Mutations in the KRAS2 oncogene during progressive stages of human colon carcinoma

Biglycan as a potential regulator of tumorgenicity and immunogenicity in K-RAS-transformed cells

The extracellular matrix component biglycan (BGN) plays an essential role in various physiological and pathophysiological processes. A deficient BGN expression associated with reduced immunogenicity was found in HER-2/neu-overexpressing cells. To determine whether BGN is suppressed by oncogene-driven regulatory networks, the expression and function of BGN was analyzed in murine and human BGNlow/BGNhigh K-RASG12V-transformed model systems as well as in different patients' datasets of colorectal carcinoma (CRC) lesions. K-RAS-mutated CRC tissues expressed low BGN mRNA and protein levels when compared to normal colon epithelial cells, which was associated with a reduced patients' survival. Transfection of BGN in murine and human BGNlow K-RAS-expressing cells resulted in a reduced growth and migration of BGNhigh vs BGNlow K-RAS cells. In addition, increased MHC class I surface antigens as a consequence of an enhanced antigen processing machinery component expression was found upon restoration of BGN, which was confirmed by RNA-sequencing of BGNlow vs. BGNhigh K-RAS models. Furthermore, a reduced tumor formation of BGNhigh versus BGNlow K-RAS-transformed fibroblasts associated with an enhanced MHC class I expression and an increased frequency of tumor-infiltrating lymphocytes in tumor lesions was found. Our data provide for the first time an inverse link between BGN and K-RAS expression in murine and human K-RAS-overexpressing models and CRC lesions associated with altered growth properties, reduced immunogenicity and worse patients' outcome. Therefore, reversion of BGN might be a novel therapeutic option for K-RAS-associated malignancies.

Effects of molecular markers on the treatment decision and prognosis of colorectal cancer: a narrative review

OBJECTIVE

To summarize the effects of molecular markers on the treatment decision and prognosis of colorectal cancer.

BACKGROUND

Colorectal cancer is a highly heterogeneous disease. Even colorectal cancers of the same pathological type and clinical stage may have significant differences in treatment efficacy and prognosis. There are three main molecular mechanisms for the occurrence and development of colorectal cancer: chromosomal instability (CIN) pathway, microsatellite instability (MSI), and CpG island methylate phenotype (CIMP). There are multiple molecular markers distributed on each pathway.

METHODS

We performed a literature search on the PubMed database for studies published in English (from the date of initiation of the database to the year of 2020) using the following subject terms: "colon cancer", "rectal cancer", "colorectal cancer", "molecular markers", "biomarkers", "treatment strategies", and "prognosis".

CONCLUSIONS

The different expression states of molecular markers have a significant impact on the treatment decision and prognosis of colorectal cancer. Main colorectal cancer molecular markers include MSI and some important genes. Individualized treatments for tumors with different molecular phenotypes have improved the treatment effectiveness for colorectal cancer. The rational use of molecular markers is valuable for treatment decision-making and the prognosis of patients with colorectal cancer.

The landscape and driver potential of site-specific hotspots across cancer genomes

Large sets of whole cancer genomes make it possible to study mutation hotspots genome-wide. Here we detect, categorize, and characterize site-specific hotspots using 2279 whole cancer genomes from the Pan-Cancer Analysis of Whole Genomes project and provide a resource of annotated hotspots genome-wide. We investigate the excess of hotspots in both protein-coding and gene regulatory regions and develop measures of positive selection and functional impact for individual hotspots. Using cancer allele fractions, expression aberrations, mutational signatures, and a variety of genomic features, such as potential gain or loss of transcription factor binding sites, we annotate and prioritize all highly mutated hotspots. Genome-wide we find more high-frequency SNV and indel hotspots than expected given mutational background models. Protein-coding regions are generally enriched for SNV hotspots compared to other regions. Gene regulatory hotspots show enrichment of potential same-patient second-hit missense mutations, consistent with enrichment of hotspot driver mutations compared to singletons. For protein-coding regions, splice-sites, promoters, and enhancers, we see an excess of hotspots associated with cancer genes. Interestingly, missense hotspot mutations in tumor suppressors are associated with elevated expression, suggesting localized amino-acid changes with functional impact. For individual non-coding hotspots, only a small number show clear signs of positive selection, including known sites in the TERT promoter and the 5' UTR of TP53. Most of the new candidates have few mutations and limited driver evidence. However, a hotspot in an enhancer of the oncogene POU2AF1, which may create a transcription factor binding site, presents multiple lines of driver-consistent evidence.

Detection of Somatic Mutations with ddPCR from Liquid Biopsy of Colorectal Cancer Patients

Liquid biopsy and cell-free DNA (cfDNA) show great promise in cancer diagnostics. In this study, we designed a custom droplet digital PCR (ddPCR) assay for the quantification and quality control of cfDNA isolated from serum. The assay was validated on a group of locally advanced colorectal cancer (CRC) patients and two control groups-patients with hemorrhoids and healthy individuals. The assay shows a high correlation with Qubit measurement (r = 0.976) but offers a higher dynamic range. Mean concentrations of cfDNA were 12.36 ng/µL, 5.17 ng/µL, and 0.29 ng/µL for CRC, hemorrhoid patients, and healthy controls, respectively. The quality of cfDNA was assessed with the measurement of B-cell DNA contamination. On a subset of CRC patients, we compared the mutation status on KRAS (G12A, G12D, G12V, G13D) and BRAF (V600E) genes in the primary tumor and cfDNA isolated from the serum. A total of 70.6% of primary tumor samples were mutated, and the mean fractional abundance of mutations was 9.50%. The matching serum samples were mutated in 38% cases with an average fractional abundance of 0.23%. We conclude that any decisions based solely on the amount of cfDNA present in patient serum must be interpreted carefully and in the context of co-morbidities. This study explores the potential of ddPCR somatic mutations detection from liquid biopsy as a supplement to tissue biopsy in targeted personalized CRC patient management.

A Pterin-FAM-TAMRA Tri-color Fluorescence Biosensor to Detect the Level of KRAS Point Mutation

Monitoring the changes in the level of KRAS point mutation (the concentration fraction of the KRAS point mutated DNA to the total DNA) in clinical treatment progress can guide and greatly improve the personalized therapy and therapeutic evaluation of patients with cancer. In this work, based on FRET fluorescence quenching and apyrimidinic site-induced guanine/pterin specific binding, we developed a pterin-FAM-TAMRA tri-color fluorescence sensing system to assess the level of KRAS point mutation in one step. The responses from TAMRA displayed good and similar linear correlations in the range from 60 nM to 2 μM for all four types of DNA, resulting in a common linear equation related to the T-DNA concentration (N_ΔFTAMRA = 2.908c_T-DNA + 0.364). Meanwhile, the responses from pterin showed excellent selectivity to W-DNA and an excellent linear correlation to the W-DNA in the concentration range from 60 nM to 1 μM (N_ΔFpterin = -0.364c_gDNA-G + 0.034). This biosensor has an effective concentration range for detecting KRAS point mutations. Especially, because the apyrimidinic site-induced guanine/pterin binding is selective for the detection of wild-type DNA, the sensing system can be applied for clinical mutation level detection of all kinds of KRAS point mutations (G → A, G → C and G → T) in blood samples, which is crucial for the personalized therapy and therapeutic evaluation of patients with most KRAS-related cancer types.

Targeting Epidermal Growth Factor Receptor in Non-Small-Cell-Lung Cancer: Current State and Future Perspective

BACKGROUND

Lung cancer is one of the leading cause of cancer death worldwide, the most common histological type of lung cancer is non-small cell lung cancer (NSCLC), whose occurrence and development is closely related to the mutation and amplification of epidermal growth factor receptors (EGFR). Currently , a series of targeted drugs were developed on the inhibition of EGFR such as epidermal growth factor receptortyrosine kinase inhibitor EGFR-TKI and monoclonal antibody (McAb).

OBJECTIVE

We sought to summarizes the current drugs targeting Epidermal Growth Factor Receptor in nonsmall- cell-lung.

METHODS

We conducted a comprehensive review of the development and application of EGFR-TKI and McAb which targeted EGFR in NSCLC and compared the mechanisms of PROTAC with the traditional inhibitors.

RESULTS

The drugs targeted EGFR in NSCLC have been widely used in clinic practices. Compared to traditional chemotherapy, these drugs excel with their clear and specific targeting, better curative effects, and less toxic and side effects. However, the mechanism comes with some insurmountable weaknesses like serious toxic and other side effects, as well as proneness to producing drug resistance.

CONCLUSION

The emerging PROTAC (Proteolysis Targeting Chimera) technology has been successfully applied to selective degradation of multiple protein targets, including EGFR. It also highlights the potential and challenges of PROTAC therapy regarding future combination therapeutic options in NSCLC treatment.

Integration of Enzymatic Labeling with Single-Molecule Detection for Sensitive Quantification of Diverse DNA Damages

DNA damage plays an important role in the regulation of gene expression and disease processes. The accurate measurement of DNA damage is essential to the discovery of potential disease biomarkers for risk assessment, early clinical diagnosis, and therapy monitoring. However, the low abundance, random location in genomic elements, diversity, and the incapability to specifically amplify the DNA damages hinder the accurate quantification of various DNA damages within human genomes. Herein, we demonstrate the integration of enzymatic labeling with single-molecule detection for sensitive quantification of diverse DNA damages. A significant advantage of our method is that only the damaged base-containing DNA sequence can be labeled by the biotin-conjugated deoxynucleotide triphosphate (biotin-dNTP) and separated from the normal DNAs, which greatly improves the detection specificity. In addition, high sensitivity can be achieved by the terminal deoxynucleotidyl transferase (TdT)-induced polymerization of multiple Alexa Fluor 488-labeled-deoxyuridine triphosphates (AF488-dUTPs) and the introduction of single-molecule detection. This method can measure DNA damage with a detection limit as low as 1.1 × 10^-16 M, and it can distinguish DNA damage at low abundance down to 1.3 × 10^-4%. Importantly, it can provide information about the occurrence of DNA damage in a specific gene and ascertain the DNA damage level in different cancer cell lines, offering a new approach for studying the physiological function of various DNA damages in human diseases.

Genome-wide CRISPR Screen to Identify Genes that Suppress Transformation in the Presence of Endogenous KrasG12D

Cooperating gene mutations are typically required to transform normal cells enabling growth in soft agar or in immunodeficient mice. For example, mutations in Kras and transformation-related protein 53 (Trp53) are known to transform a variety of mesenchymal and epithelial cells in vitro and in vivo. Identifying other genes that can cooperate with oncogenic Kras and substitute for Trp53 mutation has the potential to lead to new insights into mechanisms of carcinogenesis. Here, we applied a genome-wide CRISPR/Cas9 knockout screen in Kras^G12D immortalized mouse embryonic fibroblasts (MEFs) to search for genes that when mutated cooperate with oncogenic Kras to induce transformation. We also tested if mutation of the identified candidate genes could cooperate with Kras^G12D to generate primary sarcomas in mice. In addition to identifying the well-known tumor suppressor cyclin dependent kinase inhibitor 2A (Cdkn2a), whose alternative reading frame product p19 activates Trp53, we also identified other putative tumor suppressors, such as F-box/WD repeat-containing protein 7 (Fbxw7) and solute carrier family 9 member 3 (Slc9a3). Remarkably, the TCGA database indicates that both FBXW7 and SLC9A3 are commonly co-mutated with KRAS in human cancers. However, we found that only mutation of Trp53 or Cdkn2a, but not Fbxw7 or Slc9a3 can cooperate with Kras^G12D to generate primary sarcomas in mice. These results show that mutations in oncogenic Kras and either Fbxw7 or Slc9a3 are sufficient for transformation in vitro, but not for in vivo sarcomagenesis.

Mutation Profiling of Premalignant Colorectal Neoplasia

Accumulation of allelic variants in genes that regulate cellular proliferation, differentiation, and apoptosis may result in expansion of the aberrant intestinal epithelium, generating adenomas. Herein, we compared the mutation profiles of conventional colorectal adenomas (CNADs) across stages of progression towards early carcinoma. DNA was isolated from 17 invasive adenocarcinomas (ACs) and 58 large CNADs, including 19 with low-grade dysplasia (LGD), 21 with LGD adjacent to areas of high-grade dysplasia and/or carcinoma (LGD-H), and 28 with high-grade dysplasia (HGD). Ion AmpliSeq Comprehensive Cancer Panel libraries were prepared and sequenced on the Ion Proton. We identified 956 unique allelic variants; of these, 499 were considered nonsynonymous variants. Eleven genes (APC, KRAS, SYNE1, NOTCH4, BLNK, FBXW7, GNAS, KMT2D, TAF1L, TCF7L2, and TP53) were mutated in at least 15% of all samples. Out of frequently mutated genes, TP53 and BCL2 had a consistent trend in mutation prevalence towards malignancy, while two other genes (HNF1A and FBXW7) exhibited the opposite trend. HGD adenomas had significantly higher mutation rates than LGD adenomas, while LGD-H adenomas exhibited mutation frequencies similar to those of LGD adenomas. A significant increase in copy number variant frequency was observed from LGD through HGD to malignant samples. The profiling of advanced CNADs demonstrated variations in mutation patterns among colorectal premalignancies. Only limited numbers of genes were repeatedly mutated while the majority were altered in single cases. Most genetic alterations in adenomas can be considered early contributors to colorectal carcinogenesis.

Small Molecule KRAS Agonist for Mutant KRAS Cancer Therapy

Background

Lung cancer patients with KRAS mutation(s) have a poor prognosis due in part to the development of resistance to currently available therapeutic interventions. Development of a new class of anticancer agents that directly targets KRAS may provide a more attractive option for the treatment of KRAS-mutant lung cancer.

Results

Here we identified a small molecule KRAS agonist, KRA-533, that binds the GTP/GDP-binding pocket of KRAS. In vitro GDP/GTP exchange assay reveals that KRA-533 activates KRAS by preventing the cleavage of GTP into GDP, leading to the accumulation of GTP-KRAS, an active form of KRAS. Treatment of human lung cancer cells with KRA-533 resulted in increased KRAS activity and suppression of cell growth. Lung cancer cell lines with KRAS mutation were relatively more sensitive to KRA-533 than cell lines without KRAS mutation. Mutating one of the hydrogen-bonds among the KRA-533 binding amino acids in KRAS (mutant K117A) resulted in failure of KRAS to bind KRA-533. KRA-533 had no effect on the activity of K117A mutant KRAS, suggesting that KRA-533 binding to K117 is required for KRA-533 to enhance KRAS activity. Intriguingly, KRA-533-mediated KRAS activation not only promoted apoptosis but also autophagic cell death. In mutant KRAS lung cancer xenografts and genetically engineered mutant KRAS-driven lung cancer models, KRA-533 suppressed malignant growth without significant toxicity to normal tissues.

Conclusions

The development of this KRAS agonist as a new class of anticancer drug offers a potentially effective strategy for the treatment of lung cancer with KRAS mutation and/or mutant KRAS-driven lung cancer.

Electronic supplementary material

The online version of this article (10.1186/s12943-019-1012-4) contains supplementary material, which is available to authorized users.

Long-peptide vaccination with driver gene mutations in p53 and Kras induces cancer mutation-specific effector as well as regulatory T cell responses

Mutated proteins arising from somatic mutations in tumors are promising targets for cancer immunotherapy. They represent true tumor-specific antigens (TSAs) as they are exclusively expressed in tumors, reduce the risk of autoimmunity and are more likely to overcome tolerance compared to wild-type (wt) sequences. Hence, we designed a panel of long peptides (LPs, 28–35 aa) comprising driver gene mutations in TP35 and KRAS frequently found in gastrointestinal tumors to test their combined immunotherapeutic potential. We found increased numbers of T cells responsive against respective mutated and wt peptides in colorectal cancer patients that carry the tested mutations in their tumors than patients with other mutations. Further, active immunization of HLA(-A2/DR1)-humanized mice with mixes of the same mutated LPs yielded simultaneous, polyvalent CD8⁺/CD4⁺ T cell responses against the majority of peptides. Peptide-specific T cells possessed a multifunctional cytokine profile with CD4⁺ T cells showing a T_H1-like phenotype. Two mutated peptides (Kras[G12V], p53[R248W]) induced significantly higher T cell responses than corresponding wt sequences and comprised HLA-A2/DR1-restricted mutated epitopes. However, vaccination with the same highly immunogenic LPs strongly increased systemic regulatory T cells (T_reg) numbers in a syngeneic sarcoma model over-expressing these mutated protein variants and resulted in accelerated tumor outgrowth. In contrast, tumor outgrowth was delayed when vaccination was directed against tumor-intrinsic Kras/Tp53 mutations of lower immunogenicity. Conclusively, we show that LP vaccination targeting multiple mutated TSAs elicits polyvalent, multifunctional, and mutation-specific effector T cells capable of targeting tumors. However, the success of this therapeutic approach can be hampered by vaccination-induced, TSA-specific T_regs.

KRAS and TP53 mutations in inflammatory bowel disease-associated colorectal cancer: a meta-analysis

Although KRAS and TP53 mutations are common in both inflammatory bowel disease-associated colorectal cancer (IBD-CRC) and sporadic colorectal cancer (S-CRC), molecular events leading to carcinogenesis may be different. Previous studies comparing the frequency of KRAS and TP53 mutations in IBD-CRC and S-CRC were inconsistent. We performed a meta-analysis to compare the presence of KRAS and TP53 mutations among patients with IBD-CRC, S-CRC, and IBD without dysplasia. A total of 19 publications (482 patients with IBD-CRC, 4,222 with S-CRC, 281 with IBD without dysplasia) met the study inclusion criteria. KRAS mutation was less frequent (RR=0.71, 95%CI 0.56-0.90; P=0.004) while TP53 mutation was more common (RR=1.24, 95%CI 1.10-1.39; P<0.001) in patients with IBD-CRC compared to S-CRC. Both KRAS (RR=3.09, 95%CI 1.47-6.51; P=0.003) and TP53 (RR=2.15, 95%CI 1.07-4.31 P=0.03) mutations were more prevalent in patients with IBD-CRC compared to IBD without dysplasia. In conclusion, IBD-CRC and S-CRC appear to have biologically different molecular pathways. TP53 appears to be more important than KRAS in IBD-CRC compared to S-CRC. Our findings suggest possible roles of TP53 and KRAS as biomarkers for cancer and dysplasia screening among patients with IBD and may also provide targeted therapy in patients with IBD-CRC.

Mutational frequency of KRAS, NRAS, IDH2, PIK3CA, and EGFR in North Indian gallbladder cancer patients

BACKGROUND

Gallbladder cancer (GBC) has a peculiar geographical distinction, with a high prevalence seen in North India and Chile. There are various aetiopathogenetic mechanisms of GBC causation; one of them is a series of pathogenic mutations, which is responsible for the malignant transformation of gallbladder epithelium. Therefore, the present study aimed to find out cancer-specific hot spot mutations in five major cancer-related genes KRAS exon1 &2, NRAS exon1, IDH2 exon, PIK3CA exon 20, IDH2 exon 4 and EGFR exon 20 in North Indian GBC patients and their association with clinicopathological variables.

MATERIAL AND METHODS

This study included 34 histopathologically confirmed GBC cases. The clinical material consisted of formalin-fixed paraffin-embedded (FFPE) blocks of the patients. DNA isolation was done from FFPE tissue. DNA sequencing was performed by the capillary electrophoresis method. The chi-square (χ²) test was used to test for a statistically significant relationship between two categorical study variables.

RESULTS

The overall incidence of somatic mutations in KRAS exon 1&2, NRAS exon1, IDH2 exon4, PIK3CA exon20, and EGFR exon 20 in Indian GBC patients was found in 8/34 (23.5%), 3/34 (8.8%), 4/34 (11.7%), 7/34 (20.6%), 7/34 (20.6%), respectively. KRAS exon 1 and two mutations were found to be significantly associated with advanced stage GBC patients.

CONCLUSION

KRAS, PIK3CA, and EGFR were found to be the most frequently mutated genes among the five tested in this study.

KRAS mutation as a prognostic factor in ampullary adenocarcinoma: a meta-analysis and review

Ampullary adenocarcinoma (A-AC) is a rare malignancy arising from the ampulla of Vater. KRAS mutation is detected in 30-40% of patients with A-AC, but its clinical implication and prognostic value are not well described. We conducted this meta-analysis to investigate the association between KRAS mutation and prognosis in patients with A-AC. We searched Pubmed, MEDLINE, EMBASE, and the Cochrane Library databases for articles including following terms in their titles, abstracts, or keywords: 'ampullary or periampullary or ampulla of vater', 'cancer or carcinoma', and 'KRAS'. There were five studies with survival data of patients. A total of 388 patients with A-AC from the 5 studies were included in the overall survival (OS) analysis, and 169 patients from 2 studies were eligible for the relapse-free-survival (RFS) analysis. Out of 388 patients, 175 (45%) had KRAS mutation. There was no association between KRAS mutation and OS (HR = 1.06, 95% CI: 0.87-1.29, P = 0.58). However, there was a significant correlation between KRAS mutation and worse RFS (HR = 2.74, 95% CI: 1.52-4.92, P = 0.0008). In conclusion, this meta-analysis indicates that KRAS mutation is associated with poor RFS, but not with OS in patients with A-AC.

Depletion of Abundant Sequences by Hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications

Next-generation sequencing has generated a need for a broadly applicable method to remove unwanted high-abundance species prior to sequencing. We introduce DASH (Depletion of Abundant Sequences by Hybridization). Sequencing libraries are 'DASHed' with recombinant Cas9 protein complexed with a library of guide RNAs targeting unwanted species for cleavage, thus preventing them from consuming sequencing space. We demonstrate a more than 99 % reduction of mitochondrial rRNA in HeLa cells, and enrichment of pathogen sequences in patient samples. We also demonstrate an application of DASH in cancer. This simple method can be adapted for any sample type and increases sequencing yield without additional cost.

G4 DNA in ras genes and its potential in cancer therapy

It is now well established that in the human genome the canonical double helix coexists with folded G-quadruplex structures that are known to have important biological functions. In this review we summarize the current knowledge on quadruplex formation in the promoters of the ras genes that are mutated in about 30% of all human cancers. We describe the nuclear proteins that recognize these unusual DNA structures and discuss their function in transcription. We also examine the formation of G-quadruplexes in the 5'-untranslated region of the ras transcripts and conclude this review by reporting strategies that use either ras G-quadruplexes or proteins recognizing the ras G-quadruplexes as targets of anticancer small molecules.

The value of preoperative screening colonoscopies in patients with biliary tract cancer

BACKGROUND

The purpose of this study was to evaluate the value of preoperative screening colonoscopies in patients with biliary tract cancer.

METHODS

A total of 544 patients with biliary tract cancer who underwent preoperative screening colonoscopies between January 2005 and December 2012 were retrospectively analyzed.

RESULTS

Synchronous colorectal neoplasia was detected in 199 patients (36.7 %), with adenocarcinomas detected in 21 (3.9 %) patients, carcinoids in two (0.4 %) patients, and adenomas in 176 (32.4 %) patients. Of those with adenomas, 32 patients were diagnosed with advanced adenomas, defined as adenomas with a maximum diameter of >1 cm, villous histology, or high-grade dysplasia because these characteristics implied the risk of malignant transformation. Fifty-five (10.1 %) of the patients with colorectal neoplasia required resection (11 surgical and 44 endoscopic resections). There were no major adverse events related to the resection. Univariate and multivariate analyses revealed that smoking status [ex-smoker + current smoker vs. non-smoker: odds ratio (OR) 2.32; 95 % confidence interval (CI) 1.30-4.21] and advanced age (≥70 vs. ≤69 years: OR 2.22; 95 % CI 1.24-3.91) were independent risk factors of having a colorectal neoplasia that required resection.

CONCLUSIONS

In patients with biliary tract cancer, preoperative screening colonoscopy was feasible and provided valuable clinical information. Synchronous colorectal neoplasia was detected in a substantial number of patients. Preoperative screening colonoscopies should be considered especially in high-risk patients such as smokers and elderly patients.

Sequencing of DNA Lesions Facilitated by Site-Specific Excision via Base Excision Repair DNA Glycosylases Yielding Ligatable Gaps

Modifications to nucleotides in the genome can lead to mutations or are involved in regulation of gene expression, and therefore, finding the site of modification is a worthy goal. Robust methods for sequencing modification sites on commercial sequencers have not been developed beyond the epigenetic marks on cytosine. Herein, a method to sequence DNA modification sites was developed that utilizes DNA glycosylases found in the base excision repair pathway to excise the modification. This approach yields a gap at the modification site that is sealed by T4-DNA ligase, yielding a product strand missing the modification. Upon sequencing, the modified nucleotide is reported as a deletion mutation, identifying its location. This approach was used to detect a uracil (U) or 8-oxo-7,8-dihydroguanine (OG) in codon 12 of the KRAS gene in synthetic oligodeoxynucleotides. Additionally, an OG modification site was placed in the VEGF promoter in a plasmid and sequenced. This method requires only commercially available materials and can be put into practice on any sequencing platform, allowing this method to have broad potential for finding modifications in DNA.

Identification of DNA lesions using a third base pair for amplification and nanopore sequencing

Damage to the genome is implicated in the progression of cancer and stress-induced diseases. DNA lesions exist in low levels, and cannot be amplified by standard PCR because they are frequently strong blocks to polymerases. Here, we describe a method for PCR amplification of lesion-containing DNA in which the site and identity could be marked, copied and sequenced. Critical for this method is installation of either the dNaM or d5SICS nucleotides at the lesion site after processing via the base excision repair process. These marker nucleotides constitute an unnatural base pair, allowing large quantities of marked DNA to be made by PCR amplification. Sanger sequencing confirms the potential for this method to locate lesions by marking, amplifying and sequencing a lesion in the KRAS gene. Detection using the α-hemolysin nanopore is also developed to analyse the markers in individual DNA strands with the potential to identify multiple lesions per strand.

Genomic DNA lesions exist in low levels and cannot be amplified by standard PCR. Here, Riedl et al. report a method to amplify damaged DNA sites by replacing them via DNA repair with unnatural base pairs, which are subsequently identified by Sanger sequencing or α-hemolysin nanopore sequencing.

Quantitative proteomics reveals differentially expressed proteins in murine preneoplastic intestine in a model of intestinal tumorigenesis induced by low dietary folate and MTHFR deficiency

Colorectal cancer risk is increased when dietary folate intake is low, with or without a deficiency in methylenetetrahydrofolate reductase (MTHFR). We have observed that intestinal tumors are induced in mice fed low-folate diets, and that tumor incidence is increased when these mice also have MTHFR deficiency. This study was undertaken to identify differentially expressed proteins in conditions favoring initial steps of murine carcinogenesis in normal preneoplastic intestine. We compared the proteome of BALB/c normal intestine in Mthfr(+/+) mice fed control diets for 1 year (low susceptibility to tumorigenesis) with the proteome of Mthfr(+/-) animals fed low folate diets (higher tumor susceptibility). Our data suggest that the NuRD complex, KRAS-related proteins, the protein synthetic machinery, and fatty acid-related metabolic proteins are upregulated in the early stages of tumorigenesis. These proteins may serve as biomarkers or targets for colorectal cancer diagnosis or therapy.

Adenoma and carcinoma components in colonic tumors show discordance for KRAS mutation

Activating mutations in KRAS are common events in the pathogenesis of colorectal carcinoma and predict response to treatment with anti-EGFR antibodies. Molecular pathology testing for KRAS mutations has become the standard of practice for patients with metastatic colorectal carcinoma. Despite the known histologic and molecular differences between adenomas and carcinomas, the concordance of KRAS mutation between adenomas and carcinomas has not been established leaving some open questions regarding the appropriate choice of tissue for KRAS mutation analysis and correct interpretation of the test results. To address these questions, we analyzed the concordance of KRAS mutation in 70 tumors that contained both adenoma and carcinoma components (2 cases of intramucosal carcinoma, 66 cases with invasion of the submucosa, and 2 invading the muscularis propria). For each case, DNA was separately isolated from the adenoma and the carcinoma component and analyzed for KRAS mutation using direct sequencing. Overall, 30 (43%) of the adenoma cases and 36 (51%) of the carcinoma cases were positive for KRAS mutation. Of the 70 cases, 16 (23%) showed discordant results. Interestingly, the fraction of discordant cases went down as the depth of carcinoma invasion increased. In summary, we identified significant KRAS mutation discordance between the adenoma and carcinoma component of the lesion. Our results suggest that effort should be made to analyze only the invasive component of the lesion and that caution should be taken when interpreting a result based on DNA extracted from noninvasive elements.

Repositioning metformin in cancer: genetics, drug targets, and new ways of delivery

After sitting many years on the shelves of drug stores as a harmless antidiabetic drug, metformin comes back in the spotlight of the scientific community as a surprisingly effective antineoplastic drug. Metformin targets multiple pathways that play pivotal roles in cancer progression, impacting various cellular processes, such as proliferation, cell death, metabolism, and even the cancer stemness features. The biomolecular characteristics of tumors, such as appropriate expression of organic cation transporters or genetic alterations including p53, K-ras, LKB1, and PI3K may impact metformin's anticancer efficiency. This could indicate a need for tumor genetic profiling in order to identify patients most likely to benefit from metformin treatment. Considering that the majority of experimental models suggest that higher, supra-clinical doses of metformin should be used in order to obtain an antineoplastic effect, new ways of drug delivery could be developed, such as metformin-loaded nanoparticles or incorporation of metformin into microparticles used in transarterial chemoembolization, with the aim of obtaining higher intratumoral drug concentrations and a targeted therapy which will ultimately maximize metformin's efficacy.

Identification of potential synthetic lethal genes to p53 using a computational biology approach

BACKGROUND

Identification of genes that are synthetic lethal to p53 is an important strategy for anticancer therapy as p53 mutations have been reported to occur in more than half of all human cancer cases. Although genome-wide RNAi screening is an effective approach to finding synthetic lethal genes, it is costly and labor-intensive.

METHODS

To illustrate this approach, we identified potentially druggable genes synthetically lethal for p53 using three microarray datasets for gene expression profiles of the NCI-60 cancer cell lines, one next-generation sequencing (RNA-Seq) dataset from the Cancer Genome Atlas (TCGA) project, and one gene expression data from the Cancer Cell Line Encyclopedia (CCLE) project. We selected the genes which encoded kinases and had significantly higher expression in the tumors with functional p53 mutations (somatic mutations) than in the tumors without functional p53 mutations as the candidates of druggable synthetic lethal genes for p53. We identified important regulatory networks and functional categories pertinent to these genes, and performed an extensive survey of literature to find experimental evidence that support the synthetic lethality relationships between the genes identified and p53. We also examined the drug sensitivity difference between NCI-60 cell lines with functional p53 mutations and NCI-60 cell lines without functional p53 mutations for the compounds that target the kinases encoded by the genes identified.

RESULTS

Our results indicated that some of the candidate genes we identified had been experimentally verified to be synthetic lethal for p53 and promising targets for anticancer therapy while some other genes were putative targets for development of cancer therapeutic agents.

CONCLUSIONS

Our study indicated that pre-screening of potential synthetic lethal genes using gene expression profiles is a promising approach for improving the efficiency of synthetic lethal RNAi screening.

Prognostic and predictive roles of KRAS mutation in colorectal cancer

The RAS gene family is among the most studied and best characterized of the known cancer-related genes. Of the three human ras isoforms, KRAS is the most frequently altered gene, with mutations occurring in 17%-25% of all cancers. In particular, approximately 30%-40% of colon cancers harbor a KRAS mutation. KRAS mutations in colon cancers have been associated with poorer survival and increased tumor aggressiveness. Additionally, KRAS mutations in colorectal cancer lead to resistance to select treatment strategies. In this review we examine the history of KRAS, its prognostic value in patients with colorectal cancer, and evidence supporting its predictive value in determining appropriate therapies for patients with colorectal cancer.

Mechanism of EGER-related cancer drug resistance

Drug resistance in cancer arises from a complex range of biochemical and molecular events, which ultimately result in tumor cell survival. Identifying key genes and signal pathways involved in the molecular mechanisms of drug resistance is essential for establishment of new drug targets for preventing further resistance development and spreading. Epidermal growth factor receptor (EGFR) was the first growth factor receptor proposed as a target for cancer therapy. Significant progress in studying EGFR gene expression and mutation has been made in understanding the molecular events involved in EGFR-targeted agents. Recently, some individual chromosomal features such as EGFR copy number variation were demonstrated as new aspects related to drug sensitivity. Identifying these functional regulators of drug resistance will benefit therapeutic decision-making. In this study, we describe an extensive investigation of the published literature on mutation, amplification, and expression of EGFR and its downstream signaling that directly contribute to EGFR inhibitor resistance, including the gene status of KRAS, BRAF, PIK3CA, PTEN, MEK, and AKT on response to therapy. Analysis of these gene signatures identified reveals general modes of action of multicomponent therapies and the mechanisms of specific drug combinations, highlights the potential value of molecular interaction profiles in the discovery of novel therapies, and provides more information for personalized cancer medicine.

KRAS mutational status of endoscopic biopsies matches resection specimens

Aims

This study was performed to determine systematically whether KRAS mutational analysis in biopsy tissue is a reliable indicator of KRAS status in subsequent corresponding resection specimens.

Methods

30 colorectal cancer (CRC) patients with biopsy and corresponding subsequent surgical resection specimens were studied. KRAS mutational analysis was performed on each biopsy sample as well as two separate samples from each resection specimen by PCR and Sanger sequencing.

Results

Overall, KRAS mutations were identified in 12/30 (40%) of the tumours. There was 100% correlation between biopsy and resection specimens regarding the presence or absence of KRAS mutations. In fact, the same point mutation was identified in both biopsy and corresponding resection specimens in 12/12 (100%) cases. In addition, in two cases, there were two different point mutations detected within the same biopsy specimen.

Conclusion

This study shows perfect correlation between KRAS mutation status in biopsy and resection specimens from an individual patient, and suggests that biopsy material is adequate for KRAS mutational analysis in CRC patients.

miR-216b suppresses tumor growth and invasion by targeting KRAS in nasopharyngeal carcinoma

MicroRNAs (miRNAs) are small noncoding RNAs that are involved in various diseases, including cancer. In the present study, we found that miR-216b was downregulated in nasopharyngeal carcinoma (NPC) cell lines and specimens. Decreased expression of miR-216b was directly related to advanced clinical stage and lymph node metastasis. miR-216b levels correlated inversely with levels of KRAS protein during nasopharyngeal tumorigenesis. Furthermore, we demonstrated that miR-216b can bind to the 3' untranslated region (UTR) of KRAS and inhibit expression of the KRAS protein. Both in vitro and in vivo assays revealed that miR-216b attenuated NPC cell proliferation, invasion and tumor growth in nude mice. miR-216b exerts its tumor suppressor function through inhibition of the KRAS-related AKT and ERK pathways. Our findings provide, for the first time, significant clues regarding the role of miR-216b as a tumor suppressor by targeting KRAS in NPC.

Uptake of KRAS mutation testing in patients with metastatic colorectal cancer in Europe, Latin America and Asia

The mutation status of the KRAS gene in the tumors of patients with metastatic colorectal cancer (mCRC) is a predictive biomarker for the efficacy of epidermal growth factor receptor monoclonal antibody therapy. The establishment of KRAS mutation testing in this setting represents a significant change to standard diagnostic procedures and a major advance in the personalization of cancer care. Against a changing regulatory background, three cross-sectional surveys of physicians in 14 countries in Europe, Latin America and Asia were conducted in 2008, 2009, and 2010 to investigate the uptake and outcome of KRAS testing for patients with mCRC. Physicians in each year answered questions on four patients (last patient seen and last seen in first-, second- and third-line settings). Fieldwork was carried out February-May 2008, January-April 2009, and January-April 2010. Data from 3,819, 3,740 and 3,820 anonymized, uncoded patient records were collated. The frequency of KRAS testing in patients with mCRC increased from 3% in 2008 to 47% in 2009 and 69% in 2010. The 2010 survey revealed that test results were available within 15 days for 82%, 51% and 98% of the 1679, 679, and 261 tested patients in the European, Latin American and Asian regions, respectively. Cetuximab was the most commonly administered targeted agent in tested patients with KRAS wild-type mCRC (798/1607 patients; 50%) and bevacizumab was the most commonly administered targeted agent in tested patients with KRAS mutant tumors (396/893; 44% overall). In conclusion, KRAS testing is now widely established as a routine diagnostic procedure for patients with mCRC and is used increasingly to guide treatment selection.

EGFR Signaling in Colorectal Carcinoma

The epidermal growth factor receptor (EGFR) and its downstream signaling pathways are involved in the development and progression of several human tumors, including colorectal cancer. Much attention has been given to the EGFR pathway as of lately because both EGFR and some downstream components serve as targets for anticancer therapy. In addition to playing a critical role in targeted therapy, alterations in this pathway can have prognostic implications. The EGFR pathway and its impact on colorectal carcinogenesis and prognosis are the emphasis of this paper. Since prognosis is tightly related to response to various therapies, the predictive value of the components of this pathway will be briefly discussed, but this is not the focus of this paper.

KRAS status in patients with colorectal cancer peritoneal carcinomatosis and its impact on outcome

BACKGROUND

KRAS mutated colorectal cancers (CRC) are reported to be associated with a poor response to anti-EGFR monoclonal antibody therapy and poor prognosis. We studied the rates of KRAS mutated tumors in patients with peritoneal carcinomatosis from CRC and investigated the association of KRAS status with specific clinicopathologic factors.

METHODS

A retrospective observational study of tumor specimens from 23 patients with peritoneal carcinomatosis from CRC was performed using standard genomic DNA sampling techniques to identify KRAS mutations. Correlation between clinicopathologic factors and KRAS mutation status was performed using the Fisher exact test or χ test, as appropriate.

RESULTS

Eleven (48%) of 23 patients had KRAS mutations. There were no statistically significant correlations in patient demographics, tumor pathology, surgical evaluation, treatments, or survival outcomes for peritoneal carcinomatosis between patients with KRAS mutations or wild-type KRAS status.

CONCLUSION

The prevalence of KRAS mutation in CRC patients with peritoneal carcinomatosis is 48% in this preliminary study and clinicopathologic factors appear to be independent of mutation status.

Genes mediating programmed cell death: an immunohistochemical study of bcl-2, c-myc and p53 expression in colorectal neoplasia

Aims-To describe the expression of three genes involved in the regulation of cell proliferation and programmed cell death (apoptosis) in normal, dysplastic and malignant large bowel epithelium, and to relate any alterations to important biological and clinical variables.Methods-Immunohistochemistry was used to assess bcl-2, c-myc and p53 gene expression in 70 colorectal carcinomas, 36 adenomas and three samples of normal mucosa.Results-Bcl-2 and c-myc protein were detected in all samples of normal mucosa and most adenomas. P53 was never found in normal mucosa and was expressed in only 5% of adenomas. Sixty nine of 70 carcinomas expressed c-myc protein; p53 was found in 46% and bcl-2 was present in 35%. Bcl-2 expression correlated with a higher degree of tumour differentiation whereas the opposite was true for c-myc. Strong staining for c-myc protein predicted survival in univariate analysis. No correlation was found between p53 and bcl-2 expression.Conclusions-While c-myc and bcl-2 proteins are overexpressed at an early stage of the large bowel adenoma-carcinoma sequence, alterations to the p53 protein level only occur as a late event in large, highly dysplastic adenomas and carcinomas. Bcl-2 may therefore protect the growing adenoma against excessive programmed cell death and mutated p53 may play a similar role in carcinomas. In vitro there is a reciprocal relation between p53 and bcl-2 expression. This could not be confirmed in vivo. Similarly, there was no relation between bcl-2 and c-myc status, despite evidence that these proteins cooperate to cause neoplastic transformation. C-myc may be a prognostic indicator in large bowel cancer. There is no evidence in the present series that bcl-2 status will affect survival.

Colorectal cancer in review: the role of the EGFR pathway

IMPORTANCE OF THE FIELD

The overexpression of EGFR has been documented in 30-90% of cases of advanced colorectal cancer (CRC). An increased understanding of the EGFR pathway in CRC has paved the way for the development of other targeted agents to augment therapeutic efficacy as well as for efforts to circumvent tumor resistance to therapy.

AREAS COVERED IN THIS REVIEW

Our aim is to discuss the recent progress in the role of the EGFR pathway, the status of anti-EGFR therapeutic agents currently in use and the rationale for the development of novel agents that work along the pathway for the treatment of CRC.

WHAT THE READER WILL GAIN

The readers will learn about the development and evolution of mAbs directed against EGFR as well as tyrosine kinase inhibitors in the management of CRC patients. In the same vein, determination of optimal dosing and better methods of defining those subsets of patients most likely to benefit will be discussed.

TAKE HOME MESSAGE

All these data must encourage clinicians and basic researches to continue in their efforts to untangle the network behind EGFR and try to focus all that effort towards improving patient's quality of life as well as survival.

The frequency of KRAS mutation detection in human colon carcinoma is influenced by the sensitivity of assay methodology: a comparison between direct sequencing and real-time PCR

PURPOSE

Kirsten rat sarcoma (KRAS) gene mutations occur early in the progression of colorectal adenoma to carcinoma. The mutation status of the KRAS gene determines the benefits of molecular targeting drugs in patients with advanced colorectal cancer, although many methods are available to detect such mutations. The purpose of this study was to evaluate the influence of assay sensitivity on the detection frequency of mutated genes.

METHODS

Colorectal tumors in 224 colorectal cancer patients were characterized for KRAS mutations using PCR amplification following by direct sequencing as well as a peptide nucleic acid (PNA)-clamp real-time PCR-based assay.

RESULTS

KRAS mutations were observed in 32.1% (72/224) patients by direct sequencing, and 43.3% (97/224) by PNA-clamp PCR. The chi-square test revealed that the difference in the frequency of KRAS mutations determined by direct sequencing and PNA-clamped PCR (threshold for 1% detection) was statistically significant (p<0.015).

CONCLUSIONS

Our data suggest that assay method sensitivity clearly influences the detection frequency of mutated genes. As more sensitive assays detect more mutated genes in clinical samples, this must be taken into consideration when determining KRAS gene status in clinical practice.

Comparison of EGFR and K-RAS gene status between primary tumours and corresponding metastases in NSCLC

In non-small-cell lung cancer (NSCLC), epidermal growth factor receptor (EGFR) and K-RAS mutations of the primary tumour are associated with responsiveness and resistance to tyrosine kinase inhibitors (TKIs), respectively. However, the EGFR and K-RAS mutation status in metastases is not well studied. We compared the mutation status of these genes between the primary tumours and the corresponding metastases of 25 patients. Epidermal growth factor receptor and K-RAS mutation status was different between primary tumours and corresponding metastases in 7 (28%) and 6 (24%) of the 25 patients, respectively. Among the 25 primary tumours, three ‘hotspot’ and two non-classical EGFR mutations were found; none of the corresponding metastases had the same mutation pattern. Among the five (20%) K-RAS mutations detected in the primary tumours, two were maintained in the corresponding metastasis. Epidermal growth factor receptor and K-RAS mutations were detected in the metastatic tumours of three (12%) and five (20%) patients, respectively. The expressions of EGFR and phosphorylated EGFR showed 10 and 50% discordance, in that order. We conclude that there is substantial discordance in EGFR and K-RAS mutational status between the primary tumours and corresponding metastases in patients with NSCLC and this might have therapeutic implications when treatment with TKIs is considered.

Protein hnRNP A1 and its derivative Up1 unfold quadruplex DNA in the human KRAS promoter: implications for transcription

The promoter of the human KRAS proto-oncogene contains a structurally polymorphic nuclease hypersensitive element (NHE) whose purine strand forms a parallel G-quadruplex structure (called 32R). In a previous work we reported that quadruplex 32R is recognized by three nuclear proteins: PARP-1, Ku70 and hnRNP A1. In this study we describe the interaction of recombinant hnRNP A1 (A1) and its derivative Up1 with the KRAS G-quadruplex. Mobility-shift experiments show that A1/Up1 binds specifically, and also with a high affinity, to quadruplex 32R, while CD demonstrates that the proteins strongly reduce the intensity of the 260 nm-ellipticity—the hallmark for parallel G4-DNA—and unfold the G-quadruplex. Fluorescence resonance energy transfer melting experiments reveal that A1/Up1 completely abrogates the cooperative quadruplex-to-ssDNA transition that characterizes the KRAS quadruplex and facilitates the association between quadruplex 32R and its complementary polypyrimidine strand. When quadruplex 32R is stabilized by TMPyP4, A1/Up1 brings about only a partial destabilization of the G4-DNA structure. The possible role played by hnRNP A1 in the mechanism of KRAS transcription is discussed.

Targeting the purinome

Purines are critical cofactors in the enzymatic reactions that create and maintain living organisms. In humans, there are approximately 3,266 proteins that utilize purine cofactors and these proteins constitute the so-called purinome. The human purinome encompasses a wide-ranging functional repertoire and many of these proteins are attractive drug targets. For example, it is estimated that 30% of modern drug discovery projects target protein kinases and that modulators of small G-proteins comprise more than 50% of currently marketed drugs. Given the importance of purine-binding proteins to drug discovery, the following review will discuss the forces that mediate protein:purine recognition, the factors that determine druggability of a protein target, and the process of structure-based drug design. A review of purine recognition in representatives of the various purine-binding protein families, as well as the challenges faced in targeting members of the purinome in drug discovery campaigns will also be given.

Wild-type KRAS is required for panitumumab efficacy in patients with metastatic colorectal cancer

PURPOSE

Panitumumab, a fully human antibody against the epidermal growth factor receptor (EGFR), has activity in a subset of patients with metastatic colorectal cancer (mCRC). Although activating mutations in KRAS, a small G-protein downstream of EGFR, correlate with poor response to anti-EGFR antibodies in mCRC, their role as a selection marker has not been established in randomized trials.

PATIENTS AND METHODS

KRAS mutations were detected using polymerase chain reaction on DNA from tumor sections collected in a phase III mCRC trial comparing panitumumab monotherapy to best supportive care (BSC). We tested whether the effect of panitumumab on progression-free survival (PFS) differed by KRAS status.

RESULTS

KRAS status was ascertained in 427 (92%) of 463 patients (208 panitumumab, 219 BSC). KRAS mutations were found in 43% of patients. The treatment effect on PFS in the wild-type (WT) KRAS group (hazard ratio [HR], 0.45; 95% CI: 0.34 to 0.59) was significantly greater (P < .0001) than in the mutant group (HR, 0.99; 95% CI, 0.73 to 1.36). Median PFS in the WT KRAS group was 12.3 weeks for panitumumab and 7.3 weeks for BSC. Response rates to panitumumab were 17% and 0%, for the WT and mutant groups, respectively. WT KRAS patients had longer overall survival (HR, 0.67; 95% CI, 0.55 to 0.82; treatment arms combined). Consistent with longer exposure, more grade III treatment-related toxicities occurred in the WT KRAS group. No significant differences in toxicity were observed between the WT KRAS group and the overall population.

CONCLUSION

Panitumumab monotherapy efficacy in mCRC is confined to patients with WT KRAS tumors. KRAS status should be considered in selecting patients with mCRC as candidates for panitumumab monotherapy.

Colon cancer and gene alterations: their immunological implications and suggestions for prognostic indices and improvements in biotherapy

Studies have shown that changes occur in c-Ki-ras, p53, and Bcl2 gene structure and function during the various stages of human colon carcinogenesis. Alterations of these genes are responsible for the establishment of a state of continuous stimulus for cell division and apoptotic inhibition at physiological and pharmacological levels. This paper focuses on the results of our research aimed at investigating how these gene alterations influence tumoral mechanisms on an immunological level and how immunological parameters can be used as prognostic markers for the passage of normal tissue to adenoma and adenoma to carcinoma. Overall, our data suggest that an alteration in the c-Ki-ras gene results in a switch to a suppressive type of immune response, determining an impairment of immune cell activation at both antigen- presenting-cell and T-cell levels. c-Ki-ras gene mutations, p53 deletions, and Bc12 expression, on the other hand, can be used as prognostic markers for the passage of normal tissue to adenoma and adenoma to carcinoma. The p53 oncogene does not appear to impair patients' immunological response further. In conclusion, an evaluation of c-Ki-ras, rather than p53 gene alterations, would seem to be more relevant in colon cancer prevention programs and biotherapy improvement.

Comethylation of p16 and MGMT genes in colorectal carcinoma: Correlation with clinicopathological features and prognostic value

AIM: To investigate the significance of p16 and O⁶-methylguanine-DNA methyltransferase (MGMT) genes promoter hypermethylation and K-ras mutations on colorectal tumorigenesis and progression.

METHODS: p16 and MGMT methylation status was examined on 47 tumor samples, and K-ras mutational status was examined on 85 tumor samples. For methylation analysis, a methylation specific PCR (MS-PCR) method was used.

RESULTS: p16 and MGMT promoter methylation was found in 51% (24/47) and 43% (20/47) of CRCs, respectively, and the K-ras mutation was found in 44% (37/85) of CRCs. Comethylation of p16 and MGMT genes was significantly associated with lower aggressiveness of the disease within a two-year period of observation. Only 27% of patients with simultaneous p16 and MGMT methylation showed the detectible occurrence of metastasis and/or death, compared to 67% of patients without double methylation or with no methylation (3/11 vs 22/33, P < 0.05, χ²-test). In addition, p16 and MGMT comethylation showed a trend toward an association with longer survival in patients with CRCs (35.5 ± 6.0 mo vs 23.1 ± 3.2 mo, P = 0.072, Log-rank test). Progression of the disease within a two-year period was observed in 66% of patients carrying the K-ras mutation, compared to only 19% of patients with wild type K-ras (29/44 vs 7/37, P < 0.001, χ²-test). The presence of the K-ras mutation significantly correlated to shortened overall survival (20.0 ± 1.9 mo vs 37.0 ± 1.8 mo, P < 0.001, Log-rank test). The comethylation of p16 and MGMT genes was significantly associated with lower aggressiveness of the disease even when K-ras mutations were included in the analysis as an independent variable.

CONCLUSION: Our data suggest that comethylation of promoters of p16 and MGMT genes could have a prognostic value in patients with CRC. Specifically, concurrent methylation of both genes correlates with better prognosis.

A Monotonous Population of Elongated Cells (MPECs) in Colorectal Adenoma Indicates a High Risk of Metachronous Cancer

Accurate predictors for metachronous colorectal cancer (CRC) development after polypectomy are lacking. We evaluated the prognostic value of classical clinicopathologic features and a monotonous population of elongated cells (MPECs) in colorectal adenomas from 171 consecutively selected population-based patients with long-term follow-up. Quantitative image analysis, and univariate and multivariate regression analysis were applied. Ten of 171 adenomas (5.8%) developed metachronous CRC (defined as >24 mo interval and >5 cm from the index adenoma to the cancer). Median follow-up of adenomas with metachronous CRC was 68.4 and without cancer 149.7 months (range: 25 to 192 and 25 to 256, respectively). The most prognostic classical features were the localization of the marker adenoma as proximal (ie, in the cecum through transverse colon) versus distal from the transverse colon [P=0.0003, hazard ratio (HR)=8] and the number of polyps found during colonoscopy (<or=2 vs.>2, P=0.002, HR=6). Quantitative features of the MPECs included the longest nuclear axis and variance of the number of nuclei with 2 neighbors (higher and lower in cancer cases, respectively). Of the 171 adenomas, 50 (29%) had MPECs, of which 9 (18%) patients developed metachronous CRC at follow-up, contrasting 1/121 (0.8%) without MPECs (P=0.0003, HR=23). MPECs occurred in both low-grade and high-grade dysplasia, and in tubular and (tubulo) villous adenomas. MPECs had the strongest predictive value for metachronous CRC development. Adenomas proximally located had additional value but only if they were MPEC positive (which only occurred in 5 adenomas, 3 of which (60%) developed cancer). Having more than 2 polyps also had additional prognostic value but only in MPEC-negative adenomas [10 cases; 1 (10%) developed cancer]. Dysplasia grade and histologic growth pattern had no additional value. Thus, colorectal adenomas with subsequent metachronous cancer development can be identified more accurately with MPECs than with classical prognostic factors.

Adequacy of Colonoscopic Biopsy Specimens for Molecular Analysis: A Comparative Study With Colectomy Tissue

Molecular analyses of tumors are increasingly useful for prognosis and for guiding therapy. Colonoscopic biopsy provides the first source of tissue for most cases of colorectal carcinoma and therefore might become an important source for molecular analyses. We have addressed the question whether molecular analyses of colonoscopic biopsy yield results similar to the findings from the surgical specimen. Further, we analyzed 2 separate areas of the colectomy specimen to assess tumor heterogeneity. We evaluated 3 samples from each of 67 patients for point mutations in the KRAS gene, loss of heterozygosity (LOH) at the Adenomatous Polyposis Coli (APC) and Deleted in Colon Cancer (DCC) genes and for microsatellite instability (MSI) using polymerase chain reaction based techniques. The average time interval between biopsy and surgery was 2.2+/-0.15 weeks. Lesions were from all colon segments and all surgical stages. The degree of agreement between the biopsy and surgical sites was high for APC LOH, MSI, and KRAS mutations (kappa=0.85, 1.00, and 0.93, respectively) but less so for DCC LOH (kappa=0.62). Colonoscopic biopsies are an acceptable source of neoplastic DNA for studies of KRAS, APC LOH, and MSI, but less so for DCC LOH, primarily resulting from technical considerations.

K-ras, p53 mutations, and microsatellite instability (MSI) in gallbladder cancer

Despite the considerable progress in understanding the molecular pathology of carcinogenesis, the genetic mechanisms underlying the development and progression of gallbladder cancer (GC) are poorly understood. The survival of GC patients is generally poor. Therefore, it is very useful to define valuable prognostic factors. The most extensively studied oncogenes in gallbladder carcinogenesis are ras, commonly mutated in neoplasms of the gastrointestinal tract. K-ras oncogene is altered in a subset of gallbladder patients and mainly in those having anomalous junction of the pancreaticobiliary tract. Most of the studies of genetic abnormalities in GC have focused on p53 gene. p53 mutation/overexpression and/or LOH is present in more than 50% of gallbladder carcinomas, suggesting an important role in their pathogenesis. However, these results have not any predictive value yet. Moreover, the involvement of an alternative molecular pathway, that of microsatellite instability (MSI), is found in a limited group of GC patients. Additional research is necessary to establish its possible relation to defects of the mismatch repair (MMR) system and its proposed prognostic significance. Further elucidation of the molecular events specific to GC will help to identify novel molecular targets for the diagnosis and clinical management of the patients.

Mutant KRAS, chromosomal instability and prognosis in colorectal cancer

The RAS gene family provides a global effect on gene expression by encoding small GTP-binding proteins which act as molecular switches connecting extracellular signals with nuclear transcription factors. While wild type RAS proteins are switched off shortly after activation, mutant RAS proteins remain constitutively activated leading to complex interactions among their downstream effectors. For some human tumor types, these interactions were shown to contribute to cancer genesis and progression by inducing changes in cell survival, apoptosis, angiogenesis, invasion and metastasis. This review addresses the controversial link of KRAS mutations in colorectal cancer with chromosomal instability and patient prognosis.

Frequency and spectrum of K-RAS codons 12 and 13 mutations in colorectal adenocarcinomas from Taiwan

Mutations in codons 12 and 13 of the K-RAS oncogene are detected at a remarkably high frequency in colorectal adenocarcinoma and are believed to be a critical event in oncogenesis. In the present study, we evaluated colorectal tumor specimens from Taiwan for mutations in K-RAS codons 12 and 13 using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis and direct DNA sequencing. Mutations were found in 48 of 181 (26.5%) tumors, 30 mutations were G-->A transitions (62.5% of all mutations), 14 were G-->T transversions (29.2%), and only 4 were G-->C transversions (8.3%). Similar relative mutation frequencies and spectra were found regardless of the sex of the patient, the tumor grade, or the tumor stage. The high frequency of transitions among K-RAS mutation suggests that G/T mismatches play an important role in the oncogenesis of colorectal adenocarcinoma, implying that alkylating carcinogens may be involved in the colorectal carcinogenesis. Although the frequency of mutation (26.5%) appears to be lower than those reported in the United States (40%), France (49%), and the Netherlands (34%), the spectrum of point mutations in codons 12 and 13 of the K-RAS gene in the Taiwan Chinese population appears to be similar. The reason for these results may be that diet and ethnicity are not rate limit factors in controlling the spectra of mutations but influence on the frequency of K-RAS mutations in human colorectal adenocarcinomas.

Ki-ras gene mutations, LOH of the APC and DCC genes, and microsatellite instability in primary colorectal carcinoma are not associated with micrometastases in pericolonic lymph nodes or with patients' survival

AIMS

The primary aim of this study was to look for possible correlations between molecular genetic changes in primary colorectal cancer and the presence or absence of micrometastases in the accompanying pericolonic lymph nodes. The secondary aim was to correlate the data on these molecular genetic changes and micrometastases with survival.

METHODS

One hundred and twenty five Dukes's stage B colorectal cancers from 1989 to 1992 were analysed. The primary tumours were evaluated for Ki-ras mutation, adenomatous polyposis coli (APC) loss of heterozygosity (LOH), deleted in colon cancer (DCC) LOH, and microsatellite instability using standard molecular techniques. All available lymph nodes were immunohistochemically stained for micrometastases.

RESULTS

Micrometastases were present in 41% of patients. There were significantly more lymph nodes removed in the patients with micrometastases. Micrometastases were not associated with Ki-ras mutation, APC LOH, DCC LOH, or microsatellite instability, even when controlling for the number of lymph nodes removed. None of the molecular variables considered had a significant impact on either overall survival or on death with disease.

CONCLUSIONS

There are insufficient data to justify using molecular genetic changes in primary colorectal carcinomas as prognostic markers. Micrometastases do not provide prognostic information on survival. There is value in increasing the numbers of lymph nodes removed and analysed along with the primary tumour.