Chang Hyeok An

Somatic mutations of the KEAP1 gene in common solid cancers.

Yoo N J, Kim H R, Kim Y R, An C H & Lee S H 
(2012) Histopathology 60, 943–952

Detection of Low-Level KRAS Mutations Using PNA-Mediated Asymmetric PCR Clamping and Melting Curve Analysis with Unlabeled Probes

Detection of somatic mutations in clinical cancer specimens is often hampered by excess wild-type DNA. The aim of this study was to develop a simple and economical protocol without using fluorescent probes to detect low-level mutations. In this study, we combined peptide nucleic acid (PNA)-clamping PCR with asymmetric primers and a melting curve analysis using an unlabeled detection probe. PNA-clamping PCR, which suppressed amplification of the wild-type allele, was more sensitive for KRAS codon 12 mutation detection than nonclamping PCR in 5 different mutant cell lines. Three detection probes were tested (a perfectly matched antisense, a mismatched antisense, and a mismatched sense), and the mismatched sense detection probe showed the highest sensitivity (0.1% mutant detection) under clamping conditions. With this probe, we were able to detect not only the perfectly matched KRAS mutation, but also 4 other mismatched mutations of KRAS. We then applied this protocol to 10 human colon cancer tissues with KRAS codon 12 mutations, successfully detecting the mutations in all of them. Our data indicate that the combination of perfectly matched antisense PNA and a mismatched sense detection probe can detect KRAS mutations with a high sensitivity in both cell lines and human tissues. Moreover, this study might prove an easily applicable protocol for the detection of low-level mutations in other cancer genes.

Mutational and expressional analyses of ATG5, an autophagy-related gene, in gastrointestinal cancers.

There is mounting evidence that alterations of cell death processes are involved in cancer pathogenesis. ATG5 is a key regulator of autophagic and apoptotic cell death. The aim of this study was to see whether alterations of ATG5 protein expression and somatic mutation of ATG5 gene are features of human gastrointestinal cancers. In this study, we analyzed ATG5 somatic mutation in 45 gastric, 45 colorectal, and 45 hepatocellular carcinomas by single-strand conformation polymorphism (SSCP). Also, we analyzed ATG5 protein expression in 100 gastric, as well as in 95 colorectal and hepatocellular carcinomas using immunohistochemistry. Overall, we detected two somatic missense mutations of ATG5 gene in the coding sequences p.Leu112Phe and p.His41Tyr. The mutations were observed in one gastric and one hepatocellular carcinoma. Immunohistochemically, ATG5 protein was well expressed in normal stomach, colon, and liver epithelial cells, while it was lost in 21 (21%) of the gastric carcinomas, in 22 (23%) of the colorectal carcinomas, and in 5 (10%) of the hepatocellular carcinomas. Our data suggest that ATG5 gene could be altered in gastrointestinal cancers at the mutational or expressional level. Despite the low incidences of the alterations, our data led us to conclude that somatic mutation and loss of expression of ATG5 gene might play a role in gastrointestinal cancer pathogenesis by altering autophagic and apoptotic cell death.

Frameshift mutations of vacuolar protein sorting genes in gastric and colorectal cancers with microsatellite instability

Vacuolar protein sorting plays crucial roles in the traffic of molecules between cellular organelles. Although involvement of vacuolar protein sorting proteins in cancer is known, genetic alterations of VPS genes have not been reported in cancers. We found that VPS4B, VPS13A, VPS13B, VPS13C, VPS33A, VPS35, VPS37B, VPS37D, VPS41, and VPS54 have mononucleotide repeats in their coding sequences. To see whether these genes are mutated in cancers with microsatellite instability, we analyzed the mononucleotide repeats in 30 gastric cancers with high microsatellite instability, 13 gastric cancers with low microsatellite instability, and 45 gastric cancers with stable microsatellites and 40 colorectal cancers with high microsatellite instability, 14 colorectal cancers with low microsatellite instability, and 45 colorectal cancers with stable microsatellites by single-strand conformation polymorphism. We found mutations of VPS13A, VPS13B, VPS13C, VPS33A, VPS35, VPS37B, VPS41, and VPS54 in 9, 3, 12, 3, 5, 9, 2, and 2 cancers, respectively, all in cancers with high microsatellite instability. The gastric cancers and colorectal cancers with high microsatellite instability harbored one or more mutations of the VPS genes in 53.3% and 50.0%, respectively. Loss of Vps13A expression was observed in 30% of the gastric cancers and 35% of the colorectal cancers, whereas loss of Vps35 was observed in 55% of the gastric cancers and 55% of the colorectal cancers. Our data indicate that frameshift mutations of VPS genes and losses of expression of Vps13A and Vps35 proteins are common in gastric cancers and colorectal cancers with high microsatellite instability and suggest that these alterations might contribute to development of cancers with high microsatellite instability by deregulating vacuolar protein sorting proteins.

Detection of low‐level EGFR T790M mutation in lung cancer tissues

Oh JE, An CH, Yoo NJ, Lee SH. Detection of low‐level EGFR T790M mutation in lung cancer tissues. APMIS 2011; 119: 403–11.

Frameshift mutations of chromosome cohesion–related genes SGOL1 and PDS5B in gastric and colorectal cancers with high microsatellite instability

Cohesin is a protein complex that regulates chromatid cohesion and plays a role in preventing aneuploidy and maintaining chromosomal stability. SGOL1 encodes a cohesin protector, and PDS5B encodes a regulatory cohesion factor. Both SGOL1 and PDS5B are considered putative tumor suppressor genes. The aim of this study was to explore whether SGOL1 and PDS5B genes are mutated and expressionally altered in gastric and colorectal cancers. A genome database indicated that both genes possessed mononucleotide repeats in coding sequences, which could be mutation targets in cancers with microsatellite instability. We analyzed mutations in 91 gastric cancers and 100 colorectal cancers with high microsatellite instability or stable/low microsatellite instability by single-strand conformation polymorphism analysis and DNA sequencing. We also analyzed SGOL1 and PDS5B expression by immunohistochemistry. Overall, we found 21 SGOL1 frameshift mutations in 21 cases and 18 PDS5B frameshift mutations in 16 cases. SGOL1 and PDS5B frameshift mutations were detected in 26.6% and 20.3%, respectively, of high microsatellite instability but not in stable/low microsatellite instability (0/112). By immunohistochemistry, losses of SGOL1 and PDS5B were identified in 19% to 47% of the gastric and colorectal cancers irrespective of microsatellite instability status. The losses were more common in those with frameshift mutations or high microsatellite instability than those without mutations or high microsatellite instability. The data indicate that frameshift mutations of SGOL1 and PDS5B and the loss of their expression may be a feature of gastric and colorectal cancers with high microsatellite instability. In addition, the data suggest that these alterations might contribute to cancer pathogenesis by deregulating cohesin-related functions.

Mutational and expressional analysis of RFC3, a clamp loader in DNA replication, in gastric and colorectal cancers.

Parts of gastric (GC) and colorectal cancers (CRC) exhibit microsatellite instability (MSI) that causes frameshift mutations and contributes to cancer development. DNA replication and repair play crucial roles in maintenance of genome stability, and their alterations contribute to cancer development. In this study, we analyzed mutation of RFC1 and RFC3, clamp loaders in DNA replication, in GC and CRC with MSI. We analyzed mononucleotide repeats in RFC1 and RFC3 in 29 GC with high MSI (MSI-H), 20 GC with low MSI (MSI-L), 45 GC with stable MSI (MSS), 35 CRC with MSI-H, 20 CRC with MSI-L, and 45 CRC with MSS by single-strand conformation polymorphism. We also analyzed RFC3 expression in the GC and CRC. We found RFC3 frameshift mutations in 7 GC (24.1%) and 9 CRC with MSI-H (25.7%) but not in cancers with MSI-L or MSS. The mutations consisted of 14 c.244delA, one 243_244delAA, and one c.244dupA, which would result in premature stops of RFC3 amino acid synthesis. Loss of RFC3 expression was observed in 51% of the GC and 65% of the CRC, but all of the cancers with RFC3 frameshift mutations were weak or negative. Our data indicate RFC3 mutation and loss of RFC3 expression occur in large fractions of GC and CRC and suggest that these alterations may contribute to the cancer pathogenesis by deregulating DNA repair and replication.

Frameshift mutations of ATBF1, WNT9A, CYLD and PARK2 in gastric and colorectal carcinomas with high microsatellite instability

implication on the treatment. In all of the subsequent cases reported after the original report, the short term prognosis has been good with no recurrence or metastasis reported. The long term prognosis is unclear at this stage but will become clearer with further patient monitoring and follow-up. In this study, we described an additional case of PAMT of the stomach. Our current case shares the clinical, histological, immunophenotypical and ultrastructural features of the previously described cases (Table 1).

Mutational and expressional analyses of NRF2 and KEAP1 in sarcomas.

AIMS AND BACKGROUND Nuclear factor erythroid 2-related factor 2 (NRF2) activates expression of cytoprotective proteins such as GCLC and enhances cancer cell survival, whereas KEAP1 inhibits NRF2 by mediating NRF2 degradation. Somatic mutation of NRF2 and KEAP1 genes and loss of KEAP1 expression are detected in many carcinomas and contribute to cancer development. The aim of this study was to see whether mutational and expressional alterations of NRF2 and KEAP1 genes are features of human sarcomas as well. METHODS We analyzed somatic mutations of NRF2 and KEAP1 genes in 108 sarcoma tissues from malignant fibrous histiocytomas, rhabdomyosarcomas, osteosarcomas, malignant peripheral nerve sheath tumors, leiomyosarcomas, synovial sarcomas, liposarcomas, angiosarcomas, chondrosarcomas and Ewing sarcomas by single-strand conformation polymorphism. Also, we analyzed expressions of NRF2, KEAP1 and GCLC in sarcoma tissues by immunohistochemistry. RESULTS Tissue expressions of NRF2 and GCLC were found in 93% and 76% of the sarcomas, respectively, indicating that NRF2 signaling might be activated in most sarcomas. Loss of KEAP1 expression was observed in 24% of the sarcomas, whereas neither NRF2 nor KEAP1 somatic gene mutation was seen in the sarcomas. CONCLUSIONS Our data suggest a possible activation of the NRF2/KEAP1 system in sarcomas and a possible contribution to cytopretection of sarcoma cells.

Frameshift mutations of poly(adenosine diphosphate-ribose) polymerase genes in gastric and colorectal cancers with microsatellite instability.

Poly(adenosine diphosphate-ribose) polymerases consist of 16 members that modify nuclear proteins by building adenosine diphosphate-ribose polymers. Poly(adenosine diphosphate-ribose) polymerase 1, the prototype poly(adenosine diphosphate-ribose) polymerase, and some poly(adenosine diphosphate-ribose) polymerases are involved in many cellular processes including DNA damage response/repair, cell death, and inflammation. Inactivation of poly(adenosine diphosphate-ribose) polymerase proteins frequently enhances genomic instability and apoptosis inactivation, suggesting their roles in cancer development. However, genetic alterations of poly(adenosine diphosphate-ribose) polymerase genes have not been reported in cancers. In a public database, we found that poly(adenosine diphosphate-ribose) polymerase 1, poly(adenosine diphosphate-ribose) polymerase 11, poly(adenosine diphosphate-ribose) polymerase 14, poly(adenosine diphosphate-ribose) polymerase 15, tankyrase-1 (TNKS1), and tankyrase-2 (TNKS2) genes have mononucleotide repeats in coding DNA sequences. To see whether these genes are mutated in cancers with microsatellite instability, we analyzed the mononucleotide repeats in 30 gastric cancers with high microsatellite instability, 13 gastric cancers with low microsatellite instability, 45 gastric cancers with stable microsatellite instability, 40 colorectal cancers with high microsatellite instability, 14 colorectal cancers with low microsatellite instability, and 45 colorectal cancers with stable microsatellite instability by single-strand conformation polymorphism. We found poly(adenosine diphosphate-ribose) polymerase 14, TNKS1, and TNKS2 mutations in 8, 4, and 18 cancers, respectively. They were detected in cancers with high microsatellite instability but not in cancers with low microsatellite instability or stable microsatellite instability. The gastric cancers and colorectal cancers with high microsatellite instability harbored one or more mutations of the poly(adenosine diphosphate-ribose) polymerase genes in 50.0% and 27.5%, respectively. Of the genes with mutations, we analyzed poly(adenosine diphosphate-ribose) polymerase 14 protein expression in gastric and colorectal cancers with high microsatellite instability. Loss of poly(adenosine diphosphate-ribose) polymerase 14 expression was observed in 33% of the gastric cancers and 35% of the colorectal cancers with high microsatellite instability, whereas its loss was observed in 31% of the gastric cancers and 36% of the colorectal cancers with low microsatellite instability/stable microsatellite instability. Our data indicate that frameshift mutations of poly(adenosine diphosphate-ribose) polymerases genes and losses of expression of poly(adenosine diphosphate-ribose) polymerase 14 protein are features of gastric and colorectal cancers with high microsatellite instability and suggest that these alterations might contribute to development of cancers with high microsatellite instability by deregulating poly(adenosine diphosphate-ribose) polymerase-mediated signaling.