Research IndicatorsGraph generated 31 August 2019 using data from PubMed using criteria.
Mouse over the terms for more detail; many indicate links which you can click for dedicated pages about the topic. Tag cloud generated 31 August, 2019 using data from PubMed, MeSH and CancerIndex
Specific Cancers (5)
Data table showing topics related to specific cancers and associated disorders. Scope includes mutations and abnormal protein expression.
Note: list is not exhaustive. Number of papers are based on searches of PubMed (click on topic title for arbitrary criteria used).
OMIM, Johns Hopkin University
Referenced article focusing on the relationship between phenotype and genotype.
International Cancer Genome Consortium.
Summary of gene and mutations by cancer type from ICGC
Cancer Genome Anatomy Project, NCI
COSMIC, Sanger Institute
Somatic mutation information and related details
GEO Profiles, NCBI
Search the gene expression profiles from curated DataSets in the Gene Expression Omnibus (GEO) repository.
Latest Publications: GOLGA5 (cancer-related)
Longo T, McGinley KF, Freedman JA, et al.Targeted Exome Sequencing of the Cancer Genome in Patients with Very High-risk Bladder Cancer.
Eur Urol. 2016; 70(5):714-717 [PubMed
] Related Publications
We completed targeted exome sequencing of the tumors of 50 patients with pTis-pT4b bladder cancer. Mutations were categorized by type, stratified against previously identified cancer loci in the Catalogue of Somatic Mutations in Cancer and The Cancer Genome Atlas databases, and evaluated in pathway analysis and comutation plots. We analyzed mutation associations with receipt of neoadjuvant chemotherapy, nodal involvement, metastatic disease development, and survival. Compared with The Cancer Genome Atlas, we found higher mutation rates in genes encoding products involved in epigenetic regulation and cell cycle regulation. Of the pathways examined, PI3K/mTOR and Cell Cycle/DNA Repair exhibited the greatest frequencies of mutation. RB1 and TP53, as well as NF1 and PIK3CA were frequently comutated. We identified no association between mutations in specific genes and key clinical outcomes of interest when corrected for multiple testing. Discovery phase analysis of the somatic mutations in 50 high-risk bladder cancer patients revealed novel mutations and mutational patterns, which may be useful for developing targeted therapy regimens or new biomarkers for patients at very high risk of disease metastasis and death.
PATIENT SUMMARY: In this report we found known, as well as previously unreported, genetic mutations in the tumors of patients with high-risk bladder cancer. These mutations, if validated, may serve as actionable targets for new trials.
Varghese S, Burness M, Xu H, et al.Site-specific gene expression profiles and novel molecular prognostic factors in patients with lower gastrointestinal adenocarcinoma diffusely metastatic to liver or peritoneum.
Ann Surg Oncol. 2007; 14(12):3460-71 [PubMed
] Related Publications
BACKGROUND: Generally, colorectal and high-grade appendiceal cancers are treated similarly; treatment approach is primarily based on tumor histology and stage of disease. Patients with adenocarcinoma of the lower gastrointestinal tract frequently experience diffuse metastases isolated to liver or peritoneum and have a poor survival. Identification of novel molecular pathways in metastases from these patients may identify novel targets and prognostic factors.
METHODS: Microarray analyses of 20 metastatic tumors from patients with colorectal adenocarcinoma isolated to liver or peritoneum and eight high-grade appendiceal adenocarcinoma metastatic to peritoneum were performed using oligonucleotide microarray.
RESULTS: In an unsupervised hierarchical cluster analysis of 2-fold upregulated or downregulated genes, there was a clear site-specific segregation of liver versus peritoneal metastases. Genes primarily involved in metastasis, angiogenesis, cell cycle regulation, cell proliferation, and cell adhesion were distinctly altered between these two metastatic sites. Among the metastasis genes, the average expression levels of LI-cadherin, ALCAM, CD2, and CD14 were significantly higher in both metastatic sites. TIMP1 was overexpressed in both sites where as TIMP-2, IGF-1, and HIF-1alpha were upregulated only in peritoneal metastases demonstrating the potential benefit of metastasis site-specific treatments. Subsets of genes significantly associated with poor survival were defined, a RET proto-oncogene interacting gene, GOLGA5, was highly predictive for survival in patients with colorectal adenocarcinoma.
CONCLUSIONS: These results demonstrate that liver and peritoneal metastases of lower GI adenocarcinoma have distinct gene expression patterns; these distinctions may help in the development of therapies based on site of metastases.
Rabes HMGene rearrangements in radiation-induced thyroid carcinogenesis.
Med Pediatr Oncol. 2001; 36(5):574-82 [PubMed
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BACKGROUND: Radiation is an accepted risk factor for thyroid carcinogenesis in children. Recent observations in large cohorts of children and young adults who developed papillary thyroid carcinomas (PTC) related to accidental radiation exposure after the Chernobyl reactor accident revealed typical genetic aberrations shedding light on genetic determinants and mechanisms of radiation-induced carcinogenesis.
PROCEDURE: A molecular genetic analysis was performed on 191 post-Chernobyl PTC by RT-PCR, multiplex PCR, DNA sequencing, and in some cases 5'RACE. Determination of point mutations was by means of PCR and either allele-specific oligonucleotide hybridization or SSCP and DNA sequencing.
RESULTS: In various sporadic thyroid tumor types of adults structural genetic aberrations have been found involving mutations of RAS (codon 12, 13, 61), p53 (exons 5 to 8), Gsalpha (codon 201 and 227), and, at a low prevalence, the receptor tyrosine kinases RET or NTRK1. In contrast, in radiation-induced PTC of children RET rearrangements are by far the most prevalent genetic aberrations. In these RET rearrangements, the transmembrane and extracellular domains of RET are lost, and are replaced by parts of other genes at the 5' end. These genes always contain coiled-coil domains with dimerization potential and lead to constitutive, ligand-independent activation of the ret tyrosine kinase domain at the 3' end of the fusion product. The most frequent radiation-induced RET gene fusions involve the ELE1 (ARA70) gene, a transcription coactivator of the androgen receptor (PTC3), and H4, a gene of unknown function (PTC1). Both rearrangements originate from DNA double strand breaks with repair by intrachromosomal balanced paracentric inversion and recombination by illegitimate DNA endjoining at small stretches of homologous nucleotide sequences and direct or inverted repeats, without significant breakpoint clusters in the involved introns. In addition, five different RET-fused genes, RIalpha, GOLGA5, HTIF, RFG7 and RFG8, have been detected leading to the PTC2, 5, 6, 7 and 8 types of RET rearrangements, respectively. Each fusion leads, in principle, to the same effect: The ret tyrosine kinase is uncoupled from its stringent physiological regulation by replacement of its 5' end and is aberrantly activated by the 5' parts of fused genes in thyrocytes that do not normally express ret tyrosine kinase. Ectopic ret expression, clonal expansion and early invasion are peculiar to the affected cells. The RET-fused gene is obviously decisive for modulating tumor development: ELE1/RET rearrangements lead to most rapid tumor progression and are related to the solid variant of PTC, in contrast to H4/RET rearrangements connected with papillary or follicular variants of PTC.
CONCLUSIONS: Typical genetic aberrations are produced by radioiodine uptake in the juvenile thyroid gland. They act as determinants of phenotype, biology, and clinical course of radiation-induced papillary thyroid carcinomas.
Rabes HM, Demidchik EP, Sidorow JD, et al.Pattern of radiation-induced RET and NTRK1 rearrangements in 191 post-chernobyl papillary thyroid carcinomas: biological, phenotypic, and clinical implications.
Clin Cancer Res. 2000; 6(3):1093-103 [PubMed
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Molecular genetic aberrations and the related phenotypes were investigated in 191 papillary thyroid carcinomas (PTCs) from patients exposed at young age to radioiodine released from the Chernobyl reactor. A high prevalence of RET gene rearrangements (62.3%) with a significant predominance of ELE1/RET (PTC3) over H4/RET (PTC1) rearrangements was found in PTCs of the first post-Chernobyl decade. NTRK1 rearrangements were rare (3.3%). In 3.3%, we observed novel types of RET rearrangements: GOLGA5/ RET (PTC5), HTIF/RET (PTC6), RFG7/RET (PTC7), and an as yet undefined RFGX/RET.RET rearrangements, preferentially ELE1/RET, are related to rapid tumor development. At longer intervals after exposure to ionizing radiation, the prevalence of RET rearrangements declines with a shift from ELE1/RET to H4/RET, most significantly in female patients. The prevalence of specific types of rearrangements is independent of age at irradiation. A significantly higher prevalence of ELE1/RET was observed in the most heavily contaminated Oblasts, Gomel and Brest, suggesting a preferential formation of this type of rearrangement after high thyroid doses. RET rearrangement is related to aggressive growth: Rearrangement-positive PTCs were in a more advanced pT category and more frequently in the pN1 category at presentation than rearrangement-negative PTCs. ELE1/RET is related to the solid variant of PTC, H4/RET more frequently to typical papillary structures. The genotype/phenotype evaluation of post-Chernobyl PTCs reveals a characteristic spectrum of gene rearrangements that lead to typical phenotypes with important biological and clinical implications.
Rabes HM, Klugbauer SMolecular genetics of childhood papillary thyroid carcinomas after irradiation: high prevalence of RET rearrangement.
Recent Results Cancer Res. 1998; 154:248-64 [PubMed
] Related Publications
Epidemiological studies have revealed a connection between thyroid carcinogenesis and a history of radiation. The molecular mechanisms involved are not well understood. It has been claimed that RAS, p53 or GSP mutations and RET or TRK rearrangements might play a role in adult thyroid tumors. In childhood, the thyroid gland is particularly sensitive to ionizing radiation. The reactor accident in Chernobyl provided a unique chance to study molecular genetic aberrations in a cohort of children who developed papillary thyroid carcinomas after a short latency time after exposure to high doses of radioactive iodine isotopes. According to the concepts of molecular genetic epidemiology, exposure to a specific type of irradiation might result in a typical molecular lesion. Childhood papillary thyroid tumors after Chernobyl exhibit a high prevalence of RET rearrangement as almost the only molecular alteration. The majority showed RET/PTC3 (i.e., ELE/RET rearrangements), including several subtypes. Less frequently, RET/PTC1 (i.e., H4/RET rearrangements), and a novel type (RET/PTC5, i.e., RFG5/RET) were observed. Proof of reciprocal transcripts suggests that a balanced intrachromosomal inversion leads to this rearrangement. Breakpoint analyses revealed short homologous nucleotide stretches at the fusion points. In all types of rearrangement, the RET tyrosine kinase domain becomes controlled by 5' fused regulatory sequences of ubiquitously expressed genes that display coiled-coil regions with dimerization potential. Oncogenic activation of RET is apparently due to ligand-independent constitutive ectopic RET tyrosine kinase activity. The analysis of this cohort of children with radiation-induced thyroid tumors after Chernobyl provides insights into typical molecular aberrations in relation to a specific mode of environmental exposure and may serve as a paradigm for molecular genetic epidemiology.
Klugbauer S, Demidchik EP, Lengfelder E, Rabes HMDetection of a novel type of RET rearrangement (PTC5) in thyroid carcinomas after Chernobyl and analysis of the involved RET-fused gene RFG5.
Cancer Res. 1998; 58(2):198-203 [PubMed
] Related Publications
A novel type of RET rearrangement, PTC5, was detected in papillary thyroid carcinomas of two patients exposed to radioactive fallout after Chernobyl. Reverse transcription-PCR and rapid amplification of 5'-cDNA ends revealed a fusion of the ret tyrosine kinase (TK) domain with a sequence identical to that described previously as ret-II. Ret-II is a transfection artifact in NIH3T3 cells and has not yet been detected in any human tumor. Overlapping sequences found in the expressed sequence tag databases enabled us to sequence the COOH terminus of the ret-fused gene 5 (RFG5). The combined data made it possible to assemble a full-length rfg5 protein sequence. Computer-assisted analysis of this sequence reveals four putative coiled-coil structures, possibly involved in dimerization, but no membrane-binding sequences. Northern blots show a ubiquitous RFG5 expression in various normal tissues, including the thyroid gland. In addition to the RFG5/RET, we also detected the reciprocal RET/RFG5 transcript in both tumor samples, suggesting that the rearrangement is based on a balanced reciprocal translocation. In agreement with other rearranged TKs, it is concluded that the transforming action of the new fusion protein rfg5/ret in thyroid tumors may be due to an activation of the ret TK by constitutive expression and dimerization potential of the 5'-fused rfg5 protein. Ret immunohistochemistry indicates that the fusion protein is expressed in all cells of PTC5 tumors, suggesting that RFG5/RET rearrangement is an early event in thyroid carcinogenesis.
A poly(ADP-ribose) polymerase inhibitor, benzamide (BA), was found to induce flat revertants of NIH 3T3 cells that had been transformed by human Ha-ras, rat Ki-ras, rat c-raf, and human ret-II. These genes had been amplified in original transformants, but they were completely eliminated by BA. Contrary to this, endogenous activated Ha-ras in a human bladder carcinoma cell line, T24, was not eliminated by BA. The gene loss seemed to be restricted to exogenous and/or amplified sequences. BA also eliminated the amplified c-myc gene in HL-60 cells, concomitant with differentiation into granulocytes. We demonstrated that the amplified c-myc gene was not present as episomes. It is probably present as double minutes or a homogeneously staining region. Dimethylsulfoxide also induced differentiation at a concentration that did not inhibit poly(ADP-ribose) polymerase. The cell lost the c-myc gene in association with this differentiation. The amplified c-myc gene in a colon adenocarcinoma cell line, COLO 320HSR, and the amplified mdr-1 gene in an adriamycin-resistant myelogenous leukemia cell line, K562/ADM, were not eliminated by BA. Various poly(ADP-ribose) polymerase inhibitors also eliminated human Ha-ras in the NIH 3T3 transformant and the c-myc gene in HL-60 cells.
Ishizaka Y, Ushijima T, Sugimura T, Nagao McDNA cloning and characterization of ret activated in a human papillary thyroid carcinoma cell line.
Biochem Biophys Res Commun. 1990; 168(2):402-8 [PubMed
] Related Publications
We obtained activated ret cDNAs (retTPC) from a human papillary thyroid carcinoma cell line, TPC-1, and characterized its structure. The nucleotide sequence indicated that the recombination had occurred just upstream of the kinase domain of ret proto-oncogene and that the position, where the conserved sequence of ret proto-oncogene starts in retTPC transcripts, was exactly the same as that of ret-II which we have previously analyzed. Furthermore, a unique 13-glycine stretch, which is also present in a small subunit of the calcium dependent protease, calpain, was detected in the replaced sequence of retTPC. The aberrant tyrosine kinase activity induced by the rearrangement of ret proto-oncogene could be involved in the development of papillary thyroid carcinoma.
Ishizaka Y, Ochiai M, Tahira T, et al.Activation of the ret-II oncogene without a sequence encoding a transmembrane domain and transforming activity of two ret-II oncogene products differing in carboxy-termini due to alternative splicing.
Oncogene. 1989; 4(6):789-94 [PubMed
] Related Publications
We previously reported the cloning of a transforming gene, ret-II, which contains the proto-ret kinase domain. In the present study ret-II cDNAs were cloned from a transformant and analyzed. The restriction map and nucleotide sequence indicated that the sequence upstream of the proto-ret kinase domain was replaced by another sequence, which encoded a fusion protein composed of 899 amino acids. This non-proto-ret sequence differed from that of the ret previously reported and had no hydrophobic amino acid stretch for a transmembrane domain. Furthermore, we obtained two kinds of ret-II cDNAs differing in their 3' regions and found that the differences were generated by alternative splicing. From these cDNAs, two types of oncogene products differing in their carboxy-terminal amino acid residues were predicted. The two products exhibited similar transforming activity in NIH3T3 cells. These data indicate that activation of proto-ret can occur as a result of replacement of the extra-cellular and transmembrane domains with the hydrophilic sequence. In addition, differences in the carboxy-terminal amino acid residues in the two types of ret-II oncogene products have no influence on the transforming activity of the ret-II oncogene.