Molecular evolutionary rates of oncogenes

Summary Using nine sets of viral and cellular oncogenes, the rates of nucleotide substitutions were computed by using Gojobori and Yokoyama's (1985) method. The results obtained confirmed our previous conclusion that the rates of nucleotide substitution for the viral oncogenes are about a million times higher than those for their cellular counterparts. For cellular oncogenes and most viral oncogenes, however, the rate of synonymous substitution is higher than that of nonsynonymous substitution. Moreover, the pattern of nucleotide substitutions for viral oncogenes is more similar to that for functional genes (such as cellular oncongenes) than for pseudogenes. This implies that nucleotide substitutions in viral oncogenes may be functionally constrained. Thus, our observation supports that nucleotide substitutions for the oncogenes in those DNA and RNA genomes are consistent with Kimura's neutral theory of molecular evolution (Kimura 1968, 1983).     

Automated oncogene detection in complex protein networks with applications to the MAPK signal transduction pathway

Activation of the extracellular signal-regulated kinases (ERK1/2; p42/p44 mitogen-activated protein kinase (MAPK)) is one of the most extensively studied signaling pathways not least because it occurs downstream of oncogenic RAS. Here, we take advantage of the wealth of experimental data available on the canonical RAS/RAF/MEK/ERK pathway of Bhalla et al. to test the utility of a newly developed nonlinear analysis algorithm designed to predict likelihood of cellular transformation. By using ERK phosphorylation as an "output signal", the method analyzes experimentally determined kinetic data and predicts putative oncogenes and tumor suppressor gene products impacting the RAS/MAPK module using a purely theoretical approach. This analysis identified several modifiers of ERK/MAPK activation described previously. In addition, several novel enzymes are identified which are not previously described to affect ERK/MAPK phosphorylation. Importantly, the nonlinear analysis enables a ranking of modifiers of MAPK activation predicting their relative importance in RAS-dependent oncogenesis. The results are compared with a linearized analysis based on sensitivity analysis about the steady state or metabolic control analysis (MCA). The results are favorable, pointing to the utility of first-order sensitivity analysis and MCA in the analysis of complex signaling networks for oncogenes.     

Oncogene expression in myelopoiesis

Oncogenes are a class of genes hypothesized to be causally related to neoplasia. To date, specific oncogenes have been recognized chiefly by their ability to transform test cells to a neoplastic phenotype. This has been accomplished largely through mutational analysis of the genotype of retroviruses or through the analysis of tumor cell DNA by in vitro transfection of rodent fibroblasts. Oncogenes are believed to arise by some genetic alteration from normal cellular genes called proto-oncogenes. Although the normal function of most proto-oncogenes is unknown, it has been proposed that they may function as tissue-specific and temporally specific regulators of differentiation. The role of oncogenes in lymphoid malignancies has been extensively analyzed. Less is known about their role in myeloid leukemias and especially in normal myelopoiesis. Space limitations permit discussion of only salient features of a limited number of oncogenes; we have arbitrarily selected myc, myb, fos, fms, fes, sis, and abl.     

Discovery Proteomics Analysis Determines That Driver Oncogenes Suppress Antiviral Defense Pathways Through Reduction in Interferon-β Autocrine Stimulation

Since the discovery of oncogenes, there has been tremendous interest to understand their mechanistic basis and to develop broadly actionable therapeutics. Some of the most frequently activated oncogenes driving diverse cancers are c-MYC, EGFR, HER2, AKT, KRAS, BRAF, and MEK. Using a reductionist approach, we explored how cellular proteomes are remodeled in isogenic cell lines engineered with or without these driver oncogenes. The most striking discovery for all oncogenic models was the systematic downregulation of scores of antiviral proteins regulated by type 1 interferon. These findings extended to cancer cell lines and patient-derived xenograft models of highly refractory pancreatic cancer and osteosarcoma driven by KRAS and MYC oncogenes. The oncogenes reduced basal expression of and autocrine stimulation by type 1 interferon causing remarkable convergence on common phenotypic and functional profiles. In particular, there was dramatically lower expression of dsRNA sensors including DDX58 (RIG-I) and OAS proteins, which resulted in attenuated functional responses when the oncogenic cells were treated with the dsRNA mimetic, polyI:C, and increased susceptibility to infection with an RNA virus shown using SARS-CoV-2. Our reductionist approach provides molecular and functional insights connected to immune evasion hallmarks in cancers and suggests therapeutic opportunities.     

Discovery Proteomics Analysis Determines That Driver Oncogenes Suppress Antiviral Defense Pathways Through Reduction in Interferon-β Autocrine Stimulation

Since the discovery of oncogenes, there has been tremendous interest to understand their mechanistic basis and to develop broadly actionable therapeutics. Some of the most frequently activated oncogenes driving diverse cancers are c-MYC, EGFR, HER2, AKT, KRAS, BRAF, and MEK. Using a reductionist approach, we explored how cellular proteomes are remodeled in isogenic cell lines engineered with or without these driver oncogenes. The most striking discovery for all oncogenic models was the systematic downregulation of scores of antiviral proteins regulated by type 1 interferon. These findings extended to cancer cell lines and patient-derived xenograft models of highly refractory pancreatic cancer and osteosarcoma driven by KRAS and MYC oncogenes. The oncogenes reduced basal expression of and autocrine stimulation by type 1 interferon causing remarkable convergence on common phenotypic and functional profiles. In particular, there was dramatically lower expression of dsRNA sensors including DDX58 (RIG-I) and OAS proteins, which resulted in attenuated functional responses when the oncogenic cells were treated with the dsRNA mimetic, polyI:C, and increased susceptibility to infection with an RNA virus shown using SARS-CoV-2. Our reductionist approach provides molecular and functional insights connected to immune evasion hallmarks in cancers and suggests therapeutic opportunities.     

Identification of novel candidate oncogenes in chromosome region 17p11.2-p12 in human osteosarcoma

Osteosarcoma is the most common primary malignancy of bone. The tumours are characterized by high genomic instability, including the occurrence of multiple regions of amplifications and deletions. Chromosome region 17p11.2-p12 is amplified in about 25% of cases. In previous studies, COPS3 and PMP22 have been identified as candidate oncogenes in this region. Considering the complexity and variation of the amplification profiles for this segment, the involvement of additional causative oncogenes is to be expected. The aim of the present investigation is to identify novel candidate oncogenes in 17p11.2-p12. We selected 26 of in total 85 osteosarcoma samples (31%) with amplification events in 17p11.2-p12, using quantitative PCR for 8 marker genes. These were subjected to high-resolution SNP array analysis and subsequent GISTIC analysis to identify the most significantly amplified regions. Two major amplification peaks were found in the 17p11.2-p12 region. Overexpression as a consequence of gene amplification is a major mechanism for oncogene activation in tumours. Therefore, to identify the causative oncogenes, we next determined expression levels of all genes within the two segments using expression array data that could be generated for 20 of the selected samples. We identified 11 genes that were overexpressed through amplification in at least 50% of cases. Nine of these, c17orf39, RICH2, c17orf45, TOP3A, COPS3, SHMT1, PRPSAP2, PMP22, and RASD1, demonstrated a significant association between copy number and expression level. We conclude that these genes, including COPS3 and PMP22, are candidate oncogenes in 17p11.2-p12 of importance in osteosarcoma tumourigenesis.     

Transcription of cellular oncogenes in human tumors

The analysis of 11 various oncogenes expression in different human tumors showed that each tumor is characterised by a specific functioning program of these genes. In 40-50% of tumors the oncogenes ras, fos and myc are expressed. All other oncogenes are either considered to be "silent" or are expressed only in few cases. The increased expression of sis and myb oncogenes is observed in metastases.     

Amplification of cellular oncogenes in cancer cells

Regulatory or structural alterations of cellular oncogenes have been implicated in the causation of various cancers. Oncogene alteration by point mutations can result in a protein product with strongly enhanced oncogenic potential. Aberrant expression of cellular oncogenes may be due to tumor-specific chromosomal translocations that dysregulate the normal functions of a proto-oncogene. Amplification of cellular oncogenes can also augment their expression by increasing the amount of DNA template available for the production of mRNA. It appears that amplification of certain oncogenes is a common correlate of the progression of some tumours and also occurs as a rare sporadic event affecting various oncogenes in different types of cancer. Amplified copies of oncogenes may or may not be associated with chromosomal abnormalities signifying DNA amplification: double minute chromosomes and homogeneously staining chromosomal regions. Amplified oncogenes, whether sporadic or tumour type-specific, are expressed at elevated levels, in some cases in cells where their diploid forms are normally silent. Increased dosage of an amplified oncogene may contribute to the multistep progression of at least some cancers.     

Establishing a link between oncogenes and tumor angiogenesis.

We have tried to stress that mutant oncogenes or overexpressed, nonmutated proto-oncogenes, in addition to their direct affect on promoting aberrant tumor cell proliferation (and survival), may possess a crucial indirect means of stimulating tumor cell growth through regulation of angiogenesis. This effect would never be observed in tissue culture studies of oncogene function using pure cultures of tumor cells, which probably helps explain why the pro-angiogenic function of oncogenes has not been appreciated until only relatively recently. Indeed, the very first indication of a possible contributory role of oncogenes, such as ras and myc, to tumor angiogenesis was first reported by Thompson et al. in 1989, who used reconstituted organ cultures of the mouse prostate gland for their studies (69). This potentially important contribution of oncogenes to tumor growth and development may prove to have an impact on how various signal transduction inhibitors that are now in early phase clinical trials, e.g., monoclonal neutralizing antibodies to the human EGF receptor (70), function in vivo as anti-tumor agents.     

Nuclear matrix protein,prohibitin, was down‐regulated and translocated from nucleus to cytoplasm during the differentiation of osteosarcoma MG‐63 cells induced by ginsenoside Rg1, cinnamic acid,and tanshinone IIA (RCT)

Ginsenoside Rg1, cinnamic acid, and tanshinone IIA (RCT) are effective anticancer and antioxidant constituents of traditional Chinese herbal medicines of Ginseng, Xuanseng, and Danseng. The molecular mechanisms of anticancer effects of those constituents and their targets are unknown. Prohibitin, an inner membrane‐bound chaperone in mitochondrion involved in the regulation of cell growth, proliferation, differentiation, aging, and apoptosis, was chosen as a candidate molecular target because of its frequent up‐regulation in various cancer cells. We demonstrated that prohibitin existed in the filaments of the nuclear matrix of the MG‐63 cell and its expression was down‐regulated by the treatment of RCT using proteomic methodologies and Western blot analysis. Immunogold electro‐microscopy also found that prohibitin was localized on nuclear matrix intermediate filaments (NM‐IF) that had undergone restorational changes after RCT treatment. Prohibitin may function as a molecular chaperone that might interact with multiple oncogenes and tumor suppressor genes. We found that oncogenes c‐myc and c‐fos and tumor suppressor genes P53 and Rb were regulated by RCT as well and that these gene products co‐localized with prohibitin. Our study identified prohibitin as a molecular target of the effective anticancer constituents of Ginseng, Xuanseng, and Danseng that down‐regulated prohibitin in nuclear matrix, changed prohibtin trafficking from nucleolus to cytoplasm, and regulated several oncogenes and tumor suppressor genes. Prohibitin downregulation and cellular trafficking from nucleolus to cytoplasm indicated RCT protective roles in cancer prevention and treatment. J. Cell. Biochem. 108: 926–934, 2009. © 2009 Wiley‐Liss, Inc.     

人膀胱癌中某些癌基因的研究

本实验应用Northern和斑点印渍杂交技术探测了人膀胱癌细胞株中c-myc、c-fos、erbB等癌基因的表达,以及TPA对这些癌基因表达的调控,发现BIU-87细胞有这些癌基因的表达,并能被TPA所增强,同时也发现人膀胱癌组织有c-myc、c-fos、erbB、N-ras基因的高表达。提示蛋白激酶C的激活可以诱导某些癌基因的表达。多种癌基因的表达异常可能在膀胱癌中起重要作用。     

On the path to understanding the nature of cancer

In this essay crucial problems of the origin of cancer and the development of malignancy are discussed. The problem of precancer and three ways leading to malignancy are considered: induction of tumor precursors, accumulation of genetic traits common for tumor growth, and the role of inflammation in tumor induction. The nature of viral oncogenes and modes of their action are described in the context of their origin as a component of the viral genome. Oncogenes of RNA-containing viruses and DNA-containing tumorigenic viruses are described together with cellular protooncogenes, which are progenitors of RNA-containing viral oncogenes. Hematological malignancies are described as an intermediate form between simple tumors induced by a single oncogene and more complicated epithelial tumors. The roles of tumor suppressor genes and the interaction of several oncogenes in the formation of carcinomas and also the role of progression in tumor evolution are discussed.     

A new recipient cell line for transfection of biologically active oncogenes]

The properties of the new immortalized rat cell line (REF-1) were analyzed. These cells can be used as recipient ones in transfection assays. REF-1 cells never convert spontaneously to transformed phenotype during long-term passages in vitro unlike NIH3T3 cells. This peculiarity allowed to use REF-1 cells for identification of oncogenes, which induce slow-growing tumors. The following oncogenes were used in gene transfection experiments in order to test their effects: activated human EJ-ras; N-ras; v-myc; v-mos; activated tpr-met and c-hu-met. REF-1 cells, transfected with the members of ras family; v-mos and tpr-met were found to be transformed in vitro and induce tumors in nude mice, on the contrary of c-hu-met- and v-myc-transfected cells, which are non-tumorogenic. A number of clonal cell lines carrying different oncogenes were obtained. The detailed analyses of integration and expression of exogenous sequences of different oncogenes has been presented in 18 clonal cell lines.