The epigenomics of cancer.

The Human Plasma Proteome History, Character, and Diagnostic Prospects

There is increasing evidence that the pathogenesis of cancer proceeds by sequential steps from normal cells to premalignant foci to localized tumors to invasive tumors and to metastatic lesions. The concept of stages of tumor progression was initially analyzed by Foulds (1), and a model for tumor progression based on genetic instability and clonal selection has been pro posed by Nowell (2). Individual steps in tumor progression have been operationally delineated in mouse skin by the responses of cells to different chemicals (3). A progression of phenotypic changes has been described in human tumors, the anatomical localization of which has made it feasible to obtain serial biopsies (2, 4). Sequential somatic chromosomal abnormalities have been reported in human cancers including malignant mel anoma (5), colon cancer (6), gliomas (7), adenocarcinoma of the esophagus (8), and small cell carcinomas of the lung (9). In addition, a multiplicity of different mutations has been carefully documented in human breast cancer (10). The dilemma is that there are too many mutations in human tumors. In this perspective, I will consider the relationships between mutation rates and cancer. At least two mutations are required to account for the chromosomal changes observed in certain human inherited diseases (11). An analysis of the literature indicates that the spontaneous mutation rate in cells is of sufficient magnitude to account for a two mutation hypothesis for the initiation of cancer. However, a larger number of mu tations are observed in many human tumors. The spontaneous mutation rate in somatic cells is not sufficient to account for these multiple mutations. If the multiple mutations in tumors are causally associated with and not just an accompaniment of cancer, then I argue that an early step in tumor progression is one that induces a mutator phenotype. An increased mutation rate in tumors could be the basis for the multiple mutations that characterize many cancers.

https://cancerres.aacrjournals.org/content/canres/51/12/3075.full.pdf

Mutator Phenotype May Be Required for Multistage Carcinogenesis

Heat shock proteins (Hsps) are overexpressed in a wide range of human cancers and are implicated in tumor cell proliferation, differentiation, invasion, metastasis, death, and recognition by the immune system. We review the current status of the role of Hsp expression in cancer with special emphasis on the clinical setting. Although Hsp levels are not informative at the diagnostic level, they are useful biomarkers for carcinogenesis in some tissues and signal the degree of differentiation and the aggressiveness of some cancers. In addition, the circulating levels of Hsp and anti-Hsp antibodies in cancer patients may be useful in tumor diagnosis. Furthermore, several Hsp are implicated with the prognosis of specific cancers, most notably Hsp27, whose expression is associated with poor prognosis in gastric, liver, and prostate carcinoma, and osteosarcomas, and Hsp70, which is correlated with poor prognosis in breast, endometrial, uterine cervical, and bladder carcinomas. Increased Hsp expression may also predict the response to some anticancer treatments. For example, Hsp27 and Hsp70 are implicated in resistance to chemotherapy in breast cancer, Hsp27 predicts a poor response to chemotherapy in leukemia patients, whereas Hsp70 expression predicts a better response to chemotherapy in osteosarcomas. Implication of Hsp in tumor progression and response to therapy has led to its successful targeting in therapy by 2 main strategies, including: (1) pharmacological modification of Hsp expression or molecular chaperone activity and (2) use of Hsps in anticancer vaccines, exploiting their ability to act as immunological adjuvants. In conclusion, the present times are of importance for the field of Hsps in cancer, with great contributions to both basic and clinical cancer research.

/pdf/heat-shock-proteins-in-cancer-diagnostic-prognostic-nu0q5u09ni.pdf

Heat shock proteins in cancer: diagnostic, prognostic, predictive, and treatment implications

Proteomics is an increasingly powerful and indispensable technology in molecular cell biology. It can be used to identify the components of small protein complexes and large organelles, to determine post-translational modifications and in sophisticated functional screens. The key — but little understood — technology in mass-spectrometry-based proteomics is peptide sequencing, which we describe and review here in an easily accessible format.

/pdf/the-abc-s-and-xyz-s-of-peptide-sequencing-58wrj1in70.pdf

The ABC's (and XYZ's) of peptide sequencing

The sequencing of the human genome and that of numerous pathogens has opened the door for proteomics by providing a sequence-based framework for mining proteomes. As a result, there is intense interest in applying proteomics to foster a better understanding of disease processes, develop new biomarkers for diagnosis and early detection of disease, and accelerate drug development. This interest creates numerous opportunities as well as challenges to meet the needs for high sensitivity and high throughput required for disease-related investigations.

Disease proteomics : Proteomics

Inhibitors of DNA methylation, such as 5-azacytidine, induce gene expression. We have previously reported that cloned T cells treated with 5-azacytidine lose the requirement for Ag and can be activated by autologous HLA-D molecules alone, thus becoming auto-reactive. This phenomenon could potentially mediate an autoimmune disease in vivo. Inasmuch as several drugs are known to cause autoimmune disease, we asked whether they exert the same effects on T cells as 5-azacytidine. We report that hydralazine and procainamide, two drugs associated with a lupus-like autoimmune disease, also inhibit DNA methylation and induce self-reactivity in cloned T cell lines. These results suggest that drug-induced autoimmune disease may be due to activation of as yet unidentified genes through mechanisms involving DNA methylation.

Hydralazine and procainamide inhibit T cell DNA methylation and induce autoreactivity.

Identification of a polypeptide associated with the malignant phenotype in acute leukemia.

Substantial evidence implicates amplification of the N-myc gene with aggressive tumor growth and poor outcome in neuroblastoma. However some evidence suggests that this gene alone is not the sole determinant of outcome in N-myc amplified tumors. We have searched for genes that co-amplify with N-myc in neuroblastoma by means of two-dimensional analysis of genomic restriction digests. Using this approach, we have identified and cloned a novel genomic fragment which is co-amplified with N-myc in neuroblastomas. This fragment was mapped in close vicinity to N-myc on chromosome arm 2p24. It was amplified in 5/8 N-myc amplified neuroblastoma cell lines and in 9/13 N-myc amplified tumors. Using a PCR-based approach we isolated a 4.5 kb c-DNA sequence that is partly contained in the genomic fragment. The open reading frame of the cDNA encodes a predicted protein of 1353 amino acids (aa). The homology of the predicted protein, which we designated NAG (neuroblastoma amplified gene), to a C. elegans protein of as yet unknown function, and its ubiquitous expression suggest that NAG may serve an essential function. By Northern blot analysis we showed that amplification of the cloned gene correlates with over-expression in neuroblastoma cell lines. Amplification and consequent over-expression of NAG may, therefore, contribute to the phenotype of a subset of neuroblastomas.

S. M. Hanash

Papers

Disease proteomics : Proteomics

Hydralazine and procainamide inhibit T cell DNA methylation and induce autoreactivity.

Identification of a polypeptide associated with the malignant phenotype in acute leukemia.

Co-amplification of a novel gene, NAG, with the N-myc gene in neuroblastoma

Involvement of OP18 in cell proliferation.