Cancer: the evolved consequence of a destabilized genome.

The genome is a stable repository of vastly intricate genetic information developed over eons of evolution; this information is replicated at the highest fidelity and expressed within each cell at the highest selectivity. Non-leukemia cancers break this standard; the intricate genetic information qualitatively and progressively deteriorates, resulting in a somatic Darwinian free-for-all. In a process lasting several years, a genomically heterogeneous population replicates from a single cell that originally lost the ability to preserve its genomic integrity. Cells selected for their abilities to proliferate and spread, while evading host defenses, inexorably expand their numbers. The clinical consequences of this become severe, as the genomically diverse cell population that evolves contains members that can evade most therapeutic approaches aimed at "the tumor cell".

Intrachromosomal genomic instability in human sporadic colorectal cancer measured by genome-wide allelotyping and inter-(simple sequence repeat) PCR.

We have used genome-wide allelotyping with 348 polymorphic autosomal markers spaced, on average, 10 cM apart to quantitate the extent of intrachromosomal instability in 59 human sporadic colorectal carcinomas. We have compared instability measured by this method with that measured by inter-(simple sequence repeat) PCR and microsatellite instability assays. Instability quantitated by fractional allelic loss rates was found to be independent of that detected by microsatellite instability analyses but was weakly associated with that measured by inter-(simple sequence repeat) PCR. A set of seven loci were identified that were most strongly associated with elevated rates of fractional allelic loss and/or inter-(simple sequence repeat) PCR instability; these seven loci were on chromosomes 3, 8, 11, 13, 14, 18, and 20. A lesser association was seen with two loci flanking p53 on chromosome 17. Coordinate loss patterns for these loci suggest that at least two separate sets of cooperating loci exist for intrachromosomal genomic instability in human colorectal cancer.

Germline and somatic mutation analyses in the DNA mismatch repair gene MLH3: Evidence for somatic mutation in colorectal cancers.

DNA mismatch repair is of considerable scientific and medical importance because of its essential role in maintaining genomic integrity, and its association with hereditary non-polyposis colon cancer (HNPCC). Germline mutations in five mismatch repair genes (MLH1, MSH2, PMS1, PMS2, and MSH6) have been associated with HNPCC susceptibility. Our laboratory recently identified MLH3, a novel DNA mismatch repair gene. We screened the MLH3 coding sequence in 60 probands with increased genetic risk factors for colorectal cancer susceptibility and no mutations in the other candidate genes. No definite MLH3 germline mutations were found. We subsequently screened 36 colon tumors, and discovered an appreciable frequency of somatic MLH3 coding mutations in MSI-H tumors (25%). In four of six tumors, evidence of biallelic inactivation was noted. Furthermore, MLH3 nonsense mutations were identified in two of 12 microsatellite stable (MSS) tumors with 14q24 loss of heterozygosity. While our analyses do not exclude the existence of germline MLH3 mutations in patients with increased genetic risk factors for colorectal cancer susceptibility, they suggest such mutations are uncommon in this patient population. The finding of an appreciable frequency of somatic MLH3 mutations is consistent with a possible role for this gene in the progression of colorectal cancer tumorigenesis. Hum Mutat 17:389-396, 2001. Published 2001 Wiley-Liss, Inc.

Stereotactic core biopsy breast and blood cell by-products: a source of material for molecular genetics research--initial experience.

Stereotactic core biopsy washings and blood drop samples, routinely discarded by-products, provide satisfactory fresh cellular material for flow cytometry and molecular genetics microsatellite polymerase chain reaction (PCR) analysis for detection of loss of DNA alleles (loss of heterozygosity). Cytokeratin-positive (epithelial) cells from the core biopsy washings were sorted by means of flow cytometry prior to PCR analysis. DNA allele loss was detected in benign breast epithelial cells in three (20%) of 15 patients.

Colorectal cancer: how does it start? How does it metastasize?

Colorectal carcinogenesis is a multistep process with an apparently orderly progression from benign tissue to invasive malignancy and metastases. Yet at the genome level, a considerably more chaotic situation exists, with order arising through the process of natural selection in the midst of genomic instability. Major pathways for colorectal carcinogenesis begin with suppressor loss or acquisition of a mutator phenotype, but there are other pathways known and yet to be described. These pathways result in the natural selection of cells with unstable genomes leading to malignancy and metastases.

p53 tumor suppressor gene mutations predict decreased survival of patients with sporadic colorectal carcinoma.

BACKGROUND: Mutations of the p53 tumor suppressor gene play an integral role in sporadic colorectal carcinogenesis but prior studies have failed to show their prognostic significance consistently. METHODS: Fifty-six consecutive sporadic colorectal tumors were analyzed for their p53 status. Polymerase chain reaction amplification with primers for exons 5-9 was conducted and these products were subjected to single strand conformation polymorphism analysis. Suspected mutations were confirmed with DNA sequencing. p53 status was entered into a colorectal clinical database and these patients then were followed prospectively. Patient status with regard to disease recurrence and survival was updated every 6 months. Survival and disease free survival were calculated according to the method of Kaplan and Meier. The association between p53 status and clinical and pathologic factors with survival and recurrence was statistically determined using univariate analysis and the Cox proportional hazards model for multivariate analysis. RESULTS: p53 mutations were detected in 28 of 56 patients (50%). The median follow-up time was 45 months (range, 3-72 months). There were 33 patients (59%) who were alive at last follow-up. Fifteen of the 23 patients who died (65%) had p53 mutations and 8 (35%) had wild-type p53. Thirteen patients developed a disease recurrence, 9 of whom (69%) had tumors with p53 mutations. Overall 4-year survival rates for patients with wild-type p53 and mutant p53 were 71% and 54%, respectively (P = 0.05). The 4-year disease free survival rates for patients with wild-type p53 and mutant p53 were 83% and 62%, respectively (P = 0.09). p53 status and stage were found to be independent significant predictors for survival (p53 negative: P = 0. 02; stage: P = 0.0002.) Stage was found to be the sole significant predictor for disease free survival (P = 0.006). CONCLUSIONS: In this group of colorectal carcinoma patients, p53 mutations were a significant negative prognostic indicator for overall survival. This finding holds prognostic and therapeutic implications for the management of colorectal carcinoma patients.

The onset and extent of genomic instability in sporadic colorectal tumor progression.

Cancer cell genomes contain alterations beyond known etiologic events, but their total number has been unknown at even the order of magnitude level. By sampling colorectal premalignant polyp and carcinoma cell genomes through use of the technique inter-(simple sequence repeat) PCR, we have found genomic alterations to be considerably more abundant than expected, with the mean number of genomic events per carcinoma cell totaling approximately 11,000. Colonic polyps early in the tumor progression pathway showed similar numbers of events. These results indicate that, as with certain hereditary cancer syndromes, genomic destabilization is an early step in sporadic tumor development. Together these results support the model of genomic instability being a cause rather than an effect of malignancy, facilitating vastly accelerated somatic cell evolution, with the observed orderly steps of the colon cancer progression pathway reflecting the consequences of natural selection.

Genome-wide allelotyping indicates increased loss of heterozygosity on 9p and 14q in early age of onset colorectal cancer.

Colorectal cancer remains a significant public health challenge, despite our increased understanding of the genetic mechanisms involved in the initiation and progression of this disorder. It has become clear that multiple mechanisms lead to the tumorigenic phenotype, with familial predisposition syndromes accounting for less than 15% of all colorectal cancers. A genome-wide scan for loss of heterozygosity (LOH) was carried out with 150 highly polymorphic markers in an effort to identify additional loci involved in colorectal tumorigenesis in DNA samples from 42 colorectal cancer patients. The results confirm earlier observations that tumor DNAs from patients with hereditary nonpolyposis colon cancer (HNPCC) either maintain heterozygosity or exhibit altered or additional alleles. DNAs from patients with early onset colorectal carcinomas (diagnosed prior to age 50) revealed a higher overall degree of LOH than DNAs from patients with sporadic colorectal cancers diagnosed later in life (after age 50). While regions on 1p, 10q and 14q are suggestive, statistical analysis of LOH at these regions failed to reach significance. However, LOH at 9p did reveal a statistically significant increase in the early onset patient group, compared to the greater than age 50 group. LOH on 9p may involve inactivation of p16/CDKN2 through aberrant DNA methylation on the remaining chromosome, resulting in a situation analogous to a homozygous deletion of p16 and providing a selective growth advantage to these cells. This marker may prove to be a useful prognostic indicator for patient stratification in the design of therapy for early onset colorectal cancer patients.

Absence of frequent involvement of modifier of Min(APC) in sporadic colorectal cancer.

BACKGROUND: Mutations in the multiple intestinal neoplasia (Min) gene, the mouse homologue of the APC gene, result in the development of intestinal tumors. The degree of tumor expression is suppressed by the modifier of Min (MOM). Alterations in the MOM gene result in markedly increased tumor expression in the mouse. The human homologue of the MOM gene has been mapped to a locus on chromosome 1p35-36, but the role of the MOM gene in the development of human sporadic colorectal cancers has not been defined. METHODS: The microsatellite marker D1S199 has been previously mapped to the region of the MOM gene and was used as a primer for PCR amplification. The PCR products were subjected to denaturing electrophoresis and analyzed for loss of heterozygosity (LOH) and the mismatch repair phenomenon (RER) of each tumor compared to its mucosal control. RESULTS: 48 consecutive sporadic colorectal cancers and normal adjacent mucosa were analyzed. LOH was noted in 2 of 48 tumors and the RER phenomenon was noted in 6 of 48 tumors. Thus, 8 of 48 tumors (16.7%) showed alterations in the region of the locus of the MOM gene. There was no association between alterations in this region and TNM stage, disease-free survival, overall survival, or p53 mutation. CONCLUSIONS: Although mutation of the APC gene is an integral component of sporadic colorectal carcinogenesis, alteration in the region including the MOM gene does not appear to play a significant role in the development or clinicopathologic behavior of human sporadic colorectal tumors.

Genomic DNA-based hMSH2 and hMLH1 mutation screening in 32 Eastern United States hereditary nonpolyposis colorectal cancer pedigrees.

Hereditary nonpolyposis colorectal cancer (HNPCC) is an autosomal dominant cancer syndrome characterized by early age of onset colorectal cancer (mean 45 years) as well as endometrial, urinary tract, and upper gastrointestinal adenocarcinomas. The HNPCC phenotype has been shown to segregate with germline mutations in the human homologues of the DNA mismatch repair genes MSH2, MLH1, PMS1, and PMS2. However, the majority of published DNA mismatch repair gene mutation surveys associated with HNPCC kindreds report multiple levels of preselection, including 2p and 3p chromosomal linkage analysis and the evaluation of microsatellite instability of proband colorectal cancers prior to mutation analysis. For this reason, the concise contribution of each of the known DNA mismatch repair genes to the HNPCC phenotype remains unknown. We report the results of a genomic DNA-based analysis of hMSH2 and hMLH1 germline mutations in 32 unrelated Eastern United States HNPCC kindreds. These families were selected for study on the basis of phenotype only. We identified three hMSH2 and six hMLH1 mutations in eight families, for a positive mutation rate of 25%. Two mutations were identified in one of the families. Four of the mutations detected have not been reported in the literature previously. One of the mutation-positive families is African American; the others were of European-American ancestry. These results provide a clarification of the contribution of hMSH2 and hMLH1 to the HNPCC phenotype and suggest that in the majority of Eastern United States HNPCC kindreds selected by phenotype alone, the molecular genetic basis for the disease remains unknown.

Genomic instability in sporadic colorectal cancer quantitated by inter-simple sequence repeat PCR analysis.

Genomic instability plays a major role in cancer by facilitating tumor progression and tumor heterogeneity. Inter-simple sequence repeat (inter-SSR) PCR has been developed to provide a rapid and reproducible technique for quantitation of the major type of genomic instability observed in sporadic tumors, namely, that manifesting itself as amplifications, deletions, translocations, and insertions. Evaluation of 59 sporadic colorectal cancers by inter-SSR PCR has demonstrated a wide range of instability, independent of tumor stage at diagnosis. Comparison of these data and the results of microsatellite PCR analysis reveals an association of high genomic instability with loss of heterozygosity but no association with the replication error phenomenon arising from defects in mismatch repair.

p53 tumor suppressor gene status and the degree of genomic instability in sporadic colorectal cancers.

BACKGROUND: Genomic instability reflects the propensity and the susceptibility of the genome to acquire multiple alterations and, in turn, is believed to be a driving force behind multistep carcinogenesis. Although the molecular basis of genomic instability in sporadic colorectal cancers remains largely a mystery, mutation of the p53 tumor suppressor gene (also known as TP53) has been proposed to play an integral role in this process. However, a dilemma exists in that p53 mutation appears to be a late event in the progression of sporadic colorectal tumors, whereas genomic instability, serving as a facilitator of tumor progression, is envisioned as occurring early in this process. PURPOSE: We evaluated the relationship between p53 mutation and the major form of genomic instability in sporadic colorectal tumors, namely, that involving DNA breakage, which leads to chromosomal translocations, insertions, deletions, and gene amplification. METHODS: Fifty-eight sporadic colorectal tumors that had been previously evaluated for genomic instability were analyzed for p53 mutations. These tumors were from consecutively diagnosed patients. Genomic instability was quantified by use of inter-simple sequence repeat polymerase chain reaction analysis that employed (CA)8RG and (CA)8RY primers (R = purine [A or G]; Y = pyrimidine [C or T]); a genomic instability index (a measure of the number of alterations in tumor DNA in comparison with normal DNA, expressed as a percent) was calculated for each tumor. Mutation of the p53 gene in exons 5-9 was determined by use of single-strand conformational polymorphism-polymerase chain reaction analysis and DNA sequencing. Chi-squared analysis was used to determine the statistical significance of differences between groups of tumors. Reported P values are two-sided. RESULTS: p53 mutations were identified in 29 (50%) of the 58 tumors. The median genomic instability index value was 3.3%. Nineteen (65.5%) of the 29 tumors with p53 mutations had genomic instability indices that were less than the median value (range, 0%-2.6%); the remaining 10 (34.5%) tumors had genomic instability indices that were greater than the median (range, 3.9%-13.0%). Eleven (37.9%) of the 29 tumors with wild-type p53 genes had genomic instability indices that were less than the median value (range, 0%-2.6%), whereas the remaining 18 tumors had genomic instability indices above the median (range, 3.9%-11.7%). There was a statistically significant association between a lesser degree of genomic instability and the presence of p53 mutations (P = .032). CONCLUSIONS AND IMPLICATIONS: Tumors with no or minimal evidence of genomic instability are more likely to harbor p53 mutations than tumors with evidence of substantial genomic instability. p53 mutations play an important role in the development of cancers but do not appear to initiate or promote genomic instability in sporadic colorectal tumors.

Mutations involving the endogenous ecotropic murine leukemia virus in primary mammary carcinomas of BALB/c mice.

Endogenous murine leukemia virus-related elements (MLVEs) are often overexpressed in primary mammary carcinomas of BALB/c mice. We therefore searched for mutations associated with MLVEs and found amplified sequences of the ecotropic MLVE in hormonally and chemically induced mammary neoplasms. Restriction fragment length polymorphism (RFLP) analysis revealed DNA rearrangements consistent with 1-10 or more new copies of the ecotropic MLVE in the genome of these tumors. This is the first evidence of mutations involving an endogenous retrovirus other than mouse mammary tumor virus in mouse mammary carcinomas.

The anoxic fibroblast response is an early-stage wound healing program.

When fibroblasts experience anoxia, a cellular program is initiated which results in stepwise activation of an endogenous SVL30 retroelement, metabolic adaptation to reliance on glycolysis, protease secretion, and endonuclease induction. This response is reversible and occurs with no reduction in cellular viability. Examination of experimental wounds reveals that this same response is physiologically activated during the early phase of wound healing when near-anoxic conditions prevail and wound debridement predominates. Procathepsin D has been identified as one of three major anoxia-inducible secretory proteins; its secretion is the result of altered routing within the cell, with no apparent change in the amount of the protein synthesized. A delayed cellular contractile response occurs approximately 1 week after fibroblasts experience as little as 16 hr of anoxia; this response appears to contribute to wound contraction.

Anoxic induction of a sarcoma virus-related VL30 retrotransposon is mediated by a cis-acting element which binds hypoxia-inducible factor 1 and an anoxia-inducible factor.

Cells exposed to hypoxia undergo substantial changes in gene expression generally associated with metabolic adaptation and increasing oxygen delivery. In contrast, responses distinct from those elicited by hypoxia are induced in anoxic fibroblasts; this includes activation of a set of VL30 elements. The responses seen in anoxically cultured fibroblasts are expressed physiologically in vivo during the anaerobic phase of wound healing. A fundamental question is whether transcriptional regulatory pathways utilized during anoxia are distinct from those already characterized for hypoxic cells. We report here the isolation of a 14-bp sequence within a VL30 retrotransposon promoter which mediates its anoxia responsiveness. Analyses of the protein complexes binding to this sequence demonstrated the presence of two distinct inducible DNA binding activities. The first is present in both hypoxic and anoxic fibroblasts and is indistinguishable from hypoxia-inducible factor 1. The second activity, which is present only in anoxic fibroblasts, is a previously uncharacterized heterodimeric DNA binding activity that appears to arise via posttranslational modification of an existing complex found in aerobic cells. These results indicate that the strong VL30 transcriptional induction seen with anoxia occurs through a mechanism specific to anoxia.

Normal fibroblasts induce the C/EBP beta and ATF-4 bZIP transcription factors in response to anoxia.

Fibroblasts exhibit a complex response to temporary anoxia; this response, which is associated with no loss of viability, includes enhanced secretion of proteases and endonucleases along with an increase in glycolytic metabolism. Physiologically, this response is activated during the early stages of wound healing. We have been investigating the mechanisms by which gene expression is regulated in fibroblasts during conditions of oxygen deprivation. We show that normal fibroblasts in response to anoxia induce several members of the C/EBP and ATF subfamilies of the bZIP (basic/leucine zipper domain) transcription factor class. Although anoxia substantially elevated the levels of the corresponding proteins, we detected only slight changes in the activity of reporters containing consensus bZIP binding sites. In the case of C/EBP beta this was apparently related to the failure to detect an increase in the DNA binding of the induced factor to its consensus binding site. In contrast, we show that anoxia strongly increases ATF-4 or an immunologically related protein's DNA binding activity on a variant site, although this variant sequence by itself is insufficient for anoxia-inducible transactivation. This suggests that anoxic exposure of fibroblasts may promote the formation of variant bZIP proteins in nonpermissive conformations or they require the interaction with additional transcription factors at adjacent promoter elements for functional activity.

An anoxia inducible endonuclease and enhanced DNA breakage as contributors to genomic instability in cancer.

Fischer rat embryo fibroblasts subjected to temporary anoxia followed by an aerobic recovery period show genomic instability in the form of highly elevated CAD gene amplification rates. As revealed by flow cytometric analysis this is associated with DNA breakage in vivo, followed by repair during the recovery period. Such genomic instability parallels expression of a M(r) 29,000/31,000 endonuclease; this enzyme requires no added divalent metal ion and has a pH optimum of about 6.5. The same endonuclease was found to be expressed within healing wounds and in four of ten human colorectal cancers but was not seen in eight normal colorectal tissue samples. Our results indicate that DNA breakage resulting from endogenous endonuclease activity can have a substantial effect in modulating genomic instability.

Anoxia-inducible rat VL30 elements and their relationship to ras-containing sarcoma viruses.

VL30 elements are associated with cancer by their overexpression in rodent malignancies, their induction in a fibroblast response to anoxia which shares features with the malignant phenotype, and their presence recombined into Harvey murine sarcoma virus (HaSV) and Kirsten murine sarcoma virus. These sarcoma viruses contain ras oncogenes flanked on both sides by retrotransposon VL30 element sequences, in turn flanked by mouse leukemia virus sequences. Three very basic questions have existed about the VL30 element sequences found in sarcoma viruses: (i) how did they become recombined, (ii) what are their exact boundaries, and (iii) why are they there? To help decipher the nature of VL30 elements in sarcoma viruses, we examined VL30 clones isolated from an anoxic fibroblast cDNA library and independently by polymerase chain reaction cloning from rat cell DNA. Sequence comparisons with HaSV revealed that HaSV was formed by the substitution of 0.7 kb of VL30 sequences by 0.9 kb of c-Ha-ras sequences, with this event possibly facilitated by the presence of an identical Alu-like repeat found upstream of the 5' recombination point in both the VL30 element and c-Ha-ras. Recombination occurred 42 bases beyond the Alu-like sequences in VL30 and 1596 bases beyond them in c-Ha-ras, at position 926 of HaSV. The 3' ras-VL30 recombination event in HaSV occurred within a seven-base region of shared sequence identity, between HaSV bases 1825 and 1825 and 1831. Recombination between Moloney leukemia virus (MoLV) and VL30 appears to have occurred at a point corresponding to base 218 or 219 of MoLV and was near a TAR-like VL30 sequence; such recombination at the 3' end was between positions 7445 and 7456 of MoLV (HaSV positions 4694 to 4703). Kirsten murine sarcoma virus was found to be closely analogous to HaSV, and limited similar features were also seen with Rasheed sarcoma virus.

Comparative expression of endogenous retrotransposons in adult mouse mammary gland during normal development and differentiation.

Amplified expression of the endogenous retrotransposons, intracisternal A particles (IAPs) and murine leukemia virus-related elements (MLVEs), along with decreased expression of VL30 elements frequently occurs during mouse mammary tumorigenesis. We have now analyzed the expression of these retroelements during the normal developmental and differentiation cycle of the mammary gland as found in virgin, pregnant, lactating, and postlactation adult female BALB/c mice. Retrotransposon expression was either unchanged or decreased during the progressive stages of the cycle compared to virgin tissue. Likewise, growth of mammary epithelial cells in primary culture had little or no effect on expression of IAPs, MLVEs and VL30 sequences. Thus, the dramatic changes involving these retrotransposons in many mouse mammary tumors appear unrelated to any normal state.