The histopathology archive represents a vast, well-characterized source of specimens covering virtually every disease and is available for molecular biological investigation. The archive has in recent years become widely used for molecular genetic analysis and DNA can be routinely extracted from formalin-fixed, paraffin-embedded tissue. More recently, archival specimens have become a source of material for extensive analysis of mRNA expression utilizing DNA microarrays, real-time quantitative reverse transcriptase polymerase chain reaction (PCR), and in situ hybridization and amplification techniques. These techniques will enable a greater understanding of the changes that occur in gene function during every stage of the development of disease and will lead to better diagnosis, better evaluation of prognosis, and better treatment through targeted therapeutic regimes.

Achaete-scute like (ASCL)2 is a basic helix-loop-helix transcription factor essential for the maintenance of proliferating trophoblasts during placental development. Using oligonucleotide microarrays we identified ascl2 as a gene significantly upregulated in colorectal adenocarcinomas (n ¼ 36 cancers, n ¼ 16 normals; 15-fold, Po0.0001). This finding was confirmed by quantitative reverse transcriptase (RT)-PCR on large intestinal cancers (n ¼ 29 cancers, n ¼ 16 normals; 10-fold, Po0.0001).In situ hybridization for ascl2 demonstrated expression at the base of small and large intestinal crypts (n ¼ 304), but in no other normal tissues excepting placenta. By in situ hybridization, 52-71% of colorectal adenomas (n ¼ 187), 50-73% of large (n ¼ 327) and 33-64% of small intestinal adenocarcinomas (n ¼ 124) were positive for ascl2 expression. Upregulation of murine ascl2 was also observed using oligonucleotide microarrays, quantitative RT-PCR and in situ hybridization on apc min/ þ and apc 1638N/ þ smad4 À/ þ tumours. Tumour cell lines stably transfected with LEF1 DN or APC2, or transiently transfected with short-interfering RNA (siRNA) against b-catenin showed a significant downregulation of ascl2. Colocalization of ascl2 with nuclear b-catenin was observed in 73 small intestinal adenocarcinomas (P ¼ 0.0008) and apc min/ þ tumours. Preliminary in vitro data suggest ascl2 may promote progression through the G2/M cell cycle checkpoint. In summary, ascl2 is a putative regulator of proliferation that is overexpressed in intestinal neoplasia.

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Variations in nodal yield are due to idiosyncratic patient and tumor characteristics and differences in the quality of surgery and pathology undertaken. Adequate lymphadenectomy is essential to ensure correct stage allocation and optimal survival.

Purpose: The double-strand break (DSB) is the major DNA lesion leading to chromosomal aberrations and faithful repair is crucial for maintaining genomic instability. Very little is known about the expression of DNA DSB repair proteins in colorectal cancer. To address this issue, we examined the expression pattern of DSB repair key proteins ATM, BRCA1, BRCA2, Ku70, and Ku80 and their putative role in patients survival in a large series of colorectal cancer. Experimental Design: 342 sporadic colorectal cancer were subjected to immunohistochemistry by using specific antibodies for the various proteins investigated. Staining results were compared with clinicopathologic data, patient survival, as well as expression of mismatch repair proteins MLH1 and MSH2. Results: The expression pattern of both ATM and BRCA1 predicted survival in all colorectal cancer patients as well as in the small subgroup of patients that received adjuvant therapy. Low expression of ATM and BRCA1 was associated with loss of MLH1 or MSH2 expression. Conclusions: This is the first study to show a relationship between the expression of DNA DSB repair proteins ATM and BRCA1 and survival in colorectal cancer patients. Studies in tumors from large randomized trials are now necessary to validate our pilot data and establish the clinical usefulness of the immunohistochemical assay in predicting response to a particular adjuvant therapy regimen. Furthermore, our results indicate a possible link between expression of DNA mismatch repair and DNA DSB repair proteins in sporadic colorectal cancer, which warrants further investigation. Genetic instability has been proposed to be a driving force in colorectal carcinogenesis (1). Two major types of genetic instability have been described in colorectal cancer: chromosomal instability and microsatellite instability (2). Up to 15% of colorectal cancer show a high frequency of microsatellite instability which is caused by a defect of the DNA mismatch repair pathway (3). The vast majority of colorectal cancer, however, shows chromosomal instability, which is characterized by gains and losses of whole chromosomes or large chromosomal regions.Whereas a large number of genes that trigger chromosomal instability have been identified in yeast in the past (reviewed in ref. 4), the underlying mechanisms leading to chromosomal instability in colorectal cancer remain to be characterized. The DNA double-strand break (DSB) is regarded as the most critical of all DNA lesions (5, 6) and it has been shown that defects in the cellular response to DSBs can lead to genetic alteration, chromosomal instability, and ultimately malignant transformation (7).In mammalian cells, DSBs can be repaired by two distinct pathways: homologous recombination and nonhomologous end joining (8). DSB repair by nonhomologous end joining involves the formation of a Ku70/Ku80 protein heterodimer and recruitment of DNA-dependent protein kinase C to the site of DNA damage (9). DSB repair by homologous recombination is mediated by a large number of...

Chromosomal instable colorectal cancer is marked by specific large chromosomal copy number aberrations. Recently, focal aberrations of 3 Mb or smaller have been identified as a common phenomenon in cancer. Inherent to their limited size, these aberrations harbour one or few genes. The aim of this study was to identify recurrent focal chromosomal aberrations and their candidate driver genes in a well-defined series of stage II colon cancers and assess their potential clinical relevance. High-resolution DNA copy number profiles were obtained from 38 formalin-fixed, paraffin-embedded colon cancer samples with matched normal mucosa as a reference using array comparative genomic hybridization. In total, 81 focal chromosomal aberrations were identified that harboured 177 genes. Statistical validation of focal aberrations and identification of candidate driver genes were performed by enrichment analysis and mapping copy number and mutation data of colorectal, breast, and pancreatic cancer and glioblastomas to loci of focal aberrations in stage II colon cancer. This analysis demonstrated a significant overlap with previously identified focal amplifications in colorectal cancer, but not with cancers from other sites. In contrast, focal deletions seemed less tumour type-specific since they also showed significant overlap with focal deletions of other sites. Focal deletions detected were significantly enriched for cancer genes and genes frequently mutated in colorectal cancer. The mRNA expression of these genes was significantly correlated with DNA copy number status, supporting the relevance of focal aberrations. Loss of 5q34 and gain of 13q22.1 were identified as independent prognostic factors of survival in this series of patients. In conclusion, focal chromosomal copy number aberrations in stage II colon cancer are enriched in cancer genes that contribute to and drive the process of colorectal cancer development. DNA copy number status of these genes correlates with mRNA expression and some are associated with clinical outcome.

Quality of colorectal cancer pathology reports is related to individual patient prognosis and future treatment options. This study sought to validate the prognostic utility of the Royal College of Pathologists minimum pathology dataset (MPD), regarded as the 'gold standard', within a population. Retrospective study of the survival of 5947 surgically resected colorectal cancer patients for whom an MPD had been collected. Variables were related to survival. The study population was representative of the Yorkshire colorectal cancer population. Survival was poorer in older patients and colonic tumours and improved over the study period. Local invasion, total number of lymph nodes retrieved, nodal stage, extramural vascular invasion, peritoneal involvement, distance of invasion beyond the muscularis propria, and in rectal cancers, circumferential resection margin involvement and distance to this margin were all validated as of prognostic significance within a population. Failure to report extramural vascular invasion, peritoneal involvement or circumferential resection margin status was associated with a worse survival than absence of the factor. All variables within the Royal College of Pathologists MPD are of prognostic significance. High-quality pathology reports are essential in providing accurate prognostic information and guiding optimal patient management.

DNA microarrays are a new technology that allows the analysis of large numbers of genes at a high resolution by the hybridization of labelled DNA, which may be reverse-transcribed from mRNA, to a substrate containing thousands of spotted cDNAs or oligonucleotides. The amount of hybridized target is analysed, giving information on gene expression, polymorphisms or mutations present and allowing the gene profiling of different subtypes of disease. This technique has massive implications for the further understanding of the complicated genetic alterations involved in tumourigenesis and other disease processes and also for the generation of accurate prognostic information and optimization of treatment in these situations.