Microarray analysis of newly synthesized RNA in cells and animals

Current methods to analyze gene expression measure steady-state levels of mRNA. To specifically analyze mRNA transcription, we have developed a technique that can be applied in vivo in intact cells and animals. Our method makes use of the cellular pyrimidine salvage pathway and is based on affinity-chromatographic isolation of thiolated mRNA. When combined with data on mRNA steady-state levels, this method is able to assess the relative contributions of mRNA synthesis and degradation/stabilization. It overcomes limitations associated with currently available methods such as mechanistic intervention that disrupts cellular physiology, or the inability to apply the techniques in vivo. Our method was first tested in serum response of cultured fibroblast cells and then applied to the study of renal ischemia reperfusion injury, demonstrating its applicability for whole organs in vivo. Combined with data on mRNA steady-state levels, this method provided a detailed analysis of regulatory mechanisms of mRNA expression and the relative contributions of RNA synthesis and turnover within distinct pathways, and identification of genes expressed at low abundance at the transcriptional level.

Development of a citrus genome-wide EST collection and cDNA microarray as resources for genomic studies

A functional genomics project has been initiated to approach the molecular characterization of the main biological and agronomical traits of citrus. As a key part of this project, a citrus EST collection has been generated from 25 cDNA libraries covering different tissues, developmental stages and stress conditions. The collection includes a total of 22,635 high-quality ESTs, grouped in 11,836 putative unigenes, which represent at least one third of the estimated number of genes in the citrus genome. Functional annotation of unigenes which have Arabidopsis orthologues (68% of all unigenes) revealed gene representation in every major functional category, suggesting that a genome-wide EST collection was obtained. A Citrus clementina Hort. ex Tan. cv. Clemenules genomic library, that will contribute to further characterization of relevant genes, has also been constructed. To initiate the analysis of citrus transcriptome, we have developed a cDNA microarray containing 12,672 probes corresponding to 6875 putative unigenes of the collection. Technical characterization of the microarray showed high intra- and inter-array reproducibility, as well as a good range of sensitivity. We have also validated gene expression data achieved with this microarray through an independent technique such as RNA gel blot analysis.

Cytogenetic characterization of two colon cell lines by using conventional G-banding, comparative genomic hybridization, and whole chromosome painting

The heterogeneous nature of genetic alterations in cancer cells handicaps the full characterization of its occurrence and the analysis of their molecular bases and relation to biological processes. Although many cancer cells are highly aneuploid, in other cases, as in a subset of colorectal carcinomas displaying microsatellite instability, chromosomal aberrations are scarce. The aim of this study was to fully characterize both qualitatively and quantitatively, the karyotypes of two established colon carcinoma cell lines (LoVo and HCT 116) previously reported as being near diploid. An array of complementary cytogenetic techniques were used: G-banding, comparative genome hybridization (CGH), and whole-chromosome painting (WCP). Combinations of these techniques provided an accurate karyotype for the two cell lines: LoVo cells showed 49,XY,t(2;12)(q13;p11.2),+5,+7,+12,i(15)(q10) and HCT 116 cells showed 45,X,-Y,dup(10)(q24q26),der(16)t(8;16)(q13;p13), der(18)t(17;18)(q21;p11.3). Heterogeneity was also observed in both cell lines as shown by G-banding. Chromosomal unbalances determined by CGH (many of them related to structural reorganizations) were characterized by WCP, allowing the reliable identification of those chromosome markers that could not be completely identified by G-banding. We show that combined analysis with classical and molecular cytogenetic techniques provides an accurate map of chromosomal aberrations in these two cell lines not identified in previous investigations.

Prospective assessment of allelic losses at 4p14-16 in colorectal cancer: two mutational patterns and a locus associated with poorer survival

Previous studies have shown that allelic losses in a locus mapping to the chromosomal region 4p14-16 are indicative of poor prognosis in colorectal cancer. To further characterize the region involved and to confirm earlier observations, we have analyzed losses of heterozygosity (LOH) in nine microsatellite markers spanning this region in a prospective series of 181 colorectal carcinomas. The extent and the nature of the allelic imbalance were also ascertained by comparative genomic hybridization analysis of selected cases. The minimum common deleted region was confined to marker D4S2397 (LOH in 35% of the informative cases). Surrounding markers displayed LOH in 13-25% of informative cases and (other than the D4S2397 marker itself) showed a higher rate of allelic imbalances in association with mutations in the p53 tumor suppressor gene. Tumors with lymph node invasion also displayed increased rates of LOH in most markers. Regarding patient outcome, LOH solely at the D4S2397 locus was indicative of a shorter disease-free survival (P = 0.027). In consequence, two patterns of allelic loss are defined within the 4p14-16 region: (a) gross losses associated with tumor progression and probably attributable to the genomic instability related to the inactivation of the p53 tumor suppressor gene; and (b) specific losses limited to the D4S2397 locus (within an estimated fragment of 2 Mb) and associated with increased tumor aggressiveness. The presence of one or more putative tumor suppressor genes in this region is postulated.

p53 and K-ras gene mutations correlate with tumor aggressiveness but are not of routine prognostic value in colorectal cancer

PURPOSE

p53 gene and K-ras mutations are among the most common genetic alterations present in colorectal cancer. The prognostic utility of such mutations remains controversial. The purpose of this study was to prospectively evaluate the prognostic significance of p53 and K-ras gene mutations in colorectal cancer.

PATIENTS AND METHODS

One hundred forty patients were analyzed. Tumors belonging to the microsatellite mutator phenotype were excluded (n = 8). Mutations at the K-ras and p53 genes were detected and characterized by restriction fragment length polymorphism, single-strand conformation polymorphism, and sequencing, as appropriate.

RESULTS

p53 mutations were detected in 66 (50%) and K-ras mutations were detected in 54 (41%) of the 132 patients. In 26 cases (20%), ras and p53 mutations coexisted; in 38 cases (29%), neither mutation was found. Multivariate analysis of the whole population analyzed (n = 132) showed that survival was strongly correlated with the presence of p53 mutations alone or in combination with K-ras mutations (P = .002; log-rank test). When only patients undergoing a radical resection were considered (R0; n = 101), p53 mutations were no longer of prognostic significance.

CONCLUSION

p53 mutations alone or in combination with K-ras mutations are correlated with a worse outcome. However, the routine use of these mutations as prognostic markers in the clinical setting is not recommended.

Tracking recurrent quantitative genomic alterations in colorectal cancer: allelic losses in chromosome 4 correlate with tumor aggressiveness

Allelic imbalances are common events in cancer cells. Quantitative alterations in specific chromosomal loci have been linked to activation (gain) or inactivation (loss) of genes with a proven impact on tumor cell biology. The aim of this study was to detect new chromosomal regions recurrently altered in colorectal tumorigenesis and with a potential effect on patient's outcome. We have analyzed a series of human colorectal tumor biopsy specimens by using the DNA fingerprinting technique arbitrarily primed PCR. This approach provided information on 95 different loci randomly selected and distributed through out the cell's genome. Eight sequences displayed recurrent alterations associated with diminished patient survival. Four of them (showing allelic losses) were located in chromosome 4, one sequence in chromosome 2, and one sequence in chromosome 17. The chromosomal origin of the two remaining sequences could not be determined. Fine mapping of chromosome 4 bands suggested that there are at least two regions in chromosome 4 (4p14-16 and 4q21-28) susceptible to containing tumor suppressor genes the loss of which may affect tumor aggressiveness.

Moderate amplifications of the c-myc gene correlate with molecular and clinicopathological parameters in colorectal cancer

C-myc gene activation is a common event in multiple types of neoplasia and has been associated with different cellular processes relevant to the malignant transformation of cancer cells. C-myc gene amplification has been analysed in colorectal carcinomas by means of an innovative DNA fingerprinting method based on the arbitrarily primed PCR. This method requires a low amount of DNA, uses multiple internal controls and appears sensitive and reproducible. Clinicopathological and molecular correlates have been investigated in a series of 70 colorectal carcinomas. The incidence of c-myc amplification was 26%, ranging from two- to fivefold increase in copy number. C-myc amplification occurrence was more frequent in more advanced stages of tumour invasion (P < 0.001) and was associated with mutations in the p53 tumour-suppressor gene (P = 0.048). The presence of c-myc amplification was indicative of a shorter disease-free survival period but, because of its strong association with Dukes' stage, its prognostic value is questionable.

Assessment of genomic damage in colorectal cancer by DNA fingerprinting: prognostic applications

PURPOSE

Here we evaluate the prognostic significance of the relative value of genomic damage assessed by DNA fingerprinting in colorectal cancer.

MATERIALS AND METHODS

Sixty-three tumor and paired normal mucosa samples were included in the study. Genomic damage was assessed by comparative analysis of paired normal and tumor tissue DNA fingerprints by the arbitrarily primed polymerase chain reaction (AP-PCR). Decreases and increases of intensity in bands were computed and referred to the total number of visualized bands per case. An index reflecting the genomic damage fraction (GDF), with separated values for losses and gains, was obtained for each tumor. This index was used to determine molecular and clinicopathologic correlates after exclusion of eight cases displaying microsatellite instability.

RESULTS

Fifty-five cases were considered for the statistical analysis. The average fraction of altered bands per tumor was 0.287+/-0.121. When losses and gains were computed separately, the average fraction of changes was 0.126+/-0.113 and 0.161+/-0.120, respectively. Tumors lacking a ras mutation showed an increased GDF, primarily because of a higher fraction of gains. Tumors that were at advanced Dukes' stages and that were poorly differentiated also displayed a higher GDF. Finally, disease-free survival was significantly diminished in tumors with a GDF greater than 0.314 (P < .001). The prognostic significance of the GDF was independent of Dukes' stage (Cox multivariate analysis, P = .005).

CONCLUSION

The degree of genomic damage assessed by unbiased DNA fingerprinting correlates with genotypic, phenotypic, and clinical variables in colorectal carcinoma and may be useful in assessing prognosis in colorectal cancer.

Chromosomal assignment of human DNA fingerprint sequences by simultaneous hybridization to arbitrarily primed PCR products from human/rodent monochromosome cell hybrids

We have developed a technique for the simultaneous chromosomal assignment of multiple human DNA sequences from DNA fingerprints obtained by the arbitrarily primed polymerase chain reaction (AP-PCR). Radioactively labeled human AP-PCR products are hybridized to DNA fingerprints generated with the same arbitrary primer from human/rodent monochromosome cell hybrids after electroblotting to a nylon membrane. Human-specific hybridization bands in the human/rodent fingerprints unambiguously determine their chromosome of origin. We named this method simultaneous hybridization of arbitrarily primed PCR DNA fingerprinting products (SHARP). Using this approach, we determined the chromosomal origins of most major bands of human AP-PCR fingerprints obtained with two arbitrary primers. Altogether, the chromosomal localization of near 50 DNA fragments, comprehensive of all human chromosomes except chromosomes 21 and Y, was achieved in this simple manner. Chromosome assignment of fingerprint bands is essential for molecular karyotyping of cancer by AP-PCR DNA fingerprinting. The SHARP method provides a convenient and powerful tool for this purpose.

Lysosomal alpha-glucosidase: cell-specific processing and altered maturation in HT-29 colon cancer cells

We have previously described the abnormal localization of resident Golgi proteins and O-glycans in the rough endoplasmic reticulum of mucin-secreting HT-29 M6 colon cancer cells, suggesting altered protein trafficking in these cells [Egea, Francí, Gambús, Lesuffleur, Zweibaum and Real (1993) J. Cell Sci. 105, 819-830]. In the present work, we have chosen lysosomal alpha-glucosidase as a reporter to examine the intracellular traffic of glycoproteins in M6 cells. We have compared the synthesis and processing of alpha-glucosidase in mucin-secreting M6 cells and in Caco-2 colon cancer cells, the latter resembling normal absorptive intestinal epithelium. Our results show that alpha-glucosidase processing and secretion is markedly delayed in M6 cells as compared to Caco-2 cells or normal fibroblasts, and this delay is caused by an accumulation of alpha-glucosidase precursor form in the trans-Golgi network. Furthermore, treatment in Caco-2 cells with brefeldin A led to changes in alpha-glucosidase maturation similar to those observed in untreated M6 cells. To determine whether altered processing occurs in other cultured cells, a panel of cancer cell lines and cultures from normal exocrine pancreas were examined. In pancreas-derived cultures, alpha-glucosidase showed a processing pattern different from that described until now. Only HT-29 cells and HT-29-derived subpopulations displayed a defect in alpha-glucosidase maturation. In conclusion, alpha-glucosidase processing is more diverse than has previously been described; this finding may have tissue-specific functional implications.

Invasive pulmonary aspergillosis: a rare presentation of non-Hodgkin's lymphoma

We describe a patient with rapidly progressive pneumonia and a high level of serum lactate dehydrogenase, in whom postmortem study revealed the presence of a diffuse, small and large-cell multicentric non-Hodgkin's lymphoma, together with an invasive pulmonary aspergillosis. Aspergillosis is rare as a presenting feature of a lymphoproliferative disease; only one previous case has been reported to the best of our knowledge. Invasive aspergillosis and lymphoma should be considered in patients presenting with pneumonia and high level of lactate dehydrogenase.

[Endoscopic retrograde cholangiopancreatography in Mirizzi's syndrome]

Mirizzi's syndrome is characterized by compression and or stenosis of the common duct as a consequence of impaction of a stone in the gallbladder neck, the cystic duct and eventually by a cholecystobiliary fistula. Preoperative diagnosis is important to avoid iatrogenic injury of the biliary tree. We present two cases with Mirizzi's syndrome confirmed at operation in whom ERCP was done prior to the operation. In one of them the examination was diagnostic, while in the other, cystic duct compression and absence of the gallbladder image were the non-specific findings.

[Treatment of residual choledochal calculi in patients with Kehr's T drainage: role and results of endoscopic sphincterotomy]

The results of sphincterotomy in the treatment of residual gallstones after cholecystectomy in a series of 62 patients, bearers of a T tube are reported. The mean time after surgery was 26.4 +/- 19.2 days. The procedure was technically successful in 59/62 (95.1%). Stones were passed spontaneously or were retrieved in 55/62 patients (88.7%). In four patients gallstones persisted in spite of sphincterotomy. All were operated with favorable results. Complications were observed in 4 patients (6.4%), without mortality. Sphincterotomy is a safe and relatively efficient technique in the treatment of cholecystectomized patients with residual gallstones and a T tube drainage.

[Long-term results of endoscopic sphincterotomy in the treatment of residual/recurrent choledocholithiasis]

Endoscopic sphincterotomy is widely accepted as the technique of choice in the treatment of residual or recidivant choledocholithiasis since the results obtained with this technique are favorable when compared to biliary surgery in most series. However, the experience of long term follow up of patients with choledocholithiasis in whom this technique would have been applied as the only treatment is still scarce up to date. We have studied 40 patients (mean age 65.6 +/- 11.1 years) with residual or recidivant choledocholithiasis who had undergone endoscopic treatment successfully before the 30th of June 1985, who could be contacted by a mailed questionnaire or by phone by August 1990. The follow up time 70.7 +/- 19.4 months (mean +/- typical deviation). Out of them, 36 (90%) had been asymptomatic up to the contact date (30 cases) or up to death due to causes not related to biliary pathology (6 patients). Out of the 4 remaining patients, 2 presented mild dyspepsia and another patient has probably developed recidivant choledocholithiasis (according to I.V. cholangiography). The fourth patient presented a severe episode of cholangitis and acute pancreatitis, related to a new episode of choledocholithiasis and died 5 and a half years after the endoscopic sphincterectomy. This represents a 2.5% mortality. These long term results of endoscopic sphincterotomy in patients with residual or recidivant choledocholithiasis are an other point in favour of using this technique as the single treatment of choice in patients above 60 years old.

[Endoscopic choledochoduodenostomy in the treatment of impacted calculi in Vater's papilla]

In a series of 204 patients with common duct stones, sphincterotomy was not possible in 10, due to an impacted stone in the papilla. An endoscopic choledocho-duodenostomy was performed which was effective in all cases. One patient suffered a retroperitoneal perforation which was managed medically. This technique is an effective alternative to sphincterotomy in the treatment of impacted papillary stones. Retroperitoneal perforation is a major risk to be taken into account.

Choledocholithiasis in cirrhotic patients: is endoscopic sphincterotomy the safest choice?

Of the 18 endoscopic sphincterotomies performed on 18 cirrhotic patients for choledocholithiasis, a mortality rate of 16.6% was registered. However, this figure can be limited to 6.6% if we take only successful sphincterotomies (15/18, 83.3%) into account. After closely reviewing relevant literature, it would appear that operative mortality in comparable cases is much higher. We therefore recommend that endoscopic sphincterotomy, despite higher mortality rates when compared to the general population, should be the initial choice of management of choledocholithiasis in cirrhotic patients.

[The value of endoscopic biopsy in the diagnosis of carcinoma of Vater's ampulla]

In a series of 23 ampullary carcinomas, confirmed by the pathological examination of the duodenopancreatectomy specimens, 17 were biopsied during the previous ERCP examination. Biopsies were diagnostic of carcinoma in 12 (70.5%). Among 11 exophytic tumours biopsy was positive in 8 (72.7%) while in 6 tumours growing inside the papilla biopsies were positive in 4 (66.6%) (NS). It is concluded that endoscopic biopsy may be diagnostic in two-thirds of ampullary carcinomas.