Metka Ravnik-Glavač

Naturally occurring mutations and functional polymorphisms in multidrug resistance 1 gene: correlation with microsatellite instability and lymphoid infiltration in colorectal cancers

Pglycoprotein (Pgp), encoded by the MDR1 gene, is a transmembrane transporter that acts as an efflux pump in an ATP dependent fashion.1 Multidrug resistance, the main problem in efficient cancer chemotherapy, is mainly caused by increased expression and acquired mutations in the MDR1 gene.2 Pgp is expressed physiologically in epithelial cells of the kidney, liver, pancreas, and colon, suggesting its role in secretion of toxic compounds.3 Pgp is also expressed in the blood-brain barrier, adrenal glands, and lymphocytes where its role is still uncertain. Recently, additional functions for Pgp, including immune response4 and regulation of apoptosis,5 have been suggested in normal tissues and in cancers. High expression of Pgp at the apical surface of differentiated tubular structures was identified in previously untreated colorectal cancers (CRC)6 and its high expression at the leading edge of a colorectal carcinoma was associated with tumour progression.7 In contrast to the majority of CRC, which develop as a result of chromosomal instability (CIN), a proportion of sporadic CRC and 90% of cancers in patients with hereditary non-polyposis colorectal cancer (HNPCC) exhibit microsatellite instability (MSI).8 In MSI CRC, chromosomal aberrations such as large deletions, translocations, and gene amplifications are rare; the great majority of MSI tumours are usually diploid or near diploid. In MSI CRC, inactivation of the mismatch repair (MMR) system owing to mutations or methylation of MMR genes results in a 1000-fold accumulation of point mutations in oncogenes and tumour suppressor genes which trigger tumour progression. Therefore, in addition to genes mutated in microsatellite stable (MSS) CRC, such as APC , p53 , and K-ras , there are other genes important in the development of MSI cancers. Interestingly, MSI CRCs are also more often resistant to several chemotherapy drugs; the selection of cells for resistance to …

Long Noncoding RNAs as Biomarkers in Cancer

Long noncoding RNAs (lncRNAs) are a relatively well-characterized class of noncoding RNA (ncRNA) molecules, involved in the regulation of various cell processes, including transcription, intracellular trafficking, and chromosome remodeling. Their deregulation has been associated with the development and progression of various cancer types, the fact which makes them suitable as biomarkers for cancer diagnosis and prognosis. In recent years, detection of cancer-associated lncRNAs in body fluids of cancer patients has proven itself as an especially valuable method to effectively diagnose cancer. Cancer diagnosis and prognosis employing circulating lncRNAs are preferential when compared to classical biopsies of tumor tissues, especially due to their noninvasiveness, and have great potential for routine usage in clinical practice. Thus, this review focuses on summarizing the perspectives of lncRNAs as biomarkers in cancer, based on evaluating their expression profiles determined in body fluids of cancer patients.

Cystic fibrosis gene mutations detected in hereditary pancreatitis

To determine the potential role of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene in the etiology of Hereditary Pancreatits (HP), we analyzed this gene in two HP families. PCR-SSCP analysis was employed, followed by direct sequencing of DNA samples showing alterations by SSCP. A new alteration not yet detected in connection with CF was detected in one HP family. The alteration is in exon 7 and causes an amino acid change from Len to Arg at position 327 (L327R). L327R segregates with the disease within the family. We discovered another novel alteration (V1190P) in an HP patient of the second family. These results indicate that CFTR gene mutations may be involved in the etiology of HP and represent a challenge for further study of the role of (CTFR) in other digestive diseases.

ATP2A3 gene is involved in cancer susceptibility

The sarco/endoplasmatic reticulum calcium-ATPase (SERCA) translocates Ca(2+) from cytosol to the lumen of the ER and thus regulates Ca(2+) homeostasis, perturbations of which have been suggested to contribute to cancer. We have previously detected an increased number of alterations in the ATP2A2 gene in various cancer types and in the ATP2A3 gene in head and neck squamous cell carcinoma. Here, we further analyzed the ATP2A3 gene in colon, lung, and CNS cancers. We identified a statistically significant increase of alterations in each (colon cancer, p=0.0052, lung cancer, p=0.0026, CNS tumors, p=0.0045) cancer type, and all 3 types together (p=0.0016). Epigenetic study of the ATP2A3 gene indicated an unchanged methylation status, whereas expression of the ATP2A3 gene was normal for exon 14 mutations and reduced in connection with a nucleotide change in intron VI in all studied cancer types. Identification of a significant number of alterations in cancer patients suggests that ATP2A3 is involved in increased cancer susceptibility in humans. The mostly normal expression and methylation status of the ATP2A3 gene, as well as the absence of somatic alterations, further suggest that the ATP2A3 gene may not act as a classical tumor suppressor gene, but rather haplo-insufficiency of this gene may be enough to change the cell and tissue environment in such a way to predispose to cancer development.

Alterations in genes encoding sarcoplasmic-endoplasmic reticulum Ca2+ pumps in association with head and neck squamous cell carcinoma

Recent studies have suggested that a perturbation of intracellular Ca(2+) homeostasis or signaling could contribute to cancer development. The purpose of this study was to evaluate whether germline variants of the ATP2A2 and ATP2A3 genes might act as susceptibility alleles in head and neck squamous cell carcinoma. In both genes, we identified eight different alterations in 11 patients with head and neck squamous cell carcinoma (11/79; P = 0.0002, odds ratio = 0.054, 95% confidence interval = 0.0069-0.4236). We also detected low expression level of both genes in connection with some of alterations, but could not correlate low expression level with methylation in the promoter region of either gene. The results suggest that Ca(2+) pumps of sarcoplasmic-endoplasmic reticulum are involved in an increased susceptibility to develop head and neck squamous cell carcinoma in humans.

Low microsatellite instability and high loss of heterozygosity rates indicate dominant role of the suppressor pathway in squamous cell carcinoma of head and neck and loss of heterozygosity of 11q14.3 correlates with tumor grade

Loss of heterozygosity (LOH) and microsatellite instability (MSI) have been recognized as important events in squamous cell carcinoma of the head and neck (HNSCC), suggesting involvement of both suppressor and mutator pathways. We analyzed 153 HNSCC with 8 Bethesda reference panel markers and 14 microsatellite markers selected from chromosomal regions known to harbor either tumor-suppressor genes or oncogenes. A combination of multiplex fluorescence-based polymerase chain reaction and automatic fragment analysis was performed. LOH was observed in 78% of all tumors. 2% to 17% LOH frequency was observed with Bethesda reference panel markers comparing to higher 8% to 48% LOH in chromosomal areas 3p, 9p, 11q, and 17p. LOH of 11q14.3 correlated with tumor grade. The proportions of high- and low-MSI tumors were 3% and 10%, respectively, but no mutation was identified in MLH1 and MSH2 mismatch repair genes. These results indicate the dominant role of the suppressor in comparison with the mutator pathway in HNSCC carcinogenesis.

Screening for germline mutations of MLH1, MSH2, MSH6 and PMS2 genes in Slovenian colorectal cancer patients: implications for a population specific detection strategy of Lynch syndrome

Microsatellite instability (MSI) is present in more than 90% of colorectal cancers of patients with Lynch syndrome, and is therefore a feasible marker for the disease. Mutations in MLH1, MSH2, MSH6 and PMS2, which are one of the main causes of deficient mismatch repair and subsequent MSI, have been linked to the disease. In order to establish the role of each of the 4 genes in Slovenian Lynch syndrome patients, we performed MSI analysis on 593 unselected CRC patients and subsequently searched for the presence of point mutations, larger genomic rearrangements and MLH1 promoter hypermethylation in patients with MSI-high tumours. We detected 43 (7.3%) patients with MSI-H tumours, of which 7 patients (1.3%) harboured germline defects: 2 in MLH1, 4 in MSH2, 1 in PMS2 and none in MSH6. Twenty-nine germline sequence variations of unknown significance and 17 deleterious somatic mutations were found. MLH1 promoter methylation was detected in 56% of patients without detected germline defects and in 1 (14%) suspected Lynch syndrome. Due to the minor role of germline MSH6 mutations, we adapted the Lynch syndrome detection strategy for the Slovenian population of CRC patients, whereby germline alterations should be first sought in MLH1 and MSH2 followed by a search for larger genomic rearrangements in these two genes. When no germline mutations are found tumors should be further tested for the presence of germline defects in PMS2 and MSH6. The choice about which gene should be tested first can be guided more accurately by the immunohistochemical analysis. Our study demonstrates that the incidence of MMR mutations in a population should be known prior to the application of one of several suggested strategies for detection of Lynch syndrome.

Genomic DNA sequence of Rhesus (M. mulatta) cystic fibrosis (CFTR) gene

Cystic fibrosis is a common human genetic disease caused by mutations in CFTR, a gene that codes for a chloride channel that is regulated by phosphorylation and cytosolic nucleotides. As part of a program to discover natural animal models for human genetic diseases, we have determined the genomic sequence of CFTR in the Rhesus monkey, Macaca mulatto. The coding region of rhesus CFTR is 98.3% identical to human CFTR at the nucleotide level and 98.2% identical and 99.7% similar at the amino acid level. Partial sequences of flanking introns (5582 base pair positions analyzed) revealed 91.1% identity with human introns. Relative to rhesus intronic sequence, the human sequences had 27 insertions and 22 deletions. Primer sequences for amplification of rhesus genomic CFTR sequences are provided. The accession number is AF013753 (all 27 exons and some flanking intronic sequence).

Polymorphisms in the 3′ untranslated region of the IκB/MAD-3 (NFKBI) gene located on chromosome 14

The NF-κB transcription factor regulates the expression of a number of genes, including immune function and growth control loci, and several viruses. For example, the long terminal repeat of the human immunodeficiency virus contains NF-κB binding sites. NF-κB activity in the nucleus is regulated by a cellular inhibitory protein IκB. To analyze the potential role of these genes in genetic disease we have mapped the NF-κB (NFKB2) and IκB/MAD-3 (NFKBI) loci in a panel of somatic cell hybrids to chromosomes 4 and 14, respectively. Amplification of the 3′ untranslated region of NFKBI allows the detection of three independent polymorphisms within 410 bp. In combination these polymorphisms were informative in 27 of 36 CEPH families and allowed the gene to be placed onto the linkage map of chromosome 14, between the D14S32 and D14S42 markers.

Genetic analysis of amyotrophic lateral sclerosis in the Slovenian population.

Amyotrophic lateral sclerosis (ALS) is a complex fatal neurodegenerative disease characterized by progressive degeneration and loss of upper motor neurons in the cerebral cortex and lower motor neurons in brainstem and spinal cord. We established the frequencies of mutations in 4 major ALS-associated genes, SOD1, TARDBP, FUS, and C9ORF72 in a representative cohort of 85 Slovenian patients with sporadic form of ALS. Pathogenic massive hexanucleotide repeat expansion mutation in C9ORF72 was detected in 5.9% of patients and was the most common cause of the disease. In the remaining 3 genes, we identified 4 changes in 3 patients, p.Val14Met in SOD1, silent mutation p.Arg522Arg in FUS, and p.Gly93Cys in SOD1 together with a novel synonymous variant c.990A>G (p.Leu330Leu) in TARDBP gene, respectively. This study represents the first genetic screening of major causative genes for ALS in a cohort of sporadic ALS patients from Slovenia and is according to our knowledge the first such study in Slavic population. Overall, we genetically characterized 8.2% sporadic ALS patients.