Detection of somatic changes in human renal cell carcinomas with oligonucleotide probes specific for simple repeat motifs

Somatic DNA alterations in breast carcinomas of different lymph-node status by DNA fingerprint analyses

The purpose of this study was to screen for somatic changes in invasive breast tumors by multilocus DNA fingerprints comparing normal (blood) and malignant tissue samples from 34 patients. The comparison of lymph node-positive and node-negative breast carcinomas was of primary interest. After restriction enzyme digestion with HinfI and HaeIII, altered banding patterns were detected by using the oligonucleotide probe (GTG)5 in 7 of 34 (20.5%) and in 3 of 34 (8.8%) tumors after hybridization with (GACA)4. The overall frequency of changes thus amounted to 29.4%. Because long (GACA)n repeat motifs, generating predominant DNA fingerprint bands, are localized on the short arms of the human acrocentric chromosomes, sequences that are important in breast carcinogenesis may be present in these regions. The overall methylation status of the DNA does not appear to be responsible for DNA fingerprint differences, as can be demonstrated with the restriction endonuclease HaeIII. DNA fingerprint differences did not correlate with tumor grade, stage, and hormone receptor status. Tumors with lymph-node metastases expressed DNA fingerprint differences more frequently.

DNA fingerprint detection of somatic mutations in benign prostatic hyperplasia and prostatic adenocarcinoma

Genetic alterations within diseased prostate tissue were analysed by genomic DNA fingerprinting using a minisatellite probe (lambda 33.6), a simple repetitive oligonucleotide probe (GTG)5, and an additional human multilocus probe (pV47-2). In prostatic adenocarcinoma, somatic mutations were detected in 77% of the samples compared with 38% of the benign prostatic hyperplasia samples. No correlation was evident with either the tissue histopathology or the grading or staging classification of the malignant tissue. Because one of the probes (pV47-2) did not demonstrate any changes in the tumour tissue, and because the probes exhibited specificity for different regions of the genome, it is possible to conclude that mutations occur widely throughout the genome, perhaps with the exception of certain domains. The results suggest that somatic mutations accompany the development of both benign and malignant pathologies of the prostate. Furthermore, benign prostatic hyperplasia should be considered as a risk indicator for processes leading to prostatic adenocarcinoma.

Analysis of loss of heterozygosity in murine hepatocellular tumors

Because allelotype analysis of tumors has been important in the identification of new tumor suppressor genes, here we studied loss of heterozygosity (LOH) in a well-defined animal experimental system. We analyzed spontaneous liver tumors from C3HHc x C57BL/6J (B6C3F1) mice and urethane-induced hepatocellular tumors from (C3H/He x Mus spretus) x C57BL/6JBy (HSB) interspecific mice. A total of 95 different genetic markers were tested: 13 in 24 B6C3F1 tumors, 76 in 58 HSB tumors, and six in both groups. Minisatellite finger-printing analysis detected one case of LOH and less than 1% genomic rearrangements in polymorphic and nonpolymorphic bands, respectively. There were no changes at hepatocellular susceptibility loci or at markers homologous to loci frequently lost in human hepatocellular carcinomas. Therefore, our results suggest that LOH and genomic rearrangements are uncommon in mouse hepatocellular tumors.

Indirect gene diagnoses for complex (multifactorial) diseases--a review

The analysis of multifactorial diseases requires the efficient investigation of large numbers of (gene) loci and patient (family) samples. Since simple repetitive DNA markers are dispersed all over the chromosomes, molecular techniques employing these tools render most conventional screening procedures obsolete. Examples of tumors, autoimmune diseases and infections are presented to validate concepts of indirect gene diagnoses via simple, tandemly arranged, repetitive DNA sequences. The salient advantages of microsatellite technologies vs. those of multilocus DNA fingerprinting are weighed.

DNA fingerprint analysis in acute leukemias

Restriction fragment length polymorphism (RFLP) analysis by Southern blotting or direct in-gel hybridization is a routine procedure in any genetic laboratory. Minisatellites and simple repeat probes for RFLP analysis have proved to be highly informative genetic markers, depending on their degree of homology and index of heterozygosity. Several of these probes have considerable individualization potential, thus yielding 'fingerprint' pattern. In the setting of acute leukemia DNA fingerprint (DNA-F) analysis is able to provide considerable information concerning the genetic instability of the leukemic clone. DNA-F is capable of detecting randomly occurring genetic alterations of unknown localization and to identify new hotspots of malignant transformation. As DNA-F analysis is not likely to be hampered by the effects of chemotherapy or DNA methylation, altered fingerprints may be regarded as characteristic of the leukemic clone. With the introduction of polymerase chain reaction (PCR) and increasing sensitivity, DNA-F analysis is likely to be of significant importance in monitoring minimal residual disease in human leukemia.

Exploiting the informativity of 'meaningless' simple repetitive DNA from indirect gene diagnosis to multilocus genome scanning

Most eukaryotic genomes are characterized by excessively large amounts of non-coding DNA sequences among which redundant (repetitive) elements constitute a sizable portion. The functional role of an abundant subclass of repetitive sequences--simple, tandemly arranged repeats--remained mysterious so far. Even the biological meaning of most of these elements appears quite refractory to present-day techniques in molecular genetics. Notwithstanding simple repetitive sequences have been developed into superb tools for various aspects of eukaryotic genome research: Using oligonucleotide probes carrying simple repeat motifs multilocus DNA fingerprinting can be applied for individual identification and genetic relationship analyses in plants, animals and humans. Microsatellite analyses via polymerase chain reaction of simple repeat blocks allow for efficient investigations of such divers subject matters as criminal stains, detailed genome maps and indirect gene diagnoses.

Changes of telomere lengths in human intracranial tumours

The termini of human chromosomes comprise stretches of G-rich repeats that are about 5-20 kilobase (kb) in length. The size of the telomeres can be determined by hybridization with probes specific for these (ttaggg)n sequences after digestion of chromosomal DNA with appropriate restriction enzymes and electrophoretic separation of the fragments. Here, probing with the 32P-labelled synthetic (TTAGGG)3 oligonucleotide revealed length changes of the telomeres occurring in intracranial tumours. Among 60 samples, analysed, 41.7% showed telomere elongation, and 21.7% telomere reduction, whereas 36.7% of the tumours exhibited equal lengths compared with the patients' peripheral blood leukocytes. Most of the elongated glioma telomeres exceeded in length those of untransformed astrocytes derived from human fetal tissue.

On the essence of "meaningless" simple repetitive DNA in eukaryote genomes

Various kinds of simple tandemly repetitive DNA sequences are abundantly interspersed in the genomes of practically all eukaryotic species studied. The comparatively elevated mutation rates of simple repeat blocks result in highly polymorphic and therefore extremely informative investigation systems for studies on forensic, ecological and genetic relationship questions. Recently the techniques for analyzing simple repeats have achieved great effectivity and simplicity. Beyond their utility as tools for differentiation and individualization, certain of these repeated elements harbor quite unexpected qualities which may be discussed in the context of their biological meaning. i) A specific subset of simple (cac)n or (gtg)n repeats is expressed in mature mRNA and total cellular RNA. ii) Despite the apparently high mutation rate certain (gt)n or mixed (gt)n/(ga)m stretches of intronic simple repeats are preserved in immunologically relevant genes for at least 70 x 10(6) years and they bind nuclear protein molecules with high affinities. Consequently in addition to their tool character, the biological aspects of simple repeated DNA should be taken into consideration.