Ju Yan

The labeling efficiency of human telomeres is increased by double-strand PRINS

Telomeres are composed of tandem repeated sequences, TTAGGG, that can be detected either by fluorescence in situ hybridization (FISH), more efficiently by using a peptide nucleic acid (PNA) probe, or by the primed in situ (PRINS) technique. However, the efficiency of human telomere labeling using PRINS is somewhat lower than the efficiency using PNA-FISH. To solve this problem, we developed a double-strand PRINS technique, which uses two primers, (TTAGGG)7 and (CCCTAA)7, to label both forward and reverse telomeric DNA strands. A total of 120 lymphocyte metaphases obtained from three normal adults were scored to evaluate the labeling efficiency based upon the telomere signal frequency present in chromatid ends and chromosome arms. As a comparison, 30 metaphases from the same three individuals were evaluated using PNA-FISH. The average labeling efficiency of PRINS was increased to a level very close to that obtained with PNA-FISH. Therefore, we demonstrated that the low labeling efficiency of human telomeres with regular PRINS was likely caused by uneven annealing of primers at the relatively short human telomere sequences, resulting in some telomere sites with very weak or absent labeling. We suggest that the present double-strand labeling protocol is critical to maximize the labeling efficiency of the human telomere sequence when using the PRINS technique.

Different TP53 mutations are associated with specific chromosomal rearrangements, telomere length changes, and remodeling of the nuclear architecture of telomeres

TP53 mutations are the most common mutations in human cancers, and TP53‐R175H and TP53‐R273H are the most frequent. The impact of these mutations on genomic instability after tumor initiation is still uncovered. To gain insight into this, we studied the effects of three specific TP53 mutants (TP53‐V143A, TP53‐R175H, and TP53‐R273H) on genomic instability using four isogenic lines of LoVo cells. Multicolor fluorescence in situ hybridization (FISH), three‐dimensional (3D) quantitative FISH (Q‐FISH) on interphase and Q‐FISH on metaphases were used to investigate genomic instability. We found that LoVo cells expressing mutant TP53‐R175H displayed the highest level of chromosomal instability among the LoVo cell lines. Furthermore, we observed that mutant TP53‐R175H and TP53‐V143A showed more alterations in their 3D nuclear architecture of telomeres than the mutant TP53‐R273H and the wild type. Moreover, we noted an association between some chromosomal abnormalities and telomere elongation in the mutant TP53‐R175H. Taken together, our results indicate that the mutation TP53‐R175H is more likely to cause higher levels of genomic instability than the other TP53 mutations. We proposed that the type of TP53 mutations and the genetic background of a cancer cell are major determinants of the TP53‐dependent genomic instability.

Identification of a human chromosome-specific interstitial telomere-like sequence (ITS) at 22q11.2 using double-strand PRINS

Interstitial telomeric sequences (ITSs), telomere-like repeats at intrachromosomal sites, are common in mammals and consist of tandem repeats of the canonical telomeric repeat, TTAGGG, or a repeat similar to this. We report that the ITS in human chromosome region 22q11.2 is, in the sequenced genome database, 101 tandem repeats of the sequence TTAGGGAGG. Using the primed in situ labeling (PRINS) technique and primers against the canonical telomeric repeat (TTAGGG), we illuminated telomeric sites for all chromosomes and an ITS locus at 22q11.2. Using the TTAGGGAGG sequence, we designed PRINS primers that efficiently and specifically illuminate the 22q11.2 ITS locus without illuminating telomeric and other ITS loci. The 22q11.2 locus has more repeat units than other ITSs loci enabling an unprecedented high detection frequency for this interstitial telomere locus. The 22q11.2 is associated with hot spots for disease-related chromosome breaks for multiple disorders, such as DiGeorge syndrome and chronic myeloid leukemia. We describe our findings that the ITS at 22q11.2 is in the same area of, and proximal to the common rearrangement region of multiple disorders. We suggest that the ITS might be involved in DNA repair processes in this area to protect the chromosome from more serious damage.

Presence of alternative lengthening of telomeres associated circular extrachromosome telomere repeats in primary leukemia cells of chronic myeloid leukemia

BackgroundThe predominant mechanism by which human tumors maintain telomere length is via telomerase. In ~10% of tumor samples, however, telomere length is conserved, despite no detectable telomerase activity, in part through activation of the alternative lengthening of telomeres (ALT) pathway.MethodsWe studied the circular extra-chromosomal telomeric repeat (ECTR), an ALT hallmark, and telomerase activity in 24 chronic myeloid leukemia (CML) patients in chronic phase (CP).ResultsWe identified the presence of ECTR in primary leukemia cells from some of these samples, which indicates the possible involvement of an ALT mechanism. Moreover, we found that some samples exhibited both circular ECTR and telomerase activities, suggesting that both mechanisms can contribute to the onset of CML.ConclusionWe propose that ALT or the combined activities of ALT and telomerase might be required for the early stages of leukemogenesis. These findings shed new light into the oncogenic pathways responsible for the maintenance of telomere length in leukemia, which will ultimately determine the effectiveness of anti-telomerase-based treatment protocols.

Nuclear remodeling of telomeres in chronic myeloid leukemia.

Chronic myeloid leukemia (CML) is a hematologic cancer characterized by the proliferation of myeloid cells and the translocation between chromosomes 9 and 22, [t(9;22)(q34.1;q11.2)]. At the chronic phase (CP), CML cells present longer telomeres than at the other clinical phases, display arm‐specific maintenance of individual telomere lengths, and are chromosomally stable. We asked whether an alteration of nuclear organization of telomeres, which is associated with genomic instability, occurs in CML cells at the CP. We used fluorescent in situ hybridization of telomeres combined with three‐dimensional (3D) quantification to study the nuclear telomeric architecture of CML cells at the CP. We found that cells can exhibit high telomere numbers, different telomere distributions, and alterations in peripheral or central nuclear location of telomeres. Also, we show that CML cells can be categorized in two groups according to the number of their telomere aggregates (TAs). We propose that the presence of high TAs in some samples is associated with the increased genomic instability and could be an indication of the clinical transitional phase. Also, alterations of nuclear organization of telomeres at the CP confirm that nuclear remodeling of telomeres can occur at an early clinical stage of a cancer.

Polymorphism in a human chromosome-specific interstitial telomere-like sequence at 22q11.2.

Interstitial telomeric sequences (ITSs) are common in human. We previously reported the presence of an ITS at 22q11.2 which is in the vicinity of the genomically unstable region involved in 22q11 rearrangements. Recently, we studied the molecular status of the ITS 22q11.2 in the normal population. The amplification of an ITS at 22q11.2 showed different patterns ranging from 1–4 kb, confirming the highly polymorphic nature of this sequence. The linkage analysis of the ITS at 22q11.2 in members of 10 different families demonstrated a strong relation between offspring and parents. In contrast, the study of a DiGeorge case and his 2 parents revealed the presence of a novel allele probably inherited from the father. These results open an avenue for the use of this sequence as an allelic marker, and its implication in 22q11.2-related pathogenesis.

Application of Multi-PRINS to Simultaneously Identify Chromosomes 18, X, and Y in Prenatal Diagnosis

Since its discovery by Koch in 1989, primed in situ labeling (PRINS) reaction provides an alternative approach for direct detection of human chromosomes. The multiple color (multi)-PRINS technique can simultaneously and specifically display different chromosomes with different colors in the same metaphase or interphase nucleus by using sequential labeling of different chromosome targets. We developed a triple-PRINS reaction on uncultured amniotic cells by omitting the blocking step and taking advantage of mixing two fluorochromes (fluorescein and rhodamine) to create a third color for simultaneous detection in the same amniocytes of three different chromosome targets, e.g., chromosomes 18, X, and Y. Fluorescent signals corresponding to chromosomes 18, X, and Y were shown as yellow, red, and green color spots, respectively. Multi-PRINS is as accurate and reliable as multicolor fluorescent in situ hybridization (multi-FISH) for the detection of aneuploidies involving chromosomes 18, X, and Y. Furthermore, multi-PRINS represents a faster and more cost-effective alternative to FISH for prenatal testing of aneuploidy in uncultured amniocytes.

Dual-color PRINS for in situ detection of fetal cells in maternal blood.

Fetal nucleated cells circulating in the peripheral blood during pregnancy are potential targets for noninvasive genetic testing. Fluorescence in situ hybridization (FISH) frequently is used to quantify the total number of fetal cells in peripheral blood of pregnant women. We describe an alternative molecular cytogenetic procedure that is the primed in situ labeling (PRINS). This technique consists of annealing oligonucleotides specific to individual chromosome targets and in situ elongation using Taq DNA polymerase to incorporate labeled dUTPs. The sites of the newly synthesized DNA sequences were revealed as fluorescent signals using an immunochemical reaction. The dual-color PRINS was specifically performed for simultaneous detection of two chromosome targets, X and Y. The fluorescent signals corresponding to chromosomes X and Y were displayed as red and green color spots, respectively. The sensitivity and specificity of PRINS are similar to FISH and allow us to efficiently and reliably detect fetal cells in maternal blood. Moreover, dual-color PRINS is faster and more cost-effective than FISH.

DNAc: A Clustering Method for Identifying Kinship Relations Between DNA Profiles Using a Novel Similarity Measure*

Abstract:  After decades of refinement, DNA testing methods have become essential tools in forensic sciences. They are essentially based on likelihood ratio test principle, which is utilized specifically, by using as prior knowledge the allele frequencies in the population, to confirm or refute a given kinship hypothesis made on two genotypes. This makes these methods ill suited when allele frequencies or kinship hypotheses are unavailable. In this paper, we introduce DNAc, a new clustering methodology for DNA testing based on a new similarity measure that allows an accurate retrieval of the degree of relatedness among two or more genotypes, without relying on kinship hypotheses or allele frequencies in the population. We used DNAc in analyzing microsatellite DNA sequences distributed among 12 genotypes from normal individuals from two distinct families. The results show that DNAc accurately determines kinship among genotypes and further gathers them in the appropriate kinship groups.

Expression of Genes Associated with Telomere Homeostasis in TP53 Mutant LoVo Cell Lines as a Model for Genomic Instability

We describe a method that assesses the impact of specific mutations of TP53 and genomic instability on gene expression of the most important genes involved in telomere length and structure homeostasis. The approaches consist of using a reverse transcriptase method and a quantitative PCR that were applied to isogenic cell lines from a colon cancer.