Rapid single tube genotyping of ACP1 by FRET based amplification and dual color melting curve analysis

Small amplicons high resolution melting analysis (SA-HRMA) allows successful genotyping of acid phosphatase 1 (ACP1) polymorphisms in the Italian population

BACKGROUND

The ACP1 gene, encoding a low-molecular-weight phosphotyrosine phosphatase (LMW-PTP), has been suggested as a common genetic factor of several human diseases, including inflammatory and autoimmune diseases, favism and tumors. For this reason, the ACP1 enzyme has been investigated by case-control studies for decades. Initially based on protein electrophoresis, the ACP1 phenotype is now determined by DNA-based techniques.

METHODS

Here, we report a rapid optimized method which employs HRMA for ACP1 polymorphism identification, a molecular approach that we used to screen 80 healthy Italian subjects.

RESULTS

HRMA proved particularly suitable for detecting ACP1 genotypes. In fact, HRMA results were 100% concordant with direct sequencing. In addition, ACP1 genotype frequency in the Italian population was in accordance with the literature [4% (*A/A), 36% (*A/B), 4% (*A/C), 50% (*B/B), 6% (*B/C)].

CONCLUSIONS

HRMA was found to be a simple, rapid, sensitive and low cost method potentially useful in research and diagnostic laboratories. Finally, use of small amplicons for the set-up allowed us a better optimization of HRMA. For this reason, we present such an approach as small amplicons high resolution melting analysis (SA-HRMA). Finally, ACP1 genotype frequency in the Italian population reported in this study may contribute to a better interpretation of ACP1 allelic frequency variation.

Computational identification of phospho-tyrosine sub-networks related to acanthocyte generation in neuroacanthocytosis

Acanthocytes, abnormal thorny red blood cells (RBC), are one of the biological hallmarks of neuroacanthocytosis syndromes (NA), a group of rare hereditary neurodegenerative disorders. Since RBCs are easily accessible, the study of acanthocytes in NA may provide insights into potential mechanisms of neurodegeneration. Previous studies have shown that changes in RBC membrane protein phosphorylation state affect RBC membrane mechanical stability and morphology. Here, we coupled tyrosine-phosphoproteomic analysis to topological network analysis. We aimed to predict signaling sub-networks possibly involved in the generation of acanthocytes in patients affected by the two core NA disorders, namely McLeod syndrome (MLS, XK-related, Xk protein) and chorea-acanthocytosis (ChAc, VPS13A-related, chorein protein). The experimentally determined phosphoproteomic data-sets allowed us to relate the subsequent network analysis to the pathogenetic background. To reduce the network complexity, we combined several algorithms of topological network analysis including cluster determination by shortest path analysis, protein categorization based on centrality indexes, along with annotation-based node filtering. We first identified XK- and VPS13A-related protein-protein interaction networks by identifying all the interactomic shortest paths linking Xk and chorein to the corresponding set of proteins whose tyrosine phosphorylation was altered in patients. These networks include the most likely paths of functional influence of Xk and chorein on phosphorylated proteins. We further refined the analysis by extracting restricted sets of highly interacting signaling proteins representing a common molecular background bridging the generation of acanthocytes in MLS and ChAc. The final analysis pointed to a novel, very restricted, signaling module of 14 highly interconnected kinases, whose alteration is possibly involved in generation of acanthocytes in MLS and ChAc.

A real-time multiplex SNP melting assay to discriminate individuals

A method that quickly and inexpensively differentiates crime scene samples from multiple donors would expedite casework analysis by allowing the selection of probative items requiring comprehensive testing. This new method need not be perfectly definitive nor give a complete 13 locus short tandem repeat (STR) profile; it simply must be able to differentiate between most victim and suspect samples. We describe the development of multiplex, single nucleotide polymorphism (SNP), fluorescence resonance energy transfer-based real-time polymerase chain reaction (PCR) assays to fulfill this need. Dual probes, one fluorescently labeled and the other labeled with a quencher, are monitored during a melt analysis to reveal an increase in fluorescence, which allows the assessment of the two SNP alleles. Two alternate 6-plex assays (with and without gender determination) have been developed for the six-color RG6000 real-time instrument (Corbett Robotics, Inc.) and one seven SNP plus gender assay (performed as two 4-plex assays, one with gender the other without) have been developed for use in four/five color real-time instruments. This technique can discriminate between 95% and 99% of samples from different individuals. This assay is fast (approximately 2 h), much less expensive than STR analysis, and uses a real-time PCR instrument which is found in most forensic and molecular biology labs.