Rapid and sensitive detection of UGT1A1 polymorphisms associated with irinotecan toxicity by a novel DNA microarray

C-Mannosyl tryptophan is a novel biomarker for thrombocytosis of myeloproliferative neoplasms

C-Mannosyl tryptophan (CMW), a unique glycosylated amino acid, is considered to be produced by degradation of C-mannosylated proteins in living organism. Although protein C-mannosylation is involved in the folding and secretion of substrate proteins, the pathophysiological function in the hematological system is still unclear. This study aimed to assess CMW in the human hematological disorders. The serum CMW levels of 94 healthy Japanese workers were quantified using hydrophilic interaction liquid chromatography. Platelet count was positively correlated with serum CMW levels. The clinical significance of CMW in thrombocytosis of myeloproliferative neoplasms (T-MPN) including essential thrombocythemia (ET) were investigated. The serum CMW levels of the 34 patients with T-MPN who presented with thrombocytosis were significantly higher than those of the 52 patients with control who had other hematological disorders. In patients with T-MPN, serum CMW levels were inversely correlated with anemia, which was related to myelofibrosis (MF). Bone marrow biopsy samples were obtained from 18 patients with ET, and serum CMW levels were simultaneously measured. Twelve patients with bone marrow fibrosis had significantly higher CMW levels than 6 patients without bone marrow fibrosis. Collectively, these results suggested that CMW could be a novel biomarker to predict MF progression in T-MPN.

Development of a clinical microarray system for genetic analysis screening

Objectives

Research on the relationship between diseases and genes and the advancement of genetic analysis technologies have made genetic testing in medical care possible. There are various methods for genetic testing, including PCR-based methods and next-generation sequencing; however, screening tests in clinical laboratories are becoming more diverse; therefore, novel measurement systems and equipment are required to meet the needs of each situation. In this study, we aimed to develop a novel microarray-based genetic analysis system that uses a Peltier element to overcome the issues of conventional microarrays, such as the long measurement time and high cost.

Methods

We constructed a microarray system to detect the UDP-glucuronosyltransferase gene polymorphisms UGT1A1*6 and UGT1A1*28 in patients eligible for irinotecan hydrochloride treatment for use in clinical laboratories. To evaluate the performance of the system, the hybridization temperature and reaction time were determined, and the results were compared with those obtained using a conventional hybridization oven.

Results

The hybridization temperature reached its target in 1/27th of the time required by the conventional system. We assessed 111 human clinical samples and found that our results agreed with those obtained using existing methods. The total time for the newly developed device was reduced by 85 min compared to that for existing methods, as the automated DNA microarray eliminates the time that existing methods spend on manual operation.

Conclusions

The surface treatment technology used in our system enables high-density and strong DNA fixation, allowing the construction of a measurement system suitable for clinical applications.

Human variability in isoform-specific UDP-glucuronosyltransferases: markers of acute and chronic exposure, polymorphisms and uncertainty factors

UDP-glucuronosyltransferases (UGTs) are involved in phase II conjugation reactions of xenobiotics and differences in their isoform activities result in interindividual kinetic differences of UGT probe substrates. Here, extensive literature searches were performed to identify probe substrates (14) for various UGT isoforms (UGT1A1, UGT1A3, UGT1A4, UGT1A6, UGT1A9, UGT2B7 and UGT2B15) and frequencies of human polymorphisms. Chemical-specific pharmacokinetic data were collected in a database to quantify interindividual differences in markers of acute (Cmax) and chronic (area under the curve, clearance) exposure. Using this database, UGT-related uncertainty factors were derived and compared to the default factor (i.e. 3.16) allowing for interindividual differences in kinetics. Overall, results show that pharmacokinetic data are predominantly available for Caucasian populations and scarce for other populations of different geographical ancestry. Furthermore, the relationships between UGT polymorphisms and pharmacokinetic parameters are rarely addressed in the included studies. The data show that UGT-related uncertainty factors were mostly below the default toxicokinetic uncertainty factor of 3.16, with the exception of five probe substrates (1-OH-midazolam, ezetimibe, raltegravir, SN38 and trifluoperazine), with three of these substrates being metabolised by the polymorphic isoform 1A1. Data gaps and future work to integrate UGT-related variability distributions with in vitro data to develop quantitative in vitro-in vivo extrapolations in chemical risk assessment are discussed.

Rapid and sensitive detection of UGT1A1 polymorphisms associated with irinotecan toxicity by a novel DNA microarray

Recent developments in the field of human genomics have greatly enhanced the potential for precision and personalized medicine. We have developed a novel DNA microarray, using a 3‐mm square chip coated with diamond‐like carbon to enhance the signal‐to‐background ratio, for use as an in vitro diagnostic tool in precision medicine. To verify the genotyping effectiveness of this newly developed DNA microarray we examined UDP‐glucuronosyltransferase 1A1 (UGT1A1) polymorphisms in DNA extracted from patients with metastatic colorectal cancer. It is established that the polymorphisms of UGT1A1*28 and UGT1A1*6 are significantly associated with severe toxicity induced by the anti‐cancer drug irinotecan. For each sample, the results obtained with the novel microarray platform were compared with those obtained using other, more established, methods, including direct sequencing and the Invader assay. The polymorphisms tested included a single nucleotide substitution (UGT1A1*6) and a TA‐repeat polymorphism (UGT1A1*28), both of which were detected simultaneously and accurately using our method. Moreover, our method required 1.5‐fold less time to assay and 20‐fold less sample than those required by the Invader assay. In summary, our newly developed DNA microarray is more practical than established methods, and is at least as accurate; this will increase the efficiency of polymorphism detection prior to diagnosis and the commencement of treatment, and can feasibly be applied in precision medicine.

A universal genotyping–microarray constructed by ligating a universal fluorescence-probe with SNP-encoded flaps cleaved from multiplex invasive reactions

The universal chip and fluorescence probe enable genotyping multiple SNPs more labor-saving and cost-saving.