LightSNiP assay is a good strategy for pharmacogenetics test

The predictive and prognostic role of single nucleotide gene variants of PD-1 and PD-L1 in patients with advanced melanoma treated with PD-1 inhibitors

Background

Despite having revolutionized the treatment paradigm for advanced melanoma, not all patients benefit from immune checkpoint inhibitor therapy. To date, there are no predictive biomarkers for response or the occurrence of immune-related adverse events (irAEs) to programmed cell death protein 1 (PD-1) inhibitors. Our aim was to investigate the predictive and prognostic role of single nucleotide variants (SNVs) of genes involved in the PD-1 axis.

Methods

We analysed, in metastatic melanoma patients treated with nivolumab or pembrolizumab, five PD-1 SNVs, namely PD1.3 G>A (rs11568821), PD1.5 C>T (rs2227981), PD1.6 G>A (rs10204525), PD1.7 T>C(rs7421861), PD1.10 C>G (rs5582977) and three programmed death-ligand 1 (PD-L1) SNVs: +8293 C>A (rs2890658), PD-L1 C>T (rs2297136) and PD-L1 G>C (rs4143815). Association of SNV genotypic frequencies with best overall response to PD-1 inhibitors and development of irAEs were estimated through a modified Poisson regression. A Cox regression modelling approach was applied to evaluate the SNV association with OS.

Results

A total of 125 patients with advanced melanoma were included in the analysis. A reduction in irAEs risk was observed in patients carrying the PD-L1 +8293 C/A genotype compared with those carrying the C/C genotype (risk ratio = 0.45; 95% CL 0.22-0.93; P = 0.031). A trend for a reduction in irAEs was also observed with the PD1.5 T allele (risk ratio = 0.70, 95% confidence limits 0.48-1.01 versus C allele). None of the SNVs was associated with response to therapy. Finally, a survival benefit was observed in patients harbouring the PD1.7 C/C genotype (hazard ratio = 0.37; 95% confidence limits 0.14-0.96; P = 0.028) in the homozygous model.

Conclusions

Our study showed that PD-1.5 and PD-L1 +8293 SNVs may play a role as a predictive biomarker of development of irAEs to PD-1 inhibitors. PD1.7 SNV may also be associated with a reduction of the risk of death, although further translational research is needed to confirm these results.

Pharmacogenetic Practice of Anticancer Drugs: Multiple Approaches for an Accurate and Comprehensive Genotyping

The application of pharmacogenetics in oncology is part of the routine clinical practice. In particular, genotyping of dihydropyrimidine dehydrogenase (DPYD) and UDP-glucuronosyltransferase (UGT1A1) is crucial to manage the treatment of patients taking fluoropyrimidines and irinotecan. The unique approach of our laboratory to the pharmacogenetic diagnostic service in oncology is to combine two real-time PCR methods, LightSNiP assay (TIB MOLBIOL), and more recently FRET (Fluorescent Resonance Energy Transfer) probes technology (Nuclear Laser Medicine), plus TaqMan assay (Thermo Fisher) for the confirmation of the presence of variant alleles on DNA from a second extraction. We found that both the FRET and LightSNiP assays, where detection occurs by melting curve analysis, offer an advantage over the competing TaqMan technology. Whereas unexpected genetic variants may be missed using a mutation-specific TaqMan assay, the information thus obtained can be useful to adjust the therapy in case of unexpected post-treatment toxicity. The combination of TaqMan and FRET assays helped us to achieve more accurate genotyping and a correct result for the patient. The added value of the DPYD FRET assay is the possibility of detecting, with the same amplification profile of the polymorphisms detailed in the guidelines, also the c.2194G>A (*6 rs1801160), cited in the recommendations as a variant to be investigated in case of severe toxicity. Regarding the UGT1A1 (TA)n promoter polymorphism (rs3064744), the distinctive and positive feature of the FRET assay is to allow clearly identifying all those potential variant alleles, including the (TA)5 and (TA)8 alleles, that are frequent in African Americans. Our clinical practice emphasizes the importance of not only rapid and easy-to-use assays, such as the new FRET ones, but also of accurate and comprehensive genotyping for good pharmacogenetic diagnostic activity.

Searching for New Genetic Biomarkers of Axial Spondyloarthritis

Background: Axial spondyloarthritis (axSpA) is a chronic inflammatory condition of the spine. In addition to musculoskeletal symptoms, there are also extra-articular manifestations. The aim of this study was to search for new biomarkers associated with the clinical presentation and treatment response in axSpA patients. Methods: In this study, 106 axSpA patients and 110 healthy controls were enrolled. Six single-nucleotide polymorphisms (SNPs) were selected for genotyping: ERAP1 rs2287987, ERAP2 rs2549782, TNF rs1800629, TNFRSF1A rs767455, TNFRSF1B rs1061622, and FCGR2A rs1801274. Participants were examined at baseline and after 12 and 24 weeks of anti-TNF therapy. Results: SNPs associated with high axSpA initial activity were TNFRSF1A rs767455 and TNFRSF1B rs1061622 (p < 0.008). The ERAP1 rs2287987 AA genotype was more frequently observed in patients with enthesitis (AA vs. G+, p = 0.049), while the TNFRSF1B rs1061622 GG genotype was more common in participants with uveitis (GG vs. TT, p = 0.042). Potential in predicting anti-TNF treatment response was demonstrated by ERAP1 rs2287987, ERAP2 rs2549782, TNFRSF1B rs1061622, and FCGR2A rs1801274. Conclusions: SNPs can be used to identify patients at risk of severe disease to initiate treatment earlier. Genetic testing will allow clinicians to choose the right drug for the patient.

Rapid screening method for the detection of SARS-CoV-2 variants of concern

Background

Comprehensive and up-to-date monitoring of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC) is crucial as these are characterized by their increased transmissibility, immune evasion and virulence.

Objectives

To describe the wide-scale implementation of a reverse transcriptase polymerase chain reaction (RT-PCR) multiple variants assay with melting curve analysis as a routine procedure.

Study design

We prospectively performed multiple variants RT-PCR on consecutive SARS-CoV-2 RT-PCR positive samples from patients, healthcare workers and nursing home residents from our hospital catchment area. This technique was implemented in our automated Roche FLOW system with a turn-around time of 6 h.

Results

Between February 1 and May 2, 2021, 989 samples were tested by the variant RT-PCR. Our method was validated by comparison of variant RT-PCR to whole genome sequencing testing. We observed an increase over time in the proportion of UK variant that became the dominant variant, and the concurrent emergence of the South-African and Brazilian variants. Prompt public health responses for infection control were possible because of this rapid screening method, resulting in early detection and reduction of unnoticed spread of VOC as early as possible.

Conclusion

A variant RT-PCR with additional melting curve analyses is a feasible, rapid and efficient screening strategy that can be implemented in routine microbiological laboratories.

G82S polymorphism of receptor for advanced glycation end products gene and serum soluble RAGE levels in mild cognitive impairment and dementia of Alzheimer's type patients in Turkish population

Alzheimer's disease (AD) is a chronic, neurodegenaration resulting in progressive cognitive decline leading to dementia. Mild cognitive impairment (MCI) is also a clinical definition of cognitive decline without functional impairment. Receptor for advanced glycation end products (RAGE) is one of the neuronal membrane receptors that binds amyloid beta peptide (Aβ) triggering Aβ-related pathologic signalling mechanisms. Soluble RAGE (sRAGE) is the soluble isoform of RAGE and it collects peripheral Aβ by acting as a sink, prevents both RAGE-AGE interaction and transfer of Aβ into brain. In this study, an association was investigated in Turkish cohorts of patients with dementia with Alzheimer's Type (DAT) and MCI patients by measuring serum sRAGE levels and by genotyping G82S polymorphism and comparing them to healthy control (HC) subjects. Although the serum sRAGE levels showed a decreasing manner among the groups, these differences were not statistically significant (p = 0.2). This is the first study for Turkish population.