SNPs affecting the clinical outcomes of regularly used immunosuppressants

TPMT and NUDT15 testing for thiopurine therapy: A major tertiary hospital experience and lessons learned

Variants in thiopurine methyltransferase (TPMT) and nudix hydrolase 15 (NUDT15) are associated with an accumulation of cytotoxic metabolites leading to increased risk of drug-related toxicity with standard doses of thiopurine drugs. We established TPMT and NUDT15 genetic testing for clinical use and evaluated the utilization, service outcomes and potential value of multi-gene PGx testing for 210 patients that underwent pharmacogenetics (PGx) testing for thiopurine therapy with the aim to optimize service delivery for future prescribing. The test was most commonly ordered for Gastroenterology (40.0%) and Neurology (31.4%), with an average turnaround time of 2 days. Following testing, 24.3% patients were identified as intermediate or poor metabolizers, resulting in 51 recommendations for a drug or dose change in thiopurine therapy, which were implemented in 28 (54.9%) patients. In the remaining patients, 14 were not adjusted and 9 had no data available. Focusing on drug gene interactions available for testing in our laboratory, multi-gene PGx results would present opportunities for treatment optimization for at least 33.8% of these patients who were on 2 or more concurrent medications with actionable PGx guidance. However, the use of PGx panel testing in clinical practice will require the development of guidelines and education as revealed by a survey with the test providers. The evaluation demonstrated successful implementation of single gene PGx testing and this experience guides the transition to a pre-emptive multi-gene testing approach that provides the opportunity to improve clinical care.

Development and application of sensitive, specific, and rapid CRISPR-Cas13-based diagnosis

Nucleic acid detection is a necessary part of medical treatment and fieldwork. However, the current detection technologies are far from ideal. A lack of timely and accessible testing for identifying cases and close contacts has allowed severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2), the causative virus of the ongoing coronavirus disease‐2019 (COVID‐19) pandemic, to spread uncontrollably. The slow and expensive detection of mutations—predictors for chronic diseases such as cancer—form a barrier to personalized treatment. A recently developed diagnostic assay is ideal and field‐ready—it relies on CRISPR‐Cas13. CRISPR‐Cas13 works similarly to other CRISPR systems: Cas13 is guided by a crRNA to cleave next to a specific RNA target sequence. Additionally, Cas13 boasts a unique collateral cleavage activity; collateral cleavage of a fluorescent reporter detects the presence of the target sequence in sample RNA. This system forms the basis of CRISPR‐Cas13 diagnostic assays. CRISPR‐Cas13 assays have >95% sensitivity and >99% specificity. Detection is rapid (<2 h), inexpensive ($0.05 per test), and portable—a test using lateral flow strips is akin to a pregnancy test. The recent adaptation of micro‐well chips facilitates high‐level multiplexing and is high‐throughput. In this review, we cover the development of CRISPR‐Cas13 assays for medical diagnosis, discuss the advantages of CRISPR‐Cas13‐based diagnosis over the traditional reverse transcription polymerase chain reaction (RT‐PCR), and present examples of detection from real patient samples.

In the CRISPR‐Cas13 system, Cas13 is guided by a crRNA to cleave sample RNA at a specific target sequence.

Cas13 has collateral cleavage activity that when used with a fluorescent reporter detects a specific target sequence.

CRISPR‐Cas13‐based diagnostics are highly sensitive (>95%), specific (>99%), rapid (<2 h), inexpensive ($0.05 per test), and portable‐recent adaptions of micro‐well chips facilitate high‐evel multiplexing and are high‐throughput.

CRISPR‐Cas13‐based diagnostics have been validated in the detection of viral RNA and mutations in patient samples, including SARS‐CoV‐2 RNA during the ongoing COVID‐19 pandemic.

CRISPR‐Cas13 is also applied to RNA editing, thereby creating a full system of diagnostics and therapeutics.

Multiple genetic factors affecting the pharmacokinetic and pharmacodynamic processes of tacrolimus in Chinese myasthenia gravis patients

PURPOSE

Tacrolimus is a novel effective immunosuppressant for myasthenia gravis (MG) patients. However, the narrow therapeutic window, and high inter- and intrapatient variation in bioavailability largely limited its clinical application. This article intended to find the SNPs influencing clinical outcome and discover the possible mechanisms.

METHODS

Based on the tagSNPs genotyped by Improved Multiple Ligase Detection Reaction, Plink 1.07 was used to find the SNPs having close interaction to tacrolimus serum concentration, QMG score changes or even reasonable drug dose. Then we searched several databases to predict the possible miRNA binding rs15524 sequence. Based on the prediction, dual-luciferase reporter assay and miRNA transfection were used to discover the mechanism of how SNP rs15524 controls tacrolimus serum concentration through influencing CYP3A5 expression.

RESULTS

In this article, we found multiple SNPs on CYP3A4, CYP3A5, FKBP1A, NFATC2 genes were predicted closely related to tacrolimus serum concentration, therapeutic effect which reflected by QMG score changes or even reasonable drug dose. After in silico miRNA selection, possible relationship between hsa-miR-500a and rs15524 was found. With the help of dual-luciferase reporter assay, wild-type rs15524 (T allele) was found having a stronger binding affinity for hsa-miR-500a. Higher expression of CYP3A5 may also led by lower hsa-miR-500a level.

CONCLUSIONS

SNP rs15524 may control CYP3A5 expression by affecting the binding affinity between CYP3A5 3'UTR and hsa-miR-500a. Wild type (T allele) 3'UTR of CYP3A5 has stronger binding affinity to hsa-miR-500a and cause lower CYP3A5 expression and higher tacrolimus serum concentration.

IL-2 gene polymorphisms affect tacrolimus response in myasthenia gravis

PURPOSE

The IL-2 gene polymorphisms have been reported to be associated with the development of autoimmune disease. However, there are no published studies examining the influence of the IL-2 gene polymorphisms on the response of myasthenia gravis (MG) patients to tacrolimus (Tac). The goal of this study was to investigate the relationship between the polymorphisms of IL-2 and Tac response in MG patients.

METHODS

Ninety-two MG patients treated with Tac were studied, including 57 Tac-effective patients and 35 Tac-ineffective patients. Then, we selected four single-nucleotide polymorphisms (SNPs: rs2069776, rs2069772, rs2069762, rs2069763) in the IL-2 gene. Next, we analyzed the distribution of genotypes, allelic frequencies of SNPs, and haplotype frequencies among polymorphisms in the two groups of patients.

RESULTS

The distribution of the allelic frequency of the rs2069762 variant differed between the Tac-effective and Tac-ineffective patients (P = 0.02). Genotypes G/T and G/G of rs2069762 were differently distributed between the two groups when the wild genotype T/T was assigned as a reference (P < 0.001 for G/T; P = 0.003 for G/G). Patients with the TAGG haplotype tended to be Tac-ineffective (P < 0.001, OR: 0.15, 95% CI: 0.05-0.43).

CONCLUSION

Myasthenia gravis patients with the rs2069762 variant, rs2069762 G/T and G/G genotype, and TAGG haplotype for IL-2 tended to respond poorly to Tac treatment.