Development of a high resolution melting analysis assay for rapid identification of JAK2 V617F missense mutation and its validation

An investigation into the manganese superoxide dismutase (MnSOD Val-9Ala) gene polymorphisms employing high-resolution melting in patients with gastric cancer: A preliminary study

BACKGROUND

Gastric cancer with complex carcinogenesis and a multi-factorial immunopathophysiology is well-known as the third life-threatening type of cancer in Asia. In this regard, it has been demonstrated that the role of Reactive Oxygen Species (ROS) in these processes should not be underestimated. Besides, mitochondrial Manganese Superoxide Dismutase (MnSOD) with antioxidant properties show protective effects against ROS. On the other hand, MnSOD catalyzes the dismutation of superoxide radicals to H2O2 and oxygen reactions. A replacement of T with C at nucleotide 47 (Val-9Ala) leads to a change in MnSOD nascent protein signal sequences and builds a relationship with gastric cancer. Therefore, the authors aimed at investigating the Single Nucleotide Polymorphisms (SNPs) in patients with gastric cancer by employing High-Resolution Melting.

METHODOLOGY

In order to investigate the (T/C) polymorphisms of MnSOD, the genomic DNA of 30 paraffin-embedded tissue samples were collected from patients with gastric cancer and 30 healthy people, respectively. An investigation was conducted into the T/C polymorphisms of MnSOD by employing High Resolution Melting (HRM) in different melting temperatures (Tm). Afterward, the sequencing was carried out.

RESULTS

Our findings obtained from HRM methods confirmed the SNP genotypes in each group. It is worth mentioning that frequencies of Ala/Ala, Ala/Val, and Val/Val genotypes in MnSOD in the healthy group were 13 (43.3 %), 13 (43.3 %), and 4 (13.3 %), respectively. On the other hand, in the understudy case group, frequencies for the aforementioned genotypes were 5 (16.6 %), 16 (53.3 %), and 9 (30 %), respectively. Besides, the frequencies of the Ala allele in gastric cancer were reported to be 43 % and 54 % for healthy people. Frequencies for the Val allele in the studied case and the control groups were 44 % and 56 %, respectively. The sensitivity and the specificity of the HRM method in detecting MnSOD SNPs were reported to be 100 %.

CONCLUSION

by taking into account the contributing roles of MnSOD SNPs in the induction of gastric cancer, it is highly recommended to create collaboration among basic medical scientists, geneticists, gastroenterologists, medical laboratory scientists, pathologists, and hematologists for more promising results and improved outcome of the diagnosis. Accordingly, we conducted an investigation with diagnostic purposes into the frequencies in SNPs for patients with gastric cancer.

High-resolution melting assay for rapid, simultaneous detection of JAK2, MPL and CALR variants

AIMS

Identification of recurrent genetic alterations in JAK2, MPL and CALR remains crucial in the diagnosis of Philadelphia-negative myeloproliferative neoplasms (MPNs). Current laboratory testing algorithms may entail batching and/or sequential testing, involving multiple testing modalities and sometimes send-out testing that increase the technical and economic demands on laboratories while delaying patient diagnoses. To address this gap, an assay based on PCR and high-resolution melting (HRM) analysis was developed for simultaneous evaluation of JAK2 exons 12-14, MPL exon 10 and CALR exon 9, embodied in the HemeScreen® (hereafter 'HemeScreen') MPN assay.

METHODS

The HemeScreen MPN assay was validated with blood and bone marrow samples from 982 patients with clinical suspicion for MPN. The HRM assay and Sanger sequencing were performed in independent Clinical Laboratory Improvement Amendments (CLIA)-certified laboratories with Sanger sequencing (supported by droplet digital PCR) serving as the gold standard.

RESULTS

HRM and Sanger sequencing had an overall concordance of 99.4% with HRM detecting 133/139 (96%) variants confirmed by sequencing (9/10 MPL, 25/25 CALR, 99/104 JAK2), including 114 single nucleotide variants and 25 indels (3-52 bp). Variants consisted of disease-associated (DA) variants (89%), variants of unclear significance (2%) and non-DA variants (9%) with a positive predictive value of 92.3% and negative predictive value of 99.5%.

CONCLUSIONS

These studies demonstrate the exquisite accuracy, sensitivity and specificity of the HRM-based HemeScreen MPN assay, which serves as a powerful, clinically applicable platform for rapid, simultaneous detection of clinically relevant, somatic disease variants.

Association of DNA repair genes polymorphisms with childhood acute lymphoblastic leukemia: a high-resolution melting analysis

Objective

Acute lymphoblastic leukemia (ALL) is one of the most common cancers in children for which the exact pathogenesis is not yet known. Single-nucleotide variants (SNVs) in different DNA repair genes are reported to be associated with ALL risk. This study aimed to determine the association between XRCC1 (rs1799782) and NBN (rs1805794, rs709816) SNVs and childhood ALL risk in a sample of the Iranian population. Fifty children with ALL and 50 age- and sex-matched healthy children were included in this case–control study. Genotyping of the mentioned SNVs was done by high-resolution melting (HRM) analysis.

Results

The prevalence of all three SNVs in XRCC1 and NBN genes did not differ between the patient and control groups, and these polymorphisms were not associated with childhood ALL risk (P > 0.05). HRM was a practical method for the detection of SNVs in XRCC1 and NBN genes. We found no significant association between XRCC1 (rs1799782) and NBN (rs1805794, rs709816) SNVs and childhood ALL risk.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13104-022-05918-3.

Comparative evaluation of BMI-1 proto-oncogene expression in normal tissue, adenoma and papillary carcinoma of human thyroid in pathology samples

Objective

Papillary Thyroid carcinoma accounts for more than 60% of adult thyroid carcinomas. Finding a helpful marker is vital to determine the correct treatment approach. The present study was aimed to evaluate the expression of the B cell-specific Moloney murine leukemia virus integration site 1 (BMI-1) gene in papillary carcinoma, adenoma, and adjacent healthy thyroid tissues. Pathology blocks of thyroid tissues at the pathology department of patients who have undergone thyroid surgery between 2015 and 2019 were examined; papillary carcinoma, adenoma, and healthy tissues were selected and sectioned. Total RNA was extracted, and the relative expression level of the BMI-1 gene was examined using the Real-Time qPCR method.

Results

In the papillary and adenoma tissues, BMI-1 was overexpressed (1.047-fold and 1.042-fold) in comparison to healthy tissues (p < 0.05 for both comparisons). However, no statistically significant differences were observed between adenoma and papillary carcinoma tissues regarding BMI-1 gene expression. This study demonstrated a new biomarker for thyroid malignancies and found that the mRNA levels of the BMI-1 gene were higher in tumor tissues compared with healthy tissues. Further studies are needed to evaluate the BMI1 gene expression in other thyroid cancers.

High resolution melting analysis and detection of Leishmania resistance: the role of multi drug resistance 1 gene

Background

Pentavalent antimonial compounds are currently used to treat leishmaniasis and resistance to these drugs is a serious problem. Multidrug resistance protein is an efflux pump of the cell membrane that expels foreign compounds. This study designed to evaluate the mutations in the multi-drug resistance 1 (MDR1) gene, in biopsy specimens of Leishmania tropica, with high resolution melting (HRM) method. In this experimental study, genomic DNA was extracted from 130 patients with skin leishmaniasis. Then, nucleotide changes were investigated throughout the gene using HRM and sequencing methods. The samples categorized in 5 groups by differences in the melting temperature (Tm).

Result

The nucleotide changes analysis showed that 61% of the samples of different groups that were unresponsive to drug had mutations in the MDR1 gene, which were also confirmed by the sequencing method. These mutations can be one of the factors responsible for non-responsiveness to the treatment.

Conclusion

According to the findings, it seems that mutation in MDR1 gene could be responsible for drug resistance to pentavalent antimonial compounds. Furthermore, HRM method can be used to diagnose drug resistance in leishmaniasis. It is also recommended that further studies be done regarding the importance of drug resistance in the leishmania affected patients.

Comparison of high-resolution melting analysis with direct sequencing for detection of FLT3-TKD, FLT3-ITD and WT1 mutations in acute myeloid leukemia

BACKGROUND

Acute Myeloid Leukemia (AML) is a group of hematologic diseases characterized by a variety of clinically important genetic alterations. Genetic mutations affecting the FMS-like receptor tyrosine kinase-3 (FLT3) and Wilm's tumor (WT-1) genes are associated with poor prognosis in AML. In this work, efficiency of HRM method for detection of FLT3-ITD, FLT3-TKD, and WT-1 mutations was assessed in comparison with direct sequencing.

METHOD

A total of 58 formalin-fixed, paraffin-embedded BM biopsy specimens of AML patients were analyzed. Mutation detection was performed by HRM method and the results were consequently compared with direct sequencing RESULTS: FLT3 and WT-1 mutations were detected in 21 (36.2%) and 3 (5.17%) samples, respectively. Among all FLT3 mutations, 10 (17.2%) and 11 (18.2%) samples were harboring the FLT3-ITD and-TKD gene mutations, respectively. Frequency of the FLT3-ITD was not statistically different in females (51%) and males (49%). Also, FLT3-TKD was more common in males although the differences in gender distribution were not statistically significant (P = 0.721 and P = 0.626, respectively).

CONCLUSIONS

Regarded as the desirable characteristic, the present study is generally distinguished by the similar previous ones due to assessing the FFPE BM tissue from the perspective of the type of assessed sample. This discrepancy between our results and those in prior studies may be due to the disparity of the studied population size, adopted methods as well as the sample type. In this survey, regarding to low amount of extracted DNA from the paraffinized samples, the HRM method was efficient in determining the mentioned mutations.

Screening of somatic mutations in the JAK2 and CALR genes by high-resolution melting curve analysis

Somatic mutations associated with oncological diseases, including Ph-myeloproliferative neoplasms (Ph-MPN), are very diverse, occur with different frequencies and different allelic burden levels. Therefore, at the initial stage of performing molecular-genetic diagnostic procedures, it is desirable to be able to conduct screening tests in the laboratory. This is especially important when analyzing rare and diverse mutations. Analysis of high resolution melting curves (HRM analysis), which has high sensitivity and is suitable for screening all types of mutations, in a number of studies is proposed for the analysis of Ph-MPN associated mutations in the JAK2 and CALR genes. For analysis of somatic mutations in the majority of literature sources that we reviewed, the authors use the LightCycler (Roche) thermocycler and much rarely the CFX96 (Bio-Rad), which is often presented in Russian scientific and practical and medical organizations. The aim of the study was to screen the somatic JAK2 and CALR mutations by HRM analysis using the CFX96 thermocycler and the Precision Melt Analysis software (Bio-Rad, USA) for patients with Ph-MPN. In the present research, HRM analysis was conducted on the DNA samples from patients with mutations in the JAK2 or in the CALR gene. The Precision Melt Analysis software identified all variants of the analyzed mutations, both a single nucleotide substitution in the JAK2 gene (with allelic burden level in the range of 5-40%), and various indel mutations in the CALR gene (with allelic burden level in the range of 40-50%) Therefore, the HRM analysis that was conducted on the CFX96 allows screening of highly specific mutation for the diagnosis of Ph-MPN in the exon 14 of the JAK2 gene and in the exon 9 of the CALR gene. The inclusion of this screening research in the laboratory testing algorithm improves the efficiency and accessibility of molecular genetic technologies in the diagnosis of Ph-MPN.

An Overview of the Management of the Most Important Invasive Fungal Infections in Patients with Blood Malignancies

In patients with hematologic malignancies due to immune system disorders, especially persistent febrile neutropenia, invasive fungal infections (IFI) occur with high mortality. Aspergillosis, candidiasis, fusariosis, mucormycosis, cryptococcosis and trichosporonosis are the most important infections reported in patients with hematologic malignancies that undergo hematopoietic stem cell transplantation. These infections are caused by opportunistic fungal pathogens that do not cause severe issues in healthy individuals, but in patients with hematologic malignancies lead to disseminated infection with different clinical manifestations. Prophylaxis and creating a safe environment with proper filters and air pressure for patients to avoid contact with the pathogens in the surrounding environment can prevent IFI. Furthermore, due to the absence of specific symptoms in IFI, rapid and accurate diagnosis reduces the mortality rate of these infections and using molecular techniques along with standard mycological methods will improve the diagnosis of disseminated fungal infection in patients with hematologic disorders. Amphotericin B products, extended-spectrum azoles, and echinocandins are the essential drugs to control invasive fungal infections in patients with hematologic malignancies, and according to various conditions of patients, different results of treatment with these drugs have been reported in different studies. On the other hand, drug resistance in recent years has led to therapeutic failures and deaths in patients with blood malignancies, which indicates the need for antifungal susceptibility tests to use appropriate therapies. Life-threatening fungal infections have become more prevalent in patients with hematologic malignancies in recent years due to the emergence of new risk factors, new species, and increased drug resistance. Therefore, in this review, we discuss the different dimensions of the most critical invasive fungal infections in patients with hematologic malignancies and present a list of these infections with different clinical manifestations, treatment, and outcomes.

Significance of CXCL12/CXCR4 Ligand/Receptor Axis in Various Aspects of Acute Myeloid Leukemia

Acute myeloid leukemia (AML) is defined as an aggressive disorder which is described by accumulation of immature malignant cells into the bone marrow. Chemokine-receptor axes are defined as factors involved in AML pathogenesis and prognosis. The chemokine receptor CXCR4 along with its ligand, CXCL12 fit in important players that are actively involved in the cross-talk between leukemia cells and bone marrow microenvironment. Therefore, according to the above introductory comments, in this review article, we have focused on delineating some parts played by CXCL12/CXCR4 axis in various aspects of AML malignancy. Targeting both leukemic and stromal cell interaction is nowadays accepted as a wide and attractive strategy for improving the outcome of treatment in AML in a non-cell autonomous manner. This strategy might be employed in a wide variety of AML patients regardless of their causative mutations. In addition to several potential targets involved in the disruption of malignant leukemic cells from their specific protective niches, compounds which interfere with CXCL12/CXCR4 axis have also been explored in multiple early-phase established clinical trials. Moreover, extensive research programs are exploring novel leading mechanisms for leukemia-stromal interactions that appear to find out novel therapeutic targets within the near future.

Gene mutational analysis by NGS and its clinical significance in patients with myelodysplastic syndrome and acute myeloid leukemia

Background

In this study, we retrospectively summarized the differences of molecular gene mutations between MDS and AML patients, as well as the young and older age groups of MDS and AML patients. We also analyzed the response of newly diagnosed AML patients to standard DA or IA induction chemotherapy and the relationship between the chemotherapy outcome and the frequency of different gene mutation abnormalities.

Methods

NGS assay covering 43 genes was studied in 93 de novo MDS and 325 non-M3 AML patients. Bone marrow samples from all patients underwent gene mutational analysis by NGS.

Results

At least one non-synonymous gene mutation was detected in 279 AML patients (85.8%) and 85 MDS patients (91.4%). Contrary to 59 years and younger AML patients, there was a significantly higher incidence of gene mutation in 60 years and older AML patients (2.37 vs 1.94, p = 0.034). Gene mutation incidence in 60 years and older MDS patients increased, but no statistical significance was present (1.95 vs 1.64, p = 0.216). AML patients had a significantly higher gene mutation incidence compared with MDS-MLD patients (2.02 vs 1.63, p = 0.046). Gene mutation incidence was higher in patients with MDS-EB1/EB2 compared with patients with MDS-MLD but there was no statistical significance present (2.14 vs 1.63, p = 0.081). AML patients had significantly higher incidences of CEBPA, FLT3-ITD, DNMT3A, NPM1 and IDH1/2 gene mutations (p = 0.0043, 0.000, 0.030962, 0.002752, and 0.000628, respectively) and a lower incidence of TET2 and U2AF1 gene mutations (p = 0.000004 and 0.000, respectively) compared with MDS patients. Among the individual genes in different age groups, there were significantly higher incidences of RUNX1, IDH2, TP53 and SF3B1 gene mutations (p = 0.0478, 0.0028, 0.0024 and 0.005, respectively) as well as a trend of higher ASXL gene mutation (p = 0.057) in 60 years and older AML patients compared to 59 years and younger patients. There was no statistically significant difference in MDS patients with the different age groups and among the individual genes. Between AML patients and MDS patients among the different gene functional groups, AML patients had a significantly higher incidence of transcriptional deregulation (27.4% vs 15.1%, p = 0.014963), activated signalling (36.3% vs 10.8%, p = 0.000002) related gene mutations as well as a significantly lower incidence of RNA spliceosome (6.15% vs 60.1%, p = 0.000) related gene mutations. Furthermore, among the patients who received either IA or DA regimen for induction chemotherapy, patients with IA regimen had a significantly better CR rate than those with DA regimen (76.6% vs 57.1%, p = 0.0228).

Conclusions

Different gene mutations had been found in majority of MDS and AML patients. MDS and AML patients had different gene mutation patterns. AML patients with fewer or no gene mutations had a better chance of achieving CR when treated with IA and DA regimen induction chemotherapy.

Analysis of the reannealing- instead of melting-curve in the detection of JAK2 V617F mutation by HRM method

BACKGROUND

The Janus kinase 2 (JAK2) has an important role in the intracellular signaling in normal and neoplastic cells. JAK2 mutation, called JAK2 V617F, is frequently found in Philadelphia chromosome-negative myeloproliferative neoplasms. We aimed to assess the analytical efficiency of high-resolution melting (HRM) method using reannealing-curve analysis in comparison with routine melting-curve analysis for JAK2 V617F mutation detection.

METHOD

Twenty-three samples including one negative synthetic standard DNA, two 50% and 75% positive synthetic standard DNA samples, five wild-type samples and 15 samples positive for JAK2 V617F were examined by HRM. Melting and reannealing stages were performed, and then, raw and normalized curves were compared between the two stages.

RESULTS

In melting-curve analysis, the wild-type and mutant samples had different melting temperatures (75/53°C and 75/10°C, respectively). In normalized curves corresponding to reannealing method, mutant samples were better separated from the baseline than in melting method as well as for samples with different mutant DNA burden from each other. Furthermore, wild-type samples were more homogenous in the normalized curves corresponding to reannealing than in melting method. This means that patients with a low allelic burden may be wrongly interpreted as normal in the common melting method.

CONCLUSION

We suggest the use of reannealing instead of the melting-curve analysis for the detection of sequence variations, especially for large-scale mutation and allele burden measurement in clinical settings. However, more evaluations with more sample size will better improve the benefits of reannealing-curve analysis in research and clinic.