Influence of cytochrome P450 and glutathione S transferase polymorphisms on response to nilotinib therapy among chronic myeloidleukemia patients from Pakistan

Background

Cytochrome P450 (CYP) and glutathione S transferases (GSTs) are important biotransforming enzymes responsible for detoxification of anticancer drugs and carcinogens. Polymorphisms in these enzymes may greatly influence the susceptibility to CML and overall efficacy of tyrosine kinase inhibitors. This study was aimed to estimate the possible influence of the polymorphisms of GSTs and CYP in the occurrence of CML as well as in predicting therapeutic outcome of nilotinib therapy in Pakistani CML patients.

Methods

The polymorphic variability in CYP 1A1*2C, GSTP1 (A3131G), GSTT1 and GSTM1 was assessed either by RFLP or multiplex PCR. The BCR ABL1 transcripts were quantified by qPCR to monitor response to nilotinib.

Results

The CYP1A1*2C heterozygous and GSTP1 homozygous polymorphisms seemed to be a contributing factor in developing CML. Altogether, there were 12 non-responders, 66 responders and 21 partial responders. The most frequent genotype was null GSTM1 in responders followed by CYP 1A1 and GSTP1 -wild type (p =  < 0.05). Whereas, homozygous GSTP1 and GSTT1 null genotype is significantly higher only among nilotinib non-responders.

Conclusion

Hence, it can be concluded that wild type CYP1A1, GSTP1 and null GSTM1 may be frequently linked to favorable outcome in patients treated with nilotinib as depicted by sustained deep molecular response in most CML patients.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12885-022-09605-1.

Sequencing of SARS-CoV-2 in local transmission cases through Oxford Nanopore MinION platform from Karachi Pakistan

INTRODUCTION

The first case of severe acute respiratory syndrome 2 (SARS-CoV-2) was imported to Pakistan in February 2020, since then 8,260 deaths have been witnessed. The virus has been constantly mutating and local transmission cases from different countries vary due to host dependent viral adaptation. Many distinct clusters of variant SARS-CoV-2 have been defined globally. In this study, the epidemiology of SARS-CoV-2 was studied and locally transmitted SARS-CoV-2 isolates from Karachi were sequenced to compared and identify any possible variants.

METHODOLOGY

The real time PCR was performed on nasopharyngeal specimen to confirm SARS-CoV-2 with Orf 1ab and E gene as targets. The virus isolates were sequenced through oxford nanopore technology MinION platform. Isolates from the first and second wave of COVID-19 outbreak in Karachi were compared.

RESULTS

The overall positivity rate for PCR was 26.24% with the highest number of positive cases in June. Approximately, 37.45% PCR positive subjects aged between 19-40 years. All the isolates belonged to GH clade and shared missense mutation D614G in spike protein linked to increased transmission rate worldwide. Another spike protein mutation A222V coexisted with D614G in the virus from the second wave of COVID-19.

CONCLUSIONS

Based on the present findings it is suggested that the locally transmitted virus from Karachi varies from those reported from other parts of Pakistan. Slight variability was also observed between viruses from the first and second wave. Variability in any potential vaccine target may result in failed trials, therefore information on any local viral variants is always useful for effective vaccine design and/or selection.

Usefulness of convalescent plasma transfusion for the treatment of severely ill COVID-19 patients in Pakistan

Background

Convalescent plasma(CP) was utilized as potential therapy during COVID-19 pandemic in Pakistan. The study aimed at appraisal of CP transfusion safety and usefulness in COVID pneumonia.

Methods

Single arm, MEURI study design of non-randomized open label trial was conducted in five centers. Patients werecategorized as moderately severe, severe, and critical. The primary endpoint was a) improvement in clinical status and change in category of disease severity; secondary endpoint was b) CP ability to halt disease progression to invasive ventilation. CP transfused to hospitalized patients. Statistical tests including median (interquartile ranges), Mann-Whitney U test, Fisher’s exact test using SPSS ver. 23, ANOVA and Chi-square test were applied for the analysis of results parameters before and after CP treatment. SOFA score was applied for multiorgan failure in severe and critical cases.

Results

A total of 50 adult patients; median age 58.5 years (range: 29–92 years) received CP with infusion titers; median 1:320 U/mL (Interquartile range 1:80–1:320) between April 4 to May 5, 2020. The median time from onset of symptoms to enrollment in trial was 3 to 7 days with shortness of breath and lung infiltration as severity criterion. In 35 (70%) recipients, oxygen saturation improved from 80 to 95% within 72h, with resolution of lung infiltrates. Primary endpoint was achieved in 44 (88%) recipients whereas secondary endpoint was achieved in 42 (84%). No patient experienced severe adverse events. A high SOFA score (> 7) correlated with deaths in severe and critical patients. Eight (16%) patients expired due to comorbidities; cardiac arrest in 2 (4%), multiorgan failure secondary to cytokine storm in 5 (10%) and ventilator associated complications in 1 (2%).

Conclusion

CP transfusion can be used as a safe and useful treatment in moderately severe and severe patients.

Trial registration

The trial registration number is NCT04352751 (https://www.irct.ir/search/result?query=IRCT20200414047072N1). Trial Registration date is 28th April 2020.

Possible correlation of electrochemiluminescence based numerical cut off index value with concentration of anti-SARS-CoV-2 antibody: Is it worth reporting?

Background: Many laboratories are reporting a numerical cutoff index value (COI) value for most anti-SARS-CoV-2 qualitative tests. These numerical values in patients' report ultimately created great confusion in the public and physicians, therefore this study was designed to evaluate the correlation of electrochemiluminescence (ECLIA) based numerical COI values with quantitative ELISA of anti-SARS-CoV-2 antibody. Design and Methods: Two hundred and twenty-eight (228) recovered COVID-19 patients were included; their serum samples were analyzed by quantitative ELISA and ECLIA for anti-SARSCOV- 2 antibodies. Results: One hundred and seventy-three (75.8%) patients tested positive by ECLIA and ELISA assay and thirty-seven (6.2%) were tested negative by both methods. A weak positive correlation (r=0.37) was found between numerical COI value of ECLIA with ELISA concentration, which was statistically significant with p<0.001. All values were dispersed on scatter plot and there was no significant linear relationship between ECLIA and ELISA assay. Conclusions: As both testing techniques are base upon the same immunological phenomena of detecting antibodies against nucleocapsid protein. We suggest that COI values are not meant to describe the immunity level of the individuals thus the physicians should not consider it as a quantitative value for antibody levels in COVID-19 patients.

A distinct molecular mutational profile and its clinical impact in essential thrombocythemia and primary myelofibrosis patients

BACKGROUND

Classical MPNs including ET and PMF have a chronic course and potential for leukaemic transformation. Timely diagnosis is obligatory to ensure appropriate management and positive outcomes. The aim of this study was to determine the mutational profile, clinical characteristics and outcome of ET and PMF patients in Pakistani population.

METHODS

This was a prospective observational study conducted between 2012 and 2017 at NIBD. Patients were diagnosed and risk stratified according to international recommendations. Response to treatment was assessed by IWG criteria.

RESULTS

Of the total 137 patients analysed, 75 were ET and 62 were PMF. JAK2 positivity was seen in 51 cases (37.2%), CALR in 41 cases (29.9%), while triple-negative in 17 (12.4%) cases. None of the patients in the present study were MPL positive. Overall survival for patients with ET and PMF was 92.5 and 86.0% respectively and leukaemia free survival was 100 and 91.6% respectively, at a median follow-up of 12 months. Leukaemic transformation occurred in 6.5% of MF patients; among them, JAK2 mutation was frequently found. Molecular mutations did not influence the OS in ET whereas in PMF, OS was shortest in the triple-negative PMF group as compared to the JAK2 and CALR positive patient groups.

CONCLUSION

This study shows a different spectrum of molecular mutations in ET and PMF patients in Pakistani population as compared to other Asian countries. Similarly, the risk of leukaemic transformation in ET and PMF is relatively lower in our population of patients. The factors responsible for these phenotypic and genotypic differences need to be analysed in large scale studies with longer follow-up of patients.

Evaluation of efficacy of serological methods for detection of HCV infection in blood donors: A single centre experience

Background and Objective:

Blood transfusion is an essential and life-saving medical intervention. Despite multiple preventive measures transfusion-transmitted hepatitis C virus (HCV) infection continues to be a major healthcare issue in Pakistan. This study was conducted at National Institute of Blood Diseases & Bone Marrow Transplantation to evaluate the frequency of active HCV infection with or without co-infection in blood donors and also to determine comparative efficacy of Multisure HCV antibody assay (MHAA); a new serological device.

Methods:

A total of 14652 blood donors visiting National Institute of Blood Diseases & Bone Marrow Transplantation (NIBD) Blood Bank from January 2013 to July 2014 were enrolled and screened for a range of blood borne infections such as HBV, HCV, HIV, malaria and syphilis. The HCV was screened simultaneously by Abbot Architect anti-HCV assay (CLIA) and MHAA. The active HCV infection was confirmed by nucleic acid testing (NAT) in reactive donors. Later; for determination of comparative efficacy of MHAA; all NAT positive samples were further tested using Monolisa™, HCV blot 3.0, Anti-HCV plus V2 and Anti-HCV-MPBIO-EIA.

Results:

The HCV reactive sera were observed in 1.563% (226) donors. The NAT confirmed active HCV infection in 138 donors. Overall 27.84% of HCV positive donors exhibited co-infection either with HBV (2.57%), syphilis (22.78%). Triple infection was not observed in any donor. The efficacy of MHAA is comparable to all the serological tests with a sensitivity of about 96.89%.

Conclusion:

Active HCV infection was present in 0.94% donors. With a sensitivity of 96.89% (95% CI: 95.66-98.12) the multi-parametric device MHAA can effectively detect HCV infection in donors. Thus, it can be used in limited health care settings for HCV screening.

Expression of aberrant antigens in hematological malignancies: A single center experience

Background and Objective

Aberrant phenotype is a phenomenon of abnormal expression or loss of expression of cell specific lineage marker not associated with specific cell type. Aberrant phenotype expression due to genetic defects may be associated with unfavorable outcome. It can be used to determine minimal residual disease status. The purpose of the study was to find out the occurrence of aberrant phenotypes in leukemia/lymphoma patients.

Methods

One milliliter peripheral blood or bone marrow samples were analyzed on FACS Calibur flowcytometer. The cells were lysed and stained following standard protocol. Data was acquired and analyzed by CellQuest-Pro software. The Antigenic expression was rated as positive when the percentage of positive blast cells was ≥ 20%. In that manner, aberrant phenotype was considered positive when 20% of blast cells show expression of markers.

Results

Of a total 145 cases analyzed, 26 were acute myeloid leukemia, 71 of acute lymphoblastic leukaemia, 48 were of Chronic Lymphoid leukemia on the basis of morphological features and confirmed by flow cytometry. Overall, 19% (28) cases showed aberrant expression of antigens. In 32% (9/28) AML patients, CD5, CD7, CD64dim, CD10, CD117, CD25 and TdT were expressed while in 25% (7/28) ALL patients CD33, CD13, HLA-DR and CD3 were detected. Among chronic leukemia, all aberrant expressions were seen in cases of B-CLL (10/28) only; with CD11c, CD3 and CD10 as the aberrantly expressed markers.

Conclusion

Variability in aberrant phenotype expression was observed in different types of acute and chronic leukemia patients with no prognostic implications on treatment response.

Importance of immature platelet fraction as predictor of immune thrombocytopenic purpura

Background and Objective:

Immune thrombocytopenic purpura (ITP) is a clinical syndrome in which a decreased number of circulating platelets (thrombocytopenia) manifests as a bleeding tendency, easy bruising (purpura) or extravasation of blood from capillaries into skin and mucous membranes (petechiae). The diagnosis of ITP can be made clinically on the basis of symptoms, we need to see if ITP can be confirmed in patients by quantification of residual RNA containing immature platelets (megakaryocytic mass) or immature platelets fraction (IPF) using automated hematology analyzers (Sysmex XE-2100).

Methods:

In order to check the efficacy of IPF% parameter of Sysmex XE-2100 a total of 231 patients of thrombocytopenia were included in this study. Complete blood count (CBC) was estimated. The data was statistically analyzed by SPSS version 17.

Results:

About 62 patients were diagnosed as ITP and 169 patients were diagnosed as non ITP on the basis of clinical history. The mean IPF % value of ITP patients was 16.39% and the IPF % value of Non ITP patients was ~7.69% respectively. There was no significant difference in IPF% values with respect to time between sampling and acquisition of complete blood count. The diagnostic sensitivity of IPF% as biomarker for ITP and non-ITP was 85.71% (95%CI: 84.04% to 85.96%) and 41.76% (95% CI: 39.87% to 43.65%).

Conclusion:

The mean IPF % value by Sysmex XE-2100 can be used to predict ITP.