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Gupta DG, Varma N, Abdulkadir SA, Sreedharanunni S, Sachdeva MUS, Naseem S, Bose P, Binota J, Malhotra P, Khadwal A, Trehan A, Varma S. A surrogate molecular approach for the detection of Philadelphia chromosome-like B-acute lymphoblastic leukemia. Cancer 2024; 130:713-726. [PMID: 37819686 DOI: 10.1002/cncr.35051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 07/13/2023] [Accepted: 09/08/2023] [Indexed: 10/13/2023]
Abstract
BACKGROUND Philadelphia chromosome (Ph)-like B-acute lymphoblastic leukemia (B-ALL) is a clinically significant, high-risk genetic subtype of B-ALL cases. There are few data on the incidence, characterization, and treatment outcomes of Ph-like ALL cases from low- and middle-income countries. There is a pressing need to establish a well-organized/cost-effective approach for identifying Ph-like ALL instances. METHODS Multiplex reverse transcriptase polymerase chain reaction, nCounter NanoString, and fluorescence in situ hybridization were used to detect and characterize Ph-like ALL cases among recurrent genetic abnormalities (RGA)neg B-ALL cases. At the end of induction therapy, flow cytometry-minimal residual disease (MRD) assay was used to quantify MRD positivity in Ph-like ALL cases. RESULTS Of 130 newly diagnosed B-ALL cases, 25% (BCR::ABL1), 4% (ETV6::RUNX1), 5% (TCF3::PBX1), 2% (KM2TA::AFF1), and 65% RGAneg B-ALL cases were revealed by multiplex reverse transcriptase polymerase chain reaction. Among RGAneg B-ALL cases, 24% Ph-like ALL cases using nCounter NanoString were identified, with 48% CRLF2high cases with 45% CRLF2::P2RY8 and 18% CRLF2::IGH rearrangements(∼r) revealed by fluorescence in situ hybridization. In 52% of CRLF2low cases, 17% ABL1 and JAK2∼r 8% EPOR::IGH & PDGRFB∼r were identified. Ph-like ALL cases had higher total leukocyte count (p < .05), male preponderance (p < .05), and high MRD-positivity/induction failure compared with RGAneg B-ALL cases. Furthermore, in Ph-like ALL cases, 11 significant genes using quantitative polymerase chain reaction were identified and validated. CRLF2, IGJ, CEACAM6, MUC4, SPATS2L and NRXN3 genes were overexpressed and show statistical significance (p < .05) in Ph-like ALL cases. CONCLUSIONS This study showed the high incidence of Ph-like ALL cases with kinase activating alterations and treatment outcomes from low- and middle-income region. Furthermore, a surrogate cost-effective multiplex panel of 11 overexpressed genes for the prompt detection of Ph-like ALL cases is proposed. PLAIN LANGUAGE SUMMARY Identification of recurrent gene abnormalities (RGA)neg B-acute lymphoblastic leukemia (B-ALL) cases using multiplex-reverse transcriptase polymerase chain reaction. Identification and characterization of Philadelphia (Ph)-like ALL cases using nCounter NanoString gene expression profiling and fluorescence in situ hybridization. Furthermore, Ph-like ALL cases were characterized according to CRLF2 expression and kinase-activating genomic alterations. Minimal residual disease of Ph-like ALL cases were quantified using flow cytometry-minimal residual disease assay. A surrogate molecular approach was established to detect Ph-like ALL cases from low- and middle-income countries.
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Affiliation(s)
- Dikshat Gopal Gupta
- Department of Urology & Pathology, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Neelam Varma
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Sarki Abba Abdulkadir
- Department of Urology & Pathology, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Sreejesh Sreedharanunni
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Man Updesh Singh Sachdeva
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Shano Naseem
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Parveen Bose
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Jogeshwar Binota
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Pankaj Malhotra
- Department of Clinical Hematology & Medical Oncology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Alka Khadwal
- Department of Clinical Hematology & Medical Oncology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Amita Trehan
- Department of Pediatrics, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Subhash Varma
- Department of Internal Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
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Gupta DG, Varma N, Abdulkadir SA, Singh P, Sachdeva MUS, Naseem S, Siddiqui MR, Bose P, Binota J, Malhotra P, Khadwal A, Varma S. Identification and validation of the optimal reference genes for standardizing the gene expression profiling diagnostic panel of Ph-like B-lineage acute lymphoblastic leukemia. Clin Exp Med 2023; 23:4539-4551. [PMID: 37470909 DOI: 10.1007/s10238-023-01131-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 06/25/2023] [Indexed: 07/21/2023]
Abstract
Gene expression profiling is the criterion standard for recognizing Ph-like ALL signatures among B-ALLs. The prerequisite of GEP is the accurate normalization of target genes with stable expression of housekeeping genes in a quantitative PCR. HKGs exhibit differential expression in the different experimental conditions and affect the target genes' expression, leading to imprecise qPCR results. The selection of stable HKGs is crucial in GEP experiments, especially in identifying high-risk Ph-like ALL cases. We have evaluated the expression stability of nine HKGs (GAPDH, ACTB, GUSB, RNA18S, EEF2, PGK1, B2M, TBP and ABL1) in identified Ph-like ALLs and Ph-negative (n = 23 each) using six algorithms, 4 traditional softwares; geNorm, BestKeeper, NormFinder, Delta Cq value method, and two algorithms, RefFinderTM and ComprFinder. Further, we have validated the expression of 8 overexpressed normalized genes in Ph-like ALL cases (JCHAIN, CA6, MUC4, SPATS2L, BMPR1B, CRLF2, ADGRF1 and NRXN3). GeNorm, BestKeeper, NormFinder, Delta Cq value method, RefFinderTM and ComprFinder algorithm analysis revealed that EEF2, GAPDH, and PGK1 form the best representative HKGs in Ph-like ALL cases, while RNA18s, ß-actin, and ABL1 in Ph-negative ALLs. Lastly, we performed a correlation analysis and found that the combination of EEF2, GAPDH, and PGK1 represents the best combination with a very high correlation in Ph-like ALL cases. This is the first report that shows EEF2, GAPDH, and PGK1 are the best HKG genes and can be used in the diagnostic panel of Ph-like ALL cases using qPCR at baseline diagnosis.
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Affiliation(s)
- Dikshat Gopal Gupta
- Department of Urology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Neelam Varma
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India.
| | - Sarki Abba Abdulkadir
- Department of Urology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Parmod Singh
- Department of Anatomy, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Man Updesh Singh Sachdeva
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Shano Naseem
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Mohammad Rizwan Siddiqui
- Department of Pediatrics, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Parveen Bose
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Jogeshwar Binota
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Pankaj Malhotra
- Department of Clinical Hematology and Medical Oncology, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Alka Khadwal
- Department of Internal Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Subhash Varma
- Department of Clinical Hematology and Medical Oncology, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
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Gupta DG, Varma N, Sharma P, Truica MI, Abdulkadir SA, Singh P, Singh Sachdeva MU, Naseem S, Siddiqui MR, Bose P, Binota J, Malhotra P, Khadwal A, Trehan A, Varma S. Hematological, clinical, immunophenotypic characterization, and treatment outcomes of prognostically significant genetic subtypes of B-lineage acute lymphoblastic leukemia: A report of 1021 patients from India. Cancer 2023; 129:3390-3404. [PMID: 37498973 DOI: 10.1002/cncr.34957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 07/29/2023]
Abstract
BACKGROUND The published literature on hematological, clinical, flowcytometric-immunophenotyping, and minimal residual disease outcomes of the prognostically important genetic subtypes of acute lymphoblastic leukemia (ALL) is scarce from low-income countries. For newer classifications such as BCR::ABL1-like ALLs, the scarcity of patient-level data is even more pronounced. METHODS The authors performed comprehensive detection of recurrent gene fusions and BCR::ABL1-like ALL cases followed by immunophenotypic profiling and obtained clinical outcome parameters for a large cohort (n = 1021) of patients from India. This cohort included a significant number of patients with BCR::ABL1-like ALL subtype and other genetic subtypes of ALL. RESULTS Patients with BCR::ABL1-positive and BCR::ABL1-like ALL were significantly older, had male preponderance, and expressed a higher white blood cell count than BCR::ABL1-negative cases (p < .05). Logistic regression modeling of B-lineage-ALL (B-ALL) subtypes revealed that cluster of differentiation (CD)36 is a strong statistically significant predictive marker of BCR::ABL1-like ALL (p < .05). Furthermore, patients with BCR::ABL1-like ALLs show a significantly higher frequency of CD36 expression compared to BCR::ABL1-negative ALLs (p < .05). In terms of clinical symptoms, lymphadenopathy is a strong statistically significant predictive marker in BCR::ABL1-like ALLs compared to BCR::ABL1-negative ALL cases (p < .05). In terms of treatment outcomes, minimal residual disease (MRD) positivity in BCR::ABL1-positive ALL cases were statistically significant (p < .05), and BCR::ABL1-like ALL cases had high MRD-positivity as compared to BCR::ABL1-negative ALL cases but did not show statistical significance. CONCLUSIONS The findings evince the use of novel therapies and personalized treatment regimens to improve the overall survival of the newer incorporated entities in B-ALLs. This is the first report characterizing the hematological, clinical, flowcytometric-immunophenotyping, and minimal residual disease outcomes of the prognostically significant subtypes of ALLs in patients from India. PLAIN LANGUAGE SUMMARY Characterizing the hematological, clinical, flowcytometric-immunophenotyping, and minimal residual disease outcomes of the prognostically significant subtypes (n = 1021) of acute lymphoblastic leukemia (ALLs) in patients from India. We have made two independent logistic regression models of cluster of differentiation (CD) markers and clinical symptoms to differentiate prognostically significant subtypes of ALLs. Logistic regression analysis of CD markers revealed CD36 as a strong predictor in BCR::ABL1-like ALL cases compared to BCR::ABL1-negative ALL cases. Logistic regression analysis of clinical symptoms revealed lymphadenopathy significantly predicts BCR::ABL1-like ALLs (p < .05). In terms of treatment outcomes, BCR::ABL1-positive ALL had statistically significant minimal residual disease (MRD) (p < .05), and BCR::ABL1-like ALL cases had high MRD-positivity but did not show statistical significance as compared to BCR::ABL1-negative ALLs.
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Affiliation(s)
- Dikshat Gopal Gupta
- Department of Urology and Pathology, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Neelam Varma
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Praveen Sharma
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Mihai I Truica
- Department of Urology and Pathology, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Sarki A Abdulkadir
- Department of Urology and Pathology, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Parmod Singh
- Department of Anatomy, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Man Updesh Singh Sachdeva
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Shano Naseem
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Mohammad Rizwan Siddiqui
- Department of Pediatrics, Northwestern University Feinberg School of Medicine and Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Parveen Bose
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Jogeshwar Binota
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Pankaj Malhotra
- Department of Clinical Hematology and Medical Oncology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Alka Khadwal
- Department of Internal Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Amita Trehan
- Pediatric Hematology Oncology Unit, Department of Pediatrics, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Subhash Varma
- Department of Internal Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
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Gupta DG, Varma N, Sreedharanunni S, Abdulkadir SA, Naseem S, Sachdeva MUS, Binota J, Bose P, Malhotra P, Khadwal A, Varma S. 'Evaluation of adverse prognostic gene alterations & MRD positivity in BCR::ABL1-like B-lineage acute lymphoblastic leukaemia patients, in a resource-constrained setting. Br J Cancer 2023; 129:143-152. [PMID: 37156894 PMCID: PMC10307811 DOI: 10.1038/s41416-023-02294-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 04/12/2023] [Accepted: 04/21/2023] [Indexed: 05/10/2023] Open
Abstract
BACKGROUND Early detection of BCR::ABL1-like ALL could impact treatment management and improve the overall survival/outcome. BCR::ABL1-like ALL cases are characterised by diverse genetic alterations activating cytokine receptors and kinase signalling. Its detection is still an unmet need in low-middle-income countries due to the unavailability of a patented TLDA assay. METHODS This study's rationale is to identify BCR::ABL1-like ALLs using the PHi-RACE classifier, followed by the characterisation of underlying adverse genetic alterations in recurrent gene abnormalities negative (RGAneg) B-ALLs (n = 108). RESULTS We identified 34.25% (37/108) BCR::ABL1-like ALLs using PHi-RACE classifier, characterised by TSLPR/CRLF2 expression (11.58%), IKZF1 (Δ4-7) deletion (18.9%) and chimeric gene fusions (34.61%). In overexpressed TSLPR/CRLF2 BCR::ABL1-like ALLs, we identified 33.33% (1/3) CRLF2::IGH and 33.33% (1/3) EPOR::IGH rearrangements with concomitant JAK2 mutation R683S (50%). We identified 18.91% CD13 (P = 0.02) and 27.02% CD33 (P = 0.05) aberrant myeloid markers positivity, which was significantly higher in BCR::ABL1-like ALLs compared to non-BCR::ABL1-like ALLs. MRD positivity was considerably higher (40% in BCR::ABL1-like vs. 19.29% in non-BCR::ABL1-like ALLs). CONCLUSIONS With this practical approach, we reported a high incidence of BCR::ABL1-like ALLs, and a lower frequency of CRLF2 alteration & associated CGFs. Recognising this entity, early at diagnosis is crucial to optimise personalised treatment strategies.
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Affiliation(s)
- Dikshat Gopal Gupta
- Department of Urology, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Neelam Varma
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, Chandigarh, 160012, India.
| | - Sreejesh Sreedharanunni
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, Chandigarh, 160012, India
| | - Sarki Abba Abdulkadir
- Department of Urology, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Shano Naseem
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, Chandigarh, 160012, India
| | - Man Updesh Singh Sachdeva
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, Chandigarh, 160012, India
| | - Jogeshwar Binota
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, Chandigarh, 160012, India
| | - Parveen Bose
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, Chandigarh, 160012, India
| | - Pankaj Malhotra
- Department of Clinical Hematology & Medical Oncology, Post Graduate Institute of Medical Education and Research, Chandigarh, Chandigarh, 160012, India
| | - Alka Khadwal
- Department of Clinical Hematology & Medical Oncology, Post Graduate Institute of Medical Education and Research, Chandigarh, Chandigarh, 160012, India
| | - Subhash Varma
- Department of Internal Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, Chandigarh, 160012, India
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Gupta DG, Varma N, Kumar A, Naseem S, Sachdeva MUS, Sreedharanunni S, Binota J, Bose P, Khadwal A, Malhotra P, Varma S. Genomic and proteomic characterization of Philadelphia-like B-lineage acute lymphoblastic leukemia: A report of Indian patients. Cancer 2023; 129:1217-1226. [PMID: 36738086 DOI: 10.1002/cncr.34665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 02/05/2023]
Abstract
BACKGROUND The gold standard for the identification of Philadelphia (Ph)-like acute lymphoblastic leukemia (ALL) patients is gene expression profiling. Because of its diverse nature, its identification is extremely difficult and expensive. On the genomic and proteomic landscape of Ph-like ALL patients, there is a paucity of published literature from developing countries. METHODS The authors used digital barcoded nCounter NanoString gene expression profiling for its detection, followed by molecular and proteomic characterization using fluorescence in situ hybridization and liquid chromatography-tandem mass spectrometry (LC-MS/MS). RESULTS The authors found 32.05% Ph-like ALL patients and their median age at presentation was considerably higher than Ph-negative ALL cases (p = .0306). Furthermore, we identified 20% CRLF2 overexpressed cases having 8.33% CRLF2-IGH translocation with concomitant R683S mutation and 8.33% CRLF2-P2RY8 translocation. In 80% of CRLF2 downregulated cases, we identified 10% as having JAK2 rearrangement. Minimal residual disease-positivity was more common in Ph-like ALL cases (55.55% vs. 25% in Ph-negative ALL cases). Immunoglobulin J chain (Jchain), small nuclear ribonucleoprotein SmD1 (SNRPD1), immunoglobulin κ constant (IGKC), NADH dehydrogenase (ubiquinone) 1 α subcomplex subunit 2 (NDUFA2), histone H2AX (H2AFX), charged multivesicular body protein 4b (CHMP4B), and carbonyl reductase (NADPH) (CBR1) proteins were identified to be substantially expressed in Ph-like ALL patients, using LC-MS/MS. Gene enrichment analysis indicated that involvement of spliceosomal mediated messenger RNA splicing pathway and four microRNAs was statistically significant in Ph-like ALL patients. CONCLUSIONS For the first time, we have described incidence, molecular, and proteomic characterization of Ph-like ALL, in developing nations. PLAIN LANGUAGE SUMMARY In developing countries, detecting Philadelphia (Ph)-like B-lineage acute lymphoblastic leukemia is complicated and challenging due to its diverse genetic landscape. There is no well-defined and cost-effective methodology for its detection. The incidence of this high-risk subtype is very high in adult cases, and there is an urgent need for its accurate detection. We have developed an online PHi-RACE classifier for its rapid detection, followed by delineating the genomic and proteomic landscape of Ph-like acute lymphoblastic leukemias for the first time in Indian patients.
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Affiliation(s)
- Dikshat Gopal Gupta
- Department of Pediatrics, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Neelam Varma
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Ashish Kumar
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Shano Naseem
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Man Updesh Singh Sachdeva
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Sreejesh Sreedharanunni
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Jogeshwar Binota
- Department of Pediatrics, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Parveen Bose
- Department of Pediatrics, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Alka Khadwal
- Department of Internal Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Pankaj Malhotra
- Department of Clinical Hematology and Medical Oncology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Subhash Varma
- Department of Internal Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
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Gupta DG, Varma N, Kumar A, Naseem S, Sachdeva MUS, Bose P, Binota J, Gupta M, Sonam P, Rana P, Malhotra P, Varma S. Identification and validation of suitable housekeeping genes for gene expression studies in BCR-ABL1 positive B-lineage acute lymphoblastic leukemia. Mol Biol Rep 2022; 49:4841-4848. [PMID: 35344115 DOI: 10.1007/s11033-022-07337-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 03/04/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND The stability of the housekeeping gene (HKG) expression is an absolute prerequisite for accurate normalization of target gene expression in a quantitative real-time polymerase chain reaction (RQ-PCR). In RQ-PCR, the widely used normalization approach involves the standardization of target genes to the most stable HKG control genes. According to the recent literature, in different experimental conditions the HKGs exhibit either up or down-regulation and thus affecting the gene expression profiles of target genes which leads to erroneous results. This implies that it is very important to select the appropriate HKG and verify the expression stability of the HKG before quantification of the target gene. METHODS AND RESULTS The present study aims to analyze six different HKGs for their expression profiles and stability in BCR-ABL1 negative cases and validate them in BCR-ABL1 positive cases, detected by multiplex reverse transcribed polymerase chain reaction (RT-PCR). Six commonly used reference genes (GAPDH, ABL1, RNA18S, ACTB, GUSB, and EEF2) were selected in this study. RQ-PCR was performed on 24 BCR-ABL1 negative cases and the outcomes were validated on 24 BCR-ABL1 positive cases. RefFinder™, a web-based composite software was used to check the stability of HKG genes by different algorithms and comprehensive ranking of each HKG gene in BCR-ABL1 negative cases and finally validated in BCR-ABL1 positive cases. CONCLUSIONS It was found that RNA18S, ABL1 and GUSB are good stable HKG genes, which showed minimum variability in gene expression compared to GAPDH, EEF2, and ACTB, the most commonly used HKG.
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Affiliation(s)
- Dikshat Gopal Gupta
- Department of Hematology, Post Graduate Institute of Medical Education and Research (PGIMER), Sector 12, Chandigarh, 160012, India
| | - Neelam Varma
- Department of Hematology, Post Graduate Institute of Medical Education and Research (PGIMER), Sector 12, Chandigarh, 160012, India.
| | - Ashish Kumar
- International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Shano Naseem
- Department of Hematology, Post Graduate Institute of Medical Education and Research (PGIMER), Sector 12, Chandigarh, 160012, India
| | - Man Updesh Singh Sachdeva
- Department of Hematology, Post Graduate Institute of Medical Education and Research (PGIMER), Sector 12, Chandigarh, 160012, India
| | - Parveen Bose
- Department of Hematology, Post Graduate Institute of Medical Education and Research (PGIMER), Sector 12, Chandigarh, 160012, India
| | - Jogeshwar Binota
- Department of Hematology, Post Graduate Institute of Medical Education and Research (PGIMER), Sector 12, Chandigarh, 160012, India
| | - Minakshi Gupta
- Department of Hematology, Post Graduate Institute of Medical Education and Research (PGIMER), Sector 12, Chandigarh, 160012, India
| | - Priti Sonam
- Department of Hematology, Post Graduate Institute of Medical Education and Research (PGIMER), Sector 12, Chandigarh, 160012, India
| | - Palak Rana
- Department of Hematology, Post Graduate Institute of Medical Education and Research (PGIMER), Sector 12, Chandigarh, 160012, India
| | - Pankaj Malhotra
- Department of Internal Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Subhash Varma
- Department of Internal Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
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