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Arjuna S, Shah M, Dono A, Nunez-Rubiano L, Pichardo-Rojas PS, Zhu JJ, Riascos RF, Luthra R, Roy-Chowdhuri S, Duose D, Wang DH, Lang FF, Esquenazi Y, Ballester LY. Rapid detection of mutations in CSF-cfTNA with the Genexus Integrated Sequencer. J Neurooncol 2024; 166:39-49. [PMID: 38160230 DOI: 10.1007/s11060-023-04487-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/20/2023] [Indexed: 01/03/2024]
Abstract
PURPOSE Genomic alterations are fundamental for molecular-guided therapy in patients with breast and lung cancer. However, the turn-around time of standard next-generation sequencing assays is a limiting factor in the timely delivery of genomic information for clinical decision-making. METHODS In this study, we evaluated genomic alterations in 54 cerebrospinal fluid samples from 33 patients with metastatic lung cancer and metastatic breast cancer to the brain using the Oncomine Precision Assay on the Genexus sequencer. There were nine patients with samples collected at multiple time points. RESULTS Cell-free total nucleic acids (cfTNA) were extracted from CSF (0.1-11.2 ng/μl). Median base coverage was 31,963× with cfDNA input ranging from 2 to 20 ng. Mutations were detected in 30/54 CSF samples. Nineteen (19/24) samples with no mutations detected had suboptimal DNA input (< 20 ng). The EGFR exon-19 deletion and PIK3CA mutations were detected in two patients with increasing mutant allele fraction over time, highlighting the potential of CSF-cfTNA analysis for monitoring patients. Moreover, the EGFR T790M mutation was detected in one patient with prior EGFR inhibitor treatment. Additionally, ESR1 D538G and ESR1::CCDC170 alterations, associated with endocrine therapy resistance, were detected in 2 mBC patients. The average TAT from cfTNA-to-results was < 24 h. CONCLUSION In summary, our results indicate that CSF-cfTNA analysis with the Genexus-OPA can provide clinically relevant information in patients with brain metastases with short TAT.
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Affiliation(s)
- Srividya Arjuna
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center Houston, Houston, TX, USA
| | - Mauli Shah
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center Houston, Houston, TX, USA
| | - Antonio Dono
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School at UT Health, Houston, TX, USA
| | - Luis Nunez-Rubiano
- Department of Diagnostic and Interventional Imaging, McGovern Medical School at UT Health, Houston, TX, USA
| | - Pavel S Pichardo-Rojas
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School at UT Health, Houston, TX, USA
| | - Jay-Jiguang Zhu
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School at UT Health, Houston, TX, USA
- Memorial Hermann Hospital-TMC, Houston, TX, USA
| | - Roy F Riascos
- Department of Diagnostic and Interventional Imaging, McGovern Medical School at UT Health, Houston, TX, USA
| | - Rajyalakshmi Luthra
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center at Houston, Houston, TX, USA
| | - Sinchita Roy-Chowdhuri
- Department of Pathology, The University of Texas MD Anderson Cancer Center Houston, Houston, TX, USA
| | - Dzifa Duose
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center Houston, Houston, TX, USA
| | - Daniel H Wang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center Houston, Houston, TX, USA
| | - Frederick F Lang
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center Houston, Houston, TX, USA
| | - Yoshua Esquenazi
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School at UT Health, Houston, TX, USA.
- Memorial Hermann Hospital-TMC, Houston, TX, USA.
- Center for Precision Health, Vivian L. Smith Department of Neurosurgery, The University of Texas Health Science Center at Houston, Houston, TX, USA.
| | - Leomar Y Ballester
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center Houston, Houston, TX, USA.
- Department of Pathology, The University of Texas MD Anderson Cancer Center Houston, Houston, TX, USA.
- Neuropathology and Molecular Genetic Pathology, Department of Pathology, The University of Texas MD Anderson Cancer Center Houston, Houston, TX, USA.
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Nanjappa DP, De Saffel H, Kalladka K, Arjuna S, Babu N, Prasad K, Sips P, Chakraborty A. Poly (A)-specific ribonuclease deficiency impacts oogenesis in zebrafish. Sci Rep 2023; 13:10026. [PMID: 37340076 DOI: 10.1038/s41598-023-37226-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 06/18/2023] [Indexed: 06/22/2023] Open
Abstract
Poly (A)-specific ribonuclease (PARN) is the most important 3'-5'exonuclease involved in the process of deadenylation, the removal of poly (A) tails of mRNAs. Although PARN is primarily known for its role in mRNA stability, recent studies suggest several other functions of PARN including a role in telomere biology, non-coding RNA maturation, trimming of miRNAs, ribosome biogenesis and TP53 function. Moreover, PARN expression is de-regulated in many cancers, including solid tumours and hematopoietic malignancies. To better understand the in vivo role of PARN, we used a zebrafish model to study the physiological consequences of Parn loss-of-function. Exon 19 of the gene, which partially codes for the RNA binding domain of the protein, was targeted for CRISPR-Cas9-directed genome editing. Contrary to the expectations, no developmental defects were observed in the zebrafish with a parn nonsense mutation. Intriguingly, the parn null mutants were viable and fertile, but turned out to only develop into males. Histological analysis of the gonads in the mutants and their wild type siblings revealed a defective maturation of gonadal cells in the parn null mutants. The results of this study highlight yet another emerging function of Parn, i.e., its role in oogenesis.
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Affiliation(s)
- Dechamma Pandyanda Nanjappa
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education & Research, NITTE (Deemed to be University), Deralakatte, Mangaluru, 575018, India
| | - Hanna De Saffel
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Krithika Kalladka
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education & Research, NITTE (Deemed to be University), Deralakatte, Mangaluru, 575018, India
| | - Srividya Arjuna
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education & Research, NITTE (Deemed to be University), Deralakatte, Mangaluru, 575018, India
| | - Nishith Babu
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education & Research, NITTE (Deemed to be University), Deralakatte, Mangaluru, 575018, India
| | - Kishan Prasad
- Department of Pathology, KS Hegde Medical Academy, NITTE (Deemed to be University), Deralakatte, Mangaluru, 575018, India
| | - Patrick Sips
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Anirban Chakraborty
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education & Research, NITTE (Deemed to be University), Deralakatte, Mangaluru, 575018, India.
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Babu N, Nanjappa DP, Nazareth S, Arjuna S, Chakraborty A. PARN Knockdown in Cell Lines Results in Differential and Cell-Specific Alterations in the Expression of Cancer-Associated mRNAs. Asian Pac J Cancer Prev 2022; 23:207-215. [PMID: 35092390 PMCID: PMC9258649 DOI: 10.31557/apjcp.2022.23.1.207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Indexed: 12/02/2022] Open
Abstract
Ribonucleases (RNases) is the collective term used for the group of enzymes that are involved in mRNA degradation. The shortening of the poly (A) tail through deadenylation is the preferred mechanism of degradation of most eukaryotic mRNAs and poly (A)-specific ribonuclease (PARN) is the most important player in deadenylation. Besides its primarily role in mRNA stability, PARN is also involved in several non-conventional functions. It is conceivable that a decreased RNase activity can alter the stability of cancer-associated mRNAs and this alteration may be differential in cells of different origin.
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Affiliation(s)
- Nishith Babu
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), NITTE (Deemed to be University), Deralakatte, Mangaluru, Karnataka, India
| | - Dechamma Pandyanda Nanjappa
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), NITTE (Deemed to be University), Deralakatte, Mangaluru, Karnataka, India
| | - Sandra Nazareth
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Srividya Arjuna
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), NITTE (Deemed to be University), Deralakatte, Mangaluru, Karnataka, India
| | - Anirban Chakraborty
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), NITTE (Deemed to be University), Deralakatte, Mangaluru, Karnataka, India
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Venkataram R, Arjuna S, Hosmane GB, Chakraborty A. Quantitative analysis of cell-free DNA by droplet digital PCR reveals the presence of EGFR mutations in non-malignant lung pathologies. Monaldi Arch Chest Dis 2021; 91. [PMID: 33960186 DOI: 10.4081/monaldi.2021.1748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 04/18/2021] [Indexed: 11/23/2022] Open
Abstract
Tyrosine kinase inhibitors (TKIs) targeting epidermal growth factor receptor (EGFR) are effectively used in treatment of non-small cell lung cancer (NSCLC). Mutation profile of tyrosine kinase domain of EGFR determines the eligibility of the patients for tyrosine kinase inhibitor (TKI) therapy. Liquid biopsy, which relies on circulating tumor-derived nucleic acids, has emerged as an effective tool in lung cancer management with proven diagnostic, prognostic and predictive applications. We screened 100 subjects, suspected to have lung malignancy, for four hotspot mutations including three activating (G719S, Ex19del E746-A750 and L858R) and one acquired (T790M, de novo) in EGFR gene by droplet digital PCR (ddPCR). While 97 subjects were subsequently confirmed to have lung malignancy based on histo/cytopathological studies, three cases turned out to be non-malignant lung pathologies that were completely cured by antibiotic therapy. Intriguingly, ddPCR revealed the presence of EGFR mutations in these non-malignant subjects. Two cases showed the presence of G719S and T790M mutations respectively and another had compound mutations (T790M and L858R). The detection of EGFR mutations in non-malignant pulmonary conditions opens up a new area of research.
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Affiliation(s)
- Rajesh Venkataram
- Department of Pulmonary Medicine, KS Hegde Medical Academy (Deemed to be University), Nitte, Mangalore .
| | - Srividya Arjuna
- Division of Molecular Genetics and Cancer, Nitte University Centre For Science Education and Research (NUCSER), Nitte (Deemed to be University), Mangalore .
| | - Giridhar Belur Hosmane
- Department of Pulmonary Medicine, KS Hegde Medical Academy (Deemed to be University), Nitte, Mangalore.
| | - Anirban Chakraborty
- Division of Molecular Genetics and Cancer, Nitte University Centre For Science Education and Research (NUCSER), Nitte (Deemed to be University), Mangalore .
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Babu N, Nanjappa DP, Arjuna S, Rajesh V, Shetty V, Chakraborty A. Expression of Poly(A)-Specific Ribonuclease in Solid Tumours and Haematopoietic Malignancies. J Clin Diagn Res 2021. [DOI: 10.7860/jcdr/2021/50670.15777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Arjuna S, Venkataram R, Dechamma PN, Chakraborty G, Babu N, D'Cruz A, Hosmane GB, Chakraborty A. Non-invasive detection of EGFR mutations by cell-free loop-mediated isothermal amplification (CF-LAMP). Sci Rep 2020; 10:17559. [PMID: 33067539 PMCID: PMC7568567 DOI: 10.1038/s41598-020-74689-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/05/2020] [Indexed: 11/17/2022] Open
Abstract
Targeting epidermal growth factor receptor (EGFR) through tyrosine kinase inhibitors (TKI) is a successful therapeutic strategy in non-small cell lung cancer. However, the response to TKI therapy depends on specific activating and acquired mutations in the tyrosine kinase domain of the EGFR gene. Therefore, confirming the EGFR status of patients is crucial, not only for determining the eligibility, but also for monitoring the emergence of mutations in patients under TKI therapy. In this study, our aim was to develop a cost effective, yet sensitive, technique that allows the detection of therapeutically-relevant EGFR hotspot mutations at isothermal conditions in a non-invasive manner. Previously, we developed an allele-specific loop-mediated isothermal amplification (AS-LAMP) assay for screening germline and somatic de novo T790M EGFR mutation in lung cancer patients. In this study, we used cell free DNA as a template in AS-LAMP assay (CF-LAMP) for non-invasive detection of two hotspot EGFR mutations (T790M, and L858R) and compared its efficiency with ultrasensitive droplet digital PCR (ddPCR) assay. The results of CF-LAMP assay were consistent with those obtained in ddPCR assay, indicating the robustness of the method. CF-LAMP may serve as a valuable and cost-effective alternative for liquid biopsy techniques used in molecular diagnosis of non-small cell lung cancer.
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Affiliation(s)
- Srividya Arjuna
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), Nitte (Deemed to be University), Kotekar-Beeri Road, Deralakatte, Mangaluru, 575018, India
| | - Rajesh Venkataram
- Department of Pulmonary Medicine, K S Hegde Medical Academy, Nitte (Deemed to be University), Mangaluru, 575018, India
| | - Pandyanda Nanjappa Dechamma
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), Nitte (Deemed to be University), Kotekar-Beeri Road, Deralakatte, Mangaluru, 575018, India
| | - Gunimala Chakraborty
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), Nitte (Deemed to be University), Kotekar-Beeri Road, Deralakatte, Mangaluru, 575018, India
| | - Nishith Babu
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), Nitte (Deemed to be University), Kotekar-Beeri Road, Deralakatte, Mangaluru, 575018, India
| | - Audrey D'Cruz
- Department of Health Dentistry, A B Shetty Memorial Institute of Dental Sciences, Nitte (Deemed to be University), Mangaluru, India
| | - Giridhar Belur Hosmane
- Department of Pulmonary Medicine, K S Hegde Medical Academy, Nitte (Deemed to be University), Mangaluru, 575018, India
| | - Anirban Chakraborty
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), Nitte (Deemed to be University), Kotekar-Beeri Road, Deralakatte, Mangaluru, 575018, India.
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Arjuna S, Chakraborty G, Venkataram R, Dechamma PN, Chakraborty A. Detection of epidermal growth factor receptor T790M mutation by allele-specific loop mediated isothermal amplification. J Carcinog 2020; 19:3. [PMID: 32684851 PMCID: PMC7363156 DOI: 10.4103/jcar.jcar_6_20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/10/2020] [Accepted: 04/17/2020] [Indexed: 01/11/2023] Open
Abstract
INTRODUCTION Targeted therapy using specific inhibitors against tyrosine kinases (TKs) is a paradigm in non-small-cell lung cancer management. However, the success of TK inhibitor (TKI) therapy depends on certain activating or acquired mutations, which render sensitivity or resistance to TKIs in the patients. The acquisition of epidermal growth factor receptor (EGFR) T790M point mutation is the most common mechanism of resistance to TKI in non-small cell lung cancer. A number of molecular strategies are now available for molecular testing of non-small cell lung cancers. However, almost all of them are cost-intensive and laborious and require high-end advanced equipment. Thus, assays that are rapid, simple, and cost-effective, yet sensitive, are most ideal in clinical settings for screening such therapeutically relevant mutations. MATERIALS AND METHODS Allele-specific loop-mediated isothermal amplification assay (AS-LAMP), which is a variant of the original LAMP assay, is a promising diagnostic technique for screening single-nucleotide polymorphisms. Using commercially available plasmid constructs as template DNA, AS-LAMP assay for EGFR T790M mutation was optimized with six different sets of reaction mixture containing varying concentrations of buffer and primers. The results of AS-LAMP assay were further validated by ultrasensitive droplet digital polymerase chain reaction. RESULTS Only one of the six sets of reaction mixture could accurately distinguish between wild type and mutated DNA, indicating that the primers and buffer are the two most critical components that determine the accuracy of AS-LAMP. The optimized AS-LAMP assay was further used to screen germ line and somatic T790M mutations in non-small cell lung cancer using blood and tissue samples collected from patients. CONCLUSION Development of an accurate and rapid diagnostic assay that can detect resistant mutations without the need for sequencing is highly useful for clinicians in deciding on the eligibility of patients for TKI therapy. Considering its several inherent advantages, AS-LAMP assay could become an effective molecular tool for screening baseline or acquired EGFR T790M mutations in non-small cell lung cancer patients.
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Affiliation(s)
- Srividya Arjuna
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research, Nitte (Deemed to be University), Mangaluru, Karnataka, India
| | - Gunimala Chakraborty
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research, Nitte (Deemed to be University), Mangaluru, Karnataka, India
| | - Rajesh Venkataram
- Department of Pulmonary Medicine, K S Hegde Medical Academy, Nitte (Deemed to be University), Mangaluru, Karnataka, India
| | - Pandyanda Nanjappa Dechamma
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research, Nitte (Deemed to be University), Mangaluru, Karnataka, India
| | - Anirban Chakraborty
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research, Nitte (Deemed to be University), Mangaluru, Karnataka, India
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