1
|
Bhamidimarri PM, Salameh L, Mahdami A, Abdullah HW, Mahboub B, Hamoudi R. LINCATRA: Two-cycle method to amplify RNA for transcriptome analysis from formalin-fixed paraffin-embedded tissue. Heliyon 2024; 10:e32896. [PMID: 38988576 PMCID: PMC11234047 DOI: 10.1016/j.heliyon.2024.e32896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/21/2024] [Accepted: 06/11/2024] [Indexed: 07/12/2024] Open
Abstract
Whole transcriptome analysis (WTA) using RNA extracted from Formalin Fixed Paraffin Embedded (FFPE) tissue is an invaluable tool to understand the molecular pathology of disease. RNA extracted from FFPE tissue is either degraded and/or in very low quantities hampering gene expression analysis. Earlier studies described protocols applied for cellular RNA using poly-A primer-based linear amplification. The current study describes a method, LINCATRA (LINear amplifiCAtion of RNA for whole TRAnscriptome analysis). It employs random nonamer primer based method which can amplify short, fragmented RNA with high fidelity from as low as 5 ng to obtain enough material for WTA. The two-cycle method significantly amplified RNA at ∼1000 folds (p < 0.0001) improving the mean read lengths (p < 0.05) in WTA. Overall, increased mean read length positively correlated with on-target reads (Pearson's r = 0.71, p < 0.0001) in both amplified and unamplified RNA-seq analysis. Gene expression analysis compared between unamplified and amplified group displayed substantial overlap of the differentially expressed genes (DEGs) (log2 fold change cut-off < -2 and >2, p < 0.05) identified between lung cancer and asthma cohorts validating the method developed. This method is applicable in clinical molecular pathology field for both diagnostics and elucidation of disease mechanisms.
Collapse
Affiliation(s)
- Poorna Manasa Bhamidimarri
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Laila Salameh
- Rashid Hospital, Dubai Health, Dubai, 4545, United Arab Emirates
| | - Amena Mahdami
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Hanan Wael Abdullah
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Bassam Mahboub
- Rashid Hospital, Dubai Health, Dubai, 4545, United Arab Emirates
- Clinical Sciences Department, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Rifat Hamoudi
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- Clinical Sciences Department, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Division of Surgery and Interventional Sciences, University College London, London, United Kingdom
- BIMAI-Lab, Biomedically Informed Artificial Inelligence Laboratory, University of Sharjah, Sharjah, 27272, United Arab Emirates
- Centre of Excelence for Precision Medicine, Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
| |
Collapse
|
2
|
Zacarías-Fluck MF, Soucek L, Whitfield JR. MYC: there is more to it than cancer. Front Cell Dev Biol 2024; 12:1342872. [PMID: 38510176 PMCID: PMC10952043 DOI: 10.3389/fcell.2024.1342872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/20/2024] [Indexed: 03/22/2024] Open
Abstract
MYC is a pleiotropic transcription factor involved in multiple cellular processes. While its mechanism of action and targets are not completely elucidated, it has a fundamental role in cellular proliferation, differentiation, metabolism, ribogenesis, and bone and vascular development. Over 4 decades of research and some 10,000 publications linking it to tumorigenesis (by searching PubMed for "MYC oncogene") have led to MYC becoming a most-wanted target for the treatment of cancer, where many of MYC's physiological functions become co-opted for tumour initiation and maintenance. In this context, an abundance of reviews describes strategies for potentially targeting MYC in the oncology field. However, its multiple roles in different aspects of cellular biology suggest that it may also play a role in many additional diseases, and other publications are indeed linking MYC to pathologies beyond cancer. Here, we review these physiological functions and the current literature linking MYC to non-oncological diseases. The intense efforts towards developing MYC inhibitors as a cancer therapy will potentially have huge implications for the treatment of other diseases. In addition, with a complementary approach, we discuss some diseases and conditions where MYC appears to play a protective role and hence its increased expression or activation could be therapeutic.
Collapse
Affiliation(s)
- Mariano F. Zacarías-Fluck
- Models of Cancer Therapies Laboratory, Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Laura Soucek
- Models of Cancer Therapies Laboratory, Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Peptomyc S.L., Barcelona, Spain
| | - Jonathan R. Whitfield
- Models of Cancer Therapies Laboratory, Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| |
Collapse
|
3
|
Dakilah I, Harb A, Abu-Gharbieh E, El-Huneidi W, Taneera J, Hamoudi R, Semreen MH, Bustanji Y. Potential of CDC25 phosphatases in cancer research and treatment: key to precision medicine. Front Pharmacol 2024; 15:1324001. [PMID: 38313315 PMCID: PMC10834672 DOI: 10.3389/fphar.2024.1324001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/04/2024] [Indexed: 02/06/2024] Open
Abstract
The global burden of cancer continues to rise, underscoring the urgency of developing more effective and precisely targeted therapies. This comprehensive review explores the confluence of precision medicine and CDC25 phosphatases in the context of cancer research. Precision medicine, alternatively referred to as customized medicine, aims to customize medical interventions by taking into account the genetic, genomic, and epigenetic characteristics of individual patients. The identification of particular genetic and molecular drivers driving cancer helps both diagnostic accuracy and treatment selection. Precision medicine utilizes sophisticated technology such as genome sequencing and bioinformatics to elucidate genetic differences that underlie the proliferation of cancer cells, hence facilitating the development of customized therapeutic interventions. CDC25 phosphatases, which play a crucial role in governing the progression of the cell cycle, have garnered significant attention as potential targets for cancer treatment. The dysregulation of CDC25 is a characteristic feature observed in various types of malignancies, hence classifying them as proto-oncogenes. The proteins in question, which operate as phosphatases, play a role in the activation of Cyclin-dependent kinases (CDKs), so promoting the advancement of the cell cycle. CDC25 inhibitors demonstrate potential as therapeutic drugs for cancer treatment by specifically blocking the activity of CDKs and modulating the cell cycle in malignant cells. In brief, precision medicine presents a potentially fruitful option for augmenting cancer research, diagnosis, and treatment, with an emphasis on individualized care predicated upon patients' genetic and molecular profiles. The review highlights the significance of CDC25 phosphatases in the advancement of cancer and identifies them as promising candidates for therapeutic intervention. This statement underscores the significance of doing thorough molecular profiling in order to uncover the complex molecular characteristics of cancer cells.
Collapse
Affiliation(s)
- Ibraheem Dakilah
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Amani Harb
- Department of Basic Sciences, Faculty of Arts and Sciences, Al-Ahliyya Amman University, Amman, Jordan
| | - Eman Abu-Gharbieh
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Waseem El-Huneidi
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Jalal Taneera
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Rifat Hamoudi
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Division of Surgery and Interventional Science, University College London, London, United Kingdom
| | - Mohammed H Semreen
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
| | - Yasser Bustanji
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- School of Pharmacy, The University of Jordan, Amman, Jordan
| |
Collapse
|