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Balaji S, Rao A, Saraswathi KK, Sethu Nagarajan R, Santhi R, Kim U, Muthukkaruppan V, Vanniarajan A. Focused cancer pathway analysis revealed unique therapeutic targets in retinoblastoma. Med Oncol 2024; 41:168. [PMID: 38834895 DOI: 10.1007/s12032-024-02391-9] [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: 03/12/2024] [Accepted: 04/24/2024] [Indexed: 06/06/2024]
Abstract
Retinoblastoma (RB) is a pediatric cancer of the eye that occurs in 1/15000 live births worldwide. Albeit RB is initiated by the inactivation of RB1 gene, the disease progression relies largely on transcriptional alterations. Therefore, evaluating gene expression is vital to unveil the therapeutic targets in RB management. In this study, we employed an RT2 Profiler™ PCR array for a focused analysis of 84 cancer-specific genes in RB. An interaction network was built with gene expression data to identify the dysregulated pathways in RB. The key transcript alterations identified in 13 tumors by RT2 Profiler™ PCR array was further validated in 15 tumors by independent RT-qPCR. Out of 84 cancer-specific genes, 68 were dysregulated in RB tumors. Among the 68 genes, 23 were chosen for further analysis based on statistical significance and abundance across multiple tumors. Pathway analysis of altered genes showed the frequent perturbations of cell cycle, angiogenesis and apoptotic pathways in RB. Notably, upregulation of MCM2, MKI67, PGF, WEE1, CDC20 and downregulation of COX5A were found in all the tumors. Western blot confirmed the dysregulation of identified targets at protein levels as well. These alterations were more prominent in invasive RB, correlating with the disease pathogenesis. Our molecular analysis thus identified the potential therapeutic targets for improving retinoblastoma treatment. We also suggest that PCR array can be used as a tool for rapid and cost-effective gene expression analysis.
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Affiliation(s)
- Sekaran Balaji
- Department of Molecular Genetics, Aravind Medical Research Foundation, 1, Anna Nagar, Madurai, Tamil Nadu, 625 020, India
| | - Anindita Rao
- Department of Molecular Genetics, Aravind Medical Research Foundation, 1, Anna Nagar, Madurai, Tamil Nadu, 625 020, India
| | - Karuvel Kannan Saraswathi
- Department of Molecular Genetics, Aravind Medical Research Foundation, 1, Anna Nagar, Madurai, Tamil Nadu, 625 020, India
- Department of Molecular Biology, Aravind Medical Research Foundation - Affiliated to Alagappa University, Karaikudi, Tamil Nadu, 630003, India
| | - Rathinavel Sethu Nagarajan
- Department of Molecular Genetics, Aravind Medical Research Foundation, 1, Anna Nagar, Madurai, Tamil Nadu, 625 020, India
- Department of Molecular Biology, Aravind Medical Research Foundation - Affiliated to Alagappa University, Karaikudi, Tamil Nadu, 630003, India
| | - Radhakrishnan Santhi
- Department of Pathology, Aravind Eye Hospital, Madurai, Tamil Nadu, 625 020, India
| | - Usha Kim
- Department of Orbit, Oculoplasty and Ocular Oncology, Aravind Eye Hospital, Madurai, Tamil Nadu, 625 020, India
| | - Veerappan Muthukkaruppan
- Department of Immunology and Stem Cell Biology, Aravind Medical Research Foundation, Madurai, Tamil Nadu, 625 020, India
| | - Ayyasamy Vanniarajan
- Department of Molecular Genetics, Aravind Medical Research Foundation, 1, Anna Nagar, Madurai, Tamil Nadu, 625 020, India.
- Department of Molecular Biology, Aravind Medical Research Foundation - Affiliated to Alagappa University, Karaikudi, Tamil Nadu, 630003, India.
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Dakal TC, Dhabhai B, Pant A, Moar K, Chaudhary K, Yadav V, Ranga V, Sharma NK, Kumar A, Maurya PK, Maciaczyk J, Schmidt‐Wolf IGH, Sharma A. Oncogenes and tumor suppressor genes: functions and roles in cancers. MedComm (Beijing) 2024; 5:e582. [PMID: 38827026 PMCID: PMC11141506 DOI: 10.1002/mco2.582] [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: 09/18/2023] [Revised: 04/21/2024] [Accepted: 04/26/2024] [Indexed: 06/04/2024] Open
Abstract
Cancer, being the most formidable ailment, has had a profound impact on the human health. The disease is primarily associated with genetic mutations that impact oncogenes and tumor suppressor genes (TSGs). Recently, growing evidence have shown that X-linked TSGs have specific role in cancer progression and metastasis as well. Interestingly, our genome harbors around substantial portion of genes that function as tumor suppressors, and the X chromosome alone harbors a considerable number of TSGs. The scenario becomes even more compelling as X-linked TSGs are adaptive to key epigenetic processes such as X chromosome inactivation. Therefore, delineating the new paradigm related to X-linked TSGs, for instance, their crosstalk with autosome and involvement in cancer initiation, progression, and metastasis becomes utmost importance. Considering this, herein, we present a comprehensive discussion of X-linked TSG dysregulation in various cancers as a consequence of genetic variations and epigenetic alterations. In addition, the dynamic role of X-linked TSGs in sex chromosome-autosome crosstalk in cancer genome remodeling is being explored thoroughly. Besides, the functional roles of ncRNAs, role of X-linked TSG in immunomodulation and in gender-based cancer disparities has also been highlighted. Overall, the focal idea of the present article is to recapitulate the findings on X-linked TSG regulation in the cancer landscape and to redefine their role toward improving cancer treatment strategies.
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Affiliation(s)
- Tikam Chand Dakal
- Department of BiotechnologyGenome and Computational Biology LabMohanlal Sukhadia UniversityUdaipurRajasthanIndia
| | - Bhanupriya Dhabhai
- Department of BiotechnologyGenome and Computational Biology LabMohanlal Sukhadia UniversityUdaipurRajasthanIndia
| | - Anuja Pant
- Department of BiochemistryCentral University of HaryanaMahendergarhHaryanaIndia
| | - Kareena Moar
- Department of BiochemistryCentral University of HaryanaMahendergarhHaryanaIndia
| | - Kanika Chaudhary
- School of Life Sciences. Jawaharlal Nehru UniversityNew DelhiIndia
| | - Vikas Yadav
- School of Life Sciences. Jawaharlal Nehru UniversityNew DelhiIndia
| | - Vipin Ranga
- Dearptment of Agricultural BiotechnologyDBT‐NECAB, Assam Agricultural UniversityJorhatAssamIndia
| | | | - Abhishek Kumar
- Manipal Academy of Higher EducationManipalKarnatakaIndia
- Institute of Bioinformatics, International Technology ParkBangaloreIndia
| | - Pawan Kumar Maurya
- Department of BiochemistryCentral University of HaryanaMahendergarhHaryanaIndia
| | - Jarek Maciaczyk
- Department of Stereotactic and Functional NeurosurgeryUniversity Hospital of BonnBonnGermany
| | - Ingo G. H. Schmidt‐Wolf
- Department of Integrated OncologyCenter for Integrated Oncology (CIO)University Hospital BonnBonnGermany
| | - Amit Sharma
- Department of Stereotactic and Functional NeurosurgeryUniversity Hospital of BonnBonnGermany
- Department of Integrated OncologyCenter for Integrated Oncology (CIO)University Hospital BonnBonnGermany
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Zeng Q, Wang S, Chen L, Wang J. Transcriptome analysis reveals molecularly distinct subtypes in retinoblastoma. Sci Rep 2023; 13:16475. [PMID: 37777551 PMCID: PMC10542806 DOI: 10.1038/s41598-023-42253-4] [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: 03/19/2023] [Accepted: 09/07/2023] [Indexed: 10/02/2023] Open
Abstract
Retinoblastoma is the most frequent intraocular malignancy in children. Little is known on the molecular basis underlying the biological and clinical behavior of this cancer. Here, using gene expression profiles, we demonstrate the existence of two major retinoblastoma subtypes that can be divided into six subgroups. Subtype 1 has higher expression of cone related genes and higher percentage of RB1 germline mutation. By contrast, subtype 2 tumors harbor more genes with ganglion/neuronal features. The dedifferentiation in subtype 2 is associated with stemness features including low immune infiltration. Gene Otology analysis demonstrates that immune response regulations and visual related pathways are the key molecular difference between subtypes. Subtype 1b has the highest risk of invasiveness across all subtypes. The recognition of these molecular subtypes shed a light on the important biological and clinical perspectives for retinoblastomas.
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Affiliation(s)
- Qi Zeng
- Hunan Provincial People's Hospital (The First-Affiliated Hospital of Hunan Normal University), Changsha, 410005, China
| | - Sha Wang
- Eye Center of Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, China.
- Hunan Key Laboratory of Ophthalmology, 87 Xiangya Road, Changsha, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.
| | - Lu Chen
- Eye Center of Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, China
- Hunan Key Laboratory of Ophthalmology, 87 Xiangya Road, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Jinwei Wang
- Eye Center of Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, China
- Hunan Key Laboratory of Ophthalmology, 87 Xiangya Road, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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Mandal M, Banerjee I, Mandal M. Nanoparticle-mediated gene therapy as a novel strategy for the treatment of retinoblastoma. Colloids Surf B Biointerfaces 2022; 220:112899. [DOI: 10.1016/j.colsurfb.2022.112899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/26/2022] [Accepted: 10/01/2022] [Indexed: 11/05/2022]
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Lee C, Kim J. Genome maintenance in retinoblastoma: Implications for therapeutic vulnerabilities (Review). Oncol Lett 2022; 23:192. [PMID: 35527780 PMCID: PMC9073582 DOI: 10.3892/ol.2022.13312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/08/2022] [Indexed: 11/19/2022] Open
Abstract
Retinoblastoma (RB) is a pediatric ocular malignancy that is initiated mostly by biallelic inactivation of the RB transcriptional corepressor 1 (RB1) tumor suppressor gene in the developing retina. Unlike the prevailing prediction based on multiple studies involving RB1 gene disruption in experimental models, human RB tumors have been demonstrated to possess a relatively stable genome, characterized by a low mutation rate and a few recurrent chromosomal alterations related to somatic copy number changes. This suggests that RB may harbor heightened genome maintenance mechanisms to counteract or compensate for the risk of massive genome instability, which can potentially be driven by the early RB1 loss as a tumor-initiating event. Although the genome maintenance mechanisms might have been evolved to promote RB cell survival by preventing lethal genomic defects, emerging evidence suggests that the dependency of RB cells on these mechanisms also exposes their unique vulnerability to chemotherapy, particularly when the genome maintenance machineries are tumor cell-specific. This review summarizes the genome maintenance mechanisms identified in RB, including findings on the roles of chromatin regulators in DNA damage response/repair and protein factors involved in maintaining chromosome stability and promoting survival in RB. In addition, advantages and challenges for exploiting these therapeutic vulnerabilities in RB are discussed.
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Affiliation(s)
- Chunsik Lee
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat‑sen University, Guangzhou, Guangdong 510060, P.R. China
| | - Jong Kim
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat‑sen University, Guangzhou, Guangdong 510060, P.R. China
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