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Banda A, Impomeni O, Singh A, Baloch AR, Hu W, Jaijyan DK. Precision in Action: The Role of Clustered Regularly Interspaced Short Palindromic Repeats/Cas in Gene Therapies. Vaccines (Basel) 2024; 12:636. [PMID: 38932365 DOI: 10.3390/vaccines12060636] [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: 04/14/2024] [Revised: 05/21/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated enzyme-CAS holds great promise for treating many uncured human diseases and illnesses by precisely correcting harmful point mutations and disrupting disease-causing genes. The recent Food and Drug Association (FDA) approval of the first CRISPR-based gene therapy for sickle cell anemia marks the beginning of a new era in gene editing. However, delivering CRISPR specifically into diseased cells in vivo is a significant challenge and an area of intense research. The identification of new CRISPR/Cas variants, particularly ultra-compact CAS systems with robust gene editing activities, paves the way for the low-capacity delivery vectors to be used in gene therapies. CRISPR/Cas technology has evolved beyond editing DNA to cover a wide spectrum of functionalities, including RNA targeting, disease diagnosis, transcriptional/epigenetic regulation, chromatin imaging, high-throughput screening, and new disease modeling. CRISPR/Cas can be used to engineer B-cells to produce potent antibodies for more effective vaccines and enhance CAR T-cells for the more precise and efficient targeting of tumor cells. However, CRISPR/Cas technology has challenges, including off-target effects, toxicity, immune responses, and inadequate tissue-specific delivery. Overcoming these challenges necessitates the development of a more effective and specific CRISPR/Cas delivery system. This entails strategically utilizing specific gRNAs in conjunction with robust CRISPR/Cas variants to mitigate off-target effects. This review seeks to delve into the intricacies of the CRISPR/Cas mechanism, explore progress in gene therapies, evaluate gene delivery systems, highlight limitations, outline necessary precautions, and scrutinize the ethical considerations associated with its application.
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Affiliation(s)
- Amrutha Banda
- Department of Biology, The College of New Jersey, Ewing Township, NJ 08618, USA
| | - Olivia Impomeni
- Department of Biology, The College of New Jersey, Ewing Township, NJ 08618, USA
| | - Aparana Singh
- Department of Chemistry, National Institute of Technology Agartala, Agartala 799046, India
| | - Abdul Rasheed Baloch
- Department of Anatomy and Neurobiology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Wenhui Hu
- Department of Anatomy and Neurobiology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Dabbu Kumar Jaijyan
- Department of Anatomy and Neurobiology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23284, USA
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Eigenfeld M, Lupp KFM, Schwaminger SP. Role of Natural Binding Proteins in Therapy and Diagnostics. Life (Basel) 2024; 14:630. [PMID: 38792650 PMCID: PMC11122601 DOI: 10.3390/life14050630] [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: 03/31/2024] [Revised: 05/02/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
This review systematically investigates the critical role of natural binding proteins (NBPs), encompassing DNA-, RNA-, carbohydrate-, fatty acid-, and chitin-binding proteins, in the realms of oncology and diagnostics. In an era where cancer continues to pose significant challenges to healthcare systems worldwide, the innovative exploration of NBPs offers a promising frontier for advancing both the diagnostic accuracy and therapeutic efficacy of cancer management strategies. This manuscript provides an in-depth examination of the unique mechanisms by which NBPs interact with specific molecular targets, highlighting their potential to revolutionize cancer diagnostics and therapy. Furthermore, it discusses the burgeoning research on aptamers, demonstrating their utility as 'nucleic acid antibodies' for targeted therapy and precision diagnostics. Despite the promising applications of NBPs and aptamers in enhancing early cancer detection and developing personalized treatment protocols, this review identifies a critical knowledge gap: the need for comprehensive studies to understand the diverse functionalities and therapeutic potentials of NBPs across different cancer types and diagnostic scenarios. By bridging this gap, this manuscript underscores the importance of NBPs and aptamers in paving the way for next-generation diagnostics and targeted cancer treatments.
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Affiliation(s)
- Marco Eigenfeld
- Otto-Loewi Research Center, Division of Medicinal Chemistry, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
| | - Kilian F. M. Lupp
- Otto-Loewi Research Center, Division of Medicinal Chemistry, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
| | - Sebastian P. Schwaminger
- Otto-Loewi Research Center, Division of Medicinal Chemistry, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
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Kotsifaki A, Maroulaki S, Armakolas A. Exploring the Immunological Profile in Breast Cancer: Recent Advances in Diagnosis and Prognosis through Circulating Tumor Cells. Int J Mol Sci 2024; 25:4832. [PMID: 38732051 PMCID: PMC11084220 DOI: 10.3390/ijms25094832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024] Open
Abstract
This review offers a comprehensive exploration of the intricate immunological landscape of breast cancer (BC), focusing on recent advances in diagnosis and prognosis through the analysis of circulating tumor cells (CTCs). Positioned within the broader context of BC research, it underscores the pivotal role of the immune system in shaping the disease's progression. The primary objective of this investigation is to synthesize current knowledge on the immunological aspects of BC, with a particular emphasis on the diagnostic and prognostic potential offered by CTCs. This review adopts a thorough examination of the relevant literature, incorporating recent breakthroughs in the field. The methodology section succinctly outlines the approach, with a specific focus on CTC analysis and its implications for BC diagnosis and prognosis. Through this review, insights into the dynamic interplay between the immune system and BC are highlighted, with a specific emphasis on the role of CTCs in advancing diagnostic methodologies and refining prognostic assessments. Furthermore, this review presents objective and substantiated results, contributing to a deeper understanding of the immunological complexity in BC. In conclusion, this investigation underscores the significance of exploring the immunological profile of BC patients, providing valuable insights into novel advances in diagnosis and prognosis through the utilization of CTCs. The objective presentation of findings emphasizes the crucial role of the immune system in BC dynamics, thereby opening avenues for enhanced clinical management strategies.
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Affiliation(s)
| | | | - Athanasios Armakolas
- Physiology Laboratory, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (A.K.); (S.M.)
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Jayaprakash B, Suresh AR, Thiruvengadam R, Alharbi NS, Kadaikunnan S, Sankaran S, Thiruvengadam M, Senthil R, Venkidasamy B. Evaluation of oyster mushroom ( Pleurotus ostreatus)-derived anthraquinone on the induction of apoptosis and suppression of MMP-2 and MMP-9 expression in breast cancer cells. Int J Med Sci 2024; 21:1016-1026. [PMID: 38774755 PMCID: PMC11103395 DOI: 10.7150/ijms.93334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/26/2024] [Indexed: 05/24/2024] Open
Abstract
Introduction: Breast cancer results from tissue degradation caused by environmental and genetic factors that affect cells in the body. Matrix metalloproteinases, such as MMP-2 and MMP-9, are considered potential putative markers for tumor diagnosis in clinical validation due to their easy detection in body fluids. In addition, recent reports have suggested multiple roles for MMPs, rather than simply degeneration of the extracellular matrix, which comprises mobilizing growth factors and processing surface molecules. Methods: In this study, the chemotherapeutic effects of anthraquinone (AQ) extracted from edible mushrooms (Pleurotus ostreatus Jacq. ex Fr.) cells was examined in MCF-7 breast cancer cells. The cytotoxic potential and oxidative stress induced by purified anthraquinone were assessed in MCF-7 cells using MTT and ROS estimation assays. Gelatin Zymography, and DNA fragmentation assays were performed to examine MMP expression and apoptotic induction in the MCF-7 cells treated with AQ. The genes crucial for mutations were examined, and the mutated RNA knockout plausibility was analyzed using the CRISPR spcas9 genome editing software. Results: MCF-7 cells were attenuated in a concentration-dependent manner by the administration of AQ purified from P. ostreatus compared with the standard anticancer drug paclitaxel. AQ supplementation decreased oxidative stress and mitochondrial impairment in MCF-7 cells. Treatment with AQ and AQ with paclitaxel consistently decreased the expression of crucial marker genes such as MMP2 and MMP9. The mutated genes MMP2, MMP7, and MMP9 were assessed and observed to reveal four putative gene knockdown potentials for breast cancer treatment. Conclusions: The synergistic application of AQ and paclitaxel exerted a strong inhibitory effect on the MCF-7 breast cancer cells. Extensive studies are imperative to better understand the action of bioactive mixes on the edible oyster fungus P. ostreatus. The gene knockout potential detected by CRISPR SpCas9 will aid in elite research into anticancer treatments.
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Affiliation(s)
- Bindhu Jayaprakash
- Department of Biotechnology, Sri Shakthi Institute of Engineering & Technology, Coimbatore 641062, India
| | - Ashwin Raj Suresh
- Department of Biotechnology, Bannari Amman Institute of Technology, Sathyamangalam 638401, India
| | - Rekha Thiruvengadam
- Center for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai 600077, India
| | - Naiyf S. Alharbi
- Department of Botany and Microbiology, College of Science, King Saud University, P. O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Shine Kadaikunnan
- Department of Botany and Microbiology, College of Science, King Saud University, P. O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Sathianarayanan Sankaran
- Department of Pharmaceutical Chemistry, NGSM Institute of Pharmaceutical Sciences, Nitte (Deemed to be University), Deralakatte, Mangaluru 575018, India
| | - Muthu Thiruvengadam
- Department of Applied Bioscience, College of Life and Environmental Science, Konkuk University, Seoul 05029, Republic of Korea
| | - Rethinam Senthil
- Department of Pharmacology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai 600077, India
| | - Baskar Venkidasamy
- Department of Oral and Maxillofacial Surgery, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, India
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Liu C, Yuan ZY, Zhang XX, Chang JJ, Yang Y, Sun SJ, Du Y, Zhan HQ. Novel molecular classification and prognosis of papillary renal cell carcinoma based on a large-scale CRISPR-Cas9 screening and machine learning. Heliyon 2024; 10:e23184. [PMID: 38163209 PMCID: PMC10754875 DOI: 10.1016/j.heliyon.2023.e23184] [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: 07/11/2023] [Revised: 11/18/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024] Open
Abstract
Papillary renal cell carcinoma (PRCC) is a highly heterogeneous cancer, and PRCC patients with advanced/metastatic subgroup showed obviously shorter survival compared to other kinds of renal cell carcinomas. However, the molecular mechanism and prognostic predictors of PRCC remain unclear and are worth deep studying. The aim of this study is to identify novel molecular classification and construct a reliable prognostic model for PRCC. The expression data were retrieved from TCGA, GEO, GTEx and TARGET databases. CRISPR data was obtained from Depmap database. The key genes were selected by the intersection of CRISPR-Cas9 screening genes, differentially expressed genes, and genes with prognostic capacity in PRCC. The molecular classification was identified based on the key genes. Drug sensitivity, tumor microenvironment, somatic mutation, and survival were compared among the novel classification. A prognostic model utilizing multiple machine learning algorithms based on the key genes was developed and tested by independent external validation set. Our study identified three clusters (C1, C2 and C3) in PRCC based on 41 key genes. C2 had obviously higher expression of the key genes and lower survival than C1 and C3. Significant differences in drug sensitivity, tumor microenvironment, and mutation landscape have been observed among the three clusters. By utilizing 21 combinations of 9 machine learning algorithms, 9 out of 41 genes were chosen to construct a robust prognostic signature, which exhibited good prognostic ability. SERPINH1 was identified as a critical gene for its strong prognostic ability in PRCC by univariate and multiple Cox regression analyses. Quantitative real-time PCR and Western blot demonstrated that SERPINH1 mRNA and protein were highly expressed in PRCC cells compared with normal human renal cells. This study exhibited a new molecular classification and prognostic signature for PRCC, which may provide a potential biomarker and therapy target for PRCC patients.
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Affiliation(s)
- Chang Liu
- Department of Pathology, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, PR China
- Department of Pathology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, PR China
| | - Zhan-Yuan Yuan
- Department of Plastic Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, PR China
| | - Xiao-Xun Zhang
- Department of Pathology, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, PR China
| | - Jia-Jun Chang
- Department of Pathology, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, PR China
| | - Yang Yang
- First School of Clinical Medicine, Anhui Medical University, Hefei, 230032, PR China
| | - Sheng-Jia Sun
- School of Clinical Medicine, Anhui Medical University, Hefei, 230031, PR China
| | - Yinan Du
- Department of Pathogenic microbiology, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, PR China
| | - He-Qin Zhan
- Department of Pathology, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, PR China
- Department of Pathology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, PR China
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Kafita D, Nkhoma P, Dzobo K, Sinkala M. Shedding light on the dark genome: Insights into the genetic, CRISPR-based, and pharmacological dependencies of human cancers and disease aggressiveness. PLoS One 2023; 18:e0296029. [PMID: 38117798 PMCID: PMC10732413 DOI: 10.1371/journal.pone.0296029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/05/2023] [Indexed: 12/22/2023] Open
Abstract
Investigating the human genome is vital for identifying risk factors and devising effective therapies to combat genetic disorders and cancer. Despite the extensive knowledge of the "light genome", the poorly understood "dark genome" remains understudied. In this study, we integrated data from 20,412 protein-coding genes in Pharos and 8,395 patient-derived tumours from The Cancer Genome Atlas (TCGA) to examine the genetic and pharmacological dependencies in human cancers and their treatment implications. We discovered that dark genes exhibited high mutation rates in certain cancers, similar to light genes. By combining the drug response profiles of cancer cells with cell fitness post-CRISPR-mediated gene knockout, we identified the crucial vulnerabilities associated with both dark and light genes. Our analysis also revealed that tumours harbouring dark gene mutations displayed worse overall and disease-free survival rates than those without such mutations. Furthermore, dark gene expression levels significantly influenced patient survival outcomes. Our findings demonstrated a similar distribution of genetic and pharmacological dependencies across the light and dark genomes, suggesting that targeting the dark genome holds promise for cancer treatment. This study underscores the need for ongoing research on the dark genome to better comprehend the underlying mechanisms of cancer and develop more effective therapies.
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Affiliation(s)
- Doris Kafita
- Department of Biomedical Sciences, University of Zambia, School of Health Sciences, Lusaka, Zambia
| | - Panji Nkhoma
- Department of Biomedical Sciences, University of Zambia, School of Health Sciences, Lusaka, Zambia
| | - Kevin Dzobo
- Department of Medicine, Division of Dermatology, Hair and Skin Research Laboratory, Wound and Keloid Scarring Research Unit, The South African Medical Research Council, University of Cape Town, Cape Town, South Africa
| | - Musalula Sinkala
- Department of Biomedical Sciences, University of Zambia, School of Health Sciences, Lusaka, Zambia
- Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine and Department of Integrative Biomedical Sciences, University of Cape Town, Computational Biology Division, Cape Town, South Africa
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Gupta S, Nagtode N, Chandra V, Gomase K. From Diagnosis to Treatment: Exploring the Latest Management Trends in Cervical Intraepithelial Neoplasia. Cureus 2023; 15:e50291. [PMID: 38205499 PMCID: PMC10776490 DOI: 10.7759/cureus.50291] [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: 09/11/2023] [Accepted: 12/10/2023] [Indexed: 01/12/2024] Open
Abstract
Cervical intraepithelial neoplasia (CIN) stands as a precancerous condition with the potential to progress to invasive cervical cancer. This comprehensive review explores the intricacies of CIN management, beginning with its definition, classification, and etiology. It emphasizes the significance of early detection and outlines the latest trends in diagnosis, including Pap smears, human papillomavirus (HPV) testing, and colposcopy. Grading and staging, pivotal in treatment selection, are elucidated. Current management approaches, encompassing watchful waiting, surgical interventions, emerging minimally invasive techniques, and immunotherapy, are detailed. The factors influencing treatment decisions, informed consent, and patient education are discussed. Potential complications following treatment, the importance of long-term follow-up, and the role of HPV vaccination in prevention are underscored. Finally, the review looks to the future, discussing advances in detection, novel treatments, and the promise of precision medicine. In conclusion, early detection and management remain the cornerstone of CIN care, offering hope for a future where cervical cancer is a preventable and treatable condition.
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Affiliation(s)
- Saloni Gupta
- Community Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Nikhilesh Nagtode
- Community Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Vaibhav Chandra
- Community Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Kavita Gomase
- Obstetrics and Gynecology, Smt. Radhikabai Meghe Memorial College of Nursing, Datta Meghe Institute of Higher Education and Research, Wardha, IND
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