1
|
Fasano C, Lepore Signorile M, De Marco K, Forte G, Disciglio V, Sanese P, Grossi V, Simone C. In Silico Deciphering of the Potential Impact of Variants of Uncertain Significance in Hereditary Colorectal Cancer Syndromes. Cells 2024; 13:1314. [PMID: 39195204 DOI: 10.3390/cells13161314] [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: 06/05/2024] [Revised: 07/23/2024] [Accepted: 08/03/2024] [Indexed: 08/29/2024] Open
Abstract
Colorectal cancer (CRC) ranks third in terms of cancer incidence worldwide and is responsible for 8% of all deaths globally. Approximately 10% of CRC cases are caused by inherited pathogenic mutations in driver genes involved in pathways that are crucial for CRC tumorigenesis and progression. These hereditary mutations significantly increase the risk of initial benign polyps or adenomas developing into cancer. In recent years, the rapid and accurate sequencing of CRC-specific multigene panels by next-generation sequencing (NGS) technologies has enabled the identification of several recurrent pathogenic variants with established functional consequences. In parallel, rare genetic variants that are not characterized and are, therefore, called variants of uncertain significance (VUSs) have also been detected. The classification of VUSs is a challenging task because each amino acid has specific biochemical properties and uniquely contributes to the structural stability and functional activity of proteins. In this scenario, the ability to computationally predict the effect of a VUS is crucial. In particular, in silico prediction methods can provide useful insights to assess the potential impact of a VUS and support additional clinical evaluation. This approach can further benefit from recent advances in artificial intelligence-based technologies. In this review, we describe the main in silico prediction tools that can be used to evaluate the structural and functional impact of VUSs and provide examples of their application in the analysis of gene variants involved in hereditary CRC syndromes.
Collapse
Affiliation(s)
- Candida Fasano
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, 70013 Castellana Grotte, Italy
| | - Martina Lepore Signorile
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, 70013 Castellana Grotte, Italy
| | - Katia De Marco
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, 70013 Castellana Grotte, Italy
| | - Giovanna Forte
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, 70013 Castellana Grotte, Italy
| | - Vittoria Disciglio
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, 70013 Castellana Grotte, Italy
| | - Paola Sanese
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, 70013 Castellana Grotte, Italy
| | - Valentina Grossi
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, 70013 Castellana Grotte, Italy
| | - Cristiano Simone
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, 70013 Castellana Grotte, Italy
- Medical Genetics, Department of Precision and Regenerative Medicine and Jonic Area (DiMePRe-J), University of Bari Aldo Moro, 70124 Bari, Italy
| |
Collapse
|
2
|
Chuang HH, Huang CG, Chou SH, Li HY, Lee CC, Lee LA. Comparative analysis of gut microbiota in children with obstructive sleep apnea: assessing the efficacy of 16S rRNA gene sequencing in metabolic function prediction based on weight status. Front Endocrinol (Lausanne) 2024; 15:1344152. [PMID: 38948515 PMCID: PMC11211266 DOI: 10.3389/fendo.2024.1344152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 05/13/2024] [Indexed: 07/02/2024] Open
Abstract
Background Analyzing bacterial microbiomes consistently using next-generation sequencing (NGS) is challenging due to the diversity of synthetic platforms for 16S rRNA genes and their analytical pipelines. This study compares the efficacy of full-length (V1-V9 hypervariable regions) and partial-length (V3-V4 hypervariable regions) sequencing of synthetic 16S rRNA genes from human gut microbiomes, with a focus on childhood obesity. Methods In this observational and comparative study, we explored the differences between these two sequencing methods in taxonomic categorization and weight status prediction among twelve children with obstructive sleep apnea. Results The full-length NGS method by Pacbio® identified 118 genera and 248 species in the V1-V9 regions, all with a 0% unclassified rate. In contrast, the partial-length NGS method by Illumina® detected 142 genera (with a 39% unclassified rate) and 6 species (with a 99% unclassified rate) in the V3-V4 regions. These approaches showed marked differences in gut microbiome composition and functional predictions. The full-length method distinguished between obese and non-obese children using the Firmicutes/Bacteroidetes ratio, a known obesity marker (p = 0.046), whereas the partial-length method was less conclusive (p = 0.075). Additionally, out of 73 metabolic pathways identified through full-length sequencing, 35 (48%) were associated with level 1 metabolism, compared to 28 of 61 pathways (46%) identified through the partial-length method. The full-length NGS also highlighted complex associations between body mass index z-score, three bacterial species (Bacteroides ovatus, Bifidobacterium pseudocatenulatum, and Streptococcus parasanguinis ATCC 15912), and 17 metabolic pathways. Both sequencing techniques revealed relationships between gut microbiota composition and OSA-related parameters, with full-length sequencing offering more comprehensive insights into associated metabolic pathways than the V3-V4 technique. Conclusion These findings highlight disparities in NGS-based assessments, emphasizing the value of full-length NGS with amplicon sequence variant analysis for clinical gut microbiome research. They underscore the importance of considering methodological differences in future meta-analyses.
Collapse
Affiliation(s)
- Hai-Hua Chuang
- Department of Family Medicine, Chang Gung Memorial Hospital, Taipei Branch and Linkou Main Branch, Taoyuan, Taiwan
- School of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Sleep Center, Metabolism and Obesity Institute, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- School of Medicine, College of Life Science and Medicine, National Tsing Hua University, Hsinchu, Taiwan
- Department of Industrial Engineering and Management, National Taipei University of Technology, Taipei, Taiwan
| | - Chung-Guei Huang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
| | - Shih-Hsuan Chou
- Graduate Institute of Biomedical and Pharmaceutical Science, Fu Jen Catholic University, New Taipei City, Taiwan
- Biotools Co., Ltd., New Taipei City, Taiwan
| | - Hsueh-Yu Li
- School of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Sleep Center, Metabolism and Obesity Institute, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Otorhinolaryngology - Head and Neck Surgery, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chin-Chia Lee
- Taipei Wego Private Bilingual Senior High School, Taipei, Taiwan
| | - Li-Ang Lee
- School of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Sleep Center, Metabolism and Obesity Institute, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- School of Medicine, College of Life Science and Medicine, National Tsing Hua University, Hsinchu, Taiwan
- Department of Otorhinolaryngology - Head and Neck Surgery, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| |
Collapse
|
3
|
Kiran N, Yashaswini C, Maheshwari R, Bhattacharya S, Prajapati BG. Advances in Precision Medicine Approaches for Colorectal Cancer: From Molecular Profiling to Targeted Therapies. ACS Pharmacol Transl Sci 2024; 7:967-990. [PMID: 38633600 PMCID: PMC11019743 DOI: 10.1021/acsptsci.4c00008] [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: 01/10/2024] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 04/19/2024]
Abstract
Precision medicine is transforming colorectal cancer treatment through the integration of advanced technologies and biomarkers, enhancing personalized and effective disease management. Identification of key driver mutations and molecular profiling have deepened our comprehension of the genetic alterations in colorectal cancer, facilitating targeted therapy and immunotherapy selection. Biomarkers such as microsatellite instability (MSI) and DNA mismatch repair deficiency (dMMR) guide treatment decisions, opening avenues for immunotherapy. Emerging technologies such as liquid biopsies, artificial intelligence, and machine learning promise to revolutionize early detection, monitoring, and treatment selection in precision medicine. Despite these advancements, ethical and regulatory challenges, including equitable access and data privacy, emphasize the importance of responsible implementation. The dynamic nature of colorectal cancer, with its tumor heterogeneity and clonal evolution, underscores the necessity for adaptive and personalized treatment strategies. The future of precision medicine in colorectal cancer lies in its potential to enhance patient care, clinical outcomes, and our understanding of this intricate disease, marked by ongoing evolution in the field. The current reviews focus on providing in-depth knowledge on the various and diverse approaches utilized for precision medicine against colorectal cancer, at both molecular and biochemical levels.
Collapse
Affiliation(s)
- Neelakanta
Sarvashiva Kiran
- Department
of Biotechnology, School of Applied Sciences, REVA University, Bengaluru, Karnataka 560064, India
| | - Chandrashekar Yashaswini
- Department
of Biotechnology, School of Applied Sciences, REVA University, Bengaluru, Karnataka 560064, India
| | - Rahul Maheshwari
- School
of Pharmacy and Technology Management, SVKM’s
Narsee Monjee Institute of Management Studies (NMIMS) Deemed-to-University, Green Industrial Park, TSIIC,, Jadcherla, Hyderabad 509301, India
| | - Sankha Bhattacharya
- School
of Pharmacy and Technology Management, SVKM’S
NMIMS Deemed-to-be University, Shirpur, Maharashtra 425405, India
| | - Bhupendra G. Prajapati
- Shree.
S. K. Patel College of Pharmaceutical Education and Research, Ganpat University, Kherva, Gujarat 384012, India
| |
Collapse
|
4
|
Kasprzak A. Prognostic Biomarkers of Cell Proliferation in Colorectal Cancer (CRC): From Immunohistochemistry to Molecular Biology Techniques. Cancers (Basel) 2023; 15:4570. [PMID: 37760539 PMCID: PMC10526446 DOI: 10.3390/cancers15184570] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/04/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common and severe malignancies worldwide. Recent advances in diagnostic methods allow for more accurate identification and detection of several molecular biomarkers associated with this cancer. Nonetheless, non-invasive and effective prognostic and predictive testing in CRC patients remains challenging. Classical prognostic genetic markers comprise mutations in several genes (e.g., APC, KRAS/BRAF, TGF-β, and TP53). Furthermore, CIN and MSI serve as chromosomal markers, while epigenetic markers include CIMP and many other candidates such as SERP, p14, p16, LINE-1, and RASSF1A. The number of proliferation-related long non-coding RNAs (e.g., SNHG1, SNHG6, MALAT-1, CRNDE) and microRNAs (e.g., miR-20a, miR-21, miR-143, miR-145, miR-181a/b) that could serve as potential CRC markers has also steadily increased in recent years. Among the immunohistochemical (IHC) proliferative markers, the prognostic value regarding the patients' overall survival (OS) or disease-free survival (DFS) has been confirmed for thymidylate synthase (TS), cyclin B1, cyclin D1, proliferating cell nuclear antigen (PCNA), and Ki-67. In most cases, the overexpression of these markers in tissues was related to worse OS and DFS. However, slowly proliferating cells should also be considered in CRC therapy (especially radiotherapy) as they could represent a reservoir from which cells are recruited to replenish the rapidly proliferating population in response to cell-damaging factors. Considering the above, the aim of this article is to review the most common proliferative markers assessed using various methods including IHC and selected molecular biology techniques (e.g., qRT-PCR, in situ hybridization, RNA/DNA sequencing, next-generation sequencing) as prognostic and predictive markers in CRC.
Collapse
Affiliation(s)
- Aldona Kasprzak
- Department of Histology and Embryology, University of Medical Sciences, Swiecicki Street 6, 60-781 Poznan, Poland
| |
Collapse
|
5
|
Ciurea AM, Schenker M, Ciofiac CM, Streba L, Schenker R, Streba CT. Genomic Profiling - A Need for Clinical Decision? -Case Reports. CURRENT HEALTH SCIENCES JOURNAL 2023; 49:467-473. [PMID: 38314216 PMCID: PMC10832885 DOI: 10.12865/chsj.49.03.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 06/21/2023] [Indexed: 02/06/2024]
Abstract
Cancer is still an important health issue worldwide due to increased incidence and mortality. Personalized medicine is the future of cancer treatment. Development in technology improved technical skills in DNA/RNA sequencing. NGS technology in solid-tumor samples can describe DNA or RNA analysis by including the entire genome to detect clinical relevant mutations. Genetic results may be considered having a dynamic impact because of heterogenous molecular alterations depending of time and treatment influence. We conducted a retrospective study of all NGS tests made in the last five years for the patients from 'Sf. Nectarie' Oncology Center, Craiova, Romania. We selected three relevant clinical cases where NGS analysis was performed and the results changed the perspective of the clinical decision. Our aim is to evaluate the importance of NGS results in clinical approach. Although medicine known an important development during the last decades, only a few patients can benefit of advanced personalized treatments. It is still hard to identify the alterations or gene mutations because of genetic tests are not easily available and only a small proportion of patients carries genetic alterations.
Collapse
Affiliation(s)
- Ana-Maria Ciurea
- Department of Oncology, University of Medicine and Pharmacy of Craiova, Romania
| | - Michael Schenker
- Department of Oncology, University of Medicine and Pharmacy of Craiova, Romania
| | - Cristina Mihaela Ciofiac
- Doctoral School, Department of Radiology and Medical Imaging, University of Medicine and Pharmacy of Craiova
| | - Liliana Streba
- Department of Oncology, University of Medicine and Pharmacy of Craiova, Romania
| | - Ramona Schenker
- Psychology Department, Sf Nectarie Oncology Center, Craiova, Romania
| | - Costin Teodor Streba
- Department of Pulmonology, University of Medicine and Pharmacy of Craiova, Romania
| |
Collapse
|