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Kumar P, Benjamin DJ, Darabi S, Kloecker G, Rezazadeh Kalebasty A. Implications of genetic testing and informed consent before and after genetic testing in individuals with cancer. World J Clin Oncol 2024; 15:975-981. [DOI: 10.5306/wjco.v15.i8.975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 07/15/2024] [Accepted: 07/23/2024] [Indexed: 08/16/2024] Open
Abstract
Recent advancements in next generation sequencing have allowed for genetic information become more readily available in the clinical setting for those affected by cancer and by treating clinicians. Given the lack of access to geneticists, medical oncologists and other treating physicians have begun ordering and interpreting genetic tests for individuals with cancer through the process of "mainstreaming". While this process has allowed for quicker access to genetic tests, the process of "mainstreaming" has also brought several challenges including the dissemination of variants of unknown significance results, ordering of appropriate tests, and accurate interpretation of genetic results with appropriate follow-up testing and interventions. In this editorial, we seek to explore the process of informed consent of individuals before obtaining genetic testing and offer potential solutions to optimize the informed consent process including categorization of results as well as a layered consent model.
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Affiliation(s)
- Priyanka Kumar
- Department of Hematology and Medical Oncology, Harbor-UCLA Medical Center, Torrance, CA 90502, United States
| | - David J Benjamin
- Department of Medical Oncology, Hoag Family Cancer Institute, Newport Beach, CA 92663, United States
| | - Sourat Darabi
- Department of Precision Medicine, Hoag Family Cancer Institute, Newport Beach, CA 92663, United States
| | - Goetz Kloecker
- Department of Hematology and Medical Oncology, University of Louisville, Louisville, KY 40202, United States
| | - Arash Rezazadeh Kalebasty
- Department of Hematology and Medical Oncology, University of California-Irvine, Orange, CA 92868, United States
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2
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Fanelli A, Licenziato L, Mazzone E, Divari S, Rinaldi A, Marino M, Maga I, Bertoni F, Marconato L, Aresu L. The K9 lymphoma assay allows a genetic subgrouping of canine lymphomas with improved risk classification. Sci Rep 2024; 14:18687. [PMID: 39134766 PMCID: PMC11319785 DOI: 10.1038/s41598-024-69716-6] [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: 03/12/2024] [Accepted: 08/07/2024] [Indexed: 08/15/2024] Open
Abstract
We present here the K9 lymphoma assay, a novel 31-gene targeted next-generation sequencing panel designed for genomic profiling of canine lymphoid neoplasms. Addressing the growing demand for advanced diagnostics in veterinary oncology, this assay enables sensitive identification of known and actionable mutations specific to canine lymphomas, while evaluating its prognostic potential to facilitate diagnosis and prognosis. Our analysis, spanning several B- and T-cell lymphoma histotypes, unveiled distinct mutational landscapes distinguishing tumors derived from immature versus mature lymphocytes. Clustering analysis revealed a shared genetic origin between diffuse large B-cell lymphoma and marginal zone lymphoma, aligning with findings in human lymphomas, with TRAF3 emerging as the most frequently mutated gene across B-cell lymphoma subtypes. Significantly, TP53 mutations demonstrated universal adverse prognostic implications across B-cell lymphomas. Additionally, SETD2 mutations contributed to shorter time-to-progression, underscoring the role of epigenetic dysregulation in B-cell tumors. In T-cell lymphomas, SATB1 and FBXW7 were frequently mutated, warranting further investigation in larger cohorts. Our findings advocate for tailored therapeutic approaches based on the genetic profile, impacting treatment decisions and outcomes in canine lymphoma management. This study provides pivotal insights bridging veterinary and human oncology, paving the way for comprehensive genomic diagnostics and therapeutic strategies in comparative oncology.
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Affiliation(s)
- Antonella Fanelli
- Department of Veterinary Sciences, University of Turin, Grugliasco, Turin, Italy
| | - Luca Licenziato
- Department of Veterinary Sciences, University of Turin, Grugliasco, Turin, Italy
| | - Eugenio Mazzone
- Department of Veterinary Sciences, University of Turin, Grugliasco, Turin, Italy
| | - Sara Divari
- Department of Veterinary Sciences, University of Turin, Grugliasco, Turin, Italy
| | - Andrea Rinaldi
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Michele Marino
- MyLav Veterinary Diagnostic Laboratory, Passirana di Rho, Milan, Italy
| | - Ilaria Maga
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell'Emilia, Bologna, Italy
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | - Laura Marconato
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell'Emilia, Bologna, Italy.
| | - Luca Aresu
- Department of Veterinary Sciences, University of Turin, Grugliasco, Turin, Italy.
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3
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Abbasi AF, Asim MN, Ahmed S, Vollmer S, Dengel A. Survival prediction landscape: an in-depth systematic literature review on activities, methods, tools, diseases, and databases. Front Artif Intell 2024; 7:1428501. [PMID: 39021434 PMCID: PMC11252047 DOI: 10.3389/frai.2024.1428501] [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: 05/07/2024] [Accepted: 06/12/2024] [Indexed: 07/20/2024] Open
Abstract
Survival prediction integrates patient-specific molecular information and clinical signatures to forecast the anticipated time of an event, such as recurrence, death, or disease progression. Survival prediction proves valuable in guiding treatment decisions, optimizing resource allocation, and interventions of precision medicine. The wide range of diseases, the existence of various variants within the same disease, and the reliance on available data necessitate disease-specific computational survival predictors. The widespread adoption of artificial intelligence (AI) methods in crafting survival predictors has undoubtedly revolutionized this field. However, the ever-increasing demand for more sophisticated and effective prediction models necessitates the continued creation of innovative advancements. To catalyze these advancements, it is crucial to bring existing survival predictors knowledge and insights into a centralized platform. The paper in hand thoroughly examines 23 existing review studies and provides a concise overview of their scope and limitations. Focusing on a comprehensive set of 90 most recent survival predictors across 44 diverse diseases, it delves into insights of diverse types of methods that are used in the development of disease-specific predictors. This exhaustive analysis encompasses the utilized data modalities along with a detailed analysis of subsets of clinical features, feature engineering methods, and the specific statistical, machine or deep learning approaches that have been employed. It also provides insights about survival prediction data sources, open-source predictors, and survival prediction frameworks.
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Affiliation(s)
- Ahtisham Fazeel Abbasi
- Department of Computer Science, Rhineland-Palatinate Technical University of Kaiserslautern-Landau, Kaiserslautern, Germany
- Smart Data & Knowledge Services, Deutsches Forschungszentrum für Künstliche Intelligenz (DFKI), Kaiserslautern, Germany
| | - Muhammad Nabeel Asim
- Smart Data & Knowledge Services, Deutsches Forschungszentrum für Künstliche Intelligenz (DFKI), Kaiserslautern, Germany
| | - Sheraz Ahmed
- Smart Data & Knowledge Services, Deutsches Forschungszentrum für Künstliche Intelligenz (DFKI), Kaiserslautern, Germany
| | - Sebastian Vollmer
- Department of Computer Science, Rhineland-Palatinate Technical University of Kaiserslautern-Landau, Kaiserslautern, Germany
- Smart Data & Knowledge Services, Deutsches Forschungszentrum für Künstliche Intelligenz (DFKI), Kaiserslautern, Germany
| | - Andreas Dengel
- Department of Computer Science, Rhineland-Palatinate Technical University of Kaiserslautern-Landau, Kaiserslautern, Germany
- Smart Data & Knowledge Services, Deutsches Forschungszentrum für Künstliche Intelligenz (DFKI), Kaiserslautern, Germany
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4
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Pilenzi L, Anaclerio F, Dell'Elice A, Minelli M, Giansante R, Cicirelli M, Tinari N, Grassadonia A, Pantalone A, Grossi S, Canale N, Bruno A, Calabrese G, Ballerini P, Stuppia L, Antonucci I. The Crucial Role of Hereditary Cancer Panel Testing in Unaffected Individuals with a Strong Family History of Cancer: A Retrospective Study of a Cohort of 103 Healthy Subjects. Cancers (Basel) 2024; 16:2327. [PMID: 39001389 PMCID: PMC11240828 DOI: 10.3390/cancers16132327] [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: 05/24/2024] [Revised: 06/16/2024] [Accepted: 06/21/2024] [Indexed: 07/16/2024] Open
Abstract
Hereditary cancer syndromes caused by germline mutations account for 5-10% of all cancers. The finding of a genetic mutation could have far-reaching consequences for pharmaceutical therapy, personalized prevention strategies, and cascade testing. According to the National Comprehensive Cancer Network's (NCCN) and the Italian Association of Medical Oncology (AIOM) guidelines, unaffected family members should be tested only if the affected one is unavailable. This article explores whether germline genetic testing may be offered to high-risk families for hereditary cancer even if a living affected relative is missing. A retrospective study was carried out on 103 healthy subjects tested from 2017 to 2023. We enrolled all subjects with at least two first- or second-degree relatives affected by breast, ovarian, pancreatic, gastric, prostate, or colorectal cancer. All subjects were tested by Next Generation Sequencing (NGS) multi-gene panel of 27 cancer-associated genes. In the study population, 5 (about 5%) pathogenic/likely pathogenic variants (PVs/LPVs) were found, while 40 (42%) had a Variant of Uncertain Significance (VUS). This study highlights the importance of genetic testing for individuals with a strong family history of hereditary malignancies. This approach would allow women who tested positive to receive tailored treatment and prevention strategies based on their personal mutation status.
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Affiliation(s)
- Lucrezia Pilenzi
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
| | - Federico Anaclerio
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
| | - Anastasia Dell'Elice
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
| | - Maria Minelli
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
- Department of Medical Genetics, "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
| | - Roberta Giansante
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
- Department of Medical Genetics, "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
| | - Michela Cicirelli
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
- Department of Medical Genetics, "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
| | - Nicola Tinari
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
| | - Antonino Grassadonia
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
- Department of Innovative Technologies in Medicine and Dentistry, "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
| | - Andrea Pantalone
- Orthopaedic and Traumatology Department, "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
| | - Simona Grossi
- U.O.C. Chirurgia Generale ad Indirizzo Senologico, Eusoma Breast Center ASL2 Abruzzo, 66026 Ortona, Italy
| | - Nicole Canale
- U.O.C. Chirurgia Generale ad Indirizzo Senologico, Eusoma Breast Center ASL2 Abruzzo, 66026 Ortona, Italy
| | - Annalisa Bruno
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
- Department of Innovative Technologies in Medicine and Dentistry, "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
| | | | - Patrizia Ballerini
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
- Department of Innovative Technologies in Medicine and Dentistry, "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
| | - Liborio Stuppia
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
- Department of Psychological, Health and Territorial Sciences, "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
| | - Ivana Antonucci
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
- Department of Psychological, Health and Territorial Sciences, "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
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Zhang YW, Gvozdenovic A, Aceto N. A Molecular Voyage: Multiomics Insights into Circulating Tumor Cells. Cancer Discov 2024; 14:920-933. [PMID: 38581442 DOI: 10.1158/2159-8290.cd-24-0218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/08/2024] [Accepted: 03/13/2024] [Indexed: 04/08/2024]
Abstract
Circulating tumor cells (CTCs) play a pivotal role in metastasis, the leading cause of cancer-associated death. Recent improvements of CTC isolation tools, coupled with a steady development of multiomics technologies at single-cell resolution, have enabled an extensive exploration of CTC biology, unlocking insights into their molecular profiles. A detailed molecular portrait requires CTC interrogation across various levels encompassing genomic, epigenetic, transcriptomic, proteomic and metabolic features. Here, we review how state-of-the-art multiomics applied to CTCs are shedding light on how cancer spreads. Further, we highlight the potential implications of CTC profiling for clinical applications aimed at enhancing cancer diagnosis and treatment. SIGNIFICANCE Exploring the complexity of cancer progression through cutting-edge multiomics studies holds the promise of uncovering novel aspects of cancer biology and identifying therapeutic vulnerabilities to suppress metastasis.
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Affiliation(s)
- Yu Wei Zhang
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich, Switzerland
| | - Ana Gvozdenovic
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich, Switzerland
| | - Nicola Aceto
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich, Switzerland
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6
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Tsai YY, Cheng D, Huang SW, Hung SJ, Wang YF, Lin YJ, Tsai HP, Chu JJH, Wang JR. The molecular epidemiology of a dengue virus outbreak in Taiwan: population wide versus infrapopulation mutation analysis. PLoS Negl Trop Dis 2024; 18:e0012268. [PMID: 38870242 PMCID: PMC11207123 DOI: 10.1371/journal.pntd.0012268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 06/26/2024] [Accepted: 06/03/2024] [Indexed: 06/15/2024] Open
Abstract
Dengue virus (DENV) causes approximately 390 million dengue infections worldwide every year. There were 22,777 reported DENV infections in Tainan, Taiwan in 2015. In this study, we sequenced the C-prM-E genes from 45 DENV 2015 strains, and phylogenetic analysis based on C-prM-E genes revealed that all strains were classified as DENV serotype 2 Cosmopolitan genotype. Sequence analysis comparing different DENV-2 genotypes and Cosmopolitan DENV-2 sequences prior to 2015 showed a clade replacement event in the DENV-2 Cosmopolitan genotype. Additionally, a major substitution C-A314G (K73R) was found in the capsid region which may have contributed to the clade replacement event. Reverse genetics virus rgC-A314G (K73R) showed slower replication in BHK-21 and C6/36 cells compared to wildtype virus, as well as a decrease in NS1 production in BHK-21-infected cells. After a series of passaging, the C-A314G (K73R) mutation reverted to wildtype and was thus considered to be unstable. Next generation sequencing (NGS) of three sera collected from a single DENV2-infected patient at 1-, 2-, and 5-days post-admission was employed to examine the genetic diversity over-time and mutations that may work in conjunction with C-A314G (K73R). Results showed that the number of haplotypes decreased with time in the DENV-infected patient. On the fifth day after admission, two new haplotypes emerged, and a single non-synonymous NS4A-L115I mutation was identified. Therefore, we have identified a persistent mutation C-A314G (K73R) in all of the DENV-2 isolates, and during the course of an infection, a single new non-synonymous mutation in the NS4A region appears in the virus population within a single host. The C-A314G (K73R) thus may have played a role in the DENV-2 2015 outbreak while the NS4A-L115I may be advantageous during DENV infection within the host.
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Affiliation(s)
- You-Yuan Tsai
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Dayna Cheng
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Sheng-Wen Huang
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Tainan, Taiwan
| | - Su-Jhen Hung
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Tainan, Taiwan
| | - Ya-Fang Wang
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Tainan, Taiwan
| | - Yih-Jyh Lin
- Division of General Surgery, Department of Surgery, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Huey-Pin Tsai
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Justin Jang Hann Chu
- Infectious Diseases Translational Research Program and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jen-Ren Wang
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan
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Duraisamy AJ, Liu R, Sureshkumar S, Rose R, Jagannathan L, da Silva C, Coovadia A, Ramachander V, Chandrasekar S, Raja I, Sajnani M, Selvaraj SM, Narang B, Darvishi K, Bhayal AC, Katikala L, Guo F, Chen-Deutsch X, Balciuniene J, Ma Z, Nallamilli BRR, Bean L, Collins C, Hegde M. Focused Exome Sequencing Gives a High Diagnostic Yield in the Indian Subcontinent. J Mol Diagn 2024; 26:510-519. [PMID: 38582400 DOI: 10.1016/j.jmoldx.2024.03.005] [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: 02/15/2023] [Revised: 09/11/2023] [Accepted: 03/01/2024] [Indexed: 04/08/2024] Open
Abstract
The genetically isolated yet heterogeneous and highly consanguineous Indian population has shown a higher prevalence of rare genetic disorders. However, there is a significant socioeconomic burden for genetic testing to be accessible to the general population. In the current study, we analyzed next-generation sequencing data generated through focused exome sequencing from individuals with different phenotypic manifestations referred for genetic testing to achieve a molecular diagnosis. Pathogenic or likely pathogenic variants are reported in 280 of 833 cases with a diagnostic yield of 33.6%. Homozygous sequence and copy number variants were found as positive diagnostic findings in 131 cases (15.7%) because of the high consanguinity in the Indian population. No relevant findings related to reported phenotype were identified in 6.2% of the cases. Patients referred for testing due to metabolic disorder and neuromuscular disorder had higher diagnostic yields. Carrier testing of asymptomatic individuals with a family history of the disease, through focused exome sequencing, achieved positive diagnosis in 54 of 118 cases tested. Copy number variants were also found in trans with single-nucleotide variants and mitochondrial variants in a few of the cases. The diagnostic yield and the findings from this study signify that a focused exome test is a good lower-cost alternative for whole-exome and whole-genome sequencing and as a first-tier approach to genetic testing.
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Affiliation(s)
| | - Ruby Liu
- Revvity Omics, Pittsburgh, Pennsylvania
| | | | - Rajiv Rose
- PerkinElmer Genomics, Revvity Omics, Chennai, India
| | | | | | | | | | | | - Indu Raja
- PerkinElmer Genomics, Revvity Omics, Chennai, India
| | | | | | | | | | | | | | - Fen Guo
- Revvity Omics, Pittsburgh, Pennsylvania
| | | | | | | | | | - Lora Bean
- Revvity Omics, Pittsburgh, Pennsylvania
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Mahmood M, Taufiq I, Mazhar S, Hafeez F, Malik K, Afzal S. Revolutionizing personalized cancer treatment: the synergy of next-generation sequencing and CRISPR/Cas9. Per Med 2024; 21:175-190. [PMID: 38708901 DOI: 10.1080/17410541.2024.2341610] [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: 10/26/2023] [Accepted: 04/08/2024] [Indexed: 05/07/2024]
Abstract
In the context of cancer heterogeneity, the synergistic action of next-generation sequencing (NGS) and CRISPR/Cas9 plays a promising role in the personalized treatment of cancer. NGS enables high-throughput genomic profiling of tumors and pinpoints specific mutations that primarily lead to cancer. Oncologists use this information obtained from NGS in the form of DNA profiling or RNA analysis to tailor precision strategies based on an individual's unique molecular signature. Furthermore, the CRISPR technique enables precise editing of cancer-specific mutations, allowing targeted gene modifications. Harnessing the potential insights of NGS and CRISPR/Cas9 heralds a remarkable frontier in cancer therapeutics with unprecedented precision, effectiveness and minimal off-target effects.
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Affiliation(s)
- Muniba Mahmood
- Centre for Excellence in Molecular Biology, University of the Punjab, Lahore, Punjab, 53700, Pakistan
| | - Izza Taufiq
- Centre for Excellence in Molecular Biology, University of the Punjab, Lahore, Punjab, 53700, Pakistan
| | - Sana Mazhar
- Centre for Excellence in Molecular Biology, University of the Punjab, Lahore, Punjab, 53700, Pakistan
| | - Faiqa Hafeez
- Centre for Excellence in Molecular Biology, University of the Punjab, Lahore, Punjab, 53700, Pakistan
| | - Kausar Malik
- Centre for Excellence in Molecular Biology, University of the Punjab, Lahore, Punjab, 53700, Pakistan
| | - Samia Afzal
- Centre for Excellence in Molecular Biology, University of the Punjab, Lahore, Punjab, 53700, Pakistan
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9
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Wu Y, Yu S, de Lázaro I. Advances in lipid nanoparticle mRNA therapeutics beyond COVID-19 vaccines. NANOSCALE 2024; 16:6820-6836. [PMID: 38502114 DOI: 10.1039/d4nr00019f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
The remarkable success of two lipid nanoparticle-mRNA vaccines against coronavirus disease (COVID-19) has placed the therapeutic and prophylactic potential of messenger RNA (mRNA) in the spotlight. It has also drawn attention to the indispensable role of lipid nanoparticles in enabling the effects of this nucleic acid. To date, lipid nanoparticles are the most clinically advanced non-viral platforms for mRNA delivery. This is thanks to their favorable safety profile and efficiency in protecting the nucleic acid from degradation and allowing its cellular uptake and cytoplasmic release upon endosomal escape. Moreover, the development of lipid nanoparticle-mRNA therapeutics was already a very active area of research even before the COVID-19 pandemic, which has likely only begun to bear its fruits. In this Review, we first discuss key aspects of the development of lipid nanoparticles as mRNA carriers. We then highlight promising preclinical and clinical studies involving lipid nanoparticle-mRNA formulations against infectious diseases and cancer, and to enable protein replacement or supplementation and genome editing. Finally, we elaborate on the challenges in advancing lipid nanoparticle-mRNA technology to widespread therapeutic use.
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Affiliation(s)
- Yeung Wu
- Department of Biomedical Engineering, NYU Tandon School of Engineering, New York University, USA.
| | - Sinuo Yu
- Department of Biomedical Engineering, NYU Tandon School of Engineering, New York University, USA.
| | - Irene de Lázaro
- Department of Biomedical Engineering, NYU Tandon School of Engineering, New York University, USA.
- Cardiovascular Research Center, Division of Cardiology, Department of Medicine, NYU Grossman School of Medicine, New York University, USA
- Harvard John A. Paulson School of Engineering and Applied Science, Harvard University, USA
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10
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Shen G, Li W, Zhang Y, Chen L. Next-generation sequencing based newborn screening and comparative analysis with MS/MS. BMC Pediatr 2024; 24:230. [PMID: 38561707 PMCID: PMC10985934 DOI: 10.1186/s12887-024-04718-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 03/21/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Newborn screening (NBS), such as tandem mass spectrometry (MS/MS), may yield false positive/negative results. Next-generation sequencing (NGS) has the potential to provide increased data output, efficiencies, and applications. This study aimed to analyze the types and distribution of pathogenic gene mutations in newborns in Huzhou, Zhejiang province, China and explore the applicability of NGS and MS/MS in NBS. METHODS Blood spot samples from 1263 newborns were collected. NGS was employed to screen for pathogenic variants in 542 disease-causing genes, and detected variants were validated using Sanger sequencing. Simultaneously, 26 inherited metabolic diseases (IMD) were screened using MS/MS. Positive or suspicious samples identified through MS/MS were cross-referenced with the results of NGS. RESULTS Among all newborns, 328 had no gene mutations detected. NGS revealed at least one gene mutation in 935 newborns, with a mutation rate of 74.0%. The top 5 genes were FLG, GJB2, UGT1A1, USH2A, and DUOX2. According to American College of Medical Genetics guidelines, gene mutations in 260 cases were classified as pathogenic or likely pathogenic mutation, with a positive rate of 20.6%. The top 5 genes were UGT1A1, FLG, GJB2, MEFV, and G6PD. MS/MS identified 18 positive or suspicious samples for IMD and 1245 negative samples. Verification of these cases by NGS results showed no pathogenic mutations, resulting in a false positive rate of 1.4% (18/1263). CONCLUSION NBS using NGS technology broadened the range of diseases screened, and enhanced the accuracy of diagnoses in comparison to MS/MS for screening IMD. Combining NGS and biochemical screening would improve the efficiency of current NBS.
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Affiliation(s)
- Guosong Shen
- Medical Laboratory Center, Huzhou Maternity & Child Health Care Hospital, Huzhou, Zhejiang Province, 313000, China.
| | - Wenwen Li
- Medical Laboratory Center, Huzhou Maternity & Child Health Care Hospital, Huzhou, Zhejiang Province, 313000, China
| | - Yaqin Zhang
- Medical Laboratory Center, Huzhou Maternity & Child Health Care Hospital, Huzhou, Zhejiang Province, 313000, China
| | - Lyuyan Chen
- Institut for Neuroscience, Technical University of Munich, 80802, Munich, Germany
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Liu W, Cheng H, Huang Z, Li Y, Zhang Y, Yang Y, Jin T, Sun Y, Deng Z, Zhang Q, Lou F, Cao S, Wang H, Niu X. The correlation between clinical outcomes and genomic analysis with high risk factors for the progression of osteosarcoma. Mol Oncol 2024; 18:939-955. [PMID: 37727135 PMCID: PMC10994228 DOI: 10.1002/1878-0261.13526] [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: 06/15/2023] [Revised: 08/30/2023] [Accepted: 09/18/2023] [Indexed: 09/21/2023] Open
Abstract
Osteosarcoma (OS) is a rare but aggressive malignancy. Despite previous reports, molecular characterization of this disease is not well understood, and little is known regarding OS in Chinese patients. Herein, we analyzed the genomic signatures of 73 Chinese OS cases. TP53, NCOR1, LRP1B, ATRX, RB1, and TFE3 were the most frequently mutated gene in our OS cohort. In addition, the genomic analysis of Western OS patients was performed. Notably, there were remarkable disparities in mutational landscape, base substitution pattern, and tumor mutational burden between the Chinese and Western OS cohorts. Specific molecular mechanisms, including DNA damage repair (DDR) gene mutations, copy number variation (CNV) presence, aneuploidy, and intratumoral heterogeneity, were associated with disease progression. Additionally, 30.1% of OS patients carried clinically actionable alterations, which were mainly enriched in PI3K, MAPK, DDR, and RTK signaling pathways. A specific molecular subtype incorporating DDR alterations and CNVs was significantly correlated with distant metastasis-free survival and event-free survival, and this correlation was observed in all subgroups with different characteristics. These findings comprehensively elucidated the genomic profile and revealed novel prognostic factors in OS, which would contribute to understanding this disease and promoting precision medicine of this population.
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Affiliation(s)
- Weifeng Liu
- Department of Orthopaedic Oncology Surgery, Beijing Jishuitan HospitalPeking UniversityBeijingChina
- Fourth Medical College of Peking UniversityBeijingChina
- National Center for OrthopeadicsBeijingChina
| | | | - Zhen Huang
- Department of Orthopaedic Oncology Surgery, Beijing Jishuitan HospitalPeking UniversityBeijingChina
- Fourth Medical College of Peking UniversityBeijingChina
- National Center for OrthopeadicsBeijingChina
| | - Yaping Li
- Acornmed Biotechnology Co., Ltd.BeijingChina
| | | | - Yongkun Yang
- Department of Orthopaedic Oncology Surgery, Beijing Jishuitan HospitalPeking UniversityBeijingChina
- Fourth Medical College of Peking UniversityBeijingChina
- National Center for OrthopeadicsBeijingChina
| | - Tao Jin
- Department of Orthopaedic Oncology Surgery, Beijing Jishuitan HospitalPeking UniversityBeijingChina
- Fourth Medical College of Peking UniversityBeijingChina
- National Center for OrthopeadicsBeijingChina
| | - Yang Sun
- Department of Orthopaedic Oncology Surgery, Beijing Jishuitan HospitalPeking UniversityBeijingChina
- Fourth Medical College of Peking UniversityBeijingChina
- National Center for OrthopeadicsBeijingChina
| | - Zhiping Deng
- Department of Orthopaedic Oncology Surgery, Beijing Jishuitan HospitalPeking UniversityBeijingChina
- Fourth Medical College of Peking UniversityBeijingChina
- National Center for OrthopeadicsBeijingChina
| | - Qing Zhang
- Department of Orthopaedic Oncology Surgery, Beijing Jishuitan HospitalPeking UniversityBeijingChina
- Fourth Medical College of Peking UniversityBeijingChina
- National Center for OrthopeadicsBeijingChina
| | - Feng Lou
- Acornmed Biotechnology Co., Ltd.BeijingChina
| | - Shanbo Cao
- Acornmed Biotechnology Co., Ltd.BeijingChina
| | - Huina Wang
- Acornmed Biotechnology Co., Ltd.BeijingChina
| | - Xiaohui Niu
- Department of Orthopaedic Oncology Surgery, Beijing Jishuitan HospitalPeking UniversityBeijingChina
- Fourth Medical College of Peking UniversityBeijingChina
- National Center for OrthopeadicsBeijingChina
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12
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Kaur K, Ai R, Perry AG, Riley B, Roberts EL, Montano EN, Han J, Roacho J, Lopez BG, Skelsey MK, Childs MV, Childs JN, Dobak J, Ibarra C, Jansen B, Clarke LE, Stone S, Whitaker JW. Skin Cancer Risk Is Increased by Somatic Mutations Detected Noninvasively in Healthy-Appearing Sun-Exposed Skin. J Invest Dermatol 2024:S0022-202X(24)00176-3. [PMID: 38513819 DOI: 10.1016/j.jid.2024.02.017] [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: 10/04/2023] [Revised: 01/08/2024] [Accepted: 02/16/2024] [Indexed: 03/23/2024]
Abstract
Skin cancer risk is increased by exposure to ultraviolet radiation (UVR). Because UVR exposure accumulates over time and lighter skin is more susceptible to UVR, age and skin tone are risk factors for skin cancer. However, measurements of somatic mutations in healthy-appearing skin have not been used to calculate skin cancer risk. In this study, we developed a noninvasive test that quantifies somatic mutations in healthy-appearing sun-exposed skin and applied it to a 1038-subject cohort. Somatic mutations were combined with other known skin cancer risk factors to train a model to calculate risk. The final model (DNA-Skin Cancer Assessment of Risk) was trained to predict personal history of skin cancer from age, family history, skin tone, and mutation count. The addition of mutation count significantly improved model performance (OR = 1.3, 95% confidence interval = 1.14-1.48; P = 5.3 × 10-6) and made a more significant contribution than skin tone. Calculations of skin cancer risk matched the known United States population prevalence, indicating that DNA-Skin Cancer Assessment of Risk was well-calibrated. In conclusion, somatic mutations in healthy-appearing sun-exposed skin increase skin cancer risk, and mutations capture risk information that is not accounted for by other risk factors. Clinical utility is supported by the noninvasive nature of skin sample collection through adhesive patches.
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Affiliation(s)
| | - Rizi Ai
- DermTech, San Diego, California, USA
| | | | - Bae Riley
- DermTech, San Diego, California, USA
| | | | | | | | | | | | - Maral K Skelsey
- Department of Dermatology, School of Medicine, Georgetown University, Washington, District of Columbia, USA
| | - Maria V Childs
- Department of Dermatology, Texas A&M University College of Medicine, Temple, Texas, USA
| | - James N Childs
- Department of Dermatology, Texas A&M University College of Medicine, Temple, Texas, USA
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13
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Capasso A, Nehoray B, Gorman N, Quinn EA, Bucio D, Blazer KR. Genetic counselors' and community clinicians' implementation and perceived barriers to informed consent during pre-test counseling for hereditary cancer risk. J Genet Couns 2024. [PMID: 38480478 DOI: 10.1002/jgc4.1887] [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: 09/14/2023] [Revised: 02/01/2024] [Accepted: 02/03/2024] [Indexed: 04/21/2024]
Abstract
As demand for genetic cancer risk assessment (GCRA) continues to increase, so does the sense of urgency to scale up efforts to triage patients, facilitate informed consent, and order genetic testing for cancer risk. The National Society of Genetic Counselors outlines the elements of informed consent that should be addressed in a GCRA session. While this practice resource aims to improve health equity, research on how well the elements of informed consent are implemented in practice is lacking. This retrospective and prospective mixed-methods study assessed how adequately the elements of informed consent are addressed during pre-test GCRA among 307 community clinicians (CC) and 129 cancer genetic counselors (GC), and barriers they face to addressing these elements. Results revealed that more than 90% of both cohorts consistently addressed components of at least 5 of the 10 elements of informed consent during a pre-test consultation. Technical aspects and accuracy of the test and utilization of test results were the most similarly addressed elements. Notably, GCs more often review the purpose of the test and who to test, general information about the gene(s), and economic considerations whereas CCs more often review alternatives to testing. Both cohorts reported psychosocial aspects of the informed consent process as the least adequately addressed element. Time constraints and patient-related concerns were most often cited by both cohorts as barriers to optimal facilitation of informed consent. Additional barriers reported by CCs included provider lack of awareness, experience, or education, and availability of resources and institutional support. Findings from this study may contribute to the development of alternative delivery models that incorporate supplementary educational tools to enhance patient understanding about the utility of genetic testing, while helping to mitigate the barrier of time constraints. Equally important is the use of this information to develop continuing education tools for providers.
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Affiliation(s)
- Alexandra Capasso
- School of Pharmacy and Health Sciences, Keck Graduate Institute, Claremont, California, USA
- Division of Clinical Cancer Genomics, City of Hope National Medical Center, Duarte, California, USA
| | - Bita Nehoray
- Division of Clinical Cancer Genomics, City of Hope National Medical Center, Duarte, California, USA
| | - Nicholas Gorman
- School of Pharmacy and Health Sciences, Keck Graduate Institute, Claremont, California, USA
| | - Emily A Quinn
- School of Pharmacy and Health Sciences, Keck Graduate Institute, Claremont, California, USA
| | - Daiana Bucio
- Clinical Consultation Services, Invitae Corporation, San Francisco, California, USA
| | - Kathleen R Blazer
- Division of Clinical Cancer Genomics, City of Hope National Medical Center, Duarte, California, USA
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14
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Jose A, Kulkarni P, Thilakan J, Munisamy M, Malhotra AG, Singh J, Kumar A, Rangnekar VM, Arya N, Rao M. Integration of pan-omics technologies and three-dimensional in vitro tumor models: an approach toward drug discovery and precision medicine. Mol Cancer 2024; 23:50. [PMID: 38461268 PMCID: PMC10924370 DOI: 10.1186/s12943-023-01916-6] [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: 08/05/2023] [Accepted: 12/15/2023] [Indexed: 03/11/2024] Open
Abstract
Despite advancements in treatment protocols, cancer is one of the leading cause of deaths worldwide. Therefore, there is a need to identify newer and personalized therapeutic targets along with screening technologies to combat cancer. With the advent of pan-omics technologies, such as genomics, transcriptomics, proteomics, metabolomics, and lipidomics, the scientific community has witnessed an improved molecular and metabolomic understanding of various diseases, including cancer. In addition, three-dimensional (3-D) disease models have been efficiently utilized for understanding disease pathophysiology and as screening tools in drug discovery. An integrated approach utilizing pan-omics technologies and 3-D in vitro tumor models has led to improved understanding of the intricate network encompassing various signalling pathways and molecular cross-talk in solid tumors. In the present review, we underscore the current trends in omics technologies and highlight their role in understanding genotypic-phenotypic co-relation in cancer with respect to 3-D in vitro tumor models. We further discuss the challenges associated with omics technologies and provide our outlook on the future applications of these technologies in drug discovery and precision medicine for improved management of cancer.
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Affiliation(s)
- Anmi Jose
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Pallavi Kulkarni
- Department of Biochemistry, All India Institute of Medical Sciences Bhopal, Bhopal, Madhya Pradesh, 462020, India
| | - Jaya Thilakan
- Department of Biochemistry, All India Institute of Medical Sciences Bhopal, Bhopal, Madhya Pradesh, 462020, India
| | - Murali Munisamy
- Department of Translational Medicine, All India Institute of Medical Sciences Bhopal, Bhopal, Madhya Pradesh, 462020, India
| | - Anvita Gupta Malhotra
- Department of Translational Medicine, All India Institute of Medical Sciences Bhopal, Bhopal, Madhya Pradesh, 462020, India
| | - Jitendra Singh
- Department of Translational Medicine, All India Institute of Medical Sciences Bhopal, Bhopal, Madhya Pradesh, 462020, India
| | - Ashok Kumar
- Department of Biochemistry, All India Institute of Medical Sciences Bhopal, Bhopal, Madhya Pradesh, 462020, India
| | - Vivek M Rangnekar
- Markey Cancer Center and Department of Radiation Medicine, University of Kentucky, Lexington, KY, 40536, USA
| | - Neha Arya
- Department of Translational Medicine, All India Institute of Medical Sciences Bhopal, Bhopal, Madhya Pradesh, 462020, India.
| | - Mahadev Rao
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
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15
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Taris N, Luporsi E, Osada M, Thiblet M, Mathelin C. [News in breast oncology genetics for female and male population]. GYNECOLOGIE, OBSTETRIQUE, FERTILITE & SENOLOGIE 2024; 52:149-157. [PMID: 38190969 DOI: 10.1016/j.gofs.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 12/30/2023] [Indexed: 01/10/2024]
Abstract
OBJECTIVES Breast oncology genetics emerged almost 30 years ago with the discovery of the BRCA1 and BRCA2 genes. The evolution of analytical practices has progressively allowed access to tests whose results now have a considerable impact on the management of both female and male breast cancers. The Sénologie commission of the Collège national des gynécologues et obstétriciens français (CNGOF) asked five specialists in breast surgery, oncology and oncological genetics to draw up a summary of the oncogenetic testing criteria used and the clinical implications for the female and male population of the test results, with or without an identified causal variant. In the case of proven genetic risk, surveillance, risk-reduction strategies, and the specificities of surgical and medical management (with PARP inhibitors in particular) were updated. METHODS This summary was based on national and international guidelines on the monitoring and therapeutic management of genetic risk, and a recent review of the literature covering the last five years. RESULTS Despite successive technical developments, the probability of identifying a causal variant in a situation suggestive of a predisposition to breast and ovarian cancer remains around 10% in France. The risk of breast cancer in women with a causal variant of the BRCA1, BRCA2, PALB2, TP53, CDH1 and PTEN genes is estimated at between 35% and 85% at age 70. The presence of a causal variant in one of these genes is the subject of different recommendations for men and women, concerning both surveillance, the age of onset and imaging modalities of which vary according to the genes involved, and risk-reduction surgery, which is possible for women as soon as their risk level exceeds 30% and remains exceptionally indicated for men. In the case of breast cancer, PARP inhibitors are a promising new class of treatment for BRCA germline mutations. CONCLUSION A discipline resolutely focused on understanding molecular mechanisms, screening and preventive medicine/surgery, oncology genetics is currently also involved in new medical/surgical approaches, the long-term benefits/risks of which will need to be monitored.
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Affiliation(s)
- Nicolas Taris
- Unité de génétique oncologique, ICANS, avenue Albert-Calmette, 67200 Strasbourg, France.
| | - Elisabeth Luporsi
- Service de génétique, hôpital Femme-Mère-Enfant, CHR de Metz-Thionville, Site de Mercy, 1, allée du Château, 57085 Metz cedex, France.
| | - Marine Osada
- Service de chirurgie, ICANS, avenue Albert-Calmette, 67200 Strasbourg, France; CHRU, avenue Molière, 67200 Strasbourg, France.
| | - Marie Thiblet
- Service de chirurgie, ICANS, avenue Albert-Calmette, 67200 Strasbourg, France; CHRU, avenue Molière, 67200 Strasbourg, France.
| | - Carole Mathelin
- Service de chirurgie, ICANS, avenue Albert-Calmette, 67200 Strasbourg, France; CHRU, avenue Molière, 67200 Strasbourg, France.
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16
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Yan L, Fan E, Tan B. Characteristics of Ovarian Cancer Immune Cell Invasion and Bioinformatics to Predict the Effect of Immunotherapy. Horm Metab Res 2024; 56:197-205. [PMID: 38242159 DOI: 10.1055/a-2231-8475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2024]
Abstract
Recent studies have confirmed that tumor immune cell infiltration (ICI) is associated with sensitivity of ovarian cancer (OC) immunotherapy and disease progression of OC patients. However, studies related to immune infiltration in OC, has not been elucidated. Two algorithms are used to analyze the OC data in the TCGA and GEO databases. After combining the two data sets, the immune cell content of the sample was estimated by Cell-type Identification By Estimate Relative Subsets of RNA Transcripts (CIBERSORT method). An unsupervised consistent clustering algorithm was used to analyze ICI subtypes and their differentially expressed genes (DEGs). Two subgroups and three ICI gene clusters were identified by unsupervised consensus clustering algorithm. The ICI score was obtained by analyzing the gene characteristics through principal component analysis (PCA). The ICI score ranged from -15.8132 to 18.7211, which was associated with the prognosis of OC patients with immunotherapy. The Toll-like receptor pathway, B-cell receptor pathway, antigen processing and presentation pathway, NK-cell-mediated cytotoxicity pathway, and arginine-proline metabolism pathway were activated in the high ICI score group, suggesting that immune cells in the high ICI score group were activated, thus leading to a better prognosis in this group of patients. Patients with G3-G4 in the high ICI rating group were more sensitive to immunotherapy and had a better prognosis in patients with high tumor mutation burden (TMB). This study suggests that ICI scores can be used as a feasible auxiliary indicator for predicting the prognosis of patients with OC.
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Affiliation(s)
- Lingli Yan
- Department of Transfusion Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Erxi Fan
- Department of Ultrasound, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Bin Tan
- Department of Transfusion Medicine, West China Hospital of Sichuan University, Chengdu, China
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17
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Qiu C, Xiang YK, Da XB, Zhang HL, Kong XY, Hou NZ, Zhang C, Tian FZ, Yang YL. Phospholipase A2 enzymes PLA2G2A and PLA2G12B as potential diagnostic and prognostic biomarkers in cholangiocarcinoma. World J Gastrointest Surg 2024; 16:289-306. [PMID: 38463362 PMCID: PMC10921223 DOI: 10.4240/wjgs.v16.i2.289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/19/2023] [Accepted: 01/15/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND Phospholipase A2 (PLA2) enzymes are pivotal in various biological processes, such as lipid mediator production, membrane remodeling, bioenergetics, and maintaining the body surface barrier. Notably, these enzymes play a significant role in the development of diverse tumors. AIM To systematically and comprehensively explore the expression of the PLA2 family genes and their potential implications in cholangiocarcinoma (CCA). METHODS We conducted an analysis of five CCA datasets from The Cancer Genome Atlas and the Gene Expression Omnibus. The study identified differentially expressed genes between tumor tissues and adjacent normal tissues, with a focus on PLA2G2A and PLA2G12B. Gene Set Enrichment Analysis was utilized to pinpoint associated pathways. Moreover, relevant hub genes and microRNAs for PLA2G2A and PLA2G12B were predicted, and their correlation with the prognosis of CCA was evaluated. RESULTS PLA2G2A and PLA2G12B were discerned as differentially expressed in CCA, manifesting significant variations in expression levels in urine and serum between CCA patients and healthy individuals. Elevated expression of PLA2G2A was correlated with poorer overall survival in CCA patients. Additionally, the study delineated pathways and miRNAs associated with these genes. CONCLUSION Our findings suggest that PLA2G2A and PLA2G12B may serve as novel potential diagnostic and prognostic markers for CCA. The increased levels of these genes in biological fluids could be employed as non-invasive markers for CCA, and their expression levels are indicative of prognosis, underscoring their potential utility in clinical settings.
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Affiliation(s)
- Chen Qiu
- Center of Gallbladder Disease, Shanghai East Hospital, Institute of Gallstone Disease, School of Medicine, Tongji University, Shanghai 200092, China
| | - Yu-Kai Xiang
- Center of Gallbladder Disease, Shanghai East Hospital, Institute of Gallstone Disease, School of Medicine, Tongji University, Shanghai 200092, China
| | - Xuan-Bo Da
- Center of Gallbladder Disease, Shanghai East Hospital, Institute of Gallstone Disease, School of Medicine, Tongji University, Shanghai 200092, China
| | - Hong-Lei Zhang
- Center of Gallbladder Disease, Shanghai East Hospital, Institute of Gallstone Disease, School of Medicine, Tongji University, Shanghai 200092, China
| | - Xiang-Yu Kong
- Center of Gallbladder Disease, Shanghai East Hospital, Institute of Gallstone Disease, School of Medicine, Tongji University, Shanghai 200092, China
| | - Nian-Zong Hou
- Center of Gallbladder Disease, Shanghai East Hospital, Institute of Gallstone Disease, School of Medicine, Tongji University, Shanghai 200092, China
| | - Cheng Zhang
- Center of Gallbladder Disease, Shanghai East Hospital, Institute of Gallstone Disease, School of Medicine, Tongji University, Shanghai 200092, China
| | - Fu-Zhou Tian
- General Surgery Center, Chengdu Military General Hospital, Chengdu 610083, Sichuan Province, China
| | - Yu-Long Yang
- Center of Gallbladder Disease, Shanghai East Hospital, Institute of Gallstone Disease, School of Medicine, Tongji University, Shanghai 200092, China
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Yu SH, Kim SS, Kim S, Lee H, Kang TW. FGFR3 Mutations in Urothelial Carcinoma: A Single-Center Study Using Next-Generation Sequencing. J Clin Med 2024; 13:1305. [PMID: 38592174 PMCID: PMC10931944 DOI: 10.3390/jcm13051305] [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: 01/20/2024] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 04/10/2024] Open
Abstract
Background: Mutations of fibroblast growth factor receptor 3 (FGFR3) are associated with urothelial carcinoma (UC) oncogenesis and are considered an important therapeutic target. Therefore, we evaluated the FGFR3 mutation rate and its clinical significance in urothelial carcinoma (UC) using next-generation sequencing. Methods: A total of 123 patients with UC who were treated at Chonnam National University Hospital (Gwang-ju, Korea) from January 2018 to December 2020 were enrolled. We performed NGS using the Oncomine panel with tumor specimens and blood samples corresponding to each specimen. We analyzed the FGFR3 mutation results according to the type of UC and the effects on early recurrence and progression. Results: The mean age of the patients was 71.39 ± 9.33 years, and 103 patients (83.7%) were male. Overall, the FGFR3 mutation rate was 30.1% (37 patients). The FGFR3 mutation rate was the highest in the non-muscle-invasive bladder cancer (NMIBC) group (45.1%), followed by the muscle-invasive bladder cancer (22.7%) and upper tract UC (UTUC) (14.3%) groups. Patients with FGFR3 mutations had a significantly lower disease stage (p = 0.019) but a high-risk of NMIBC (p < 0.001). Conclusions: Our results revealed that FGFR3 mutations were more prevalent in patients with NMIBC and lower stage UC and associated with a high-risk of NMIBC. Large multicenter studies are needed to clarify the clinical significance of FGFR3 mutations in UC.
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Affiliation(s)
- Seong Hyeon Yu
- Department of Urology, Chonnam National University Medical School, Chonnam National University Hospital, Gwangju 61469, Republic of Korea;
| | - Sung sun Kim
- Department of Pathology, Chonnam National University Medical School, Chonnam National University Hospital, Gwangju 61469, Republic of Korea;
| | - Shinseung Kim
- MediCloud Corporation, Hwasun 58128, Republic of Korea; (S.K.); (H.L.)
| | - Hyungki Lee
- MediCloud Corporation, Hwasun 58128, Republic of Korea; (S.K.); (H.L.)
| | - Taek Won Kang
- Department of Urology, Chonnam National University Medical School, Chonnam National University Hospital, Gwangju 61469, Republic of Korea;
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19
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Sun C, España S, Richarz N, Solé-Blanch C, Boada A, Martinez-Cardús A, Chu A, Liu Z, Manzano JL. Targeted therapy or immunotherapy in BRAF-mutated metastatic melanoma: a Spanish center's decade of experience. Front Oncol 2024; 14:1322116. [PMID: 38450188 PMCID: PMC10915752 DOI: 10.3389/fonc.2024.1322116] [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: 10/15/2023] [Accepted: 01/30/2024] [Indexed: 03/08/2024] Open
Abstract
Background Targeted therapies and immunotherapy are currently considered the mainstay first-line treatment for advanced BRAF-mutated melanoma. However, the impact of treatment (targeted therapy and immunotherapy) and the prognostic factors are still not clear. Material and methods Medical records of 140 patients diagnosed with advanced melanoma between 2011 and 2021 were retrospectively reviewed to extract demographic, BRAF status, treatment, performance status, and survival data. ORR, PFS, and OS were compared between patients diagnosed with advanced melanoma and treated with first-line IT or BRAF/MEKi. The prognostic factors were assessed using Cox regression models. Results In all patients and those treated with immunotherapy, we did not find any effect of BRAF status on ORR, PFS, or OS. In patients with BRAF-mutated melanoma, ORR was 43.8% vs. 70% (P=0.04), PFS was 19.2 vs. 11.5 months (p=0.22), and OS was 33.4 vs. 16.4 months for the immunotherapy and targeted therapy groups, respectively (P=0.04). ECOG, presence of brain metastases, and high LDH level from initiation of first-line treatment were all associated with differences in PFS and OS. Conclusion Patients with advanced BRAF-mutated melanoma treated with first-line immunotherapy had a significantly longer PFS and OS than those treated with first-line BRAF/MEKi; however, first-line BRAF/MEKi treatment had a significantly higher ORR than first-line immunotherapy.
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Affiliation(s)
- Chen Sun
- Department of Radiation Oncology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Sofia España
- Medical Oncology Department, Institut Catala d´Oncologia Badalona, Universitari Hospital Germans Trias i Pujol, Badalona-Applied Research Group in Oncology (B-ARGO), Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Nina Richarz
- Dermatology Department, Universitari Hospital Germans Trias i Pujol, Badalona, Spain
| | - Carme Solé-Blanch
- Badalona-Applied Research Group in Oncology (BARGO), Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Aram Boada
- Dermatology Department, Universitari Hospital Germans Trias i Pujol, Germans Trias i Pujol Research Institute, Autonoma University of Barcelona, Badalona, Spain
| | - Anna Martinez-Cardús
- Badalona-Applied Research Group in Oncology (BARGO), Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Alan Chu
- Department of Radiation Oncology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zongwen Liu
- Department of Radiation Oncology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jose Luis Manzano
- Medical Oncology Department, Institut Catala d´Oncologia Badalona, Universitari Hospital Germans Trias i Pujol, Badalona-Applied Research Group in Oncology (B-ARGO), Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
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20
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Canino F, Tornincasa A, Bettelli S, Manfredini S, Barbolini M, Moscetti L, Omarini C, Toss A, Tamburrano F, Antonelli G, Baglio F, Belluzzi L, Martinelli G, Natalizio S, Ponzoni O, Dominici M, Piacentini F. Real-World Data and Clinical Implications of Next-Generation Sequencing (NGS)-Based Analysis in Metastatic Breast Cancer Patients. Int J Mol Sci 2024; 25:2490. [PMID: 38473737 DOI: 10.3390/ijms25052490] [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: 01/16/2024] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024] Open
Abstract
Over the last two decades, the use of Next-Generation Sequencing (NGS) in medical oncology has increased the likelihood of identifying druggable mutations that may be potentially susceptible to targeted treatments. The European Society for Medical Oncology (ESMO) currently does not recommend the use of the NGS test to determine the therapeutic course of patients with metastatic breast cancer (mBC) in daily clinical practice. However, the aim of this work is to evaluate the potential contribution of the NGS test in selecting targeted therapies for patients with mBC. Data were retrospectively collected from 101 patients diagnosed with metastatic breast cancer and treated at the Modena Cancer Center between January 2015 and April 2022. A NGS test was performed on the tumor tissue of each patient at the Laboratory of Molecular Pathology of the University Hospital of Modena. This study analyzed the clinical-pathological characteristics and mutational profile of the population using NGS tests, with a focus on actionable mutations that could be targeted in advanced stages of clinical development. The indicator of this study was to quantify the actionable mutations that resulted in a change of cancer treatment. In total, 101 patients with metastatic breast cancer were analyzed, including 86 with luminal phenotype, 10 who were HER2-positive and 5 who were triple-negative. Median age was 52 years. NGS analysis was conducted on 47 samples of primary breast cancer, 52 on metastatic sites of disease and 2 on liquid biopsies. A total of 85 gene mutations were found. The most common mutations were identified in the PIK3CA (47%), FGFR (19%) and ERBB2 genes (12%), and to a lesser extent in other genes. Of the 61 patients with pathogenic mutations, 46 (75%) had at least one actionable mutation. Of these, nine received treatment with a molecular target drug: eight patients with a mutation of the PIK3CA gene were treated with alpelisib and fulvestrant; one patient with FGFR1/2 amplifications received TAS120. Median PFS for these patients was 3.8 months. The study results show that using the NGS test on cancer tissue of metastatic breast cancer could influence the therapeutic choices, considering the small sample size and limited follow-up. About 9% of the study population had their therapy modified based on the results of NGS. The growing number of detectable mutations and increased accessibility of the test may lead to a greater number of potential therapeutic implications for the NGS assay. Perspectives suggest that NGS analysis can be implemented in daily clinical practice, particularly in contexts where a Molecular Tumor Board (MTB) is active.
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Affiliation(s)
- Fabio Canino
- Division of Medical Oncology, Department of Medical and Surgical Sciences for Children and Adults, University Hospital of Modena, 41124 Modena, Italy
- Gruppo Oncologico Italiano di Ricerca Clinica (GOIRC), 43126 Parma, Italy
| | - Antonio Tornincasa
- Unità Operativa di Oncologia, ASL I dell'Umbria, 06012 Città di Castello, Italy
| | - Stefania Bettelli
- Molecular Pathology and Predictive Medicine, Azienda Ospedaliero, Universitaria Policlinico di Modena, 41124 Modena, Italy
| | - Samantha Manfredini
- Molecular Pathology and Predictive Medicine, Azienda Ospedaliero, Universitaria Policlinico di Modena, 41124 Modena, Italy
| | - Monica Barbolini
- Division of Medical Oncology, Department of Medical and Surgical Sciences for Children and Adults, University Hospital of Modena, 41124 Modena, Italy
- Gruppo Oncologico Italiano di Ricerca Clinica (GOIRC), 43126 Parma, Italy
| | - Luca Moscetti
- Gruppo Oncologico Italiano di Ricerca Clinica (GOIRC), 43126 Parma, Italy
- Division of Medical Oncology, Department of Oncology and Ematology, Azienda Ospedaliero, Universitaria Policlinico di Modena, 41124 Modena, Italy
| | - Claudia Omarini
- Gruppo Oncologico Italiano di Ricerca Clinica (GOIRC), 43126 Parma, Italy
- Division of Medical Oncology, Department of Oncology and Ematology, Azienda Ospedaliero, Universitaria Policlinico di Modena, 41124 Modena, Italy
| | - Angela Toss
- Division of Medical Oncology, Department of Medical and Surgical Sciences for Children and Adults, University Hospital of Modena, 41124 Modena, Italy
| | - Fabio Tamburrano
- Division of Medical Oncology, Department of Medical and Surgical Sciences for Children and Adults, University Hospital of Modena, 41124 Modena, Italy
| | - Giuseppina Antonelli
- Division of Medical Oncology, Department of Medical and Surgical Sciences for Children and Adults, University Hospital of Modena, 41124 Modena, Italy
| | - Federica Baglio
- Division of Medical Oncology, Department of Medical and Surgical Sciences for Children and Adults, University Hospital of Modena, 41124 Modena, Italy
| | - Lorenzo Belluzzi
- Division of Medical Oncology, Department of Medical and Surgical Sciences for Children and Adults, University Hospital of Modena, 41124 Modena, Italy
| | - Giulio Martinelli
- Division of Medical Oncology, Department of Medical and Surgical Sciences for Children and Adults, University Hospital of Modena, 41124 Modena, Italy
- Gruppo Oncologico Italiano di Ricerca Clinica (GOIRC), 43126 Parma, Italy
| | - Salvatore Natalizio
- Division of Medical Oncology, Department of Medical and Surgical Sciences for Children and Adults, University Hospital of Modena, 41124 Modena, Italy
| | - Ornella Ponzoni
- Division of Medical Oncology, Department of Medical and Surgical Sciences for Children and Adults, University Hospital of Modena, 41124 Modena, Italy
| | - Massimo Dominici
- Division of Medical Oncology, Department of Medical and Surgical Sciences for Children and Adults, University Hospital of Modena, 41124 Modena, Italy
| | - Federico Piacentini
- Division of Medical Oncology, Department of Medical and Surgical Sciences for Children and Adults, University Hospital of Modena, 41124 Modena, Italy
- Gruppo Oncologico Italiano di Ricerca Clinica (GOIRC), 43126 Parma, Italy
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21
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Zhao JY, He YX, Wu ML, Wang RQ. The application of high-throughput sequencing technology in corneal diseases. Int Ophthalmol 2024; 44:53. [PMID: 38340174 PMCID: PMC10858842 DOI: 10.1007/s10792-024-03049-1] [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: 04/27/2023] [Accepted: 01/18/2024] [Indexed: 02/12/2024]
Abstract
High-throughput sequencing technology, also known as next-generation sequencing technology, can explore new biomarkers and specific gene mutations. It has a pivotal role in promoting the gene research, which can limit the detection area, lessen the time needed for sequencing. Also, it can quickly screen out the suspected pathogenic genes of patients, gain the necessary genetic data, and provide the basis for clinical diagnosis and genetic counseling. In the research of corneal diseases, through the DNA sequencing of patients' diseased cells, it can provide a deeper understanding of corneal diseases and improve the diagnosis, classification and treatment alternatives of various corneal diseases. This article will introduce the application progress of high-throughput sequencing technology in corneal diseases, which will help to understand the application of this technology in various corneal diseases.
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Affiliation(s)
- Jing Yi Zhao
- The Second Clinical Medical College of Jilin University, Changchun, 130012, Jilin, China
| | - Yu Xi He
- The Eye Center, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China
| | - Mei Liang Wu
- The Eye Center, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China
| | - Rui Qing Wang
- The Eye Center, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China.
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22
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Bayle A, Marino P, Baffert S, Margier J, Bonastre J. [Cost of high-throughput sequencing (NGS) technologies: Literature review and insights]. Bull Cancer 2024; 111:190-198. [PMID: 37852801 DOI: 10.1016/j.bulcan.2023.08.013] [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: 03/21/2023] [Revised: 08/02/2023] [Accepted: 08/28/2023] [Indexed: 10/20/2023]
Abstract
Although high-throughput sequencing technologies (Next-Generation Sequencing [NGS]) are revolutionizing medicine, the estimation of their production cost for pricing/tariffication by health systems raises methodological questions. The objective of this review of cost studies of high-throughput sequencing techniques is to draw lessons for producing robust cost estimates of these techniques. We analyzed, using an eleven item analysis framework, micro-costing studies of high-throughput sequencing technologies (n=17), including two studies conducted in the French context. The factors of variability between the studies that we identified were temporality (early evaluation of the innovation vs. evaluation of a mature technology), the choice of cost evaluation method (scope, micro- vs. gross-costing technique), the choice of production steps observed and the transposability of these studies. The lessons we have learned are that it is necessary to have a comprehensive vision of the sequencing production process by integrating all the steps from the collection of the biological sample to the delivery of the result to the clinician. It is also important to distinguish between what refers to the local context and what refers to the general context, by favouring the use of mixed methods to calculate costs. Finally, sensitivity analyses and periodic re-estimation of the costs of the techniques must be carried out in order to be able to revise the tariffs according to changes linked to the diffusion of the technology and to competition between reagent suppliers.
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Affiliation(s)
- Arnaud Bayle
- Gustave-Roussy, université Paris-Saclay, bureau biostatistique et épidémiologie, Villejuif, France; Inserm, université Paris-Saclay, CESP U1018 Oncostat, labelisé Ligue contre le cancer, Villejuif, France.
| | - Patricia Marino
- Institut Paoli-Calmettes, SESSTIM, équipe CAN-BIOS, Marseille, France
| | | | - Jennifer Margier
- Hospices civils de Lyon, service d'évaluation économique en santé (SEES), Lyon, France
| | - Julia Bonastre
- Gustave-Roussy, université Paris-Saclay, bureau biostatistique et épidémiologie, Villejuif, France; Inserm, université Paris-Saclay, CESP U1018 Oncostat, labelisé Ligue contre le cancer, Villejuif, France
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23
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Malgundkar SH, Tamimi Y. The pivotal role of long non-coding RNAs as potential biomarkers and modulators of chemoresistance in ovarian cancer (OC). Hum Genet 2024; 143:107-124. [PMID: 38276976 DOI: 10.1007/s00439-023-02635-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024]
Abstract
Ovarian cancer (OC) is a fatal gynecological disease that is often diagnosed at later stages due to its asymptomatic nature and the absence of efficient early-stage biomarkers. Previous studies have identified genes with abnormal expression in OC that couldn't be explained by methylation or mutation, indicating alternative mechanisms of gene regulation. Recent advances in human transcriptome studies have led to research on non-coding RNAs (ncRNAs) as regulators of cancer gene expression. Long non-coding RNAs (lncRNAs), a class of ncRNAs with a length greater than 200 nucleotides, have been identified as crucial regulators of physiological processes and human diseases, including cancer. Dysregulated lncRNA expression has also been found to play a crucial role in ovarian carcinogenesis, indicating their potential as novel and non-invasive biomarkers for improving OC management. However, despite the discovery of several thousand lncRNAs, only one has been approved for clinical use as a biomarker in cancer, highlighting the importance of further research in this field. In addition to their potential as biomarkers, lncRNAs have been implicated in modulating chemoresistance, a major problem in OC. Several studies have identified altered lncRNA expression upon drug treatment, further emphasizing their potential to modulate chemoresistance. In this review, we highlight the characteristics of lncRNAs, their function, and their potential to serve as tumor markers in OC. We also discuss a few databases providing detailed information on lncRNAs in various cancer types. Despite the promising potential of lncRNAs, further research is necessary to fully understand their role in cancer and develop effective strategies to combat this devastating disease.
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Affiliation(s)
- Shika Hanif Malgundkar
- Biochemistry Department, College of Medicine and Health Sciences, Sultan Qaboos University, PC 123, PO Box 35, Muscat, Sultanate of Oman
| | - Yahya Tamimi
- Biochemistry Department, College of Medicine and Health Sciences, Sultan Qaboos University, PC 123, PO Box 35, Muscat, Sultanate of Oman.
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24
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Wang JZ, Yuan D, Yang XH, Sun CH, Hou LL, Zhang Y, Gao YX. Etiology of lower respiratory tract in pneumonia based on metagenomic next-generation sequencing: a retrospective study. Front Cell Infect Microbiol 2024; 13:1291980. [PMID: 38264726 PMCID: PMC10803656 DOI: 10.3389/fcimb.2023.1291980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 12/13/2023] [Indexed: 01/25/2024] Open
Abstract
Introduction Pneumonia are the leading cause of death worldwide, and antibiotic treatment remains fundamental. However, conventional sputum smears or cultures are still inefficient for obtaining pathogenic microorganisms.Metagenomic next-generation sequencing (mNGS) has shown great value in nucleic acid detection, however, the NGS results for lower respiratory tract microorganisms are still poorly studied. Methods This study dealt with investigating the efficacy of mNGS in detecting pathogens in the lower respiratory tract of patients with pulmonary infections. A total of 112 patients admitted at the First Affiliated Hospital of Zhengzhou University between April 30, 2018, and June 30, 2020, were enrolled in this retrospective study. The bronchoalveolar lavage fluid (BALF) was obtained from lower respiratory tract from each patient. Routine methods (bacterial smear and culture) and mNGS were employed for the identification of pathogenic microorganisms in BALF. Results The average patient age was 53.0 years, with 94.6% (106/112) obtaining pathogenic microorganism results. The total mNGS detection rate of pathogenic microorganisms significantly surpassed conventional methods (93.7% vs. 32.1%, P < 0.05). Notably, 75% of patients (84/112) were found to have bacteria by mNGS, but only 28.6% (32/112) were found to have bacteria by conventional approaches. The most commonly detected bacteria included Acinetobacter baumannii (19.6%), Klebsiella pneumoniae (17.9%), Pseudomonas aeruginosa (14.3%), Staphylococcus faecium (12.5%), Enterococcus faecium (12.5%), and Haemophilus parainfluenzae (11.6%). In 29.5% (33/112) of patients, fungi were identified using mNGS, including 23 cases of Candida albicans (20.5%), 18 of Pneumocystis carinii (16.1%), and 10 of Aspergillus (8.9%). However, only 7.1 % (8/112) of individuals were found to have fungi when conventional procedures were used. The mNGS detection rate of viruses was significantly higher than the conventional method rate (43.8% vs. 0.9%, P < 0.05). The most commonly detected viruses included Epstein-Barr virus (15.2%), cytomegalovirus (13.4%), circovirus (8.9%), human coronavirus (4.5%), and rhinovirus (4.5%). Only 29.4% (33/112) of patients were positive, whereas 5.4% (6/112) of patients were negative for both detection methods as shown by Kappa analysis, indicating poor consistency between the two methods (P = 0.340; Kappa analysis). Conclusion Significant benefits of mNGS have been shown in the detection of pathogenic microorganisms in patients with pulmonary infection. For those with suboptimal therapeutic responses, mNGS can provide an etiological basis, aiding in precise anti-infective treatment.
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Affiliation(s)
- Jin-zhu Wang
- Emergency Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Emergency and Critical Care Center, Intensive Care Unit, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Ding Yuan
- Emergency Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xiang-hong Yang
- Emergency and Critical Care Center, Intensive Care Unit, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Chang-hua Sun
- Emergency Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lin-lin Hou
- Emergency Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yan Zhang
- Emergency Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yan-xia Gao
- Emergency Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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25
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Friedrich B, Vindrola-Padros C, Lucassen AM, Patch C, Clarke A, Lakhanpaul M, Lewis C. "A very big challenge": a qualitative study to explore the early barriers and enablers to implementing a national genomic medicine service in England. Front Genet 2024; 14:1282034. [PMID: 38239852 PMCID: PMC10794539 DOI: 10.3389/fgene.2023.1282034] [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: 08/23/2023] [Accepted: 11/27/2023] [Indexed: 01/22/2024] Open
Abstract
Background: The Genomic Medicine Service (GMS) was launched in 2018 in England to create a step-change in the use of genomics in the NHS, including offering whole genome sequencing (WGS) as part of routine care. In this qualitative study on pediatric rare disease diagnosis, we used an implementation science framework to identify enablers and barriers which have influenced rollout. Methods: Semi-structured interviews were conducted with seven participants tasked with designing the GMS and 14 tasked with leading the implementation across the seven Genomic Medicine Service Alliances (GMSAs) and/or Genomic Laboratory Hubs (GLHs) between October 2021 and February 2022. Results: Overall, those involved in delivering the service strongly support its aims and ambitions. Challenges include: 1) concerns around the lack of trained and available workforce (clinicians and scientists) to seek consent from patients, interpret findings and communicate results; 2) the lack of a digital, coordinated infrastructure in place to support and standardize delivery with knock-on effects including onerous administrative aspects required to consent patients and order WGS tests; 3) that the "mainstreaming agenda", whilst considered important, encountered reluctance to become engaged from those who did not see it as a priority or viewed it as being politically rather than clinically driven; 4) the timelines and targets set for the GMS were perceived by some as too ambitious. Interviewees discussed local adaptations and strategies employed to address the various challenges they had encountered, including 1) capacity-building, 2) employing genomic associates and other support staff to support the consent and test ordering process, 3) having "genomic champions" embedded in mainstream services to impart knowledge and best practice, 4) enhancing collaboration between genetic and mainstream specialties, 5) building evaluation into the service and 6) co-creating services with patients and the public. Conclusion: Our findings highlight the challenges of implementing system-wide change within a complex healthcare system. Local as well as national solutions can undoubtedly address many of these barriers over time.
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Affiliation(s)
- Bettina Friedrich
- Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Cecilia Vindrola-Padros
- Department of Targeted Intervention and Rapid Research Evaluation and Appraisal Lab (RREAL), University College London, London, United Kingdom
| | - Anneke M. Lucassen
- Clinical Ethics and Law, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Centre for Personalised Medicine, The Wellcome Centre for Human Genetics, Oxford, United Kingdom
| | - Chris Patch
- Engagement and Society, Wellcome Connecting Science Wellcome Genome Campus, Hinxton, United Kingdom
| | - Angus Clarke
- Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Monica Lakhanpaul
- Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Celine Lewis
- Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
- London North Genomic Laboratory Hub, London, United Kingdom
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26
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Diamantopoulos MA, Georgoulia KK, Levis P, Kotronopoulos G, Stravodimos K, Kontos CK, Avgeris M, Scorilas A. 28S rRNA-Derived Fragments Represent an Independent Molecular Predictor of Short-Term Relapse in Prostate Cancer. Int J Mol Sci 2023; 25:239. [PMID: 38203408 PMCID: PMC10779029 DOI: 10.3390/ijms25010239] [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: 11/28/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Prostate cancer (PCa) is a global health concern, being a leading cause of cancer-related mortality among males. Early detection and accurate prognosis are crucial for effective management. This study delves into the diagnostic and prognostic potential of 28S rRNA-derived fragments (rRFs) in PCa. Total RNA extracted from 89 PCa and 53 benign prostate hyperplasia (BPH) tissue specimens. After 3'-end polyadenylation, we performed reverse transcription to create first-strand cDNA. Using an in-house quantitative real-time PCR (qPCR) assay, we quantified 28S rRF levels. Post-treatment biochemical relapse served as the clinical endpoint event for survival analysis, which we validated internally through bootstrap analysis. Our results revealed downregulated 28S rRF levels in PCa compared to BPH patients. Additionally, we observed a significant positive correlation between 28S rRF levels and higher Gleason scores and tumor stages. Furthermore, PCa patients with elevated 28S rRF expression had a significantly higher risk of post-treatment disease relapse independently of clinicopathological data. In conclusion, our study demonstrates, for the first time, the prognostic value of 28S rRF in prostate adenocarcinoma. Elevated 28S rRF levels independently predict short-term PCa relapse and enhance risk stratification. This establishes 28S rRF as a potential novel molecular marker for PCa prognosis.
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Affiliation(s)
- Marios A. Diamantopoulos
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701 Athens, Greece; (M.A.D.); (K.K.G.); (C.K.K.); (M.A.)
| | - Konstantina K. Georgoulia
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701 Athens, Greece; (M.A.D.); (K.K.G.); (C.K.K.); (M.A.)
| | - Panagiotis Levis
- First Department of Urology, “Laiko” General Hospital, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece; (P.L.); (G.K.); (K.S.)
| | - Georgios Kotronopoulos
- First Department of Urology, “Laiko” General Hospital, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece; (P.L.); (G.K.); (K.S.)
| | - Konstantinos Stravodimos
- First Department of Urology, “Laiko” General Hospital, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece; (P.L.); (G.K.); (K.S.)
| | - Christos K. Kontos
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701 Athens, Greece; (M.A.D.); (K.K.G.); (C.K.K.); (M.A.)
| | - Margaritis Avgeris
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701 Athens, Greece; (M.A.D.); (K.K.G.); (C.K.K.); (M.A.)
- Laboratory of Clinical Biochemistry-Molecular Diagnostics, Second Department of Pediatrics, “P. & A. Kyriakou” Children’s Hospital, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701 Athens, Greece; (M.A.D.); (K.K.G.); (C.K.K.); (M.A.)
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Di Rado S, Giansante R, Cicirelli M, Pilenzi L, Dell’Elice A, Anaclerio F, Rimoldi M, Grassadonia A, Grossi S, Canale N, Ballerini P, Stuppia L, Antonucci I. Detection of Germline Mutations in a Cohort of 250 Relatives of Mutation Carriers in Multigene Panel: Impact of Pathogenic Variants in Other Genes beyond BRCA1/2. Cancers (Basel) 2023; 15:5730. [PMID: 38136276 PMCID: PMC10741895 DOI: 10.3390/cancers15245730] [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: 10/13/2023] [Revised: 11/20/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND Several hereditary-familial syndromes associated with various types of tumors have been identified to date, evidencing that hereditary cancers caused by germline mutations account for 5-10% of all tumors. Advances in genetic technology and the implementation of Next-Generation Sequencing (NGS) have accelerated the discovery of several susceptibility cancer genes, allowing for the detection of cancer-predisposing mutations in a larger number of cases. The aim of this study is to highlight how the application of an NGS-multigene panel to a group of oncological patients subsequently leads to improvement in the identification of carriers of healthy pathogenic variants/likely pathogenic variants (PVs/LPVs) and prevention of the disease in these cases. METHODS Starting from a total of 110 cancer patients carrying PVs/LPVs in genes involved in cancer susceptibility detected via a customized NGS panel of 27 cancer-associated genes, we enrolled 250 healthy collateral family members from January 2020 to July 2022. The specific PVs/LPVs identified in each proband were tested in healthy collateral family members via Sanger sequencing. RESULTS A total of 131 out of the 250 cases (52%) were not carriers of the mutation detected in the affected relative, while 119 were carriers. Of these, 81/250 patients carried PVs/LPVs on BRCA1/2 (33%), 35/250 harbored PVs/LPVs on other genes beyond BRCA1 and BRCA2 (14%), and 3/250 (1%) were PVs/LPVs carriers both on BRCA1/2 and on another susceptibility gene. CONCLUSION Our results show that the analysis of BRCA1/2 genes would have only resulted in a missed diagnosis in a number of cases and in the lack of prevention of the disease in a considerable percentage of healthy carriers with a genetic mutation (14%).
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Affiliation(s)
- Sara Di Rado
- Center for Advanced Studies and Technology (CAST), “G. D’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy; (S.D.R.); (R.G.); (M.C.); (L.P.); (F.A.); (A.G.); (P.B.); (L.S.); (I.A.)
| | - Roberta Giansante
- Center for Advanced Studies and Technology (CAST), “G. D’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy; (S.D.R.); (R.G.); (M.C.); (L.P.); (F.A.); (A.G.); (P.B.); (L.S.); (I.A.)
- Department of Medical Genetics, “G. D’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy
| | - Michela Cicirelli
- Center for Advanced Studies and Technology (CAST), “G. D’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy; (S.D.R.); (R.G.); (M.C.); (L.P.); (F.A.); (A.G.); (P.B.); (L.S.); (I.A.)
- Department of Medical Genetics, “G. D’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy
| | - Lucrezia Pilenzi
- Center for Advanced Studies and Technology (CAST), “G. D’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy; (S.D.R.); (R.G.); (M.C.); (L.P.); (F.A.); (A.G.); (P.B.); (L.S.); (I.A.)
| | - Anastasia Dell’Elice
- Center for Advanced Studies and Technology (CAST), “G. D’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy; (S.D.R.); (R.G.); (M.C.); (L.P.); (F.A.); (A.G.); (P.B.); (L.S.); (I.A.)
| | - Federico Anaclerio
- Center for Advanced Studies and Technology (CAST), “G. D’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy; (S.D.R.); (R.G.); (M.C.); (L.P.); (F.A.); (A.G.); (P.B.); (L.S.); (I.A.)
| | - Martina Rimoldi
- SD Genetica Medica, IRCCS Fondazione Ca’Granda Ospedale Maggiore Policlinico, 20122 Milano, Italy;
| | - Antonino Grassadonia
- Center for Advanced Studies and Technology (CAST), “G. D’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy; (S.D.R.); (R.G.); (M.C.); (L.P.); (F.A.); (A.G.); (P.B.); (L.S.); (I.A.)
- Department of Innovative Technologies in Medicine and Dentistry, “G. D’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy
| | - Simona Grossi
- U.O.C. Chirurgia Generale ad Indirizzo Senologico, Eusoma Breast Center ASL2 Abruzzo, 66026 Ortona, Italy; (S.G.); (N.C.)
| | - Nicole Canale
- U.O.C. Chirurgia Generale ad Indirizzo Senologico, Eusoma Breast Center ASL2 Abruzzo, 66026 Ortona, Italy; (S.G.); (N.C.)
| | - Patrizia Ballerini
- Center for Advanced Studies and Technology (CAST), “G. D’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy; (S.D.R.); (R.G.); (M.C.); (L.P.); (F.A.); (A.G.); (P.B.); (L.S.); (I.A.)
| | - Liborio Stuppia
- Center for Advanced Studies and Technology (CAST), “G. D’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy; (S.D.R.); (R.G.); (M.C.); (L.P.); (F.A.); (A.G.); (P.B.); (L.S.); (I.A.)
| | - Ivana Antonucci
- Center for Advanced Studies and Technology (CAST), “G. D’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy; (S.D.R.); (R.G.); (M.C.); (L.P.); (F.A.); (A.G.); (P.B.); (L.S.); (I.A.)
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Li B, Chen X, Xian H, Wen Q, Wang T. Gene mutation analysis of oral submucous fibrosis cancerization in Hainan Island. PeerJ 2023; 11:e16392. [PMID: 38050610 PMCID: PMC10693820 DOI: 10.7717/peerj.16392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/11/2023] [Indexed: 12/06/2023] Open
Abstract
Objective The sequencing panel composed of 61 target genes was used to explore the related mutation genes of oral squamous cell carcinoma (OSCC) and oral submucous fibrosis (OSF) cancerization, so as to provide a theoretical basis for the early diagnosis of oral submucous fibrosis cancerization, find the most important mutations in OSF cancerization, and more targeted prevention of OSF cancerization. Methods A total of 74 clinically diagnosed samples were included, including 36 cases of OSCC and 38 cases of OSF cancer patients. DNA was extracted, and targeted gene panel sequencing technology was used to analyze the gene frequency of pathogenic mutation sites in clinical samples. Results Gene panel sequencing analysis showed that there were 69 mutations in 18 genes in OSCC and OSF cancerous specimens. The results of gene panel sequencing were screened, and 18 mutant genes were finally screened out and their mutation frequencies in the samples were analyzed. According to the frequency of gene mutations from high to low, they were TP53, FLT4, PIK3CA, CDKN2A, FGFR4, HRAS, BRCA1, PTPN11, NF1, KMT2A, RB1, PTEN, MSH2, MLH1, KMT2D, FLCN, BRCA2, APC. The mutation frequency of FLT4 gene was significantly higher than that of OSCC group (P < 0.05). Conclusion FLT4 gene may be related to OSF cancerization and is expected to be an early diagnostic biomarker for OSF cancerization.
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Affiliation(s)
- Bingxia Li
- Department of stomatology, Hainan General Hospital, Haikou, China
- The Affiliated Hainan Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Xinyu Chen
- College of Stomatology, Hospital of Stomatology, Guangxi Medical University, Nanning, Guangxi, China
| | - Haiyu Xian
- Department of stomatology, Hainan General Hospital, Haikou, China
- The Affiliated Hainan Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Qitao Wen
- Department of stomatology, Hainan General Hospital, Haikou, China
- The Affiliated Hainan Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Tao Wang
- Department of stomatology, Hainan General Hospital, Haikou, China
- The Affiliated Hainan Hospital of Hainan Medical University, Haikou, Hainan, China
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Crespo-Lopez ME, Barthelemy JL, Lopes-Araújo A, Santos-Sacramento L, Leal-Nazaré CG, Soares-Silva I, Macchi BM, do Nascimento JLM, Arrifano GDP, Augusto-Oliveira M. Revisiting Genetic Influence on Mercury Exposure and Intoxication in Humans: A Scoping Review. TOXICS 2023; 11:967. [PMID: 38133368 PMCID: PMC10747380 DOI: 10.3390/toxics11120967] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/21/2023] [Accepted: 11/26/2023] [Indexed: 12/23/2023]
Abstract
Human intoxication to mercury is a worldwide health problem. In addition to the type and length of exposure, the genetic background plays an important role in mercury poisoning. However, reviews on the genetic influence in mercury toxicity are scarce and not systematic. Therefore, this review aimed to systematically overview the most recent evidence on the genetic influence (using single nucleotide polymorphisms, SNPs) on human mercury poisoning. Three different databases (PubMed/Medline, Web of Science and Scopus) were searched, and 380 studies were found that were published from 2015 to 2022. After applying inclusion/exclusion criteria, 29 studies were selected and data on characteristics (year, country, profile of participants) and results (mercury biomarkers and quantitation, SNPs, main findings) were extracted and analyzed. The largest number of studies was performed in Brazil, mainly involving traditional populations of the Tapajós River basin. Most studies evaluated the influence of the SNPs related to genes of the glutathione system (GST, GPx, etc.), the ATP-binding cassette transporters and the metallothionein proteins. The recent findings regarding other SNPs, such as those of apolipoprotein E and brain-derived neurotrophic factor genes, are also highlighted. The importance of the exposure level is discussed considering the possible biphasic behavior of the genetic modulation phenomena that could explain some SNP associations. Overall, recommendations are provided for future studies based on the analysis obtained in this scoping review.
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Affiliation(s)
- Maria Elena Crespo-Lopez
- Laboratório de Farmacologia Molecular, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil (L.S.-S.); (C.G.L.-N.)
| | - Jean Ludger Barthelemy
- Laboratório de Farmacologia Molecular, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil (L.S.-S.); (C.G.L.-N.)
| | - Amanda Lopes-Araújo
- Laboratório de Farmacologia Molecular, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil (L.S.-S.); (C.G.L.-N.)
| | - Leticia Santos-Sacramento
- Laboratório de Farmacologia Molecular, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil (L.S.-S.); (C.G.L.-N.)
| | - Caio Gustavo Leal-Nazaré
- Laboratório de Farmacologia Molecular, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil (L.S.-S.); (C.G.L.-N.)
| | - Isabela Soares-Silva
- Laboratório de Farmacologia Molecular, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil (L.S.-S.); (C.G.L.-N.)
| | - Barbarella M. Macchi
- Laboratório de Neuroquímica Molecular e Celular, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil (J.L.M.d.N.)
| | - José Luiz M. do Nascimento
- Laboratório de Neuroquímica Molecular e Celular, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil (J.L.M.d.N.)
| | - Gabriela de Paula Arrifano
- Laboratório de Farmacologia Molecular, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil (L.S.-S.); (C.G.L.-N.)
| | - Marcus Augusto-Oliveira
- Laboratório de Farmacologia Molecular, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil (L.S.-S.); (C.G.L.-N.)
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30
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Xiao H, Hu L, Tan Q, Jia J, Xie P, Li J, Wang M. Transcriptional profiles reveal histologic origin and prognosis across 33 The Cancer Genome Atlas tumor types. Transl Cancer Res 2023; 12:2764-2780. [PMID: 37969389 PMCID: PMC10643977 DOI: 10.21037/tcr-23-234] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/18/2023] [Indexed: 11/17/2023]
Abstract
Background In recent years, with the development of transcriptome sequencing, the molecular characteristics of tumors are gradually revealed. Because of the complexity of tumor transcriptome, there is a need to look for the molecular signatures which can be used to evaluate the tissue origin and cell stemness of tumors in order to promote the diagnosis and treatment of tumors. Methods Tumor tissue-specific gene sets (TTSGs) consisting of 200 genes were selected using RNA expression data of 9,875 patients from 33 tumor types. t-distributed Stochastic Neighbor Embedding (t-SNE) was used for dimensionality reduction and visualization of TTSGs in each tumor type. To evaluate oncogenic dedifferentiation and loss of cell stemness, Euclidean distance from each sample to a human embryo single-cell RNA-seq dataset (GSE36552) of TTSGs was calculated as TTSGs index indicating dissimilarity of tumors and embryo. TTSGs index was evaluated for prognosis in each tumor type. Two published signature indexes, the mRNA signature index (mRNAsi) and CIBERSORT, were compared to assess the correlation between the TTSGs index with cell stemness and immune microenvironment. Finally, the difference of prognosis, immune microenvironment and radiotherapy outcomes were compared between patients with high and low TTSGs index. Results In this study, all 33 tumor types in The Cancer Genome Atlas (TCGA) were embedded into isolated clusters by t-SNE and confirmed by k-nearest neighbors (kNN) algorithm. Clusters of squamous-cell carcinoma were adjacent to each other revealing similar histologic origin. Basal-like breast cancer was separated from luminal and HER-2-amplified subtypes and closed to squamous-cell carcinoma. TTSGs index was related to overall survival outcomes in cancers derived from liver, thyroid, brain, cervical and kidney. There was a positive correlation between mRNAsi and TTSGs index in pan-kidney and pan-neuronal cancers. Furthermore, cell fractions of M2 macrophages and total leukocytes increased in the group with higher TTSGs index. Patients with higher TTSGs index had longer overall survival time and less radiation therapy resistance compared to patients with lower TTSGs index. Conclusions The signature of TTSGs is related to tumor expression features that distinguish tumors of different histologic origin using t-SNE. The signature also relates to prognosis of certain kinds of tumors.
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Affiliation(s)
- Hui Xiao
- Department of Pathology, The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Shenzhen & Longgang District People’s Hospital of Shenzhen, Shenzhen, China
| | - Liang Hu
- Central Laboratory, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City, Shenzhen, China
| | - Qi Tan
- Department of Pathology, The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Shenzhen & Longgang District People’s Hospital of Shenzhen, Shenzhen, China
| | - Jinping Jia
- Department of Pathology, The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Shenzhen & Longgang District People’s Hospital of Shenzhen, Shenzhen, China
| | - Ping Xie
- Department of Pathology, The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Shenzhen & Longgang District People’s Hospital of Shenzhen, Shenzhen, China
| | - Junai Li
- Department of Pathology, The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Shenzhen & Longgang District People’s Hospital of Shenzhen, Shenzhen, China
| | - Minghua Wang
- Department of Pathology, The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Shenzhen & Longgang District People’s Hospital of Shenzhen, Shenzhen, China
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Stout LA, Hunter C, Schroeder C, Kassem N, Schneider BP. Clinically significant germline pathogenic variants are missed by tumor genomic sequencing. NPJ Genom Med 2023; 8:30. [PMID: 37833309 PMCID: PMC10575977 DOI: 10.1038/s41525-023-00374-9] [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: 05/24/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
A germline pathogenic variant may be present even if the results of tumor genomic sequencing do not suggest one. There are key differences in the assay design and reporting of variants between germline and somatic laboratories. When appropriate, both tests should be completed to aid in therapy decisions and determining optimal screening and risk-reduction interventions.
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Affiliation(s)
- Leigh Anne Stout
- Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana University Health Precision Genomics, Indianapolis, IN, USA
| | - Cynthia Hunter
- Indiana University Health Precision Genomics, Indianapolis, IN, USA
| | | | - Nawal Kassem
- Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana University Health Precision Genomics, Indianapolis, IN, USA
| | - Bryan P Schneider
- Indiana University School of Medicine, Indianapolis, IN, USA.
- Indiana University Health Precision Genomics, Indianapolis, IN, USA.
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32
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Yu SH, Kim SS, Lee H, Kim S, Kang TW. Somatic Mutation of the Non-Muscle-Invasive Bladder Cancer Associated with Early Recurrence. Diagnostics (Basel) 2023; 13:3201. [PMID: 37892022 PMCID: PMC10606398 DOI: 10.3390/diagnostics13203201] [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: 08/23/2023] [Revised: 09/29/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Next-generation sequencing (NGS) is widely used in muscle-invasive bladder cancer but has limited use in non-muscle-invasive bladder cancer (NMIBC) due to significant heterogeneity and high cancer-specific survival. Therefore, we evaluated the genomic information of NMIBC and identified molecular alterations associated with tumour recurrence. A total of 43 patients with NMIBC who underwent transurethral resection of the bladder were enrolled. We performed NGS using an Oncomine panel of tumour specimens and blood samples corresponding to each specimen. The somatic mutation results were analysed by pairwise comparison and logistic regression according to the recurrence of bladder tumours within 1 year. The median incidence of genetic variations in 43 tumour samples was 56 variations per sample, and a high tumour mutation burden (TMB) was associated with tumour recurrence (median variation 33 vs. 64, p = 0.023). The most mutated gene was adipose tissue macrophages (ATM) (79%), followed by neurofibromatosis-1 (NF1) (79%), and neurogenic locus notch homolog protein 1 (NOTCH1) (79%). In multivariable analysis, mutation of epidermal growth factor receptor (EGFR) (odds ratio [OR], 9.95; 95% confidence interval [CI], 1.40-70.96; p = 0.022) and telomerase reverse transcriptase (TERT) (OR, 7.92; 95% CI, 1.22-51.51; p = 0.030) were significant factors associated with the recurrence of bladder tumour within 1 year. Our results revealed that high TMB, EGFR mutation, and TERT mutation had a significant association with tumour recurrence in NMIBC. In addition, somatic mutations in EGFR and TERT could be useful prognostic biomarkers in NMIBC.
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Affiliation(s)
- Seong Hyeon Yu
- Department of Urology, Chonnam National University Medical School, Chonnam National University Hospital, Gwangju 61469, Republic of Korea;
| | - Sung Sun Kim
- Department of Pathology, Chonnam National University Medical School, Chonnam National University Hospital, Gwangju 61469, Republic of Korea;
| | - Hyungki Lee
- MediCloud Corporation, Hwasun 58128, Republic of Korea; (H.L.); (S.K.)
| | - Shinseung Kim
- MediCloud Corporation, Hwasun 58128, Republic of Korea; (H.L.); (S.K.)
| | - Taek Won Kang
- Department of Urology, Chonnam National University Medical School, Chonnam National University Hospital, Gwangju 61469, Republic of Korea;
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33
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Davidson AL, Dressel U, Norris S, Canson DM, Glubb DM, Fortuno C, Hollway GE, Parsons MT, Vidgen ME, Holmes O, Koufariotis LT, Lakis V, Leonard C, Wood S, Xu Q, McCart Reed AE, Pickett HA, Al-Shinnag MK, Austin RL, Burke J, Cops EJ, Nichols CB, Goodwin A, Harris MT, Higgins MJ, Ip EL, Kiraly-Borri C, Lau C, Mansour JL, Millward MW, Monnik MJ, Pachter NS, Ragunathan A, Susman RD, Townshend SL, Trainer AH, Troth SL, Tucker KM, Wallis MJ, Walsh M, Williams RA, Winship IM, Newell F, Tudini E, Pearson JV, Poplawski NK, Mar Fan HG, James PA, Spurdle AB, Waddell N, Ward RL. The clinical utility and costs of whole-genome sequencing to detect cancer susceptibility variants-a multi-site prospective cohort study. Genome Med 2023; 15:74. [PMID: 37723522 PMCID: PMC10507925 DOI: 10.1186/s13073-023-01223-1] [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: 10/04/2022] [Accepted: 08/18/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND Many families and individuals do not meet criteria for a known hereditary cancer syndrome but display unusual clusters of cancers. These families may carry pathogenic variants in cancer predisposition genes and be at higher risk for developing cancer. METHODS This multi-centre prospective study recruited 195 cancer-affected participants suspected to have a hereditary cancer syndrome for whom previous clinical targeted genetic testing was either not informative or not available. To identify pathogenic disease-causing variants explaining participant presentation, germline whole-genome sequencing (WGS) and a comprehensive cancer virtual gene panel analysis were undertaken. RESULTS Pathogenic variants consistent with the presenting cancer(s) were identified in 5.1% (10/195) of participants and pathogenic variants considered secondary findings with potential risk management implications were identified in another 9.7% (19/195) of participants. Health economic analysis estimated the marginal cost per case with an actionable variant was significantly lower for upfront WGS with virtual panel ($8744AUD) compared to standard testing followed by WGS ($24,894AUD). Financial analysis suggests that national adoption of diagnostic WGS testing would require a ninefold increase in government annual expenditure compared to conventional testing. CONCLUSIONS These findings make a case for replacing conventional testing with WGS to deliver clinically important benefits for cancer patients and families. The uptake of such an approach will depend on the perspectives of different payers on affordability.
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Affiliation(s)
- Aimee L Davidson
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Uwe Dressel
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Sarah Norris
- Faculty of Medicine and Health, University of Sydney, L2.22 The Quadrangle (A14), Sydney, NSW, 2006, Australia
| | - Daffodil M Canson
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Dylan M Glubb
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Cristina Fortuno
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Georgina E Hollway
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Michael T Parsons
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Miranda E Vidgen
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Australian Genomics, Melbourne, VIC, Australia
| | - Oliver Holmes
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Lambros T Koufariotis
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Vanessa Lakis
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Conrad Leonard
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Scott Wood
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Qinying Xu
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Amy E McCart Reed
- Centre for Clinical Research, University of Queensland, Brisbane, QLD, Australia
| | - Hilda A Pickett
- Children's Medical Research Institute, University of Sydney, Westmead, NSW, Australia
| | - Mohammad K Al-Shinnag
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Rachel L Austin
- Australian Genomics, Melbourne, VIC, Australia
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Jo Burke
- Tasmanian Clinical Genetics Service, Royal Hobart Hospital, Hobart, TAS, Australia
| | - Elisa J Cops
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Cassandra B Nichols
- Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, WA, Australia
| | - Annabel Goodwin
- Cancer Genetics Department, Royal Prince Alfred Hospital, Sydney, NSW, Australia
- University of Sydney, Sydney, NSW, Australia
| | - Marion T Harris
- Monash Health Familial Cancer, Monash Health, Melbourne, VIC, Australia
- Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia
| | - Megan J Higgins
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Emilia L Ip
- Cancer Genetics, Liverpool Hospital, Sydney, NSW, Australia
| | | | - Chiyan Lau
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Genomics, Pathology Queensland, Brisbane, QLD, Australia
| | - Julia L Mansour
- Tasmanian Clinical Genetics Service, Royal Hobart Hospital, Hobart, TAS, Australia
| | - Michael W Millward
- Tasmanian Clinical Genetics Service, Royal Hobart Hospital, Hobart, TAS, Australia
| | - Melissa J Monnik
- Adult Genetics Unit, Royal Adelaide Hospital, Adelaide, SA, Australia
| | - Nicholas S Pachter
- Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, WA, Australia
- Faculty of Health and Medical Sciences, University of Western Australia, Perth, WA, Australia
| | - Abiramy Ragunathan
- Familial Cancer Services, The Crown Princess Mary Cancer Centre, Westmead Hospital, Westmead, NSW, Australia
| | - Rachel D Susman
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Sharron L Townshend
- Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, WA, Australia
| | - Alison H Trainer
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, Australia
- Department of Medicine, University of Melbourne, Melbourne, VIC, Australia
| | - Simon L Troth
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Katherine M Tucker
- Prince of Wales Clinical School, UNSW Medicine and Health, The University of New South Wales, Sydney, NSW, Australia
- Hereditary Cancer Centre, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Mathew J Wallis
- Tasmanian Clinical Genetics Service, Royal Hobart Hospital, Hobart, TAS, Australia
- School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Maie Walsh
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Rachel A Williams
- Prince of Wales Clinical School, UNSW Medicine and Health, The University of New South Wales, Sydney, NSW, Australia
- Hereditary Cancer Centre, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Ingrid M Winship
- Department of Medicine, University of Melbourne, Melbourne, VIC, Australia
- Genomic Medicine and Familial Cancer Clinic, Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Felicity Newell
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Emma Tudini
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Australian Genomics, Melbourne, VIC, Australia
| | - John V Pearson
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Nicola K Poplawski
- Adult Genetics Unit, Royal Adelaide Hospital, Adelaide, SA, Australia
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Helen G Mar Fan
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Paul A James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Amanda B Spurdle
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia.
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia.
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Robyn L Ward
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia.
- Faculty of Medicine and Health, University of Sydney, L2.22 The Quadrangle (A14), Sydney, NSW, 2006, Australia.
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Tian Y, Wang Y, Yang J, Gao P, Xu H, Wu Y, Li M, Chen H, Lu D, Yan H. Integrative preimplantation genetic testing analysis for a Chinese family with hereditary spherocytosis caused by a novel splicing variant of SPTB. Front Genet 2023; 14:1221853. [PMID: 37795245 PMCID: PMC10545875 DOI: 10.3389/fgene.2023.1221853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 08/30/2023] [Indexed: 10/06/2023] Open
Abstract
Hereditary spherocytosis (HS), the most common inherited hemolytic anemia disorder, is characterized by osmotically fragile microspherocytic red cells with a reduced surface area on the peripheral blood smear. Pathogenic variants in five erythrocyte membrane structure-related genes ANK1 (Spherocytosis, type 1; MIM#182900), SPTB (Spherocytosis, type 2; MIM#616649), SPTA1 (Spherocytosis, type 3; MIM#270970), SLC4A1 (Spherocytosis, type 4; MIM#612653) and EPB42 (Spherocytosis, type 5; MIM#612690) have been confirmed to be related to HS. There have been many studies on the pathogenic variants and mechanisms of HS, however, studies on how to manage the transmission of HS to the next-generation have not been reported. In this study, we recruited a patient with HS. Targeted next-generation sequencing with a panel of 208 genes related to blood system diseases detected a novel heterozygous variant in the SPTB: c.300+2dup in the proband. Sanger sequencing of variant alleles and haplotype linkage analysis of single nucleotide polymorphism (SNP) based on next-generation sequencing were performed simultaneously. Five embryos were identified with one heterozygous and four not carrying the SPTB variant. Single-cell amplification and whole genome sequencing showed that three embryos had varying degrees of trisomy mosaicism. One of two normal embryos was transferred to the proband. Ultimately, a healthy boy was born, confirmed by noninvasive prenatal testing for monogenic conditions (NIPT-M) to be disease-free. This confirmed our successful application of PGT in preventing transmission of the pathogenic variant allele in the HS family.
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Affiliation(s)
- Yafei Tian
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yao Wang
- Department of Reproductive Heredity Center, Navy Medical University, Shanghai, China
| | - Jingmin Yang
- NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute, Chongqing, China
- Institute of Medical Genetics and Genomics, Fudan University, Shanghai, China
- Shanghai WeHealth BioMedical Technology Co., Ltd.Shanghai, China
| | - Pengfei Gao
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai WeHealth BioMedical Technology Co., Ltd.Shanghai, China
| | - Hui Xu
- Shanghai WeHealth BioMedical Technology Co., Ltd.Shanghai, China
| | - Yiming Wu
- Shanghai WeHealth BioMedical Technology Co., Ltd.Shanghai, China
| | - Mengru Li
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, China
| | - Hongyan Chen
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, China
| | - Daru Lu
- NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute, Chongqing, China
- Institute of Medical Genetics and Genomics, Fudan University, Shanghai, China
| | - Hongli Yan
- Department of Reproductive Heredity Center, Navy Medical University, Shanghai, China
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Murata M, Bilim V, Shirono Y, Kazama A, Hiruma K, Tasaki M, Tomita Y. MicroRNAs as Potential Regulators of GSK-3β in Renal Cell Carcinoma. Curr Issues Mol Biol 2023; 45:7432-7448. [PMID: 37754254 PMCID: PMC10529713 DOI: 10.3390/cimb45090470] [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: 07/03/2023] [Revised: 09/07/2023] [Accepted: 09/09/2023] [Indexed: 09/28/2023] Open
Abstract
The prognosis of patients with advanced renal cell carcinoma (RCC) has improved with newer therapies, including molecular-targeted therapies and immuno-oncology agents. Despite these therapeutic advances, many patients with metastatic disease remain uncured. Inhibition of glycogen synthase kinase-3β (GSK-3β) is a promising new therapeutic strategy for RCC; however, the precise regulatory mechanism has not yet been fully elucidated. MicroRNAs (miRNAs) act as post-translational regulators of target genes, and we investigated the potential regulation of miRNAs on GSK-3β in RCC. We selected nine candidate miRNAs from three databases that could potentially regulate GSK-3β. Among these, hsa-miR-4465 (miR-4465) was downregulated in RCC cell lines and renal cancer tissues. Furthermore, luciferase assays revealed that miR-4465 directly interacted with the 3' untranslated region of GSK-3β, and Western blot analysis showed that overexpression of miR-4465 significantly decreased GSK-3β protein expression. Functional assays showed that miR-4465 overexpression significantly suppressed cell invasion of A498 and Caki-1 cells; however, cell proliferation and migration were suppressed only in Caki-1 and A498 cells, respectively, with no effect on cell cycle and apoptosis. In conclusion, miR-4465 regulates GSK-3β expression but does not consistently affect RCC cell function as a single molecule. Further comprehensive investigation of regulatory networks is required in this field.
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Affiliation(s)
- Masaki Murata
- Department of Urology, Division of Molecular Oncology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan; (V.B.); (Y.S.); (A.K.); (K.H.); (M.T.); (Y.T.)
| | - Vladimir Bilim
- Department of Urology, Division of Molecular Oncology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan; (V.B.); (Y.S.); (A.K.); (K.H.); (M.T.); (Y.T.)
- Department of Urology, Kameda Daiichi Hospital, Niigata 950-0165, Japan
| | - Yuko Shirono
- Department of Urology, Division of Molecular Oncology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan; (V.B.); (Y.S.); (A.K.); (K.H.); (M.T.); (Y.T.)
| | - Akira Kazama
- Department of Urology, Division of Molecular Oncology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan; (V.B.); (Y.S.); (A.K.); (K.H.); (M.T.); (Y.T.)
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Kaede Hiruma
- Department of Urology, Division of Molecular Oncology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan; (V.B.); (Y.S.); (A.K.); (K.H.); (M.T.); (Y.T.)
| | - Masayuki Tasaki
- Department of Urology, Division of Molecular Oncology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan; (V.B.); (Y.S.); (A.K.); (K.H.); (M.T.); (Y.T.)
| | - Yoshihiko Tomita
- Department of Urology, Division of Molecular Oncology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan; (V.B.); (Y.S.); (A.K.); (K.H.); (M.T.); (Y.T.)
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São José C, Garcia-Pelaez J, Ferreira M, Arrieta O, André A, Martins N, Solís S, Martínez-Benítez B, Ordóñez-Sánchez ML, Rodríguez-Torres M, Sommer AK, Te Paske IBAW, Caldas C, Tischkowitz M, Tusié MT, Hoogerbrugge N, Demidov G, de Voer RM, Laurie S, Oliveira C. Combined loss of CDH1 and downstream regulatory sequences drive early-onset diffuse gastric cancer and increase penetrance of hereditary diffuse gastric cancer. Gastric Cancer 2023; 26:653-666. [PMID: 37249750 PMCID: PMC10361908 DOI: 10.1007/s10120-023-01395-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/30/2023] [Indexed: 05/31/2023]
Abstract
BACKGROUND Germline CDH1 pathogenic or likely pathogenic variants cause hereditary diffuse gastric cancer (HDGC). Once a genetic cause is identified, stomachs' and breasts' surveillance and/or prophylactic surgery is offered to asymptomatic CDH1 carriers, which is life-saving. Herein, we characterized an inherited mechanism responsible for extremely early-onset gastric cancer and atypical HDGC high penetrance. METHODS Whole-exome sequencing (WES) re-analysis was performed in an unsolved HDGC family. Accessible chromatin and CDH1 promoter interactors were evaluated in normal stomach by ATAC-seq and 4C-seq, and functional analysis was performed using CRISPR-Cas9, RNA-seq and pathway analysis. RESULTS We identified a germline heterozygous 23 Kb CDH1-TANGO6 deletion in a family with eight diffuse gastric cancers, six before age 30. Atypical HDGC high penetrance and young cancer-onset argued towards a role for the deleted region downstream of CDH1, which we proved to present accessible chromatin, and CDH1 promoter interactors in normal stomach. CRISPR-Cas9 edited cells mimicking the CDH1-TANGO6 deletion display the strongest CDH1 mRNA downregulation, more impacted adhesion-associated, type-I interferon immune-associated and oncogenic signalling pathways, compared to wild-type or CDH1-deleted cells. This finding solved an 18-year family odyssey and engaged carrier family members in a cancer prevention pathway of care. CONCLUSION In this work, we demonstrated that regulatory elements lying down-stream of CDH1 are part of a chromatin network that control CDH1 expression and influence cell transcriptome and associated signalling pathways, likely explaining high disease penetrance and very young cancer-onset. This study highlights the importance of incorporating scientific-technological updates and clinical guidelines in routine diagnosis, given their impact in timely genetic diagnosis and disease prevention.
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Affiliation(s)
- Celina São José
- i3S-Instituto de Investigação e Inovação em Saúde, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
- Doctoral Programme in Biomedicine, Faculty of Medicine, University of Porto, Porto, Portugal
| | - José Garcia-Pelaez
- i3S-Instituto de Investigação e Inovação em Saúde, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
- Doctoral Programme in Biomedicine, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Marta Ferreira
- i3S-Instituto de Investigação e Inovação em Saúde, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
- Department Computer Science Faculty of Science, University of Porto, Porto, Portugal
| | - Oscar Arrieta
- Thoracic Oncology Unit, Department of Thoracic Oncology, Instituto Nacional de Cancerología, Mexico City, Mexico
| | - Ana André
- i3S-Instituto de Investigação e Inovação em Saúde, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Nelson Martins
- i3S-Instituto de Investigação e Inovação em Saúde, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
- Master Programme in Molecular Medicine and Oncology, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Samantha Solís
- INCMNSZ/Instituto de Investigaciones Biomédicas, Unidad de Biología Molecular y Medicina Genómica Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, UNAM Mexico City, Mexico
| | - Braulio Martínez-Benítez
- Pathology Department, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, INCMNSZ Mexico City, Mexico
| | - María Luisa Ordóñez-Sánchez
- INCMNSZ/Instituto de Investigaciones Biomédicas, Unidad de Biología Molecular y Medicina Genómica Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, UNAM Mexico City, Mexico
| | - Maribel Rodríguez-Torres
- INCMNSZ/Instituto de Investigaciones Biomédicas, Unidad de Biología Molecular y Medicina Genómica Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, UNAM Mexico City, Mexico
| | - Anna K Sommer
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Iris B A W Te Paske
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
- Cambridge Experimental Cancer Medicine Centre (ECMC), CRUK Cambridge Centre, NIHR Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Maria Teresa Tusié
- INCMNSZ/Instituto de Investigaciones Biomédicas, Unidad de Biología Molecular y Medicina Genómica Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, UNAM Mexico City, Mexico
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - German Demidov
- Institute of Medical Genetics and Applied Genomics, Tübingen, Germany
| | - Richarda M de Voer
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Steve Laurie
- The Barcelona Institute of Science and Technology, CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - Carla Oliveira
- i3S-Instituto de Investigação e Inovação em Saúde, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.
- IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal.
- FMUP-Faculty of Medicine of the University of Porto, Porto, Portugal.
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Li Z, Lu T, Chen Z, Yu X, Wang L, Shen G, Huang H, Li Z, Ren Y, Guo W, Hu Y. HOXA11 promotes lymphatic metastasis of gastric cancer via transcriptional activation of TGFβ1. iScience 2023; 26:107346. [PMID: 37539033 PMCID: PMC10393827 DOI: 10.1016/j.isci.2023.107346] [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: 05/13/2023] [Revised: 06/09/2023] [Accepted: 07/06/2023] [Indexed: 08/05/2023] Open
Abstract
Most gastric cancer (GC) patients with early stage often have no lymph node (LN) metastases, while LN metastases appear in the advanced stage. However, there are some patients who present with early stage LN metastases and no LN metastases in the advanced stage. To explore the deeper molecular mechanisms involved, we collected clinical samples from early and advanced stage GC with and without LN metastases, as well as metastatic lymph nodes. Herein, we identified a key target, HOXA11, that was upregulated in GC tissues and closely associated with lymphatic metastases. HOXA11 transcriptionally regulates TGFβ1 expression and activates the TGFβ1/Smad2 pathway, which not only promotes EMT development but also induces VEGF-C secretion and lymphangiogenesis. These findings provide a plausible mechanism for HOXA11-modulated tumor in lymphatic metastasis and suggest that HOXA11 may represent a potential therapeutic target for clinical intervention in LN-metastatic gastric cancer.
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Affiliation(s)
- Zhenyuan Li
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, the First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
| | - Tailiang Lu
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, the First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
| | - Zhian Chen
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, the First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
| | - Xiang Yu
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, the First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
| | - Lingzhi Wang
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, the First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
| | - Guodong Shen
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, the First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
| | - Huilin Huang
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, the First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
| | - Zhenhao Li
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, the First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
| | - Yingxin Ren
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, the First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
| | - Weihong Guo
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, the First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
| | - Yanfeng Hu
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, the First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, P.R. China
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Liu SC, Gong LL, Huang FC, Xu N, Yang KX, Liu XH, Li WL. RNF114 facilitates the proliferation, stemness, and metastasis of colorectal cancer. Pathol Res Pract 2023; 248:154716. [PMID: 37523804 DOI: 10.1016/j.prp.2023.154716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 07/17/2023] [Accepted: 07/25/2023] [Indexed: 08/02/2023]
Abstract
BACKGROUND Colorectal cancer (CRC), the fourth of the world's major common malignancy, poses a serious threat to the physical and mental health of the population. Nevertheless, the prognosis of CRC patients remains unsatisfactory. Consequently, it is still imperative to continuously discover the CRC mechanisms. METHODS The expression profiles of mRNAs were recognized by whole transcriptome sequencing to identity differentially expressed mRNA (DE-mRNA). TCGA COAD cohort, PPOGgene and Kaplan-Meier Plotter databases were utilized to validate RNF114 relevance to CRC prognosis. The effect of RNF114 on the malignant biological behavior of CRC was explored in CRC cells and subcutaneous tumor models and lung metastasis model after exogenous regulation of RNF114. RESULTS A total of 1358 DE-mRNAs were identified, including 617 up-regulated and 741 down-regulated DE-mRNAs, and they were mainly involved in the term of receptor ligand activity, Wnt signaling pathway and pathway in cancer. Notably, RNF114 was hyper-expressed in tissues and cell of CRC, and significantly correlated with tumor invasion depth and TNM stage of CRC patients. RNF114 expression were significantly associated with overall survival, and had superior diagnostic value in CRC. In vitro, knockdown of RNF114 statistically diminished the proliferation, stemness, invasion and wound healing of CRC cells and facilitated their apoptosis, and the opposite result was observed for overexpression of RNF114. In vivo, knockdown of RNF114 effectively diminished the mass and volume of tumors, and lung metastasis in animal model. CONCLUSIONS In summary, we identified DE-mRNAs in CRC, and elucidated that RNF114 facilitates CRC process. The discovery will contribute to theoretical foundation for RNF114 as a potential therapeutic target and biomarker, and offer new perspectives for CRC research.
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Affiliation(s)
- Shi-Cheng Liu
- Department of Colorectal Surgery, the Third Affiliated Hospital of Kunming Medical University (the Tumor Hospital of Yunnan), China
| | - Le-Lan Gong
- Department of Colorectal Surgery, the Third Affiliated Hospital of Kunming Medical University (the Tumor Hospital of Yunnan), China
| | - Feng-Chang Huang
- Department of Oncology, the First Affiliated Hospital of Kunming Medical University, China
| | - Ning Xu
- Department of Oncology, the First Affiliated Hospital of Kunming Medical University, China
| | - Ke-Xin Yang
- Department of Colorectal Surgery, the Third Affiliated Hospital of Kunming Medical University (the Tumor Hospital of Yunnan), China
| | - Xi-Hong Liu
- Department of Oncology, the First Affiliated Hospital of Kunming Medical University, China
| | - Wen-Liang Li
- Department of Colorectal Surgery, the Third Affiliated Hospital of Kunming Medical University (the Tumor Hospital of Yunnan), China.
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Loong HH, Shimizu T, Prawira A, Tan AC, Tran B, Day D, Tan DSP, Ting FIL, Chiu JW, Hui M, Wilson MK, Prasongsook N, Koyama T, Reungwetwattana T, Tan TJ, Heong V, Voon PJ, Park S, Tan IB, Chan SL, Tan DSW. Recommendations for the use of next-generation sequencing in patients with metastatic cancer in the Asia-Pacific region: a report from the APODDC working group. ESMO Open 2023; 8:101586. [PMID: 37356359 PMCID: PMC10319859 DOI: 10.1016/j.esmoop.2023.101586] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/27/2023] [Accepted: 05/18/2023] [Indexed: 06/27/2023] Open
Abstract
INTRODUCTION Next-generation sequencing (NGS) diagnostics have shown clinical utility in predicting survival benefits in patients with certain cancer types who are undergoing targeted drug therapies. Currently, there are no guidelines or recommendations for the use of NGS in patients with metastatic cancer from an Asian perspective. In this article, we present the Asia-Pacific Oncology Drug Development Consortium (APODDC) recommendations for the clinical use of NGS in metastatic cancers. METHODS The APODDC set up a group of experts in the field of clinical cancer genomics to (i) understand the current NGS landscape for metastatic cancers in the Asia-Pacific (APAC) region; (ii) discuss key challenges in the adoption of NGS testing in clinical practice; and (iii) adapt/modify the European Society for Medical Oncology guidelines for local use. Nine cancer types [breast cancer (BC), gastric cancer (GC), nasopharyngeal cancer (NPC), ovarian cancer (OC), prostate cancer, lung cancer, and colorectal cancer (CRC) as well as cholangiocarcinoma and hepatocellular carcinoma (HCC)] were identified, and the applicability of NGS was evaluated in daily practice and/or clinical research. Asian ethnicity, accessibility of NGS testing, reimbursement, and socioeconomic and local practice characteristics were taken into consideration. RESULTS The APODDC recommends NGS testing in metastatic non-small-cell lung cancer (NSCLC). Routine NGS testing is not recommended in metastatic BC, GC, and NPC as well as cholangiocarcinoma and HCC. The group suggested that patients with epithelial OC may be offered germline and/or somatic genetic testing for BReast CAncer gene 1 (BRCA1), BRCA2, and other OC susceptibility genes. Access to poly (ADP-ribose) polymerase inhibitors is required for NGS to be of clinical utility in prostate cancer. Allele-specific PCR or a small-panel multiplex-gene NGS was suggested to identify key alterations in CRC. CONCLUSION This document offers practical guidance on the clinical utility of NGS in specific cancer indications from an Asian perspective.
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Affiliation(s)
- H H Loong
- Department of Clinical Oncology, The Chinese University of Hong Kong, Hong Kong, China
| | - T Shimizu
- Department of Pulmonary Medicine and Medical Oncology, Wakayama Medical University Graduate School of Medicine, Wakayama, Japan
| | - A Prawira
- Cancer Trials and Research Unit, Prince of Wales Hospital, Sydney, Australia
| | - A C Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - B Tran
- Department of Oncology, Peter MacCallum Cancer Centre, Melbourne
| | - D Day
- Department of Oncology, Monash Health and Monash University, Australia
| | - D S P Tan
- Department of Haematology-Oncology, National University Cancer Institute, Singapore
| | - F I L Ting
- Department of Medicine, Dr. Pablo O. Torre Memorial Hospital, Bacolod, Philippines
| | - J W Chiu
- Department of Medicine, The University of Hong Kong, HKSAR, Pok Fu Lam, Hong Kong, China
| | - M Hui
- Department of Medical Oncology, Chris O'Brien Lifehouse, Camperdown, Australia
| | - M K Wilson
- Department of Medical Oncology, Auckland City Hospital, Auckland, New Zealand
| | - N Prasongsook
- Division of Medical Oncology, Phramongkutklao Hospital, Bangkok, Thailand
| | - T Koyama
- Department of Experimental Therapeutics, National Cancer Center Hospital, Tokyo, Japan
| | - T Reungwetwattana
- Division of Medical Oncology, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - T J Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - V Heong
- Department Medical Oncology, Tan Tock Seng Hospital, Singapore
| | - P J Voon
- Radiotherapy and Oncology Department, Hospital Umum Sarawak, Kuching, Malaysia
| | - S Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - I B Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - S L Chan
- Department of Clinical Oncology, The Chinese University of Hong Kong, Hong Kong, China
| | - D S W Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore.
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Satam H, Joshi K, Mangrolia U, Waghoo S, Zaidi G, Rawool S, Thakare RP, Banday S, Mishra AK, Das G, Malonia SK. Next-Generation Sequencing Technology: Current Trends and Advancements. BIOLOGY 2023; 12:997. [PMID: 37508427 PMCID: PMC10376292 DOI: 10.3390/biology12070997] [Citation(s) in RCA: 82] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023]
Abstract
The advent of next-generation sequencing (NGS) has brought about a paradigm shift in genomics research, offering unparalleled capabilities for analyzing DNA and RNA molecules in a high-throughput and cost-effective manner. This transformative technology has swiftly propelled genomics advancements across diverse domains. NGS allows for the rapid sequencing of millions of DNA fragments simultaneously, providing comprehensive insights into genome structure, genetic variations, gene expression profiles, and epigenetic modifications. The versatility of NGS platforms has expanded the scope of genomics research, facilitating studies on rare genetic diseases, cancer genomics, microbiome analysis, infectious diseases, and population genetics. Moreover, NGS has enabled the development of targeted therapies, precision medicine approaches, and improved diagnostic methods. This review provides an insightful overview of the current trends and recent advancements in NGS technology, highlighting its potential impact on diverse areas of genomic research. Moreover, the review delves into the challenges encountered and future directions of NGS technology, including endeavors to enhance the accuracy and sensitivity of sequencing data, the development of novel algorithms for data analysis, and the pursuit of more efficient, scalable, and cost-effective solutions that lie ahead.
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Affiliation(s)
- Heena Satam
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Kandarp Joshi
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Upasana Mangrolia
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Sanober Waghoo
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Gulnaz Zaidi
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Shravani Rawool
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Ritesh P. Thakare
- Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605, USA; (R.P.T.); (S.B.); (A.K.M.)
| | - Shahid Banday
- Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605, USA; (R.P.T.); (S.B.); (A.K.M.)
| | - Alok K. Mishra
- Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605, USA; (R.P.T.); (S.B.); (A.K.M.)
| | - Gautam Das
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Sunil K. Malonia
- Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605, USA; (R.P.T.); (S.B.); (A.K.M.)
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Jeroch J, Riedlinger T, Schmitt C, Ebner S, Winkelmann R, Wild PJ, Demes M. A Comparison of Two Different FFPE Tissue Dissection Methods for Routine Diagnostics in Molecular Pathology: Manual Macrodissection versus Automated Microdissection Using the Roche "AVENIO Millisect" System. Cancers (Basel) 2023; 15:3249. [PMID: 37370864 DOI: 10.3390/cancers15123249] [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: 04/13/2023] [Revised: 05/31/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Currently, in routine diagnostics, most molecular testing is performed on formalin-fixed, paraffin-embedded tissue after a histomorphological assessment. In order to find the best possible and targeted individual therapy, knowing the mutational status of the tumour is crucial. The "AVENIO Millisect" system Roche introduced an automation solution for the dissection of tissue on slides. This technology allows the precise and fully automated dissection of the tumour area without wasting limited and valuable patient material. In this study, the digitally guided microdissection was directly compared to the manual macrodissection regarding the precision and duration of the procedure, their DNA concentrations as well as DNA qualities, and the overall costs in 24 FFPE samples. In 21 of 24 cases (87.5%), the DNA yields of the manually dissected samples were higher in comparison to the automatically dissected samples. Shorter execution times and lower costs were also benefits of the manual scraping process. Nevertheless, the DNA quality achieved with both methods was comparable, which is essential for further molecular testing. Therefore, it could be used as an additional tool for precise tumour enrichment.
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Affiliation(s)
- Jan Jeroch
- Wildlab, University Hospital Frankfurt MVZ GmbH, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Tobias Riedlinger
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Christina Schmitt
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Silvana Ebner
- Wildlab, University Hospital Frankfurt MVZ GmbH, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Ria Winkelmann
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Peter J Wild
- Wildlab, University Hospital Frankfurt MVZ GmbH, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Melanie Demes
- Wildlab, University Hospital Frankfurt MVZ GmbH, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
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42
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Yap TA, Stadler ZK, Stout LA, Schneider BP. Aligning Germline Cancer Predisposition With Tumor-Based Next-Generation Sequencing for Modern Oncology Diagnosis, Interception, and Therapeutic Development. Am Soc Clin Oncol Educ Book 2023; 43:e390738. [PMID: 37390373 DOI: 10.1200/edbk_390738] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2023]
Abstract
In the era of precision medicine, genomic interrogation for identification of both germline and somatic genetic alterations has become increasingly important. While such germline testing was usually undertaken via a phenotype-driven single-gene approach, with the advent of next-generation sequencing (NGS) technologies, the widespread utilization of multigene panels, often agnostic of cancer phenotype, has become a commonplace in many different cancer types. At the same time, somatic tumor testing in oncology performed for the purpose of guiding therapeutic decisions for targeted therapies has also rapidly expanded, recently starting to incorporate not just patients with recurrent or metastatic cancer but even patients with early-stage disease. An integrated approach may be the best approach for the optimal management of patients with different cancers. The lack of complete congruence between germline and somatic NGS tests does not minimize the power or importance of either, but highlights the need to understand their limitations so as not to overlook an important finding or omission. NGS tests built to more uniformly and comprehensively evaluate both the germline and tumor simultaneously are urgently required and are in development. In this article, we discuss approaches to somatic and germline analyses in patients with cancer and the knowledge gained from integration of tumor-normal sequencing. We also detail strategies for the incorporation of genomic analysis into oncology care delivery models and the important emergence of poly(ADP-ribose) polymerase and other DNA Damage Response inhibitors in the clinic for patients with cancer with germline and somatic BRCA1 and BRCA2 mutations.
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Affiliation(s)
- Timothy A Yap
- University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Leigh Anne Stout
- Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN
| | - Bryan P Schneider
- Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN
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43
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Enko D, Schaflinger E, Müller DJ. [Clinical Application Examples of a Next-Generation Sequencing based Multi-Genepanel Analysis]. Dtsch Med Wochenschr 2023; 148:695-702. [PMID: 37216946 DOI: 10.1055/a-2033-5329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
This review provides an overview of clinically useful applications of a next-generation sequencing (NGS)-based multi-gene panel testing strategy in the areas of oncology, hereditary tumor syndromes, and hematology. In the case of solid tumors (e.g. lung carcinoma, colon-rectal carcinoma), the detection of somatic mutations contributes not only to a better diagnostic but also therapeutic stratification of those affected. The increasing genetic complexity of hereditary tumor syndromes (e.g. breast and ovarian carcinoma, lynch syndrome/polyposis) requires a multi-gene panel analysis of germline mutations in affected families. Another useful indication for a multi-gene panel diagnostics and prognosis assessment are acute and chronic myeloid diseases. The criteria of the WHO-classification and the European LeukemiaNet-prognosis system for acute myeloid leukemia can only be met by a multi-gene panel test strategy.
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Affiliation(s)
- Dietmar Enko
- Medizinische Universität Graz Klinisches Institut für Medizinische und Chemische Labordiagnostik, Graz, Austria
| | - Erich Schaflinger
- Institut für Humangenetik, Medizinische Universität Graz, Neue Stiftingtalstraße 2, 8010 Graz, Austria
| | - Daniel J Müller
- Klinisches Institut für Pharmakogenetische Wissenschaft, Cambell Family Mental Health Research Institute, Zentrum für Suchtkrankheit und psychische Gesundheit, College Street 250, Toronto, ON M5T 1R8, Toronto, Kanada
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44
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Albitar M, Zhang H, Charifa A, Ip A, Ma W, McCloskey J, Donato M, Siegel D, Waintraub S, Gutierrez M, Pecora A, Goy A. Combining cell-free RNA with cell-free DNA in liquid biopsy for hematologic and solid tumors. Heliyon 2023; 9:e16261. [PMID: 37251903 PMCID: PMC10208940 DOI: 10.1016/j.heliyon.2023.e16261] [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: 03/16/2023] [Revised: 05/07/2023] [Accepted: 05/11/2023] [Indexed: 05/31/2023] Open
Abstract
Current use of liquid biopsy is based on cell-free DNA (cfDNA) and the evaluation of mutations or methylation pattern. However, expressed RNA can capture mutations, changes in expression levels due to methylation, and provide information on cell of origin, growth, and proliferation status. We developed an approach to isolate cell-free total nucleic acid (cfDNA) and used targeted next generation sequencing to sequence cell-free RNA (cfRNA) and cfDNA as new approach in liquid biopsy. We demonstrate that cfRNA is overall more sensitive than cfDNA in detecting mutations. We show that cfRNA is reliable in detecting fusion genes and cfDNA is reliable in detecting chromosomal gains and losses. cfRNA levels of various solid tumor biomarkers were significantly higher (P < 0.0001) in samples from solid tumors as compared with normal control. Similarly, cfRNA lymphoid markers and cfRNA myeloid markers were all higher in lymphoid and myeloid neoplasms, respectively as compared with control (P < 0.0001). Using machine learning we demonstrate cfRNA was highly predictive of diagnosis (AUC >0.98) of solid tumors, B-cell lymphoid neoplasms, T-cell lymphoid neoplasms, and myeloid neoplasms. In evaluating the host immune system, cfRNA CD4:CD8B and CD3D:CD19 ratios in normal controls were as expected (median: 5.92 and 6.87, respectively) and were significantly lower in solid tumors (P < 0.0002). This data suggests that liquid biopsy combining analysis of cfRNA with cfDNA is practical and may provide helpful information in predicting genomic abnormalities, diagnosis of neoplasms and evaluating both the tumor biology and the host response.
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Affiliation(s)
- Maher Albitar
- Genomic Testing Cooperative, LCA, Irvine, CA, 92618, USA
| | - Hong Zhang
- Genomic Testing Cooperative, LCA, Irvine, CA, 92618, USA
| | - Ahmad Charifa
- Genomic Testing Cooperative, LCA, Irvine, CA, 92618, USA
| | - Andrew Ip
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Wanlong Ma
- Genomic Testing Cooperative, LCA, Irvine, CA, 92618, USA
| | - James McCloskey
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Michele Donato
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - David Siegel
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Stanley Waintraub
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Martin Gutierrez
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Andrew Pecora
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Andre Goy
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, 07601, USA
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Alsaafin A, Safarpoor A, Sikaroudi M, Hipp JD, Tizhoosh HR. Learning to predict RNA sequence expressions from whole slide images with applications for search and classification. Commun Biol 2023; 6:304. [PMID: 36949169 PMCID: PMC10033650 DOI: 10.1038/s42003-023-04583-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 02/13/2023] [Indexed: 03/24/2023] Open
Abstract
Deep learning methods are widely applied in digital pathology to address clinical challenges such as prognosis and diagnosis. As one of the most recent applications, deep models have also been used to extract molecular features from whole slide images. Although molecular tests carry rich information, they are often expensive, time-consuming, and require additional tissue to sample. In this paper, we propose tRNAsformer, an attention-based topology that can learn both to predict the bulk RNA-seq from an image and represent the whole slide image of a glass slide simultaneously. The tRNAsformer uses multiple instance learning to solve a weakly supervised problem while the pixel-level annotation is not available for an image. We conducted several experiments and achieved better performance and faster convergence in comparison to the state-of-the-art algorithms. The proposed tRNAsformer can assist as a computational pathology tool to facilitate a new generation of search and classification methods by combining the tissue morphology and the molecular fingerprint of the biopsy samples.
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Affiliation(s)
- Areej Alsaafin
- Rhazes Lab, Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN, USA
- Kimia Lab, University of Waterloo, Waterloo, ON, Canada
| | | | | | - Jason D Hipp
- Division of Computational Pathology and AI, Mayo Clinic, Rochester, MN, USA
| | - H R Tizhoosh
- Rhazes Lab, Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN, USA.
- Kimia Lab, University of Waterloo, Waterloo, ON, Canada.
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Karpel H, Manderski E, Pothuri B. Frequency of actionable germline pathogenic variants identified through tumor next-generation sequencing in a gynecologic cancer cohort. Int J Gynecol Cancer 2023:ijgc-2022-004142. [PMID: 36889816 DOI: 10.1136/ijgc-2022-004142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023] Open
Abstract
BACKGROUND Tumor next-generation sequencing can identify potential germline pathogenic variants associated with cancer susceptibility. OBJECTIVE To describe the frequency of tumor sequencing results that met European Society of Medical Oncology (ESMO) recommendations for further germline genetic testing, and the frequency of germline variants among a cohort with gynecologic cancer. METHODS Patients with gynecologic cancer who underwent tumor sequencing between September 2019 and February 2022 in a large healthcare system in New York City were retrospectively identified. Eligible patients with suspected germline pathogenic variants on tumor sequencing were identified based on ESMO guidelines. Logistic regression was used to explore variables associated with referral and completion of germline testing. RESULTS Of 358 patients with gynecologic cancers who underwent tumor sequencing, 81 (22.6%) had ≥1 suspected germline variant according to ESMO guidelines. Of the 81 patients with qualifying tumor sequencing results, 56 (69.1%) received germline testing: 41/46 (89.1%) eligible patients with ovarian cancer and 15/33 (45.5%) with endometrial cancer. In the endometrial cancer cohort, 11/33 (33.3%) eligible patients were not referred for germline testing and the majority of these patients had tumor variants in genes commonly known to cause hereditary cancer. Of the 56 patients who underwent germline testing, 40 (71.4%) had pathogenic germline variants. In multivariable analysis, race/ethnicity other than non-Hispanic white was associated with lower odds of germline testing referral and completion (OR=0.1, 95% CI 0.01 to 0.5 and OR=0.2, 95% CI 0.04 to 0.6, respectively). CONCLUSION Given the high rate of pathogenic germline variant detection and the importance of identifying such variants for both patients and their family, it is imperative that eligible patients undergo germline testing. Additional education for providers on multidisciplinary guidelines and development of clinical pathways to ensure germline testing of suspected pathogenic variants identified on tumor sequencing is warranted, especially in light of the racial/ethnic inequity observed.
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Affiliation(s)
- Hannah Karpel
- New York University Grossman School of Medicine, New York, New York, USA
| | - Elizabeth Manderski
- Perlmutter Cancer Center, New York University Langone Health, New York, New York, USA
| | - Bhavana Pothuri
- Department of Obstetrics and Gynecology, Perlmutter Cancer Center, New York University Langone Health, New York, New York, USA
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Cine N, Ugurtas C, Gokbayrak M, Aydin D, Demir G, Kuru S, Sunnetci-Akkoyunlu D, Eren-Keskin S, Simsek T, Cabuk D, Aksu MG, Canturk NZ, Savli H. The role of next-generation sequencing in the examination of signaling genes in Brca1/2-negative breast cancer cases. Ann Hum Genet 2023; 87:28-49. [PMID: 36479692 DOI: 10.1111/ahg.12488] [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: 12/28/2021] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Breast cancer is the most prevalent malignancy in women worldwide. Although pathogenic variants in the BRCA1/2 genes are responsible for the majority of hereditary breast cancer cases, a substantial proportion of patients are negative for pathogenic variations in these genes. In cancers, the signal transduction pathways of the cell are usually affected first. Therefore, this study aimed to detect and classified genetic variations in non-BRCA signaling genes and investigate the underlying genetic causes of susceptibility to breast cancer. METHODS Ninety-six patients without pathogenic variants in the BRCA1/2 genes who met the inclusion criteria were enrolled in the study, and 34 genes were analyzed using next-generation sequencing (NGS) for genetic analysis. RESULTS Based on the ClinVar database or American College of Medical Genetics criteria, a total of 55 variants of 16 genes were detected in 43 (44.8%) of the 96 patients included in the study. The pathogenic variants were found in the TP53, CHEK2, and RET genes, whereas the likely pathogenic variants were found in the FGFR1, FGFR3, EGFR, and NOTCH1 genes. CONCLUSION The examination of signaling genes in patients who met the established criteria for hereditary breast cancer but were negative for BRCA1/2 pathogenic variants provided additional information for approximately 8% of the families. The results of the present study suggest that NGS is a powerful tool for investigating the underlying genetic causes of occurrence and progression of breast cancer.
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Affiliation(s)
- Naci Cine
- Department of Medical Genetics, Kocaeli University Faculty of Medicine, Kocaeli, Turkey.,Department of Medical Genetics and Molecular Biology, Kocaeli University Institute of Health Sciences, Kocaeli, Turkey
| | - Cansu Ugurtas
- Department of Medical Genetics, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Merve Gokbayrak
- Department of Medical Genetics, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Duygu Aydin
- Department of Medical Genetics, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Gulhan Demir
- Department of Medical Genetics, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Seda Kuru
- Department of Medical Genetics, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | | | - Seda Eren-Keskin
- Department of Medical Genetics, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Turgay Simsek
- Department of General Surgery, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Devrim Cabuk
- Department of Medical Oncology, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Maksut Gorkem Aksu
- Department of Radiation Oncology, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Nuh Zafer Canturk
- Department of General Surgery, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Hakan Savli
- Department of Medical Genetics, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
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Jiang S, Liu Y, Xu Y, Sang X, Lu X. Research on liquid biopsy for cancer: A bibliometric analysis. Heliyon 2023; 9:e14145. [PMID: 36915518 PMCID: PMC10006671 DOI: 10.1016/j.heliyon.2023.e14145] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
BACKGROUND In recent years, liquid biopsy has shown great potential for improving cancer diagnosis and treatment. This study aimed to explore the trends and prospects in liquid biopsy for cancer from a bibliometric perspective. METHODS Reviews and articles on liquid biopsy and cancer were collected from the Web of Science Core Collection (WoSCC). Key bibliometric characteristics were analyzed using CiteSpace. Co-occurrence analysis of keywords and co-citation analysis of references was performed. RESULTS A total of 6331 publications from 11 years of scientific research were retrieved. Ninety-five countries and 7004 institutions in liquid biopsy and cancer contributed. The United States (US) and China published the most articles. The institution with the most published articles was the University of Texas MD Anderson Cancer Center. The most published journals were Cancer and Frontiers in Oncology. "Bettegowda (2014)" was the most cited reference with the highest burst strength in the last decade. Cluster analysis revealed that the recent hot topics were "circulating tumor cells," "cancer," and "exosomes." CONCLUSIONS This bibliometric analysis maps the basic knowledge structure of the field of liquid biopsy for cancer. The field is entering a phase of rapid development. The hot spots identified in this study deserve further investigation.
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Affiliation(s)
- Shitao Jiang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yaoge Liu
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yiyao Xu
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xinting Sang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xin Lu
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Udagawa S, Ooki A, Shinozaki E, Fukuda K, Yamaguchi K, Osumi H. Circulating Tumor DNA: The Dawn of a New Era in the Optimization of Chemotherapeutic Strategies for Metastatic Colo-Rectal Cancer Focusing on RAS Mutation. Cancers (Basel) 2023; 15:cancers15051473. [PMID: 36900264 PMCID: PMC10001242 DOI: 10.3390/cancers15051473] [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: 01/03/2023] [Revised: 02/10/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Genotyping of tumor tissues to assess RAS and BRAF V600E mutations enables us to select optimal molecularly targeted therapies when considering treatment strategies for patients with metastatic colorectal cancer. Tissue-based genetic testing is limited by the difficulty of performing repeated tests, due to the invasive nature of tissue biopsy, and by tumor heterogeneity, which can limit the usefulness of the information it yields. Liquid biopsy, represented by circulating tumor DNA (ctDNA), has attracted attention as a novel method for detecting genetic alterations. Liquid biopsies are more convenient and much less invasive than tissue biopsies and are useful for obtaining comprehensive genomic information on primary and metastatic tumors. Assessing ctDNA can help track genomic evolution and the status of alterations in genes such as RAS, which are sometimes altered following chemotherapy. In this review, we discuss the potential clinical applications of ctDNA, summarize clinical trials focusing on RAS, and present the future prospects of ctDNA analysis that could change daily clinical practice.
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Affiliation(s)
| | | | | | | | | | - Hiroki Osumi
- Correspondence: ; Tel.: +81-3-3520-0111 or +81-3-3570-0515
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50
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Blood-Based mRNA Tests as Emerging Diagnostic Tools for Personalised Medicine in Breast Cancer. Cancers (Basel) 2023; 15:cancers15041087. [PMID: 36831426 PMCID: PMC9954278 DOI: 10.3390/cancers15041087] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Molecular diagnostic tests help clinicians understand the underlying biological mechanisms of their patients' breast cancer (BC) and facilitate clinical management. Several tissue-based mRNA tests are used routinely in clinical practice, particularly for assessing the BC recurrence risk, which can guide treatment decisions. However, blood-based mRNA assays have only recently started to emerge. This review explores the commercially available blood mRNA diagnostic assays for BC. These tests enable differentiation of BC from non-BC subjects (Syantra DX, BCtect), detection of small tumours <10 mm (early BC detection) (Syantra DX), detection of different cancers (including BC) from a single blood sample (multi-cancer blood test Aristotle), detection of BC in premenopausal and postmenopausal women and those with high breast density (Syantra DX), and improvement of diagnostic outcomes of DNA testing (variant interpretation) (+RNAinsight). The review also evaluates ongoing transcriptomic research on exciting possibilities for future assays, including blood transcriptome analyses aimed at differentiating lymph node positive and negative BC, distinguishing BC and benign breast disease, detecting ductal carcinoma in situ, and improving early detection further (expression changes can be detected in blood up to eight years before diagnosing BC using conventional approaches, while future metastatic and non-metastatic BC can be distinguished two years before BC diagnosis).
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