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Murali H, Wang P, Liao EC, Wang K. Genetic variant classification by predicted protein structure: A case study on IRF6. Comput Struct Biotechnol J 2024; 23:892-904. [PMID: 38370976 PMCID: PMC10869248 DOI: 10.1016/j.csbj.2024.01.019] [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: 12/02/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/20/2024] Open
Abstract
Next-generation genome sequencing has revolutionized genetic testing, identifying numerous rare disease-associated gene variants. However, to impute pathogenicity, computational approaches remain inadequate and functional testing of gene variant is required to provide the highest level of evidence. The emergence of AlphaFold2 has transformed the field of protein structure determination, and here we outline a strategy that leverages predicted protein structure to enhance genetic variant classification. We used the gene IRF6 as a case study due to its clinical relevance, its critical role in cleft lip/palate malformation, and the availability of experimental data on the pathogenicity of IRF6 gene variants through phenotype rescue experiments in irf6-/- zebrafish. We compared results from over 30 pathogenicity prediction tools on 37 IRF6 missense variants. IRF6 lacks an experimentally derived structure, so we used predicted structures to explore associations between mutational clustering and pathogenicity. We found that among these variants, 19 of 37 were unanimously predicted as deleterious by computational tools. Comparing in silico predictions with experimental findings, 12 variants predicted as pathogenic were experimentally determined as benign. Even with the recently published AlphaMissense model, 15/18 (83%) of the predicted pathogenic variants were experimentally determined as benign. In comparison, mapping variants to the protein revealed deleterious mutation clusters around the protein binding domain, whereas N-terminal variants tend to be benign, suggesting the importance of structural information in determining pathogenicity of mutations in this gene. In conclusion, incorporating gene-specific structural features of known pathogenic/benign mutations may provide meaningful insights into pathogenicity predictions in a gene-specific manner and facilitate the interpretation of variant pathogenicity.
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Affiliation(s)
- Hemma Murali
- Graduate Program in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA 19104, United States
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
| | - Peng Wang
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
- Master of Biotechnology Program, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Eric C. Liao
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
- Center for Craniofacial Innovation, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
| | - Kai Wang
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
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2
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Tateo V, Cigliola A, Mercinelli C, Agarwal N, Grivas P, Kamat AM, Gibb EA, Moschini M, Brausi M, Dyrskjøt L, Loriot Y, Gupta S, Colecchia M, Spiess PE, Ross JS, Necchi A. Optimizing the Use of Next-Generation Sequencing Assays in Patients With Urothelial Carcinoma: Recommendations by the 2023 San Raffaele Retreat Panel. Clin Genitourin Cancer 2024; 22:102091. [PMID: 38735133 DOI: 10.1016/j.clgc.2024.102091] [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: 03/08/2024] [Revised: 04/03/2024] [Accepted: 04/06/2024] [Indexed: 05/14/2024]
Abstract
BACKGROUND The application of precision medicine in clinical practice implies a thorough evaluation of actionable genomic alterations to streamline therapeutic decision making. Comprehensive genomic profiling of tumor via next-generation sequencing (NGS) represents a great opportunity but also several challenges. During the 2023 San Raffaele Retreat, we aimed to provide expert recommendations for the optimal use of NGS in urothelial carcinoma (UC). MATERIALS AND METHODS A modified Delphi method was utilized, involving a panel of 12 experts in UC from European and United States centers, including oncologists, urologists, pathologists, and translational scientists. An initial survey, conducted before the meeting, delivered 15 statements to the panel. A consensus was defined when ≥70% agreement was reached for each statement. Statements not meeting the consensus threshold were discussed during the meeting. RESULTS Nine of the 15 statements covering patient selection, cancer characteristics, and type of NGS assay, achieved a consensus during the survey. The remaining six statements addressing the optimal timing of NGS use, the ideal source of tumor biospecimen for NGS testing, and the subsequent need to evaluate the germline nature of certain genomic findings were discussed during the meeting, leading to unanimous agreement at the end of the conference. CONCLUSION This consensus-building effort addressed multiple unanswered questions regarding the use of NGS in UC. The opinion of experts was in favor of broader use of NGS. In a setting where recommendations/guidelines may be limited, these insights may aid clinicians to provide informed counselling and raise the bar of precision and personalized therapy.
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Affiliation(s)
- Valentina Tateo
- Department of Medical Oncology, IRCCS San Raffaele Hospital, Milan, Italy.
| | - Antonio Cigliola
- Department of Medical Oncology, IRCCS San Raffaele Hospital, Milan, Italy
| | - Chiara Mercinelli
- Department of Medical Oncology, IRCCS San Raffaele Hospital, Milan, Italy
| | - Neeraj Agarwal
- Huntsman Cancer Institute (NCI-CCC), University of Utah, Salt Lake City, UT
| | - Petros Grivas
- Division of Hematology Oncology, Department of Medicine, University of Washington, Seattle, WA
| | - Ashish M Kamat
- Department of Urology, University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Marco Moschini
- Department of Urology, IRCCS San Raffaele Hospital, Milan, Italy
| | - Maurizio Brausi
- Department of Urology, Cure Hesperia Hospital, Modena, Italy
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Yohann Loriot
- Département de Médecine Oncologique, Institut Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Shilpa Gupta
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Maurizio Colecchia
- Department of Pathology, IRCCS San Raffaele Hospital, Milan, Italy; Vita-Salute San Raffaele University, Milan, Italy
| | - Philippe E Spiess
- Department of GU Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Jeffrey S Ross
- Foundation Medicine, Inc., Cambridge, MA; SUNY Upstate Medical University, Syracuse, NY
| | - Andrea Necchi
- Department of Medical Oncology, IRCCS San Raffaele Hospital, Milan, Italy; Vita-Salute San Raffaele University, Milan, Italy
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3
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Tao Y, Feng T, Zhou L, Han L. Identification of key differentially expressed immune related genes in patients with persistent atrial fibrillation: an integrated bioinformation analysis. BMC Cardiovasc Disord 2024; 24:346. [PMID: 38977948 PMCID: PMC11229288 DOI: 10.1186/s12872-024-04007-6] [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: 03/14/2024] [Accepted: 06/24/2024] [Indexed: 07/10/2024] Open
Abstract
OBJECTIVE We aimed to investigate key differentially expressed immune related genes in persistent atrial fibrillation. METHODS Gene expression profiles were downloaded from Gene Expression Omnibus (GEO) using "GEO query" package. "limma" package and "sva" package were used to conduct normalization and eliminate batch effects, respectively. We screened out differentially expressed genes (DEGs) based on "limma" package with the standard of |log fold change (FC)| ≥ 1.5 and false discovery rate (FDR) < 0.05. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of DEGs were performed by "clusterProfler" package. We further applied LASSO to select key DEGs, and intersected key DEGs with immune related genes from ImmPort database. The ROC curve of each DEIRG was constructed to evaluate its diagnostic efficiency for AF. RESULTS A total of 103 DEGs we were screened out, of them, 48 genes were down-regulated and 55 genes were up-regulated. Result of functional enrichment analysis show that, most of DEGs were related to immune response, inflammation, and oxidative stress. Ultimately, CYBB, RORB, S100A12, and CHGB were determined as key DEIRGs, each of which displayed a favor efficiency for diagnosing persistent AF. CONCLUSION CYBB, RORB, S100A12, and CHGB were identified as key DEIRGs in persistent AF, and future studies are needed to further explore the underlying roles of CYBB, RORB, S100A12, and CHGB in persistent AF.
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Affiliation(s)
- Yijing Tao
- Department of Cardiology, Changshu Hospital Affiliated to Soochow University, Changshu No. 1 People's Hospital, Changshu, 215500, China
| | - Tonghui Feng
- Department of Anesthesia Surgery, Zhejiang Hospital, Hangzhou, 310000, China.
| | - Lucien Zhou
- Independent researcher, Changshu, 215500, China.
| | - Leng Han
- Department of Cardiology, Changshu Hospital Affiliated to Soochow University, Changshu No. 1 People's Hospital, Changshu, 215500, China.
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Li Y, Zhu R, Jin J, Guo H, Zhang J, He Z, Liang T, Guo L. Exploring the Role of Clustered Mutations in Carcinogenesis and Their Potential Clinical Implications in Cancer. Int J Mol Sci 2024; 25:6744. [PMID: 38928450 PMCID: PMC11203652 DOI: 10.3390/ijms25126744] [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: 04/23/2024] [Revised: 06/07/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Abnormal cell proliferation and growth leading to cancer primarily result from cumulative genome mutations. Single gene mutations alone do not fully explain cancer onset and progression; instead, clustered mutations-simultaneous occurrences of multiple mutations-are considered to be pivotal in cancer development and advancement. These mutations can affect different genes and pathways, resulting in cells undergoing malignant transformation with multiple functional abnormalities. Clustered mutations influence cancer growth rates, metastatic potential, and drug treatment sensitivity. This summary highlights the various types and characteristics of clustered mutations to understand their associations with carcinogenesis and discusses their potential clinical significance in cancer. As a unique mutation type, clustered mutations may involve genomic instability, DNA repair mechanism defects, and environmental exposures, potentially correlating with responsiveness to immunotherapy. Understanding the characteristics and underlying processes of clustered mutations enhances our comprehension of carcinogenesis and cancer progression, providing new diagnostic and therapeutic approaches for cancer.
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Affiliation(s)
- Yi Li
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Rui Zhu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Jiaming Jin
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (J.J.); (Z.H.)
| | - Haochuan Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Jiaxi Zhang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Zhiheng He
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (J.J.); (Z.H.)
| | - Tingming Liang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Li Guo
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (J.J.); (Z.H.)
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Robertson AJ, Mallett AJ, Stark Z, Sullivan C. It Is in Our DNA: Bringing Electronic Health Records and Genomic Data Together for Precision Medicine. JMIR BIOINFORMATICS AND BIOTECHNOLOGY 2024; 5:e55632. [PMID: 38935958 PMCID: PMC11211701 DOI: 10.2196/55632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/08/2024] [Accepted: 04/09/2024] [Indexed: 06/29/2024]
Abstract
Health care is at a turning point. We are shifting from protocolized medicine to precision medicine, and digital health systems are facilitating this shift. By providing clinicians with detailed information for each patient and analytic support for decision-making at the point of care, digital health technologies are enabling a new era of precision medicine. Genomic data also provide clinicians with information that can improve the accuracy and timeliness of diagnosis, optimize prescribing, and target risk reduction strategies, all of which are key elements for precision medicine. However, genomic data are predominantly seen as diagnostic information and are not routinely integrated into the clinical workflows of electronic medical records. The use of genomic data holds significant potential for precision medicine; however, as genomic data are fundamentally different from the information collected during routine practice, special considerations are needed to use this information in a digital health setting. This paper outlines the potential of genomic data integration with electronic records, and how these data can enable precision medicine.
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Affiliation(s)
- Alan J Robertson
- Faculty of Medicine, University of Queensland, Hertson, Australia
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Queensland Digital Health Centre, University of Queensland, Brisbane, Australia
- The Genomic Institute, Department of Health, Queensland Government, Brisbane, Australia
| | - Andrew J Mallett
- Department of Renal Medicine, Townsville University Hospital, Townsville, Australia
- College of Medicine and Dentistry, James Cook University, Townsville, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
- Australian Genomics, Melbourne, Australia
- University of Melbourne, Melbourne, Australia
| | - Clair Sullivan
- Queensland Digital Health Centre, University of Queensland, Brisbane, Australia
- Centre for Health Services Research, Faculty of Medicine, University of Queensland, Woolloongabba, Australia
- Metro North Hospital and Health Service, Department of Health, Queensland Government, Brisbane, Australia
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Matsuoka T, Yashiro M. Bioinformatics Analysis and Validation of Potential Markers Associated with Prediction and Prognosis of Gastric Cancer. Int J Mol Sci 2024; 25:5880. [PMID: 38892067 PMCID: PMC11172243 DOI: 10.3390/ijms25115880] [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: 04/18/2024] [Revised: 05/23/2024] [Accepted: 05/25/2024] [Indexed: 06/21/2024] Open
Abstract
Gastric cancer (GC) is one of the most common cancers worldwide. Most patients are diagnosed at the progressive stage of the disease, and current anticancer drug advancements are still lacking. Therefore, it is crucial to find relevant biomarkers with the accurate prediction of prognoses and good predictive accuracy to select appropriate patients with GC. Recent advances in molecular profiling technologies, including genomics, epigenomics, transcriptomics, proteomics, and metabolomics, have enabled the approach of GC biology at multiple levels of omics interaction networks. Systemic biological analyses, such as computational inference of "big data" and advanced bioinformatic approaches, are emerging to identify the key molecular biomarkers of GC, which would benefit targeted therapies. This review summarizes the current status of how bioinformatics analysis contributes to biomarker discovery for prognosis and prediction of therapeutic efficacy in GC based on a search of the medical literature. We highlight emerging individual multi-omics datasets, such as genomics, epigenomics, transcriptomics, proteomics, and metabolomics, for validating putative markers. Finally, we discuss the current challenges and future perspectives to integrate multi-omics analysis for improving biomarker implementation. The practical integration of bioinformatics analysis and multi-omics datasets under complementary computational analysis is having a great impact on the search for predictive and prognostic biomarkers and may lead to an important revolution in treatment.
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Affiliation(s)
- Tasuku Matsuoka
- Department of Molecular Oncology and Therapeutics, Osaka Metropolitan University Graduate School of Medicine, 1-4-3 Asahi-machi, Abeno-ku, Osaka 5458585, Japan;
- Institute of Medical Genetics, Osaka Metropolitan University, 1-4-3 Asahi-machi, Abeno-ku, Osaka 5458585, Japan
| | - Masakazu Yashiro
- Department of Molecular Oncology and Therapeutics, Osaka Metropolitan University Graduate School of Medicine, 1-4-3 Asahi-machi, Abeno-ku, Osaka 5458585, Japan;
- Institute of Medical Genetics, Osaka Metropolitan University, 1-4-3 Asahi-machi, Abeno-ku, Osaka 5458585, Japan
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7
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Durand M, Cabaud Gibouin V, Duplomb L, Salmi L, Caillot M, Sola B, Camus V, Jardin F, Garrido C, Jego G. A first-in-class inhibitor of HSP110 to potentiate XPO1-targeted therapy in primary mediastinal B-cell lymphoma and classical Hodgkin lymphoma. J Exp Clin Cancer Res 2024; 43:148. [PMID: 38773631 PMCID: PMC11110392 DOI: 10.1186/s13046-024-03068-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] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 05/10/2024] [Indexed: 05/24/2024] Open
Abstract
BACKGROUND Primary mediastinal B-cell lymphoma (PMBL) and classical Hodgkin lymphoma (cHL) are distinct hematological malignancies of B-cell origin that share many biological, molecular, and clinical characteristics. In particular, the JAK/STAT signaling pathway is a driver of tumor development due to multiple recurrent mutations, particularly in STAT6. Furthermore, the XPO1 gene that encodes exportin 1 (XPO1) shows a frequent point mutation (E571K) resulting in an altered export of hundreds of cargo proteins, which may impact the success of future therapies in PMBL and cHL. Therefore, targeted therapies have been envisioned for these signaling pathways and mutations. METHODS To identify novel molecular targets that could overcome the treatment resistance that occurs in PMBL and cHL patients, we have explored the efficacy of a first-in-class HSP110 inhibitor (iHSP110-33) alone and in combination with selinexor, a XPO1 specific inhibitor, both in vitro and in vivo. RESULTS We show that iHSP110-33 decreased the survival of several PMBL and cHL cell lines and the size of tumor xenografts. We demonstrate that HSP110 is a cargo of XPO1wt as well as of XPO1E571K. Using immunoprecipitation, proximity ligation, thermophoresis and kinase assays, we showed that HSP110 directly interacts with STAT6 and favors its phosphorylation. The combination of iHSP110-33 and selinexor induces a synergistic reduction of STAT6 phosphorylation and of lymphoma cell growth in vitro and in vivo. In biopsies from PMBL patients, we show a correlation between HSP110 and STAT6 phosphorylation levels. CONCLUSIONS These findings suggest that HSP110 could be proposed as a novel target in PMBL and cHL therapy.
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Affiliation(s)
- Manon Durand
- INSERM, UMR1231, Team HSP-Pathies Labellisée « Ligue Nationale Contre Le Cancer » and Labex LipSTIC, Dijon, 21000, France
- University of Burgundy, Medical Sciences Faculty, Dijon, 21078, France
| | - Vincent Cabaud Gibouin
- INSERM, UMR1231, Team HSP-Pathies Labellisée « Ligue Nationale Contre Le Cancer » and Labex LipSTIC, Dijon, 21000, France
- University of Burgundy, Medical Sciences Faculty, Dijon, 21078, France
| | - Laurence Duplomb
- INSERM, UMR1231, Equipe GAD, University of Burgundy, Dijon, 21078, France
| | - Leila Salmi
- INSERM, UMR1231, Team HSP-Pathies Labellisée « Ligue Nationale Contre Le Cancer » and Labex LipSTIC, Dijon, 21000, France
- University of Burgundy, Medical Sciences Faculty, Dijon, 21078, France
| | | | - Brigitte Sola
- INSERM, U1245, Normandy University, Caen, 14000, France
| | - Vincent Camus
- Department of Hematology, Centre Henri Becquerel, Rouen, 76000, France
| | - Fabrice Jardin
- Department of Hematology, Centre Henri Becquerel, Rouen, 76000, France
| | - Carmen Garrido
- INSERM, UMR1231, Team HSP-Pathies Labellisée « Ligue Nationale Contre Le Cancer » and Labex LipSTIC, Dijon, 21000, France
- University of Burgundy, Medical Sciences Faculty, Dijon, 21078, France
- Georges François Leclerc Cancer Centre, CGFL, Dijon, France
| | - Gaëtan Jego
- INSERM, UMR1231, Team HSP-Pathies Labellisée « Ligue Nationale Contre Le Cancer » and Labex LipSTIC, Dijon, 21000, France.
- University of Burgundy, Medical Sciences Faculty, Dijon, 21078, France.
- INSERM, UMR1231, Université Bourgogne, 7 Boulevard Jeanne d'Arc, Dijon, 21078, France.
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Hora J, Rambhia N, Mani I. Drug repurposing for personalized medicine. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 207:107-122. [PMID: 38942534 DOI: 10.1016/bs.pmbts.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Personalized medicine has emerged as a revolutionary approach to healthcare in the 21st century. By understanding a patient's unique genetic and biological characteristics, it aims to tailor treatments specifically to the individual. This approach takes into account factors such as an individual's lifestyle, genetic makeup, and environmental factors to provide targeted therapies that have the potential to be more effective and lower the risk of side reactions or ineffective treatments. It is a paradigm shift from the traditional "one size fits all" approach in medicine, where patients with similar symptoms or diagnoses receive the same standard treatments regardless of their differences. It leads to improved clinical outcomes and more efficient use of healthcare resources. Drug repurposing is a strategy that uses existing drugs for new indications and aims to take advantage of the known safety profiles, pharmacokinetics, and mechanisms of action of these drugs to accelerate the development process. Precision medicine may undergo a revolutionary change as a result, enabling the rapid development of novel treatment plans utilizing drugs that traditional methods would not otherwise link to. In this chapter, we have focused on a few strategies wherein drug repurposing has shown great success for precision medicine. The approach is particularly useful in oncology as there are many variations induced in the genetic material of cancer patients, so tailored treatment approaches go a long way. We have discussed the cases of breast cancer, glioblastoma and hepatocellular carcinoma. Other than that, we have also looked at drug repurposing approaches in anxiety disorders and COVID-19.
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Affiliation(s)
- Jahnvi Hora
- Manipal School of Life Science, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Nishita Rambhia
- Manipal School of Life Science, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Indra Mani
- Department of Microbiology, Gargi College, University of Delhi, New Delhi, India.
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Savchenko E, Bunimovich-Mendrazitsky S. Investigation toward the economic feasibility of personalized medicine for healthcare service providers: the case of bladder cancer. Front Med (Lausanne) 2024; 11:1388685. [PMID: 38808135 PMCID: PMC11130437 DOI: 10.3389/fmed.2024.1388685] [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: 02/20/2024] [Accepted: 04/26/2024] [Indexed: 05/30/2024] Open
Abstract
In today's complex healthcare landscape, the pursuit of delivering optimal patient care while navigating intricate economic dynamics poses a significant challenge for healthcare service providers (HSPs). In this already complex dynamic, the emergence of clinically promising personalized medicine-based treatment aims to revolutionize medicine. While personalized medicine holds tremendous potential for enhancing therapeutic outcomes, its integration within resource-constrained HSPs presents formidable challenges. In this study, we investigate the economic feasibility of implementing personalized medicine. The central objective is to strike a balance between catering to individual patient needs and making economically viable decisions. Unlike conventional binary approaches to personalized treatment, we propose a more nuanced perspective by treating personalization as a spectrum. This approach allows for greater flexibility in decision-making and resource allocation. To this end, we propose a mathematical framework to investigate our proposal, focusing on Bladder Cancer (BC) as a case study. Our results show that while it is feasible to introduce personalized medicine, a highly efficient but highly expensive one would be short-lived relative to its less effective but cheaper alternative as the latter can be provided to a larger cohort of patients, optimizing the HSP's objective better.
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10
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Blanluet C, Kuo CJ, Bhattacharya A, Santiago JG. Design and Evaluation of a Robust CRISPR Kinetic Assay for Hot-Spot Genotyping. Anal Chem 2024; 96:7444-7451. [PMID: 38684052 DOI: 10.1021/acs.analchem.3c05657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Next-generation sequencing offers highly multiplexed and accurate detection of nucleic acid sequences but at the expense of complex workflows and high input requirements. The ease of use of CRISPR-Cas12 assays is attractive and may enable highly accurate detection of sequences implicated in, for example, cancer pathogenic variants. CRISPR assays often employ end-point measurements of Cas12 trans-cleavage activity after Cas12 activation by the target; however, end point-based methods can be limited in accuracy and robustness by arbitrary experimental choices. To overcome such limitations, we develop and demonstrate here an accurate assay targeting a mutation of the epidermal growth factor gene implicated in lung cancer (exon 19 deletion). The assay is based on characterizing the kinetics of Cas12 trans-cleavage to discriminate the mutant from wild-type targets. We performed extensive experiments (780 reactions) to calibrate key assay design parameters, including the guide RNA sequence, reporter sequence, reporter concentration, enzyme concentration, and DNA target type. Interestingly, we observed a competitive reaction between the target and reporter molecules that has important consequences for the design of CRISPR assays, which use preamplification to improve sensitivity. Finally, we demonstrate the assay on 18 tumor-extracted amplicons and 100 training iterations with 99% accuracy and discuss discrimination parameters and models to improve wild type versus mutant classification.
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Affiliation(s)
- Charles Blanluet
- CentraleSupelec─Universite Paris-Saclay, 91190 Gif-sur-Yvette, France
- Department of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
| | - Calvin J Kuo
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Asmita Bhattacharya
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Juan G Santiago
- Department of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
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11
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Shalata W, Maimon Rabinovich N, Agbarya A, Yakobson A, Dudnik Y, Abu Jama A, Cohen AY, Shalata S, Abu Hamed A, Ilan Ber T, Machluf O, Shoham Levin G, Meirovitz A. Efficacy of Pembrolizumab vs. Nivolumab Plus Ipilimumab in Metastatic NSCLC in Relation to PD-L1 and TMB Status. Cancers (Basel) 2024; 16:1825. [PMID: 38791905 PMCID: PMC11119071 DOI: 10.3390/cancers16101825] [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: 04/08/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
The efficacy of immune checkpoint inhibitor (ICI) therapy concerning programmed death ligand 1 (PD-L1) status is well established in patients diagnosed with non-small cell lung cancer (NSCLC). However, there remains a paucity of evidence regarding the efficacy concerning tumor mutational burden (TMB) in both clinical trials and real-world data (RWD). In the current article, clinicopathological and molecular epidemiological data were meticulously collected, and treatment modalities were meticulously recorded. The final analysis included a study population of 194 patients. Median age was 67 years (range 37-86), with the majority being male (71.13%), and 85.71% of patients were either current or former smokers at diagnosis. Adenocarcinoma accounted for most diagnoses (71.65%), followed by squamous cell carcinoma (24.23%). In terms of PD-L1 status, 42.78% had an expression level below 1%, 28.35% had an expression between 1-49%, and 28.87% had an expression above 50%. The TMB ranged from 0 to 75, with a median of 10.31 (range 0-75) for PD-L1 expression below 1%, with a median of 9.73 (range 0.95-39.63) for PD-L1 expression between 1-49%, and a median of 9.72 (range 0.95-48) for PD-L1 expression above 50%. Corresponding to patients with low PDL-1 less than 1% and low TMB (0-5), the median overall survival (mOS) was 16 (p = 0.18), and 15 months (p = 0.22), patients with medium PDL-1 (1-49%) and medium TMB (5-10), the mOS was 15 (p = 0.18) and 16 months (p = 0.22), patients with high PDL-1 (>50) and high TMB (>10), the mOS was 24 (p = 0.18) and 21 (p = 0.22) months. This study represents the largest academic RWD dataset concerning PD-L1 and TMB status in patients with locally advanced and metastatic NSCLC.
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Affiliation(s)
- Walid Shalata
- The Legacy Heritage Cancer Center and Dr. Larry Norton Institute, Soroka Medical Center, Beer-Sheva 84105, Israel
- Medical School for International Health, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | | | - Abed Agbarya
- Oncology Department, Bnai Zion Medical Center, Haifa 31048, Israel
| | - Alexander Yakobson
- The Legacy Heritage Cancer Center and Dr. Larry Norton Institute, Soroka Medical Center, Beer-Sheva 84105, Israel
- Medical School for International Health, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Yulia Dudnik
- The Legacy Heritage Cancer Center and Dr. Larry Norton Institute, Soroka Medical Center, Beer-Sheva 84105, Israel
- Medical School for International Health, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Ashraf Abu Jama
- The Legacy Heritage Cancer Center and Dr. Larry Norton Institute, Soroka Medical Center, Beer-Sheva 84105, Israel
- Medical School for International Health, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Ahron Yehonatan Cohen
- The Legacy Heritage Cancer Center and Dr. Larry Norton Institute, Soroka Medical Center, Beer-Sheva 84105, Israel
- Medical School for International Health, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Sondos Shalata
- Nutrition Unit, Galilee Medical Center, Nahariya 22000, Israel;
| | - Ahmad Abu Hamed
- The Legacy Heritage Cancer Center and Dr. Larry Norton Institute, Soroka Medical Center, Beer-Sheva 84105, Israel
| | | | | | | | - Amichay Meirovitz
- The Legacy Heritage Cancer Center and Dr. Larry Norton Institute, Soroka Medical Center, Beer-Sheva 84105, Israel
- Medical School for International Health, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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12
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Chang P, Amaral LJ, Asher A, Clauw D, Jones B, Thompson P, Warner AS. A perspective on a precision approach to pain in cancer; moving beyond opioid therapy. Disabil Rehabil 2024; 46:2174-2183. [PMID: 37194659 DOI: 10.1080/09638288.2023.2212916] [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: 09/11/2022] [Accepted: 05/07/2023] [Indexed: 05/18/2023]
Abstract
PURPOSE Cancer-related pain is primarily treated with opioids which while effective can add significant patient burden due to side effects, associated stigma, and timely access. The purpose of this perspective discussion is to argue for a precision approach to pain in cancer based on a biopsychosocial and spiritual model which we argue can offer a higher quality of life while limiting opioid use. CONCLUSIONS Pain in cancer represents a heterogenous process with multiple contributing and modulating factors. Specific characterization of pain as either nociceptive, neuropathic, nociplastic, or mixed can allow for targeted treatments. Additional assessment of biopsychosocial and spiritual issues can elucidate further points of targeted intervention which can lead to overall greater pain control.
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Affiliation(s)
- Philip Chang
- Philip Chang - Cedars Sinai Medical Center, Los Angeles, CA
| | | | - Arash Asher
- Arash Asher - Cedars Sinai Medical Center, Los Angeles, CA
| | | | - Bronwen Jones
- Bronwen Jones - Cedars Sinai Medical Center, Los Angeles, CA
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13
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Matsukiyo Y, Yamanaka C, Yamanishi Y. De Novo Generation of Chemical Structures of Inhibitor and Activator Candidates for Therapeutic Target Proteins by a Transformer-Based Variational Autoencoder and Bayesian Optimization. J Chem Inf Model 2024; 64:2345-2355. [PMID: 37768595 DOI: 10.1021/acs.jcim.3c00824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
Deep generative models for molecular generation have been gaining much attention as structure generators to accelerate drug discovery. However, most previously developed methods are chemistry-centric approaches, and comprehensive biological responses in the cell have not been taken into account. In this study, we propose a novel computational method, TRIOMPHE-BOA (transcriptome-based inference and generation of molecules with desired phenotypes using the Bayesian optimization algorithm), to generate new chemical structures of inhibitor or activator candidates for therapeutic target proteins by integrating chemically and genetically perturbed transcriptome profiles. In the algorithm, the substructures of multiple molecules that were selected based on the transcriptome analysis are fused in the design of new chemical structures by exploring the latent space of a Transformer-based variational autoencoder using Bayesian optimization. Our results demonstrate the usefulness of the proposed method in terms of having high reproducibility of existing ligands for 10 therapeutic target proteins when compared with previous methods. Moreover, this method can be applied to proteins without detailed 3D structures or known ligands and is expected to become a powerful tool for more efficient hit identification.
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Affiliation(s)
- Yuki Matsukiyo
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan
| | - Chikashige Yamanaka
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan
| | - Yoshihiro Yamanishi
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan
- Graduate School of Informatics, Nagoya University, Chikusa, Nagoya, Aichi 464-8601, Japan
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14
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Grynberg S, Vered M, Shapira-Frommer R, Asher N, Ben-Betzalel G, Stoff R, Steinberg Y, Amariglio N, Greenberg G, Barshack I, Toren A, Yahalom R, Schachter J, Rechavi G, Hirschhorn A, Abebe Campino G. Neoadjuvant BRAF-targeted therapy for ameloblastoma of the mandible: an organ preservation approach. J Natl Cancer Inst 2024; 116:539-546. [PMID: 37966914 DOI: 10.1093/jnci/djad232] [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: 06/15/2023] [Revised: 10/06/2023] [Accepted: 11/03/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND Ameloblastoma is a rare odontogenic neoplasm frequently located in the mandible. Standard treatment involves radical bone resection and immediate reconstruction, causing functional, aesthetic, and psychological impairments. The BRAF V600E mutation is present in approximately 80% of mandible ameloblastomas, and BRAF inhibitors have demonstrated sustained responses in unresectable cases. METHODS We identified ameloblastoma patients planned for ablative surgery and screened them for BRAF V600E mutation. Neoadjuvant BRAF inhibitors were offered to facilitate jaw preservation surgery. Retrospective data collection encompassed treatment regimens, tolerability, tumor response, and conversion to mandible preservation surgery. RESULTS Between 2017 and 2022, a total of 11 patients received dabrafenib (n = 6) or dabrafenib with trametinib (n = 5). The median age was 19 (range = 10-83) years. Median treatment duration was 10 (range = 3-20) months. All (100%) patients achieved a radiological response. Ten (91%) patients successfully converted to mandible preservation surgery with residual tumor enucleation. One patient attained complete radiological response, and surgery was not performed. Among the 10 surgically treated patients, all exhibited a pathological response, with 4 achieving near complete response and 6 partial response. At a median follow-up of 14 (range = 7-37) months after surgery, 1 case of recurrence was observed. Grade 1-2 adverse effects were reported in 8 (73%) patients, with a single case of grade 3 (hepatitis). Dose modification was necessary for 3 patients, and 4 experienced treatment interruptions, while 1 patient permanently discontinued therapy. CONCLUSIONS Neoadjuvant BRAF inhibition may offer a safe and effective strategy for organ preservation in mandible ameloblastoma treatment.
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Affiliation(s)
- Shirly Grynberg
- Ella Lemelbaum Institute of Immuno-Oncology and Melanoma, Sheba Medical Center, Tel Hashomer, Israel
| | - Marilena Vered
- Institue of Pathology, Sheba Medical Center, Tel Hashomer, Israel
| | - Ronnie Shapira-Frommer
- Ella Lemelbaum Institute of Immuno-Oncology and Melanoma, Sheba Medical Center, Tel Hashomer, Israel
| | - Nethanel Asher
- Ella Lemelbaum Institute of Immuno-Oncology and Melanoma, Sheba Medical Center, Tel Hashomer, Israel
| | - Guy Ben-Betzalel
- Ella Lemelbaum Institute of Immuno-Oncology and Melanoma, Sheba Medical Center, Tel Hashomer, Israel
| | - Ronen Stoff
- Ella Lemelbaum Institute of Immuno-Oncology and Melanoma, Sheba Medical Center, Tel Hashomer, Israel
| | - Yael Steinberg
- Ella Lemelbaum Institute of Immuno-Oncology and Melanoma, Sheba Medical Center, Tel Hashomer, Israel
| | - Ninette Amariglio
- Sheba Cancer Research Center, Wohl Institute of Translational Medicine, Sheba Medical Center, Tel Hashomer, Israel
| | - Gahl Greenberg
- Department of Diagnostic Imaging, Sheba Medical Center, Tel Hashomer, Israel
| | - Iris Barshack
- Institue of Pathology, Sheba Medical Center, Tel Hashomer, Israel
| | - Amos Toren
- Division of Pediatric Hemato-Oncology, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Ran Yahalom
- Department of Cranio-Maxillofacial Surgery, Sheba Medical Center, Tel Hashomer, Israel
| | - Jacob Schachter
- Ella Lemelbaum Institute of Immuno-Oncology and Melanoma, Sheba Medical Center, Tel Hashomer, Israel
| | - Gideon Rechavi
- Sheba Cancer Research Center, Wohl Institute of Translational Medicine, Sheba Medical Center, Tel Hashomer, Israel
| | - Ariel Hirschhorn
- Department of Cranio-Maxillofacial Surgery, Sheba Medical Center, Tel Hashomer, Israel
| | - Gadi Abebe Campino
- Division of Pediatric Hemato-Oncology, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
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15
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Li S, Zhang H, Chen T, Zhang X, Shang G. Current treatment and novel insights regarding ROS1-targeted therapy in malignant tumors. Cancer Med 2024; 13:e7201. [PMID: 38629293 PMCID: PMC11022151 DOI: 10.1002/cam4.7201] [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: 05/20/2023] [Revised: 03/22/2024] [Accepted: 04/06/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND The proto-oncogene ROS1 encodes an intrinsic type I membrane protein of the tyrosine kinase/insulin receptor family. ROS1 facilitates the progression of various malignancies via self-mutations or rearrangements. Studies on ROS1-directed tyrosine kinase inhibitors have been conducted, and some have been approved by the FDA for clinical use. However, the adverse effects and mechanisms of resistance associated with ROS1 inhibitors remain unknown. In addition, next-generation ROS1 inhibitors, which have the advantage of treating central nervous system metastases and alleviating endogenous drug resistance, are still in the clinical trial stage. METHOD In this study, we searched relevant articles reporting the mechanism and clinical application of ROS1 in recent years; systematically reviewed the biological mechanisms, diagnostic methods, and research progress on ROS1 inhibitors; and provided perspectives for the future of ROS1-targeted therapy. RESULTS ROS1 is most expressed in malignant tumours. Only a few ROS1 kinase inhibitors are currently approved for use in NSCLC, the efficacy of other TKIs for NSCLC and other malignancies has not been ascertained. There is no effective standard treatment for adverse events or resistance to ROS1-targeted therapy. Next-generation TKIs appear capable of overcoming resistance and delaying central nervous system metastasis, but with a greater incidence of adverse effects. CONCLUSIONS Further research on next-generation TKIs regarding the localization of ROS1 and its fusion partners, binding sites for targeted drugs, and coadministration with other drugs is required. The correlation between TKIs and chemotherapy or immunotherapy in clinical practice requires further study.
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Affiliation(s)
- Shizhe Li
- Department of OrthopedicsShengjing Hospital of China Medical UniversityShenyangLiaoning ProvinceChina
| | - He Zhang
- Department of OrthopedicsShengjing Hospital of China Medical UniversityShenyangLiaoning ProvinceChina
| | - Ting Chen
- Department of OrthopedicsShengjing Hospital of China Medical UniversityShenyangLiaoning ProvinceChina
| | - Xiaowen Zhang
- Medical Research CenterShengjing Hospital of China Medical UniversityShenyangLiaoning ProvinceChina
| | - Guanning Shang
- Department of OrthopedicsShengjing Hospital of China Medical UniversityShenyangLiaoning ProvinceChina
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16
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Gallo E. The rise of big data: deep sequencing-driven computational methods are transforming the landscape of synthetic antibody design. J Biomed Sci 2024; 31:29. [PMID: 38491519 PMCID: PMC10943851 DOI: 10.1186/s12929-024-01018-5] [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: 10/16/2023] [Accepted: 03/05/2024] [Indexed: 03/18/2024] Open
Abstract
Synthetic antibodies (Abs) represent a category of artificial proteins capable of closely emulating the functions of natural Abs. Their in vitro production eliminates the need for an immunological response, streamlining the process of Ab discovery, engineering, and development. These artificially engineered Abs offer novel approaches to antigen recognition, paratope site manipulation, and biochemical/biophysical enhancements. As a result, synthetic Abs are fundamentally reshaping conventional methods of Ab production. This mirrors the revolution observed in molecular biology and genomics as a result of deep sequencing, which allows for the swift and cost-effective sequencing of DNA and RNA molecules at scale. Within this framework, deep sequencing has enabled the exploration of whole genomes and transcriptomes, including particular gene segments of interest. Notably, the fusion of synthetic Ab discovery with advanced deep sequencing technologies is redefining the current approaches to Ab design and development. Such combination offers opportunity to exhaustively explore Ab repertoires, fast-tracking the Ab discovery process, and enhancing synthetic Ab engineering. Moreover, advanced computational algorithms have the capacity to effectively mine big data, helping to identify Ab sequence patterns/features hidden within deep sequencing Ab datasets. In this context, these methods can be utilized to predict novel sequence features thereby enabling the successful generation of de novo Ab molecules. Hence, the merging of synthetic Ab design, deep sequencing technologies, and advanced computational models heralds a new chapter in Ab discovery, broadening our comprehension of immunology and streamlining the advancement of biological therapeutics.
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Affiliation(s)
- Eugenio Gallo
- Department of Medicinal Chemistry, Avance Biologicals, 950 Dupont Street, Toronto, ON, M6H 1Z2, Canada.
- Department of Protein Engineering, RevivAb, Av. Ipiranga, 6681, Partenon, Porto Alegre, RS, 90619-900, Brazil.
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17
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d’Amati A, Bargiacchi L, Rossi S, Carai A, Bertero L, Barresi V, Errico ME, Buccoliero AM, Asioli S, Marucci G, Del Baldo G, Mastronuzzi A, Miele E, D’Antonio F, Schiavello E, Biassoni V, Massimino M, Gessi M, Antonelli M, Gianno F. Pediatric CNS tumors and 2021 WHO classification: what do oncologists need from pathologists? Front Mol Neurosci 2024; 17:1268038. [PMID: 38544524 PMCID: PMC10966132 DOI: 10.3389/fnmol.2024.1268038] [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: 07/27/2023] [Accepted: 02/23/2024] [Indexed: 05/14/2024] Open
Abstract
The fifth edition of the WHO Classification of Tumors of the Central Nervous System (CNS), published in 2021, established new approaches to both CNS tumor nomenclature and grading, emphasizing the importance of integrated diagnoses and layered reports. This edition increased the role of molecular diagnostics in CNS tumor classification while still relying on other established approaches such as histology and immunohistochemistry. Moreover, it introduced new tumor types and subtypes based on novel diagnostic technologies such as DNA methylome profiling. Over the past decade, molecular techniques identified numerous key genetic alterations in CSN tumors, with important implications regarding the understanding of pathogenesis but also for prognosis and the development and application of effective molecularly targeted therapies. This review summarizes the major changes in the 2021 fifth edition classification of pediatric CNS tumors, highlighting for each entity the molecular alterations and other information that are relevant for diagnostic, prognostic, or therapeutic purposes and that patients' and oncologists' need from a pathology report.
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Affiliation(s)
- Antonio d’Amati
- Unit of Anatomical Pathology, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari “Aldo Moro”, Bari, Italy
- Unit of Human Anatomy and Histology, Department of Translational Biomedicine and Neuroscience (DiBraiN), University of Bari “Aldo Moro”, Bari, Italy
- Unit of Anatomical Pathology, Department of Radiology, Oncology and Anatomical Pathology, University La Sapienza, Rome, Italy
- Neuropathology Unit, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Università Cattolica S. Cuore, Roma, Italy
| | - Lavinia Bargiacchi
- Unit of Anatomical Pathology, Department of Radiology, Oncology and Anatomical Pathology, University La Sapienza, Rome, Italy
| | - Sabrina Rossi
- Pathology Unit, Department of Laboratories, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Andrea Carai
- Department of Neuroscience and Neurorehabilitation, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Luca Bertero
- Pathology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Valeria Barresi
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Maria Elena Errico
- Department of Pathology, AORN Santobono Pausilipon, Pediatric Hospital, Naples, Italy
| | | | - Sofia Asioli
- Department of Biomedical and Neuromotor Sciences (DIBINEM), Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Gianluca Marucci
- Neuropathology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Giada Del Baldo
- Department of Paediatric Haematology/Oncology, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Angela Mastronuzzi
- Department of Paediatric Haematology/Oncology, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Evelina Miele
- Department of Paediatric Haematology/Oncology, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Federica D’Antonio
- Department of Paediatric Haematology/Oncology, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Elisabetta Schiavello
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Veronica Biassoni
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Maura Massimino
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Marco Gessi
- Neuropathology Unit, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Università Cattolica S. Cuore, Roma, Italy
| | - Manila Antonelli
- Unit of Anatomical Pathology, Department of Radiology, Oncology and Anatomical Pathology, University La Sapienza, Rome, Italy
- IRCCS Neuromed, Pozzilli, Isernia, Italy
| | - Francesca Gianno
- Unit of Anatomical Pathology, Department of Radiology, Oncology and Anatomical Pathology, University La Sapienza, Rome, Italy
- IRCCS Neuromed, Pozzilli, Isernia, Italy
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18
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Wang P, Leong QY, Lau NY, Ng WY, Kwek SP, Tan L, Song SW, You K, Chong LM, Zhuang I, Ong YH, Foo N, Tadeo X, Kumar KS, Vijayakumar S, Sapanel Y, Raczkowska MN, Remus A, Blasiak A, Ho D. N-of-1 medicine. Singapore Med J 2024; 65:167-175. [PMID: 38527301 PMCID: PMC11060644 DOI: 10.4103/singaporemedj.smj-2023-243] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/19/2024] [Indexed: 03/27/2024]
Abstract
ABSTRACT The fields of precision and personalised medicine have led to promising advances in tailoring treatment to individual patients. Examples include genome/molecular alteration-guided drug selection, single-patient gene therapy design and synergy-based drug combination development, and these approaches can yield substantially diverse recommendations. Therefore, it is important to define each domain and delineate their commonalities and differences in an effort to develop novel clinical trial designs, streamline workflow development, rethink regulatory considerations, create value in healthcare and economics assessments, and other factors. These and other segments are essential to recognise the diversity within these domains to accelerate their respective workflows towards practice-changing healthcare. To emphasise these points, this article elaborates on the concept of digital health and digital medicine-enabled N-of-1 medicine, which individualises combination regimen and dosing using a patient's own data. We will conclude with recommendations for consideration when developing novel workflows based on emerging digital-based platforms.
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Affiliation(s)
- Peter Wang
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore
| | - Qiao Ying Leong
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
| | - Ni Yin Lau
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
| | - Wei Ying Ng
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
| | - Siong Peng Kwek
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
| | - Lester Tan
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore
| | - Shang-Wei Song
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore
| | - Kui You
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore
| | - Li Ming Chong
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore
| | - Isaiah Zhuang
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
| | - Yoong Hun Ong
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
| | - Nigel Foo
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore
| | - Xavier Tadeo
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
| | - Kirthika Senthil Kumar
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
| | - Smrithi Vijayakumar
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
| | - Yoann Sapanel
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
- Singapore’s Health District @ Queenstown, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Marlena Natalia Raczkowska
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
| | - Alexandria Remus
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore
- Heat Resilience Performance Centre (HRPC), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Agata Blasiak
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Dean Ho
- Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore
- Singapore’s Health District @ Queenstown, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- The Bia-Echo Asia Centre for Reproductive Longevity and Equality, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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Huang Z, Fu Y, Yang H, Zhou Y, Shi M, Li Q, Liu W, Liang J, Zhu L, Qin S, Hong H, Liu Y. Liquid biopsy in T-cell lymphoma: biomarker detection techniques and clinical application. Mol Cancer 2024; 23:36. [PMID: 38365716 PMCID: PMC10874034 DOI: 10.1186/s12943-024-01947-7] [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: 11/03/2023] [Accepted: 01/25/2024] [Indexed: 02/18/2024] Open
Abstract
T-cell lymphoma is a highly invasive tumor with significant heterogeneity. Invasive tissue biopsy is the gold standard for acquiring molecular data and categorizing lymphoma patients into genetic subtypes. However, surgical intervention is unfeasible for patients who are critically ill, have unresectable tumors, or demonstrate low compliance, making tissue biopsies inaccessible to these patients. A critical need for a minimally invasive approach in T-cell lymphoma is evident, particularly in the areas of early diagnosis, prognostic monitoring, treatment response, and drug resistance. Therefore, the clinical application of liquid biopsy techniques has gained significant attention in T-cell lymphoma. Moreover, liquid biopsy requires fewer samples, exhibits good reproducibility, and enables real-time monitoring at molecular levels, thereby facilitating personalized health care. In this review, we provide a comprehensive overview of the current liquid biopsy biomarkers used for T-cell lymphoma, focusing on circulating cell-free DNA (cfDNA), circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), Epstein-Barr virus (EBV) DNA, antibodies, and cytokines. Additionally, we discuss their clinical application, detection methodologies, ongoing clinical trials, and the challenges faced in the field of liquid biopsy.
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Affiliation(s)
- Zongyao Huang
- Department of Pathology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Yao Fu
- Department of Pathology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Hong Yang
- Department of Pathology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Yehan Zhou
- Department of Pathology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Min Shi
- Department of Pathology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Qingyun Li
- Genecast Biotechnology Co., Ltd, Wuxi, 214104, China
| | - Weiping Liu
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Junheng Liang
- Nanjing Geneseeq Technology Inc., Nanjing, 210032, Jiangsu, China
| | - Liuqing Zhu
- Nanjing Geneseeq Technology Inc., Nanjing, 210032, Jiangsu, China
| | - Sheng Qin
- Department of Pathology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China.
| | - Huangming Hong
- Department of Medical Oncology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China.
| | - Yang Liu
- Department of Pathology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China.
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20
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Gallo E. Revolutionizing Synthetic Antibody Design: Harnessing Artificial Intelligence and Deep Sequencing Big Data for Unprecedented Advances. Mol Biotechnol 2024:10.1007/s12033-024-01064-2. [PMID: 38308755 DOI: 10.1007/s12033-024-01064-2] [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: 11/03/2023] [Accepted: 01/02/2024] [Indexed: 02/05/2024]
Abstract
Synthetic antibodies (Abs) represent a category of engineered proteins meticulously crafted to replicate the functions of their natural counterparts. Such Abs are generated in vitro, enabling advanced molecular alterations associated with antigen recognition, paratope site engineering, and biochemical refinements. In a parallel realm, deep sequencing has brought about a paradigm shift in molecular biology. It facilitates the prompt and cost-effective high-throughput sequencing of DNA and RNA molecules, enabling the comprehensive big data analysis of Ab transcriptomes, including specific regions of interest. Significantly, the integration of artificial intelligence (AI), based on machine- and deep- learning approaches, has fundamentally transformed our capacity to discern patterns hidden within deep sequencing big data, including distinctive Ab features and protein folding free energy landscapes. Ultimately, current AI advances can generate approximations of the most stable Ab structural configurations, enabling the prediction of de novo synthetic Abs. As a result, this manuscript comprehensively examines the latest and relevant literature concerning the intersection of deep sequencing big data and AI methodologies for the design and development of synthetic Abs. Together, these advancements have accelerated the exploration of antibody repertoires, contributing to the refinement of synthetic Ab engineering and optimizations, and facilitating advancements in the lead identification process.
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Affiliation(s)
- Eugenio Gallo
- Avance Biologicals, Department of Medicinal Chemistry, 950 Dupont Street, Toronto, ON, M6H 1Z2, Canada.
- RevivAb, Department of Protein Engineering, Av. Ipiranga, 6681, Partenon, Porto Alegre, RS, 90619-900, Brazil.
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21
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Cruz-Romero SD, González S, Juez JY, Becerra DS, Baldión AM, Hakim JA, González-Devia D, Perdomo S, Rodríguez-Urrego PA. TIROSEC: Molecular, Clinical and Histopathological Profile of Papillary Thyroid Carcinoma in a Colombian Cohort. Adv Ther 2024; 41:792-805. [PMID: 38170436 DOI: 10.1007/s12325-023-02756-y] [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: 09/11/2023] [Accepted: 11/29/2023] [Indexed: 01/05/2024]
Abstract
INTRODUCTION In Colombia, thyroid cancer ranks among the highest incidences, yet our population lacks studies on its molecular profile. This study aims to characterize clinical, histopathologic and molecular data in a Colombian cohort with papillary thyroid carcinoma (PTC). METHODS A retrospective review of clinical history, clinicopathologic characteristics, treatment and 5-10-year follow-up for all patients was done. DNA and RNA were extracted from formalin-fixed paraffin-embedded (FFPE) tissue using the Quick-DNA & RNA FFPE Min iPrep kit (Zymo Research). Next-generation sequencing (NGS) analysis was performed with SOPHiA Solid Tumor Solutions kit (SOPHiA GENETICS). Tumor mutation genomic analysis used SOPHiA DDM™ platform, with descriptive analysis reporting frequencies, means and associations via chi-square analysis. RESULTS Among 231 sequenced patients, mean age at diagnosis was 46 (± 12.35) years, with higher frequency in women (81.82%). Two cases were reclassified as non-invasive follicular thyroid neoplasm (NIFT-P); an NRAS mutation was found in one of them. Predominant histologic subtype was classic PTC (57.64%) followed by tall cell (28.82%). Of the 229 sequenced carcinomas, mutations were identified in 186 cases, including BRAF, IDH1, RAS and PIK3CA. Notable copy number variations (CNVs) were PDGFRA, CDK4 and KIT, with RET being the most frequent gene fusion, including CCDC6-RET in two classic subtype cases. CONCLUSION This is the first study in Colombia (TIROSEC) to our knowledge that integrates molecular and histopathologic profiles enriching our local comprehension and knowledge of PTC. The identification of target mutations such as BRAF, RET and NTRK fusions holds the potential to guide targeted therapies for tumor recurrence and predict aggressive behavior.
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Affiliation(s)
- Sergio D Cruz-Romero
- Pathology Department, Univeristy Hospital Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - Sebastián González
- Pathology Department, Univeristy Hospital Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - José Y Juez
- School of Engineer, Los Andes University, Bogotá, Colombia
| | | | - Ana M Baldión
- Pathology Department, Univeristy Hospital Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - José A Hakim
- Head and Neck Surgery, University Hospital Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | | | - Sandra Perdomo
- Nutrition, Genetics, and Metabolism Research Group, El Bosque University, Bogotá, Colombia
- Genomic Epidemiology Branch, International Agency for Research On Cancer (IARC/WHO), Lyon, France
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22
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Philips AO, Panda SS, Cyriac S, Moharana L, Kilaru S, Kolluri S, Rathnam K, Saju S, Raju HS, Kayal S, Biswajit D, Sehrawat A, Sundriyal D, Jose AT, Raju S, Paul P, Ganesan P. Real-World Experiences of Next-Generation Sequencing in Oncology: From an Indian Multicenter Registry and Collaborative Centers. Indian J Med Paediatr Oncol 2024. [DOI: 10.1055/s-0044-1779275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024] Open
Abstract
Abstract
Background The integration of next-generation sequencing (NGS) in guiding personalized therapy for oncology faces the challenges, primarily, of cost and drug accessibility. Limited data from Indian academic centers accentuate the need for comprehensive insights into the real-world applications of NGS in oncology.
Methods The Network of Oncology Clinical Trials in India (NOCI), accessible at www.noci-india.com, compiled data on patients who underwent NGS for solid organ cancers from January 1, 2018, to December 31, 2021. This study aimed to elucidate the testing indications, sample types analyzed, and the resultant impact on patient care.
Results Analysis of data from six centers included 278 subjects, with 24 specimens (9%) excluded due to quality test failure. Tissue constituted 59.7% of specimens, blood 38.5%, and both 1.8%. Predominantly, NGS was employed for identifying BRCA1/2 mutations (56%) and for targeted therapy in non-small-cell lung cancer (NSCLC; 28%). Only 41 (16%) patients with other cancers underwent multigene NGS panels in pursuit of targetable mutations. Among them, 13 exhibited targetable mutations, and 3 received treatment based on NGS findings.
Conclusion This study underscores that the majority of NGS applications focused on screening for BRCA1/2 mutations and identifying targetable mutations in NSCLC. However, among those undergoing NGS for advanced cancers, only a limited number received personalized therapy. The findings underscore the challenges of utilizing NGS in off-label indications within resource-constrained settings.
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Affiliation(s)
| | - Soumya Surath Panda
- Department of Medical Oncology, Institute of Medical Sciences and Sum Hospital, Odhisha, India
| | - Sunu Cyriac
- Department of Medical Oncology, Amala Institute of Medical Sciences, Kerala, India
| | - Lalatendu Moharana
- Department of Medical Oncology, Institute of Medical Sciences and Sum Hospital, Odhisha, India
| | - Sindhu Kilaru
- Department of Medical Oncology, Institute of Medical Sciences and Sum Hospital, Odhisha, India
| | - Spoorty Kolluri
- Department of Medical Oncology, Institute of Medical Sciences and Sum Hospital, Odhisha, India
| | - Krishnakumar Rathnam
- Department of Medical Oncology, Meenakshi Mission Medical College and Research Center, Madurai, India
| | - S.V. Saju
- Department of Medical Oncology, Meenakshi Mission Medical College and Research Center, Madurai, India
| | - Honey Susan Raju
- Department of Medical Oncology, Meenakshi Mission Medical College and Research Center, Madurai, India
| | - Smita Kayal
- Department of Medical Oncology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Dubashi Biswajit
- Department of Medical Oncology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Amit Sehrawat
- Department of Medical Oncology, All India Institute of Medical Sciences Rishikesh, India
| | - Deepak Sundriyal
- Department of Medical Oncology, All India Institute of Medical Sciences Rishikesh, India
| | - Anil T. Jose
- Department of Medical Oncology, Amala Institute of Medical Sciences, Kerala, India
| | - Sreeja Raju
- Department of Pathology, Amala Institute of Medical Sciences, Kerala, India
| | - Preethi Paul
- Department of Pathology, Christian Medical College, Ludhiana, Punjab, India
| | - Prasanth Ganesan
- Department of Medical Oncology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
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23
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Park JW, Bae SJ, Yun JH, Kim S, Park M. Assessment of Genetic Stability in Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes by Using Droplet Digital PCR. Int J Mol Sci 2024; 25:1101. [PMID: 38256178 PMCID: PMC10815998 DOI: 10.3390/ijms25021101] [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: 12/19/2023] [Revised: 01/04/2024] [Accepted: 01/13/2024] [Indexed: 01/24/2024] Open
Abstract
Unintended genetic modifications that occur during the differentiation and proliferation of human induced pluripotent stem cells (hiPSCs) can lead to tumorigenicity. This is a crucial concern in the development of stem cell-based therapies to ensure the safety and efficacy of the final product. Moreover, conventional genetic stability testing methods are limited by low sensitivity, which is an issue that remains unsolved. In this study, we assessed the genetic stability of hiPSCs and hiPSC-derived cardiomyocytes using various testing methods, including karyotyping, CytoScanHD chip analysis, whole-exome sequencing, and targeted sequencing. Two specific genetic mutations in KMT2C and BCOR were selected from the 17 gene variants identified by whole-exome and targeted sequencing methods, which were validated using droplet digital PCR. The applicability of this approach to stem cell-based therapeutic products was further demonstrated with associated validation according to the International Council for Harmonisation (ICH) guidelines, including specificity, precision, robustness, and limit of detection. Our droplet digital PCR results showed high sensitivity and accuracy for quantitatively detecting gene mutations, whereas conventional qPCR could not avoid false positives. In conclusion, droplet digital PCR is a highly sensitive and precise method for assessing the expression of mutations with tumorigenic potential for the development of stem cell-based therapeutics.
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Affiliation(s)
| | | | | | | | - Misun Park
- Advanced Bioconvergence Product Research Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju-si 28159, Republic of Korea; (J.W.P.); (S.J.B.); (J.H.Y.); (S.K.)
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24
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Hafeez A, Shabbir M, Khan K, Trembley JH, Badshah Y, Zafar S, Shahid K, Shah H, Ashraf NM, Hamid A, Afsar T, Almajwal A, Marium A, Razak S. Possible prognostic impact of PKCι genetic variants in prostate cancer. Cancer Cell Int 2024; 24:24. [PMID: 38200472 PMCID: PMC10782671 DOI: 10.1186/s12935-023-03182-4] [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: 10/08/2023] [Accepted: 12/17/2023] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Single nucleotide polymorphisms (SNPs) have been linked with prostate cancer (PCa) and have shown potential as prognostic markers for advanced stages. Loss of function mutations in PKCι have been linked with increased risk of malignancy by enhancing tumor cell motility and invasion. We have evaluated the impact of two coding region SNPs on the PKCι gene (PRKCI) and their prognostic potential. METHODS Genotypic association of non-synonymous PKCι SNPs rs1197750201 and rs1199520604 with PCa was determined through tetra-ARMS PCR. PKCι was docked with interacting partner Par-6 to determine the effect of these variants on PKCι binding capabilities. Molecular dynamic simulations of PKCι docked with Par-6 were performed to determine variant effects on PKCι protein interactions. The possible impact of changes in PKCι protein interactions on epithelial cell polarity was hypothesized. RESULTS PKCι rs1199520604 mutant genotype TT showed association with PCa (p = 0.0055), while rs1197750201 mutant genotype AA also showed significant association with PCa (P = 0.0006). The binding interaction of PKCι with Par-6 was altered for both variants, with changes in Van der Waals energy and electrostatic energy of docked structures. CONCLUSION Genotypic analysis of two non-synonymous PKCι variants in association with PCa prognosis was performed. Both variants in the PB1 domain showed potential as a prognostic marker for PCa. In silico analysis of the effect of the variants on PKCι protein interactions indicated they may be involved in PCa progression through aberration of epithelial cell polarity pathways.
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Affiliation(s)
- Amna Hafeez
- Department of Healthcare Biotechnology, Rahman School of Applied Biosciences, National University of Sciences and Technology, Atta-Ur, Islamabad, Pakistan
| | - Maria Shabbir
- Department of Healthcare Biotechnology, Rahman School of Applied Biosciences, National University of Sciences and Technology, Atta-Ur, Islamabad, Pakistan.
| | - Khushbukhat Khan
- Department of Healthcare Biotechnology, Rahman School of Applied Biosciences, National University of Sciences and Technology, Atta-Ur, Islamabad, Pakistan
| | - Janeen H Trembley
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Minneapolis VA Health Care System Research Service, Minneapolis, MN, USA
| | - Yasmin Badshah
- Department of Healthcare Biotechnology, Rahman School of Applied Biosciences, National University of Sciences and Technology, Atta-Ur, Islamabad, Pakistan
| | - Sameen Zafar
- Department of Healthcare Biotechnology, Rahman School of Applied Biosciences, National University of Sciences and Technology, Atta-Ur, Islamabad, Pakistan
| | - Kanza Shahid
- Department of Healthcare Biotechnology, Rahman School of Applied Biosciences, National University of Sciences and Technology, Atta-Ur, Islamabad, Pakistan
| | - Hania Shah
- Department of Healthcare Biotechnology, Rahman School of Applied Biosciences, National University of Sciences and Technology, Atta-Ur, Islamabad, Pakistan
| | - Naeem Mahmood Ashraf
- Department of Biochemistry and Biotechnology, University of Gujrat, Hafiz Hayat Campus, Gujrat, 50700, Punjab, Pakistan
| | - Arslan Hamid
- University of Bonn, LIMES Institute (AG-Netea), Carl-Troll-Str. 31, 53115, Bonn, Germany
| | - Tayyaba Afsar
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Ali Almajwal
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Afifa Marium
- Department of Healthcare Biotechnology, Rahman School of Applied Biosciences, National University of Sciences and Technology, Atta-Ur, Islamabad, Pakistan
| | - Suhail Razak
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia.
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Madaci L, Gard C, Nin S, Sarrabay A, Baier C, Venton G, Rihet P, Puthier D, Loriod B, Costello R. Single-Cell Transcriptome Analysis of Acute Myeloid Leukemia Cells Using Methanol Fixation and Cryopreservation. Diseases 2023; 12:1. [PMID: 38275564 PMCID: PMC10814800 DOI: 10.3390/diseases12010001] [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: 11/16/2023] [Revised: 12/08/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
INTRODUCTION The application of single-cell RNA sequencing has greatly improved our understanding of various cellular and molecular mechanisms involved in physiological and pathophysiological processes. However, obtaining living cells for this technique can be difficult under certain conditions. To solve this problem, the methanol fixation method appeared as a promising alternative for routine clinical use. MATERIALS AND METHODS In this study, we selected two AML samples that had been fixed in methanol for 12-18 months. Once the cells were rehydrated, these samples were subjected to single-cell RNA sequencing. We then compared the results obtained from these samples with those obtained from the same samples cryopreserved in DMSO. RESULTS We used a previously validated methanol fixation protocol to perform scRNA-seq on DMSO cryopreserved cells and cells fixed in methanol for more than one year. Preliminary results show that methanol fixation induces some genetic and transcriptional modification compared with DMSO cryopreservation but remains a valuable method for single-cell analysis of primary human leukemia cells. CONCLUSIONS The initial findings from this study highlight certain resemblances in methanol fixation over a 12-month period and cryopreservation with DMSO, along with associated transcriptional level modifications. However, we observed genetic degradation in the fixation condition when extending beyond one year. Despite certain study limitations, it is evident that short-term methanol fixation can be effectively used for leukemia blast samples. Its ease of implementation holds the potential to simplify the integration of this technique into routine clinical practice.
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Affiliation(s)
- Lamia Madaci
- TAGC, TGML, INSERM, UMR1090, Aix-Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France; (L.M.); (C.G.); (S.N.); (G.V.); (P.R.); (D.P.); (B.L.)
| | - Charlyne Gard
- TAGC, TGML, INSERM, UMR1090, Aix-Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France; (L.M.); (C.G.); (S.N.); (G.V.); (P.R.); (D.P.); (B.L.)
| | - Sébastien Nin
- TAGC, TGML, INSERM, UMR1090, Aix-Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France; (L.M.); (C.G.); (S.N.); (G.V.); (P.R.); (D.P.); (B.L.)
| | - Alexandre Sarrabay
- TAGC, TGML, INSERM, UMR1090, Aix-Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France; (L.M.); (C.G.); (S.N.); (G.V.); (P.R.); (D.P.); (B.L.)
| | - Céline Baier
- Advanced BioDesign, Parc Technologique de Lyon, 655 Allée des Parcs, 69800 Saint Priest, France
| | - Geoffroy Venton
- TAGC, TGML, INSERM, UMR1090, Aix-Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France; (L.M.); (C.G.); (S.N.); (G.V.); (P.R.); (D.P.); (B.L.)
- Hematology and Cellular Therapy Department, Conception University Hospital, 13005 Marseille, France
| | - Pascal Rihet
- TAGC, TGML, INSERM, UMR1090, Aix-Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France; (L.M.); (C.G.); (S.N.); (G.V.); (P.R.); (D.P.); (B.L.)
| | - Denis Puthier
- TAGC, TGML, INSERM, UMR1090, Aix-Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France; (L.M.); (C.G.); (S.N.); (G.V.); (P.R.); (D.P.); (B.L.)
| | - Béatrice Loriod
- TAGC, TGML, INSERM, UMR1090, Aix-Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France; (L.M.); (C.G.); (S.N.); (G.V.); (P.R.); (D.P.); (B.L.)
| | - Régis Costello
- TAGC, TGML, INSERM, UMR1090, Aix-Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France; (L.M.); (C.G.); (S.N.); (G.V.); (P.R.); (D.P.); (B.L.)
- Hematology and Cellular Therapy Department, Conception University Hospital, 13005 Marseille, France
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Ladwig A, Gupta S, Ehlers P, Sekora A, Alammar M, Koczan D, Wolkenhauer O, Junghanss C, Langer P, Murua Escobar H. Exploring Thiazolopyridine AV25R: Unraveling of Biological Activities, Selective Anti-Cancer Properties and In Silico Target and Binding Prediction in Hematological Neoplasms. Molecules 2023; 28:8120. [PMID: 38138609 PMCID: PMC10745743 DOI: 10.3390/molecules28248120] [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: 10/28/2023] [Revised: 11/24/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Thiazolopyridines are a highly relevant class of small molecules, which have previously shown a wide range of biological activities. Besides their anti-tubercular, anti-microbial and anti-viral activities, they also show anti-cancerogenic properties, and play a role as inhibitors of cancer-related proteins. Herein, the biological effects of the thiazolopyridine AV25R, a novel small molecule with unknown biological effects, were characterized. Screening of a set of lymphoma (SUP-T1, SU-DHL-4) and B- acute leukemia cell lines (RS4;11, SEM) revealed highly selective effects of AV25R. The selective anti-proliferative and metabolism-modulating effects were observed in vitro for the B-ALL cell line RS4;11. Further, we were able to detect severe morphological changes and the induction of apoptosis. Gene expression analysis identified a large number of differentially expressed genes after AV25R exposure and significant differentially regulated cancer-related signaling pathways, such as VEGFA-VEGFR2 signaling and the EGF/EGFR pathway. Structure-based pharmacophore screening approaches using in silico modeling identified potential biological AV25R targets. Our results indicate that AV25R binds with several proteins known to regulate cell proliferation and tumor progression, such as FECH, MAP11, EGFR, TGFBR1 and MDM2. The molecular docking analyses indicates that AV25R has a higher binding affinity compared to many of the experimentally validated small molecule inhibitors of these targets. Thus, here we present in vitro and in silico analyses which characterize, for the first time, the molecular acting mechanism of AV25R, including cellular and molecular biologic effects. Additionally, this predicted the target binding of the molecule, revealing a high affinity to cancer-related proteins and, thus, classified AVR25 for targeted intervention approaches.
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Affiliation(s)
- Annika Ladwig
- Department of Medicine, Clinic III—Hematology, Oncology and Palliative Care, Rostock University Medical Center, 18057 Rostock, Germany; (A.L.); (A.S.); (M.A.); (C.J.)
| | - Shailendra Gupta
- Department of Systems Biology and Bioinformatics, University of Rostock, 18057 Rostock, Germany; (S.G.); (O.W.)
| | - Peter Ehlers
- Institute of Chemistry, University of Rostock, 18057 Rostock, Germany; (P.E.); (P.L.)
| | - Anett Sekora
- Department of Medicine, Clinic III—Hematology, Oncology and Palliative Care, Rostock University Medical Center, 18057 Rostock, Germany; (A.L.); (A.S.); (M.A.); (C.J.)
| | - Moosheer Alammar
- Department of Medicine, Clinic III—Hematology, Oncology and Palliative Care, Rostock University Medical Center, 18057 Rostock, Germany; (A.L.); (A.S.); (M.A.); (C.J.)
| | - Dirk Koczan
- Core Facility Genomics, Rostock University Medical Center, 18057 Rostock, Germany;
| | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, University of Rostock, 18057 Rostock, Germany; (S.G.); (O.W.)
| | - Christian Junghanss
- Department of Medicine, Clinic III—Hematology, Oncology and Palliative Care, Rostock University Medical Center, 18057 Rostock, Germany; (A.L.); (A.S.); (M.A.); (C.J.)
| | - Peter Langer
- Institute of Chemistry, University of Rostock, 18057 Rostock, Germany; (P.E.); (P.L.)
| | - Hugo Murua Escobar
- Department of Medicine, Clinic III—Hematology, Oncology and Palliative Care, Rostock University Medical Center, 18057 Rostock, Germany; (A.L.); (A.S.); (M.A.); (C.J.)
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Yao S, Han Y, Yang M, Jin K, Lan H. Integration of liquid biopsy and immunotherapy: opening a new era in colorectal cancer treatment. Front Immunol 2023; 14:1292861. [PMID: 38077354 PMCID: PMC10702507 DOI: 10.3389/fimmu.2023.1292861] [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: 09/12/2023] [Accepted: 11/03/2023] [Indexed: 12/18/2023] Open
Abstract
Immunotherapy has revolutionized the conventional treatment approaches for colorectal cancer (CRC), offering new therapeutic prospects for patients. Liquid biopsy has shown significant potential in early screening, diagnosis, and postoperative monitoring by analyzing circulating tumor cells (CTC) and circulating tumor DNA (ctDNA). In the era of immunotherapy, liquid biopsy provides additional possibilities for guiding immune-based treatments. Emerging technologies such as mass spectrometry-based detection of neoantigens and flow cytometry-based T cell sorting offer new tools for liquid biopsy, aiming to optimize immune therapy strategies. The integration of liquid biopsy with immunotherapy holds promise for improving treatment outcomes in colorectal cancer patients, enabling breakthroughs in early diagnosis and treatment, and providing patients with more personalized, precise, and effective treatment strategies.
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Affiliation(s)
- Shiya Yao
- Department of Colorectal Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Yuejun Han
- Department of Colorectal Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Mengxiang Yang
- Department of Colorectal Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Ketao Jin
- Department of Colorectal Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Huanrong Lan
- Department of Surgical Oncology, Hangzhou Cancer Hospital, Hangzhou, Zhejiang, China
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28
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Shin DW. [Treatment of Ampullary Adenocarcinoma]. THE KOREAN JOURNAL OF GASTROENTEROLOGY = TAEHAN SOHWAGI HAKHOE CHI 2023; 82:159-170. [PMID: 37876255 DOI: 10.4166/kjg.2023.110] [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: 09/13/2023] [Revised: 09/28/2023] [Accepted: 10/03/2023] [Indexed: 10/26/2023]
Abstract
The ampulla of Vater is a small projection formed by the confluence of the main pancreatic duct and common bile duct in the second part of the duodenum. Primary ampullary adenocarcinoma is a rare malignancy, accounting for only 0.2% of gastrointestinal cancers and approximately 7% of all periampullary cancers. Jaundice from a biliary obstruction is the most common symptom of ampullary adenocarcinoma. In the early stages, radical pancreatoduodenectomy is the standard surgical approach. On the other hand, no randomized controlled trial has provided evidence to guide physicians on the choice of adjuvant/palliative chemotherapy because of the rarity of the disease and the paucity of related research. This paper reports the biology, histology, current therapeutic strategies, and potential future therapies of ampullary adenocarcinoma.
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Affiliation(s)
- Dong Woo Shin
- Division of Gastroenterology, Department of Internal Medicine, Hallym University College of Medicine, Hallym University Sacred Heart Hospital, Anyang, Korea
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29
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Zheng H, Grayling MJ, Mozgunov P, Jaki T, Wason JMS. Bayesian sample size determination in basket trials borrowing information between subsets. Biostatistics 2023; 24:1000-1016. [PMID: 35993875 DOI: 10.1093/biostatistics/kxac033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 07/22/2022] [Accepted: 07/29/2022] [Indexed: 12/31/2022] Open
Abstract
Basket trials are increasingly used for the simultaneous evaluation of a new treatment in various patient subgroups under one overarching protocol. We propose a Bayesian approach to sample size determination in basket trials that permit borrowing of information between commensurate subsets. Specifically, we consider a randomized basket trial design where patients are randomly assigned to the new treatment or control within each trial subset ("subtrial" for short). Closed-form sample size formulae are derived to ensure that each subtrial has a specified chance of correctly deciding whether the new treatment is superior to or not better than the control by some clinically relevant difference. Given prespecified levels of pairwise (in)commensurability, the subtrial sample sizes are solved simultaneously. The proposed Bayesian approach resembles the frequentist formulation of the problem in yielding comparable sample sizes for circumstances of no borrowing. When borrowing is enabled between commensurate subtrials, a considerably smaller trial sample size is required compared to the widely implemented approach of no borrowing. We illustrate the use of our sample size formulae with two examples based on real basket trials. A comprehensive simulation study further shows that the proposed methodology can maintain the true positive and false positive rates at desired levels.
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Affiliation(s)
- Haiyan Zheng
- MRC Biostatistics Unit, University of Cambridge, Cambridge, CB2 0SR, UK and Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | - Michael J Grayling
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | - Pavel Mozgunov
- MRC Biostatistics Unit, University of Cambridge, Cambridge, CB2 0SR, UK
| | - Thomas Jaki
- MRC Biostatistics Unit, University of Cambridge, Cambridge, CB2 0SR, UK and University of Regensburg, 93040 Regensburg, Germany
| | - James M S Wason
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
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30
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Yang HY, Du YX, Hou YJ, Lu DR, Xue P. Hyperprogression after anti-programmed death-1 therapy in a patient with urothelial bladder carcinoma: A case report. World J Clin Cases 2023; 11:6841-6849. [PMID: 37901032 PMCID: PMC10600846 DOI: 10.12998/wjcc.v11.i28.6841] [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: 06/22/2023] [Revised: 08/22/2023] [Accepted: 09/04/2023] [Indexed: 09/25/2023] Open
Abstract
BACKGROUND Immune checkpoint inhibitors, including programmed death-ligand 1 (PD-L1) and programmed death-1 (PD-1) have recently been approved to treat locally advanced and metastatic urothelial carcinoma (UC). However, some patients experience rapid tumor progression rather than any clinical benefit from anti-PD-L1/PD-1 therapy. CASE SUMMARY A 73-year-old woman with bladder UC showed the progression of multiple metastases after surgery and chemotherapy for over 12 mo. The patient could not tolerate further chemotherapy. Next-generation sequencing was performed, and the results indicated that the tumor mutational burden was 6.4 mutations/Mb. The patient received the anti-PD-L1 agent toripalimab combined with albumin-bound paclitaxel. Compared with the baseline staging before immunotherapy, the patient had a treatment failure time of < 2 mo, an increase in tumor burden of > 50%, and a > 2-fold increase in progression, indicating hyperprogression. CONCLUSION Selecting patients most likely to respond to treatment with immunotherapeutic agents remains challenging. For older patients with advanced UC who have already exhausted multi-line chemotherapy options, immunotherapy should be used prudently if no effective biomarker is available. Further studies are required to clarify the causes and mechanisms of hyperprogression.
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Affiliation(s)
- Hong-Yu Yang
- Department of Oncology, Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing 100000, China
- Department of Oncology, Tianjin University of Chinese Medicine, Tianjin 300000, China
| | - Yu-Xuan Du
- Traditional Chinese Medical Science, Tianjin University of Chinese Medicine, Tianjin 300000, China
| | - Yu-Jia Hou
- Department of Oncology, Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing 100000, China
| | - Dian-Rong Lu
- Department of Oncology, Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing 100000, China
| | - Peng Xue
- Department of Oncology, Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing 100000, China
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31
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Ratajska M, Sette C, Cunliffe HE. Editorial: 365 days of progress in cancer genetics. Front Oncol 2023; 13:1270902. [PMID: 37823056 PMCID: PMC10562717 DOI: 10.3389/fonc.2023.1270902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/16/2023] [Indexed: 10/13/2023] Open
Affiliation(s)
- Magdalena Ratajska
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
- Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, University of the Sacred Hearth, Rome, Italy
- Gemelli Science and Technology Park (GSTeP)-Organoids Research Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy
| | - Heather E. Cunliffe
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
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32
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Yamanaka C, Uki S, Kaitoh K, Iwata M, Yamanishi Y. De novo drug design based on patient gene expression profiles via deep learning. Mol Inform 2023; 42:e2300064. [PMID: 37475603 DOI: 10.1002/minf.202300064] [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: 03/16/2023] [Revised: 05/25/2023] [Accepted: 07/20/2023] [Indexed: 07/22/2023]
Abstract
Computational de novo drug design is a challenging issue in medicine, and it is desirable to consider all of the relevant information of the biological systems in a disease state. Here, we propose a novel computational method to generate drug candidate molecular structures from patient gene expression profiles via deep learning, which we call DRAGONET. Our model can generate new molecules that are likely to counteract disease-specific gene expression patterns in patients, which is made possible by exploring the latent space constructed by a transformer-based variational autoencoder and integrating the substructures of disease-correlated molecules. We applied DRAGONET to generate drug candidate molecules for gastric cancer, atopic dermatitis, and Alzheimer's disease, and demonstrated that the newly generated molecules were chemically similar to registered drugs for each disease. This approach is applicable to diseases with unknown therapeutic target proteins and will make a significant contribution to the field of precision medicine.
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Affiliation(s)
- Chikashige Yamanaka
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
| | - Shunya Uki
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
| | - Kazuma Kaitoh
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
- Graduate School of Informatics, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Michio Iwata
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
| | - Yoshihiro Yamanishi
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
- Graduate School of Informatics, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
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33
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Bodén E, Sveréus F, Olm F, Lindstedt S. A Systematic Review of Mesenchymal Epithelial Transition Factor ( MET) and Its Impact in the Development and Treatment of Non-Small-Cell Lung Cancer. Cancers (Basel) 2023; 15:3827. [PMID: 37568643 PMCID: PMC10417792 DOI: 10.3390/cancers15153827] [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: 06/14/2023] [Revised: 07/20/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Lung cancer represents the leading cause of annual cancer-related deaths worldwide, accounting for 12.9%. The available treatment options for patients who experience disease progression remain limited. Targeted therapeutic approaches are promising but further understanding of the role of genetic alterations in tumorigenesis is imperative. The MET gene has garnered great interest in this regard. The aim of this systematic review was to analyze the findings from multiple studies to provide a comprehensive and unbiased summary of the evidence. A systematic search was conducted in the reputable scientific databases Embase and PubMed, leading to the inclusion of twenty-two articles, following the PRISMA guidelines, elucidating the biological role of MET in lung cancer and targeted therapies. The systematic review was registered in PROSPERO with registration ID: CRD42023437714. MET mutations were detected in 7.6-11.0% of cases while MET gene amplification was observed in 3.9-22.0%. Six studies showed favorable treatment outcomes utilizing MET inhibitors compared to standard treatment or placebo, with increases in PFS and OS ranging from 0.9 to 12.4 and 7.2 to 24.2 months, respectively, and one study reporting an increase in ORR by 17.3%. Furthermore, patients with a higher mutational burden may derive greater benefit from treatment with MET tyrosine kinase inhibitors (TKIs) than those with a lower mutational burden. Conversely, two studies reported no beneficial effect from adjunctive treatment with a MET targeted therapy. Given these findings, there is an urgent need to identify effective therapeutic strategies specifically targeting the MET gene in lung cancer patients.
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Affiliation(s)
- Embla Bodén
- Department of Clinical Sciences, Lund University, 22184 Lund, Sweden; (E.B.); (F.S.); (F.O.)
- Wallenberg Center for Molecular Medicine, Lund University, 22184 Lund, Sweden
- Lund Stem Cell Center, Lund University, 22184 Lund, Sweden
| | - Fanny Sveréus
- Department of Clinical Sciences, Lund University, 22184 Lund, Sweden; (E.B.); (F.S.); (F.O.)
- Wallenberg Center for Molecular Medicine, Lund University, 22184 Lund, Sweden
- Lund Stem Cell Center, Lund University, 22184 Lund, Sweden
| | - Franziska Olm
- Department of Clinical Sciences, Lund University, 22184 Lund, Sweden; (E.B.); (F.S.); (F.O.)
- Wallenberg Center for Molecular Medicine, Lund University, 22184 Lund, Sweden
- Lund Stem Cell Center, Lund University, 22184 Lund, Sweden
- Department of Cardiothoracic Surgery and Transplantation, Skåne University Hospital, 22242 Lund, Sweden
| | - Sandra Lindstedt
- Department of Clinical Sciences, Lund University, 22184 Lund, Sweden; (E.B.); (F.S.); (F.O.)
- Wallenberg Center for Molecular Medicine, Lund University, 22184 Lund, Sweden
- Lund Stem Cell Center, Lund University, 22184 Lund, Sweden
- Department of Cardiothoracic Surgery and Transplantation, Skåne University Hospital, 22242 Lund, Sweden
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34
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Sadee W, Wang D, Hartmann K, Toland AE. Pharmacogenomics: Driving Personalized Medicine. Pharmacol Rev 2023; 75:789-814. [PMID: 36927888 PMCID: PMC10289244 DOI: 10.1124/pharmrev.122.000810] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 03/09/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023] Open
Abstract
Personalized medicine tailors therapies, disease prevention, and health maintenance to the individual, with pharmacogenomics serving as a key tool to improve outcomes and prevent adverse effects. Advances in genomics have transformed pharmacogenetics, traditionally focused on single gene-drug pairs, into pharmacogenomics, encompassing all "-omics" fields (e.g., proteomics, transcriptomics, metabolomics, and metagenomics). This review summarizes basic genomics principles relevant to translation into therapies, assessing pharmacogenomics' central role in converging diverse elements of personalized medicine. We discuss genetic variations in pharmacogenes (drug-metabolizing enzymes, drug transporters, and receptors), their clinical relevance as biomarkers, and the legacy of decades of research in pharmacogenetics. All types of therapies, including proteins, nucleic acids, viruses, cells, genes, and irradiation, can benefit from genomics, expanding the role of pharmacogenomics across medicine. Food and Drug Administration approvals of personalized therapeutics involving biomarkers increase rapidly, demonstrating the growing impact of pharmacogenomics. A beacon for all therapeutic approaches, molecularly targeted cancer therapies highlight trends in drug discovery and clinical applications. To account for human complexity, multicomponent biomarker panels encompassing genetic, personal, and environmental factors can guide diagnosis and therapies, increasingly involving artificial intelligence to cope with extreme data complexities. However, clinical application encounters substantial hurdles, such as unknown validity across ethnic groups, underlying bias in health care, and real-world validation. This review address the underlying science and technologies germane to pharmacogenomics and personalized medicine, integrated with economic, ethical, and regulatory issues, providing insights into the current status and future direction of health care. SIGNIFICANCE STATEMENT: Personalized medicine aims to optimize health care for the individual patients with use of predictive biomarkers to improve outcomes and prevent adverse effects. Pharmacogenomics drives biomarker discovery and guides the development of targeted therapeutics. This review addresses basic principles and current trends in pharmacogenomics, with large-scale data repositories accelerating medical advances. The impact of pharmacogenomics is discussed, along with hurdles impeding broad clinical implementation, in the context of clinical care, ethics, economics, and regulatory affairs.
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Affiliation(s)
- Wolfgang Sadee
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus Ohio (W.S., A.E.T.); Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, Florida (D.W.); Department of Radiology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania (K.H.); Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, California (W.S.); and Aether Therapeutics, Austin, Texas (W.S.)
| | - Danxin Wang
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus Ohio (W.S., A.E.T.); Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, Florida (D.W.); Department of Radiology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania (K.H.); Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, California (W.S.); and Aether Therapeutics, Austin, Texas (W.S.)
| | - Katherine Hartmann
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus Ohio (W.S., A.E.T.); Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, Florida (D.W.); Department of Radiology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania (K.H.); Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, California (W.S.); and Aether Therapeutics, Austin, Texas (W.S.)
| | - Amanda Ewart Toland
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus Ohio (W.S., A.E.T.); Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, Florida (D.W.); Department of Radiology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania (K.H.); Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, California (W.S.); and Aether Therapeutics, Austin, Texas (W.S.)
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35
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Yang J, Nittala MR, Velazquez AE, Buddala V, Vijayakumar S. An Overview of the Use of Precision Population Medicine in Cancer Care: First of a Series. Cureus 2023; 15:e37889. [PMID: 37113463 PMCID: PMC10129036 DOI: 10.7759/cureus.37889] [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] [Accepted: 04/19/2023] [Indexed: 04/29/2023] Open
Abstract
Advances in science and technology in the past century and a half have helped improve disease management, prevention, and early diagnosis and better health maintenance. These have led to a longer life expectancy in most developed and middle-income countries. However, resource- and infrastructure-scarce countries and populations have not enjoyed these benefits. Furthermore, in every society, including in developed nations, the lag time from new advances, either in the laboratory or from clinical trials, to using those findings in day-to-day medical practice often takes many years and sometimes close to or longer than a decade. A similar trend is seen in the application of "precision medicine" (PM) in terms of improving population health (PH). One of the reasons for such lack of application of precision medicine in population health is the misunderstanding of equating precision medicine with genomic medicine (GM) as if they are the same. Precision medicine needs to be recognized as encompassing genomic medicine in addition to other new developments such as big data analytics, electronic health records (EHR), telemedicine, and information communication technology. By leveraging these new developments together and applying well-tested epidemiological concepts, it can be posited that population/public health can be improved. In this paper, we take cancer as an example of the benefits of recognizing the potential of precision medicine in applying it to population/public health. Breast cancer and cervical cancer are taken as examples to demonstrate these hypotheses. There exists significant evidence already to show the importance of recognizing "precision population medicine" (PPM) in improving cancer outcomes not only in individual patients but also for its applications in early detection and cancer screening (especially in high-risk populations) and achieving those goals in a more cost-efficient manner that can reach resource- and infrastructure-scarce societies and populations. This is the first report of a series that will focus on individual cancer sites in the future.
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Affiliation(s)
- Johnny Yang
- Radiation Oncology, University of Mississippi Medical Center, Jackson, USA
| | - Mary R Nittala
- Radiation Oncology, University of Mississippi Medical Center, Jackson, USA
| | | | - Vedanth Buddala
- Radiation Oncology, University of Mississippi Medical Center, Jackson, USA
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36
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Monné Rodríguez JM, Frisk AL, Kreutzer R, Lemarchand T, Lezmi S, Saravanan C, Stierstorfer B, Thuilliez C, Vezzali E, Wieczorek G, Yun SW, Schaudien D. European Society of Toxicologic Pathology (Pathology 2.0 Molecular Pathology Special Interest Group): Review of In Situ Hybridization Techniques for Drug Research and Development. Toxicol Pathol 2023; 51:92-111. [PMID: 37449403 PMCID: PMC10467011 DOI: 10.1177/01926233231178282] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
In situ hybridization (ISH) is used for the localization of specific nucleic acid sequences in cells or tissues by complementary binding of a nucleotide probe to a specific target nucleic acid sequence. In the last years, the specificity and sensitivity of ISH assays were improved by innovative techniques like synthetic nucleic acids and tandem oligonucleotide probes combined with signal amplification methods like branched DNA, hybridization chain reaction and tyramide signal amplification. These improvements increased the application spectrum for ISH on formalin-fixed paraffin-embedded tissues. ISH is a powerful tool to investigate DNA, mRNA transcripts, regulatory noncoding RNA, and therapeutic oligonucleotides. ISH can be used to obtain spatial information of a cell type, subcellular localization, or expression levels of targets. Since immunohistochemistry and ISH share similar workflows, their combination can address simultaneous transcriptomics and proteomics questions. The goal of this review paper is to revisit the current state of the scientific approaches in ISH and its application in drug research and development.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Seong-Wook Yun
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Dirk Schaudien
- Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
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37
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Deshpande D, Chhugani K, Chang Y, Karlsberg A, Loeffler C, Zhang J, Muszyńska A, Munteanu V, Yang H, Rotman J, Tao L, Balliu B, Tseng E, Eskin E, Zhao F, Mohammadi P, P. Łabaj P, Mangul S. RNA-seq data science: From raw data to effective interpretation. Front Genet 2023; 14:997383. [PMID: 36999049 PMCID: PMC10043755 DOI: 10.3389/fgene.2023.997383] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 02/24/2023] [Indexed: 03/14/2023] Open
Abstract
RNA sequencing (RNA-seq) has become an exemplary technology in modern biology and clinical science. Its immense popularity is due in large part to the continuous efforts of the bioinformatics community to develop accurate and scalable computational tools to analyze the enormous amounts of transcriptomic data that it produces. RNA-seq analysis enables genes and their corresponding transcripts to be probed for a variety of purposes, such as detecting novel exons or whole transcripts, assessing expression of genes and alternative transcripts, and studying alternative splicing structure. It can be a challenge, however, to obtain meaningful biological signals from raw RNA-seq data because of the enormous scale of the data as well as the inherent limitations of different sequencing technologies, such as amplification bias or biases of library preparation. The need to overcome these technical challenges has pushed the rapid development of novel computational tools, which have evolved and diversified in accordance with technological advancements, leading to the current myriad of RNA-seq tools. These tools, combined with the diverse computational skill sets of biomedical researchers, help to unlock the full potential of RNA-seq. The purpose of this review is to explain basic concepts in the computational analysis of RNA-seq data and define discipline-specific jargon.
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Affiliation(s)
- Dhrithi Deshpande
- Department of Pharmacology and Pharmaceutical Sciences, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, Los Angeles, CA, United States
| | - Karishma Chhugani
- Department of Pharmacology and Pharmaceutical Sciences, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, Los Angeles, CA, United States
| | - Yutong Chang
- Department of Pharmacology and Pharmaceutical Sciences, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, Los Angeles, CA, United States
| | - Aaron Karlsberg
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, Los Angeles, CA, United States
| | - Caitlin Loeffler
- Department of Computer Science, University of California, Los Angeles, CA, United States
| | - Jinyang Zhang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Agata Muszyńska
- Małopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
- Institute of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland
| | - Viorel Munteanu
- Department of Computers, Informatics and Microelectronics, Technical University of Moldova, Chisinau, Moldova
| | - Harry Yang
- Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, United States
| | - Jeremy Rotman
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, Los Angeles, CA, United States
| | - Laura Tao
- Department of Computational Medicine, David Geffen School of Medicine at UCLA, CHS, Los Angeles, CA, United States
| | - Brunilda Balliu
- Department of Computational Medicine, David Geffen School of Medicine at UCLA, CHS, Los Angeles, CA, United States
| | | | - Eleazar Eskin
- Department of Computer Science, University of California, Los Angeles, CA, United States
- Department of Computational Medicine, David Geffen School of Medicine at UCLA, CHS, Los Angeles, CA, United States
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Pejman Mohammadi
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
| | - Paweł P. Łabaj
- Małopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
- Department of Biotechnology, Boku University Vienna, Vienna, Austria
| | - Serghei Mangul
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, Los Angeles, CA, United States
- Department of Quantitative and Computational Biology, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA, United States
- *Correspondence: Serghei Mangul,
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38
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Wilkes RP. Next-Generation Diagnostics for Pathogens. Vet Clin North Am Food Anim Pract 2023; 39:165-173. [PMID: 36731996 DOI: 10.1016/j.cvfa.2022.09.003] [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] [Indexed: 02/04/2023] Open
Abstract
Next-generation sequencing (NGS) was initially developed to aid sequencing of the human genome. This molecular method is cost effective for sequencing and characterizing genomes, not only those of humans or animals but also those of bacteria and other pathogens. However, rather than sequencing a single organism, a targeted NGS method can be used to specifically amplify pathogens of interest in a clinical sample for detection and characterization by sequencing. Targeted NGS is an ideal method for ruminant syndromic testing due to its ability to detect a variety of pathogens in a sample with a single test.
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Affiliation(s)
- Rebecca P Wilkes
- Department of Comparative Pathobiology and Molecular Section Head, Animal Disease Diagnostic Laboratory, Purdue University College of Veterinary Medicine, 406 South University St., West Lafayette, IN 47907-2065, USA.
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39
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D'Alise AM, Scarselli E. Getting personal in metastatic melanoma: neoantigen-based vaccines as a new therapeutic strategy. Curr Opin Oncol 2023; 35:94-99. [PMID: 36721894 PMCID: PMC9894148 DOI: 10.1097/cco.0000000000000923] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
PURPOSE OF REVIEW Cancer vaccines are facing renewed interest, thanks to the progress recently achieved in the immunotherapy field, including the success of immune checkpoint inhibitors (CPIs). The advances in understanding the CPI mode of action revealed a central role of neoantigens for the outcome of such treatments. Neoantigens became the preferred antigens for cancer vaccines and have been evaluated in several clinical trials. Here, we review the recent results from neoantigen-based vaccines in melanoma patients and discuss avenues for improvement. RECENT FINDINGS The importance of neoantigens for tumor control comes from the positive correlation between tumor mutational burden (TMB) and response to CPI. Preclinical studies have proved the effectiveness of neoantigen vaccines in models, expediting their clinical testing. Tumor mutations are not shared in most tumor types including melanoma, mandating the need of a personalized approach. Several clinical studies have shown the safety, feasibility, immunogenicity and preliminary evidence of antitumor activity of personalized vaccination. Currently, new trials have been started aiming to both confirm clinical activity and combining vaccines with other immunotherapies for improved efficacy. SUMMARY Personalized vaccines hold the promise for highly mutated and immunogenic cancers, including melanoma. Continuous efforts are underway to increase their likelihood of success.
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Spatial RNA sequencing methods show high resolution of single cell in cancer metastasis and the formation of tumor microenvironment. Biosci Rep 2023; 43:232194. [PMID: 36459212 PMCID: PMC9950536 DOI: 10.1042/bsr20221680] [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: 08/04/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/03/2022] Open
Abstract
Cancer metastasis often leads to death and therapeutic resistance. This process involves the participation of a variety of cell components, especially cellular and intercellular communications in the tumor microenvironment (TME). Using genetic sequencing technology to comprehensively characterize the tumor and TME is therefore key to understanding metastasis and therapeutic resistance. The use of spatial transcriptome sequencing enables the localization of gene expressions and cell activities in tissue sections. By examining the localization change as well as gene expression of these cells, it is possible to characterize the progress of tumor metastasis and TME formation. With improvements of this technology, spatial transcriptome sequencing technology has been extended from local regions to whole tissues, and from single sequencing technology to multimodal analysis combined with a variety of datasets. This has enabled the detection of every single cell in tissue slides, with high resolution, to provide more accurate predictive information for tumor treatments. In this review, we summarize the results of recent studies dealing with new multimodal methods and spatial transcriptome sequencing methods in tumors to illustrate recent developments in the imaging resolution of micro-tissues.
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Verna R. From alchemy to personalised medicine: the journey of laboratory medicine. J Clin Pathol 2023; 76:301-307. [PMID: 36828620 DOI: 10.1136/jcp-2022-208492] [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: 07/12/2022] [Accepted: 02/02/2023] [Indexed: 02/26/2023]
Abstract
This review summarises the long period in which man has approached nature to understand its powers, and has tried to control it through physical and chemical, and also magical, practices. From the attempt to manage nature to the development of primordial drugs and medical practices and later to achieve modern biomedical science, laboratory practices always played a pivotal role. Over the years and centuries, the laboratory has acquired more and more importance in the improvement of health.In addition to the well-known importance of laboratory medicine in the early diagnosis and appropriateness, the discoveries of the last 50 years have also given the Laboratory a decisive role in regenerative and personalised medicine.This paper examines the evolution of the laboratory and is not meant to be a treatise on the history of medicine. The goal is to highlight the moments of the transition from magic and alchemy to laboratory science.-------------------------------Roberto Verna is President of the World Association of Societies of Pathology and Laboratory Medicine and President of the Academy for Health and Clinical Research.
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Affiliation(s)
- Roberto Verna
- Experimental Medicine - Systems Biology Group, University of Rome La Sapienza Faculty of Medicine and Dentistry, Roma, Italy
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Ma S, Zhou M, Xu Y, Gu X, Zou M, Abudushalamu G, Yao Y, Fan X, Wu G. Clinical application and detection techniques of liquid biopsy in gastric cancer. Mol Cancer 2023; 22:7. [PMID: 36627698 PMCID: PMC9832643 DOI: 10.1186/s12943-023-01715-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/02/2023] [Indexed: 01/12/2023] Open
Abstract
Gastric cancer (GC) is one of the most common tumors worldwide and the leading cause of tumor-related mortality. Endoscopy and serological tumor marker testing are currently the main methods of GC screening, and treatment relies on surgical resection or chemotherapy. However, traditional examination and treatment methods are more harmful to patients and less sensitive and accurate. A minimally invasive method to respond to GC early screening, prognosis monitoring, treatment efficacy, and drug resistance situations is urgently needed. As a result, liquid biopsy techniques have received much attention in the clinical application of GC. The non-invasive liquid biopsy technique requires fewer samples, is reproducible, and can guide individualized patient treatment by monitoring patients' molecular-level changes in real-time. In this review, we introduced the clinical applications of circulating tumor cells, circulating free DNA, circulating tumor DNA, non-coding RNAs, exosomes, and proteins, which are the primary markers in liquid biopsy technology in GC. We also discuss the current limitations and future trends of liquid biopsy technology as applied to early clinical biopsy technology.
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Affiliation(s)
- Shuo Ma
- grid.452290.80000 0004 1760 6316Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009 Jiangsu China ,grid.263826.b0000 0004 1761 0489Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, 210009 Jiangsu China
| | - Meiling Zhou
- grid.452290.80000 0004 1760 6316Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009 Jiangsu China ,grid.263826.b0000 0004 1761 0489Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, 210009 Jiangsu China
| | - Yanhua Xu
- grid.452743.30000 0004 1788 4869Department of Laboratory Medicine, Northern Jiangsu People’s Hospital Affiliated to Yangzhou University, Yangzhou, 225000 Jiangsu China
| | - Xinliang Gu
- grid.440642.00000 0004 0644 5481Department of Laboratory Medicine, Medical School, Affiliated Hospital of Nantong University, Nantong University, Nantong, 226001 Jiangsu China
| | - Mingyuan Zou
- grid.452290.80000 0004 1760 6316Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009 Jiangsu China ,grid.263826.b0000 0004 1761 0489Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, 210009 Jiangsu China
| | - Gulinaizhaer Abudushalamu
- grid.452290.80000 0004 1760 6316Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009 Jiangsu China ,grid.263826.b0000 0004 1761 0489Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, 210009 Jiangsu China
| | - Yuming Yao
- grid.452290.80000 0004 1760 6316Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009 Jiangsu China ,grid.263826.b0000 0004 1761 0489Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, 210009 Jiangsu China
| | - Xiaobo Fan
- grid.452290.80000 0004 1760 6316Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009 Jiangsu China ,grid.263826.b0000 0004 1761 0489Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, 210009 Jiangsu China
| | - Guoqiu Wu
- grid.452290.80000 0004 1760 6316Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009 Jiangsu China ,grid.263826.b0000 0004 1761 0489Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, 210009 Jiangsu China ,grid.263826.b0000 0004 1761 0489Jiangsu Provincial Key Laboratory of Critical Care Medicine, Southeast University, Nanjing, 210009 Jiangsu China
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Ji T, Gao X, Li D, Huai S, Chi Y, An X, Ji W, Yang S, Li J. Identification and validation of signature for prognosis and immune microenvironment in gastric cancer based on m6A demethylase ALKBH5. Front Oncol 2023; 12:1079402. [PMID: 36686788 PMCID: PMC9853004 DOI: 10.3389/fonc.2022.1079402] [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: 10/25/2022] [Accepted: 12/07/2022] [Indexed: 01/07/2023] Open
Abstract
Background N6-methyladenosine (m6A) RNA regulators play important roles in cancers, but their functions and mechanism have not been demonstrated clearly in gastric cancer (GC). Methods In this study, the GC samples with clinical information and RNA transcriptome were downloaded from The Cancer Genome Atlas database. The different expression genes were compared by the absolute value and median ± standard deviation. Samples with complete information were randomly divided into a training dataset and a test dataset. The differential expression genes (DEGs) between ALKBH5-low and ALKBH5-high subgroups were identified in the training dataset and constructed a risk model by Cox and least absolute shrinkage and selection operator regression. The model was testified in test datasets, overall survival (OS) was compared with the Kaplan-Meier method, and immune cell infiltration was calculated by the CIBERSORT algorithm in the low-risk and high-risk subgroups based on the model. The protein levels of ALKBH5 were detected with immunohistochemistry. The relative expression of messenger-ribonucleic acid (mRNA) was detected with quantitative polymerase chain reaction. Results ALKBH5 was the only regulator whose expression was lower in tumor samples than that in normal samples. The low expression of ALKBH5 led to the poor OS of GC patients and seemed to be an independent protective factor. The model based on ALKBH5-regulated genes was validated in both datasets (training/test) and displayed a potential capacity to predict a clinical prognosis. Gene Ontology analysis implied that the DEGs were involved in the immune response; CIBERSORT results indicated that ALKBH5 and its related genes could alter the immune microenvironment of GC. The protein levels of ALKBH5 were verified as lowly expressed in GC tissues. SLC7A2 and CGB3 were downregulated with ALKBH5 knockdown. Conclusions In this study, we found that ALKBH5 might be a suppressor of GC; ALKBH5 and its related genes were latent biomarkers and immunotherapy targets.
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Affiliation(s)
- Tiannan Ji
- Medical School of Chinese PLA, Beijing, China,Department of Radiotherapy, Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Xiaohui Gao
- Department of Radiotherapy, Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, Beijing, China,Department of Clinical Medicine, Graduate School of Hebei North University, Zhangjiakou, Hebei, China
| | - Dan Li
- Department of Radiotherapy, Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Siyuan Huai
- Department of Radiotherapy, Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Yajing Chi
- Department of Radiotherapy, Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, Beijing, China,School of Medicine, Nankai University, Tianjin, China
| | - Xian An
- Department of Radiotherapy, Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Wenyu Ji
- Department of Radiotherapy, Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, Beijing, China,Department of Clinical Medicine, Graduate School of Hebei North University, Zhangjiakou, Hebei, China
| | - Siming Yang
- Department of Radiotherapy, Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Jianxiong Li
- Department of Radiotherapy, Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, Beijing, China,*Correspondence: Jianxiong Li,
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Yao J, Ding Y, Liu X, Huang J, Zhang M, Zhang Y, Lv Y, Xie Z, Zuo J. Application value of whole exome sequencing in screening and identifying novel mutations of hypopharyngeal cancer. Sci Rep 2023; 13:107. [PMID: 36596842 PMCID: PMC9810646 DOI: 10.1038/s41598-022-27273-w] [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: 05/06/2022] [Accepted: 12/29/2022] [Indexed: 01/05/2023] Open
Abstract
The research on targeted therapy of hypopharyngeal cancer is very scarce. The discovery of new targeted driver genes will promote the progress of hypopharyngeal cancer therapy to a great extent. In our research, whole-exome sequencing in 10 patients with hypopharyngeal cancer was performed to identify single nucleotide variations (SNVs) and insertions and deletions (INDELs). American College of Medical Genetics and Genomics (ACMG) guidelines were used to evaluate the pathogenicity of the selected variants. 8113 mutation sites in 5326 genes were identified after strict screening. We identified 72 pathogenic mutations in 53 genes according to the ACMG guidelines. Gene Ontology (GO) annotation and KEGG enrichment analysis show the effect of these genes on cancer. Protein-protein interaction (PPI) was analyzed by string online software. The validation results of the ualcan database showed that 22 of the 53 genes may be related to the poor prognosis of patients with hypopharyngeal cancer. RBM20 has the most significant correlation with hypopharyngeal cancer, and it is likely to be the driver gene of hypopharyngeal cancer. In conclusion, we found possible therapeutic targets for hypopharyngeal cancer, especially RBM20 and KMT2C. Our study provides a basis for the pathogenesis and targeted therapy of hypopharyngeal cancer.
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Affiliation(s)
- Jingwei Yao
- grid.412017.10000 0001 0266 8918Gastroenterology Department, The Affiliated Nanhua Hospital of University of South China, Hengyang, 421001 Hunan People’s Republic of China ,grid.12955.3a0000 0001 2264 7233Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, 361003 People’s Republic of China ,grid.412017.10000 0001 0266 8918Transformation Research Lab, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Hengyang Medical School, University of South China, Hengyang, 421001 Hunan People’s Republic of China ,grid.412017.10000 0001 0266 8918Clinical Laboratory, The Third Affiliated Hospital of University of South China, Hengyang, 421000 Hunan People’s Republic of China
| | - Yubo Ding
- grid.412017.10000 0001 0266 8918Gastroenterology Department, The Affiliated Nanhua Hospital of University of South China, Hengyang, 421001 Hunan People’s Republic of China ,grid.412017.10000 0001 0266 8918Transformation Research Lab, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Hengyang Medical School, University of South China, Hengyang, 421001 Hunan People’s Republic of China
| | - Xiong Liu
- grid.284723.80000 0000 8877 7471Department of Otolaryngology-Head and Neck Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515 People’s Republic of China
| | - Jialu Huang
- grid.412017.10000 0001 0266 8918Transformation Research Lab, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Hengyang Medical School, University of South China, Hengyang, 421001 Hunan People’s Republic of China
| | - Minghui Zhang
- grid.412017.10000 0001 0266 8918Transformation Research Lab, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Hengyang Medical School, University of South China, Hengyang, 421001 Hunan People’s Republic of China
| | - Yu Zhang
- grid.412017.10000 0001 0266 8918Transformation Research Lab, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Hengyang Medical School, University of South China, Hengyang, 421001 Hunan People’s Republic of China
| | - Yufan Lv
- grid.412017.10000 0001 0266 8918Gastroenterology Department, The Affiliated Nanhua Hospital of University of South China, Hengyang, 421001 Hunan People’s Republic of China ,grid.412017.10000 0001 0266 8918Transformation Research Lab, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Hengyang Medical School, University of South China, Hengyang, 421001 Hunan People’s Republic of China
| | - Zhuoyi Xie
- grid.412017.10000 0001 0266 8918Transformation Research Lab, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Hengyang Medical School, University of South China, Hengyang, 421001 Hunan People’s Republic of China
| | - Jianhong Zuo
- grid.412017.10000 0001 0266 8918Gastroenterology Department, The Affiliated Nanhua Hospital of University of South China, Hengyang, 421001 Hunan People’s Republic of China ,grid.412017.10000 0001 0266 8918Transformation Research Lab, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Hengyang Medical School, University of South China, Hengyang, 421001 Hunan People’s Republic of China ,grid.412017.10000 0001 0266 8918Clinical Laboratory, The Third Affiliated Hospital of University of South China, Hengyang, 421000 Hunan People’s Republic of China
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Liu X, Yang F, Jia D, Dong X, Zhang Y, Wu Z. Case report: A case study on the treatment using icaritin soft capsules in combination with lenvatinib achieving impressive PR and stage reduction in unresectable locally progressive pancreatic cancer and a literature review. Front Genet 2023; 14:1167470. [PMID: 37152980 PMCID: PMC10156971 DOI: 10.3389/fgene.2023.1167470] [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: 02/16/2023] [Accepted: 04/03/2023] [Indexed: 05/09/2023] Open
Abstract
Background: Pancreatic cancer is one of the most deadly malignancies in the world. It is characterized by rapid progression and a very poor prognosis. The five-year survival rate of pancreatic cancer in China is only 7.2%, which is the lowest among all cancers and the use of combined paclitaxel albumin, capecitabine, and digital has been the clinical standard treatment for advanced pancreatic cancer since 1997. Also, the application of multidrug combinations is often limited by the toxicity of chemotherapy. Therefore, there is an urgent need for a more appropriate and less toxic treatment modality for pancreatic cancer. Case presentation: The patient was a 79-year-old woman, admitted to the hospital with a diagnosis of unresectable locally advanced pancreatic cancer (T3N0M0, stage IIA), with its imaging showing overgrowth of SMV involvement and unresectable reconstruction of the posterior vein after evaluation. As the patient refused chemotherapy, lenvatinib (8 mg/time, qd) and icaritin soft capsules (three tablets/time, bid) were recommended according to our past experience and a few clinical research cases. The tumor lesion was greatly reduced by 57.5% after the treatment, and the extent of vascular involvement also decreased. The aforementioned medication resulted in a significant downstaging of the patient's tumor. Conclusion: Better results were achieved in the treatment with icaritin soft capsules and lenvatinib in this case. Because of its less toxic effect on the liver and kidney and bone marrow suppression, it was suitable to combine icaritin soft capsules with targeted drugs for treating intermediate and advanced malignancies, which brings hope to patients who cannot or refuse to take chemotherapy.
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Affiliation(s)
- Xiaolong Liu
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Feimin Yang
- Department of Nursing, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Dunmao Jia
- Department of General Surgery, Affiliated Run Run Shaw Hospital, Jiangshan Branch, Harbin Medical University, Quzhou, China
| | - Xinyu Dong
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yizhuo Zhang
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhengrong Wu
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- *Correspondence: Zhengrong Wu,
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Expert consensus of the Spanish Society of Pathology and the Spanish Society of Medical Oncology on the determination of biomarkers in pancreatic and biliary tract cancer. REVISTA ESPANOLA DE PATOLOGIA : PUBLICACION OFICIAL DE LA SOCIEDAD ESPANOLA DE ANATOMIA PATOLOGICA Y DE LA SOCIEDAD ESPANOLA DE CITOLOGIA 2023; 56:32-44. [PMID: 36599598 DOI: 10.1016/j.patol.2022.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 06/25/2022] [Indexed: 01/31/2023]
Abstract
Pancreatic cancer and biliary tract cancer have a poor prognosis. In recent years, the development of new diagnostic techniques has enabled the identification of the main genetic alterations involved in the development of these tumours. Multiple studies have assessed the ability to predict response to treatment of certain biomarkers, such as BRCA in pancreatic cancer, IDH1 or FGFR2 in biliary tract cancer and microsatellite instability or NTRK fusions in an agnostic tumour fashion. In this consensus, a group of experts selected by the Spanish Society of Medical Oncology (SEOM) and the Spanish Society of Pathology (SEAP) reviewed the role played by these mutations in the process of carcinogenesis and their clinical implications. Based on their results, a series of recommendations are made to optimize the determination of these biomarkers and thus help standardize the diagnosis and treatment of these tumours.
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Vera R, Ibarrola-de-Andrés C, Adeva J, Pérez-Rojas J, García-Alfonso P, Rodríguez-Gil Y, Macarulla T, Serrano-Piñol T, Mondéjar R, Madrigal-Rubiales B. Expert consensus of the Spanish Society of Pathology and the Spanish Society of Medical Oncology on the determination of biomarkers in pancreatic and biliary tract cancer. Clin Transl Oncol 2022; 24:2107-2119. [PMID: 36008616 PMCID: PMC9522813 DOI: 10.1007/s12094-022-02873-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/06/2022] [Indexed: 10/26/2022]
Abstract
Pancreatic cancer and biliary tract cancer have a poor prognosis. In recent years, the development of new diagnostic techniques has enabled the identification of the main genetic alterations involved in the development of these tumours. Multiple studies have assessed the ability of certain biomarkers, such as BRCA in pancreatic cancer, IDH1 or FGFR2 in biliary tract cancer and microsatellite instability or NTRK fusions in an agnostic tumour fashion, to predict response to treatment.In this consensus, a group of experts selected by the Spanish Society of Medical Oncology (SEOM) and the Spanish Society of Pathology (SEAP) reviewed the role played by these mutations in the process of carcinogenesis and their clinical implications. As a result, this article proposes a series of recommendations to optimize the determination of these biomarkers to help standardize the diagnosis and treatment of these tumours.
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Affiliation(s)
- Ruth Vera
- Navarra University Hospital, Spanish Society of Medical Oncology (SEOM), Calle Irunlarrea, 3, Navarra, 31008, Pamplona, Spain.
| | | | - Jorge Adeva
- 12 de Octubre University Hospital, Spanish Society of Medical Oncology (SEOM), Madrid, Spain
| | - Judith Pérez-Rojas
- La Fe University and Polytechnic Hospital, Spanish Society of Pathology (SEAP), Valencia, Spain
| | - Pilar García-Alfonso
- Gregorio Marañón University Hospital, Spanish Society of Medical Oncology (SEOM), Madrid, Spain
| | - Yolanda Rodríguez-Gil
- 12 de Octubre University Hospital, Spanish Society of Pathology (SEAP), Madrid, Spain
| | - Teresa Macarulla
- Vall d'Hebron University Hospital, Spanish Society of Medical Oncology (SEOM), Barcelona, Spain
| | - Teresa Serrano-Piñol
- Bellvitge University Hospital, Spanish Society of Pathology (SEAP), Barcelona, Spain
| | - Rebeca Mondéjar
- La Princesa University Hospital, Spanish Society of Medical Oncology (SEOM), Madrid, Spain
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Zhuo Z, Lin L, Miao L, Li M, He J. Advances in liquid biopsy in neuroblastoma. FUNDAMENTAL RESEARCH 2022; 2:903-917. [PMID: 38933377 PMCID: PMC11197818 DOI: 10.1016/j.fmre.2022.08.005] [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: 04/27/2022] [Revised: 07/18/2022] [Accepted: 08/09/2022] [Indexed: 10/15/2022] Open
Abstract
Even with intensive treatment of high-risk neuroblastoma (NB) patients, half of high-risk NB patients still relapse. New therapies targeting the biological characteristics of NB have important clinical value for the personalized treatment of NB. However, the current biological markers for NB are mainly analyzed by tissue biopsy. In recent years, circulating biomarkers of NB based on liquid biopsy have attracted more and more attention. This review summarizes the analytes and methods for liquid biopsy of NB. We focus on the application of liquid biopsy in the diagnosis, prognosis assessment, and monitoring of NB. Finally, we discuss the prospects and challenges of liquid biopsy in NB.
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Affiliation(s)
- Zhenjian Zhuo
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
- Laboratory Animal Center, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Lei Lin
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Lei Miao
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Meng Li
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Jing He
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
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Hamamoto R, Koyama T, Kouno N, Yasuda T, Yui S, Sudo K, Hirata M, Sunami K, Kubo T, Takasawa K, Takahashi S, Machino H, Kobayashi K, Asada K, Komatsu M, Kaneko S, Yatabe Y, Yamamoto N. Introducing AI to the molecular tumor board: one direction toward the establishment of precision medicine using large-scale cancer clinical and biological information. Exp Hematol Oncol 2022; 11:82. [PMID: 36316731 PMCID: PMC9620610 DOI: 10.1186/s40164-022-00333-7] [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: 08/31/2022] [Accepted: 10/05/2022] [Indexed: 11/10/2022] Open
Abstract
Since U.S. President Barack Obama announced the Precision Medicine Initiative in his New Year's State of the Union address in 2015, the establishment of a precision medicine system has been emphasized worldwide, particularly in the field of oncology. With the advent of next-generation sequencers specifically, genome analysis technology has made remarkable progress, and there are active efforts to apply genome information to diagnosis and treatment. Generally, in the process of feeding back the results of next-generation sequencing analysis to patients, a molecular tumor board (MTB), consisting of experts in clinical oncology, genetic medicine, etc., is established to discuss the results. On the other hand, an MTB currently involves a large amount of work, with humans searching through vast databases and literature, selecting the best drug candidates, and manually confirming the status of available clinical trials. In addition, as personalized medicine advances, the burden on MTB members is expected to increase in the future. Under these circumstances, introducing cutting-edge artificial intelligence (AI) technology and information and communication technology to MTBs while reducing the burden on MTB members and building a platform that enables more accurate and personalized medical care would be of great benefit to patients. In this review, we introduced the latest status of elemental technologies that have potential for AI utilization in MTB, and discussed issues that may arise in the future as we progress with AI implementation.
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Affiliation(s)
- Ryuji Hamamoto
- grid.272242.30000 0001 2168 5385Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.509456.bCancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027 Japan
| | - Takafumi Koyama
- grid.272242.30000 0001 2168 5385Department of Experimental Therapeutics, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan
| | - Nobuji Kouno
- grid.272242.30000 0001 2168 5385Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.258799.80000 0004 0372 2033Department of Surgery, Graduate School of Medicine, Kyoto University, Yoshida-konoe-cho, Sakyo-ku, Kyoto, 606-8303 Japan
| | - Tomohiro Yasuda
- grid.272242.30000 0001 2168 5385Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.417547.40000 0004 1763 9564Research and Development Group, Hitachi, Ltd., 1-280 Higashi-koigakubo, Kokubunji, Tokyo, 185-8601 Japan
| | - Shuntaro Yui
- grid.272242.30000 0001 2168 5385Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.417547.40000 0004 1763 9564Research and Development Group, Hitachi, Ltd., 1-280 Higashi-koigakubo, Kokubunji, Tokyo, 185-8601 Japan
| | - Kazuki Sudo
- grid.272242.30000 0001 2168 5385Department of Experimental Therapeutics, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.272242.30000 0001 2168 5385Department of Medical Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan
| | - Makoto Hirata
- grid.272242.30000 0001 2168 5385Department of Genetic Medicine and Services, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan
| | - Kuniko Sunami
- grid.272242.30000 0001 2168 5385Department of Laboratory Medicine, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan
| | - Takashi Kubo
- grid.272242.30000 0001 2168 5385Department of Laboratory Medicine, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan
| | - Ken Takasawa
- grid.272242.30000 0001 2168 5385Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.509456.bCancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027 Japan
| | - Satoshi Takahashi
- grid.272242.30000 0001 2168 5385Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.509456.bCancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027 Japan
| | - Hidenori Machino
- grid.272242.30000 0001 2168 5385Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.509456.bCancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027 Japan
| | - Kazuma Kobayashi
- grid.272242.30000 0001 2168 5385Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.509456.bCancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027 Japan
| | - Ken Asada
- grid.272242.30000 0001 2168 5385Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.509456.bCancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027 Japan
| | - Masaaki Komatsu
- grid.272242.30000 0001 2168 5385Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.509456.bCancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027 Japan
| | - Syuzo Kaneko
- grid.272242.30000 0001 2168 5385Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.509456.bCancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027 Japan
| | - Yasushi Yatabe
- grid.272242.30000 0001 2168 5385Department of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.272242.30000 0001 2168 5385Division of Molecular Pathology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan
| | - Noboru Yamamoto
- grid.272242.30000 0001 2168 5385Department of Experimental Therapeutics, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan
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Liu S, Liu W, Ding Z, Yang X, Jiang Y, Wu Y, Liu Y, Wu J. Identification and validation of a novel tumor driver gene signature for diagnosis and prognosis of head and neck squamous cell carcinoma. Front Mol Biosci 2022; 9:912620. [PMID: 36339718 PMCID: PMC9631213 DOI: 10.3389/fmolb.2022.912620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 10/04/2022] [Indexed: 11/12/2023] Open
Abstract
Objective: Head and neck squamous cell carcinoma (HNSCC) is a common heterogeneous cancer with complex carcinogenic factors. However, the current TNM staging criteria to judge its severity to formulate treatment plans and evaluate the prognosis are particularly weak. Therefore, a robust diagnostic model capable of accurately diagnosing and predicting HNSCC should be established. Methods: Gene expression and clinical data were retrieved from The Cancer Genome Atlas and Gene Expression Omnibus databases. Key prognostic genes associated with HNSCC were screened with the weighted gene co-expression network analysis and least absolute shrinkage and selection operator (LASSO) Cox regression model analysis. We used the timeROC and survival R packages to conduct time-dependent receiver operating characteristic curve analyses and calculated the area under the curve at different time points of model prediction. Patients in the training and validation groups were divided into high- and low-risk subgroups, and Kaplan-Meier (K-M) survival curves were plotted for all subgroups. Subsequently, LASSO and support vector machine algorithms were used to screen genes to construct diagnostic model. Furthermore, we used the Wilcoxon signed-rank test to compare the half-maximal inhibitory concentrations of common chemotherapy drugs among patients in different risk groups. Finally, the expression levels of eight genes were measured using quantitative real-time polymerase chain reaction and immunohistochemistry. Results: Ten genes (SSB, PFKP, NAT10, PCDH9, SHANK2, PAX8, CELSR3, DCLRE1C, MAP2K7, and ODF4) with prognostic potential were identified, and a risk score was derived accordingly. Patients were divided into high- and low-risk groups based on the median risk score. The K-M survival curves confirmed that patients with high scores had significantly worse overall survival. Receiver operating characteristic curves proved that the prognostic signature had good sensitivity and specificity for predicting the prognosis of patients with HNSCC. Univariate and multivariate Cox regression analyses confirmed that the gene signature was an independent prognostic risk factor for HNSCC. Diagnostic model was built by identifying eight genes (SSB, PFKP, NAT10, PCDH9, CELSR3, DCLRE1C, MAP2K7, and ODF4). The high-risk group showed higher sensitivity to various common chemotherapeutic drugs. DCLRE1C expression was higher in normal tissues than in HNSCC tissues. Conclusion: Our study identified the important role of tumor-driver genes in HNSCC and their potential clinical diagnostic and prognostic values to facilitate individualized management of patients with HNSCC.
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Affiliation(s)
- Shixian Liu
- Department of Otolaryngology-Head & Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Medical University, Hefei, China
- Graduate School of Anhui Medical University, Hefei, China
| | - Weiwei Liu
- Department of Otolaryngology-Head & Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Medical University, Hefei, China
- Graduate School of Anhui Medical University, Hefei, China
| | - Zhao Ding
- Department of Otolaryngology-Head & Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Medical University, Hefei, China
- Graduate School of Anhui Medical University, Hefei, China
| | - Xue Yang
- Department of Otolaryngology-Head & Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Medical University, Hefei, China
- Graduate School of Anhui Medical University, Hefei, China
| | - Yuan Jiang
- Department of Otolaryngology-Head & Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Medical University, Hefei, China
- Graduate School of Anhui Medical University, Hefei, China
| | - Yu Wu
- Department of Otolaryngology-Head & Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Medical University, Hefei, China
- Graduate School of Anhui Medical University, Hefei, China
| | - Yehai Liu
- Department of Otolaryngology-Head & Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jing Wu
- Department of Otolaryngology-Head & Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
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