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Budhbaware T, Rathored J, Shende S. Molecular methods in cancer diagnostics: a short review. Ann Med 2024; 56:2353893. [PMID: 38753424 PMCID: PMC11100444 DOI: 10.1080/07853890.2024.2353893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND One of the ailments with the greatest fatality rates in the 21st century is cancer. Globally, molecular methods are widely employed to treat cancer-related disorders, and the body of research on this subject is growing yearly. A thorough and critical summary of the data supporting molecular methods for illnesses linked to cancer is required. OBJECTIVE In order to guide clinical practice and future research, it is important to examine and summarize the systematic reviews (SRs) that evaluate the efficacy and safety of molecular methods for disorders associated to cancer. METHODS We developed a comprehensive search strategy to find relevant articles from electronic databases like PubMed, Google Scholar, Web of Science (WoS), or Scopus. We looked through the literature and determined which diagnostic methods in cancer genetics were particularly reliable. We used phrases like 'cancer genetics', genetic susceptibility, Hereditary cancer, cancer risk assessment, 'cancer diagnostic tools', cancer screening', biomarkers, and molecular diagnostics, reviews and meta-analyses evaluating the efficacy and safety of molecular therapies for cancer-related disorders. Research that only consider treatment modalities that don't necessitate genetic or molecular diagnostics fall under the exclusion criteria. RESULTS The results of this comprehensive review clearly demonstrate the transformative impact of molecular methods in the realm of cancer genetics.This review underscores how these technologies have empowered researchers and clinicians to identify and understand key genetic alterations that drive malignancy, ranging from point mutations to structural variations. Such insights are instrumental in pinpointing critical oncogenic drivers and potential therapeutic targets, thus opening the door for methods in precision medicine that can significantly improve patient outcomes. LIMITATION The search does not specify a timeframe for publication inclusion, it may have missed recent advancements or changes in the field's landscape of molecular methods for cancer. As a result, it may not have included the most recent developments in the field. CONCLUSION After conducting an in-depth study on the molecular methods in cancer genetics, it is evident that these cutting-edge technologies have revolutionized the field of oncology, providing researchers and clinicians with powerful tools to unravel the complexities of cancer at the genetic level. The integration of molecular methods techniques has not only enhanced our understanding of cancer etiology, progression, and treatment response but has also opened new avenues for personalized medicine and targeted therapies, leading to improved patient outcomes.
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Affiliation(s)
- Tanushree Budhbaware
- Department of ‘School of Allied Health Sciences’, Central Research Laboratory (CRL) and Molecular Diagnostics, Datta Meghe Institute of Higher Education and Research, Sawangi (Meghe), Wardha, India
| | - Jaishriram Rathored
- Department of ‘School of Allied Health Sciences’, Central Research Laboratory (CRL) and Molecular Diagnostics, Datta Meghe Institute of Higher Education and Research, Sawangi (Meghe), Wardha, India
| | - Sandesh Shende
- Department of ‘School of Allied Health Sciences’, Central Research Laboratory (CRL) and Molecular Diagnostics, Datta Meghe Institute of Higher Education and Research, Sawangi (Meghe), Wardha, India
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2
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Quan S, Huang H. Epigenetic contribution to cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2024; 387:1-25. [PMID: 39179345 DOI: 10.1016/bs.ircmb.2024.05.003] [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: 08/26/2024]
Abstract
Epigenetics has transformed our understanding of cancer by revealing how changes in gene activity, which do not alter the DNA itself, can initiate and progress the disease. These changes include adjustments in DNA methylation, histone configuration, and non-coding RNA activity. For instance, DNA methylation can inactivate genes that typically protect against cancer, leading to broader genomic instability. Histone modifications can alter how tightly DNA is wound, influencing which genes are active or silenced; while non-coding RNAs can interfere with the messages that direct protein production, impacting cancer-related processes. Unlike genetic mutations, which are permanent and irreversible, epigenetic changes provide a malleable target for therapeutic intervention, allowing potentially reversible adjustments to gene expression patterns. This flexibility is essential in the complex landscape of cancer where static genetic solutions may be insufficient. Additionally, epigenetics bridges the gap between genetic predispositions and environmental influences on cancer, offering a comprehensive framework for understanding how lifestyle factors and external exposures impact cancer risk and progression. The integration of epigenetics into cancer research not only enhances our understanding of the disease but also opens innovative avenues for intervention that were previously unexplored in traditional genetic-focused studies. Technologies like advanced sequencing and precise epigenetic modification are paving the way for early cancer detection and more personalized treatment approaches, highlighting the critical role of epigenetics in modern cancer care.
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Affiliation(s)
- Songhua Quan
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Hao Huang
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States.
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3
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Malakar S, Gontor EN, Dugbaye MY, Shah K, Sinha S, Sutaoney P, Chauhan NS. Cancer treatment with biosimilar drugs: A review. CANCER INNOVATION 2024; 3:e115. [PMID: 38946928 PMCID: PMC11212292 DOI: 10.1002/cai2.115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/04/2023] [Accepted: 12/11/2023] [Indexed: 07/02/2024]
Abstract
Biosimilars are biological drugs created from living organisms or that contain living components. They share an identical amino-acid sequence and immunogenicity. These drugs are considered to be cost-effective and are utilized in the treatment of cancer and other endocrine disorders. The primary aim of biosimilars is to predict biosimilarity, efficacy, and treatment costs; they are approved by the Food and Drug Administration (FDA) and have no clinical implications. They involve analytical studies to understand the similarities and dissimilarities. A biosimilar manufacturer sets up FDA-approved reference products to evaluate biosimilarity. The contribution of next-generation sequencing is evolving to study the organ tumor and its progression with its impactful therapeutic approach on cancer patients to showcase and target rare mutations. The study shall help to understand the future perspectives of biosimilars for use in gastro-entero-logic diseases, colorectal cancer, and thyroid cancer. They also help target specific organs with essential mutational categories and drug prototypes in clinical practices with blood and liquid biopsy, cell treatment, gene therapy, recombinant therapeutic proteins, and personalized medications. Biosimilar derivatives such as monoclonal antibodies like trastuzumab and rituximab are common drugs used in cancer therapy. Escherichia coli produces more than six antibodies or antibody-derived proteins to treat cancer such as filgrastim, epoetin alfa, and so on.
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Affiliation(s)
- Shilpa Malakar
- Department of MicrobiologyKalinga UniversityRaipurChhattisgarhIndia
| | | | - Moses Y. Dugbaye
- Department of MicrobiologyKalinga UniversityRaipurChhattisgarhIndia
| | - Kamal Shah
- Institute of Pharmaceutical ResearchGLA UniversityMathuraUttar PradeshIndia
| | - Sakshi Sinha
- Department of MicrobiologyKalinga UniversityRaipurChhattisgarhIndia
| | - Priya Sutaoney
- Department of MicrobiologyKalinga UniversityRaipurChhattisgarhIndia
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Wu Z, Gu T, Xiong C, Shi J, Wang J, Guo T, Xing X, Pang F, He N, Miao R, Shan F, Zhou Y, Li Z, Ji J. Genomic characterization of peritoneal lavage cytology-positive gastric cancer. Chin J Cancer Res 2024; 36:66-77. [PMID: 38455368 PMCID: PMC10915641 DOI: 10.21147/j.issn.1000-9604.2024.01.07] [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: 07/25/2023] [Accepted: 02/04/2024] [Indexed: 03/09/2024] Open
Abstract
Objective Positive peritoneal lavege cytology (CY1) gastric cancer is featured by dismal prognosis, with high risks of peritoneal metastasis. However, there is a lack of evidence on pathogenic mechanism and signature of CY1 and there is a continuous debate on CY1 therapy. Therefore, exploring the mechanism of CY1 is crucial for treatment strategies and targets for CY1 gastric cancer. Methods In order to figure out specific driver genes and marker genes of CY1 gastric cancer, and ultimately offer clues for potential marker and risk assessment of CY1, 17 cytology-positive gastric cancer patients and 31 matched cytology-negative gastric cancer patients were enrolled in this study. The enrollment criteria were based on the results of diagnostic laparoscopy staging and cytology inspection of exfoliated cells. Whole exome sequencing was then performed on tumor samples to evaluate genomic characterization of cytology-positive gastric cancer. Results Least absolute shrinkage and selection operator (LASSO) algorithm identified 43 cytology-positive marker genes, while MutSigCV identified 42 cytology-positive specific driver genes. CD3G and CDKL2 were both driver and marker genes of CY1. Regarding mutational signatures, driver gene mutation and tumor subclone architecture, no significant differences were observed between CY1 and negative peritoneal lavege cytology (CY0). Conclusions There might not be distinct differences between CY1 and CY0, and CY1 might represent the progression of CY0 gastric cancer rather than constituting an independent subtype. This genomic analysis will thus provide key molecular insights into CY1, which may have a direct effect on treatment recommendations for CY1 and CY0 patients, and provides opportunities for genome-guided clinical trials and drug development.
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Affiliation(s)
- Zhouqiao Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Tingfei Gu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Changxian Xiong
- Department of Biomedical Informatics, Department of Physiology and Pathophysiology, Center for Noncoding RNA Medicine, MOE Key Lab of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Jinyao Shi
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Jingpu Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Ting Guo
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Xiaofang Xing
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Fei Pang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Ning He
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Rulin Miao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Fei Shan
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Yuan Zhou
- Department of Biomedical Informatics, Department of Physiology and Pathophysiology, Center for Noncoding RNA Medicine, MOE Key Lab of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Ziyu Li
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Jiafu Ji
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing 100142, China
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Karunakaran C, Niranjan V, Setlur AS, Pradeep D, Kumar J. Exploring the Role of Non-synonymous and Deleterious Variants Identified in Colorectal Cancer: A Multi-dimensional Computational Scrutiny of Exomes. Curr Genomics 2024; 25:41-64. [PMID: 38544823 PMCID: PMC10964087 DOI: 10.2174/0113892029285310231227105503] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/25/2023] [Accepted: 12/13/2023] [Indexed: 08/25/2024] Open
Abstract
Introduction Colorectal cancers are the world's third most commonly diagnosed type of cancer. Currently, there are several diagnostic and treatment options to combat it. However, a delay in detection of the disease is life-threatening. Additionally, a thorough analysis of the exomes of cancers reveals potential variation data that can be used for early disease prognosis. Methods By utilizing a comprehensive computational investigation, the present study aimed to reveal mutations that could potentially predispose to colorectal cancer. Ten colorectal cancer exomes were retrieved. Quality control assessments were performed using FastQC and MultiQC, gapped alignment to the human reference genome (hg19) using Bowtie2 and calling the germline variants using Haplotype caller in the GATK pipeline. The variants were filtered and annotated using SIFT and PolyPhen2 successfully categorized the mutations into synonymous, non-synonymous, start loss and stop gain mutations as well as marked them as possibly damaging, probably damaging and benign. This mutational profile helped in shortlisting frequently occurring mutations and associated genes, for which the downstream multi-dimensional expression analyses were carried out. Results Our work involved prioritizing the non-synonymous, deleterious SNPs since these polymorphisms bring about a functional alteration to the phenotype. The top variations associated with their genes with the highest frequency of occurrence included LGALS8, CTSB, RAD17, CPNE1, OPRM1, SEMA4D, MUC4, PDE4DIP, ELN and ADRA1A. An in-depth multi-dimensional downstream analysis of all these genes in terms of gene expression profiling and analysis and differential gene expression with regard to various cancer types revealed CTSB and CPNE1 as highly expressed and overregulated genes in colorectal cancer. Conclusion Our work provides insights into the various alterations that might possibly lead to colorectal cancer and suggests the possibility of utilizing the most important genes identified for wet-lab experimentation.
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Affiliation(s)
- Chandrashekar Karunakaran
- Department of Biotechnology, R V College of Engineering, Bangalore, 560059, affiliated to Visveswaraya Technological University, Belagavi, 590018, India
| | - Vidya Niranjan
- Department of Biotechnology, R V College of Engineering, Bangalore, 560059, affiliated to Visveswaraya Technological University, Belagavi, 590018, India
| | - Anagha S. Setlur
- Department of Biotechnology, R V College of Engineering, Bangalore, 560059, affiliated to Visveswaraya Technological University, Belagavi, 590018, India
| | - Dhanya Pradeep
- Department of Biotechnology, BMS College of Engineering, Bangalore, 560019, India
| | - Jitendra Kumar
- Biotechnology Industry Research Assistance Council (BIRAC), CGO complex Lodhi Road, New Delhi, India
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6
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Zazo S, Pérez‐Buira S, Carvajal N, Plaza‐Sánchez J, Manso R, Pérez‐González N, Dominguez C, Prieto‐Potin I, Rubio J, Dómine M, Lozano V, Mohedano P, Carcedo D, Carias R, Rojo F. Actionable mutational profiling in solid tumors using hybrid-capture-based next-generation sequencing in a real-world setting in Spain. Cancer Med 2024; 13:e6827. [PMID: 38213074 PMCID: PMC10905216 DOI: 10.1002/cam4.6827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/09/2023] [Accepted: 12/08/2023] [Indexed: 01/13/2024] Open
Abstract
OBJECTIVE This study aimed to describe the performance of a next-generation sequencing (NGS) panel for the detection of precise genomic alterations in cancer in Spanish clinical practice. The impact of tumor characteristics was evaluated on informative NGS and actionable mutation rates. MATERIALS AND METHODS A cross-sectional study was conducted at the Fundación Jiménez Díaz University Hospital (May 2021-March 2022) where molecular diagnostic of 537 Formalin-Fixed Paraffin-Embedded (FFPE) tissue samples of diverse solid tumors (lung, colorectal, melanoma, gastrointestinal stromal, among others) was performed using AVENIO Tumor Tissue Targeted Kit. A descriptive analysis of the features of all samples was carried out. Multivariable logistic analysis was conducted to assess the impact of sample characteristics on NGS performance defined by informative results rate (for all tumors and for lung tumors), and on actionable mutations rate (for lung tumors only). RESULTS AVENIO performance rate was 75.2% in all tumor samples and 75.3% in lung cancer samples, and the multivariable analysis showed that surgical specimens are most likely to provide informative results than diagnostic biopsies. Regarding the mutational findings, 727 pathogenic, likely pathogenic, or variant of unknown significance mutations were found in all tumor samples. Single nucleotide variant was the most common genomic alteration, both for all tumor samples (85.3% and 81.9% for all solid tumors and lung samples, respectively). In lung tumors, multivariable analysis showed that it is more likely to find actionable mutations from non-smokers and patients with adenocarcinoma, large cell, or undifferentiated histologies. CONCLUSION This is the largest cohort-level study in Spain to profile the analyses of biopsy samples of different tumors using NGS in routine clinical practice. Our findings showed that the use of NGS routinely provides good rates of informative results and can improve tumor characterization and identify a greater number of actionable mutations.
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Affiliation(s)
- Sandra Zazo
- Department of PathologyFundación Jiménez Díaz University HospitalMadridSpain
- IIS‐Fundación Jimenez DiazCenter for Biomedical Network Research on Cancer (CIBERONC)MadridSpain
| | - Sandra Pérez‐Buira
- Department of PathologyFundación Jiménez Díaz University HospitalMadridSpain
| | - Nerea Carvajal
- Department of PathologyFundación Jiménez Díaz University HospitalMadridSpain
| | | | - Rebeca Manso
- Department of PathologyFundación Jiménez Díaz University HospitalMadridSpain
| | | | - Carolina Dominguez
- IIS‐Fundación Jimenez DiazCenter for Biomedical Network Research on Cancer (CIBERONC)MadridSpain
| | - Iván Prieto‐Potin
- Department of PathologyFundación Jiménez Díaz University HospitalMadridSpain
| | - Jaime Rubio
- Medical Oncology DepartmentFundación Jiménez Díaz University HospitalMadridSpain
| | - Manuel Dómine
- IIS‐Fundación Jimenez DiazCenter for Biomedical Network Research on Cancer (CIBERONC)MadridSpain
- Medical Oncology DepartmentFundación Jiménez Díaz University HospitalMadridSpain
| | | | | | | | - Rafael Carias
- Department of PathologyFundación Jiménez Díaz University HospitalMadridSpain
| | - Federico Rojo
- Department of PathologyFundación Jiménez Díaz University HospitalMadridSpain
- IIS‐Fundación Jimenez DiazCenter for Biomedical Network Research on Cancer (CIBERONC)MadridSpain
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Wang Q, Liang Q, Wei W, Niu W, Liang C, Wang X, Wang X, Pan H. Concordance analysis of cerebrospinal fluid with the tumor tissue for integrated diagnosis in gliomas based on next-generation sequencing. Pathol Oncol Res 2023; 29:1611391. [PMID: 37822669 PMCID: PMC10562547 DOI: 10.3389/pore.2023.1611391] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/12/2023] [Indexed: 10/13/2023]
Abstract
Purpose: The driver mutations of gliomas have been identified in cerebrospinal fluid (CSF). Here we compared the concordance between CSF and tumor tissue for integrated diagnosis in gliomas using next-generation sequencing (NGS) to evaluate the feasibility of CSF detection in gliomas. Patients and methods: 27 paired CSF/tumor tissues of glioma patients were sequenced by a customized gene panel based on NGS. All CSF samples were collected through lumbar puncture before surgery. Integrated diagnosis was made by analysis of histology and tumor DNA molecular pathology according to the 2021 WHO classification of the central nervous system tumors. Results: A total of 24 patients had detectable circulating tumor DNA (ctDNA) and 22 had at least one somatic mutation or chromosome alteration in CSF. The ctDNA levels varied significantly across different ages, Ki-67 index, magnetic resonance imaging signal and glioma subtypes (p < 0.05). The concordance between integrated ctDNA diagnosis and the final diagnosis came up to 91.6% (Kappa, 0.800). We reclassified the clinical diagnosis of 3 patients based on the results of CSF ctDNA sequencing, and 4 patients were reassessed depending on tumor DNA. Interestingly, a rare IDH1 R132C was identified in CSF ctDNA, but not in the corresponding tumor sample. Conclusion: This study demonstrates a high concordance between integrated ctDNA diagnosis and the final diagnosis of gliomas, highlighting the practicability of NGS based detection of mutations of CSF in assisting integrated diagnosis of gliomas, especially glioblastoma.
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Affiliation(s)
- Qiang Wang
- Department of Neurosurgery, Jinling Hospital, Nanjing, China
| | - Qiujin Liang
- State Key Laboratory of Neurology and Oncology Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
| | - Wuting Wei
- Department of Neurosurgery, Jinling Hospital, Nanjing, China
| | - Wenhao Niu
- Department of Neurosurgery, Jinling Hospital, Nanjing, China
| | - Chong Liang
- Department of Neurosurgery, Jinling Hospital, Nanjing, China
| | - Xiaoliang Wang
- Department of Neurosurgery, Jinling Hospital, Nanjing, China
| | - Xiaoxuan Wang
- State Key Laboratory of Neurology and Oncology Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
| | - Hao Pan
- Department of Neurosurgery, Jinling Hospital, Nanjing, China
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Asl ER, Sarabandi S, Shademan B, Dalvandi K, sheikhansari G, Nourazarian A. MicroRNA targeting: A novel therapeutic intervention for ovarian cancer. Biochem Biophys Rep 2023; 35:101519. [PMID: 37521375 PMCID: PMC10382632 DOI: 10.1016/j.bbrep.2023.101519] [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: 06/13/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 08/01/2023] Open
Abstract
Ovarian cancer, a perilous form of cancer affecting the female reproductive system, exhibits intricate communication networks that contribute to its progression. This study aims to identify crucial molecular abnormalities linked to the disease to enhance diagnostic and therapeutic strategies. In particular, we investigate the role of microRNAs (miRNAs) as diagnostic biomarkers and explore their potential in treating ovarian cancer. By targeting miRNAs, which can influence multiple pathways and genes, substantial therapeutic benefits can be attained. In this review we want to shed light on the promising application of miRNA-based interventions and provide insights into the specific miRNAs implicated in ovarian cancer pathogenesis.
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Affiliation(s)
- Elmira Roshani Asl
- Social Determinants of Health Research Center, Saveh University of Medical Sciences, Saveh, Iran
| | - Sajed Sarabandi
- Department of Veterinary, Faculty of Medicine Sciences, Islamic Azad University of Karaj, Karaj, Iran
| | - Behrouz Shademan
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Kourosh Dalvandi
- Ministry of Health and Medical Education, Health Department, Tehran, Iran
| | | | - Alireza Nourazarian
- Department of Basic Medical Sciences, Khoy University of Medical Sciences, Khoy, Iran
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Sutera P, Skinner H, Witek M, Mishra M, Kwok Y, Davicioni E, Feng F, Song D, Nichols E, Tran PT, Bergom C. Histology Specific Molecular Biomarkers: Ushering in a New Era of Precision Radiation Oncology. Semin Radiat Oncol 2023; 33:232-242. [PMID: 37331778 PMCID: PMC10446901 DOI: 10.1016/j.semradonc.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Histopathology and clinical staging have historically formed the backbone for allocation of treatment decisions in oncology. Although this has provided an extremely practical and fruitful approach for decades, it has long been evident that these data alone do not adequately capture the heterogeneity and breadth of disease trajectories experienced by patients. As efficient and affordable DNA and RNA sequencing have become available, the ability to provide precision therapy has become within grasp. This has been realized with systemic oncologic therapy, as targeted therapies have demonstrated immense promise for subsets of patients with oncogene-driver mutations. Further, several studies have evaluated predictive biomarkers for response to systemic therapy within a variety of malignancies. Within radiation oncology, the use of genomics/transcriptomics to guide the use, dose, and fractionation of radiation therapy is rapidly evolving but still in its infancy. The genomic adjusted radiation dose/radiation sensitivity index is one such early and exciting effort to provide genomically guided radiation dosing with a pan-cancer approach. In addition to this broad method, a histology specific approach to precision radiation therapy is also underway. Herein we review select literature surrounding the use of histology specific, molecular biomarkers to allow for precision radiotherapy with the greatest emphasis on commercially available and prospectively validated biomarkers.
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Affiliation(s)
- Philip Sutera
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Heath Skinner
- Department of Radiation Oncology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Matthew Witek
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mark Mishra
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Young Kwok
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Felix Feng
- Departments of Radiation Oncology, Medicine and Urology, UCSF, San Francisco, CA, USA
| | - Daniel Song
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elizabeth Nichols
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Phuoc T. Tran
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Carmen Bergom
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
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Fang W, Wu J, Cheng M, Zhu X, Du M, Chen C, Liao W, Zhi K, Pan W. Diagnosis of invasive fungal infections: challenges and recent developments. J Biomed Sci 2023; 30:42. [PMID: 37337179 DOI: 10.1186/s12929-023-00926-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/13/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND The global burden of invasive fungal infections (IFIs) has shown an upsurge in recent years due to the higher load of immunocompromised patients suffering from various diseases. The role of early and accurate diagnosis in the aggressive containment of the fungal infection at the initial stages becomes crucial thus, preventing the development of a life-threatening situation. With the changing demands of clinical mycology, the field of fungal diagnostics has evolved and come a long way from traditional methods of microscopy and culturing to more advanced non-culture-based tools. With the advent of more powerful approaches such as novel PCR assays, T2 Candida, microfluidic chip technology, next generation sequencing, new generation biosensors, nanotechnology-based tools, artificial intelligence-based models, the face of fungal diagnostics is constantly changing for the better. All these advances have been reviewed here giving the latest update to our readers in the most orderly flow. MAIN TEXT A detailed literature survey was conducted by the team followed by data collection, pertinent data extraction, in-depth analysis, and composing the various sub-sections and the final review. The review is unique in its kind as it discusses the advances in molecular methods; advances in serology-based methods; advances in biosensor technology; and advances in machine learning-based models, all under one roof. To the best of our knowledge, there has been no review covering all of these fields (especially biosensor technology and machine learning using artificial intelligence) with relevance to invasive fungal infections. CONCLUSION The review will undoubtedly assist in updating the scientific community's understanding of the most recent advancements that are on the horizon and that may be implemented as adjuncts to the traditional diagnostic algorithms.
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Affiliation(s)
- Wenjie Fang
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Junqi Wu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, 200433, China
| | - Mingrong Cheng
- Department of Anorectal Surgery, The Third Affiliated Hospital of Guizhou Medical University, Guizhou, 558000, China
| | - Xinlin Zhu
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Mingwei Du
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Chang Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, 200433, China
| | - Wanqing Liao
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Kangkang Zhi
- Department of Vascular and Endovascular Surgery, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China.
| | - Weihua Pan
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China.
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Ionita I, Malita D, Dehelean C, Olteanu E, Marcovici I, Geamantan A, Chiriac S, Roman A, Radu D. Experimental Models for Rare Melanoma Research-The Niche That Needs to Be Addressed. Bioengineering (Basel) 2023; 10:673. [PMID: 37370604 DOI: 10.3390/bioengineering10060673] [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: 04/19/2023] [Revised: 05/09/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Melanoma, the tumor arising from the malignant transformation of pigment-producing cells-the melanocytes-represents one of the most severe cancer types. Despite their rarity compared to cutaneous melanoma, the extracutaneous subtypes such as uveal melanoma (UM), acral lentiginous melanoma (ALM), and mucosal melanoma (MM) stand out due to their increased aggressiveness and mortality rate, demanding continuous research to elucidate their specific pathological features and develop efficient therapies. Driven by the emerging progresses made in the preclinical modeling of melanoma, the current paper covers the most relevant in vitro, in vivo, and in ovo systems, providing a deeper understanding of these rare melanoma subtypes. However, the preclinical models for UM, ALM, and MM that were developed so far remain scarce, and none of them is able to completely simulate the complexity that is characteristic to these melanomas; thus, a continuous expansion of the existing library of experimental models is pivotal for driving advancements in this research field. An overview of the applicability of precision medicine in the management of rare melanoma subtypes is also provided.
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Affiliation(s)
- Ioana Ionita
- Faculty of Medicine, "Victor Babes" University of Medicine and Pharmacy, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
| | - Daniel Malita
- Faculty of Medicine, "Victor Babes" University of Medicine and Pharmacy, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
| | - Cristina Dehelean
- Faculty of Pharmacy, "Victor Babes" University of Medicine and Pharmacy, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
- Research Center for Pharmaco-Toxicological Evaluations, Faculty of Pharmacy, "Victor Babes" University of Medicine and Pharmacy, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
| | - Emilian Olteanu
- Faculty of Pharmacy, "Victor Babes" University of Medicine and Pharmacy, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
- Research Center for Pharmaco-Toxicological Evaluations, Faculty of Pharmacy, "Victor Babes" University of Medicine and Pharmacy, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
- Center for Research and Innovation in Personalized Medicine of Respiratory Diseases, "Victor Babes" University of Medicine and Pharmacy, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
| | - Iasmina Marcovici
- Faculty of Pharmacy, "Victor Babes" University of Medicine and Pharmacy, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
- Research Center for Pharmaco-Toxicological Evaluations, Faculty of Pharmacy, "Victor Babes" University of Medicine and Pharmacy, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
| | - Andreea Geamantan
- Faculty of Pharmacy, "Victor Babes" University of Medicine and Pharmacy, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
- Research Center for Pharmaco-Toxicological Evaluations, Faculty of Pharmacy, "Victor Babes" University of Medicine and Pharmacy, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
| | - Sorin Chiriac
- Faculty of Medicine, "Victor Babes" University of Medicine and Pharmacy, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
| | - Andrea Roman
- Faculty of Medicine, "Victor Babes" University of Medicine and Pharmacy, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
| | - Daniela Radu
- Faculty of Medicine, "Victor Babes" University of Medicine and Pharmacy, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
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12
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Shukla N, Kour B, Sharma D, Vijayvargiya M, Sadasukhi TC, Medicherla KM, Malik B, Bissa B, Vuree S, Lohiya NK, Suravajhala P. Towards Understanding the Key Signature Pathways Associated from Differentially Expressed Gene Analysis in an Indian Prostate Cancer Cohort. Diseases 2023; 11:diseases11020072. [PMID: 37218885 DOI: 10.3390/diseases11020072] [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: 02/20/2023] [Revised: 04/13/2023] [Accepted: 04/18/2023] [Indexed: 05/24/2023] Open
Abstract
Prostate cancer (PCa) is one of the most prevalent cancers among men in India. Although studies on PCa have dealt with genetics, genomics, and the environmental influence in the causality of PCa, not many studies employing the Next Generation Sequencing (NGS) approaches of PCa have been carried out. In our previous study, we identified some causal genes and mutations specific to Indian PCa using Whole Exome Sequencing (WES). In the recent past, with the help of different cancer consortiums such as The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC), along with differentially expressed genes (DEGs), many cancer-associated novel non-coding RNAs have been identified as biomarkers. In this work, we attempt to identify differentially expressed genes (DEGs) including long non-coding RNAs (lncRNAs) associated with signature pathways from an Indian PCa cohort using the RNA-sequencing (RNA-seq) approach. From a cohort of 60, we screened six patients who underwent prostatectomy; we performed whole transcriptome shotgun sequencing (WTSS)/RNA-sequencing to decipher the DEGs. We further normalized the read counts using fragments per kilobase of transcript per million mapped reads (FPKM) and analyzed the DEGs using a cohort of downstream regulatory tools, viz., GeneMANIA, Stringdb, Cytoscape-Cytohubba, and cbioportal, to map the inherent signatures associated with PCa. By comparing the RNA-seq data obtained from the pairs of normal and PCa tissue samples using our benchmarked in-house cuffdiff pipeline, we observed some important genes specific to PCa, such as STEAP2, APP, PMEPA1, PABPC1, NFE2L2, and HN1L, and some other important genes known to be involved in different cancer pathways, such as COL6A1, DOK5, STX6, BCAS1, BACE1, BACE2, LMOD1, SNX9, CTNND1, etc. We also identified a few novel lncRNAs such as LINC01440, SOX2OT, ENSG00000232855, ENSG00000287903, and ENST00000647843.1 that need to be characterized further. In comparison with publicly available datasets, we have identified characteristic DEGs and novel lncRNAs implicated in signature PCa pathways in an Indian PCa cohort which perhaps have not been reported. This has set a precedent for us to validate candidates further experimentally, and we firmly believe this will pave a way toward the discovery of biomarkers and the development of novel therapies.
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Affiliation(s)
- Nidhi Shukla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Statue Circle, Jaipur 302001, India
- Department of Chemistry, School of Basic Sciences, Manipal University Jaipur, Jaipur 303007, India
| | - Bhumandeep Kour
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144001, India
| | - Devendra Sharma
- Department of Urology, Rukmani Birla Hospital, Jaipur 302018, India
| | - Maneesh Vijayvargiya
- Department of Pathology, Mahatma Gandhi University of Medical Sciences and Technology, Jaipur 302022, India
| | - T C Sadasukhi
- Department of Urology, Mahatma Gandhi University of Medical Sciences and Technology, Jaipur 302022, India
| | - Krishna Mohan Medicherla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Statue Circle, Jaipur 302001, India
- Department of Bioengineering, Birla Institute of Technology, Mesra Jaipur Campus, 27-Malaviya Industrial Area, Jaipur 302017, India
| | - Babita Malik
- Department of Chemistry, School of Basic Sciences, Manipal University Jaipur, Jaipur 303007, India
| | - Bhawana Bissa
- Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, India
| | - Sugunakar Vuree
- Bioclues.org, Hyderabad 500072, India
- MNR Foundation for Research & Innovation, MNR University, Sangareddy 502294, India
| | - Nirmal Kumar Lohiya
- Department of Zoology, Center for Advanced Studies, University of Rajasthan, Jaipur 302004, India
| | - Prashanth Suravajhala
- Bioclues.org, Hyderabad 500072, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India
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Menon T, Gopal S, Rastogi Verma S. Targeted therapies in non-small cell lung cancer and the potential role of AI interventions in cancer treatment. Biotechnol Appl Biochem 2023; 70:344-356. [PMID: 35609005 DOI: 10.1002/bab.2356] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 04/17/2022] [Indexed: 11/12/2022]
Abstract
Non-small cell lung cancer is the most prevalent lung cancer, and almost three-fourths of patients are diagnosed in the advanced stage directly. In this stage, chemotherapy gives only a 15% 5-year survival rate. As people have varied symptoms and reactions to a specific cancer type, treatment for the tumor is likely to fall short, complicating cancer therapy. Immunotherapy is a breakthrough treatment involving drugs targeting novel immune checkpoint inhibitors like CTLA-4 and PD-1/PD-L1, along with combination therapies. In addition, the utility of engineered CAR-T and CAR-NK cells can be an effective strategy to promote the immune response against tumors. The concept of personalized cancer vaccines with the discovery of neoantigens loaded on dendritic cell vectors can also be an effective approach to cure cancer. Advances in genetic engineering tools like CRISPR/Cas9-mediated gene editing of T cells to enhance their effector function is another ray of hope. This review aims to provide an overview of recent developments in cancer immunotherapy, which can be used in first- and second-line treatments in the clinical space. Further, the intervention of artificial intelligence to detect cancer tumors at an initial stage with the help of machine learning techniques is also explored.
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Affiliation(s)
- Tarunya Menon
- Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Shubhang Gopal
- Department of Information Technology, Delhi Technological University, Delhi, India
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14
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Siddique A, Bashir S, Abbas M. Pharmacogenetics of Anticancer Drugs: Clinical Response and Toxicity. Cancer Treat Res 2023; 185:141-175. [PMID: 37306909 DOI: 10.1007/978-3-031-27156-4_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cancer is the most challenging disease for medical professionals to treat. The factors underlying the complicated situation include anticancer drug-associated toxicity, non-specific response, low therapeutic window, variable treatment outcomes, development of drug resistance, treatment complications, and cancer recurrence. The remarkable advancement in biomedical sciences and genetics, over the past few decades, however, is changing the dire situation. The discovery of gene polymorphism, gene expression, biomarkers, particular molecular targets and pathways, and drug-metabolizing enzymes have paved the way for the development and provision of targeted and individualized anticancer treatment. Pharmacogenetics is the study of genetic factors having the potential to affect clinical responses and pharmacokinetic and pharmacodynamic behaviors of drugs. This chapter emphasizes pharmacogenetics of anticancer drugs and its applications in improving treatment outcomes, selectivity, toxicity of the drugs, and discovering and developing personalized anticancer drugs and genetic methods for prediction of drug response and toxicity.
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Affiliation(s)
- Ammara Siddique
- Faculty of Pharmacy, Bahauddin Zakariya University, Multan, Pakistan
| | - Samra Bashir
- Faculty of Pharmacy, Capital University of Science and Technology, Islamabad, Pakistan.
| | - Mateen Abbas
- Faculty of Pharmacy, Capital University of Science and Technology, Islamabad, Pakistan
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15
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Herreros-Villanueva M, Bujanda L, Ruiz-Rebollo L, Torremocha R, Ramos R, Martín R, Artigas MC. Circulating tumor DNA tracking in patients with pancreatic cancer using next-generation sequencing. GASTROENTEROLOGIA Y HEPATOLOGIA 2022; 45:637-644. [PMID: 35092761 DOI: 10.1016/j.gastrohep.2021.12.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/08/2021] [Accepted: 12/29/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND Pancreatic cancer remains one of the most devastating malignancies due to the absence of techniques for early diagnosis and the lack of target therapeutic options for advanced disease. Next Generation Sequencing (NGS) generates high throughput and valuable genetic information when evaluating circulating tumor DNA (ctDNA); however clinical utility of liquid biopsy in pancreatic cancer has not been demonstrated yet. The aim of this study was to evaluate whether results from a Next Generation Sequencing panel on plasma samples from pancreatic cancer patients could have a clinical significance. METHODS From December 2016 to January 2020, plasma samples from 27 patients with pancreatic ductal adenocarcinoma at two different tertiary Spanish Hospitals underwent ctDNA testing using a commercial NGS panel of 65 genes. Clinical data were available for these patients. VarsSome Clinical software was used to analyse NGS data and establish pathogenicity. RESULTS Evaluable NGS results were obtained in 18 out of the 27 plasma samples. Somatic pathogenic mutations were found mainly in KRAS, BRCA2, FLT3 and HNF1A, genes. Pathogenic mutations were detected in 50% of plasma samples from patient diagnosed at stages III-IV samples. FLT3 mutations were observed in 22.22% of samples which constitute a novel result in the field. CONCLUSIONS Liquid biopsy using NGS is a valuable tool but still not sensitive or specific enough to provide clinical utility in pancreatic cancer patients.
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Affiliation(s)
- Marta Herreros-Villanueva
- Facultad de Ciencias de la Salud, Universidad Isabel I, Burgos, Spain; Department of Gastroenterology, Hospital Donostia/Instituto Biodonostia, San Sebastián, Spain.
| | - Luis Bujanda
- Department of Gastroenterology, Hospital Donostia/Instituto Biodonostia, San Sebastián, Spain; Department of Gastroenterology, Hospital Donostia/Instituto Biodonostia, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Universidad del País Vasco UPV/EHU, San Sebastián, Spain
| | - Lourdes Ruiz-Rebollo
- Department of Gastroenterology, Hospital Clínico de Valladolid, Valladolid, Spain
| | | | | | - Rubén Martín
- Facultad de Ciencias de la Salud, Universidad Isabel I, Burgos, Spain
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16
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Kumari P, Kumar S, Sethy M, Bhue S, Mohanta BK, Dixit A. Identification of therapeutically potential targets and their ligands for the treatment of OSCC. Front Oncol 2022; 12:910494. [PMID: 36203433 PMCID: PMC9530560 DOI: 10.3389/fonc.2022.910494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/15/2022] [Indexed: 11/30/2022] Open
Abstract
Recent advancements in cancer biology have revealed molecular changes associated with carcinogenesis and chemotherapeutic exposure. The available information is being gainfully utilized to develop therapies targeting specific molecules involved in cancer cell growth, survival, and chemoresistance. Targeted therapies have dramatically increased overall survival (OS) in many cancers. Therefore, developing such targeted therapies against oral squamous cell carcinoma (OSCC) is anticipated to have significant clinical implications. In the current work, we have identified drug-specific sensitivity-related prognostic biomarkers (BOP1, CCNA2, CKS2, PLAU, and SERPINE1) using gene expression, Cox proportional hazards regression, and machine learning in OSCC. Dysregulation of these markers is significantly associated with OS in many cancers. Their elevated expression is related to cellular proliferation and aggressive malignancy in various cancers. Mechanistically, inhibition of these biomarkers should significantly reduce cellular proliferation and metastasis in OSCC and should result in better OS. It is pertinent to note that no effective small-molecule candidate has been identified against these biomarkers to date. Therefore, a comprehensive in silico drug design strategy assimilating homology modeling, extensive molecular dynamics (MD) simulation, and ensemble molecular docking has been applied to identify potential compounds against identified targets, and potential molecules have been identified. We hope that this study will help in deciphering potential genes having roles in chemoresistance and a significant impact on OS. It will also result in the identification of new targeted therapeutics against OSCC.
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Affiliation(s)
- Pratima Kumari
- Computational Biology and Bioinformatics Laboratory, Institute of Life Sciences, Bhubaneswar, India
- Regional Centre for Biotechnology (RCB), Faridabad, India
| | - Sugandh Kumar
- Computational Biology and Bioinformatics Laboratory, Institute of Life Sciences, Bhubaneswar, India
| | - Madhusmita Sethy
- Computational Biology and Bioinformatics Laboratory, Institute of Life Sciences, Bhubaneswar, India
| | - Shyamlal Bhue
- Computational Biology and Bioinformatics Laboratory, Institute of Life Sciences, Bhubaneswar, India
- Regional Centre for Biotechnology (RCB), Faridabad, India
| | - Bineet Kumar Mohanta
- Computational Biology and Bioinformatics Laboratory, Institute of Life Sciences, Bhubaneswar, India
- Regional Centre for Biotechnology (RCB), Faridabad, India
| | - Anshuman Dixit
- Computational Biology and Bioinformatics Laboratory, Institute of Life Sciences, Bhubaneswar, India
- *Correspondence: Anshuman Dixit,
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17
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Evaluation of the Available Variant Calling Tools for Oxford Nanopore Sequencing in Breast Cancer. Genes (Basel) 2022; 13:genes13091583. [PMID: 36140751 PMCID: PMC9498802 DOI: 10.3390/genes13091583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 11/23/2022] Open
Abstract
The goal of biomarker testing, in the field of personalized medicine, is to guide treatments to achieve the best possible results for each patient. The accurate and reliable identification of everyone’s genome variants is essential for the success of clinical genomics, employing third-generation sequencing. Different variant calling techniques have been used and recommended by both Oxford Nanopore Technologies (ONT) and Nanopore communities. A thorough examination of the variant callers might give critical guidance for third-generation sequencing-based clinical genomics. In this study, two reference genome sample datasets (NA12878) and (NA24385) and the set of high-confidence variant calls provided by the Genome in a Bottle (GIAB) were used to allow the evaluation of the performance of six variant calling tools, including Human-SNP-wf, Clair3, Clair, NanoCaller, Longshot, and Medaka, as an integral step in the in-house variant detection workflow. Out of the six variant callers understudy, Clair3 and Human-SNP-wf that has Clair3 incorporated into it achieved the highest performance rates in comparison to the other variant callers. Evaluation of the results for the tool was expressed in terms of Precision, Recall, and F1-score using Hap.py tools for the comparison. In conclusion, our findings give important insights for identifying accurate variants from third-generation sequencing of personal genomes using different variant detection tools available for long-read sequencing.
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18
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Sutera P, Deek MP, Van der Eecken K, Wyatt AW, Kishan AU, Molitoris JK, Ferris MJ, Minhaj Siddiqui M, Rana Z, Mishra MV, Kwok Y, Davicioni E, Spratt DE, Ost P, Feng FY, Tran PT. Genomic biomarkers to guide precision radiotherapy in prostate cancer. Prostate 2022; 82 Suppl 1:S73-S85. [PMID: 35657158 PMCID: PMC9202472 DOI: 10.1002/pros.24373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/30/2022] [Accepted: 04/29/2022] [Indexed: 11/08/2022]
Abstract
Our ability to prognosticate the clinical course of patients with cancer has historically been limited to clinical, histopathological, and radiographic features. It has long been clear however, that these data alone do not adequately capture the heterogeneity and breadth of disease trajectories experienced by patients. The advent of efficient genomic sequencing has led to a revolution in cancer care as we try to understand and personalize treatment specific to patient clinico-genomic phenotypes. Within prostate cancer, emerging evidence suggests that tumor genomics (e.g., DNA, RNA, and epigenetics) can be utilized to inform clinical decision making. In addition to providing discriminatory information about prognosis, it is likely tumor genomics also hold a key in predicting response to oncologic therapies which could be used to further tailor treatment recommendations. Herein we review select literature surrounding the use of tumor genomics within the management of prostate cancer, specifically leaning toward analytically validated and clinically tested genomic biomarkers utilized in radiotherapy and/or adjunctive therapies given with radiotherapy.
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Affiliation(s)
- Philip Sutera
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Matthew P. Deek
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USA
| | - Kim Van der Eecken
- Department of Pathology, Ghent University Hospital, Cancer Research Institute (CRIG), Ghent, Belgium
| | - Alexander W. Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amar U. Kishan
- Department of Radiation Oncology, UCLA, Los Angeles, CA, USA
| | - Jason K. Molitoris
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Matthew J. Ferris
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - M. Minhaj Siddiqui
- Department of Surgery, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Zaker Rana
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mark V. Mishra
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Young Kwok
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Daniel E. Spratt
- Department of Radiation Oncology, University Hospitals, Cleveland, OH, USA
| | - Piet Ost
- Department of Radiation Oncology, Iridium Network, Antwerp, Belgium and Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Felix Y. Feng
- Departments of Radiation Oncology, Medicine and Urology, UCSF, San Francisco, CA, USA
| | - Phuoc T. Tran
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
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Duplex sequencing identifies genomic features that determine susceptibility to benzo(a)pyrene-induced in vivo mutations. BMC Genomics 2022; 23:542. [PMID: 35902794 PMCID: PMC9331077 DOI: 10.1186/s12864-022-08752-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/04/2022] [Indexed: 11/20/2022] Open
Abstract
Exposure to environmental mutagens increases the risk of cancer and genetic disorders. We used Duplex Sequencing (DS), a high-accuracy error-corrected sequencing technology, to analyze mutation induction across twenty 2.4 kb intergenic and genic targets in the bone marrow of MutaMouse males exposed to benzo(a)pyrene (BaP), a widespread environmental pollutant. DS revealed a linear dose-related induction of mutations across all targets with low intra-group variability. Heterochromatic and intergenic regions exhibited the highest mutation frequencies (MF). C:G > A:T transversions at CCA, CCC and GCC trinucleotides were enriched in BaP-exposed mice consistent with the known etiology of BaP mutagenesis. However, GC-content had no effect on mutation susceptibility. A positive correlation was observed between DS and the “gold-standard” transgenic rodent gene mutation assay. Overall, we demonstrate that DS is a promising approach to study in vivo mutagenesis and yields critical insight into the genomic features governing mutation susceptibility, spectrum, and variability across the genome.
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20
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Sharma K, Sayed S, Saleh M. Promoting Best Practice in Cancer Care in Sub Saharan Africa. Front Med (Lausanne) 2022; 9:950309. [PMID: 35872798 PMCID: PMC9299371 DOI: 10.3389/fmed.2022.950309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 06/15/2022] [Indexed: 11/21/2022] Open
Abstract
Promoting best practice in the management of a cancer patient is rooted in the application of new knowledge derived through various sources including population science, laboratory advances, and translational research. Ultimately, the impact of these advances depends on their application at the patient's bedside. A close collaboration between the oncologist and the pathologist is critical in underwriting progress in the management of the cancer patient. Recent advancements have shown that more granular characteristics of the tumor and the microenvironment are defining determinants when it comes to disease course and overall outcome. Whereas, histologic features and basic immunohistochemical characterization were previously adequate to define the tumor and establish treatment recommendation, the growing capability of the pathologist to provide molecular characterization of the tumor and its microenvironment, as well as, the availability of novel therapeutic agents have revolutionized cancer treatment paradigms and improved patient-outcomes and survival. While such capacity and capability appear readily available in most developed high-income countries (HIC), it will take a concerted and collaborative effort of all stakeholders to pave the way in the same stride in the low and middle-income countries (LMIC), which bear a disproportionate burden of human illness and cancers. Patients in the LMIC present with disease at advanced stage and often display characteristics unlike those encountered in the developed world. To keep stride and avoid the disenfranchisement of patients in the LMIC will require greater participation of LMIC patients on the global clinical trial platform, and a more equitable and affordable sharing of diagnostic and therapeutic capabilities between the developed and developing world. Key to the success of this progress and improvement of patient outcomes in the developing world is the close collaboration between the oncologist and the pathologist in this new era of precision and personalized medicine.
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Affiliation(s)
- Karishma Sharma
- Clinical Research Unit, Aga Khan University Cancer Center, Aga Khan University, Nairobi, Kenya
| | - Shahin Sayed
- Department of Pathology, Aga Khan University Hospital, Nairobi, Kenya
| | - Mansoor Saleh
- Clinical Research Unit, Aga Khan University Cancer Center, Aga Khan University, Nairobi, Kenya
- Department of Hematology and Oncology, Aga Khan University Hospital, Nairobi, Kenya
- *Correspondence: Mansoor Saleh
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21
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Guarnaccia M, Guarnaccia L, La Cognata V, Navone SE, Campanella R, Ampollini A, Locatelli M, Miozzo M, Marfia G, Cavallaro S. A Targeted Next-Generation Sequencing Panel to Genotype Gliomas. LIFE (BASEL, SWITZERLAND) 2022; 12:life12070956. [PMID: 35888045 PMCID: PMC9320073 DOI: 10.3390/life12070956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 12/12/2022]
Abstract
Gliomas account for the majority of primary brain tumors. Glioblastoma is the most common and malignant type. Based on their extreme molecular heterogeneity, molecular markers can be used to classify gliomas and stratify patients into diagnostic, prognostic, and therapeutic clusters. In this work, we developed and validated a targeted next-generation sequencing (NGS) approach to analyze variants or chromosomal aberrations correlated with tumorigenesis and response to treatment in gliomas. Our targeted NGS analysis covered 13 glioma-related genes (ACVR1, ATRX, BRAF, CDKN2A, EGFR, H3F3A, HIST1H3B, HIST1H3C, IDH1, IDH2, P53, PDGFRA, PTEN), a 125 bp region of the TERT promoter, and 54 single nucleotide polymorphisms (SNPs) along chromosomes 1 and 19 for reliable assessment of their copy number alterations (CNAs). Our targeted NGS approach provided a portrait of gliomas’ molecular heterogeneity with high accuracy, specificity, and sensitivity in a single workflow, enabling the detection of variants associated with unfavorable outcomes, disease progression, and drug resistance. These preliminary results support its use in routine diagnostic neuropathology.
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Affiliation(s)
- Maria Guarnaccia
- Institute for Biomedical Research and Innovation, National Research Council, Via P. Gaifami 18, 95126 Catania, Italy; (M.G.); (V.L.C.)
| | - Laura Guarnaccia
- Laboratory of Experimental Neurosurgery and Cell Therapy, Neurosurgery Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, Italy; (L.G.); (S.E.N.); (R.C.); (A.A.); (M.L.); (G.M.)
- Department of Clinical Sciences and Community Health, University of Milan, Via Festa del Perdono 7, 20122 Milan, Italy
| | - Valentina La Cognata
- Institute for Biomedical Research and Innovation, National Research Council, Via P. Gaifami 18, 95126 Catania, Italy; (M.G.); (V.L.C.)
| | - Stefania Elena Navone
- Laboratory of Experimental Neurosurgery and Cell Therapy, Neurosurgery Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, Italy; (L.G.); (S.E.N.); (R.C.); (A.A.); (M.L.); (G.M.)
| | - Rolando Campanella
- Laboratory of Experimental Neurosurgery and Cell Therapy, Neurosurgery Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, Italy; (L.G.); (S.E.N.); (R.C.); (A.A.); (M.L.); (G.M.)
| | - Antonella Ampollini
- Laboratory of Experimental Neurosurgery and Cell Therapy, Neurosurgery Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, Italy; (L.G.); (S.E.N.); (R.C.); (A.A.); (M.L.); (G.M.)
| | - Marco Locatelli
- Laboratory of Experimental Neurosurgery and Cell Therapy, Neurosurgery Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, Italy; (L.G.); (S.E.N.); (R.C.); (A.A.); (M.L.); (G.M.)
- “Aldo Ravelli” Research Center, Via Antonio di Rudinì 8, 20142 Milan, Italy
- Department of Medical-Surgical Physiopathology and Transplantation, University of Milan, Via Francesco Sforza 35, 20122 Milan, Italy
| | - Monica Miozzo
- Department of Health Sciences, University of Milan, 20122 Milan, Italy;
- Unit of Medical Genetics, ASST Santi Paolo e Carlo, 20142 Milan, Italy
| | - Giovanni Marfia
- Laboratory of Experimental Neurosurgery and Cell Therapy, Neurosurgery Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, Italy; (L.G.); (S.E.N.); (R.C.); (A.A.); (M.L.); (G.M.)
- Clinical Pathology Unit, Aerospace Medicine Institute “A. Mosso”, Italian Air Force, Viale dell’Aviazione 1, 20138 Milan, Italy
| | - Sebastiano Cavallaro
- Institute for Biomedical Research and Innovation, National Research Council, Via P. Gaifami 18, 95126 Catania, Italy; (M.G.); (V.L.C.)
- Correspondence: ; Tel.: +39-09-57338128
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22
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Thevendran R, Foo KL, Hussin MH, Moses EJ, Citartan M, Prasad HR, Maheswaran S. Reverse Electrochemical Sensing of FLT3-ITD Mutations in Acute Myeloid Leukemia Using Gold Sputtered ZnO-Nanorod Configured DNA Biosensors. BIOSENSORS 2022; 12:170. [PMID: 35323440 PMCID: PMC8946250 DOI: 10.3390/bios12030170] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/19/2022] [Accepted: 02/21/2022] [Indexed: 11/17/2022]
Abstract
Detection of genetic mutations leading to hematological malignancies is a key factor in the early diagnosis of acute myeloid leukemia (AML). FLT3-ITD mutations are an alarming gene defect found commonly in AML patients associated with high cases of leukemia and low survival rates. Available diagnostic assessments for FLT3-ITD are incapable of combining cost-effective detection platforms with high analytical performances. To circumvent this, we developed an efficient DNA biosensor for the recognition of AML caused by FLT3-ITD mutation utilizing electrochemical impedance characterization. The system was designed by adhering gold-sputtered zinc oxide (ZnO) nanorods onto interdigitated electrode (IDE) sensor chips. The sensing surface was biointerfaced with capture probes designed to hybridize with unmutated FLT3 sequences instead of the mutated FLT3-ITD gene, establishing a reverse manner of target detection. The developed biosensor demonstrated specific detection of mutated FLT3 genes, with high levels of sensitivity in response to analyte concentrations as low as 1 nM. The sensor also exhibited a stable functional life span of more than five weeks with good reproducibility and high discriminatory properties against FLT3 gene targets. Hence, the developed sensor is a promising tool for rapid and low-cost diagnostic applications relevant to the clinical prognosis of AML stemming from FLT3-ITD mutations.
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Affiliation(s)
- Ramesh Thevendran
- Infectomics Cluster, Advanced Medical & Dental Institute, Universiti Sains Malaysia, Bertam, Kepala Batas 13200, Malaysia; (R.T.); (M.C.)
| | - Kai Loong Foo
- Nano Biochip Research Group, Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, Kangar 01000, Malaysia;
| | - Mohd Hazwan Hussin
- Materials Technology Research Group (MaTReC), School of Chemical Sciences, Universiti Sains Malaysia, Minden 11800, Malaysia;
| | - Emmanuel Jairaj Moses
- Regenerative Medicine Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, Kepala Batas 13200, Malaysia;
| | - Marimuthu Citartan
- Infectomics Cluster, Advanced Medical & Dental Institute, Universiti Sains Malaysia, Bertam, Kepala Batas 13200, Malaysia; (R.T.); (M.C.)
| | | | - Solayappan Maheswaran
- Regenerative Medicine Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, Kepala Batas 13200, Malaysia;
- Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Bedong 08100, Malaysia
- Centre of Excellence for Nanobiotechnology & Nanomedicine (CoExNano), Faculty of Applied Sciences, AIMST University, Bedong 08100, Malaysia
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23
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Elsink K, Huibers MMH, Hollink IHIM, Simons A, Zonneveld-Huijssoon E, van der Veken LT, Leavis HL, Henriet SSV, van Deuren M, van de Veerdonk FL, Potjewijd J, Berghuis D, Dalm VASH, Vermont CL, van de Ven AAJM, Lambeck AJA, Abbott KM, van Hagen PM, de Bree GJ, Kuijpers TW, Frederix GWJ, van Gijn ME, van Montfrans JM. Implementation of Early Next-Generation Sequencing for Inborn Errors of Immunity: A Prospective Observational Cohort Study of Diagnostic Yield and Clinical Implications in Dutch Genome Diagnostic Centers. Front Immunol 2022; 12:780134. [PMID: 34992599 PMCID: PMC8724043 DOI: 10.3389/fimmu.2021.780134] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 12/01/2021] [Indexed: 01/07/2023] Open
Abstract
Objective Inborn errors of immunity (IEI) are a heterogeneous group of disorders, affecting different components of the immune system. Over 450 IEI related genes have been identified, with new genes continually being recognized. This makes the early application of next-generation sequencing (NGS) as a diagnostic method in the evaluation of IEI a promising development. We aimed to provide an overview of the diagnostic yield and time to diagnosis in a cohort of patients suspected of IEI and evaluated by an NGS based IEI panel early in the diagnostic trajectory in a multicenter setting in the Netherlands. Study Design We performed a prospective observational cohort study. We collected data of 165 patients with a clinical suspicion of IEI without prior NGS based panel evaluation that were referred for early NGS using a uniform IEI gene panel. The diagnostic yield was assessed in terms of definitive genetic diagnoses, inconclusive diagnoses and patients without abnormalities in the IEI gene panel. We also assessed time to diagnosis and clinical implications. Results For children, the median time from first consultation to diagnosis was 119 days versus 124 days for adult patients (U=2323; p=0.644). The median turn-around time (TAT) of genetic testing was 56 days in pediatric patients and 60 days in adult patients (U=1892; p=0.191). A definitive molecular diagnosis was made in 25/65 (24.6%) of pediatric patients and 9/100 (9%) of adults. Most diagnosed disorders were identified in the categories of immune dysregulation (n=10/25; 40%), antibody deficiencies (n=5/25; 20%), and phagocyte diseases (n=5/25; 20%). Inconclusive outcomes were found in 76/165 (46.1%) patients. Within the patient group with a genetic diagnosis, a change in disease management occurred in 76% of patients. Conclusion In this cohort, the highest yields of NGS based evaluation for IEI early in the diagnostic trajectory were found in pediatric patients, and in the disease categories immune dysregulation and phagocyte diseases. In cases where a definitive diagnosis was made, this led to important disease management implications in a large majority of patients. More research is needed to establish a uniform diagnostic pathway for cases with inconclusive diagnoses, including variants of unknown significance.
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Affiliation(s)
- Kim Elsink
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina's Children Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Manon M H Huibers
- Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Iris H I M Hollink
- Department of Clinical Genetics, Erasmus Medical Center, Erasmus University Rotterdam, Rotterdam, Netherlands
| | - Annet Simons
- Department of Human Genetics, Nijmegen Center for Molecular Life Sciences, Radboud University Medical Centre, Radboud University, Nijmegen, Netherlands.,Radboud Institute for Oncology, Radboud University Medical Center, Radboud University, Nijmegen, Netherlands
| | - Evelien Zonneveld-Huijssoon
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Lars T van der Veken
- Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Helen L Leavis
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Stefanie S V Henriet
- Department of Pediatric Infectious Diseases and Immunology, Amalia's Children Hospital, Radboud University Nijmegen Medical Centre, Radboud University, Nijmegen, Netherlands
| | - Marcel van Deuren
- Department of Internal Medicine, Radboud University Medical Center, Radboud Center for Infectious Diseases, Nijmegen, Netherlands
| | - Frank L van de Veerdonk
- Department of Internal Medicine, Radboud University Medical Center, Radboud Center for Infectious Diseases, Nijmegen, Netherlands
| | - Judith Potjewijd
- Department of Nephrology and Clinical Immunology, Maastricht University Medical Center, Maastricht University, Maastricht, Netherlands
| | - Dagmar Berghuis
- Willem-Alexander Children's Hospital, Department of Pediatrics, Leiden University Medical Center, Leiden University, Leiden, Netherlands
| | - Virgil A S H Dalm
- Department of Internal Medicine, Division of Allergy & Clinical Immunology; Department of Immunology, Erasmus University Medical Center Rotterdam, Erasmus University Rotterdam, Rotterdam, Netherlands
| | - Clementien L Vermont
- Department of Pediatric Infectious Diseases, Immunology and Rheumatology, Sophia Children's Hospital, Erasmus Medical Center, Erasmus University Rotterdam, Rotterdam, Netherlands
| | - Annick A J M van de Ven
- Department of Internal Medicine and Allergology, Rheumatology and Clinical Immunology, University Medical Center Groningen, Groningen, Netherlands
| | - Annechien J A Lambeck
- Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Kristin M Abbott
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - P Martin van Hagen
- Department of Internal Medicine, Division of Allergy & Clinical Immunology; Department of Immunology, Erasmus University Medical Center Rotterdam, Erasmus University Rotterdam, Rotterdam, Netherlands
| | - Godelieve J de Bree
- Department of Internal Medicine, Institute for Infection and Immunity, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Taco W Kuijpers
- Department of Pediatric Hematology, Immunology and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Geert W J Frederix
- Julius Center for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Mariëlle E van Gijn
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Joris M van Montfrans
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina's Children Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
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24
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Solis RN, Silverman DA, Birkeland AC. Current Trends in Precision Medicine and Next-Generation Sequencing in Head and Neck Cancer. Curr Treat Options Oncol 2022; 23:254-267. [PMID: 35195839 PMCID: PMC9196261 DOI: 10.1007/s11864-022-00942-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2021] [Indexed: 12/20/2022]
Abstract
OPINION STATEMENT As the field of oncology enters the era of precision medicine and targeted therapies, we have come to realize that there may be no single "magic bullet" for patients with head and neck cancer. While immune check point inhibitors and some targeted therapeutics have shown great promise in improving oncologic outcomes, the current standard of care in most patients with head and neck squamous cell carcinoma (HNSCC) remains a combination of surgery, radiation, and/or cytotoxic chemotherapy. Nevertheless, advances in precision medicine, next-generation sequencing (NGS), and targeted therapies have a potential future in the treatment of HNSCC. These roles include increased patient treatment stratification based on predictive biomarkers or targetable mutations and novel combinatorial regimens with existing HNSCC treatments. There remain challenges to precision medicine and NGS in HNSCC, including intertumor and intratumor heterogeneity, challenging targets, and need for further trials validating the utility of NGS and precision medicine. Additionally, there is a need for evidence-based practice guidelines to assist clinicians on how to appropriately incorporate NGS in care for HNSCC. In this review, we describe the current state of precision medicine and NGS in HNSCC and opportunities for future advances in this challenging but important field.
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Affiliation(s)
- Roberto N Solis
- Department of Otolaryngology-Head and Neck Surgery, University of California, Davis, 2521 Stockton Blvd., Suite 7200, Sacramento, CA, 95817, USA
| | - Dustin A Silverman
- Department of Otolaryngology-Head and Neck Surgery, University of California, Davis, 2521 Stockton Blvd., Suite 7200, Sacramento, CA, 95817, USA
| | - Andrew C Birkeland
- Department of Otolaryngology-Head and Neck Surgery, University of California, Davis, 2521 Stockton Blvd., Suite 7200, Sacramento, CA, 95817, USA.
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25
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Lebedeva A, Shaykhutdinova Y, Seriak D, Ignatova E, Rozhavskaya E, Vardhan D, Manicka S, Sharova M, Grigoreva T, Baranova A, Mileyko V, Ivanov M. Incidental germline findings during molecular profiling of tumor tissues for precision oncology: molecular survey and methodological obstacles. J Transl Med 2022; 20:29. [PMID: 35033101 PMCID: PMC8760669 DOI: 10.1186/s12967-022-03230-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 01/05/2022] [Indexed: 12/13/2022] Open
Abstract
Background A fraction of patients referred for complex molecular profiling of biopsied tumors may harbor germline variants in genes associated with the development of hereditary cancer syndromes (HCS). Neither the bioinformatic analysis nor the reporting of such incidental germline findings are standardized. Methods Data from Next-Generation Sequencing (NGS) of biopsied tumor samples referred for complex molecular profiling were analyzed for germline variants in HCS-associated genes. Analysis of variant origin was performed employing bioinformatic algorithms followed by manual curation. When possible, the origin of the variant was validated by Sanger sequencing of the sample of normal tissue. The variants’ pathogenicity was assessed according to ACMG/AMP. Results Tumors were sampled from 183 patients (Males: 75 [41.0%]; Females: 108 [59.0%]; mean [SD] age, 57.7 [13.3] years) and analysed by targeted NGS. The most common tumor types were colorectal (19%), pancreatic (13%), and lung cancer (10%). A total of 56 sequence variants in genes associated with HCS were detected in 40 patients. Of them, 17 variants found in 14 patients were predicted to be of germline origin, with 6 variants interpreted as pathogenic (PV) or likely pathogenic (LPV), and 9 as variants of uncertain significance (VUS). For the 41 out of 42 (97%) missense variants in HCS-associated genes, the results of computational prediction of variant origin were concordant with that of experimental examination. We estimate that Sanger sequencing of a sample of normal tissue would be required for ~ 1–7% of the total assessed cases with PV or LPV, when necessity to follow with genetic counselling referral in ~ 2–15% of total assessed cases (PV, LPV or VUS found in HCS genes). Conclusion Incidental findings of pathogenic germline variants are common in data from cancer patients referred for complex molecular profiling. We propose an algorithm for the management of patients with newly detected variants in genes associated with HCS.
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Affiliation(s)
- Alexandra Lebedeva
- Atlas Oncodiagnostics, LLC, Moscow, Russia. .,Sechenov University, Moscow, Russia.
| | | | | | - Ekaterina Ignatova
- Atlas Oncodiagnostics, LLC, Moscow, Russia.,Department of chemotherapy №2, Federal State Budgetary Institution «N.N. Blokhin National Medical Research Center of Oncology» of the Ministry of Health of the Russian Federation, Moscow, Russia.,Department of Oncogenetics, Institute of Higher and Additional Professional Education, Research Centre for Medical Genetics, Moscow, Russia
| | | | | | - Sofia Manicka
- School of Systems Biology, George Mason University, Mannas, VA, USA
| | | | | | - Ancha Baranova
- School of Systems Biology, George Mason University, Mannas, VA, USA
| | | | - Maxim Ivanov
- Atlas Oncodiagnostics, LLC, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
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26
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Undifferentiated Pleomorphic Sarcoma Presenting With Cardiac Tamponade: A Case Report and Review. J Investig Med High Impact Case Rep 2022; 10:23247096221141190. [DOI: 10.1177/23247096221141190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Soft tissue sarcomas (STS) comprise a large group of heterogeneous malignant tumors that form approximately 1% of all adult malignancies. Most sarcomas originate from soft tissue and the rest arise from the bone. Undifferentiated pleomorphic sarcoma (UPS) is an aggressive tumor that usually presents as an asymptomatic subcutaneous mass that exhibits rapid growth with unremarkable skin findings. The diagnosis is usually made with histopathology or immunohistochemistry; once the diagnosis is confirmed, evaluation and workup of the primary tumor, lymph nodes, and metastasis should be made. Treatment is stage-dependent but generally involves en-bloc resection followed by a review of pathology with a discussion of the benefits of adjuvant radiation or chemotherapy. Here, we discuss a case of a 77-year-old patient who presented with a large mass over the right shoulder and echocardiographic findings of cardiac tamponade.
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27
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Siddiqui MF, Mouna A, Nicolas G, Rahat SAA, Mitalipova A, Emmanuel N, Tashmatova N. Computational Intelligence: A Step Forward in Cancer Biomarker Discovery and Therapeutic Target Prediction. COMPUTATIONAL INTELLIGENCE IN ONCOLOGY 2022:233-250. [DOI: 10.1007/978-981-16-9221-5_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/24/2024]
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28
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Garland-Kledzik M, Scholer A, Ensenyat-Mendez M, Orozco JIJ, Khader A, Santamaria-Barria J, Fischer T, Pigazzi A, Marzese DM. Establishing Novel Molecular Subtypes of Appendiceal Cancer. Ann Surg Oncol 2021; 29:2118-2125. [PMID: 34718915 DOI: 10.1245/s10434-021-10945-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 09/24/2021] [Indexed: 01/03/2023]
Abstract
PURPOSE Appendiceal cancer is a rare disease process with complex treatment strategies. The objective of this study was to identify mutation-based genetic subtypes that may differ from the current histological classification, compare the genetic make-up of primaries and metastases, and find novel targetable alterations. METHODS The analyses involved the curation and normalization of gene mutation panels from appendiceal adenocarcinoma and mucinous adenocarcinoma (n = 196) stored in the AACR GENIE Database v6.0. Genes mutated in less than one patient and tumors profiled with incomplete mutation panels were excluded from the study. The optimal number of AC subtypes was established using the Nonnegative Matrix Factorization algorithm. Statistical comparisons of mutation frequencies were performed using Pearson's χ2 test. RESULTS AC patients were stratified into five mutation subtypes, based on a final set of 41 cancer-related genes. AC0 had no mutations. The most frequently mutated genes varied between the subtypes were: AC1: KRAS (91.9%) and GNAS (77.4%); AC2: KRAS (52.5%), APC (32.5%), and GNAS (30%); AC3: KMT2D (38.7%), TP53 (38.7%), KRAS (35.5%), EP300 (22.6%); and AC4: TP53 (97.2%), KRAS (77.8%), and SMAD4 (36.1%). Additionally, AC3 was less likely to be mucinous (22.6% vs. 50.0-74.2%, p < 0.001) and had a higher mutation frequency (3.6 vs. 0-3.1, p < 0.001). There were no significant differences between primary tumors and metastases in the 41 assessed genes (p = 0.35). CONCLUSIONS The characterization of these subtypes suggests a need for molecular approaches to complement anatomical and histopathological staging for AC. A prospective comparison of subtype prognosis and response to surgery and adjuvant treatment is needed to identify the clinical applications of the novel molecular subtypes.
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Affiliation(s)
| | - Anthony Scholer
- Department of Surgery, Saint John's Cancer Institute at Providence St. John's Health Center, Santa Monica, CA, USA
| | - Miquel Ensenyat-Mendez
- Cancer Epigenetic Laboratory, Health Research Institute of the Balearic Islands (IdISBa), Palma, Islas Baleares, Spain
| | - Javier I J Orozco
- Cancer Epigenetics Laboratory, Saint John's Cancer Institute at Providence St. John's Health Center, Santa Monica, CA, USA
| | - Adam Khader
- Department of Surgery, Saint John's Cancer Institute at Providence St. John's Health Center, Santa Monica, CA, USA
| | - Juan Santamaria-Barria
- Department of Surgery, Saint John's Cancer Institute at Providence St. John's Health Center, Santa Monica, CA, USA
| | - Trevan Fischer
- Department of Surgery, Saint John's Cancer Institute at Providence St. John's Health Center, Santa Monica, CA, USA
| | - Alessio Pigazzi
- Colon and Rectal Surgery, Weill Cornell Medicine, New York-Presbyterian Hospital, New York, NY, USA
| | - Diego M Marzese
- Cancer Epigenetic Laboratory, Health Research Institute of the Balearic Islands (IdISBa), Palma, Islas Baleares, Spain
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29
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Jung Y, Son M, Nam YR, Choi J, Heath JR, Yang S. Microfluidic Single-Cell Proteomics Assay Chip: Lung Cancer Cell Line Case Study. MICROMACHINES 2021; 12:mi12101147. [PMID: 34683198 PMCID: PMC8541572 DOI: 10.3390/mi12101147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/16/2021] [Accepted: 09/20/2021] [Indexed: 12/22/2022]
Abstract
Cancer is a dynamic disease involving constant changes. With these changes, cancer cells become heterogeneous, resulting in varying sensitivity to chemotherapy. The heterogeneity of cancer cells plays a key role in chemotherapy resistance and cancer recurrence. Therefore, for effective treatment, cancer cells need to be analyzed at the single-cell level by monitoring various proteins and investigating their heterogeneity. We propose a microfluidic chip for a single-cell proteomics assay that is capable of analyzing complex cellular signaling systems to reveal the heterogeneity of cancer cells. The single-cell assay chip comprises (i) microchambers (n = 1376) for manipulating single cancer cells, (ii) micropumps for rapid single-cell lysis, and (iii) barcode immunosensors for detecting nine different secretory and intracellular proteins to reveal the correlation among cancer-related proteins. Using this chip, the single-cell proteomics of a lung cancer cell line, which may be easily masked in bulk analysis, were evaluated. By comparing changes in the level of protein secretion and heterogeneity in response to combinations of four anti-cancer drugs, this study suggests a new method for selecting the best combination of anti-cancer drugs. Subsequent preclinical and clinical trials should enable this platform to become applicable for patient-customized therapies.
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Affiliation(s)
- Yugyung Jung
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea; (Y.J.); (M.S.); (Y.R.N.)
| | - Minkook Son
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea; (Y.J.); (M.S.); (Y.R.N.)
| | - Yu Ri Nam
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea; (Y.J.); (M.S.); (Y.R.N.)
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Jongchan Choi
- School of Mechanical Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea;
- Institute for Systems Biology, Seattle, WA 98109, USA;
| | - James R. Heath
- Institute for Systems Biology, Seattle, WA 98109, USA;
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
| | - Sung Yang
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea; (Y.J.); (M.S.); (Y.R.N.)
- School of Mechanical Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea;
- Correspondence:
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30
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Hur JY, Lee KY. Characteristics and Clinical Application of Extracellular Vesicle-Derived DNA. Cancers (Basel) 2021; 13:3827. [PMID: 34359729 PMCID: PMC8345206 DOI: 10.3390/cancers13153827] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/25/2021] [Accepted: 07/27/2021] [Indexed: 02/06/2023] Open
Abstract
Extracellular vesicles (EVs) carry RNA, proteins, lipids, and diverse biomolecules for intercellular communication. Recent studies have reported that EVs contain double-stranded DNA (dsDNA) and oncogenic mutant DNA. The advantage of EV-derived DNA (EV DNA) over cell-free DNA (cfDNA) is the stability achieved through the encapsulation in the lipid bilayer of EVs, which protects EV DNA from degradation by external factors. The existence of DNA and its stability make EVs a useful source of biomarkers. However, fundamental research on EV DNA remains limited, and many aspects of EV DNA are poorly understood. This review examines the known characteristics of EV DNA, biogenesis of DNA-containing EVs, methylation, and next-generation sequencing (NGS) analysis using EV DNA for biomarker detection. On the basis of this knowledge, this review explores how EV DNA can be incorporated into diagnosis and prognosis in clinical settings, as well as gene transfer of EV DNA and its therapeutic potential.
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Affiliation(s)
- Jae Young Hur
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul 05030, Korea;
- Department of Pathology, Konkuk University Medical Center, Seoul 05030, Korea
| | - Kye Young Lee
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul 05030, Korea;
- Department of Pulmonary Medicine, Konkuk University School of Medicine, Seoul 05030, Korea
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31
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Rojano E, Córdoba-Caballero J, Jabato FM, Gallego D, Serrano M, Pérez B, Parés-Aguilar Á, Perkins JR, Ranea JAG, Seoane-Zonjic P. Evaluating, Filtering and Clustering Genetic Disease Cohorts Based on Human Phenotype Ontology Data with Cohort Analyzer. J Pers Med 2021; 11:730. [PMID: 34442375 PMCID: PMC8398478 DOI: 10.3390/jpm11080730] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/13/2021] [Accepted: 07/20/2021] [Indexed: 12/21/2022] Open
Abstract
Exhaustive and comprehensive analysis of pathological traits is essential to understanding genetic diseases, performing precise diagnosis and prescribing personalized treatments. It is particularly important for disease cohorts, as thoroughly detailed phenotypic profiles allow patients to be compared and contrasted. However, many disease cohorts contain patients that have been ascribed low numbers of very general and relatively uninformative phenotypes. We present Cohort Analyzer, a tool that measures the phenotyping quality of patient cohorts. It calculates multiple statistics to give a general overview of the cohort status in terms of the depth and breadth of phenotyping, allowing us to detect less well-phenotyped patients for re-examining or excluding from further analyses. In addition, it performs clustering analysis to find subgroups of patients that share similar phenotypic profiles. We used it to analyse three cohorts of genetic diseases patients with very different properties. We found that cohorts with the most specific and complete phenotypic characterization give more potential insights into the disease than those that were less deeply characterised by forming more informative clusters. For two of the cohorts, we also analysed genomic data related to the patients, and linked the genomic data to the patient-subgroups by mapping shared variants to genes and functions. The work highlights the need for improved phenotyping in this era of personalized medicine. The tool itself is freely available alongside a workflow to allow the analyses shown in this work to be applied to other datasets.
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Affiliation(s)
- Elena Rojano
- Department of Molecular Biology and Biochemistry, University of Málaga, 29071 Málaga, Spain; (E.R.); (J.C.-C.); (Á.P.-A.); (J.A.G.R.); (P.S.-Z.)
- Institute of Biomedical Research in Málaga (IBIMA), 29010 Málaga, Spain;
| | - José Córdoba-Caballero
- Department of Molecular Biology and Biochemistry, University of Málaga, 29071 Málaga, Spain; (E.R.); (J.C.-C.); (Á.P.-A.); (J.A.G.R.); (P.S.-Z.)
| | - Fernando M. Jabato
- Institute of Biomedical Research in Málaga (IBIMA), 29010 Málaga, Spain;
- Supercomputation and Bioinformatics (SCBI), University of Malaga, 29071 Malaga, Spain
- LifeWatch-ERIC, 41071 Seville, Spain
| | - Diana Gallego
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), [Madrid, Málaga, Barcelona], Instituto de Salud Carlos III, 28029 Madrid, Spain; (D.G.); (M.S.); (B.P.)
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Campus de Cantoblanco, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Instituto de Investigación Sanitaria idiPAZ, 28049 Madrid, Spain
| | - Mercedes Serrano
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), [Madrid, Málaga, Barcelona], Instituto de Salud Carlos III, 28029 Madrid, Spain; (D.G.); (M.S.); (B.P.)
- Neuropediatric Department, Institut de Recerca Hospital Sant Joan de Déu, 08950 Barcelona, Spain
| | - Belén Pérez
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), [Madrid, Málaga, Barcelona], Instituto de Salud Carlos III, 28029 Madrid, Spain; (D.G.); (M.S.); (B.P.)
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Campus de Cantoblanco, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Instituto de Investigación Sanitaria idiPAZ, 28049 Madrid, Spain
| | - Álvaro Parés-Aguilar
- Department of Molecular Biology and Biochemistry, University of Málaga, 29071 Málaga, Spain; (E.R.); (J.C.-C.); (Á.P.-A.); (J.A.G.R.); (P.S.-Z.)
| | - James R. Perkins
- Department of Molecular Biology and Biochemistry, University of Málaga, 29071 Málaga, Spain; (E.R.); (J.C.-C.); (Á.P.-A.); (J.A.G.R.); (P.S.-Z.)
- Institute of Biomedical Research in Málaga (IBIMA), 29010 Málaga, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), [Madrid, Málaga, Barcelona], Instituto de Salud Carlos III, 28029 Madrid, Spain; (D.G.); (M.S.); (B.P.)
| | - Juan A. G. Ranea
- Department of Molecular Biology and Biochemistry, University of Málaga, 29071 Málaga, Spain; (E.R.); (J.C.-C.); (Á.P.-A.); (J.A.G.R.); (P.S.-Z.)
- Institute of Biomedical Research in Málaga (IBIMA), 29010 Málaga, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), [Madrid, Málaga, Barcelona], Instituto de Salud Carlos III, 28029 Madrid, Spain; (D.G.); (M.S.); (B.P.)
| | - Pedro Seoane-Zonjic
- Department of Molecular Biology and Biochemistry, University of Málaga, 29071 Málaga, Spain; (E.R.); (J.C.-C.); (Á.P.-A.); (J.A.G.R.); (P.S.-Z.)
- Institute of Biomedical Research in Málaga (IBIMA), 29010 Málaga, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), [Madrid, Málaga, Barcelona], Instituto de Salud Carlos III, 28029 Madrid, Spain; (D.G.); (M.S.); (B.P.)
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Park JK, Lee JH, Noh DH, Park JK, Lee KT, Lee JK, Lee KH, Jang KT, Cho J. Factors of Endoscopic Ultrasound-Guided Tissue Acquisition for Successful Next-Generation Sequencing in Pancreatic Ductal Adenocarcinoma. Gut Liver 2021; 14:387-394. [PMID: 31581388 PMCID: PMC7234878 DOI: 10.5009/gnl19011] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/11/2019] [Accepted: 05/12/2019] [Indexed: 12/15/2022] Open
Abstract
Background/Aims Recent advances in understanding the genetics of pancreatic ductal adenocarcinoma (PDAC) have led to the potential for a personalized approach. Several studies have described the feasibility of generating genetic profiles of PDAC with next-generation sequencing (NGS) of samples obtained through endoscopic ultrasound-guided tissue acquisition (EUS-TA). The aim of this study was to find the best EUS-TA approach for successful NGS of PDAC. Methods We attempted to perform NGS with tissues from 190 patients with histologically proven PDAC by endoscopic ultrasound-guided fine-needle aspiration and endoscopic ultrasound-guided fine-needle biopsy at Samsung Medical Center between November 2011 and February 2015. The medical records of these patients were retrospectively reviewed for parameters including tumor factors (size, location, and T stage), EUS-TA factors (needle gauge [G], needle type, and number of needle passes) and histologic factors (cellularity and blood contamination). The sample used for NGS was part of the EUS-TA specimen that underwent cytological and histological analysis. Results NGS could be successfully performed in 109 patients (57.4%). In the univariate analysis, a large needle G (p=0.003) and tumor located in the body/tail (p=0.005) were associated with successful NGS. The multivariate logistic regression analysis revealed that the needle G was an independent factor of successful NGS (odds ratio, 2.19; 95% confidence interval, 1.08 to 4.47; p=0.031). Conclusions The needle G is an independent factor associated with successful NGS. This finding may suggest that the quantity of cells obtained from EUS-TA specimens is important for successful NGS.
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Affiliation(s)
- Jae Keun Park
- Digestive Disease Center and Research Institute, Department of Internal Medicine, Soonchunhyang University School of Medicine, Bucheon, Korea
| | - Ji Hyeon Lee
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Dong Hyo Noh
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Joo Kyung Park
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Kyu Taek Lee
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jong Kyun Lee
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Kwang Hyuck Lee
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Clinical Research Design and Evaluation, Samsung Advanced Institute for Health Sciences & Technology (SAIHST), Sungkyunkwan University, Seoul, Korea
| | - Kee-Taek Jang
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Juhee Cho
- Department of Clinical Research Design and Evaluation, Samsung Advanced Institute for Health Sciences & Technology (SAIHST), Sungkyunkwan University, Seoul, Korea.,Center for Clinical Epidemiology, Samsung Medical Center, Sungkyunkwan University, Seoul, Korea.,Department of Epidemiology and Medicine and Welch Center for Prevention, Epidemiology and Clinical Research, Johns Hopkins Medical Institutions, Baltimore, MD, USA
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Alam W, Bouferraa Y, Haibe Y, Shamseddine A. Complete Radiological Response of Recurrent Metastatic Adrenocortical Carcinoma to Pembrolizumab and Mitotane. CLINICAL MEDICINE INSIGHTS-ONCOLOGY 2021; 15:11795549211007682. [PMID: 33889043 PMCID: PMC8040600 DOI: 10.1177/11795549211007682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 03/10/2021] [Indexed: 11/29/2022]
Abstract
Adrenocortical carcinoma (ACC) is a rare malignancy with a poor prognosis. Treatment options for ACC are limited, with resection the main intervention. Most cases present in late metastatic cases, and data regarding effective therapies is limited. We report a case of ACC in a 40-year-old woman with history of ACC postadrenalectomy, who presented with recurrent metastatic ACC in the left perinephric space. She was started on pembrolizumab which was added to her mitotane maintenance therapy. Complete radiological response was achieved after 4 cycles of pembrolizumab. As far as we know, this is the first case to achieve complete radiological response with mitotane and pembrolizumab in recurrent metastatic ACC, with negative prognostic markers and no prior radiotherapy. As our findings are in the setting of one clinical case, we suggest the need to perform a trial to assess the benefit of combining mitotane and pembrolizumab in treating metastatic ACC.
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Affiliation(s)
- Walid Alam
- Division of Hematology-Oncology, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Youssef Bouferraa
- Division of Hematology-Oncology, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Yolla Haibe
- Division of Hematology-Oncology, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Ali Shamseddine
- Division of Hematology-Oncology, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
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Padmavathi P, Setlur AS, Chandrashekar K, Niranjan V. A comprehensive in-silico computational analysis of twenty cancer exome datasets and identification of associated somatic variants reveals potential molecular markers for detection of varied cancer types. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100762] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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Ergoren MC, Cobanogulları H, Temel SG, Mocan G. Functional coding/non-coding variants in EGFR, ROS1 and ALK genes and their role in liquid biopsy as a personalized therapy. Crit Rev Oncol Hematol 2020; 156:103113. [PMID: 33038629 DOI: 10.1016/j.critrevonc.2020.103113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 02/06/2023] Open
Abstract
Personalized medicine holds promise to tailor the treatment options for patients' unique genetic make-up, behavioral and environmental background. Liquid biopsy is non-invasive technique and precise diagnosis and treatment approach. Significantly, NGS technologies have revolutionized the genomic medicine by novel identifying SNPs, indel mutations in both coding and non-coding regions and also a promising technology to accelerate the early detection and finding new biomarkers for diagnosis and treatment. The number of the bioinformatics tools have been rapidly increasing with the aim of learning more about the detected mutations either they have a pathogenic role or not. EGFR, ROS1 and ALK genes are members of the RTK family. Until now, mutations within these genes have been associated with many cancers and involved in resistance formation to TKIs. This review article summarized the findings about the mostly investigated variations in EGFR, ROS1 and ALK genes and their potential role in liquid biopsy approach.
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Affiliation(s)
- Mahmut Cerkez Ergoren
- Department of Medical Biology, Faculty of Medicine, Near East University, Nicosia, 99138, Cyprus; DESAM Institute, Near East University, 99138, Nicosia, Cyprus.
| | - Havva Cobanogulları
- Department of Medical Biology, Faculty of Medicine, Near East University, Nicosia, 99138, Cyprus; DESAM Institute, Near East University, 99138, Nicosia, Cyprus
| | - Sehime Gulsun Temel
- Department of Medical Genetics, Faculty of Medicine, Bursa Uludag University, Bursa, Turkey; Department of Histology & Embryology, Faculty of Medicine, Bursa Uludag University, Bursa, Turkey; Department of Translational Medicine, Institute of Health Sciences, Bursa Uludag University, Bursa, Turkey
| | - Gamze Mocan
- Department of Medical Biology, Faculty of Medicine, Near East University, Nicosia, 99138, Cyprus; Department of Medical Pathology, Faculty of Medicine, Near East University, Nicosia, 99138, Cyprus
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Odogwu NM, Olayemi OO, Omigbodun AO. The vaginal microbiome of sub-Saharan African women: revealing important gaps in the era of next-generation sequencing. PeerJ 2020; 8:e9684. [PMID: 32879794 PMCID: PMC7441984 DOI: 10.7717/peerj.9684] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 07/18/2020] [Indexed: 12/14/2022] Open
Abstract
Accurate characterization of the vaginal microbiome remains a fundamental goal of the Human Microbiome project (HMP). For over a decade, this goal has been made possible deploying high-throughput next generation sequencing technologies (NGS), which indeed has revolutionized medical research and enabled large-scale genomic studies. The 16S rRNA marker-gene survey is the most commonly explored approach for vaginal microbial community studies. With this approach, prior studies have elucidated substantial variations in the vaginal microbiome of women from different ethnicities. This review provides a comprehensive account of studies that have deployed this approach to describe the vaginal microbiota of African women in health and disease. On the basis of published data, the few studies reported from the African population are mainly in non-pregnant post pubertal women and calls for more detailed studies in pregnant and postnatal cohorts. We provide insight on the use of more sophisticated cutting-edge technologies in characterizing the vaginal microbiome. These technologies offer high-resolution detection of vaginal microbiome variations and community functional capabilities, which can shed light into several discrepancies observed in the vaginal microbiota of African women in an African population versus women of African descent in the diaspora.
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Affiliation(s)
- Nkechi Martina Odogwu
- Pan African University of Life and Earth Science Institute, Department of Obstetrics and Gynecology, University College Hospital, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Oladapo O. Olayemi
- Department of Obstetrics and Gynecology, College of Medicine, University College Hospital, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Akinyinka O. Omigbodun
- Department of Obstetrics and Gynecology, College of Medicine, University College Hospital, University of Ibadan, Ibadan, Oyo, Nigeria
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Kim E, Kim M, So K, Park YS, Woo CG, Hyun SH. Characterization and comparison of genomic profiles between primary cancer cell lines and parent atypical meningioma tumors. Cancer Cell Int 2020; 20:345. [PMID: 32742192 PMCID: PMC7388534 DOI: 10.1186/s12935-020-01438-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 07/20/2020] [Indexed: 12/18/2022] Open
Abstract
Background Meningiomas are the second most common primary tumors of the central nervous system. However, there is a paucity of data on meningioma biology due to the lack of suitable preclinical in vitro and in vivo models. In this study, we report the establishment and characterization of patient-derived, spontaneously immortalized cancer cell lines derived from World Health Organization (WHO) grade I and atypical WHO grade II meningiomas. Methods We evaluated high-resolution 3T MRI neuroimaging findings in meningioma patients which were followed by histological analysis. RT-qPCR and immunostaining analyses were performed to determine the expression levels of meningioma-related factors. Additionally, flow cytometry and sorting assays were conducted to investigate and isolate the CD133 and CD44 positive cells from primary atypical meningioma cells. Further, we compared the gene expression profiles of meningiomas and cell lines derived from them by performing whole-exome sequencing of the blood and tumor samples from the patients, and the primary cancer cell lines established from the meningioma tumor. Results Our results were consistent with earlier studies that reported mutations in NF2, SMO, and AKT1 genes in atypical meningiomas, and we also observed mutations in MYBL2, a gene that was recently discovered. Significantly, the genomic signature was consistent between the atypical meningioma cancer cell lines and the tumor and blood samples from the patient. Conclusion Our results lead us to conclude that established meningioma cell lines with a genomic signature identical to tumors might be a valuable tool for understanding meningioma tumor biology, and for screening therapeutic agents to treat recurrent meningiomas.
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Affiliation(s)
- Eunhye Kim
- Laboratory of Veterinary Embryology and Biotechnology (VETEMBIO), Veterinary Medical Center and College of Veterinary Medicine, Chungbuk National University, 1 Chungdae-ro, Seowon-gu, Cheongju, 28644 Republic of Korea.,Institute for Stem Cell & Regenerative Medicine (ISCRM), Chungbuk National University, 1 Chungdae-ro, Seowon-gu, Cheongju, 28644 Republic of Korea
| | - Mirae Kim
- Laboratory of Veterinary Embryology and Biotechnology (VETEMBIO), Veterinary Medical Center and College of Veterinary Medicine, Chungbuk National University, 1 Chungdae-ro, Seowon-gu, Cheongju, 28644 Republic of Korea.,Institute for Stem Cell & Regenerative Medicine (ISCRM), Chungbuk National University, 1 Chungdae-ro, Seowon-gu, Cheongju, 28644 Republic of Korea
| | - Kyungha So
- Laboratory of Veterinary Embryology and Biotechnology (VETEMBIO), Veterinary Medical Center and College of Veterinary Medicine, Chungbuk National University, 1 Chungdae-ro, Seowon-gu, Cheongju, 28644 Republic of Korea.,Institute for Stem Cell & Regenerative Medicine (ISCRM), Chungbuk National University, 1 Chungdae-ro, Seowon-gu, Cheongju, 28644 Republic of Korea
| | - Young Seok Park
- Department of Neurosurgery, Chungbuk National University Hospital, Chungbuk National University, College of Medicine, Cheongju, 28644 Republic of Korea
| | - Chang Gok Woo
- Department of Pathology, Chungbuk National University Hospital, Chungbuk National University, College of Medicine, Cheongju, 28644 Republic of Korea
| | - Sang-Hwan Hyun
- Laboratory of Veterinary Embryology and Biotechnology (VETEMBIO), Veterinary Medical Center and College of Veterinary Medicine, Chungbuk National University, 1 Chungdae-ro, Seowon-gu, Cheongju, 28644 Republic of Korea.,Institute for Stem Cell & Regenerative Medicine (ISCRM), Chungbuk National University, 1 Chungdae-ro, Seowon-gu, Cheongju, 28644 Republic of Korea
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Investigation on the prognostic impact of concurrent genomic alterations in crizotinib-treated EML4-ALK-rearranged advanced non-small cell lung cancer patients. Lung Cancer 2020; 146:209-216. [PMID: 32563740 DOI: 10.1016/j.lungcan.2020.05.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 05/14/2020] [Accepted: 05/20/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Despite the efficacy of crizotinib in non-small cell lung cancer (NSCLC) with genomic rearrangement between echinoderm microtubule-associated protein-like 4 (EML4) and anaplastic lymphoma kinase (ALK), clinical outcomes are heterogeneous among these patients. In our study, we investigated concurrent molecular factors that could contribute to the heterogeneity of their clinical outcomes to crizotinib therapy. METHODS We retrospectively analyzed the clinical and targeted sequencing data from 32 crizotinib-treated patients with EML4-ALK-rearranged advanced NSCLC. RESULTS Analysis of the mutation profile revealed the detection of concurrent deleterious mutations in 17 patients (53 %, 17/32). Of which, 5 patients had deleterious copy number variations and 12 patients had deleterious single nucleotide variations. Seven patients did not harbor any concurrent mutations from the genes included in the panel. The remaining 8 patients harbored concurrent mutations which were either non-deleterious or variants of uncertain significance. TP53, detected from 34 % (11/32) of the patients and the most commonly co-occurring mutation in our cohort, was not significantly associated with survival outcomes. Interestingly, significantly shorter progression-free survival (P = 0.032) was observed in patients harboring concurrent deleterious mutations, particularly copy number amplifications (PFS, P = 0.0021; OS, P = 0.034), than those without concurrent deleterious mutations. Harboring more copy number variations, reflected by chromosomal fluctuation coefficient varscore, was associated with shorter progression-free survival (P = 0.02). CONCLUSION Our study revealed that concurrent deleterious mutations, particularly copy number amplifications in oncogenic genes have prognostic implications in patients with EML4-ALK-rearranged NSCLC receiving crizotinib therapy. These observations advance the understanding of the heterogeneity of treatment responses among patients with EML4-ALK-rearranged tumors.
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do Nascimento PM, Medeiros IG, Falcão RM, Stransky B, de Souza JES. A decision tree to improve identification of pathogenic mutations in clinical practice. BMC Med Inform Decis Mak 2020; 20:52. [PMID: 32151256 PMCID: PMC7063785 DOI: 10.1186/s12911-020-1060-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 02/21/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND A variant of unknown significance (VUS) is a variant form of a gene that has been identified through genetic testing, but whose significance to the organism function is not known. An actual challenge in precision medicine is to precisely identify which detected mutations from a sequencing process have a suitable role in the treatment or diagnosis of a disease. The average accuracy of pathogenicity predictors is 85%. However, there is a significant discordance about the identification of mutational impact and pathogenicity among them. Therefore, manual verification is necessary for confirming the real effect of a mutation in its casuistic. METHODS In this work, we use variables categorization and selection for building a decision tree model, and later we measure and compare its accuracy with four known mutation predictors and seventeen supervised machine-learning (ML) algorithms. RESULTS The results showed that the proposed tree reached the highest precision among all tested variables: 91% for True Neutrals, 8% for False Neutrals, 9% for False Pathogenic, and 92% for True Pathogenic. CONCLUSIONS The decision tree exceptionally demonstrated high classification precision with cancer data, producing consistently relevant forecasts for the sample tests with an accuracy close to the best ones achieved from supervised ML algorithms. Besides, the decision tree algorithm is easier to apply in clinical practice by non-IT experts. From the cancer research community perspective, this approach can be successfully applied as an alternative for the determination of potential pathogenicity of VOUS.
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Affiliation(s)
| | - Inácio Gomes Medeiros
- Bioinformatics Postgraduate Program, Metrópole Digital Institute, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Raul Maia Falcão
- Bioinformatics Postgraduate Program, Metrópole Digital Institute, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Beatriz Stransky
- Biomedical Engineering Department, Center of Technology, Federal University of Rio Grande do Norte, Natal, Brazil
- Bioinformatics Multidisciplinary Environment (BioME), Metrópole Digital Institute, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Jorge Estefano Santana de Souza
- Bioinformatics Postgraduate Program, Metrópole Digital Institute, Federal University of Rio Grande do Norte, Natal, Brazil.
- Bioinformatics Multidisciplinary Environment (BioME), Metrópole Digital Institute, Federal University of Rio Grande do Norte, Natal, Brazil.
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Kruse A, Abdel-Azim N, Kim HN, Ruan Y, Phan V, Ogana H, Wang W, Lee R, Gang EJ, Khazal S, Kim YM. Minimal Residual Disease Detection in Acute Lymphoblastic Leukemia. Int J Mol Sci 2020; 21:E1054. [PMID: 32033444 PMCID: PMC7037356 DOI: 10.3390/ijms21031054] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/30/2020] [Accepted: 02/03/2020] [Indexed: 02/04/2023] Open
Abstract
Minimal residual disease (MRD) refers to a chemotherapy/radiotherapy-surviving leukemia cell population that gives rise to relapse of the disease. The detection of MRD is critical for predicting the outcome and for selecting the intensity of further treatment strategies. The development of various new diagnostic platforms, including next-generation sequencing (NGS), has introduced significant advances in the sensitivity of MRD diagnostics. Here, we review current methods to diagnose MRD through phenotypic marker patterns or differential gene patterns through analysis by flow cytometry (FCM), polymerase chain reaction (PCR), real-time quantitative polymerase chain reaction (RQ-PCR), reverse transcription polymerase chain reaction (RT-PCR) or NGS. Future advances in clinical procedures will be molded by practical feasibility and patient needs regarding greater diagnostic sensitivity.
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Affiliation(s)
- Aaron Kruse
- Children’s Hospital Los Angeles, University of Southern California, 4650 Sunset Boulevard, MS #57, Los Angeles, CA 90027, USA; (A.K.); (N.A.-A.); (H.N.K.); (Y.R.); (V.P.); (H.O.); (W.W.); (R.L.); (E.J.G.)
| | - Nour Abdel-Azim
- Children’s Hospital Los Angeles, University of Southern California, 4650 Sunset Boulevard, MS #57, Los Angeles, CA 90027, USA; (A.K.); (N.A.-A.); (H.N.K.); (Y.R.); (V.P.); (H.O.); (W.W.); (R.L.); (E.J.G.)
| | - Hye Na Kim
- Children’s Hospital Los Angeles, University of Southern California, 4650 Sunset Boulevard, MS #57, Los Angeles, CA 90027, USA; (A.K.); (N.A.-A.); (H.N.K.); (Y.R.); (V.P.); (H.O.); (W.W.); (R.L.); (E.J.G.)
| | - Yongsheng Ruan
- Children’s Hospital Los Angeles, University of Southern California, 4650 Sunset Boulevard, MS #57, Los Angeles, CA 90027, USA; (A.K.); (N.A.-A.); (H.N.K.); (Y.R.); (V.P.); (H.O.); (W.W.); (R.L.); (E.J.G.)
| | - Valerie Phan
- Children’s Hospital Los Angeles, University of Southern California, 4650 Sunset Boulevard, MS #57, Los Angeles, CA 90027, USA; (A.K.); (N.A.-A.); (H.N.K.); (Y.R.); (V.P.); (H.O.); (W.W.); (R.L.); (E.J.G.)
| | - Heather Ogana
- Children’s Hospital Los Angeles, University of Southern California, 4650 Sunset Boulevard, MS #57, Los Angeles, CA 90027, USA; (A.K.); (N.A.-A.); (H.N.K.); (Y.R.); (V.P.); (H.O.); (W.W.); (R.L.); (E.J.G.)
| | - William Wang
- Children’s Hospital Los Angeles, University of Southern California, 4650 Sunset Boulevard, MS #57, Los Angeles, CA 90027, USA; (A.K.); (N.A.-A.); (H.N.K.); (Y.R.); (V.P.); (H.O.); (W.W.); (R.L.); (E.J.G.)
| | - Rachel Lee
- Children’s Hospital Los Angeles, University of Southern California, 4650 Sunset Boulevard, MS #57, Los Angeles, CA 90027, USA; (A.K.); (N.A.-A.); (H.N.K.); (Y.R.); (V.P.); (H.O.); (W.W.); (R.L.); (E.J.G.)
| | - Eun Ji Gang
- Children’s Hospital Los Angeles, University of Southern California, 4650 Sunset Boulevard, MS #57, Los Angeles, CA 90027, USA; (A.K.); (N.A.-A.); (H.N.K.); (Y.R.); (V.P.); (H.O.); (W.W.); (R.L.); (E.J.G.)
| | - Sajad Khazal
- Department of Pediatrics Patient Care, Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Yong-Mi Kim
- Children’s Hospital Los Angeles, University of Southern California, 4650 Sunset Boulevard, MS #57, Los Angeles, CA 90027, USA; (A.K.); (N.A.-A.); (H.N.K.); (Y.R.); (V.P.); (H.O.); (W.W.); (R.L.); (E.J.G.)
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Zelli V, Compagnoni C, Cannita K, Capelli R, Capalbo C, Di Vito Nolfi M, Alesse E, Zazzeroni F, Tessitore A. Applications of Next Generation Sequencing to the Analysis of Familial Breast/Ovarian Cancer. High Throughput 2020; 9:ht9010001. [PMID: 31936873 PMCID: PMC7151204 DOI: 10.3390/ht9010001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/02/2020] [Accepted: 01/07/2020] [Indexed: 12/24/2022] Open
Abstract
Next generation sequencing (NGS) provides a powerful tool in the field of medical genetics, allowing one to perform multi-gene analysis and to sequence entire exomes (WES), transcriptomes or genomes (WGS). The generated high-throughput data are particularly suitable for enhancing the understanding of the genetic bases of complex, multi-gene diseases, such as cancer. Among the various types of tumors, those with a familial predisposition are of great interest for the isolation of novel genes or gene variants, detectable at the germline level and involved in cancer pathogenesis. The identification of novel genetic factors would have great translational value, helping clinicians in defining risk and prevention strategies. In this regard, it is known that the majority of breast/ovarian cases with familial predisposition, lacking variants in the highly penetrant BRCA1 and BRCA2 genes (non-BRCA), remains unexplained, although several less penetrant genes (e.g., ATM, PALB2) have been identified. In this scenario, NGS technologies offer a powerful tool for the discovery of novel factors involved in familial breast/ovarian cancer. In this review, we summarize and discuss the state of the art applications of NGS gene panels, WES and WGS in the context of familial breast/ovarian cancer.
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Affiliation(s)
- Veronica Zelli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
- Center for Molecular Diagnostics and Advanced Therapies, University of L’Aquila, Via Petrini, 67100 L’Aquila, Italy
| | - Chiara Compagnoni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Katia Cannita
- Medical Oncology Unit, St Salvatore Hospital, Via L. Natali 1, 67100 L’Aquila, Italy;
| | - Roberta Capelli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Carlo Capalbo
- Department of Molecular Medicine, University of Rome “La Sapienza”, Viale Regina Elena 324, 00161 Rome, Italy;
| | - Mauro Di Vito Nolfi
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Edoardo Alesse
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Francesca Zazzeroni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Alessandra Tessitore
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
- Center for Molecular Diagnostics and Advanced Therapies, University of L’Aquila, Via Petrini, 67100 L’Aquila, Italy
- Correspondence:
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42
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Park JK, Lee KH. Present and Future of Endoscopic Ultrasound-Guided Tissue Acquisition in Solid Pancreatic Tumors. Clin Endosc 2019; 52:541-548. [PMID: 31812159 PMCID: PMC6900303 DOI: 10.5946/ce.2019.127] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 11/03/2019] [Indexed: 12/16/2022] Open
Abstract
Endoscopic ultrasound-guided tissue acquisition (EUS-TA) is a well-established method for pathological diagnosis of solid pancreatic neoplasm. It can be performed either as EUS-guided fine-needle aspiration (EUS-FNA) or EUS-guided fine-needle biopsy (EUSFNB). The incidence of adverse events related to EUS-TA is less than 1%. The factors that affect the diagnostic accuracy and specimen adequacy include the techniques used, type and size of the needle, competency of endosonographers, presence of cytopathologists/ cytotechnologists, and rapid on-site examination. EUS-TA may contribute to precision medicine through obtaining tissue samples for next-generation sequencing. The current status, several clinical issues for diagnostic yield and adverse events, and future perspectives of EUS-FNA/FNB for diagnosing pancreatic neoplasm have been discussed in this review article.
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Affiliation(s)
- Jae Keun Park
- Digestive Disease Center and Research Institute, Department of Internal Medicine, Soon Chun Hyang University School of Medicine, Bucheon, Korea
| | - Kwang Hyuck Lee
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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43
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Musci RJ, Fairman B, Masyn KE, Uhl G, Maher B, Sisto DY, Kellam SG, Ialongo NS. Polygenic Score × Intervention Moderation: an Application of Discrete-Time Survival Analysis to Model the Timing of First Marijuana Use Among Urban Youth. PREVENTION SCIENCE : THE OFFICIAL JOURNAL OF THE SOCIETY FOR PREVENTION RESEARCH 2019; 19:6-14. [PMID: 27817095 DOI: 10.1007/s11121-016-0729-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The present study examines the interaction between a polygenic score and an elementary school-based universal preventive intervention trial and its effects on a discrete-time survival analysis of time to first smoking marijuana. Research has suggested that initiation of substances is both genetically and environmentally driven (Rhee et al., Archives of general psychiatry 60:1256-1264, 2003; Verweij et al., Addiction 105:417-430, 2010). A previous work has found a significant interaction between the polygenic score and the same elementary school-based intervention with tobacco smoking (Musci et al., in press). The polygenic score reflects the contribution of multiple genes and has been shown in prior research to be predictive of smoking cessation, tobacco use, and marijuana use (Uhl et al., Molecular Psychiatry 19:50-54, 2014). Using data from a longitudinal preventive intervention study (N = 678), we examined age of first marijuana use from sixth grade to age 18. Genetic data were collected during emerging adulthood and were genotyped using the Affymetrix 6.0 microarray (N = 545). The polygenic score was computed using these data. Discrete-time survival analysis was employed to test for intervention main and interaction effects with the polygenic score. We found main effect of the polygenic score approaching significance, with the participants with higher polygenic scores reporting their first smoking marijuana at an age significantly later than controls (p = .050). We also found a significant intervention × polygenic score interaction effect at p = .003, with participants at the higher end of the polygenic score benefiting the most from the intervention in terms of delayed age of first use. These results suggest that genetics may play an important role in the age of first use of marijuana and that differences in genetics may account for the differential effectiveness of classroom-based interventions in delaying substance use experimentation.
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Affiliation(s)
- Rashelle J Musci
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, 624 North Broadway, Baltimore, MD, 21205, USA.
| | - Brian Fairman
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, 624 North Broadway, Baltimore, MD, 21205, USA
| | - Katherine E Masyn
- School of Public Health, Georgia State University, One Park Place, Atlanta, GA, 30303, USA
| | - George Uhl
- New Mexico VA Healthcare System, 1501 San Pedro Drive, DE, Albuquerque, NM, 87108, USA
| | - Brion Maher
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, 624 North Broadway, Baltimore, MD, 21205, USA
| | - Danielle Y Sisto
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, 624 North Broadway, Baltimore, MD, 21205, USA
| | - Sheppard G Kellam
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, 624 North Broadway, Baltimore, MD, 21205, USA
| | - Nicholas S Ialongo
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, 624 North Broadway, Baltimore, MD, 21205, USA
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Morley-Bunker A, Pearson J, Currie MJ, Morrin H, Whitehead MR, Eglinton T, Walker LC. Assessment of intra-tumoural colorectal cancer prognostic biomarkers using RNA in situ hybridisation. Oncotarget 2019; 10:1425-1439. [PMID: 30858927 PMCID: PMC6402718 DOI: 10.18632/oncotarget.26675] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 02/01/2019] [Indexed: 01/01/2023] Open
Abstract
Genome-wide expression studies using microarrays and RNAseq have increased our understanding of colorectal cancer development. Translating potential gene biomarkers from these studies for clinical utility has typically relied on PCR-based technology and immunohistochemistry. Results from these techniques are limited by tumour sample heterogeneity and the lack of correlation between mRNA transcript abundance and corresponding protein levels. The aim of this research was to investigate the clinical utility of the RNA in situ hybridisation technique, RNAscope®, for measuring intra-tumoural gene expression of potential prognostic markers in a colorectal cancer cohort. Two candidate gene markers (GFI1 and TNFRSF11A) assessed in this study were identified from a previous study led by the The Cancer Genome Atlas (TCGA) Network, and analysis was performed on 112 consecutively collected, archival FFPE colorectal cancer tumour samples. Consistent with the TCGA Network study, we found reduced GFI1 expression was associated with high-grade and left-sided tumours, and reduced TNFRSF11A expression was associated with metastasis and high nodal involvement. RNAscope® combined with image analysis also enabled quantification of GFI1 and TNFRSF11A mRNA expression levels at the single cell level, allowing cell-type determination. These data showed that reduced mRNA transcript abundance measured in patients with poorer prognosis occurred in carcinoma cells, and not lymphocytes, stromal cells or normal epithelial cells. To our knowledge, this is the first study to assess the intra-tumoural expression patterns of GFI1 and TNFRSF11A and to validate their microarray expression profiles using RNAscope. We also demonstrate the utility of RNAscope® technology to show that expression differences are derived from carcinoma cells rather than from cells located in the tumour microenvironment.
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Affiliation(s)
- Arthur Morley-Bunker
- Mackenzie Cancer Research Group, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - John Pearson
- Biostatistics and Computational Biology Unit, University of Otago, Christchurch, New Zealand
| | - Margaret J Currie
- Mackenzie Cancer Research Group, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Helen Morrin
- Mackenzie Cancer Research Group, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.,Cancer Society Tissue Bank, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Martin R Whitehead
- Canterbury Health Laboratories, Christchurch Hospital, Christchurch, New Zealand
| | - Tim Eglinton
- Department of Surgery, University of Otago, Christchurch, New Zealand
| | - Logan C Walker
- Mackenzie Cancer Research Group, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
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45
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Mambetsariev I, Pharaon R, Nam A, Knopf K, Djulbegovic B, Villaflor VM, Vokes EE, Salgia R. Heuristic value-based framework for lung cancer decision-making. Oncotarget 2018; 9:29877-29891. [PMID: 30042820 PMCID: PMC6057456 DOI: 10.18632/oncotarget.25643] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 06/04/2018] [Indexed: 11/25/2022] Open
Abstract
Heuristics and the application of fast-and-frugal trees may play a role in establishing a clinical decision-making framework for value-based oncology. We determined whether clinical decision-making in oncology can be structured heuristically based on the timeline of the patient's treatment, clinical intuition, and evidence-based medicine. A group of 20 patients with advanced non-small cell lung cancer (NSCLC) were enrolled into the study for extensive treatment analysis and sequential decision-making. The extensive clinical and genomic data allowed us to evaluate the methodology and efficacy of fast-and-frugal trees as a way to quantify clinical decision-making. The results of the small cohort will be used to further advance the heuristic framework as a way of evaluating a large number of patients within registries. Among the cohort whose data was analyzed, substitution and amplification mutations occurred most frequently. The top five most prevalent genomic alterations were TP53 (45%), ALK (40%), LRP1B (30%), CDKN2A (25%), and MYC (25%). These 20 cases were analyzed by this clinical decision-making process and separated into two distinctions: 10 straightforward cases that represented a clearer decision-making path and 10 complex cases that represented a more intricate treatment pathway. The myriad of information from each case and their distinct pathways was applied to create the foundation of a framework for lung cancer decision-making as an aid for oncologists. In late-stage lung cancer patients, the fast-and-frugal heuristics can be utilized as a strategy of quantifying proper decision-making with limited information.
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Affiliation(s)
- Isa Mambetsariev
- Department of Medical Oncology and Therapeutics Research, City of Hope, Duarte, CA, USA
| | - Rebecca Pharaon
- Department of Medical Oncology and Therapeutics Research, City of Hope, Duarte, CA, USA
| | - Arin Nam
- Department of Medical Oncology and Therapeutics Research, City of Hope, Duarte, CA, USA
| | - Kevin Knopf
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | | | - Victoria M. Villaflor
- Department of Medicine (Hematology and Oncology), Northwestern University, Chicago, IL, USA
| | | | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope, Duarte, CA, USA
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46
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Ahmed AA, Abedalthagafi M. Cancer diagnostics: The journey from histomorphology to molecular profiling. Oncotarget 2018; 7:58696-58708. [PMID: 27509178 PMCID: PMC5295463 DOI: 10.18632/oncotarget.11061] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 07/19/2016] [Indexed: 12/15/2022] Open
Abstract
Although histomorphology has made significant advances into the understanding of cancer etiology, classification and pathogenesis, it is sometimes complicated by morphologic ambiguities, and other shortcomings that necessitate the development of ancillary tests to complement its diagnostic value. A new approach to cancer patient management consists of targeting specific molecules or gene mutations in the cancer genome by inhibitory therapy. Molecular diagnostic tests and genomic profiling methods are increasingly being developed to identify tumor targeted molecular profile that is the basis of targeted therapy. Novel targeted therapy has revolutionized the treatment of gastrointestinal stromal tumor, renal cell carcinoma and other cancers that were previously difficult to treat with standard chemotherapy. In this review, we discuss the role of histomorphology in cancer diagnosis and management and the rising role of molecular profiling in targeted therapy. Molecular profiling in certain diagnostic and therapeutic difficulties may provide a practical and useful complement to histomorphology and opens new avenues for targeted therapy and alternative methods of cancer patient management.
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Affiliation(s)
- Atif A Ahmed
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri, USA
| | - Malak Abedalthagafi
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,The Saudi Human Genome Laboratory, Department of Pathology, King Fahad Medical City, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
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47
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Del Vecchio F, Mastroiaco V, Di Marco A, Compagnoni C, Capece D, Zazzeroni F, Capalbo C, Alesse E, Tessitore A. Next-generation sequencing: recent applications to the analysis of colorectal cancer. J Transl Med 2017; 15:246. [PMID: 29221448 PMCID: PMC5723063 DOI: 10.1186/s12967-017-1353-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/27/2017] [Indexed: 02/07/2023] Open
Abstract
Since the establishment of the Sanger sequencing method, scientists around the world focused their efforts to progress in the field to produce the utmost technology. The introduction of next-generation sequencing (NGS) represents a revolutionary step and promises to lead to massive improvements in our understanding on the role of nucleic acids functions. Cancer research began to use this innovative and highly performing method, and interesting results started to appear in colorectal cancer (CRC) analysis. Several studies produced high-quality data in terms of mutation discovery, especially about actionable or less frequently mutated genes, epigenetics, transcriptomics. Analysis of results is unveiling relevant perspectives aiding to evaluate the response to therapies. Novel evidences have been presented also in other directions such as gut microbiota or CRC circulating tumor cells. However, despite its unquestioned potential, NGS poses some issues calling for additional studies. This review intends to offer a view of the state of the art of NGS applications to CRC through examination of the most important technologies and discussion of recent published results.
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Affiliation(s)
- Filippo Del Vecchio
- Division of Cancer Sciences, University of Southampton, Southampton, Hampshire, SO16 6YD UK
| | - Valentina Mastroiaco
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, 67100 Italy
| | - Antinisca Di Marco
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, 67100 Italy
| | - Chiara Compagnoni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, 67100 Italy
| | - Daria Capece
- Department of Medicine, Centre for Cell Signaling and Inflammation, Imperial College London, London, W12 0NN UK
| | - Francesca Zazzeroni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, 67100 Italy
| | - Carlo Capalbo
- Department of Molecular Medicine, La Sapienza University, Rome, 00161 Italy
| | - Edoardo Alesse
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, 67100 Italy
| | - Alessandra Tessitore
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, 67100 Italy
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49
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Morley-Bunker A, Walker LC, Currie MJ, Pearson J, Eglinton T. Translating colorectal cancer genetics into clinically useful biomarkers. Colorectal Dis 2016; 18:749-62. [PMID: 26990814 DOI: 10.1111/codi.13334] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 01/22/2016] [Indexed: 12/23/2022]
Abstract
Colorectal cancer (CRC) is a major health problem worldwide accounting for over a million deaths annually. While many patients with Stage II and III CRC can be cured with combinations of surgery, radiotherapy and chemotherapy, this is morbid costly treatment and a significant proportion will suffer recurrence and eventually die of CRC. Increased understanding of the molecular pathogenesis of CRC has the potential to identify high risk patients and target therapy more appropriately. Despite increased understanding of the molecular events underlying CRC development, established molecular techniques have only produced a limited number of biomarkers suitable for use in routine clinical practice to predict risk, prognosis and response to treatment. Recent rapid technological developments, however, have made genomic sequencing of CRC more economical and efficient, creating potential for the discovery of genetic biomarkers that have greater diagnostic, prognostic and therapeutic capabilities for the management of CRC. This paper reviews the current understanding of the molecular pathogenesis of CRC, and summarizes molecular biomarkers that surgeons will encounter in current clinical use as well as those under development in clinical and preclinical trials. New molecular technologies are reviewed together with their potential impact on the understanding of the molecular pathogenesis of CRC and their potential clinical utility in classification, diagnosis, prognosis and targeting of therapy.
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Affiliation(s)
- A Morley-Bunker
- Mackenzie Cancer Research Group, Department of Pathology, University of Otago, Christchurch, New Zealand
| | - L C Walker
- Mackenzie Cancer Research Group, Department of Pathology, University of Otago, Christchurch, New Zealand
| | - M J Currie
- Mackenzie Cancer Research Group, Department of Pathology, University of Otago, Christchurch, New Zealand
| | - J Pearson
- Biostatistics and Computational Biology Unit, University of Otago, Christchurch, New Zealand
| | - T Eglinton
- Department of Surgery, University of Otago, Christchurch, New Zealand.
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50
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Roy-Chowdhuri S, Stewart J. Preanalytic Variables in Cytology: Lessons Learned From Next-Generation Sequencing—The MD Anderson Experience. Arch Pathol Lab Med 2016; 140:1191-1199. [DOI: 10.5858/arpa.2016-0117-ra] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Context.—
As our understanding of genomic alterations underlying solid tumor malignancies continues to evolve, molecular testing of tumor samples is increasingly used to guide therapeutic management. Next-generation sequencing (NGS) provides a novel platform for the simultaneous screening of multiple genes using small amounts of DNA. Several recent studies have described NGS mutational analysis using cytologic specimens. The cytopathologist's role in specimen assessment and triaging is critical to effectively implementing NGS in routine cytology practice.
Objectives.—
To review the NGS experience and a variety of preanalytic factors that affect NGS success rates of cytologic specimens at our institution.
Data Sources.—
To evaluate cytology specimen adequacy rates for NGS, we reviewed a 14-month period of image-guided fine-needle aspiration and core needle biopsies used for testing. In addition, we reviewed data from our previously published studies to evaluate preanalytic factors affecting NGS success in these specimens.
Conclusions.—
Identifying factors that affect NGS success rates in cytology specimens is crucial for a better understanding of specimen adequacy requirements and for proper use of limited-volume tissue samples. In our practice, which uses direct smears as well as cell block sections, NGS success rates in core needle biopsy and fine-needle aspiration samples are comparable. The chance of successful testing is further increased by procuring concurrent fine-needle aspiration and core needle biopsy samples. The type of glass slides used for direct smears and the method of tissue extraction affect our DNA yield. Validating a DNA input for cytology samples that is lower than that recommended by the manufacturer has significantly increased our NGS success rate.
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Affiliation(s)
- Sinchita Roy-Chowdhuri
- From the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston
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