1
|
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.
Collapse
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
| |
Collapse
|
2
|
Alsaab HO, Alzahrani MS, Bahauddin AA, Almutairy B. Circulating tumor DNA (ctDNA) application in investigation of cancer: Bench to bedside. Arch Biochem Biophys 2024; 758:110066. [PMID: 38906310 DOI: 10.1016/j.abb.2024.110066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/02/2024] [Accepted: 06/18/2024] [Indexed: 06/23/2024]
Abstract
Now, genomics forms the core of the precision medicine concept. Comprehensive investigations of tumor genomes have made it possible to characterize tumors at the molecular level and, specifically, to identify the fundamental processes that cause condition. A variety of kinds of tumors have seen better outcomes for patients as a result of the development of novel medicines to tackle these genetic-driving processes. Since therapy may exert selective pressure on cancers, non-invasive methods such as liquid biopsies can provide the opportunity for rich reservoirs of crucial and real-time genetic data. Liquid biopsies depend on the identification of circulating cells from tumors, circulating tumor DNA (ctDNA), RNA, proteins, lipids, and metabolites found in patient biofluids, as well as cell-free DNA (cfDNA), which exists in those with cancer. Although it is theoretically possible to examine biological fluids other than plasma, such as pleural fluid, urine, saliva, stool, cerebrospinal fluid, and ascites, we will limit our discussion to blood and solely cfDNA here for the sake of conciseness. Yet, the pace of wider clinical acceptance has been gradual, partly due to the increased difficulty of choosing the best analysis for the given clinical issue, interpreting the findings, and delaying proof of value from clinical trials. Our goal in this review is to discuss the current clinical value of ctDNA in cancers and how clinical oncology systems might incorporate procedures for ctDNA testing.
Collapse
Affiliation(s)
- Hashem O Alsaab
- Department of Pharmaceutics and Pharmaceutical Technology, Taif University, Taif, 21944, Saudi Arabia.
| | - Mohammad S Alzahrani
- Department of Clinical Pharmacy, College of Pharmacy, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia.
| | - Ammar A Bahauddin
- Department of Pharmacology and Toxicology, College of Pharmacy, Taibah University, Medina Al-Munawarah, Saudi Arabia.
| | - Bandar Almutairy
- Department of Pharmacology, College of Pharmacy, Shaqra University, Shaqra 11961, Saudi Arabia.
| |
Collapse
|
3
|
Zhang J, Li Y, Huang W, Sun G, Ren H, Tang M. An ultrasensitive DNA-enhanced amplification method for detecting cfDNA drug-resistant mutations in non-small cell lung cancer with selective FEN-assisted degradation of dominant somatic fragments. Clin Chem Lab Med 2024; 0:cclm-2024-0614. [PMID: 39089988 DOI: 10.1515/cclm-2024-0614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 07/18/2024] [Indexed: 08/04/2024]
Abstract
OBJECTIVES Blood cell-free DNA (cfDNA) can be a new reliable tool for detecting epidermal growth factor receptor (EGFR) mutations in non-small cell lung cancer (NSCLC) patients. However, the currently reported cfDNA assays have a limited role in detecting drug-resistant mutations due to their deficiencies in sensitivity, stability, or mutation detection rate. METHODS We developed an Archaeoglobus fulgidus-derived flap endonuclease (Afu FEN)-based DNA-enhanced amplification system of mutated cfDNA by designing a pair of hairpin probes to anneal with wild-type cfDNA to form two 5'-flaps, allowing for the specific cleavage of wild-type cfDNA by Afu FEN. When the dominant wild-type somatic cfDNA fragments were cleaved by structure-recognition-specific Afu FEN, the proportion of mutated cfDNA in the reaction system was greatly enriched. As the amount of mutated cfDNA in the system was further increased by PCR amplification, the mutation status could be easily detected through first-generation sequencing. RESULTS In a mixture of synthetic wild-type and T790M EGFR DNA fragments, our new assay still could detect T790M mutation at the fg level with remarkably high sensitivity. We also tested its performance in detecting low variant allele frequency (VAF) mutations in clinical samples from NSCLC patients. The plasma cfDNA samples with low VAF (0.1 and 0.5 %) could be easily detected by DNA-enhanced amplification. CONCLUSIONS This system with enhanced amplification of mutated cfDNA is an effective tool used for the early screening and individualized targeted therapy of NSCLC by providing a rapid, sensitive, and economical way for the detection of drug-resistant mutations in tumors.
Collapse
Affiliation(s)
- Junhua Zhang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 117555 Beijing Hospital/National Center of Gerontology of National Health Commission , Beijing, P.R. China
| | - Yifei Li
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Wei Huang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 117555 Beijing Hospital/National Center of Gerontology of National Health Commission , Beijing, P.R. China
| | - Gaoyuan Sun
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Hongjun Ren
- Advanced Research Institute and Department of Chemistry, Taizhou University, Jiaojiang 318000, P.R. China
| | - Min Tang
- Department of Oncology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, P.R. China
| |
Collapse
|
4
|
Chen HS, Negoita S, Schwartz S, Hsu E, Hafterson J, Coyle L, Stevens J, Fernandez A, Potts M, Feuer EJ. Toward real-time reporting of cancer incidence: methodology, pilot study, and SEER Program implementation. J Natl Cancer Inst Monogr 2024; 2024:123-131. [PMID: 39102887 DOI: 10.1093/jncimonographs/lgae024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/18/2024] [Accepted: 04/23/2024] [Indexed: 08/07/2024] Open
Abstract
BACKGROUND A lag time between cancer case diagnosis and incidence reporting impedes the ability to monitor the impact of recent events on cancer incidence. Currently, the data submission standard is 22 months after a diagnosis year ends, and the reporting standard is 27.5 months after a diagnosis year ends. This paper presents the National Cancer Institute (NCI) Surveillance, Epidemiology, and End Results (SEER) Program's efforts to minimize the lag and achieve "real-time" reporting, operationalized as submission within 2 months from the end of a diagnosis year. METHODS Technology for rapidly creating a consolidated tumor case (CTC) from electronic pathology (e-path) reports is described. Statistical methods are extended to adjust for biases in incidence rates due to reporting delays for the most recent diagnosis years. RESULTS A registry pilot study demonstrated that real-time submissions can approximate rates obtained from 22-month submissions after adjusting for reporting delays. A plan to be implemented across the SEER Program rapidly ascertains unstructured e-path reports and uses machine learning algorithms to translate the reports into the core data items that comprise a CTC for incidence reporting. Across the program, cases were submitted 2 months after the end of the calendar year. Registries with the most promising baseline values and a willingness to modify registry operations have joined a program to become certified as real-time reporting. CONCLUSION Advances in electronic reporting, natural language processing, registry operations, and statistical methodology, energized by the SEER Program's mobilization and coordination of these efforts, will make real-time reporting an achievable goal.
Collapse
Affiliation(s)
- Huann-Sheng Chen
- Division of Cancer Control and Population Sciences, National Cancer Institute, Rockville, MD, USA
| | - Serban Negoita
- Division of Cancer Control and Population Sciences, National Cancer Institute, Rockville, MD, USA
| | - Steve Schwartz
- Fred Hutch Cancer Surveillance System (CSS), Seattle, WA, USA
| | - Elizabeth Hsu
- Division of Cancer Control and Population Sciences, National Cancer Institute, Rockville, MD, USA
| | | | - Linda Coyle
- Information Management Services (IMS), Inc, Calverton, MD, USA
| | | | - Anna Fernandez
- Division of Cancer Control and Population Sciences, National Cancer Institute, Rockville, MD, USA
| | - Mary Potts
- Fred Hutch Cancer Surveillance System (CSS), Seattle, WA, USA
| | - Eric J Feuer
- Division of Cancer Control and Population Sciences, National Cancer Institute, Rockville, MD, USA
| |
Collapse
|
5
|
Adugna A, Muche Y, Melkamu A, Jemal M, Belew H, Amare GA. Current updates on the molecular and genetic signals as diagnostic and therapeutic targets for hepatitis B virus-associated hepatic malignancy. Heliyon 2024; 10:e34288. [PMID: 39100497 PMCID: PMC11295980 DOI: 10.1016/j.heliyon.2024.e34288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 05/28/2024] [Accepted: 07/07/2024] [Indexed: 08/06/2024] Open
Abstract
Liver cancer caused by the hepatitis B virus (HBV) is the third most common cancer-related cause of death worldwide. Early detection of HBV-caused hepatic tumors increases the likelihood of a successful cure. Molecular and genetic signals are becoming more and more recognized as possible indicators of HBV-associated hepatic malignancy and of how well a treatment is working. As a result, we have discussed the current literature on molecular and genetic sensors, including extracellular vesicle microRNAs (EV-miRNAs), long non-coding circulating RNAs (lncRNAs), extracellular vesicles (EVs), and cell free circulating DNA (cfDNA), for the diagnosis and forecasting of HBV-related hepatic cancer. Extracellular vesicle microRNAs such as miR-335-5p, miR-172-5p, miR-1285-5p, miR-497-5p, miR-636, miR-187-5p, miR-223-3p, miR-21, miR-324-3p, miR-210-3p, miR-718, miR-122, miR-522, miR-0308-3p, and miR-375 are essential for the posttranscriptional regulation of oncogenes in hepatic cells as well as the epigenetic modulation of many internal and external signaling pathways in HBV-induced hepatic carcinogenesis. LncRNAs like lnc01977, HULC (highly up-regulated in liver cancer), MALAT1 (metastasis-associated lung adenocarcinoma transcript 1), and HOTAIR (hox transcript antisense intergenic RNA) have been demonstrated to control hepatic-tumors cell growth, relocation, encroachment, and cell death resiliency. They are also becoming more and more involved in immune tracking, hepatic shifting, vasculature oversight, and genomic destabilization. EVs are critical mediators involved in multiple aspects of liver-tumors like angiogenesis, immunology, tumor formation, and the dissemination of malignant hepatocytes. Furthermore, cfDNA contributes to signals associated with tumors, including mutations and abnormal epigenetic changes during HBV-related hepatic tumorigenesis.
Collapse
Affiliation(s)
- Adane Adugna
- Medical Laboratory Sciences, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Yalew Muche
- Medical Laboratory Sciences, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Abateneh Melkamu
- Medical Laboratory Sciences, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Mohammed Jemal
- Department of Biomedical Sciences, School of Medicine, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Habtamu Belew
- Medical Laboratory Sciences, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Gashaw Azanaw Amare
- Medical Laboratory Sciences, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| |
Collapse
|
6
|
Mareso C, Crosta L, De Vita MG, Cristofoli F, Tanzi B, Benedetti S, Bonetti G, Donofrio CA, Cominetti M, Riccio L, Fioravanti A, Generali D, Lucci Cordisco E, Chiurazzi P, Gatta V, Stuppia L, Cecchin S, Bertelli M, Marceddu G. Assessing the efficacy of an innovative diagnostic method for identifying 5 % variants in somatic ctDNA. Gene 2024; 928:148771. [PMID: 39032702 DOI: 10.1016/j.gene.2024.148771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 07/05/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024]
Abstract
BACKGROUND Liquid biopsy is considered a complementary and recently also an alternative method to surgical biopsy. It allows for the acquisition of valuable information regarding the potential presence of tumors, particularly through the analysis of circulating tumor DNA (ctDNA). CtDNA is a fraction of circulating free DNA (cfDNA) that can be extracted from various tissues, with blood being the most readily available. RESULTS To maximize the yield of plasma separation, specific Streck tubes are recommended for blood collection. The MagPurix CFC DNA Extraction Kit can be used for cfDNA extraction, and the TWIST Library Preparation protocol can be optimized for further analysis. Next-generation sequencing (NGS) can be employed to compare somatic and germline lineages, enabling the identification of somatic variants with a Variant Allele Frequency (VAF) of 5 % or higher, which are absent in the germline lineage. CONCLUSION This analysis helps in the assessment of recurrence, analysis, and monitoring of cancer tissue.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Gabriele Bonetti
- MAGI'S LAB, 38068 Rovereto (TN), Italy; Department of Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy.
| | - Carmine Antonio Donofrio
- Neurosurgery, ASST Cremona, 26100 Cremona, Italy; Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | | | - Lucia Riccio
- Neurosurgery, ASST Cremona, 26100 Cremona, Italy
| | | | - Daniele Generali
- Dipartimento Universitario Clinico di Scienze Mediche, Chirurgiche e della Salute, Università degli Studi di Trieste, 34127 Trieste, Italy
| | - Emanuela Lucci Cordisco
- Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; UOC Genetica Medica, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, 00168 Rome, Italy
| | - Pietro Chiurazzi
- Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; UOC Genetica Medica, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, 00168 Rome, Italy
| | - Valentina Gatta
- Department of Psychological Health and Territorial Sciences, School of Medicine and Health Sciences, G. d'Annunzio University, 66100 Chieti, Italy; Unit of Molecular Genetics, Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
| | - Liborio Stuppia
- Department of Psychological Health and Territorial Sciences, School of Medicine and Health Sciences, G. d'Annunzio University, 66100 Chieti, Italy; Unit of Molecular Genetics, Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
| | | | - Matteo Bertelli
- MAGI EUREGIO, 39100 Bolzano, Italy; MAGI'S LAB, 38068 Rovereto (TN), Italy; MAGISNAT, Atlanta Tech Park, Peachtree Corners, 30092 GA, USA
| | | |
Collapse
|
7
|
Tao XY, Li QQ, Zeng Y. Clinical application of liquid biopsy in colorectal cancer: detection, prediction, and treatment monitoring. Mol Cancer 2024; 23:145. [PMID: 39014366 PMCID: PMC11250976 DOI: 10.1186/s12943-024-02063-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 07/09/2024] [Indexed: 07/18/2024] Open
Abstract
Colorectal cancer (CRC) is one of the most prevalent malignancies affecting the gastrointestinal tract and is ranked third among cancers with the highest incidence and second-highest mortality rate worldwide. CRC exhibits a slow progression providing a wide treatment window. The currently employed CRC screening methods have shown great potential to prevent CRC and reduce CRC-related morbidity and mortality. The diagnosis of CRC is achieved by colonoscopy and tissue biopsy, with studies showing that liquid biopsy is more effective in detecting and diagnosing early CRC patients. Increasing number of studies have shown that the tumor components shed into circulating blood can be detected in liquid form, and can be applied in the clinical management of CRC. Analysis of circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), or tumor-associated platelets (TEPs) in the blood can be used for early screening and diagnosis of CRC, aid tumor staging, treatment response monitoring, and prediction of CRC recurrence and metastasis in a minimally invasive manner. This chapter provides an updated review of CTCs, ctDNA, and TEPs as novel biomarkers for CRC, highlighting their strengths and limitations.
Collapse
Affiliation(s)
- Xiang-Yuan Tao
- Translational Medicine Center, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- School of Pharmacy, University of South China, Hengyang, China
| | - Qian-Qian Li
- Translational Medicine Center, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- School of Pharmacy, University of South China, Hengyang, China
| | - Yong Zeng
- Translational Medicine Center, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.
- School of Pharmacy, University of South China, Hengyang, China.
| |
Collapse
|
8
|
Zalis M, Viana Veloso GG, Aguiar Jr. PN, Gimenes N, Reis MX, Matsas S, Ferreira CG. Next-generation sequencing impact on cancer care: applications, challenges, and future directions. Front Genet 2024; 15:1420190. [PMID: 39045325 PMCID: PMC11263191 DOI: 10.3389/fgene.2024.1420190] [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: 04/19/2024] [Accepted: 06/13/2024] [Indexed: 07/25/2024] Open
Abstract
Fundamentally precision oncology illustrates the path in which molecular profiling of tumors can illuminate their biological behavior, diversity, and likely outcomes by identifying distinct genetic mutations, protein levels, and other biomarkers that underpin cancer progression. Next-generation sequencing became an indispensable diagnostic tool for diagnosis and treatment guidance in current clinical practice. Nowadays, tissue analysis benefits from further support through methods like comprehensive genomic profiling and liquid biopsies. However, precision medicine in the field of oncology presents specific hurdles, such as the cost-benefit balance and widespread accessibility, particularly in countries with low- and middle-income. A key issue is how to effectively extend next-generation sequencing to all cancer patients, thus empowering treatment decision-making. Concerns also extend to the quality and preservation of tissue samples, as well as the evaluation of health technologies. Moreover, as technology advances, novel next-generation sequencing assessments are being developed, including the study of Fragmentomics. Therefore, our objective was to delineate the primary uses of next-generation sequencing, discussing its' applications, limitations, and prospective paths forward in Oncology.
Collapse
Affiliation(s)
- Mariano Zalis
- Oncoclínicas&Co/MedSir, Rio de Janeiro, Brazil
- Medical School of the Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gilson Gabriel Viana Veloso
- Oncoclínicas&Co/MedSir, Rio de Janeiro, Brazil
- Santa Casa de Misericórdia de Belo Horizonte, Belo Horizonte, Brazil
| | | | | | | | - Silvio Matsas
- Centro de Estudos e Pesquisas de Hematologia e Oncologia (CEPHO), Sao Paulo, Brazil
| | | |
Collapse
|
9
|
Rodríguez-Ces AM, Rapado-González Ó, Salgado-Barreira Á, Santos MA, Aroso C, Vinhas AS, López-López R, Suárez-Cunqueiro MM. Liquid Biopsies Based on Cell-Free DNA Integrity as a Biomarker for Cancer Diagnosis: A Meta-Analysis. Diagnostics (Basel) 2024; 14:1465. [PMID: 39061602 PMCID: PMC11276058 DOI: 10.3390/diagnostics14141465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/28/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024] Open
Abstract
Liquid biopsies have been identified as a viable source of cancer biomarkers. We aim to evaluate the diagnostic accuracy of cell-free DNA integrity (cfDI) in liquid biopsies for cancer. A comprehensive literature search was conducted through PubMed, Embase, Web of Science, and Cochrane Library up to June 2024. Seventy-two study units from forty-six studies, comprising 4286 cancer patients, were identified and evaluated. The Quality Assessment for Studies of Diagnostic Accuracy-2 (QUADAS-2) was used to assess study quality. Meta-regression analysis was employed to investigate the underlying factors contributing to heterogeneity, alongside an evaluation of publication bias. The bivariate random-effect model was utilized to compute the primary diagnostic outcomes and their corresponding 95% confidence intervals (CIs). The pooled sensitivity, specificity, and positive and negative likelihood ratios of cfDI in cancer diagnosis were 0.70 and 0.77, 3.26 and 0.34, respectively. The overall area under the curve was 0.84, with a diagnostic odds ratio of 10.63. This meta-analysis suggested that the cfDI index has a promising potential as a non-invasive and accurate diagnostic tool for cancer. Study registration: The study was registered at PROSPERO (reference No. CRD42021276290).
Collapse
Affiliation(s)
- Ana María Rodríguez-Ces
- Department of Surgery and Medical-Surgical Specialties, Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain; (A.M.R.-C.); (Ó.R.-G.)
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain;
- Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), 15706 Santiago de Compostela, Spain
| | - Óscar Rapado-González
- Department of Surgery and Medical-Surgical Specialties, Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain; (A.M.R.-C.); (Ó.R.-G.)
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain;
- Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), 15706 Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/CI-IPOP@RISE (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Ángel Salgado-Barreira
- Department of Public Health, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain;
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBER Epidemiology and Public Health—CIBERESP), 28029 Madrid, Spain
- Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain
| | - María Arminda Santos
- UNIPRO-Oral Pathology and Rehabilitation Research Unit, University Institute of Health Sciences (IUCS), CESPU, 4585-116 Gandra, Portugal; (M.A.S.); (C.A.); (A.S.V.)
| | - Carlos Aroso
- UNIPRO-Oral Pathology and Rehabilitation Research Unit, University Institute of Health Sciences (IUCS), CESPU, 4585-116 Gandra, Portugal; (M.A.S.); (C.A.); (A.S.V.)
| | - Ana Sofia Vinhas
- UNIPRO-Oral Pathology and Rehabilitation Research Unit, University Institute of Health Sciences (IUCS), CESPU, 4585-116 Gandra, Portugal; (M.A.S.); (C.A.); (A.S.V.)
| | - Rafael López-López
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain;
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (CHUS, SERGAS), 15706 Santiago de Compostela, Spain
| | - María Mercedes Suárez-Cunqueiro
- Department of Surgery and Medical-Surgical Specialties, Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain; (A.M.R.-C.); (Ó.R.-G.)
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain;
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (CHUS, SERGAS), 15706 Santiago de Compostela, Spain
| |
Collapse
|
10
|
Turabi K, Klute K, Radhakrishnan P. Decoding the Dynamics of Circulating Tumor DNA in Liquid Biopsies. Cancers (Basel) 2024; 16:2432. [PMID: 39001494 PMCID: PMC11240538 DOI: 10.3390/cancers16132432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/16/2024] Open
Abstract
Circulating tumor DNA (ctDNA), a fragment of tumor DNA found in the bloodstream, has emerged as a revolutionary tool in cancer management. This review delves into the biology of ctDNA, examining release mechanisms, including necrosis, apoptosis, and active secretion, all of which offer information about the state and nature of the tumor. Comprehensive DNA profiling has been enabled by methods such as whole genome sequencing and methylation analysis. The low abundance of the ctDNA fraction makes alternative techniques, such as digital PCR and targeted next-generation exome sequencing, more valuable and accurate for mutation profiling and detection. There are numerous clinical applications for ctDNA analysis, including non-invasive liquid biopsies for minimal residual disease monitoring to detect cancer recurrence, personalized medicine by mutation profiling for targeted therapy identification, early cancer detection, and real-time evaluation of therapeutic response. Integrating ctDNA analysis into routine clinical practice creates promising avenues for successful and personalized cancer care, from diagnosis to treatment and follow-up.
Collapse
Affiliation(s)
- Khadija Turabi
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Kelsey Klute
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Division of Oncology and Hematology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Prakash Radhakrishnan
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| |
Collapse
|
11
|
Gromek P, Senkowska Z, Płuciennik E, Pasieka Z, Zhao LY, Gielecińska A, Kciuk M, Kłosiński K, Kałuzińska-Kołat Ż, Kołat D. Revisiting the standards of cancer detection and therapy alongside their comparison to modern methods. World J Methodol 2024; 14:92982. [PMID: 38983668 PMCID: PMC11229876 DOI: 10.5662/wjm.v14.i2.92982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/15/2024] [Accepted: 04/28/2024] [Indexed: 06/13/2024] Open
Abstract
In accordance with the World Health Organization data, cancer remains at the forefront of fatal diseases. An upward trend in cancer incidence and mortality has been observed globally, emphasizing that efforts in developing detection and treatment methods should continue. The diagnostic path typically begins with learning the medical history of a patient; this is followed by basic blood tests and imaging tests to indicate where cancer may be located to schedule a needle biopsy. Prompt initiation of diagnosis is crucial since delayed cancer detection entails higher costs of treatment and hospitalization. Thus, there is a need for novel cancer detection methods such as liquid biopsy, elastography, synthetic biosensors, fluorescence imaging, and reflectance confocal microscopy. Conventional therapeutic methods, although still common in clinical practice, pose many limitations and are unsatisfactory. Nowadays, there is a dynamic advancement of clinical research and the development of more precise and effective methods such as oncolytic virotherapy, exosome-based therapy, nanotechnology, dendritic cells, chimeric antigen receptors, immune checkpoint inhibitors, natural product-based therapy, tumor-treating fields, and photodynamic therapy. The present paper compares available data on conventional and modern methods of cancer detection and therapy to facilitate an understanding of this rapidly advancing field and its future directions. As evidenced, modern methods are not without drawbacks; there is still a need to develop new detection strategies and therapeutic approaches to improve sensitivity, specificity, safety, and efficacy. Nevertheless, an appropriate route has been taken, as confirmed by the approval of some modern methods by the Food and Drug Administration.
Collapse
Affiliation(s)
- Piotr Gromek
- Department of Functional Genomics, Medical University of Lodz, Lodz 90-752, Lodzkie, Poland
| | - Zuzanna Senkowska
- Department of Functional Genomics, Medical University of Lodz, Lodz 90-752, Lodzkie, Poland
| | - Elżbieta Płuciennik
- Department of Functional Genomics, Medical University of Lodz, Lodz 90-752, Lodzkie, Poland
| | - Zbigniew Pasieka
- Department of Biomedicine and Experimental Surgery, Medical University of Lodz, Lodz 90-136, Lodzkie, Poland
| | - Lin-Yong Zhao
- Department of General Surgery & Laboratory of Gastric Cancer, State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
- Gastric Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Adrianna Gielecińska
- Department of Molecular Biotechnology and Genetics, University of Lodz, Lodz 90-237, Lodzkie, Poland
- Doctoral School of Exact and Natural Sciences, University of Lodz, Lodz 90-237, Lodzkie, Poland
| | - Mateusz Kciuk
- Department of Molecular Biotechnology and Genetics, University of Lodz, Lodz 90-237, Lodzkie, Poland
| | - Karol Kłosiński
- Department of Biomedicine and Experimental Surgery, Medical University of Lodz, Lodz 90-136, Lodzkie, Poland
| | - Żaneta Kałuzińska-Kołat
- Department of Functional Genomics, Medical University of Lodz, Lodz 90-752, Lodzkie, Poland
- Department of Biomedicine and Experimental Surgery, Medical University of Lodz, Lodz 90-136, Lodzkie, Poland
| | - Damian Kołat
- Department of Functional Genomics, Medical University of Lodz, Lodz 90-752, Lodzkie, Poland
- Department of Biomedicine and Experimental Surgery, Medical University of Lodz, Lodz 90-136, Lodzkie, Poland
| |
Collapse
|
12
|
Gerke MB, Jansen CS, Bilen MA. Circulating Tumor DNA in Genitourinary Cancers: Detection, Prognostics, and Therapeutic Implications. Cancers (Basel) 2024; 16:2280. [PMID: 38927984 PMCID: PMC11201475 DOI: 10.3390/cancers16122280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 06/18/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
CtDNA is emerging as a non-invasive clinical detection method for several cancers, including genitourinary (GU) cancers such as prostate cancer, bladder cancer, and renal cell carcinoma (RCC). CtDNA assays have shown promise in early detection of GU cancers, providing prognostic information, assessing real-time treatment response, and detecting residual disease and relapse. The ease of obtaining a "liquid biopsy" from blood or urine in GU cancers enhances its potential to be used as a biomarker. Interrogating these "liquid biopsies" for ctDNA can then be used to detect common cancer mutations, novel genomic alterations, or epigenetic modifications. CtDNA has undergone investigation in numerous clinical trials, which could address clinical needs in GU cancers, for instance, earlier detection in RCC, therapeutic response prediction in castration-resistant prostate cancer, and monitoring for recurrence in bladder cancers. The utilization of liquid biopsy for ctDNA analysis provides a promising method of advancing precision medicine within the field of GU cancers.
Collapse
Affiliation(s)
- Margo B. Gerke
- Emory University School of Medicine, Atlanta, GA 30322, USA; (M.B.G.); (C.S.J.)
| | - Caroline S. Jansen
- Emory University School of Medicine, Atlanta, GA 30322, USA; (M.B.G.); (C.S.J.)
- Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Mehmet A. Bilen
- Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
| |
Collapse
|
13
|
Hou Y, Meng XY, Zhou X. Systematically Evaluating Cell-Free DNA Fragmentation Patterns for Cancer Diagnosis and Enhanced Cancer Detection via Integrating Multiple Fragmentation Patterns. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2308243. [PMID: 38881520 DOI: 10.1002/advs.202308243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 04/12/2024] [Indexed: 06/18/2024]
Abstract
Cell-free DNA (cfDNA) fragmentation patterns have immense potential for early cancer detection. However, the definition of fragmentation varies, ranging from the entire genome to specific genomic regions. These patterns have not been systematically compared, impeding broader research and practical implementation. Here, 1382 plasma cfDNA sequencing samples from 8 cancer types are collected. Considering that cfDNA within open chromatin regions is more susceptible to fragmentation, 10 fragmentation patterns within open chromatin regions as features and employed machine learning techniques to evaluate their performance are examined. All fragmentation patterns demonstrated discernible classification capabilities, with the end motif showing the highest diagnostic value for cross-validation. Combining cross and independent validation results revealed that fragmentation patterns that incorporated both fragment length and coverage information exhibited robust predictive capacities. Despite their diagnostic potential, the predictive power of these fragmentation patterns is unstable. To address this limitation, an ensemble classifier via integrating all fragmentation patterns is developed, which demonstrated notable improvements in cancer detection and tissue-of-origin determination. Further functional bioinformatics investigations on significant feature intervals in the model revealed its impressive ability to identify critical regulatory regions involved in cancer pathogenesis.
Collapse
Affiliation(s)
- Yuying Hou
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiang-Yu Meng
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
- Health Science Center, Hubei Minzu University, Enshi, 445000, China
- Hubei Provincial Clinical Medical Research Center for Nephropathy, Hubei Minzu University, Enshi, 445000, China
| | - Xionghui Zhou
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Smart Farming for Agricultural Animals, Ministry of Agriculture and Rural Affairs, Wuhan, 430070, China
| |
Collapse
|
14
|
Fuentes-Rodriguez A, Mitchell A, Guérin SL, Landreville S. Recent Advances in Molecular and Genetic Research on Uveal Melanoma. Cells 2024; 13:1023. [PMID: 38920653 PMCID: PMC11201764 DOI: 10.3390/cells13121023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/08/2024] [Accepted: 06/09/2024] [Indexed: 06/27/2024] Open
Abstract
Uveal melanoma (UM), a distinct subtype of melanoma, presents unique challenges in its clinical management due to its complex molecular landscape and tendency for liver metastasis. This review highlights recent advancements in understanding the molecular pathogenesis, genetic alterations, and immune microenvironment of UM, with a focus on pivotal genes, such as GNAQ/11, BAP1, and CYSLTR2, and delves into the distinctive genetic and chromosomal classifications of UM, emphasizing the role of mutations and chromosomal rearrangements in disease progression and metastatic risk. Novel diagnostic biomarkers, including circulating tumor cells, DNA and extracellular vesicles, are discussed, offering potential non-invasive approaches for early detection and monitoring. It also explores emerging prognostic markers and their implications for patient stratification and personalized treatment strategies. Therapeutic approaches, including histone deacetylase inhibitors, MAPK pathway inhibitors, and emerging trends and concepts like CAR T-cell therapy, are evaluated for their efficacy in UM treatment. This review identifies challenges in UM research, such as the limited treatment options for metastatic UM and the need for improved prognostic tools, and suggests future directions, including the discovery of novel therapeutic targets, immunotherapeutic strategies, and advanced drug delivery systems. The review concludes by emphasizing the importance of continued research and innovation in addressing the unique challenges of UM to improve patient outcomes and develop more effective treatment strategies.
Collapse
Affiliation(s)
- Aurélie Fuentes-Rodriguez
- Department of Ophthalmology and Otorhinolaryngology-Cervico-Facial Surgery, Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada; (A.F.-R.); (A.M.); (S.L.G.)
- Hôpital du Saint-Sacrement, Regenerative Medicine Division, CHU de Québec-Université Laval Research Centre, Quebec City, QC G1S 4L8, Canada
- Centre de Recherche en Organogénèse Expérimentale de l‘Université Laval/LOEX, Quebec City, QC G1J 1Z4, Canada
- Université Laval Cancer Research Center, Quebec City, QC G1R 3S3, Canada
| | - Andrew Mitchell
- Department of Ophthalmology and Otorhinolaryngology-Cervico-Facial Surgery, Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada; (A.F.-R.); (A.M.); (S.L.G.)
- Hôpital du Saint-Sacrement, Regenerative Medicine Division, CHU de Québec-Université Laval Research Centre, Quebec City, QC G1S 4L8, Canada
- Centre de Recherche en Organogénèse Expérimentale de l‘Université Laval/LOEX, Quebec City, QC G1J 1Z4, Canada
- Université Laval Cancer Research Center, Quebec City, QC G1R 3S3, Canada
| | - Sylvain L. Guérin
- Department of Ophthalmology and Otorhinolaryngology-Cervico-Facial Surgery, Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada; (A.F.-R.); (A.M.); (S.L.G.)
- Hôpital du Saint-Sacrement, Regenerative Medicine Division, CHU de Québec-Université Laval Research Centre, Quebec City, QC G1S 4L8, Canada
- Centre de Recherche en Organogénèse Expérimentale de l‘Université Laval/LOEX, Quebec City, QC G1J 1Z4, Canada
| | - Solange Landreville
- Department of Ophthalmology and Otorhinolaryngology-Cervico-Facial Surgery, Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada; (A.F.-R.); (A.M.); (S.L.G.)
- Hôpital du Saint-Sacrement, Regenerative Medicine Division, CHU de Québec-Université Laval Research Centre, Quebec City, QC G1S 4L8, Canada
- Centre de Recherche en Organogénèse Expérimentale de l‘Université Laval/LOEX, Quebec City, QC G1J 1Z4, Canada
- Université Laval Cancer Research Center, Quebec City, QC G1R 3S3, Canada
| |
Collapse
|
15
|
Jary A, Kim Y, Rozemeijer K, Eijk PP, van der Zee RP, Bleeker MCG, Wilting SM, Steenbergen RDM. Accurate detection of copy number aberrations in FFPE samples using the mFAST-SeqS approach. Exp Mol Pathol 2024; 137:104906. [PMID: 38820761 DOI: 10.1016/j.yexmp.2024.104906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 05/17/2024] [Accepted: 05/22/2024] [Indexed: 06/02/2024]
Abstract
BACKGROUND Shallow whole genome sequencing (Shallow-seq) is used to determine the copy number aberrations (CNA) in tissue samples and circulating tumor DNA. However, costs of NGS and challenges of small biopsies ask for an alternative to the untargeted NGS approaches. The mFAST-SeqS approach, relying on LINE-1 repeat amplification, showed a good correlation with Shallow-seq to detect CNA in blood samples. In the present study, we evaluated whether mFAST-SeqS is suitable to assess CNA in small formalin-fixed paraffin-embedded (FFPE) tissue specimens, using vulva and anal HPV-related lesions. METHODS Seventy-two FFPE samples, including 36 control samples (19 vulva;17 anal) for threshold setting and 36 samples (24 vulva; 12 anal) for clinical evaluation, were analyzed by mFAST-SeqS. CNA in vulva and anal lesions were determined by calculating genome-wide and chromosome arm-specific z-scores in comparison with the respective control samples. Sixteen samples were also analyzed with the conventional Shallow-seq approach. RESULTS Genome-wide z-scores increased with the severity of disease, with highest values being found in cancers. In vulva samples median and inter quartile ranges [IQR] were 1[0-2] in normal tissues (n = 4), 3[1-7] in premalignant lesions (n = 9) and 21[13-48] in cancers (n = 10). In anal samples, median [IQR] were 0[0-1] in normal tissues (n = 4), 14[6-38] in premalignant lesions (n = 4) and 18[9-31] in cancers (n = 4). At threshold 4, all controls were CNA negative, while 8/13 premalignant lesions and 12/14 cancers were CNA positive. CNA captured by mFAST-SeqS were mostly also found by Shallow-seq. CONCLUSION mFAST-SeqS is easy to perform, requires less DNA and less sequencing reads reducing costs, thereby providing a good alternative for Shallow-seq to determine CNA in small FFPE samples.
Collapse
Affiliation(s)
- Aude Jary
- Department of Pathology, Amsterdam UMC, location Vrije Universiteit Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Biomarkers and Imaging, Amsterdam, the Netherlands
| | - Yongsoo Kim
- Department of Pathology, Amsterdam UMC, location Vrije Universiteit Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Biomarkers and Imaging, Amsterdam, the Netherlands
| | - Kirsten Rozemeijer
- Department of Pathology, Amsterdam UMC, location Vrije Universiteit Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Biomarkers and Imaging, Amsterdam, the Netherlands
| | - Paul P Eijk
- Department of Pathology, Amsterdam UMC, location Vrije Universiteit Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Biomarkers and Imaging, Amsterdam, the Netherlands
| | - Ramon P van der Zee
- Department of Pathology, Amsterdam UMC, location Vrije Universiteit Amsterdam, Amsterdam, the Netherlands; Department of Internal Medicine, division of Infectious Diseases, Amsterdam UMC, location Universiteit van Amsterdam, Amsterdam, the Netherlands
| | - Maaike C G Bleeker
- Department of Pathology, Amsterdam UMC, location Vrije Universiteit Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Biomarkers and Imaging, Amsterdam, the Netherlands
| | - Saskia M Wilting
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Renske D M Steenbergen
- Department of Pathology, Amsterdam UMC, location Vrije Universiteit Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Biomarkers and Imaging, Amsterdam, the Netherlands.
| |
Collapse
|
16
|
Duffy MJ, Crown J. Circulating tumor DNA (ctDNA): can it be used as a pan-cancer early detection test? Crit Rev Clin Lab Sci 2024; 61:241-253. [PMID: 37936529 DOI: 10.1080/10408363.2023.2275150] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/21/2023] [Indexed: 11/09/2023]
Abstract
Circulating tumor DNA (ctDNA, DNA shed by cancer cells) is emerging as one of the most transformative cancer biomarkers discovered to-date. Although potentially useful at all the phases of cancer detection and patient management, one of its most exciting possibilities is as a relatively noninvasive pan-cancer screening test. Preliminary findings with ctDNA tests such as Galleri or CancerSEEK suggest that they have high specificity (> 99.0%) for malignancy. Their sensitivity varies depending on the type of cancer and stage of disease but it is generally low in patients with stage I disease. A major advantage of ctDNA over existing screening strategies is the potential ability to detect multiple cancer types in a single test. A limitation of most studies published to-date is that they are predominantly case-control investigations that were carried out in patients with a previous diagnosis of malignancy and that used apparently healthy subjects as controls. Consequently, the reported sensitivities, specificities and positive predictive values might be lower if the tests are used for screening in asymptomatic populations, that is, in the population where these tests are likely be employed. To demonstrate clinical utility in an asymptomatic population, these tests must be shown to reduce cancer mortality without causing excessive overdiagnosis in a large randomized prospective randomized trial. Such trials are currently ongoing for Galleri and CancerSEEK.
Collapse
Affiliation(s)
- Michael J Duffy
- UCD School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
- UCD Clinical Research Centre, St. Vincent's University Hospital, Dublin, Ireland
| | - John Crown
- Department of Medical Oncology, St Vincent's University Hospital, Dublin, Ireland
| |
Collapse
|
17
|
Pandya D, Tomita S, Rhenals MP, Swierczek S, Reid K, Camacho-Vanegas O, Camacho C, Engelman K, Polukort S, RoseFigura J, Chuang L, Andikyan V, Cohen S, Fiedler P, Sieber S, Shih IM, Billaud JN, Sebra R, Reva B, Dottino P, Martignetti JA. Mutations in cancer-relevant genes are ubiquitous in histologically normal endometrial tissue. Gynecol Oncol 2024; 185:194-201. [PMID: 38452634 DOI: 10.1016/j.ygyno.2024.02.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/17/2024] [Accepted: 02/20/2024] [Indexed: 03/09/2024]
Abstract
OBJECTIVE Endometrial cancer (EndoCA) is the most common gynecologic cancer and incidence and mortality rate continue to increase. Despite well-characterized knowledge of EndoCA-defining mutations, no effective diagnostic or screening tests exist. To lay the foundation for testing development, our study focused on defining the prevalence of somatic mutations present in non-cancerous uterine tissue. METHODS We obtained ≥8 uterine samplings, including separate endometrial and myometrial layers, from each of 22 women undergoing hysterectomy for non-cancer conditions. We ultra-deep sequenced (>2000× coverage) samples using a 125 cancer-relevant gene panel. RESULTS All women harbored complex mutation patterns. In total, 308 somatic mutations were identified with mutant allele frequencies ranging up to 96.0%. These encompassed 56 unique mutations from 24 genes. The majority of samples possessed predicted functional cancer mutations but curiously no growth advantage over non-functional mutations was detected. Functional mutations were enriched with increasing patient age (p = 0.045) and BMI (p = 0.0007) and in endometrial versus myometrial layers (68% vs 39%, p = 0.0002). Finally, while the somatic mutation landscape shared similar mutation prevalence in key TCGA-defined EndoCA genes, notably PIK3CA, significant differences were identified, including NOTCH1 (77% vs 10%), PTEN (9% vs 61%), TP53 (0% vs 37%) and CTNNB1 (0% vs 26%). CONCLUSIONS An important caveat for future liquid biopsy/DNA-based cancer diagnostics is the repertoire of shared and distinct mutation profiles between histologically unremarkable and EndoCA tissues. The lack of selection pressure between functional and non-functional mutations in histologically unremarkable uterine tissue may offer a glimpse into an unrecognized EndoCA protective mechanism.
Collapse
Affiliation(s)
- Deep Pandya
- The Rudy L. Ruggles Biomedical Research Institute, Nuvance Health, Danbury, CT 06902, United States of America
| | - Shannon Tomita
- Departments of Obstetrics/Gynecology & Reproductive Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America
| | - Maria Padron Rhenals
- Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America
| | - Sabina Swierczek
- The Rudy L. Ruggles Biomedical Research Institute, Nuvance Health, Danbury, CT 06902, United States of America; Department of Obstetrics, Gynecology and Reproductive Sciences, Larner College of Medicine, University of Vermont, Burlington, VT, United States of America
| | - Katherine Reid
- Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America
| | - Olga Camacho-Vanegas
- Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America
| | - Catalina Camacho
- Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America
| | - Kelsey Engelman
- Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America
| | - Stephanie Polukort
- The Rudy L. Ruggles Biomedical Research Institute, Nuvance Health, Danbury, CT 06902, United States of America
| | | | - Linus Chuang
- The Rudy L. Ruggles Biomedical Research Institute, Nuvance Health, Danbury, CT 06902, United States of America
| | - Vaagn Andikyan
- The Rudy L. Ruggles Biomedical Research Institute, Nuvance Health, Danbury, CT 06902, United States of America
| | - Samantha Cohen
- Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America
| | - Paul Fiedler
- The Rudy L. Ruggles Biomedical Research Institute, Nuvance Health, Danbury, CT 06902, United States of America
| | - Steven Sieber
- The Rudy L. Ruggles Biomedical Research Institute, Nuvance Health, Danbury, CT 06902, United States of America
| | - Ie-Ming Shih
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States of America
| | - Jean-Noël Billaud
- QIAGEN Bioinformatics, 1001 Marshall Street, Redwood City, CA 94063, United States of America
| | - Robert Sebra
- Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America
| | - Boris Reva
- Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America
| | - Peter Dottino
- Departments of Obstetrics/Gynecology & Reproductive Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America; MDDx Inc., Tarrytown, NY 10591., United States of America
| | - John A Martignetti
- The Rudy L. Ruggles Biomedical Research Institute, Nuvance Health, Danbury, CT 06902, United States of America; Departments of Obstetrics/Gynecology & Reproductive Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America; Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America; MDDx Inc., Tarrytown, NY 10591., United States of America.
| |
Collapse
|
18
|
Peng H, Pan M, Zhou Z, Chen C, Xing X, Cheng S, Zhang S, Zheng H, Qian K. The impact of preanalytical variables on the analysis of cell-free DNA from blood and urine samples. Front Cell Dev Biol 2024; 12:1385041. [PMID: 38784382 PMCID: PMC11111958 DOI: 10.3389/fcell.2024.1385041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Cell-free DNA (cfDNA), a burgeoning class of molecular biomarkers, has been extensively studied across a variety of biomedical fields. As a key component of liquid biopsy, cfDNA testing is gaining prominence in disease detection and management due to the convenience of sample collection and the abundant wealth of genetic information it provides. However, the broader clinical application of cfDNA is currently impeded by a lack of standardization in the preanalytical procedures for cfDNA analysis. A number of fundamental challenges, including the selection of appropriate preanalytical procedures, prevention of short cfDNA fragment loss, and the validation of various cfDNA measurement methods, remain unaddressed. These existing hurdles lead to difficulties in comparing results and ensuring repeatability, thereby undermining the reliability of cfDNA analysis in clinical settings. This review discusses the crucial preanalytical factors that influence cfDNA analysis outcomes, including sample collection, transportation, temporary storage, processing, extraction, quality control, and long-term storage. The review provides clarification on achievable consensus and offers an analysis of the current issues with the goal of standardizing preanalytical procedures for cfDNA analysis.
Collapse
Affiliation(s)
- Hongwei Peng
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ming Pan
- Taihe Skills Training Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Zongning Zhou
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Congbo Chen
- Department of Urology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Xing Xing
- Department of Urology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Shaoping Cheng
- Department of Urology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Shanshan Zhang
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hang Zheng
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kaiyu Qian
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| |
Collapse
|
19
|
Bang G, Park M, Seon JY, Park SY. Comparative analysis of genetic testing utilization rates among people with and without disabilities in South Korea from 2016 to 2019, focusing on malignant neoplasms: A national population-based study. Cancer Med 2024; 13:e7102. [PMID: 38711356 DOI: 10.1002/cam4.7102] [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: 07/26/2023] [Revised: 02/13/2024] [Accepted: 03/02/2024] [Indexed: 05/08/2024] Open
Abstract
INTRODUCTION Oncogene testing is widely used to detect or direct cancer treatments. Compared to people without disabilities, people with disabilities in Korea have a lower cancer incidence rate but a fivefold higher cancer mortality rate, implying delayed detection. METHODS We used an administrative database combining disability status and care utilization to analyze every case of cancer-related genetic testing paid for by the National Health Insurance Services of Korea between 2016 and 2019. We first compared percentages of individuals who had taken a registered genetic test by their disability statuses. We then compared the most frequently utilized tests between individuals with and without disabilities. RESULTS Korean citizens, 175,000 in total, underwent at least one of the 192 registered cancer-related genetic tests between 2016 and 2019. People with disabilities utilized these genetic tests at higher rates than those without disabilities, regardless of sex or age. Among people aged ≥40 years, lung and colorectal cancer-related tests were most frequently utilized, regardless of disability status. CONCLUSION Although the cancer-related genetic test uptake rate is higher among people with disabilities than among those without disabilities, it is still possible that information on these tests is not as readily available to people with disabilities. Therefore, it is imperative for the government to actively devise strategies to enhance national cancer screening rates among people with disabilities.
Collapse
Affiliation(s)
- Gwanwook Bang
- Department of Medical Education and Humanities, College of Medicine, Kyunghee University, Seoul, South Korea
- Disability Health Research Center of Kyunghee University, Seoul, South Korea
| | - Minji Park
- Kyunghee University Hospital at Gangdong, Seoul, South Korea
| | - Jeong-Yeon Seon
- Health Insurance Research Institute, National Health Insurance Service, Wonju, South Korea
| | - So-Youn Park
- Department of Medical Education and Humanities, College of Medicine, Kyunghee University, Seoul, South Korea
- Disability Health Research Center of Kyunghee University, Seoul, South Korea
| |
Collapse
|
20
|
Garg P, Krishna M, Subbalakshmi AR, Ramisetty S, Mohanty A, Kulkarni P, Horne D, Salgia R, Singhal SS. Emerging biomarkers and molecular targets for precision medicine in cervical cancer. Biochim Biophys Acta Rev Cancer 2024; 1879:189106. [PMID: 38701936 DOI: 10.1016/j.bbcan.2024.189106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/18/2024] [Accepted: 04/28/2024] [Indexed: 05/06/2024]
Abstract
Cervical cancer remains a significant global health burden, necessitating innovative approaches for improved diagnostics and personalized treatment strategies. Precision medicine has emerged as a promising paradigm, leveraging biomarkers and molecular targets to tailor therapy to individual patients. This review explores the landscape of emerging biomarkers and molecular targets in cervical cancer, highlighting their potential implications for precision medicine. By integrating these biomarkers into comprehensive diagnostic algorithms, clinicians can identify high-risk patients at an earlier stage, enabling timely intervention and improved patient outcomes. Furthermore, the identification of specific molecular targets has paved the way for the development of targeted therapies aimed at disrupting key pathways implicated in cervical carcinogenesis. In conclusion, the evolving landscape of biomarkers and molecular targets presents exciting opportunities for advancing precision medicine in cervical cancer. By harnessing these insights, clinicians can optimize treatment selection, enhance patient outcomes, and ultimately transform the management of this devastating disease.
Collapse
Affiliation(s)
- Pankaj Garg
- Department of Chemistry, GLA University, Mathura, Uttar Pradesh 281406, India
| | - Madhu Krishna
- Departments of Medical Oncology & Therapeutics Research and Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - Ayalur Raghu Subbalakshmi
- Departments of Medical Oncology & Therapeutics Research and Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - Sravani Ramisetty
- Departments of Medical Oncology & Therapeutics Research and Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - Atish Mohanty
- Departments of Medical Oncology & Therapeutics Research and Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - Prakash Kulkarni
- Departments of Medical Oncology & Therapeutics Research and Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - David Horne
- Departments of Molecular Medicine, Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - Ravi Salgia
- Departments of Medical Oncology & Therapeutics Research and Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - Sharad S Singhal
- Departments of Medical Oncology & Therapeutics Research and Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA.
| |
Collapse
|
21
|
Yang R, He J, Luo W, Xiang R, Zou G, Zhang X, Liu H, Deng J. Comprehensive analysis and prognostic assessment of senescence-associated genes in bladder cancer. Discov Oncol 2024; 15:130. [PMID: 38668876 PMCID: PMC11052743 DOI: 10.1007/s12672-024-00987-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/18/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND The prevalence and mortality of bladder cancer (BLCA) present a significant medical challenge. While the function of senescence-related genes in tumor development is recognized, their prognostic significance in BLCA has not been thoroughly explored. METHODS BLCA transcriptome datasets were sourced from the TCGA and GEO repositories. Gene groupings were determined through differential gene expression and non-negative matrix factorization (NMF) methodologies. Key senescence-linked genes were isolated using singular and multivariate Cox regression analyses, combined with lasso regression. Validation was undertaken with GEO database information. Predictive models, or nomograms, were developed by merging risk metrics with clinical records, and their efficacy was gauged using ROC curve methodologies. The immune response's dependency on the risk metric was assessed through the immune phenomenon score (IPS). Additionally, we estimated IC50 metrics for potential chemotherapeutic agents. RESULTS Reviewing 406 neoplastic and 19 standard tissue specimens from the TCGA repository facilitated the bifurcation of subjects into two unique clusters (C1 and C2) according to senescence-related gene expression. After a stringent statistical evaluation, a set of ten pivotal genes was discerned and applied for risk stratification. Validity tests for the devised nomograms in forecasting 1, 3, and 5-year survival probabilities for BLCA patients were executed via ROC and calibration plots. IC50 estimations highlighted a heightened responsiveness in the low-risk category to agents like cisplatin, cyclopamine, and sorafenib. CONCLUSIONS In summation, our research emphasizes the prospective utility of risk assessments rooted in senescence-related gene signatures for enhancing BLCA clinical oversight.
Collapse
Affiliation(s)
- Ruilin Yang
- Jinan University, 601 Huangpu Avenue West, Tianhe District, Guangzhou, 511400, China
- Andrology Clinic, The Affiliated Panyu Central Hospital of Guangzhou Medical University, 8 East Fuyu Road, Qiaonan Street, Panyu District, Guangzhou, 511400, China
| | - Jieling He
- Ultrasonography Department, The Affiliated Panyu Central Hospital of Guangzhou Medical University, Guangzhou, 511400, China
| | - Wenfeng Luo
- Central Laboratory, The Affiliated Panyu Central Hospital of Guangzhou Medical University, Guangzhou, 511400, China
| | - Renyang Xiang
- Department of Surgery, The University of HongKong-Shenzhen Hospital, Shenzhen, 518053, Guangdong, China
| | - Ge Zou
- Urology Department, The Affiliated Panyu Central Hospital of Guangzhou Medical University, Guangzhou, 511400, China
| | - Xintao Zhang
- Department of Urology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, 511400, China.
| | - Huang Liu
- National Health Commission (NHC) Key Laboratory of Male Reproduction and Genetics, Department of Andrology, Guangdong Provincial Reproductive Science Institute (Guangdong Provincial Fertility Hospital), Human Sperm Bank of Guangdong Province, Guangzhou, China.
| | - Junhong Deng
- Department of Andrology, Guangzhou First People's Hospital, The Second Affiliated Hospital of South China University of Technology, Guangzhou, China.
| |
Collapse
|
22
|
Pomerantz T, Brooks R. Circulating Tumor DNA (ctDNA) and Its Role in Gynecologic Malignancies. Curr Treat Options Oncol 2024; 25:510-522. [PMID: 38472567 DOI: 10.1007/s11864-024-01180-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2024] [Indexed: 03/14/2024]
Abstract
OPINION STATEMENT Circulating tumor DNA (ctDNA) refers to small fragments of DNA released into the bloodstream by cancer cells. It is obtained through "liquid biopsy;" which most commonly refers to plasma or blood samples, but can be obtained from a number of bodily fluids including ascitic fluid, saliva, and even urine and stool. ctDNA is detected via polymerase chain reaction (PCR) or next-generation sequencing (NGS). The DNA from these samples is analyzed for the detection of point mutations, copy-number alterations, gene fusion, and DNA methylation. These results have the potential for use in cancer diagnosis, determining prognosis, targeting gene-specific therapies, and monitoring for/predicting disease recurrence and response to treatment. ctDNA offers an alternative to tissue biopsy; it is less invasive and can be monitored serially over time without multiple procedures. Moreover it may have the ability to detect disease recurrence or predict behavior in a way that solid tissue biopsies, tumor marker surveillance, and imaging cannot. Recent explosion in interest in ctDNA shows promising developments for widespread adoption of these techniques in cancer care. However, the use of ctDNA in diagnosis and treatment of gynecologic malignancies is currently limited, compared to adoption in other solid-organ tumors such as breast and colorectal cancers. Compared to other cancer types, there appear to be fewer comprehensive studies and clinical validations specifically focusing on the use of ctDNA in gynecologic cancers. More research is needed in this area to advance the potential for use of ctDNA in ovarian, endometrial, and cervical cancers before this can be routinely adopted to improve care for patients with gynecologic malignancies.
Collapse
Affiliation(s)
- Tali Pomerantz
- University of California Davis Medical Center, 4860 Y Street, Suite 2500, Sacramento, CA, 95817, USA.
| | - Rebecca Brooks
- University of California Davis Medical Center, 4860 Y Street, Suite 2500, Sacramento, CA, 95817, USA
| |
Collapse
|
23
|
Kim YJ, Rho WY, Park SM, Jun BH. Optical nanomaterial-based detection of biomarkers in liquid biopsy. J Hematol Oncol 2024; 17:10. [PMID: 38486294 PMCID: PMC10938695 DOI: 10.1186/s13045-024-01531-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/02/2024] [Indexed: 03/18/2024] Open
Abstract
Liquid biopsy, which is a minimally invasive procedure as an alternative to tissue biopsy, has been introduced as a new diagnostic/prognostic measure. By screening disease-related markers from the blood or other biofluids, it promises early diagnosis, timely prognostication, and effective treatment of the diseases. However, there will be a long way until its realization due to its conceptual and practical challenges. The biomarkers detected by liquid biopsy, such as circulating tumor cell (CTC) and circulating tumor DNA (ctDNA), are extraordinarily rare and often obscured by an abundance of normal cellular components, necessitating ultra-sensitive and accurate detection methods for the advancement of liquid biopsy techniques. Optical biosensors based on nanomaterials open an important opportunity in liquid biopsy because of their enhanced sensing performance with simple and practical properties. In this review article, we summarized recent innovations in optical nanomaterials to demonstrate the sensitive detection of protein, peptide, ctDNA, miRNA, exosome, and CTCs. Each study prepares the optical nanomaterials with a tailored design to enhance the sensing performance and to meet the requirements of each biomarker. The unique optical characteristics of metallic nanoparticles (NPs), quantum dots, upconversion NPs, silica NPs, polymeric NPs, and carbon nanomaterials are exploited for sensitive detection mechanisms. These recent advances in liquid biopsy using optical nanomaterials give us an opportunity to overcome challenging issues and provide a resource for understanding the unknown characteristics of the biomarkers as well as the mechanism of the disease.
Collapse
Affiliation(s)
- Young Jun Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Won-Yeop Rho
- School of International Engineering and Science, Jeonbuk National University, Chonju, 54896, Republic of Korea
| | - Seung-Min Park
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, 637459, Singapore.
| | - Bong-Hyun Jun
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea.
| |
Collapse
|
24
|
Wang B, Wang M, Lin Y, Zhao J, Gu H, Li X. Circulating tumor DNA methylation: a promising clinical tool for cancer diagnosis and management. Clin Chem Lab Med 2024; 0:cclm-2023-1327. [PMID: 38443752 DOI: 10.1515/cclm-2023-1327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/19/2024] [Indexed: 03/07/2024]
Abstract
Cancer continues to pose significant challenges to the medical community. Early detection, accurate molecular profiling, and adequate assessment of treatment response are critical factors in improving the quality of life and survival of cancer patients. Accumulating evidence shows that circulating tumor DNA (ctDNA) shed by tumors into the peripheral blood preserves the genetic and epigenetic information of primary tumors. Notably, DNA methylation, an essential and stable epigenetic modification, exhibits both cancer- and tissue-specific patterns. As a result, ctDNA methylation has emerged as a promising molecular marker for noninvasive testing in cancer clinics. In this review, we summarize the existing techniques for ctDNA methylation detection, describe the current research status of ctDNA methylation, and present the potential applications of ctDNA-based assays in the clinic. The insights presented in this article could serve as a roadmap for future research and clinical applications of ctDNA methylation.
Collapse
Affiliation(s)
- Binliang Wang
- Department of Respiratory Medicine, Huangyan Hospital Affiliated to Wenzhou Medical University, Taizhou, P.R. China
| | - Meng Wang
- Institute of Health Education, Hangzhou Center for Disease Control and Prevention, Hangzhou, P.R. China
| | - Ya Lin
- Zhejiang University of Chinese Medicine, Hangzhou, P.R. China
| | - Jinlan Zhao
- Scientific Research Department, Zhejiang Shengting Medical Company, Hangzhou, P.R. China
| | - Hongcang Gu
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, P.R. China
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei, P.R. China
| | - Xiangjuan Li
- Department of Gynaecology, Hangzhou Obstetrics and Gynecology Hospital, Hangzhou, P.R. China
| |
Collapse
|
25
|
Shang X, Zhang C, Kong R, Zhao C, Wang H. Construction of a Diagnostic Model for Small Cell Lung Cancer Combining Metabolomics and Integrated Machine Learning. Oncologist 2024; 29:e392-e401. [PMID: 37706531 PMCID: PMC10911920 DOI: 10.1093/oncolo/oyad261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 08/09/2023] [Indexed: 09/15/2023] Open
Abstract
BACKGROUND To date, no study has systematically explored the potential role of serum metabolites and lipids in the diagnosis of small cell lung cancer (SCLC). Therefore, we aimed to conduct a case-cohort study that included 191 cases of SCLC, 91 patients with lung adenocarcinoma, 82 patients with squamous cell carcinoma, and 97 healthy controls. METHODS Metabolomics and lipidomics were applied to analyze different metabolites and lipids in the serum of these patients. The SCLC diagnosis model (d-model) was constructed using an integrated machine learning technology and a training cohort (n = 323) and was validated in a testing cohort (n=138). RESULTS Eight metabolites, including 1-mristoyl-sn-glycero-3-phosphocholine, 16b-hydroxyestradiol, 3-phosphoserine, cholesteryl sulfate, D-lyxose, dioctyl phthalate, DL-lactate and Leu-Phe, were successfully selected to distinguish SCLC from controls. The d-model was constructed based on these 8 metabolites and showed improved diagnostic performance for SCLC, with the area under curve (AUC) of 0.933 in the training cohort and 0.922 in the testing cohort. Importantly, the d-model still had an excellent diagnostic performance after adjusting the stage and related clinical variables and, combined with the progastrin-releasing peptide (ProGRP), showed the best diagnostic performance with 0.975 of AUC for limited-stage patients. CONCLUSION This study is the first to analyze the difference between metabolomics and lipidomics and to construct a d-model to detect SCLC using integrated machine learning. This study may be of great significance for the screening and early diagnosis of SCLC patients.
Collapse
Affiliation(s)
- Xiaoling Shang
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong University, Jinan, People’s Republic of China
| | - Chenyue Zhang
- Department of Integrated Therapy, Fudan University Shanghai Cancer Center, Shanghai Medical College, Shanghai, People’s Republic of China
| | - Ronghua Kong
- Department of Breast Surgery, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, People’s Republic of China
| | - Chenglong Zhao
- Department of Pathology, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, People’s Republic of China
| | - Haiyong Wang
- Department of Internal Medicine-Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, People’s Republic of China
| |
Collapse
|
26
|
Ruan D, Fang J, Teng X. Efficient 18F-fluorodeoxyglucose positron emission tomography/computed tomography-based machine learning model for predicting epidermal growth factor receptor mutations in non-small cell lung cancer. THE QUARTERLY JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING : OFFICIAL PUBLICATION OF THE ITALIAN ASSOCIATION OF NUCLEAR MEDICINE (AIMN) [AND] THE INTERNATIONAL ASSOCIATION OF RADIOPHARMACOLOGY (IAR), [AND] SECTION OF THE SOCIETY OF... 2024; 68:70-83. [PMID: 35420272 DOI: 10.23736/s1824-4785.22.03441-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
BACKGROUND Beyond the human eye's limitations, radiomics provides more information that can be used for diagnosis. We develop a personalized and efficient model based on 18F-fluorodeoxyglucose (18F-FDG) positron emission tomography/computed tomography (PET/CT) to predict epidermal growth factor receptor (EGFR) mutations to help identify which non-small cell cancer (NSCLC) patients are candidates for EGFR-tyrosine kinase inhibitors (TKIs) therapy. METHODS We retrospectively included 100 patients with NSCLC and randomized them according to 70 patients in the training group and 30 patients in the validation group. The least absolute shrinkage and selection operator logistic regression (LLR) algorithm and support vector machine (SVM) classifier were used to build the models and predict whether EGFR is mutated or not. The predictive efficacy of the LLR algorithm-based model and the SVM classifier-based model was evaluated by plotting the receiver operating characteristic (ROC) curves and calculating the area under the curve (AUC). RESULTS The AUC, sensitivity and specificity of our radiomics model by LLR algorithm were 0.792, 0.967, and 0.600 for the training group and 0.643, 1.00, and 0.378 for the validation group, respectively, in predicting EGFR mutations. The AUC was 0.838 for the training group and 0.696 for the validation group after combining radiomics features with clinical features. The prediction results based on the SVM classifier showed that the validation group had the best performance when based on radial kernel function with AUC, sensitivity, and specificity of 0.741, 0.667, and 0.825, respectively. CONCLUSIONS Radiomics models based on 18F-FDG PET/CT modeled with different machine learning algorithms can improve the predictive efficacy of the models. Models that combine clinical features are more clinically valuable.
Collapse
Affiliation(s)
- Dan Ruan
- Department of Nuclear Medicine, Xiamen Branch, Zhongshan Hospital, Fudan University, Fujian, China -
| | - Janyao Fang
- Department of Nuclear Medicine, Xiamen Branch, Zhongshan Hospital, Fudan University, Fujian, China
| | - Xinyu Teng
- Department of Nuclear Medicine, Xiamen Branch, Zhongshan Hospital, Fudan University, Fujian, China
| |
Collapse
|
27
|
Xin W, Tu S, Yi S, Xiong Y, Fang K, Sun G, Xiao W. Clinical significance of tumor suppressor genes methylation in circulating tumor DNA of patients with pancreatic cancer. Gene 2024; 897:148078. [PMID: 38097094 DOI: 10.1016/j.gene.2023.148078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 11/14/2023] [Accepted: 12/11/2023] [Indexed: 12/17/2023]
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) has emerged as a potential diagnostic and prognostic biomarker in various tumors. However, the role of tumor suppressor genes (TSGs) methylation in ctDNA of patients with pancreatic cancer (PC) remains largely unclear. METHODS Patients with PC (n = 43), pancreatic benign diseases (n = 39), and healthy controls (n = 20) were enrolled in the study. Quantitative analysis of methylation pattern of five candidate TSGs including NPTX2, RASSF1A, EYA2, p16, and ppENK in ctDNA was performed by next generation sequencing (NGS). The diagnostic performances of these 5-TSGs methylation were assessed by the operating characteristic (ROC) curve and clinicopathological features correlation analysis. Meanwhile, the changes in methylation levels of these 5-TSGs on the 7th postoperative day were evaluated in 23 PC patients who underwent radical resection. RESULTS The methylation levels of RASSF1A, EYA2, ppENK and p16 genes in patients with PC were significantly higher than those in healthy controls. EYA2, p16 and ppENK genes showed significantly hypermethylation in PC than those in pancreatic benign diseases. NPTX2, RASSF1A, EYA2, p16 and ppENK genes showed significantly hypermethylation in pancreatic benign diseases than those in healthy controls (P < 0.05). The methylation levels of these 5 candidate TSGs were not correlated with the tumor size, nerve invasion, lymph node metastasis and TNM stage of PC. The AUC of these biomarkers for diagnosis of PC ranged from 0.65 to 0.96. The AUC values of these methylated genes and CpG sites for differentiating malignant and benign pancreatic diseases were ranging from 0.68 to 0.92. Combined the hypermethylated genes improved the detective ability of PC than single gene. The methylation levels of NPTX2, EYA2 and ppENK genes were significantly decreased after radical resection of PC. CONCLUSION Quantitative analysis of methylation pattern of NPTX2, RASSF1A, EYA2, p16 and ppENK in ctDNA by NGS could be a valuable non-invasive tool for detection and monitoring of PC.
Collapse
Affiliation(s)
- WanPeng Xin
- Department of General Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi, China
| | - Shuju Tu
- Department of General Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi, China
| | - Siqing Yi
- Department of General Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi, China
| | - Yuanpeng Xiong
- Department of General Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi, China
| | - Kang Fang
- Department of General Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi, China
| | - Gen Sun
- Department of General Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi, China
| | - Weidong Xiao
- Department of General Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi, China; Institute of Digestive Surgery, Nanchang University, Nanchang, Jiangxi, China.
| |
Collapse
|
28
|
Matza LS, Howell TA, Fung ET, Janes SM, Seiden M, Hackshaw A, Nadauld L, Karn H, Chung KC. Health State Utilities Associated with False-Positive Cancer Screening Results. PHARMACOECONOMICS - OPEN 2024; 8:263-276. [PMID: 38189869 PMCID: PMC10884390 DOI: 10.1007/s41669-023-00443-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/14/2023] [Indexed: 01/09/2024]
Abstract
INTRODUCTION Early cancer detection can significantly improve patient outcomes and reduce mortality rates. Novel cancer screening approaches, including multi-cancer early detection tests, have been developed. Cost-utility analyses will be needed to examine their value, and these models require health state utilities. The purpose of this study was to estimate the disutility (i.e., decrease in health state utility) associated with false-positive cancer screening results. METHODS In composite time trade-off interviews using a 1-year time horizon, UK general population participants valued 10 health state vignettes describing cancer screening with true-negative or false-positive results. Each false-positive vignette described a common diagnostic pathway following a false-positive result suggesting lung, colorectal, breast, or pancreatic cancer. Every pathway ended with a negative result (no cancer detected). The disutility of each false positive was calculated as the difference between the true-negative and each false-positive health state, and because of the 1-year time horizon, each disutility can be interpreted as a quality-adjusted life-year decrement associated with each type of false-positive experience. RESULTS A total of 203 participants completed interviews (49.8% male; mean age = 42.0 years). The mean (SD) utility for the health state describing a true-negative result was 0.958 (0.065). Utilities for false-positive health states ranged from 0.847 (0.145) to 0.932 (0.059). Disutilities for false positives ranged from - 0.031 to - 0.111 (- 0.041 to - 0.111 for lung cancer; - 0.079 for colorectal cancer; - 0.031 to - 0.067 for breast cancer; - 0.048 to - 0.088 for pancreatic cancer). CONCLUSION All false-positive results were associated with a disutility. Greater disutility was associated with more invasive follow-up diagnostic procedures, longer duration of uncertainty regarding the eventual diagnosis, and perceived severity of the suspected cancer type. Utility values estimated in this study would be useful for economic modeling examining the value of cancer screening procedures.
Collapse
Affiliation(s)
| | | | - Eric T Fung
- GRAIL, LLC., a subsidiary of Illumina Inc., Menlo Park, CA, USA
| | - Sam M Janes
- UCL Respiratory, University College London, London, UK
| | - Michael Seiden
- Physician in Residence, GRAIL, LLC., Menlo Park, CA, USA
| | | | | | | | - Karen C Chung
- GRAIL, LLC., a subsidiary of Illumina Inc., Menlo Park, CA, USA
| |
Collapse
|
29
|
Yan L, Fan E, Tan B. Characteristics of Ovarian Cancer Immune Cell Invasion and Bioinformatics to Predict the Effect of Immunotherapy. Horm Metab Res 2024; 56:197-205. [PMID: 38242159 DOI: 10.1055/a-2231-8475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2024]
Abstract
Recent studies have confirmed that tumor immune cell infiltration (ICI) is associated with sensitivity of ovarian cancer (OC) immunotherapy and disease progression of OC patients. However, studies related to immune infiltration in OC, has not been elucidated. Two algorithms are used to analyze the OC data in the TCGA and GEO databases. After combining the two data sets, the immune cell content of the sample was estimated by Cell-type Identification By Estimate Relative Subsets of RNA Transcripts (CIBERSORT method). An unsupervised consistent clustering algorithm was used to analyze ICI subtypes and their differentially expressed genes (DEGs). Two subgroups and three ICI gene clusters were identified by unsupervised consensus clustering algorithm. The ICI score was obtained by analyzing the gene characteristics through principal component analysis (PCA). The ICI score ranged from -15.8132 to 18.7211, which was associated with the prognosis of OC patients with immunotherapy. The Toll-like receptor pathway, B-cell receptor pathway, antigen processing and presentation pathway, NK-cell-mediated cytotoxicity pathway, and arginine-proline metabolism pathway were activated in the high ICI score group, suggesting that immune cells in the high ICI score group were activated, thus leading to a better prognosis in this group of patients. Patients with G3-G4 in the high ICI rating group were more sensitive to immunotherapy and had a better prognosis in patients with high tumor mutation burden (TMB). This study suggests that ICI scores can be used as a feasible auxiliary indicator for predicting the prognosis of patients with OC.
Collapse
Affiliation(s)
- Lingli Yan
- Department of Transfusion Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Erxi Fan
- Department of Ultrasound, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Bin Tan
- Department of Transfusion Medicine, West China Hospital of Sichuan University, Chengdu, China
| |
Collapse
|
30
|
Otsuji R, Fujioka Y, Hata N, Kuga D, Hatae R, Sangatsuda Y, Nakamizo A, Mizoguchi M, Yoshimoto K. Liquid Biopsy for Glioma Using Cell-Free DNA in Cerebrospinal Fluid. Cancers (Basel) 2024; 16:1009. [PMID: 38473369 DOI: 10.3390/cancers16051009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 02/24/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Glioma is one of the most common primary central nervous system (CNS) tumors, and its molecular diagnosis is crucial. However, surgical resection or biopsy is risky when the tumor is located deep in the brain or brainstem. In such cases, a minimally invasive approach to liquid biopsy is beneficial. Cell-free DNA (cfDNA), which directly reflects tumor-specific genetic changes, has attracted attention as a target for liquid biopsy, and blood-based cfDNA monitoring has been demonstrated for other extra-cranial cancers. However, it is still challenging to fully detect CNS tumors derived from cfDNA in the blood, including gliomas, because of the unique structure of the blood-brain barrier. Alternatively, cerebrospinal fluid (CSF) is an ideal source of cfDNA and is expected to contribute significantly to the liquid biopsy of gliomas. Several successful studies have been conducted to detect tumor-specific genetic alterations in cfDNA from CSF using digital PCR and/or next-generation sequencing. This review summarizes the current status of CSF-based cfDNA-targeted liquid biopsy for gliomas. It highlights how the approaches differ from liquid biopsies of other extra-cranial cancers and discusses the current issues and prospects.
Collapse
Affiliation(s)
- Ryosuke Otsuji
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yutaka Fujioka
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Nobuhiro Hata
- Department of Neurosurgery, Oita University Faculty of Medicine, Yufu 879-5593, Japan
| | - Daisuke Kuga
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Ryusuke Hatae
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yuhei Sangatsuda
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Akira Nakamizo
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Masahiro Mizoguchi
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
- Department of Neurosurgery, National Hospital Organization Kyushu Medical Center, Clinical Research Institute, Fukuoka 810-8563, Japan
| | - Koji Yoshimoto
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| |
Collapse
|
31
|
Huang Z, Fu Y, Yang H, Zhou Y, Shi M, Li Q, Liu W, Liang J, Zhu L, Qin S, Hong H, Liu Y. Liquid biopsy in T-cell lymphoma: biomarker detection techniques and clinical application. Mol Cancer 2024; 23:36. [PMID: 38365716 PMCID: PMC10874034 DOI: 10.1186/s12943-024-01947-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/25/2024] [Indexed: 02/18/2024] Open
Abstract
T-cell lymphoma is a highly invasive tumor with significant heterogeneity. Invasive tissue biopsy is the gold standard for acquiring molecular data and categorizing lymphoma patients into genetic subtypes. However, surgical intervention is unfeasible for patients who are critically ill, have unresectable tumors, or demonstrate low compliance, making tissue biopsies inaccessible to these patients. A critical need for a minimally invasive approach in T-cell lymphoma is evident, particularly in the areas of early diagnosis, prognostic monitoring, treatment response, and drug resistance. Therefore, the clinical application of liquid biopsy techniques has gained significant attention in T-cell lymphoma. Moreover, liquid biopsy requires fewer samples, exhibits good reproducibility, and enables real-time monitoring at molecular levels, thereby facilitating personalized health care. In this review, we provide a comprehensive overview of the current liquid biopsy biomarkers used for T-cell lymphoma, focusing on circulating cell-free DNA (cfDNA), circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), Epstein-Barr virus (EBV) DNA, antibodies, and cytokines. Additionally, we discuss their clinical application, detection methodologies, ongoing clinical trials, and the challenges faced in the field of liquid biopsy.
Collapse
Affiliation(s)
- Zongyao Huang
- Department of Pathology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Yao Fu
- Department of Pathology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Hong Yang
- Department of Pathology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Yehan Zhou
- Department of Pathology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Min Shi
- Department of Pathology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Qingyun Li
- Genecast Biotechnology Co., Ltd, Wuxi, 214104, China
| | - Weiping Liu
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Junheng Liang
- Nanjing Geneseeq Technology Inc., Nanjing, 210032, Jiangsu, China
| | - Liuqing Zhu
- Nanjing Geneseeq Technology Inc., Nanjing, 210032, Jiangsu, China
| | - Sheng Qin
- Department of Pathology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China.
| | - Huangming Hong
- Department of Medical Oncology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China.
| | - Yang Liu
- Department of Pathology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China.
| |
Collapse
|
32
|
Alberca-del Arco F, Prieto-Cuadra D, Santos-Perez de la Blanca R, Sáez-Barranquero F, Matas-Rico E, Herrera-Imbroda B. New Perspectives on the Role of Liquid Biopsy in Bladder Cancer: Applicability to Precision Medicine. Cancers (Basel) 2024; 16:803. [PMID: 38398192 PMCID: PMC10886494 DOI: 10.3390/cancers16040803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Bladder cancer (BC) is one of the most common tumors in the world. Cystoscopy and tissue biopsy are the standard methods in screening and early diagnosis of suspicious bladder lesions. However, they are invasive procedures that may cause pain and infectious complications. Considering the limitations of both procedures, and the recurrence and resistance to BC treatment, it is necessary to develop a new non-invasive methodology for early diagnosis and multiple evaluations in patients under follow-up for bladder cancer. In recent years, liquid biopsy has proven to be a very useful diagnostic tool for the detection of tumor biomarkers. This non-invasive technique makes it possible to analyze single tumor components released into the peripheral circulation and to monitor tumor progression. Numerous biomarkers are being studied and interesting clinical applications for these in BC are being presented, with promising results in early diagnosis, detection of microscopic disease, and prediction of recurrence and response to treatment.
Collapse
Affiliation(s)
- Fernardo Alberca-del Arco
- Departamento de Urología, Hospital Universitario Virgen de la Victoria (HUVV), 29010 Málaga, Spain; (F.A.-d.A.); (R.S.-P.d.l.B.); (F.S.-B.)
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA Plataforma BIONAND), 29590 Málaga, Spain
| | - Daniel Prieto-Cuadra
- Departamento de Anatomía Patológica, Hospital Universitario Virgen de la Victoria (HUVV), 29010 Málaga, Spain;
- Unidad de Gestion Clinica de Anatomia Patologica, IBIMA, Hospital Universitario Virgen de la Victoria, 29010 Málaga, Spain
- SYNLAB Pathology, 29007 Málaga, Spain
| | - Rocio Santos-Perez de la Blanca
- Departamento de Urología, Hospital Universitario Virgen de la Victoria (HUVV), 29010 Málaga, Spain; (F.A.-d.A.); (R.S.-P.d.l.B.); (F.S.-B.)
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA Plataforma BIONAND), 29590 Málaga, Spain
- Genitourinary Alliance for Research and Development (GUARD Consortium), 29071 Málaga, Spain
| | - Felipe Sáez-Barranquero
- Departamento de Urología, Hospital Universitario Virgen de la Victoria (HUVV), 29010 Málaga, Spain; (F.A.-d.A.); (R.S.-P.d.l.B.); (F.S.-B.)
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA Plataforma BIONAND), 29590 Málaga, Spain
- Genitourinary Alliance for Research and Development (GUARD Consortium), 29071 Málaga, Spain
| | - Elisa Matas-Rico
- Departamento de Urología, Hospital Universitario Virgen de la Victoria (HUVV), 29010 Málaga, Spain; (F.A.-d.A.); (R.S.-P.d.l.B.); (F.S.-B.)
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA Plataforma BIONAND), 29590 Málaga, Spain
- Genitourinary Alliance for Research and Development (GUARD Consortium), 29071 Málaga, Spain
- Departamento de Biología Celular, Genética y Fisiología, Universidad de Málaga (UMA), 29071 Málaga, Spain
| | - Bernardo Herrera-Imbroda
- Departamento de Urología, Hospital Universitario Virgen de la Victoria (HUVV), 29010 Málaga, Spain; (F.A.-d.A.); (R.S.-P.d.l.B.); (F.S.-B.)
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA Plataforma BIONAND), 29590 Málaga, Spain
- Genitourinary Alliance for Research and Development (GUARD Consortium), 29071 Málaga, Spain
- Departamento de Especialidades Quirúrgicas, Bioquímica e Inmunología, Universidad de Málaga (UMA), 29071 Málaga, Spain
| |
Collapse
|
33
|
Shishido SN, Lin E, Nissen N, Courcoubetis G, Suresh D, Mason J, Osipov A, Hendifar AE, Lewis M, Gaddam S, Pandol S, Kuhn P, Lo SK. Cancer-related cells and oncosomes in the liquid biopsy of pancreatic cancer patients undergoing surgery. NPJ Precis Oncol 2024; 8:36. [PMID: 38360856 PMCID: PMC10869814 DOI: 10.1038/s41698-024-00521-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 01/15/2024] [Indexed: 02/17/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) has a five-year survival rate of less than 10% due to its late diagnosis, rapid metastasis, and chemotherapeutic resistance. For a small proportion (10-20%) of early-stage patients however, surgical resection of the pancreatic tumor offers the best chance for survival but the effect of surgery on disease dissemination is unknown. The primary objective of this study was to characterize cellular and acellular blood-based analytes in portal and peripheral blood before pancreatic manipulation, during tumor dissection and immediately after surgical resection to determine the effects of the surgery. This study used the non-enriching third generation High-Definition Single Cell Assay (HDSCA3.0) workflow to investigate heterogeneous circulating rare cell population in the blood. Blood from both sites taken before surgical manipulation of the pancreas had significantly greater incidence of total rare cellular and acellular analytes than normal donor samples. Post-surgery portal and peripheral blood had significantly greater incidence of specific cellular and acellular subtypes compared to the matched pre- and during-surgery samples. Our results reveal that in patients with PDAC liquid biopsy analytes are increased in both the portal and peripheral blood; portal blood contains a higher frequency of analytes than in the peripheral blood; total analytes in the portal and peripheral blood samples were significantly associated with the tumor volume and pathological T stage; and the surgical procedure increased the blood levels of circulating cellular and acellular analytes, but not Epi.CTCs or Mes.CTCs. This study demonstrates liquid biopsy's utility in monitoring patients with PDAC with surgically resectable disease.
Collapse
Affiliation(s)
- Stephanie N Shishido
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA, 90089, USA
| | - Emmeline Lin
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA, 90089, USA
| | - Nicholas Nissen
- Pancreatic and Biliary Diseases Program, Cedars Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - George Courcoubetis
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA, 90089, USA
| | - Divya Suresh
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA, 90089, USA
| | - Jeremy Mason
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA, 90089, USA
- Institute of Urology, Catherine & Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Arsen Osipov
- IM Hematology Oncology, Cedars Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Andrew E Hendifar
- IM Hematology Oncology, Cedars Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Michael Lewis
- Pancreatic and Biliary Diseases Program, Cedars Sinai Medical Center, Los Angeles, CA, 90048, USA
- Greater Los Angeles Veterans Affairs System, Los Angeles, CA, 90073, USA
- Clark Atlanta University, Center for Cancer Research and Therapeutic Development, Atlanta, GA, 30314, USA
| | - Srinivas Gaddam
- Pancreatic and Biliary Diseases Program, Cedars Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Stephen Pandol
- Pancreatic and Biliary Diseases Program, Cedars Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Peter Kuhn
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA, 90089, USA.
- Institute of Urology, Catherine & Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, 90089, USA.
- Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, 90089, USA.
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
| | - Simon K Lo
- Pancreatic and Biliary Diseases Program, Cedars Sinai Medical Center, Los Angeles, CA, 90048, USA.
| |
Collapse
|
34
|
Galant N, Nicoś M, Kuźnar-Kamińska B, Krawczyk P. Variant Allele Frequency Analysis of Circulating Tumor DNA as a Promising Tool in Assessing the Effectiveness of Treatment in Non-Small Cell Lung Carcinoma Patients. Cancers (Basel) 2024; 16:782. [PMID: 38398173 PMCID: PMC10887123 DOI: 10.3390/cancers16040782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Despite the different possible paths of treatment, lung cancer remains one of the leading causes of death in oncological patients. New tools guiding the therapeutic process are under scientific investigation, and one of the promising indicators of the effectiveness of therapy in patients with NSCLC is variant allele frequency (VAF) analysis. VAF is a metric characterized as the measurement of the specific variant allele proportion within a genomic locus, and it can be determined using methods based on NGS or PCR. It can be assessed using not only tissue samples but also ctDNA (circulating tumor DNA) isolated from liquid biopsy. The non-invasive characteristic of liquid biopsy enables a more frequent collection of material and increases the potential of VAF analysis in monitoring therapy. Several studies have been performed on patients with NSCLC to evaluate the possibility of VAF usage. The research carried out so far demonstrates that the evaluation of VAF dynamics may be useful in monitoring tumor progression, remission, and recurrence during or after treatment. Moreover, the use of VAF analysis appears to be beneficial in making treatment decisions. However, several issues require better understanding and standardization before VAF testing can be implemented in clinical practice. In this review, we discuss the difficulties in the application of ctDNA VAF analysis in clinical routine, discussing the diagnostic and methodological challenges in VAF measurement in liquid biopsy. We highlight the possible applications of VAF-based measurements that are under consideration in clinical trials in the monitoring of personalized treatments for patients with NSCLC.
Collapse
Affiliation(s)
- Natalia Galant
- Department of Pneumonology, Oncology and Allergology, Medical University of Lublin, 20-059 Lublin, Poland
| | - Marcin Nicoś
- Department of Pneumonology, Oncology and Allergology, Medical University of Lublin, 20-059 Lublin, Poland
| | - Barbara Kuźnar-Kamińska
- Department of Pulmonology, Allergology and Respiratory Oncology, Poznan University of Medical Sciences, 61-710 Poznan, Poland;
| | - Paweł Krawczyk
- Department of Pneumonology, Oncology and Allergology, Medical University of Lublin, 20-059 Lublin, Poland
| |
Collapse
|
35
|
Ye L, Chu X, Ni J, Chu L, Yang X, Zhu Z. NGS-based Tissue-Blood TMB Comparison and Blood-TMB Monitoring in Stage-III Non-Small Cell Lung Cancer Treated with Concurrent Chemoradiotherapy. Cancer Invest 2024; 42:165-175. [PMID: 38390854 DOI: 10.1080/07357907.2024.2316297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 02/05/2024] [Indexed: 02/24/2024]
Abstract
In this study, we analyzed the blood-based TMB (b-TMB) and its dynamic changes in patients with locally advanced non-small cell lung cancer (LA-NSCLC) who received concurrent chemoradiotherapy. Baseline tissue and blood TMB from 15 patients showed a strong positive correlation (Pearson correlation = 0.937), and nearly all mutations were markedly reduced in the later course of treatment, indicating a treatment-related response. This study suggests that in patients with LA-NSCLC, b-TMB is a reliable biomarker, and its dynamic monitoring can help distinguish patients who might benefit most from the consolidated immunotherapy.
Collapse
Affiliation(s)
- Luxi Ye
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiao Chu
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jianjiao Ni
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Li Chu
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xi Yang
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhengfei Zhu
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
| |
Collapse
|
36
|
Heinrich MC, Jones RL, George S, Gelderblom H, Schöffski P, von Mehren M, Zalcberg JR, Kang YK, Razak AA, Trent J, Attia S, Le Cesne A, Siontis BL, Goldstein D, Boye K, Sanchez C, Steeghs N, Rutkowski P, Druta M, Serrano C, Somaiah N, Chi P, Reichmann W, Sprott K, Achour H, Sherman ML, Ruiz-Soto R, Blay JY, Bauer S. Ripretinib versus sunitinib in gastrointestinal stromal tumor: ctDNA biomarker analysis of the phase 3 INTRIGUE trial. Nat Med 2024; 30:498-506. [PMID: 38182785 PMCID: PMC10878977 DOI: 10.1038/s41591-023-02734-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 11/22/2023] [Indexed: 01/07/2024]
Abstract
INTRIGUE was an open-label, phase 3 study in adult patients with advanced gastrointestinal stromal tumor who had disease progression on or intolerance to imatinib and who were randomized to once-daily ripretinib 150 mg or sunitinib 50 mg. In the primary analysis, progression-free survival (PFS) with ripretinib was not superior to sunitinib. In clinical and nonclinical studies, ripretinib and sunitinib have demonstrated differential activity based on the exon location of KIT mutations. Therefore, we hypothesized that mutational analysis using circulating tumor DNA (ctDNA) might provide further insight. In this exploratory analysis (N = 362), baseline peripheral whole blood was analyzed by a 74-gene ctDNA next-generation sequencing-based assay. ctDNA was detected in 280/362 (77%) samples with KIT mutations in 213/362 patients (59%). Imatinib-resistant mutations were found in the KIT ATP-binding pocket (exons 13/14) and activation loop (exons 17/18). Mutational subgroup assessment showed 2 mutually exclusive populations with differential treatment effects. Patients with only KIT exon 11 + 13/14 mutations (ripretinib, n = 21; sunitinib, n = 20) had better PFS with sunitinib versus ripretinib (median, 15.0 versus 4.0 months). Patients with only KIT exon 11 + 17/18 mutations (ripretinib, n = 27; sunitinib, n = 25) had better PFS with ripretinib versus sunitinib (median, 14.2 versus 1.5 months). The results of this exploratory analysis suggest ctDNA sequencing may improve the prediction of the efficacy of single-drug therapies and support further evaluation of ripretinib in patients with KIT exon 11 + 17/18 mutations. ClinicalTrials.gov identifier: NCT03673501.
Collapse
Affiliation(s)
- Michael C Heinrich
- Division of Hematology/Oncology, Portland VA Health Care System, Portland, OR, USA
- Department of Medicine, OHSU Knight Cancer Institute, Portland, OR, USA
| | - Robin L Jones
- Sarcoma Unit, The Royal Marsden NHS Foundation Trust and Institute of Cancer Research, London, UK
| | - Suzanne George
- Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Hans Gelderblom
- Department of Medical Oncology, Leiden University Medical Center, Leiden, Netherlands
| | - Patrick Schöffski
- Department of General Medical Oncology, University Hospitals Leuven, Leuven Cancer Institute, KU Leuven, Leuven, Belgium
| | - Margaret von Mehren
- Department of Hematology/Oncology, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA, USA
| | - John R Zalcberg
- Department of Medical Oncology, Monash University School of Public Health and Preventive Medicine, Alfred Health, Melbourne, Victoria, Australia
| | - Yoon-Koo Kang
- Department of Oncology, Asan Medical Center, University of Ulsan, Seoul, Korea
| | - Albiruni Abdul Razak
- Division of Medical Oncology, Toronto Sarcoma Program, Princess Margaret Cancer Center, Toronto, ON, Canada
| | - Jonathan Trent
- Department of Medical Oncology, Sylvester Comprehensive Cancer Center, University of Miami Health System, Miami, FL, USA
| | - Steven Attia
- Department of Medical Oncology, Mayo Clinic, Jacksonville, FL, USA
| | - Axel Le Cesne
- Medical Oncology Department, Gustave Roussy, Villejuif, France
| | | | - David Goldstein
- Department of Medical Oncology, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Kjetil Boye
- Department of Tumor Biology, Oslo University Hospital, Oslo, Norway
| | - Cesar Sanchez
- Department of Hematology-Oncology, Centro de Cáncer, Hospital Clínico Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Neeltje Steeghs
- Department of Medical Oncology, The Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, Netherlands
| | - Piotr Rutkowski
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie National Research Institute of Oncology, Warszawa, Poland
| | - Mihaela Druta
- Sarcoma Program, Moffitt Cancer Center, Tampa, FL, USA
| | - César Serrano
- Sarcoma Translational Research Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Neeta Somaiah
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ping Chi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Kam Sprott
- Biometrics, Deciphera Pharmaceuticals, LLC, Waltham, MA, USA
- Translational Medicine, Deciphera Pharmaceuticals, LLC, Waltham, MA, USA
| | - Haroun Achour
- Biometrics, Deciphera Pharmaceuticals, LLC, Waltham, MA, USA
- Clinical Development, Deciphera Pharmaceuticals, LLC, Waltham, MA, USA
| | - Matthew L Sherman
- Clinical Development, Deciphera Pharmaceuticals, LLC, Waltham, MA, USA
| | - Rodrigo Ruiz-Soto
- Clinical Development, Deciphera Pharmaceuticals, LLC, Waltham, MA, USA
| | - Jean-Yves Blay
- Department of Medical Oncology, Centre Léon Bérard, Lyon, France
| | - Sebastian Bauer
- Department of Medical Oncology and Sarcoma Center, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, Essen, Germany.
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, Essen, Germany.
| |
Collapse
|
37
|
Anitha K, Posinasetty B, Naveen Kumari K, Chenchula S, Padmavathi R, Prakash S, Radhika C. Liquid biopsy for precision diagnostics and therapeutics. Clin Chim Acta 2024; 554:117746. [PMID: 38151071 DOI: 10.1016/j.cca.2023.117746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/22/2023] [Accepted: 12/23/2023] [Indexed: 12/29/2023]
Abstract
Liquid biopsy (LB) has emerged as a highly promising and non-invasive diagnostic approach, particularly in the field of oncology, and has garnered interest in various medical disciplines. This technique involves the examination of biomolecules released into physiological fluids, such as urine samples, blood, and cerebrospinal fluid (CSF). The analysed biomolecules included circulating tumour DNA (ctDNA), circulating tumour cells (CTCs), cell-free DNA (cfDNA), exosomes, and other cell-free components. In contrast to conventional tissue biopsies, LB provides minimally invasive diagnostics, offering invaluable insights into tumor characteristics, treatment response, and early disease detection. This Review explores the contemporary landscape of technologies and clinical applications in the realm of LB, with a particular emphasis on the isolation and analysis of ctDNA and/or cfDNA. Various methodologies have been employed, including droplet digital polymerase chain reaction (DDP), BEAMing (beads, emulsion, amplification, and magnetics), TAm-Seq (tagged-amplicon deep sequencing), CAPP-Seq (cancer personalized profiling by deep sequencing), WGBS-Seq (whole genome bisulfite sequencing), WES (whole exome sequencing), and WGS (whole-genome sequencing). Additionally, CTCs have been successfully isolated through biomarker-based cell capture, employing both positive and negative enrichment strategies based on diverse biophysical and other inherent properties. This approach also addresses challenges and limitations associated with liquid biopsy techniques, such as sensitivity, specificity, standardization and interpretability of findings. This review seeks to identify the current technologies used in liquid biopsy samples, emphasizing their significance in identifying tumor markers for cancer detection, prognosis, and treatment outcome monitoring.
Collapse
Affiliation(s)
- Kuttiappan Anitha
- Department of Pharmacology, School of Pharmacy and Technology Management (SPTM), SVKM's Narsee Monjee Institute of Management Studies (NMIMS) Deemed-to-University, Shirpur 425405, India
| | | | - K Naveen Kumari
- Sri Krishna Teja Pharmacy College, Tirupati, Andhra Pradesh 517502, India
| | | | - R Padmavathi
- SVS Medical College, Hyderabad, Telangana, India
| | - Satya Prakash
- All India Institute of Medical Sciences, Bhopal 462020, India
| | | |
Collapse
|
38
|
Eugene T, Roy Sg J, S N, Rappai M. Assessment of the Efficacy of Circulating Tumor Cells by Liquid Biopsy in the Diagnosis and Prediction of Tumor Behavior of Gliomas: A Systematic Review. Cureus 2024; 16:e54101. [PMID: 38357405 PMCID: PMC10865163 DOI: 10.7759/cureus.54101] [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: 12/16/2023] [Accepted: 02/13/2024] [Indexed: 02/16/2024] Open
Abstract
In the realm of glioma management, the ability to accurately diagnose and predict tumor behavior remains a formidable task. Emerging as a beacon of hope, liquid biopsy (LB), with its potential to detect circulating tumor (CT) cells, offers a novel and promising avenue for addressing these challenges. This systematic review delves into the effectiveness of LB in transforming the landscape of glioma analysis as well as prognosis, shedding light on its clinical significance and implications. We conducted a comprehensive literature search from 2015 to 2023, using multiple sources. We assessed titles and abstracts first, followed by full-text review if they met our criteria. We included those studies that fulfill the inclusion criteria of the study. For bias assessment, we used a two-part tool for specific domains and a quality assessment tool for diagnostic accuracy studies. In this review, we incorporated eight studies. A total of 498 patients were identified across eight studies. The average sensitivity was 72.28% in seven of these studies, while the average specificity was 91.52% in the same seven studies. Our review revealed a sensitivity of 72.28% and an impressive specificity of 91.52%. This underscores the potential of LB as a valuable prognostic tool for detecting CT cells. However, the early detection of tumor cells and the prediction of tumor behavior in gliomas continue to be topics of debate, necessitating further research for more precise and reliable outcomes.
Collapse
Affiliation(s)
- Teena Eugene
- Pathology, SRM Medical College Hospital and Research Centre, SRM Institute of Science and Technology (SRMIST), Chennai, IND
| | - Jano Roy Sg
- Pathology, SRM Medical College Hospital and Research Centre, SRM Institute of Science and Technology (SRMIST), Chennai, IND
| | - Nivethitha S
- Pathology, SRM Medical College Hospital and Research Centre, SRM Institute of Science and Technology (SRMIST), Chennai, IND
| | - Meethu Rappai
- Pathology, SRM Medical College Hospital and Research Centre, SRM Institute of Science and Technology (SRMIST), Chennai, IND
| |
Collapse
|
39
|
Shbeer AM, Robadi IA. liquid biopsy holds a promising approach for the early detection of cancer: Current information and future perspectives. Pathol Res Pract 2024; 254:155082. [PMID: 38246032 DOI: 10.1016/j.prp.2023.155082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/24/2023] [Accepted: 12/30/2023] [Indexed: 01/23/2024]
Abstract
Cancer is becoming a global pandemic, and its occurrence is increasing rapidly, putting a strain on people's families, health systems, and finances, in addition to their physical, mental, and emotional well-being. Many cancer types lack screening programs, and many people at high risk of developing cancer do not follow recommended medical screening regimens because of the nature of currently available screening tests and other compliance issues, despite cancer being the second leading cause of death worldwide. Furthermore, a lot of liquid biopsy methods for early cancer screening are not sensitive enough to catch cancer early. Cancer treatment costs increase with the time it takes to diagnose the disease; therefore, early detection is essential to enhance the quality of life and survival rates. The current status of the liquid biopsy sector is examined in this paper.
Collapse
Affiliation(s)
- Abdullah M Shbeer
- Department of Surgery, Faculty of Medicine, Jazan University, Jazan, Saudi Arabia.
| | - Ibrahim Ahmed Robadi
- Department of Pathology, Faculty of Medicine, Jazan University, Jazan, Saudi Arabia.
| |
Collapse
|
40
|
Martínez-Herrera JF, Sánchez Domínguez G, Juárez-Vignon Whaley JJ, Carrasco-Cara Chards S, López Vrátný C, Guzmán Casta J, Riera Sala RF, Alatorre-Alexander JA, Seidman Sorsby A, Cruz Zermeño M, Conde Flores E, Flores-Mariñelarena RR, Sánchez-Ríos CP, Martínez-Barrera LM, Gerson-Cwilich R, Santillán-Doherty P, Jiménez López JC, López Hernández W, Rodríguez-Cid JR. Mutation profile in liquid biopsy tested by next generation sequencing in Mexican patients with non-small cell lung carcinoma and its impact on survival. J Thorac Dis 2024; 16:161-174. [PMID: 38410597 PMCID: PMC10894362 DOI: 10.21037/jtd-23-1029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 11/24/2023] [Indexed: 02/28/2024]
Abstract
Background Lung cancer represents a significant global health concern, often diagnosed in its advanced stages. The advent of massive DNA sequencing has revolutionized the landscape of cancer treatment by enabling the identification of target mutations and the development of tailored therapeutic approaches. Unfortunately, access to DNA sequencing technology remains limited in many developing countries. In this context, we emphasize the critical importance of integrating this advanced technology into healthcare systems in developing nations to improve treatment outcomes. Methods We conducted an analysis of electronic clinical records of patients with confirmed advanced non-small cell lung cancer (NSCLC) and a verified negative status for the epidermal growth factor receptor (EGFR) mutation. These patients underwent next-generation sequencing (NGS) for molecular analysis. We performed descriptive statistical analyses for each variable and conducted both univariate and multivariate statistical analyses to assess their impact on progression-free survival (PFS) and overall survival (OS). Additionally, we classified genetic mutations as actionable or non-actionable based on the European Society for Medical Oncology Scale of Clinical Actionability of Molecular Targets (ESCAT) guidelines. Results Our study included a total of 127 patients, revealing the presence of twenty-one distinct mutations. The most prevalent mutations were EGFR (18.9%) and Kirsten rat sarcoma viral oncogene homolog (KRAS) (15.7%). Notably, anaplastic lymphoma kinase (ALK) [hazard ratio (HR): 0.258, P<0.001], tumor mutation burden (TMB) (HR: 2.073, P=0.042) and brain magnetic resonance imaging (MRI) (HR: 0.470, P=0.032) demonstrated statistical significance in both the univariate and multivariate analyses with respect to PFS. In terms of OS, ALK (HR: 0.285, P<0.001) and EGFR (HR: 0.482, P=0.024) exhibited statistical significance in both analyses. Applying the ESCAT classification system, we identified actionable genomic variations (ESCAT level-1), including EGFR, ALK, breast cancer (BRAF) gene, c-ros oncogene 1 (ROS1), and rearranged during transfection (RET) gene, in 32.3% of the patients. Conclusions Our findings from massive DNA sequencing underscore that 32.3% of patients who test negative for the EGFR mutation possess other targetable mutations, enabling them to receive personalized, targeted therapies at an earlier stage of their disease. Implementing massive DNA sequencing in developing countries is crucial to enhance survival rates among NSCLC patients and guide more effective treatment strategies.
Collapse
Affiliation(s)
- José Fabián Martínez-Herrera
- Department of Thoracic Oncology, Instituto Nacional de Enfermedades Respiratorias, Dr. Ismael Cosío Villegas, Mexico City, Mexico
- Cancer Center, Medical Center American British Cowdray, Mexico City, Mexico
- Cancer Research Networking, Universidad Cientifica del Sur, Lima, Perú
| | - Gisela Sánchez Domínguez
- Department of Thoracic Oncology, Instituto Nacional de Enfermedades Respiratorias, Dr. Ismael Cosío Villegas, Mexico City, Mexico
| | - Juan J. Juárez-Vignon Whaley
- Centro de Investigación en Ciencias de la Salud (CICSA), FCS, Universidad Anáhuac México Campus Norte, Mexico City, Mexico
| | | | | | - Jordi Guzmán Casta
- Department of Thoracic Oncology, Instituto Nacional de Enfermedades Respiratorias, Dr. Ismael Cosío Villegas, Mexico City, Mexico
| | - Rodrigo F. Riera Sala
- Department of Thoracic Oncology, Instituto Nacional de Enfermedades Respiratorias, Dr. Ismael Cosío Villegas, Mexico City, Mexico
| | - Jorge A. Alatorre-Alexander
- Department of Thoracic Oncology, Instituto Nacional de Enfermedades Respiratorias, Dr. Ismael Cosío Villegas, Mexico City, Mexico
| | | | | | | | | | - Carla P. Sánchez-Ríos
- Department of Thoracic Oncology, Instituto Nacional de Enfermedades Respiratorias, Dr. Ismael Cosío Villegas, Mexico City, Mexico
| | - Luis M. Martínez-Barrera
- Department of Thoracic Oncology, Instituto Nacional de Enfermedades Respiratorias, Dr. Ismael Cosío Villegas, Mexico City, Mexico
| | | | - Patricio Santillán-Doherty
- Department of Thoracic Oncology, Instituto Nacional de Enfermedades Respiratorias, Dr. Ismael Cosío Villegas, Mexico City, Mexico
- Medical Direction, Instituto Nacional de Enfermedades Respiratorias, Dr. Ismael Cosío Villegas, Mexico City, Mexico
| | | | - William López Hernández
- Department of Thoracic Oncology, Instituto Nacional de Enfermedades Respiratorias, Dr. Ismael Cosío Villegas, Mexico City, Mexico
| | - Jerónimo R. Rodríguez-Cid
- Department of Thoracic Oncology, Instituto Nacional de Enfermedades Respiratorias, Dr. Ismael Cosío Villegas, Mexico City, Mexico
- Oncology Center, Medica Sur Hospital, Mexico City, Mexico
| |
Collapse
|
41
|
Greene MP, Vassy JL. Helping patients understand multi-cancer early detection tests: a scoping review. Per Med 2024; 21:131-137. [PMID: 38269535 DOI: 10.2217/pme-2023-0090] [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: 08/08/2023] [Accepted: 01/12/2024] [Indexed: 01/26/2024]
Abstract
Multi-cancer early detection tests are emerging as a revolutionary technology for the early detection of dozens of cancers from a single blood sample, including cancers without proven screening methods. However, they also come with challenges, including false-positive and false-negative results. To help patients make informed decisions, patient education materials are crucial. A review of available materials reveals that, while some materials provide understandable and actionable information, most lack a balanced presentation of the current benefits and risks of multi-cancer early detection testing. The dynamic nature of this field necessitates continuous updates to educational materials, incorporating current evidence and uncertainties.
Collapse
Affiliation(s)
| | - Jason L Vassy
- Harvard Medical School, Boston, 02115 MA, USA
- Veterans Affairs Boston Healthcare System, Boston, 02130 MA, USA
- Brigham and Women's Hospital, Boston, 02115 MA, USA
- Precision Population Health, Ariadne Labs, Boston, 02215 MA, USA
| |
Collapse
|
42
|
Yang L, Gu X, Liu J, Wu L, Qin Y. Functionalized nanomaterials-based electrochemiluminescent biosensors and their application in cancer biomarkers detection. Talanta 2024; 267:125237. [PMID: 37757698 DOI: 10.1016/j.talanta.2023.125237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023]
Abstract
To detect a range of trace biomarkers associated with human diseases, researchers have been focusing on developing biosensors that possess high sensitivity and specificity. Electrochemiluminescence (ECL) biosensors have emerged as a prominent research tool in recent years, owing to their potential superiority in low background signal, high sensitivity, straightforward instrumentation, and ease of operation. Functional nanomaterials (FNMs) exhibit distinct advantages in optimizing electrical conductivity, increasing reaction rate, and expanding specific surface area due to their small size effect, quantum size effect, and surface and interface effects, which can significantly improve the stability, reproducibility, and sensitivity of the biosensors. Thereby, various nanomaterials (NMs) with excellent properties have been developed to construct efficient ECL biosensors. This review provides a detailed summary and discussion of FNMs-based ECL biosensors and their applications in cancer biomarkers detection.
Collapse
Affiliation(s)
- Luxia Yang
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China
| | - Xijuan Gu
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China
| | - Jinxia Liu
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China.
| | - Li Wu
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China.
| | - Yuling Qin
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China.
| |
Collapse
|
43
|
Ma Y, Chu Y, Xu Z, Xie C, Ma X, Zhang L, Hu J, Zou B, Wu H, Zhou G. Ultrafast and Highly Specific Detection of One-Base Mutated Cell-Free DNA at a Very Low Abundance. Anal Chem 2024; 96:117-126. [PMID: 38114445 DOI: 10.1021/acs.analchem.3c03326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Liquid biopsy as well as genotyping plays important roles in guiding the use of tumor-targeted drugs and monitoring the generation of drug resistance. However, current methods, such as next-generation sequencing (NGS) and pyrosequencing, require long analysis time and complicated steps. To achieve ultrafast and highly specific detection of cell-free DNA (cfDNA) from blood, we improved our recently developed FEN1-aided RPA (FARPA), which combined flap endonuclease 1 (FEN1)-catalyzed invasive reactions with recombinase polymerase amplification (RPA) by inactivating the RPA enzymes before invasive reactions, designing short RPA primers, and changing invasive reaction conditions. Using the L858R and T790M mutations as examples, FARPA was sensitive to detect 5 copies of targeted mutants, specific to sense the mutants with an abundance as low as 0.01% from blood, and ultrafast to get results within 40 min. The method was readily expended to genotyping, and 15 min was enough to report the allele species directly from oral swab samples by coupling quick DNA extraction reagents. Validation was carried out by detecting clinical samples, including 20 cfDNA from patients with non-small cell lung cancer (NSCLC) for liquid biopsy and 43 human genomic DNA (gDNA) purified from blood (33) or lysed from oral swabs (10) for genotyping, giving 100% agreement with NGS and pyrosequencing, respectively. Furthermore, a portable battery-driven device with dual-channel fluorescence detection was successfully constructed to facilitate point-of-care testing (POCT) of liquid biopsy and genotyping, providing doctors with a potential tool to achieve genotyping- or mutant-guided personalized medicine at emergency or source-limited regions.
Collapse
Affiliation(s)
- Yi Ma
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210002, China
| | - Yanan Chu
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210002, China
| | - Zhaoluo Xu
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210002, China
| | - Chunmei Xie
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210002, China
| | - Xueping Ma
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210002, China
| | - Likun Zhang
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210002, China
| | - Jingjing Hu
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210002, China
| | - Bingjie Zou
- Key Laboratory of Drug Quality Control and Pharmacovigilance of Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Haiping Wu
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210002, China
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Guohua Zhou
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210002, China
| |
Collapse
|
44
|
Derbal Y. Adaptive Cancer Therapy in the Age of Generative Artificial Intelligence. Cancer Control 2024; 31:10732748241264704. [PMID: 38897721 PMCID: PMC11189021 DOI: 10.1177/10732748241264704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/17/2024] [Accepted: 06/06/2024] [Indexed: 06/21/2024] Open
Abstract
Therapeutic resistance is a major challenge facing the design of effective cancer treatments. Adaptive cancer therapy is in principle the most viable approach to manage cancer's adaptive dynamics through drug combinations with dose timing and modulation. However, there are numerous open issues facing the clinical success of adaptive therapy. Chief among these issues is the feasibility of real-time predictions of treatment response which represent a bedrock requirement of adaptive therapy. Generative artificial intelligence has the potential to learn prediction models of treatment response from clinical, molecular, and radiomics data about patients and their treatments. The article explores this potential through a proposed integration model of Generative Pre-Trained Transformers (GPTs) in a closed loop with adaptive treatments to predict the trajectories of disease progression. The conceptual model and the challenges facing its realization are discussed in the broader context of artificial intelligence integration in oncology.
Collapse
Affiliation(s)
- Youcef Derbal
- Ted Rogers School of Information Technology Management, Toronto Metropolitan University, Toronto, ON, Canada
| |
Collapse
|
45
|
Heidrich I, Roeper CMT, Rautmann C, Pantel K, Smit DJ. [Liquid Biopsy - A new diagnostic concept in oncology]. Laryngorhinootologie 2024; 103:40-46. [PMID: 37748502 DOI: 10.1055/a-2144-4262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
The analysis of tumor cells circulating in the blood or of products of tumor cells circulating in other body fluids has gained increasing attention in recent years and is summarized under the term liquid biopsy (LB). LB includes the analysis of circulating tumor cells, cell-free circulating tumor-associated nucleic acids, extracellular vesicles, proteins, or other products that are released into the peripheral bloodstream by the primary or metastatic tumor. For a huge number of solid tumor entities, LB has already been successfully applied in preclinical and clinical studies for the detection, risk stratification, treatment monitoring and relapse detection. LB provides valuable real-time information on tumor cell development, therapeutic targets, and mechanisms of therapy resistance using a non-invasive peripheral blood test. In this article, the most important LB analytes and the current state of research are presented. In addition, the remaining obstacles and the diverse efforts to implement LB in clinical routine are critically discussed.
Collapse
Affiliation(s)
- Isabel Heidrich
- Klinik und Poliklinik für Dermatologie und Venerologie, Fleur Hiege-Centrum für Hautkrebsforschung, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Deutschland
- Institut für Tumorbiologie, Fleur Hiege-Centrum für Hautkrebsforschung, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Deutschland
- Mildred-Scheel-Nachwuchszentrum, Universitäres Cancer Center Hamburg, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Deutschland
| | - Carmen M T Roeper
- Klinik und Poliklinik für Dermatologie und Venerologie, Fleur Hiege-Centrum für Hautkrebsforschung, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Deutschland
| | - Charlotte Rautmann
- Klinik und Poliklinik für Dermatologie und Venerologie, Fleur Hiege-Centrum für Hautkrebsforschung, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Deutschland
| | - Klaus Pantel
- Institut für Tumorbiologie, Fleur Hiege-Centrum für Hautkrebsforschung, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Deutschland
| | - Daniel J Smit
- Institut für Tumorbiologie, Fleur Hiege-Centrum für Hautkrebsforschung, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Deutschland
| |
Collapse
|
46
|
Robinson SD, de Boisanger J, Pearl FMG, Critchley G, Rosenfelder N, Giamas G. A brain metastasis liquid biopsy: Where are we now? Neurooncol Adv 2024; 6:vdae066. [PMID: 38770219 PMCID: PMC11102938 DOI: 10.1093/noajnl/vdae066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024] Open
Abstract
Brain metastases remain a challenging and feared complication for patients with cancer and research in this area has lagged behind research into metastases to other organs. Due to their location and the risks associated with neurosurgical biopsies, the biology underpinning brain metastases response to treatment and evolution over time remains poorly understood. Liquid biopsies are proposed to overcome many of the limitations present with tissue biopsies, providing a better representation of tumor heterogeneity, facilitating repeated sampling, and providing a noninvasive assessment of tumor biology. Several different liquid biopsy approaches have been investigated including circulating tumor cells, circulating tumor DNA, extracellular vesicles, and tumor-educated platelets; however, these have generally been less effective in assessing brain metastases compared to metastases to other organs requiring improved techniques to investigate these approaches, studies combining different liquid biopsy approaches and/or novel liquid biopsy approaches. Through this review, we highlight the current state of the art and define key unanswered questions related to brain metastases liquid biopsies.
Collapse
Affiliation(s)
- Stephen David Robinson
- Sussex Cancer Centre, University Hospitals Sussex NHS Foundation Trust, Brighton, UK
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - James de Boisanger
- Neuro-Oncology Unit, The Royal Marsden Hospital NHS Foundation Trust, London, UK
| | - Frances M G Pearl
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Giles Critchley
- Department of Neurosurgery, University Hospitals Sussex NHS Foundation Trust, Brighton, UK
- Section of Neurosurgery, Department of Surgical Sciences, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Nicola Rosenfelder
- Neuro-Oncology Unit, The Royal Marsden Hospital NHS Foundation Trust, London, UK
| | - Georgios Giamas
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| |
Collapse
|
47
|
Xiang Z, Xie Q, Yu Z. Exosomal DNA: Role in Reflecting Tumor Genetic Heterogeneity, Diagnosis, and Disease Monitoring. Cancers (Basel) 2023; 16:57. [PMID: 38201485 PMCID: PMC10778000 DOI: 10.3390/cancers16010057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 12/17/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Extracellular vesicles (EVs), with exosomes at the forefront, are key in transferring cellular information and assorted biological materials, including nucleic acids. While exosomal RNA has been thoroughly examined, exploration into exosomal DNA (exoDNA)-which is stable and promising for cancer diagnostics-lags behind. This hybrid genetic material, combining contributions from both nuclear and mitochondrial DNA (mtDNA), is rooted in the cytoplasm. The enigmatic process concerning its cytoplasmic encapsulation continues to captivate researchers. Covering the entire genetic landscape, exoDNA encases significant oncogenic alterations in genes like TP53, ALK, and IDH1, which is vital for clinical assessment. This review delves into exosomal origins, the ins and outs of DNA encapsulation, and exoDNA's link to tumor biology, underscoring its superiority to circulating tumor DNA in the biomarker arena for both detection and therapy. Amidst scientific progress, there are complexities in the comprehension and practical application of the exoDNA surface. Reflecting on these nuances, we chart the prospective research terrain and potential pitfalls, forging a path for future inquiry. By illuminating both the known and unknown facets of exoDNA, the objective of this review is to provide guidance to the field of liquid biopsy (LB) while minimizing the occurrence of avoidable blind spots and detours.
Collapse
Affiliation(s)
- Ziyi Xiang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China;
| | - Qihui Xie
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China;
| | - Zili Yu
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China;
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Wuhan University, Wuhan 430079, China
| |
Collapse
|
48
|
Qi J, Qi Q, Zhou Z, Wu Y, Cai A, Wu J, Chen B, Wang Q, Chen L, Wang F. PER-CRISPR/Cas14a system-based electrochemical biosensor for the detection of ctDNA EGFR L858R. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 16:51-61. [PMID: 38058174 DOI: 10.1039/d3ay01615c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
The detection of epidermal growth factor receptor (EGFR) mutation L858R in circulating tumor DNA (ctDNA) is beneficial for the clinical diagnosis and personalized therapy of non-small cell lung cancer (NSCLC). Herein, for the first time, the combination of the primer exchange reaction (PER) and clustered regularly interspaced short palindromic repeats (CRISPR) and its associated nucleases (Cas) 14a was used in electrochemical biosensor construction for the detection of ctDNA EGFR L858R. EGFR L858R, as the target, induced the isothermal amplification of the PER reaction, and then the CRISPR/Cas14a system was activated; subsequently, the substrate ssDNA-MB was cleaved and the electron on the surface of the gold electrode transferred, resulting in the fluctuation of the electrochemical redox signal on the electrode surface, whereas the electrochemical signal will be stable when EGFR L858R is absent. Therefore, the concentration of EGFR L858R can be quantified by electrochemical signal analysis. The low detection limit is 0.34 fM and the dynamic detection range is from 1 fM to 1 μM in this work. The PER-CRISPR/Cas14a electrochemical biosensor greatly improved the analytical sensitivity. In addition, this platform also exhibited excellent specificity, reproducibility, stability and good recovery. This study provides an efficient and novel strategy for the detection of ctDNA EGFR L858R, which has great potential for application in the diagnosis and treatment of NSCLC.
Collapse
Affiliation(s)
- Jing Qi
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China.
| | - Qianyi Qi
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China.
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| | - Zhou Zhou
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China.
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| | - Yixuan Wu
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China.
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| | - Aiting Cai
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China.
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| | - Jinran Wu
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China.
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| | - Bairong Chen
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China.
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| | - Qingxiang Wang
- College of Chemistry and Environment, Minnan Normal University, Zhangzhou 363000, China
- Nantong Institute of Liver Diseases, Nantong Third People's Hospital Affiliated Nantong Hospital 3 of Nantong University, Nantong 226006, China.
| | - Lin Chen
- Nantong Institute of Liver Diseases, Nantong Third People's Hospital Affiliated Nantong Hospital 3 of Nantong University, Nantong 226006, China.
| | - Feng Wang
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China.
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| |
Collapse
|
49
|
Lu D, Wu X, Wu W, Wu S, Li H, Zhang Y, Yan X, Zhai J, Dong X, Feng S, Zhang X, Sun F, Wang S, Cai K. Plasma cell-free DNA 5-hydroxymethylcytosine and whole-genome sequencing signatures for early detection of esophageal cancer. Cell Death Dis 2023; 14:843. [PMID: 38114477 PMCID: PMC10730877 DOI: 10.1038/s41419-023-06329-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 11/05/2023] [Accepted: 11/23/2023] [Indexed: 12/21/2023]
Abstract
Esophageal cancer is a highly incidence and deadly disease with a poor prognosis, especially in developing countries. Owing to the lack of specific symptoms and early diagnostic biomarkers, most patients are diagnosed with advanced disease, leading to a 5-year survival rate of less than 15%. Early (n = 50) and middle-advanced (n = 50) esophageal squamous cell carcinoma (ESCC) patients, as well as 71 healthy individuals, underwent 5-hydroxymethylcytosine (5hmC) sequencing on their plasma cell-free DNA (cfDNA). A Northern Chinese cohort of cfDNA 5hmC dataset of 150 ESCC patients and 183 healthy individuals were downloaded for validation. A diagnostic model was developed using cfDNA 5hmC signatures and then improved by low-pass whole genome sequencing (WGS) features of cfDNA. Conserved cfDNA 5hmC modification motifs were observed in the two independent ESCC cohorts. The diagnostic model with 5hmC features achieved an AUC of 0.810 and 0.862 in the Southern and Northern cohorts, respectively, with sensitivities of 69.3-74.3% and specificities of 82.4-90.7%. The performance was well maintained in Stage I to Stage IV, with accuracy of 70-100%, but low in Stage 0, 33.3%. Low-pass WGS of cfDNA improved the AUC to 0.934 with a sensitivity of 82.4%, a specificity of 88.2%, and an accuracy of 84.3%, particularly significantly in Stage 0, with an accuracy up to 80%. 5hmC and WGS could efficiently differentiate very early ESCC from healthy individuals. These findings imply a non-invasive and convenient method for ESCC detection when clinical treatments are available and may eventually prolong survival.
Collapse
Affiliation(s)
- Di Lu
- Department of Thoracic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Xuanzhen Wu
- Department of Thoracic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Wendy Wu
- Berry Oncology Corporation, Beijing, 100102, China
| | - Shuangxiu Wu
- Berry Oncology Corporation, Beijing, 100102, China
| | - Hui Li
- Berry Oncology Corporation, Beijing, 100102, China
| | - Yuhong Zhang
- Berry Oncology Corporation, Beijing, 100102, China
| | - Xuebin Yan
- Department of Thoracic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Jianxue Zhai
- Department of Thoracic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Xiaoying Dong
- Department of Thoracic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Siyang Feng
- Department of Thoracic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | | | - Fuming Sun
- Berry Oncology Corporation, Beijing, 100102, China
| | - Shaobo Wang
- Berry Oncology Corporation, Beijing, 100102, China
| | - Kaican Cai
- Department of Thoracic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| |
Collapse
|
50
|
Zavarykina TM, Lomskova PK, Pronina IV, Khokhlova SV, Stenina MB, Sukhikh GT. Circulating Tumor DNA Is a Variant of Liquid Biopsy with Predictive and Prognostic Clinical Value in Breast Cancer Patients. Int J Mol Sci 2023; 24:17073. [PMID: 38069396 PMCID: PMC10706922 DOI: 10.3390/ijms242317073] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
This paper introduces the reader to the field of liquid biopsies and cell-free nucleic acids, focusing on circulating tumor DNA (ctDNA) in breast cancer (BC). BC is the most common type of cancer in women, and progress with regard to treatment has been made in recent years. Despite this, there remain a number of unresolved issues in the treatment of BC; in particular, early detection and diagnosis, reliable markers of response to treatment and for the prediction of recurrence and metastasis, especially for unfavorable subtypes, are needed. It is also important to identify biomarkers for the assessment of drug resistance and for disease monitoring. Our work is devoted to ctDNA, which may be such a marker. Here, we describe its main characteristics and potential applications in clinical oncology. This review considers the results of studies devoted to the analysis of the prognostic and predictive roles of various methods for the determination of ctDNA in BC patients. Currently known epigenetic changes in ctDNA with clinical significance are reviewed. The possibility of using ctDNA as a predictive and prognostic marker for monitoring BC and predicting the recurrence and metastasis of cancer is also discussed, which may become an important part of a precision approach to the treatment of BC.
Collapse
Affiliation(s)
- Tatiana M. Zavarykina
- N.M. Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Moscow 119334, Russia;
- “B.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology of Ministry of Health of the Russian Federation, Moscow 117997, Russia; (S.V.K.); (G.T.S.)
| | - Polina K. Lomskova
- N.M. Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Moscow 119334, Russia;
| | - Irina V. Pronina
- Institute of General Pathology and Pathophysiology, Moscow 125315, Russia;
| | - Svetlana V. Khokhlova
- “B.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology of Ministry of Health of the Russian Federation, Moscow 117997, Russia; (S.V.K.); (G.T.S.)
| | - Marina B. Stenina
- “N.N. Blokhin National Medical Research Center of Oncology of Ministry of Health of the Russian Federation, Moscow 115522, Russia;
| | - Gennady T. Sukhikh
- “B.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology of Ministry of Health of the Russian Federation, Moscow 117997, Russia; (S.V.K.); (G.T.S.)
| |
Collapse
|