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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; 62:2111-2127. [PMID: 38443752 DOI: 10.1515/cclm-2023-1327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [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.
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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
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Kumar S, Poria R, Kala D, Nagraik R, Dhir Y, Dhir S, Singh B, Kaushik NK, Noorani MS, Kumar D, Gupta S, Kaushal A. Recent advances in ctDNA detection using electrochemical biosensor for cancer. Discov Oncol 2024; 15:517. [PMID: 39356360 PMCID: PMC11448507 DOI: 10.1007/s12672-024-01365-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 09/18/2024] [Indexed: 10/03/2024] Open
Abstract
In the quest for early cancer diagnosis, early identification and treatment are paramount. Recently, ctDNA detection has emerged as a viable avenue for early screening of cancer. The examination of ctDNA in fluid biopsies has gained substantial attention in tumor diagnosis and therapy. Both the scientific community and industry are actively exploring this field. However, developing cost-effective, portable, and real-time ctDNA measurement methods using conventional gene detection equipment poses a significant challenge. This challenge has led to the exploration of alternative approaches. Electrochemical biosensors, distinguished by their heightened sensitivity, remarkable specificity, affordability, and excellent portability, have emerged as a promising avenue for ctDNA detection. This review is dedicated to the specific focus on ctDNA detection, highlighting recent advancements in this evolving detection technology. We aimed to reference previous studies related to ctDNA-targeted cancer detection using electrochemical biosensors to advocate the utilization of electrochemical biosensors in healthcare diagnostics. Further research is imperative for the effective integration of ctDNA analysis into point-of-care cancer testing. Innovative approaches utilizing multiple markers need to be explored to advance this technology and make substantial contributions to societal well-being.
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Affiliation(s)
- Sahil Kumar
- Department of Bio-Sciences and Technology, Maharishi Markandeshwar (Deemed to Be) University, Mullana, 133203, Ambala, India
| | - Renu Poria
- Department of Bio-Sciences and Technology, Maharishi Markandeshwar (Deemed to Be) University, Mullana, 133203, Ambala, India
| | - Deepak Kala
- NL-11 Centera Tetrahertz Laboratory, Institute of High Pressure Physics, Polish Academy of Sciences, 29/37 Sokolowska Street, Warsaw, 01142, Poland
| | - Rupak Nagraik
- School of Bioengineering and Food Technology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, India
| | - Yashika Dhir
- Department of Bio-Sciences and Technology, Maharishi Markandeshwar (Deemed to Be) University, Mullana, 133203, Ambala, India
| | - Sunny Dhir
- Department of Bio-Sciences and Technology, Maharishi Markandeshwar (Deemed to Be) University, Mullana, 133203, Ambala, India
| | - Bharat Singh
- Department of Bio-Sciences and Technology, Maharishi Markandeshwar (Deemed to Be) University, Mullana, 133203, Ambala, India
| | - Naveen Kumar Kaushik
- Department of Industrial Biotechnology, College of Biotechnology, Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, India
| | - Md Salik Noorani
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, 110062, India
| | - Deepak Kumar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Shoolini University, Solan, 173229, Himachal Pradesh, India.
| | - Shagun Gupta
- Department of Bio-Sciences and Technology, Maharishi Markandeshwar (Deemed to Be) University, Mullana, 133203, Ambala, India.
| | - Ankur Kaushal
- Department of Bio-Sciences and Technology, Maharishi Markandeshwar (Deemed to Be) University, Mullana, 133203, Ambala, India.
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Heesterbeek CJ, Tjan-Heijnen VC, Heimovaara JH, Lenaerts L, Lok C, Vriens IJ, Van Opstal D, Boon EM, Sie D, de Die-Smulders CE, Amant F, Macville MV. Prenatal cell-free DNA testing of women with pregnancy-associated cancer: a retrospective cross-sectional study. THE LANCET REGIONAL HEALTH. EUROPE 2024; 45:101024. [PMID: 39220433 PMCID: PMC11363838 DOI: 10.1016/j.lanepe.2024.101024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 07/14/2024] [Accepted: 07/23/2024] [Indexed: 09/04/2024]
Abstract
Background Incidentally, the non-invasive prenatal test (NIPT) shows chromosomal aberrations suspicious of a maternal malignancy, especially after genome-wide testing. The aim of this study is to determine how many cases of cancer in pregnancy are diagnosed or missed with NIPT and whether in retrospect subtle changes in NIPT results could have detected cancer. Methods We identified Dutch patients diagnosed in 2017-2021 with pregnancy-associated cancer from the International Network on Cancer, Infertility and Pregnancy (INCIP) Registry, who underwent NIPT in the Dutch NIPT implementation study (TRIDENT-2). We retrospectively assessed how many of these women showed a malignancy suspicious-NIPT, their tumour types and -stages, and the time interval between NIPT and cancer diagnosis. Findings Of 143 women with pregnancy-associated cancer, we included 65 patients that underwent an NIPT. Fifty-four women had a solid tumour and 11 a haematological malignancy. Sixteen (24.6%) NIPTs were malignancy suspicious (15 genome-wide, one targeted). All 10 haematological cancer patients with genome-wide NIPT had a malignancy suspicious-NIPT, irrespective of the disease stage. Only five patients with a solid tumour had a genome-wide malignancy suspicious-NIPT (4/5 advanced cancer stage III or IV). The mean time between date of NIPT and cancer diagnosis was significantly shorter after a malignancy suspicious-NIPT compared to a non-suspicious-NIPT, respectively 49.9 days (± SD 31.8) and 100.7 days (± SD 74.9), p = 0.001. Interpretation All genome-wide NIPT in women with pregnancy-associated haematological malignancies were malignancy suspicious. Women with a solid tumour showed a malignancy suspicious-NIPT in only a minority of cases, mainly the advanced stages. Funding None.
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Affiliation(s)
- Catharina J. Heesterbeek
- Department of Medical Oncology, GROW School for Oncology and Reproduction, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Vivianne C.G. Tjan-Heijnen
- Department of Medical Oncology, GROW School for Oncology and Reproduction, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Joosje H. Heimovaara
- Department of Gynaecology, Antoni van Leeuwenhoek-Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Oncology, Catholic University Leuven, Leuven, Belgium
| | | | - Christianne Lok
- Department of Gynaecologic Oncology, Centre of Gynaecologic Oncology Amsterdam, Amsterdam, the Netherlands
| | - Ingeborg J.H. Vriens
- Department of Medical Oncology, GROW School for Oncology and Reproduction, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Diane Van Opstal
- Department of Clinical Genetics, Erasmus MC University Medical Centre, Rotterdam, the Netherlands
| | - Elles M.J. Boon
- Department of Human Genetics, VU University Medical Centre Amsterdam, Amsterdam University Medical Centres, Amsterdam, the Netherlands
| | - Daoud Sie
- Department of Human Genetics, VU University Medical Centre Amsterdam, Amsterdam University Medical Centres, Amsterdam, the Netherlands
| | | | - Frédéric Amant
- Department of Gynaecologic Oncology, Catholic University Leuven, Leuven, Belgium
- Department of Gynaecologic Oncology, Antoni van Leeuwenhoek-The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Merryn V.E. Macville
- Department of Clinical Genetics, GROW School for Oncology and Reproduction, Maastricht University Medical Centre, Maastricht, the Netherlands
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Rubio-Alarcón C, Stelloo E, Vessies DCL, Erve IV, Mekkes NJ, Swennenhuis J, Lakbir S, van Bree EJ, Tijssen M, Diemen PDV, Lanfermeijer M, Linders T, van den Broek D, Punt CJA, Heringa J, Meijer GA, Abeln S, Feitsma H, Fijneman RJA. High Prevalence of Chromosomal Rearrangements and LINE Retrotranspositions Detected in Formalin-Fixed, Paraffin-Embedded Colorectal Cancer Tissue. J Mol Diagn 2024:S1525-1578(24)00206-X. [PMID: 39332629 DOI: 10.1016/j.jmoldx.2024.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 07/04/2024] [Accepted: 08/23/2024] [Indexed: 09/29/2024] Open
Abstract
Structural variants (SVs) caused by chromosomal rearrangements in common fragile sites or long interspersed nuclear element (LINE) retrotranspositions are highly prevalent in colorectal cancer. However, methodology for the targeted detection of these SVs is lacking. This article reports the use of formalin-fixed paraffin-embedded targeted-locus capture (FFPE-TLC) sequencing as a novel technology for the targeted detection of tumor-specific SVs. Analysis of 29 FFPE colorectal tumor samples and 8 matched normal samples revealed tumor-specific SVs in 24 patients (83%), with a median of 2 SVs per patient (range, 1 to 21). A total of 104 SVs were found in the common fragile site-associated genes MACROD2, PRKN, FHIT, and WWOX in 18 patients (62%), and 39 SVs caused by three LINE transposable elements were found in 15 patients (52%). Tumor specificity of SVs was independently verified by Droplet Digital PCR of tumor tissue DNA, and their applicability as plasma circulating tumor DNA biomarkers was demonstrated. It was concluded that FFPE-TLC sequencing enables the detection of tumor-specific SVs caused by chromosomal rearrangements and LINE retrotranspositions in FFPE tissue. Therefore, FFPE-TLC sequencing facilitates the investigation of the biological and clinical effects of SVs using FFPE material from (retrospective) cohorts of cancer patients and has potential clinical applicability in the detection of SV biomarkers in the routine molecular diagnostics setting.
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Affiliation(s)
- Carmen Rubio-Alarcón
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ellen Stelloo
- Cergentis B.V., a Solvias company, Utrecht, The Netherlands
| | - Daan C L Vessies
- Department of Laboratory Medicine, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Iris Van't Erve
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Nienke J Mekkes
- Bioinformatics Group, Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | | | - Soufyan Lakbir
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands; Bioinformatics Group, Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Elisabeth J van Bree
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marianne Tijssen
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Pien Delis-van Diemen
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Mirthe Lanfermeijer
- Department of Laboratory Medicine, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Theodora Linders
- Department of Laboratory Medicine, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daan van den Broek
- Department of Laboratory Medicine, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Cornelis J A Punt
- Department of Epidemiology, Julius Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jaap Heringa
- Bioinformatics Group, Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Gerrit A Meijer
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Sanne Abeln
- Bioinformatics Group, Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands; AI Technology for Life Group, Department of Information and Computing Sciences, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Harma Feitsma
- Cergentis B.V., a Solvias company, Utrecht, The Netherlands
| | - Remond J A Fijneman
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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Puvvula PK, Johnson A, Bernal-Mizrachi L. Unveiling retrotransposon-derived DNA zip code for myeloma cell internalization. Oncoscience 2024; 11:58-64. [PMID: 39015604 PMCID: PMC11251427 DOI: 10.18632/oncoscience.606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Indexed: 07/18/2024] Open
Affiliation(s)
| | - Anthony Johnson
- Kodikaz Therapeutic Solutions, (INC), New York, NY 10014, USA
| | - Leon Bernal-Mizrachi
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
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Ikliptikawati DK, Makiyama K, Hazawa M, Wong RW. Unlocking the Gateway: The Spatio-Temporal Dynamics of the p53 Family Driven by the Nuclear Pores and Its Implication for the Therapeutic Approach in Cancer. Int J Mol Sci 2024; 25:7465. [PMID: 39000572 PMCID: PMC11242911 DOI: 10.3390/ijms25137465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 07/03/2024] [Accepted: 07/04/2024] [Indexed: 07/16/2024] Open
Abstract
The p53 family remains a captivating focus of an extensive number of current studies. Accumulating evidence indicates that p53 abnormalities rank among the most prevalent in cancer. Given the numerous existing studies, which mostly focus on the mutations, expression profiles, and functional perturbations exhibited by members of the p53 family across diverse malignancies, this review will concentrate more on less explored facets regarding p53 activation and stabilization by the nuclear pore complex (NPC) in cancer, drawing on several studies. p53 integrates a broad spectrum of signals and is subject to diverse regulatory mechanisms to enact the necessary cellular response. It is widely acknowledged that each stage of p53 regulation, from synthesis to degradation, significantly influences its functionality in executing specific tasks. Over recent decades, a large body of data has established that mechanisms of regulation, closely linked with protein activation and stabilization, involve intricate interactions with various cellular components. These often transcend canonical regulatory pathways. This new knowledge has expanded from the regulation of genes themselves to epigenomics and proteomics, whereby interaction partners increase in number and complexity compared with earlier paradigms. Specifically, studies have recently shown the involvement of the NPC protein in such complex interactions, underscoring the further complexity of p53 regulation. Furthermore, we also discuss therapeutic strategies based on recent developments in this field in combination with established targeted therapies.
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Affiliation(s)
- Dini Kurnia Ikliptikawati
- Cell-Bionomics Research Unit, Innovative Integrated Bio-Research Core, Institute for Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa 9201192, Japan;
| | - Kei Makiyama
- Laboratory of Molecular Cell Biology, Division of Transdisciplinary Sciences, Graduate School of Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa 9201192, Japan
| | - Masaharu Hazawa
- Cell-Bionomics Research Unit, Innovative Integrated Bio-Research Core, Institute for Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa 9201192, Japan;
- Laboratory of Molecular Cell Biology, Division of Transdisciplinary Sciences, Graduate School of Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa 9201192, Japan
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 9201192, Japan
| | - Richard W. Wong
- Cell-Bionomics Research Unit, Innovative Integrated Bio-Research Core, Institute for Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa 9201192, Japan;
- Laboratory of Molecular Cell Biology, Division of Transdisciplinary Sciences, Graduate School of Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa 9201192, Japan
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 9201192, Japan
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Gao L, Medford A, Spring L, Bar Y, Hu B, Jimenez R, Isakoff SJ, Bardia A, Peppercorn J. Searching for the "Holy Grail" of breast cancer recurrence risk: a narrative review of the hunt for a better biomarker and the promise of circulating tumor DNA (ctDNA). Breast Cancer Res Treat 2024; 205:211-226. [PMID: 38355821 DOI: 10.1007/s10549-024-07253-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 01/08/2024] [Indexed: 02/16/2024]
Abstract
BACKGROUND This paper is a narrative review of a major clinical challenge at the heart of breast cancer care: determining which patients are at risk of recurrence, which require systemic therapy, and which remain at risk in the survivorship phase of care despite initial therapy. METHODS We review the literature on prognostic and predictive biomarkers in breast cancer with a focus on detection of minimal residual disease. RESULTS While we have many tools to estimate and refine risk that are used to individualize local and systemic therapy, we know that we continue to over treat many patients and undertreat others. Many patients also experience what is, at least in hindsight, needless fear of recurrence. In this review, we frame this dilemma for the practicing breast oncologist and discuss the search for what we term the "holy grail" of breast cancer evaluation: the ideal biomarker of residual distant disease. We review the history of attempts to address this problem and the up-to-date science on biomarkers, circulating tumor cells and circulating tumor DNA (ctDNA). CONCLUSION This review suggests that the emerging promise of ctDNA may help resolve a crticical dilemma at the heart of breast cancer care, and improve prognostication, treatment selection, and outcomes for patients with breast cancer.
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Affiliation(s)
- Lucy Gao
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Arielle Medford
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Laura Spring
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Yael Bar
- Massachusetts General Hospital, Boston, MA, USA
| | - Bonnie Hu
- Massachusetts General Hospital, Boston, MA, USA
| | - Rachel Jimenez
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Steven J Isakoff
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Aditya Bardia
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Jeffrey Peppercorn
- Massachusetts General Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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O'Sullivan NJ, Temperley HC, Kyle ET, Sweeney KJ, O'Neill M, Gilham C, O'Sullivan J, O'Kane G, Mehigan B, O'Toole S, Larkin J, Gallagher D, McCormick P, Kelly ME. Assessing circulating tumour DNA (ctDNA) as a prognostic biomarker in locally advanced rectal cancer: a systematic review and meta-analysis. Int J Colorectal Dis 2024; 39:82. [PMID: 38809315 PMCID: PMC11136793 DOI: 10.1007/s00384-024-04656-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/23/2024] [Indexed: 05/30/2024]
Abstract
INTRODUCTION Circulating tumour DNA (ctDNA) has emerged as a promising biomarker in various cancer types, including locally advanced rectal cancer (LARC), offering potential insights into disease progression, treatment response and recurrence. This review aims to comprehensively evaluate the utility of ctDNA as a prognostic biomarker in LARC. METHODS PubMed, EMBASE and Web of Science were searched as part of our review. Studies investigating the utility of ctDNA in locally advanced rectal cancer (LARC) were assessed for eligibility. Quality assessment of included studies was performed using the Newcastle Ottawa Scale (NOS) risk of bias tool. Outcomes extracted included basic participant characteristics, ctDNA details and survival data. A meta-analysis was performed on eligible studies to determine pooled recurrence-free survival (RFS). RESULTS Twenty-two studies involving 1676 participants were included in our analysis. Methodological quality categorised by the Newcastle Ottawa Scale was generally satisfactory across included studies. ctDNA detected at various time intervals was generally associated with poor outcomes across included studies. Meta-analysis demonstrated a pooled hazard ratio of 8.87 (95% CI 4.91-16.03) and 15.15 (95% CI 8.21-27.95), indicating an increased risk of recurrence with ctDNA positivity in the post-neoadjuvant and post-operative periods respectively. CONCLUSION Our systematic review provides evidence supporting the prognostic utility of ctDNA in patients with LARC, particularly in identifying patients at higher risk of disease recurrence in the post-neoadjuvant and post-operative periods.
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Affiliation(s)
- Niall J O'Sullivan
- Department of Surgery, St. James's Hospital, Dublin 8, Ireland.
- School of Medicine, Trinity College Dublin, Dublin 2, Ireland.
| | - Hugo C Temperley
- Department of Surgery, St. James's Hospital, Dublin 8, Ireland
- School of Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Eimear T Kyle
- Department of Surgery, St. James's Hospital, Dublin 8, Ireland
| | - Kevin J Sweeney
- Department of Surgery, St. James's Hospital, Dublin 8, Ireland
| | - Maeve O'Neill
- Department of Surgery, St. James's Hospital, Dublin 8, Ireland
| | - Charles Gilham
- School of Medicine, Trinity College Dublin, Dublin 2, Ireland
- Department of Radiation Oncology, St. James's Hospital, Dublin 8, Ireland
| | - Jacintha O'Sullivan
- School of Medicine, Trinity College Dublin, Dublin 2, Ireland
- Trinity Translational Medicine Institute, Trinity St. James's Cancer Institute, Trinity College, St. James's Hospital, Dublin, Ireland
| | - Grainne O'Kane
- Department of Medical Oncology, St. James's Hospital, Dublin 8, Ireland
| | - Brian Mehigan
- Department of Surgery, St. James's Hospital, Dublin 8, Ireland
| | - Sharon O'Toole
- School of Medicine, Trinity College Dublin, Dublin 2, Ireland
- Trinity Translational Medicine Institute, Trinity St. James's Cancer Institute, Trinity College, St. James's Hospital, Dublin, Ireland
| | - John Larkin
- Department of Surgery, St. James's Hospital, Dublin 8, Ireland
| | - David Gallagher
- School of Medicine, Trinity College Dublin, Dublin 2, Ireland
- Department of Medical Oncology, St. James's Hospital, Dublin 8, Ireland
- Department of Genetics, St. James's Hospital, Dublin 8, Ireland
| | - Paul McCormick
- Department of Surgery, St. James's Hospital, Dublin 8, Ireland
| | - Michael E Kelly
- Department of Surgery, St. James's Hospital, Dublin 8, Ireland
- School of Medicine, Trinity College Dublin, Dublin 2, Ireland
- Trinity St. James's Cancer Institute, St. James's Hospital, Dublin 8, Ireland
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9
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Casolino R, Beer PA, Chakravarty D, Davis MB, Malapelle U, Mazzarella L, Normanno N, Pauli C, Subbiah V, Turnbull C, Westphalen CB, Biankin AV. Interpreting and integrating genomic tests results in clinical cancer care: Overview and practical guidance. CA Cancer J Clin 2024; 74:264-285. [PMID: 38174605 DOI: 10.3322/caac.21825] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/07/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024] Open
Abstract
The last decade has seen rapid progress in the use of genomic tests, including gene panels, whole-exome sequencing, and whole-genome sequencing, in research and clinical cancer care. These advances have created expansive opportunities to characterize the molecular attributes of cancer, revealing a subset of cancer-associated aberrations called driver mutations. The identification of these driver mutations can unearth vulnerabilities of cancer cells to targeted therapeutics, which has led to the development and approval of novel diagnostics and personalized interventions in various malignancies. The applications of this modern approach, often referred to as precision oncology or precision cancer medicine, are already becoming a staple in cancer care and will expand exponentially over the coming years. Although genomic tests can lead to better outcomes by informing cancer risk, prognosis, and therapeutic selection, they remain underutilized in routine cancer care. A contributing factor is a lack of understanding of their clinical utility and the difficulty of results interpretation by the broad oncology community. Practical guidelines on how to interpret and integrate genomic information in the clinical setting, addressed to clinicians without expertise in cancer genomics, are currently limited. Building upon the genomic foundations of cancer and the concept of precision oncology, the authors have developed practical guidance to aid the interpretation of genomic test results that help inform clinical decision making for patients with cancer. They also discuss the challenges that prevent the wider implementation of precision oncology.
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Affiliation(s)
- Raffaella Casolino
- Wolfson Wohl Cancer Research Center, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Philip A Beer
- Wolfson Wohl Cancer Research Center, School of Cancer Sciences, University of Glasgow, Glasgow, UK
- Hull York Medical School, York, UK
| | | | - Melissa B Davis
- Department of Surgery, Weill Cornell Medicine, New York City, New York, USA
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Luca Mazzarella
- Laboratory of Translational Oncology and Division of Gastrointestinal Medical Oncology and Neuroendocrine Tumors IEO European Institute of Oncology, IRCCS, Milan, Italy
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori, IRCCS "Fondazione G. Pascale", Naples, Italy
| | - Chantal Pauli
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Vivek Subbiah
- Sarah Cannon Research Institute, Nashville, Tennessee, USA
| | - Clare Turnbull
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- National Cancer Registration and Analysis Service, National Health Service (NHS) England, London, UK
- Cancer Genetics Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - C Benedikt Westphalen
- Department of Medicine III, Ludwig Maximilians University (LMU) Hospital Munich, Munich, Germany
- Comprehensive Cancer Center, LMU Hospital Munich, Munich, Germany
- German Cancer Consortium, LMU Hospital Munich, Munich, Germany
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Center, School of Cancer Sciences, University of Glasgow, Glasgow, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK
- South Western Sydney Clinical School, Liverpool, New South Wales, Australia
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10
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Rashid S, Sun Y, Ali Khan Saddozai U, Hayyat S, Munir MU, Akbar MU, Khawar MB, Ren Z, Ji X, Ihsan Ullah Khan M. Circulating tumor DNA and its role in detection, prognosis and therapeutics of hepatocellular carcinoma. Chin J Cancer Res 2024; 36:195-214. [PMID: 38751441 PMCID: PMC11090798 DOI: 10.21147/j.issn.1000-9604.2024.02.07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/15/2024] [Indexed: 05/18/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is considered the fifth most prevalent cancer among all types of cancers and has the third most morbidity value. It has the most frequent duplication time and a high recurrence rate. Recently, the most unique technique used is liquid biopsies, which carry many markers; the most prominent is circulating tumor DNA (ctDNA). Varied methods are used to investigate ctDNA, including various forms of polymerase chain reaction (PCR) [emulsion PCR (ePCR), digital PCR (dPCR), and bead, emulsion, amplification, magnetic (BEAMing) PCR]. Hence ctDNA is being recognized as a potential biomarker that permits early cancer detection, treatment monitoring, and predictive data on tumor burden are subjective to therapy or surgery. Numerous ctDNA biomarkers have been investigated based on their alterations such as 1) single nucleotide variations (either insertion or deletion of a nucleotide) markers including TP53, KRAS, and CCND1; 2) copy number variations which include markers such as CDK6, EFGR, MYC and BRAF; 3) DNA methylation (RASSF1A, SEPT9, KMT2C and CCNA2); 4) homozygous mutation includes ctDNA markers as CDKN2A, AXIN1; and 5) gain or loss of function of the genes, particularly for HCC. Various researchers have conducted many studies and gotten fruitful results. Still, there are some drawbacks to ctDNA namely low quantity, fragment heterogeneity, less stability, limited mutant copies and standards, and differential sensitivity. However, plenty of investigations demonstrate ctDNA's significance as a polyvalent biomarker for cancer and can be viewed as a future diagnostic, prognostic and therapeutic agent. This article overviews many conditions in genetic changes linked to the onset and development of HCC, such as dysregulated signaling pathways, somatic mutations, single-nucleotide polymorphisms, and genomic instability. Additionally, efforts are also made to develop treatments for HCC that are molecularly targeted and to unravel some of the genetic pathways that facilitate its early identification.
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Affiliation(s)
- Sana Rashid
- Institute of Molecular Biology and Biotechnology, University of Lahore, Lahore 54590, Pakistan
| | - Yingchuan Sun
- Department of Internal Oncology (Section I), Xuchang Municipal Central Hospital, Xuchang 461000, China
| | - Umair Ali Khan Saddozai
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225001, China
| | - Sikandar Hayyat
- Institute of Molecular Biology and Biotechnology, University of Lahore, Lahore 54590, Pakistan
| | - Muhammad Usman Munir
- Australian Institute for Bioengineering & Nanotechnology, the University of Queensland, Brisbane 4072, Australia
| | - Muhammad Usman Akbar
- Gomal Center of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29111, Pakistan
| | - Muhammad Babar Khawar
- Institute of Molecular Biology and Biotechnology, University of Lahore, Lahore 54590, Pakistan
- Applied Molecular Biology and Biomedicine Lab, Department of Zoology, University of Narowal, Narowal Punjab 51600, Pakistan
| | - Zhiguang Ren
- Kaifeng Municipal Key Laboratory for Infection and Biosafety, Henan International Joint Laboratory of Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
| | - Xinying Ji
- Faculty of Basic Medical Subjects, Shu-Qing Medical College of Zhengzhou, Zhengzhou 450064, China
- Department of Medicine, Huaxian County People’s Hospital, Huaxian 456400, China
| | - Malik Ihsan Ullah Khan
- Institute of Molecular Biology and Biotechnology, University of Lahore, Lahore 54590, Pakistan
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11
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Zafra J, Onieva JL, Oliver J, Garrido-Barros M, González-Hernández A, Martínez-Gálvez B, Román A, Ordóñez-Marmolejo R, Pérez-Ruiz E, Benítez JC, Mesas A, Vera A, Chicas-Sett R, Rueda-Domínguez A, Barragán I. Novel Blood Biomarkers for Response Prediction and Monitoring of Stereotactic Ablative Radiotherapy and Immunotherapy in Metastatic Oligoprogressive Lung Cancer. Int J Mol Sci 2024; 25:4533. [PMID: 38674117 PMCID: PMC11050102 DOI: 10.3390/ijms25084533] [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: 03/27/2024] [Revised: 04/12/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
Up to 80% of patients under immune checkpoint inhibitors (ICI) face resistance. In this context, stereotactic ablative radiotherapy (SABR) can induce an immune or abscopal response. However, its molecular determinants remain unknown. We present early results of a translational study assessing biomarkers of response to combined ICI and SABR (I-SABR) in liquid biopsy from oligoprogressive patients in a prospective observational multicenter study. Cohort A includes metastatic patients in oligoprogression to ICI maintaining the same ICI due to clinical benefit and who receive concomitant SABR. B is a comparative group of oligometastatic patients receiving only SABR. Blood samples are extracted at baseline (T1), after the first (T2) and last (T3) fraction, two months post-SABR (T4) and at further progression (TP). Response is evaluated by iRECIST and defined by the objective response rate (ORR)-complete and partial responses. We assess peripheral blood mononuclear cells (PBMCs), circulating cell-free DNA (cfDNA) and small RNA from extracellular vesicles. Twenty-seven patients could be analyzed (cohort A: n = 19; B: n = 8). Most were males with non-small cell lung cancer and one progressing lesion. With a median follow-up of 6 months, the last ORR was 63% (26% complete and 37% partial response). A decrease in cfDNA from T2 to T3 correlated with a good response. At T2, CD8+PD1+ and CD8+PDL1+ cells were increased in non-responders and responders, respectively. At T2, 27 microRNAs were differentially expressed. These are potential biomarkers of response to I-SABR in oligoprogressive disease.
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Affiliation(s)
- Juan Zafra
- Group of Translational Research in Cancer Immunotherapy (CIMO2), Department of Radiation Oncology, Virgen de la Victoria University Hospital, Institute of Biomedical Research in Malaga (IBIMA), 29010 Málaga, Spain;
- Faculty of Medicine, University of Malaga (UMA), 29071 Málaga, Spain; (J.L.O.); (M.G.-B.); (A.G.-H.)
| | - Juan Luis Onieva
- Faculty of Medicine, University of Malaga (UMA), 29071 Málaga, Spain; (J.L.O.); (M.G.-B.); (A.G.-H.)
- Group of Translational Research in Cancer Immunotherapy (CIMO2), Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria Hospitals, Institute of Biomedical Research in Malaga (IBIMA), 29010 Málaga, Spain; (J.O.); (B.M.-G.); (E.P.-R.); (J.C.B.)
| | - Javier Oliver
- Group of Translational Research in Cancer Immunotherapy (CIMO2), Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria Hospitals, Institute of Biomedical Research in Malaga (IBIMA), 29010 Málaga, Spain; (J.O.); (B.M.-G.); (E.P.-R.); (J.C.B.)
| | - María Garrido-Barros
- Faculty of Medicine, University of Malaga (UMA), 29071 Málaga, Spain; (J.L.O.); (M.G.-B.); (A.G.-H.)
- Group of Translational Research in Cancer Immunotherapy (CIMO2), Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria Hospitals, Institute of Biomedical Research in Malaga (IBIMA), 29010 Málaga, Spain; (J.O.); (B.M.-G.); (E.P.-R.); (J.C.B.)
| | - Andrea González-Hernández
- Faculty of Medicine, University of Malaga (UMA), 29071 Málaga, Spain; (J.L.O.); (M.G.-B.); (A.G.-H.)
- Group of Translational Research in Cancer Immunotherapy (CIMO2), Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria Hospitals, Institute of Biomedical Research in Malaga (IBIMA), 29010 Málaga, Spain; (J.O.); (B.M.-G.); (E.P.-R.); (J.C.B.)
| | - Beatriz Martínez-Gálvez
- Group of Translational Research in Cancer Immunotherapy (CIMO2), Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria Hospitals, Institute of Biomedical Research in Malaga (IBIMA), 29010 Málaga, Spain; (J.O.); (B.M.-G.); (E.P.-R.); (J.C.B.)
| | - Alicia Román
- Department of Radiation Oncology, Virgen de la Victoria University Hospital, Institute of Biomedical Research in Malaga (IBIMA), 29010 Málaga, Spain; (A.R.); (R.O.-M.)
| | - Rafael Ordóñez-Marmolejo
- Department of Radiation Oncology, Virgen de la Victoria University Hospital, Institute of Biomedical Research in Malaga (IBIMA), 29010 Málaga, Spain; (A.R.); (R.O.-M.)
| | - Elisabeth Pérez-Ruiz
- Group of Translational Research in Cancer Immunotherapy (CIMO2), Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria Hospitals, Institute of Biomedical Research in Malaga (IBIMA), 29010 Málaga, Spain; (J.O.); (B.M.-G.); (E.P.-R.); (J.C.B.)
| | - José Carlos Benítez
- Group of Translational Research in Cancer Immunotherapy (CIMO2), Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria Hospitals, Institute of Biomedical Research in Malaga (IBIMA), 29010 Málaga, Spain; (J.O.); (B.M.-G.); (E.P.-R.); (J.C.B.)
| | - Andrés Mesas
- Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria Hospitals, 29010 Málaga, Spain;
| | - Andrés Vera
- Department of Radiation Oncology, Dr Negrín University Hospital, 35010 Las Palmas de Gran Canaria, Spain;
| | - Rodolfo Chicas-Sett
- Department of Radiation Oncology, La Fe University Hospital, 46026 Valencia, Spain;
- Group of Clinical and Translational Cancer Research, Le Fe Health Research Institute, 46026 Valencia, Spain
| | - Antonio Rueda-Domínguez
- Group of Translational Research in Cancer Immunotherapy (CIMO2), Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria Hospitals, Institute of Biomedical Research in Malaga (IBIMA), 29010 Málaga, Spain; (J.O.); (B.M.-G.); (E.P.-R.); (J.C.B.)
| | - Isabel Barragán
- Group of Translational Research in Cancer Immunotherapy (CIMO2), Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria Hospitals, Institute of Biomedical Research in Malaga (IBIMA), 29010 Málaga, Spain; (J.O.); (B.M.-G.); (E.P.-R.); (J.C.B.)
- Group of Pharmacoepigenetics, Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden
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12
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Valerius AR, Webb MJ, Hammad N, Sener U, Malani R. Cerebrospinal Fluid Liquid Biopsies in the Evaluation of Adult Gliomas. Curr Oncol Rep 2024; 26:377-390. [PMID: 38488990 DOI: 10.1007/s11912-024-01517-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2024] [Indexed: 03/17/2024]
Abstract
PURPOSE OF REVIEW This review aims to discuss recent research regarding the biomolecules explored in liquid biopsies and their potential clinical uses for adult-type diffuse gliomas. RECENT FINDINGS Evaluation of tumor biomolecules via cerebrospinal fluid (CSF) is an emerging technology in neuro-oncology. Studies to date have already identified various circulating tumor DNA, extracellular vesicle, micro-messenger RNA and protein biomarkers of interest. These biomarkers show potential to assist in multiple avenues of central nervous system (CNS) tumor evaluation, including tumor differentiation and diagnosis, treatment selection, response assessment, detection of tumor progression, and prognosis. In addition, CSF liquid biopsies have the potential to better characterize tumor heterogeneity compared to conventional tissue collection and CNS imaging. Current imaging modalities are not sufficient to establish a definitive glioma diagnosis and repeated tissue sampling via conventional biopsy is risky, therefore, there is a great need to improve non-invasive and minimally invasive sampling methods. CSF liquid biopsies represent a promising, minimally invasive adjunct to current approaches which can provide diagnostic and prognostic information as well as aid in response assessment.
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Affiliation(s)
| | - Mason J Webb
- Department of Medical Oncology, Mayo Clinic, Rochester, MN, USA
| | - Nouran Hammad
- Jordan University of Science and Technology School of Medicine, Irbid, Jordan
| | - Ugur Sener
- Department of Neurology, Department of Medical Oncology, Mayo Clinic, Rochester, MN, USA
| | - Rachna Malani
- University of UT - Huntsman Cancer Institute (Department of Neurosurgery), Salt Lake City, UT, USA
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13
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Grossi I, Assoni C, Lorini L, Smussi D, Gurizzan C, Grisanti S, Paderno A, Mattavelli D, Piazza C, Pelisenco IA, De Petro G, Salvi A, Bossi P. Evaluation of DNA methylation levels of SEPT9 and SHOX2 in plasma of patients with head and neck squamous cell carcinoma using droplet digital PCR. Oncol Rep 2024; 51:52. [PMID: 38299234 PMCID: PMC10865173 DOI: 10.3892/or.2024.8711] [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: 07/14/2023] [Accepted: 12/12/2023] [Indexed: 02/02/2024] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the seventh most commonly diagnosed cancer globally. HNSCC develops from the mucosa of the oral cavity, pharynx and larynx. Methylation levels of septin 9 (SEPT9) and short stature homeobox 2 (SHOX2) genes in circulating cell‑free DNA (ccfDNA) are considered epigenetic biomarkers and have shown predictive value in preliminary reports in HNSCC. Liquid biopsy is a non‑invasive procedure that collects tumor‑derived molecules, including ccfDNA. In the present study, a droplet digital PCR (ddPCR)‑based assay was developed to detect DNA methylation levels of circulating SEPT9 and SHOX2 in the plasma of patients with HNSCC. The assay was first set up using commercial methylated and unmethylated DNA. The dynamic changes in the methylation levels of SEPT9 and SHOX2 were then quantified in 20 patients with HNSCC during follow‑up. The results highlighted: i) The ability of the ddPCR‑based assay to detect very low copies of methylated molecules; ii) the significant decrease in SEPT9 and SHOX2 methylation levels in the plasma of patients with HNSCC at the first time points of follow‑up with respect to T0; iii) a different trend of longitudinally DNA methylation variations in small groups of stratified patients. The absolute and precise quantification of SEPT9 and SHOX2 methylation levels in HNSCC may be useful for studies with translational potential.
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Affiliation(s)
- Ilaria Grossi
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, I-25123 Brescia, Italy
| | - Claudia Assoni
- Unit of Medical Oncology, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
| | - Luigi Lorini
- Unit of Medical Oncology, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
| | - Davide Smussi
- Unit of Medical Oncology, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
| | - Cristina Gurizzan
- Unit of Medical Oncology, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
| | - Salvatore Grisanti
- Unit of Medical Oncology, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
| | - Alberto Paderno
- Unit of Otorhinolaryngology-Head and Neck Surgery, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
| | - Davide Mattavelli
- Unit of Otorhinolaryngology-Head and Neck Surgery, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
| | - Cesare Piazza
- Unit of Otorhinolaryngology-Head and Neck Surgery, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
| | - Iulia Andreea Pelisenco
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, I-25123 Brescia, Italy
| | - Giuseppina De Petro
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, I-25123 Brescia, Italy
| | - Alessandro Salvi
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, I-25123 Brescia, Italy
| | - Paolo Bossi
- Unit of Medical Oncology, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
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14
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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.
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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
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Nishino K, Shih JY, Nakagawa K, Reck M, Garon EB, Carlsen M, Matsui T, Visseren-Grul C, Nadal E. RELAY, Erlotinib Plus Ramucirumab in Untreated, EGFR-Mutated, Metastatic NSCLC: Outcomes by EGFR Exon 19 Deletion Variants. JTO Clin Res Rep 2024; 5:100624. [PMID: 38304857 PMCID: PMC10832259 DOI: 10.1016/j.jtocrr.2023.100624] [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: 09/08/2023] [Revised: 12/04/2023] [Accepted: 12/15/2023] [Indexed: 02/03/2024] Open
Abstract
Introduction EGFR gene mutations are drivers of NSCLC. The RELAY double-blind, placebo (PBO)-controlled phase 3 study revealed superior progression-free survival (PFS) for ramucirumab plus erlotinib (RAM + ERL) versus PBO (PBO + ERL) in patients with untreated advanced NSCLC and an EGFR-activating mutation. This exploratory analysis evaluated potential associations between EGFR exon 19 deletion (ex19del) variants and clinical outcomes. Methods Patients (N = 449) were randomized (1:1) to RAM plus ERL or PBO plus ERL. Plasma samples were collected at baseline, on treatment, and at 30-day post-study treatment discontinuation follow-up. Baseline and treatment-emergent gene alterations were investigated by Guardant360 next-generation sequencing. Patients with a valid baseline plasma sample and ex19del were included (RAM + ERL, n = 62; PBO + ERL, n = 72). Results The most common ex19del variant was E746_A750del (67.2%); EGFR E746 deletions (E746del) occurred more frequently than L747 deletions (74.6% versus 25.4%, respectively). TP53 mutations were the most frequently co-occurring baseline gene alterations. With treatment arms combined, median PFS was 18.0 months versus 12.5 months for patients with uncommon (non-E746_A750del, n = 44) versus common (E746_A750del, n = 90) ex19del variants (hazard ratio [HR] = 1.657 [95% confidence interval or CI:1.044-2.630]). Median PFS was longer with RAM plus ERL versus PBO plus ERL for patients with the common (15.2 versus 9.9 mo; HR = 0.564 [95% CI: 0.344-0.926]) and E746del (15.4 versus 9.9 mo; HR = 0.587 [95% CI: 0.363-0.951]) variants. Treatment-emergent post-progression EGFR T790M rates were higher in the common versus uncommon and E746del versus L747 deletion subgroups. Conclusions RAM plus ERL provides benefit and improves treatment outcomes for patients with metastatic NSCLC with EGFR ex19del variants.
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Affiliation(s)
- Kazumi Nishino
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Jin-Yuan Shih
- Department of Internal Medicine, National Taiwan University Hospital, Taipei City, Taiwan
| | - Kazuhiko Nakagawa
- Department of Medical Oncology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Martin Reck
- Lung Clinic, Airway Research Center North, German Center of Lung Research, Grosshansdorf, Germany
| | - Edward B. Garon
- Department of Medicine, David Geffen School of Medicine at UCLA/TRIO-US Network, Los Angeles, California
| | | | | | | | - Ernest Nadal
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), and Preclinical and Experimental Research Group in Thoracic Tumors, Oncobell, l’Institut d’Investigació Biomèdica de Bellvitge (IDIBELL), L’Hospitalet, Barcelona, Spain
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16
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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.
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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.
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17
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Roque R, Ribeiro IP, Figueiredo-Dias M, Gourley C, Carreira IM. Current Applications and Challenges of Next-Generation Sequencing in Plasma Circulating Tumour DNA of Ovarian Cancer. BIOLOGY 2024; 13:88. [PMID: 38392306 PMCID: PMC10886635 DOI: 10.3390/biology13020088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/25/2024] [Accepted: 01/27/2024] [Indexed: 02/24/2024]
Abstract
Circulating tumour DNA (ctDNA) facilitates longitudinal study of the tumour genome, which, unlike tumour tissue biopsies, globally reflects intratumor and intermetastatis heterogeneity. Despite its costs, next-generation sequencing (NGS) has revolutionised the study of ctDNA, ensuring a more comprehensive and multimodal approach, increasing data collection, and introducing new variables that can be correlated with clinical outcomes. Current NGS strategies can comprise a tumour-informed set of genes or the entire genome and detect a tumour fraction as low as 10-5. Despite some conflicting studies, there is evidence that ctDNA levels can predict the worse outcomes of ovarian cancer (OC) in both early and advanced disease. Changes in those levels can also be informative regarding treatment efficacy and tumour recurrence, capable of outperforming CA-125, currently the only universally utilised plasma biomarker in high-grade serous OC (HGSOC). Qualitative evaluation of sequencing shows that increasing copy number alterations and gene variants during treatment may correlate with a worse prognosis in HGSOC. However, following tumour clonality and emerging variants during treatment poses a more unique opportunity to define treatment response, select patients based on their emerging resistance mechanisms, like BRCA secondary mutations, and discover potential targetable variants. Sequencing of tumour biopsies and ctDNA is not always concordant, likely as a result of clonal heterogeneity, which is better captured in the plasma samples than it is in a large number of biopsies. These incoherences may reflect tumour clonality and reveal the acquired alterations that cause treatment resistance. Cell-free DNA methylation profiles can be used to distinguish OC from healthy individuals, and NGS methylation panels have been shown to have excellent diagnostic capabilities. Also, methylation signatures showed promise in explaining treatment responses, including BRCA dysfunction. ctDNA is evolving as a promising new biomarker to track tumour evolution and clonality through the treatment of early and advanced ovarian cancer, with potential applicability in prognostic prediction and treatment selection. While its role in HGSOC paves the way to clinical applicability, its potential interest in other histological subtypes of OC remains unknown.
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Affiliation(s)
- Ricardo Roque
- Cytogenetics and Genomics Laboratory, Institute of Cellular and Molecular Biology, Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal
- Centre of Investigation on Environment Genetics and Oncobiology (CIMAGO), Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal
- Portuguese Institute of Oncology of Coimbra, 3000-075 Coimbra, Portugal
| | - Ilda Patrícia Ribeiro
- Cytogenetics and Genomics Laboratory, Institute of Cellular and Molecular Biology, Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal
- Centre of Investigation on Environment Genetics and Oncobiology (CIMAGO), Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Margarida Figueiredo-Dias
- Faculty of Medicine, Gynecology Department, University of Coimbra, 3004-504 Coimbra, Portugal
- Coimbra Academic and Clinical Centre, 3000-370 Coimbra, Portugal
- Gynecology Department, Hospital University Centre of Coimbra, 3004-561 Coimbra, Portugal
| | - Charlie Gourley
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Isabel Marques Carreira
- Cytogenetics and Genomics Laboratory, Institute of Cellular and Molecular Biology, Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal
- Centre of Investigation on Environment Genetics and Oncobiology (CIMAGO), Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal
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Stenzinger A, Vogel A, Lehmann U, Lamarca A, Hofman P, Terracciano L, Normanno N. Molecular profiling in cholangiocarcinoma: A practical guide to next-generation sequencing. Cancer Treat Rev 2024; 122:102649. [PMID: 37984132 DOI: 10.1016/j.ctrv.2023.102649] [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: 09/20/2023] [Accepted: 10/29/2023] [Indexed: 11/22/2023]
Abstract
Cholangiocarcinomas (CCA) are a heterogeneous group of tumors that are classified as intrahepatic, perihilar, or distal according to the anatomic location within the biliary tract. Each CCA subtype is associated with distinct genomic alterations, including single nucleotide variants, copy number variants, and chromosomal rearrangements or gene fusions, each of which can influence disease prognosis and/or treatment outcomes. Molecular profiling using next-generation sequencing (NGS) is a powerful technique for identifying unique gene variants carried by an individual tumor, which can facilitate their accurate diagnosis as well as promote the optimal selection of gene variant-matched targeted treatments. NGS is particularly useful in patients with CCA because between one-third and one-half of these patients have genomic alterations that can be targeted by drugs that are either approved or in clinical development. NGS can also provide information about disease evolution and secondary resistance alterations that can develop during targeted therapy, and thus facilitate assessment of prognosis and choice of alternative targeted treatments. Pathologists play a critical role in assessing the viability of biopsy samples for NGS, and advising treating clinicians whether NGS can be performed and which of the available platforms should be used to optimize testing outcomes. This review aims to provide clinical pathologists and other healthcare professionals with practical step-by-step guidance on the use of NGS for molecular profiling of patients with CCA, with respect to tumor biopsy techniques, pre-analytic sample preparation, selecting the appropriate NGS panel, and understanding and interpreting results of the NGS test.
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Affiliation(s)
- Albrecht Stenzinger
- Institute of Pathology Heidelberg (IPH), Center for Molecular Pathology, University Hospital Heidelberg, In Neuenheimer Feld 224, 69120 Heidelberg, Building 6224, Germany.
| | - Arndt Vogel
- Division of Gastroenterology and Hepatology, Toronto General Hospital Medical Oncology, Princess Margaret Cancer Centre, Schwartz Reisman Liver Research Centre, 200 Elizabeth Street, Office: 9 EB 236 Toronto, ON, M5G 2C4, Canada.
| | - Ulrich Lehmann
- Institute for Pathology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany.
| | - Angela Lamarca
- Department of Medical Oncology, Oncohealth Institute, Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Fundación Jiménez Díaz University Hospital, Av. de los Reyes Católicos, 2, 28040 Madrid, Spain; Department of Medical Oncology, The Christie NHS Foundation Trust, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, FHU OncoAge, IHU RespirERA, Siège de l'Université: Grand Château, 28 Avenue de Valrose, 06103 Nice CEDEX 2, France.
| | - Luigi Terracciano
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini, 4, 20072 Pieve Emanuele, Milan, Italy; IRCCS Humanitas Research Hospital, Via Alessandro Manzoni, 56, 20089 Rozzano, Milan, Italy.
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy.
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Bibikova M, Fan J. Liquid biopsy for early detection of lung cancer. CHINESE MEDICAL JOURNAL PULMONARY AND CRITICAL CARE MEDICINE 2023; 1:200-206. [PMID: 39171286 PMCID: PMC11332910 DOI: 10.1016/j.pccm.2023.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Indexed: 08/23/2024]
Abstract
Lung cancer is the leading cause of cancer-related mortality worldwide. Early cancer detection plays an important role in improving treatment success and patient prognosis. In the past decade, liquid biopsy became an important tool for cancer diagnosis, as well as for treatment selection and response monitoring. Liquid biopsy is a broad term that defines a non-invasive test done on a sample of blood or other body fluid to look for cancer cells or other analytes that can include DNA, RNA, or other molecules released by tumor cells. Liquid biopsies mainly include circulating tumor DNA, circulating RNA, microRNA, proteins, circulating tumor cells, exosomes, and tumor-educated platelets. This review summarizes the progress and clinical application potential of liquid biopsy for early detection of lung cancer.
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Affiliation(s)
- Marina Bibikova
- AnchorDx, Inc., 46305 Landing Parkway, Fremont, CA 94538, USA
| | - Jianbing Fan
- Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou, Guangdong 510515, China
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20
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Lindskrog SV, Birkenkamp-Demtröder K, Nordentoft I, Laliotis G, Lamy P, Christensen E, Renner D, Andreasen TG, Lange N, Sharma S, ElNaggar AC, Liu MC, Sethi H, Aleshin A, Agerbæk M, Jensen JB, Dyrskjøt L. Circulating Tumor DNA Analysis in Advanced Urothelial Carcinoma: Insights from Biological Analysis and Extended Clinical Follow-up. Clin Cancer Res 2023; 29:4797-4807. [PMID: 37782315 PMCID: PMC10690087 DOI: 10.1158/1078-0432.ccr-23-1860] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/21/2023] [Accepted: 09/28/2023] [Indexed: 10/03/2023]
Abstract
PURPOSE To investigate whether circulating tumor DNA (ctDNA) assessment in patients with muscle-invasive bladder cancer predicts treatment response and provides early detection of metastatic disease. EXPERIMENTAL DESIGN We present full follow-up results (median follow-up: 68 months) from a previously described cohort of 68 neoadjuvant chemotherapy (NAC)-treated patients who underwent longitudinal ctDNA testing (712 plasma samples). In addition, we performed ctDNA evaluation of 153 plasma samples collected before and after radical cystectomy (RC) in a separate cohort of 102 NAC-naïve patients (median follow-up: 72 months). Total RNA sequencing of tumors was performed to investigate biological characteristics of ctDNA shedding tumors. RESULTS Assessment of ctDNA after RC identified metastatic relapse with a sensitivity of 94% and specificity of 98% using the expanded follow-up data for the NAC-treated patients. ctDNA dynamics during NAC was independently associated with patient outcomes when adjusted for pathologic downstaging (HR = 4.7; P = 0.029). For the NAC-naïve patients, ctDNA was a prognostic predictor before (HR = 3.4; P = 0.0005) and after RC (HR = 17.8; P = 0.0002). No statistically significant difference in recurrence-free survival for patients without detectable ctDNA at diagnosis was observed between the cohorts. Baseline ctDNA positivity was associated with the Basal/Squamous (Ba/Sq) subtype and enrichment of epithelial-to-mesenchymal transition and cell cycle-associated gene sets. CONCLUSIONS ctDNA is prognostic in NAC-treated and NAC-naïve patients with more than 5 years follow-up and outperforms pathologic downstaging in predicting treatment efficacy. Patients without detectable ctDNA at diagnosis may benefit significantly less from NAC, but additional studies are needed.
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Affiliation(s)
- Sia V. Lindskrog
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Karin Birkenkamp-Demtröder
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Iver Nordentoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | | | - Philippe Lamy
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Emil Christensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | | | - Tine G. Andreasen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Naja Lange
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | | | | | | | | | | | - Mads Agerbæk
- Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Jørgen B. Jensen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
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21
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Li J, Wang L, Dong Z, Song Q, Wang Z. A meta-analysis of circulating tumor DNA as a survival indicator in small cell lung cancer patients. Clin Exp Med 2023; 23:3935-3945. [PMID: 37027065 DOI: 10.1007/s10238-023-01052-x] [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: 02/27/2023] [Accepted: 03/17/2023] [Indexed: 04/08/2023]
Abstract
A high level of circulating tumor DNA (ctDNA) has been linked to poor survival in patients with certain solid tumors. In spite of this, it is still unclear whether ctDNA is associated with poor survival in small cell lung cancer (SCLC). To investigate the above association, we conducted a systematic review and meta-analysis. PubMed, Web of Science, Cochrane's Library, and Embase were searched for relevant cohort studies from the inception of the databases to November 28, 2022. Data collection, literature search, and statistical analysis were carried out independently by two authors. To account for heterogeneity, we used a random-effects model. In this meta-analysis, 391 patients with SCLC were identified, and the data were pooled from nine observational studies and followed for 11.4 to 25.0 months. A high ctDNA was associated with worse overall survival (OS, risk ratio [RR] 2.50, 95% confidence interval [CI]1.85 to 3.38, p < 0.001; I2 = 25%) and progression-free survival (PFS, RR 2.33, 95% CI 1.48 to 3.64, p < 0.001, I2 = 42%). Subgroup analyses retrieved consistent results in prospective and retrospective studies, in studies with ctDNA measured with polymerase chain reaction or next-generation sequencing, and in studies analyzed with univariate or multivariate regression models. Studies suggest that ctDNA may be an important factor in predicting poor OS and PFS in SCLC patients.
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Affiliation(s)
- Jie Li
- Department of Pathology, The First Medical Center of Chinese PLA General Hospital, No. 28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Liqun Wang
- Department of Pathology, The First Medical Center of Chinese PLA General Hospital, No. 28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Zhouhuan Dong
- Department of Pathology, The First Medical Center of Chinese PLA General Hospital, No. 28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Qi Song
- Department of Oncology, The First Medical Center of Chinese PLA General Hospital, Beijing, 100853, China
| | - Zhanbo Wang
- Department of Pathology, The First Medical Center of Chinese PLA General Hospital, No. 28 Fuxing Road, Haidian District, Beijing, 100853, China.
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22
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Wang W, Zheng Z, Lei J. CTC, ctDNA, and Exosome in Thyroid Cancers: A Review. Int J Mol Sci 2023; 24:13767. [PMID: 37762070 PMCID: PMC10530859 DOI: 10.3390/ijms241813767] [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: 06/11/2023] [Revised: 08/29/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Thyroid cancer has become more common in recent years all around the world. Many issues still need to be urgently addressed in the diagnosis, treatment, and prognosis of thyroid cancer. Liquid biopsy (mainly circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), and circulating exosomes) may provide a novel and ideal approach to solve these issues, allows us to assess the features of diseases more comprehensively, and has a function in a variety of malignancies. Recently, liquid biopsy has been shown to be critical in thyroid cancer diagnosis, treatment, and prognosis in numerous previous studies. In this review, by testing CTCs, ctDNA, and exosomes, we focus on the possible clinical role of liquid biopsy in thyroid cancer, including diagnostic and prognostic biomarkers and response to therapy. We briefly review how liquid biopsy components have progressed in thyroid cancer by consulting the existing public information. We also discuss the clinical potential of liquid biopsy in thyroid cancer and provide a reference for liquid biopsy research. Liquid biopsy has the potential to be a useful tool in the early detection, monitoring, or prediction of response to therapies and prognosis in thyroid cancer, with promising clinical applications.
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Affiliation(s)
- Wenwen Wang
- Division of Thyroid Surgery, Department of General Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zhiyao Zheng
- Division of Thyroid Surgery, Department of General Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Jianyong Lei
- Division of Thyroid Surgery, Department of General Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
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23
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Luo M, Liu Y, Zhao M. Identifying the Common Cell-Free DNA Biomarkers across Seven Major Cancer Types. BIOLOGY 2023; 12:934. [PMID: 37508365 PMCID: PMC10376459 DOI: 10.3390/biology12070934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/25/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023]
Abstract
Blood-based detection of circulating cell-free DNA (cfDNA) is a non-invasive and easily accessible method for early cancer detection. Despite the extensive utility of cfDNA, there are still many challenges to developing clinical biomarkers. For example, cfDNA with genetic alterations often composes a small portion of the DNA circulating in plasma, which can be confounded by cfDNA contributed by normal cells. Therefore, filtering out the potential false-positive cfDNA mutations from healthy populations will be important for cancer-based biomarkers. Additionally, many low-frequency genetic alterations are easily overlooked in a small number of cfDNA-based cancer tests. We hypothesize that the combination of diverse types of cancer studies on cfDNA will provide us with a new perspective on the identification of low-frequency genetic variants across cancer types for promoting early diagnosis. By building a standardized computational pipeline for 1358 cfDNA samples across seven cancer types, we prioritized 129 shard genetic variants in the major cancer types. Further functional analysis of the 129 variants found that they are mainly enriched in ribosome pathways such as cotranslational protein targeting the membrane, some of which are tumour suppressors, oncogenes, and genes related to cancer initiation. In summary, our integrative analysis revealed the important roles of ribosome proteins as common biomarkers in early cancer diagnosis.
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Affiliation(s)
- Mingyu Luo
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4558, Australia
| | - Yining Liu
- The School of Public Health, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 510120, China
| | - Min Zhao
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4558, Australia
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24
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Souza VGP, Forder A, Brockley LJ, Pewarchuk ME, Telkar N, de Araújo RP, Trejo J, Benard K, Seneda AL, Minutentag IW, Erkan M, Stewart GL, Hasimoto EN, Garnis C, Lam WL, Martinez VD, Reis PP. Liquid Biopsy in Lung Cancer: Biomarkers for the Management of Recurrence and Metastasis. Int J Mol Sci 2023; 24:ijms24108894. [PMID: 37240238 DOI: 10.3390/ijms24108894] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 05/11/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Liquid biopsies have emerged as a promising tool for the detection of metastases as well as local and regional recurrence in lung cancer. Liquid biopsy tests involve analyzing a patient's blood, urine, or other body fluids for the detection of biomarkers, including circulating tumor cells or tumor-derived DNA/RNA that have been shed into the bloodstream. Studies have shown that liquid biopsies can detect lung cancer metastases with high accuracy and sensitivity, even before they are visible on imaging scans. Such tests are valuable for early intervention and personalized treatment, aiming to improve patient outcomes. Liquid biopsies are also minimally invasive compared to traditional tissue biopsies, which require the removal of a sample of the tumor for further analysis. This makes liquid biopsies a more convenient and less risky option for patients, particularly those who are not good candidates for invasive procedures due to other medical conditions. While liquid biopsies for lung cancer metastases and relapse are still being developed and validated, they hold great promise for improving the detection and treatment of this deadly disease. Herein, we summarize available and novel approaches to liquid biopsy tests for lung cancer metastases and recurrence detection and describe their applications in clinical practice.
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Affiliation(s)
- Vanessa G P Souza
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
- Molecular Oncology Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, SP 18618-687, Brazil
| | - Aisling Forder
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Liam J Brockley
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | | | - Nikita Telkar
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
- British Columbia Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
| | - Rachel Paes de Araújo
- Molecular Oncology Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, SP 18618-687, Brazil
| | - Jessica Trejo
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Katya Benard
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Ana Laura Seneda
- Molecular Oncology Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, SP 18618-687, Brazil
| | - Iael W Minutentag
- Molecular Oncology Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, SP 18618-687, Brazil
| | - Melis Erkan
- Department of Pathology and Laboratory Medicine, IWK Health Centre, Halifax, NS B3K 6R8, Canada
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS B3K 6R8, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS B3H 4R2, Canada
| | - Greg L Stewart
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Erica N Hasimoto
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University (UNESP), Botucatu, SP 18618-687, Brazil
| | - Cathie Garnis
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
- Division of Otolaryngology, Department of Surgery, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Wan L Lam
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Victor D Martinez
- Department of Pathology and Laboratory Medicine, IWK Health Centre, Halifax, NS B3K 6R8, Canada
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS B3K 6R8, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS B3H 4R2, Canada
| | - Patricia P Reis
- Molecular Oncology Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, SP 18618-687, Brazil
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University (UNESP), Botucatu, SP 18618-687, Brazil
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25
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Jha P, Lenaerts L, Vermeesch J, Norton M, Amant F, Glanc P, Poder L. Noninvasive prenatal screening and maternal malignancy: role of imaging. Abdom Radiol (NY) 2023; 48:1590-1598. [PMID: 37095202 DOI: 10.1007/s00261-023-03913-1] [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: 11/25/2022] [Revised: 01/21/2023] [Accepted: 01/23/2023] [Indexed: 04/26/2023]
Abstract
Noninvasive prenatal screening (NIPS) tests for fetal chromosomal anomalies through maternal blood sampling. It is becoming widely available and standard of care for pregnant women in many countries. It is performed in the first trimester of pregnancy, usually between 9 and 12 weeks. Fragments of fetal cell-free deoxyribonucleic acid (DNA) floating in maternal plasma are detected and analyzed by this test to assess for chromosomal aberrations. Similarly, maternal tumor-derived cell-free DNA (ctDNA) released from the tumor cells also circulates in the plasma. Hence, the presence of genomic anomalies originating from maternal tumor-derived DNA may be detected on the NIPS-based fetal risk assessment in pregnant patients. Presence of multiple aneuploidies or autosomal monosomies are the most commonly reported NIPS abnormalities detected with occult maternal malignancies. When such results are received, the search for an occult maternal malignancy begins, in which imaging plays a crucial role. The most commonly detected malignancies via NIPS are leukemia, lymphoma, breast and colon cancers. Ultrasound is a reasonable radiation-free modality for imaging during pregnancy, specially when there are localizing symptoms or findings, such as palpable lumps. While there are no consensus guidelines on the imaging evaluation for these patients, when there are no localizing symptoms or clinically palpable findings, whole body MRI is recommended as the radiation-free modality of choice to search for an occult malignancy. Based on clinical symptoms, practice patterns, and available resources, breast ultrasound, chest radiographs, and targeted ultrasound evaluations can also be performed initially or as a follow-up for MRI findings. CT is reserved for exceptional circumstances due to its higher radiation dose. This article intends to increase awareness of this rare but stressful clinical scenario and guide imaging evaluation for occult malignancy detected via NIPS during pregnancy.
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Affiliation(s)
- Priyanka Jha
- Department of Radiology, Division of Body Imaging, Stanford University School of Medicine, Palo Alto, CA, USA.
| | | | - Joris Vermeesch
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Centre of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Mary Norton
- Department of Obstetrics and Gynecology, University of California San Francisco, San Francisco, CA, USA
| | - Frédéric Amant
- Department of Oncology, KU Leuven, Leuven, Belgium
- Gynecology and Obstetrics, University Hospitals Leuven, Leuven, Belgium
- Center for Gynecological Oncology Amsterdam, Academic Medical Centre Amsterdam, University of Amsterdam, Amsterdam, The Netherlands
- The Netherlands Cancer Institute, Antoni Van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Phyllis Glanc
- Department of Radiology, Obstetrics & Gynecology, University of Toronto, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Liina Poder
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA
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Brockley LJ, Souza VGP, Forder A, Pewarchuk ME, Erkan M, Telkar N, Benard K, Trejo J, Stewart MD, Stewart GL, Reis PP, Lam WL, Martinez VD. Sequence-Based Platforms for Discovering Biomarkers in Liquid Biopsy of Non-Small-Cell Lung Cancer. Cancers (Basel) 2023; 15:2275. [PMID: 37190212 PMCID: PMC10136462 DOI: 10.3390/cancers15082275] [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: 03/07/2023] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
Lung cancer detection and monitoring are hampered by a lack of sensitive biomarkers, which results in diagnosis at late stages and difficulty in tracking response to treatment. Recent developments have established liquid biopsies as promising non-invasive methods for detecting biomarkers in lung cancer patients. With concurrent advances in high-throughput sequencing technologies and bioinformatics tools, new approaches for biomarker discovery have emerged. In this article, we survey established and emerging biomarker discovery methods using nucleic acid materials derived from bodily fluids in the context of lung cancer. We introduce nucleic acid biomarkers extracted from liquid biopsies and outline biological sources and methods of isolation. We discuss next-generation sequencing (NGS) platforms commonly used to identify novel biomarkers and describe how these have been applied to liquid biopsy. We highlight emerging biomarker discovery methods, including applications of long-read sequencing, fragmentomics, whole-genome amplification methods for single-cell analysis, and whole-genome methylation assays. Finally, we discuss advanced bioinformatics tools, describing methods for processing NGS data, as well as recently developed software tailored for liquid biopsy biomarker detection, which holds promise for early diagnosis of lung cancer.
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Affiliation(s)
- Liam J. Brockley
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.P.S.); (A.F.); (M.E.P.); (N.T.); (K.B.); (J.T.); (M.D.S.); (G.L.S.); (W.L.L.)
| | - Vanessa G. P. Souza
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.P.S.); (A.F.); (M.E.P.); (N.T.); (K.B.); (J.T.); (M.D.S.); (G.L.S.); (W.L.L.)
- Molecular Oncology Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu 18618-687, SP, Brazil;
| | - Aisling Forder
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.P.S.); (A.F.); (M.E.P.); (N.T.); (K.B.); (J.T.); (M.D.S.); (G.L.S.); (W.L.L.)
| | - Michelle E. Pewarchuk
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.P.S.); (A.F.); (M.E.P.); (N.T.); (K.B.); (J.T.); (M.D.S.); (G.L.S.); (W.L.L.)
| | - Melis Erkan
- Department of Pathology and Laboratory Medicine, IWK Health Centre, Halifax, NS B3K 6R8, Canada;
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS B3K 6R8, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS B3H 4R2, Canada
| | - Nikita Telkar
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.P.S.); (A.F.); (M.E.P.); (N.T.); (K.B.); (J.T.); (M.D.S.); (G.L.S.); (W.L.L.)
- British Columbia Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
| | - Katya Benard
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.P.S.); (A.F.); (M.E.P.); (N.T.); (K.B.); (J.T.); (M.D.S.); (G.L.S.); (W.L.L.)
| | - Jessica Trejo
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.P.S.); (A.F.); (M.E.P.); (N.T.); (K.B.); (J.T.); (M.D.S.); (G.L.S.); (W.L.L.)
| | - Matt D. Stewart
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.P.S.); (A.F.); (M.E.P.); (N.T.); (K.B.); (J.T.); (M.D.S.); (G.L.S.); (W.L.L.)
| | - Greg L. Stewart
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.P.S.); (A.F.); (M.E.P.); (N.T.); (K.B.); (J.T.); (M.D.S.); (G.L.S.); (W.L.L.)
| | - Patricia P. Reis
- Molecular Oncology Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu 18618-687, SP, Brazil;
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University (UNESP), Botucatu 18618-687, SP, Brazil
| | - Wan L. Lam
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.P.S.); (A.F.); (M.E.P.); (N.T.); (K.B.); (J.T.); (M.D.S.); (G.L.S.); (W.L.L.)
| | - Victor D. Martinez
- Department of Pathology and Laboratory Medicine, IWK Health Centre, Halifax, NS B3K 6R8, Canada;
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS B3K 6R8, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS B3H 4R2, Canada
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Ruas JS, Silva FLT, Euzébio MF, Biazon TO, Daiggi CMM, Nava D, Franco MT, Cardinalli IA, Cassone AE, Pereira LH, Seidinger AL, Maschietto M, Jotta PY. Somatic Copy Number Alteration in Circulating Tumor DNA for Monitoring of Pediatric Patients with Cancer. Biomedicines 2023; 11:biomedicines11041082. [PMID: 37189699 DOI: 10.3390/biomedicines11041082] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/02/2023] [Accepted: 03/08/2023] [Indexed: 04/07/2023] Open
Abstract
Pediatric tumors share few recurrent mutations and are instead characterized by copy number alterations (CNAs). The cell-free DNA (cfDNA) is a prominent source for the detection of cancer-specific biomarkers in plasma. We profiled CNAs in the tumor tissues for further evaluation of alterations in 1q, MYCN and 17p in the circulating tumor DNA (ctDNA) in the peripheral blood at diagnosis and follow-up using digital PCR. We report that among the different kinds of tumors (neuroblastoma, Wilms tumor, Ewing sarcoma, rhabdomyosarcoma, leiomyosarcoma, osteosarcoma and benign teratoma), neuroblastoma presented the greatest amount of cfDNA, in correlation with tumor volume. Considering all tumors, cfDNA levels correlated with tumor stage, metastasis at diagnosis and metastasis developed during therapy. In the tumor tissue, at least one CNA (at CRABP2, TP53, surrogate markers for 1q and 17p, respectively, and MYCN) was observed in 89% of patients. At diagnosis, CNAs levels were concordant between tumor and ctDNA in 56% of the cases, and for the remaining 44%, 91.4% of the CNAs were present only in cfDNA and 8.6% only in the tumor. Within the cfDNA, we observed that 46% and 23% of the patients had MYCN and 1q gain, respectively. The use of specific CNAs as targets for liquid biopsy in pediatric patients with cancer can improve diagnosis and should be considered for monitoring of the disease response.
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Affiliation(s)
| | - Felipe Luz Torres Silva
- Research Center, Boldrini Children’s Hospital, Campinas 13083-884, SP, Brazil
- Genetics and Molecular Biology, Institute of Biology, State University of Campinas, Campinas 13083-862, SP, Brazil
| | - Mayara Ferreira Euzébio
- Research Center, Boldrini Children’s Hospital, Campinas 13083-884, SP, Brazil
- Genetics and Molecular Biology, Institute of Biology, State University of Campinas, Campinas 13083-862, SP, Brazil
| | - Tássia Oliveira Biazon
- Research Center, Boldrini Children’s Hospital, Campinas 13083-884, SP, Brazil
- Genetics and Molecular Biology, Institute of Biology, State University of Campinas, Campinas 13083-862, SP, Brazil
| | | | - Daniel Nava
- Boldrini Children’s Hospital, Campinas 13083-210, SP, Brazil
| | | | | | | | | | - Ana Luiza Seidinger
- Research Center, Boldrini Children’s Hospital, Campinas 13083-884, SP, Brazil
| | - Mariana Maschietto
- Research Center, Boldrini Children’s Hospital, Campinas 13083-884, SP, Brazil
- Genetics and Molecular Biology, Institute of Biology, State University of Campinas, Campinas 13083-862, SP, Brazil
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Tichà V, Patelli G, Basso G, Prino A, Repetti E, Grugni M, Damascelli B. Case Report: Potential role of selective venous sampling for liquid biopsy in complex clinical settings: Three case presentations. Front Genet 2023; 14:1065537. [PMID: 37056288 PMCID: PMC10086121 DOI: 10.3389/fgene.2023.1065537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
Tumor mutation profiling from a blood sample, known as liquid biopsy, is a reality that has already been approved for some cancers. This molecular diagnostic method complements tissue biopsy but is less invasive and therefore more easily applied, especially during tumor evolution. Its use should allow detection of residual disease, evaluation of treatment response or resistance, and selection of targeted treatments. However, implementation of liquid biopsy in routine clinical practice is hindered by unsolved issues, one of which is the scarcity of circulating tumor DNA in blood samples drawn from peripheral veins. To address this problem, we propose minimally invasive selective venous sampling from the region of interest, as used for some hormonal studies and for mapping of endocrine tumors. Intuitively, selective sampling should improve the sensitivity of liquid biopsy by avoiding the dilution of tumor biomarkers that occurs in the peripheral circulation. We report three cases that illustrate the potential utility of selective liquid biopsy in complex clinical settings, providing implications for diagnosis and treatment as well as for monitoring over time, disease localization, identification of drug resistance, and differential diagnosis.
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Affiliation(s)
- Vladimira Tichà
- Department of Interventional Oncology, EMO GVM Centrocuore Columbus, Milan, Italy
| | - Gianluigi Patelli
- Department of Radiology, ASST Bergamo Est-Bolognini Hospital, Seriate, Italy
| | - Gianpaolo Basso
- School of Medicine and Surgery, San Gerardo Hospital, University of Milano-Bicocca, Monza, Italy
| | - Aurelio Prino
- Palliative Care Department and Hospice, University Hospital Maggiore Della Carità, Novara, Italy
| | - Elena Repetti
- TOMA Advanced Biomedical Assays S.p.A, Busto Arsizio, Varese, Italy
| | - Maria Grugni
- TOMA Advanced Biomedical Assays S.p.A, Busto Arsizio, Varese, Italy
| | - Bruno Damascelli
- Department of Interventional Oncology, EMO GVM Centrocuore Columbus, Milan, Italy
- *Correspondence: Bruno Damascelli,
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Impact of Whole Genome Doubling on Detection of Circulating Tumor DNA in Colorectal Cancer. Cancers (Basel) 2023; 15:cancers15041136. [PMID: 36831479 PMCID: PMC9954709 DOI: 10.3390/cancers15041136] [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: 12/16/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
OBJECTIVE Circulating tumor DNA (ctDNA) is a candidate biomarker of cancer with practice-changing potential in the detection of both early and residual disease. Disease stage and tumor size affect the probability of ctDNA detection, whereas little is known about the influence of other tumor characteristics on ctDNA detection. This study investigates the impact of tumor cell whole-genome doubling (WGD) on the detection of ctDNA in plasma collected preoperatively from newly diagnosed colorectal cancer (CRC) patients. METHODS WGD was estimated from copy numbers derived from whole-exome sequencing (WES) data of matched tumor and normal DNA from 833 Danish CRC patients. To explore if tumor WGD status impacts ctDNA detection, we applied tumor-informed ctDNA analysis to preoperative plasma samples from all patients. RESULTS Patients with WGD+ tumors had 53% increased odds of being ctDNA positive (OR = 1.53, 95%CI: 1.12-2.09). After stratification for UICC stage, the association persisted for Stage I (OR = 2.44, 95%CI: 1.22-5.03) and Stage II (OR = 1.76, 95%CI: 1.11-2.81) but not for Stage III (OR = 0.83, 95%CI: 0.44-1.53) patients. CONCLUSION The presence of WGD significantly increases the probability of detecting ctDNA, particularly for early-stage disease. In patients with more advanced disease, the benefit of WGD on ctDNA detection is less pronounced, consistent with increased DNA shedding from these tumors, making ctDNA detection less dependent on the amount of ctDNA released per tumor cell.
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Stejskal P, Goodarzi H, Srovnal J, Hajdúch M, van ’t Veer LJ, Magbanua MJM. Circulating tumor nucleic acids: biology, release mechanisms, and clinical relevance. Mol Cancer 2023; 22:15. [PMID: 36681803 PMCID: PMC9862574 DOI: 10.1186/s12943-022-01710-w] [Citation(s) in RCA: 64] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/29/2022] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Despite advances in early detection and therapies, cancer is still one of the most common causes of death worldwide. Since each tumor is unique, there is a need to implement personalized care and develop robust tools for monitoring treatment response to assess drug efficacy and prevent disease relapse. MAIN BODY Recent developments in liquid biopsies have enabled real-time noninvasive monitoring of tumor burden through the detection of molecules shed by tumors in the blood. These molecules include circulating tumor nucleic acids (ctNAs), comprising cell-free DNA or RNA molecules passively and/or actively released from tumor cells. Often highlighted for their diagnostic, predictive, and prognostic potential, these biomarkers possess valuable information about tumor characteristics and evolution. While circulating tumor DNA (ctDNA) has been in the spotlight for the last decade, less is known about circulating tumor RNA (ctRNA). There are unanswered questions about why some tumors shed high amounts of ctNAs while others have undetectable levels. Also, there are gaps in our understanding of associations between tumor evolution and ctNA characteristics and shedding kinetics. In this review, we summarize current knowledge about ctNA biology and release mechanisms and put this information into the context of tumor evolution and clinical utility. CONCLUSIONS A deeper understanding of the biology of ctDNA and ctRNA may inform the use of liquid biopsies in personalized medicine to improve cancer patient outcomes.
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Affiliation(s)
- Pavel Stejskal
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University and University Hospital in Olomouc, Olomouc, 779 00 Czech Republic
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158 USA
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158 USA
- Department of Urology, University of California San Francisco, San Francisco, CA 94158 USA
| | - Josef Srovnal
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University and University Hospital in Olomouc, Olomouc, 779 00 Czech Republic
| | - Marián Hajdúch
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University and University Hospital in Olomouc, Olomouc, 779 00 Czech Republic
| | - Laura J. van ’t Veer
- Department of Laboratory Medicine, University of California San Francisco, 2340 Sutter Street, San Francisco, CA USA
| | - Mark Jesus M. Magbanua
- Department of Laboratory Medicine, University of California San Francisco, 2340 Sutter Street, San Francisco, CA USA
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