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Labiano I, Huerta AE, Alsina M, Arasanz H, Castro N, Mendaza S, Lecumberri A, Gonzalez-Borja I, Guerrero-Setas D, Patiño-Garcia A, Alkorta-Aranburu G, Hernández-Garcia I, Arrazubi V, Mata E, Gomez D, Viudez A, Vera R. Building on the clinical applicability of ctDNA analysis in non-metastatic pancreatic ductal adenocarcinoma. Sci Rep 2024; 14:16203. [PMID: 39003322 PMCID: PMC11246447 DOI: 10.1038/s41598-024-67235-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 07/09/2024] [Indexed: 07/15/2024] Open
Abstract
Pancreatic ductal adenocarcinoma represents one of the solid tumors showing the worst prognosis worldwide, with a high recurrence rate after adjuvant or neoadjuvant therapy. Circulating tumor DNA analysis raised as a promising non-invasive tool to characterize tumor genomics and to assess treatment response. In this study, surgical tumor tissue and sequential blood samples were analyzed by next-generation sequencing and were correlated with clinical and pathological characteristics. Thirty resectable/borderline pancreatic ductal adenocarcinoma patients treated at the Hospital Universitario de Navarra were included. Circulating tumoral DNA sequencing identified pathogenic variants in KRAS and TP53, and in other cancer-associated genes. Pathogenic variants at diagnosis were detected in patients with a poorer outcome, and were correlated with response to neoadjuvant therapy in borderline pancreatic ductal adneocarcinoma patients. Higher variant allele frequency at diagnosis was associated with worse prognosis, and thesum of variant allele frequency was greater in samples at progression. Our results build on the potential value of circulating tumor DNA for non-metastatic pancreatic ductal adenocarcinoma patients, by complementing tissue genetic information and as a non-invasive tool for treatment decision. Confirmatory studies are needed to corroborate these findings.
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Affiliation(s)
- Ibone Labiano
- Oncobiona Group, Navarrabiomed-Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008, Pamplona, Spain
| | - Ana E Huerta
- Oncobiona Group, Navarrabiomed-Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008, Pamplona, Spain
| | - Maria Alsina
- Oncobiona Group, Navarrabiomed-Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008, Pamplona, Spain.
- Medical Oncology Department, Hospital Universitario de Navarra (HUN), Irunlarrea 3, 31008, Pamplona, Spain.
| | - Hugo Arasanz
- Oncobiona Group, Navarrabiomed-Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008, Pamplona, Spain
- Medical Oncology Department, Hospital Universitario de Navarra (HUN), Irunlarrea 3, 31008, Pamplona, Spain
| | - Natalia Castro
- Oncobiona Group, Navarrabiomed-Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008, Pamplona, Spain
| | - Saioa Mendaza
- Oncobiona Group, Navarrabiomed-Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008, Pamplona, Spain
| | - Arturo Lecumberri
- Oncobiona Group, Navarrabiomed-Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008, Pamplona, Spain
- Medical Oncology Department, Hospital Universitario de Navarra (HUN), Irunlarrea 3, 31008, Pamplona, Spain
| | - Iranzu Gonzalez-Borja
- Oncobiona Group, Navarrabiomed-Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008, Pamplona, Spain
| | - David Guerrero-Setas
- Molecular Pathology of Cancer Group, Navarrabiomed, Hospital Universitario de Navarra (HUN), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008, Pamplona, Spain
| | - Ana Patiño-Garcia
- Department of Pediatrics and Clinical Genetics, Clínica Universidad de Navarra (CUN), Cancer Center Clínica Universidad de Navarra (CCUN), Program in Solid Tumors, Center for Applied Medical Research (CIMA) and Navarra Institute for Health Research (IdiSNA), University of Navarra, Pamplona, Spain
| | | | - Irene Hernández-Garcia
- Oncobiona Group, Navarrabiomed-Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008, Pamplona, Spain
- Medical Oncology Department, Hospital Universitario de Navarra (HUN), Irunlarrea 3, 31008, Pamplona, Spain
| | - Virginia Arrazubi
- Oncobiona Group, Navarrabiomed-Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008, Pamplona, Spain
- Medical Oncology Department, Hospital Universitario de Navarra (HUN), Irunlarrea 3, 31008, Pamplona, Spain
| | - Elena Mata
- Oncobiona Group, Navarrabiomed-Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008, Pamplona, Spain
- Medical Oncology Department, Hospital Universitario de Navarra (HUN), Irunlarrea 3, 31008, Pamplona, Spain
| | - David Gomez
- Oncobiona Group, Navarrabiomed-Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008, Pamplona, Spain
- Medical Oncology Department, Hospital Universitario de Navarra (HUN), Irunlarrea 3, 31008, Pamplona, Spain
| | - Antonio Viudez
- Oncobiona Group, Navarrabiomed-Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008, Pamplona, Spain
| | - Ruth Vera
- Oncobiona Group, Navarrabiomed-Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008, Pamplona, Spain
- Medical Oncology Department, Hospital Universitario de Navarra (HUN), Irunlarrea 3, 31008, Pamplona, Spain
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2
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Capella MP, Fallah P, Basik M. Personalized circulating tumor DNA response to local radiotherapy in a patient with an early lobular breast cancer: A case report. Oncol Lett 2024; 27:282. [PMID: 38736743 PMCID: PMC11082640 DOI: 10.3892/ol.2024.14415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/26/2024] [Indexed: 05/14/2024] Open
Abstract
The detection of circulating tumor DNA (ctDNA) in the plasma of cancer patients is emerging as a very sensitive and specific prognostic biomarker. Previous studies with ctDNA have focused on the ability of ctDNA detection to predict micrometastatic and eventual clinical metastatic relapse. There are few data on the role of ctDNA in monitoring response to local therapy. The present study reports the case of a patient with early-stage lobular breast cancer, with a detectable ctDNA test which resolved with local radiotherapy to the breast. This case suggests that ctDNA is sensitive enough to detect the response of minimal residual disease, localized in the breast, to radiation therapy, and thus may assist in providing indications for local breast cancer treatment.
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Affiliation(s)
- Mariana Pilon Capella
- Department of Medicine and Oncology, Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, McGill University Montreal, Montreal, QC H3T 1E2, Canada
| | - Parvaneh Fallah
- Department of Medicine and Oncology, Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, McGill University Montreal, Montreal, QC H3T 1E2, Canada
| | - Mark Basik
- Division of Oncology, Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, McGill University Montreal, Montreal, QC H3T 1E2, Canada
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Oh Y, Yoon SM, Lee J, Park JH, Lee S, Hong T, Chung LI, Sudhaman S, Riddell T, Palsuledesai CC, Krainock M, Liu MC, Chae YK. Personalized, tumor-informed, circulating tumor DNA assay for detecting minimal residual disease in non-small cell lung cancer patients receiving curative treatments. Thorac Cancer 2024; 15:1095-1102. [PMID: 38558374 PMCID: PMC11062881 DOI: 10.1111/1759-7714.15281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 02/24/2024] [Accepted: 02/29/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) has emerged as a prognostic and predictive biomarker for detection of minimal residual disease (MRD), monitoring treatment response, and early detection of recurrence in cancer patients. In this study, we explored the utility of ctDNA-based MRD detection to predict recurrence in a real-world cohort of primarily early-stage non-small cell lung cancer (NSCLC) patients treated with curative intent. METHODS Longitudinal plasma samples were collected post curative-intent treatment from 36 patients with stage I-IV NSCLC. A personalized, tumor-informed assay was used to detect and quantify ctDNA in plasma samples. RESULTS Of the 24 patients with plasma samples available during the MRD window (within 6 months of curative surgery and before adjuvant therapy), ctDNA was detectable in two patients. Patients with ctDNA-positivity during the MRD window were 15 times more likely to recur compared to ctDNA-negative patients (HR: 15.0, 95% CI: 1.0-253.0, p = 0.010). At any time post-curative intent treatment, ctDNA-positivity was associated with significantly poorer recurrence-free survival compared to persistently ctDNA-negative patients (p < 0.0001). CONCLUSION Our real-world data indicate that longitudinal, personalized, tumor-informed ctDNA monitoring is a valuable tool in patients with NSCLC receiving curative treatment to identify patients at high risk for recurrence.
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Affiliation(s)
- Youjin Oh
- Feinberg School of Medicine, Northwestern UniversityChicagoIllinoisUSA
- Department of internal medicineJohn H. Stroger Hospital of Cook CountyChicagoIllinoisUSA
| | - Sung Mi Yoon
- Feinberg School of Medicine, Northwestern UniversityChicagoIllinoisUSA
- North Central Bronx Hospital, Albert Einstein College of MedicineBronxNew YorkUSA
| | - Jeeyeon Lee
- Feinberg School of Medicine, Northwestern UniversityChicagoIllinoisUSA
- Kyungpook National University School of Medicine, Kyungpook National University Chilgok HospitalDaeguRepublic of Korea
| | - Joo Hee Park
- Feinberg School of Medicine, Northwestern UniversityChicagoIllinoisUSA
| | - Soowon Lee
- Feinberg School of Medicine, Northwestern UniversityChicagoIllinoisUSA
- Baylor UniversityWacoTexasUSA
| | - Timothy Hong
- Feinberg School of Medicine, Northwestern UniversityChicagoIllinoisUSA
| | | | | | | | | | | | | | - Young Kwang Chae
- Feinberg School of Medicine, Northwestern UniversityChicagoIllinoisUSA
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Valladares-Ayerbes M, Safont MJ, González Flores E, García-Alfonso P, Aranda E, Muñoz AML, Falcó Ferrer E, Cirera Nogueras L, Rodríguez-Salas N, Aparicio J, Llanos Muñoz M, Pimentel Cáceres PP, Castillo Trujillo OA, Vidal Tocino R, Salgado Fernández M, Salud-Salvia A, Massuti Sureda B, Garcia-Carbonero R, Vicente Conesa MÁ, Lloansí Vila A. Sequential RAS mutations evaluation in cell-free DNA of patients with tissue RAS wild-type metastatic colorectal cancer: the PERSEIDA (Cohort 2) study. Clin Transl Oncol 2024:10.1007/s12094-024-03487-4. [PMID: 38642257 DOI: 10.1007/s12094-024-03487-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 03/25/2024] [Indexed: 04/22/2024]
Abstract
PURPOSE RAS (KRAS/NRAS) mutational status on a tumor biopsy is mandatory to guide the best treatment in metastatic colorectal cancer (mCRC). Determining the RAS mutational status by tumor-tissue biopsy is essential in guiding the optimal treatment decision for mCRC. RAS mutations are negative predictive factors for the use of EGFR monoclonal antibodies. Cell-free DNA (cfDNA) analysis enables minimally invasive monitoring of tumor evolution. METHODS/PATIENTS PERSEIDA was an observational, prospective study assessing cfDNA RAS, BRAF and EGFR mutations (using Idylla™) in first-line mCRC, RAS wild-type (baseline tumor-tissue biopsy) patients (cohort 2). Plasma samples were collected before first-line treatment, after 20 ± 2 weeks, and at disease progression. RESULTS 117 patients were included (103 received panitumumab + chemotherapy as first-line treatment). At baseline, 7 (6.8%) patients had RAS mutations, 4 (3.9%) BRAF mutations and no EGFR mutations were detected (cfDNA, panitumumab + chemotherapy subpopulation [panitumumab + Ch]). The baseline RAS mutational status concordance between tissue and liquid biopsies was 94.0% (93.2%, panitumumab + Ch). At 20 weeks, only one patient in the study (included in the panitumumab + Ch) had an emerging cfDNA RAS mutation. No emerging BRAF or EGFR mutations were reported. At disease progression, 6 patients had emergent mutations not present at baseline (RAS conversion rate: 13.3% [6/45]; 15.0% [6/40], panitumumab + Ch). CONCLUSIONS The concordance rate between liquid and solid biopsies at baseline was very high, as previously reported, while our results suggest a considerable emergence of RAS mutations during disease progression. Thus, the dynamics of the genomic landscape in ctDNA may provide relevant information for the management of mCRC patients.
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Affiliation(s)
| | - Maria José Safont
- Consorcio Hospital General Universitario de Valencia, Universidad de Valencia, Valencia; CIBERONC, Valencia, Spain
| | | | - Pilar García-Alfonso
- Medical Oncology Service, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Universidad Complutense, Madrid, Spain
| | | | | | | | | | | | - Jorge Aparicio
- Hospital Universitari i Politècnic La Fe, Valencia, Spain
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5
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Pomerantz T, Brooks R. Circulating Tumor DNA (ctDNA) and Its Role in Gynecologic Malignancies. Curr Treat Options Oncol 2024; 25:510-522. [PMID: 38472567 DOI: 10.1007/s11864-024-01180-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2024] [Indexed: 03/14/2024]
Abstract
OPINION STATEMENT Circulating tumor DNA (ctDNA) refers to small fragments of DNA released into the bloodstream by cancer cells. It is obtained through "liquid biopsy;" which most commonly refers to plasma or blood samples, but can be obtained from a number of bodily fluids including ascitic fluid, saliva, and even urine and stool. ctDNA is detected via polymerase chain reaction (PCR) or next-generation sequencing (NGS). The DNA from these samples is analyzed for the detection of point mutations, copy-number alterations, gene fusion, and DNA methylation. These results have the potential for use in cancer diagnosis, determining prognosis, targeting gene-specific therapies, and monitoring for/predicting disease recurrence and response to treatment. ctDNA offers an alternative to tissue biopsy; it is less invasive and can be monitored serially over time without multiple procedures. Moreover it may have the ability to detect disease recurrence or predict behavior in a way that solid tissue biopsies, tumor marker surveillance, and imaging cannot. Recent explosion in interest in ctDNA shows promising developments for widespread adoption of these techniques in cancer care. However, the use of ctDNA in diagnosis and treatment of gynecologic malignancies is currently limited, compared to adoption in other solid-organ tumors such as breast and colorectal cancers. Compared to other cancer types, there appear to be fewer comprehensive studies and clinical validations specifically focusing on the use of ctDNA in gynecologic cancers. More research is needed in this area to advance the potential for use of ctDNA in ovarian, endometrial, and cervical cancers before this can be routinely adopted to improve care for patients with gynecologic malignancies.
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Affiliation(s)
- Tali Pomerantz
- University of California Davis Medical Center, 4860 Y Street, Suite 2500, Sacramento, CA, 95817, USA.
| | - Rebecca Brooks
- University of California Davis Medical Center, 4860 Y Street, Suite 2500, Sacramento, CA, 95817, USA
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6
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Iseas S, Mariano G, Gros L, Baba-Hamed N, De Parades V, Adam J, Raymond E, Abba MC. Unraveling Emerging Anal Cancer Clinical Biomarkers from Current Immuno-Oncogenomics Advances. Mol Diagn Ther 2024; 28:201-214. [PMID: 38267771 PMCID: PMC10925578 DOI: 10.1007/s40291-023-00692-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/26/2023] [Indexed: 01/26/2024]
Abstract
Anal squamous cell carcinoma (ASCC) is a rare gastrointestinal malignancy associated with high-risk human papillomavirus (HPV) and is currently one of the fastest-growing causes of cancer incidence and mortality in developed countries. Although next-generation sequencing technologies (NGS) have revolutionized cancer and immuno-genomic research in various tumor types, a limited amount of clinical research has been developed to investigate the expression and the functional characterization of genomic data in ASCC. Herein, we comprehensively assess recent advancements in "omics" research, including a systematic analysis of genome-based studies, aiming to identify the most relevant ASCC cancer driver gene expressions and their associated signaling pathways. We also highlight the most significant biomarkers associated with anal cancer progression, gene expression of potential diagnostic biomarkers, expression of therapeutic drug targets, and emerging treatment opportunities. This review stresses the urgent need for developing target-specific therapies in ASCC. By illuminating the molecular characteristics and drug-target expression in ASCC, this study aims to provide insights for the development of precision medicine in anal cancer.
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Affiliation(s)
- Soledad Iseas
- Medical Oncology Department, Paris-St Joseph Hospital, 185 rue Raymond Losserand, 75014, Paris, France.
| | - Golubicki Mariano
- Oncology Unit, Gastroenterology Hospital "Dr. Carlos Bonorino Udaondo", Av. Caseros 2061, C1264, Ciudad Autónoma de Buenos Aires, Argentina
| | - Louis Gros
- Medical Oncology Department, Paris-St Joseph Hospital, 185 rue Raymond Losserand, 75014, Paris, France
| | - Nabil Baba-Hamed
- Medical Oncology Department, Paris-St Joseph Hospital, 185 rue Raymond Losserand, 75014, Paris, France
| | - Vincent De Parades
- Proctology Unit, Paris-St Joseph Hospital, 185 rue Raymond Losserand, 75014, Paris, France
| | - Julien Adam
- Pathology Department, Paris-St Joseph Hospital, 185 rue Raymond Losserand, 75014, Paris, France
| | - Eric Raymond
- Medical Oncology Department, Paris-St Joseph Hospital, 185 rue Raymond Losserand, 75014, Paris, France
| | - Martin Carlos Abba
- Basic and Applied Immunological Research Center (CINIBA), School of Medical Sciences, NationalUniversity of La Plata, Calle 60 y 120, C1900, La Plata, Argentina.
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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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8
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Wang Z, Liu M, Lin H, Zhu G, Dong Z, Wu N, Fan Y, Xu G, Chang L, Wang Y. An Ion Concentration Polarization Microplatform for Efficient Enrichment and Analysis of ctDNA. ACS NANO 2024; 18:2872-2884. [PMID: 38236597 DOI: 10.1021/acsnano.3c07137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Strategies for rapid, effective nucleic acid processing hold tremendous significance to the clinical analysis of circulating tumor DNA (ctDNA), a family of important markers indicating tumorigenesis and metastasis. However, traditional techniques remain challenging to achieve efficient DNA enrichment, further bringing about complicated operation and limited detection sensitivity. Here, we developed an ion concentration polarization microplatform that enabled highly rapid, efficient enrichment and purification of ctDNA from a variety of clinical samples, including serum, urine, and feces. The platform demonstrated efficiently separating and enriching ctDNA within 30 s, with a 100-fold improvement over traditional methods. Integrating an on-chip isothermal amplification module, the platform further achieved 100-fold enhanced sensitivity in ctDNA detection, which significantly eliminated false-negative results in the serum or urine samples due to the low abundance of ctDNA. Such a simple-designed platform offers a user-friendly yet powerful diagnosis technique with a wide applicability, ranging from early tumor diagnosis to infection screening.
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Affiliation(s)
- Zhiying Wang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
| | - Ming Liu
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
| | - Haocheng Lin
- Department of Urology, Peking University Third Hospital, Beijing, 100191, China
| | - Guiying Zhu
- School of Biomedical Engineering/Med-X, Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Zaizai Dong
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
- School of Engineering Medicine, Beihang University, Beijing 100083, China
| | - Nan Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Yubo Fan
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
- School of Engineering Medicine, Beihang University, Beijing 100083, China
| | - Gaolian Xu
- School of Biomedical Engineering/Med-X, Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- Shanghai Sci-Tech InnoCenter for Infection & Immunity, Shanghai, 200000, China
| | - Lingqian Chang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
| | - Yang Wang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
- School of Engineering Medicine, Beihang University, Beijing 100083, China
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9
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Astier C, Ngo C, Colmet-Daage L, Marty V, Bawa O, Nicotra C, Ngo-Camus M, Italiano A, Massard C, Scoazec JY, Smolenschi C, Ducreux M, Hollebecque A, Postel-Vinay S. Molecular profiling of biliary tract cancers reveals distinct genomic landscapes between circulating and tissue tumor DNA. Exp Hematol Oncol 2024; 13:2. [PMID: 38191492 PMCID: PMC10775454 DOI: 10.1186/s40164-023-00470-7] [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: 10/13/2023] [Accepted: 12/30/2023] [Indexed: 01/10/2024] Open
Abstract
Biliary tract cancers (BTCs) are heterogeneous malignancies with dismal prognosis due to tumor aggressiveness and poor response to limited current therapeutic options. Tumor exome profiling has allowed to successfully establish targeted therapeutic strategies in the clinical management of cholangiocarcinoma (CCA). Still, whether liquid biopsy profiling could inform on BTC biology and patient management is unknown. In order to test this and generate novel insight into BTC biology, we analyzed the molecular landscape of 128 CCA patients, using a 394-gene NGS panel (Foundation Medicine). Among them, 32 patients had matched circulating tumor (ct) DNA and tumor DNA samples, where both samples were profiled. In both tumor and liquid biopsies, we identified an increased frequency of alterations in genes involved in genome integrity or chromatin remodeling, including ARID1A (15%), PBRM1 (9%), and BAP1 (14%), which were validated using an in-house-developed immunohistochemistry panel. ctDNA and tumor DNA showed variable concordance, with a significant correlation in the total number of detected variants, but some heterogeneity in the detection of actionable mutations. FGFR2 mutations were more frequently identified in liquid biopsies, whereas KRAS alterations were mostly found in tumors. All IDH1 mutations detected in tumor DNA were also identified in liquid biopsies. These findings provide novel insights in the concordance between the tumor and liquid biopsies genomic landscape in a large cohort of patients with BTC and highlight the complementarity of both analyses when guiding therapeutic prescription.
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Affiliation(s)
- Clémence Astier
- ERC Chromatin Remodeling, DNA Repair and Epigenetics Laboratory, INSERM U981, Gustave Roussy, Villejuif, France
- Université Paris-Saclay, Université Paris-Sud XI, Faculté de Médicine, Le Kremlin Bicêtre, France
| | - Carine Ngo
- ERC Chromatin Remodeling, DNA Repair and Epigenetics Laboratory, INSERM U981, Gustave Roussy, Villejuif, France
- Department of Pathology, Gustave Roussy, Villejuif, France
| | - Léo Colmet-Daage
- ERC Chromatin Remodeling, DNA Repair and Epigenetics Laboratory, INSERM U981, Gustave Roussy, Villejuif, France
| | - Virginie Marty
- INSERM US23, CNRS UAR 3655, AMMICa, Experimental and Translational Pathology Platform, Gustave Roussy, Villejuif, France
| | - Olivia Bawa
- INSERM US23, CNRS UAR 3655, AMMICa, Experimental and Translational Pathology Platform, Gustave Roussy, Villejuif, France
| | - Claudio Nicotra
- Drug Development Department (DITEP), Gustave Roussy - Cancer Campus, Villejuif, France
| | - Maud Ngo-Camus
- Drug Development Department (DITEP), Gustave Roussy - Cancer Campus, Villejuif, France
| | - Antoine Italiano
- Drug Development Department (DITEP), Gustave Roussy - Cancer Campus, Villejuif, France
- Department of Early Phase Trial Unit, Institut Bergonié Comprehensive Cancer Centre, Bordeaux, France
- Faculty of Medicine, University of Bordeaux, Bordeaux, France
| | - Christophe Massard
- Drug Development Department (DITEP), Gustave Roussy - Cancer Campus, Villejuif, France
- INSERM U1030, Molecular Radiotherapy, Gustave Roussy, Université Paris-Saclay, Paris, France
| | - Jean-Yves Scoazec
- INSERM US23, CNRS UAR 3655, AMMICa, Experimental and Translational Pathology Platform, Gustave Roussy, Villejuif, France
- Department of Pathology and Laboratory Medicine, Translational Research Laboratory and Biobank, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy, Villejuif, France
| | - Cristina Smolenschi
- Drug Development Department (DITEP), Gustave Roussy - Cancer Campus, Villejuif, France
| | - Michel Ducreux
- Drug Development Department (DITEP), Gustave Roussy - Cancer Campus, Villejuif, France
- Université Paris-Saclay, Gustave Roussy, INSERM, Dynamique des Cellules Tumorales (U-1279), Villejuif, France
| | - Antoine Hollebecque
- Drug Development Department (DITEP), Gustave Roussy - Cancer Campus, Villejuif, France
| | - Sophie Postel-Vinay
- ERC Chromatin Remodeling, DNA Repair and Epigenetics Laboratory, INSERM U981, Gustave Roussy, Villejuif, France.
- Drug Development Department (DITEP), Gustave Roussy - Cancer Campus, Villejuif, France.
- University College of London Cancer Institute, London, UK.
- Institut Gustave Roussy, 114 rue Edouard Vaillant, 94805, Villejuif, France.
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10
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Dong Q, Chen C, Hu Y, Zhang W, Yang X, Qi Y, Zhu C, Chen X, Shen X, Ji W. Clinical application of molecular residual disease detection by circulation tumor DNA in solid cancers and a comparison of technologies: review article. Cancer Biol Ther 2023; 24:2274123. [PMID: 37955635 PMCID: PMC10653633 DOI: 10.1080/15384047.2023.2274123] [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: 05/11/2023] [Accepted: 08/04/2023] [Indexed: 11/14/2023] Open
Abstract
Molecular residual disease (MRD), detected by circulating tumor DNA (ctDNA) can be involved in the entire process of solid tumor management, including recurrence prediction, efficacy evaluation, and risk stratification. Currently, the detection technologies are divided into two main categories, as follows: tumor-agnostic and tumor informed. Tumor-informed assay obtains mutation information by sequencing tumor tissue samples before blood MRD monitoring, followed by formulation of a personalized MRD panel. Tumor-agnostic assays are carried out using a fixed panel without the mutation information from primary tumor tissue. The choice of testing strategy may depend on the level of evidence from ongoing randomized clinical trials, investigator preference, cost-effectiveness, patient economics, and availability of tumor tissue. The review describes the difference between tumor informed and tumor agnostic detection. In addition, the clinical application of ctDNA MRD in solid tumors was introduced, with emphasis on lung cancer, colorectal cancer, Urinary system cancer, and breast cancer.
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Affiliation(s)
- Qiantong Dong
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
| | - Chenbin Chen
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
- Department of Gastrointestinal Surveillance, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou City, Zhejiang, China
| | - Yuanbo Hu
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
- Department of Gastrointestinal Surveillance, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou City, Zhejiang, China
| | - Weiteng Zhang
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
| | - Xinxin Yang
- Department of Gastrointestinal Surveillance, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou City, Zhejiang, China
| | - Yingxue Qi
- The Medical Department, Jiangsu Simcere Diagnostics Co.Ltd, The state Key Laboratory of Neurology and Oncology Drug Development, Nanjing, China
| | - Chan Zhu
- The Medical Department, Jiangsu Simcere Diagnostics Co.Ltd, The state Key Laboratory of Neurology and Oncology Drug Development, Nanjing, China
| | - Xiaodong Chen
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
| | - Xian Shen
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
- Department of Gastrointestinal Surveillance, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou City, Zhejiang, China
| | - Weiping Ji
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
- Department of Gastrointestinal Surveillance, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou City, Zhejiang, China
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11
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Shefer A, Tutanov O, Belenikin M, Tsentalovich YP, Tamkovich S. Blood Plasma Circulating DNA-Protein Complexes: Involvement in Carcinogenesis and Prospects for Liquid Biopsy of Breast Cancer. J Pers Med 2023; 13:1691. [PMID: 38138918 PMCID: PMC10744380 DOI: 10.3390/jpm13121691] [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: 10/12/2023] [Revised: 11/21/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Circulating DNA (cirDNA) is a promising tool in translational medicine. However, studies of cirDNA have neglected its association with proteins, despite ample evidence that this interaction may affect the fate of DNA in the bloodstream and its molecular functions. The goal of the current study is to shed light on the differences between the proteomic cargos of histone-containing nucleoprotein complexes (NPCs) from healthy female (HFs) and breast cancer patients (BCPs), and to reveal the proteins involved in carcinogenesis. NPCs were isolated from the blood samples of HFs and BCPs using affinity chromatography. A total of 177 and 169 proteins were identified in NPCs from HFs and BCPs using MALDI-TOF mass spectrometry. A bioinformatics analysis revealed that catalytically active proteins, as well as proteins that bind nucleic acids and regulate the activity of receptors, are the most represented among the unique proteins of blood NPCs from HFs and BCPs. In addition, the proportion of proteins participating in ion channels and proteins binding proteins increases in the NPCs from BCP blood. However, the involvement in transport and signal transduction was greater in BCP NPCs compared to those from HFs. Gene ontology term (GO) analysis revealed that the NPC protein cargo from HF blood was enriched with proteins involved in the negative regulation of cell proliferation, and in BCP blood, proteins involved in EMT, invasion, and cell migration were observed. The combination of SPG7, ADRB1, SMCO4, PHF1, and PSMG1 NPC proteins differentiates BCPs from HFs with a sensitivity of 100% and a specificity of 80%. The obtained results indirectly indicate that, in tandem with proteins, blood cirDNA is an important part of intercellular communication, playing a regulatory and integrating role in the physiology of the body.
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Affiliation(s)
- Aleksei Shefer
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Oleg Tutanov
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, USA;
| | | | - Yuri P. Tsentalovich
- International Tomography Center, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Svetlana Tamkovich
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, 630090 Novosibirsk, Russia;
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12
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Yahya J, Baber M, Nabavizadeh N, Goodyear SM, Kardosh A. A Review of Circulating Tumor DNA as a Biomarker Guide for Total Neoadjuvant Therapy in Patients with Locally Advanced Rectal Cancer. J Gastrointest Cancer 2023; 54:1140-1150. [PMID: 36719559 PMCID: PMC10754735 DOI: 10.1007/s12029-022-00906-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2022] [Indexed: 02/01/2023]
Abstract
PURPOSE Non-operative management of patients with locally advanced rectal cancer (LARC) is emerging as a popular approach for patients that have no evidence of disease following neoadjuvant therapy. However, high rates of local recurrence or distant metastases have highlighted the urgent need for robust biomarker strategies to aid clinical management of these patients. METHODS This review summarizes recent advances in the utility of cell-free (cf) and circulating tumor (ct) DNA as potential biomarkers to help guide individualized non-operative management strategies for LARC patients receiving neoadjuvant therapy. RESULTS Liquid biopsies and the detection of cfDNA/ctDNA is an emerging technology with the potential to provide a non-invasive approach to monitor disease response and improve the identification of patients with LARC that would best benefit from non-operative management. CONCLUSIONS Substantial work is still needed before cfDNA/ctDNA monitoring can be widely adopted in the clinical setting. Studies reviewed herein highlight several areas of opportunity for improving the effectiveness and utility of cfDNA/ctDNA for managing patients with LARC.
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Affiliation(s)
- Jehan Yahya
- Department of Radiation Medicine, Oregon Health & Science University (OHSU), Portland, OR, USA
| | - Miriam Baber
- University of Kansas School of Medicine-Wichita, Wichita, KS, USA
| | - Nima Nabavizadeh
- Department of Radiation Medicine, Oregon Health & Science University (OHSU), Portland, OR, USA
- Knight Cancer Institute, OHSU, Portland, OR, USA
| | - Shaun M Goodyear
- Knight Cancer Institute, OHSU, Portland, OR, USA
- Division of Hematology and Oncology, School of Medicine, OHSU, Portland, OR, USA
| | - Adel Kardosh
- Knight Cancer Institute, OHSU, Portland, OR, USA.
- Division of Hematology and Oncology, School of Medicine, OHSU, Portland, OR, USA.
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13
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Jafri HSMO, Mushtaq S, Baig S, Bhatty A, Siraj S. Comparison of KRAS gene in circulating tumor DNA levels vs histological grading of colorectal cancer patients through liquid biopsy. Saudi J Gastroenterol 2023; 29:371-375. [PMID: 37602638 PMCID: PMC10754382 DOI: 10.4103/sjg.sjg_85_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/15/2023] [Accepted: 07/04/2023] [Indexed: 08/22/2023] Open
Abstract
Background To determine KRAS gene in circulating tumor DNA in comparison with histological grading through liquid biopsy in colorectal cancer patients. Methods This dual-centered cross-sectional study included 73 diagnosed patients of colorectal cancer at different grading levels [Grade I, well differentiated (n = 7, 9.5%); Grade II, moderately differentiated (n = 14,18.9%); and Grade III, poorly differentiated (n = 52, 70%)]. Blood was collected, and plasma was separated. ctDNA was extracted, using magnetic bead-based technique (MagMAX Cell-Free DNA kit). KRAS gene was quantified through qPCR. STRING database was used to find KRAS interactomes. Results Mean threshold cycle (CT value) of KRAS gene in Grade III samples showed significantly higher (P = 0.001) levels of ctDNA (2.7 ± 1.14) compared with Grade II and Grade I (3.1 ± 0.68, 2.3 ± 0.60), respectively. Grading characterization showed that rectal cancer (n = 22, 42.3%) with Grade III (68.8%) was more prevalent than colon and sigmoid cancer (n = 19, 36.5%, n = 11, 21%, respectively). STRING database showed 10 functional genes interacting with KRAS expressed as gene/proteins. Conclusion Liquid biopsy can be used to detect ctDNA in plasma of CRC patients and enabled to detect the KRAS gene by qPCR. The technique being less invasive and cost-effective is convenient for multiple biopsies in different cancers.
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Affiliation(s)
| | - Shamim Mushtaq
- Department of Biochemistry, Basic Health Sciences, Ziauddin University, Karachi, Pakistan
| | - Saeeda Baig
- Department of Biochemistry, Basic Health Sciences, Ziauddin University, Karachi, Pakistan
| | - Afreen Bhatty
- Department of Biochemistry, Basic Health Sciences, Ziauddin University, Karachi, Pakistan
| | - Sabra Siraj
- Department of Pharmacology, Basic Health Sciences, Ziauddin University, Karachi, Pakistan
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14
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Fernandez SV, Tan YF, Rao S, Fittipaldi P, Sheriff F, Borghaei H, Dotan E, Winn JS, Edelman MJ, Treat J, Judd J, Alpaugh RK, Wang YL, Yu JQ, Wasik M, Baldwin DA. Validation of a Molecular Diagnostic Test for Circulating Tumor DNA by Next-Gen Sequencing. Int J Mol Sci 2023; 24:15779. [PMID: 37958763 PMCID: PMC10648112 DOI: 10.3390/ijms242115779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 10/26/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
A modified version of the PGDx elioTM Plasma Resolve assay was validated as a laboratory-developed test (LDT) for clinical use in the Molecular Diagnostics Laboratory at Fox Chase Cancer Center. The test detects single nucleotide variants (SNVs) and small insertions and deletions (indels) in 33 target genes using fragmented genomic DNA extracted from plasma. The analytical performance of this assay was assessed with reference standard DNA and 29 samples from cancer patients and detected 66 SNVs and 23 indels. Using 50 ng of input DNA, the sensitivity was 95.5% to detect SNVs at 0.5% allele frequency, and the specificity was 92.3%. The sensitivity to detect indels at 1% allele frequency was 70.4%. A cutoff of 0.25% variant allele frequency (VAF) was set up for diagnostic reporting. An inter-laboratory study of concordance with an orthologous test resulted in a positive percent agreement (PPA) of 91.7%.
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Affiliation(s)
- Sandra V. Fernandez
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (Y.F.T.); (S.R.); (Y.L.W.); (M.W.)
| | - Yin Fei Tan
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (Y.F.T.); (S.R.); (Y.L.W.); (M.W.)
| | - Shilpa Rao
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (Y.F.T.); (S.R.); (Y.L.W.); (M.W.)
| | - Patricia Fittipaldi
- Protocol Support Laboratory, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (P.F.); (R.K.A.)
| | - Fathima Sheriff
- Office of Clinical Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA;
| | - Hossein Borghaei
- Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (H.B.); (E.D.); (J.S.W.); (M.J.E.); (J.T.); (J.J.)
| | - Efrat Dotan
- Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (H.B.); (E.D.); (J.S.W.); (M.J.E.); (J.T.); (J.J.)
| | - Jennifer S. Winn
- Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (H.B.); (E.D.); (J.S.W.); (M.J.E.); (J.T.); (J.J.)
| | - Martin J. Edelman
- Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (H.B.); (E.D.); (J.S.W.); (M.J.E.); (J.T.); (J.J.)
| | - Joseph Treat
- Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (H.B.); (E.D.); (J.S.W.); (M.J.E.); (J.T.); (J.J.)
| | - Julia Judd
- Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (H.B.); (E.D.); (J.S.W.); (M.J.E.); (J.T.); (J.J.)
| | - R. Katherine Alpaugh
- Protocol Support Laboratory, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (P.F.); (R.K.A.)
| | - Y. Lynn Wang
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (Y.F.T.); (S.R.); (Y.L.W.); (M.W.)
| | - Jian Q. Yu
- Department of Radiology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA;
| | - Mariusz Wasik
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (Y.F.T.); (S.R.); (Y.L.W.); (M.W.)
| | - Don A. Baldwin
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (Y.F.T.); (S.R.); (Y.L.W.); (M.W.)
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15
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Jiang L, Lin X, Chen F, Qin X, Yan Y, Ren L, Yu H, Chang L, Wang Y. Current research status of tumor cell biomarker detection. MICROSYSTEMS & NANOENGINEERING 2023; 9:123. [PMID: 37811123 PMCID: PMC10556054 DOI: 10.1038/s41378-023-00581-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/26/2023] [Accepted: 07/23/2023] [Indexed: 10/10/2023]
Abstract
With the annual increases in the morbidity and mortality rates of tumors, the use of biomarkers for early diagnosis and real-time monitoring of tumor cells is of great importance. Biomarkers used for tumor cell detection in body fluids include circulating tumor cells, nucleic acids, protein markers, and extracellular vesicles. Among them, circulating tumor cells, circulating tumor DNA, and exosomes have high potential for the prediction, diagnosis, and prognosis of tumor diseases due to the large amount of valuable information on tumor characteristics and evolution; in addition, in situ monitoring of telomerase and miRNA in living cells has been the topic of extensive research to understand tumor development in real time. Various techniques, such as enzyme-linked immunosorbent assays, immunoblotting, and mass spectrometry, have been widely used for the detection of these markers. Among them, the detection of tumor cell markers in body fluids based on electrochemical biosensors and fluorescence signal analysis is highly preferred because of its high sensitivity, rapid detection and portable operation. Herein, we summarize recent research progress in the detection of tumor cell biomarkers in body fluids using electrochemical and fluorescence biosensors, outline the current research status of in situ fluorescence monitoring and the analysis of tumor markers in living cells, and discuss the technical challenges for their practical clinical application to provide a reference for the development of new tumor marker detection methods.
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Affiliation(s)
- Liying Jiang
- School of Electrical and Information Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450002 China
- Academy for Quantum Science and Technology, Zhengzhou University of Light Industry, Zhengzhou, 450002 China
| | - Xinyi Lin
- School of Electrical and Information Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450002 China
| | - Fenghua Chen
- School of Electrical and Information Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450002 China
| | - Xiaoyun Qin
- School of Electrical and Information Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450002 China
| | - Yanxia Yan
- School of Electrical and Information Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450002 China
| | - Linjiao Ren
- School of Electrical and Information Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450002 China
| | - Hongyu Yu
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Lingqian Chang
- key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083 China
| | - Yang Wang
- key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083 China
- School of Engineering Medicine, Beihang University, Beijing, 100083 China
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16
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Tsai HL, Lin CC, Sung YC, Chen SH, Chen LT, Jiang JK, Wang JY. The emergence of RAS mutations in patients with RAS wild-type mCRC receiving cetuximab as first-line treatment: a noninterventional, uncontrolled multicenter study. Br J Cancer 2023; 129:947-955. [PMID: 37488448 PMCID: PMC10491612 DOI: 10.1038/s41416-023-02366-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/30/2023] [Accepted: 07/11/2023] [Indexed: 07/26/2023] Open
Abstract
ABSRTACT BACKGROUND: Patients treated with anti-epidermal growth factor receptor (anti-EGFR) will ultimately develop acquired resistance promoted by clonal selection, mainly the emergence of mutations in the MAPK pathway (mostly RAS mutations). Baseline assessment of RAS mutations in the blood of patients correlates well with RAS tumour tissue testing and is currently an alternative option in routine clinical practice to guide first-line therapy. The aim of this study was the prevalence of acquired genomic alterations detected in the auxiliary tool of ctDNA testing and investigated the role of RAS ctDNA status for detecting tumour response and predicting benefit to anti-EGFR therapy. METHODS Only patients with concordant wild-type formalin-fixed, paraffin-embedded (FFPE) tumour tissue and baseline ctDNA RAS wild-type were included. RAS mutations in plasma were evaluated using MassARRAY platform. Blood samples were collected at baseline, every 3 months during first-line treatment, and at disease progression. The primary endpoint was the detection rate of RAS mutations during cetuximab treatment. The correlation between response and survival outcomes and the emergence of circulating RAS mutations was also analysed. RESULTS The detection rate of RAS mutations during treatment was 9.3% (10/108). RAS mutations detection occurred a median of 3 months prior to radiologic documentation. The subgroup of patients with RAS mutations exhibited significantly inferior progression-free survival and overall survival (P = 0.002 and 0.027, respectively) but the baseline characteristics, response rates, disease control rates, and metastatectomy were not significant (all P > 0.05). CONCLUSIONS We demonstrated that RAS ctDNA status might be a valuable biomarker for detecting early tumour response and predicting benefit to anti-EGFR therapy. CLINICAL TRIAL REGISTRATION NCT03401957 (January 17, 2018).
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Affiliation(s)
- Hsiang-Lin Tsai
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Surgery, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chun-Chi Lin
- Division of Colorectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Surgery, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yung-Chung Sung
- School of Medicine, Fu-Jen Catholic University, New Taipei City, Taiwan
- Division of Hematology/Oncology, Internal Medicine, Cathay General Hospital, Taipei, Taiwan
| | - Shang-Hung Chen
- Division of Hematology and Oncology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | - Li-Tzong Chen
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
- Division of Medical Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Internal Medicine, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jeng-Kai Jiang
- Division of Colorectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.
- Department of Surgery, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.
| | - Jaw-Yuan Wang
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.
- Department of Surgery, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
- Center for Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan.
- Pingtung Hospital, Ministry of Health and Welfare, Pingtung, Taiwan.
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17
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Ponomaryova AA, Rykova EY, Solovyova AI, Tarasova AS, Kostromitsky DN, Dobrodeev AY, Afanasiev SA, Cherdyntseva NV. Genomic and Transcriptomic Research in the Discovery and Application of Colorectal Cancer Circulating Markers. Int J Mol Sci 2023; 24:12407. [PMID: 37569782 PMCID: PMC10419249 DOI: 10.3390/ijms241512407] [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] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/24/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023] Open
Abstract
Colorectal cancer (CRC) is the most frequently occurring malignancy in the world. However, the mortality from CRC can be reduced through early diagnostics, selection of the most effective treatment, observation of the therapy success, and the earliest possible diagnosis of recurrences. A comprehensive analysis of genetic and epigenetic factors contributing to the CRC development is needed to refine diagnostic, therapeutic, and preventive strategies and to ensure appropriate decision making in managing specific CRC cases. The liquid biopsy approach utilizing circulating markers has demonstrated its good performance as a tool to detect the changes in the molecular pathways associated with various cancers. In this review, we attempted to brief the main tendencies in the development of circulating DNA and RNA-based markers in CRC such as cancer-associated DNA mutations, DNA methylation changes, and non-coding RNA expression shifts. Attention is devoted to the existing circulating nucleic acid-based CRC markers, the possibility of their application in clinical practice today, and their future improvement. Approaches to the discovery and verification of new markers are described, and the existing problems and potential solutions for them are highlighted.
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Affiliation(s)
- Anastasia A. Ponomaryova
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia
| | - Elena Yu. Rykova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Engineering Problems of Ecology, Novosibirsk State Technical University, 630087 Novosibirsk, Russia
| | - Anastasia I. Solovyova
- Department of Biochemistry, Medico-Biological Faculty, Siberian State Medical University, 634050 Tomsk, Russia
| | - Anna S. Tarasova
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia
| | - Dmitry N. Kostromitsky
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia
| | - Alexey Yu. Dobrodeev
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia
| | - Sergey A. Afanasiev
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia
| | - Nadezhda V. Cherdyntseva
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia
- Faculty of Chemistry, National Research Tomsk State University, 634050 Tomsk, Russia
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18
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Domrazek K, Pawłowski K, Jurka P. Usefulness of BRCA and ctDNA as Prostate Cancer Biomarkers: A Meta-Analysis. Cancers (Basel) 2023; 15:3452. [PMID: 37444562 DOI: 10.3390/cancers15133452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/23/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Prostate cancer represents the most common male urologic neoplasia. Tissue biopsies are the gold standard in oncology for diagnosing prostate cancer. We conducted a study to find the most reliable and noninvasive diagnostic tool. We performed a systematic review and meta-analysis of two biomarkers which we believe are the most interesting: BRCA (BRCA1 and 2) and ctDNA. Our systematic research yielded 248 articles. Forty-five duplicates were first excluded and, upon further examination, a further 203 articles were excluded on the basis of the inclusion and exclusion criteria, leaving 25 articles. A statistical analysis of the obtained data has been performed. With a collective calculation, BRCA1 was expressed in 2.74% of all cases from 24,212 patients examined and BRCA2 in 1.96% of cases from 20,480 patients. In a total calculation using ctDNA, it was observed that 89% of cases from 1198 patients exhibited high expression of circulating tumor DNA. To date, no ideal PCa biomarker has been found. Although BRCA1 and BRCA2 work well for breast and ovarian cancers, they do not seem to be reliable for prostate cancer. ctDNA seems to be a much better biomarker; however, there are few studies in this area. Further studies need to be performed.
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Affiliation(s)
- Kinga Domrazek
- Department of Small Animal Diseases and Clinic, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Nowoursynowska 159c, 02-776 Warsaw, Poland
| | - Karol Pawłowski
- Department of Pathology and Veterinary Diagnostics, Faculty of Veterinary Medicine, Warsaw University of Life Sciences, Nowoursynowska 159c, 02-776 Warsaw, Poland
| | - Piotr Jurka
- Department of Small Animal Diseases and Clinic, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Nowoursynowska 159c, 02-776 Warsaw, Poland
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Neagu AN, Whitham D, Bruno P, Morrissiey H, Darie CA, Darie CC. Omics-Based Investigations of Breast Cancer. Molecules 2023; 28:4768. [PMID: 37375323 DOI: 10.3390/molecules28124768] [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: 05/19/2023] [Revised: 06/08/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Breast cancer (BC) is characterized by an extensive genotypic and phenotypic heterogeneity. In-depth investigations into the molecular bases of BC phenotypes, carcinogenesis, progression, and metastasis are necessary for accurate diagnoses, prognoses, and therapy assessments in predictive, precision, and personalized oncology. This review discusses both classic as well as several novel omics fields that are involved or should be used in modern BC investigations, which may be integrated as a holistic term, onco-breastomics. Rapid and recent advances in molecular profiling strategies and analytical techniques based on high-throughput sequencing and mass spectrometry (MS) development have generated large-scale multi-omics datasets, mainly emerging from the three "big omics", based on the central dogma of molecular biology: genomics, transcriptomics, and proteomics. Metabolomics-based approaches also reflect the dynamic response of BC cells to genetic modifications. Interactomics promotes a holistic view in BC research by constructing and characterizing protein-protein interaction (PPI) networks that provide a novel hypothesis for the pathophysiological processes involved in BC progression and subtyping. The emergence of new omics- and epiomics-based multidimensional approaches provide opportunities to gain insights into BC heterogeneity and its underlying mechanisms. The three main epiomics fields (epigenomics, epitranscriptomics, and epiproteomics) are focused on the epigenetic DNA changes, RNAs modifications, and posttranslational modifications (PTMs) affecting protein functions for an in-depth understanding of cancer cell proliferation, migration, and invasion. Novel omics fields, such as epichaperomics or epimetabolomics, could investigate the modifications in the interactome induced by stressors and provide PPI changes, as well as in metabolites, as drivers of BC-causing phenotypes. Over the last years, several proteomics-derived omics, such as matrisomics, exosomics, secretomics, kinomics, phosphoproteomics, or immunomics, provided valuable data for a deep understanding of dysregulated pathways in BC cells and their tumor microenvironment (TME) or tumor immune microenvironment (TIMW). Most of these omics datasets are still assessed individually using distinct approches and do not generate the desired and expected global-integrative knowledge with applications in clinical diagnostics. However, several hyphenated omics approaches, such as proteo-genomics, proteo-transcriptomics, and phosphoproteomics-exosomics are useful for the identification of putative BC biomarkers and therapeutic targets. To develop non-invasive diagnostic tests and to discover new biomarkers for BC, classic and novel omics-based strategies allow for significant advances in blood/plasma-based omics. Salivaomics, urinomics, and milkomics appear as integrative omics that may develop a high potential for early and non-invasive diagnoses in BC. Thus, the analysis of the tumor circulome is considered a novel frontier in liquid biopsy. Omics-based investigations have applications in BC modeling, as well as accurate BC classification and subtype characterization. The future in omics-based investigations of BC may be also focused on multi-omics single-cell analyses.
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Affiliation(s)
- Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, "Alexandru Ioan Cuza" University of Iasi, Carol I Bvd, No. 20A, 700505 Iasi, Romania
| | - Danielle Whitham
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Pathea Bruno
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Hailey Morrissiey
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Celeste A Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Costel C Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
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Li S, Zhang H, Zhu M, Kuang Z, Li X, Xu F, Miao S, Zhang Z, Lou X, Li H, Xia F. Electrochemical Biosensors for Whole Blood Analysis: Recent Progress, Challenges, and Future Perspectives. Chem Rev 2023. [PMID: 37262362 DOI: 10.1021/acs.chemrev.1c00759] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Whole blood, as one of the most significant biological fluids, provides critical information for health management and disease monitoring. Over the past 10 years, advances in nanotechnology, microfluidics, and biomarker research have spurred the development of powerful miniaturized diagnostic systems for whole blood testing toward the goal of disease monitoring and treatment. Among the techniques employed for whole-blood diagnostics, electrochemical biosensors, as known to be rapid, sensitive, capable of miniaturization, reagentless and washing free, become a class of emerging technology to achieve the target detection specifically and directly in complex media, e.g., whole blood or even in the living body. Here we are aiming to provide a comprehensive review to summarize advances over the past decade in the development of electrochemical sensors for whole blood analysis. Further, we address the remaining challenges and opportunities to integrate electrochemical sensing platforms.
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Affiliation(s)
- Shaoguang Li
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Hongyuan Zhang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Man Zhu
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Zhujun Kuang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Xun Li
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Fan Xu
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Siyuan Miao
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Zishuo Zhang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Xiaoding Lou
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Hui Li
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
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Quraish RU, Hirahata T, Quraish AU, ul Quraish S. An Overview: Genetic Tumor Markers for Early Detection and Current Gene Therapy Strategies. Cancer Inform 2023; 22:11769351221150772. [PMID: 36762284 PMCID: PMC9903029 DOI: 10.1177/11769351221150772] [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: 07/05/2022] [Accepted: 12/24/2022] [Indexed: 02/04/2023] Open
Abstract
Genomic instability is considered a fundamental factor involved in any neoplastic disease. Consequently, the genetically unstable cells contribute to intratumoral genetic heterogeneity and phenotypic diversity of cancer. These genetic alterations can be detected by several diagnostic techniques of molecular biology and the detection of alteration in genomic integrity may serve as reliable genetic molecular markers for the early detection of cancer or cancer-related abnormal changes in the body cells. These genetic molecular markers can detect cancer earlier than any other method of cancer diagnosis, once a tumor is diagnosed, then replacement or therapeutic manipulation of these cancer-related abnormal genetic changes can be possible, which leads toward effective and target-specific cancer treatment and in many cases, personalized treatment of cancer could be performed without the adverse effects of chemotherapy and radiotherapy. In this review, we describe how these genetic molecular markers can be detected and the possible ways for the application of this gene diagnosis for gene therapy that can attack cancerous cells, directly or indirectly, which lead to overall improved management and quality of life for a cancer patient.
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Affiliation(s)
| | - Tetsuyuki Hirahata
- Tetsuyuki Hirahata, Hirahata Gene Therapy Laboratory, HIC Clinic #1105, Itocia Office Tower 11F, 2-7-1, Yurakucho, Chiyoda-ku, Tokyo 100-0006, Japan.
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22
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Zhao M, Li Q, Yang J, Zhang M, Liu X, Zhang H, Huang Y, Li J, Bao J, Wang J, Du J, Guan T, Su L. Application of circulating tumour DNA in terms of prognosis prediction in Chinese follicular lymphoma patients. Front Genet 2023; 14:1066808. [PMID: 37152994 PMCID: PMC10157236 DOI: 10.3389/fgene.2023.1066808] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 03/27/2023] [Indexed: 05/09/2023] Open
Abstract
Background: Follicular lymphoma (FL), an indolent non-Hodgkin lymphoma (NHL), is generally incurable. Favourable prognosis and durable remission are crucial for FL patients. The genetic mutation spectrum provides novel biomarkers for determining the prognosis of FL patients, but its detection is easily affected by the collection of tumour tissue biopsies. In this study, we aimed to describe the mutational landscape of FL using circulating tumour DNA (ctDNA) samples and to explore the relationship between mutations and prognostic indicators of clinical outcome in patients with newly diagnosed follicular lymphoma and the prognostic value of such mutations. Methods: A total of 28 patients with newly diagnosed FL were included in this study. A targeted NGS-based 59-gene panel was used to assess the ctDNA mutation profiles. Differences in clinical factors between patients carrying mutations and those without mutations were analysed. We also explored the relationship between gene mutation status, mean VAFs (variant allele frequencies) and clinical factors. The Kaplan‒Meier method was applied to analyse the overall survival (OS) and progression-free survival (PFS) of patients carrying mutations and those without mutations. Results: ctDNA mutations were detectable in 21 (75%) patients. The most commonly mutated genes were CREBBP (54%, 15/28), KMT2D (50%, 14/28), STAT6 (29%, 8/28), CARD11 (18%, 5/28), PCLO (14%, 4/28), EP300 (14%, 4/28), BCL2 (11%, 3/28), and TNFAIP3 (11%, 3/28), with a mutation frequency of >10%. Patients with detectable ctDNA mutation tended to present with advanced Ann Arbor stage (III-IV) (p = 0.009), high FLIPI risk (3-5) (p = 0.023) and severe lymph node involvement (No. of involved areas ≥5) (p = 0.02). In addition, we found that the mean VAF was significantly higher in patients with advanced Ann Arbor stage, high-risk FLIPI, elevated lactate dehydrogenase (LDH: 0-248U/L), advanced pathology grade, bone marrow involvement (BMI) and lymph node involvement. Additionally, KMT2D, EP300, and STAT6 mutations were associated with inferior PFS (p < 0.05). Conclusion: We described the ctDNA mutation landscapes in Chinese patients with newly diagnosed FL and found that ctDNA VAF means reflect tumour burden. Moreover, PFS was shorter in patients with KMT2D, EP300 and STAT6 mutations.
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Affiliation(s)
- Mengjing Zhao
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Shanxi Medical University, Taiyuan, China
- Department of Hematology, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Qingjuan Li
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Shanxi Medical University, Taiyuan, China
| | - Jing Yang
- Department of Hematology, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Min Zhang
- Department of Hematology, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Xiaolan Liu
- Department of Hematology, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Hongwei Zhang
- Department of Hematology, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Yunpeng Huang
- Department of Hematology, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Jing Li
- Department of Pathology, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Jiangping Bao
- Department of Hematology, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Jingfang Wang
- Department of Hematology, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Jun Du
- Department of Microbial and Biochemical Pharmacy, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Tao Guan
- Department of Hematology, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
- *Correspondence: Tao Guan, ; Liping Su,
| | - Liping Su
- Department of Hematology, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
- *Correspondence: Tao Guan, ; Liping Su,
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23
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Telekes A, Horváth A. The Role of Cell-Free DNA in Cancer Treatment Decision Making. Cancers (Basel) 2022; 14:6115. [PMID: 36551600 PMCID: PMC9776613 DOI: 10.3390/cancers14246115] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022] Open
Abstract
The aim of this review is to evaluate the present status of the use of cell-free DNA and its fraction of circulating tumor DNA (ctDNA) because this year July 2022, an ESMO guideline was published regarding the application of ctDNA in patient care. This review is for clinical oncologists to explain the concept, the terms used, the pros and cons of ctDNA; thus, the technical aspects of the different platforms are not reviewed in detail, but we try to help in navigating the current knowledge in liquid biopsy. Since the validated and adequately sensitive ctDNA assays have utility in identifying actionable mutations to direct targeted therapy, ctDNA may be used for this soon in routine clinical practice and in other different areas as well. The cfDNA fragments can be obtained by liquid biopsy and can be used for diagnosis, prognosis, and selecting among treatment options in cancer patients. A great proportion of cfDNA comes from normal cells of the body or from food uptake. Only a small part (<1%) of it is related to tumors, originating from primary tumors, metastatic sites, or circulating tumor cells (CTCs). Soon the data obtained from ctDNA may routinely be used for finding minimal residual disease, detecting relapse, and determining the sites of metastases. It might also be used for deciding appropriate therapy, and/or emerging resistance to the therapy and the data analysis of ctDNA may be combined with imaging or other markers. However, to achieve this goal, further clinical validations are inevitable. As a result, clinicians should be aware of the limitations of the assays. Of course, several open questions are still under research and because of it cfDNA and ctDNA testing are not part of routine care yet.
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Affiliation(s)
- András Telekes
- Omnimed-Etosz, Ltd., 81 Széher Rd., 1021 Budapest, Hungary
- Semmelweis University, 26. Üllői Rd., 1085 Budapest, Hungary
| | - Anna Horváth
- Department of Internal Medicine and Haematology, Semmelweis University, 46. Szentkirályi Rd., 1088 Budapest, Hungary
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24
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Guan T, Zhang M, Liu X, Li J, Xin B, Ren Y, Yang Y, Wang H, Zhao M, Huang Y, Guo X, Du J, Qian W, Su L. Circulating tumor DNA mutation profile is associated with the prognosis and treatment response of Chinese patients with newly diagnosed diffuse large B-cell lymphoma. Front Oncol 2022; 12:1003957. [DOI: 10.3389/fonc.2022.1003957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/17/2022] [Indexed: 11/18/2022] Open
Abstract
BackgroundCharacterization of gene mutation profiles can provide new treatment options for patients with diffuse large B-cell lymphoma (DLBCL). However, this method is challenged by the limited source of tissue specimens, especially those of DLBCL patients at advanced stages. Therefore, in the current study, we aimed to describe the gene mutation landscape of DLBCL using circulating tumor DNA (ctDNA) samples obtained from patients’ blood samples, as well as to explore the relationship between ctDNA mutations and the prognosis and treatment response of patients with newly diagnosed DLBCL.MethodsA total of 169 newly diagnosed Chinese DLBCL patients were included in this study, among which 85 patients were divided into a training set and 84 were assigned into a validation set. The mutation profile of a 59-gene panel was analyzed by targeted next generation sequencing (NGS) of the patients’ ctDNA samples. Differences in clinical factors between patients with and without ctDNA mutations were analyzed. In addition, we also explored gene mutation frequencies between GCB and non-GCB subtypes, and the relationship between gene mutation status, clinical factors, mean VAF (variant allele frequencies) and the patients’ overall survival (OS) and progression-free survival (PFS).ResultsctDNA mutations were detected in 64 (75.3%) patients of the training set and 67 (79.8%) patients of the validation set. The most commonly mutated genes in both sets were PCLO, PIM1, MYD88, TP53, KMT2D, CD79B, HIST1H1E and LRP1B, with mutation frequencies of >10%. Patients with detectable ctDNA mutations trended to present advanced Ann Arbor stages (III-IV), elevated LDH (lactate dehydrogenase) levels, shorter OS and PFS, and a lower complete response (CR) rate to the R-CHOP regimen compared with DLBCL patients without ctDNA mutations. In addition, mean VAF (≥4.94%) and PCLO mutations were associated with poor OS and PFS.ConclusionWe investigated the ctDNA mutation landscape in Chinese patients with newly diagnosed DLBCL and found that ctDNA could reflect tumor burden and patients with detectable ctDNA mutations trended to have shorter OS and PFS and a lower CR rate.
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25
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Puccini A, Seeber A, Berger MD. Biomarkers in Metastatic Colorectal Cancer: Status Quo and Future Perspective. Cancers (Basel) 2022; 14:4828. [PMID: 36230751 PMCID: PMC9564318 DOI: 10.3390/cancers14194828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/20/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
Colorectal cancer (CRC) is the third most frequent cancer worldwide, and its incidence is steadily increasing. During the last two decades, a tremendous improvement in outcome has been achieved, mainly due to the introduction of novel drugs, targeted treatment, immune checkpoint inhibitors (CPIs) and biomarker-driven patient selection. Moreover, progress in molecular diagnostics but also improvement in surgical techniques and local ablative treatments significantly contributed to this success. However, novel therapeutic approaches are needed to further improve outcome in patients diagnosed with metastatic CRC. Besides the established biomarkers for mCRC, such as microsatellite instability (MSI) or mismatch repair deficiency (dMMR), RAS/BRAF, sidedness and HER2 amplification, new biomarkers have to be identified to better select patients who derive the most benefit from a specific treatment. In this review, we provide an overview about therapeutic relevant and established biomarkers but also shed light on potential promising markers that may help us to better tailor therapy to the individual mCRC patient in the near future.
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Affiliation(s)
- Alberto Puccini
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
- Department of Internal Medicine and Medical Specialties (DIMI), School of Medicine, University of Genoa, 16132 Genoa, Italy
| | - Andreas Seeber
- Department of Hematology and Oncology, Comprehensive Cancer Center Innsbruck, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Martin D Berger
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland
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Methodology established for the detection of circulating tumor DNA by hybridization capture. Biotechniques 2022; 73:151-158. [PMID: 36065956 DOI: 10.2144/btn-2022-0029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Roche's AVENIO ctDNA analysis kits and bioinformatics analysis (the AVENIO system) are accessible to all NGS laboratories. We have developed an approach, namely the Sec-Seq system, and compared the accuracy, sensitivity, repeatability and economic cost between the AVENIO system and the Sec-Seq system. Both methods share the comparable accuracy and sensitivity in detecting the variant allele frequency of 0.0005, while the Sec-Seq system shows better accuracy in detecting the variant allele frequency of 0.001. Furthermore, the Sec-Seq system displays a much better detection sensitivity than the AVENIO system. The Sec-Seq system has satisfactory performance in detecting the rare genetic variants in ctDNA with lower economic cost compared with the AVENIO system.
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Liu Z, Han Y, Dang Q, Xu H, Zhang Y, Duo M, Lv J, Li H, Kong Y, Han X. Roles of circulating tumor DNA in PD-1/PD-L1 immune checkpoint Inhibitors: Current evidence and future directions. Int Immunopharmacol 2022; 111:109173. [PMID: 35998502 DOI: 10.1016/j.intimp.2022.109173] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/11/2022] [Accepted: 08/14/2022] [Indexed: 12/18/2022]
Abstract
Circulating tumor DNA (ctDNA) sequencing holds considerable promise for early diagnosis and detection of surveillance and minimal residual disease. Blood ctDNA monitors specific cancers by detecting the alterations found in cancer cells, such as apoptosis and necrosis. Due to the short half-life, ctDNA reflects the actual burden of other treatments on tumors. In addition, ctDNA might be preferable to monitor tumor development and treatment compared with invasive tissue biopsy. ctDNA-based liquid biopsy brings remarkable strength to targeted therapy and precision medicine. Notably, multiple ctDNA analysis platforms have been broadly applied in clinical immunotherapy. Through targeted sequencing, early variations in ctDNA could predict response to immune checkpoint inhibitor (ICI). Several studies have demonstrated a correlation between ctDNA kinetics and anti-PD1 antibodies. The need for further research and development remains, although this biomarker holds significant prospects for early cancer detection. This review focuses on describing the basis of ctDNA and its current utilities in oncology and immunotherapy, either for clinical management or early detection, highlighting its advantages and inherent limitations.
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Affiliation(s)
- Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China; Interventional Institute of Zhengzhou University, Zhengzhou, Henan 450052, China; Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan 450052, China.
| | - Yilin Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Qin Dang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Hui Xu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Yuyuan Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Mengjie Duo
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Jinxiang Lv
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Huanyun Li
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Ying Kong
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China; Interventional Institute of Zhengzhou University, Zhengzhou, Henan 450052, China; Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan 450052, China.
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28
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Liu S, Wang J. Current and Future Perspectives of Cell-Free DNA in Liquid Biopsy. Curr Issues Mol Biol 2022; 44:2695-2709. [PMID: 35735625 PMCID: PMC9222159 DOI: 10.3390/cimb44060184] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/01/2022] [Accepted: 06/09/2022] [Indexed: 11/16/2022] Open
Abstract
A liquid biopsy is a minimally invasive or non-invasive method to analyze a range of tumor material in blood or other body fluids, including circulating tumor cells (CTCs), cell-free DNA (cfDNA), messenger RNA (mRNA), microRNA (miRNA), and exosomes, which is a very promising technology. Among these cancer biomarkers, plasma cfDNA is the most widely used in clinical practice. Compared with a tissue biopsy of traditional cancer diagnosis, in assessing tumor heterogeneity, a liquid biopsy is more reliable because all tumor sites release cfDNA into the blood. Therefore, a cfDNA liquid biopsy is less invasive and comprehensive. Moreover, the development of next-generation sequencing technology makes cfDNA sequencing more sensitive than a tissue biopsy, with higher clinical applicability and wider application. In this publication, we aim to review the latest perspectives of cfDNA liquid biopsy clinical significance and application in cancer diagnosis, treatment, and prognosis. We introduce the sequencing techniques and challenges of cfDNA detection, analysis, and clinical applications, and discuss future research directions.
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