1
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Ren S, Yu C, Huang Q. Diagnostic value of combined detection of plasma cfDNA concentration and integrity in NSCLC. Lung Cancer Manag 2024; 13:LMT64. [PMID: 38812772 PMCID: PMC11131340 DOI: 10.2217/lmt-2023-0009] [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: 08/28/2023] [Accepted: 12/12/2023] [Indexed: 05/31/2024] Open
Abstract
Aim: To evaluate the value of combined detection of plasma cfDNA concentration and integrity in the early diagnosis of NSCLC. Methods: Real-time fluorescence quantitative PCR was used to determine the concentration and integrity of plasma cfDNA in 71 NSCLC patients and 53 healthy people. Results: Combined detection of plasma cfDNA concentration and integrity had higher diagnostic power in differentiating NSCLC patients with stage I/II from healthy people than detection of plasma cfDNA concentration alone or integrity alone. The AUC, sensitivity and specificity of the combined detection of plasma cfDNA concentration and integrity were 0.781, 0.62 and 0.85. Conclusion: Combined detection of plasma cfDNA concentration and integrity could improve the diagnostic value in NSCLC detection.
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Affiliation(s)
- Sai Ren
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, 400042, PR China
- Department of Laboratory Medicine, People's Hospital of Chongqing Liang Jiang New Area, Chongqing, 401121, PR China
| | - Chunli Yu
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, 400042, PR China
- Department of Laboratory Medicine, Chengdu Xinhua Hospital, Chengdu, 610055, PR China
| | - Qing Huang
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, 400042, PR China
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2
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Deng E, Fan X. Categorizing Extrachromosomal Circular DNA as Biomarkers in Serum of Cancer. Biomolecules 2024; 14:488. [PMID: 38672504 PMCID: PMC11048305 DOI: 10.3390/biom14040488] [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: 02/23/2024] [Revised: 04/07/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Extrachromosomal circular DNA (eccDNA), a double-stranded circular DNA molecule found in multiple organisms, has garnered an increasing amount of attention in recent years due to its close association with the initiation, malignant progression, and heterogeneous evolution of cancer. The presence of eccDNA in serum assists in non-invasive tumor diagnosis as a biomarker that can be assessed via liquid biopsies. Furthermore, the specific expression patterns of eccDNA provide new insights into personalized cancer therapy. EccDNA plays a pivotal role in tumorigenesis, development, diagnosis, and treatment. In this review, we comprehensively outline the research trajectory of eccDNA, discuss its role as a diagnostic and prognostic biomarker, and elucidate its regulatory mechanisms in cancer. In particular, we emphasize the potential application value of eccDNA in cancer diagnosis and treatment and anticipate the development of novel tumor diagnosis strategies based on serum eccDNA in the future.
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Affiliation(s)
- Enze Deng
- Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, China
| | - Xiaoying Fan
- Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, China
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510005, China
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3
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Ali M, Choudhary R, Singh K, Kumari S, Kumar R, Graham BB, Pasha MAQ, Rabyang S, Thinlas T, Mishra A. Hypobaric hypoxia modulated structural characteristics of circulating cell-free DNA in high-altitude pulmonary edema. Am J Physiol Lung Cell Mol Physiol 2024; 326:L496-L507. [PMID: 38349115 DOI: 10.1152/ajplung.00245.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 01/10/2024] [Accepted: 01/25/2024] [Indexed: 04/07/2024] Open
Abstract
The utility of cell-free (cf) DNA has extended as a surrogate or clinical biomarker for various diseases. However, a more profound and expanded understanding of the diverse cfDNA population and its correlation with physiological phenotypes and environmental factors is imperative for using its full potential. The high-altitude (HA; altitude > 2,500 m above sea level) environment characterized by hypobaric hypoxia offers an observational case-control design to study the differential cfDNA profile in patients with high-altitude pulmonary edema (HAPE) (number of subjects, n = 112) and healthy HA sojourners (n = 111). The present study investigated cfDNA characteristics such as concentration, fragment length size, degree of integrity, and subfractions reflecting mitochondrial-cfDNA copies in the two groups. The total cfDNA level was significantly higher in patients with HAPE, and the level increased with increasing HAPE severity (P = 0.0036). A lower degree of cfDNA integrity of 0.346 in patients with HAPE (P = 0.001) indicated the prevalence of shorter cfDNA fragments in circulation in patients compared with the healthy HA sojourners. A significant correlation of cfDNA characteristics with the peripheral oxygen saturation levels in the patient group demonstrated the translational relevance of cfDNA molecules. The correlation was further supported by multivariate logistic regression and receiver operating characteristic curve. To our knowledge, our study is the first to highlight the association of higher cfDNA concentration, a lower degree of cfDNA integrity, and increased mitochondrial-derived cfDNA population with HAPE disease severity. Further deep profiling of cfDNA fragments, which preserves cell-type specific genetic and epigenetic features, can provide dynamic physiological responses to hypoxia.NEW & NOTEWORTHY This study observed altered cell-free (cf) DNA fragment patterns in patients with high-altitude pulmonary edema and the significant correlation of these patterns with peripheral oxygen saturation levels. This suggests deep profiling of cfDNA fragments in the future may identify genetic and epigenetic mechanisms underlying physiological and pathophysiological responses to hypoxia.
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Affiliation(s)
- Manzoor Ali
- Cardio Respiratory Disease Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Raushni Choudhary
- Cardio Respiratory Disease Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Kanika Singh
- Cardio Respiratory Disease Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Swati Kumari
- Cardio Respiratory Disease Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rahul Kumar
- Department of Medicine, University of California, San Francisco, California, United States
- Lung Biology Center, Zuckerberg San Francisco General Hospital, San Francisco, California, United States
| | - Brian B Graham
- Department of Medicine, University of California, San Francisco, California, United States
- Lung Biology Center, Zuckerberg San Francisco General Hospital, San Francisco, California, United States
| | | | - Stanzen Rabyang
- Department of Medicine, Sonam Norboo Memorial Hospital, Leh, India
| | - Tashi Thinlas
- Department of Medicine, Sonam Norboo Memorial Hospital, Leh, India
| | - Aastha Mishra
- Cardio Respiratory Disease Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Shim SM, Lee M, Jeon JP. Assessment of the Impact of Preanalytical DNA Integrity on the Genome Data Quality. Biopreserv Biobank 2024. [PMID: 38563611 DOI: 10.1089/bio.2023.0050] [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: 04/04/2024] Open
Abstract
Many molecular approaches have been employed for the quality control (QC) of biobanked DNA samples. Since 2003, the National Biobank of Korea (NBK) has provided various studies with over half a million quality-controlled genomic DNA samples using conventional agarose gel electrophoresis and spectrophotometry. We assessed the postanalytical genomic data quality of DNA samples (n = 41) with a different range of the DNA quality index such as genomic quality number (GQN) for developing an evidence-based best practice for DNA quality criteria. We examined the quality indices of three different platforms, including single nucleotide polymorphism arrays, methylation arrays, and next-generation sequencing, using the same DNA samples (n = 41) of different quality, ranging from 4.0 to 10.0 values of the GQN. Our data analysis revealed that higher GQN value and/or double-stranded DNA concentration resulted in higher quality genomic data. In addition, all the analyzed DNA samples successfully generated good-quality genomic data. This study provides a guide for the QC of biobanked DNA samples for genomic analysis platforms.
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Affiliation(s)
- Sung-Mi Shim
- Division of Biobank, Department of Precision Medicine, Korea National Institute of Health, Cheongju-si, Republic of Korea
| | - Meehee Lee
- Division of Biobank, Department of Precision Medicine, Korea National Institute of Health, Cheongju-si, Republic of Korea
| | - Jae-Pil Jeon
- Division of Biobank, Department of Precision Medicine, Korea National Institute of Health, Cheongju-si, Republic of Korea
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Bruno V, Logoteta A, Chiofalo B, Mancini E, Betti M, Fabrizi L, Piccione E, Vizza E. It is time to implement molecular classification in endometrial cancer. Arch Gynecol Obstet 2024; 309:745-753. [PMID: 37410149 DOI: 10.1007/s00404-023-07128-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] [Received: 12/06/2022] [Accepted: 05/11/2023] [Indexed: 07/07/2023]
Abstract
A huge effort has been done in redefining endometrial cancer (EC) risk classes in the last decade. However, known prognostic factors (FIGO staging and grading, biomolecular classification and ESMO-ESGO-ESTRO risk classes stratification) are not able to predict outcomes and especially recurrences. Biomolecular classification has helped in re-classifying patients for a more appropriate adjuvant treatment and clinical studies suggest that currently used molecular classification improves the risk assessment of women with EC, however, it does not clearly explain differences in recurrence profiles. Furthermore, a lack of evidence appears in EC guidelines. Here, we summarize the main concepts why molecular classification is not enough in the management of endometrial cancer, by highlighting some promising innovative examples in scientific literature studies with a clinical potential significant impact.
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Affiliation(s)
- Valentina Bruno
- Gynecologic Oncology Unit, Department of Experimental Clinical Oncology, IRCCS "Regina Elena" National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - Alessandra Logoteta
- Department of Maternal and Child Health and Urological Sciences, University of Rome "Sapienza", Policlinico "Umberto I", Rome, Italy
| | - Benito Chiofalo
- Gynecologic Oncology Unit, Department of Experimental Clinical Oncology, IRCCS "Regina Elena" National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy.
| | - Emanuela Mancini
- Gynecologic Oncology Unit, Department of Experimental Clinical Oncology, IRCCS "Regina Elena" National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - Martina Betti
- Biostatistics, Bioinformatics and Clinical Trial Center, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Luana Fabrizi
- Department of Anesthesiology, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Emilio Piccione
- Department of Surgical Sciences, Catholic University Our Lady of Good Counsel, Tirane, Albania
| | - Enrico Vizza
- Gynecologic Oncology Unit, Department of Experimental Clinical Oncology, IRCCS "Regina Elena" National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
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6
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Wang M, Lv X, Wang Y, Li Y, Li H, Shen Z, Zhao L. Biomarkers of peripheral blood neutrophil extracellular traps in the diagnosis and progression of malignant tumors. Cancer Med 2024; 13:e6935. [PMID: 38230764 PMCID: PMC10905219 DOI: 10.1002/cam4.6935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 12/20/2023] [Accepted: 12/24/2023] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND AND AIMS The mortality rate associated with malignant tumors remains high and there is a lack of effective diagnostic and tumor progression markers. Neutrophil extracellular traps (NETs) can promote tumor-associated thrombosis, invasive metastasis, and inflammatory responses, but there is a lack of research on the value of measuring NETs in the peripheral blood of patients with malignancies. METHODS We included 263 patients with malignancies (55 gliomas, 101 ovarian, 64 colorectal, and 43 lung cancers) and 75 healthy controls in this study. We compared the levels of citrullinated histone H3 (citH3), cell-free DNA (cfDNA), and systemic inflammation-related parameters, including neutrophils, lymphocytes, monocytes, platelets, neutrophil-to-lymphocyte ratio, monocyte-to-lymphocyte ratio, platelet-to-lymphocyte ratio, systemic immune inflammation index, and systemic inflammation response index. We assessed the value of changes in NETs in peripheral blood to determine the diagnosis, venous thromboembolism, clinical staging, and systemic inflammatory response in patients with malignancy. RESULTS The levels of citH3 and cfDNA in peripheral blood can distinguish between healthy controls and tumor patients. The levels of citH3 and cfDNA before clinical intervention did not predict the risk of combined venous thromboembolism in oncology patients in the short-term after clinical intervention. The levels of citH3, cfDNA, and systemic inflammation-related parameters in the peripheral blood of tumor patients increased with the clinical stage. There was a correlation between cfDNA levels in peripheral blood and systemic inflammation-related parameters in tumor patients, and this correlation was more significant in patients with advanced tumors. CONCLUSIONS Changes in NETs in the peripheral blood differ between healthy controls and patients with malignant tumors. NETs may be involved in tumor-induced systemic inflammatory responses through interaction with circulating inflammatory cells, thus promoting tumor progression. NETs may be used as markers to assist in the diagnosis and progression of tumor malignancy.
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Affiliation(s)
- Min Wang
- Department of Blood TransfusionSecond Hospital of Jilin UniversityChangchunChina
| | - Xiaoyan Lv
- Department of Experimental MedicineSecond Hospital of Jilin UniversityChangchunChina
| | - Ying Wang
- Department of Experimental MedicineSecond Hospital of Jilin UniversityChangchunChina
| | - Yao Li
- Department of Blood TransfusionSecond Hospital of Jilin UniversityChangchunChina
| | - Honghong Li
- Department of Blood TransfusionSecond Hospital of Jilin UniversityChangchunChina
| | - Zhongjun Shen
- Department of Blood TransfusionSecond Hospital of Jilin UniversityChangchunChina
| | - Liyan Zhao
- Department of Blood TransfusionSecond Hospital of Jilin UniversityChangchunChina
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7
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Tagawa M, Aoki M. Clinical utility of liquid biopsy in canine oral malignant melanoma using cell-free DNA. Front Vet Sci 2023; 10:1182093. [PMID: 37408834 PMCID: PMC10319414 DOI: 10.3389/fvets.2023.1182093] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 06/05/2023] [Indexed: 07/07/2023] Open
Abstract
Introduction Cell-free DNA (cfDNA), an extracellular free DNA released into the bloodstream by cells, is a potentially useful noninvasive marker to detect human malignancies and monitor response to treatment. In the present study, we evaluated the utility of circulating cfDNA in canine patients with oral malignant melanoma (OMM) in assessing therapeutic response and clinical outcomes. Methods Plasma samples were collected from 12 dogs with OMM and 9 healthy controls. cfDNA concentration was quantified by real-time PCR resulting in short (99bp) and long (218bp) fragments of long interspersed nuclear element-1 (LINE-1), and the DNA integrity index (DII) was then calculated (218/99). A follow-up study was conducted on 6 dogs with OMM, and the plasma cfDNA and DII were quantified throughout disease progression. Results Although cfDNA levels obtained from dogs with OMM were not significantly different compared to those obtained from healthy controls, the DII was significantly lower in dogs with OMM than in healthy controls. The DII tended to decrease as the disease stage progressed. Moreover, changes in cfDNA concentration and DII along the clinical course were observed when major changes, such as metastasis or apparent tumor progression, were observed. Discussion The results of our study suggest that measurements of serum cfDNA and DII using LINE-1 might be valuable new biomarkers for monitoring OMM progression in dogs. This preliminary study demonstrated the potential clinical utility of monitoring plasma cfDNA in canine patients with OMM.
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Affiliation(s)
- Michihito Tagawa
- Veterinary Medical Center, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan
- Department of Veterinary Associated Science, Okayama University of Science, Imabari, Japan
| | - Minori Aoki
- Veterinary Medical Center, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan
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Shen Y, Yang W, Liu J, Zhang Y. Minimally invasive approaches for the early detection of endometrial cancer. Mol Cancer 2023; 22:53. [PMID: 36932368 PMCID: PMC10022290 DOI: 10.1186/s12943-023-01757-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 03/07/2023] [Indexed: 03/19/2023] Open
Abstract
Endometrial cancer (EC) is one of the most common gynecologic cancers and its incidence is rising globally. Although advanced EC has a poor prognosis; diagnosing EC at an earlier stage could improve long-term patient outcomes. However, there is no consensus on the early detection strategies for EC and the current diagnostic practices such as transvaginal ultrasound, hysteroscopy and endometrial biopsy are invasive, costly and low in specificity. Thus, accurate and less invasive screening tests that detect EC in women with early stages of the disease are needed. Current research has revolutionized novel EC early detection methodologies in many aspects. This review aims to comprehensively characterizes minimally invasive screening techniques that can be applied to EC in the future, and fully demonstrate their potential in the early detection of EC.
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Affiliation(s)
- Yufei Shen
- Department of Gynecology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wenqing Yang
- Department of Gynecology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Gynaecology Oncology Research and Engineering Central of Hunan Province, Changsha, Hunan, China
| | - Jiacheng Liu
- The Center of Systems Biology and Data Science, School of Basic Medical Science, Central South University, Changsha, Hunan, China.
| | - Yu Zhang
- Department of Gynecology, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Gynaecology Oncology Research and Engineering Central of Hunan Province, Changsha, Hunan, China.
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Caputo V, Ciardiello F, Corte CMD, Martini G, Troiani T, Napolitano S. Diagnostic value of liquid biopsy in the era of precision medicine: 10 years of clinical evidence in cancer. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2023; 4:102-138. [PMID: 36937316 PMCID: PMC10017193 DOI: 10.37349/etat.2023.00125] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 11/13/2022] [Indexed: 03/06/2023] Open
Abstract
Liquid biopsy is a diagnostic repeatable test, which in last years has emerged as a powerful tool for profiling cancer genomes in real-time with minimal invasiveness and tailoring oncological decision-making. It analyzes different blood-circulating biomarkers and circulating tumor DNA (ctDNA) is the preferred one. Nevertheless, tissue biopsy remains the gold standard for molecular evaluation of solid tumors whereas liquid biopsy is a complementary tool in many different clinical settings, such as treatment selection, monitoring treatment response, cancer clonal evolution, prognostic evaluation, as well as the detection of early disease and minimal residual disease (MRD). A wide number of technologies have been developed with the aim of increasing their sensitivity and specificity with acceptable costs. Moreover, several preclinical and clinical studies have been conducted to better understand liquid biopsy clinical utility. Anyway, several issues are still a limitation of its use such as false positive and negative results, results interpretation, and standardization of the panel tests. Although there has been rapid development of the research in these fields and recent advances in the clinical setting, many clinical trials and studies are still needed to make liquid biopsy an instrument of clinical routine. This review provides an overview of the current and future clinical applications and opening questions of liquid biopsy in different oncological settings, with particular attention to ctDNA liquid biopsy.
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Affiliation(s)
- Vincenza Caputo
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Fortunato Ciardiello
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Carminia Maria Della Corte
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Giulia Martini
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Teresa Troiani
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Stefania Napolitano
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
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Nair MG, Ramesh RS, Naidu CM, Mavatkar AD, V. P. S, Ramamurthy V, Somashekaraiah VM, C. E. A, Raghunathan K, Panigrahi A, Das M, Dhar SK, Prabhu JS. Estimation of ALU Repetitive Elements in Plasma as a Cost-Effective Liquid Biopsy Tool for Disease Prognosis in Breast Cancer. Cancers (Basel) 2023; 15:cancers15041054. [PMID: 36831397 PMCID: PMC9953974 DOI: 10.3390/cancers15041054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 02/10/2023] Open
Abstract
BACKGROUND Liquid biopsy is widely recognized as an efficient diagnostic method in oncology for disease detection and monitoring. Though the examination of circulating tumor cells (CTC) is mostly implemented for the assessment of genomic aberrations, the need of complex methodologies for their detection has impeded its acceptance in low-resource settings. We evaluated cell-free DNA (cfDNA) as a liquid biopsy tool and investigated its utility in breast cancer patients. METHODS Total cell-free DNA was extracted from the plasma of breast cancer patients (n = 167) with a median follow-up of more than 5 years, at various stages of the disease. Quantitative PCR was performed to estimate the copy numbers of two fractions of ALU repetitive elements (ALU 115 and ALU 247), and DNA integrity (DI) was calculated as the ratio of ALU 247/115. Mutations in TP53 and PIK3CA in the cfDNA were estimated by next-gen sequencing (NGS) in a subset of samples. Associations of the levels of both the ALU fragments with various clinico-pathological factors and disease-free survival at various stages were examined. Nomogram models were constructed with clinical variables and ALU 247 levels to predict disease-free survival and the best performing model was evaluated by decision curve analysis. RESULTS DI and ALU 247 levels were significantly lower (p < 0.0001) in the post-operative plasma when compared to their pre-surgery levels. DI and ALU 247 were found to be significantly higher in patients with metastasis (p < 0.05). Patients with higher levels of ALU 247 in their post-operative plasma had significant poor disease-free survival (p = 0.005). Higher levels of ALU 247 in the circulation also correlated with low tumor-infiltrating lymphocytes (TIL) within their primary tumors in the ER-negative breast cancer subtype (p = 0.01). Cox proportional hazard analysis confirmed ALU 247 as an independent variable of disease-free survival both in univariate and multivariate analysis [HR 1.3 (95% CI 1.047 to 1.613, p = 0.017)]. The nomogram model showed that the addition of ALU 247 with other variables significantly improved (C-index 0.823) the predictive ability of the model. CONCLUSION Our results confirm the utility of cfDNA as an evolving liquid biopsy tool for molecular analysis. Evaluation of larger fragments of cfDNA estimated through ALU 247 can provide vital information concurrent with the pathological process of disease evolution in breast cancer and warrants expansion to other cancer types.
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Affiliation(s)
- Madhumathy G. Nair
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, India
- Correspondence: (M.G.N.); (J.S.P.)
| | - Rakesh S. Ramesh
- Department of Surgical Oncology, St. John’s Medical College and Hospital, Bangalore 560034, India
| | - Chandrakala M. Naidu
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, India
| | - Apoorva D. Mavatkar
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, India
| | - Snijesh V. P.
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, India
| | - Vishakha Ramamurthy
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, India
| | - Vidya M. Somashekaraiah
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, India
| | - Anupama C. E.
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, India
| | | | - Anuradha Panigrahi
- Molecular Immunology Program, MSMF, Narayana Health City, Bangalore 560099, India
| | - Manjula Das
- Molecular Immunology Program, MSMF, Narayana Health City, Bangalore 560099, India
| | - Sujan K. Dhar
- Molecular Immunology Program, MSMF, Narayana Health City, Bangalore 560099, India
| | - Jyothi S. Prabhu
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, India
- Correspondence: (M.G.N.); (J.S.P.)
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11
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Huang Q, Ji M, Li F, Li Y, Zhou X, Hsueh CY, Zhou L. Diagnostic and prognostic value of plasma cell-free DNA combined with VEGF-C in laryngeal squamous cell carcinoma. Mol Cell Probes 2023; 67:101895. [PMID: 36682577 DOI: 10.1016/j.mcp.2023.101895] [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: 09/12/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 01/20/2023]
Abstract
BACKGROUND Circulating cell-free DNA (cfDNA) and vascular endothelial growth factor-C (VEGF-C) can be utilized to detect cancer and predict its prognosis. However, their potential application in laryngeal squamous cell carcinoma (LSCC) is unclear. PURPOSE This study aimed to identify the diagnostic and prognostic value of cfDNA and VEGF-C in LSCC patients. METHODS The plasma cfDNA of 148 LSCC patients and 43 non-tumor patients were isolated. Quantitative real-time PCR (qRT-PCR) was performed to assess long and short DNA fragments in plasma by amplifying the ALU repeats. ALU-qPCR results (ALU247/ALU115) were used to calculate cfDNA integrity index. Vascular endothelial growth factor-C (VEGF-C) level was detected by ELISA assay. Correlation between cfDNA and clinical features was analyzed. For detecting the sensitivity and specificity of cfDNA and VEGF-C alone or in combination for diagnosing LSCC, receiver operator characteristic (ROC) was established. For evaluating the overall survival (OS) of LSCC, Kaplan-Meier curves were established. RESULTS LSCC patients had significantly higher levels of plasma cfDNA (ALU115, ALU247, and cfDNA integrity index) and VEGF-C than those without cancer (p < 0.05), showing area under the curve (AUC) values of 0.79, 0.74, 0.62 and 0.80, when cutoff value was correspondingly defined at 2.14 ng/mL, 1.39 ng/mL, 0.73 and 412.90 pg/mL, respectively. The AUC for distinguishing LSCC patients from non-tumor patients by plasma cfDNA combined with VEGF-C was 0.89 (95% CI: 0.83-0.94). A significant correlation was found between plasma cfDNA levels and Ki-67, tumor size, pT stage, and smoking history (p < 0.05). Based on survival analysis, low VEGF-C concentration groups had longer OS than those with high VEGF-C concentration (p = 0.02). CONCLUSION Indicators such as plasma cfDNA and VEGF-C may be used to diagnose and monitor LSCC for its noninvasiveness and rapid accessibility.
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Affiliation(s)
- Qiang Huang
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China
| | - Mengyou Ji
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China
| | - Feiran Li
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China
| | - Yufeng Li
- Department of Anesthesiology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China
| | - Xuehua Zhou
- Department of Anesthesiology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China
| | - Chi-Yao Hsueh
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China.
| | - Liang Zhou
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China.
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12
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Grant BM, Pugh TJ, Oza AM. Molecular Monitoring in Endometrial Cancer-Ready for Prime Time? Clin Cancer Res 2023; 29:305-308. [PMID: 36354753 DOI: 10.1158/1078-0432.ccr-22-2781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/26/2022] [Accepted: 11/03/2022] [Indexed: 11/12/2022]
Abstract
SUMMARY Efforts are under way to define the role of minimally invasive strategies for molecular monitoring and risk stratification in endometrial cancer. A recent publication aims to define the association between circulating tumor DNA level and disease stage in patients with newly diagnosed endometrial cancer and determine whether sequencing of longitudinal cell-free DNA samples can be used for disease monitoring and detection of progression or recurrence. These results accelerate the current knowledge of molecular follow-up in endometrial cancer. See related article by Ashley et al., p. 410.
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Affiliation(s)
- Brooke M Grant
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Amit M Oza
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada
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13
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Kumar S, Nadda N, Paul S, Gamanagatti S, Dash NR, Vanamail P, Saraya A, Shalimar, Nayak B. Evaluation of the cell-free DNA integrity index as a liquid biopsy marker to differentiate hepatocellular carcinoma from chronic liver disease. Front Mol Biosci 2022; 9:1024193. [PMID: 36483538 PMCID: PMC9723134 DOI: 10.3389/fmolb.2022.1024193] [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: 08/21/2022] [Accepted: 11/08/2022] [Indexed: 08/19/2023] Open
Abstract
Background: Hepatocellular carcinoma (HCC) occurs in the majority of patients with underlying chronic liver disease (CLD) of viral and non-viral etiologies, which requires screening for early HCC diagnosis. Liquid biopsy holds great promise now for early detection, prognosis, and assessment of response to cancer therapy. Cell-free DNA (cfDNA) as a liquid biopsy marker can be easily detected by a real-time quantitative PCR (RT-qPCR) assay for a change in its concentration, integrity, and fragmentation in cancer. Methods: Patients with HCC (n = 100), CLD (n = 100), and healthy (n = 30) controls were included in the study. The cfDNA was isolated from serum and real-time quantitative PCR (RT-qPCR) was carried out using primer pairs for large (>205 bp) and small (110 bp) fragments of repetitive elements (ALU and LINE1) and housekeeping genes (β-Actin and GAPDH). Total cfDNA concentrations and integrity index were determined by the absolute quantitation method (L/S ratio or cfDII-integrity). The cfDII as a measure of fragmentation was determined by comparative Ct (2-ΔΔCt) method of relative quantification (cfDII-fragmentation). Using a receiver operating characteristic (ROC) curve, cfDII-integrity and cfDII-fragmentation were used to differentiate HCC from CLD patients or healthy controls. Results: The total cfDNA concentrations in the sera of HCC (244 ng/ml) patients were significantly higher than those of CLD (33 ng/ml) patients and healthy (16.88 ng/ml) controls. HCC patients have shown poor DNA integrity or excess cfDNA fragmentation than CLD patients and healthy controls. The cfDII-integrity of GAPDH and ALU fragment significantly differentiate HCC from CLD at AUROC 0.72 and 0.67, respectively. The cfDII-fragmentation following normalization with cfDNA of healthy control has shown significant differential capabilities of HCC from CLD at AUROC 0.67 using GAPDH and 0.68 using the ALU element. The ROC curve of LINE1 and β-actin cfDII was not found significant for any of the above methods. The cfDII-fragmentation trend in HCC patients of different etiologies was similar indicating increased cfDNA fragmentation irrespective of its etiology. Conclusion: The cfDII measuring both DNA integrity (L/S ratio) and fragmentation of the Alu and GAPDH genes can differentiate HCC from CLD patients and healthy individuals.
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Affiliation(s)
- Sonu Kumar
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Neeti Nadda
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Shashi Paul
- Department of Radiodiagnosis, All India Institute of Medical Sciences, New Delhi, India
| | - Shivanand Gamanagatti
- Department of Radiodiagnosis, All India Institute of Medical Sciences, New Delhi, India
| | - Nihar Ranjan Dash
- Department of Gastrointestinal Surgery, All India Institute of Medical Sciences, New Delhi, India
| | - Perumal Vanamail
- Department of Biostatistics in Obstetrics and Gynaecology, All India Institute of Medical Sciences, New Delhi, India
- Trichy SRM Medical College Hospital & Research Centre, Tiruchirappalli, Tamil Nadu, India
| | - Anoop Saraya
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Shalimar
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Baibaswata Nayak
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
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14
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Exosomal miR-155-5p derived from glioma stem-like cells promotes mesenchymal transition via targeting ACOT12. Cell Death Dis 2022; 13:725. [PMID: 35986010 PMCID: PMC9391432 DOI: 10.1038/s41419-022-05097-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 07/07/2022] [Accepted: 07/12/2022] [Indexed: 01/21/2023]
Abstract
Tumor-associated exosomes play essential roles in intercellular communication and the foundation of cancer microenvironment in glioma. Many mRNAs, microRNAs (miRNAs) and proteins contained in tumor-associated exosomes can be transferred to recipient cells and contribute to the progression of tumor. Nevertheless, the cellular communication between malignant cells with different heterogeneities or characteristics and resultant tumor progression are still unclear in glioma. Here, we show that exosomes released from glioma stem-like cells (GSCs) contain a significant increasing level of miR-155-5p and could be horizontally transferred to surrounding glioma cells. High expression of miR-155-5p in plasma exosomes from patients was associated with glioma diagnosis and grading. Mechanically, we found that miR-155-5p markedly reduced the expression of acetyl-CoA thioesterase 12 (ACOT12), which played as a tumor suppressor in glioma. Furthermore, mesenchymal transition was significantly promoted in glioma cells treated with GSCs-derived exosomes. In conclusion, GSCs-derived exosomal miR-155-5p play a critical role in glioma progression and facilitating tumor aggressive growth by targeting ACOT12 and promoting mesenchymal transition. Exosomal miR-155-5p is also a potential predictive biomarker for glioma, which may provoke the development of novel diagnostic and therapeutic strategies against glioma.
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15
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The Utility of Repetitive Cell-Free DNA in Cancer Liquid Biopsies. Diagnostics (Basel) 2022; 12:diagnostics12061363. [PMID: 35741173 PMCID: PMC9221655 DOI: 10.3390/diagnostics12061363] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 02/05/2023] Open
Abstract
Liquid biopsy is a broad term that refers to the testing of body fluids for biomarkers that correlate with a pathological condition. While a variety of body-fluid components (e.g., circulating tumor cells, extracellular vesicles, RNA, proteins, and metabolites) are studied as potential liquid biopsy biomarkers, cell-free DNA (cfDNA) has attracted the most attention in recent years. The total cfDNA population in a typical biospecimen represents an immensely rich source of biological and pathological information and has demonstrated significant potential as a versatile biomarker in oncology, non-invasive prenatal testing, and transplant monitoring. As a significant portion of cfDNA is composed of repeat DNA sequences and some families (e.g., pericentric satellites) were recently shown to be overrepresented in cfDNA populations vs their genomic abundance, it holds great potential for developing liquid biopsy-based biomarkers for the early detection and management of patients with cancer. By outlining research that employed cell-free repeat DNA sequences, in particular the ALU and LINE-1 elements, we highlight the clinical potential of the repeat-element content of cfDNA as an underappreciated marker in the cancer liquid biopsy repertoire.
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16
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Rapado-González Ó, López-Cedrún JL, Lago-Lestón RM, Abalo A, Rubin-Roger G, Salgado-Barreira Á, López-López R, Muinelo-Romay L, Suárez-Cunqueiro MM. Integrity and quantity of salivary cell-free DNA as a potential molecular biomarker in oral cancer: A preliminary study. J Oral Pathol Med 2022; 51:429-435. [PMID: 35416334 PMCID: PMC9322526 DOI: 10.1111/jop.13299] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/20/2022] [Accepted: 03/30/2022] [Indexed: 11/28/2022]
Abstract
Background Differences in cell‐free DNA (cfDNA) fragments have been described as a valuable tool to distinguish cancer patients from healthy individuals. We aim to investigate the concentration and integrity of cfDNA fragments in saliva from oral squamous cell carcinoma (OSCC) patients and healthy individuals in order to explore their value as diagnostic biomarkers. Methods Saliva samples were collected from a total of 34 subjects (19 OSCC patients and 15 healthy controls). The total concentration of salivary cfDNA (scfDNA) was determined using a fluorometry method and quantitative real‐time polymerase chain reaction (qPCR). To evaluate the scfDNA quantity and integrity, qPCR targeting Arthobacter luteus (ALU) sequences at three amplicons of different lengths (60, 115, and 247 bp, respectively) was carried out. ScfDNA integrity indexes (ALU115/ALU60 and ALU247/ALU60) were calculated as the ratio between the absolute concentration of the longer amplicons 115 bp and 247 bp and the total scfDNA amount (amplicon 60 bp). Results The total scfDNA concentration (ALU60) was higher in OSCC than in healthy donors, but this trend was not statistically significant. The medians of scfDNA integrity indexes, ALU115/ALU60 and ALU247/ALU60, were significantly higher in OSCC, showing area under the curve values of 0.8211 and 0.7018, respectively. Conclusion Our preliminary results suggest that scfDNA integrity indexes (ALU115/ALU60 and ALU247/ALU60) have potential as noninvasive diagnostic biomarkers for OSCC.
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Affiliation(s)
- Óscar Rapado-González
- Department of Surgery and Medical-Surgical Specialties, Medicine and Dentistry School, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago IDIS, Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS), Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Cáncer CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - José Luis López-Cedrún
- Department of Oral and Maxillofacial Surgery, Complexo Hospitalario Universitario de A Coruña SERGAS, A Coruña, Spain
| | - Ramón Manuel Lago-Lestón
- Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago IDIS, Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS), Santiago de Compostela, Spain
| | - Alicia Abalo
- Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago IDIS, Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS), Santiago de Compostela, Spain
| | - Guillermo Rubin-Roger
- Department of Oral and Maxillofacial Surgery, Complexo Hospitalario Universitario de A Coruña SERGAS, A Coruña, Spain
| | - Ángel Salgado-Barreira
- Department of Preventive Medicine, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Epidemiology, Health Public and Health Technology Assessment, Health Research Institute of Santiago de Compostela (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS), Santiago de Compostela, Spain
| | - Rafael López-López
- Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS), Santiago de Compostela, Spain
| | - Laura Muinelo-Romay
- Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago IDIS, Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS), Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Cáncer CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - María Mercedes Suárez-Cunqueiro
- Department of Surgery and Medical-Surgical Specialties, Medicine and Dentistry School, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Cáncer CIBERONC, Instituto de Salud Carlos III, Madrid, Spain.,Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS), Santiago de Compostela, Spain
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Njoku K, Barr CE, Crosbie EJ. Current and Emerging Prognostic Biomarkers in Endometrial Cancer. Front Oncol 2022; 12:890908. [PMID: 35530346 PMCID: PMC9072738 DOI: 10.3389/fonc.2022.890908] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 03/28/2022] [Indexed: 12/19/2022] Open
Abstract
Endometrial cancer is the most common gynaecological malignancy in high income countries and its incidence is rising. Whilst most women with endometrial cancer are diagnosed with highly curable disease and have good outcomes, a significant minority present with adverse clinico-pathological characteristics that herald a poor prognosis. Prognostic biomarkers that reliably select those at greatest risk of disease recurrence and death can guide management strategies to ensure that patients receive appropriate evidence-based and personalised care. The Cancer Genome Atlas substantially advanced our understanding of the molecular diversity of endometrial cancer and informed the development of simplified, pragmatic and cost-effective classifiers with prognostic implications and potential for clinical translation. Several blood-based biomarkers including proteins, metabolites, circulating tumour cells, circulating tumour DNA and inflammatory parameters have also shown promise for endometrial cancer risk assessment. This review provides an update on the established and emerging prognostic biomarkers in endometrial cancer.
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Affiliation(s)
- Kelechi Njoku
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
- Stoller Biomarker Discovery Centre, University of Manchester, Manchester, United Kingdom
- Department of Obstetrics and Gynaecology, St Mary’s Hospital, Manchester, University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Chloe E. Barr
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
- Department of Obstetrics and Gynaecology, St Mary’s Hospital, Manchester, University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Emma J. Crosbie
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
- Department of Obstetrics and Gynaecology, St Mary’s Hospital, Manchester, University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
- *Correspondence: Emma J. Crosbie,
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18
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Ronchetti L, Terrenato I, Ferretti M, Corrado G, Goeman F, Donzelli S, Mandoj C, Merola R, Zampa A, Carosi M, Blandino G, Conti L, Lobascio AM, Iacobelli M, Vizza E, Piaggio G, Gurtner A. Circulating cell free DNA and citrullinated histone H3 as useful biomarkers of NETosis in endometrial cancer. J Exp Clin Cancer Res 2022; 41:151. [PMID: 35449078 PMCID: PMC9027343 DOI: 10.1186/s13046-022-02359-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 04/06/2022] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Cancer mortality is mainly caused by organ failure and thrombotic events. It has been demonstrated that NETosis, a chromatin release mechanism implemented by neutrophils, may contribute to these lethal systemic effects. Our aim was to investigate NETosis biomarkers in endometrial cancer (EC). METHODS The experiments were conducted on 21 healthy subjects (HS) with no gynecological conditions, and on 63 EC patients. To assess the presence of NETosis features, IHC and IF was performed using antibodies against citrullinated histone H3 (citH3), neutrophil elastase (NE) and histone 2B. Serum levels of cell free DNA (cfDNA), cell free mitochondrial DNA (cfmtDNA) and citH3 were measured by qPCR using one microliter of deactivated serum, and by ELISA assay respectively. Fragmentation pattern of serum cfDNA was analyzed using the Agilent 2100 Bioanalyzer and High Sensitivity DNA Chips. Receiver operating characteristic (ROC) analysis was used to identify a cut off for cfDNA and cfmtDNA values able to discriminate between ECs and HSs. Correlation analysis and multiple correspondence analysis (MCA) between cfDNA, mtcfDNA, citH3 and blood parameters were used to identify the potential association among serum parameters in EC grades. RESULTS We demonstrated the presence of NETosis features in tissues from all EC grades. Serum cfDNA and cfmtDNA levels discriminate ECs from HSs and a direct correlation between citH3 and cfDNA content and an inverse correlation between cfmtDNA and citH3 in EC sera was observed, not detectable in HSs. MCA indicates cfDNA, cfmtDNA and citH3 as features associated to G1 and G2 grades. A correlation between increased levels of cfDNA, citH3 and inflammation features was found. Finally, serum nucleosomal cfDNA fragmentation pattern varies in EC sera and correlates with increased levels of cfDNA, citH3, lymphocytes and fibrinogen. CONCLUSION Our data highlight the occurrence of NETosis in EC and indicate serum cfDNA and citH3 as noninvasive biomarkers of tumor-induced systemic effects in endometrial cancer.
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Affiliation(s)
- Livia Ronchetti
- SAFU Unit, IRCCS - Regina Elena National Cancer Institute, via Elio Chianesi 53, 00144, Rome, Italy
| | - Irene Terrenato
- Clinical Trial Center - Biostatistics & Bioinformatics, IRCCS - Regina Elena National Cancer Institute, Rome, Italy
| | - Margherita Ferretti
- SAFU Unit, IRCCS - Regina Elena National Cancer Institute, via Elio Chianesi 53, 00144, Rome, Italy
| | - Giacomo Corrado
- Department of Women and Children Health, Gynecologic Oncology Unit, Fondazione Policlinico Universitario A. Gemelli, IRCCS - Università Cattolica del Sacro Cuore, Roma, Italy
| | - Frauke Goeman
- SAFU Unit, IRCCS - Regina Elena National Cancer Institute, via Elio Chianesi 53, 00144, Rome, Italy
| | - Sara Donzelli
- Oncogenomics and Epigenetics Unit, IRCCS - Regina Elena National Cancer Institute, Rome, Italy
| | - Chiara Mandoj
- Clinical Pathology Unit, IRCCS - Regina Elena National Cancer Institute, Rome, Italy
| | - Roberta Merola
- Clinical Pathology Unit, IRCCS - Regina Elena National Cancer Institute, Rome, Italy
| | - Ashanti Zampa
- Gynecologic Oncology Unit, IRCCS - Regina Elena National Cancer Institute, Rome, Italy
| | - Mariantonia Carosi
- Anatomy Pathology Unit, IRCCS - Regina Elena National Cancer Institute, Rome, Italy
| | - Giovanni Blandino
- Oncogenomics and Epigenetics Unit, IRCCS - Regina Elena National Cancer Institute, Rome, Italy
| | - Laura Conti
- Clinical Pathology Unit, IRCCS - Regina Elena National Cancer Institute, Rome, Italy
| | - Anna Maria Lobascio
- Gynecologic Oncology Unit, IRCCS - Regina Elena National Cancer Institute, Rome, Italy
| | - Marcello Iacobelli
- Gynecologic Oncology Unit, IRCCS - Regina Elena National Cancer Institute, Rome, Italy
| | - Enrico Vizza
- Gynecologic Oncology Unit, IRCCS - Regina Elena National Cancer Institute, Rome, Italy
| | - Giulia Piaggio
- SAFU Unit, IRCCS - Regina Elena National Cancer Institute, via Elio Chianesi 53, 00144, Rome, Italy
| | - Aymone Gurtner
- SAFU Unit, IRCCS - Regina Elena National Cancer Institute, via Elio Chianesi 53, 00144, Rome, Italy.
- Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy.
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19
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Piñeiro-Pérez R, Abal M, Muinelo-Romay L. Liquid Biopsy for Monitoring EC Patients: Towards Personalized Treatment. Cancers (Basel) 2022; 14:cancers14061405. [PMID: 35326558 PMCID: PMC8946652 DOI: 10.3390/cancers14061405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/02/2022] [Accepted: 03/07/2022] [Indexed: 01/27/2023] Open
Abstract
Simple Summary Although the field of liquid biopsy is clearly having an effect on other tumour types, in endometrial cancer (EC) there is important work to do to implement the analysis of circulating biomarkers into the clinical routine. One of the most evident contexts of application is the disease follow-up in both localized and advanced diseases, which at present is primarily made by imaging techniques. In the present review, we conducted an overview of the circulating biomarkers with the potential to be used as monitoring biomarkers in endometrial tumours and highlighted the key challenges for their translation into the patients’ management in order to help researchers to better focus their work in this field. Abstract Endometrial cancer (EC) is the most frequent gynecological cancer in developed countries and its incidence shows an increasing trend. Fortunately, the prognosis of the disease is good when the tumour is diagnosed in an early phase, but some patients recur after surgery and develop distant metastasis. The therapy options for EC for advanced disease are more limited than for other tumours. Therefore, the application of non-invasive strategies to anticipate the recurrence of localized tumours and guide the treatment in advanced stages represents a clear requirement to improve the survival and quality of life of patients with EC. To achieve this desired precision oncology, it is necessary to invest in the identification and validation of circulating markers that allow a more effective stratification and monitoring of patients. We here review the main advances made for the evaluation of circulating tumour DNA (ctDNA), circulating tumour cells (CTCs), circulating extracellular vesicles (cEVs), and other non-invasive biomarkers as a monitoring tool in the context of localized and advanced endometrial tumours, with the aim of providing a global perspective of the achievements and the key areas in which the use of these markers can be developed into a real clinical tool.
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Affiliation(s)
- Raquel Piñeiro-Pérez
- Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago de Compostela (IDIS), University Hospital of Santiago de Compostela (SERGAS), Trav. Choupana s/n, 15706 Santiago de Compostela, Spain;
| | - Miguel Abal
- Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago de Compostela (IDIS), University Hospital of Santiago de Compostela (SERGAS), Trav. Choupana s/n, 15706 Santiago de Compostela, Spain;
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Monforte de Lemos 3-5, 28029 Madrid, Spain
- Correspondence: (M.A.); (L.M.-R.); Tel.: +34-981-955-073 (M.A. & L.M.-R.)
| | - Laura Muinelo-Romay
- Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago de Compostela (IDIS), University Hospital of Santiago de Compostela (SERGAS), Trav. Choupana s/n, 15706 Santiago de Compostela, Spain;
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Monforte de Lemos 3-5, 28029 Madrid, Spain
- Correspondence: (M.A.); (L.M.-R.); Tel.: +34-981-955-073 (M.A. & L.M.-R.)
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20
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Shaban S, Al‑Rahim A, Suleiman A. ALU repeat as potential molecular marker in the detection and prognosis of different cancer types: A systematic review. Mol Clin Oncol 2022; 16:86. [PMID: 35251637 PMCID: PMC8892463 DOI: 10.3892/mco.2022.2519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/13/2022] [Indexed: 11/25/2022] Open
Abstract
Cancer is a major health issue worldwide. cfDNA integrity has been reported as a potential diagnostic molecular marker for different types of cancer, identifying the importance of liquid biopsy. The aim of this review was to evaluate the prognostic and diagnostic performance of Arthrobacter luteus (ALU) repeat in tumor. Following a thorough review of the literature published from January, 2000 to September 2021, 36 studies were included. All of the study descriptions were analyzed. According to several studies, there were increased concentrations of ALU repetitive elements in cancer patients, while these concentrations were decreased in control, benign, different cancer stage, and other diseases. The total ALU (115 and 247) sequence levels are potential biomarkers for the purpose of investigations and cancer prognosis.
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Affiliation(s)
- Semaa Shaban
- Department of Biology, College of Sciences, Tikrit University, Tikrit, Saladin 34001, Iraq
| | - Aya Al‑Rahim
- Department of Molecular and Medical Biotechnology, College of Biotechnology, Al‑Nahrain University, Baghdad 64074, Iraq
| | - Ahmed Suleiman
- Department of Biotechnology, Science College, University of Anbar, Ramadi, Anbar 46006, Iraq
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21
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Yin L, Guo Z, Wang T, Wang X. Increase of circulating cfDNA by chronic training or overtraining in human and rat and its possible mechanisms. Sci Sports 2022. [DOI: 10.1016/j.scispo.2021.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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22
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Abouali H, Hosseini SA, Purcell E, Nagrath S, Poudineh M. Recent Advances in Device Engineering and Computational Analysis for Characterization of Cell-Released Cancer Biomarkers. Cancers (Basel) 2022; 14:288. [PMID: 35053452 PMCID: PMC8774172 DOI: 10.3390/cancers14020288] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/21/2021] [Accepted: 01/04/2022] [Indexed: 02/04/2023] Open
Abstract
During cancer progression, tumors shed different biomarkers into the bloodstream, including circulating tumor cells (CTCs), extracellular vesicles (EVs), circulating cell-free DNA (cfDNA), and circulating tumor DNA (ctDNA). The analysis of these biomarkers in the blood, known as 'liquid biopsy' (LB), is a promising approach for early cancer detection and treatment monitoring, and more recently, as a means for cancer therapy. Previous reviews have discussed the role of CTCs and ctDNA in cancer progression; however, ctDNA and EVs are rapidly evolving with technological advancements and computational analysis and are the subject of enormous recent studies in cancer biomarkers. In this review, first, we introduce these cell-released cancer biomarkers and briefly discuss their clinical significance in cancer diagnosis and treatment monitoring. Second, we present conventional and novel approaches for the isolation, profiling, and characterization of these markers. We then investigate the mathematical and in silico models that are developed to investigate the function of ctDNA and EVs in cancer progression. We convey our views on what is needed to pave the way to translate the emerging technologies and models into the clinic and make the case that optimized next-generation techniques and models are needed to precisely evaluate the clinical relevance of these LB markers.
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Affiliation(s)
- Hesam Abouali
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (H.A.); (S.A.H.)
| | - Seied Ali Hosseini
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (H.A.); (S.A.H.)
| | - Emma Purcell
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109-2800, USA; (E.P.); (S.N.)
| | - Sunitha Nagrath
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109-2800, USA; (E.P.); (S.N.)
| | - Mahla Poudineh
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (H.A.); (S.A.H.)
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Katopodis P, Anikin V, Kishore U, Carter T, Hall M, Asadi N, Polychronis A, Karteris E. Circulating tumour cells and circulating cell-free DNA in patients with lung cancer: a comparison between thoracotomy and video-assisted thoracoscopic surgery. BMJ Open Respir Res 2021; 8:8/1/e000917. [PMID: 34493540 PMCID: PMC8424856 DOI: 10.1136/bmjresp-2021-000917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 08/07/2021] [Indexed: 11/03/2022] Open
Abstract
INTRODUCTION The type of lung cancer surgery impacts on tumour manipulation during surgery and may drive dissemination of cancer cells into the vasculature, thus facilitating metastatic spread. The aim of this study was to investigate the impact of surgically induced trauma using peripheral blood from preoperative and postoperative patients with non-small cell lung cancer (NSCLC) undergoing thoracotomy or video-assisted thoracoscopic surgery (VATS) resection. METHODS Imaging flow cytometry was used to measure circulating cancer-associated cells (CCs). Circulating cell-free DNA (ccfDNA) isolation was performed using Promega dsDNA HS Assay Kit. DNA integrity measurements were calculated by the ALU247 to ALU115 ratio and cytokine levels measured using the Luminex screening assay. RESULTS CCs were increased in postoperative blood samples in 54 patients with NSCLC. Patients who underwent thoracotomy instead of VATS had higher numbers of EpCAM (p=0.004) and PanCK-labelled (p=0.03) CCs postoperatively. ccfDNA and DNA integrity index were also significantly increased in postoperative samples (p=0.0009 and p=0.04), with concomitant increase in interleukin 6 and interleukin 10 levels in the same cohorts (p=0.0004 and p=0.034, respectively). CONCLUSIONS In this study we have shown the potential clinical utility of several biomarkers from liquid biopsies to guide perioperative management, as well as provide a snapshot of the type of surgical resection in terms of circulating tumour cell release. Obtaining reliable readouts from blood can provide crucial information for disease progression, as well as being of prognostic value monitoring patients' response to treatment.
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Affiliation(s)
- Periklis Katopodis
- Biosciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK.,Thoracic Surgery, Royal Brompton & Harefield NHS Foundation Trust, Harefield, UK
| | - Vladimir Anikin
- Biosciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK.,Thoracic Surgery, Royal Brompton & Harefield NHS Foundation Trust, Harefield, UK.,Department of Oncology and Reconstructive Surgery, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Uday Kishore
- Biosciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK
| | | | - Marcia Hall
- Biosciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK.,Mount Vernon Cancer Centre, Northwood, UK
| | - Nizar Asadi
- Royal Brompton and Harefield NHS Trust, London, UK
| | | | - Emmanouil Karteris
- Biosciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK .,Thoracic Surgery, Royal Brompton & Harefield NHS Foundation Trust, Harefield, UK
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24
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Ronchetti L, Boubaker NS, Barba M, Vici P, Gurtner A, Piaggio G. Neutrophil extracellular traps in cancer: not only catching microbes. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:231. [PMID: 34261496 PMCID: PMC8281578 DOI: 10.1186/s13046-021-02036-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/05/2021] [Indexed: 12/16/2022]
Abstract
Neutrophils are the most abundant type of white blood cells circulating throughout the bloodstream and are often considered the frontline defenders in innate immunity. However, neutrophils are increasingly being recognized as having an important role in tumorigenesis and carcinogenesis due to their aberrant activation by molecules released into the tumor microenvironment. One defensive response of neutrophils that is aberrantly triggered during the neoplastic process is called NETosis, where activated neutrophils expel their DNA and intracellular contents in a web-like structure known as a neutrophil extracellular trap (NET). In cancer, NETosis has been linked to increased disease progression, metastasis, and complications such as venous thromboembolism. NET structures released by neutrophils can also serve as a scaffold for clot formation, shining new light on the role of neutrophils and NETosis in coagulation-mediated diseases. Here, we review current available knowledge regarding NET and the related NETosis process in cancer patients, with an emphasis on pre-clinical and clinical data fostering the identification and validation of biomarkers of NET with a predictive/prognostic role in cancer patients treated with immunotherapy agents. NETosis biomarkers, e.g., citH3, may integrate correlates of immunogenicity currently available (e.g., PD-L1 expression, TMB, TILs) and help select the subsets of patients who may most benefit from the use of the therapeutic weapons under discussion.
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Affiliation(s)
- Livia Ronchetti
- SAFU Unit, IRCCS - Regina Elena National Cancer Institute, Rome, Italy
| | - Nouha Setti Boubaker
- SAFU Unit, IRCCS - Regina Elena National Cancer Institute, Rome, Italy.,Laboratory of proteins engineering and bioactive molecules (LIP-MB), National Institute of Applied Sciences and Technology of Tunis (INSAT), The University of Carthage, Tunis, Tunisia
| | - Maddalena Barba
- Division of Medical Oncology 2, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Patrizia Vici
- Division of Medical Oncology 2, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Aymone Gurtner
- SAFU Unit, IRCCS - Regina Elena National Cancer Institute, Rome, Italy. .,Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy.
| | - Giulia Piaggio
- SAFU Unit, IRCCS - Regina Elena National Cancer Institute, Rome, Italy
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25
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Grassi T, Harris FR, Smadbeck JB, Murphy SJ, Block MS, Multinu F, Schaefer Klein JL, Zhang P, Karagouga G, Liu MC, Larish A, Lemens MA, Sommerfield MKS, Cappuccio S, Cheville JC, Vasmatzis G, Mariani A. Personalized tumor-specific DNA junctions to detect circulating tumor in patients with endometrial cancer. PLoS One 2021; 16:e0252390. [PMID: 34111149 PMCID: PMC8192008 DOI: 10.1371/journal.pone.0252390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 05/17/2021] [Indexed: 01/08/2023] Open
Abstract
INTRODUCTION There are no reliable blood biomarkers for monitoring endometrial cancer patients in the current clinical practice. Circulating tumor DNA (ctDNA) is emerging as a promising non-invasive method to measure tumor burden, define prognosis and monitor disease status in many solid cancers. In this pilot study, we investigated if unique tumor-specific DNA junctions can be used to detect ctDNA levels in patients with endometrial cancer. METHODS Chromosomal rearrangements in primary tumors of eleven patients with high-grade or advanced stage endometrial cancer were determined by whole-genome Mate-Pair sequencing. Identified unique tumor-specific junctions were evaluated in pre- and six-week post-surgery patient plasma using individualized quantitative polymerase chain reaction (qPCR) assays. The relationship between clinicopathological features and detection of ctDNA was investigated. RESULTS CtDNA was detected in 60% (6/10) of cases pre-surgery and in 27% (3/11) post-surgery. The detection of ctDNA pre-surgery was consistent with clinical indicators of aggressive disease such as advanced stage (80% - 4/5), lymphatic spread of disease (100% - 3/3), serous histology (80% - 4/5), deep myometrial invasion (100% - 3/3), lympho-vascular space invasion (75% - 3/4). All patients in which ctDNA was detected post-surgically had type II endometrial cancer. DISCUSSION This pilot study demonstrates the feasibility of using personalized tumor-specific junction panels for detecting ctDNA in the plasma of endometrial cancer patients. Larger studies and longer follow-up are needed to validate the potential association between pre-surgical ctDNA detection and the presence of cancers with aggressive pathologic tumor characteristics or advanced stage observed in this study.
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Affiliation(s)
- Tommaso Grassi
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, United States of America
- Clinic of Obstetrics and Gynecology, University of Milan-Bicocca, San Gerardo Hospital, Monza, Italy
| | - Faye R. Harris
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States of America
| | - James B. Smadbeck
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States of America
| | - Stephen J. Murphy
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States of America
| | - Matthew S. Block
- Department of Oncology, Mayo Clinic, Rochester, MN, United States of America
| | - Francesco Multinu
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, United States of America
- Department of Gynecology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | | | - Piyan Zhang
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States of America
| | - Giannoula Karagouga
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States of America
| | - Minetta C. Liu
- Department of Oncology, Mayo Clinic, Rochester, MN, United States of America
| | - Alyssa Larish
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, United States of America
| | - Maureen A. Lemens
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, United States of America
| | | | - Serena Cappuccio
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, United States of America
- Department of Women and Child Health, Catholic University of the Sacred Heart, Rome, Italy
| | - John C. Cheville
- Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - George Vasmatzis
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States of America
- * E-mail:
| | - Andrea Mariani
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, United States of America
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26
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Poulet G, Garlan F, Garrigou S, Zonta E, Benhaim L, Carrillon MJ, Didelot A, Le Corre D, Mulot C, Nizard P, Ginot F, Boutonnet-Rodat A, Blons H, Bachet JB, Taïeb J, Zaanan A, Geromel V, Pellegrina L, Laurent-Puig P, Wang-Renault SF, Taly V. Characterization of Plasma Cell-Free DNA Integrity Using Droplet-Based Digital PCR: Toward the Development of Circulating Tumor DNA-Dedicated Assays. Front Oncol 2021; 11:639675. [PMID: 34094923 PMCID: PMC8174096 DOI: 10.3389/fonc.2021.639675] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/16/2021] [Indexed: 01/05/2023] Open
Abstract
Background: Cellular-cell free-DNA (ccfDNA) is being explored as a diagnostic and prognostic tool for various diseases including cancer. Beyond the evaluation of the ccfDNA mutational status, its fragmentation has been investigated as a potential cancer biomarker in several studies. However, probably due to a lack of standardized procedures dedicated to preanalytical and analytical processing of plasma samples, contradictory results have been published. Methods: ddPCR assays allowing the detection of KRAS wild-type and mutated sequences (KRAS p.G12V, pG12D, and pG13D) were designed to target different fragments sizes. Once validated on fragmented and non-fragmented DNA extracted from cancer cell lines, these assays were used to investigate the influence of the extraction methods on the non-mutated and mutated ccfDNA integrity reflected by the DNA integrity index (DII). The DII was then analyzed in two prospective cohorts of metastatic colorectal cancer patients (RASANC study n = 34; PLACOL study n = 12) and healthy subjects (n = 49). Results and Discussion: Our results demonstrate that ccfDNA is highly fragmented in mCRC patients compared with healthy individuals. These results strongly suggest that the characterization of ccfDNA integrity hold great promise toward the development of a universal biomarker for the follow-up of mCRC patients. Furthermore, they support the importance of standardization of sample handling and processing in such analysis.
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Affiliation(s)
- Geoffroy Poulet
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France.,Eurofins-Biomnis, Specialized Medical Biology Laboratory, Lyon, France
| | - Fanny Garlan
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
| | - Sonia Garrigou
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
| | - Eleonora Zonta
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
| | - Leonor Benhaim
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France.,Department of Visceral and Surgical Oncology, Gustave Roussy, Villejuif, France
| | - Marie-Jennifer Carrillon
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
| | - Audrey Didelot
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
| | - Delphine Le Corre
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
| | - Claire Mulot
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France.,CIC-EC4 URC, HEGP, Hôpitaux Universitaires Paris Ouest AP-HP, Paris, France
| | - Philippe Nizard
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
| | | | | | - Helene Blons
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France.,Department of Oncology, European Georges-Pompidou Hospital, AP-HP, Paris Descartes University, Paris, France
| | - Jean-Baptiste Bachet
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France.,Sorbonne Universités, UPMC Université, Paris, France.,Department of Hepato-gastroenterology, Groupe Hospitalier Pitié Salpêtrière, Paris, France.,AGEO (Association des Gastroentérologues Oncologues), Paris, France
| | - Julien Taïeb
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France.,Department of Oncology, European Georges-Pompidou Hospital, AP-HP, Paris Descartes University, Paris, France.,AGEO (Association des Gastroentérologues Oncologues), Paris, France
| | - Aziz Zaanan
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France.,Department of Oncology, European Georges-Pompidou Hospital, AP-HP, Paris Descartes University, Paris, France
| | - Vanna Geromel
- Eurofins-Biomnis, Specialized Medical Biology Laboratory, Lyon, France
| | | | - Pierre Laurent-Puig
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France.,Department of Oncology, European Georges-Pompidou Hospital, AP-HP, Paris Descartes University, Paris, France
| | - Shu-Fang Wang-Renault
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
| | - Valerie Taly
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale Contre le Cancer, CNRS SNC 5096, Paris, France
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27
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González de Aledo-Castillo JM, Casanueva-Eliceiry S, Soler-Perromat A, Fuster D, Pastor V, Reguart N, Viñolas N, Reyes R, Vollmer I, Paredes P, Puig-Butillé JA. Cell-free DNA concentration and fragment size fraction correlate with FDG PET/CT-derived parameters in NSCLC patients. Eur J Nucl Med Mol Imaging 2021; 48:3631-3642. [PMID: 33797597 DOI: 10.1007/s00259-021-05306-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/07/2021] [Indexed: 01/26/2023]
Abstract
PURPOSE The aim of our study was to investigate the correlation between cfDNA concentration and fragment size fraction with FDG PET/CT- and CT-derived parameters in untreated NSCLC patient. METHODS Fifty-three patients diagnosed of locally advanced or metastatic NSCLC who had undergone FDG PET/CT, CT and cfDNA analysis prior to any treatment were included in this retrospective study. CfDNA concentration was measured by fluorometry and fragment size fractions were determined by microchip electrophoresis. [18F]F-FDG PET/CT was performed and standardised uptake values (SUV), metabolic tumour volume (MTV) and total lesion glycolysis (TLG) were calculated for primary, extrapulmonary and total disease. CT scans were evaluated according to RECIST 1.1 criteria. RESULTS CfDNA concentration showed a positive correlation with extrapulmonary MTV (r2 = 0.36, P = 0.009), and extrapulmonary TLG (r2 = 0.35, P = 0.009) and their whole-body (wb) ratios. Higher concentrations of total cfDNA were found in patients with liver lesions. Short fragments of cfDNA (100-250 bp) showed a positive correlation with extrapulmonary MTV (r2 = 0.49, P = 0.0005) and extrapulmonary TLG (r2 = 0.39, P = 0.006) and their respective wb ratios, and a negative correlation with SUVmean (r2 = -0.31, P = 0.03) and SUVmean/SUVmax ratio (r2 = -0.34, P = 0.02). A higher fraction of short cfDNA fragments was found in patients with liver and pleural lesions. CONCLUSIONS This study supports the hypothesis that cfDNA concentration and short cfDNA fragment size fraction reflect the tumour burden as well as metabolic activity in advanced NSCLC patients. This suggests their suitability as complementary tests for a more accurate diagnosis of tumour metabolic behaviour and to allow personalised therapies.
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Affiliation(s)
| | | | | | - D Fuster
- Nuclear Medicine Department, Hospital Clínic, Barcelona, Spain.,Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.,Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - V Pastor
- Molecular Biology CORE, Hospital Clínic, Villarroel 170, 08036, Barcelona, Spain
| | - N Reguart
- Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain.,Medical Oncology Department, Hospital Clínic, Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - N Viñolas
- Medical Oncology Department, Hospital Clínic, Barcelona, Spain
| | - R Reyes
- Medical Oncology Department, Hospital Clínic, Barcelona, Spain
| | - I Vollmer
- Radiology Department, Hospital Clínic, Barcelona, Spain.,Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain
| | - P Paredes
- Nuclear Medicine Department, Hospital Clínic, Barcelona, Spain.,Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.,Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - J A Puig-Butillé
- Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain. .,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain. .,Molecular Biology CORE, Hospital Clínic, Villarroel 170, 08036, Barcelona, Spain.
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28
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Han Y, Li X, Zhang M, Yang Y, Ge G, Wang K, Gong Y, Liang Y, Niu H, Ci W. Enhanced Detection of Genitourinary Cancers Using Fragmentation and Copy Number Profiles Obtained from Urinary Cell-Free DNA. Clin Chem 2020; 67:394-403. [PMID: 33523215 DOI: 10.1093/clinchem/hvaa283] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/23/2020] [Indexed: 12/30/2022]
Abstract
BACKGROUND Recent studies have reported that examining the fragmentation profiles (FP) of plasma cell-free DNA (cfDNA) further improves the clinical sensitivity of tumor detection. We hypothesized that considering the differences of the FP of urinary cfDNA would increase the clinical sensitivity of genitourinary (GU) cancer detection. METHODS 177 patients with GU cancer and 94 individuals without tumors were enrolled in the discovery cohort. An independent validation dataset comprising 30 patients without tumors and 66 patients with GU cancer was also collected. We constructed an ensemble classifier, GUIDER, to detect and localize GU cancers using fragmentation and copy number profiles obtained from shallow whole-genome sequencing of urinary cfDNA. RESULTS Urinary cfDNA of patients with GU cancer had a higher proportion of long fragments (209-280 bp) and a lower proportion of short fragments (140-208 bp) compared to controls. The overall mean classification accuracy of the FP was 74.62%-85.39% for different algorithms, and integration of the FP and copy number alteration (CNA) features further enhanced the classification of samples from patients with GU cancer. The mean diagnostic accuracy was further improved by the ensemble classifier GUIDER, which integrated the FP and CNA profiles and resulted in a higher mean accuracy (87.52%) compared to the analysis performed without FP features (74.62%). GUIDER performed well in an independent validation dataset. CONCLUSIONS The lengthening and shortening of urinary cfDNA within specific size ranges were identified in patients with GU cancer. Integration of the FP should further enhance the ability to use urinary cfDNA as a molecular diagnostic tool.
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Affiliation(s)
- Yang Han
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing China.,China National Center for Bioinformation, Beijing China.,University of the Chinese Academy of Sciences, Beijing China
| | - Xinxin Li
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing China.,China National Center for Bioinformation, Beijing China
| | - Mingxin Zhang
- Department of Urology, the Affiliated Hospital of Qingdao University, Qingdao China
| | - Yang Yang
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing China.,China National Center for Bioinformation, Beijing China.,University of the Chinese Academy of Sciences, Beijing China
| | - Guangzhe Ge
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing China.,China National Center for Bioinformation, Beijing China
| | - Kunxiang Wang
- Department of Urology, the Affiliated Hospital of Qingdao University, Qingdao China
| | - Yanqing Gong
- Department of Urology, Peking University First Hospital, Beijing China.,Institute of Urology, Peking University, Beijing China.,National Urological Cancer Center, Beijing China
| | - Yuan Liang
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing China.,China National Center for Bioinformation, Beijing China
| | - Haitao Niu
- Department of Urology, the Affiliated Hospital of Qingdao University, Qingdao China
| | - Weimin Ci
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing China.,China National Center for Bioinformation, Beijing China.,University of the Chinese Academy of Sciences, Beijing China.,Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing China
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29
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Ray SK, Mukherjee S. Cell free DNA as an evolving liquid biopsy biomarker for initial diagnosis and therapeutic nursing in Cancer- An evolving aspect in Medical Biotechnology. Curr Pharm Biotechnol 2020; 23:112-122. [PMID: 33308128 DOI: 10.2174/1389201021666201211102710] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/26/2020] [Accepted: 10/20/2020] [Indexed: 11/22/2022]
Abstract
Cell-free DNA (cfDNA) is present in numerous body fluids in addition to initiates generally from blood cells. It is undoubtedly the utmost promising tool among all components of liquid biopsy. Liquid biopsy is a specialized method investigating the nonsolid biological tissue by revealing of circulating cells, cell free DNA etc. that enter body fluids. Since, cancer cells disengage from compact tumors circulate in peripheral blood, evaluating blood of cancer patients holds the opportunities for capture and molecular level analysis of various tumor-derived constituents. Cell free DNA samples can deliver a significant perceptions into oncology, for instance tumor heterogeneity, instantaneous tumor development, response to therapy and treatment, comprising immunotherapy and mechanisms of cancer metastasis. Malignant growth at any phase can outhouse tumor cells in addition to fragments of neoplasticity causing DNA into circulatory system giving noble sign of mutation in the tumor at sampling time. Liquid biopsy distinguishes diverse blood based evolving biomarkers comprising circulating tumor cells (CTCs), circulating tumor DNA (ctDNA) or cfDNA, circulating RNA (cfRNA) and exosomes. Cell free DNA are little DNA fragments found circulating in plasma or serum, just as other fluids present in our body. Cell free DNA involves primarily double stranded nuclear DNA and mitochondrial DNA, present both on a surface level and in the lumen of vesicles. The probable origins of the tumor-inferred portion of cfDNA are apoptosis or tumor necrosis, lysis of CTCs or release of DNA from the tumor cells into circulation. The evolution of innovations, refinement and improvement in therapeutics for determination of cfDNA fragment size and its distribution provide significant information related with pathological conditions of the cell, thus emerging as promising indicator for clinical output in medical biotechnology.
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Affiliation(s)
| | - Sukhes Mukherjee
- Department of Biochemistry. All India Institute of Medical Sciences. Bhopal, Madhya pradesh-462020. India
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30
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Risk factors of progression to endometrial cancer in women with endometrial hyperplasia: A retrospective cohort study. PLoS One 2020; 15:e0243064. [PMID: 33259545 PMCID: PMC7707482 DOI: 10.1371/journal.pone.0243064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 11/15/2020] [Indexed: 11/19/2022] Open
Abstract
Objective This study aimed to investigate risk factors of progression to endometrial cancer (EC) in women with non-atypical and atypical endometrial hyperplasia (EH). Methods The data of 62,333 women with EH diagnostic codes from 2007 to 2018 were sourced from the Korean Health Insurance Review and Assessment Service databases. The data from 11,525 women with non-atypical EH and 2,219 women with atypical EH who met the selection criteria were extracted for analysis. Results Risk of EC in women with EH decreased in 40–49 year olds compared to other ages (non-atypical EH: [≤39 vs. 40–49 years] HR, 0.557; 95% CI, 0.439–0.708; P<0.001; [≤39 vs. ≥50 years] P = 0.739; atypical EH: [≤39 vs. 40–49 years] HR, 0.391; 95% CI, 0.229–0.670; P = 0.001; [≤39 vs. ≥50 years] P = 0.712). Risk of EC increased with increase in number of follow-up biopsies in women with non-atypical EH (1 biopsy: HR, 1.835; 95% CI, 1.282–2.629; P = 0.001; ≥2 biopsies: HR, 3.644; 95% CI, 2.585–5.317; P<0.001) and in women receiving ≥2 follow-up biopsies with atypical EH (HR, 3.827; 95% CI, 1.924–7.612; P = 0.001). Time of progression to EC decreased in women ≥50 years old with non-atypical EH compared to other ages (P = 0.004) and showed no differences among ages in women with atypical EH (P = 0.576). Progestational agents were a protective factor for EC in women with non-atypical EH (HR, 0.703; 95% CI, 0.565–0.876; P = 0.002). Conclusions In this claim data analysis, women ≤39 and ≥50 years old with EH were at a high risk for progression to EC, and repeat follow-up biopsy after a diagnosis of EH increased detection of EC. Progestational agents were an effective modality to prevent EC in women with non-atypical EH.
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De Palma FDE, Luglio G, Tropeano FP, Pagano G, D’Armiento M, Kroemer G, Maiuri MC, De Palma GD. The Role of Micro-RNAs and Circulating Tumor Markers as Predictors of Response to Neoadjuvant Therapy in Locally Advanced Rectal Cancer. Int J Mol Sci 2020; 21:E7040. [PMID: 32987896 PMCID: PMC7582560 DOI: 10.3390/ijms21197040] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/18/2020] [Accepted: 09/22/2020] [Indexed: 02/08/2023] Open
Abstract
The response to neoadjuvant chemoradiation (nCRT) is a critical step in the management of locally advanced rectal cancer (LARC) patients. Only a minority of LARC patients responds completely to neoadjuvant treatments, thus avoiding invasive radical surgical resection. Moreover, toxic side effects can adversely affect patients' survival. The difficulty in separating in advances responder from non-responder patients affected by LARC highlights the need for valid biomarkers that guide clinical decision-making. In this context, microRNAs (miRNAs) seem to be promising candidates for predicting LARC prognosis and/or therapy response, particularly due to their stability, facile detection, and disease-specific expression in human tissues, blood, serum, or urine. Although a considerable number of studies involving potential miRNA predictors to nCRT have been conducted over the years, to date, the identification of the perfect miRNA signatures or single miRNA, as well as their use in the clinical practice, is still representing a challenge for the management of LARC patients. In this review, we will first introduce LARC and its difficult management. Then, we will trace the scientific history and the key obstacles for the identification of specific miRNAs that predict responsiveness to nCRT. There is a high potential to identify non-invasive biomarkers that circulate in the human bloodstream and that might indicate the LARC patients who benefit from the watch-and-wait approach. For this, we will critically evaluate recent advances dealing with cell-free nucleic acids including miRNAs and circulating tumor cells as prognostic or predictive biomarkers.
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Affiliation(s)
- Fatima Domenica Elisa De Palma
- Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM UMRS 1138, Sorbonne Université, Université of Paris, 75005 Paris, France; (G.K.); (M.C.M.)
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, 94800 Villejuif, France
- CEINGE-Biotecnologie Avanzate, 80131 Naples, Italy
| | - Gaetano Luglio
- Department of Public Health, University of Naples “Federico II”, 80138 Naples, Italy; (G.L.); (M.D.)
| | - Francesca Paola Tropeano
- Department of Clinical Medicine and Surgery, University of Naples “Federico II”, 80138 Naples, Italy; (F.P.T.); (G.P.)
| | - Gianluca Pagano
- Department of Clinical Medicine and Surgery, University of Naples “Federico II”, 80138 Naples, Italy; (F.P.T.); (G.P.)
| | - Maria D’Armiento
- Department of Public Health, University of Naples “Federico II”, 80138 Naples, Italy; (G.L.); (M.D.)
| | - Guido Kroemer
- Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM UMRS 1138, Sorbonne Université, Université of Paris, 75005 Paris, France; (G.K.); (M.C.M.)
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, 94800 Villejuif, France
- Suzhou Institute for Systems Medicine, Chinese Academy of Sciences, Suzhou 100864, China
- Department of Women’s and Children’s Health, Karolinska Institutet, 171 77 Stockholm, Sweden
- Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, 75015 Paris, France
| | - Maria Chiara Maiuri
- Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM UMRS 1138, Sorbonne Université, Université of Paris, 75005 Paris, France; (G.K.); (M.C.M.)
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, 94800 Villejuif, France
| | - Giovanni Domenico De Palma
- Department of Clinical Medicine and Surgery, University of Naples “Federico II”, 80138 Naples, Italy; (F.P.T.); (G.P.)
- Centro Interuniversitario di Studi per l’Innovazione Tecnologica in Chirurgia, University of Naples Federico II, 80138 Naples, Italy
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Gressel GM, Maggi EC, Harmon BE, Ye KQ, Kuo DYS, Dolan SM, Montagna C. Low molecular weight serum cell-free DNA concentration is associated with clinicopathologic indices of poor prognosis in women with uterine cancer. J Transl Med 2020; 18:323. [PMID: 32854748 PMCID: PMC7457235 DOI: 10.1186/s12967-020-02493-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 08/20/2020] [Indexed: 12/12/2022] Open
Abstract
Background Serum cell-free DNA (cfDNA) holds promise as a non-invasive cancer biomarker. The objective of this study was to evaluate the association of cfDNA concentration with clinicopathologic variables of poor prognosis and overall survival among women with uterine cancer compared to benign cancer-free controls. Methods cfDNA was extracted from the serum of 91 women with multiple uterine cancer histologies and 22 post-menopausal controls without cancer. Low molecular weight (LMW) cfDNA was separated from contaminating genomic high molecular weight cfDNA using paramagnetic bead purification and its concentration was measured using fluorometric quantification. Clinicopathologic data was abstracted from the electronic medical record. The association between serum cfDNA concentration, clinicopathologic variables, and overall survival was assessed using linear regression modelling, Cox proportional hazards modelling, and the Kaplan–Meier method. Results Median total serum cfDNA concentration for the cohort was 69.2 ng/mL (IQR 37.4, 132.3) and median LMW cfDNA concentration was 23.8 ng/mL (IQR 14.9, 44.4). There were no significant differences in total serum cfDNA concentration with any clinicopathologic variables. However, LMW cfDNA concentration was significantly higher in serum of women with cancer (25.8 ng/mL IQR 16.0, 49.6) compared to benign controls (15.5 ng/mL IQR 9.3, 25.8 ng/mL) (p < 0.01). It is also significantly higher among women with early stage cancer than benign controls (p < 0.01). There were also significant associations between LMW cfDNA concentration and stage of cancer (p = 0.01) and histology (p = 0.02). Patients with leiomyosarcoma and carcinosarcoma had higher cfDNA concentrations than those with endometrioid cancer. Over a median follow-up of 51.9 months, 75th percentile for overall survival for women with cancer was 24.0 months. Higher LMW cfDNA concentrations is associated with lower survival among women with cancer (p < 0.01). Conclusions Serum LMW cfDNA concentration is associated with overall survival in women with uterine cancer, and it is higher among women with uterine cancer compared to those of controls.
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Affiliation(s)
- Gregory M Gressel
- Department of Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Elaine C Maggi
- Department of Genetics, Albert Einstein College of Medicine Price Center/Block Research Pavilion, Room 401, 1301 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Bryan E Harmon
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Kenny Q Ye
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY, USA.,Department of Systems & Computational Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - D Y S Kuo
- Department of Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Siobhan M Dolan
- Department of Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Cristina Montagna
- Department of Genetics, Albert Einstein College of Medicine Price Center/Block Research Pavilion, Room 401, 1301 Morris Park Avenue, Bronx, NY, 10461, USA.
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Aberrant Telomere Length in Circulating Cell-Free DNA as Possible Blood Biomarker with High Diagnostic Performance in Endometrial Cancer. Pathol Oncol Res 2020; 26:2281-2289. [PMID: 32462419 DOI: 10.1007/s12253-020-00819-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 05/12/2020] [Indexed: 02/07/2023]
Abstract
To investigate the diagnostic performance of relative telomere length (RTL) in cell-free DNA (cfDNA) for endometrioid endometrial cancer (EC). We measured RTL in cfDNA of 40 EC patients (65 ± 12 years) and 31 healthy controls (HC) (63 ± 13 years), excluding in both groups other oncologic and severe non-oncologic diseases to limit confounders. Circulating cfDNA was extracted from serum using the QIAamp DNA Blood Mini kit (Qiagen, Hilden, Germany). After the quantitative real-time polymerase chain reaction, telomere repeat copy number to single-gene copy number ratio was calculated. RTL in cfDNA was found to be significantly lower in EC patients than in HC (p < 0.0001). The diagnostic performance of cfDNA RTL was estimated with receiver operating characteristics (ROC) curve analysis, which showed a diagnostic accuracy for EC of 0.87 (95% CI: 0.79-0.95, p < 0.0001). The cutoff cfDNA RTL value of 2.505 (T/S copy ratio) reported a sensitivity of 80.0% (95% CI: 64.35-90.95) and a specificity of 80.65% (95% CI: 62.53-92.55). Significant differences of RTL among EC stages or grades (p = 0.85 and p = 0.89, respectively) were not observed. Our results suggest that cfDNA RTL analysis may be a diagnostic tool for EC detection since the early stage, whilst its diagnostic performance seems unsatisfactory for cancer progression, staging, and grading. However, further studies are needed to confirm these preliminary findings. In particular, future investigations should focus on high-risk patients (such as those with atypical endometrial hyperplasia) that may benefit from this tool, because TL shortening is not specific for EC and is influenced by other oncologic and non-oncologic diseases.
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Bruno V, Corrado G, Baci D, Chiofalo B, Carosi MA, Ronchetti L, Piccione E, Albini A, Noonan DM, Piaggio G, Vizza E. Endometrial Cancer Immune Escape Mechanisms: Let Us Learn From the Fetal-Maternal Interface. Front Oncol 2020; 10:156. [PMID: 32226771 PMCID: PMC7080858 DOI: 10.3389/fonc.2020.00156] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 01/29/2020] [Indexed: 12/14/2022] Open
Abstract
The immune escape mechanisms at the base of tumor progression in endometrial cancer mimic immune tolerance mechanisms occurring at the maternal-fetal interface. The biological and immunological processes behind the maternal-fetal interface are finely tuned in time and space during embryo implantation and subsequent pregnancy stages; conversely, those behind cancer progression are often aberrant. The environment composition at the maternal-fetal interface parallels the pro-tumor microenvironment identified in many cancers, pointing to the possibility for the use of the maternal-fetal interface as a model to depict immune therapeutic targets in cancer. The framework of cancer environment signatures involved in immune adaptations, precisely timed in cancer progression, could reveal a specific "immune clock" in endometrial cancer, which might guide clinicians in patient risk class assessment, diagnostic workup, management, surgical and therapeutic approach, and surveillance strategies. Here, we review studies approaching this hypothesis, focusing on what is known so far about oncofetal similarities in immunity with the idea to individualize personalized immunotherapy targets, through the downregulation of the immune escape stage or the reactivation of the pro-inflammatory processes suppressed by the tumor.
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Affiliation(s)
- Valentina Bruno
- Gynecologic Oncology Unit, Department of Experimental Clinical Oncology, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Giacomo Corrado
- Gynecologic Oncology Unit, Department of Women and Children Health, Fondazione Policlinico Universitario A. Gemelli, IRCCS-Università Cattolica del Sacro Cuore, Rome, Italy
| | - Denisa Baci
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Benito Chiofalo
- Gynecologic Oncology Unit, Department of Experimental Clinical Oncology, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Maria Antonia Carosi
- Anatomy Pathology Unit, Department of Research, Diagnosis and Innovative Technologies, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Livia Ronchetti
- Anatomy Pathology Unit, Department of Research, Diagnosis and Innovative Technologies, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Emilio Piccione
- Section of Gynecology, Academic Department of Surgical Sciences, Tor Vergata University Hospital, University of Rome "Tor Vergata", Rome, Italy
| | - Adriana Albini
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy.,Vascular Biology and Angiogenesis Laboratory, Science and Technology Pole (PST), IRCCS MultiMedica, Milan, Italy
| | - Douglas M Noonan
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy.,Vascular Biology and Angiogenesis Laboratory, Science and Technology Pole (PST), IRCCS MultiMedica, Milan, Italy
| | - Giulia Piaggio
- Department of Research, Diagnosis and Innovative Technologies, UOSD SAFU, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Enrico Vizza
- Gynecologic Oncology Unit, Department of Experimental Clinical Oncology, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
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Mayo-de-Las-Casas C, Velasco A, Sanchez D, Martínez-Bueno A, Garzón-Ibáñez M, Gatius S, Ruiz-Miró M, Gonzalez-Tallada X, Llordella I, Tresserra F, Rodríguez S, Aldeguer E, Roman-Canal B, Bertran-Alamillo J, García-Peláez B, Rosell R, Molina-Vila MA, Matias-Guiu X. Detection of somatic mutations in peritoneal lavages and plasma of endometrial cancer patients: A proof-of-concept study. Int J Cancer 2020; 147:277-284. [PMID: 31953839 DOI: 10.1002/ijc.32872] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/10/2019] [Accepted: 01/03/2020] [Indexed: 12/18/2022]
Abstract
Endometrial cancer (EC) is the most common gynecologic malignancy in developed countries. Although most patients are diagnosed at early stages, 15-20% will relapse despite local treatment. Presently, there are no reliable markers to identify patients with worse outcomes who may benefit from adjuvant treatments, such as chemotherapy, and liquid biopsies may be of use in this setting. Peritoneal lavages are systematically performed during endometrial surgery but little data are available about their potential as liquid biopsies. We analyzed KRAS and PIK3CA mutations in paired surgical biopsies, blood and cytology-negative peritoneal lavages in a cohort of 50 EC patients. Surgical biopsies were submitted to next-generation sequencing (NGS) while circulating-free DNA (cfDNA) purified from plasma and peritoneal lavages was analyzed for KRAS and PIK3CA hotspot mutations using a sensitive quantitative polymerase chain reaction (PCR) assay. NGS of biopsies revealed KRAS, PIK3CA or concomitant KRAS + PIK3CA mutations in 33/50 (66%) EC patients. Of those, 19 cases carried hotspot mutations. Quantitative PCR revealed KRAS and/or PIK3CA mutations in the lavages of 9/19 (47.4%) hotspot EC patients. In contrast, only 2/19 (10.5%) blood samples from hotspot EC patients were positive. Mutations found in cfDNA consistently matched those in paired biopsies. One of the two patients positive in plasma and lavage died in less than 6 months. In conclusion, mutational analysis in peritoneal lavages and blood from early stage EC is feasible. Further studies are warranted to determine if it might help to identify patients with worse prognosis. Human genes discussed: KRAS, KRAS proto-oncogene, GTPase; PIK3CA, phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha.
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Affiliation(s)
- Clara Mayo-de-Las-Casas
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Ana Velasco
- Department of Pathology, Hospital Universitari Arnau de Vilanova, IRBLLEIDA, Lleida, Spain
| | - Douglas Sanchez
- Department of Pathology, Hospital Universitari Arnau de Vilanova, IRBLLEIDA, Lleida, Spain
| | | | - Mónica Garzón-Ibáñez
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Sònia Gatius
- Department of Pathology, Hospital Universitari Arnau de Vilanova, IRBLLEIDA, Lleida, Spain
| | | | | | - Ivana Llordella
- Department of Gynecology, Hospital Universitari Arnau de Vilanova, IRBLLEIDA, Lleida, Spain
| | - Francesc Tresserra
- Department of Pathology, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Sonia Rodríguez
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Erika Aldeguer
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | | | - Jordi Bertran-Alamillo
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Beatriz García-Peláez
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Rafael Rosell
- Dr Rosell Oncology Institute, Quirón Dexeus University Hospital, Barcelona, Spain
- Cancer Biology and Precision Medicine Program, Catalan Institute of Oncology, Germans Trias i Pujol Health Sciences Institute and Hospital, Badalona, Spain
| | - Miguel A Molina-Vila
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Xavier Matias-Guiu
- Department of Pathology, Hospital Universitari Arnau de Vilanova, IRBLLEIDA, Lleida, Spain
- Hospital Universitari de Bellvitge, IDIBELL, Barcelona, Spain
- University of Lleida, CIBERONC, Lleida, Spain
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De Bruyn C, Baert T, Van den Bosch T, Coosemans A. Circulating Transcripts and Biomarkers in Uterine Tumors: Is There a Predictive Role? Curr Oncol Rep 2020; 22:12. [PMID: 31997106 DOI: 10.1007/s11912-020-0864-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
PURPOSE OF REVIEW Uterine cancer comprises endometrial carcinoma and the uterine sarcoma. Endometrial carcinomas are the most frequent variant and have early symptoms and a solid diagnostic work up, resulting in a rather fair prognosis. However, in case of advanced stage disease and relapse, treatment options are limited and prognosis is impaired. Uterine sarcomas are rare, often lacking symptoms and no diagnostic tool for correct pre-operative diagnosis are available. Prognosis is poor. RECENT FINDINGS Circulating biomarkers as a liquid biopsy could be beneficial as a diagnostic tool in uterine sarcomas. For both carcinomas and sarcomas, circulating biomarkers could be of use in predicting early disease recurrence. This review in endometrial carcinoma and uterine sarcoma focus on circulating biomarkers; such as proteins; circulating tumor cells; circulating tumor DNA; microRNA; and immune cells.
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Affiliation(s)
- Christine De Bruyn
- Department of Oncology, Laboratory of Tumor Immunology and Immunotherapy, ImmunOvar Research Group, KU Leuven, Leuven, Belgium
- Department of Obstetrics and Gynecology, University Hospital Antwerp, Edegem, Belgium
| | - Thaïs Baert
- Department of Oncology, Laboratory of Tumor Immunology and Immunotherapy, ImmunOvar Research Group, KU Leuven, Leuven, Belgium
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen Mitte (KEM), Essen, Germany
| | - Thierry Van den Bosch
- Department of Oncology, Laboratory of Tumor Immunology and Immunotherapy, ImmunOvar Research Group, KU Leuven, Leuven, Belgium
- Department of Obstetrics and Gynecology, University Hospitals Leuven, Leuven, Belgium
| | - An Coosemans
- Department of Oncology, Laboratory of Tumor Immunology and Immunotherapy, ImmunOvar Research Group, KU Leuven, Leuven, Belgium.
- Department of Obstetrics and Gynecology, University Hospitals Leuven, Leuven, Belgium.
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Chen Q, Zhang ZH, Wang S, Lang JH. Circulating Cell-Free DNA or Circulating Tumor DNA in the Management of Ovarian and Endometrial Cancer. Onco Targets Ther 2019; 12:11517-11530. [PMID: 31920340 PMCID: PMC6938177 DOI: 10.2147/ott.s227156] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 11/27/2019] [Indexed: 12/14/2022] Open
Abstract
Ovarian cancer (OC) is the most lethal cancer of all gynecological malignancies, while endometrial cancer (EC) is the most common one. Current strategies for OC/EC diagnosis consist of the extraction of a solid tissue from the affected area. This sample enables the study of specific biomarkers and the genetic nature of the tumor. However, the tissue extraction is risky and painful for the patient and in some cases is unavailable in inaccessible tumors. Moreover, a tissue biopsy is expensive and requires a highly skilled gynecological surgery to pinpoint accurately which cannot be applied repeatedly. New alternatives that overcome these drawbacks are rising up nowadays, such as liquid biopsy. A liquid biopsy is the analysis of biomarkers in a non-solid biological tissue, mainly blood, which has remarkable advantages over the traditional method. The most studied cancer non-invasive biomarkers are circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), and circulating free DNA (cfDNA). These circulating biomarkers play a key role in the understanding of metastasis and tumorigenesis, which could provide a better insight into the evolution of the tumor dynamics during treatment and disease progression. Liquid biopsy is an emerging non-invasive, safe and effective method with considerable potential for clinical diagnosis and treatment management in patients with OC and EC. Analysis of cfDNA and ctDNA will provide a better characterization of biomarkers and give rise to a wide range of clinical applications, such as early detection of OC/EC, the prediction of treatment responses due to the discovery of personalized tumor-related biomarkers, and therapeutic response monitoring.
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Affiliation(s)
- Qian Chen
- Department of Gynecology and Obstetrics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Zi-Han Zhang
- Department of Gynecology and Obstetrics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Shu Wang
- Department of Gynecology and Obstetrics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Jing-He Lang
- Department of Gynecology and Obstetrics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
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Zou Y, Yang R, Huang ML, Kong YG, Sheng JF, Tao ZZ, Gao L, Chen SM. NOTCH2 negatively regulates metastasis and epithelial-Mesenchymal transition via TRAF6/AKT in nasopharyngeal carcinoma. J Exp Clin Cancer Res 2019; 38:456. [PMID: 31699119 PMCID: PMC6836530 DOI: 10.1186/s13046-019-1463-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 10/21/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Clinically, distant metastasis after primary treatment remains a key problem in nasopharyngeal carcinoma (NPC). Thus, identification of the underlying mechanisms and development of novel therapeutic strategies are urgently needed. NOTCH has been shown to function as a tumor promotor that enhances angiogenesis, cancer invasion and metastasis in NPC. However, the precise roles of the four individual NOTCH receptors and their mechanisms of action are unclear. METHODS We used Western blot analysis, immunofluorescence, immunohistochemical analysis, phalloidin staining, mouse tumor metastatic dissemination models, gene set enrichment analysis, immunoprecipitation assays and a series of functional assays to determine the potential role of NOTCH2 in regulating NPC metastasis. RESULTS NOTCH2 expression in the NPC tissues of patients with cervical lymph node metastasis was lower than that of patients without cervical lymph node metastasis. Correspondingly, NOTCH2 expression was low in metastatic and poorly differentiated NPC cells. NOTCH2 expression correlated negatively with survival time in patients with NPC. Suppression of NOTCH2 expression promoted NPC cell metastasis, whereas NOTCH2 overexpression inhibited this process. Furthermore, NOTCH2 attenuated the TRAF6-AKT signaling axis via an interaction between the NOTCH2 intracellular domain (N2ICD) and TRAF6, which inhibited epithelial-mesenchymal transition (EMT) and eventually suppressed NPC metastasis. CONCLUSIONS These findings reveal that loss of NOTCH2 activates the TRAF6/AKT axis and promotes metastasis in NPC, suggesting that NOTCH2 may represent a therapeutic target for the treatment of NPC.
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Affiliation(s)
- You Zou
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, 238 Jie-Fang Road, Wuhan, 430060 Hubei People’s Republic of China
| | - Rui Yang
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, 238 Jie-Fang Road, Wuhan, 430060 Hubei People’s Republic of China
| | - Mao-Ling Huang
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, 238 Jie-Fang Road, Wuhan, 430060 Hubei People’s Republic of China
| | - Yong-Gang Kong
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, 238 Jie-Fang Road, Wuhan, 430060 Hubei People’s Republic of China
| | - Jian-Fei Sheng
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, 238 Jie-Fang Road, Wuhan, 430060 Hubei People’s Republic of China
| | - Ze-Zhang Tao
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, 238 Jie-Fang Road, Wuhan, 430060 Hubei People’s Republic of China
| | - Ling Gao
- Department of Endocrinology & Metabolism, Renmin Hospital of Wuhan University, Jinan, China
| | - Shi-Ming Chen
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, 238 Jie-Fang Road, Wuhan, 430060 Hubei People’s Republic of China
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Quantitative Methylation-Specific PCR: A Simple Method for Studying Epigenetic Modifications of Cell-Free DNA. Methods Mol Biol 2019; 1909:137-162. [PMID: 30580429 DOI: 10.1007/978-1-4939-8973-7_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Aberrant DNA methylation of cell-free circulating DNA (cfDNA) has recently gained attention for its use as biomarker in cancer diagnosis, prognosis, and prediction of therapeutic response. Quantification of cfDNA methylation levels requires methods with high sensitivity and specificity due to low amounts of cfDNA available in plasma, high degradation of cfDNA, and/or contamination with genomic DNA. To date, several approaches for measuring cfDNA methylation have been established, including quantitative methylation-specific PCR (qMSP), which represents a simple, fast, and cost-effective technique that can be easily implemented into clinical practice. In this chapter, we provide a detailed protocol for SYBR Green qMSP analysis which is currently used in our laboratory for cfDNA methylation detection. Useful information regarding successful qMSP primers design are also provided.
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Mari R, Lambaudie É, Provansal M, Sabatier R. [Circulating tumor DNA assessment for gynaecological cancers management]. Bull Cancer 2019; 106:237-252. [PMID: 30765097 DOI: 10.1016/j.bulcan.2018.11.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 11/19/2018] [Accepted: 11/27/2018] [Indexed: 01/05/2023]
Abstract
Gynaecological cancers are frequent, with more than 16,000 cases per year in France for 6500 deaths. Few improvements in diagnostic methods, prognostic tools, and therapeutic strategies have occurred in the last two decades. Tumour genomic analyses from, at least in part, the Cancer Genome Atlas have identified some of the molecular alterations involved in gynaecological tumours growth and spreading. However, these data remain incomplete and have not led to dramatic changes in the clinical management of our patients. Moreover, they require invasive samples that are not suitable to objectives like screening/early diagnosis, assessment of treatment efficacy, monitoring of residual disease or early diagnosis of relapse. In the last years, the analysis of circulating tumour biomarkers (also called "liquid biopsies") based on tumour cells (circulating tumour cells) or tumour nucleotides (circulating DNA or RNA) has been massively explored through various indications, platforms, objectives; data related to circulating tumour DNA being the most important in terms of number of publications and interest for clinical practice. This review aims to describe the methods of analysis as well as the observations from the analysis of circulating tumour DNA in gynaecological tumours, from screening/early diagnosis to the adaptation of treatment for advanced stages, through choice of treatments and monitoring of subclinical disease.
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Affiliation(s)
- Roxane Mari
- Aix-Marseille university, CNRS U7258, Inserm U1068, institut Paoli-Calmettes, département d'oncologie médicale, CRCM, Marseille cedex 9, France
| | - Éric Lambaudie
- Aix-Marseille university, CNRS U7258, Inserm U1068, institut Paoli-Calmettes, département de chirurgie oncologique, CRCM, Marseille cedex 9, France; Aix-Marseille university, CNRS U7258, Inserm U1068, institut Paoli-Calmettes, CRCM, laboratoire d'oncologie prédictive, Marseille cedex 9, France
| | - Magali Provansal
- Aix-Marseille university, CNRS U7258, Inserm U1068, institut Paoli-Calmettes, département d'oncologie médicale, CRCM, Marseille cedex 9, France
| | - Renaud Sabatier
- Aix-Marseille university, CNRS U7258, Inserm U1068, institut Paoli-Calmettes, département d'oncologie médicale, CRCM, Marseille cedex 9, France; Aix-Marseille university, CNRS U7258, Inserm U1068, institut Paoli-Calmettes, CRCM, laboratoire d'oncologie prédictive, Marseille cedex 9, France.
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Qi J, Chen LY, Shen XJ, Ju SQ. Analytical Value of Cell-Free DNA Based on Alu in Psychiatric Disorders. Front Psychiatry 2019; 10:992. [PMID: 32038328 PMCID: PMC6985436 DOI: 10.3389/fpsyt.2019.00992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 12/13/2019] [Indexed: 11/17/2022] Open
Abstract
Psychiatric disorders impose a huge burden on individuals, families, and society. The Alu repeat sequence is a member of the short interspersed nuclear element (SINE) family of mammalian genomes, however, its expression pattern and role in psychiatric disorders is unclear. The current paper aimed at determining the concentrations of Alu in patients with schizophrenia (SZ), major depressive disorder (MDD), and alcohol-induced psychotic disorder (AIPD), and to further define the role and value of Alu as a potential biomarker in psychiatric disorders. In this work, we found that the concentration of Alu was considerably incremented in patients with SZ, and a significant difference existed between patients diagnosed with SZ and MDD or AIPD. ROC analysis also indicated that Alu was effective in the complementary diagnosis of SZ, and differentially diagnosed between SZ patients and patients with MDD or AIPD. In addition, we found a positive relationship between the Alu concentrations and interleukin-1β (IL-1β) in patients with SZ, MDD, and AIPD, and between the concentrations of Alu and interleukin-18 (IL-18) in patients with SZ. Overall, the present work indicates that Alu might be an innovative biomarker for diagnosing psychiatric disorders, and provides the basis for hypotheses about the pathophysiology of psychiatric disorders.
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Affiliation(s)
- Jing Qi
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Ling-Yun Chen
- Center of Laboratory Medicine, Nantong Mental Health Center, Nantong, China
| | - Xian-Juan Shen
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Shao-Qing Ju
- Center of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
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Muinelo-Romay L, Casas-Arozamena C, Abal M. Liquid Biopsy in Endometrial Cancer: New Opportunities for Personalized Oncology. Int J Mol Sci 2018; 19:E2311. [PMID: 30087246 PMCID: PMC6121388 DOI: 10.3390/ijms19082311] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 07/24/2018] [Accepted: 08/02/2018] [Indexed: 12/16/2022] Open
Abstract
The identification of new molecular targets and biomarkers associated with high risk of recurrence and response to therapy represents one of the main clinical challenges in the management of advanced disease in endometrial cancer. In this sense, the field of liquid biopsy has emerged as a great revolution in oncology and is considered "the way" to reach personalised medicine. In this review, we discuss the promising but already relatively limited advances of liquid biopsy in endometrial cancer compared to other types of tumours like breast, colorectal or prostate cancer. We present recent data analysing circulating tumour material in minimally-invasive blood samples, but also in alternative forms of liquid biopsy like uterine aspirates. Proteomic and genomic studies focused on liquid-based uterine samples are resulting not only in optimal diagnostic tools but also in reliable approaches to address tumour heterogeneity. Likewise, circulating tumour cells (CTCs) and circulating tumour DNA (ctDNA) represent an opportunity for the correct stratification of patients, for the assessment of early recurrent disease or for the real-time monitoring of therapy responses. Appropriately designed studies and implementation in clinical trials will determine the value of liquid biopsy for precision oncology in endometrial cancer.
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Affiliation(s)
- Laura Muinelo-Romay
- Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (Oncomet), CIBERONC, Health Research Institute of Santiago de Compostela (IDIS), University Hospital of Santiago de Compostela (SERGAS), Trav. Choupana s/n, 15706 Santiago de Compostela, Spain.
| | - Carlos Casas-Arozamena
- Translational Medical Oncology Group (Oncomet), CIBERONC, Health Research Institute of Santiago (IDIS), University Hospital of Santiago de Compostela (SERGAS), Trav. Choupana s/n, 15706 Santiago de Compostela, Spain.
| | - Miguel Abal
- Translational Medical Oncology Group (Oncomet), CIBERONC, Health Research Institute of Santiago (IDIS), University Hospital of Santiago de Compostela (SERGAS), Trav. Choupana s/n, 15706 Santiago de Compostela, Spain.
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Vizza E, Corrado G, De Angeli M, Carosi M, Mancini E, Baiocco E, Chiofalo B, Patrizi L, Zampa A, Piaggio G, Cicchillitti L. Correction to: Serum DNA integrity index as a potential molecular biomarker in endometrial cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2018; 37:35. [PMID: 29463277 PMCID: PMC5820798 DOI: 10.1186/s13046-018-0708-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 02/02/2018] [Indexed: 11/10/2022]
Abstract
CORRECTION In the publication of this article [1], there is an error in the first sentence of the Acknowledgements section.
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Affiliation(s)
- Enrico Vizza
- Department of Experimental Clinical Oncology, Gynecologic Oncology Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Giacomo Corrado
- Department of Health of Woman and Child, Gynecologic Oncology Unit, Catholic University of the Sacred Heart, Rome, Italy.
| | - Martina De Angeli
- Department of Biomedicine and Prevention, Obstetrics and Gynecology Unit, University of Rome "Tor Vergata", Rome, Italy
| | - Mariantonia Carosi
- Department of Research, Advanced Diagnostics and Technological Innovation, Anatomy Pathology Unit Regina Elena National Cancer Institute, Rome, Italy
| | - Emanuela Mancini
- Department of Experimental Clinical Oncology, Gynecologic Oncology Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Ermelinda Baiocco
- Department of Experimental Clinical Oncology, Gynecologic Oncology Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Benito Chiofalo
- Department of Experimental Clinical Oncology, Gynecologic Oncology Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Lodovico Patrizi
- Department of Biomedicine and Prevention, Obstetrics and Gynecology Unit, University of Rome "Tor Vergata", Rome, Italy
| | - Ashanti Zampa
- Department of Experimental Clinical Oncology, Gynecologic Oncology Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Giulia Piaggio
- Department of Research, Advanced Diagnostics and Technological Innovation, Area of Translational Research, IRCCS Regina Elena National Cancer Institute, Rome, Italy.
| | - Lucia Cicchillitti
- Department of Experimental Clinical Oncology, Gynecologic Oncology Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
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