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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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New Perspectives on the Importance of Cell-Free DNA Biology. Diagnostics (Basel) 2022; 12:diagnostics12092147. [PMID: 36140548 PMCID: PMC9497998 DOI: 10.3390/diagnostics12092147] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/24/2022] [Accepted: 08/31/2022] [Indexed: 11/28/2022] Open
Abstract
Body fluids are constantly replenished with a population of genetically diverse cell-free DNA (cfDNA) fragments, representing a vast reservoir of information reflecting real-time changes in the host and metagenome. As many body fluids can be collected non-invasively in a one-off and serial fashion, this reservoir can be tapped to develop assays for the diagnosis, prognosis, and monitoring of wide-ranging pathologies, such as solid tumors, fetal genetic abnormalities, rejected organ transplants, infections, and potentially many others. The translation of cfDNA research into useful clinical tests is gaining momentum, with recent progress being driven by rapidly evolving preanalytical and analytical procedures, integrated bioinformatics, and machine learning algorithms. Yet, despite these spectacular advances, cfDNA remains a very challenging analyte due to its immense heterogeneity and fluctuation in vivo. It is increasingly recognized that high-fidelity reconstruction of the information stored in cfDNA, and in turn the development of tests that are fit for clinical roll-out, requires a much deeper understanding of both the physico-chemical features of cfDNA and the biological, physiological, lifestyle, and environmental factors that modulate it. This is a daunting task, but with significant upsides. In this review we showed how expanded knowledge on cfDNA biology and faithful reverse-engineering of cfDNA samples promises to (i) augment the sensitivity and specificity of existing cfDNA assays; (ii) expand the repertoire of disease-specific cfDNA markers, thereby leading to the development of increasingly powerful assays; (iii) reshape personal molecular medicine; and (iv) have an unprecedented impact on genetics research.
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Ferchiou S, Caza F, de Boissel PGJ, Villemur R, St-Pierre Y. Applying the concept of liquid biopsy to monitor the microbial biodiversity of marine coastal ecosystems. ISME COMMUNICATIONS 2022; 2:61. [PMID: 37938655 PMCID: PMC9723566 DOI: 10.1038/s43705-022-00145-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 06/28/2022] [Accepted: 07/08/2022] [Indexed: 10/04/2023]
Abstract
Liquid biopsy (LB) is a concept that is rapidly gaining ground in the biomedical field. Its concept is largely based on the detection of circulating cell-free DNA (ccfDNA) fragments that are mostly released as small fragments following cell death in various tissues. A small percentage of these fragments are from foreign (nonself) tissues or organisms. In the present work, we applied this concept to mussels, a sentinel species known for its high filtration capacity of seawater. We exploited the capacity of mussels to be used as natural filters to capture environmental DNA fragments of different origins to provide information on the biodiversity of marine coastal ecosystems. Our results showed that hemolymph of mussels contains DNA fragments that varied considerably in size, ranging from 1 to 5 kb. Shotgun sequencing revealed that a significant amount of DNA fragments had a nonself microbial origin. Among these, we found DNA fragments derived from bacteria, archaea, and viruses, including viruses known to infect a variety of hosts that commonly populate coastal marine ecosystems. Taken together, our study shows that the concept of LB applied to mussels provides a rich and yet unexplored source of knowledge regarding the microbial biodiversity of a marine coastal ecosystem.
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Affiliation(s)
- Sophia Ferchiou
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, H7V 1B7, Canada
| | - France Caza
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, H7V 1B7, Canada
| | | | - Richard Villemur
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, H7V 1B7, Canada
| | - Yves St-Pierre
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, H7V 1B7, Canada.
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Mohamadzaheri M, Cheraghi H, Shirani D, Hatamkhani A. Relationship between plasma cell-free DNA changes and lysyl oxidase during the treatment and prognosis of canine transmissible venereal tumors. BMC Vet Res 2022; 18:76. [PMID: 35189882 PMCID: PMC8862336 DOI: 10.1186/s12917-022-03173-z] [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: 11/01/2021] [Accepted: 02/09/2022] [Indexed: 11/22/2022] Open
Abstract
Background Transmissible venereal tumors (TVT) are a wide range of canine tumors for which there are no effective markers to monitor the therapeutic response in real-time. Circulating biomarkers can be valuable in early cancer diagnosis and prognosis. Accordingly, this study aimed to investigate the significance of the cell-free DNA (cfDNA) and cfDNA integrity index to monitor the response of TVTs to vincristine and compare them with lysyl oxidase activity. Plasma and sera were collected from fifteen male dogs within four weeks before drug administration. The analytical method was mainly based on the quantitative polymerase chain reaction (qPCR) technique for short and long cfDNAs and lysyl oxidase activity was measured in serum. Results The results of the cfDNA integrity index showed a significant (p < 0.05) difference in the baseline concentration compared to the second and third weeks (with cut-off values of 1.118 and 93.33% specificity). The cfDNA integrity index increased over time due to the reduction of short cfDNAs in the first week after treatment. Lysyl oxidase activity increased during the fourth week (p < 0.001), but there were no significant differences in the other weeks compared to the baseline. The ROC analysis of lysyl oxidase revealed high sensitivity (100%) and specificity (90%) on the second and third weeks compared to the baseline. Multivariate analysis between cfDNA integrity index and lysyl oxidase showed significant correlation (p < 0.05) only in baseline results. Conclusions Overall, short cfDNA, the cfDNA integrity index, and lysyl oxidase activity can be proposed as diagnostic biomarkers and putative prognostic candidates in TVT patients. These biomarkers can be combined with cytology to quickly diagnose TVT. Supplementary Information The online version contains supplementary material available at 10.1186/s12917-022-03173-z.
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Affiliation(s)
- Mona Mohamadzaheri
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Razi University, Kermanshah, Iran
| | - Hadi Cheraghi
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Razi University, Kermanshah, Iran.
| | - Darioush Shirani
- Department of Small Animal Internal Medicine, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
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Kayes D, Blacklock B. Feline Uveal Melanoma Review: Our Current Understanding and Recent Research Advances. Vet Sci 2022; 9:vetsci9020046. [PMID: 35202299 PMCID: PMC8877522 DOI: 10.3390/vetsci9020046] [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: 12/02/2021] [Revised: 01/21/2022] [Accepted: 01/23/2022] [Indexed: 02/01/2023] Open
Abstract
Melanocytic neoplasia is the most common form of ocular tumour in cats, accounting for 67% of cases in an analysis of 2614 cases of primary ocular neoplasia. Feline diffuse iris melanoma (FDIM) is by far the most common form of ocular melanocytic neoplasia, with limbal melanomas and atypical melanoma (melanoma affecting the choroid or ciliary body) infrequently recognised. Early lesions begin as flat areas of pigmentation of the iris, known as iris melanosis. This melanosis is a precursor lesion that can become FDIM when pigmented cells infiltrate the anterior iris stroma, commonly alongside a transition in cell morphology. The differentiation between FDIM and benign iris melanosis is only recognisable though histologic examination, with no in vivo means of identifying the malignant transformation. The behaviour of FDIM is variable and difficult to predict. Some FDIM lesions have a more benign progression and can slowly grow or remain static for years without affecting the ocular or systemic health of the individual, whilst other tumours behave aggressively, invading the ocular structures and significantly affecting the life expectancy of cats through metastatic disease. This makes management and timely enucleation of these cases challenging in practice. This article aims to review our current knowledge of FDIM.
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Guerra Guimarães T, Menezes Cardoso K, Tralhão P, Marto CM, Alexandre N, Botelho MF, Laranjo M. Current Therapeutics and Future Perspectives to Ocular Melanocytic Neoplasms in Dogs and Cats. Bioengineering (Basel) 2021; 8:bioengineering8120225. [PMID: 34940378 PMCID: PMC8698280 DOI: 10.3390/bioengineering8120225] [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: 11/29/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 12/24/2022] Open
Abstract
Neoplasms of melanocytic origin are diseases relevant to dogs and cats' ophthalmic oncology due to their incidence, potential visual loss, and consequent decrease in life quality and expectancy. Despite its non-specific clinical presentation, melanocytic neoplasms can be histologically distinguished in melanocytomas, which present benign characteristics, and malignant melanomas. The diagnosis often occurs in advanced cases, limiting the therapeutic options. Surgery, cryotherapy, radiotherapy, photodynamic therapy (PDT), and laser are currently available therapeutic strategies. As no clinical guidelines are available, the treatment choice is primarily based on the clinician's preference, proficiency, and the owner's financial constraints. While surgery is curative in benign lesions, ocular melanomas present a variable response to treatments, besides the potential of tumour recurrences or metastatic disease. This review presents the currently available therapies for ocular melanocytic neoplasms in dogs and cats, describing the therapeutic, indications, and limitations. Additionally, new therapeutics being developed are presented and discussed, as they can improve the current treatment options.
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Affiliation(s)
- Tarcísio Guerra Guimarães
- Institute of Research and Advanced Training (IIFA), University of Évora, 7002-554 Évora, Portugal; (T.G.G.); (K.M.C.)
- Mediterranean Institute for Agriculture, Environment and Development (MED), University of Évora, 7006-554 Évora, Portugal;
- Institute of Biophysics, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (C.M.M.); (M.F.B.)
- Institute for Clinical and Biomedical Research (iCBR), Area of Environment, Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3000-548 Coimbra, Portugal
| | - Karla Menezes Cardoso
- Institute of Research and Advanced Training (IIFA), University of Évora, 7002-554 Évora, Portugal; (T.G.G.); (K.M.C.)
- Mediterranean Institute for Agriculture, Environment and Development (MED), University of Évora, 7006-554 Évora, Portugal;
- Institute of Biophysics, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (C.M.M.); (M.F.B.)
- Institute for Clinical and Biomedical Research (iCBR), Area of Environment, Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3000-548 Coimbra, Portugal
| | - Pedro Tralhão
- Center of Veterinary Ophthalmology, Oftalvet, 4050-102 Porto, Portugal;
| | - Carlos Miguel Marto
- Institute of Biophysics, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (C.M.M.); (M.F.B.)
- Institute for Clinical and Biomedical Research (iCBR), Area of Environment, Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3000-548 Coimbra, Portugal
- Institute of Experimental Pathology, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-561 Coimbra, Portugal
| | - Nuno Alexandre
- Mediterranean Institute for Agriculture, Environment and Development (MED), University of Évora, 7006-554 Évora, Portugal;
- Department of Veterinary Medicine, University of Évora, 7004-516 Évora, Portugal
| | - Maria Filomena Botelho
- Institute of Biophysics, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (C.M.M.); (M.F.B.)
- Institute for Clinical and Biomedical Research (iCBR), Area of Environment, Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3000-548 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-561 Coimbra, Portugal
| | - Mafalda Laranjo
- Institute of Biophysics, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (C.M.M.); (M.F.B.)
- Institute for Clinical and Biomedical Research (iCBR), Area of Environment, Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3000-548 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-561 Coimbra, Portugal
- Correspondence:
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Colmer SF, Luethy D, Abraham M, Stefanovski D, Hurcombe SD. Utility of cell-free DNA concentrations and illness severity scores to predict survival in critically ill neonatal foals. PLoS One 2021; 16:e0242635. [PMID: 33901192 PMCID: PMC8075268 DOI: 10.1371/journal.pone.0242635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/13/2021] [Indexed: 11/18/2022] Open
Abstract
Plasma cell-free DNA (cfDNA) levels have been associated with disease and survival status in septic humans and dogs. To date, studies investigating cfDNA levels in association with critical illness in foals are lacking. We hypothesized that cfDNA would be detectable in the plasma of foals, that septic and sick-nonseptic foals would have significantly higher cfDNA levels compared to healthy foals, and that increased cfDNA levels would be associated with non-survival. Animals used include 80 foals of 10 days of age or less admitted to a tertiary referral center between January and July, 2020 were stratified into three categories: healthy (n = 34), sick non-septic (n = 11) and septic (n = 35) based on specific criteria. This was a prospective clinical study. Blood was collected from critically ill foals at admission or born in hospital for cfDNA quantification and blood culture. Previously published sepsis score (SS) and neonatal SIRS score (NSIRS) were also calculated. SS, NSIRS, blood culture status and cfDNA concentrations were evaluated to predict survival. Continuous variables between groups were compared using Kruskal-Wallis ANOVA with Dunn’s post hoc test. Comparisons between two groups were assessed using the Mann-Whitney U-test or Spearman rank for correlations. The performance of cfDNA, sepsis score and NSIRS score to predict survival was assessed by receiver operator characteristic (ROC) curve analysis including area under the curve, sensitivity and specificity using cutoffs. Plasma cfDNA was detectable in all foals. No significant differences in cfDNA concentration were detected between healthy foals and septic foals (P = 0.65) or healthy foals and sick non-septic foals (P = 0.88). There was no significant association between cfDNA and culture status, SS, NSIRS or foal survival. SS (AUC 0.85) and NSIRS (AUC 0.83) were superior to cfDNA (AUC 0.64) in predicting survival. Although cfDNA was detectable in foal plasma, it offers negligible utility to diagnose sepsis or predict survival in critical illness in neonates.
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Affiliation(s)
- Sarah Florence Colmer
- Department of Clinical Sciences, The University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Philadelphia, Pennsylvania, United States of America
| | - Daniela Luethy
- Department of Clinical Sciences, The University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Philadelphia, Pennsylvania, United States of America
| | - Michelle Abraham
- Department of Clinical Sciences, The University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Philadelphia, Pennsylvania, United States of America
| | - Darko Stefanovski
- Department of Clinical Sciences, The University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Philadelphia, Pennsylvania, United States of America
| | - Samuel David Hurcombe
- Department of Clinical Sciences, The University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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