scholarly journals Horizons in Veterinary Precision Oncology: Fundamentals of Cancer Genomics and Applications of Liquid Biopsy for the Detection, Characterization, and Management of Cancer in Dogs

2021 ◽  
Vol 8 ◽  
Author(s):  
Jason Chibuk ◽  
Andi Flory ◽  
Kristina M. Kruglyak ◽  
Nicole Leibman ◽  
Alexis Nahama ◽  
...  
Keyword(s):  
Veterinary Medicine ◽  
Liquid Biopsy ◽  
Cancer Genomics ◽  
Residual Disease ◽  
Clinical Signs ◽  
Human Medicine ◽  
Response Monitoring ◽  
Precision Oncology ◽  
Technological Advances ◽  
The One

Cancer is the leading cause of death in dogs, in part because many cases are identified at an advanced stage when clinical signs have developed, and prognosis is poor. Increased understanding of cancer as a disease of the genome has led to the introduction of liquid biopsy testing, allowing for detection of genomic alterations in cell-free DNA fragments in blood to facilitate earlier detection, characterization, and management of cancer through non-invasive means. Recent discoveries in the areas of genomics and oncology have provided a deeper understanding of the molecular origins and evolution of cancer, and of the “one health” similarities between humans and dogs that underlie the field of comparative oncology. These discoveries, combined with technological advances in DNA profiling, are shifting the paradigm for cancer diagnosis toward earlier detection with the goal of improving outcomes. Liquid biopsy testing has already revolutionized the way cancer is managed in human medicine – and it is poised to make a similar impact in veterinary medicine. Multiple clinical use cases for liquid biopsy are emerging, including screening, aid in diagnosis, targeted treatment selection, treatment response monitoring, minimal residual disease detection, and recurrence monitoring. This review article highlights key scientific advances in genomics and their relevance for veterinary oncology, with the goal of providing a foundational introduction to this important topic for veterinarians. As these technologies migrate from human medicine into veterinary medicine, improved awareness and understanding will facilitate their rapid adoption, for the benefit of veterinary patients.

scholarly journals Liquid Biopsy in Early Breast Cancer: A Preliminary Report

2020 ◽  
pp. 1-8
Author(s):  
Antonio Rulli ◽  
Antognelli Cinzia ◽  
Antonio Rulli ◽  
Covarelli Piero ◽  
Izzo Luciano ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Liquid Biopsy ◽  
Residual Disease ◽  
Early Stage ◽  
Dynamic Monitoring ◽  
Molecular Profile ◽  
Precision Oncology ◽  
Surgical Biopsy ◽  
Post Surgery ◽  
Genetic Landscape

Background: Liquid biopsy (LB) is a technique that utilizes circulating biomarkers from cancer patients to provide information regarding the genetic landscape of the cancer. LB is emerging as an alternative and complementary diagnostic and prognostic tool to surgical biopsy and is expected to provide the tool for the implementation of precision oncology in clinical settings. In fact, it may contribute to enhance understanding of tumor heterogeneity and permitting the dynamic monitoring of treatment responses and genomic variations. Thus, LB is a promising method for the management of cancer, including breast cancer (BC), whose incidence in Italy is progressively increasing. Previous studies focused mainly on patients with advanced-stage BC. In the present study we evaluated the number of circulating tumor cells (CTCs), the quantity of cell free tumor DNA (cftDNA) and the analysis of the mutational profile of DNA from CTCs (ctcDNA) and cftDNA in early stage BC patients. Methods: Matched pre- and post-surgery blood samples were collected from 47 early stage BC patients. CTCs enumeration was done using Isoflux system, molecular profile of ctcDNA and cftDNA was performed with the Spotlight 59 Panels kit on a MiSeq Illumina instrument. Results: Eighty percent of samples was CTCs-positive, while healthy controls were all CTCs-negative. Forty-four patients provided a pre-surgery and 21 post-surgery sample. By comparing the number of CTCs post-surgery with that of pre-surgery, we found that 66% of patients showed a decreased number of CTCs, 14% of patients continued to have the same number of CTCs, while, interestingly, 19% of patients showed an increased number of CTCs. Next Generation Sequencing (NGS) of ctcDNA and cftDNA showed that 52% of samples had mutations in 9 genes (TP53, CDKN2A, FBXW7, PTPN11, KRAS, NRAS, BRAF, IDH1, ALK) and in 5 genes (PIK3CA, APC ALK, KRAS, TSC1), respectively, with KRAS and ALK overlapping and TP53 being the most frequently mutated gene in ctcDNA analysis. Conclusions: LB could facilitate early detection of minimal residual disease, aiding in the initiation of adjuvant therapy to prevent recurrence and progression towards metastasis, enhance individualized treatment and longitudinal screening, thus improving the clinical management and outcome of patients with early BC.

scholarly journals Precision Medicine for Colorectal Cancer with Liquid Biopsy and Immunotherapy

Cancers ◽  
2021 ◽  
Vol 13 (19) ◽  
pp. 4803
Author(s):  
Satoshi Nagayama ◽  
Siew-Kee Low ◽  
Kazuma Kiyotani ◽  
Yusuke Nakamura
Keyword(s):  
Colorectal Cancer ◽  
Early Detection ◽  
Liquid Biopsy ◽  
Residual Disease ◽  
Point Of View ◽  
Liquid Biopsies ◽  
Cell Therapies ◽  
Technological Advances ◽  
Diagnostic Modalities ◽  
Tumor Genome

In the field of colorectal cancer (CRC) treatment, diagnostic modalities and chemotherapy regimens have progressed remarkably in the last two decades. However, it is still difficult to identify minimal residual disease (MRD) necessary for early detection of recurrence/relapse of tumors and to select and provide appropriate drugs timely before a tumor becomes multi-drug-resistant and more aggressive. We consider the leveraging of in-depth genomic profiles of tumors as a significant breakthrough to further improve the overall prognosis of CRC patients. With the recent technological advances in methodologies and bioinformatics, the genomic profiles can be analyzed profoundly without delay by blood-based tests—‘liquid biopsies’. From a clinical point of view, a minimally-invasive liquid biopsy is thought to be a promising method and can be implemented in routine clinical settings in order to meet unmet clinical needs. In this review, we highlighted clinical usefulness of liquid biopsies in the clinical management of CRC patients, including cancer screening, detection of MRD, selection of appropriate molecular-targeted drugs, monitoring of the treatment responsiveness, and very early detection of recurrence/relapse of the disease. In addition, we addressed a possibility of adoptive T cell therapies and a future personalized immunotherapy based on tumor genome information.

scholarly journals The pitfalls and promise of liquid biopsies for diagnosing and treating solid tumors in children: a review

2020 ◽  
Vol 179 (2) ◽  
pp. 191-202 ◽  
Author(s):  
Ruben Van Paemel ◽  
Roos Vlug ◽  
Katleen De Preter ◽  
Nadine Van Roy ◽  
Frank Speleman ◽  
...  
Keyword(s):  
Solid Tumors ◽  
Liquid Biopsy ◽  
Residual Disease ◽  
Therapy Response ◽  
Response Monitoring ◽  
Liquid Biopsies ◽  
Cell Free Dna ◽  
Pediatric Solid Tumors ◽  
Free Dna ◽  
Tumor Types

AbstractCell-free DNA profiling using patient blood is emerging as a non-invasive complementary technique for cancer genomic characterization. Since these liquid biopsies will soon be integrated into clinical trial protocols for pediatric cancer treatment, clinicians should be informed about potential applications and advantages but also weaknesses and potential pitfalls. Small retrospective studies comparing genetic alterations detected in liquid biopsies with tumor biopsies for pediatric solid tumor types are encouraging. Molecular detection of tumor markers in cell-free DNA could be used for earlier therapy response monitoring and residual disease detection as well as enabling detection of pathognomonic and therapeutically relevant genomic alterations.Conclusion: Existing analyses of liquid biopsies from children with solid tumors increasingly suggest a potential relevance for molecular diagnostics, prognostic assessment, and therapeutic decision-making. Gaps remain in the types of tumors studied and value of detection methods applied. Here we review the current stand of liquid biopsy studies for pediatric solid tumors with a dedicated focus on cell-free DNA analysis. There is legitimate hope that integrating fully validated liquid biopsy–based innovations into the standard of care will advance patient monitoring and personalized treatment of children battling solid cancers. What is Known:• Liquid biopsies are finding their way into routine oncological screening, diagnosis, and disease monitoring in adult cancer types fast.• The most widely adopted source for liquid biopsies is blood although other easily accessible body fluids, such as saliva, pleural effusions, urine, or cerebrospinal fluid (CSF) can also serve as sources for liquid biopsies What is New:• Retrospective proof-of-concept studies in small cohorts illustrate that liquid biopsies in pediatric solid tumors yield tremendous potential to be used in diagnostics, for therapy response monitoring and in residual disease detection.• Liquid biopsy diagnostics could tackle some long-standing issues in the pediatric oncology field; they can enable accurate genetic diagnostics in previously unbiopsied tumor types like renal tumors or brain stem tumors leading to better treatment strategies

Dissolution of cholelithiasis in a Cavalier King Charles Spaniel receiving conservative management with ursodeoxycholic acid

2020 ◽  
Vol 8 (3) ◽  
pp. e001206
Author(s):  
Frederik Allan ◽  
Katie Elizabeth McCallum ◽  
Marie-Aude Genain ◽  
Benjamin John Harris ◽  
Penny J Watson
Keyword(s):  
Veterinary Medicine ◽  
Ursodeoxycholic Acid ◽  
Conservative Management ◽  
Clinical Signs ◽  
Human Medicine ◽  
Complete Dissolution ◽  
Abdominal Ultrasonography ◽  
Cavalier King Charles Spaniel ◽  
Low Fat Diet

A six-year-old female neutered Cavalier King Charles Spaniel presented with recurrent diarrhoea, intermittent vomiting and anorexia. She was diagnosed with partially obstructive cholelithiasis with concurrent suspected chronic pancreatitis based on abdominal ultrasonography and blood biochemistry. The dog responded to conservative management with ursodeoxycholic acid (UDCA), paracetamol and a low-fat diet with resolution of clinical signs attributable to obstructive cholelithiasis and near-complete dissolution of the cholelith at follow-up eight months after presentation. In human medicine, UDCA has been reported to be effective in cholelith dissolution, prevention of cholelith formation and resolution of clinical signs due to cholelithiasis but the non-surgical literature in veterinary medicine is limited. To the authors’ knowledge, this is the first reported case of dissolution of a cholelith in a dog receiving conservative management.

scholarly journals Future perspectives of circulating tumor DNA in colorectal cancer

Tumor Biology ◽  
2017 ◽  
Vol 39 (5) ◽  
pp. 101042831770574 ◽  
Author(s):  
C Nadal ◽  
T Winder ◽  
A Gerger ◽  
David Tougeron
Keyword(s):  
Colorectal Cancer ◽  
Liquid Biopsy ◽  
Residual Disease ◽  
Genetic Material ◽  
Treatment Resistance ◽  
Circulating Tumor Dna ◽  
Tumor Burden ◽  
Response Monitoring ◽  
Cancer Management ◽  
Tumor Dna

Tumor biopsy is currently the gold standard for diagnosis and in determining cell signaling pathways involved in the development of treatment resistance. However, there are major challenges with this technique, including the need for serial sampling to monitor treatment resistance, which is invasive and also has the potential for selection bias due to intra-tumoral and inter-tumoral heterogeneity. These challenges highlight the need for more effective methods for obtaining Tumor samples. Liquid biopsy analyzes genetic material or tumor cells shed into the blood from the primary tumor and metastatic sites and consequently provides a comprehensive, real-time picture of the tumor burden in an individual patient. Indeed, liquid biopsy has the potential to revolutionize cancer management. Here, we review recent studies on the potential clinical applications of liquid biopsy using circulating tumor DNA in colorectal cancer, including screening, diagnosis, detection of minimal residual disease after surgery, detection of recurrence, prognosis, predicting treatment response, monitoring tumor burden or response during treatment, and tracking resistance. We also discuss recent data demonstrating the utility of detecting KRAS-mutated circulating tumor DNA, both at diagnosis to determine an appropriate treatment strategy and during anti-epidermal growth factor receptor therapy to predict treatment resistance. The future integration of liquid biopsy into clinical practice is discussed, together with alternative approaches and key questions that need to be answered in future clinical studies before this technology can be implemented and used routinely.

scholarly journals Liquid biopsy in early breast cancer. A preliminary report

2019 ◽  
Author(s):  
ANTONIO RULLI ◽  
CINZIA ANTOGNELLI ◽  
ANNAMARIA SIGGILLINO ◽  
VINCENZO TALESA ◽  
ZAYIK SVITLANA ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Liquid Biopsy ◽  
Residual Disease ◽  
Early Stage ◽  
Dynamic Monitoring ◽  
Molecular Profile ◽  
Precision Oncology ◽  
Surgical Biopsy ◽  
Post Surgery ◽  
Genetic Landscape

Abstract Background Liquid biopsy (LB) is a technique that utilizes circulating biomarkers from cancer patients to provide information regarding the genetic landscape of the cancer. LB is emerging as an alternative and complementary diagnostic and prognostic tool to surgical biopsy and is expected to provide the tool for the implementation of precision oncology in clinical settings. In fact, it may contribute to enhance understanding of tumor heterogeneity and permitting the dynamic monitoring of treatment responses and genomic variations. Thus, LB is a promising method for the management of cancer, including breast cancer (BC), whose incidence in Italy is progressively increasing. Previous studies focused mainly on patients with advanced-stage BC. In the present study we evaluated the number of circulating tumor cells (CTCs), the quantity of cell free tumor DNA (cftDNA) and the analysis of the mutational profile of DNA from CTCs (ctcDNA) and cftDNA in early stage BC patients. Methods Matched pre- and post-surgery blood samples were collected from 47 early stage BC patients. CTCs enumeration was done using Isoflux system, molecular profile of ctcDNA and cftDNA was performed with the Spotlight 59 Panels kit on a MiSeq Illumina instrument. Results Eighty percent of samples was CTCs-positive, while healthy controls were all CTCs-negative. Forty-four patients provided a pre-surgery and 21 post-surgery sample. By comparing the number of CTCs post-surgery with that of pre-surgery, we found that 66% of patients showed a decreased number of CTCs, 14% of patients continued to have the same number of CTCs, while, interestingly, 19% of patients showed an increased number of CTCs. NGS of ctcDNA and cftDNA showed that 52% of samples had mutations in 9 genes (TP53, CDKN2A, FBXW7, PTPN11, KRAS, NRAS, BRAF, IDH1, ALK) and in 5 genes (PIK3CA, APC ALK, KRAS, TSC1), respectively, with KRAS and ALK overlapping and TP53 being the most frequently mutated gene in ctcDNA analysis. Conclusions LB could facilitate early detection of minimal residual disease, aiding in the initiation of adjuvant therapy to prevent recurrence and progression towards metastasis, enhance individualized treatment and longitudinal screening, thus improving the clinical management and outcome of patients with early BC.

Avenues to Precision Oncology

2020 ◽  
pp. 36-45
Author(s):  
Alexander Meisel
Keyword(s):  
Precision Medicine ◽  
Trial Design ◽  
Ad Hoc ◽  
Molecular Targets ◽  
Clinical Trial Design ◽  
Predictive Biomarkers ◽  
Precision Oncology ◽  
Companion Diagnostics ◽  
Bona Fide ◽  
The One

Until recently, the clinical management of cancer heavily relied on anatomical and histopathological criteria, with ad hoc guidelines directing the therapeutic choices in specific indications. In the last years, the development and therapeutic implementation of novel anticancer therapies significantly improved the clinical outcome of cancer patients. Nonetheless, such cutting-edge approaches revealed the limitation of the one-size-fits-all paradigm. The newly discovered molecular targets can be exploited either as bona fide targets for subsequent drug development, or as tools to precision medicine, in the form of prognostic and/or predictive biomarkers. This article provides an overview of some of the most recent advances in precision medicine in oncology, with a focus on novel tissue-agnostic anticancer therapies. The definition and implementation of biomarkers and companion diagnostics in clinical trials and clinical practice are also discussed, as well as the changing landscape in clinical trial design.

scholarly journals ctDNA-Based Liquid Biopsy of Cerebrospinal Fluid in Brain Cancer

Cancers ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 1989
Author(s):  
Laura Escudero ◽  
Francisco Martínez-Ricarte ◽  
Joan Seoane
Keyword(s):  
Cerebrospinal Fluid ◽  
Brain Cancer ◽  
Liquid Biopsy ◽  
Therapeutic Strategy ◽  
Residual Disease ◽  
Imaging Techniques ◽  
Prognostic Information ◽  
Tumour Heterogeneity ◽  
Diagnosis And Prognosis ◽  
Cns Malignancies

The correct characterisation of central nervous system (CNS) malignancies is crucial for accurate diagnosis and prognosis and also the identification of actionable genomic alterations that can guide the therapeutic strategy. Surgical biopsies are performed to characterise the tumour; however, these procedures are invasive and are not always feasible for all patients. Moreover, they only provide a static snapshot and can miss tumour heterogeneity. Currently, monitoring of CNS cancer is performed by conventional imaging techniques and, in some cases, cytology analysis of the cerebrospinal fluid (CSF); however, these techniques have limited sensitivity. To overcome these limitations, a liquid biopsy of the CSF can be used to obtain information about the tumour in a less invasive manner. The CSF is a source of cell-free circulating tumour DNA (ctDNA), and the analysis of this biomarker can characterise and monitor brain cancer. Recent studies have shown that ctDNA is more abundant in the CSF than plasma for CNS malignancies and that it can be sequenced to reveal tumour heterogeneity and provide diagnostic and prognostic information. Furthermore, analysis of longitudinal samples can aid patient monitoring by detecting residual disease or even tracking tumour evolution at relapse and, therefore, tailoring the therapeutic strategy. In this review, we provide an overview of the potential clinical applications of the analysis of CSF ctDNA and the challenges that need to be overcome in order to translate research findings into a tool for clinical practice.

scholarly journals DEEPGENTM—A Novel Variant Calling Assay for Low Frequency Variants

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 507
Author(s):  
Bernd Timo Hermann ◽  
Sebastian Pfeil ◽  
Nicole Groenke ◽  
Samuel Schaible ◽  
Robert Kunze ◽  
...  
Keyword(s):  
Cancer Detection ◽  
Genetic Variants ◽  
Liquid Biopsy ◽  
Hot Spot ◽  
Treatment Success ◽  
Low Frequency ◽  
Variant Calling ◽  
Subsequent Treatment ◽  
Precision Oncology ◽  
Orthogonal Comparison

Detection of genetic variants in clinically relevant genomic hot-spot regions has become a promising application of next-generation sequencing technology in precision oncology. Effective personalized diagnostics requires the detection of variants with often very low frequencies. This can be achieved by targeted, short-read sequencing that provides high sequencing depths. However, rare genetic variants can contain crucial information for early cancer detection and subsequent treatment success, an inevitable level of background noise usually limits the accuracy of low frequency variant calling assays. To address this challenge, we developed DEEPGENTM, a variant calling assay intended for the detection of low frequency variants within liquid biopsy samples. We processed reference samples with validated mutations of known frequencies (0%–0.5%) to determine DEEPGENTM’s performance and minimal input requirements. Our findings confirm DEEPGENTM’s effectiveness in discriminating between signal and noise down to 0.09% variant allele frequency and an LOD(90) at 0.18%. A superior sensitivity was also confirmed by orthogonal comparison to a commercially available liquid biopsy-based assay for cancer detection.

scholarly journals Tick-borne zoonoses and commonly used diagnostic methods in human and veterinary medicine

2021 ◽  
Author(s):  
Andrea Springer ◽  
Antje Glass ◽  
Julia Probst ◽  
Christina Strube
Keyword(s):  
Veterinary Medicine ◽  
Diagnostic Tests ◽  
One Health ◽  
Animal Health ◽  
Diagnostic Techniques ◽  
Diagnostic Methods ◽  
Diagnostic Tools ◽  
Zoonotic Pathogens ◽  
Health Concept ◽  
The One

AbstractAround the world, human health and animal health are closely linked in terms of the One Health concept by ticks acting as vectors for zoonotic pathogens. Animals do not only maintain tick cycles but can either be clinically affected by the same tick-borne pathogens as humans and/or play a role as reservoirs or sentinel pathogen hosts. However, the relevance of different tick-borne diseases (TBDs) may vary in human vs. veterinary medicine, which is consequently reflected by the availability of human vs. veterinary diagnostic tests. Yet, as TBDs gain importance in both fields and rare zoonotic pathogens, such as Babesia spp., are increasingly identified as causes of human disease, a One Health approach regarding development of new diagnostic tools may lead to synergistic benefits. This review gives an overview on zoonotic protozoan, bacterial and viral tick-borne pathogens worldwide, discusses commonly used diagnostic techniques for TBDs, and compares commercial availability of diagnostic tests for humans vs. domestic animals, using Germany as an example, with the aim of highlighting existing gaps and opportunities for collaboration in a One Health framework.

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