Exosomes from Plasma of Neuroblastoma Patients Contain Doublestranded DNA Reflecting the Mutational Status of Parental Tumor Cells

Neuroblastoma (NB) is an aggressive infancy tumor, leading cause of death among preschool age diseases. Here we focused on characterization of exosomal DNA (exo-DNA) isolated from plasma cell-derived exosomes of neuroblastoma patients, and its potential use for detection of somatic mutations present in the parental tumor cells. Exosomes are small extracellular membrane vesicles secreted by most cells, playing an important role in intercellular communications. Using an enzymatic method, we provided evidence for the presence of double-stranded DNA in the NB exosomes. Moreover, by whole exome sequencing, we demonstrated that NB exo-DNA represents the entire exome and that it carries tumor-specific genetic mutations, including those occurring on known oncogenes and tumor suppressor genes in neuroblastoma (ALK, CHD5, SHANK2, PHOX2B, TERT, FGFR1, and BRAF). NB exo-DNA can be useful to identify variants responsible for acquired resistance, such as mutations of ALK, TP53, and RAS/MAPK genes that appear in relapsed patients. The possibility to isolate and to enrich NB derived exosomes from plasma using surface markers, and the quick and easy extraction of exo-DNA, gives this methodology a translational potential in the clinic. Exo-DNA can be an attractive non-invasive biomarker for NB molecular diagnostic, especially when tissue biopsy cannot be easily available.

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Emerging Advances of Detection Strategies for Tumor-Derived Exosomes

International Journal of Molecular Sciences ◽

10.3390/ijms23020868 ◽

2022 ◽

Vol 23 (2) ◽

pp. 868

Author(s):

Huijuan Cheng ◽

Qian Yang ◽

Rongrong Wang ◽

Ruhua Luo ◽

Shanshan Zhu ◽

...

Keyword(s):

Tumor Cells ◽

Cancer Diagnosis ◽

Theoretical Basis ◽

Biological Origin ◽

Intrinsic Nature ◽

Non Invasive ◽

Parental Tumor ◽

Molecular Components ◽

The Relationship ◽

Detection Strategies

Exosomes derived from tumor cells contain various molecular components, such as proteins, RNA, DNA, lipids, and carbohydrates. These components play a crucial role in all stages of tumorigenesis and development. Moreover, they reflect the physiological and pathological status of parental tumor cells. Recently, tumor-derived exosomes have become popular biomarkers for non-invasive liquid biopsy and the diagnosis of numerous cancers. The interdisciplinary significance of exosomes research has also attracted growing enthusiasm. However, the intrinsic nature of tumor-derived exosomes requires advanced methods to detect and evaluate the complex biofluid. This review analyzes the relationship between exosomes and tumors. It also summarizes the exosomal biological origin, composition, and application of molecular markers in clinical cancer diagnosis. Remarkably, this paper constitutes a comprehensive summary of the innovative research on numerous detection strategies for tumor-derived exosomes with the intent of providing a theoretical basis and reference for early diagnosis and clinical treatment of cancer.

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Epithelial-Mesenchymal Transition and MicroRNAs in Colorectal Cancer Chemoresistance to FOLFOX

Pharmaceutics ◽

10.3390/pharmaceutics13010075 ◽

2021 ◽

Vol 13 (1) ◽

pp. 75

Author(s):

Paula I. Escalante ◽

Luis A. Quiñones ◽

Héctor R. Contreras

Keyword(s):

Colorectal Cancer ◽

Tumor Cells ◽

Methylenetetrahydrofolate Reductase ◽

Epithelial Mesenchymal Transition ◽

Late Onset ◽

Dihydropyrimidine Dehydrogenase ◽

Acquired Resistance ◽

Potential Effect ◽

Mesenchymal Transition ◽

Folfox Chemotherapy

The FOLFOX scheme, based on the association of 5-fluorouracil and oxaliplatin, is the most frequently indicated chemotherapy scheme for patients diagnosed with metastatic colorectal cancer. Nevertheless, development of chemoresistance is one of the major challenges associated with this disease. It has been reported that epithelial-mesenchymal transition (EMT) is implicated in microRNA-driven modulation of tumor cells response to 5-fluorouracil and oxaliplatin. Moreover, from pharmacogenomic research, it is known that overexpression of genes encoding dihydropyrimidine dehydrogenase (DPYD), thymidylate synthase (TYMS), methylenetetrahydrofolate reductase (MTHFR), the DNA repair enzymes ERCC1, ERCC2, and XRCC1, and the phase 2 enzyme GSTP1 impair the response to FOLFOX. It has been observed that EMT is associated with overexpression of DPYD, TYMS, ERCC1, and GSTP1. In this review, we investigated the role of miRNAs as EMT promotors in tumor cells, and its potential effect on the upregulation of DPYD, TYMS, MTHFR, ERCC1, ERCC2, XRCC1, and GSTP1 expression, which would lead to resistance of CRC tumor cells to 5-fluorouracil and oxaliplatin. This constitutes a potential mechanism of epigenetic regulation involved in late-onset of acquired resistance in mCRC patients under FOLFOX chemotherapy. Expression of these biomarker microRNAs could serve as tools for personalized medicine, and as potential therapeutic targets in the future.

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The Increasing Impact of Translational Research in the Molecular Diagnostics of Neuromuscular Diseases

International Journal of Molecular Sciences ◽

10.3390/ijms22084274 ◽

2021 ◽

Vol 22 (8) ◽

pp. 4274

Author(s):

Dèlia Yubero ◽

Daniel Natera-de Benito ◽

Jordi Pijuan ◽

Judith Armstrong ◽

Loreto Martorell ◽

...

Keyword(s):

Molecular Diagnosis ◽

Clinical Symptoms ◽

Neuromuscular Diseases ◽

Genomic Analysis ◽

Molecular Diagnostic ◽

Diagnostic Process ◽

Targeted Analysis ◽

Whole Exome ◽

Referral Hospitals ◽

Uncertain Significance

The diagnosis of neuromuscular diseases (NMDs) has been progressively evolving from the grouping of clinical symptoms and signs towards the molecular definition. Optimal clinical, biochemical, electrophysiological, electrophysiological, and histopathological characterization is very helpful to achieve molecular diagnosis, which is essential for establishing prognosis, treatment and genetic counselling. Currently, the genetic approach includes both the gene-targeted analysis in specific clinically recognizable diseases, as well as genomic analysis based on next-generation sequencing, analyzing either the clinical exome/genome or the whole exome or genome. However, as of today, there are still many patients in whom the causative genetic variant cannot be definitely established and variants of uncertain significance are often found. In this review, we address these drawbacks by incorporating two additional biological omics approaches into the molecular diagnostic process of NMDs. First, functional genomics by introducing experimental cell and molecular biology to analyze and validate the variant for its biological effect in an in-house translational diagnostic program, and second, incorporating a multi-omics approach including RNA-seq, metabolomics, and proteomics in the molecular diagnosis of neuromuscular disease. Both translational diagnostics programs and omics are being implemented as part of the diagnostic process in academic centers and referral hospitals and, therefore, an increase in the proportion of neuromuscular patients with a molecular diagnosis is expected. This improvement in the process and diagnostic performance of patients will allow solving aspects of their health problems in a precise way and will allow them and their families to take a step forward in their lives.

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Interleukin 2 gene transfer into tumor cells abrogates tumorigenicity and induces protective immunity.

Journal of Experimental Medicine ◽

10.1084/jem.172.4.1217 ◽

1990 ◽

Vol 172 (4) ◽

pp. 1217-1224 ◽

Cited By ~ 443

Author(s):

B Gansbacher ◽

K Zier ◽

B Daniels ◽

K Cronin ◽

R Bannerji ◽

...

Keyword(s):

Gene Transfer ◽

Tumor Cells ◽

Interleukin 2 ◽

Retroviral Vectors ◽

Cytolytic Activity ◽

Tumor Formation ◽

Tumor Bearing ◽

Low Levels ◽

Parental Tumor ◽

Observation Period

To study the effects of localized secretion of cytokines on tumor progression, the gene for human interleukin 2 (IL-2) was introduced via retroviral vectors into CMS-5 cells, a weakly immunogenic mouse fibrosarcoma cell line of BALB/c origin. Secretion of low levels of IL-2 from the tumor cells abrogated their tumorigenicity and induced a long-lasting protective immune response against a challenge with a tumorigenic dose of parental CMS-5 cells. Co-injection of IL-2-producing CMS-5 cells with unmodified tumor cells inhibited tumor formation even when highly tumorigenic doses of CMS-5 cells were used. Cytolytic activity in mice injected with parental CMS-5 cells was transient and was greatly diminished 3 wk after injection, as commonly observed in tumor-bearing animals. However, in mice injected with IL-2-producing cells, tumor-specific cytolytic activity persisted at high levels for the duration of the observation period (at least 75 d). High levels of tumor-specific cytolytic activity could also be detected in parental CMS-5 tumor-bearing animals 18 d after inoculation with tumor cells, if IL-2-producing CMS-5 cells but not unmodified parental tumor cells were used as targets. These studies highlight the potential advantages of localized secretion of cytokines mediated via gene transfer to induce potent anti-tumor immune responses.

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The Clinical Application of Circulating Tumor Cells and DNAs as Prognostic and Predictive Biomarkers in Gastrointestinal Cancer

Current Cancer Drug Targets ◽

10.2174/1568009621666210311090531 ◽

2021 ◽

Vol 21 ◽

Author(s):

Sara Memarpour ◽

Ghazaleh Khalili-Tanha ◽

Awa Alizadeh Ghannad ◽

Masoud Sharifian Razavi ◽

Mona Joudi ◽

...

Keyword(s):

Tumor Cells ◽

Circulating Tumor Cells ◽

Tumor Biology ◽

Predictive Biomarkers ◽

Invasive Approach ◽

New Approach ◽

Non Invasive ◽

Gi Cancer ◽

Gi Cancers ◽

Tumor Dna

: Gastrointestinal (GI) cancer is one of the most common cancers globally. Genetic and epigenetic mechanisms are involved in its pathogenesis. The conventional methods for diagnosis and screening for GI cancers are often invasive and have other limitations. In the era of personalized medicine, a novel non-invasive approach called liquid biopsy has been introduced for the detection and management of GI cancers, which focuses on the analysis of circulating tumor cells (CTCs) and circulating cell-free tumor DNA (ctDNA). Several studies have shown that this new approach allows for an improved understanding of GI tumor biology and will lead to an improvement in clinical management. The aim of the current review is to explore the clinical applications of CTCs and ctDNA in patients with GI cancer.

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Epigenetic Targeting of Autophagy via HDAC Inhibition in Tumor Cells: Role of p53

International Journal of Molecular Sciences ◽

10.3390/ijms19123952 ◽

2018 ◽

Vol 19 (12) ◽

pp. 3952 ◽

Cited By ~ 14

Author(s):

Maria Mrakovcic ◽

Lauren Bohner ◽

Marcel Hanisch ◽

Leopold F. Fröhlich

Keyword(s):

Cell Death ◽

Tumor Cells ◽

Histone Deacetylase ◽

Stress Responses ◽

Histone Deacetylase Inhibitors ◽

Tumor Therapy ◽

Regulatory System ◽

Anticancer Activities ◽

Mutational Status

Tumor development and progression is the consequence of genetic as well as epigenetic alterations of the cell. As part of the epigenetic regulatory system, histone acetyltransferases (HATs) and deacetylases (HDACs) drive the modification of histone as well as non-histone proteins. Derailed acetylation-mediated gene expression in cancer due to a delicate imbalance in HDAC expression can be reversed by histone deacetylase inhibitors (HDACi). Histone deacetylase inhibitors have far-reaching anticancer activities that include the induction of cell cycle arrest, the inhibition of angiogenesis, immunomodulatory responses, the inhibition of stress responses, increased generation of oxidative stress, activation of apoptosis, autophagy eliciting cell death, and even the regulation of non-coding RNA expression in malignant tumor cells. However, it remains an ongoing issue how tumor cells determine to respond to HDACi treatment by preferentially undergoing apoptosis or autophagy. In this review, we summarize HDACi-mediated mechanisms of action, particularly with respect to the induction of cell death. There is a keen interest in assessing suitable molecular factors allowing a prognosis of HDACi-mediated treatment. Addressing the results of our recent study, we highlight the role of p53 as a molecular switch driving HDACi-mediated cellular responses towards one of both types of cell death. These findings underline the importance to determine the mutational status of p53 for an effective outcome in HDACi-mediated tumor therapy.

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OA 10.05 Non-Invasive Molecular Profiling in NSCLC by Targeted and Whole Exome Analysis of Plasma cfDNA

Journal of Thoracic Oncology ◽

10.1016/j.jtho.2017.09.385 ◽

2017 ◽

Vol 12 (11) ◽

pp. S1772

Author(s):

M. Cheng ◽

J. Yang ◽

M. Shady ◽

P. Ulz ◽

E. Heitzer ◽

...

Keyword(s):

Molecular Profiling ◽

Non Invasive ◽

Whole Exome ◽

Exome Analysis

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The genomic landscape of intrinsic and acquired resistance to cyclin-dependent kinase 4/6 inhibitors in patients with hormone receptor positive metastatic breast cancer

10.1101/857839 ◽

2019 ◽

Author(s):

Seth A. Wander ◽

Ofir Cohen ◽

Xueqian Gong ◽

Gabriela N. Johnson ◽

Jorge Buendia-Buendia ◽

...

Keyword(s):

Breast Cancer ◽

Acquired Resistance ◽

Metastatic Breast ◽

Resistance Mechanisms ◽

Akt Activation ◽

Hormone Receptor Positive ◽

Ras Activation ◽

Whole Exome ◽

Clinical Resistance

AbstractClinical resistance mechanisms to CDK4/6 inhibitors in HR+ breast cancer have not been clearly defined. Whole exome sequencing of 59 tumors with CDK4/6i exposure revealed multiple candidate resistance mechanisms including RB1 loss, activating alterations in AKT1, RAS, AURKA, CCNE2, ERBB2, and FGFR2, and loss of ER expression. In vitro experiments confirmed that these alterations conferred CDK4/6i resistance. Cancer cells cultured to resistance with CDK4/6i also acquired RB1, KRAS, AURKA, or CCNE2 alterations, which conferred sensitivity to AURKA, ERK, or CHEK1 inhibition. Besides inactivation of RB1, which accounts for ∼5% of resistance, seven of these mechanisms have not been previously identified as clinical mediators of resistance to CDK4/6 inhibitors in patients. Three of these—RAS activation, AKT activation, and AURKA activation—have not to our knowledge been previously demonstrated preclinically. Together, these eight mechanisms were present in 80% of resistant tumors profiled and may define therapeutic opportunities in patients.SignificanceWe identified eight distinct mechanisms of resistance to CDK4/6 inhibitors present in 80% of resistant tumors profiled. Most of these have a therapeutic strategy to overcome or prevent resistance in these tumors. Taken together, these findings have critical implications related to the potential utility of precision-based approaches to overcome resistance in many patients with HR+ MBC.

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