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1.
Heliyon ; 9(11): e21853, 2023 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-38027900

RESUMO

The detection of RAS mutations and co-mutations in liquid biopsy offers a novel paradigm for the dynamic management of metastatic colorectal cancer (mCRC) patients. Expanding the results of the prospective OMITERC (OMIcs application from solid to liquid biopsy for a personalized ThERapy of Cancer) project, we collected blood samples at specific time points from patients who received a first-line chemotherapy (CT) for KRAS-mutated mCRC. CTC quantification was performed by CellSearch® system. Libraries from cfDNA were prepared using the Oncomine™ Colon cfDNA Assay to detect tumour-derived DNA in cfDNA. The analysis involved >240 hotspots in 14 genes. Twenty patients with KRAS-mutated mCRC treated at the Medical Oncology Unit of Careggi University Hospital were prospectively enrolled. Nine patients had available data for longitudinal monitoring of cfDNA. After 6 weeks of first-line CT an increase of KRAS-mutated clone was reported in the only patient who did not obtain disease control, while all patients with decrease of KRAS clones obtained disease control. Overall, in patients with a short (<9 months) progression-free survival (PFS) we registered, at 6 weeks, an increase in cfDNA levels and in KRAS mutations or other co-mutations, i.e. PIK3CA, FBXW7, GNAS, and TP53. In selected cases, co-mutations were able to better anticipate radiological progressive disease (PD) than the increase of KRAS-mutated clones. In conclusion, our study confirms plasma ctDNA as a crucial tool for anticipating PD at an early time point and highlights the value of a comprehensive assessment of clonal dynamics to improve the management of patients with mCRC.

2.
N Biotechnol ; 78: 13-21, 2023 Dec 25.
Artigo em Inglês | MEDLINE | ID: mdl-37730172

RESUMO

Analysis of circulating cell-free DNA (ccfDNA) isolated from liquid biopsies is rapidly being implemented into clinical practice. However, diagnostic accuracy is significantly impacted by sample quality and standardised approaches for assessing the quality of ccfDNA are not yet established. In this study we evaluated the application of nucleic acid "spike-in" control materials to aid quality control (QC) and standardisation of cfDNA isolation for use in in vitro diagnostic assays. We describe an approach for the design and characterisation of in-process QC materials, illustrating it with a spike-in material containing an exogenous Arabidopsis sequence and DNA fragments approximating to ccfDNA and genomic DNA lengths. Protocols for inclusion of the spike-in material in plasma ccfDNA extraction and quantification of its recovery by digital PCR (dPCR) were assessed for their suitability for process QC in an inter-laboratory study between five expert laboratories, using a range of blood collection devices and ccfDNA extraction methods. The results successfully demonstrated that spiking plasmid-derived material into plasma did not deleteriously interfere with endogenous ccfDNA recovery. The approach performed consistently across a range of commonly-used extraction protocols and was able to highlight differences in efficiency and variability between the methods, with the dPCR quantification assay performing with good repeatability (generally CV <5%). We conclude that initial findings demonstrate that this approach appears "fit for purpose" and spike-in recovery can be combined with other extraction QC metrics for monitoring the performance of a process over time, or in the context of external quality assessment.


Assuntos
Ácidos Nucleicos Livres , Ácidos Nucleicos Livres/análise , Biópsia Líquida/métodos , Controle de Qualidade , DNA , Reação em Cadeia da Polimerase/métodos
3.
Histopathology ; 81(3): 389-401, 2022 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-35791778

RESUMO

OBJECTIVE: Chondroblastoma-like osteosarcoma (CBLOS) is a rare and poorly understood variant of OS. We examined the clinicopathological, immunohistochemical and molecular features of six CBLOSs to highlight the differences with conventional high-grade OS (CHGOS) and CB, including CB with aggressive features. METHODS: We performed histone 3.3 mutation analysis by gene sequencing and/or immunohistochemistry in all cases, while whole exome sequencing (WES) was performed on two CB-like osteosarcomas and 11 conventional high-grade OS. RESULTS: CBLOSs were predominantly localised at acral sites and involved mainly male subjects with a mean age of 29 years. One patient who had metastases at presentation died of disease, while another patient who developed multiple local recurrences and lung metastases was alive with no evidence of disease (ANED) at 294 months. The remaining patients were ANED after a mean interval of 70.8 months. Histologically, all CBLOS presented aggressive features, including nuclear atypia and infiltrative growth. Immunohistochemistry with H3F3 K36M mutant antibody was negative in all CBLOSs, and none of the five tumours tested by gene sequencing had H3F3B mutations. Conversely, all CBs presented the H3F3B K36M variant and were positive for immunostaining with the H3F3 K36M antibody. Two CBLOSs analysed by WES differed in amount and type of mutation from 11 cases of CHGOS. Moreover, CBLOSs showed lower copy number alteration (CNA) score values than CHGOSs. CONCLUSIONS: CBLOS presents a different genetic background and a less aggressive clinical behaviour in comparison with CHGOS. Search of the H3F3B K36M mutation is useful in the differential diagnosis with CB.


Assuntos
Neoplasias Ósseas , Condroblastoma , Osteossarcoma , Adulto , Anticorpos , Neoplasias Ósseas/patologia , Condroblastoma/diagnóstico , Condroblastoma/genética , Condroblastoma/patologia , Feminino , Histonas/genética , Humanos , Imuno-Histoquímica , Masculino , Osteossarcoma/patologia
4.
Med Oncol ; 39(8): 119, 2022 Jun 10.
Artigo em Inglês | MEDLINE | ID: mdl-35687207

RESUMO

Circulating tumor cells detection and ARV7 expression are associated with worse clinical outcomes in metastatic Castration-Resistant Prostate Cancer (mCRPC) undergoing Androgen Receptor Targeted Agents. ARFL, PSMA and PSA may help to refine prognostic models. In our institution, a prospective observational trial testing CTC detection in mCPRC undergoing I line ARTA therapy terminated the planned enrollment in 2020. Here, we present a pre-planned interim analysis with 18 months of median follow-up. RT-qPCR was used to determine the CTC expression of PSA, PSMA, AR and ARV7 before starting ARTA. PSA-drop, Progression-Free and Overall Survival (PFS and OS) and their correlation with CTC detection were reported. Forty-four patients were included. CTC were detected in 43.2% of patients, of whom 8.94% expressed PSA, 15.78% showed ARV7, 63.15% and 73.68% displayed ARFL and PSMA, respectively. Biochemical response was significantly improved in CTC + vs CTC- patients, with median PSA-drop of 18.5 vs 2.5 ng/ml (p = 0.03). After a median follow-up of 18 months, 50% of patients progressed. PFS was significantly longer in CTC- patients (NR vs 16 months). Eight (18.2%) patients died, a non-significant trend in terms of OS was detected in favor of CTC- patients (NR vs 29 months, p = 0.05). AR, PSA and PSMA expression in CTC + had no significant impact on PSA-drop, PFS or OS. PRIMERA-trial confirmed the CTC detection predictive importance in mCRPC patients.


Assuntos
Antineoplásicos , Células Neoplásicas Circulantes , Neoplasias de Próstata Resistentes à Castração , Antineoplásicos/uso terapêutico , Biomarcadores Tumorais/genética , Humanos , Masculino , Células Neoplásicas Circulantes/patologia , Estudos Prospectivos , Antígeno Prostático Específico , Neoplasias de Próstata Resistentes à Castração/tratamento farmacológico , Neoplasias de Próstata Resistentes à Castração/genética , Receptores Androgênicos/genética , Receptores Androgênicos/metabolismo , Resultado do Tratamento
5.
Br J Cancer ; 125(1): 94-100, 2021 07.
Artigo em Inglês | MEDLINE | ID: mdl-33953347

RESUMO

BACKGROUND: Within the OMITERC prospective study (OMIcs application from solid to liquid biopsy for a personalised ThERapy of Cancer), we explored the prognostic role of liquid biopsy encompassing cell-free DNA (cfDNA) and circulating tumour cells (CTCs) in KRAS mutated metastatic colorectal cancer (mCRC). METHODS: We defined a workflow including pre-analytical and analytical procedures collecting blood before therapy and every 3 months until disease progression (PD). CTCs were counted by CellSearch® and isolated by DEPArray™. NGS sequencing of CTCs and cfDNA was performed using a panel of cancer/CRC related genes respectively. RESULTS: KRAS mutational status was mostly concordant between tumour tissues and liquid biopsy. The percentage of cfDNA samples with mutations in CRC driver genes was in line with literature. In longitudinal monitoring circulating biomarkers anticipated or overlapped conventional diagnostic tools in predicting PD. The presence of CTCs at baseline was confirmed a negative prognostic marker. CONCLUSIONS: Cell-free DNA and CTCs are readily available candidates for clinical application in mCRC. While CTCs demonstrated a prognostic significance at baseline, cfDNA was confirmed an easily accessible material for monitoring the mutational status of the tumour over time. Moreover, in the longitudinal study, the two markers emerged as complementary in assessing disease progression.


Assuntos
Biomarcadores Tumorais/genética , Ácidos Nucleicos Livres/genética , Neoplasias Colorretais/patologia , Células Neoplásicas Circulantes/patologia , Proteínas Proto-Oncogênicas p21(ras)/genética , Análise de Sequência de DNA/métodos , Idoso , Idoso de 80 Anos ou mais , Neoplasias Colorretais/genética , Progressão da Doença , Feminino , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Estudos Longitudinais , Masculino , Pessoa de Meia-Idade , Mutação , Metástase Neoplásica , Prognóstico , Estudos Prospectivos
6.
Clin Chem Lab Med ; 59(7): 1181-1200, 2021 06 25.
Artigo em Inglês | MEDLINE | ID: mdl-33544478

RESUMO

Despite advances in screening and therapeutics cancer continues to be one of the major causes of morbidity and mortality worldwide. The molecular profile of tumor is routinely assessed by surgical or bioptic samples, however, genotyping of tissue has inherent limitations: it represents a single snapshot in time and it is subjected to spatial selection bias owing to tumor heterogeneity. Liquid biopsy has emerged as a novel, non-invasive opportunity of detecting and monitoring cancer in several body fluids instead of tumor tissue. Circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), RNA (mRNA and microRNA), microvesicles, including exosomes and tumor "educated platelets" were recently identified as a source of genomic information in cancer patients which could reflect all subclones present in primary and metastatic lesions allowing sequential monitoring of disease evolution. In this review, we summarize the currently available information concerning liquid biopsy in breast cancer, colon cancer, lung cancer and melanoma. These promising issues still need to be standardized and harmonized across laboratories, before fully adopting liquid biopsy approaches into clinical practice.


Assuntos
DNA Tumoral Circulante , MicroRNAs , Células Neoplásicas Circulantes , Biomarcadores Tumorais , Humanos , Biópsia Líquida , MicroRNAs/genética
7.
J Biophotonics ; 14(3): e202000365, 2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-33305912

RESUMO

Malignant melanoma is an aggressive form of skin cancer, which develops from the genetic mutations of melanocytes - the most frequent involving BRAF and NRAS genes. The choice and the effectiveness of the therapeutic approach depend on tumour mutation; therefore, its assessment is of paramount importance. Current methods for mutation analysis are destructive and take a long time; instead, Raman spectroscopy could provide a fast, label-free and non-destructive alternative. In this study, confocal Raman microscopy has been used for examining three in vitro melanoma cell lines, harbouring different molecular profiles and, in particular, specific BRAF and NRAS driver mutations. The molecular information obtained from Raman spectra has served for developing two alternative classification algorithms based on linear discriminant analysis and artificial neural network. Both methods provide high accuracy (≥90%) in discriminating all cell types, suggesting that Raman spectroscopy may be an effective tool for detecting molecular differences between melanoma mutations.


Assuntos
Melanoma , Neoplasias Cutâneas , Linhagem Celular , Humanos , Melanócitos , Melanoma/genética , Mutação , Neoplasias Cutâneas/genética , Aprendizado de Máquina Supervisionado
8.
Cancers (Basel) ; 12(11)2020 Oct 29.
Artigo em Inglês | MEDLINE | ID: mdl-33138000

RESUMO

Adrenocortical carcinoma (ACC), a rare and aggressive neoplasia, presents poor prognosis when metastatic at diagnosis and limited therapies are available. Specific and sensitive markers for early diagnosis and a monitoring system of therapy and tumor evolution are urgently needed. The liquid biopsy represents a source of tumor material within a minimally invasive blood draw that allows the recovery of circulating tumor cells (CTCs). CTCs have been recently shown to be detectable in ACC. In the present paper, we evaluated the prognostic value of CTCs obtained by size-filtration in a small pilot cohort of 19 ACC patients. We found CTCs in 68% of pre-surgery and in 38% of post-surgery blood samples. In addition, CTC clusters (CTMs) and cancer associated macrophages (CAMLs) were detectable in some ACC patients. The median number of CTCs significantly decreased after the mass removal. Finally, stratifying patients in high and low pre-surgery CTC number groups, assuming the 75th percentile CTC value as cut-off, CTCs significantly predicted patients' overall survival (log rank = 0.005), also in a multivariate analysis adjusted for age and tumor stage. In conclusion, though preliminary and performed in a small cohort of patients, our study suggests that CTC number may represent a promising marker for prognosis and disease monitoring in ACC.

9.
Urol Int ; 104(11-12): 865-870, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32957110

RESUMO

INTRODUCTION: Microchimerism (MC) is the presence of a small amount of foreign cells or DNA within a person's circulation or tissues. It has been identified also in recipients of solid organ transplants where it seems to be critical for the development and maintenance of immunological tolerance. Nevertheless, natural and/or iatrogenic MC can be acquired prior to transplantation, through pregnancy and/or blood transfusion. OBJECTIVE: The aim of this study was to detect the presence of MC in women after renal transplantation from male cadaveric donors and its relationship with graft outcomes. METHODS: We studied by qPCR the presence of the DYS14 gene sequence of the Y chromosome in 12 females who received a kidney graft from a male donor before transplantation (T0), after 15 days (T1) and 1 year of transplantation (T2). We found the sequence in all recipients after renal transplantation. RESULTS: All the women were negative for this sequence prior to transplantation (T0). Mean (SD) Y-related DNA quantity was 0.80 (0.69) ng/mL plasma and 0.15 (0.26) ng/mL plasma at T1 and T2, respectively. No acute rejection was observed, and mean (SD) estimated Cr clearance was 68.8 (16.9) mL/min within 1 year from transplantation. CONCLUSIONS: Presence of MC was associated with good kidney graft outcomes after 1 year of transplantation, but further studies will be needed to investigate the relationship between clinical outcomes and the development of MC in renal transplant recipient.


Assuntos
Quimerismo , Transplante de Rim , Reação em Cadeia da Polimerase , Adulto , Idoso , Cadáver , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Estudos Prospectivos , Fatores de Tempo , Resultado do Tratamento
10.
Andrology ; 8(5): 1256-1264, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32406197

RESUMO

BACKGROUND: Recently, alterations in miRNAs expression profile in semen have been linked to damaged spermatogenesis, suggesting miRNAs could be used as potential infertility biomarkers. In previous animal studies, miR-20a-5p was found to be down-expressed in low motile spermatozoa, implying its potential target of genes associated with cell apoptosis. OBJECTIVE: To investigate miR-20a-5p expression in blood plasma of patients suffering from non-obstructive azoospermia (NOA), compared to normozoospermic controls. MATERIALS AND METHODS: Between January 2018 and December 2019, from 52 infertile couples eligible for the study, 24 couples were finally enrolled in this monocentric observational prospective pilot study. Patients were included into two groups: Group 1 comprised men with NOA (n = 14) and Group 2 fertile men partners of women with female tubal factor infertility (n = 10). All NOA patients underwent testicular sperm extraction. The expression of circulating miR-20a-5p in plasma samples was assessed by RT-qPCR. A relative quantification strategy was adopted using the 2-ΔCq method to calculate the target miR-20a-5p expression with respect to miR-16-5p as endogenous control. RESULTS: Median blood plasma miR-20a-5p was significantly higher in patients affected by NOA (0.16 2-ΔCt , range: 0.05-0.79 2-ΔCt ) than in fertile controls (0.06 2-ΔCt , range: 0.04-0.10 2-ΔCt ), P < .001. MiR-20a-5p was positively correlated with follicle-stimulating hormone (FSH) (rrho  = -0.490, P = .015) and luteinizing hormone (LH) (rrho  = -0.462, P = .023), and negatively correlated with serum total testosterone (TT) (rrho  = -0.534, P = .007) and right and left testicular size (rrho  = -0.473, P = .020 and rrho  = -0.471, P = .020, respectively). Successful sperm retrieval (SR) rate was 50.0%. Median value of miR-20a-5p did not differ significantly among patients with successful SR and those with negative SR. Testicular histological examination showed: hypospermatogenesis in 6/14 (42.8%), maturation arrest in 4/14 (28.6%), sertoli cell-only syndrome in 4/14 (28.6%). No significant differences in miR-20a-5p were found between histopathological patterns (P > .05). CONCLUSIONS: MiR-20a-5p could represent a novel non-invasive diagnostic biomarker of male infertility.


Assuntos
Azoospermia/sangue , Azoospermia/diagnóstico , Biomarcadores/sangue , MicroRNAs/sangue , Adulto , Azoospermia/patologia , Feminino , Humanos , Projetos Piloto
11.
N Biotechnol ; 55: 19-29, 2020 Mar 25.
Artigo em Inglês | MEDLINE | ID: mdl-31580920

RESUMO

The term 'liquid biopsy', introduced in 2013 in reference to the analysis of circulating tumour cells (CTCs) in cancer patients, was extended to cell-free nucleic acids (cfNAs) circulating in blood and other body fluids. CTCs and cfNAs are now considered diagnostic and prognostic markers, used as surrogate materials for the molecular characterisation of solid tumours, in particular for research on tumour-specific or actionable somatic mutations. Molecular characterisation of cfNAs and CTCs (especially at the single cell level) is technically challenging, requiring highly sensitive and specific methods and/or multi-step processes. The analysis of the liquid biopsy relies on a plethora of methods whose standardisation cannot be accomplished without disclosing criticisms related to the pre-analytical phase. Thus, pre-analytical factors potentially influencing downstream cellular and molecular analyses must be considered in order to translate the liquid biopsy approach into clinical practice. The present review summarises the most recent reports in this field, discussing the main pre-analytical aspects related to CTCs, cfNAs and exosomes in blood samples for liquid biopsy analysis. A short discussion on non-blood liquid biopsy samples is also included.


Assuntos
Biópsia Líquida/métodos , Fase Pré-Analítica/métodos , Animais , Líquidos Corporais/metabolismo , Ácidos Nucleicos Livres/análise , Exossomos/metabolismo , Humanos , Células Neoplásicas Circulantes/patologia
12.
Clin Chem ; 66(1): 149-160, 2020 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-31628139

RESUMO

BACKGROUND: In cancer patients, circulating cell-free DNA (ccfDNA) can contain tumor-derived DNA (ctDNA), which enables noninvasive diagnosis, real-time monitoring, and treatment susceptibility testing. However, ctDNA fractions are highly variable, which challenges downstream applications. Therefore, established preanalytical work flows in combination with cost-efficient and reproducible reference materials for ccfDNA analyses are crucial for analytical validity and subsequently for clinical decision-making. METHODS: We describe the efforts of the Innovative Medicines Initiative consortium CANCER-ID (http://www.cancer-id.eu) for comparing different technologies for ccfDNA purification, quantification, and characterization in a multicenter setting. To this end, in-house generated mononucleosomal DNA (mnDNA) from lung cancer cell lines carrying known TP53 mutations was spiked in pools of plasma from healthy donors generated from 2 different blood collection tubes (BCTs). ccfDNA extraction was performed at 15 partner sites according to their respective routine practice. Downstream analysis of ccfDNA with respect to recovery, integrity, and mutation analysis was performed centralized at 4 different sites. RESULTS: We demonstrate suitability of mnDNA as a surrogate for ccfDNA as a process quality control from nucleic acid extraction to mutation detection. Although automated extraction protocols and quantitative PCR-based quantification methods yielded the most consistent and precise results, some kits preferentially recovered spiked mnDNA over endogenous ccfDNA. Mutated TP53 fragments derived from mnDNA were consistently detected using both next-generation sequencing-based deep sequencing and droplet digital PCR independently of BCT. CONCLUSIONS: This comprehensive multicenter comparison of ccfDNA preanalytical and analytical work flows is an important contribution to establishing evidence-based guidelines for clinically feasible (pre)analytical work flows.


Assuntos
Ácidos Nucleicos Livres/metabolismo , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Reação em Cadeia da Polimerase em Tempo Real/métodos , Coleta de Amostras Sanguíneas , Linhagem Celular Tumoral , Ácidos Nucleicos Livres/química , Ácidos Nucleicos Livres/normas , DNA Tumoral Circulante/sangue , Análise Mutacional de DNA , Sequenciamento de Nucleotídeos em Larga Escala/normas , Humanos , Neoplasias/genética , Neoplasias/patologia , Nucleossomos/genética , Polimorfismo de Nucleotídeo Único , Fase Pré-Analítica , Reação em Cadeia da Polimerase em Tempo Real/normas , Padrões de Referência , Proteína Supressora de Tumor p53/genética
13.
Methods Mol Biol ; 2065: 95-104, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31578690

RESUMO

This chapter reports the use of real-time quantitative PCR to detect Diplodia sapinea, a fungal plant pathogen that causes shoot tip dieback and tree mortality on pine trees. This molecular approach represents a reliable and sensitive tool to detect fungal pathogens in DNA extracted from plant tissues and its use can be also recommended to study fungal behavior in host tissues by quantifying fungal growth in the latent phase, when symptoms in the host are not present yet.


Assuntos
Ascomicetos/isolamento & purificação , Pinus/microbiologia , Doenças das Plantas/prevenção & controle , Reação em Cadeia da Polimerase em Tempo Real/métodos , Ascomicetos/genética , DNA Fúngico/isolamento & purificação , Doenças das Plantas/microbiologia , Reprodutibilidade dos Testes , Sensibilidade e Especificidade , Árvores
14.
Methods Mol Biol ; 2065: 139-151, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31578693

RESUMO

We propose two different approaches involving the use of quantitative real-time PCR for the detection or analysis of circulating tumor cells. In one case cells are indirectly identified through the expression of a marker mRNA, while in the other one cells are enriched by size prior to be submitted to mutational analysis for a specific target. Both methods have been successfully applied to the study of circulating melanoma cells.


Assuntos
Biomarcadores Tumorais/isolamento & purificação , Melanoma/diagnóstico , Células Neoplásicas Circulantes/patologia , RNA Mensageiro/isolamento & purificação , Reação em Cadeia da Polimerase em Tempo Real/métodos , Biomarcadores Tumorais/genética , Análise Mutacional de DNA , Humanos , Biópsia Líquida/métodos , Melanoma/sangue , Melanoma/genética , Melanoma/patologia , Monofenol Mono-Oxigenase/genética , RNA Mensageiro/genética
15.
Cancer Biomark ; 26(3): 271-279, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31524142

RESUMO

BACKGROUND: Circulating tumor cells (CTCs) and circulating cell free DNA (ccfDNA) represent a liquid biopsy of a tumor allowing real time disease monitoring especially in advanced stages of cancer, but their analysis is technically challenging. OBJECTIVE: We aimed to demonstrate the feasibility of two different technical approaches to detect the BRAFV600E mutation in the liquid biopsy of 20 metastatic melanoma patients by using both the enriched CTC fraction and circulating ccfDNA from the same blood sample. METHODS: We detected CTCs by a filtration method in 20 metastatic melanoma patients and detected the BRAFV600E variant on CTCs and ccfDNA by an allele-specific qPCR assay; the mutated samples were confirmed by ICE-COLD PCR followed by Sanger sequencing. RESULTS: We found CTCs in 70% of the samples, and identified the BRAFV600E variant on CTCs. We correlated the results with those obtained on ccfDNA from the same blood draw. We found some discordant results between CTCs and ccfDNA. CONCLUSIONS: Our results underline the importance of investigating both CTCs and ccfDNA in a liquid biopsy approach to melanoma patients.


Assuntos
Biomarcadores Tumorais/sangue , DNA Tumoral Circulante/sangue , Melanoma/diagnóstico , Células Neoplásicas Circulantes/patologia , Proteínas Proto-Oncogênicas B-raf/genética , Neoplasias Cutâneas/diagnóstico , Substituição de Aminoácidos , Biomarcadores Tumorais/genética , DNA Tumoral Circulante/isolamento & purificação , Análise Mutacional de DNA/métodos , Estudos de Viabilidade , Ácido Glutâmico/genética , Humanos , Biópsia Líquida/métodos , Melanoma/sangue , Melanoma/patologia , Mutação , Reação em Cadeia da Polimerase em Tempo Real , Neoplasias Cutâneas/sangue , Neoplasias Cutâneas/patologia , Valina/genética
16.
Diagnostics (Basel) ; 9(3)2019 Sep 12.
Artigo em Inglês | MEDLINE | ID: mdl-31547467

RESUMO

Next Generation Sequencing (NGS) is a promising tool for the improvement of tumor molecular profiling in view of the identification of a personalized treatment in oncologic patients. To verify the potentiality of a targeted NGS (Ion AmpliSeq™ Cancer Hotspot Panel v2), selected melanoma samples (n = 21) were retrospectively analyzed on S5 platform in order to compare NGS performance with the conventional techniques adopted in our routine clinical setting (Sequenom MassARRAY system, Sanger sequencing, allele-specific real-time PCR). The capability in the identification of rare and low-frequency mutations in the main genes involved in melanoma (BRAF and NRAS genes) was verified and integrated with the results deriving from other oncogenes and tumor suppressor genes. The analytical evaluation was carried out by the analysis of DNA derived from control cell lines and FFPE (Formalin-Fixed, Paraffin-Embedded) samples to verify that the achieved resolution of uncommon mutations and low-frequency variants was suitable to meet the technical and clinical requests. Our results demonstrate that the amplicon-based NGS approach can reach the sensitivity proper of the allele-specific assays together with the high specificity of a sequencing method. An overall concordance among the tested methods was observed in the identification of classical and uncommon mutations. The assessment of the quality parameters and the comparison with the orthogonal methods suggest that the NGS method could be implemented in the clinical setting for melanoma molecular characterization.

17.
N Biotechnol ; 52: 121-125, 2019 Sep 25.
Artigo em Inglês | MEDLINE | ID: mdl-31102798

RESUMO

In May 2017, the European In Vitro Diagnostic Regulation (IVDR) entered into force and will apply to in vitro diagnostics from May 26th, 2022. This will have a major impact on the in vitro diagnostics (IVD) industry as all devices falling under the scope of the IVDR will require new or re-certification. It will also affect health institutions developing and using in-house devices. The IVDR also has implications with respect to product performance validation and verification including the pre-analytics of biological samples used by IVD developers and diagnostic service providers. In parallel to the IVDR, a series of standards on pre-analytical sample processing has been published by the International Organization for Standardization (ISO) and the European Committee for Standardization (CEN). These standards describe pre-analytical requirements for various types of analyses in various types of biospecimens. They are of relevance for IVD product developers in the context of (re)certification under the IVDR and to some extent also to devices manufactured and used only within health institutions. This review highlights the background and the rational for the pre-analytical standards. It describes the procedure that leads to these standards, the major implications of the standards and the requirements on pre-analytical workflows. In addition, it discusses the relationship between the standards and the IVDR.


Assuntos
Técnicas e Procedimentos Diagnósticos/normas , Fase Pré-Analítica/normas , Controle Social Formal , Equipamentos e Provisões/normas , Humanos , Padrões de Referência
18.
Int J Cancer ; 145(9): 2580-2593, 2019 11 01.
Artigo em Inglês | MEDLINE | ID: mdl-30973654

RESUMO

Five-year overall survival of stage III colorectal cancer (CRC) patients treated with standard adjuvant chemotherapy (ACHT) is highly variable. Genomic biomarkers and/or transcriptomic profiles identified lack of adequate validation. Aim of our study was to identify and validate molecular biomarkers predictive of ACHT response in stage III CRC patients by a transcriptomic approach. From a series of CRC patients who received ACHT, two stage III extreme cohorts (unfavorable vs. favorable prognosis) were selected. RNA-sequencing was performed from fresh frozen explants. Tumors were characterized for somatic mutations. Validation was performed in stage III CRC patients extracted from two GEO datasets. According to disease-free survival (DFS), 108 differentially expressed genes (104/4 up/downregulated in the unfavorable prognosis group) were identified. Among 104 upregulated genes, 42 belonged to olfactory signaling pathways, 62 were classified as pseudogenes (n = 17), uncharacterized noncoding RNA (n = 10), immune response genes (n = 4), microRNA (n = 1), cancer-related genes (n = 14) and cancer-unrelated genes (n = 16). Three out of four down-regulated genes were cancer-related. Mutational status (i.e., RAS, BRAF, PIK3CA) did not differ among the cohorts. In the validation cohort, multivariate analysis showed high PNN and KCNQ1OT1 expression predictive of shorter DFS in ACHT treated patients (p = 0.018 and p = 0.014, respectively); no difference was observed in untreated patients. This is the first study that identifies by a transcriptomic approach and validates PNN and KCNQ1OT1 as molecular biomarkers predictive of chemotherapy response in stage III CRC patients. After a further validation in an independent cohort, PNN and KCNQ1OT1 evaluation could be proposed to prospectively identify stage III CRC patients benefiting from ACHT.


Assuntos
Biomarcadores Tumorais/genética , Moléculas de Adesão Celular/genética , Neoplasias Colorretais/genética , Proteínas Nucleares/genética , Idoso , Quimioterapia Adjuvante/métodos , Classe I de Fosfatidilinositol 3-Quinases/genética , Estudos de Coortes , Neoplasias Colorretais/patologia , Intervalo Livre de Doença , Regulação para Baixo/genética , Feminino , Perfilação da Expressão Gênica/métodos , Humanos , Masculino , Pessoa de Meia-Idade , Mutação/genética , Estadiamento de Neoplasias/métodos , Canais de Potássio de Abertura Dependente da Tensão da Membrana/genética , Prognóstico , Análise de Sequência de RNA/métodos , Transdução de Sinais/genética , Transcriptoma/genética , Regulação para Cima/genética
19.
Oncotarget ; 8(56): 96062-96078, 2017 Nov 10.
Artigo em Inglês | MEDLINE | ID: mdl-29221187

RESUMO

The anti-arthritic drug auranofin exerts also potent antitumour activity in in vitro and in vivo models, whose mechanisms are not yet well defined. From an auranofin-sensitive human ovarian cancer cell line A2780, a highly resistant (>20-fold) subline (A2780/AF-R) was developed and characterized. Marked reduction of gold accumulation occurred in auranofin-resistant A2780 cells. Also, moderately higher thioredoxin reductase activity in A2780/AF-R cells was observed while no changes in intracellular glutathione content occurred. Resistance to auranofin was associated with a low level of cross-resistance to some investigational gold compounds as well as to oxaliplatin and other anticancer drugs with different mode of action (i.e. melphalan, vinblastine, doxorubicin, etoposide, and paclitaxel). Reduced gold accumulation was associated to substantial gene expression changes in various influx (e.g. SLC22A1, SLC47A1, SLCO1B1) and efflux (e.g. ABCB1, ABCC2, ABCC3) transporters. The expression levels of selected proteins (i.e. SLC22A1, SLC47A1, P-gp) were also changed accordingly. These data provide evidence that multiple drug transporters may act as mediators of transport of auranofin and other gold compounds in cancer cells. Further investigation into the molecular mechanisms mediating transport of auranofin and new gold complexes in view of their potential clinical application in the treatment of cancer is warranted.

20.
Oncotarget ; 8(39): 65525-65533, 2017 Sep 12.
Artigo em Inglês | MEDLINE | ID: mdl-29029450

RESUMO

Adrenocortical cancer (ACC) is a rare aggressive malignancy. Recent ACC integrated genomics analysis contributed to redefine the risk groups on molecular basis, including tumor microRNAs (miRs), detectable also in the bloodstream. We developed a quantitative real-time (RT) assay for the measurement of miR483 and miR483-5p absolute levels in plasma samples. miR483/miR483-5p levels were evaluated in plasma samples of 27 patients with ACC before surgery and at follow-up. Statistically significant differences in miR483-5p and miR483 levels were found between stage 1/2 and stage 3/4 ACCs in pre-surgery and post-surgery samples. ROC curve analysis of miR483-5p levels gave a prediction of the clinical stage (accuracy 0.917±0.084), with the best cut-off value of 0.221 ng/ml, prognosticating overall and recurrence-free survival. In a multivariate Cox analysis (HR 16.2, 95%CI[1.39-188.6, P<0.026]), miR483-5p was the only variable that significantly predicted recurrence, but not overall survival. In addition, miR483 and miR483-5p levels correlated with the number of circulating tumor cells (CTCs) detected in the same blood samples, independently of the timing of sampling. In conclusion, we demonstrated that miR483-5p absolute plasma levels in ACC patients are powerful molecular markers that may help in the follow-up of patients after surgery and chemotherapy, and contribute to more accurately classify and predict tumor progression.

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