Molecular profiling of lung cancer specimens and liquid biopsies using MALDI-TOF mass spectrometry

Bonaparte, Eleonora; Pesenti, Chiara; Fontana, Laura; Falcone, Rossella; Paganini, Leda; Marzorati, A.; Ferrero, Stefano; Nosotti, Mario; Mendogni, Paolo; Bareggi, Claudia; Sirchia, Silvia Maria; Tabano, Silvia; Bòsari, Silvano; Miozzo, Monica

doi:10.1186/s13000-017-0683-7

Cited by 15 publications

(10 citation statements)

References 29 publications

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“…The Matrix-Assisted Laser Desorption Ionization Time of Flight (MALDI-TOF) genotyping system was used to genotype 612 individuals for 28 inflammation-related gene polymorphisms. MALDI-TOF is a medium-to-high-throughput technology platform that takes both sensitivity and specific into account and used mass spectrometry for direct detection (46). Amplification and extension primers were designed by BGI.…”

Section: Snp Genotypingmentioning

confidence: 99%

Association of Inflammation-Related Gene Polymorphisms With Susceptibility and Radiotherapy Sensitivity in Head and Neck Squamous Cell Carcinoma Patients in Northeast China

et al. 2021

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BackgroundInflammation-related gene polymorphisms are some of the most important determinants for cancer susceptibility, clinical phenotype diversity, and the response to radiotherapy and chemotherapy. However, the relationship between these polymorphisms and head and neck squamous cell carcinoma (HNSCC) remains unclear. The aim of this study was to investigate the role of inflammation-related gene polymorphisms in the developmental risk and radiotherapy sensitivity of HNSCC.MethodsThe Matrix-Assisted Laser Desorption Ionization Time of Flight (MALDI-TOF) genotyping system was used to genotype 612 individuals from a Chinese population for 28 inflammation-related gene polymorphisms.ResultsThe protein kinase B (AKT1) rs1130233 TT, dominance model (CT+TT vs. CC), recessive model (TT vs. CT+CC), and rs2494732 CC genotypes were associated with reduced risk of HNSCC (P=0.014; P=0.041; P=0.043). The polymeric immunoglobulin receptor (PIGR) rs291097 GA, dominance model (GA+AA vs. GG), and rs291102 dominance model (GA+AA vs. GG) were associated with increased risk of HNSCC (P=0.025; P=0.025; P=0.040). The interleukin-4 receptor-α (IL-4RA) rs1801275 AA genotype was significantly correlated with increased radiotherapy sensitivity of HNSCC patients (P=0.030). In addition, age ≤ 60 years, non-smoker status, and normal levels of squamous cell carcinoma antigen (SCC) were found to be associated with increased radiotherapy sensitivity of HNSCC patients (P=0.033; P=0.033; P=0.030).ConclusionThe AKT1 rs1130233, AKT1 rs2494732, PIGR rs291097, and PIGR rs291102 polymorphisms were significantly related to the risk of HNSCC. The IL-4RA rs1801275 polymorphism, age ≤ 60 years, non-smoker status, and normal levels of SCC were significantly associated with increased radiotherapy sensitivity of HNSCC.

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Section: Snp Genotypingmentioning

confidence: 99%

Association of Inflammation-Related Gene Polymorphisms With Susceptibility and Radiotherapy Sensitivity in Head and Neck Squamous Cell Carcinoma Patients in Northeast China

et al. 2021

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“…A limitation of MALDI-ToF MS, however, is its relative lack of specificity in differentiating closely related strains of bacterial species. In molecular diagnostics, genotyping and mutational analysis in liquid biopsy have been in development using MALDI-ToF MS 32–34 50. Please see recent review on other clinical and near clinical applications of MALDI-ToF MS for details 51–53…”

Section: Current Clinical Applications Of Ms In Clinical Laboratoriesmentioning

confidence: 99%

Emerging role of clinical mass spectrometry in pathology

et al. 2019

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Mass spectrometry-based assays have been increasingly implemented in various disciplines in clinical diagnostic laboratories for their combined advantages in multiplexing capacity and high analytical specificity and sensitivity. It is now routinely used in areas including reference methods development, therapeutic drug monitoring, toxicology, endocrinology, paediatrics, immunology and microbiology to identify and quantify biomolecules in a variety of biological specimens. As new ionisation methods, instrumentation and techniques are continuously being improved and developed, novel mass spectrometry-based clinical applications will emerge for areas such as proteomics, metabolomics, haematology and anatomical pathology. This review will summarise the general principles of mass spectrometry and specifically highlight current and future clinical applications in anatomical pathology.

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“…Using the MALDI‐TOF mass spectrometry and MassARRAY technology, multiplex panels such as OncoCarta, LungCarta, OncoFOCUS and UltraSEEK have been developed . Other groups have developed customized panels using MALDI‐TOF technology to detect for somatic mutations in NSCLC …”

Section: Maldi‐tof Mass Spectrometrymentioning

confidence: 99%

“…52 Other groups have developed customized panels using MALDI-TOF technology to detect for somatic mutations in NSCLC. 53 This technology is based on PCR amplification and allele-specific single-based primer extension. Each nucleotide or base added to the primer has a defined mass and is analysed using MALDI-TOF where the time of flight is proportional to the mass and is linked to specific genotype calls.…”

Section: Maldi-tof Mass Spectrometrymentioning

confidence: 99%

Somatic mutations and immune checkpoint biomarkers

et al. 2019

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The development of molecular testing for identifying somatic mutations and immune checkpoint biomarkers has directed treatment towards personalized medicine for patients with non‐small cell lung cancer. The choice of molecular testing in a clinical setting is influenced by cost, expertise in the technology, instrumentation setup and sample type availability. The molecular techniques described in this review include immunohistochemistry (IHC), fluorescent in situ hybridization, direct sequencing, real‐time polymerase chain reaction (PCR), denaturing high‐performance liquid chromatography, matrix‐assisted laser desorption/ionization time of flight mass spectrometry and next‐generation sequencing (NGS). IHC is routinely used in clinical practice for the classification, differentiation, histology and identification of targetable alterations of epidermal growth factor receptor (EGFR), anaplastic lymphoma kinase (ALK) and programmed death ligand‐1 (PD‐L1). Recently, the PD‐L1 pathway was identified as being exploited by tumour cells, allowing immune resistance and tumour evasion. The development of immune checkpoint inhibitors as treatment for tumours expressing checkpoints has highlighted the need for standardized IHC assays to inform treatment decisions for patients. Direct sequencing was historically the gold standard for mutation testing for EGFR, KRAS (Kirsten rat sarcoma viral oncogene homologue) and BRAF (v‐Raf murine sarcoma viral oncogene homologue B1) requiring a high ratio of tumour to normal cells, but this has been superseded by more sensitive methods. NGS is a new emerging technique, which allows high‐throughput coverage of frequently mutated genes, including less common BRAF and MET mutations and alterations in tumour suppressor genes. When an NGS platform is unavailable, PCR‐based technologies offer an efficient and cost‐effective single gene test to guide patient treatment. This article will review these techniques and discuss the future of molecular platforms underpinning clinical management decisions.

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Molecular profiling of lung cancer specimens and liquid biopsies using MALDI-TOF mass spectrometry

Cited by 15 publications

References 29 publications

Association of Inflammation-Related Gene Polymorphisms With Susceptibility and Radiotherapy Sensitivity in Head and Neck Squamous Cell Carcinoma Patients in Northeast China

Association of Inflammation-Related Gene Polymorphisms With Susceptibility and Radiotherapy Sensitivity in Head and Neck Squamous Cell Carcinoma Patients in Northeast China

Emerging role of clinical mass spectrometry in pathology

Somatic mutations and immune checkpoint biomarkers

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