A Systematic Analysis Workflow for High-Density Customized Protein Microarrays in Biomarker Screening

García-Valiente, Rodrigo; Fernández-García, Jonatan; Carabias-Sánchez, Javier; Landeira-Viñuela, Alicia; Góngora, Rafael; González‐González, María; Fuentes, Manuel

doi:10.1007/978-1-4939-8814-3_7

Cited by 4 publications

(6 citation statements)

References 23 publications

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“…In this sense, comparing with mass spectroscopy used for the most abundant APRs, our novel method provided the possibility of exploring all the proteins in one single assay with low amount of sample and in a relative short time, testing more than 1000 analytes in just one array [22]. According to our previous experience in novel microarrays, we also have established a complete pipeline for development and analysis from the platform design to the final results useful for clinical outcome [23,30,31].…”

Section: Discussionmentioning

confidence: 99%

“…The fluorescence signal retrieved from images processed in the previous section was corrected by subtracting background signal and then transformed into Z score as previously reported [30,31]. Overall raw fluorescence and log 2 (Z score) density distribution were compared to validate signal correction at each microarray employed.…”

Section: Aprs and Aab Microarray Data Pre-processing And Quality Controlmentioning

confidence: 99%

“…Protein microarray allows the miniaturization of thousands of immunoassays in a single device, evaluating many biomolecules presented in one biological sample with high-sensitivity and reproducibility with a small amount of sample [22,23]. Moreover, protein microarrays have been reported as useful methodology to analyze differential protein profiles of study samples by antigen-antibody interaction [24,25]. In the lack of a feasible methodology for determining all the APRs in one single step, in this report, it is explored protein microarrays as a suitable tool to carry out a high-throughput and simultaneous screening of APRs, allowing the detection in their corresponding dynamic range.…”

Section: Introductionmentioning

confidence: 99%

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Systematic evaluation of plasma signaling cascades by functional proteomics approaches: SARS‐CoV‐2 infection as model

Juanes-Velasco

García-Vaquero

Landeira-Viñuela

et al. 2022

Proteomics Clinical Apps

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Purpose : Acute phase reactants play a critical role in inflammation. The difference in their physiological functions or the different dynamic ranges of these proteins in plasma makes it difficult to detect them simultaneously and to use several of these proteins as a tool in clinical practice. Experimental Design : a novel multiplex assays has been designed and optimized to carry out a high‐throughput and simultaneous screening of acute phase reactants, allowing the detection of each of them at the same time and in their corresponding dynamic range. Results : Using Sars‐CoV‐2 infection as a model, it has been possible to profile different patterns of acute phase proteins that vary significantly between healthy and infected patients. In addition, severity profiles (acute respiratory distress syndrome and sepsis) have been established. Conclusions and Clinical Relevance : Differential profiles in acute phase proteins can serve as a diagnostic and prognostic tools, among patient stratification. The design of this new platform for their simultaneous detection paves the way for them to be more extensive use in clinical practice. This article is protected by copyright. All rights reserved

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Section: Discussionmentioning

confidence: 99%

Section: Aprs and Aab Microarray Data Pre-processing And Quality Controlmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Systematic evaluation of plasma signaling cascades by functional proteomics approaches: SARS‐CoV‐2 infection as model

Juanes-Velasco

García-Vaquero

Landeira-Viñuela

et al. 2022

Proteomics Clinical Apps

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“…The array images were analyzed by GenePix ® Pro 4.0 software ( Figure S2B ). In all of the arrays, the fluorescence signals were normalized (after background subtraction), as described by Valiente-Garcia R. et al (2019) [ 39 ] ( Figure S3 ), by a quartile normalization (based on all the arrays having the same homogeneous distribution).…”

Section: Methodsmentioning

confidence: 99%

Deciphering Biomarkers for Leptomeningeal Metastasis in Malignant Hemopathies (Lymphoma/Leukemia) Patients by Comprehensive Multipronged Proteomics Characterization of Cerebrospinal Fluid

Juanes-Velasco

Galicia

et al. 2022

Cancers

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In the present work, leptomeningeal disease, a very destructive form of systemic cancer, was characterized from several proteomics points of view. This pathology involves the invasion of the leptomeninges by malignant tumor cells. The tumor spreads to the central nervous system through the cerebrospinal fluid (CSF) and has a very grim prognosis; the average life expectancy of patients who suffer it does not exceed 3 months. The early diagnosis of leptomeningeal disease is a challenge because, in most of the cases, it is an asymptomatic pathology. When the symptoms are clear, the disease is already in the very advanced stages and life expectancy is low. Consequently, there is a pressing need to determine useful CSF proteins to help in the diagnosis and/or prognosis of this disease. For this purpose, a systematic and exhaustive proteomics characterization of CSF by multipronged proteomics approaches was performed to determine different protein profiles as potential biomarkers. Proteins such as PTPRC, SERPINC1, sCD44, sCD14, ANPEP, SPP1, FCGR1A, C9, sCD19, and sCD34, among others, and their functional analysis, reveals that most of them are linked to the pathology and are not detected on normal CSF. Finally, a panel of biomarkers was verified by a prediction model for leptomeningeal disease, showing new insights into the research for potential biomarkers that are easy to translate into the clinic for the diagnosis of this devastating disease.

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“…The fluorescence signal retrieved from images processed in the previous section was corrected by subtracting background signal and then transformed into Z score as described in previous reports (26,27). Overall raw fluorescence and log 2 (Z score) density distribution were compared to validate signal correction at each microarray employed.…”

Section: Apps and Aab Microarray Data Pre-processing And Qcmentioning

confidence: 99%

SARS-CoV-2 Infection Triggers Auto-Immune Response in ARDS

et al. 2022

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Acute respiratory distress syndrome (ARDS) is a severe pulmonary disease, which is one of the major complications in COVID-19 patients. Dysregulation of the immune system and imbalances in cytokine release and immune cell activation are involved in SARS-CoV-2 infection. Here, the inflammatory, antigen, and auto-immune profile of patients presenting COVID-19-associated severe ARDS has been analyzed using functional proteomics approaches. Both, innate and humoral responses have been characterized through acute-phase protein network and auto-antibody signature. Severity and sepsis by SARS-CoV-2 emerged to be correlated with auto-immune profiles of patients and define their clinical progression, which could provide novel perspectives in therapeutics development and biomarkers of COVID-19 patients. Humoral response in COVID-19 patients’ profile separates with significant differences patients with or without ARDS. Furthermore, we found that this profile can be correlated with COVID-19 severity and results more common in elderly patients.

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A Systematic Analysis Workflow for High-Density Customized Protein Microarrays in Biomarker Screening

Cited by 4 publications

References 23 publications

Systematic evaluation of plasma signaling cascades by functional proteomics approaches: SARS‐CoV‐2 infection as model

Systematic evaluation of plasma signaling cascades by functional proteomics approaches: SARS‐CoV‐2 infection as model

Deciphering Biomarkers for Leptomeningeal Metastasis in Malignant Hemopathies (Lymphoma/Leukemia) Patients by Comprehensive Multipronged Proteomics Characterization of Cerebrospinal Fluid

SARS-CoV-2 Infection Triggers Auto-Immune Response in ARDS

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