Proteomics and Proteogenomics Approaches for Oral Diseases

Bragazzi, Nicola Luigi; Pechkova, Eugenia; Nicolini, Claudio

doi:10.1016/b978-0-12-800453-1.00004-x

Cited by 18 publications

(13 citation statements)

References 182 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…As already extensively explained in our previous articles [9,[11][12][13][17][18][19] We analyzed the conductance curves acquired in NAPPAQCs in different steps of the expressing and capturing process: after the addition of human IVTT lysate at 30°C ("IVTT addition"), i.e. prior protein expression; after 10 minutes from the addition of human IVTT lysate, i.e.…”

Section: Resultsmentioning

confidence: 99%

“…Our laboratory had previously introduced novel approaches in the field of nanogenomics [7][8][9] and nanoproteomics [10][11], pioneering in both fields. Only by coupling and combining proteomics and genomics within a highly integrated, coherent framework, with an emphasis on proteomics, clinical problems can be successfully addressed (Figure 1) [12][13].…”

Section: Figurementioning

confidence: 99%

See 1 more Smart Citation

Determination of Protein-Protein Interaction for Cancer Control via Mass Spectrometry and Nanoconductimetry of NAPPA SNAP Arrays: An Overview

Nicolini¹,

Bragazzi²,

Pechkova³

2015

NanoWorld J

Self Cite

View full text Add to dashboard Cite

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Figurementioning

confidence: 99%

Determination of Protein-Protein Interaction for Cancer Control via Mass Spectrometry and Nanoconductimetry of NAPPA SNAP Arrays: An Overview

Nicolini¹,

Bragazzi²,

Pechkova³

2015

NanoWorld J

Self Cite

View full text Add to dashboard Cite

show abstract

“…On the light of the sixteen recently published experimental papers, referred in the last section [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16], we have successfully completed the feasibility study on Microarray-based Functional Nanoproteomics for an Industrial Approach to Cancer.…”

Section: Introductionmentioning

confidence: 99%

Microarray-based Functional Nanoproteomics for an Industrial Approach to Cancer. II Mass Spectrometry and Nanoconductimetry

Nicolini¹,

Bragazzi²,

Pechkova³

2016

NanoWorld J

Self Cite

View full text Add to dashboard Cite

Using the New England BioLabs (NEBL) SNAP-based Genes Expression in conjunction with our "sub-micron arrays" (Anodic Porous Allumina and/ or Kapton based Nanopores), we exploit our proprietary microarrays scanner (DNASER, DNA analyzer) and Label Free Nanotechnologies to carry out the following tasks: 1) Construction of SNAP-based Genes Nanoarrays, using gold surface coated for 10 minutes with 2% solution of 3-Aminopropyltriethoxysilane (APTES) in acetone, rinsed in acetone and dried with filtered air. Full length complementary DNAs (cDNAs) for onco-suppressor 53 (p53), Cyclin-dependent kinase 2 (CDK2), SH2 (Src Homology 2) domain of the proto-oncogene tyrosine-protein kinase (Src) and tyrosine-protein phosphatase non-receptor type 11 (PTPN11) were amplified and cloned. Printing mix was prepared with 0.66 μg/μl DNA capture reagent BG-PEG-NH2 for the one-step synthesis of SNAP-tag substrates from esters on labels or surfaces;2) Determination of Protein-Protein Interaction for the chosen cancer following the identification of leader genes (or hub genes, investigated with theoretical ab initio bioinformatics analysis using in-house software and algorithms, and then experimentally confirmed via DNASER). These genes are expressed by PURE (Protein synthesis Using Recombinant Elements) Express in spots less than 1 micron size piezo-microdispensed and then characterized via Label Free proprietary Autoflex Mass Spectrometry (MS) integrated with ad hoc software, namely the Spectrum Analyzer and Data Set manager (SpADS) and a proprietary Quartz Crystal Micro-balance with Dissipation factor monitoring (QCM_D) Nanoconductimetry, enabling to describe properties such as changes in frequency and conductance, viscoelasticity and dissipation factor. Solutions without DNA were prepared (called Master Mix, MM), as negative controls, in printing mix. Negative controls were prepared with a varying concentration range of SNAP capture reagent. As a positive control (for fluorescence analysis) mouse IgG or rabbit IgG (Pierce, IL, USA) were added in a printing mix instead of DNA.

show abstract

“…D N is more strictly related to the curve shape, reflecting the conductance variation (Bragazzi et al, 2014a;Spera et al, 2013).…”

Section: Qcm_d Conductometermentioning

confidence: 99%

Drug-Protein Interactions for Clinical Research by Nucleic Acid Programmable Protein Arrays-Quartz Crystal Microbalance with Dissipation Factor Monitoring Nanoconductometric Assay

Nicolini¹,

Spera²,

Bragazzi³

et al. 2014

American Journal of Biochemistry and Biotechnology

Self Cite

View full text Add to dashboard Cite

Conductometric monitoring of drug-gene and drug-protein interactions is of fundamental importance in the field of molecular pharmacology. Here, we present our main findings and characterizations of an important antiblastic used in neuro-oncology (Temozolomide), interacting with selected proteins that represent predictive biomarkers of the rate survival of the patients, of the outcome of chemotherapy and resistance to drug itself (namely, BRIP1 and MLH1). We use our previously introduced two genes along with previously described Nucleic Acid Programmable Protein Arrays (NAPPA)-based nanoconductometric sensor. We performed a positive control (Temozolomide plus MLH1 protein), a negative control (Temozolomide plus BRIP1 protein) and a multi-gene experiment (Temozolomide plus BRIP1&MLH1 being coexpressed), showing that we are able to properly perform pharmacoproteomics tasks, discriminating each protein and drug unique conductance curve as well as their interactions, even in the presence of multi-proteins being immobilized. Moreover, in the last part of our paper, we used a multiple regression model in order to predict the behavior of Temozolomide when exposed to BRIP1&MLH1 co-expressed and we showed that we are able to predict the drug-protein interaction profile with a good regression coefficient.

show abstract

Proteomics and Proteogenomics Approaches for Oral Diseases

Cited by 18 publications

References 182 publications

Determination of Protein-Protein Interaction for Cancer Control via Mass Spectrometry and Nanoconductimetry of NAPPA SNAP Arrays: An Overview

Determination of Protein-Protein Interaction for Cancer Control via Mass Spectrometry and Nanoconductimetry of NAPPA SNAP Arrays: An Overview

Microarray-based Functional Nanoproteomics for an Industrial Approach to Cancer. II Mass Spectrometry and Nanoconductimetry

Drug-Protein Interactions for Clinical Research by Nucleic Acid Programmable Protein Arrays-Quartz Crystal Microbalance with Dissipation Factor Monitoring Nanoconductometric Assay

Contact Info

Product

Resources

About