By Type: Book Chapter

Nanotheranostics in Gene Therapy, Oliveira, {Beatriz B. }, Fernandes {Alexandra R. }, and Baptista {Pedro V. } , Advances in Cancer Nanotheranostics for Experimental and Personalized Medicine, jan, United Kingdom, p.82–115, (2020) Abstract

The continuous advances in molecular genetics have prompt for a wealth of tools capable to modulate genome and the corresponding gene expression. These innovative technologies have broadened the range of possibilities for gene therapy, either to decrease expression of malignant genes and mutations or edition of genomes for correction of errors. These strategies rely on the delivery of therapeutic nucleic acids to cells and tissues that must overcome several biological barriers. Indeed, a key element for the success of any gene therapy formulation is the carrier agent capable to deliver the therapeutic nucleic acid moieties to a specific target and promote efficient cellular uptake, while preventing deleterious off-target effects and degradation by endogenous nucleases. The initial vectorization strategies proved to be rather immunogenic, limited in the amount of genetic material that can be packed and raised severe toxicity concerns. Nowadays, a new generation of nanotechnology-based gene delivery systems are making an impact on the way we use therapeutic nucleic acids. These nanovectorization platforms have been developed so as to show low immunogenicity, low toxicity, ease of assembly and scale-up with higher loading capacity. Some of these nanoscale systems have also allowed for controlled release system and for the simultaneous capability of monitorization of effect - nanotheranostics. Herein, we provide a review on the variety of gene delivery vectors and platforms at the nanoscale.

RNA Quantification Using Noble Metal Nanoprobes: Simultaneous Identification of Several Different mRNA Targets Using Color Multiplexing and Application to Chronic Myeloid Leukemia Diagnostics, Baptista, {Pedro Viana} , Nanoparticles in Biology and Medicine, United States, p.251–268, (2020) Abstract

Nanotechnology provides new tools for gene expression analysis that allow for sensitive and specific characterization of prognostic signatures related to cancer. Cancer is a complex disease where multiple gene loci contribute to the phenotype. The ability to simultaneously monitor differential expression originating from each locus allows for a more accurate indication into the degree of cancerous activity than either locus alone. Metal nanoparticles have been widely used as labels for in vitro identification and quantification of target sequences. Here we describe the synthesis of nanoparticles with different noble metal compositions in an alloy format that are then functionalized with thiol-modified ssDNA (nanoprobes). We also show how such nanoprobes are used in a non-cross-linking colorimetric method for the direct detection and quantification of specific mRNA targets, without the need for enzymatic amplification or reverse-transcription steps. The different metals in the alloy provide for distinct absorption spectra due to their characteristic plasmon resonance peaks. The color multiplexing allows for simultaneous identification of different mRNA targets involved in cancer development. A comparison of the absorption spectra of the nanoprobe mixtures taken before and after induced aggregation of metal nanoparticles allows to both identify and quantify each mRNA target. We describe the use of gold and gold–silver alloy nanoprobes for the development of the non-cross-linking method to detect a specific BCR-ABL fusion gene (e.g., e1a2 and e14a2) mRNA target associated with chronic myeloid leukemia (CML) using 10 ng/μL of unamplified total human RNA. Additionally, we demonstrate the use of this approach for the direct diagnostics of CML. This simple methodology takes less than 50 min to complete after total RNA extraction with comparable specificity and sensitivity to the more commonly used methods.

Nanoparticles as Delivery Systems in Cancer Therapy: Focus on Gold Nanoparticles and Drugs, Carvalho, Andreia, Fernandes {Alexandra R. }, and Baptista {Pedro V. } , Applications of Targeted Nano Drugs and Delivery Systems, jan, Netherlands, p.257–295, (2018) Abstract

Conventional cancer chemotherapy presents several bottlenecks, such as lack of specificity that impacts healthy tissues, rapid drug metabolism, and both intrinsic/acquired drug resistances varying in patient status, which altogether lead to reduction of efficacy. To overcome these issues and improve efficacy, combination with novel nanotechnology approaches-cancer nanomedicine-in the areas of imaging, diagnosis, and drug delivery are being proposed. These developments have been focused upon the preparation and application of nanoparticles for cancer therapy. Gold nanoparticle (AuNP) applications have been projected for improved imaging, diagnosis, and therapy, due to their exquisite physicochemical and optical properties showing potential applications as drug/gene carriers, photothermal and contrast agents. All these features may potentiate selective drug delivery, thus improving efficacy and reducing side effects. In this chapter, we shall discuss applications of nanoparticles with focus on AuNPs as efficient targeted (drug) delivery systems in cancer therapy.

Gold nanoparticles in molecular diagnostics and molecular therapeutics, Matias, {Ana S. }, Carlos {Fábio F. }, Pedrosa P., Fernandes {Alexandra R. }, and Baptista {Pedro V. } , Metal Nanoparticles in Pharma, jan, Switzerland, p.365–387, (2017) Abstract

Gold nanoparticles, due to their unique physicochemical properties, are among the most widely used nanoscale-based platforms for molecular diagnostics. The intrinsic chemical stability and apparent lack of toxicity have also prompted for application in therapeutics, e.g., for imaging modalities and as vectorization strategies for molecular modulators, i.e., gene silencing, specific targeting of cellular pathways, etc. Because of their common molecular ground, these approaches have been synergistically coupled together into molecular theranostic systems that allow for radical new in vivo diagnostics modalities with simultaneous tackling of molecular disequilibria leading to disease. Despite this tremendous potential, gold nanoparticle- based systems still have to make their effective translation to the clinics. This chapter focuses on the use of gold nanoparticles for molecular diagnostics and molecular therapeutics and their application in theranostics. Attention is paid to those systems that have moved toward the clinics.

Gene silencing using multifunctionalized gold nanoparticles for cancer therapy, Fernandes, {Alexandra R. }, and Baptista {Pedro V. } , Methods in Molecular Biology, Volume 1530, United States, p.319–336, (2017) Abstract

Multifunctionalized gold nanobeacons (Au-nanobeacon) combine, in a single and unique platform, targeting, detection and silencing providing an effective impact in clinics boosting cancer theranostics. Here, we describe a nano-integrated platform based on Au-nanobeacons able to detect and inhibit gene expression specifically in cancer cells. The surfaces of gold nanoparticles (AuNPs) are functionalized with targeting peptides to enhance tumor cell recognition and uptake, and with fluorescently labeled antisense DNA hairpin oligonucleotides to detect AuNPs. These oligonucleotides, upon recognition and hybridization to the target, open their structure resulting in separating apart the dye and the quencher allowing the fluorophore to emit light and to monitor the intracellular interactions of AuNPs with the target and the specific silencing of gene expression. This strategy allows inhibiting KRAS gene expression in colorectal carcinoma cell lines with no relevant toxicity for healthy fibroblasts. Importantly, this nano-integrated platform can be easily adapted to hybridize with any specific target thus providing real benefits for the diagnosis and treatment of cancer.

Gold nanoparticles for DNA/RNA-based diagnostics, Franco, Ricardo, Pedrosa Pedro, Carlos {Fábio Ferreira}, Veigas Bruno, and Baptista {Pedro Miguel Ribeiro Viana} , Handbook of Nanoparticles, sep, Switzerland, p.1339–1370, (2015) Abstract

The remarkable physicochemical properties of gold nanoparticles (AuNPs) have prompted development in exploring biomolecular interactions with AuNPscontaining systems, pursuing biomedical applications in diagnostics. Among these applications, AuNPs have been remarkably useful for the development of DNA/RNA detection and characterization systems for diagnostics, including systems suitable for point of need. Here, emphasis will be on available molecular detection schemes of relevant pathogens and their molecular characterization, genomic sequences associated with medical conditions (including cancer), mutation and polymorphism identification, and the quantification of gene expression.

Nanoparticles for mass spectrometry applications, Larguinho, Miguel, Capelo {José Luís}, and Baptista {Pedro V. } , Handbook of Nanoparticles, sep, Switzerland, p.1371–1396, (2015) Abstract

Nanotechnology has led to the development of new and improved materials, and particular emphasis has been directed toward nanoparticles and their multiple bio-applications. Nanoparticles exhibit size-, shape-, and compositiondependent properties, e.g., surface plasmon resonance and photothermal properties, which may potentially enhance laser desorption/ionization systems for mass spectrometry-based analysis of biomolecules. Also, nanoparticles possess high surface to volume ratio that can be easily derivatized with a wide range of ligands with different functional groups. Surface modification makes nanoparticles advantageous for sample preparation procedures prior to detection by mass spectrometry. Moreover, it allows the synthesis of affinity probes, which promotes interactions between nanoparticles and analytes, greatly enhancing the ionization efficiency. This chapter provides a comprehensive discussion on the use of nanoparticles for mass spectrometry-related applications, from sample preparation methodologies to ionization surfaces. Applications will focus on nanoparticle size, composition, and functionalization, as a comparative point of view on optimal characteristics toward maximization of bioassay efficiency.

Gold and Silver Nanoparticles for Diagnostics of Infection, Pedrosa, Pedro, and Baptista {Pedro V. } , Nanotechnology in Diagnosis, Treatment and Prophylaxis of Infectious Diseases, may, Netherlands, p.1–18, (2015) Abstract

The use of noble metal nanoparticles (NPs), particularly gold and silver, in biomolecular applications has surged, ranging from innovative strategies for molecular diagnostics to radical new ways of treatment. Taking advantage of the particular optical-chemical characteristics of these metal NPs, every year new methods of molecular diagnostics of infectious diseases are reported providing higher analytical capability, sensitivity, and throughput at lower costs and with the possibility to be used where needed. Gold and silver NPs, or a combination of both, possess amazing optical/spectral properties, such as the intense localized surface plasmon resonance that, together with the ease of surface modification and functionalization with biomolecules capable of specific molecular recognition, have provided new strategies for molecular analysis, extending the detection limit of current nucleic acid and protein-based assays.This chapter focuses on the methods used for diagnostic of infectious diseases that take advantage of noble metal NPs. It discusses their use in biomolecular recognition and their most promising approaches, and it compares their advantages and disadvantages.

Mobile based gold nanoprobe TB diagnostics for point-of-need, Veigas, B., Fortunato E., and Baptista {P. V. } , Mobile Health Technologies: Methods and Protocols, jan, Volume Part 1, United States, p.41–56, (2015) Abstract

Nanotechnology based diagnostics has provided improved tools for pathogen detection and sensitive and specific characterization of antibiotic resistance signatures. Tuberculosis (TB) is caused by members of the Mycobacterium tuberculosis Complex (MTBC) and, according to the World Health Organization, is one of the most serious infectious diseases in the world. Recent advances in molecular diagnostics of TB have improved both the detection time and sensitivity but they still require specialized technical personnel and cumbersome laboratory equipment. Diagnostics at point-of-need is crucial to TB control as it may provide rapid identification of pathogen together with the resistance profile of TB strains, originated from single nucleotide polymorphisms (SNPs) in different loci , allowing for a more accurate indication of the adequate therapy.Gold nanoparticles have been widely used in molecular diagnostics platforms. Here, we describe the use of gold nanoprobes (oligonucleotide functionalized gold nanoparticles) to be used in a non-crosslinking colorimetric method for the direct detection of specific DNA targets. Due to the remarkable optical properties of gold nanoparticles, this detection system provides colorimetric detection of the pathogen together with the potential of identification of several single nucleotide polymorphisms (SNPs) involved in TB resistance to antibiotics. For point-of-need use, we adapted this strategy to a low-cost mobile scheme using a paper based revelation platform and where the spectral signature is transposed to RGB data via a smartphone device. This way, identification of pathogen and characterization of resistance signatures is achieved at point-of-need.

Application of Nanotechnology in Drug Delivery, Silva, Joana, Fernandes {Alexandra R. }, and Baptista {Pedro V. } , Application of Nanotechnology in Drug Delivery, jul, (2014) Abstract
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RNA quantification using noble metal nanoprobes: Simultaneous identification of several different mrna targets using color multiplexing and application to cancer diagnostics, Conde, João, c}alo Doria Gon{\c, {de la Fuente} {Jesus M. }, and Baptista {Pedro Viana} , Nanoparticles in Biology and Medicine: Methods and Protocols, aug, United States, p.71–87, (2012) Abstract

Nanotechnology provides new tools for gene expression analysis that allow for sensitive and specific characterization of prognostic signatures related to cancer. Cancer is a multigenic complex disease where multiple gene loci contribute to the phenotype. The ability to simultaneously monitor differential expression originating from each locus allows for a more accurate indication of degree of cancerous activity than either locus alone. Metal nanoparticles have been widely used as labels for in vitro identification and quantification of target sequences. Here we describe the synthesis of nanoparticles with different noble metal compositions in an alloy format that are then functionalized with thiol-modified ssDNA (nanoprobes). We also show how to use such nanoprobes in a non-cross-linking colorimetric method for the direct detection and quantification of specific mRNA targets, without the need for enzymatic amplification or reverse transcription steps. The different metals in the alloy provide for distinct absorption spectra due to their characteristic plasmon resonance peaks. The color multiplexing allows for simultaneous identification of several different mRNA targets involved in cancer development. Comparison of the absorption spectra of the nanoprobes mixtures taken before and after induced aggregation of metal nanoparticles allows to both identify and quantify each mRNA target. We describe the use of gold and gold:silver-alloy nanoprobes for the development of the non-cross-linking method to detect a specific BCR-ABL fusion gene (e.g., e1a2 and e14a2) mRNA target associated with chronic myeloid leukemia (CML) using 10 ng μL -1 of unamplified total human RNA. This simple methodology takes less than 50 min to complete after total RNA extraction with comparable specificity and sensitivity to the more commonly used methods.

Nanodiagnostics for tuberculosis, Veigas, Bruno, c}alo Dória Gon{\c, and Baptista {Pedro V. } , Understanding Tuberculosis, feb, p.257–276, (2012) Abstract
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RNA quantification using noble metal nanoprobes - application to cancer diagnostics, Baptista, {Pedro Miguel Ribeiro Viana} , Nanoparticles in Biology and Medicine - Methods and Applications, jan, p.71–87, (2012) Abstract
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Nanoparticles in molecular diagnostics, Baptista, {Pedro V. }, c}alo Dória Gon{\c, Quaresma Pedro, Cavadas Miguel, Neves {Cristina S. }, Gomes Inês, Eaton Peter, Pereira Eulália, and Franco Ricardo , Nanoparticles in Translational Science and Medicine, Netherlands, p.427–488, (2011) Abstract

The aim of this chapter is to provide an overview of the available and emerging molecular diagnostic methods that take advantage of the unique nanoscale properties of nanoparticles (NPs) to increase the sensitivity, detection capabilities, ease of operation, and portability of the biodetection assemblies. The focus will be on noble metal NPs, especially gold NPs, fluorescent NPs, especially quantum dots, and magnetic NPs, the three main players in the development of probes for biological sensing. The chapter is divided into four sections: a first section covering the unique physicochemical properties of NPs of relevance for their utilization in molecular diagnostics; the second section dedicated to applications of NPs in molecular diagnostics by nucleic acid detection; and the third section with major applications of NPs in the area of immunoassays. Finally, a concluding section highlights the most promising advances in the area and presents future perspectives.

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