Whole-exome sequencing of non-BRCA1/BRCA2 mutation carrier cases at high-risk for hereditary breast/ovarian cancer.

The current study aimed to identify new breast and/or ovarian cancer predisposition genes. For that, whole-exome sequencing (WES) was performed in the germline DNA of 52 non-BRCA1/BRCA2/TP53 mutation carrier women at high-risk for hereditary breast and ovarian cancer (HBOC). All variants were classified using information from population and disease specific databases, in silico prediction tools and the American College of Medical Genetics and Genomics (ACMG) criteria. Loss of heterozygosity (LOH) of tumor samples and segregation analyses were performed whenever possible. The variants identified were investigated in a second, independent cohort of 17 BC cases. Pathogenic/Likely Pathogenic variants were identified in known cancer genes such as CHEK2, MUTYH, PMS2, and RAD51C. Rare and potentially pathogenic variants were identified in DNA repair genes (FAN1, POLQ, and RAD54L) and other cancer-related genes such as DROSHA and SLC34A2. Interestingly, the variant c.149T>G in the FAN1 gene was identified in two unrelated families, and exhibited LOH in the tumor tissue of one of them. In conclusion, this is the largest Brazilian WES study involving families at high-risk for HBOC which has brought novel insights into the role of potentially new genetic risk factors for hereditary breast and ovarian cancer.

Determination of p53 biomarker using an electrochemical immunoassay based on layer-by-layer films with NiFe2O4 nanoparticles.

A disposable electrochemical immunosensors is presented suitable to detect cancer biomarker p53 using screen-printed carbon electrodes modified with a layer-by-layer (LbL) matrix of carboxylated NiFe2O4 nanoparticles and polyethyleneimine, onto which anti-p53 antibodies were adsorbed. Under optimized conditions, the immunosensors exhibited high surface coverage and high concentration of immobilized antibodies, which allowed for detection of p53 in a wide dynamic range from 1.0 to 10 × 103 pg mL-1, with a limit of detection of 5.0 fg mL-1 at a working potential of 100 mV vs. Ag/AgCl. The immunosensors also exhibited good selectivity with negligible interference upon incubation in complex matrices containing high concentrations of proteins (i.e., fetal bovine serum and cell lysate). The immunosensor performance is among the best reported in the literature for determination of p53, with the additional advantage of being disposable and operating with low-volume solutions.Graphical abstract Schematic representation of immunosensor fabrication depicting the immobilization of specific antibodies against p53 protein onto the surfaces of disposable printed electrodes modified with films of polyethyleneimine and different concentrations of carboxylated magnetic nanoparticles.

Screen-printed electrodes modified with carbon black and polyelectrolyte films for determination of cancer marker carbohydrate antigen 19-9.

Electrochemical immunosensors have been developed to determine the carbohydrate antigen 19-9 (CA19-9). They are based on screen-printed carbon electrodes (SPCEs) coated with layer-by-layer (LbL) films of carbon black (CB) and polyelectrolytes. Owing to a suitable choice of LbL film architecture, the procedures for immobilization of anti-CA19-9 antibodies on the electrode surfaces were straightforward. Mechanically flexible immunosensors were capable of detecting CA19-9 within a dynamic range of 0.01 to 40 U mL-1 and a limit of detection of 0.07 U mL-1 using differential pulse voltammetry. In addition to detecting CA19-9 at clinically relevant concentrations for pancreatic cancer in standard solutions, the immunosensors provide the determination of CA19-9 on cell lysate and human serum samples. Using LbL films led to immunosensors with superior performance compared to similar systems obtained by drop casting. The fabrication of this relatively simple, inexpensive platform is a demonstration that SPCEs modified with cost-effective materials are able to detect cancer biomarkers and may be adapted to other disposable immunosensors. Graphical abstract Schematic representation of assembly and characterization of electrochemical immunosensors for the determination of carbohydrate antigen 19-9 based on printed electrodes modified with composites of carbon black and polyelectrolyte films.

Hexane partition from Annona crassiflora Mart. promotes cytotoxity and apoptosis on human cervical cancer cell lines.

Cervical cancer is the third most commonly diagnosed tumor type and the fourth cause of cancer-related death in females. Therapeutic options for cervical cancer patients remain very limited. Annona crassiflora Mart. is used in traditional medicine as antimicrobial and antineoplastic agent. However, little is known about its antitumoral properties. In this study the antineoplastic effect of crude extract and derived partitions from A. crassiflora Mart in cervical cancer cell lines was evaluated. The crude extract significantly alters cell viability of cervical cancer cell lines as well as proliferation and migration, and induces cell death in SiHa cells. Yet, the combination of the crude extract with cisplatin leads to antagonistic effect. Importantly, the hexane partition derived from the crude extract presented cytotoxic effect both in vitro and in vivo, and initiates cell responses, such as DNA damage (H2AX activity), apoptosis via intrinsic pathway (cleavage of caspase-9, caspase-3, poly (ADP-ribose) polymerase (PARP) and mitochondrial membrane depolarization) and decreased p21 expression by ubiquitin proteasome pathway. Concluding, this work shows that hexane partition triggers several biological responses such as DNA damage and apoptosis, by intrinsic pathways, and was also able to promote a direct decrease in tumor perimeter in vivo providing a basis for further investigation on its antineoplastic activity on cervical cancer.

Low-Cost and Rapid-Production Microfluidic Electrochemical Double-Layer Capacitors for Fast and Sensitive Breast Cancer Diagnosis.

This technical note describes a new microfluidic sensor that combines low-cost (USD $0.97) with rapid fabrication and user-friendly, fast, sensitive, and accurate quantification of a breast cancer biomarker. The electrodes consisted of cost-effective bare stainless-steel capillaries, whose mass production is already well-established. These capillaries were used as received, without any surface modification. Microfluidic chips containing electrical double-layer capillary capacitors (µEDLC) were obtained by a cleanroom-free prototyping that allows the fabrication of dozens to hundreds of chips in 1 h. This sensor provided the successful quantification of CA 15-3, a biomarker protein for breast cancer, in serum samples from cancer patients. Antibody-anchored magnetic beads were utilized for immunocapture of the marker, and then, water was added to dilute the protein. Next, the CA 15-3 detection (<2 min) was made without using redox probes, antibody on electrode (sandwich immunoassay), or signal amplification strategies. In addition, the capacitance tests eliminated external pumping systems and precise volumetric sampling steps, as well as presented low sample volume (5 µL) and high sensitivity using bare capillaries in a new design for double-layer capacitors. The achieved limit-of-detection (92.0 µU mL-1) is lower than that of most methods reported in the literature for CA 15-3, which are based on nanostructured electrodes. The data shown in this technical note support the potential of the µEDLC toward breast cancer diagnosis even at early stages. We believe that accurate analyses using a simple sample pretreatment such as magnetic field-assisted immunocapture and cost-effective bare electrodes can be extended to quantify other cancer biomarkers and even biomolecules by changing the biorecognition element.

Using machine learning and an electronic tongue for discriminating saliva samples from oral cavity cancer patients and healthy individuals.

The diagnosis of cancer and other diseases using data from non-specific sensors - such as the electronic tongues (e-tongues) - is challenging owing to the lack of selectivity, in addition to the variability of biological samples. In this study, we demonstrate that impedance data obtained with an e-tongue in saliva samples can be used to diagnose cancer in the mouth. Data taken with a single-response microfluidic e-tongue applied to the saliva of 27 individuals were treated with multidimensional projection techniques and non-supervised and supervised machine learning algorithms. The distinction between healthy individuals and patients with cancer on the floor of mouth or oral cavity could only be made with supervised learning. Accuracy above 80% was obtained for the binary classification (YES or NO for cancer) using a Support Vector Machine (SVM) with radial basis function kernel and Random Forest. In the classification considering the type of cancer, the accuracy dropped to ca. 70%. The accuracy tended to increase when clinical information such as alcohol consumption was used in conjunction with the e-tongue data. With the random forest algorithm, the rules to explain the diagnosis could be identified using the concept of Multidimensional Calibration Space. Since the training of the machine learning algorithms is believed to be more efficient when the data of a larger number of patients are employed, the approach presented here is promising for computer-assisted diagnosis.

Low-cost bacterial nanocellulose-based interdigitated biosensor to detect the p53 cancer biomarker.

Low-cost sensors to detect cancer biomarkers with high sensitivity and selectivity are essential for early diagnosis. Herein, an immunosensor was developed to detect the cancer biomarker p53 antigen in MCF7 lysates using electrical impedance spectroscopy. Interdigitated electrodes were screen printed on bacterial nanocellulose substrates, then coated with a matrix of layer-by-layer films of chitosan and chondroitin sulfate onto which a layer of anti-p53 antibodies was adsorbed. The immunosensing performance was optimized with a 3-bilayer matrix, with detection of p53 in MCF7 cell lysates at concentrations between 0.01 and 1000 Ucell. mL-1, and detection limit of 0.16 Ucell mL-1. The effective buildup of the immunosensor on bacterial nanocellulose was confirmed with polarization-modulated infrared reflection absorption spectroscopy (PM-IRRAS) and surface energy analysis. In spite of the high sensitivity, full selectivity with distinction of the p53-containing cell lysates and possible interferents required treating the data with a supervised machine learning approach based on decision trees. This allowed the creation of a multidimensional calibration space with 11 dimensions (frequencies used to generate decision tree rules), with which the classification of the p53-containing samples can be explained.

Colorimetric Detection of SARS-CoV-2 Using Plasmonic Biosensors and Smartphones.

Low-cost, instrument-free colorimetric tests were developed to detect SARS-CoV-2 using plasmonic biosensors with Au nanoparticles functionalized with polyclonal antibodies (f-AuNPs). Intense color changes were noted with the naked eye owing to plasmon coupling when f-AuNPs form clusters on the virus, with high sensitivity and a detection limit of 0.28 PFU mL-1 (PFU stands for plaque-forming units) in human saliva. Plasmon coupling was corroborated with computer simulations using the finite-difference time-domain (FDTD) method. The strategies based on preparing plasmonic biosensors with f-AuNPs are robust to permit SARS-CoV-2 detection via dynamic light scattering and UV-vis spectroscopy without interference from other viruses, such as influenza and dengue viruses. The diagnosis was made with a smartphone app after processing the images collected from the smartphone camera, measuring the concentration of SARS-CoV-2. Both image processing and machine learning algorithms were found to provide COVID-19 diagnosis with 100% accuracy for saliva samples. In subsidiary experiments, we observed that the biosensor could be used to detect the virus in river waters without pretreatment. With fast responses and requiring small sample amounts (only 20 µL), these colorimetric tests can be deployed in any location within the point-of-care diagnosis paradigm for epidemiological control.

Novel enzyme-free immunomagnetic microfluidic device based on Co0.25Zn0.75Fe2O4 for cancer biomarker detection.

Early diagnosis of cancer by biomarker detection has been widely studied since it can lead to an increase in patient survival rates. Magnetic nanoparticles (MNPs) play an important role in this field acting as a valuable tool in the biomarker immunocapture and detection. In this work, Co0.25Zn0.75Fe2O4 (CoZnFeONPs) nanoparticles were synthesized and applied as enzyme mimics of peroxidase-like catalysis in a disposable enzyme-free microfluidic immunoarray device (µID). The catalytic activity of CoZnFeONPs was evaluated by hydrogen peroxide detection using cyclic voltammetry and the apparent Michaelis-Menten constant was estimated by Lineweaver-Burk equation showing good Km values. In µID, the immunosensors were assembled with monoclonal antibody against CYFRA 21-1 covalently immobilized on graphene oxide previously deposited on the screen-printed carbon-based electrodes. Under optimized conditions, the method presented a good linear response for CYFRA 21-1 in the range of 3.9-1000 fg mL-1 achieving an ultralow limit of detection (LOD) of 0.19 fg mL-1. For comparison, Fe3O4 nanoparticles (FeONPs) was also synthetized and presented results slight inferior to that obtained with CoZnFeONPs. The methods developed using both MNPs exhibited countless advantages when compared with the immunosensors developed for CYFRA-21-1, previously reported in the literature. The methods were successful applied for the detection of CYFRA 21-1 in real serum samples of healthy and prostate cancer patients and showed good correlation with results obtained with the enzyme-linked immunosorbent assay (ELISA). The CoZnFeONPs associated with the disposable microfluidic immunoarray device provides a simple and effective method for biomarker detection that could satisfy the need for a low-cost and rapid test for early diagnosis of cancer.

The role of single-nucleotide polymorphism (SNPs) in toxicity of induction chemotherapy based on cisplatin and paclitaxel in patients with advanced head and neck cancer.

BACKGROUND: Induction chemotherapy in locally-advanced head and neck squamous cell carcinoma (LAHNSCC) patients is potentially associated to serious adverse events. Biomarkers associated with toxicity could tailor its indication. This study evaluated the association between single-nucleotide polymorphisms (SNPs) in metabolic genes and toxicity to induction chemotherapy. METHODS: 59 LAHNSCC phase II clinical trial patients (NCT00959387) were assessed regarding 47 metabolic genes (366 SNPs). Toxicities were graded (CTCAE 3.0) and statistical analysis was performed. RESULTS: The SNPs rs8187710 (ABCC2) and rs1801131 (MTHFR) were associated to increased risk of gastrointestinal toxicity, whereas the SNPs rs3788007 (ABCG1) and rs4148943 (CHST3) were associated to decreased risk. Two other SNPs, rs2301159 (SLC10A2) and rs2470890 (CYP1A2), were associated with increased risk of hematological toxicity. Nevertheless, these SNPs did not remain significant after adjusting for multiple comparisons. CONCLUSIONS: This study could not demonstrate relationship between SNPs and toxicity to induction chemotherapy in LAHNSCC patients. The small number of patients may have affected the results.

Screen-printed interdigitated electrodes modified with nanostructured carbon nano-onion films for detecting the cancer biomarker CA19-9.

Nanostructured capacitive biosensors, combined with inexpensive fabrication technologies, may provide simple, sensitive devices for detecting clinically relevant cancer biomarkers. Herein, we report a novel platform for detecting the pancreatic cancer biomarker CA19-9 using low-cost screen-printed interdigitated electrodes (SPIDEs). The SPIDEs were modified by carbon nano-onions (CNOs) and graphene oxide (GO) films, on which a layer of anti-CA19-9 antibodies was immobilized. The modification with CNOs and GO significantly improved the analytical performance of the biosensor, which displayed superior results to those prepared only with GO. The biossensor exhibited high reproducibility and a relatively low limit of detection of 0.12 U mL-1. Using these devices in combination with information visualization methods we were able to detect CA19-9 in whole cell lysates of colorectal adenocarcinoma. The fabrication of these low-cost, disposable immunosensors is a successful attempt to explore CNOs in capacitive biosensors, which may be extended for detection of different cancer biomarkers.

Disposable Microfluidic Immunoarray Device for Sensitive Breast Cancer Biomarker Detection.

Breast cancer is the most common cancer in women worldwide. The detection of biomarkers has played a significant role in the early diagnosis and prognosis of breast cancer. Herein, we describe the construction of a disposable microfluidic immunoarray device (DµID) for the rapid and low-cost detection of CA15-3 (carbohydrate antigen 15-3), a protein biomarker for breast cancer. The DµID was constructed using a simple and rapid prototyping technique and was applied to detect CA15-3 in cancer patients. The DµID construction was based on the use of a double-sided adhesive card with a microfluidic channel and a screen-printed array with 8 electrodes. Both the immunoarray and microfluidic channel were designed using an inexpensive home cutter printer and using low-cost materials. The immunoarray was modified using the layer-by-layer technique aiming at immobilizing the primary antibody. For the biomarker detection, magnetic particles (MPs) modified with polyclonal antibodies and peroxidase enzymes were used as a strategy for capture, separation, and preconcentration of the biomarker, in addition to amplification of the electroanalytical signal. The preconcentration and amplification strategies integrated with the nanostructured immunosensors of the DµID meaningfully contributed toward the detection of CA15-3 with a limit of detection (LoD) of 6 µU mL-1, requiring as low as 2 µL of serum samples for 8 simultaneous detections. The obtained LoD was 1200 times lower compared to those of other immunosensors previously reported in the literature. The DµID was applied for the detection of CA15-3 in real samples of breast cancer patients and was found to present an excellent correlation with the well-established commercial electrochemiluminescence immunoassay. The association of the DµID with nanostructured surfaces and analyte capturing with bioconjugated paramagnetic particles is essentially a promising breakthrough for the low-cost and accurate detection of cancer biomarkers.

Immunosensor for Pancreatic Cancer Based on Electrospun Nanofibers Coated with Carbon Nanotubes or Gold Nanoparticles.

We report the fabrication of immunosensors based on nanostructured mats of electrospun nanofibers of polyamide 6 and poly(allylamine hydrochloride) coated either with multiwalled carbon nanotubes (MWCNTs) or gold nanoparticles (AuNPs), whose three-dimensional structure was suitable for the immobilization of anti-CA19-9 antibodies to detect the pancreatic cancer biomarker CA19-9. Using impedance spectroscopy, the sensing platform was able to detect CA19-9 with a detection limit of 1.84 and 1.57 U mL-1 for the nanostructured architectures containing MWCNTs and AuNPs, respectively. The high sensitivity achieved can be attributed to the irreversible adsorption between antibodies and antigens, as confirmed with polarization-modulated infrared reflection absorption spectroscopy. The adsorption mechanism was typical Langmuir-Freundlich processes. The high sensitivity and selectivity of the immunosensors were also explored in tests with blood serum from patients with distinct concentrations of CA19-9, for which the impedance spectra data were processed with a multidimensional projection technique. The robustness of the immunosensors in dealing with patient samples without suffering interference from analytes present in biological fluids is promising for a simple, effective diagnosis of pancreatic cancer at early stages.

Identification of hereditary cancer in the general population: development and validation of a screening questionnaire for obtaining the family history of cancer.

One of the challenges for Latin American countries is to include in their healthcare systems technologies that can be applied to hereditary cancer detection and management. The aim of the study is to create and validate a questionnaire to identify individuals with possible risk for hereditary cancer predisposition syndromes (HCPS), using different strategies in a Cancer Prevention Service in Brazil. The primary screening questionnaire (PSQ) was developed to identify families at-risk for HCPS. The PSQ was validated using discrimination measures, and the reproducibility was estimated through kappa coefficient. Patients with at least one affirmative answer had the pedigree drawn using three alternative interview approaches: in-person, by telephone, or letter. Validation of these approaches was done. Kappa and intraclass correlation coefficients were used to analyze data's reproducibility considering the presence of clinical criteria for HCPS. The PSQ was applied to a convenience sample of 20,000 women of which 3121 (15.6%) answered at least one affirmative question and 1938 had their pedigrees drawn. The PSQ showed sensitivity and specificity scores of 94.4% and 75%, respectively, and a kappa of 0.64. The strategies for pedigree drawing had reproducibility coefficients of 0.976 and 0.850 for the telephone and letter approaches, respectively. Pedigree analysis allowed us to identify 465 individuals (24.0%) fulfilling at least one clinical criterion for HCPS. The PSQ fulfills its function, allowing the identification of HCPS at-risk families. The use of alternative screening methods may reduce the number of excluded at-risk individuals/families who live in locations where oncogenetic services are not established.

Controlled Film Architectures to Detect a Biomarker for Pancreatic Cancer Using Impedance Spectroscopy.

The need for analytical devices for detecting cancer at early stages has motivated research into nanomaterials where synergy is sought to achieve high sensitivity and selectivity in low-cost biosensors. In this study, we developed a film architecture combining self-assembled monolayer (SAM) and layer-by-layer (LbL) films of polysaccharide chitosan and the protein concanavalin A, on which a layer of anti-CA19-9 antibody was adsorbed. Using impedance spectroscopy with this biosensor, we were capable of detecting low concentrations of the antigen CA19-9, an important biomarker for pancreatic cancer. The limit of detection of 0.69U/mL reached is sufficient for detecting pancreatic cancer at very early stages. The selectivity of the biosensor was inferred from a series of control experiments with samples of cell lines that were tested positive (HT29) and negative (SW620) for the biomarker CA19-9, in addition to the lack of changes in the capacitance value for other analytes and antigen that are not related to this type of cancer. The high sensitivity and selectivity are ascribed to the very specific antigen-antibody interaction, which was confirmed with PM-IRRAS and atomic force microscopy. Also significant is that used information visualization methods to show that different cell lines and commercial samples containing distinct concentrations of CA19-9 and other analytes can be easily distinguished from each other. These computational methods are generic and may be used in optimization procedures to tailor biosensors for specific purposes, as we demonstrated here by comparing the performance of two film architectures in which the concentration of chitosan was varied.

Herpes simplex virus type 1 (HSV-1)-derived amplicon vectors.

Amplicons are defective, helper-dependent, herpes simplex virus type 1 (HSV-1)-derived vectors. The main interest of these vectors as gene transfer tools stems from the fact that the amplicon vector genomes do not carry protein-encoding viral sequences. Consequently, they are completely safe for the host and nontoxic for the infected cells. Moreover, the complete absence of virus genes provides space to accommodate very large foreign DNA sequences, up to almost 150-kb, the size of the virus genome. This large transgene capacity can be used to deliver complete gene loci, including introns and exons, as well as long regulatory sequences, conferring tissue-specific expression or stable maintenance of the transgene in proliferating cells. During many years the development of these vectors and their application in gene transfer experiments was hindered by the presence of contaminating toxic helper virus particles in the vector stocks. In recent years, however, two different methodologies have been developed that allow generating amplicon stocks either completely free of helper particles or only faintly contaminated with fully defective helper particles. This chapter describes these two methodologies.