Clinical and Technical Validation of OncoIndx® Assay-A Comprehensive Genome Profiling Assay for Pan-Cancer Investigations.

Comprehensive next-generation sequencing (NGS) assays enable the identification of clinically relevant mutations, enhancing the capability for targeted therapeutic interventions. In addition, genomic alterations driving the oncogenic roadmap and leading to resistance mechanisms are reshaping precision oncology. We report the workflow and clinical and technical validation of the OncoIndx® NGS platform-a comprehensive genomic profiling (CGP)-based assay for pan-cancer investigation. We evaluated the concordance between the OncoIndx® test findings and clinically established hotspot detection using SeraSeq reference standards. OncoIndx is a hybridization capture-based NGS assay for the targeted deep sequencing of all exons and selected introns of 1080 cancer-related genes. We show the outcome in the form of tier I and tier II single nucleotide variants (SNVs), copy number alterations (CNAs), and specific gene fusions. OncoIndx® also informs genome-wide tumor mutational burden (TMB), microsatellite instability (MSI), homologous recombination deficiency (HRD), and genomic loss of heterozygosity (gLOH). A total of 63 samples were utilized for validation with reference standards, clinical samples, and orthogonal assessment for genomic alterations. In addition, 49 cross-laboratory samples were validated for microsatellite instability (MSI), and for the tumor mutation burden (TMB), 18 samples as reference standards, 6 cross-laboratory samples, and 29 TCGA samples were utilized. We show a maximum clinical sensitivity of 98% and a positive predictive value (PPV) of 100% for the clinically actionable genomic variants detected by the assay. In addition, we demonstrate analytical validation with the performance of the assay, limit of detection (LoD), precision, and orthogonal concordance for various types of SVs, CNAs, genomic rearrangements, and complex biomarkers like TMB, MSI, and HRD. The assay offers reliable genomic predictions with the high-precision detection of actionable variants, validated by established reference standards.

A multicomponent nanosystem for capturing circulating tumor cells from cancer patients with PD-L1 as an immunotherapy oncotarget.

Capturing circulating tumor cells (CTCs) from the peripheral blood of cancer patients, where they are disseminated among billions of other blood cells, is one of the most daunting challenge. We report OncoDiscover®, a multicomponent nano-system consisting of iron oxide (Fe3O4) nanoparticles (NPs), polyamidoamine generation 4 dendrimers (PAMAM-G4-NH2), graphene oxide (GO) sheets and an anti-epithelial cell adhesion molecule (anti-EpCAM) antibody (Fe-GSH-PAMAM-GO-EpCAM) for the selective and precise capture of CTCs. We further evaluated this system for therapeutically important oncotargets, exemplifying overexpression of the programmed death ligand 1 (PD-L1) as a functional assay on CTCs in cancer patients. We retrospectively evaluated 134 cancer patients for the presence of CTCs and 113 (84%) showed the presence of CTCs. About 62 (55%) of the CTC +ve patients showed CTCs with PD-L1 expression. The personalized cancer detection demonstrated by the OncoDiscover® CTC analysis tool is highly relevant for cancer monitoring and treatment outcomes.

CTC together with Shh and Nrf2 are prospective diagnostic markers for HNSCC.

BACKGROUND: The lack of appropriate prognostic biomarkers remains a significant obstacle in the early detection of Head and Neck Squamous Cell Carcinoma (HNSCC), a cancer type with a high mortality rate. Despite considerable advancements in treatment, the success in diagnosing HNSCC at an early stage still needs to be improved. Nuclear factor erythroid 2-related factor 2 (Nrf2) and Sonic Hedgehog (Shh) are overexpressed in various cancers, including HNSCC, and have recently been proposed as possible therapeutic targets for HNSCC. Circulating Tumor Cell (CTC) is a novel concept used for the early detection of cancers, and studies have suggested that a higher CTC count is associated with the aggressiveness of HNSCC and poor survival rates. Therefore, we aimed to establish molecular markers for the early diagnosis of HNSCC considering Shh/Nrf2 overexpression in the background. In addition, the relation between Shh/Nrf2 and CTCs is still unexplored in HNSCC patients. METHODS: In the present study, we selected a cohort of 151 HNSCC patients and categorized them as CTC positive or negative based on the presence or absence of CTCs in their peripheral blood. Data on demographic and clinicopathological features with the survival of the patients were analyzed to select the patient cohort to study Shh/Nrf2 expression. Shh and Nrf2 expression was measured by qRT-PCR. RESULTS: Considering significant demographic [smoking, betel leaf (p-value < 0.0001)] and clinicopathological risk factors [RBC count (p < 0.05), Platelet count (p < 0.05), Neutrophil count (p < 0.005), MCV (p < 0.0001), NLR (p < 0.05), MLR (p < 0.05)], patients who tested positive for CTC also exhibited significant overexpression of Shh/Nrf2 in both blood and tissue compared to CTC-negative patients. A strong association exists between CTCs and tumor grade. Following chemotherapy (a combination of Cisplatin, 5FU, and Paclitaxel), the frequency of CTCs was significantly decreased in patients with HNSCC who had tested positive for CTCs. The Kaplan-Meier plot illustrated that a higher number of CTCs is associated with poorer overall survival (OS) in patients with HNSCC. CONCLUSIONS: Detecting CTCs, and higher expression of Shh and Nrf2 in HNSCC patients' blood, can be a promising tool for diagnosing and prognosticating HNSCC.

Role of circulating tumour cells (CTCs) in recurrent/metastatic head and neck squamous cell carcinoma (HNSCC).

Background: Liquid biopsy is emerging as a non-invasive tool, providing a personalized snapshot of a primary and metastatic tumour. It aids in detecting early metastasis, recurrence or resistance to the disease. We aimed to assess the role of circulating tumour cells (CTCs) as a predictive biomarker in recurrent/metastatic head and neck cancer (head and neck squamous cell carcinoma (HNSCC)). Methodology: Thirty-five patients receiving palliative chemotherapy underwent blood sampling [2 mL in Ethylenediaminetetraacetic acid (EDTA) vial] at baseline and at 3 months intervals. The CTCs were isolated and evaluated using anti-epithelial cell adhesion molecule antibody-based enrichment using the OncoDiscover platform. Results: CTCs isolated from 80% of patients (n = 28) showed the sensitivity of cell detection at the baseline and 3 months intervals. The median CTC count was 1/1.5 mL of blood and the concordance with clinic-radiological outcomes was 51.4%. The median CTC count (1 (range:0-4) to 0 (range:0-1)) declined at 3 months in responders, while the non-responders had an increase in levels (0 (range :0-2) to 1 (range :0-3)). Although CTCs positively correlated with progression-free survival (PFS) and overall survival (OS), the association of CTCs did not show a significant difference with these parameters (PFS: 6 months versus 4 months; hazard ratio: 0.68; 95% confidence interval (CI): 0.29-1.58, p = 0.323; OS: 10 months versus 8 months; hazard ratio: 0.54; 95% (CI):0.18-1.57 p = 0.216) between CTC positive and CTC negative patients at 3 months. Conclusion: This study highlights the utility of CTC as a disease progression-monitoring tool in recurrent HNSCC patients. Our findings suggest the potential clinical utility of CTC and the need for exploration in upfront settings of the disease as well (NCT: CTRL/2020/02/023378).

Circulating tumor cells as a predictor for poor prognostic factors and overall survival in treatment naïve oral squamous cell carcinoma patients.

OBJECTIVE: The aim of this study was to investigate the presence of circulating tumor cells (CTCs) and their correlation with prognostic factors and clinical outcomes in treatment-naive patients with oral squamous cell carcinoma. STUDY DESIGN: CTCs were isolated using OncoDiscover technique from presurgically obtained peripheral blood of 152 patients with treatment naïve oral squamous cell carcinoma. Sensitivity analysis was performed by including 40 healthy controls. CTCs cutoff values for clinicopathologic factors were obtained from receiver operating characteristic curves. Multivariate models determined the significance of CTC as independent variables. Kaplan-Meier analysis differentiated in overall survival between CTC values corresponding to the stage. RESULTS: Sensitivity, specificity, and accuracy of CTC detection were 94.32%, 98%, and 95.17%, respectively. Platform differentiated true positives at >3.5 CTCs (P < .00001). CTCs above 20.5 were suggestive of nodal metastasis (P < .0001) with a linear trend for detecting occult metastasis (P = .061). Early and advanced stages could be differentiated by >13.5 CTCs (P < .0001). Elevated CTCs were significantly associated with extranodal extension (>21.45 CTCs, P = .025), perineural invasion (>19.35 CTCs, P = .049), and depth of invasion (>12.5 CTCs, P = .0038). Median survival was reduced by 19 months when CTCs were >13. CONCLUSIONS: Preoperative CTC levels demonstrated a strong correlation with adverse clinicopathology factors and suggested its role as a sensitive prognostic marker to predict survival outcome and disease progress.

Size and Shape Directed Novel Green Synthesis of Plasmonic Nanoparticles Using Bacterial Metabolites and Their Anticancer Effects.

The growing need for developing new synthesis methods of plasmonic nanoparticles (PNPs) stems from their various applications in nanotechnology. As a result, a variety of protocols have been developed for the synthesis of PNPs of different shapes, sizes, and compositions. Though widely practiced, the chemical synthesis of PNPs demands stringent control over the experimental conditions, often employs environmentally hazardous chemicals for surface stabilization, and is frequently energy-intensive. Additionally, chemically obtained PNPs require subsequent surface engineering steps for various optoelectronic and biomedicine applications to minimize the toxic effects and render them useful for targeted drug delivery, sensing, and imaging. Considering the pressing need to develop environmentally-friendly technology solutions, "greener" methods of nanoparticle synthesis are gaining importance. Here, we report on the biological synthesis of plasmonic nanoparticles using bacterial metabolites. A peptide-based siderophore pyoverdine and a blue-green pigment pyocyanin obtained from a marine strain of Pseudomonas aeruginosa rapidly produced plasmonic nanoparticles of gold and silver in an aqueous environment. The morphology of plasmonic nanoparticles could be modulated by tuning the concentration of these metabolites and the reaction time. The exposure of pyoverdine to chloroauric acid resulted in anisotropic gold nanoparticles. On the other hand, pyocyanin produced a highly monodispersed population of gold nanoparticles and anisotropic silver nanoparticles. Biologically obtained gold and silver nanoparticles retained pyoverdine and pyocyanin on the nanoparticle surface and were stable for an extended period of time. The biologically obtained gold and silver plasmonic nanoparticles displayed potent anticancer activities against metastatic lung cancer cells. Biogenic nanoparticles were rapidly internalized by cancer cells in high quantity to affect the cellular organization, and karyoplasmic ratio, indicating the potential of these nanoparticles for cancer nanomedicine.

Exploration of intrinsic peroxidase-like activity of Acidithiobacillus ferrooxidans spent medium and its application for glutathione detection.

Acidithiobacillus ferrooxidans (At. ferrooxidans) is a bacterium that has the ability to metabolize iron. It converts Fe2+ into Fe3+ during its metabolic cycle. Hence, the At. ferrooxidans spent medium is rich in Fe3+. The presence of Fe3+ contributes to a peroxidase-like activity. Therefore, in this study, an attempt has been made to explore the peroxidase-like activity of the At. ferrooxidans spent medium. It has been observed that the At. ferrooxidans spent medium oxidized 3,3',5,5'-tetramethylbenzidine (TMB) in the presence of hydrogen peroxide (H2O2). The effect of various process parameters on the peroxidase-like activity has been studied. Optimum peroxidase-like activity is achieved using 5 µl of the spent medium, 0.3 mM TMB concentration, 4 mM H2O2 concentration, 4.2 pH, and 40 °C temperature. The peroxidase-like activity of the At. ferrooxidans spent medium has been used to develop a colorimetric assay for detection of glutathione (GSH). GSH inhibits the peroxidase-like activity of the At. ferrooxidans spent medium in a concentration range of 0-1 mM. The limit of detection (LOD) of GSH, obtained using the calibration plot is 0.69 mM. The developed assay is selective toward GSH, as the presence of amino acids, metals, and sugars have shown a negligible effect on the GSH sensing ability.

Chemo-specific designs for the enumeration of circulating tumor cells: advances in liquid biopsy.

Advanced materials and chemo-specific designs at the nano/micrometer-scale have ensured revolutionary progress in next-generation clinically relevant technologies. For example, isolating a rare population of cells, like circulating tumor cells (CTCs) from the blood amongst billions of other blood cells, is one of the most complex scientific challenges in cancer diagnostics. The chemical tunability for achieving this degree of exceptional specificity for extra-cellular biomarker interactions demands the utility of advanced entities and multistep reactions both in solution and in the insoluble state. Thus, this review delineates the chemo-specific substrates, chemical methods, and structure-activity relationships (SARs) of chemical platforms used for isolation and enumeration of CTCs in advancing the relevance of liquid biopsy in cancer diagnostics and disease management. We highlight the synthesis of cell-specific, tumor biomarker-based, chemo-specific substrates utilizing functionalized linkers through chemistry-based conjugation strategies. The capacity of these nano/micro substrates to enhance the cell interaction specificity and efficiency with the targeted tumor cells is detailed. Furthermore, this review accounts for the importance of CTC capture and other downstream processes involving genotypic and phenotypic CTC analysis in real-time for the detection of the early onset of metastases progression and chemotherapy treatment response, and for monitoring progression free-survival (PFS), disease-free survival (DFS), and eventually overall survival (OS) in cancer patients.

Approach to nigericin derivatives and their therapeutic potential.

A new nigericin analogue that has been chemically modified was synthesized through a fluorination process from the parent nigericin, produced from a novel Streptomyces strain DASNCL-29. Fermentation strategies were designed for the optimised production of nigericin molecule and subjected for purification and structural analysis. The fermentation process resulted in the highest yield of nigericin (33% (w/w)). Initially, nigericin produced from the strain DASNCL-29 demonstrated polymorphism in its crystal structure, i.e., monoclinic and orthorhombic crystal lattices when crystallised with methanol and hexane, respectively. Furthermore, nigericin produced has been subjected to chemical modification by fluorination to enhance its efficacy. Two fluorinated analogues revealed that they possess a very potent antibacterial activity against Gram positive and Gram negative bacteria. To date, the nigericin molecule has not been reported for any reaction against Gram-negative bacteria, which are increasingly becoming resistant to antibiotics. For the first time, fluorinated analogues of nigericin have shown promising activity. In vitro cytotoxicity analysis of fluorinated analogues demonstrated tenfold lesser toxicity than the parent nigericin. This is the first type of study where the fluorinated analogues of nigericin showed very encouraging activity against Gram-negative organisms; moreover, they can be used as a candidate for treating many serious infections.

Self-propelled carbon nanotube based microrockets for rapid capture and isolation of circulating tumor cells.

Here, we report a non-invasive strategy for isolating cancer cells by autonomously propelled carbon nanotube (CNT) microrockets. H2O2-driven oxygen (O2) bubble-propelled microrockets were synthesized using CNT and Fe3O4 nanoparticles in the inner surface and covalently conjugating transferrin on the outer surface. Results show that self-propellant microrockets can specifically capture cancer cells.

Magnetic nanoparticles as mediators of ligand-free activation of EGFR signaling.

BACKGROUND: Magnetic nanoparticles (NPs) are of particular interest in biomedical research, and have been exploited for molecular separation, gene/drug delivery, magnetic resonance imaging, and hyperthermic cancer therapy. In the case of cultured cells, magnetic manipulation of NPs provides the means for studying processes induced by mechanotransduction or by local clustering of targeted macromolecules, e.g. cell surface receptors. The latter are normally activated by binding of their natural ligands mediating key signaling pathways such as those associated with the epidermal growth factor (EGFR). However, it has been reported that EGFR may be dimerized and activated even in the absence of ligands. The present study assessed whether receptor clustering induced by physical means alone suffices for activating EGFR in quiescent cells. METHODOLOGY/PRINCIPAL FINDINGS: The EGFR on A431 cells was specifically targeted by superparamagnetic iron oxide NPs (SPIONs) carrying either a ligand-blocking monoclonal anti-EGFR antibody or a streptavidin molecule for targeting a chimeric EGFR incorporating a biotinylated amino-terminal acyl carrier peptide moiety. Application of a magnetic field led to SPION magnetization and clustering, resulting in activation of the EGFR, a process manifested by auto and transphosphorylation and downstream signaling. The magnetically-induced early signaling events were similar to those inherent to the ligand dependent EGFR pathways. Magnetization studies indicated that the NPs exerted magnetic dipolar forces in the sub-piconewton range with clustering dependent on Brownian motion of the receptor-SPION complex and magnetic field strength. CONCLUSIONS/SIGNIFICANCE: We demonstrate that EGFR on the cell surface that have their ligand binding-pocket blocked by an antibody are still capable of transphosphorylation and initiation of signaling cascades if they are clustered by SPIONs either attached locally or targeted to another site of the receptor ectodomain. The results suggest that activation of growth factor receptors may be triggered by ligand-independent molecular crowding resulting from overexpression and/or sequestration in membrane microdomains.

On-chip magnetic separation and encapsulation of cells in droplets.

Single cell study is gaining importance because of the cell-to-cell variation that exists within cell population, even after significant initial sorting. Analysis of such variation at the gene expression level could impact single cell functional genomics, cancer, stem-cell research, and drug screening. The on-chip monitoring of individual cells in an isolated environment would prevent cross-contamination, provide high recovery yield, and enable study of biological traits at a single cell level. These advantages of on-chip biological experiments is a significant improvement for a myriad of cell analyses methods, compared to conventional methods, which require bulk samples and provide only averaged information on cell structure and function. We report on a device that integrates a mobile magnetic trap array with microfluidic technology to provide the possibility of separation of immunomagnetically labeled cells and their encapsulation with reagents into picoliter droplets for single cell analysis. The simultaneous reagent delivery and compartmentalization of the cells immediately following sorting are all performed seamlessly within the same chip. These steps offer unique advantages such as the ability to capture cell traits as originated from its native environment, reduced chance of contamination, minimal use of the reagents, and tunable encapsulation characteristics independent of the input flow. Preliminary assay on cell viability demonstrates the potential for the device to be integrated with other up- or downstream on-chip modules to become a powerful single-cell analysis tool.

Inorganic materials using 'unusual' microorganisms.

A promising avenue of research in materials science is to follow the strategies used by Mother Nature to fabricate ornate hierarchical structures as exemplified by organisms such as diatoms, sponges and magnetotactic bacteria. Some of the strategies used in the biological world to create functional inorganic materials may well have practical implications in the world of nanomaterials. Therefore, the strive towards exploring nature's ingenious work for designing strategies to create inorganic nanomaterials in our laboratories has led to development of biological and biomimetic synthesis routes over the past decade or so. A large proportion of these relentless efforts have explored the use of those microorganisms, which are typically not known to encounter these inorganic materials in their natural environment. Therefore, one can consider these microorganisms as 'unusual' for the purpose for which they have been utilized - it is in this context that this review has been penned down. In this extensive review, we discuss the use of these 'unusual' microorganisms for deliberate biosynthesis of various nanomaterials including biominerals, metals, sulfides and oxides nanoparticles. In addition to biosynthesis approach, we have also discussed a bioleaching approach, which can provide a noble platform for room-temperature synthesis of inorganic nanomaterials using naturally available raw materials. Moreover, the unique properties and functionalities displayed by these biogenic inorganic materials have been discussed, wherever such properties have been investigated previously. Finally, towards the end of this review, we have made efforts to summarize the common outcomes of the biosynthesis process and draw conclusions, which provide a perspective on the current status of the biosynthesis research field and highlights areas where future research in this field should be directed to realize the full potential of biological routes towards nanomaterials synthesis. Furthermore, the review clearly demonstrates that the biological route to inorganic materials synthesis is not merely an addition to the existing list of synthesis routes; biological routes using 'unusual' microorganisms might in fact provide an edge over other nanomaterials synthesis routes in terms of their eco-friendliness, low energy intensiveness, and economically-viable synthesis. This review has significant importance for colloids and interface science since it underpins the synthesis of colloidal materials using 'unusual' microorganism, wherein the role of biological interfaces for controlled synthesis of technologically important nanomaterials is clearly evident.

Bacteria-mediated precursor-dependent biosynthesis of superparamagnetic iron oxide and iron sulfide nanoparticles.

The bacterium Actinobacter sp. has been shown to be capable of extracellularly synthesizing iron based magnetic nanoparticles, namely maghemite (gamma-Fe2O3) and greigite (Fe3S4) under ambient conditions depending on the nature of precursors used. More precisely, the bacterium synthesized maghemite when reacted with ferric chloride and iron sulfide when exposed to the aqueous solution of ferric chloride-ferrous sulfate. Challenging the bacterium with different metal ions resulted in induction of different proteins, which bring about the specific biochemical transformations in each case leading to the observed products. Maghemite and iron sulfide nanoparticles show superparamagnetic characteristics as expected. Compared to the earlier reports of magnetite and greigite synthesis by magnetotactic bacteria and iron reducing bacteria, which take place strictly under anaerobic conditions, the present procedure offers significant advancement since the reaction occurs under aerobic condition. Moreover, reaction end products can be tuned by the choice of precursors used.

Bacterial enzyme mediated biosynthesis of gold nanoparticles.

Development of synthesis methods for anisotropic metal nanoparticles is of considerable interest due to their remarkable optoelectronic properties. Various shapes ranging from rods to cubes to tetrapods and prisms may be obtained by chemical methods. Here we show that anisotropic gold nanoparticles can be synthesized biologically by the bacterium Actinobacter spp. when challenged with gold chloride in the presence of Bovine serum albumin (BSA). We also observed that synthesis of gold nanoparticles occur with simultaneous induction of the protease enzyme secreted by the bacterium in the presence of BSA. The presence of BSA helps to enhance the rate of gold nanoparticles biosynthesis and may also impart some shape control. Controlling simple experimental conditions like incubation temperature and presence or absence of oxygen have drastic effect on the reaction rate and the morphology of the particles. Various assay experiments show that the presence of enzyme protease can act as a reducing as well as shape directing agent.

Extracellular biosynthesis of magnetite using fungi.

The development of synthetic processes for oxide nanomaterials is an issue of considerable topical interest. While a number of chemical methods are available and are extensively used, the collaborations are often energy intensive and employ toxic chemicals. On the other hand, the synthesis of inorganic materials by biological systems is characterized by processes that occur at close to ambient temperatures and pressures, and at neutral pH (examples include magnetotactic bacteria, diatoms, and S-layer bacteria). Here we show that nanoparticulate magnetite may be produced at room temperature extracellularly by challenging the fungi, Fusarium oxysporum and Verticillium sp., with mixtures of ferric and ferrous salts. Extracellular hydrolysis of the anionic iron complexes by cationic proteins secreted by the fungi results in the room-temperature synthesis of crystalline magnetite particles that exhibit a signature of a ferrimagnetic transition with a negligible amount of spontaneous magnetization at low temperature.

Bacterial aerobic synthesis of nanocrystalline magnetite.

The synthesis of iron oxide nanoparticles of the predominantly magnetite phase by the reaction of aqueous iron complexes with the bacterium, Actinobacter spp., is described. This reaction occurs at room temperature and under aerobic conditions, resulting in the formation of superparamagnetic magnetite.