Proteome-wide biomarker quantification and target screening.

e15205 Background: Existing drug development programs are represented by only a few hundred protein targets. A large subset of the ~20,000 proteins encoded by the human genome remain undiscovered. Proteome-wide “druggability” screening may lead to new targets for therapeutics. Methods: The NanoMosaic platform is a digital immunoassay technology that achieves sub-pg/ml level sensitivity, whole-proteome level multiplexing capability, and 7 logs of dynamic range. The platform overcomes the sensitivity and dynamic range limitations of traditional protein arrays and mass spectrometry. Results: The NanoMosaic technology is powered by silicon nanoneedle biosensors that are densely integrated on a plate and manufactured with CMOS-compatible nanofabrication processes. Each nanoneedle is a label-free biosensor, functionalized with capture antibodies. Its scattering spectrum changes when an antigen binds to its surface. Each analyte specific sensing area consists a total of ~23k nanoneedles divided into a digital region (~20k nanoneedles) and an analog region (~3k nanoneedles). The digital nanoneedles provide the single molecule sensitivity. Therefore, at ultra-low concentration when antigens that are captured by the nanoneedles follow Poisson statistics, the number of antigens can be quantitated by counting the presence or absence of color changes of individual nanoneedles in a binary fashion. As the protein concentrations increase, the binding event counts increase accordingly and achieve saturation when all nanoneedles capture more than one protein. Above the digital saturation concentration, an adjacent section of analog nanoneedles perform quantitative analysis based on the level of color change, thus providing a wider dynamic range up to 1ug/ml. Ultrahigh level multiplex can be achieved by parallelizing the detection in a microarray format without loss of the sensitivity and dynamic range. A 20,000-plex proteome-wide study can be achieved with a total of 5 billion nanoneedles on a ~70mm by 70mm chip. Conclusions: In conclusion, proteome-wide biomarker quantification and target discovery can be performed on the NanoMosaic platform at higher sensitivity, wider dynamic range, lower cost and higher throughput than is currently possible by mass spectrometry or traditional immunoassays.

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MosaicNeedles: A tool for multi-omic liquid biopsy sensitivity and specificity enhancement.

Journal of Clinical Oncology ◽

10.1200/jco.2021.39.15_suppl.e15019 ◽

2021 ◽

Vol 39 (15_suppl) ◽

pp. e15019-e15019

Author(s):

Qimin Quan ◽

Joe Wilkinson ◽

Joshua Ritchey ◽

Alaina Kaiser ◽

John Geanacopoulos ◽

...

Keyword(s):

Mass Spectrometry ◽

Single Molecule ◽

Liquid Biopsy ◽

Dynamic Range ◽

Color Change ◽

Protein Detection ◽

Target Sequence ◽

Label Free ◽

Protein Biomarkers ◽

Oncology Research

e15019 Background: Liquid biopsy has evolved to be an important method complementary to tissue biopsy. It is not only non-invasive, but also has the potential to detect cancer in its earliest stages and monitor patients in remission. The integration of proteomics into liquid biopsy may transform the molecular diagnostics of cancer and accelerate basic and clinical oncology research. A recent study showed that adding just 8 protein biomarkers to a panel of circulating DNA biomarkers increased the diagnostic accuracy up to 98% sensitivity and 99% specificity. Proteomics also bridges the gaps of functional information lost due to post-transcriptional and post-translational modifications in the genomic approach. However, the proteogenomic approach normally requires the use of multiple different assay technologies and laboratory workflows, including mass spectrometry. Methods: NanoMosaic’s Tessie platform employs a densely integrated nanoneedle sensor array (thus named MosaicNeedles) which can be used to detect both nucleic acids and proteins in a single assay process with reduced workflow complexity, without the need for mass spectrometry. Results: The NanoMosaic platform is a label-free, digital, single molecule counting technology using nanoneedles. It achieves sub-pg/ml (̃fM) level sensitivity with 7 logs of dynamic range. An array of nanoneedles is densely integrated and manufactured with CMOS-compatible nanofabrication processes. Each nanoneedle is a single molecule biosensor that is functionalized with capture probes. The capture probe can be either an antibody for protein detection or an oligonucleotide with a specific target sequence to a DNA fragment, mRNA, or miRNA of interest. The scattering spectrum of each nanoneedle changes when an analyte binds to its surface. At low abundance, analytes that are captured can be quantitated by counting the presence or absence of a color change on each individual nanoneedle in a binary fashion. As an analyte concentration increases the binding events increase accordingly and achieve saturation. In this range, an analog analysis on the spectrum shift will be performed, thus providing a wider dynamic range, up to 7 logs. Ultrahigh level multiplex can be achieved by parallelizing each analyte specific sensing area without loss of sensitivity or dynamic range. A 10,000-plex study can be achieved with a total of 2.5 billion nanoneedles on a 50mm by 50mm consumable. In this consumable, a 2,000-plex proteome and 8,000 cell-free DNA fragments can be detected. Conclusions: In conclusion, a full proteogenomic quantification can be performed on the NanoMosaic platform in one reaction, with higher sensitivity, lower cost and higher throughput than is currently possible by traditional methods. In addition, the high-plexibility of the NanoMosaic platform allows the discovery of new biomarkers across the whole proteome without the need for mass spectrometry.

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Monitoring of inflammatory response to cancer immunotherapies.

Journal of Clinical Oncology ◽

10.1200/jco.2020.38.15_suppl.e15199 ◽

2020 ◽

Vol 38 (15_suppl) ◽

pp. e15199-e15199 ◽

Cited By ~ 1

Author(s):

Qimin Quan ◽

John Geanacopoulos ◽

Joshua Ritchey ◽

Mark Clenow ◽

Joe Wilkinson ◽

...

Keyword(s):

Inflammatory Response ◽

Single Molecule ◽

Dynamic Range ◽

Color Change ◽

High Sensitivity ◽

Test Methods ◽

Label Free ◽

Cell Therapies ◽

Color Changes ◽

Cmos Compatible

e15199 Background: Inflammation observed in response to some monoclonal antibody drugs and adaptive T-Cell therapies has become a major issue in cancer immunotherapy. Prognostic monitoring of the inflammatory response requires simultaneous measurement of multiple cytokines at widely divergent concentrations. At present, no analytical method, known to us, can provide large dynamic range (> 6 logs), high sensitivity (< 1pg/ml) and high multiplex in a single test. Methods: The NanoMosaic platform is a cytokine quantification technology powered by silicon nanoneedle biosensors that are densely integrated on a plate and manufactured with CMOS-compatible nanofabrication processes. Each nanoneedle is a label-free biosensor, functionalized with capture antibodies. Each analyte specific sensing area consists a total of ~23k nanoneedles divided into a digital region (~20k nanoneedles) and an analog region (~3k nanoneedles), combined to cover the entire range of inflammatory biomarkers from 0.1pg/ml to 1ug/ml. Results: We demonstrated that the digital nanoneedles achieve the single molecule sensitivity. Therefore, at ultra-low concentrations when antigens that are captured by the nanoneedles follow Poisson statistics, the number of antigens can be quantitated by counting the presence or absence of color changes of individual nanoneedles in a binary fashion. As the protein concentrations increase, the binding events increase accordingly and achieve saturation when all nanoneedles capture more than one protein. Above the digital saturation concentration, an adjacent section of analog nanoneedles perform quantitative analysis based on the level of color change, thus providing a wider dynamic range up to 1ug/ml. Each single analyte area, including both digital and analog sensors, is less than 500um. Therefore, high level multiplex can be achieved by duplicating the detection sensor in a microarray format without loss of sensitivity and dynamic range. Conclusions: The CMOS-compatible NanoMosaic technology provides the cost-effectiveness, sensitivity, dynamic range and multiplexing capacity required to fully integrate patient immune response into therapeutic development and decision making.

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Multitarget, quantitative nanoplasmonic electrical field-enhanced resonating device (NE2RD) for diagnostics

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1510824112 ◽

2015 ◽

Vol 112 (32) ◽

pp. E4354-E4363 ◽

Cited By ~ 44

Author(s):

Fatih Inci ◽

Chiara Filippini ◽

Murat Baday ◽

Mehmet Ozgun Ozen ◽

Semih Calamak ◽

...

Keyword(s):

Dynamic Range ◽

Point Of Care ◽

Medical Diagnostics ◽

Clinical Samples ◽

Label Free ◽

Protein Biomarkers ◽

Electrical Field ◽

Color Changes ◽

Sensing Platform ◽

Broad Dynamic Range

Recent advances in biosensing technologies present great potential for medical diagnostics, thus improving clinical decisions. However, creating a label-free general sensing platform capable of detecting multiple biotargets in various clinical specimens over a wide dynamic range, without lengthy sample-processing steps, remains a considerable challenge. In practice, these barriers prevent broad applications in clinics and at patients’ homes. Here, we demonstrate the nanoplasmonic electrical field-enhanced resonating device (NE2RD), which addresses all these impediments on a single platform. The NE2RD employs an immunodetection assay to capture biotargets, and precisely measures spectral color changes by their wavelength and extinction intensity shifts in nanoparticles without prior sample labeling or preprocessing. We present through multiple examples, a label-free, quantitative, portable, multitarget platform by rapidly detecting various protein biomarkers, drugs, protein allergens, bacteria, eukaryotic cells, and distinct viruses. The linear dynamic range of NE2RD is five orders of magnitude broader than ELISA, with a sensitivity down to 400 fg/mL This range and sensitivity are achieved by self-assembling gold nanoparticles to generate hot spots on a 3D-oriented substrate for ultrasensitive measurements. We demonstrate that this precise platform handles multiple clinical samples such as whole blood, serum, and saliva without sample preprocessing under diverse conditions of temperature, pH, and ionic strength. The NE2RD’s broad dynamic range, detection limit, and portability integrated with a disposable fluidic chip have broad applications, potentially enabling the transition toward precision medicine at the point-of-care or primary care settings and at patients’ homes.

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Adaptive nanopores: A bioinspired label-free approach for protein sequencing and identification

Nano Research ◽

10.1007/s12274-020-3095-z ◽

2020 ◽

Vol 14 (1) ◽

pp. 328-333 ◽

Cited By ~ 2

Author(s):

Andrea Spitaleri ◽

Denis Garoli ◽

Moritz Schütte ◽

Hans Lehrach ◽

Walter Rocchia ◽

...

Keyword(s):

Amino Acids ◽

Single Molecule ◽

Dynamic Range ◽

Protein Sequencing ◽

High Fidelity ◽

Label Free ◽

Therapeutic Approaches ◽

Highly Sensitive ◽

Dynamics Simulations ◽

Structure Of Proteins

AbstractSingle molecule protein sequencing would tremendously impact in proteomics and human biology and it would promote the development of novel diagnostic and therapeutic approaches. However, its technological realization can only be envisioned, and huge challenges need to be overcome. Major difficulties are inherent to the structure of proteins, which are composed by several different amino-acids. Despite long standing efforts, only few complex techniques, such as Edman degradation, liquid chromatography and mass spectroscopy, make protein sequencing possible. Unfortunately, these techniques present significant limitations in terms of amount of sample required and dynamic range of measurement. It is known that proteins can distinguish closely similar molecules. Moreover, several proteins can work as biological nanopores in order to perform single molecule detection and sequencing. Unfortunately, while DNA sequencing by means of nanopores is demonstrated, very few examples of nanopores able to perform reliable protein-sequencing have been reported so far. Here, we investigate, by means of molecular dynamics simulations, how a re-engineered protein, acting as biological nanopore, can be used to recognize the sequence of a translocating peptide by sensing the “shape” of individual amino-acids. In our simulations we demonstrate that it is possible to discriminate with high fidelity, 9 different amino-acids in a short peptide translocating through the engineered construct. The method, here shown for fluorescence-based sequencing, does not require any labelling of the peptidic analyte. These results can pave the way for a new and highly sensitive method of sequencing.

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High-Throughput Mass Spectrometry for Hit Identification: Current Landscape and Future Perspectives

SLAS DISCOVERY Advancing Life Sciences ◽

10.1177/2472555220980696 ◽

2021 ◽

Vol 26 (2) ◽

pp. 168-191

Author(s):

David G. McLaren ◽

Vinit Shah ◽

Thomas Wisniewski ◽

Lucien Ghislain ◽

Chang Liu ◽

...

Keyword(s):

Mass Spectrometry ◽

High Throughput ◽

High Throughput Screening ◽

Dynamic Range ◽

Direct Detection ◽

Label Free ◽

Physiological Relevance ◽

Wide Range ◽

And Performance ◽

Sensitivity Specificity

For nearly two decades mass spectrometry has been used as a label-free, direct-detection method for both functional and affinity-based screening of a wide range of therapeutically relevant target classes. Here, we present an overview of several established and emerging mass spectrometry platforms and summarize the unique strengths and performance characteristics of each as they apply to high-throughput screening. Multiple examples from the recent literature are highlighted in order to illustrate the power of each individual technique, with special emphasis given to cases where the use of mass spectrometry was found to be differentiating when compared with other detection formats. Indeed, as many of these examples will demonstrate, the inherent strengths of mass spectrometry—sensitivity, specificity, wide dynamic range, and amenability to complex matrices—can be leveraged to enhance the discriminating power and physiological relevance of assays included in screening cascades. It is our hope that this review will serve as a useful guide to readers of all backgrounds and experience levels on the applicability and benefits of mass spectrometry in the search for hits, leads, and, ultimately, drugs.

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Label-free, mass-sensitive single-molecule imaging using interferometric scattering microscopy

Essays in Biochemistry ◽

10.1042/ebc20200023 ◽

2020 ◽

Author(s):

Nikolas Hundt

Keyword(s):

Single Molecule ◽

Cellular Systems ◽

Single Molecule Imaging ◽

Label Free ◽

Measurement Sensitivity ◽

Mass Distributions ◽

Quantitative Measurements ◽

Contrast Mechanism ◽

Cellular Components ◽

Scattering Signal

Abstract Single-molecule imaging has mostly been restricted to the use of fluorescence labelling as a contrast mechanism due to its superior ability to visualise molecules of interest on top of an overwhelming background of other molecules. Recently, interferometric scattering (iSCAT) microscopy has demonstrated the detection and imaging of single biomolecules based on light scattering without the need for fluorescent labels. Significant improvements in measurement sensitivity combined with a dependence of scattering signal on object size have led to the development of mass photometry, a technique that measures the mass of individual molecules and thereby determines mass distributions of biomolecule samples in solution. The experimental simplicity of mass photometry makes it a powerful tool to analyse biomolecular equilibria quantitatively with low sample consumption within minutes. When used for label-free imaging of reconstituted or cellular systems, the strict size-dependence of the iSCAT signal enables quantitative measurements of processes at size scales reaching from single-molecule observations during complex assembly up to mesoscopic dynamics of cellular components and extracellular protrusions. In this review, I would like to introduce the principles of this emerging imaging technology and discuss examples that show how mass-sensitive iSCAT can be used as a strong complement to other routine techniques in biochemistry.

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Single Particle Inductively Coupled Plasma Mass Spectrometry: Investigating Nonlinear Response Observed in Pulse Counting Mode and Extending the Linear Dynamic Range by Compensating for Dead Time Related Count Losses on a Microsecond Timescale

10.26434/chemrxiv.9911627 ◽

2019 ◽

Author(s):

Ingo Strenge ◽

Carsten Engelhard

Keyword(s):

Mass Spectrometry ◽

Inductively Coupled Plasma ◽

Nonlinear Response ◽

Dynamic Range ◽

Dead Time ◽

Inorganic Nanoparticles ◽

Linear Dynamic Range ◽

Inductively Coupled ◽

Icp Ms ◽

Plasma Mass Spectrometry

<p>The article demonstrates the importance of using a suitable approach to compensate for dead time relate count losses (a certain measurement artefact) whenever short, but potentially strong transient signals are to be analysed using inductively coupled plasma mass spectrometry (ICP-MS). Findings strongly support the theory that inadequate time resolution, and therefore insufficient compensation for these count losses, is one of the main reasons for size underestimation observed when analysing inorganic nanoparticles using ICP-MS, a topic still controversially discussed.</p>

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