Akoya Biosciences: Combining CODEX with Highly Multiplexed Assays
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Akoya Biosciences: Combining CODEX with Highly Multiplexed Assays

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Brian McKelligon, CEO, Akoya BiosciencesBrian McKelligon, CEO
Understanding and characterizing the complexities of the tumor microenvironment is a critical element in studying the molecular and cellular mechanisms that drive diseases and their therapeutic responses. When it comes to defining tumor heterogeneity, the role of spatial relationships between infiltrating immune cells and the remodeling of the cellular matrix is vital. Through its revolutionary CODEX Technology, a company called Akoya Biosciences is providing a comprehensive solution for spatially resolved, highly multiplexed biomarker analysis. Along with its wide array of image analysis software to chose from, the CODEX technology changing the game of processing highly multiplexed assays for bio-technicians. Akoya Biosciences, together with their strategic partners, is leading the emerging field of tissue biomarker analysis.

The CODEX (Co-detection by Indexing) technology uses an antibody comprising a unique oligonucleotide sequence, which is a part of Akoya Barcodes. The CODEX assay targets specific reporters enabling an unlimited level of flexibility in the generation of highly multiplexed panels while maintaining the tissue integrity and ensuring high-quality data. Akoya’s CODEX system is a fluidics control instrument that integrates with existing fluorescent microscopes for the synchronization of the CODEX assay and image collection. CODEX system converts a traditional fluorescent microscope into an automated, high-dimensional imaging system capable of providing in-depth analysis at a cellular and sub-cellular level. To assist with the aforementioned procedure, Akoya has developed a suite of analysis tools that enable researchers in shifting from multiplexed fluorescent images to spatially resolved cellular structure and cell phenotypes.

Akoya combines the latest technologies, algorithms, and its intuitive, easy-to-use interfaces, allowing technicians to visualize, analyze, and quantify phenotype cells labeled with multiple biomarkers.

Akoya is excited to bring unprecedented power, scale, and automation to histology through the power of multiplex immunofluorescence


Akoya’s inForm Tissue Finder is a patented image analysis software package facilitating comparative studies of multiple markers and specimens, for quick diagnoses of diseases. Its powerful separation engine eliminates weak and overlapping markers in multiplex assays. The inForm Tissue Finder is fully automated, and its algorithms are trainable. Phenoptr is another product which uses data tables and imagery exported from inForm to analyze and report on the spatial relationship between cells such as the nearest phenotype, phenotypic density across a boundary, cells count within a radius, and also to identify touching cells. The HALO Image analysis software is a collaborative project of PerkinElmer and Indica Labs that helps in extending the image analysis over the entire tissue. HALO enables fast quantification in brightfield, fluorescent whole-side imagery and multi-spectral fields of view, ideal for use in immune-oncology, neuroscience, and many other research areas.

Some of the other products to throw light upon are the CODEX Assay, wherein the antibody panel is run through iterative cycles. This is unlike the traditional immunofluorescence assay procedure. CODEX Assay uses the unique CODEX-based molecular barcodes and 50 customizable panels for a single-tissue straining. It provides customizable panel designs consisting of CODEX antibodies with barcodes. In order to enable the wide range of research areas and tissue-specific biomarkers, Akoya has developed the CODEX Conjugation Kit and individual CODEX Barcodes to prepare clones from third-party antibody suppliers.

“Akoya is excited to bring unprecedented power, scale, and automation to histology through the power of multiplex immunofluorescence,” says Brian McKelligon, the CEO of Akoya Biosciences. Founded in 2015 to commercialize the CODEX system, the company has reserved a spot for itself in the market for its ability to enable high-multiplexing for biomarker discovery. At this moment, Akoya’s portfolio spans the entire spectrum from powerful tools for the discovery of biomarkers that are essential to clinical research applications.

Akoya Biosciences News

Akoya Biosciences Appoints Joseph Driscoll as Chief Financial Officer

MENLO PARK, Calif: Akoya Biosciences, Inc., announced the appointment of Joseph Driscoll as Chief Financial Officer. Mr. Driscoll joins Akoya with more than 30 years of financial leadership experience and a proven track record of driving growth and increasing company valuations.

"I am delighted to welcome Joe to the Akoya team and look forward to working with him," said Brian McKelligon, Chief Executive Officer of Akoya. "Joe's strategic, finance, and business operations skill set will be a great asset as we continue building on our mission to revolutionize the tissue biomarker field."

Mr. Driscoll is a seasoned financial and strategic leader with extensive experience in several industries including technology, life sciences, and consumer products. He most recently served as CFO at Quanterix Corporation (NASDAQ:QTRX), where during his tenure the company successfully completed an IPO, and the valuation increased from approximately $200 million to over $500 million in two years. He also served as CFO at several other public and private companies, including Verscend, Inc. (healthcare data analytics), PC Connection, Inc. (technology service provider; NASDAQ:CNXN), Summer Infant, Inc., ACT Electronics, Inc., and Safety 1st, Inc. In addition, Mr. Driscoll held senior management positions at Staples, Inc., and he started his career as an Audit Manager of KPMG Peat Marwick. Mr. Driscoll is a Certified Public Accountant and holds a B.S. in Accounting from Boston College.

"With their comprehensive solutions for high-parameter tissue analysis, Akoya has the opportunity to drive significant advances in biomedical research and I am excited to be joining the company," said Mr. Driscoll. "Akoya's recent accomplishments and successes are impressive, and I'm looking forward to joining the rest of the experienced management team to drive the company's continued growth."

Akoya recently announced the commercial release of two new products, the CODEX platform and Phenoptics 2.0, that together form the most complete solution for high-parameter tissue imaging.

Akoya Biosciences Acquires Phenoptics Portfolio from PerkinElmer

MENLO PARK, Calif: Akoya Biosciences (Akoya), a Telegraph Hill Partners (THP) company, has acquired PerkinElmer, Inc.’s Phenoptics™ portfolio. Akoya was founded in 2015 to commercialize the CODEX® multiparameter tissue analysis technology developed in the lab of Dr. Garry Nolan at Stanford University. PerkinElmer has grown its Phenoptics business, to be an industry leader in multiplex immunofluorescence. This acquisition establishes Akoya as a leading provider of quantitative tissue biomarker evaluation, from discovery through translational and clinical research.

“With both the Phenoptics portfolio and CODEX, Akoya will provide our customers with a full suite of end-to-end solutions for high parameter tissue analysis,” said Brian McKelligon, CEO of Akoya.

High-parameter analysis of biological tissue samples provides critical spatial context in studies of autoimmune disease, immune-oncology and many other research areas. The Phenoptics portfolio, with its Mantra®, Vectra® and Vectra Polaris® systems, provides the throughput and standardization required to support large-scale translational studies. Its multispectral imaging instruments, reagents, software and research services have been adopted by hundreds of labs globally. CODEX enables biomarker discovery with detection of up to 50 markers on a single tissue section with reagents and instrumentation that integrate with our customer’s existing microscopes. CODEX includes optimized assay reagents combined with validated antibodies labeled with proprietary CODEX Barcodes to enable a simple, automated workflow.

Concurrent with the acquisition, PerkinElmer’s Phenoptics team’s management, R&D, sales and support staff have joined Akoya. Akoya will continue to operate this team out of the greater Boston area and maintain headquarters in Menlo Park, CA. Brian McKelligon will remain as Chief Executive Officer of Akoya and Terry Lo, General Manager of the Phenoptics team at PerkinElmer, will join Akoya as President.

“With both the Phenoptics portfolio and CODEX, Akoya will provide our customers with a full suite of end-to-end solutions for high parameter tissue analysis,” said Brian McKelligon, CEO of Akoya. “We now have the team and technologies to develop and deliver transformational solutions in the rapidly advancing field of tissue imaging.”

“The PerkinElmer Phenoptics team created a powerful solution already deployed at leading academic and biopharmaceutical companies with a focus on immuno-oncology,” said Terry Lo, President of Akoya. “We are excited to now join Akoya and catalyze further development of the Phenoptics platform as a leading technology for tissue analysis.”

Telegraph Hill Partners has provided Akoya with additional funding to support further growth of the organization and continue technology and product development. “By having one company with the capabilities of Phenoptics and CODEX, both PerkinElmer and THP saw the opportunity to establish the most advanced and complete solution for multiplexed tissue analysis,” said Robert Shepler, Managing Director of THP. “PerkinElmer was excellent throughout the process, and we look forward to further collaborations with them.”

Akoya Biosciences and VIB Partner to Explore Multiplexed Spatial Analysis of Single Cells Using the CODEX™ Technology Platform

MENLO PARK, Calif: Akoya Biosciences, a private biotech start-up, announced that VIB, a leading life sciences institute in Belgium, will be one of its first partners for exploring the CODEX™ (CO-Detection by indexing) technology in Europe.

The CODEX™ technology originates from Dr. Garry Nolan's lab at Stanford University and is the only technology available to provide spatial and quantitative analysis of up to 50 biomarkers of individual cells in complex tissues. This technology will accelerate VIB's ongoing effort in single cell immunology, neurology and oncology research by unraveling the spatial interactions of single cells for the very first time using a multiplex imaging tool.

Characterizing the interaction of single cells and their corresponding microenvironments is of major interest to VIB and is also one of the key goals of the newly established Single Cell Accelerator (SCA) program at the institute. This program aims to expand VIB's expertise in single cell research by optimizing, validating and developing novel and recently commercialized platforms within VIB's Technology Innovation Lab. The CODEX™ is the first imaging platform to enter the SCA and Brian McKelligon, CEO of Akoya Biosciences, further complements, "VIB is one of the leading research institutes in single cell research, and as such, we are thrilled and honored to partner with them in their SCA program by bringing the CODEX™ Technology to Europe."

The CODEX™ platform transforms traditional fluorescent microscopes into powerful high-dimensional tissue imaging stations that can analyze the tissue architecture and heterogeneity through multiplex staining. Dr. Saskia Lippens, Manager at the VIB Bioimaging Core confirms, "This platform is clearly the next step and the long-sought missing link in single cell research and imaging." Prof. Martin Guilliams, group leader at VIB – UGent Center for Inflammation Research and member of the Human Cell Atlas Initiative agrees and further adds, "There is no 'atlas' without a map, thus the ability to accurately map distinct subsets of single cells in tissues such as the liver will certainly drive the Human Cell Atlas forward!" The possibility to detect up to 50 protein markers in a single tissue section opens new research avenues. Prof. Diether Lambrechts, group leader and director of VIB – KU Leuven Center for Cancer Biology expects that this platform will continue to advance single cell research in cancer biology and adds, "The complexity of the tumor microenvironment has so far been underrepresented due to the lack of adequate research tools, with the help of the CODEX™ platform we aim to further dissect and unravel the role of the microenvironment in tumor progression and development." Prof. Adrian Liston, group leader at VIB – KU Leuven Center for Brain & Disease research, enthusiastically agrees: "The CODEX™ is a unique multiplex imaging platform and we expect this technology to bolster our understanding in immune diseases at a level never achieved before."

The collaboration between VIB and Akoya Biosciences began last year when Dr. Wai Long Tam, who is part of the Technology Innovation Lab at the institute, visited the company in Menlo Park for on-site training. He notes that "The integration and rollout of this platform have been a great success; multiple groups are now plugging in and can't wait to integrate this technology in their research pipelines." Dr. Halina Novak, Technology and Innovation Manager at VIB, confirms and feels privileged to have the CODEX™ installed at the institute. She comments, "Despite the physical distance between VIB and Akoya Biosciences, the interaction and support has so far been exceptional, and I am looking forward to expand this collaboration. We expect the CODEX™ platform to bring novel insights into both normal biological or diseases processes, with the aim to ultimately decipher novel biological questions."