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NeoProteomics Sets Sights on Biomarker Identification with Network Biology Software Suite

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By Uduak Grace Thomas

Informatics startup NeoProteomics is hoping to make its mark in the biomarker-identification and -validation markets with a suite of network biology software tools it has licensed from Case Western Reserve University.

The Cleveland-based company, which spun off from Case Western's School of Medicine in 2006, disclosed the 20-year licensing agreement last month. Under the terms of the deal, Case Western receives a 15-percent share in the company and an undisclosed royalty for each software sale (BI 09/02/2011).

Mark Chance, director of the Case Center for Proteomics and Bioinformatics and the company's chief scientific officer and co-founder, told BioInform that the licensing arrangement covers four network analysis packages, three of which the company has begun selling

These include the Subnetwork Analysis and Scoring System, or SASSy, which ranks sub-networks of interacting proteins based on corresponding gene expression data; Crosstalker, which searches protein-protein interaction networks for sub-networks with a functional role in disease; and Combinatorially Dysregulated Subnetworks, or CRANE, which searches protein interaction networks for sub-networks and expression states informative of phenotype.

The agreement with Case Western also covers a fourth tool dubbed DiseaseNet Finder that is used to predict potential protein-interaction networks. The company currently offers this software as a service but plans to release it in a web-based format in mid- to late-2012, Chance said.

The new agreements build on a previous license that NeoProteomics signed with Case Western for two mass spectrometry data-analysis tools — ProtModMS and ProtMapMS — that are used to analyze the structure of biologic drugs.

The company expects the network biology tools to be of particular interest to customers looking to discover and validate disease markers, and has already begun several partnerships in this area.

In one project, NeoProteomics is working with a Midwest-based, medium-sized, undisclosed pharma company to discover and verify biomarkers of bone growth, Chance told BioInform.

The company uses animal models to test products that are suspected to promote bone growth. NeoProteomics is analyzing the data to look for protein and gene expression changes that are stimulated by these products. The company is also trying to identify which networks the drugs are interacting with in order to cause these changes, Chance said.

A Growing Portfolio

NeoProteomics has also been awarded a two-year, $300,000 small business innovation research grant from the National Center for Research Resources that Chance said it will use to enhance the capabilities of its SASSy and Crosstalker products.

He explained that both tools emerged out of a research pipeline at Case Western that had to deal with separate silos for proteomics data, gene-expression data, and SNP data.

"The silos were filling up, but they really weren’t talking to each other," Chance said. "These software tools enabled you to analyze the data in a common framework of protein-protein interactions."

He explained that the grant is intended to develop these tools, which are currently suited for expert bioinformaticians, into software packages that academic scientists without technical skills can wrap their arms around.

Specifically, the grant will be used to convert "tools that might be written in Matlab or Perl script ... into Java," which is able to "run on any machine." Additionally, the funds will be used to develop "client-installable versions as well as web-based subscription versions of [the] software," Chance said.

The funding will also support further development of DiseaseNet Finder, which was developed to predict possible protein interactions that users can test in their laboratories.

This tool addresses issues of "low coverage" in protein-interaction databases, Chance explained, where the number of recorded interactions is "relatively low" compared to the number of interactions that actually occur in nature.

DiseaseNet Finder "takes various kinds of data from yeast or fly or other model organisms, looks at their network structure, and says, 'Well, here is a piece that might be missing in mouse or human, let me give that to you as the user and you can use it as a hypothesis to test,'" Chance explained.

The network biology suite expands the company's offerings beyond its legacy mass spec-analysis business. The ProdModMS and ProtMapMS products are targeted at pharma companies and academic institutions looking to analyze the three-dimensional structures of biologic drugs such as monoclonal antibodies, Chance said.

The software packages provide capabilities for quality-control assessment of primary structure modifications and higher-order structure analyses using oxidative labeling. They also include tools for data format conversion, detection and verification of peptide species, and confirmation of sites of peptide modification.

Market Performance

Both the network biology and mass-spec products are "performing well" in the market, Chance said, noting that the mass spec-analysis business is slightly ahead because NeoProteomics began marketing those tools earlier than the other products.

In the network biology informatics market, NeoProteomics has to contend with tools such as Ingenuity Pathway Analysis and GeneGo's MetaCore, but Chance said his company occupies a different niche because it is more focused on the analytics as opposed to developing content.

Ingenuity and GeneGo have invested in very "broad and deep database[s] of network interactions ... [as well as] creating content that’s very high quality," he said. "We are seeing ... challenges in further analyzing and integrating [that content] ... that's our opportunity."

NeoProteomics also hopes to "make it easier for customers to access public databases of network information, which are also out there and compete with IPA and MetaCore," he said. These include the Human Protein Reference Database, the IntAct molecular interaction database, and Reactome.

The company offers perpetual licenses for its software products as well as a web-based service for an undisclosed yearly subscription fee.

Prices for informatics services are based on the nature of the project, Chance said, adding that this option is for customers who aren’t looking to install the products themselves but need data analyzed for a drug development pipeline or biomarker study, for example.

NeoProteomics currently has two full-time employees and five consultants and plans to increase its headcount by hiring two additional staff members this year.


Have topics you'd like to see covered in BioInform? Contact the editor at uthomas [at] genomeweb [.] com.

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