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H3 Biomedicine's CEO Says Bioinformatics Plays 'Big Role' in Oncology Drug Discovery Efforts

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This article has been updated to clarify the tools being co-developed by H3 Biomedicine and Sage Bionetworks

Using a combination of publicly available cancer genomic data and internally developed computational pipelines, H3 Biomedicine is seeking to build an oncology drug discovery business based on identifying cancer mechanisms and pathways.

The Cambridge Mass.-based firm was launched two years ago by Japanese drug firm Eisai to help develop oncology drugs based on genetic information from public resources such as the Cancer Genome Atlas. Eisai is investing up to $200 million in the company and is so far its sole customer, though H3 plans to forge risk-sharing partnerships with other pharmaceutical firms to explore potential targeted treatments.

CEO Markus Warmuth told BioInform that bioinformatics plays a "big role" in the company's efforts to look through publicly available sequencing data to identify potential drug targets and biomarkers. It also hopes that its approach will help shorten the time required to develop drugs for clinical use since it begins with an analysis of human cancer data rather than data from animal and yeast models, he said.

He said that the company has hired roughly a dozen employees with experience in bioinformatics and computational science to help it build analysis pipelines and make use of cloud computing infrastructure.

H3 Biomedicine is using a mix of internally and externally developed bioinformatics resources. For example, it relies on databases and software developed by Compendia, which is now owned by Life Technologies (BI 10/12/2012). These include the Oncomine Concepts and Oncomine Power tools that together help users validate biomarker and gene target discoveries, better understand mechanisms of disease, and optimize clinical outcomes. H3 also uses a curated database of RNA-, exome-, and whole genome – sequencing data from public repositories such as TCGA and the International Cancer Genome Consortium that it developed in conjunction with Compendia (BI 2/17/2012).

The company is also developing query algorithms, analysis pipelines for handling internally sequenced data, and a correlation pipeline that makes it possible to find links between cancer phenotypes and genetic changes, Warmuth said.

H3 is also partnering with Sage Bionetworks to develop in silico analysis tools that correlate "pharmacological response to omic features." These tools will also be part of a screening platform that will be used by a non-profit organization called Translational Proof-of-Concept, or TransPOC, which H3 Biomedicine plans to launch at the end of this month if it reaches its fundraising goal of $10 million, Warmuth said.

Warmuth said that his firm is launching TransPOC to provide a more cost-effective way for participating companies to test their drug compounds across 1,000 cell lines without having to bear the costs of culturing multiple cell lines themselves.

He explained that H3 chose to launch TransPOC as a non-profit organization to make the idea more palatable to potential member companies who would otherwise be reluctant to share information on proprietary drug molecules.

Warmuth said that for now the company is focused on targets it is evaluating with Eisai and is currently working out the details of its broader business strategy.

He did say that H3 Biomedicine intends to partner with small companies to validate targets that they have identified. One example is a splicing protein that has been found to have mutations in cases of myelodysplastic syndrome, chronic lymphocytic leukemia, acute myeloid leukemia, pancreatic cancer, melanoma, and breast cancer.

He said that H3 has started reaching out informally to unnamed pharma and venture capital companies but that it hasn’t signed any agreements yet.

Warmuth also said while his company will have to compete with firms like Epizyme, which has adopted a similar approach to cancer drug discovery using epigenetics data, "the opportunities today in curing cancer are endless and I would much rather see us work together to [avoid] some of the redundancies and really [focus] on the diversity."

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