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TRENDSPOTTER: Treading the Thin Ice of Proteomic Patent Protection

Like genomics, the field of proteomics reverses traditional methodologies of protein characterization. It comes as no surprise, then, that proteomics can expect problems similar to those faced when attempting to patent genomics inventions.

Proteomics focuses on the analysis of the protein profile of an entire cell, tissue, or organism to identify the protein profile of a disease state or to pinpoint a target for drug activity. One particular type of proteomics invention, the so-called “orphan” receptor, has received a great deal of attention from the US Patent and Trademark Office.  

Orphan receptors are identified through analysis of protein sequence information coupled with a comparison to know protein structure function relationships. This yields enough information to classify the protein tentatively as a receptor, but gives little additional indication of the biological function or ligands of the receptor. Although it is highly desirable to obtain patents for orphan receptors because of their potential use in drug development, the lack of complete information renders it difficult to obtain broad claims.

For example, an inventor may compare protein expression in melanoma and normal skin cells using two-dimensional electrophoresis and locate several polypeptides found only in melanoma cells. Sequence analysis may then reveal two polypeptides having 50 percent identity to a receptor know to be upregulated in melanoma cells. It may also be known that blocking this type of upregulated receptor can inhibits the growth of melanoma cells.

Based on this information, the inventor might seek patent protection for the two polypeptides based on the relationship between the sequence and the known receptor (SEQ. ID. NO: 1). The patent application might also contain homology-based claims such as “an isolated polypeptide with 70 percent sequence identity to SEQ. ID. NO: 1” or “an isolated polypeptide comprising at least 40 contiguous amino acids of SEQ. ID. NO: 1.”

Without additional disclosure, such claims might be unpatentable for several reasons. First, the USPTO has asserted that the only real-world utility for a polypeptide is its use as a screening agent for drugs that may inhibit cancer cell growth. The utility may be deemed invalid because it is based solely upon an amino acid sequence relationship to a known protein. It is well known that receptors such as VEGF and PDGF exhibit high levels of homology, yet have opposite functions in vascular tissues.

The USPTO’s reasoning may seem sound. However, other valid utilities for the polypeptides may exist. For instance, polypeptides may have a use in detecting melanoma or as a targeted treatment, such as gene therapy. Essentially, any utility that might credibly be practiced in the real world and that does not assert an unverified function solely based on homology should suffice.

Second, the written description requirement must be satisfied by demonstrating that the inventor possessed the claimed invention when the patent application was filed. Possession of a protein may be shown by inter alia sequence, physical characterization and/or functional information. Possession of the sequenced polypeptides should be adequately demonstrated by sequence alone. Possession of the “genus” of homologous polypeptides is more difficult to demonstrate because of partial sequence absent other characteristics will likely not fulfill the written description requirements, and may be patentable only if the claims recite a high degree of sequence identity to a protein having a known function. Additionally, the patent application may need to provide several representative polypeptides, as well as evidence of polypeptide function, to support the claims.

Finally, homology-based claims may also be deemed to fail the enablement requirement, which requires the patent application to teach others in the field how to make and use the full scope of the claimed invention without undue experimentation. A known sequence generally serves this purpose, whereas a homology designation may not.

However, an indication of specific portions of the sequence that must be present in the polypeptide may enable a claim. Additionally, some breadth may be obtained by claiming all polypeptides containing the specified sequence.

In general, in proteomics just as in genomics, the basic information obtained from initial discovery activities affords only narrow patent protection. Additional research is generally required to provide broader protection for the full scope of an invention.

Rochelle K. Seide is a partner at the law firm of Baker Botts, where she specializes in biotechnology, intellectual property, and patent issues. She also has a PhD in human genetics. Michelle LeCointe is an associate at Baker Botts, where she specializes in biotechnology patents and licensing. They can be reached at  [email protected]  and  [email protected] .   

TrendSpotter  is a weekly column that focuses on how trends in politics, patent law, and the US and European markets will affect the genomics industry. The column appears every Friday. To access previous columns just enter the word "Trendspotter" in the archive search window on the homepage.

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