The Supreme Court’s 2013 decision in Ass'n for Molecular Pathology v. Myriad, 569 U.S. 576 (2013), which held that a naturally occurring cDNA was a product of nature and not eligible for patenting, continues to cause uncertainty in the patent bar and at the United States Patent Office. This uncertainty surfaced recently in an appeal to the Patent Trial and Appeals Board (“PTAB”) in Ex parte Kuttruff-Coqui, 2020 Pat. App. LEXIS 9989 (PTAB September 21, 2020).
The appeal in Ex parte Kuttruff-Coqui was taken from an examiner’s final rejection of claims directed to COL20A1, a collagen peptide purportedly useful for immunotherapy in certain cancers. Claim 1, which was on appeal to the PTAB, recited:
1. A peptide consisting of the amino acid sequence of SEQ ID NO: 28 [i.e. COL20A1] wherein said peptide is in the form of a pharmaceutically acceptable salt.
As can be seen, the claim recited a “pharmaceutically acceptable salt” of the peptide. There was no dispute on appeal that COL20A1 occurs naturally in the human body. There also was no dispute that COL20A1 by itself is a product of nature and ineligible for patent protection. The Applicant’s dispute with the Examiner was whether COL20A1 became eligible for a patent when the inventors formed it into a salt.
The Examiner argued that salts of COL20A1 were ineligible for patenting because such salts also occurred naturally in nature. According to the Examiner, the peptide would naturally form a salt inside the cell because:
“peptide fragments of the collagen protein degraded by a proteasome will naturally form a salt in the cytosol, the ER, or the MHC because there are counterions such as sodium, chloride and potassium present.”
The Examiner’s argument made common sense, since counterions are also always present in the body, but the Applicants were clearly up to the challenge. They submitted an expert declaration under 35 CFR 1.132 (the “Sterne Declaration”) to explain why the peptide represented by SEQ ID NO: 28 would not exist in the body as a salt. According to the Sterne Declaration, the peptide only existed for a brief moment in the cell as its protein degraded, and not long enough to form a salt. As explained by Dr. Sterne,
“peptide fragments, such as amino acid sequence SEQ ID NO: 28, that arise when proteins are degraded are themselves degraded within a few seconds if not associated with other proteins involved in degradation, ER transport and loading of the peptide onto MHC-1 molecules. … In the absence of peptide binding, neither the peptide nor the MHC molecule by itself is stable, or persists."
Even if the free peptide did exist in the cell for more than a few seconds, the cellular environment did not support salt formation. As explained by Dr. Sterne,
"there is no acid-base reaction that could occur in the cytoplasm or ER of a cell . . . that would result in formation of a peptide salt [because] [t]he formation of salts requires specific combinations of acids or bases in specific concentrations, at a defined ratio (stoichiometry), so that there is a set number of moles of acid and moles of base in a controlled environment[, and] [t]he cytoplasm of a cell is not such an environment."
The PTAB reversed the Examiner because, according to the PTAB, the Examiner had not given adequate weight to this expert testimony.
The PTAB next turned to the Supreme Court’s Myriad decision, and the Supreme Court’s holding that DNA did not become patentable simply because it was isolated from the human body. According to the PTAB, Myriad's isolated DNA claims were ineligible for patenting because the claims did not “rely in any way on the chemical changes that result from the isolation of a particular section of DNA.” A salt, in contrast, describes actual chemical changes that occur when a naturally occurring peptide binds to a counter-ion outside the body. In the words of the PTAB, the salt of COL20A1 is a new “chemical construct” that is eligible for a patent...
