Patenting Interfering RNA

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Patenting Interfering RNA

• John LeGuyader SPE Art Unit 1635
• [phone]
• John.leguyader_at_uspto.gov

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Interfering RNAGlossary of Terms

• RNAi RNA interference
• dsRNA double stranded RNA
• Dicer RNase endonuclease
• siRNA small interfering RNA, double stranded,
  21-23 nucleotides
• shRNA short hairpin RNA (doubled stranded by
  virtue of a ssRNA folding back on itself)
• ssRNA single stranded RNA
• RISC RNA-induced silencing complex
• Helicase unwinds siRNA and RNase endonuclease

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RNAi - Mechanism of Action

• Introducing long double stranded RNA leads to
  sequence-specific degradation of homologous gene
  transcripts
• Long double stranded RNA metabolized to small
  21-23-nucleotide siRNAs by endogenous RNase Dicer
• siRNAs bind to protein complex RISC with dual
  function helicase unwinding and RNase activity
• Unwinds siRNA allowing antisense strand to bind
  to target
• Hydrolyses of target by endonuclease activity of
  helicase

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RNAi
Antisense

• ssDNA - 5 deoxynucleotides
• 8-30 mer
• Endonuclease - ribonuclease
• Antisense binds homologous RNA target
• RNAse H endonuclease
• attacks DNA/RNA duplex
• Sequence-dependent degradation of cognate mRNA

• siRNA ds- or ssRNA 
• 21 mer
• Endonuclease - ribonuclease
• Antisense binds homologous RNA target
• Helicase unwinds/endonuclease
• attacks RNA/RNA duplex
• Sequence-dependent degradation of cognate mRNA

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RNAi Patentability issues

• Consider a broad claim to
• An siRNA that inhibits expression of a nucleic
  acid encoding protein X.
• Can also be claimed more broadly as short
  interfering nucleic acid.

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RNAi Patentability Issues 35 U.S.C. 101 Utility

• Credible/Specific/Substantial/Well Established
• Used to routinely investigate gene function in a
  high throughput fashion or to modulate gene
  expression in human diseases (see Chi et al.
  (PNAS) 100(11)6343-6346, 2003)
• Some knowledge of gene function required
• Enough to warrant target inhibition

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RNAi Patentability Issues 35 U.S.C. 101 Utility

• If no function for target nucleic acid (protein
  or regulatory) is shown or was known
• RNAi would likely lack utility
• also raises possible enablement (how to use)
  and/or written description issues
• probe function alone for target not sufficient to
  provide utility for RNAi

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RNAi Patentability Issues 35 U.S.C. 112, first
paragraph, Enablement

• high in vivo unpredictability due to general lack
  of knowledge regarding efficacy and in vivo
  target site determination, and delivery issues
• to date only one human antisense with FDA
  approval

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RNAi Predictability

• Highly dependent on target position
• Screening required to identify accessible target
  regions
• Antisense targets can also be RNAi targets but
  with exceptions, e.g. intron targets not active
  for RNAi
• Small mismatches (1-2 nts) can be tolerated
• Long dsRNAs cause severe sequence-non-specific
  effects
• induces apoptosis from shut down of translation
• RNAi of about 21nts required to evade effects
• Little in vivo efficacy to date

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RNAi Patentability Issues 35 U.S.C. 112, first
paragraph, Written Description

• adequate description for broad/generic claims
  relates to what is known and/or disclosed
  regarding target site accessibility for the gene
  at issue
• the example claim defines the invention in purely
  functional terms and lacks structural correlates
• RNAi described only by function may lack written
  description

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RNAi Patentability Issues 35 U.S.C. 112, first
paragraph, Written Description

• The Analysis
• identify all disclosed relevant distinguishing
  characteristics as they relate to the scope and
  content of the claims
• identify any disclosed structure/function
  relationships
• what target regions are accessible for RNAi and
  provide for inhibition
• showing of antisense targets across mRNA may be
  sufficient, but not all antisense targets are
  open to siRNA
• intron targets may not be active for siRNA but
  may be for antisense
• identify all elements claimed and their support
  in the description
• identify species explicitly or implicitly
  disclosed
• reconcile with the level of skill in the art

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RNAi Patentability Issues 35 U.S.C. 112, first
paragraph, Written Description

• A broad genus of siRNAs inhibiting expression of
  a nucleic acid encoding a protein may not be
  described by the sequence of a gene alone since
  the genus reads on targeting many different
  nucleic acids.
• Description of genus sufficient to comply with
  written description requires description of a
  representative number of species
• In the case of a small genus covering a limited
  defined target, one species may be
  respresentative

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RNAi Patentability Issues 35 U.S.C. 112, first
paragraph, Written Description

• Written Description Conclusions
• Broad claims to siRNAs inhibiting expression of a
  nucleic acid encoding a protein may lack an
  adequate written description since the claim
  reads on targeting many different nucleic acids.
• Analysis turns on what is shown in the
  specification and what was known about the
  various versions of the gene at the time of
  filing.
• Provide evidence RNAi targets shown functionally
  correlate with targeting other versions of the
  gene.
• The more you show and/or is known, the more you
  can possibly claim.

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Gene Walk
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Gene Walk Conclusions

• Probability of finding an individual functional
  RNAi is high
• A broad claim to An isolated RNAi that inhibits
  the expression of human gene X. may be enabled
  by providing the sequence for gene X and gene
  walk data (no magic number)
• Predictability of any single RNAi being effective
  is low
• claims to specific RNAi sequence may require
  evidence of function
• The current state of predictability for RNAi may
  support that breadth/scope claimed is enabled
• but this may also raise prior art issues
  depending on what was known at the time of filing

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RNAi Patentability Issues35 U.S.C. 102
Novelty/Anticipation

• Anticipation of specific RNAi
• must be explicitly taught in the prior art for
  anticipation to be applicable.

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RNAi Patentability Issues35 U.S.C. 103 -
Obviousness

• Expect an obviousness rejection against broad
  RNAi claims to known genes if the prior art
  suggested inhibiting the gene by nucleic
  acid-based methods or other means and the gene
  sequence was known.
• The current knowledge and level of skill in the
  art is high such that one of ordinary skill in
  the art would expect at least an RNAi against a
  known gene, absent evidence to the contrary.
• Narrow claims to specific RNAi sequences may be
  free of the art, where there would be no
  motivation to modify the prior art to achieve the
  specific RNAi sequence claimed.

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RNAi Patentability Issues35 U.S.C. 103 -
Obviousness

• Motivation
• used to routinely investigate gene function in a
  high throughput fashion or to modulate gene
  expression in human diseases (see Chi et al.
  (PNAS) 100(11)6343-6346, 2003)
• target identified in the prior art as desirable
  for silencing (disease gene, virus), and which
  has been inhibited in cells
• neither necessarily identifies any specific RNAi
  sequence

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RNAi Patentability Issues35 U.S.C. 103 -
Obviousness

• Expectation of Success
• expectation of RNAi gene silencing highly likely
  for target sites identified as accessible to
  antisense inhibition (see Vickers et al. (J.
  Biol. Chem.) 278 7108-7118, 2003)
• low expectation of success for in vivo
  applications
• low expectation for specific target sequences
  which are not identified
• identification of some sequence as appropriate
  target should be provided, e.g. known antisense
  target

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Case Law

• Antisense-specific
• Enzo Biochem Inc. v. Calgene Inc., 52 USPQ2d 1129
  (CAFC 1999)
• enablement - antisense highly unpredictable
• the decision is based on patents with effective
  filing dates of at least 1989 and the technology
  at that time
• decision does not necessarily determine the
  outcome for examination of antisense patent
  applications recently filed because current
  knowledge and level of skill in the art is high
  (antisense has progressed as a technology since
  1989)

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Recommendations

• Claim functional RNAi by specific sequence.
• List results of gene walk
• showing activity of each RNAi
• gene walk data may provide representative
  number of species for broad scope of a generic
  claim, but there is no magic number

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Recommendations

• Provide objective evidence that in vitro results
  are representative of in vivo applicability.
• Respond to examiner-cited unpredictable factors
  with objective evidence to the contrary.
• Expert opinions are more favorably viewed when
  supported using objective evidence.
• Provide objective evidence that a particular
  animal model is generally accepted as
  representative of disease or methods of treating,
  particularly for humans.
• Objective evidence includes arguments, case law,
  journal articles, and experimental data and
  comparisons commensurate with the disclosure as
  filed.

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RNAi

• Questions?