# Presentation: 097214

## Proteomics Examination

**Yvonne (Bonnie) Eyler**
**Technology Center 1600**
**Art Unit 1646**
**(703) 308-6564**
**yvonne.eyler@uspto.gov**

## What is a Proteome?

- All the proteins expressed by a genome.
- “Functional Proteome” = all the proteins produced by a specific cell in a single time frame.

**Notes:**
 ~30,000 genes = 300,000 to 1 million proteins when alternate splicing and post-translational modifications are considered.
While a genome remains unchanged to a large extent, the proteins in any particular cell change dramatically as genes are turned on and off in response to environment.
 	“Functional Proteome” reflects the dynamic nature fo the proteome.

## Why is the Proteome Important?

- It is the proteins within the cell that:
- Provide structure
- Produce energy
- Allow communication
- Allow movement
- Allow reproduction
- Proteins provide the structural and functional framework of cellular life

## What is Proteomics?

- Proteomics refers to the systematic analysis of protein profiles of entire cells, tissues, organisms, or species.
- It represents the protein counterpart to the analysis of gene function.

**Notes:**
 Proteomics is high capacity global analysis of gene expression
proteomics parallels and complements the related field of genomics
 Genomics, ie. DNA sequence information is static-a snapshot
proteomic information is directed more to the dynamic life cycle and changes in protein populations associated with growth, disease, death, and the interactions between proteins and groups of proteins.

## Proteomics vs Genomics

- DNA sequence does not predict if the protein is in an active form
- RNA quantitation does not always reflect corresponding protein levels
- Multiple proteins can be obtained from each gene (alternative splicing)
- Genomics cannot predict post-translational modifications and the effects thereof
- DNA/RNA analysis cannot predict the amount of a gene product made (if and when)
- DNA/RNA analysis cannot predict events involving multiple genes

**Notes:**
 Proteomics is high capacity global analysis of gene expression
proteomics parallels and complements the related field of genomics
Genetic information is static while the protein complement of a cell is dynamic
 Genomics, ie. DNA sequence information is static-a snapshot
proteomic information is directed more to the dynamic life cycle and changes in protein populations associated with growth, disease, death, and the interactions between proteins and groups of proteins.
Examples of post-translation modifications:
Phophorylation
glycosylation

## Why is Proteomics Important?

- Identification of proteins in normal and disease conditions
- Investigating epidemiology and taxonomy of pathogens
- Analysis of drug resistance
- Identification of pathogenic mechanisms
- Reveals gene regulation events involved in disease progression
- Promise in novel drug discovery via analysis of clinically relevant molecular events
- Contributes to understanding of gene function

**Notes:**
Can discriminate among disease subtypes that are not recognizable using traditional pathological criteria.

## Proteomic Methodologies

- Analysis of protein expression patterns
- Analysis of protein Sequence Information
- Analysis of protein structure/function relationships

**Notes:**
Major techniques used in proteomic research
2D gel electrophoresis (studies expression)
2D gel electrophoresis is a method where a protein sample is applied to a gel and the proteins separated by, e.g., molecular weight.  Then the strip of the gel containing the separated proteins is cut out, flipped 90 degrees and the proteins separated by another criteria, such as based on their pI (isoelectric point)
protein sequence databases
mass spectrometry-helpful in linking gel-separated proteins to sequence databases
storage, manipulation,comparison of data using bioinformatics

Might want to add bullet re: protein-protien interactions as well since there are slides dealing with orphan receptors.
Analysis of protein structure/function intra- and interrelationships

## Proteomic Methodologies

- Complex protein mixtures are separated by 2-D gel electrophoresis
- Then individual proteins are isolated from spots and are identified by using mass spectrometry
- Individual proteins are sequenced, followed by database searches
- Bioinformatics

**Notes:**
2-D gel electrophoresis
Currently used in reference to the gel-based separation of proteins by their isoelectric point in one dimension
followed by a molecular weight separation by SDS-polyacrylamide gel electrophoresis perpendicular to the
first dimension

protein sequence databases
mass spectrometry-helpful in linking gel-separated proteins to sequence databases
storage, manipulation,comparison of data using bioinformatics

Might want to add bullet re: protein-protien interactions as well since there are slides dealing with orphan receptors.
Analysis of protein structure/function intra- and interrelationships

## Proteomics Examination

## Patentability

- Patent Statutes
**35 USC 101, Utility**
- 35 USC 102, Anticipation
- 35 USC 103, Obviousness
**35 USC 112, 1st Paragraph, enablement**
**35 USC 112, 1st Paragraph, written description**
- 35 USC 112, 2nd Paragraph

## Protein Expression Pattern

## Disclosure # 1 

- The specification discloses 2D gels of proteins present in prostate cancer cell lysates and normal cell lysates.
- The specification points to several spots indicating proteins expressed in prostate cancer that are not present in normal cells.
- The specification distinguishes between these protein spots by isoelectric point and molecular weight.
- No further information is provided.

**Notes:**
SUMMARY SLIDE of WHAT SPECIFICATION DISCLOSES:

2D gels of polypeptide populations from prostate cancer cells 

compared to 2D gel of polypeptide populations from normal prostate cells 

several unique polypeptide spots on the 2D gel of prostate cancer cell

each polypeptide spot is characterized by an isoelectric point and a molecular weight.

## Example Claim

- An isolated polypeptide which is diagnostic of prostate cancer, wherein the polypeptide is identified by 2D gel electrophoretic comparison of proteins present in prostatic cancer cells as compared to normal prostatic cells.

**Notes:**
This claim is an example of the type of claim one might see in expression proteomics type applications.

## Patentability Considerations-Written Description

- 112 1st paragraph written description
- Can one skilled in the art reasonably conclude the inventor had possession of the claimed invention at the time the application was filed?

**Notes:**
The example claim is going to be analyzed for compliance with written description first. This slide states the basic requirement and the following slide lists the factors to be considered in determining if compliance is met.

## Satisfying Written Description 

- Weigh factual considerations in view of level of skill and knowledge in the art
- Complete or partial structure
- Physical and/or chemical properties
- Functional characteristics
- Correlation between structure and function
- Method of making
- Combinations of the above

## Written Description Analysis

**No structure of the polypeptide is provided in the specification**
**Physical properties of the polypeptide are disclosed, ie molecular weight and pI**
**The biological function of the polypeptide is not disclosed**
**Method of making is not disclosed,  only a method of isolating from a specific population of undefined cells.**

***An isolated polypeptide which is diagnostic of prostate cancer, wherein the polypeptide is identified by 2D gel electrophoretic comparison of proteins present in prostatic cancer cells as compared to normal prostatic cells.***

**Notes:**
The example claim is repeated for convenience on the right hand portion of this slide

The left hand portion is the written description analysis of the example  claim

The analysis follows the points that must be weighed from the previous slide I.e. : structure, properties, function, method of making

structure: no sequence provided
properties: isoelectric point and molecular weight are obtainable from the 2D gel
function: no functions or activities are provided
method of making is limited to the separation of  polypeptide populations by 2D gel electrophoresis of the specific cells used. The method is unreproducible since the specific cells are not defined. 

## Conclusion

- Applicant was not in possession of the claimed isolated polypeptide.

## Solution

- Claim a method of diagnosing prostate cancer that relies upon a particular pattern of polypeptide expression.

## Patentability Considerations-Enablement

**Patentability Considerations-Enablement**

## Factors to be considered, In re Wands, 858 F.2d 731, 8 USPQ 2d 1400 (Fed. Cir. 1988)

- Quantity of experimentation necessary
- Amount of direction or guidance presented
- Presence or absence of working examples
- Nature of the invention
- State of the prior art
- Relative skill of those in the art
- Predictability or unpredictability of the art
- Breadth of the claims

## Enablement  Analysis

**Undue experimentation necessary to isolate and identify polypeptide.**
**No guidance present regarding the structure of the polypeptide.**
**No working examples of isolated polypeptide used to diagnose prostate cancer.**
**The prior art does not teach polypeptide or it’s use to diagnose prostate cancer.**
**The structure and function isolated polypeptide is unpredictable from the disclosure.**

***	******An isolated polypeptide which is diagnostic of prostate cancer, wherein the polypeptide is identified by 2D gel electrophoretic comparison of proteins present in prostatic cancer cells as compared to normal prostatic cells.***

**Notes:**
In addition to the written description defects, this claim is also not enabled for how to make the claimed polypeptide.
The specification only discloses a method of how to separate a population of polypeptides from specific cells.
There is no information regarding how to make the individual polypeptides- what their structures are and how they may be identified.

## Conclusion

- Specification was not enabling for the claimed isolated polypeptide.

## Solution

- Claim a method of diagnosing prostate cancer that relies upon a particular pattern of polypeptide expression.

## Patentability Considerations-Utility

- Asserted utility
- specific
- substantial
- credible
- Well established utility

**Notes:**
The same expression proteomics example claim is now going to be analyzed for compliance with the Utility requirements.

## Utility Analysis

**The asserted utility is to use the polypeptide to diagnose prostate cancer**
**The asserted utility is specific**
**The asserted utility is substantial**
**The asserted utility is credible**

- 	***An isolated polypeptide which is diagnostic of prostate cancer, wherein the polypeptide is identified by 2D gel electrophoretic comparison of proteins present in prostatic cancer cells as compared to normal prostatic cells.***

**Notes:**
Is there an asserted utility? YES
to diagnose cancer
is the asserted utility specific? YES, it is based on a property of  the claimed polypeptide, not on a general feature. The property is the polypeptides’ expression in prostate cancer tissue vs normal, as indicated by the comparison 2D gels.
Is the asserted utility substantial? YES, it is a real-world use.
Is it credible? YES

## Conclusion

- The claimed invention has a specific, substantial, and credible asserted utility, i.e. for cancer diagnosis.

## Disclosure # 2

- The specification discloses 2D gels of prostate cancer and normal cell lysates.
- A polypeptide located in a spot unique to prostate cancer cells was isolated and sequenced (SEQ ID NO: 1)
- Antibodies were generated to SEQ ID NO: 1
- The antibodies were used in a series of binding assays to demonstrate a clear correlation between presence of high levels of SEQ ID NO: 1 and prostate cancer.

## An Example Claim Set

- An isolated polypeptide comprising at least 10 contiguous amino acids of SEQ ID NO: 1.
- An isolated polypeptide having at least 45% identity to the polypeptide of SEQ ID NO: 1.

## Satisfying Written Description 

- Weigh factual considerations in view of level of skill and knowledge in the art
- Complete or partial structure
- Physical and/or chemical properties
- Functional characteristics
- Correlation between structure and function
- Method of making
- Combinations of the above

## Written Description Analysis

**Physical properties of a single polypeptide are disclosed, ie molecular weight and pI by 2D gel electrophoresis and its sequence. **
**The physical properties of polypeptides comprising 10 amino acids or of polypeptides having 45% identity to SEQ ID NO: 1 are not disclosed or known in the art.**
**No biological function of the polypeptide of SEQ ID NO: 1 is disclosed. The isolated polypeptide is an “orphan” receptor. **
**No structural to functional correlation is disclosed between core structural features needed to retain function in the two claimed genus of polypeptides.**

***An isolated polypeptide comprising at least 10 contiguous amino acids of SEQ ID NO: 1. ***
***An isolated polypeptide having at least 45% identity to the polypeptide of SEQ ID NO: 1.***

**Notes:**

The analysis follows the points that must be weighed from the previous slide I.e. : structure, properties, function, method of making

## Conclusion

- Applicant was not in possession of the claimed genus of isolated polypeptides.

## Satisfying the Enablement Requirement 

**Factors to be considered, *****In re Wands, 858 F.2d 731, 8 USPQ 2d 1400 (Fed. Cir. 1988)***
- Quantity of experimentation necessary
- Amount of direction or guidance presented
- Presence or absence of working examples
- Nature of the invention
- State of the prior art
- Relative skill of those in the art
- Predictability or unpredictability of the art
- Breadth of the claims

**Notes:**
Do you need this in view of Jasemine’s part of the presentation?

## Enablement  Analysis

**No guidance regarding the critical structural features of the polypeptide of SEQ ID NO: 1.**
**Which 10 amino acids are essential to functional and physical properties?**
**Where over the length of the polypeptide may changes be made up to 45% identity and still retain functional and physical properties?**
**There is no function for the isolated polypeptide. It is an “orphan” receptor.**
**It is not predictable that the scope of the claimed polypeptides could be used to diagnose prostate cancer.**

***An isolated polypeptide comprising at least 10 contiguous amino acids of SEQ ID NO: 1. ***
***An isolated polypeptide having at least 45% identity to the polypeptide of SEQ ID NO: 1.***

**Notes:**
In addition to the written description defects, this claim is also not enabled for how to make the claimed polypeptide.
The specification only discloses a method of how to separate a population of polypeptides from specific cells.
There is no information regarding how to make the individual polypeptides- what their structures are and how they may be identified.

## Conclusion

- The specification was not enabling for the scope the claimed isolated polypeptides.

## Solution

- Claim:
- An isolated polypeptide comprising SEQ ID NO: 1.

## ??? Questions ???