Office Action 2: Notice of Allowance (2025-02-12)

CLAIMS:
AMENDMENTS TO THE CLAIMS

This listing of claims will replace all prior versions and listings of claims in the application. No new matter is added.

Listing of Claims:

1\. (currently amended) An in vitro method of detecting phosphorylation of a Rubicon protein comprising:isolating proteins from a sample;
contacting the isolated proteins with an antibody that binds to a phosphorylated Threonine at 166 of a Rubicon protein to form a complex, the antibody comprising amino acid sequences:
i) LC-CDR1: RSSQSLVHSNGNTYLH (SEQ ID NO. 4);
ii) LC-CDR2: KLSNRFS (SEQ ID NO. 5);
iii) LC-CDR3: SQSTHVPLT (SEQ ID NO. 6);
iv) HC-CDR1: NYGVS (SEQ ID NO. 7);
v) HC-CDR2: TINSNGGSKYYPDSVKG (SEQ ID NO. 8); and
vi) HC-CDR3: DVWLRRQWYFDV (SEQ ID NO. 9);
detecting the complex wherein detection of the complex that varies from a predetermined value indicates that the sample comes from a subject having a disease associated with Leucine-rich repeat kinase 2 (LRRK2).

2\. (original) The in vitro method according to claim 1, wherein the disease associated with Leucine-rich repeat kinase 2 (LRRK2) is Parkinson's disease.

3\. (previously presented) The in vitro method according to claim 1, wherein the antibody is a chimeric humanised antibody.

4\. (previously presented) The in vitro method according to claim 1, wherein the antibody is a monoclonal antibody.

5\. (previously presented) The in vitro method according to claim 1, wherein the complex is detected with an enzyme linked immunosorbent assay.

6\. (currently amended) The in vitro method according to claim 1, wherein the subject having a disease associated with Leucine-rich repeat kinase 2 (LRRK2) is treated with a compound able to block interaction of LRRK2 with Threonine 166 of the Rubicon protein, the compound comprising a treatment antibody that binds to phosphorylated Threonine at 166 of the Rubicon protein, the treatment antibody comprising amino acid sequences:i) LC-CDR1: RSSQSLVHSNGNTYLH (SEQ ID NO. 4);
ii) LC-CDR2: KLSNRFS (SEQ ID NO. 5);
iii) LC-CDR3: SQSTHVPLT (SEQ ID NO. 6);
iv) HC-CDR1: NYGVS (SEQ ID NO. 7);
v) HC-CDR2: TINSNGGSKYYPDSVKG (SEQ ID NO. 8); and
vi) HC-CDR3: DVWLRRQWYFDV (SEQ ID NO. 9).

7\. (cancelled)

8\. (currently amended) The in vitro method according to claim 76,wherein the treatment antibody is a chimeric humanised antibody.

9\. (currently amended) The in vitro method according to claim 76,wherein the treatment antibody is a monoclonal antibody.

10\. (Cancelled).

11\. (Cancelled).

12\. (currently amended) An antibody that binds to phosphorylated at-Threonine at 166 of a Rubicon protein, the antibody comprising amino acid sequences:i) LC-CDR1: RSSQSLVHSNGNTYLH (SEQ ID NO. 4);
ii) LC-CDR2: KLSNRFS (SEQ ID NO. 5);
iii) LC-CDR3: SQSTHVPLT (SEQ ID NO. 6);
iv) HC-CDR1: NYGVS (SEQ ID NO. 7);
v) HC-CDR2: TINSNGGSKYYPDSVKG (SEQ ID NO. 8); and
vi) HC-CDR3: DVWLRRQWYFDV (SEQ ID NO. 9).

13\. (cancelled)

14\. (cancelled)

15\. (previously presented) The antibody according to claim 12, wherein the antibody is a chimeric humanised antibody.

16\. (previously presented) The antibody according to claim 12, wherein the antibody is a monoclonal antibody.

17\. (cancelled)

18\. (cancelled)

19\. (currently amended) An inhibitor of Rubicon interaction with Leucine-rich repeat kinase 2 (LRRK2) comprising a compound able to block interaction of LRRK2 with Threonine 166 of the Rubicon protein, the compound comprising an antibody that binds to phosphorylated Threonine at 166 of the Rubicon protein,the antibody comprising amino acid sequences:i) LC-CDR1: RSSQSLVHSNGNTYLH (SEQ ID NO. 4);
ii) LC-CDR2: KLSNRFS (SEQ ID NO. 5);
iii) LC-CDR3: SQSTHVPLT (SEQ ID NO. 6);

iv) HC-CDR1: NYGVS (SEQ ID NO. 7);
v) HC-CDR2: TINSNGGSKYYPDSVKG (SEQ ID NO. 8); and
vi) HC-CDR3: DVWLRRQWYFDV (SEQ ID NO. 9).

20\. (cancelled)

21\. - 26 (cancelled).2225

27\. (currently amended) A method of treating a subject in need having a disease associated with Leucine-rich repeat kinase 2 (LRRK2) comprising:administering a compound able to block interaction of LRRK2 with Threonine 166 f the Rubicon protein, the compound comprising an antibody that binds to phosphorylated Threonine at 166 of the Rubicon protein, the antibody comprising amino acid sequences:
i) LC-CDR1: RSSQSLVHSNGNTYLH (SEQ ID NO. 4);
ii) LC-CDR2: KLSNRFS (SEQ ID NO. 5);
iii) LC-CDR3: SQSTHVPLT (SEQ ID NO. 6);
iv) HC-CDR1: NYGVS (SEQ ID NO. 7);
v) HC-CDR2: TINSNGGSKYYPDSVKG (SEQ ID NO. 8); and
vi) HC-CDR3: DVWLRRQWYFDV (SEQ ID NO. 9).

28\. (cancelled)

29\. (currently amended) The method according to claim 2827, wherein the antibody is a chimeric humanised antibody.

30\. (currently amended) The method according to claim 2827, wherein the antibody is a monoclonal antibody.

31\. (cancelled)

32\. (cancelled)

33\. (new) The in vitro method according to claim 1, wherein the antibody comprises a primary antibody and the step of detecting the complex comprises contacting the complex with a secondary antibody that binds to the primary antibody.

34\. (new) The in vitro method according to claim 1, wherein the antibody comprises amino acid sequences set forth in SEQ ID NO. 12 and SEQ ID NO. 13; or a functional variant with 99% amino acid sequence identity to SEQ ID NO. 12 or SEQ ID NO. 13.

35\. (new) The antibody according to claim 12, comprising amino acid sequences set forth in SEQ ID NO. 12 and SEQ ID NO. 13; or a functional variant with 99% amino acid sequence identity to SEQ ID NO. 12 or SEQ ID NO. 13.

36\. (new) The inhibitor according to claim 19, wherein the antibody comprises amino acid sequences set forth in SEQ ID NO. 12 and SEQ ID NO. 13; or a functional variant with 99% amino acid sequence identity to SEQ ID NO. 12 or SEQ ID NO. 13.

37\. (new) The method according to claim 27, wherein the antibody comprises amino acid sequences set forth in SEQ ID NO. 12 and SEQ ID NO. 13; or a functional variant with 99% amino acid sequence identity to SEQ ID NO. 12 or SEQ ID NO. 13.

OFFICE ACTION:
DETAILED ACTION
Notice of Pre-AIA  or AIA  Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Application Status
Claims 1-6, 8-9, 12, 15-16, 19, 27, 29-30, and 33-37 are pending.
Claims 1-6, 8-9, 12, 15-16, 19, 27, 29-30, and 33-37 are examined on the merits herein.
Grounds of Rejection Withdrawn
The previous rejection of claims 1-2 and 4-5 under 35 U.S.C. 101 are withdrawn in view of claim amendments.
The previous rejection of claims 1-9, 12-16, and 28-30 under 35 U.S.C. 112(b) are withdrawn in view of claim amendments and cancellations.
The previous rejection of claims 1-9, 12-16, 19-20, and 27-30 under 35 U.S.C. 112(a) are withdrawn in view of claim amendments and cancellations.
The previous rejection of claims 6, 19, and 27 under 35 U.S.C. 102 are withdrawn in view of claim amendments.
Allowable Subject Matter
Claims 1-6, 8-9, 12, 15-16, 19, 27, 29-30, and 33-37 are allowed.
The following is an examiner’s statement of reasons for allowance:
The CDRs comprising an antibody that binds to phosphorylated at 166 of the Rubicon protein comprising the amino acid sequences SEQ ID NOs: 4-9 have been found free of the prior art. Therefore independent claims 1, 12, 19, and 27 are allowable.
As claims 2-6, 8-9, 15-16, 29-30, and 33-37 are dependent from these independent claims and are therefore also allowable.
The state of the prior art teaches antibodies with specific binding to Rubicon as seen in Hartlova and Yue. Hartlova (the EMBO Journal, 2018, 37(12): e98694; IDS filed September 7, 2021) teaches an anti-rubicon mAb clone D9F7 produced by immunizing an animal with a synthetic peptide as well as a sheep anti-rubicon antibody that was used for western blot (figure 5). Yue (WO 2010/030936 A2; IDS filed September 7,2021) teaches an anti-rubicon antibody that regulates autophagy that can be used to treat neurological disease (abstract). It is not disclosed whether these antibodies are capable of binding rubicon phosphorylated at threonine 166 but they were not specifically generated to bind phosphorylated threonine 166 of Rubicon. There is no prior art that teaches antibodies that specifically bind to Rubicon protein phosphorylated at threonine 166.
Any comments considered necessary by applicant must be submitted no later than the payment of the issue fee and, to avoid processing delays, should preferably accompany the issue fee.  Such submissions should be clearly labeled “Comments on Statement of Reasons for Allowance.”
Conclusion

APPLICANT REBUTTAL: REMARKS
This is a reply to the Non-Final Office Action dated September 27, 2024. Applicant thanks the Examiner for carefully considering the application.
Status of Claims
Prior to the entry of the present Response, claims 1-9, 12-16, 19-20 and 27-30 were pending. In an interest to progress prosecution of the present application, Applicant is amending the claims as set forth herein, and following entry of these amendments, claims 1-6, 8-9, 12, 15-16, 19, 27, 29-30 and 33-37 are pending.
Claims 1-2 and 4-5 are rejected under 35 U.S.C. § 101 because the claimed invention is directed to a judicial exception without significantly more.
Claims 1-9, 12-16, and 28-30 are rejected under 35 U.S.C. § 112 as being
indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention. Claims 1-9, 12, 15- 16, 19-20 and 27-30 are rejected 35 U.S.C. § 112 as failing to comply with the written description requirement. Claims 13 and 14 are rejected under 35 U.S.C. § 112 as failing to complain with the written description requirement. Claims 6, 12-16, and 28-30 are rejected under 35 U.S.C. under § 112 for failing to comply with the enablement requirement.
Claims 6, 19, and 27 are rejected under 35 U.S.C. § 102 as being anticipated by (J Neurosci Methods, 2013, 214(1):62-8: PTO-892). Claims 12 and 16 are rejected under 35 U.S.C. § 102 as being anticipated by Gronborg (Mol Cell Proteomics. 2002 Jul; 1(7):517-27; PTO-892).
Claims 1, 6, 8-9, 12, 19, 27, 29-30 are amended. Claims 7, 10-11, 13-14, 17-18, 20-26, 28, 31-32 are cancelled. Claims 33-37 are new. No new subject matter is added to the amended claims or in the new claims.
Claims 1, 6, 12, 19 and 27 have been amended to include the limitation of an antibody comprising the CDR sequences as recited by previously pending Claim 14. Pursuant to this amendment, previously pending Claims 13, 14, 20 and 28 have been cancelled.
Claims 1 and 12 have been further amended to read "...an antibody that binds to...".Claims 6, 12, 19 and 27 have been amended to remove the feature of "Serine 189".
Claim 6 has been further amended to include the limitation of Claim 7
directed to a treatment antibody. Accordingly, claim 7 has been cancelled and the dependencies of Claims 8 and 9 have been amended to depend from Claim 6.
The dependencies of Claims 29 and 30 have been amended following the amendment to Claim 27 and cancellation of Claim 28.
New Claims 33 has been added and finds support from at least paragraph [00131] of the specification.
New Claims 34-37 have been added and find support from at least paragraphs [0059] and [00134], and [00139]-[00142] of the specification.
Applicant submits that the amendments and new claims are supported by the application as filed and do not introduce new matter. Applicant respectfully request reconsideration and allowance in view of these amendments and the following remarks.
Response to Rejections
35 U.S.C. 101
The Examiner has rejected Claims 1-2 and 4-5 under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e. law of nature) without significantly more.
In response, claim 1 has been amended to include the CDR sequences as
recited by previously pending Claim 14. Applicant submits that with the recitation of the CDR sequences in amended Claim 1, said claim includes additional elements that are sufficient to amount to significantly more than the judicial exception because neither Gronborg (Mol Cell Proteomics. 2002 Jul;1 (7):517-27; PTO-892) nor any other prior art references disclose an antibody that binds to phosphorylated Threonine at 166 of a Rubicon protein, the antibody comprising amino acid sequences:
i) LC-CDR1: RSSQSLVHSNGNTYLH (SEQ ID NO. 4);
ii) LC-CDR2: KLSNRFS (SEQ ID NO. 5);
iii) LC-CDR3: SQSTHVPLT (SEQ ID NO. 6);
iv) HC-CDR1: NYGVS (SEQ ID NO. 7);
v) HC-CDR2: TINSNGGSKYYPDSVKG (SEQ ID NO. 8); and
vi) HC-CDR3: DVWLRRQWYFDV (SEQ ID NO. 9).
The abovementioned specific CDR sequences are not well-understood, routine and/or conventional limitations of detecting phosphorylated threonine at 166 on the Rubicon protein.
In view of the above, Applicant submits that Claim 1 relates to patent eligible subject matter. Claims 2 and 4-5 which depend on Claim 1 and include the CDR sequences, would also include additional elements that are sufficient to amount to significantly more than the judicial exception and constitute patent eligible subject matter.
35 U.S.C. 112(b)
The Examiner has rejected Claims 1-9 under 35 U.S.C. 112(b) because Claim
1 recites "an antibody that hybridizes" and is indefinite.
In response, claim 1 has been amended to "...an antibody that binds to..." and Applicant submits that said claim is no longer indefinite. Claims 2-6 and 8-9 which depend from claim 1 are also no longer indefinite pursuant to this amendment to Claim 1.
The Examiner has rejected Claims 7-9 under 35 U.S.C. 112(b) because there is insufficient antecedent basis for the limitation "the compound" in line 2 of Claim
Claim 7 has been cancelled in the present Response and Applicant submits that the rejection to Claim 7 is now moot.
Claims 8-9 have been amended to depend on claim 6 which has been amended to recite "a treatment antibody" which provides antecedent basis for Claims 8-9. Applicant accordingly submits that there is sufficient antecedent basis for the limitations in Claim 8-9.
The Examiner has rejected Claims 12-16 and 28-30 under 35 U.S.C. 112(b) because Claims 12 and 28 recite "an antibody which is capable of binding" and are indefinite.
Claim 12 has been amended to "...an antibody that binds to..." and Applicant submits that said claim is no longer indefinite. Claims 15-16 which depend from Claim 12 are also no longer indefinite pursuant to this amendment to Claim 12.
Claim 28 has been cancelled and the rejection is now moot. Claims 29-30 are now dependent on Claim 27 which recites "...an antibody that binds to..." which Applicant submits is not indefinite, hence Claims 29-30 are no longer indefinite.
35 U.S.C. 112(a)
Claims 1-9, 12, 15-16, 19-20 and 27-30
The Examiner has rejected Claims 1-9, 12, 15-16, 19-20 and 27-30 under 35 U.S.C. 112(a) as failing to comply the written description requirement because "one skilled in the art would be unable to predict or envision a genus of antibodies that bind to rubicon phosphorylated at threonine 166 and/ or serine 189 or blocking the interaction between LRRK2 and rubicon at these sites".
In response, Claims 1, 6, 12, 19 and 27 have been amended to include the CDR sequences of previously pending Claim 14. Further, Claims 6, 12, 19 and 27 have been amended to remove the feature "Serine 189".
As acknowledged by the Examiner at least on pages 8 and 12 of the non-final Office Action, there is written description for an antibody that binds to phosphorylated Threonine at 166 of the Rubicon protein (paragraphs [00130] and [00132] of the PCT publication) and for an antibody comprising the 6 (six) CDR amino acid sequences disclosed at paragraphs [00139]-[00142] of the PCT publication. Accordingly, Applicant submits that with the amendments to Claims 1, 6, 12, 19 and 27, Claims 1-6, 8-9, 12, 15-16, 19, 27, 29-30 as pending in the present Response now comply with the written description requirement. New dependent Claims 33-37 also comply with the written description requirement for the same reasons.
Claims 13 and 14
The Examiner has rejected Claims 13 and 14 under 35 U.S.C. 112(a) as failing to comply the written description requirement because Claim 13 which is "directed to at least one CDR sequence, would not permit a skilled artisan to envision the subgenus of antibodies comprising such sequences and have the ability
to bind rubicon phosphorylated at threonine 166 as claimed" and with regards to Claims 13 and 14, "one skilled in the art would be unable to predict or envision which residues of the heavy and light chain CDRs of claims 13-14 may be changed to maintain 99% amino acid sequence identity, such that the resultant variant CDR residues form an antigen-binding site capable of binding rubicon phosphorylated at threonine 166".
Claims 13 and 14 have been cancelled in the present Response and Applicant submits that this rejection is now moot.
Applicant wishes to highlight that the "at least one" and "selected from" language of Claim 13 and the percentage sequence identity language of Claim 14 have been omitted in the amendments to Claims 1, 6, 12, 19 and 27 to include the CDR sequences. Accordingly, Applicant submits that these claims satisfy the written description requirement under 35 U.S.C. 112(a).
Claims 6, 12-16 and 28-30
The Examiner has rejected Claims 6, 12-16 and 28-30 under 35 U.S.C. 112(a) as failing to comply the enablement requirement because "it would require undue experimentation for one skilled in the art to generate or determine an antibody capable of binding to rubicon phosphorylated at threonine 166 and serine 189".
Claims 6 and 12 have been amended to remove the feature "Serine 189".
Claim 27 has also been amended in the same manner. Applicant accordingly submits that Claims 6, 12 and 27 now meet the enablement requirement under 35 U.S.C. 112(b) because the subject application discloses at paragraphs of [00131]-[00142] of the PCT publication, an antibody that is capable of binding to phosphorylated Threonine at 166 of the Rubicon protein. Claims dependent on Claims 6, 12 and 27 also meet the enablement requirement under 35 U.S.C. 112(a) for the same reasons.
Claims 13, 14 and 28 have been cancelled, hence this rejection is moot.
35 U.S.C. 102
The Examiner has rejected Claims 6, 19 and 27 under 35 U.S.C. 102(a)(1) as being anticipated by Gillardon (J Neurosci Methods, 2013, 214(1 ):62-8; PTO-892). The Examiner has rejected Claims 12 and 16 under 35 U.S.C. 102(a)(1) as being anticipated by Gronborg (Mal Cell Proteomics. 2002 Jul;1 (7):517-27; PTO-892).
In response, Claims 6, 12, 19 and 27 have been amended to an antibody that binds to phosphorylated Threonine at 166 of the Rubicon protein, the antibody comprising the CDR sequences of previously pending Claim 14 to which the Examiner has not found to be anticipated by Gillardon or Gronborg.
Applicant accordingly submits that Claims 6, 12, 19 and 27 are novel in view of Gillardon or Gronborg. Claim 16 is also novel in view of Gronborg because of its dependency on Claim 12.
In the present communication, any alteration to the application or claims and/or any characterization of claim scope or cited prior references are made to facilitate expeditious prosecution of this application and it is not conceded that any of the previously pending claims is not patentable. Applicant therefore reserves the right to pursue any previously pending or other broader or narrower claims and/or any subject matter therein that is supported by the present disclosure, including subject matter found to be specifically disclaimed herein or by any prior prosecution, at a later date. Accordingly, it shall not be reasonably inferred that Applicant has made any disclaimers or disavowals of any subject matter supported by the present application, in this application, or parent or child or related prosecution history.
CONCLUSION


CITED REFERENCE SUMMARIES: Ref WO2010030936A2: Claims:
1. An isolated polypeptide that has an amino acid sequence up to 99% identical to SEQ ID NO: 1, comprising at least one sequence selected from the group consisting of amino acids 75 to 95 of SEQ ID NO: 1 and amino acids 148 to 178 of SEQ ID NO: 1.
2. The isolated polypeptide of claim 1, comprising a sequence of amino acids 99 to 492 of SEQ ID NO: 1.
3. An isolated polypeptide that has an amino acid sequence up to 99% identical to SEQ ID NO: 2, comprising at least a sequence of amino acids 488 to 508 of SEQ ID NO: 2.
4. The isolated polypeptide of claim 3, comprising a sequence of amino acids 208 to 836 of SEQ ID NO: 2.
5. The isolated polypeptide of claim 3, comprising a sequence of amino acids 1 to 836 of SEQ ID NO: 2.
6. The isolated polypeptide of claim 3, comprising a sequence of amino acids 208 to 941 of SEQ ID NO: 2.
7. An isolated polypeptide that has an amino acid sequence up to 99% identical to SEQ ID NO: 3, comprising at least one sequence selected from the group consisting of amino acids 75 to 95 of SEQ ID NO: 3 and amino acids 148 to 178 of SEQ ID NO: 3.
8. An isolated polypeptide that has an amino acid sequence up to 99% identical to SEQ ID NO: 4, comprising at least a sequence of amino acids 518 to 538 of SEQ ID NO: 4.
9. A nucleic acid encoding the polypeptide of any one of claims 1 -8.
10. The nucleic acid of claim 9 which is comprised in an expression vector.
11. A pharmaceutical composition comprising a therapeutically effective amount of the polypeptide of any one of claims 1-8 in a pharmaceutically acceptable carrier.
12. A pharmaceutical composition comprising a therapeutically effective amount of the expression vector of claim 10, and a pharmaceutically acceptable carrier.
13. An isolated oligonucleotide less than 50 base pairs in length that hybridizes under physiological conditions to an ATGl 4L nucleic acid coding sequence as set forth in SEQ ID NO: 5 or a complementary sequence thereof.
14. An isolated oligonucleotide less than 50 base pairs in length that hybridizes under physiological conditions to an ATGl 4L nucleic acid coding sequence as set forth in SEQ ID NO: 6 or a complementary sequence thereof.
15. The isolated oligonucleotide of claim 13 or 14, which is an RNAi oligonucleotide.
16. The RNAi of claim 15, which has a nucleotide sequence as set forth in SEQ ID NO: 11.
17. The isolated oligonucleotide of claim 13 or 14, which is an antisense oligonucleotide.
18. An isolated oligonucleotide less than 50 base pairs in length that hybridizes under physiological conditions to a Rubicon nucleic acid coding sequence as set forth in SEQ ID NO: 7 or a complementary sequence thereof.
19. An isolated oligonucleotide less than 50 base pairs in length that hybridizes under physiological conditions to a Rubicon nucleic acid coding sequence as set forth in SEQ ID NO: 8 or a complementary sequence thereof.
20. The isolated oligonucleotide of claim 18 or 19, which is an RNAi oligonucleotide.
21. The RNAi of claim 20, which has a nucleotide sequence as set forth in SEQ ID NO: 12.
22. The isolated oligonucleotide of claim 18 or 19, which is an antisense oligonucleotide.
23. An isolated antibody, or antigen binding portion thereof, which binds to an ATG 14L protein having an amino acid sequence as set forth in SEQ ID NO: 1.
24. An isolated antibody, or antigen binding portion thereof, which binds to an ATG 14L protein having an amino acid sequence as set forth in SEQ ID NO: 3.
25. An isolated antibody, or antigen binding portion thereof, which binds to a Rubicon protein having an amino acid sequence as set forth in SEQ ID NO: 2.
26. An isolated antibody, or antigen binding portion thereof, which binds to a Rubicon protein having an amino acid sequence as set forth in SEQ ID NO: 4.
27. A method of increasing autophagic activity in a cell, which comprises administering to the cell an effective amount of an agent which increases or enhances the biological activity of ATGl 4L.
28. The method of claim 27, wherein the agent is selected from the group consisting of an ATG 14L, a functional agonistic fragment thereof, an ATG 14L polypeptide equivalent, an ATG 14L mimetic compound, a therapeutic vector comprising a nucleic acid molecule encoding ATG 14L protein, a binding enhancer which enhances or prolongs the binding between ATG 14L and a class III PI3K/Vρs34-Beclin-l autophagic complex, and a binding enhancer which enhances or prolongs the binding between ATG 14L and Beclin 1.
29. A method of increasing autophagic activity in a cell, which comprises administering to the cell an effective amount of an agent which decreases or inhibits the biological activity of Rubicon.
30. The method of claim 29, wherein the agent is selected from the group consisting of a functional antagonistic fragment of Rubicon, an anti-Rubicon antibody, an anti-Rubicon antibody fragment, an antisense nucleic acid, a ribozyme, and an RNAi.
31. A method of decreasing autophagic activity in a cell, which comprises administering to the cell an effective amount of an agent which increases or enhances the biological activity of Rubicon.
32. The method of claim 31 , wherein the agent is selected from the group consisting of a Rubicon, a functional agonistic fragment thereof, a Rubicon polypeptide equivalent, a Rubicon mimetic compound, a therapeutic vector comprising a nucleic acid molecule encoding Rubicon protein, and a binding enhancer which enhances or prolongs the binding between Rubicon and a class III PI3K/Vps34-Beclin-1 autophagic complex.
33. A method of decreasing autophagic activity in a cell, which comprises administering to the cell an effective amount of an agent which decreases or inhibits the biological activity of ATGl 4L.
34. The method of claim 33, wherein the agent is selected from the group consisting of a functional antagonistic fragment of ATGl 4L, an anti-ATG14L antibody, an anti-ATG14L antibody fragment, an antisense nucleic acid, a ribozyme, and an RNAi.
35. A method of increasing class III PI3K/Vps34 kinase activity in a cell, which comprises administering to the cell an effective amount of an agent which increases or enhances the biological activity of ATGl 4L.
36. The method of claim 35, wherein the agent is selected from the group consisting of an ATGl 4L, a functional agonistic fragment thereof, an ATG 14L polypeptide equivalent, an ATG 14L mimetic compound, a therapeutic vector comprising a nucleic acid molecule encoding ATG 14L protein, a binding enhancer which enhances or prolongs the binding between ATGl 4L and a class III PI3K/Vps34-Beclin-1 autophagic complex, and a binding enhancer which enhances or prolongs the binding between ATG 14L and Beclin 1.
37. A method of increasing class III PI3K/Vps34 kinase activity in a cell, which comprises administering to the cell an effective amount of an agent which decreases or inhibits the biological activity of Rubicon.
38. The method of claim 37, wherein the agent is selected from the group consisting of a functional antagonistic fragment of Rubicon, an anti-Rubicon antibody, an anti-Rubicon antibody fragment, an antisense nucleic acid, a ribozyme, and an RNAi.
39. A method of decreasing class III PI3K/Vps34 kinase activity in a cell, which comprises administering to the cell an effective amount of an agent which increases or enhances the biological activity of Rubicon.
40. The method of claim 39, wherein the agent is selected from the group consisting of a Rubicon, a functional agonistic fragment thereof, a Rubicon polypeptide equivalent, a Rubicon mimetic compound, a therapeutic vector comprising a nucleic acid molecule encoding Rubicon protein, and a binding enhancer which enhances or prolongs the binding between Rubicon and a class III PI3K/Vps34-Beclin-1 autophagic complex.
41. A method of decreasing class III PI3K/Vps34 kinase activity in a cell, which comprises administering to the cell an effective amount of an agent which decreases or inhibits the biological activity of ATGl 4L.
42. The method of claim 41, wherein the agent is selected from the group consisting of a functional antagonistic fragment of ATGl 4L, an anti-ATG14L antibody, an anti-ATG14L antibody fragment, an antisense nucleic acid, a ribozyme, and an RNAi.
43. A method of screening for a compound that binds to an ATGl 4L polypeptide, which comprises (a) providing the ATG 14L polypeptide; (b) contacting a candidate compound with ATG 14; and (c) determining whether the candidate compound has bound to the ATG 14L polypeptide.
44. A method of screening for a compound that binds to a Rubicon polypeptide, which comprises (a) providing an Rubicon polypeptide; (b) contacting a candidate compound with the Rubicon polypeptide; and (c) determining whether the candidate compound has bound to the Rubicon polypeptide.
45. The method of claim 43, wherein the ATG14L polypeptide is selected from the group consisting of murine ATG 14L protein having an amino acid sequence of SEQ ID NO: 1, a polypeptide having an amino acid sequence that has at least 95% identity with SEQ ID NO: 1, human ATGl 4L protein having an amino acid sequence of SEQ ID NO: 3, and a polypeptide having an amino acid sequence that has at least 95% identity with SEQ ID NO: 3.
46. The method of claim 44, wherein the Rubicon polypeptide is selected from the group consisting of murine Rubicon protein having an amino acid sequence of SEQ ID NO: 2, a polypeptide having an amino acid sequence that has at least 95% identity with SEQ ID NO: 2, human Rubicon protein having an amino acid sequence of SEQ ID NO: 4, and a polypeptide having an amino acid sequence that has at least 95% identity with SEQ ID NO: 4.
47. A transgenic knock-out mouse comprising a disruption in the endogenous ATG 14L gene, wherein disruption of the ATG 14L gene results in decreased expression of ATGl 4L protein.
48. A transgenic knock-out mouse comprising a disruption in the endogenous
Rubicon gene, wherein disruption of the Rubicon gene results in decreased expression of Rubicon protein.
49. A host cell comprising an expression vector coding for an ATG 14L protein or a functional fragment thereof, wherein the host cell expresses ATG 14L protein.
50. A host cell comprising an expression vector coding for a Rubicon protein or a functional fragment thereof, wherein the host cell expresses Rubicon protein.
51. A functional Beclin 1 fusion protein, comprising a tag for detecting the fusion protein, and a mature Beclin 1 having an amino acid sequence set forth in SEQ ID NO: 9 or SEQ ID NO: 10, or an amino acid sequence that has at least 95% sequence identify with SEQ ID NO: 9 or SEQ ID NO: 10, and which retains Beclin 1 biological activity.
52. The functional Beclin 1 fusion protein of claim 51 , wherein the biological activity of the Beclin 1 fusion protein is reduced by no more than 10% compared to the mature Beclin 1.
53. The fusion Beclin 1 fusion protein of claim 51, wherein the tag is green fluorescent protein (GFP).
54. An isolated nucleic acid molecule encoding the functional Beclin 1 fusion protein of claim 51.
55. An expression vector comprising the nucleic acid molecule of claim 54.
56. A transgenic non-human animal comprising the vector of claim 55.
57. A host cell comprising the vector of claim 55.
58. A method of screening for a compound that modulates biological activity of ATG 14L, which comprises (a) contacting ATG 14L with a candidate compound in a manner wherein the candidate compound interacts with ATG 14L; (b) evaluating the biological activity of ATGl 4L; and (c) identifying a candidate compound as a modulator of biological activity of ATGl 4L based upon observing increased or decreased biological activity of ATGl 4L in the presence of the candidate compound compared to a control sample.
59. A method of screening for a compound that modulates biological activity of Rubicon, which comprises (a) contacting Rubicon with a candidate compound in a manner wherein the candidate compound interacts with Rubicon; (b) evaluating the biological activity of Rubicon; and (c) identifying a candidate compound as a modulator of biological activity of Rubicon based upon observing increased or decreased biological activity of Rubicon in the presence of the candidate compound compared to a control sample.
60. A method of treating cancer in a subject, the method comprising administering to said subject a therapeutically effective amount of an agent which increases or enhances the biological activity of ATGl 4L.
61. The method of claim 60, wherein the agent is selected from the group consisting of an ATGl 4L, a functional agonistic fragment thereof, an ATG 14L polypeptide equivalent, an ATG 14L mimetic compound, a therapeutic vector comprising a nucleic acid molecule encoding ATG 14L protein, a binding enhancer which enhances or prolongs the binding between ATG 14L and a class III
PI3K/Vps34-Beclin-1 autophagic complex, and a binding enhancer which enhances or prolongs the binding between ATG 14L and Beclin 1.
62. A method of treating cancer in a subject, the method comprising administering to the subject a therapeutically effective amount of an agent which decreases or inhibits the biological activity of Rubicon.
63. The method of claim 62, wherein the agent is selected from the group consisting of a functional antagonistic fragment of Rubicon, an anti-Rubicon antibody, an anti-Rubicon antibody fragment, an antisense nucleic acid, a ribozyme, and an RNAi.
64. A method of treating neurodegenerative disease in a subject, the method comprising: administering to the subject a therapeutically effective amount of an agent which increases or enhances the biological activity of ATGl 4L.
65. The method of claim 64, wherein the agent is selected from the group consisting of an ATGl 4L, a functional agonistic fragment thereof, an ATG 14L polypeptide equivalent, an ATG 14L mimetic compound, a therapeutic vector comprising a nucleic acid molecule encoding ATG 14L protein, a binding enhancer which enhances or prolongs the binding between ATGl 4L and a class III
PI3K/Vps34-Beclin-1 autophagic complex, and a binding enhancer which enhances or prolongs the binding between ATG 14L and Beclin 1.
66. A method of treating neurodegenerative disease in a subject, the method comprising: administering to the subject a therapeutically effective amount of an agent which decreases or inhibits the biological activity of Rubicon.
67. The method of claim 66, wherein the agent is selected from the group consisting of a functional antagonistic fragment of Rubicon, an anti-Rubicon antibody, an anti-Rubicon antibody fragment, an antisense nucleic acid, a ribozyme, and an RNAi.
68. A method of treating inflammatory diseases in a subject, the method comprising: administering to the subject a therapeutically effective amount of an agent which increases the biological activity of ATGl 4L.
69. The method of claim 68, wherein the agent is selected from the group consisting of an ATG 14L, a functional agonistic fragment thereof, an ATG 14L  polypeptide equivalent, an ATG 14L mimetic compound, a therapeutic vector comprising a nucleic acid molecule encoding ATG 14L protein, a binding enhancer which enhances or prolongs the binding between ATG 14L and a class III PI3K/Vps34-Beclin-1 autophagic complex, and a binding enhancer which enhances or prolongs the binding between ATG 14L and Beclin 1.
70. A method of treating inflammatory diseases in a subject, the method comprising: administering to the subject a therapeutically effective amount of an agent which decreases the biological activity of Rubicon.
71. The method of claim 70, wherein the agent is selected from the group consisting of a functional antagonistic fragment of Rubicon, an anti-Rubicon antibody, an anti-Rubicon antibody fragment, an antisense nucleic acid, a ribozyme, and an RNAi.
72. A method of treating age-related diseases in a subject, the method comprising: administering to the subject a therapeutically effective amount of an agent which increases the biological activity of ATG 14L .
73. The method of claim 72, wherein the agent is selected from the group consisting of an ATGl 4L, a functional agonistic fragment thereof, an ATG 14L polypeptide equivalent, an ATG 14L mimetic compound, a therapeutic vector comprising a nucleic acid molecule encoding ATG 14L protein, a binding enhancer which enhances or prolongs the binding between ATG 14L and a class III
PI3K/Vps34— Beclin- 1 autophagic complex, and a binding enhancer which enhances or prolongs the binding between ATG 14L and Beclin 1.
74. A method of treating age-related diseases in a subject, the method comprising: administering to the subject a therapeutically effective amount of an agent which decreases the biological activity of Rubicon.
75. The method of claim 74, wherein the agent is selected from the group consisting of a functional antagonistic fragment of Rubicon, an anti-Rubicon antibody, an anti-Rubicon antibody fragment, an antisense nucleic acid, a ribozyme, and an RNAi.
76. A method of treating heart diseases in a subject, the method comprising: administering to the subject a therapeutically effective amount of an agent which modulates the biological activity of ATGl 4L.
77. The method of claim 76, wherein the agent increases the biological activity of ATG 14L during ischemia.
78. The method of claim 76, wherein the agent decreases the biological activity of ATG 14L during reperfusion.
79. A method of treating heart diseases in a subject, the method comprising: administering to the subject a therapeutically effective amount of an agent which modulates the biological activity of Rubicon.
80. The method of claim 79, wherein the agent decreases the biological activity of Rubicon during ischemia.
81. The method of claim 79 wherein the agent increases the biological activity of Rubicon during reperfusion.
82. The method of claim 77, wherein the agent is selected from the group consisting of an ATG 14L, a functional agonistic fragment thereof, an ATG 14L polypeptide equivalent, an ATG 14L mimetic compound, a therapeutic vector comprising a nucleic acid molecule encoding ATG 14L protein, a binding enhancer which enhances or prolongs the binding between ATG 14L and a class III PI3K/Vps34-Beclin-1 autophagic complex, and a binding enhancer which enhances or prolongs the binding between ATG 14L and Beclin 1.
83. The method of claim 78, wherein the agent is selected from the group consisting of a functional antagonistic fragment of ATGl 4L, an anti-ATG14L antibody, an anti-ATG14L antibody fragment, an antisense nucleic acid, a ribozyme, and an RNAi.
84. The method of claim 80, wherein the agent is selected from the group consisting of a functional antagonistic fragment of Rubicon, an anti-Rubicon antibody, an anti-Rubicon antibody fragment, an antisense nucleic acid, a ribozyme, and an RNAi.
85. The method of claim 81 , wherein the agent is selected from the group consisting of an Rubicon, a functional agonistic fragment thereof, a Rubicon polypeptide equivalent, a Rubicon mimetic compound, a therapeutic vector comprising a nucleic acid molecule encoding Rubicon protein, and a binding enhancer which enhances or prolongs the binding between Rubicon and a class III PI3K/Vps34- Beclin 1 autophagic complex.
86. A method for evaluating expression of ATG 14L in a cell in a biological sample, which comprises detecting an ATG14L polypeptide in the biological sample.
87. A method for evaluating expression of ATG14L in cells in a biological sample which comprises detecting ATG 14L mRNA in the biological sample.
88. The method of claim 86 or 87, wherein the expression of ATGl 4L correlates to autophagic activity in a manner that increased expression of ATGl 4L indicates increased autophagic activity, and decreased expression of ATGl 4L indicates decreased autophagic activity.
89. The method of claim 86 or 87, wherein the expression of ATGl 4L correlates to class III PI3K/Vps34 kinase acti
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