Patent Docs

Patent Profile: Hana Biosciences Receives Notice of Allowance for Use of Menadione to Treat EGFR Inhibitor-Associated Skin Rash

    By Nate Chongsiriwatana --

Hana Biosciences, Inc. recently announced that it received a Notice of Allowance from the U.S. Patent and Trademark Office for U.S. Application No. 11/886,803, entitled "Vitamin K for Prevention and Treatment of Skin Rash Secondary to Anti-EGFR Therapy" (U.S. Patent Application Publication No. 2009/0209652 A1).  Skin rash is a painful and common side effect of all approved epidermal growth factor receptor (EGFR) inhibitors (such as Tarceva®, Iressa®, Erbitux®, Vectibix®, and Tykerb®) that can limit treatment or make dose reduction necessary.  As its title suggests, the '803 application discloses treatment of EGFR-associated skin rash with vitamin K3 (also known as menadione), a provitamin precursor of vitamin K2.  Once issued, the patent will extend protection for this technology into 2026.  Corresponding foreign applications are pending in Australia, Canada, Europe, Hong Kong, Japan, and Korea, and Hana reports that additional applications relating to the use of menadione have been filed.

The sole independent claim allowed in the '803 application reads:

1.  A method for treating a skin rash secondary to an anti-epidermal growth factor receptor (EGFR) therapy in a subject receiving said therapy, the method comprising applying vitamin K3 to the skin in an amount effective to treat the skin rash.

A Phase I clinical study conducted by Hana demonstrated that a menadione topical lotion was generally well-tolerated, and that menadione was delivered into the skin without appreciable systemic absorption.  Recently, Hana completed enrollment for a proof-of-concept study of vitamin K3 lotion in cancer patients receiving EGFR inhibitor therapy; the company expects to present data from this study and initiate a Phase II trial by the end of 2010.

Patent Profile: Sloning Biotechnology Granted U.S. Patent on Methods for Synthesis of dsDNA Triplet Libraries

    By James DeGiulio --

On April 13, 2010, Sloning Biotechnology announced the issuance of U.S. Patent No. 7,695,906, which covers an optimized method of Slonomics, the company's platform technology.  Slonomics uses a set of double stranded DNA triplets as universal building blocks for the synthesis of combinatorial libraries.  This triplet library contains all possible sequence combinations necessary to build any desired DNA molecule.

In the first phase of Slonomics (see below; click on image to enlarge), the triplet building blocks are sequentially ligated in a series of cycles referred to as elongation.  The output of this elongation phase is a large number of sub-fragments of the target sequence referred to as E-blocks, which together comprise the complete target sequence.  These E-blocks are then assembled in a second synthesis phase, referred to as transposition, to generate the desired DNA.  Adjoining E-blocks are ligated together to create T-blocks, which are then sequentially ligated to generate larger fragments.  This process is repeated until all the blocks are combined into a single DNA molecule comprising the complete sequence.

Although this method is suitable to automation, the standard Slonomics method produces an unacceptable number of side products.  These incomplete side products can ligate in the subsequent transposition reactions and lead to the formation of incomplete T-blocks, thus reducing the yield of the correct product.

The '906 patent describes the particular reaction steps in the elongation process that results in a reduction of undesired by-products, thus increasing the efficacy of the desired nucleic acid molecule.  The patent provides three examples of this optimized process and contains 16 total claims.  The independent claims read as follows:

1. A method for the manufacture of a nucleic acid molecule comprising the steps of:
    (a) providing a first at least partially double-stranded oligonucleotide which has a modification allowing the oligonucleotide to be coupled to a surface, whereby the oligonucleotide comprises a recognition site for a first type IIS restriction enzyme which cuts outside its recognition site, and which oligonucleotide comprises a single-stranded overhang;
    (b) providing a second at least partially double-stranded oligonucleotide whereby the oligonucleotide comprises a recognition site or a part thereof or a sequence which is complementary thereto, for a second type IIS restriction enzyme which cuts outside its recognition site, and which second oligonucleotide comprises a single-stranded overhang;
    (c) ligating the first and the second oligonucleotide via their overhangs generating a first ligation product, wherein the first and second oligonucleotides are not attached to a surface during the ligation;
    (d) immobilising the first ligation product of step (c) to the surface via the modification;
    (e) cutting the immobilised ligation product with the first type IIS restriction enzyme thus releasing an elongated oligonucleotide having an overhang;
    (f) combining the elongated oligonucleotide with a further at least partially double-stranded oligonucleotide which has a modification allowing the oligonucleotide to be coupled, to a surface, whereby the further oligonucleotide comprises a recognition site for a further type IIS restriction enzyme which cuts outside its recognition site and which oligonucleotide comprises a single-stranded overhang, and ligating the elongated second oligonucleotide and the further at least partially double-stranded oligonucleotide via their overhangs forming a further ligation product;
    (g) immobilising the further ligation product to a surface via the modification;
    (h) cutting the further ligation product with the further type IIS restriction enzyme releasing an elongated oligonucleotide having an overhang; and
    (i) optionally, repeating steps f) to h).

2. A method for the manufacture of a nucleic acid molecule comprising the steps of:
    (a) providing a first at least partially double-stranded oligonucleotide which has a modification allowing the oligonucleotide to be coupled to a surface, whereby the oligonucleotide comprises a recognition site for a first type IIS restriction enzyme which cuts outside its recognition site, and which oligonucleotide comprises a single-stranded overhang;
    (b) providing a second at least partially double-stranded oligonucleotide whereby the oligonucleotide comprises a recognition site or a part thereof or a sequence which is complementary thereto, for a second type IIS restriction enzyme which cuts outside its recognition site, and which second oligonucleotide comprises a single-stranded overhang;
    (c) ligating the first and the second oligonucleotide via their overhangs generating a first ligation product, wherein the first and second oligonucleotides are not attached to a surface during the ligation;
    (d) cutting the ligation product with the first type IIS restriction enzyme thus generating an elongated oligonucleotide having an overhang and a shortened first oligonucleotide;
    (e) immobilising the shortened first oligonucleotide on a surface via the modification;
    (f) providing a further at least partially double-stranded oligonucleotide which has a modification allowing the further oligonucleotide to be coupled to a surface, whereby the further oligonucleotide comprises a recognition site for a further type IIS restriction enzyme which cuts outside its recognition site and which oligonucleotide comprises a single-stranded overhang;
    (g) combining the elongated oligonucleotide with the further oligonucleotide and ligating the elongated oligonucleotide and the further oligonucleotide via their overhangs forming a further ligation product;
    (h) cutting the further ligation product with the further type IIS restriction enzyme generating an elongated oligonucleotide having an overhang and a shortened further oligonucleotide; and
    (i) optionally, repeating steps e) to h).

7. A method for the manufacture of a nucleic acid molecule comprising the steps of:
    (a) providing a first at least partially double-stranded oligonucleotide which has a modification allowing the oligonucleotide to be coupled to a surface, whereby the oligonucleotide comprises a recognition site for a first type IIS restriction enzyme which cuts outside its recognition site, and which oligonucleotide comprises a single-stranded overhang, and whereby the oligonucleotide comprises a part of the nucleic acid molecule to be manufactured;
    (b) immobilizing the first oligonucleotide on a surface;
    (c) cutting the first oligonucleotide with the first type IIS restriction enzyme releasing a double stranded oligonucleotide having a single stranded overhang at each end and being a part of the nucleic acid molecule to be manufactured; and
    (d) combining the double stranded oligonucleotide of step c) with a second at least partially double-stranded oligonucleotide which has a modification allowing the oligonucleotide to be coupled to a surface, whereby the oligonucleotide contains a recognition site for a second type IIS restriction enzyme which cuts outside its recognition site, and which oligonucleotide further comprises a single-stranded overhang and a part of the nucleic acid molecule to be manufactured, and ligating the double-stranded oligonucleotide of step c) with the second oligonucleotide, wherein the double-stranded oligonucleotide of step c) and the second oligonucleotide are not attached to a surface during the ligation; whereby the overhang of the second oligonucleotide is essentially complementary to the overhang of the double stranded oligonucleotide of step c).

9. A method for the manufacture of a nucleic acid molecule comprising the following steps:
    (a) providing a first ligation product, whereby the first ligation product consists of a first oligonucleotide moiety comprising a recognition site for a first type IIS restriction enzyme, a second oligonucleotide moiety comprising a recognition site for a second type IIS restriction enzyme and a third oligonucleotide moiety, whereby the third oligonucleotide moiety is a part of the nucleic acid molecule to be manufactured, and whereby the first and the second type IIS restriction enzymes each generate an overhang, whereby the overhang generated by the first type IIS restriction enzyme has a length which is different from the length of the overhang generated by the second type IIS restriction enzyme;
    (b) providing a second ligation product, whereby the second ligation product consists of a first oligonucleotide moiety comprising a recognition site for a third type IIS restriction enzyme, a second oligonucleotide moiety comprising a recognition site for a fourth type IIS restriction enzyme and a third oligonucleotide moiety, whereby the third oligonucleotide moiety is a part of the nucleic acid molecule to be manufactured, and whereby the third and the fourth type IIS restriction enzyme each generate an overhang, whereby the overhang generated by the third type IIS restriction enzyme has a length which is different from the length of the overhang generated by the fourth type IIS restriction enzyme;
    (c) cutting the first ligation product with the second restriction enzyme generating a first cut ligation product and cutting the second ligation product with the fourth restriction enzyme generating a second cut ligation product;
    (d) providing a third at least partially double-stranded oligonucleotide and ligating the third oligonucleotide with the first cut ligation product, wherein the first cut ligation product and the third oligonucleotide are not attached to a surface during the ligation, whereby the third oligonucleotide comprises an overhang which is complementary to the overhang of the first cut ligation product generated in step c) and whereby the third oligonucleotide comprises a recognition site for a fifth IIS restriction enzyme;
(e) providing a fourth at least partially double-stranded oligonucleotide and ligating the fourth oligonucleotide to the second cut ligation product, wherein the second cut ligation product and the fourth oligonucleotide are not attached to a surface during the ligation, whereby the fourth oligonucleotide comprises an overhang which is complementary to the overhang of the second ligation product generated in step c) and whereby the fourth oligonucleotide comprises a recognition site for a sixth type IIS restriction enzyme;
    (f) immobilising the ligation product of step d) and step e) on a surface by means of a modification of the third oligonucleotide and the fourth oligonucleotide;
    (g) cutting the immobilised ligation product of step d) with the fifth type IIS restriction enzyme releasing an oligonucleotide;
    (h) cutting the immobilised ligation product of step e) with the third type IIS restriction enzyme; and
    (i) combining and ligating the oligonucleotide released according to step g) with the immobilised reaction product of step h), whereby the overhang generated by the first and the third restriction enzyme is complementary to the overhang generated by the fifth and sixth restriction enzyme.

James DeGiulio has a doctorate in molecular biology and genetics from Northwestern University and is a third-year law student at the Northwestern University School of Law.  Dr. DeGiulio was a member of MBHB's 2009 class of summer associates, and he can be contacted at degiulio@mbhb.com.

Patent Profile: Kylin Therapeutics Receives Patent Covering pRNA Technology

    By James DeGiulio --

On Apr. 6, 2010, Kylin Therapeutics of West Lafayette, IN announced the issuance of U.S. Patent No. 7,655,787, which broadly covers a number of functionalities for Kylin's lead technology platform, "pRNA," or "packaging RNA."  These functionalities include receptor binding, ribozyme activity, and RNA-interference.  The main feature of pRNA is its ability to enhance RNA stability in cells by altering RNA folding and protecting it from exonuclease degradation.  The '787 patent, which issued on February 2, 2010, is based on principal inventor Peixuan Guo's (below) original discovery of a virally-encoded 120-base RNA involved in bacteriophage DNA packaging.

The '787 patent issued from U.S. Application No. 10/373,612, filed February 24, 2003, and claims the benefit of U.S. Provisional Application No. 60/433,697, filed December 16, 2002.  The patent is also a continuation-in-part of International Application No. PCT/US01/26333, filed August 23, 2001, which claims the benefit of U.S. Provisional Application No. 60/227,393, filed August 23, 2000.

The Examples provided in the patent specification include construction of pRNA chimeras and in vitro pRNA-ribozyme activity assays.  The '787 patent contains 18 total claims covering pRNA chimeras, methods of making the pRNAs, and methods of delivery of DNA encoding the pRNAs.  The five independent claims recite:

1.  A pRNA chimera comprising:
    (a) a pRNA region; and
    (b) a spacer region comprising a biologically active RNA, the spacer region covalently linked at its 5' and 3' ends to the pRNA region, wherein the biologically active RNA specifically binds a pre-identified substrate; wherein the pRNA region comprises:
        (i) in the 5' to 3' direction beginning at the covalent linkage of the pRNA with the 3' end of the spacer region a first loop; a second loop; and a lower stem-loop structure comprising a bulge, a first stem section and a third loop;
        (ii) a second stem section interposed between the spacer region and the stem-loop structure;
        (iii) a third stem section interposed between the stem-loop structure and the first loop;
        (iv) a fourth stem section interposed between the first loop and the second loop; and further comprises
        (v) an opening defining 5' and 3' ends of the pRNA chimera.

14.  A pRNA chimera comprising:
    (a) a pRNA region; and
    (b) a spacer region comprising a biologically active RNA that specifically binds a pre-identified ligand or receptor, the spacer region covalently linked at its 5' and 3' ends to the pRNA region; wherein the pRNA region comprises:
        (i) in the 5' and 3' direction beginning at the covalent linkage of the pRNA with the 3' end of the spacer region a first loop; a second loop; and a lower stem-loop structure comprising a bulge, a first stem section and a third loop;
        (ii) a second stem section interposed between the spacer region and the stem-loop structure;
        (iii) a third stem section interposed between the stem-loop structure and the first loop;
        (iv) a fourth stem section interposed between the first loop and the second loop; and further comprises
        (v) an opening defining 5' and 3' ends of the pRNA chimera.

15. A pRNA chimera comprising:
    (a) a pRNA region; and
    (b) a spacer region comprising a biologically active RNA that comprises at least one of a specific binding activity and an enzymatic activity, the spacer region covalently linked at its 5' and 3' ends to the pRNA region; wherein the pRNA region comprises:
        (i) in the 5' and 3' direction beginning at the covalent linkage of the pRNA with the 3' end of the spacer region a first loop; a second loop; and a lower stem-loop structure comprising a bulge, a first stem section and a third loop;
        (ii) a second stem section interposed between the spacer region and the stem-loop structure;
        (iii) a third stem section interposed between the stem-loop structure and the first loop;
        (iv) a fourth stem section interposed between the first loop and the second loop; and further comprises
        (v) an opening defining 5' and 3' ends of the pRNA chimera.

17. A pRNA chimera comprising:
    (a) a pRNA region; and
    (b) a spacer region comprising a biologically active RNA that does not comprise the nucleotide sequence UAAUACGACUCACUAUA as set forth in SEQ ID NO:8, the spacer region covalently linked at its 5' and 3' ends to the pRNA region, wherein the biologically active RNA specifically binds a pre-identified substrate; wherein the pRNA region comprises:
        (i) in the 5' to 3' direction beginning at the covalent linkage of the pRNA with the 3' end of the spacer region a first loop; a second loop; and a lower stem-loop structure comprising a bulge, a first stem section and a third loop;
        (ii) a second stem section interposed between the spacer region and the stem-loop structure;
        (iii) a third stem section interposed between the stem-loop structure and the first loop;
        (iv) a fourth stem section interposed between the first loop and the second loop; and further comprises
        (v) an opening defining 5' and 3' ends of the pRNA chimera.

18.  A pRNA chimera comprising:
    (a) a pRNA region; and
    (b) a spacer region comprising a biologically active RNA, the spacer region covalently linked at its 5' and 3' ends to the pRNA region, wherein the biologically active RNA binds a pre-identified substrate and comprises a polyribonucleotide selected from the group consisting of an RNA of at least 25-100, 46, 47, 63, 66, 94, 120, 168 and 188 nucleotides, wherein the pRNA region comprises:
        (i) in the 5' to 3' direction beginning at the covalent linkage of the pRNA with the 3' end of the spacer region a first loop; a second loop; and a lower stem-loop structure comprising a bulge, a first stem section and a third loop;
        (ii) a second stem section interposed between the spacer region and the stem-loop structure;
        (iii) a third stem section interposed between the stem-loop structure and the first loop;
        (iv) a fourth stem section interposed between the first loop and the second loop; and further comprises
        (v) an opening defining 5' and 3' ends of the pRNA chimera.

James DeGiulio has a doctorate in molecular biology and genetics from Northwestern University and is a third-year law student at the Northwestern University School of Law.  Dr. DeGiulio was a member of MBHB's 2009 class of summer associates, and he can be contacted at degiulio@mbhb.com.

Patent Profile: Athersys Obtains U.S. and European Patents for Non-Embryonic Multipotent Stem Cells

    By James DeGiulio --

On February 9th, Athersys, Inc. was issued U.S. Patent No. 7,659,118 covering multipotent adult stem cells (MASC), their isolation and expansion, and related pharmaceutical compositions.  In a February 10, 2010 press release, the Cleveland-based company also announced the grant of European patent EP 1 218 489 B1, the counterpart to the '118 patent.  Athersys adds these patents to an already robust patent portfolio covering its stem cell technology, which includes fourteen patents and more than 120 global patent applications.

Both the '118 and '489 patents cover the company's MultiStem technology, which is an investigational stem cell therapy that has demonstrated therapeutic potential to treat a range of problems, including heart attack, stroke, bone marrow transplant rejection, and inflammatory bowel disease.  MultiStem has the ability to produce a range of factors and form multiple cell types.  MultiStem promotes tissue repair and healing in multiple ways, such as through the production of multiple therapeutic factors produced in response to signals of inflammation and tissue damage.  Unlike traditional stem cell therapies that aim to replace damaged tissue, MultiStem produces factors that regulate the immune system, protect damaged or injured cells, and promote tissue repair and healing, giving the therapy a more drug-like effect.  Thus, the company believes that MultiStem represents a unique "off-the-shelf" stem cell product.

The '118 patent describes the advantages of using cells from the developed individual rather than an embryo, specifically overcoming the problem of tissue incompatibility.  The claimed MASC are negative for many common antigens, including CD44, CD45, and HLA class I and II.  The MASC express transcription factors Oct3/4, REX-1, and ROX-1, express telomerase, and respond to the growth factor LIF.  The patent describes the method of MASC isolation from human bone marrow, after which the MASC can be maintained in undifferentiated state or differentiated into several cell types, depending on desired use.  The MASC are also suited for ex vivo genetic alteration prior to introduction or engraftment into a human patient.  The MASC are described as efficient for a number of uses, including cancer treatment, tissue damage repair, induction of immune responses to fight infection, and cardiovascular therapy.  The patent contains 11 examples, which describe the isolation, differentiation, development, characterization, and engraftment of the cells.

Both the U.S. and European patents claim the MASCs and pharmaceutical compositions, as well as methods for their production.  The '489 patent contains 21 claims, additionally claiming the use of the MASC for agent screening applications.  The '118 patent contains 12 claims; representative claims include:

1.  A cell culture comprising isolated expanded human multipotent, non-embryonic, non-germ cells that can differentiate into at least one cell type of each of the endodermal, ectodermal, and mesodermal embryonic lineages and express telomerase, said cells having undergone at least 10-40 cell doublings in culture.

9.  A pharmaceutical composition comprising a pharmaceutically acceptable carrier and isolated expanded human multipotent, non-embryonic, non-germ cells that can differentiate into at least one cell type of each of the endodermal, ectodermal, and mesodermal embryonic lineages and express telomerase, said cells having undergone at least 10-40 cell doublings in culture, said cells obtained from the cell culture of claim 1 or 2.

10.  A method for making a pharmaceutical composition comprising admixing a pharmaceutically acceptable carrier and isolated expanded human multipotent, non-embryonic, non-germ cells that can differentiate into at least one cell type of each of the endodermal, ectodermal, and mesodermal embryonic lineages and express telomerase, said cells having undergone at least 10-40 cell doublings in culture, said cells obtained from the cell culture of claim 1 or 2.

In a December 2009 press release, Athersys announced a strategic partnership with Pfizer under which the companies will jointly develop MultiStem for inflammatory bowel disease, and a partnership with Angiotech to develop MultiStem in acute myocardial infarction and other cardiovascular indications.  Athersys is still seeking partners to develop MultiStem for stroke victims as well as leukemia patients who have rejected bone marrow treatments.

On February 16, 2010, Athersys, Inc. announced that it has completed patient enrollment for its phase I clinical trial which will test administration of Multistem to individuals following acute myocardial infarction.

James DeGiulio has a doctorate in molecular biology and genetics from Northwestern University and is a third-year law student at the Northwestern University School of Law.  Dr. DeGiulio was a member of MBHB's 2009 class of summer associates, and he can be contacted at degiulio@mbhb.com.

Patent Profile: NexBio Granted U.S. Patent for Flu Therapeutic

    By James DeGiulio --

Last week, NexBio, Inc. announced the issuance of U.S. Patent No. 7,645,448, entitled "Class of Therapeutic Protein Based Molecules."  The '448 patent, issued January 12, 2010, is the company's first issued U.S. patent.  The patent covers NexBio's sialidase pharmaceutical compositions, including its lead compound DAS181 (Fludase®) and methods of treating or preventing viral infection by influenza and parainfluenza with such compositions.

Fludase® (at left) is a recombinant fusion protein that inactivates sialic viral receptors on the cells of the human respiratory tract, thereby preventing all types of influenza (including H1N1) and other viruses from both infecting the human body and amplifying in already-infected individuals.  Fludase® is currently undergoing a Phase II clinical trial for the treatment of community-acquired influenza.  More information on the clinical trial can be found here.

Current antivirals target the virus particle and thus are limited by virus resistance.  According to the patent, NexBio's technology is not limited by virus resistance because its compounds target the virus point of attachment and entry on cells, rather than the virus itself.  The patent further discloses the use of these compounds to enhance gene delivery for gene therapy applications.  Finally, the patent contains several examples of synthesizing sialidase proteins and corresponding functional assays.

The 21 allowed claims cover the peptides, pharmaceutical compositions, and methods of treating or preventing viral infection.  Representative claims include:

1.  An isolated polypeptide comprising an amino acid sequence that begins at any of the amino acids from amino acid 270 to amino acid 290 of the Actinomyces viscosus sialidase protein sequence (SEQ ID NO:12) and ends at any of the amino acids from amino acid 665 to amino acid 901 of the Actinomyces viscosus sialidase protein sequence (SEQ ID NO:12), wherein the isolated polypeptide does not comprise the sequence extending from amino acid 1 to amino acid 269 of SEQ ID NO:12 and wherein the isolated polypeptide has sialidase activity.

7.  A pharmaceutical formulation comprising the isolated polypeptide of claim 1.

9.  A method of treating or preventing viral infection by influenza, comprising:
    applying a therapeutically effective amount of the formulation of claim 7 to epithelial cells of a subject.

James DeGiulio has a doctorate in molecular biology and genetics from Northwestern University and is a third-year law student at the Northwestern University School of Law.  Dr. DeGiulio was a member of MBHB's 2009 class of summer associates, and he can be contacted at degiulio@mbhb.com.

Patent Profile: Fate Therapeutics to Receive First U.S. Patent for Induced Pluripotent Stem Cell Technology

    By James DeGiulio --

This week, Fate Therapeutics of San Diego, CA was issued a Notice of Allowance for U.S. Application No. 10/997,146 (U.S. Patent Application Publication No. 2008/0280362), titled "Methods for Reprogramming Somatic Cells."  With a priority date of November 26, 2003, the application is believed to contain the earliest allowed claims in the United States for induced pluripotent stem cell technology.  Upon issuance, the invention by Rudolf Jaenisch, M.D. (below left), founding member of the Whitehead Institute for Biomedical Research and scientific founder of Fate Therapeutics, will cover methods for generating pluripotent stem cells and compositions for identifying agents that enable the reprogramming of human somatic cells.

The application first describes the need for alternative methods of generating human pluripotent cells without using embryos, oocytes, or nuclear transfer technology and how reprogrammed somatic cells can enable autologous cell therapy, including the treatment of neurological diseases.  The application describes novel methods of reprogramming somatic cells by introducing certain pluripotency genes, such as Oct4, Nanog, or Sox2.  The application further covers compositions used in screening for agents to generate these pluripotent cells, including genes, classes of small molecules, or pluripotency proteins.  The application's lone Example describes the generation of a transgenic mouse by integration of an inducible Oct-4 gene and the resulting enhanced stem cell populations.

After a series of amendments, including an examiner's amendment, twelve total claims were allowed, including three independent claims:

17.  A primary somatic cell comprising in its genome a first endogenous pluripotency gene operably linked to DNA encoding a first selectable marker in such a manner that expression of the first selectable marker substantially matches expression of the first endogenous pluripotency gene, wherein the cell additionally comprises an exogenously introduced nucleic acid encoding a pluripotency protein and operably linked to at least one regulatory sequence, wherein the endogenous pluripotency gene is a gene that is expressed in a pluripotent embryonic stem cell, is required for the pluripotency of the embryonic stem cell, and is downregulated as the embryonic stem cell differentiates, and wherein the pluripotency protein is a protein expressed in a pluripotent embryonic stem cell, and is downregulated as the embryonic stem cell differentiates.

36.  A primary somatic cell comprising in its genome a first endogenous pluripotency gene operably linked to DNA encoding a first selectable marker in such a manner that expression of the first selectable marker substantially matches expression of the first endogenous pluripotency gene, wherein the first endogenous pluripotency gene encodes Oct4 or Nanog, and wherein the cell additionally comprises an exogenously introduced nucleic acid encoding Oct4, Nanog, or Sox2 and operably linked to at least one regulatory sequence.

38.  A composition comprising:
    (i)  a primary somatic cell comprising in its genome a first endogenous pluripotency gene operably linked to DNA encoding a first selectable marker in such a manner that expression of the first selectable marker substantially matches expression of the first endogenous pluripotency gene, and additionally comprising an exogenously introduced nucleic acid encoding Oct4, Nanog, or Sox2 and operably linked to at least one regulatory sequence; and
    (ii)  a candidate agent of interest with respect to its potential to reprogram a somatic cell, wherein the first endogenous pluripotency gene encodes Oct4 or Nanog.

James DeGiulio has a doctorate in molecular biology and genetics from Northwestern University and is a third-year law student at the Northwestern University School of Law.  Dr. DeGiulio was a member of MBHB's 2009 class of summer associates, and he can be contacted at degiulio@mbhb.com.

Patent Profile: Advaxis Granted New U.S. Patent in Protein Adjuvant Technology Portfolio

    By Sherri Oslick --

Last week, Advaxis, Inc., a biotechnology corporation focused on using a bioengineered bacterium, Listeria monocytogenes (Lm), to activate the immune system to treat cancer, infectious disease, or allergic syndromes, was issued U.S. Patent No. 7,588,930 ("Compositions and Methods for Enhancing the Immunogenicity of Antigens").  The '930 patent is directed to the use of Lm protein ActA and fragments thereof for use in the creation of antigen fusion proteins; the ActA protein was found to possess immuno-adjuvant properties.  The patent is assigned to The Trustees of the University of Pennsylvania, and licensed exclusively by Advaxis.

The claims are directed to Lm vaccine strains comprising an antigen fused to a truncated ActA protein, as well as methods of eliciting an enhanced immune response to an antigen using the claimed vaccine strains.  Representative claims include:

1.  A Listeria monocytogenes vaccine strain comprising an antigen fused to a truncated ActA protein, wherein said truncated ActA protein consists of amino acids 1-390 of said ActA protein; wherein said truncated ActA protein comprises a PEST-like sequence selected from the sequences set forth in SEQ ID No: 2-5; and wherein said antigen is selected from the group consisting of human papilloma virus (HPV) E6, HPV E7, Her-2/Neu, NY-ESO-1, human telomerase, WT-1, proteinase 3, TRP-2 and PSA antigen.

6.  A method of eliciting an enhanced immune response to an antigen, the method comprising administering to a subject an effective amount of a composition comprising a Listeria monocytogenes vaccine strain comprising said antigen fused to a truncated ActA protein, wherein said truncated ActA protein consists of amino acids 1-390 of said ActA protein; and wherein said truncated ActA protein comprises a PEST-like sequence selected from the sequences set forth in SEQ ID No: 2-5; and wherein said antigen is selected from the group consisting of human papilloma virus (HPV) E6, HPV E7, Her-2/Neu, NY-ESO-1, human telomerase, WT-1, proteinase 3, TRP-2, and PSA antigen.

This patent adds to Advaxis' patent portfolio directed toward creating specific and effective vaccines by using a variety of antigens and adjuvant proteins to target different types of cancers and infectious disease indications.

Patent Profile: OncoGenex Announces Issuance of Patent for Antisense Cancer Therapeutic

    By Donald Zuhn --

Last month, OncoGenex Pharmaceuticals, Inc. announced that the U.S. Patent and Trademark Office had issued U.S. Patent No. 7,569,551.  The '551 patent is directed to a method of enhancing cancer cell chemo- or radiation-sensitivity using an antisense oligodeoxynucleotide targeted against the testosterone-repressed prostate message-2 (TRPM-2) gene.  The inventors found that that administration of TRPM-2 antisense oligodeoxynucleotides can reduce the expression of TRPM-2, and as a result enhance the sensitivity of cancer cells to chemotherapeutic agents or radiotherapy either in vitro and in vivo.  While the '551 patent is assigned to the University of British Columbia, Oncogenex notes that it has exclusively licensed the patent.

According to the biopharmaceutical company's announcement, the '551 patent encompasses methods for treating cancers that express the protein clusterin (the historical name for TRPM-2) using Oncogenex's lead cancer drug candidate, OGX-011 (also known as custirsen sodium), or any other clusterin antisense oligonucleotide, in combination with any chemotherapeutic agent or radiation therapy.  Oncogenex President and CEO Scott Cormack stated that the '551 patent "expands [the company's] intellectual property estate for treating clusterin-expressing cancers using antisense therapy and provides us with a broad patent that applies well beyond prostate cancer."

The Onogenex release also notes that OGX-011 utilizes antisense technology licensed from Isis Pharmaceuticals, and that OncoGenex and Isis partnered in the discovery and initial development of OGX-011.  Last year, OncoGenex and Isis amended their agreement involving OGX-011 to provide OncoGenex with sole rights to the molecule and sole responsibility for its development, subject to financial obligations to Isis.  The company's website states that preliminary data in a Phase 2 clinical trial evaluating OGX-011 in combination with second-line chemotherapy in patients with hormone refractory prostate cancer has shown that retreatment with docetaxel in combination with OGX-011 may reverse docetaxel resistance and improve patient survival.  OGX-011 is also being tested for use in the treatment of non-small cell lung cancer and breast cancer.

The '551 patent issued from U.S. Application No. 09/967,726, filed September 28, 2001, which is a continuation-in-part of U.S. Application No. 09/913,325, filed August 10, 2001, which is a national stage application of International Application No. PCT/US00/0487, filed February 25, 2000, and claims the benefit of U.S. Provisional Application No. 60/236,301, filed September 28, 2000.  Independent claims 1 and 36 of the '551 patent recite:

1.  A method for enhancing the chemo- or radiation sensitivity of cancer cells in an individual suffering from a cancer that expresses TRPM-2 in amounts different from normal tissue of the same type, comprising treating the individual with either chemotherapy or radiation therapy and administering to the individual a composition comprising an oligonucleotide targeted to TRPM-2 and effective to inhibit expression of TRPM-2 by cancer cells during at least a portion of the time that the chemotherapy or radiation therapy is active against cancer cells.

36.  A method for treating a cancer which expresses TRPM-2 before or after treatment with a chemotherapy agent, comprising administering to an individual suffering from the cancer a chemotherapeutic agent which is at least partially effective against the cancer and a an oligonucleotide which is targeted to TRPM-2 and reduces the amount of TRPM-2 in cancer cell.

Patent Profile: Cytori Receives Notice of Allowance for Use of Adipose-Derived Stem Cells in Bone Disorders

    By Mark Chael --

Recently, Cytori Therapeutics, Inc. announced that the U.S. Patent and Trademark Office had issued a Notice of Allowance for claims directed to prosthetic devices seeded with adipose-derived stem cells.  According to the press release, these claims are related to the use of Cytori's Celution® System for the treatment of bone diseases.

Although not specified in Cytori's recent press release, a quick review of the online databases at the USPTO indicates that on June 23, 2009, a Notice of Allowance was issued in U.S. Patent App. No. 10/885,293 (U.S. Patent App. Pub. No. 2005/0058632) in response to the applicants' filing of amended claims, which included the following:

1.  A method of processing adipose tissue that comprises a population of cells comprising adipose-derived stem cells for reintroduction into a patient, comprising:
    removing unprocessed adipose tissue that comprises a cell population comprising adipose-derived stem cells from said patient;
    introducing the removed adipose tissue into a self-contained adipose-derived stem cell processing unit configured to maintain a closed system where said self contained adipose-derived stem cells processing unit comprises

   a tissue collection chamber that is configured to receive unprocessed adipose tissue that is removed from said patient, wherein the tissue collection chamber is defined by a closed system;
    a first filter that is disposed within said tissue collection chamber, wherein said first filter is configured to retain a first component of said unprocessed adipose tissue and pass a second component of said unprocessed adipose tissue, such that said first filter separates said first component from said second component, and wherein said first component comprises a cell population comprising adipose-derived stem cells and said second component comprises lipid, mature adipocytes, and saline;
    a processing chamber, which is configured to receive said first component comprising said population of cells comprising adipose-derived stem cells from said tissue collection chamber, wherein said processing chamber is within said closed system;
    a conduit configured to allow passage of said first component comprising said cell population comprising adipose-derived stem cells from said tissue collection chamber to said processing chamber while maintaining a closed system;
    a cell concentrator disposed with said processing chamber, which is configured to facilitate the concentration of said first component comprising said cell population comprising adipose-derived stem cell so as to obtain a concentrated population of cells comprising adipose-derived stem cells, wherein said cell concentrator comprises a centrifuge or a filter; and
    an outlet configured to allow the aseptic removal of said concentrated population of cells comprising adipose-derived stem cells;

    processing said removed, unprocessed adipose tissue to obtain said concentrated population cell comprising adipose-derived stem cells; and
    introducing said concentrated population of cells that comprises adipose-derived stem cells into a prosthetic device, wherein said prosthetic device comprises a cell carrier portion and a cell carrier containment portion, and wherein said concentrated population of cells comprising adipose-derived stem cells is introduced into said cell carrier portion of said prosthetic device.

3.  The method of claim 1, wherein said patient has a bone related disorder.

Cytori and its proprietary system were profiled in 2006 by the San Diego Union Tribune.  Also, as Patent Docs reported previously, Cytori is assembling a significant portfolio of patents and patent applications covering various uses of adipose-derived stem cells and methods for their isolation.

According to information available from Cytori's website, the Celution® System consists of a cell processing device, single use consumables and related instrumentation and reagents.  The cell processing device "rapidly and reliably delivers a clinical grade, mixed population of non-cultured adipose derived stem and regenerative cells at the patient's beside."  Cytori does not sell these cells as a pharmaceutical product, unlike other stem cell commercialization enterprises, but rather commercializes the cell processing device, related instruments, consumables, and other reagents.

Patent Profile: Immunomedics Announces Patent for Dock-and-Lock Antibody Assemblies

    By Mark Chael --

On May 5th, Immunomedics, Inc. announced that its majority-owned subsidiary, IBC Pharmaceuticals, Inc., was granted U.S. Patent No. 7,527,787, entitled "Multivalent Immunoglobulin-based Bioreactive Assemblies."  Claim 1 from the patent reads:

1.  A hexameric stably tethered structure comprising an IgG antibody attached to two AD2 moieties of SEQ ID NO: 4 and four antigen-binding antibody fragments of the same or different IgG with each fragment attached to a DDD2 moiety of SEQ ID NO: 2; the AD2 moieties bound to the DDD2 moieties.

The four antigen-binding antibody fragments can be Fab fragments.  In particular, these Fab fragments can be the Fab fragments of humanized antibody hMN-14 that binds to CEA, humanized antibody hA20 that binds to CD20, humanized antibody hLL2 that binds to CD22, humanized antibody hL243 that binds to HLA class II, humanized antibody hCC49 that binds to TAG-72, humanized antibody hLL1 that binds to CD74, humanized antibody hPAM4 that binds to MUC 1, humanized antibody hRS7 that binds to EGP-1, humanized antibody hR1 that binds to IGF1R, anti-CD 14, anti-CD 111, adalimumab, infliximab, omalizumab, palivizumab, and humanized antibody hMN-15 that binds to CEA.

The abbreviation "AD" in claim 1 refers to the Anchoring Domain of A-kinase anchoring proteins (AKAPs), while "DDD" refers to the Dimerization and Docking Domain of cyclic-AMP-dependent protein kinase (PKA).  These two domains cooperate in this Dock-and-Lock (DNL) technology.

According to a recent paper authored by the inventors of the '787 patent (and others), the Dock-and-Lock technology is:

[A] new approach to develop targeting molecules for improved cancer imaging and therapy.  It involves the use of a pair of distinct protein domains involved in the natural association between cyclic adenosine monophosphate (cAMP)-dependent protein kinase A (PKA) and A-kinase anchoring proteins (AKAPs).  The dimerization and docking domain found in the regulatory subunit of PKA and the anchoring domain (AD) of an interactive AKAP are each attached to a biologic entity, and the resulting derivatives, when combined, readily form a stably tethered complex of a defined composition that fully retains the functions of the individual constituents.

Another recent patent assigned to IBC Pharmaceuticals, U.S. Patent No. 7,521,056, relates to the same technology as the '787 patent.  These two patents may be the first drawn to the PKA/AKAP Dock-and-Lock technology.

Other similar, so-called Dock-and-Lock systems are known.  For example, scientists at SibTech, Inc. published a report in 2006 about such a system "based on mutated fragments of human RNase I that spontaneously bind to each other and form a conjugate with a disulfide bond between complimentary cysteine residues."  Each of the mutated RNase I fragments may be independently linked to functionally heterogeneous compounds.

Patent Profile: ImmunoCellular Therapeutics Announces Issuance of Patent for Method of Monitoring Myeloma or Ovarian Cancer Therapy

    By Mark Chael --

On April 29, 2009, ImmunoCellular Therapeutics, Ltd. announced that the U.S. Patent and Trademark Office issued Patent No. 7,498,129, which relates to the company's monoclonal antibody platform.  The '129 patent is entitled "Myeloma Cell and Ovarian Cancer Cell Surface Glycoproteins, Antibodies Thereto, and Uses Thereof," and according to ImmunoCellular, is directed to the use of the company's antibodies to measure the effectiveness of proposed treatments for multiple myeloma and ovarian cancer.

Claim 1 of the '129 patent reads as follows:

1.  A method for monitoring the effectiveness of therapy for a myeloma or ovarian cancer, comprising:
    a) measuring changes in the level of the antigen recognizable by a monoclonal antibody or antigen binding fragment thereof in a bodily fluid sample from a patient undergoing therapy, wherein said monoclonal antibody is produced by the hybridoma cell line deposited at the American Type Culture Collection having accession No. PTA-450; and
    b) correlating the change in the level with the effectiveness of said therapy, wherein a decrease in the level indicates a reduced tumor burden.

In 2007, ImmunoCellular acquired a portion of its monoclonal antibody-related technology from Molecular Discoveries.  One such monoclonal antibody, ICT-109, targets small cell lung cancer (SCLC) and pancreatic cancer.  ICT-109 is currently in pre-clinical development, and is useful as a diagnostic reagent to prescreen patients for the specific antigens to which it binds.  According to ImmunoCellular, this antibody has shown encouraging preliminary data in pre-clinical studies and may be ready to enter clinical trials in the near future for SCLC and/or pancreatic cancer.

According to the assignment database  at the USPTO, ImmunoCellular is the assignee of record on at least seven patents and one published patent application.

Patent Profile: Raptor Pharmaceuticals Secures Allowances for Brain Drug Delivery Methods

    By Mark Chael --

On April 29, 2009, Raptor Pharmaceuticals Corp. announced that the U.S. Patent and Trademark Office recently issued Notices of Allowance for two of its pending patent applications related to methods of delivering drugs to the brain.  The Notices were issued for U.S. Patent Application Nos. 10/812,849 and 11/202,566.  The published applications are entitled "Megalin-based Delivery of Therapeutic Compounds to the Brain and Other Tissues" and "Use of the Chaperone Receptor-associated Protein (RAP) for the Delivery of Therapeutic Compounds to the Brain and Other Tissues," respectively.  These applications are directed to the company's NeuroTrans™ drug delivery platform.

An exemplary allowed claim from the '849 patent application reads as follows:

1.  A method of delivering an active agent into the central nervous system of an animal comprising administering to said animal a conjugate comprising said agent conjugated to a Receptor Associated Protein (RAP) polypeptide consisting of an amino acid sequence at least 80% identical to amino acids 221-323 of RAP (SEQ ID NO:1), wherein said RAP polypeptide retains megalin-binding activity and wherein said agent is delivered into the central nervous system.

Similarly, one of the allowed claims from the '566 patent application reads as follows:

1.  A method of delivering a therapeutic or diagnostic/investigational agent across the blood brain barrier (BBB) into the central nervous system in a subject in need thereof, said method comprising:  administering to said subject a chimeric RAP fusion protein comprising said therapeutic or diagnostic/investigational agent, wherein the RAP portion of the chimeric RAP fusion protein consists of an amino acid sequence at least 80% identical to amino acids 221-323 of SEQ ID NO:1.

According to Raptor's website, the company was founded in 2005 by former executives and scientists from BioMarin Pharmaceutical, Inc.  In January 2006, Raptor acquired the intellectual property for the NeuroTrans™ program from BioMarin.  Since its incorporation in 2005, Raptor has completed five product and technology acquisitions, including Convivia™, which addresses the toxicity associated with ALDH2 deficiency, and DR Cysteamine, which may be useful for a variety of clinical applications.

The assignment databases at the USPTO list Raptor Pharmaceutical, Inc. as the assignee of four patent applications, and BioMarin Pharmaceutical as the assignor or assignee of a number of patents and applications.

Patent Profile: Ryogen Announces Issuance of Two Genomics Patents

    By Donald Zuhn --

Ryogen LLC recently announced that the U.S. Patent and Trademark Office had issued U.S. Patent Nos. 7,468,266 and 7,470,522.  The '266 patent is directed to an isolated genomic polynucleotide encoding human lipoprotein-associated phospholipase A2, as well as vectors and host cells comprising such polynucleotides, antisense oligonucleotides to such polynucleotides, and methods for modulating human lipoprotein-associated phospholipase A2 levels in a subject using such polynucleotides.  The '522 patent is directed to an isolated genomic polynucleotide encoding human resistin or human syntaxin binding protein 2, as well as vectors and host cells comprising such polynucleotides, antisense oligonucleotides to such polynucleotides, and methods for obtaining a polypeptide that inhibits insulin activity. 

A search of the USPTO Patent Full-Text and Image Database indicates that the '266 and '522 patents are the Suffern, NY-based genetic company's second and third U.S. patents (see "Ryogen Announces Issuance of Patent on Soluble Aminopeptidase P Gene").  According to Ryogen's website, the company, which is a portfolio company of IP Holdings LLC, was formed for the purpose of licensing U.S. Patent Nos. 6,399,349 and 7,273,718.

In Ryogen's statement regarding the issuance of the two patents, Ryogen Chief Scientist (and named inventor on both patents) Dr. James Ryan noted that the proteins encoded by the claimed genes are "thought to play important roles in serious human diseases."  In particular, human lipoprotein-associated phospholipase A2 is believed to play a central role in the development of atherosclerosis, serves as an independent risk factor for coronary artery disease, and its level of expression has been found to be altered in patients with systemic lupus erythematosis, stroke, and asthma.  Resistin is believed to provide a link between obesity and Type 2 diabetes.  Ryogen Executive Vice President Valeria Poltorak stated that Ryogen was "planning to license the newly issued patents and make these genes widely available for research to promote the development of new methods of genetic diagnostics and treatment."

The '266 patent issued on December 23, 2008 from U.S. Application No. 10/161,127, filed May 30, 2002, which claims the benefit of U.S. Provisional Application No. 60/294,404, filed May 30, 2001.  Independent claims 1, 8, and 10 of the '266 patent recite:

1.  An isolated genomic polynucleotide selected from the group consisting of:
    (a) a polynucleotide which is at least 99% identical to the polynucleotide of SEQ ID NO:2, which encodes a polypeptide which is at least 99% identical to the amino acid sequence of SEQ ID NO:1, wherein said polypeptide has human lipoprotein-associated phospholipase A2 activity;
    (b) a fragment of (a) comprising at least nucleotides 11967-30301, which encodes a polypeptide which is at least 99% identical to the amino acid sequence of SEQ ID NO:1, wherein said polypeptide has lipoprotein-associated phospholipase A2 activity; and
    (c) the full complement of (a) or (b).

8.  An isolated polynucleotide selected from the group consisting of (a) SEQ ID NO:2, which encodes lipoprotein-associated phospholipase A2 of SEQ ID NO:1; (b) a fragment of (a) comprising at least nucleotides 11967-30301 of SEQ ID NO:2, which encodes lipoprotein-associated phospholipase A2 of SEQ ID NO:1 and (c) the full complement of (a) or (b).

10.  A method of identifying a polynucleotide of SEQ ID NO:2, which encodes a lipoprotein-associated phospholipase A2 of SEQ ID NO:1, or its complementary sequence comprising:
    (a) isolating genomic DNA from a subject and
    (b) determining the presence or absence of a polynucleotide identical to the polynucleotide of SEQ ID NO:2 in a subject by comparing the nucleotide sequence of SEQ ID NO:2 with the nucleotide sequence of the isolated genomic DNA.

The '522 patent issued on December 30, 2008 from U.S. Application No. 11/483,373, filed July 7, 2006, which claims the benefit of U.S. Provisional Application No. 60/697,815, filed July 9, 2005.  Independent claims 1 and 12 recite:

1.  An isolated genomic nucleic acid molecule, said nucleic acid molecule selected from the group consisting of:
    (a) a nucleic acid molecule consisting of a nucleic acid sequence which has at least 99% identity to the nucleic acid molecule of SEQ ID NO: 3 and which encodes a polypeptide having the amino acid sequence of SEQ ID NO: 1, wherein said polypeptide inhibits the action of insulin;
    (b) a fragment of the nucleic acid molecule of (a), said fragment comprising at least nucleotides 19611-20633 of SEQ ID NO: 3 and which encodes a polypeptide having the amino acid sequence of SEQ ID NO: 1, wherein said polypeptide inhibits the action of insulin, and;
    (c) a nucleic acid molecule that is the full complement of the nucleic acid molecule of (a) or (b).

12.  A method of identifying a nucleotide sequence variant of the 5'-noncoding region, 3'-noncoding region or intron region of SEQ ID NO: 3 or its complementary sequence comprising:
    (a) isolating genomic DNA from a subject and
    (b) determining the presence or absence of a nucleotide sequence variation in said genomic DNA by comparing the nucleotide sequence of SEQ ID NO: 3 with the nucleotide sequence of the isolated genomic DNA and establishing if and where a difference occurs between the two nucleic acid sequences thereby identifying a nucleotide sequence variant of SEQ ID NO: 3, or its complement.

Patent Profile: Thrasos Therapeutics Announces Issuance of U.S. Patent No. 7,482,329

    By Sherri Oslick --

Thrasos Therapeutics, a Hopkinton, MA based biotechnology company, announced earlier this week the issuance of U.S. Patent No. 7,482,329 ("Single Domain TDF-Related Compounds and Analogs Thereof," issued January 27, 2009) directed to small molecules that selectively activate the key receptors of the bone morphogenetic protein (BMP) family.  BMPs are part of the TGF-β superfamily of proteins, and are implicated, via the SMAD signaling pathway, in the reduction and control of inflammation and fibrosis and in the prevention of apoptosis in many different cells, tissues, and organs.  BMPs are also implicated in the stimulation of the growth of cartilage and bone.

The claimed compounds selectively target key receptors of the BMP family of proteins to specifically activate the repair and regenerative effects of BMP, without stimulating bone growth, providing cell and tissue protection, repair and regenerative treatment without bone growth stimulation.  The compounds in particular offer promise in the treatment of Acute Kidney Injury and Chronic Kidney Disease.

Claim 1 of the patent recites:

1.  A compound comprising an amino acid sequence selected from the group consisting of
SEQ ID NO.45 (H)-CYFDDSSNVLCKKYRS-(OH)
SEQ ID NO.33 (H)-CYFDDSSNVLCKKYRS-(NH2)
SEQ ID NO.24 (H)-CYFDDSSNVICKRYRS-(OH)
SEQ ID NO.43 (H)-CYFDDSSOVLCKKYRS-(OH)