# US 2014/0193392 A1 · Methods and compositions to detect the level of lysosomal exocytosis activity and methods of use

> Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt

- Number: US 2014/0193392 A1
- Document ID: US20140193392A1
- Status: Published application
- Kind: A1
- Application number: 14/239,728
- Filed: 2012-08-28
- Published: 2014-07-10
- Earliest claimed: 2011-08-31
- Assignees: St. Jude Children's Research Hospital
- Inventors: Ida Annunziata; Alessandra D'Azzo; Shai White-Gilbertson
- Web page: https://patentgrep.com/patent/US20140193392A1

## CPC

- G16H 20/40: relating to mechanical, radiation or invasive therapies, e.g. surgery, laser therapy, dialysis or acupuncture
- A61K 38/47: acting on glycosyl compounds (3.2), e.g. cellulases, lactases
- A61K 38/48: acting on peptide bonds (3.4)
- A61K 38/4813: {Exopeptidases (3.4.11. to 3.4.19)}
- A61P 35/00: Antineoplastic agents
- C07B 59/005: {Sugars; Derivatives thereof; Nucleosides; Nucleotides; Nucleic acids}
- C12N 9/2402: {hydrolysing O- and S- glycosyl compounds (3.2.1)}
- C12N 9/485: {Exopeptidases (3.4.11-3.4.19)}
- C12N 15/11: DNA or RNA fragments; Modified forms thereof (DNA or RNA not used in recombinant technology, C07H21/00); {Non-coding nucleic acids having a biological activity}
- C12N 15/63: Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
- C12N 15/86: Viral vectors
- C12Q 1/34: involving hydrolase
- C12Y 302/01018: Exo-alpha-sialidase (3.2.1.18), i.e. trans-sialidase
- C12Y 304/16005: Carboxypeptidase C (3.4.16.5), i.e. carboxypeptidase Y
- G01N 33/573: for enzymes or isoenzymes
- G01N 33/5758: {involving compounds serving as markers for tumours, cancers or neoplasias, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides or metabolites}
- G01N 33/57595: {involving intracellular compounds}
- G16H 20/00: ICT specially adapted for therapies or health-improving plans, e.g. for handling prescriptions, for steering therapy or for monitoring patient compliance
- A61P 25/28: for treating neurodegenerative disorders of the central nervous system, e.g. nootropic agents, cognition enhancers, drugs for treating Alzheimer's disease or other forms of dementia
- C12N 15/00: Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor (mutants or genetically engineered microorganisms, per se C12N1/00, C12N5/00, C12N7/00; new plants per se A01H; plant reproduction by tissue culture techniques A01H4/00; new animals per se A01K67/00; use of medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases, gene therapy A61K48/00)
- C12N 2320/30: Special therapeutic applications
- C12N 2710/10031: Uses of virus other than therapeutic or vaccine, e.g. disinfectant
- C12N 2740/10041: Use of virus, viral particle or viral elements as a vector
- C12N 2750/14141: Use of virus, viral particle or viral elements as a vector
- G01N 2333/924: acting on glycosyl compounds (3.2)
- G01N 2800/2821: Alzheimer
- G01N 2800/56: Staging of a disease; Further complications associated with the disease
- Y02A 90/10: Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation
- G16H: HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
- A61K: PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES (devices or methods specially adapted for bringing pharmaceutical products into particular physical or administering forms A61J3/00; chemical aspects of, or use of materials for deodorisation of air, for disinfection or sterilisation, or for bandages, dressings, absorbent pads or surgical articles A61L; soap compositions C11D)
- A61P: SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- C07B: GENERAL METHODS OF ORGANIC CHEMISTRY; APPARATUS THEREFOR (preparation of carboxylic acid esters by telomerisation C07C67/47; telomerisation C08F)
- C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00)
- C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Y: ENZYMES
- G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q)
- Y02A: TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE

## Abstract

Methods are provided for the prognosis, diagnosis and treatment of various pathological states, including cancer, chemotherapy resistance and dementia associated with Alzheimer's disease. The methods provided herein are based on the discovery that various proteins with a high level of sialylation are shown herein to be associated with disease states, such as, cancer, chemotherapy resistance and dementia associated with Alzheimer's disease. Such methods provide a lysosomal exocytosis activity profile comprising one or more values representing lysosomal exocytosis activity. Also provided herein, is the discovery that low lysosomal sialidase activity is associated with various pathological states. Thus, the methods also provide a lysosomal sialidase activity profile, comprising one or more values representing lysosomal sialidase activity. A lysosomal sialidase activity profile is one example of a lysosomal exocytosis activity profile. As such, the level of lysosomal exocytosis activity and/or lysosomal sialidase activity is predictive of a diagnosis and/or prognosis of cancer, chemotherapy resistance or dementia associated with Alzheimer's disease.

## Claims

### Claim 1

A method of determining the prognosis for a subject with cancer, comprising the steps of
a) providing a subject profile comprising a lysosomal sialidase activity profile comprising two or more values from different lysosomal sialidase activity markers, a NEU1 substrate sialylation activity profile or a NEU1 level activity profile from a tumor sample from said subject;
b) providing a corresponding reference profile comprising a lysosomal sialidase activity profile comprising two or more values from different lysosomal sialidase activity markers, a NEU1 substrate sialylation activity profile or a NEU1 level activity profile from a control sample, wherein the subject profile and the reference profile comprise one or more values representing lysosomal sialidase activity, NEU1 substrate sialylation activity or NEU1 level activity; and
c) comparing said subject and said reference lysosomal sialidase activity profiles to thereby determine the prognosis for said subject with cancer, wherein a lower lysosomal sialidase activity, a higher NEU1 substrate sialylation activity or a higher NEU1 level activity of said subject as compared to the lysosomal sialidase activity, NEU1 substrate sialylation activity or NEU1 level activity of said reference results in a prediction of an invasive cancer for said subject.

### Claim 2

A method of diagnosing cancer in a subject, the method comprising:
a) providing a subject profile comprising a lysosomal sialidase activity profile comprising two or more values from different lysosomal sialidase activity markers, a NEU1 substrate sialylation activity profile or a NEU1 level activity profile from a tumor sample from said subject;
b) providing a corresponding reference profile comprising a NEU1 activity profile comprising two or more values from different lysosomal sialidase activity markers, a NEU1 substrate sialylation activity profile or a NEU1 level activity profile from a control sample, wherein the subject profile and the reference profile comprise one or more values representing lysosomal sialidase activity, NEU1 substrate sialylation activity or NEU1 level activity; and
c) comparing said subject and said reference lysosomal sialidase activity profiles to thereby determine the diagnosis for said subject, wherein said subject is diagnosed with cancer if said lysosomal sialidase activity of said subject is lower, the NEU1 substrate sialylation activity is higher or the NEU1 level activity is higher than the lysosomal sialidase activity, NEU1 substrate sialylation activity or NEU1 level activity of said reference.

### Claim 3

A method of determining the prognosis for a lysosomotropic chemotherapeutic agent regime in a subject with cancer, comprising the steps of
a) providing a subject lysosomal sialidase activity profile from a tumor sample from said subject;
b) providing a reference lysosomal sialidase activity profile from a control sample, wherein the subject lysosomal sialidase activity profile and the reference lysosomal sialidase activity profile comprise one or more values representing lysosomal sialidase activity; and
c) comparing said subject and said reference lysosomal sialidase activity profiles to thereby determine the prognosis for a lysosomotropic chemotherapy agent regime in the subject, wherein a lower lysosomal sialidase activity of said subject as compared to the lysosomal sialidase activity of said reference results in a prediction that said cancer will be resistant to said lysosomotropic chemotherapeutic agent.

### Claim 4 (depends on 1)

The method of claim 1, wherein the control sample is from normal tissue adjacent to said tumor from said subject.

### Claim 5 (depends on 1)

The method of claim 1, wherein the one or more values representing lysosomal sialidase activity comprise
(a) the level of LAMP-1 protein;
(b) the level of LAMP-1 and MUC-1 protein;
(c) the level of LAMP-1 sialylation;
(d) the level of MUC-1 sialylation;
(e) the level of LAMP-1 and MUC-1 sialylation;
(f) the level of LAMP-1, the level of MUC-1 protein, the level of LAMP-1 sialylation and the level of MUC-1 sialylation; or
(g) the level of MUC-1 protein.

### Claim at position 6

-11. (canceled)

### Claim 12 (depends on 1)

The method of claim 1, wherein the cancer comprises rhabdomyosarcoma, breast cancer, colon cancer, pancreatic cancer, acute lymphoblastic leukemia or Ewing's sarcoma.

### Claim 13

A method of diagnosing dementia associated with Alzheimer's disease in a subject, the method comprising:
a) providing a subject lysosomal exocytosis activity profile of a sample of cerebrospinal fluid from said subject;
b) providing a reference lysosomal exocytosis activity profile of a control sample of cerebrospinal fluid, wherein the subject lysosomal exocytosis activity profile and the corresponding reference lysosomal exocytosis activity profile comprise one or more values representing lysosomal exocytosis activity; and,
c) comparing said subject and said reference lysosomal exocytosis activity profiles, wherein said subject is diagnosed with dementia associated with Alzheimer's disease if the subject has a higher lysosomal exocytosis activity as compared to the reference lysosomal exocytosis activity.

### Claim 14 (depends on 13)

The method of claim 13, wherein said subject lysosomal exocytosis activity profile and said reference lysosomal exocytosis activity profile comprise
(a) a lysosomal sialidase activity profile, wherein the subject lysosomal sialidase activity profile and the corresponding reference lysosomal sialidase activity profile comprise one or more values representing lysosomal sialidase activity; or
(b) a sialylation activity profile, wherein the subject sialylation activity profile and the corresponding reference sialylation activity profile comprise one or more values representing sialylation activity.

### Claim 15 (depends on 13)

The method of claim 13, wherein the one or more values representing lysosomal exocytosis activity comprise
(a) the level of LAMP-1 sialylation;
(b) the level of MUC-1 sialylation;
(c) the level of LAMP-1 and MUC-1 sialylation;
(d) the level of amyloid precursor protein sialylation;
(e) the level of sialylation of one or more proteins comprising LAMP-1, MUC-1, amyloid precursor protein, Cathepsin B, Cathepsin D, Fibrinogen, Transthyretin, beta-2 microglobulin or Immunoglobulin heavy chain;
(f) the level of LAMP-1 protein;
(g) the level of MUC-1 protein;
(h) the level of amyloid precursor protein;
(i) the level of LAMP-1 and MUC-1 protein;
(j) the level of LAMP-1 protein, the level of MUC-1 protein, the level of LAMP-1 sialylation and the level of MUC-1 sialylation; or
(k) the level of protein of one or more proteins comprising LAMP-1, MUC-1, amyloid precursor protein, Cathepsin B, Cathepsin D, Fibrinogen, Hexosaminidase beta, Mannosidase alpha, Transthyretin, beta-2 microglobulin or Immunoglobulin heavy chain.

### Claim at position 11

-26. (canceled)

### Claim 27

A method of treating a subject with dementia associated with Alzheimer's disease or treating cancer comprising administering to a subject in need thereof a therapeutically effective amount of Neuramimidase 1 (NEU1) polypeptide having an amino acid sequence with at least 85% sequence identity to SEQ ID NO: 2, wherein said polypeptide has sialidase activity.

### Claim 28 (depends on 27)

The method of claim 27, further comprising the administration of Protective Protein/Cathepsin A (PPCA) polypeptide having an amino acid sequence with at least 85% sequence identity to SEQ ID NO: 4, wherein said PPCA polypeptide enhances NEU1 enzymatic activity.

### Claim 29 (depends on 28)

The method of claim 28, wherein the NEU1 polypeptide and PPCA polypeptide are administered separately or simultaneously.

### Claim 30 (depends on 29)

The method of claim 29, wherein administration of the NEU1 polypeptide comprises administration of a viral vector comprising a nucleotide sequence having at least 85% sequence identity to SEQ ID NO: 1.

### Claim 31

A method of generating a lysosomal sialidase activity profile comprising:
(a) obtaining a sample from a tumor from a subject; and,
(b) assaying for the level of LAMP-1 protein or the level of LAMP-1 sialylation.

### Claim 32 (depends on 31)

The method of claim 31, comprising assaying for one or more additional lysosomal sialidase activity markers.

### Claim 33 (depends on 32)

The method of claim 32, wherein the one or more additional lysosomal sialidase activity markers comprise a NEU1 substrate.

### Claim 34

A method of generating a lysosomal exocytosis activity profile from cerebrospinal fluid comprising:
(a) obtaining a sample of cerebrospinal fluid from a subject; and,
(b) assaying for lysosomal exocytosis activity.

### Claim 35 (depends on 34)

The method of claim 34, wherein assaying for lysosomal exocytosis activity comprises
(a) assaying for the level of LAMP-1 protein or the level of LAMP-1 sialylation;
(b) assaying for the level of one or more proteins comprising LAMP-1, MUC-1, amyloid precursor protein, Cathepsin B, Cathepsin D, Fibrinogen, Hexosaminidase beta, Mannosidase alpha, Transthyretin, beta-2 microglobulin or Immunoglobulin heavy chain.

### Claim 36

(canceled)

### Claim 37 (depends on 31)

The method of claim 31, comprising assembling a lysosomal sialidase activity profile in view of the activity values obtained.

### Claim 38 (depends on 34)

The method of claim 34, comprising assembling a lysosomal exocytosis activity profile in view of the activity values obtained.

### Claim 39

(canceled)

### Claim 40 (depends on 2)

The method of claim 2, wherein the one or more values representing lysosomal sialidase activity comprise
(a) the level of LAMP-1 protein;
(b) the level of LAMP-1 and MUC-1 protein;
(c) the level of LAMP-1 sialylation;
(d) the level of MUC-1 sialylation;
(e) the level of LAMP-1 and MUC-1 sialylation; or
(f) the level of LAMP-1, the level of MUC-1 protein, the level of LAMP-1 sialylation and the level of MUC-1 sialylation.

### Claim 41 (depends on 3)

The method of claim 3, wherein the one or more values representing lysosomal sialidase activity comprise
(a) the level of LAMP-1 protein;
(b) the level of LAMP-1 and MUC-1 protein;
(c) the level of LAMP-1 sialylation;
(d) the level of MUC-1 sialylation;
(e) the level of LAMP-1 and MUC-1 sialylation; or
(f) the level of LAMP-1, the level of MUC-1 protein, the level of LAMP-1 sialylation and the level of MUC-1 sialylation.