Mitochondrial biology expression arrays

• US 20060099578A1
• Filed: 08/30/2002
• Published: 05/11/2006
• Est. Priority Date: 08/30/2001
• Status: Abandoned Application

• Current Assignee: Emory University
• Original Assignee: Emory University
• Inventors: Levy, Shawn, Procaccio, Vincent, Kerstann, Keith, Wallace, Douglas C
• Application Number:
  US10/488,619
• Publication Number:
  US 20060099578A1
• Time in Patent Office: Days
• US Class Current: 435/6.12
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 1/6888 for detection or identification of organisms
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/158 Expression markers

Abstract

This invention provides a library of genes involved in mitochondrial biology, arrays containing probes for genes involved in mitochondrial biology, methods for making such arrays, and methods of using such arrays. Genes and probe sequences involved in mitochondrial biology in humans and mice are provided. The arrays of this invention are useful for determining mitochondrial biology gene expression profiles. Mitochondrial biology gene expression profiles are useful for determining expression profiles diagnostic of physiological conditions; diagnosing physiological conditions; identifying biochemical pathways, genes, and mutations involved in physiological conditions; identify therapeutic agents useful for preventing and/or treating such physiological conditions; evaluating and/or monitoring the efficacy of such therapies, and creating and identifying animal models of human physiologic conditions. Arrays containing probes for all genes known to be involved in mitochondrial biology are provided, as well as arrays containing subsets of such probes.

Claims

1. An array comprising at least two isolated nucleotide molecules, each molecule having a sequence capable of uniquely hybridizing to a nucleic acid molecule which is an expression product of a gene involved in mitochondrial biology.

2. An array comprising two or more isolated nucleic acid molecules or spots, each spot comprising a plurality of isolated nucleic acid molecules, each molecule having a sequence consisting essentially of a sequence selected from the group consisting of the sequences of human probe set #1, SEQ ID NOS:

1 to 994, or mouse probe set #2, SEQ ID NOS;

995 to 3040, and sequences having at least 70% homology to the foregoing sequences.

3. The array of claim 2 printed on a glass slide.

4. The array of claim 2 comprising more than about ten spots.

5. The array of claim 2 comprising more than about twenty-five spots.

6. The array of claim 2 comprising all of the isolated nucleic acid molecules having the sequences of human probe set #1, SEQ ID NOS:

1 to 994.

7. The array of claim 2 comprising all of the isolated nucleic acid molecules having the sequences of mouse probe set #2, SEQ ID NOS:

995 to 3040.

8. The array of claim 2 also comprising one or more spots comprising control nucleic acid molecules, SEQ ID NOS:

3041-3044.

9. A method for determining an expression profile of a sample containing nucleic acid comprising:

a) providing the sample;

b) providing an array of claim 2;

c) contacting said array with said sample under conditions allowing selective hybridization; and

d) measuring hybridization of nucleic acid in said sample to said array to produce an expression profile.

10. The method of claim 9 wherein said sample is from a mouse or a human.

11. A method for determining an expression profile of a first labeled sample containing nucleic acid relative to a second, differently labled sample containing nucleic acid comprising:

a) providing the first labeled sample;

b) providing the second, differently labeled sample;

c) providing an array of claim 2;

d) contacting the array with the first sample and the second sample under conditions allowing selective hybridization;

e) measuring hybridization of said first and said second samples to said array; and

f) comparing the hybridization of said first sample to the hybridization of said second sample to produce an expression profile.

12. The method of claim 11 wherein said second sample is a reference or a standard.

13. A method for determining an expression profile diagnostic of an energy-metabolism-related physiological condition comprising:

a) providing a labeled first sample from a first group of one or more individuals with said physiological condition;

b) providing a differently labeled second sample from a second group of one or more individuals without said physiological condition;

c) providing an array of claim 2;

d) contacting the array with the first sample and the said second sample under conditions allowing selective hybridization;

e) measuring hybridization of said first and said second samples to said array; and

f) comparing the hybridization of said first sample to the hybridization of said second sample to produce an expression profile diagnostic of said physiological condition.

14. A method of making an array comprising:

a) providing a prepared substrate; and

b) printing two or more spots in known positions on said substrate, each spot comprising a plurality of isolated nucleic acid molecules, each molecule having a sequence consisting essentially of a sequence selected from the group consisting of human probe set #1, SEQ ID NOS;

1 to 994, mouse probe set #2, SEQ ID NOS;

995 to 3040, and sequences having at least 70% homology to the foregoing sequences.

15. The method of claim 14 wherein said array comprises all of said isolated nucleic acid molecules in human probe set #1, SEQ ID NOS:

1 to 994.

16. The method of claim 14 wherein said array comprises all of said isolated nucleic acid molecules in mouse probe set #2, SEQ ID NOS:

995 to 3040.

17. A method of diagnosing a first individual with Complex IV Leigh'"'"'s Syndrome comprising detecting in a first sample from said first individual at least about a 1.7-fold decrease in the amount of expression of genes comprising ND4, NDL4, ND6, SURF-1, SOD2, 70 kD heat shock protein, VDAC4, ANT2, and glutathione peroxidase 3 compared to the amount of expression of said genes in a second sample from a second individual without Complex IV Leigh'"'"'s Syndrome.

18. A library of at least two isolated nucleic acid molecules, each molecule having a sequence consisting essentially of a sequence selected from the group consisting of human probe set #1, SEQ ID NOS:

1 to 994, mouse probe set #2, SEQ ID NOS;

995 to 3040, and sequences having at least 70% homology to the foregoing sequences.

19. An array comprising at least two spots, each spot comprising a plurality of isolated nucleic acid molecules, each molecule comprising a sequence with at least 70% homology to a sequence selected from the group consisting of human probe set #1, SEQ ID NOS:

1 to 994.

20. An array comprising at least two spots, each spot comprising a plurality of isolated nucleic acid molecules, each molecule comprising a sequence with at least 70% homology to a sequence selected from the group consisting of mouse probe set #2, SEQ ID NOS:

995 to 3040.