Blood-based assays for breast cancer

Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid

Reexamination Certificate

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C435S004000, C435S007920, C435S015000, C435S194000

Reexamination Certificate

active

06358683

ABSTRACT:

BACKGROUND OF THE INVENTION
Excluding cancers of the skin, breast cancer is the most common cancer among women, accounting for one out of every three cancer diagnoses in the United States. In 1997, approximately 180,200 new cases of invasive breast cancer are expected to be diagnosed, and 43,900 women are expected to die from this disease. Only lung cancer causes more cancer deaths in women.
Currently, the primary method of detecting breast cancer in women is through mammography, or by physical examination. Unlike numerous other cancers, at present no method is available to reliably detect the existence of breast cancer by examining the level of specific blood markers. For example, in the case of prostate cancer, the antigen PSA (for prostate specific antigen) can be detected in the blood and is indicative of the presence of prostate cancer. Thus, the blood of men at risk for prostate cancer can be quickly, easily, and safely screened for elevated PSA levels. No such method currently exists for women at risk of breast cancer. This invention addresses this and other needs.
SUMMARY OF THE INVENTION
The present invention provides methods of detecting markers from a biological sample from a patient, wherein the level of the marker indicates the presence of breast cancer in the patient.
In numerous embodiments of the invention, a method for assessing the presence of a breast cancer in a patient will include several steps, including providing a biological sample from the patient, detecting the level of one or more markers in the sample, and comparing the level of the one or more markers with a control level that is representative of a level in a normal, cancer-free patient. Using such methods, an elevation of marker level in a patient compared to the control level indicates the presence of breast cancer in the patient.
In preferred embodiments, the marker used in this invention will be M2 Pyruvate Kinase, or a derivative or fragment thereof. Also preferred is the use of hnRNPK, or derivatives or fragments thereof. The invention also provides methods for identifying novel molecules useful in the assays described herein.
In preferred embodiments, the level of a marker will be measured in a blood sample. The “level” as used herein can refer to MRNA level, DNA level, protein level, enzyme activity, the presence of particular isoforms, or any other marker of gene number, expression, or activity. In particularly preferred embodiments, the protein level of one or more marker described herein will be measured.
In preferred embodiments, the level of marker will be quantitated and compared with a control value or sample. In particularly preferred embodiments, the difference between an elevated level and a control level will be statistically significant.
In numerous embodiments, the present methods will further include an additional step, wherein an additional diagnostic step specific to breast cancer will be performed. For example, following a detection of an elevated level of a marker, which elevated level indicates the presence of a breast cancer, the indication will be confirmed using one or more techniques specific to breast cancer detection, such as mammography, physical examination, biopsy, etc.
Definitions
A “blood sample” refers to an amount of blood removed to allow diagnostic analysis of components within the blood. These components may be blood cells, such as lymphocytes or other white blood cells, or may be blood fractions that are partially or completely devoid of cells, e.g., plasma or serum). A blood sample can also refer to cells removed from bone marrow.
When a cell is said to have an “elevated level” of a marker, it means that it has a level of the marker that is measurably or detectably higher than the level of the marker in a normal, non-cancerous cell. The difference between the higher level of the marker and the normal level may be based on quantitative or qualitative methods of detection.
The phrase “detecting a breast cancer” refers to the ascertainment of the presence or absence of breast cancer in an animal. “Detecting a breast cancer” can also refer to obtaining indirect evidence regarding the likelihood of the presence of cancerous cells in the animal. Detecting a breast cancer can be accomplished using the methods of this invention alone, or in combination with other methods or in light of other information regarding the state of health of the animal.
A “breast cancer” in an animal refers to the presence of cells originating in the breast that possess characteristics typical of cancer-causing cells, such as uncontrolled proliferation, immortality, metastatic potential, rapid growth and proliferation rate, and certain characteristic morphological features. Often, breast cancer cells will be in the form of a tumor, but such cells may also exist alone within a patient.
“Providing a biological sample” means to obtain a biological sample for use in the methods described in this invention. Most often, this will be done by removing a sample of cells from a patient, but can also be accomplished by using previously isolated cells (e.g., isolated by another person), or by performing the methods of the invention in vivo.
A “biological sample” refers to a cell or population of cells or a quantity of tissue or fluid from a human. Most often, the sample has been removed from a human, but the term “biological sample” can also refer to cells or tissue analyzed in vivo, i.e. without removal from a human. Often, a “biological sample” will contain cells from the human, but the term can also refer to non-cellular biological material, such as non-cellular fractions of blood, saliva, or urine, that can be used to measure marker levels.
“Tissue biopsy” refers to the removal of a biological sample for diagnostic analysis. In a patient with cancer, tissue may be removed from a tumor, allowing the analysis of cells within the tumor.
“Detecting a level of a marker” refers to determining the expression level of a gene or genes encoding a target polypeptide. The copy number of a gene can be measured in multiple ways known to those of skill in the art, including, but not limited to, Comparative Genomic Hybridization (CGH) and quantitative DNA amplification (e.g., quantitative PCR). Gene expression can be monitored in a variety of ways, including by detecting mRNA levels, protein levels, or protein activity, any of which can be measured using standard techniques. Detection can involve quantification of the level of (e.g., gDNA, cDNA, MRNA, protein, or enzyme activity), or, alternatively, can be a qualitative assessment of the level of a target, in particular in comparison with a control level.
To “compare” levels of markers means to detect marker levels in two samples and to determine whether the levels are equal or if one or the other is greater. A comparison can be done between quantified levels, allowing statistical comparison between the two values, or in the absence of quantification, for example using qualitative methods of detection such as visual assessment by a human.
A “control sample” refers to a sample of biological material representative of healthy, cancer-free humans. The level of a target in a control sample is desirably typical of the general population of normal, cancer-free humans. This sample can be removed from a patient expressly for use in the methods described in this invention, or can be any biological material representative of normal, cancer-free humans, including cancer-free biological material taken from a human with cancer elsewhere in its body. A control sample can also refer to an established level of a target, representative of the cancer-free population, that has been previously established based on measurements from normal, cancer-free humans.
An “increased level of a target” means a level of a target polypeptide (e.g. M2PK), that, in comparison with a control level of the target polypeptide, is detectably higher. The method of comparison can be statistical, using quantified values for the level of the target, or can be compared using non-statistical means, s

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