Classifications

• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
  • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
  • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
  • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
  • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
  • G01N33/57484—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving compounds serving as markers for tumor, cancer, neoplasia, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides, metabolites
  • G01N33/57488—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving compounds serving as markers for tumor, cancer, neoplasia, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides, metabolites involving compounds identifable in body fluids
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P35/00—Antineoplastic agents
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
  • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
  • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
  • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
  • G01N33/6803—General methods of protein analysis not limited to specific proteins or families of proteins
  • G01N33/6848—Methods of protein analysis involving mass spectrometry
• • G—PHYSICS
  • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
  • G16C—COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
  • G16C20/00—Chemoinformatics, i.e. ICT specially adapted for the handling of physicochemical or structural data of chemical particles, elements, compounds or mixtures
  • G16C20/70—Machine learning, data mining or chemometrics
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N2800/00—Detection or diagnosis of diseases
  • G01N2800/52—Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis
• • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
  • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
  • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
  • Y02A90/00—Technologies having an indirect contribution to adaptation to climate change
  • Y02A90/10—Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation
• • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
  • Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
  • Y10T—TECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION
  • Y10T436/00—Chemistry: analytical and immunological testing
  • Y10T436/24—Nuclear magnetic resonance, electron spin resonance or other spin effects or mass spectrometry

Definitions

• This invention relates to the field of identifying cancer patients as being likely to benefit from treatment with drugs targeting the epidermal growth factor receptor (EGFR) pathway.
• the identification for initial selection for treatment involves mass spectral analysis of blood samples from the patient in conjunction with a classification algorithm using a training set of class-labeled spectra from other patients.
• EGFR epidermal growth factor receptor
• Non-Small-Cell Lung Cancer is a leading cause of death from cancer in both men and women in the United States.
• NSCLC Non-Small-Cell Lung Cancer
• Squamous cell (epidermoid) carcinoma of the lung is a microscopic type of cancer most frequently related to smoking.
• Adenocarcinoma of the lung accounts for over 50% of all lung cancer cases in the U.S. This cancer is more common in women and is still the most frequent type seen in non-smokers.
• Large cell carcinoma especially those with neuroendocrine features, is commonly associated with spread of tumors to the brain. When NSCLC enters the blood stream, it can spread to distant sites such as the liver, bones, brain, and other places in the lung.
• epidermal growth factor binds to a receptor that is found on the surface of many cells in the body.
• the receptor known as the epidermal growth factor receptor (EGFR) sends signals to the cells, through the activation of an enzyme called tyrosine kinase (TK) that is found within the cells.
• TK tyrosine kinase
• EGFR epidermal growth factor receptor
• NSCLC non-small cell lung cancer
• EGFR-Inhibitors While in some trials EGFR-Inhibitors (EGFR-I) have been shown to generate sufficient survival benefit even in unselected populations, in others there was no substantial benefit. This lead AstraZeneca to withdraw their EGFR-tyrosine kinase inhibitor (TKI) (gefitinib, Iressa) from the United States market. Even in the case of approved EGFR-Is it has become more and more clear that efficient and reliable tests are necessary to identify those patients that might benefit from treatment with EGFR-Is vs. those that are not likely to benefit. Ladanyi M, et al., Mod Pathol. 2008 May; 21 Suppl 2:S 16-22.
• TKI EGFR-tyrosine kinase inhibitor
• Head and neck squamous cell carcinoma is used here to refer to a variety of cancer characterized by squamous cell carcinomas of the oral cavity, pharynx and larynx, salivary glands, paranasal sinuses and nasal cavity, as well as the lymph nodes of the upper part of the neck. Head and neck cancers account for approximately 3 to 5 percent of all cancers in the United States. These cancers are more common in men and in people over age 50. Tobacco (including smokeless tobacco) and alcohol use are the most important risk factors for head and neck cancers, particularly those of the oral cavity, oropharynx, hypopharynx and larynx. Eighty-five percent of head and neck cancers are linked to tobacco use.
• HNSCC head and neck squamous cell carcinoma
• EGFR-I EGFR inhibitors
• TKIs small molecule tyrosine kinase inhibitors
• Erbitux monoclonal antibody EGFG-I
• panitumumab monoclonal antibody EGFG-I
• a method is disclosed of determining whether a HNSCC patient is likely to benefit from treatment with a drug targeting the EGFR pathway (e.g., an EGFR-TKI such Tarceva (erlotinib), Erbitux (cetuximab), Iressa (gefitinib), or equivalent) comprising the steps of: a) obtaining a mass spectrum from a blood-based sample from the patient; b) performing one or more predefined pre-processing steps on the mass spectrum obtained in step a); c) obtaining integrated intensity values of selected features in said spectrum at one or more predefined m/z ranges after the pre-processing steps on the mass spectrum in step b) have been performed; and d) using the values obtained in step c) in a classification algorithm using a training set comprising class-labeled spectra produced from blood-based samples from other patients to
• the drug comprises a small molecule epidermal growth factor receptor tyrosine kinase inhibitor.
• the drug comprises a monoclonal antibody epidermal growth factor receptor inhibitor.
• the predefined pre-processing steps comprise a background subtraction step producing a background-subtracted spectrum, and a normalization step performing a normalization of the background-subtracted spectrum.
• the training set comprises class-labeled spectra produced from blood-based samples obtained from non-small cell lung cancer patients.
• Figure 1 is a flow chart showing a method for selection of HNSCC cancer patients for treatment with EGFR-I in accordance with a preferred embodiment of this invention.
• Figure 2 is a Kaplan-Meier plot for a set of HNSCC patients treated with gefitinib and the class label assigned to serum samples using the method of Figure 1. The plot indicates that patients labeled "good” had a better prognosis following treatment with gefitinib than the patients labeled "poor", with a hazard ratio of 0.41 (95% CI: .22-.79) of good versus poor.
• Figure 3 is a Kaplan-Meier plot for a set of HNSCC patients treated with cetuximab and the class label assigned to serum samples using the method of Figure 1.
• a serum or plasma sample is obtained from the patient.
• the serum samples are separated into three aliquots and the mass spectroscopy and subsequent steps 104, 106 (including sub-steps 108, 1 10 and 1 12), 114, 116 and 1 18 are performed independently on each of the aliquots.
• the sample is subject to mass spectroscopy.
• a preferred method of mass spectroscopy is matrix assisted laser desorption ionization (MALDI) time of flight (TOF) mass spectroscopy, but other methods are possible.
• MALDI matrix assisted laser desorption ionization
• TOF time of flight
• Mass spectroscopy produces data points that represent intensity values at a multitude of mass/charge (m/z) values, as is conventional in the art.
• the samples are thawed and centrifuged at 1500 rpm for five minutes at four degrees Celsius.
• the serum samples may be diluted 1 : 10, or 1 :5, in MiIIiQ water. Diluted samples may be spotted in randomly allocated positions on a MALDI plate in triplicate (i.e., on three different MALDI targets).
• Mass spectra may be acquired for positive ions in linear mode using a Voyager DE- PRO or DE-STR MALDI TOF mass spectrometer with automated or manual collection of the spectra. Seventy five or one hundred spectra are collected from seven or five positions within each MALDI spot in order to generate an average of 525 or 500 spectra for each serum specimen. Spectra are externally calibrated using a mixture of protein standards (Insulin (bovine), thioredoxin (E. coli), and Apomyglobin (equine)).
• the spectra obtained in step 104 are subject to one ore more pre-defined pre-processing steps.
• the pre-processing steps 106 are implemented in a general purpose computer using software instructions that operate on the mass spectral data obtained in step 104.
• the pre-processing steps 106 include background subtraction (step 108), normalization (step 1 10) and alignment (step 112).
• the step of background subtraction preferably involves generating a robust, asymmetrical estimate of background in the spectrum and subtracts the background from the spectrum.
• Step 108 uses the background subtraction techniques described in U.S. published applications 2007/0231921 and U.S. 2005/0267689, which are incorporated by reference herein.
• the normalization step 1 10 involves a normalization of the background subtracted spectrum.
• the normalization can take the form of a partial ion current normalization, or a total ion current normalization, as described in our prior patent application U.S. 2007/0231921.
• Step 112 aligns the normalized, background subtracted spectrum to a predefined mass scale, as described in U.S. 2007/0231921, which can be obtained from investigation of the training set used by the classifier.
• step 114 of obtaining values of selected features (peaks) in the spectrum over predefined m/z ranges.
• the normalized and background subtracted amplitudes may be integrated over these m/z ranges and assigned this integrated value (i.e., the area under the curve between the width of the feature) to a feature.
• the integration range may be defined as the interval around the average m/z position of this feature with a width corresponding to the peak width at the current m/z position.
• step 114 as described in our patent application published as US 2007/0231921 , the integrated values of features in the spectrum is obtained at one or more of the following m/z ranges: 5732 to 5795 5811 to 5875 6398 to 6469 11376 to 11515
• values are obtained at at least eight of these m/z ranges, and more preferably at all 12 of these ranges. The significance, and methods of discovery of these peaks, is explained in the prior patent application publication U.S. 2007/0231921.
• the values obtained at step 114 are supplied to a classifier, which in the illustrated embodiment is a K-nearest neighbor (KNN) classifier.
• KNN K-nearest neighbor
• the classifier makes use of a training set of class labeled spectra from a multitude of other patients (which could be
• the KNN classification algorithm to the values at 1 14 and the training set is explained in our patent application publication U.S. 2007/0231921.
• Other classifiers can be used, including a probabilistic KNN classifier or other classifier.
• the classifier produces a label for the spectrum, either "good”, “poor” or
• steps 104-118 are performed in parallel on three separate aliquots from a given patient sample.
• a check is made to determine whether all three aliquots produce the same class label. If not, an undefined result is returned as indicated at step 122. If all aliquots produce the same label, the label is reported as indicated at step 124. If the label reported at step 124 is "good” it indicates that the patient is likely to benefit from administration of the EGFR pathway targeting drug, or continued administration in the case of monitoring a patient in the course of treatment. If the label reported at step 124 is "poor" it indicates that the patient is not likely to benefit from treatment by such a drug.
• steps 106, 1 14, 116 and 118 are typically performed in a programmed general purpose computer using software coding the pre-processing step 106, the obtaining of spectral values in step 114, the application of the KNN classification algorithm in step 116 and the generation of the class label in step 118.
• the training set of class labeled spectra used in step 116 is stored in memory in the computer or in a memory accessible to the computer.
• the analysis was performed in a fully blinded manner, i.e. no clinical data were available during the determination of the label. Once the labels were generated the clinical data were unblinded and a Kaplan-Meier analysis for overall survival could be performed from the clinical data for the endpoint overall survival.
• the Kaplan-Meier curves are shown in Figure 3 for the patients labeled "good” and "poor".
• the patients labeled "good” had a better prognosis following treatment with cetuximab than the patients labeled "poor” with a hazard ratio of 0.26 (95% CI: .06-1.06) of good versus poor.
• the good and poor curves are close to statistically significantly different with a log-rank p-value of 0.061 .
• a method of determining whether a HNSCC patient is likely to benefit from treatment with a drug targeting the EGFR pathway comprising the steps of: a) obtaining a mass spectrum from a blood-based sample from the patient; b) performing one or more predefined pre-processing steps on the mass spectrum obtained in step a); c) obtaining integrated intensity values of selected features in said spectrum at one or more predefined m/z ranges after the pre-processing steps on the mass spectrum in step b) have been performed; and d) using the values obtained in step c) in a classification algorithm using a training set comprising class-labeled spectra produced from blood-based samples from other patients to identify the patient as being either likely or not likely to benefit from treatment with the said drug.
• the one or more m/z ranges comprises one or more m/z ranges selected from the group of m/z ranges consisting of:
• the mass spectrum is obtained from a MALDI mass spectrometer.
• the drug for which the patient is identified as being likely to benefit from may comprise a small molecule epidermal growth factor receptor tyrosine kinase inhibitor, such as getfitinib or erlotinib, or alternatively a monoclonal antibody epidermal growth factor receptor inhibitor such as cetuximab.

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• 2009
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