WO2019226669A1 - Identifying treatment options for sclc patients - Google Patents

Abstract

Disclosed herein are methods for selecting a suitable anticancer drug for the treatment of a lung tumor to a patient in need thereof by using clinical proteomics. The methods disclosed herein comprise performing proteomic analysis of the tumor to quantify protein expression; and determining whether the anticancer drug is suitable or unsuitable for the treatment of the lung tumor by comparing the protein expression of the tumor with a pre-defined threshold for that protein.

Description

IDENTIFYING TREATMENT OPTIONS FOR SCLC PATIENTS

[0001] This application claims priority to our co-pending US provisional applications with the serial number 62/676,643, filed May 25, 2018, which is incorporated by reference herein in its entirety.

Field of the Invention

[0002] The field of the invention is in the field of proteomic analysis, especially as it relates to treatment of cancer.

Background of the Invention

[0003] The background description includes information that may be useful in understanding the present invention. It is not an admission that any of the information provided herein is prior art or relevant to the presently claimed invention, or that any publication specifically or implicitly referenced is prior art.

[0004] All publications and patent applications herein are incorporated by reference to the same extent as if each individual publication or patent application were specifically and individually indicated to be incorporated by reference. Where a definition or use of a term in an incorporated reference is inconsistent or contrary to the definition of that term provided herein, the definition of that term provided herein applies and the definition of that term in the reference does not apply.

[0005] There are two main types of lung cancer. Small-cell lung cancer (SCLC), sometimes called small-cell carcinoma, causes about 10%-15% of all lung cancer. Non-small-cell lung cancer (NSCLC) causes the rest. SCLC is characterized by tumor cells that grow rapidly and spreads quickly. The survival rate of lung cancer, and in particular SCLC, is dismal; currently, the 5-year survival rate for stage 1 SCLC is 31 percent, for stage 2 SCLC it is 19 percent, for stage 3 it is 8 percent, and only 2 percent for stage 4 disease.

[0006] Small cell lung cancer (SCLC) is the most lethal and aggressive subtype of lung carcinoma, responsible for -13-18% of lung cancer death with no appreciable improvements in outcomes or treatment options for the last 30 years. The clinical behavior of SCLC is tailor made for nihilism with excellent initial overall response rates transforming to inevitable chemotherapy resistant recurrence in the majority of patients. Targeted therapies to date have failed with little to no efficacy in unselected populations. Numerous explanations are given for this lack of efficacy of SCLC treatments in patients. One theory proposes that the rapid recurrence after initial response to chemotherapy of SCLC is suggestive of biological features consistent with stem cell biology. This strongly suggests a stem cell like phenotype, or a resistant subclonal expansion. Another theory proposes that the lack of mutational drivers and the mutational signature of SCLC appear to be principally driven by changes in tumor suppressor or

transcription factors. These targets are challenging to drug and this has hampered targeted therapy options. Another theory proposes that there are inadequate biomarkers for the delineation of SCLC subpopulations. SCLC has long been known to be a heterogeneous disease, but currently tools are not available to further characterize potential subpopulations.

[0007] WO1998035985A1 (Hanash et al) identifies protein markers for lung cancer. The‘985 publication studied computerized analysis of 2-D gels, both carrier ampholyte (CA) and immobilized pH gradient (IPG) based, of the proteins in tissue from lung tumors, and reveals proteins which are different types of tumors and in control tissues. However this publication does not disclose which subpopulations of lung cancer will benefit from which treatment.

[0008] US20160274121A1 (Wong et al) discloses cancer markers, for example cancer stem cell biomarkers for diagnostic and therapeutic use. However, the disclosure provides for general stem cell markers present in all patients, and not specific cell markers to characterize subpopulations and determine which subpopulation will respond to which treatment.

[0009] Thus, there remains a need in the art of lung cancer, and specifically small cell lung cancer, for additional improved methods of treatment. Such improved methods of treatment will preferably identify biomarkers (for example protein targets) to further characterize potential subpopulations of the patients and determine the best and most effective treatment for each patient. Summary of The Invention

[0010] The inventive subject matter is directed to various methods for selecting a suitable anticancer drug for the treatment of a lung tumor in a patient in need thereof, the method comprising: performing proteomic analysis of the tumor to quantify protein expression. The protein expression in the tumor is then compared with a pre-defined threshold to determine whether the anticancer drug is suitable or unsuitable for the treatment of the lung tumor by comparing the protein expression of the tumor with a pre-defined threshold for that protein.

[0011] Most typically, the anticancer drug is temozolomide, fluorouracil, or an antibody-drug conjugate. Preferably, temozolomide is selected as the suitable anticancer drug for the patient when the patient’s tumor has low of absent MGMT protein expression. Low or absent MGMT protein expression comprises protein expression of less than 200 attomoles per microgram of tumor. Fluorouracil is selected as the suitable anticancer drug for the patient when the patient’ s tumor overexpresses TYMP protein, and TYMP expression is more than 1335 attomoles per microgram of tumor. Variations of the level of protein expression are contemplated. For example variations of protein expression of MGMT and TYMP may be up to 10%, up to 20%, or up to 30%, or upto 50% of the values disclosed above.

[0012] Additionally, the anticancer drug may be an antibody-drug conjugate that targets the proteins DLL3, CD56, or TROP2. In this case, the presence of proteins DLL3, CD56, or TROP2 indicates that antibody-drug conjugate therapy is a suitable anticancer drug for the patient.

[0013] In some embodiments of this disclosure, the proteomic analysis is performed by using quantitative mass spectrometry. The mass spectrometry may be DIA or CID mass spectrometry.

[0014] In another aspect of this present disclosure, the method further comprises administering the selected anticancer drug to the patient for treating the disease.

[0015] In yet another aspect of the inventive subject matter, the inventors contemplate a method of determining the best treatment option for a patient having lung cancer, comprising performing proteomic analysis of a tumor sample of the patient to quantify one or more proteins in the tumor sample; and determining the best treatment option for the patient based on the quantity of the one or more proteins in the tumor sample. For example, when patient’s tumor has an underexpression of MGMT protein, then temozolomide drug therapy is the most suitable treatment option.

Alternatively, when patient’s tumor has an overexpression of TYMP protein, then fluorouracil drug therapy is the most suitable treatment option. Furthermore, when patient’s tumor expresses DLL3, CD56, or TROP2 proteins, then antibody-drug conjugate therapy is the most suitable treatment option. Most typically, the lung cancer is small cell lung cancer (SCLC).

[0016] Various objects, features, aspects and advantages of the inventive subject matter will become more apparent from the following detailed description of preferred embodiments.

Detailed Description

[0017] The inventors have now surprisingly discovered that multiplexed clinical proteomic testing can be used for identifying the best or most suitable treatment option for patients suffering from lung cancer. The method involves profiling protein targets in clinical tumor biopsies of lung cancer patients, preferably small cell lung cancer patients, by using quantitative mass spectrometry. A suitable anticancer drug is then selected for the patient by performing proteomic analysis of the tumor to quantify protein expression in the tumor. Preferably, the method also includes comparing the protein expression level in the tumor cells of the patient with a pre-defined threshold for that protein.

[0018] Healthcare practitioners have a number of treatment options available to them for Lung Cancer, such as chemotherapy, radiation therapy, antibody therapy, immune therapy etc.

Moreover, healthcare practitioners may also use different combinations of chemotherapeutic drugs, as well as drugs that do not carry a label claim for the treatment of a particular cancer, but for which there is evidence of efficacy in that cancer. Best likelihood of good treatment outcome requires that patients at highest risk of metastatic disease be identified and assigned to optimal available cancer treatment. In particular, it is important to determine the likelihood of patient response to therapeutic drugs, such as cyclophosphamide, methotrexate, 5-fluorouracil, anthracyclines, taxanes, and anti-estrogen drugs, such as tamoxifen, because these have limited efficacy and a spectrum of often severe side effects. The identification of patients who are most or least likely to need and respond to a particular available drug could increase the net benefit these drugs have to offer, and thereby increase the survival rate of lung cancer. [0019] The standard of care for most patients with SCLC is platinum doublet therapy. In the platinum doublet therapy, the most commonly used regimen comprises a platinum compound and a third-generation chemotherapy agent. The platinum compound is usually Cisplatin (CDDP), Carboplatin (CBDCA), or Nedaplatin (CDGP), while the third-generation

chemotherapy agent is usually docetaxel, paclitaxel, vinorelbine, or gemcitabine. However, even with such treatment, most patients with SCLC survive for less than one year.

[0020] For patients with refractory or relapsed disease, second-line, single-agent chemotherapy is usually recommended. These pre-treated SCLC patients may also opt to participate in clinical therapies of new chemotherapeutic agents. In one embodiment, the inventors have surprisingly found that while these therapies work for some patients, it does not work for all. The inventors sought to find an answer to this problem by using multiplexed clinical proteomic testing.

[0021] Clinical proteomic testing of SCLC biopsies using mass spectrometry, the inventors have now unexpectedly found that expression level of certain protein biomarkers may be used to find the best therapy for a particular patient having lung cancer.

[0022] In one embodiment, the inventors studied the SCLC biopsies of clinical trial agents temozolomide, fluorouracil (5FU), and antibody-drug conjugates (ADC) targeting the proteins DLL3, CD56, or TROP2. To assess the proportions of patients who would be likely to respond to these therapies, the inventors profiled protein targets in clinical tumor biopsies of SCLC using quantitative mass spectrometry.

[0023] Accordingly, archived tumor samples from 88 SCLC patients were microdissected and solubilized for proteomic quantification of 58 therapeutically relevant biomarkers. In each sample, quantities of tumor protein were compared with pre-defined thresholds based on evidence from clinical studies or on quantification limits of proteomic assays. Prevalence and protein expression levels in SCLC were compared with those of other cancer indications analyzed in the same clinical laboratory.

[0024] In one embodiment, the inventors found that 15 of 83 (18%) SCLC tumors had low or absent MGMT protein expression ( < 200 attomoles per microgram [amol/ug]), indicating likely response to temozolomide. 14 of 88 (15%) overexpressed TYMP protein ( > 1335 amol/ug), suggesting likely response to 5FU. Except for one patient, likely responders to temozolomide or 5FU were mutually exclusive. Prevalences of quantifiable levels of the ADC markers DLL3, TROP2, and CD56 were 43%, 49% and 97%, respectively. The SCLC tumors expressed a wide range of DLL3 protein (range: 101 - 1201 amol/ug); median expression in SCLC was 2 times higher than in pediatric neurological cancers, while median expression of TROP2 was lower in SCLC than in other indications. CD56 protein levels in SCLC were similar to other indications, but with higher prevalences in SCLC. Thus, in patients with SCLC, clinical proteomics identified protein targets of multiple approved and investigational therapies.

[0025] As used herein, the term“tumor” refers to, and is interchangeably used with one or more cancer cells, cancer tissues, malignant tumor cells, or malignant tumor tissue, that can be placed or found in one or more anatomical locations in a human body. It should be noted that the term “patient” as used herein includes both individuals that are diagnosed with a condition ( e.g ., cancer) as well as individuals undergoing examination and/or testing for the purpose of detecting or identifying a condition. Thus, a patient having a tumor refers to both individuals that are diagnosed with a cancer as well as individuals that are suspected to have a cancer. As used herein, the term“provide” or“providing” refers to and includes any acts of manufacturing, generating, placing, enabling to use, transferring, or making ready to use.

[0026] Any suitable methods and/or procedures to obtain proteomics data are contemplated. For example, the proteomics data can be obtained by obtaining tissues from an individual and processing the tissue to obtain DNA, RNA, protein, or any other biological substances from the tissue to further analyze relevant information. In another example, the proteomics data can be obtained directly from a database that stores omics information of an individual.

[0027] Where the proteomics data is obtained from the tissue of an individual, any suitable methods of obtaining a tumor sample (tumor cells or tumor tissue) or healthy tissue from the patient are contemplated. Most typically, a tumor sample or healthy tissue sample can be obtained from the patient via a biopsy (including liquid biopsy, or obtained via tissue excision during a surgery or an independent biopsy procedure, etc.), which can be fresh or processed (e.g., frozen, etc.) until further process for obtaining omics data from the tissue. For example, tissues or cells may be fresh or frozen. In other example, the tissues or cells may be in a form of cell/tissue extracts. In some embodiments, the tissues or cells may be obtained from a single or multiple different tissues or anatomical regions. For example, a metastatic breast cancer tissue can be obtained from the patient’s breast as well as other organs ( e.g ., liver, brain, lymph node, blood, lung, etc.) for metastasized breast cancer tissues. In another example, a healthy tissue or matched normal tissue (e.g., patient’s non-cancerous breast tissue) of the patient can be obtained from any part of the body or organs, preferably from liver, blood, or any other tissues near the tumor (in a close anatomical distance, etc.).

[0028] In some embodiments, tumor samples can be obtained from the patient in multiple time points in order to determine any changes in the tumor samples over a relevant time period. For example, tumor samples (or suspected tumor samples) may be obtained before and after the samples are determined or diagnosed as cancerous. In another example, tumor samples (or suspected tumor samples) may be obtained before, during, and/or after (e.g., upon completion, etc.) a one time or a series of anti-tumor treatment (e.g., radiotherapy, chemotherapy, immunotherapy, etc.). In still another example, the tumor samples (or suspected tumor samples) may be obtained during the progress of the tumor upon identifying a new metastasized tissues or cells.

[0029] From the obtained tumor samples (cells or tissue) or healthy samples (cells or tissue), DNA (e.g., genomic DNA, extrachromosomal DNA, etc.), RNA (e.g., mRNA, miRNA, siRNA, shRNA, etc.), and/or proteins (e.g., membrane protein, cytosolic protein, nucleic protein, etc.) can be isolated and further analyzed to obtain proteomics data. Alternatively and/or additionally, a step of obtaining proteomics data may include receiving proteomics data from a database that stores proteomics information of one or more patients and/or healthy individuals. For example, proteomics data of the patient’s tumor may be obtained from isolated DNA, RNA, and/or proteins from the patient’s tumor tissue, and the obtained proteomics data may be stored in a database (e.g., cloud database, a server, etc.) with other proteomics data set of other patients having the same type of tumor or different types of tumor. Proteomics data obtained from the healthy individual or the matched normal tissue (or healthy tissue) of the patient can be also stored in the database such that the relevant data set can be retrieved from the database upon analysis. Likewise, where protein data are obtained, these data may also include protein activity, especially where the protein has enzymatic activity ( e.g ., polymerase, kinase, hydrolase, lyase, ligase, oxidoreductase, etc.).

[0030] Moreover, it should be noted that some data sets are preferably reflective of a tumor and a matched normal sample of the same patient to so obtain patient and tumor specific information. Of course, it should be recognized that the tumor sample may be from an initial tumor, from the tumor upon start of treatment, from a recurrent tumor or metastatic site, etc. In most cases, the matched normal sample of the patient may be blood, or non-diseased tissue from the same tissue type as the tumor.

[0031] It should be recognized that proteomics data of cancer and/or normal cells comprises proteomics data set that includes protein expression levels (quantification of protein molecules), post-translational modification, protein-protein interaction, protein-nucleotide interaction, protein-lipid interaction, and so on. Thus, it should also be appreciated that proteomic analysis as presented herein may also include activity determination of selected proteins. Such proteomic analysis can be performed from freshly resected tissue, from frozen or otherwise preserved tissue, and even from FFPE tissue samples. Most preferably, proteomics analysis is quantitative ( i.e ., provides quantitative information of the expressed polypeptide) and qualitative ( ._<?., provides numeric or qualitative specified activity of the polypeptide). Any suitable types of analysis are contemplated. However, particularly preferred proteomics methods include antibody-based methods and mass spectroscopic methods. Moreover, it should be noted that the proteomics analysis may not only provide qualitative or quantitative information about the protein per se, but may also include protein activity data where the protein has catalytic or other functional activity. One exemplary technique for conducting proteomic assays is described in US 7473532, incorporated by reference herein. Further suitable methods of identification and even quantification of protein expression include various mass spectroscopic analyses (e.g., selective reaction monitoring (SRM), multiple reaction monitoring (MRM), and consecutive reaction monitoring (CRM)).

[0032] The inventors contemplate that a molecular profile or a molecular signature of the tumor tissue can be determined using proteomics data, preferably two or more types of proteomics data. Optionally, one or more subtypes of proteomics data can be used to determine the molecular profile or a molecular signature of the tumor tissue. Exemplary proteomics data includes, but not limited to, quantities of one or more proteins or peptides, post-translational modification of one or proteins or peptides ( e.g phosphorylation, glycosylation, forming a dimer, ubiquitination, etc.), and/or subcellular localization of the proteins or peptides.

[0033] Without wishing to be bound by any specific theory, the inventors contemplate that the mutational profiles and/or the protein expression profiles of the tumor tissue, either

independently or collectively, affect the way a particular drug molecule interacts with the tumor tissues or cells.

[0034] Even if a cancer drug that has high likelihood of success in treating the SCLC tumor is identified, the cancer drug may not be effectively used to treat every SCLC tumor in every patient. This may be because the cancer drug may not be metabolized in an efficient manner in some patients. Alternatively or additionally, the cancer drug may produce toxicity to the patient’s normal tissues or cells due to the patient’s specific genetic variance. The inventors used clinical proteomics to identify protein targets of multiple approved and investigative therapies for patients with SCLC. These identified protein targets were then used to select the best or most suitable drug for the patient. It should be noted that while this disclosure generally relates to lung cancer, or more specifically small cell lung cancer, the techniques disclosed herein may also be used to find a suitable treatment for various other types of cancers.

[0035] Thus, in one aspect of the inventive subject matter, the inventors have disclosed a method for selecting a suitable anticancer drug for the treatment of a lung tumor to a patient in need thereof, the method comprising: performing proteomic analysis of the tumor to quantify protein expression; and determining whether the anticancer drug is suitable or unsuitable for the treatment of the lung tumor by comparing the protein expression of the tumor with a pre-defined threshold for that protein.

[0036] The anticancer drug may be the chemotherapy agent, temozolomide. Temozolomide is an oral chemotherapy drug that is used to treat brain cancer and melanoma. Currently,

temozolomide is undergoing clinical trials for relapsed sensitive or refractory small cell lung cancer. This clinical study found that temozolomide is effective in treating some lung cancer patients, but not all. Here, in this disclosure, the inventors have shown that the treatment result of SCLC by using temozolomide can be predicted based on proteomics data. Proteomics data from the patient’s tumor is analyzed, and when the patient’s tumor has low of absent MGMT protein expression, temozolomide is selected as the suitable anticancer drug for the patient. Low or absent MGMT protein expression comprises MGMT protein expression of less than 200 attomoles per microgram of tumor. As used herein, the term“suitable anticancer drug” is one where treatment with that drug molecule results in shrinkage of the patient’s tumor.

[0037] In another embodiment of the inventive subject matter, the anticancer drug may be the chemotherapy agent, 5-fluorouracil, or a derivative thereof. 5- fluorouracil is selected as the suitable anticancer drug for the patient when the patient’s tumor overexpresses TYMP protein, and the TYMP protein expression is more than 1335 attomoles per microgram of tumor.

[0038] Alternatively, or additionally, the anticancer drug may be an antibody-drug conjugate targeting the proteins DLL3, CD56, or TROP2. For example, the presence of proteins DLL3, CD56, or TROP2 in the tumor biopsies of the patient may indicate or predict that antibody-drug conjugate therapy is a suitable anticancer drug for the patient.

[0039] The proteomic analysis may be done using any method known in the art. In one preferred embodiment, mass spectrometry is used to identify and quantify the proteins in the tumor sample. The mode of mass spectrometry may be, for example, tandem mass spectrometry, ion trap mass spectrometry, triple quadrupole mass spectrometry, MALDI-TOF mass spectrometry, MALDI mass spectrometry, hybrid ion trap/quadrupole mass spectrometry and/or time of flight mass spectrometry and may be carried out using Selected Reaction Monitoring (SRM), Multiple Reaction Monitoring (MRM), Parallel Reaction Monitoring (PRM), intelligent Selected Reaction Monitoring (iSRM), and/or multiple Selected Reaction Monitoring (mSRM).

Furthermore, the mass spectrometry may be Data Independent Acquisition (DIA) mass spectrometry or Collision-Induced Dissociation (CID) mass spectrometry.

[0040] SRM and MRM are methods of targeted mass spectrometry assays, as opposed to the shotgun method. MRM relates to the quantification of peptides in human tissue extracts by comparing spectra of unlabeled samples to those of labeled peptides. SRM, which is a newer and more targeted approach, focus on following up the quantification of a handful of proteins of interest in separate experimental conditions, performing relative or absolute quantification with high specificity and sensitivity, even in particularly complex backgrounds. Thus MRM/SRM relies on the measurement of the target protein by measuring one or ideally several surrogate proteins. The method is further described in detail in Faria, Sara S et al.“A Timely Shift from Shotgun to Targeted Proteomics and How It Can Be Groundbreaking for Cancer

Research.” Frontiers in oncology vol. 7 13. 20 Feb. 2017. SRM/MRM-based proteomics has been successfully applied on a variety of biological samples from clinical specimens.

[0041] In one embodiment, the mass spectrometry sample may be prepared using tissue microdissection. Usually, in this method the tumor tissues are sliced into sections of about lOpm thickness. The tissues are stained with hematoxylin using standard histological methods prior to dissection. Microdissection is performed on a Leica LMD6000 dissection scope according to manufacturer’s recommendations (Leica, Wetzlar, Germany). A total area of 12 mm consisting of approximately 45,000 tissue-derived cancerous cells may be transferred via laser dissection directly into the dry cap of a 0.5 ml tube. Once the entire 12 mm area is transferred to the dry cap, 20ql of 100 % acetonitrile (ACN) may be added to the cap and the cell/tissue material is transferred to the bottom of the tube by a brief centrifugation. The ACN may be removed by speedvac centrifugation at 35°C for 6 min. The dried dissection pellet may be stored at -20°C.

[0042] For SRM mass spectrometry, the dissected cells may be analyzed on an Orbitrap mass spectrometer (Thermo Scientific, San Jose, CA) equipped with a nanoAcquityLC system (Waters, Milford, MA) and on a TSQVantage triple quadrupole mass spectrometer (Thermo Scientific, San Jose, CA) equipped with a nanoAcquityLC to evaluate all peptides in the tumor tissue sample. Software programs Pinpointl.0, Xcalibur2.l (Thermo Scientific, San Jose, CA) may also be used to identify proteins and peptides based on reproducible peak heights, retention times, chromatographic ion intensities, and distinctive/reproducible transition ion ratios.

[0043] The methods disclosed herein may further comprise a step of administering the selected anticancer drug to the patient. As used herein, the term“administering” an anticancer drug therapy refers to both direct and indirect administration of the therapy, wherein direct administration is typically performed by a health care professional ( e.g physician, nurse, etc.), and wherein indirect administration includes a step of providing or making available the formulation to the health care professional for direct administration ( e.g ., via injection, infusion, oral delivery, topical delivery, etc.).

[0044] In another aspect of the inventive subject matter, the inventors have disclosed a method of determining the best treatment option for a patient having lung cancer, comprising:

performing proteomic analysis of a tumor sample of the patient to quantify one or more proteins in the tumor sample and determining the best treatment option for the patient based on the quantity of the one or more proteins in the tumor sample preferably, when patient’s tumor has an underexpression of MGMT protein, then temozolomide drug therapy is the most suitable treatment option. Alternatively, when patient’s tumor has an overexpression of TYMP protein, then fluorouracil drug therapy is the most suitable treatment option. Finally, when patient’s tumor expresses DLL3, CD56, or TROP2 proteins, then antibody-drug conjugate therapy is the most suitable treatment option.

[0045] The foregoing discussion provides many example embodiments of the inventive subject matter. Although each embodiment represents a single combination of inventive elements, the inventive subject matter is considered to include all possible combinations of the disclosed elements. Thus if one embodiment comprises elements A, B, and C, and a second embodiment comprises elements B and D, then the inventive subject matter is also considered to include other remaining combinations of A, B, C, or D, even if not explicitly disclosed. As used in the description herein and throughout the claims that follow, the meaning of“a,”“an,” and“the” includes plural reference unless the context clearly dictates otherwise. Also, as used in the description herein, the meaning of“in” includes“in” and“on” unless the context clearly dictates otherwise.

[0046] Groupings of alternative elements or embodiments of the invention disclosed herein are not to be construed as limitations. Each group member can be referred to and claimed individually or in any combination with other members of the group or other elements found herein. One or more members of a group can be included in, or deleted from, a group for reasons of convenience and/or patentability. When any such inclusion or deletion occurs, the

specification is herein deemed to contain the group as modified thus fulfilling the written description of all Markush groups used in the appended claims. [0047] It should be apparent to those skilled in the art that many more modifications besides those already described are possible without departing from the inventive concepts herein. The inventive subject matter, therefore, is not to be restricted except in the scope of the appended claims. Moreover, in interpreting both the specification and the claims, all terms should be interpreted in the broadest possible manner consistent with the context. In particular, the terms “comprises” and“comprising” should be interpreted as referring to elements, components, or steps in a non-exclusive manner, indicating that the referenced elements, components, or steps may be present, or utilized, or combined with other elements, components, or steps that are not expressly referenced. Where the specification claims refers to at least one of something selected from the group consisting of A, B, C .... and N, the text should be interpreted as requiring only one element from the group, not A plus N, or B plus N, etc.

Claims

CLAIMS What is claimed is:

1. A method for selecting a suitable anticancer drug for the treatment of a lung tumor to a patient in need thereof, the method comprising:

performing quantitative mass spectroscopic proteomic analysis on a plurality of tumor cells to quantify expression of a protein; and

determining whether the anticancer drug is suitable or unsuitable for the treatment of the lung tumor by comparing the protein expression of the tumor with a pre-defined threshold for that protein.

2. The method of claim 1, wherein the anticancer drug is temozolomide.

3. The method of claim 2, wherein temozolomide is selected as the suitable anticancer drug for the patient when the patient’s tumor has low of absent MGMT protein expression.

4. The method of claim 3, wherein low or absent MGMT protein expression comprises MGMT protein expression of less than 200 attomoles per microgram of tumor.

5. The method of claim 1, wherein the anticancer drug is fluorouracil.

6. The method of claim 5, wherein fluorouracil is selected as the suitable anticancer drug for the patient when the patient’s tumor overexpresses TYMP protein.

7. The method of claim 3, wherein overexpression of TYMP protein comprises TYMP protein expression of more than 1335 attomoles per microgram of tumor.

8. The method of claim 1, wherein the anticancer drug is an antibody-drug conjugate.

9. The method of claim 8, wherein the antibody-drug conjugate targets the proteins DLL3, CD56, or TROP2.

10. The method of claim 9, wherein the presence of proteins DLL3, CD56, or TROP2 indicates that antibody-drug conjugate therapy is a suitable anticancer drug for the patient.

11. The method of claim 1, wherein proteomic analysis is performed by using quantitative mass spectrometry.

12. The method of claim 11, wherein the mass spectrometry is Data Independent Acquisition (DIA) mass spectrometry.

13. The method of claim 11, wherein the mass spectrometry is Collision-Induced Dissociation (CID) mass spectrometry.

14. The method of claim 1, further comprising administering the selected anticancer drug to the patient.

15. A method of determining a treatment option for a patient having lung cancer, comprising: performing quantitative mass spectrometric proteomic analysis of a plurality of tumor cells of the patient to quantify one or more proteins; and

determining the treatment option for the patient based on the quantity of the one or more proteins, wherein:

a. when patient’s tumor has an underexpression of MGMT protein relative to a reference threshold, then temozolomide drug therapy is the most suitable treatment option;

b. when patient’s tumor has an overexpression of TYMP protein relative to a

reference threshold, then fluorouracil drug therapy is the most suitable treatment option; and

c. when patient’s tumor expresses DLL3, CD56, or TROP2 proteins, then antibody- drug conjugate therapy is the most suitable treatment option.

16. The method of claim 15, wherein the lung cancer is small cell lung cancer (SCLC).

17. The method of claim 15, wherein proteomic analysis is performed by using quantitative mass spectrometry.

18. The method of claim 15, wherein the mass spectrometry is Data Independent Acquisition (DIA) mass spectrometry.

19. The method of claim 15, wherein the mass spectrometry is Collision-Induced Dissociation (CID) mass spectrometry.

20. The method of claim 15, wherein underexpression of MGMT protein comprises MGMT protein expression of less than 200 attomoles per microgram of tumor.

21. The method of claim 15, wherein overexpression of TYMP protein comprises TYMP protein expression of more than 1335 attomoles per microgram of tumor.

22. The method of claim 15, further comprising administering the selected anticancer drug to the patient.