COMPOUNDS WITH ANTI-TUMOR ACTIVITY AGAINST CANCER CELLS BEARING EGFR OR HER2 EXON 20 INSERTIONS

The present disclosure provides methods of treating cancer in a patient determined to have an EGFR and/or HER2 exon 20 mutation, such as an insertion mutation, by administering a third-generation tyrosine kinase inhibitor, such as poziotinib or afatinib.

INCORPORATION OF SEQUENCE LISTING

The sequence listing that is contained in the file named “UTFCP1383WO.txt”, which is 3.59 KB (as measured in Microsoft Windows) and was created on Mar. 27, 2020, is filed herewith by electronic submission and is incorporated by reference herein.

BACKGROUND

The present invention relates generally to the field of molecular biology and medicine. More particularly, it concerns methods of treating patients with EGFR and/or HER2 exon 20 mutations, such as insertion mutations.

2. Description of Related Art

Approximately 10-15% of NSCLCs harbor activating EGFR mutations. For the majority of these patients whose tumors have “classical” sensitizing mutations (L858R and exon 19 deletions), TKIs such as gefitinib and erlotinib provide dramatic clinical benefit, with approximately 70% experiencing objective responses (OR), improved progression free survival (PFS), and quality of life compared to chemotherapy alone (Maemondo et al., 2010). However, approximately 10-12% of EGFR mutant NSCLC tumors have an in-frame insertion within exon 20 of EGFR (Arcila et al., 2012), and are generally resistant to EGFR TKIs. In addition, 90% of HER2 mutations in NSCLC are exon 20 mutations (Mazieres et al., 2013). Together, EGFR and HER2 exon 20 mutations comprise approximately 4% of NSCLC patients. The data thus far suggests that available TKIs of HER2 (afatinib, lapatinib, neratinib, dacomitinib) have limited activity in patients with HER2 mutant tumors with many studies reporting OR rates below 40% (Kosaka et al., 2017), although some preclinical activity is observed in HER2 mouse models treated with afatinib (Perera et al., 2009).

Exon 20 of EGFR and HER2 contains two major regions, the c-helix (residues 762-766 in EGFR and 770-774 in HER2) and the loop following the c-helix (residues 767-774 in EGFR and 775-783 in HER2). Crystallography of the EGFR exon 20 insertion D770insNPG has revealed a stabilized and ridged active conformation inducing resistance to first generation TKIs in insertions after residue 764. However, modeling of EGFR A763insFQEA demonstrated that insertions before residue 764 do not exhibit this effect and do not induce drug resistance (Yasuda et al., 2013). Moreover, in a patient derived xenograft (PDX) model of EGFR exon 20 driven NSCLC where insertions are in the loop after the c-helix (EGFR H773insNPH), third generation EGFR TKIs, osimertinib (AZD9291) and rociletinib (CO-1696) were found to have minimal activity (Yang et al., 2016). In a recent study of rare EGFR and HER2 exon 20 mutations, the authors found a heterogeneous response to covalent quinazoline-based second generation inhibitors such as dacomitinib and afatinib; however, concentrations required to target more common exon 20 insertion mutations were above clinically achievable concentrations (Kosaka et al., 2017). Therefore, there is a significant clinical need to identify novel therapies to overcome the innate drug resistance of NSCLC tumors harboring exon 20 mutations, particularly insertion mutations, in EGFR and HER2.

SUMMARY

Embodiments of the present disclosure provides methods and compositions for treating cancer in patients with EGFR and/or HER2 exon 20 mutations, such as exon 20 insertion mutations. In one embodiment, there is provided a method of treating cancer in a subject comprising administering an effective amount of poziotinib to the subject, wherein the subject has been determined to have one or more EGFR exon 20 mutations, such as one or more EGFR exon 20 insertion mutations. In particular aspects, the subject is human.

In some aspects, the poziotinib is further defined as poziotinib hydrochloride salt. In certain aspects, the poziotinib hydrochloride salt is formulated as a tablet. In some aspects, the one or more EGFR exon 20 mutations are further defined as de novo EGFR 20 insertion mutations.

In certain aspects, the one or more EGFR exon 20 mutations comprise one or more point mutations, insertions, and/or deletions of 3-18 nucleotides between amino acids 763-778. In some aspects, the subject has been determined to have 2, 3, or 4 EGFR exon 20 mutations. In some aspects, the one or more EGFR exon 20 mutations are at one or more residues selected from the group consisting of A763, A767, S768, V769, D770, N771, P772, H773, V774, and R776.

In some aspects, the subject is resistant or has shown resistance to the previously administered tyrosine kinase inhibitor. In certain aspects, the tyrosine kinase inhibitor is lapatinib, afatinib, dacomitinib, osimertinib, ibrutinib, nazartinib, or beratinib.

In certain aspects, the poziotinib is administered orally. In some aspects, the poziotinib is administered at a dose of 5-25 mg, such as 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 2, 23, 24, or 25 mg. In certain aspects, the poziotinib is administered at a dose of 8 mg, 12 mg, or 16 mg. In some aspects, the poziotinib is administered daily. In certain aspects, the poziotinib is administered on a continuous basis. In some aspects, the poziotinib is administered on 28 day cycles.

In certain aspects, the subject was determined to have an EGFR exon 20 mutation, such as an insertion mutation, by analyzing a genomic sample from the subject. In some aspects, the genomic sample is isolated from saliva, blood, urine, normal tissue, or tumor tissue. In particular aspects, the presence of an EGFR exon 20 mutation is determined by nucleic acid sequencing (e.g., DNA sequencing of tumor tissue or circulating free DNA from plasma) or PCR analyses.

In certain aspects, the method further comprises administering an additional anti-cancer therapy. In some aspects, the anti-cancer therapy is chemotherapy, radiotherapy, gene therapy, surgery, hormonal therapy, anti-angiogenic therapy or immunotherapy. In certain aspects, the poziotinib and/or anti-cancer therapy are administered intravenously, subcutaneously, intraosseously, orally, transdermally, in sustained release, in controlled release, in delayed release, as a suppository, or sublingually. In some aspects, administering the poziotinib and/or anti-cancer therapy comprises local, regional or systemic administration. In particular aspects, the poziotinib and/or anti-cancer therapy are administered two or more times, such as daily, every other day, or weekly.

In another embodiment, there is provided a pharmaceutical composition comprising poziotinib for a patient determined to have one or more EGFR exon 20 mutations, such as one or more EGFR exon 20 insertion mutations. In certain aspects, the one or more EGFR exon 20 mutations comprise a point mutation, insertion, and/or deletion of 3-18 nucleotides between amino acids 763-778. In certain aspects, the subject has been determined to have 2, 3, or 4 EGFR exon 20 mutations.

In some aspects, the poziotinib is further defined as poziotinib hydrochloride salt. In certain aspects, the poziotinib hydrochloride salt is formulated as a tablet. In some aspects, the one or more EGFR exon 20 mutations are further defined as de novo EGFR 20 insertion mutations.

In some aspects, the poziotinib is administered orally. In some aspects, the poziotinib is administered at a dose of 5-25 mg, such as 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 2, 23, 24, or 25 mg. In some aspects, the poziotinib is administered at a dose of 8 mg, 12 mg, or 16 mg. In certain aspects, the poziotinib is administered daily. In some aspects, the poziotinib is administered on a continuous basis. In some aspects, the poziotinib is administered on 28 day cycles.

In some aspects, the subject is resistant or has shown resistance to the previously administered tyrosine kinase inhibitor. In certain aspects, the tyrosine kinase inhibitor is lapatinib, afatinib, dacomitinib, osimertinib, ibrutinib, nazartinib, or beratinib.

In some aspects, the one or more EGFR exon 20 insertion mutations are at one or more residues selected from the group consisting of A763, A767, 5768, V769, D770, N771, P772, and H773. In certain aspects, the subject has been determined to not have an EGFR mutation at residue C797 and/or T790, such as C797S and/or T790M. In particular aspects, the one or more exon 20 mutations are selected from the group consisting of A763insFQEA, A763insLQEA, A767insASV, S768dupSVD, S768I, V769insASV, D770insSVD, D770insNPG, H773insNPH, N771del insGY, N771del insFH, N771dupNPH, A767insTLA, V769insGVV, V769L, V769insGSV, V769ins MASVD, D770del ins GY, D770insG, D770insY H773Y, N771insSVDNR, N771insHH, N771dupN, P772insDNP, H773insAH, H773insH, V774M, V774insHV, R776H, and R776C. In some aspects, the patient is being treated with an anti-cancer therapy.

In yet another embodiment, there is provided a method of predicting a response to poziotinib alone or in combination with an anti-cancer therapy in a subject having a cancer comprising detecting an EGFR exon 20 mutation (e.g., EGFR exon 20 insertion mutation) in a genomic sample obtained from said patient, wherein if the sample is positive for the presence of the EGFR exon 20 mutation, then the patient is predicted to have a favorable response to poziotinib alone or in combination with an anti-cancer therapy. In some aspects, the genomic sample is isolated from saliva, blood, urine, normal tissue, or tumor tissue. In certain aspects, the presence of an EGFR exon 20 mutation is determined by nucleic acid sequencing or PCR analyses. In certain aspects, the EGFR exon 20 mutation comprises one or more point mutations, insertions, and/or deletions of 3-18 nucleotides between amino acids 763-778. In some aspects, the EGFR exon 20 mutation is at residue A763, H773, A767, S768, V769, D770, N771, and/or D773. In some aspects, the EGFR exon 20 mutation is selected from the group consisting of A763insFQEA, A767insASV, S768dupSVD, V769insASV, D770insSVD, D770insNPG, H773insNPH, N771del insGY, N771del insFH and N771dupNPH.

In certain aspects, a favorable response to poziotinib inhibitor alone or in combination with an anti-cancer therapy comprises reduction in tumor size or burden, blocking of tumor growth, reduction in tumor-associated pain, reduction in cancer associated pathology, reduction in cancer associated symptoms, cancer non-progression, increased disease free interval, increased time to progression, induction of remission, reduction of metastasis, or increased patient survival. In further aspects, the patient predicted to have a favorable response is administered poziotinib alone or in combination with a second anti-cancer therapy.

In some aspects, the poziotinib is further defined as poziotinib hydrochloride salt. In certain aspects, the poziotinib hydrochloride salt is formulated as a tablet. In some aspects, the one or more EGFR exon 20 mutations are further defined as de novo EGFR 20 insertion mutations.

In some aspects, the poziotinib is administered orally. In some aspects, the poziotinib is administered at a dose of 5-25 mg, such as 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 2, 23, 24, or 25 mg. In some aspects, the poziotinib is administered at a dose of 8 mg, 12 mg, or 16 mg. In certain aspects, the poziotinib is administered daily. In some aspects, the poziotinib is administered on a continuous basis. In some aspects, the poziotinib is administered on 28 day cycles.

In some aspects, the subject is resistant or has shown resistance to the previously administered tyrosine kinase inhibitor. In certain aspects, the tyrosine kinase inhibitor is lapatinib, afatinib, dacomitinib, osimertinib, ibrutinib, nazartinib, or beratinib.

A further embodiment provides a method of treating cancer in a patient comprising administering an effective amount of poziotinib or afatinib to the subject, wherein the subject has been determined to have one or more HER2 exon 20 mutations selected from the group consisting of A775insV G776C, A775insYVMA, G776V, G776C V777insV, G776C V777insC, G776del insVV, G776del insVC, P780insGSP, V777L, G778insLPS, V773M, Y772dupYVMA, G776del insLC, G778dupGSP, V777insCG, G776V/S, V777M, M774dupM, A775insSVMA, A775insVA, and L786V. In some aspects, the one or more HER2 exon 20 mutations further comprise one or more point mutations, insertions, and/or deletions of 3-18 nucleotides between amino acids 770-785. In some aspects, the one or more HER2 exon 20 mutations are at residue Y772, A775, M774, G776, G778, V777, S779, P780, and/or L786. In some aspects, the one or more HER2 exon 20 mutations selected from the group consisting of A775insV G776C, A775insYVMA, G776V, G776C V777insV, G776C V777insC, G776del insVV, G776del insVC, P780insGSP, V777L, G778insLPS, and V773M. In some aspects, the HER2 exon 20 mutation is at residue V773, A775, G776, S779, G778, and/or P780. In particular aspects, the subject is human.

In some aspects, the poziotinib is further defined as poziotinib hydrochloride salt. In certain aspects, the poziotinib hydrochloride salt is formulated as a tablet. In some aspects, the one or more EGFR exon 20 mutations are further defined as de novo EGFR 20 insertion mutations.

In some aspects, the poziotinib is administered orally. In some aspects, the poziotinib is administered at a dose of 5-25 mg, such as 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 2, 23, 24, or 25 mg. In some aspects, the poziotinib is administered at a dose of 8 mg, 12 mg, or 16 mg. In certain aspects, the poziotinib is administered daily. In some aspects, the poziotinib is administered on a continuous basis. In some aspects, the poziotinib is administered on 28 day cycles.

In some aspects, the subject is resistant or has shown resistance to the previously administered tyrosine kinase inhibitor. In certain aspects, the tyrosine kinase inhibitor is lapatinib, afatinib, dacomitinib, osimertinib, ibrutinib, nazartinib, or beratinib.

In some aspects, the method further comprises administering an mTOR inhibitor. In certain aspects, the mTOR inhibitor is rapamycin, temsirolimus, everolimus, ridaforolimus or MLN4924. In particular aspects, the mTOR inhibitor is everolimus.

In certain aspects, the poziotinib or afatinib and/or mTOR inhibitor are administered intravenously, subcutaneously, intraosseously, orally, transdermally, in sustained release, in controlled release, in delayed release, as a suppository, or sublingually. In some aspects, the patient was determined to have a HER2 exon 20 mutation by analyzing a genomic sample from the patient. In certain aspects, the genomic sample is isolated from saliva, blood, urine, normal tissue, or tumor tissue. In some aspects, the presence of an HER2 exon 20 mutation is determined by nucleic acid sequencing or PCR analyses.

In additional aspects, the method further comprises administering an additional anti-cancer therapy. In some aspects, the anti-cancer therapy is chemotherapy, radiotherapy, gene therapy, surgery, hormonal therapy, anti-angiogenic therapy or immunotherapy.

In another embodiment, there is provided a pharmaceutical composition comprising poziotinib or afatinib for a patient determined to have one or more HER2 exon 20 mutations selected from the group consisting of A775insV G776C, A775insYVMA, G776V, G776C V777insV, G776C V777insC, G776del insVV, G776del insVC, P780insGSP, V777L, G778insLPS, V773M, Y772dupYVMA, G776del insLC, G778dupGSP, V777insCG, G776V/S, V777M, M774dupM, A775insSVMA, A775insVA, and L786V. In some aspects, the one or more HER2 exon 20 mutations further comprise one or more point mutations, insertions, and/or deletions of 3-18 nucleotides between amino acids 770-785. In some aspects, the one or more HER2 exon 20 mutations are at residue Y772, A775, M774, G776, G778, V777, 5779, P780, and/or L786. In some aspects, the one or more HER2 exon 20 mutations are selected from the group consisting of A775insV G776C, A775insYVMA, G776V, G776C V777insV, G776C V777insC, G776del insVV, G776del insVC, P780insGSP, V777L, G778insLPS, and V773M. In some aspects, the HER2 exon 20 mutation is at residue V773, A775, G776, S779, G778, and/or P780. In some aspects, the patient is being treated with an anti-cancer therapy.

In some aspects, the poziotinib is further defined as poziotinib hydrochloride salt. In certain aspects, the poziotinib hydrochloride salt is formulated as a tablet. In some aspects, the one or more EGFR exon 20 mutations are further defined as de novo EGFR 20 insertion mutations.

In some aspects, the subject is resistant or has shown resistance to the previously administered tyrosine kinase inhibitor. In certain aspects, the tyrosine kinase inhibitor is lapatinib, afatinib, dacomitinib, osimertinib, ibrutinib, nazartinib, or beratinib.

In yet another embodiment, there is provided a method of predicting a response to poziotinib or afatinib alone or in combination with an anti-cancer therapy in a patient having a cancer comprising detecting an HER2 exon 20 mutation (e.g., HER2 exon 20 insertion mutation) selected from the group consisting of A775insV G776C, A775insYVMA, G776V, G776C V777insV, G776C V777insC, G776del insVV, G776del insVC, P780insGSP, V777L, G778insLPS, V773M, Y772dupYVMA, G776del insLC, G778dupGSP, V777insCG, G776V/S, V777M, M774dupM, A775insSVMA, A775insVA, and L786V in a genomic sample obtained from said patient, wherein if the sample is positive for the presence of the HER2 exon 20 mutation, then the patient is predicted to have a favorable response to the poziotinib or afatinib alone or in combination with an anti-cancer therapy. In some aspects, the one or more mutations are selected from the group consisting of A775insV G776C, A775insYVMA, G776C V777insC, G776del insVV, G776del insVC, P780insGSP, V777L, G778insLPS, and V773M. In some aspects, the HER2 exon 20 mutation further comprises one or more point mutations, insertions, and/or deletions of 3-18 nucleotides between amino acids 770-785. In certain aspects, the HER2 exon 20 mutation is at residues V773, A775, G776, V777, G778, S779, and/or P780. In other aspects, the HER2 exon 20 mutation is at residue A775, G776, S779, and/or P780.

In some aspects, the genomic sample is isolated from saliva, blood, urine, normal tissue, or tumor tissue. In certain aspects, the presence of a HER2 exon 20 mutation is determined by nucleic acid sequencing or PCR analyses. In particular aspects, the anti-cancer therapy is an mTOR inhibitor. In some aspects, a favorable response to poziotinib or afatinib inhibitor alone or in combination with an anti-cancer therapy comprises reduction in tumor size or burden, blocking of tumor growth, reduction in tumor-associated pain, reduction in cancer associated pathology, reduction in cancer associated symptoms, cancer non-progression, increased disease free interval, increased time to progression, induction of remission, reduction of metastasis, or increased patient survival. In further aspects, the patient predicted to have a favorable response is administered poziotinib alone or in combination with a second anti-cancer therapy.

Also provided herein is a composition comprising nucleic acids isolated from human cancer cells; and a primer pair that can amplify at least a first portion of exon 20 of a human EGFR or HER2 coding sequence. In some aspects, the composition further comprises a labeled probe molecule that can specifically hybridize to the first portion of exon 20 of the human EGFR or HER coding sequence when there is a mutation in the sequence. In certain aspects, the composition further comprises a thermostable DNA polymerase. In some aspects, the composition further comprises dNTPS. In some aspects, the labeled probe hybridizes to the first portion of exon 20 of the human EGFR coding sequence when there is a mutation selected from the group consisting of A763insFQEA, A763insLQEA, A767insASV, S768dupSVD, 57681, V769insASV, D770insSVD, D770insNPG, H773insNPH, N771del insGY, N771del insFH, N771dupNPH, A767insTLA, V769insGVV, V769L, V769insGSV, V769ins MASVD, D770del ins GY, D770insG, D770insY H773Y, N771insSVDNR, N771insHH, N771dupN, P772insDNP, H773insAH, H773insH, V774M, V774insHV, R776H, and R776C.

In certain aspects, the labeled probe hybridizes to the first portion of exon 20 of the human HER2 coding sequence when there is a mutation selected from the group consisting of A775insV G776C, A775insYVMA, G776V, G776C V777insV, G776C V777insC, G776del insVV, G776del insVC, and P780insGSP.

In another embodiment, there is provided an isolated nucleic acid encoding a mutant EGFR protein, wherein said mutant protein differs from wild-type human EGFR by one or more EGFR exon 20 mutations comprising a point mutation, insertion, and/or deletion of 3-18 nucleotides between amino acids 763-778. In some aspects, the one or more EGFR exon 20 mutations are at one or more residues selected from the group consisting of A763, A767, 5768, V769, D770, N771, P772, H773, V774, and R776. In certain aspects, the one or more exon 20 mutations are selected from the group consisting of A763insFQEA, A763insLQEA, A767insASV, S768dupSVD, 57681, V769insASV, D770insSVD, D770insNPG, H773insNPH, N771del insGY, N771del insFH, N771dupNPH, A767insTLA, V769insGVV, V769L, V769insGSV, V769ins MASVD, D770del ins GY, D770insG, D770insY H773Y, N771insSVDNR, N771insHH, N771dupN, P772insDNP, H773insAH, H773insH, V774M, V774insHV, R776H, and R776C. In specific aspects, the nucleic acid comprises the sequence of SEQ ID NO:8, 9, 10, 11, or 12.

In yet another embodiment, there is provided an isolated nucleic acid encoding a mutant HER2 protein, wherein said mutant protein differs from wild-type human HER2 by one or more HER2 exon 20 mutations comprising one or more point mutations, insertions, and/or deletions of 3-18 nucleotides between amino acids 770-785. In some aspects, the one or more HER2 exon 20 mutations are at residue V773, A775, G776, V777, G778, S779, and/or P780. In certain aspects, the one or more HER2 exon 20 mutations selected from the group consisting of A775insV G776C, A775insYVMA, G776V, G776C V777insV, G776C V777insC, G776del insVV, G776del insVC, P780insGSP, V777L, G778insLPS, and V773M. In specific aspects, the nucleic acid comprises the sequence of SEQ ID NO:14, 15, 16, 17, or 18.

DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS

Although the majority of activating mutations of epidermal growth factor receptor (EGFR) mutant non-small cell lung cancers (NSCLCs) are sensitive to available EGFR tyrosine kinase inhibitor (TKIs), a subset with alterations in exon 20 of EGFR and HER2 are intrinsically resistant. The present studies utilized in silico, in vitro, and in vivo testing to model structural alterations induced by these exon 20 mutations and identify effective inhibitors. 3-D modeling revealed significant alterations restricting the size of the drug binding pocket, imposing the binding of large, rigid inhibitors. It was found that poziotinib, due to its small size and flexibility, was able to circumvent these steric changes, and is a potent and relatively selective inhibitor of the EGFR or HER2 exon 20 mutant proteins. Poziotinib also has potent activity in mutant exon 20 EGFR or HER2 NSCLC patient-derived xenograft (PDX) models and genetically engineered mouse models. Thus, these data identify poziotinib as a potent, clinically active inhibitor of EGFR/HER2 exon 20 mutations, and illuminate the molecular features of kinase inhibitors that may circumvent steric changes induced by these insertions.

Accordingly, certain embodiments of the present disclosure provide methods for treating cancer patients with EGFR and/or HER2 exon 20 mutations, such as exon 20 insertions. In particular, the present methods comprise the administration of poziotinib (also known as HM781-36B) or afatinib to patients identified to have EGFR and/or HER exon 20 insertion mutations. The size and flexibility of poziotinib overcomes steric hindrance, inhibiting EGFR and HER2 exon 20 mutants at low nanomolar concentrations. Thus, poziotinib or afatinib as well as structurally similar inhibitors are potent EGFR or HER2 inhibitors that can be used to target both EFGR and HER2 exon 20 insertions which are resistant to irreversible 2ndand 3rdgenerations TKIs.

The term “about” refers to the stated value plus or minus 5%.

“Treatment” or “treating” includes (1) inhibiting a disease in a subject or patient experiencing or displaying the pathology or symptomatology of the disease (e.g., arresting further development of the pathology and/or symptomatology), (2) ameliorating a disease in a subject or patient that is experiencing or displaying the pathology or symptomatology of the disease (e.g., reversing the pathology and/or symptomatology), and/or (3) effecting any measurable decrease in a disease in a subject or patient that is experiencing or displaying the pathology or symptomatology of the disease. For example, a treatment may include administration of an effective amount of poziotinib.

“Prophylactically treating” includes: (1) reducing or mitigating the risk of developing the disease in a subject or patient which may be at risk and/or predisposed to the disease but does not yet experience or display any or all of the pathology or symptomatology of the disease, and/or (2) slowing the onset of the pathology or symptomatology of a disease in a subject or patient which may be at risk and/or predisposed to the disease but does not yet experience or display any or all of the pathology or symptomatology of the disease.

As used herein, the term “patient” or “subject” refers to a living mammalian organism, such as a human, monkey, cow, sheep, goat, dog, cat, mouse, rat, guinea pig, or transgenic species thereof. In certain embodiments, the patient or subject is a primate. Non-limiting examples of human patients are adults, juveniles, infants and fetuses.

The term “effective,” as that term is used in the specification and/or claims, means adequate to accomplish a desired, expected, or intended result. “Effective amount,” “therapeutically effective amount” or “pharmaceutically effective amount” when used in the context of treating a patient or subject with a compound means that amount of the compound which, when administered to a subject or patient for treating or preventing a disease, is an amount sufficient to effect such treatment or prevention of the disease.

As used herein, the term “IC50” refers to an inhibitory dose which is 50% of the maximum response obtained. This quantitative measure indicates how much of a particular drug or other substance (inhibitor) is needed to inhibit a given biological, biochemical or chemical process (or component of a process, i.e. an enzyme, cell, cell receptor or microorganism) by half.

An “anti-cancer” agent is capable of negatively affecting a cancer cell/tumor in a subject, for example, by promoting killing of cancer cells, inducing apoptosis in cancer cells, reducing the growth rate of cancer cells, reducing the incidence or number of metastases, reducing tumor size, inhibiting tumor growth, reducing the blood supply to a tumor or cancer cells, promoting an immune response against cancer cells or a tumor, preventing or inhibiting the progression of cancer, or increasing the lifespan of a subject with cancer.

The term “insertion(s)” or “insertion mutation(s)” refers to the addition of one or more nucleotide base pairs into a DNA sequence. For example, an insertion mutation of exon 20 of EGFR can occur between amino acids 767 to 774, of about 2-21 base pairs. In another example, HER2 exon 20 insertion mutation comprises one or more insertions of 3-18 nucleotides between amino acids 770-785. Exemplary EGFR and HER exon 20 insertion mutations are depicted inFIG. 1of the present disclosure.

“Hybridize” or “hybridization” refers to the binding between nucleic acids. The conditions for hybridization can be varied according to the sequence homology of the nucleic acids to be bound. Thus, if the sequence homology between the subject nucleic acids is high, stringent conditions are used. If the sequence homology is low, mild conditions are used. When the hybridization conditions are stringent, the hybridization specificity increases, and this increase of the hybridization specificity leads to a decrease in the yield of non-specific hybridization products. However, under mild hybridization conditions, the hybridization specificity decreases, and this decrease in the hybridization specificity leads to an increase in the yield of non-specific hybridization products.

A “probe” or “probes” refers to a polynucleotide that is at least eight (8) nucleotides in length and which forms a hybrid structure with a target sequence, due to complementarity of at least one sequence in the probe with a sequence in the target region. The polynucleotide can be composed of DNA and/or RNA. Probes in certain embodiments, are detectably labeled. Probes can vary significantly in size. Generally, probes are, for example, at least 8 to 15 nucleotides in length. Other probes are, for example, at least 20, 30 or 40 nucleotides long. Still other probes are somewhat longer, being at least, for example, 50, 60, 70, 80, or 90 nucleotides long. Probes can be of any specific length that falls within the foregoing ranges as well. Preferably, the probe does not contain a sequence complementary to the sequence(s) used to prime for a target sequence during the polymerase chain reaction.

“Oligonucleotide” or “polynucleotide” refers to a polymer of a single-stranded or double-stranded deoxyribonucleotide or ribonucleotide, which may be unmodified RNA or DNA or modified RNA or DNA.

A “modified ribonucleotide” or deoxyribonucleotide refer to molecules that can be used in place of naturally occurring bases in nucleic acid and includes, but is not limited to, modified purines and pyrimidines, minor bases, convertible nucleosides, structural analogs of purines and pyrimidines, labeled, derivatized and modified nucleosides and nucleotides, conjugated nucleosides and nucleotides, sequence modifiers, terminus modifiers, spacer modifiers, and nucleotides with backbone modifications, including, but not limited to, ribose-modified nucleotides, phosphoramidates, phosphorothioates, phosphonamidites, methyl phosphonates, methyl phosphoramidites, methyl phosphonamidites, 5′-β-cyanoethyl phosphoramidites, methylenephosphonates, phosphorodithioates, peptide nucleic acids, achiral and neutral internucleotidic linkages.

A “variant” refers to a polynucleotide or polypeptide that differs relative to a wild-type or the most prevalent form in a population of individuals by the exchange, deletion, or insertion of one or more nucleotides or amino acids, respectively. The number of nucleotides or amino acids exchanged, deleted, or inserted can be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more such as 25, 30, 35, 40, 45 or 50.

A “primer” or “primer sequence” refers to an oligonucleotide that hybridizes to a target nucleic acid sequence (for example, a DNA template to be amplified) to prime a nucleic acid synthesis reaction. The primer may be a DNA oligonucleotide, a RNA oligonucleotide, or a chimeric sequence. The primer may contain natural, synthetic, or modified nucleotides. Both the upper and lower limits of the length of the primer are empirically determined. The lower limit on primer length is the minimum length that is required to form a stable duplex upon hybridization with the target nucleic acid under nucleic acid amplification reaction conditions. Very short primers (usually less than 3-4 nucleotides long) do not form thermodynamically stable duplexes with target nucleic acid under such hybridization conditions. The upper limit is often determined by the possibility of having a duplex formation in a region other than the pre-determined nucleic acid sequence in the target nucleic acid. Generally, suitable primer lengths are in the range of about 10 to about 40 nucleotides long. In certain embodiments, for example, a primer can be 10-40, 15-30, or 10-20 nucleotides long. A primer is capable of acting as a point of initiation of synthesis on a polynucleotide sequence when placed under appropriate conditions.

“Detection,” “detectable” and grammatical equivalents thereof refers to ways of determining the presence and/or quantity and/or identity of a target nucleic acid sequence. In some embodiments, detection occurs amplifying the target nucleic acid sequence. In other embodiments, sequencing of the target nucleic acid can be characterized as “detecting” the target nucleic acid. A label attached to the probe can include any of a variety of different labels known in the art that can be detected by, for example, chemical or physical means. Labels that can be attached to probes may include, for example, fluorescent and luminescence materials.

“Amplifying,” “amplification,” and grammatical equivalents thereof refers to any method by which at least a part of a target nucleic acid sequence is reproduced in a template-dependent manner, including without limitation, a broad range of techniques for amplifying nucleic acid sequences, either linearly or exponentially. Exemplary means for performing an amplifying step include ligase chain reaction (LCR), ligase detection reaction (LDR), ligation followed by Q-replicase amplification, PCR, primer extension, strand displacement amplification (SDA), hyperbranched strand displacement amplification, multiple displacement amplification (MDA), nucleic acid strand-based amplification (NASBA), two-step multiplexed amplifications, rolling circle amplification (RCA), recombinase-polymerase amplification (RPA) (TwistDx, Cambridg, UK), and self-sustained sequence replication (3 SR), including multiplex versions or combinations thereof, for example but not limited to, OLA/PCR, PCR/OLA, LDR/PCR, PCR/PCR/LDR, PCR/LDR, LCR/PCR, PCR/LCR (also known as combined chain reaction-CCR), and the like. Descriptions of such techniques can be found in, among other places, Sambrook et al. Molecular Cloning, 3rdEdition).

“EGFR” or “Epidermal growth factor receptor” or “EGFR” refers to a tyrosine kinase cell surface receptor and is encoded by one of four alternative transcripts appearing as GenBank accession NM_005228.3, NM_201282.1, NM_201283.1 and NM_201284.1. Variants of EGFR include an insertion in exon 20.

“HER2” or “ERBB2” is a member of the EGFR/ErbB family and appears as GenBank accession NM_004448.2. Variants of HER2 include an insertion in exon 20.

Certain embodiments of the present disclosure concern determining if a subject has one or more EGFR and/or HER2 exon 20 mutations, such as an insertion mutations, particularly one or more insertion mutations as depicted inFIG. 1. The subject may have 2, 3, 4, or more EGFR exon 20 mutations and/or HER2 exon 20 mutations. Mutation detection methods are known the art including PCR analyses and nucleic acid sequencing as well as FISH and CGH. In particular aspects, the exon 20 mutations are detected by DNA sequencing, such as from a tumor or circulating free DNA from plasma.

The EGFR exon 20 mutation(s) may comprise one or more point mutations, insertions, and/or deletions of 3-18 nucleotides between amino acids 763-778. The one or more EGFR exon 20 mutations may be located at one or more residues selected from the group consisting of A763, A767, 5768, V769, D770, N771, P772, H773, V774, and R776.

In some aspects, the subject may have or develop a mutation at EGFR residue C797 which may result in resistance to the TKI, such as poziotinib. Thus, in certain aspects, the subject is determined to not have a mutation at EGFR C797 and/or T790, such as C797S and/or T790M. In some aspects, subjects with T790 mutations, such as T790M, may be administered osimertinib and subjects with C797 mutations, such as C797S, may be administered chemotherapy and/or radiotherapy.

The patient sample can be any bodily tissue or fluid that includes nucleic acids from the lung cancer in the subject. In certain embodiments, the sample will be a blood sample comprising circulating tumor cells or cell free DNA. In other embodiments, the sample can be a tissue, such as a lung tissue. The lung tissue can be from a tumor tissue and may be fresh frozen or formalin-fixed, paraffin-embedded (FFPE). In certain embodiments, a lung tumor FFPE sample is obtained.

Samples that are suitable for use in the methods described herein contain genetic material, e.g., genomic DNA (gDNA). Genomic DNA is typically extracted from biological samples such as blood or mucosal scrapings of the lining of the mouth, but can be extracted from other biological samples including urine, tumor, or expectorant. The sample itself will typically include nucleated cells (e.g., blood or buccal cells) or tissue removed from the subject including normal or tumor tissue. Methods and reagents are known in the art for obtaining, processing, and analyzing samples. In some embodiments, the sample is obtained with the assistance of a health care provider, e.g., to draw blood. In some embodiments, the sample is obtained without the assistance of a health care provider, e.g., where the sample is obtained non-invasively, such as a sample comprising buccal cells that is obtained using a buccal swab or brush, or a mouthwash sample.

In some cases, a biological sample may be processed for DNA isolation. For example, DNA in a cell or tissue sample can be separated from other components of the sample. Cells can be harvested from a biological sample using standard techniques known in the art. For example, cells can be harvested by centrifuging a cell sample and resuspending the pelleted cells. The cells can be resuspended in a buffered solution such as phosphate-buffered saline (PBS). After centrifuging the cell suspension to obtain a cell pellet, the cells can be lysed to extract DNA, e.g., gDNA. See, e.g., Ausubel et al. (2003). The sample can be concentrated and/or purified to isolate DNA. All samples obtained from a subject, including those subjected to any sort of further processing, are considered to be obtained from the subject. Routine methods can be used to extract genomic DNA from a biological sample, including, for example, phenol extraction. Alternatively, genomic DNA can be extracted with kits such as the QIAamp® Tissue Kit (Qiagen, Chatsworth, Calif.) and the Wizard® Genomic DNA purification kit (Promega). Non-limiting examples of sources of samples include urine, blood, and tissue.

The presence or absence of EGFR or HER2 exon 20 mutations, such as an exon 20 insertion mutation, as described herein can be determined using methods known in the art. For example, gel electrophoresis, capillary electrophoresis, size exclusion chromatography, sequencing, and/or arrays can be used to detect the presence or absence of insertion mutations. Amplification of nucleic acids, where desirable, can be accomplished using methods known in the art, e.g., PCR. In one example, a sample (e.g., a sample comprising genomic DNA), is obtained from a subject. The DNA in the sample is then examined to determine the identity of an insertion mutation as described herein. An insertion mutation can be detected by any method described herein, e.g., by sequencing or by hybridization of the gene in the genomic DNA, RNA, or cDNA to a nucleic acid probe, e.g., a DNA probe (which includes cDNA and oligonucleotide probes) or an RNA probe. The nucleic acid probe can be designed to specifically or preferentially hybridize with a particular variant.

A set of probes typically refers to a set of primers, usually primer pairs, and/or detectably-labeled probes that are used to detect the target genetic variations (e.g., EGFR and/or HER2 exon 20 mutations) used in the actionable treatment recommendations of the present disclosure. The primer pairs are used in an amplification reaction to define an amplicon that spans a region for a target genetic variation for each of the aforementioned genes. The set of amplicons are detected by a set of matched probes. In an exemplary embodiment, the present methods may use TaqMan™ (Roche Molecular Systems, Pleasanton, Calif.) assays that are used to detect a set of target genetic variations, such as EGFR and/or HER2 exon 20 mutations. In one embodiment, the set of probes are a set of primers used to generate amplicons that are detected by a nucleic acid sequencing reaction, such as a next generation sequencing reaction. In these embodiments, for example, AmpliSEQ™ (Life Technologies/Ion Torrent, Carlsbad, Calif.) or TruSEQ™ (Illumina, San Diego, Calif.) technology can be employed.

Analysis of nucleic acid markers can be performed using techniques known in the art including, without limitation, sequence analysis, and electrophoretic analysis. Non-limiting examples of sequence analysis include Maxam-Gilbert sequencing, Sanger sequencing, capillary array DNA sequencing, thermal cycle sequencing (Sears et al., 1992), solid-phase sequencing (Zimmerman et al., 1992), sequencing with mass spectrometry such as matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS; Fu et al., 1998), and sequencing by hybridization (Chee et al., 1996; Drmanac et al., 1993; Drmanac et al., 1998). Non-limiting examples of electrophoretic analysis include slab gel electrophoresis such as agarose or polyacrylamide gel electrophoresis, capillary electrophoresis, and denaturing gradient gel electrophoresis. Additionally, next generation sequencing methods can be performed using commercially available kits and instruments from companies such as the Life Technologies/Ion Torrent PGM or Proton, the Illumina HiSEQ or MiSEQ, and the Roche/454 next generation sequencing system.

In one example, a method of identifying an EGFR and/or HER2 mutation in a sample comprises contacting a nucleic acid from said sample with a nucleic acid probe that is capable of specifically hybridizing to nucleic acid encoding a mutated EGFR or HER2 protein, or fragment thereof incorporating a mutation, and detecting said hybridization. In a particular embodiment, said probe is detectably labeled such as with a radioisotope (3H,32P, or33P), a fluorescent agent (rhodamine, or fluorescein) or a chromogenic agent. In a particular embodiment, the probe is an antisense oligomer, for example PNA, morpholino-phosphoramidates, LNA or 2′-alkoxyalkoxy. The probe may be from about 8 nucleotides to about 100 nucleotides, or about 10 to about 75, or about 15 to about 50, or about 20 to about 30. In another aspect, said probes of the present disclosure are provided in a kit for identifying EGFR or HER2 mutations in a sample, said kit comprising an oligonucleotide that specifically hybridizes to or adjacent to a site of mutation in the EGFR or HER2 gene. The kit may further comprise instructions for treating patients having tumors that contain EGFR or HER2 insertion mutations with poziotinib or afatinib based on the result of a hybridization test using the kit.

In another aspect, a method for detecting an exon 20 mutation in a sample comprises amplifying from said sample nucleic acids corresponding to exon 20 of said EGFR gene or HER2, or a fragment thereof suspected of containing a mutation, and comparing the electrophoretic mobility of the amplified nucleic acid to the electrophoretic mobility of corresponding wild-type EGFR or HER2 gene or fragment thereof. A difference in the mobility indicates the presence of a mutation in the amplified nucleic acid sequence. Electrophoretic mobility may be determined on polyacrylamide gel.

Alternatively, nucleic acids may be analyzed for detection of mutations using Enzymatic Mutation Detection (EMD) (Del Tito et al., 1998). EMD uses the bacteriophage resolvase T4 endonuclease VII, which scans along double-stranded DNA until it detects and cleaves structural distortions caused by base pair mismatches resulting from point mutations, insertions and deletions. Detection of two short fragments formed by resolvase cleavage, for example by gel electrophoresis, indicates the presence of a mutation. Benefits of the EMD method are a single protocol to identify point mutations, deletions, and insertions assayed directly from PCR reactions eliminating the need for sample purification, shortening the hybridization time, and increasing the signal-to-noise ratio. Mixed samples containing up to a 20-fold excess of normal DNA and fragments up to 4 kb in size can been assayed. However, EMD scanning does not identify particular base changes that occur in mutation positive samples requiring additional sequencing procedures to identity of the mutation if necessary. CEL I enzyme can be used similarly to resolvase T4 endonuclease VII as demonstrated in U.S. Pat. No. 5,869,245.

III. METHODS OF TREATMENT

Further provided herein are methods for treating or delaying progression of cancer in an individual comprising administering to the individual an effective amount of poziotinib, afatinib, or a structurally similar inhibitor, to a subject determined to have an EGFR and/or HER2 exon 20 mutations, such as an exon 20 insertion. The subject may have more than one EGFR and/or HER exon 20 mutation.

Examples of cancers contemplated for treatment include lung cancer, head and neck cancer, breast cancer, pancreatic cancer, prostate cancer, renal cancer, bone cancer, testicular cancer, cervical cancer, gastrointestinal cancer, lymphomas, pre-neoplastic lesions in the lung, colon cancer, melanoma, and bladder cancer. In particular aspects, the cancer is non-small cell lung cancer.

In some embodiments, the subject is a mammal, e.g., a primate, preferably a higher primate, e.g., a human (e.g., a patient having, or at risk of having, a disorder described herein). In one embodiment, the subject is in need of enhancing an immune response. In certain embodiments, the subject is, or is at risk of being, immunocompromised. For example, the subject is undergoing or has undergone a chemotherapeutic treatment and/or radiation therapy. Alternatively, or in combination, the subject is, or is at risk of being, immunocompromised as a result of an infection.

Certain embodiments concern the administration of poziotinib (also known as HM781-36B, HM781-36, and 1-[4-[4-(3,4-dichloro-2-fluoroanilino)-7-methoxyquinazolin-6-yl]oxypiperidin-1-yl]prop-2-en-1-one) to a subject determined to have EGFR or HER2 exon 20 mutation, such as an exon 20 insertion. Poziotinib is a quinazoline-based pan-HER inhibitor that irreversibly blocks signaling through the HER family of tyrosine-kinase receptors including HER1, HER2, and HER4. Poziotinib or structurally similar compounds (e.g., U.S. Pat. No. 8,188,102 and U.S. Patent Publication No. 20130071452; incorporated herein by reference) may be used in the present methods.

The poziotinib, such as poziotinib hydrochloride salt, may be administered orally, such as in a tablet. The poziotinib may be administered in a dose of 4-25 mg, such as at a dose of 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, or 24 mg. The dosing may be daily, every other day, every 3 days or weekly. The dosing may be on a continuous schedule, such as on 28 days cycles.

In some aspects, subjects with T790 mutations, such as T790M, may be administered osimertinib and subjects with C797 mutations, such as C797S, may be administered chemotherapy and/or radiotherapy as described herein. The osimertinib, chemotherapy, and/or radiation may be administered alone or in combination with poziotinib. Osimertinib may be administered at a dose of 25 to 100 mg, such as about 40 or 80 mg. The dosing may be daily, every other day, every 2 days, every 3 days, or weekly. The osimertinib may be administered orally, such as in tablet.

Afatinib may be administered at a dose of 10-50 mg, such as 10, 20, 30, 40, or 50 mg. The afatinib may be administered

Also provided herein are pharmaceutical compositions and formulations comprising poziotinib or afatinib and a pharmaceutically acceptable carrier for subjects determined to have an EGFR or HER2 exon 20 mutation, such as an exon 20 insertion.

In certain embodiments, the compositions and methods of the present embodiments involve poziotinib or afatinib in combination with at least one additional therapy. The additional therapy may be radiation therapy, surgery (e.g., lumpectomy and a mastectomy), chemotherapy, gene therapy, DNA therapy, viral therapy, RNA therapy, immunotherapy, bone marrow transplantation, nanotherapy, monoclonal antibody therapy, or a combination of the foregoing. The additional therapy may be in the form of adjuvant or neoadjuvant therapy.

In some embodiments, the additional therapy is the administration of small molecule enzymatic inhibitor or anti-metastatic agent. In some embodiments, the additional therapy is the administration of side-effect limiting agents (e.g., agents intended to lessen the occurrence and/or severity of side effects of treatment, such as anti-nausea agents, etc.). In some embodiments, the additional therapy is radiation therapy. In some embodiments, the additional therapy is surgery. In some embodiments, the additional therapy is a combination of radiation therapy and surgery. In some embodiments, the additional therapy is gamma irradiation. In some embodiments, the additional therapy is therapy targeting PBK/AKT/mTOR pathway, HSP90 inhibitor, tubulin inhibitor, apoptosis inhibitor, and/or chemopreventative agent. The additional therapy may be one or more of the chemotherapeutic agents known in the art.

The poziotinib or afatinib may be administered before, during, after, or in various combinations relative to an additional cancer therapy, such as immune checkpoint therapy. The administrations may be in intervals ranging from concurrently to minutes to days to weeks. In embodiments where the poziotinib or afatinib is provided to a patient separately from an additional therapeutic agent, one would generally ensure that a significant period of time did not expire between the time of each delivery, such that the two compounds would still be able to exert an advantageously combined effect on the patient. In such instances, it is contemplated that one may provide a patient with the antibody therapy and the anti-cancer therapy within about 12 to 24 or 72 h of each other and, more particularly, within about 6-12 h of each other. In some situations it may be desirable to extend the time period for treatment significantly where several days (2, 3, 4, 5, 6, or 7) to several weeks (1, 2, 3, 4, 5, 6, 7, or 8) lapse between respective administrations.

Various combinations may be employed. For the example below poziotinib or afatinib is “A” and an anti-cancer therapy is “B”:

Administration of any compound or therapy of the present embodiments to a patient will follow general protocols for the administration of such compounds, taking into account the toxicity, if any, of the agents. Therefore, in some embodiments there is a step of monitoring toxicity that is attributable to combination therapy.

A wide variety of chemotherapeutic agents may be used in accordance with the present embodiments. The term “chemotherapy” refers to the use of drugs to treat cancer. A “chemotherapeutic agent” is used to connote a compound or composition that is administered in the treatment of cancer. These agents or drugs are categorized by their mode of activity within a cell, for example, whether and at what stage they affect the cell cycle. Alternatively, an agent may be characterized based on its ability to directly cross-link DNA, to intercalate into DNA, or to induce chromosomal and mitotic aberrations by affecting nucleic acid synthesis.

The skilled artisan will understand that additional immunotherapies may be used in combination or in conjunction with methods of the embodiments. In the context of cancer treatment, immunotherapeutics, generally, rely on the use of immune effector cells and molecules to target and destroy cancer cells. Rituximab (RITUXAN®) is such an example. The immune effector may be, for example, an antibody specific for some marker on the surface of a tumor cell. The antibody alone may serve as an effector of therapy or it may recruit other cells to actually affect cell killing. The antibody also may be conjugated to a drug or toxin (chemotherapeutic, radionuclide, ricin A chain, cholera toxin, pertussis toxin, etc.) and serve as a targeting agent. Alternatively, the effector may be a lymphocyte carrying a surface molecule that interacts, either directly or indirectly, with a tumor cell target. Various effector cells include cytotoxic T cells and NK cells

Antibody-drug conjugates have emerged as a breakthrough approach to the development of cancer therapeutics. Cancer is one of the leading causes of deaths in the world. Antibody-drug conjugates (ADCs) comprise monoclonal antibodies (MAbs) that are covalently linked to cell-killing drugs. This approach combines the high specificity of MAbs against their antigen targets with highly potent cytotoxic drugs, resulting in “armed” MAbs that deliver the payload (drug) to tumor cells with enriched levels of the antigen. Targeted delivery of the drug also minimizes its exposure in normal tissues, resulting in decreased toxicity and improved therapeutic index. The approval of two ADC drugs, ADCETRIS® (brentuximab vedotin) in 2011 and KADCYLA® (trastuzumab emtansine or T-DM1) in 2013 by FDA validated the approach. There are currently more than 30 ADC drug candidates in various stages of clinical trials for cancer treatment (Leal et al., 2014). As antibody engineering and linker-payload optimization are becoming more and more mature, the discovery and development of new ADCs are increasingly dependent on the identification and validation of new targets that are suitable to this approach and the generation of targeting MAbs. Two criteria for ADC targets are upregulated/high levels of expression in tumor cells and robust internalization.

In one aspect of immunotherapy, the tumor cell must bear some marker that is amenable to targeting, i.e., is not present on the majority of other cells. Many tumor markers exist and any of these may be suitable for targeting in the context of the present embodiments. Common tumor markers include CD20, carcinoembryonic antigen, tyrosinase (p97), gp68, TAG-72, HMFG, Sialyl Lewis Antigen, MucA, MucB, PLAP, laminin receptor, erb B, and p155. An alternative aspect of immunotherapy is to combine anticancer effects with immune stimulatory effects. Immune stimulating molecules also exist including: cytokines, such as IL-2, IL-4, IL-12, GM-CSF, gamma-IFN, chemokines, such as MIP-1, MCP-1, IL-8, and growth factors, such as FLT3 ligand.

In some embodiments, the immunotherapy may be an immune checkpoint inhibitor. Immune checkpoints either turn up a signal (e.g., co-stimulatory molecules) or turn down a signal. Inhibitory immune checkpoints that may be targeted by immune checkpoint blockade include adenosine A2A receptor (A2AR), B7-H3 (also known as CD276), B and T lymphocyte attenuator (BTLA), cytotoxic T-lymphocyte-associated protein 4 (CTLA-4, also known as CD152), indoleamine 2,3-dioxygenase (IDO), killer-cell immunoglobulin (KIR), lymphocyte activation gene-3 (LAG3), programmed death 1 (PD-1), T-cell immunoglobulin domain and mucin domain 3 (TIM-3) and V-domain Ig suppressor of T cell activation (VISTA). In particular, the immune checkpoint inhibitors target the PD-1 axis and/or CTLA-4.

The immune checkpoint inhibitors may be drugs such as small molecules, recombinant forms of ligand or receptors, or, in particular, are antibodies, such as human antibodies (e.g., International Patent Publication WO2015016718; Pardoll,Nat Rev Cancer,12(4): 252-64, 2012; both incorporated herein by reference). Known inhibitors of the immune checkpoint proteins or analogs thereof may be used, in particular chimerized, humanized or human forms of antibodies may be used. As the skilled person will know, alternative and/or equivalent names may be in use for certain antibodies mentioned in the present disclosure. Such alternative and/or equivalent names are interchangeable in the context of the present invention. For example it is known that lambrolizumab is also known under the alternative and equivalent names MK-3475 and pembrolizumab.

In some embodiments, the PD-1 binding antagonist is a molecule that inhibits the binding of PD-1 to its ligand binding partners. In a specific aspect, the PD-1 ligand binding partners are PDL1 and/or PDL2. In another embodiment, a PDL1 binding antagonist is a molecule that inhibits the binding of PDL1 to its binding partners. In a specific aspect, PDL1 binding partners are PD-1 and/or B7-1. In another embodiment, the PDL2 binding antagonist is a molecule that inhibits the binding of PDL2 to its binding partners. In a specific aspect, a PDL2 binding partner is PD-1. The antagonist may be an antibody, an antigen binding fragment thereof, an immunoadhesin, a fusion protein, or oligopeptide. Exemplary antibodies are described in U.S. Pat. Nos. 8,735,553, 8,354,509, and 8,008,449, all incorporated herein by reference. Other PD-1 axis antagonists for use in the methods provided herein are known in the art such as described in U.S. Patent Publication Nos. US20140294898, US2014022021, and US20110008369, all incorporated herein by reference.

In some embodiments, the PD-1 binding antagonist is an anti-PD-1 antibody (e.g., a human antibody, a humanized antibody, or a chimeric antibody). In some embodiments, the anti-PD-1 antibody is selected from the group consisting of nivolumab, pembrolizumab, and CT-011. In some embodiments, the PD-1 binding antagonist is an immunoadhesin (e.g., an immunoadhesin comprising an extracellular or PD-1 binding portion of PDL1 or PDL2 fused to a constant region (e.g., an Fc region of an immunoglobulin sequence). In some embodiments, the PD-1 binding antagonist is AMP-224. Nivolumab, also known as MDX-1106-04, MDX-1106, ONO-4538, BMS-936558, and OPDIVO®, is an anti-PD-1 antibody described in WO2006/121168. Pembrolizumab, also known as MK-3475, Merck 3475, lambrolizumab, KEYTRUDA®, and SCH-900475, is an anti-PD-1 antibody described in WO2009/114335. CT-011, also known as hBAT or hBAT-1, is an anti-PD-1 antibody described in WO2009/101611. AMP-224, also known as B7-DCIg, is a PDL2-Fc fusion soluble receptor described in WO2010/027827 and WO2011/066342.

Another immune checkpoint that can be targeted in the methods provided herein is the cytotoxic T-lymphocyte-associated protein 4 (CTLA-4), also known as CD152. The complete cDNA sequence of human CTLA-4 has the Genbank accession number L15006. CTLA-4 is found on the surface of T cells and acts as an “off” switch when bound to CD80 or CD86 on the surface of antigen-presenting cells. CTLA4 is a member of the immunoglobulin superfamily that is expressed on the surface of Helper T cells and transmits an inhibitory signal to T cells. CTLA4 is similar to the T-cell co-stimulatory protein, CD28, and both molecules bind to CD80 and CD86, also called B7-1 and B7-2 respectively, on antigen-presenting cells. CTLA4 transmits an inhibitory signal to T cells, whereas CD28 transmits a stimulatory signal. Intracellular CTLA4 is also found in regulatory T cells and may be important to their function. T cell activation through the T cell receptor and CD28 leads to increased expression of CTLA-4, an inhibitory receptor for B7 molecules.

In some embodiments, the immune checkpoint inhibitor is an anti-CTLA-4 antibody (e.g., a human antibody, a humanized antibody, or a chimeric antibody), an antigen binding fragment thereof, an immunoadhesin, a fusion protein, or oligopeptide.

Anti-human-CTLA-4 antibodies (or VH and/or VL domains derived therefrom) suitable for use in the present methods can be generated using methods well known in the art. Alternatively, art recognized anti-CTLA-4 antibodies can be used. For example, the anti-CTLA-4 antibodies disclosed in: U.S. Pat. No. 8,119,129; International Patent Publication Nos. WO 01/14424, WO 98/42752, and WO 00/37504 (CP675,206, also known as tremelimumab; formerly ticilimumab); U.S. Pat. No. 6,207,156; Hurwitz et al., 1998; Camacho et al., 2004; and Mokyr et al., 1998 can be used in the methods disclosed herein. The teachings of each of the aforementioned publications are hereby incorporated by reference. Antibodies that compete with any of these art-recognized antibodies for binding to CTLA-4 also can be used. For example, a humanized CTLA-4 antibody is described in International Patent Application Nos. WO2001014424, and WO2000037504, and U.S. Pat. No. 8,017,114; all incorporated herein by reference.

An exemplary anti-CTLA-4 antibody is ipilimumab (also known as 10D1, MDX-010, MDX-101, and Yervoy®) or antigen binding fragments and variants thereof (see, e.g., WO 01/14424). In other embodiments, the antibody comprises the heavy and light chain CDRs or VRs of ipilimumab. Accordingly, in one embodiment, the antibody comprises the CDR1, CDR2, and CDR3 domains of the VH region of ipilimumab, and the CDR1, CDR2 and CDR3 domains of the VL region of ipilimumab. In another embodiment, the antibody competes for binding with and/or binds to the same epitope on CTLA-4 as the above-mentioned antibodies. In another embodiment, the antibody has at least about 90% variable region amino acid sequence identity with the above-mentioned antibodies (e.g., at least about 90%, 95%, or 99% variable region identity with ipilimumab).

Other molecules for modulating CTLA-4 include CTLA-4 ligands and receptors such as described in U.S. Pat. Nos. 5,844,905, 5,885,796 and International Patent Application Nos. WO1995001994 and WO1998042752; all incorporated herein by reference, and immunoadhesins such as described in U.S. Pat. No. 8,329,867, incorporated herein by reference.

5. Other Agents

It is contemplated that other agents may be used in combination with certain aspects of the present embodiments to improve the therapeutic efficacy of treatment. These additional agents include agents that affect the upregulation of cell surface receptors and GAP junctions, cytostatic and differentiation agents, inhibitors of cell adhesion, agents that increase the sensitivity of the hyperproliferative cells to apoptotic inducers, or other biological agents. Increases in intercellular signaling by elevating the number of GAP junctions would increase the anti-hyperproliferative effects on the neighboring hyperproliferative cell population. In other embodiments, cytostatic or differentiation agents can be used in combination with certain aspects of the present embodiments to improve the anti-hyperproliferative efficacy of the treatments. Inhibitors of cell adhesion are contemplated to improve the efficacy of the present embodiments. Examples of cell adhesion inhibitors are focal adhesion kinase (FAKs) inhibitors and Lovastatin. It is further contemplated that other agents that increase the sensitivity of a hyperproliferative cell to apoptosis, such as the antibody c225, could be used in combination with certain aspects of the present embodiments to improve the treatment efficacy.

Also within the scope of the present disclosure are kits for detecting EGFR and/or HER2 exon 20 mutations, such as those disclosed herein. An example of such a kit may include a set of exon 20 mutation-specific primer. The kit may further comprise instructions for use of the primers to detect the presence or absence of the specific EFGR and/or HER2 exon 20 mutations described herein. The kit may further comprise instructions for diagnostic purposes, indicating that a positive identification of EGFR and/or HER2 exon 20 mutations described herein in a sample from a cancer patient indicates sensitivity to the tyrosine kinase inhibitor poziotinib or afatinib or a structurally similar inhibitor. The kit may further comprise instructions that indicate that a positive identification of EGFR and/or exon 20 mutations described herein in a sample from a cancer patient indicates that a patient should be treated with poziotinib, afatinib, or a structurally similar inhibitor.

Example 1—Identification of Drugs for Cancer Cells with EGFR or HER Exon 20 Insertions

Clinical responses to TKIs were investigated in patients with tumors harboring EGFR exon 20 insertions in the clinical database; and among 280 patients with EGFR mutant NSCLC, 129 patients were identified with classical EGFR mutations (exon 19 deletion, L858R, and L861Q) and 9 patients with EGFR exon 20 insertions that were treated with single agent erlotinib, gefitinib or afatinib. NSCLC patients with classical EGFR mutations had a median PFS of 14 months, whereas patients with EGFR exon 20 insertions had a median PFS of only 2 months (p<0.0001, log rank test;FIG. 1A). Of the 9 EGFR exon 20 insertion patients, OR was observed in only 1 patient harboring an S768del-insIL mutation who received afatinib (FIG. 4A). This clinical data demonstrates the limited activity of the available EGFR TKIs in EGFR exon 20 insertion driven NSCLC and validates that alternative treatment strategies are needed for these specific tumors.

As an initial step in drug screening, 7 EGFR and 11 HER2 mutations were expressed in Ba/F3 cells. The locations of the EGFR and HER2 exon 20 mutations are summarized inFIG. 1B. To assess which exon 20 mutations of EGFR and HER2 are activating, Ba/F3 cell lines were screened for IL-3 independent survival. It was found that all EGFR exon 20 insertions tested were activating mutations (FIG. 4B), 6 HER2 exon 20 mutations and, L755P, located in exon 19, were activating mutations (FIG. 4C). Next, the sensitivity was tested for the exon 20 insertions to EGFR and HER2 TKIs that have undergone clinical evaluation including reversible (first generation), irreversible (second generation) and irreversible mutant-specific TKIs (third generation), and then compared sensitivity to EGFR L858R, a classical sensitizing mutation. With the exception of EGFR A763insFQEA, EGFR exon 20 insertions (n=6) were resistant to first (FIG. 1C, IC50=3.3->10 second (FIG. 1d, IC50=40-135 nM), and third (FIG. 1e, IC50=103-850 nM) generation EGFR TKIs (FIG. 5, Table 1). In addition, HER2 exon 20 mutants (n=6) were resistant to first (FIG. 1F, IC50=1.2-13 μM) and third (FIG. 1H, IC50=114-505 nM) generation TKIs. Second generation TKIs did have some activity against Ba/F3 HER2 exon 20 mutant cell lines (FIG. 1G, IC50=10-12 nM,FIG. 6, Table 1). Consistent with the drug screening, with the exception of EGFR A763insFQEA, which showed partial inhibition at lower doses, western blotting demonstrated erlotinib and osimertinib did not significantly inhibit p-EGFR2 in EGFR exon 20 insertion mutations, and only significantly inhibited p-HER2 in HER2 exon 20 insertions mutants at 500 nM (FIG. 7A-D).

To investigate why exon 20 insertions are resistant to first and third generation EGFR TKIs, 3-D modeling was performed on the solved crystal structures of EGFR D770insNPG with EGFR T790M and EGFR WT to visualize changes within the drug binding pocket. The modeling revealed that EGFR exon 20 insertions are similar to T790M mutations in the alignment of the gatekeeper residue T790, which results in increased affinity to ATP and a reduced binding of first generation inhibitors, rendering these mutations resistant to non-covalent inhibitors. In addition, HER2 exon 20 insertions induce a constitutively active conformation, preventing the binding of non-covalent HER2 inhibitor lapatinib, which binds to HER2 in the inactive conformation. Moreover, EGFR and HER2 exon 20 insertions have a dramatic effect on the drug binding pocket. In silico modeling of EGFR (FIG. 1I) and HER2 (FIG. 1J) exon 20 insertions revealed a significant shift of the a-c-helix into the drug binding pocket (arrow) due to the insertions at the C-terminal end of the a-c-helix (FIG. 1J), forcing a ridged placement of the a-c-helix in the inward, activated position. In addition, 3-D modeling demonstrated a significant shift of the P-loop into the drug binding pocket (FIG. 1I, 1J) of both receptors. Together these shifts result in steric hindrance of the drug biding pocket from two directions in both EGFR and HER2 exon 20 mutant proteins. Consistent with the above mentioned in vitro testing, 3-D modeling supports the observation that afatinib inhibits exon 20 insertions more effectively than osimertinib. Osimertinib has a large terminal 1-methylindole group connected directly to a rigid pyrimidine core. This large inflexible group reduces the ability of osimertinib to reach the C797 residue as effectively as afatinib in EGFR exon 20 insertions (FIG. 1I). Alternatively, afatinib has a smaller 1-chorlo-2-flurobenzene ring terminal group indirectly linked to a quinazoline core via a secondary amine group, enabling afatinib to fit into the sterically hindered binding pocket. Moreover, steric hindrance prevents binding of osimertinib to HER2 A775insYVMA. Taken together, the in vitro data and in silico modeling indicate that small, flexible quinazoline derivatives may be capable of targeting EGFR/HER2 exon 20 insertions.

It was next sought to identify TKIs with enhanced activity against exon 20 insertions. Poziotinib, like afatinib, also contains a small terminal group and a flexible quinazoline core. However, poziotinib has smaller substituent groups linking the Michael Acceptor group to the quinazoline core compared to afatinib and increased halogenation of the terminal benzene ring compared to afatinib. This electron-rich moiety also interacts with basic residues of EGFR such as K745 to further stabilize its binding. Therefore, poziotinib was tested in the Ba/F3 system. In vitro, poziotinib potently inhibited the growth of EGFR exon 20 mutant Ba/F3 cell lines (FIG. 2A) and HER2 exon 20 mutant Ba/F3 cells (FIG. 2B). Poziotinib had an average IC50value of 1.0 nM in EGFR exon 20 mutant Ba/F3 cell lines making poziotinib approximately 100 times more potent than osimertinib and 40 times more potent than afatinib in vitro. Moreover, poziotinib had an average IC50value of 1.9 nM in HER2 exon 20 mutant Ba/F3 cell lines, making poziotinib 200 times more potent than osimertinib and 6 times more potent than afatinib in vitro. These results were validated by western blotting where poziotinib inhibited phosphorylation of EGFR and HER2 at concentrations as low as 5 nM (FIG. 2C, 8A). Furthermore, to validate that poziotinib sensitivity was not due to level of expression of EGFR or HER2 mutants, expression of each mutant was determined by ELISA then plotted against IC50values (FIG. 8D). While no correlation was found between IC50and expression (R=−0.056, p=0.856), a correlation was found between poziotinib sensitivity and location of the mutation for EGFR (R=0.687, p=0.044) (FIG. 2D), suggesting that the further away the insertion is from the α-c-helix, the higher the IC50. Interestingly, this correlation was not found for HER2 exon 20 mutations which vary more in the size of the insertion rather than the location (FIG. 8E). This correlation suggests that the precise location of the mutation has varying effects on the drug binding pocket, contributing to the heterogeneity of drug response seen. In addition, poziotinib effectively inhibited growth of patient derived cell lines CUTO14 (EGFR A767dupASV) and YUL0019 (EGFR N771del insFH) with an average IC50value of 1.84 nM and 0.30 nM, respectively, which was 15 times more potent than afatinib for CUT014 and more than 100 times more potent than afatinib for YUL0019 (FIG. 2E, F). Western blotting of CUT014 cell line determined that there was significant inhibition of p-EGFR at 10 nM poziotinib treatment but p-EGFR was not significantly inhibited by afatinib until 1000 nM (FIG. 8B, C).

To determine the specificity of poziotinib to inhibit exon 20 mutants compared to T790M mutants, the IC50values of afatinib, osimertinib, rociletinib, and poziotinib were compared in exon 20 mutants to the IC50values of afatinib, osimertinib, rociletinib, and poziotinib in EGFR T790M mutant Ba/F3 cell lines. IC50values are displayed normalized to the single EGFR T790M mutation, where values less than 1 indicate specificity to exon 20 insertions compared to T790M (FIG. 2G). When compared to EGFR T790M mutants, EGFR exon 20 insertions were 65 times more sensitive to poziotinib. Moreover, EGFR exon 20 insertion mutations were 1.4 times more resistant to afatinib, 5.6 times more resistant to osimertinib, and 24 times more resistant to rociletinib than EGFR T790M mutants (FIG. 2G).

To examine why poziotinib, but not third generation TKIs such as osimertinib, selectively and potently inhibits exon 20 mutants compared to T790M mutations, 3-D modeling was performed to determine how changes in the drug binding pocket affect drug binding. While osimertinib fits into the drug binding pocket of EGFR T790M mutant receptor (FIG. 2H), in exon 20 mutants, large changes (FIG. 2I) within the binding pocket sterically hinder the binding of third generation inhibitors. However, poziotinib is smaller and has greater flexibility allowing it to fit into the sterically hindered exon 20 binding pocket (FIG. 2I). Moreover, 3-D modeling of EGFR D770insNPG with poziotinib and afatinib suggest that the shifted P-loop into the drug binding pocket causes poziotinib to bind more tightly into the drug binding pocket than afatinib. Calculations of structural modeling indicate that the free energy of binding (London ΔG) for poziotinib is lower than afatinib, indicating stronger binding affinity of poziotinib. 3-D modeling of WT HER2 with osimertinib demonstrates that the binding pocket of WT HER2 is larger than the binding pocket of HER2 A775insYVMA. Thus, poziotinib tightly binds deep into the sterically hindered drug binding pocket of HER2 A775insYVMA overcoming structural changes induced by exon 20 insertions.

The efficacy of poziotinib was tested in vivo using GEM models of EGFR and HER2 exon 20 insertion-driven NSCLC. Lung tumors were induced in previously described EGFR D770insNPG (Cho et al., 2013) and HER2 A775insYVMA (Perera et al., 2009) mice, and animals orally received poziotinib (10 mg/kg) or vehicle daily control for 4 weeks. As determined by Mill, Poziotinib reduced tumor burden by 85% in EGFR exon 20 GEMMS (FIG. 3A,C) and 60% in HER2 exon 20 GEMMS (FIG. 3B, D), a higher level of inhibition than the 37% previously observed for afatinib in the identical GEM model. Representative Mill images of tumors before and after poziotinib are shown for both EGFR and HER2 GEMMS (FIG. 3C, D). In both EGFR and HER2 GEM models, mice treated with 10 mg/kg poziotinib demonstrated durable regression, without signs of progression at 12 weeks (FIG. 3E, F). In addition, poziotinib treatment (5 or 10 mg/kg) completely reduced tumors by 14 days (>85% inhibition) in EGFR exon 20 insertions PDX model LU0387 (H773insNPH) (FIG. 3G).

To determine if poziotinib, like other irreversible inhibitors, binds covalently at C797, Ba/F3 cell lines were generated with the C797S mutation observed in ˜30% of patients with osimertinib resistance (Thress et al., 2015). It was found that the C797S mutation induced resistance to poziotinib with IC50value of >10 μM. Together these experiments suggested that poziotinib may be susceptible to similar mechanisms of acquired resistance as other third generation TKIs.

To validate the above findings, experiments were performed using a breast cancer cell line MCF10A with a HER2 G776del insVC. The cells were treated with the different inhibitors at varying doses, and it was found that the breast cancer cell line is sensitive to poziotinib as seen in the other cell lines tested (FIG. 10). Therefore, poziotinib can be used for the treatment of other cancers with exon 20 mutations.

Thus, it was found that exon 20 mutants exhibit de novo resistance to first, second, and third generation TKIs. Using 3-D modeling of EGFR D770insNPG and HER2 A775insYVMA poziotinib was identified as having structural features that could overcome changes within the drug binding pocket induced by insertions in exon 20. Moreover, the predicted activity of poziotinib was confirmed using in vitro and in vivo models demonstrating the potent anti-tumor activity of poziotinib in cells with these mutations.

Poziotinib was found to be approximately 40 times more potent than afatinib and 65 times more potent than dacomitinib in EGFR exon 20 mutants. Moreover, poziotinib was 6 times more potent that afatinib and dacomitinib in HER2 exon 20 mutants in vitro. Taken together, these data indicate that although poziotinib shares a similar quinazoline backbone with afatinib and dacomitinib, additional features of the kinase inhibitor result in increased activity and relative specificity for EGFR exon 20 mutations compared with the more common T790M mutation.

The 3-D modeling suggests that the smaller size, increased halogenation, and flexibility of poziotinib give the inhibitor a competitive advantage in the sterically hindered drug binding pocket of exon 20 mutant EGFR/HER2. A negative correlation was observed between the distance of the mutation from the a-c-helix and drug sensitivity. This relationship suggests that the precise location of the mutation affects the drug binding pocket and/or binding affinity of the TKI. Furthermore, the data indicated that the size of the insertion also affects drug sensitivity. Furthermore, the patient derived cell line, YUL0019 (N771del insFH) which had a net gain of only one amino acid, was more sensitive to quinazoline based pan-HER inhibitors than cell lines with larger EGFR exon 20 insertions.

Example 2—Materials and Methods

Patient Population and Statistical Analyses:

Patients with EGFR mutant NSCLC enrolled in the prospectively collected MD Anderson Lung Cancer Moon Shot GEMINI database were identified. EGFR mutation status was determined using one of PCR-based next generation sequencing of panels of 50, 134 or 409 genes used for routine clinical care. PFS was calculated using the Kaplan Meier method. PFS was defined as time from commencement of EGFR TKI to radiologic progression or death. Restaging scans were obtained at 6-8 week intervals during treatment and were retrospectively assessed according to the Response Evaluation Criteria in Solid Tumors (RECIST), version 1.1 to determine response rate in patients with EGFR exon 20 insertion NSCLC.

Cell Line Generation and IL-3 Deprivation:

Ba/F3 cell line, was cultured in complete RPMI-1640 (R8758; Sigma Life Science) media supplemented with L-glutamine, 10% heat inactivated FBS (Gibco), 1% penicillin/streptomycin (Sigma Life Science), and 10 ng/ml mouse IL-3 (R&D systems) under sterile conditions. Stable cell lines were generated by retroviral transduction of Ba/F3 cell line for 12 hours. Retroviruses were generated by transfecting pBabe-Puro based vectors summarized in Table 2 (Addgene and Bioinnovatise) into the Phoenix 293T ampho packing cell line (Orbigen) using Lipofectamine 2000 (Invitrogen). 72 hours after transduction, 2 μg/ml puromycin (Invitrogen) was added to the media. After 5 days of selection, cells were stained with FITC-HER2 (Biolegend) or PE-EGFR (Biolegend) and sorted via FACS. Cell lines were then grown in the absence of IL-3 for 15 days and cell viability was determined every 3 days using the Cell Titer Glo assay (Progema). Resulting stable cell lines were maintained in complete RPMI-1640 media described above without IL-3. HCC827 and HCC4006 lung cancer cell lines were obtained from ATCC and maintained in 10% RPMI media under sterile conditions. Cell line identity was confirmed by DNA fingerprinting via short tandem repeats using the PowerPlex 1.2 kit (Promega). Fingerprinting results were compared with reference fingerprints maintained by the primary source of the cell line. All cell lines were free ofMycoplasma. To generate erlotinib resistant cell lines, HCC827 and HCC4006 (both EGFR mutant) cells were cultured with increasing concentrations of erlotinib until resistant variants emerged.

Cell Viability Assay and IC50 Estimation:

Cell viability was determined using the Cell Titer Glo assay (Promega). Cells were collected from suspension media, spun down at 300×g for 5 minutes and re-suspended in fresh RPMI media and counted using a Countess automated cell counter and trypan blue (Invitrogen). 1500 cells per well were plated in 384-well plates (Greiner Bio-One) in technical triplicate. Cells were treated with seven different concentrations of inhibitors in serial three-fold diluted TKIs or vehicle alone at a final volume of 40 μL per well. After 72 hours, 11 μL of Cell Titer Glo was added to each well. Plates were shaken for 10 minutes, and bioluminescence was determined using a FLUOstar OPTIMA multi-mode micro-plate reader (BMG LABTECH). Bioluminescence values were normalized to DMSO treated cells, and normalized values were plotted in GraphPad Prism using non-linear regression fit to normalized data with a variable slope. IC50 values were calculated by GraphPad Prism at 50% inhibition. Each experiment was replicated 3 times unless indicated.

Lapatinib, afatinib, dacomitinib, AZD9291, CO-1686, EGF816, ibrutinib, and HM781-36B were purchased from Selleck Chemical. Erlotinib and gefitinib were obtained from the institutional pharmacy at The University of Texas MD Anderson Cancer Center. BI-694 was provided by Boehringer-Ingelheim. All inhibitors were dissolved in DMSO at a concentration of 10 mM and stored at −80° C.

The structure of EGFR D770insNPG protein was retrieved (Protein Data Bank entry code: 4LRM) and used it as a template to build the molecular 3-D structural model of EGFR D770insNPG. HER2 A775insYVMA was built using the previously published model in Shen et al. The homology models were built using MODELLER 9v6 and further energetically minimized using Molecular Operating Environment software package (Chemical Computing Group, Montreal, Canada). Molecular docking of TKIs into exon 20 mutant EGFR and HER2 were performed using GOLD software with default parameters unless otherwise noted. No early termination was allowed in the docking process. Restraints were used to model the covalent bond formations between receptors and inhibitors. The flexibility of residues within the binding pocket was addressed using GOLD software. Figures demonstrating interactions between EGFR/HER2 and inhibitors were visualized using PYMOL.

Western Blotting of Ba/F3 Mutants:

For Western blotting, cells were washed in phosphate-buffered saline and lysed in protein lysis buffer (ThermoFisher) and protease inhibitor cocktail tablets (Roche). Protein (30-40 μg) was loaded into gels purchased from BioRad. BioRad semi-dry transfer was used and then probed with antibodies against pEGFR (#2234), EGFR (#4267), pHER2 (#2247), HER2 (#4290) (1:1000; Cell Signaling). Blots were probed with antibodies against β-actin (Sigma-Aldrich, #A2228) or vinculin (Sigma-Aldrich, #V4505) as a loading control, and exposed using SuperSignal West Pico Chemiluminescent Substrate (ThermoFisher) and BioRad's ChemiDoc Touch Imaging System or radiographic film. Representative images are shown of two separate protein isolations and blots run in duplicate. Quantification of western blotting was completed in Photoshop and calculated as (background mean intensity—sample mean intensity) (number of pixels)=band intensity. Samples were normalized first to loading control (β-actin or vinculin), then normalized to DMSO and graphed in GraphPad Prism. Significance from DMSO was calculated in GraphPad Prism.

ELISA and Correlation of Ba/F3 Mutants:

Protein was harvested from the parental Ba/F3 cell line and each of the Ba/F3 exon 20 mutants found to be activating mutations as described above. ELISA was performed as described by the manufacture instructions for total EGFR (Cell signaling, #7250) and total HER2 (Cell Signaling, #7310). Relative expression determined by ELISA was plotted against IC50values calculated as described above. Pearson correlations and p-values were determined by GraphPad Prism.

Patient Derived Cell Line Studies:

CUTO14 cells were generated from the pleural effusion of a patient with lung adenocarcinoma following informed consent using previously described culture methods (Davies et al., 2013). Cell lines were treated with the indicated doses of afatinib or poziotinib for 72 hours and cell viability was determined by MTS assay (Promega). IC50 was calculated as previously described (n=3). Western blotting with patient derived cell lines was completed as previously described (Hong et al., 2007) (n=3). Cells were treated for 2 hours with indicated doses of afatinib or poziotinib. All antibodies were purchased from Cell Signaling Technology with the exception of total EGFR (BD Transduction Laboratories) and GAPDH (Calbiochem).

The YUL0019 cell line was established from malignant pericardial fluid obtained from a patient with advanced adenocarcinoma of the lung under an IRB-approved protocol. The cell line was cultured in RPMI+L-glutamine (Corning), supplemented with 10% heat-inactivated fetal bovine serum (Atlanta Biologicals) and 1% penicillin/streptomycin (Corning). To confirm the presence of the EGFR mutation, RNA was extracted from cell pellet using the RNeasy mini kit (Qiagen #74104) according to manufacturer's instructions. cDNA was synthesized using the Superscript III First-Strand cDNA Synthesis Kit (Invitrogen #18080-051) and used as a template to amplify EGFR. PCR product was sequenced by Sanger sequencing using the following primers: EGFR-2080F: CTTACACCC AGTGGAGAAGC (SEQ ID NO:5) and EGFR-2507R ACCAAGCGACGGTCCTCCAA (SEQ ID NO:6). Forward and reverse sequence tracings were manually reviewed. The variant detected in the patient-derived cell line was a complex insertion in exon 20 of EGFR (N771delinsFH) leading to the replacement of amino acid asparagine at position 771 by two amino acids, phenylalanine and histidine. Cell viability and IC50estimation was performed as described above.

LU0387 PDX experiments were completed by Crown BioSciences. Briefly, tumor fragments from EGFR H773insNPH expressing tumors were inoculated into 5-6 week old female nu/nu nude mice. When tumors reached 100-200 mm3mice were randomized into 3 groups: 5 mg/kg poziotinib, 10 mg/kg poziotinib, or vehicle control (20% PEG-400, 3% Tween-80 in dH2O). Tumor volumes and body weight were measured twice weekly. Mice receiving 5 mg/kg poziotinib received drug for 4-5 days then were on dosing holiday for 4 days then received 4 additional days of dosing. Mice were then observed for 2 additional days without dosing. Mice receiving 10 mg/kg poziotinib received drug for 3-4 days then were observed for 10 days without dosing. Mice humanly euthanized for events unrelated to tumor burden were excluded from final analysis.

EGFR D770insNPG and HER2 A775insYVMA GEMMs were generated as previously described (Perera et al., 2009; Cho et al., 2013). Mice were handled in accordance with Good Animal Practices as defined by the Office of Laboratory Animal Welfare and done in with approval from Dana-Farber Cancer Institute Institutional Animal Care and Use Committee (Boston, Mass.). Mice were fed a continuous doxycycline diet from 6 weeks of age. Tumor volume was determined by Mill as previously described (Perera et al., 2009; Cho et al., 2013). Mice with equal initial tumor volume were non-blindly randomized to vehicle and 10 mg/kg poziotinib daily upon obvious tumor formation determined by Mill. Mice humanly euthanized for events unrelated to tumor burden were excluded from final analysis.

Example 3—Identification of Drugs for Cancer Cells with HER2 Exon 21 Mutations

HER2 Mutations Occur Most Frequently in Cancers of the Bladder, Stomach, and Bile Duct:

To understand the diversity of HER2 mutations across cancer types, several databases were queried including cohorts from cBioPortal, MD Anderson Cancer Center, and Foundation Medicine, and a cfDNA cohort from Guardant Health. Across all databases, all non-synonymous HER2 mutations were analyzed within 25 different cancer types (Table 4). The weighted average frequency for HER2 mutations was calculated. Similar to what was observed in the AACR GENIE database (Meric-Bernstam et al., 2018), HER2 mutations occurred most frequently in bladder (8.3%), bile duct (5.3%), and stomach (4.5%) cancers (FIG. 13A); and HER2 exon 20 mutations occurred most frequently in cancers of the small intestine (1.8%), lung (1.5%), and breast (0.9%) (FIG. 13B).

HER2 Mutations Occur Most Frequently in the Tyrosine Kinase Domain of HER2 and Mutational Hotspots Vary by Malignancy:

Next, the frequency of mutations was analyzed within the various regions of the HER2 receptor reported in cBioPortal and at MD Anderson. Across all cancer types, HER2 mutations occurred most frequently in the tyrosine kinase domain (46%) which included mutations in exon 20 (20%), exon 19 (11%), and exon 21 (9%) (FIG. 14A). In addition, extra-cellular domain mutations made up 37% of HER2 mutations. Across all cancers queried, the most common HER2 mutations were p.S310F/Y (11.0%), p.Y772 A775dupYVMA (5.7%), p.L755P/S (4.6%), p.V842I (4.4%), and p.V777L/M (4.0%) (FIG. 14E). In lung cancer, the majority of HER2 mutations occurred within exon 20 (48%), with Y772 A775dupYVMA comprising 34% of all HER2 mutations (FIGS. 14B, 14F). In breast cancer, the majority of HER2 mutations occurred within exon 19 (37%), with L755 mutations being the most prevalent at 22% of HER2 mutations (FIG. 14C). However, unlike lung cancer where one variant was dominant, in breast cancer, there was more mutational diversity among exon 19 mutations (FIG. 14G). In colorectal cancer, HER2 mutations occurred most frequently in exon 21 (23%) and the extracellular domain (23%), with the V842I variant in exon 21 being the most prevalent (19%) (FIGS. 14D, 14H).

Y772dupYVMA is the Most Common HER2 Exon 20 Insertion Mutation Across Cancer Types:

HER2 exon 20 mutations are the most commonly occurring mutations within the tyrosine kinase domain of HER2 (16% of all HER2 mutations and 43% of tyrosine kinase domain mutations), and HER2 exon 20 insertion mutations remain a clinical challenge. To understand the diversity and prevalence of exon 20 insertions, the frequency of HER2 exon 20 insertion sequences was analyzed by cancer type in cBioportal, MD Anderson, and Guardant Health databases. The Y772dupYVMA insertion was the most common HER2 exon 20 insertion, comprising 70% of all HER2 exon 20 insertions, and the p.G778dupGSP (14%) and p.G776del insVC (9%) insertions occurred the second and third most frequently (FIG. 21A). Exon 20 insertion mutations in NSCLC (N=362) showed the greatest diversity in exon 20 insertion mutations (FIG. 21B), and exon 20 insertion mutations in breast cancer (N=30) showed little diversity in insertion sequence with only three distinct variants reported (FIG. 21C). Additional rare insertion mutations were seen across other cancer types, but the duplications at Y772 and G778 occurred most frequently in every cancer type analyzed (FIG. 21D).

Frequently Detected HER2 Alterations are Activating Mutations:

To assess the functional impact of common HER2 mutations, Ba/F3 cells were stably expressed with the 16 most frequently detected HER2 mutation across exons 19, 20, and 21. All 16 HER2 mutations tested were found to induce IL-3 independent survival of Ba/F3 cells (FIGS. 15A-C). Moreover, expression of these 16 HER2 mutations resulted in expression of phosphorylated HER2 (FIG. 22A), indicating that these mutations result in receptor activation.

Poziotinib was the Most Potent TKI Tested and Inhibited the Most Common HER2 Mutations In Vitro:

While recent reports highlight the effectiveness of covalent quinazolinamine-based TKIs (i.e. afatinib, dacomitinib, poziotinib, neratinib) in pre-clinical models of HER2 mutant disease, clinical studies of afatinib, dacomitinib, and neratinib have had low ORRs, as well as cancer-specific and variant-specific differences in patient outcomes. To systematically evaluate drug sensitivity across the most commonly detected HER2 variants, the panel of HER2 mutant Ba/F3 cells was screened against 11 covalent and non-covalent EGFR and HER2 TKIs. HER2 mutants showed robust resistance to non-covalent inhibitors, lapatinib and sapatinib (FIG. 16A). Covalent TKIs osimertinib, ibrutinib, and nazartinib were not effective in inhibiting cell viability in cells expressing exon 20 mutations; however, these TKIs did demonstrate activity against cells expressing D769 variants (FIG. 16A). By comparison, covalent, quinazolinamine-based TKIs, afatinib, neratinib, dacomitinib, tarloxotinib-TKI, and poziotinib, had inhibitory activity for HER2 mutants across all three exons (FIG. 16A). Across all HER2 mutation variants and TKIs tested, poziotinib had the lowest average IC50 and was significantly more effective in reducing cell viability than afatinib, neratinib, or tarloxotinib-TKI (FIG. 16B). In addition, while poziotinib was significantly more efficacious than either afatinib, neratinib, or tarloxotinib-TKI against HER2 exon 19 and 20 mutations, there was no significant difference in average IC50for exon 21 mutants (FIGS. 16C-E), suggesting that mutation location impacts drug binding. Furthermore, within exon 19, L755S and L755P variants had significant differences in drug sensitivity across all TKIs tested (FIG. 16F), indicating that specific amino acid changes at this site influenced drug binding affinity.

HER2 Mutation Location and Amino Acid Change Affects Drug Binding Affinity:

To further understand how the location of the mutation and the amino acid change can affect drug binding affinity and inhibitory efficacy, molecular dynamics simulations were used to investigate how these mutations impact the structure and dynamics of the HER2 kinase domain. Molecular models of the L755S, L755P, Y772dupYVMA, and V777L HER2 mutants (FIG. 23A) were constructed using a publicly available X-ray structure (PDB 3PP0) as a template and subjected to accelerated molecular dynamics to increase protein conformational sampling. The range of protein conformations sampled, particularly in regard to the P-loop and α-C-helix positions, varied among these HER2 mutants. Differences were clearly evident even between exon 20 mutations, especially in the α-C-helix region, where the duration of the conformation of the α-C-helix varied between the “in” (the active conformation with a smaller binding pocket), and the “out” (the inactive conformation with a larger binding pocket). The V777L mutant heavily sampled the “out” conformation while the Y772dupYVMA mutant sampled both the “in” and “out” conformations (FIG. 17A). Overall, these differences in conformational state resulted in the Y772dupYVMA mutant residing in the “in” conformation 10-times more often than the V777L mutant (FIG. 17B), and, on average, a smaller binding pocket size for Y772dupYVMA compared to V777L (FIGS. 17C and 23B). In addition, the smaller binding pocket of the Y772dupYVMA may be the cause of the weaker potency of neratinib against the Y772dupYVMA compared to the V777L since neratinib contains a pyridyl ring oriented towards the α-C-helix.

Further analysis of the HER2 mutant binding pocket volumes (FIG. 22B) demonstrated that mutations at the same residue can have drastically different effects on protein conformation. In particular, the proline residue of the L755P mutation lacks a hydrogen bond donor which breaks a backbone hydrogen bond between the (33 and (35 strands between L755 and V790, respectively. The lack of stabilization between these two β-strands resulted in destabilization of the β-sheet and a structural rearrangement in the kinase hinge region (FIG. 17D). In particular the L800 residue of L755P protruded into the active site and reduced the pocket size considerably. Changes in the β3 strand conformation also caused the P-loop to collapse inward, further reducing pocket volume and making this mutant less sensitive to most TKIs. Furthermore, the changes in hinge mobility may also play a role in kinase activation. These distinct changes in the L755P mutant confirmation contrasted with the behavior of the L755S mutant, which had a conformational and pocket volume profile that is more similar to wild-type HER2 (FIG. 23B).

HER2 Mutant Human Cancer Cell Lines Showed Enhanced Sensitivity to Poziotinib:

Clinical studies testing HER2 inhibitors have revealed cancer type specific differences in drug sensitivity (Hyman et al., 2018). To determine whether covalent, quinazolinamine-based TKIs have activity in models of HER2 mutant disease, the panel of EGFR/HER2 TKIs were tested in human cancer cell lines. Pre-neoplastic MCF10A mammary epithelial cells were transfected with HER2 exon 20 mutations and evaluated in vitro sensitivity to 12 EGFR/HER2 TKIs. MCF10A cells expressing G776del insVC, Y772dupYVMA, or G778dupGSP HER2 mutations were most sensitive to poziotinib, with IC50values of 12 nM, 8.3 nM, and 4.5 nM, respectively (FIG. 18A-C). In comparison, tarloxotinib-TKI and neratinib yielded average IC50values of 21 nM and 150 nM, respectively (FIGS. 18A-C), indicating that poziotinib is 2.6 and 19 times more potent than tarloxotinib-TKI and neratinib, respectively (p<0.001). Furthermore, Western blotting of MCF10A HER2 G776delinsVC cells with poziotinib and neratinib showed that poziotinib, but not neratinib, completely inhibits p-HER2 at 10 nM (FIG. 24A). Since wild-type (WT) HER2 does not transform Ba/F3 cells to grow independent of IL-3, MCF10A cells were used to determine the selectivity of the TKIs for mutant HER2 compared to WT HER2. To this end, the selectivity index (SI, IC50value mutant/IC50value WT) was calculated for each inhibitor, and found that poziotinib was the most mutant selective TKI tested in MCF10A cell lines (SI=0.028), followed by pyrotinib (SI=0.063) and tarloxotinib-TKI (SI=0.111), (FIG. 18D). Consistent with the data obtained using Ba/F3 cells (FIG. 15C), in a model of HER2 exon 19 mutant colorectal cancer (CW-2), differences in sensitivity between poziotinib, tarloxotinib-TKI, and neratinib were less dramatic, albeit significant (p=0.02 and p=0.0004), with average IC50values of 3.19 nM, 4.24 nM, and 68.8 nM, respectively (FIG. 18E). Furthermore, in a xenograft mouse model of CW-2 colorectal cells, at day 21, poziotinib (5 mg/kg) treated animals had showed a reduction of 58% in tumor volume compared to the vehicle treated group (p=0.011). In comparison, neratinib (30 mg/kg) treated animals showed an increased tumor volume (28%) compared to vehicle control (p=0.023), and afatinib (20 mg/kg) treatment did not significantly affect tumor growth compared to vehicle control (FIGS. 18F, 25).

Poziotinib has Anti-Tumor Activity in NSCLC Patients with HER2 Mutations:

Based on these preclinical data and previously published work on exon 20 mutations (Robichaux et al., 2018), an investigator-initiated, phase II clinical trial of poziotinib in EGFR and HER2 exon 20 mutant NSCLC (NCT03066206) was initiated. Patients were treated with poziotinib 16 mg orally daily until progression, death, or withdrawal. Objective response was evaluated every eight weeks, based on RECIST v1.1. Of the first 12 evaluable patients harboring HER2 exon 20 insertion mutations, 6/12 (50%) patients had a best response of partial response (PR). This response was confirmed by a repeat scan 2 months later in 5/12 (confirmed objective response rate, 42%) (FIG. 19A). Of these twelve patients, two patients had progressive disease (PD) at first response evaluation, resulting in a disease control rate (DCR) of 83%. As of December 2018, ten of the twelve patients had progressed, and the median PFS for the first twelve patients was 5.6 months (FIG. 19B). All patients included in the study thus far harbored one of the two most common HER2 exon 20 insertions, Y772dupYVMA and G778dupGSP (FIG. 19A). Representative images of one NSCLC patient with an Y772dupYVMA mutation pre- and post-treatment (8 weeks) showed robust tumor shrinkage in the right lung (FIG. 19C). Patient characteristics including number of previous lines of treatment can be found in Table 3. In addition, one heavily pre-treated NSCLC patient harboring a HER2 exon 19 point mutation, L755P, was treated on a compassionate care use protocol (C-IND18-0014). The patient was treated with 16 mg poziotinib daily and had tumor shrinkage at four weeks (FIG. 19D, white box). The patient had stable disease (SD) per RECIST v1.1 (−12% reduction in target legions). The patient remained on poziotinib with disease control for more than seven months until imaging revealed disease progression and poziotinib was discontinued. The patient was clinically well at the end of poziotinib treatment and proceeded to receive further systemic therapy.

Previous studies of HER2 TKI lapatinib in HER2-positive breast cancer models and EGFR inhibitors in EGFR mutant NSCLC models have shown that TKI treatment results in an increase of receptor accumulation on the cell surface, and that increased cell surface HER2/EGFR increases sensitivity to antibody-dependent cellular cytotoxicity (ADCC). To determine if poziotinib treatment increases total HER2 receptor expression on the cell surface cell surface HER2 expression was analyzed by FACS after 24 hours of low dose poziotinib treatment. It was found that, on average, poziotinib treatment increased cell surface HER2 expression 2-fold (FIG. 20A, p<0.0001). Next, it was tested whether the combination of poziotinib and T-DM1 would decrease cell viability in vitro, and it was found that while T-DM1 alone did not inhibit cell viability of MCF10A HER2 mutant cell lines, combination of T-DM1 with poziotinib resulted in significantly lower IC50 values than either agent alone in a dose-dependent manner (FIG. 20B). To validate these findings in vivo, the combination of low dose poziotinib with a single dose of T-DM1 was tested in a HER2 mutant NSCLC PDX model, HER2 Y772dupYVMA (FIG. 20C). To asses response to treatment, progression free survival (PFS) was determined, defined as time to tumor doubling from best response. Mice receiving vehicle control had a median PFS (mPFS) of 3 days, whereas mice receiving low dose poziotinib or T-DM1 had an mPFS of 15 days and 27 days, respectively. However, (14/20) mice receiving a single dose of T-DM1 in combination with low dose poziotinib remained tumor free at 45 days (FIG. 20D). Furthermore, at the time of best response, day 15, the combination of low dose poziotinib (2.5 mg/kg) and a single dose of T-DM1 (10 mg/kg) resulted in complete tumor regression in 20/20 mice (100%), compared to 2/9 mice receiving T-DM1 alone or 0/12 mice receiving low dose poziotinib (FIGS. 20C-F). By day 30, tumor growth resumed in all mice receiving T-DM1 alone; however, in 14/20 mice receiving combination treatment there was no evidence of tumor reoccurrence (FIGS. 20F, G).

Further studies validated the efficacy of poziotinib as compared to other TKIs. It was found that poziotinib was more effective than high dose osimertinib in the EGFR S768dupSVD PDX model (FIG. 26). It was also shown that poziotinib had more anti-tumor activity than neratinib in the PDX model of NSCLC harboring Y772dupYVMA (FIG. 27). Single agent poziotinib was more efficacious than neratinib in the breast cancer PDX model harboring V777L (FIG. 28). A summary of the efficacy of poziotinib anti-tumor activity in various EGFR and HER2 exon 20 mutant in vivo models is shown inFIG. 29.

Here, it is reported that HER2 mutations occur in various tumor types although the specific mutational hotspots vary by malignancy. Moreover, sensitivity to HER2 TKIs is heterogeneous across mutation location, with HER2 exon 20 insertions and L755P mutations being resistant to the majority of HER2 TKIs, likely due to the reduced volume of the drug binding pocket. Furthermore, poziotinib was identified as a potent, pan-HER2 mutant-selective inhibitor with clinical efficacy in NSCLC patients bearing HER2 exon 20 insertions and L755P mutations. Lastly, it was established that poziotinib treatment induced accumulation of HER2 on the cell surface, and that combination of poziotinib and T-DM1 treatment enhanced anti-tumor activity in vitro and in vivo.

The pan-cancer analysis reveals that HER2 mutational hotspots vary by cancer type and have differential sensitivity to HER2 TKIs in vitro, which will likely affect clinical efficacy. In the SUMMIT trial, neratinib yielded the most efficacy in breast cancer patients, with the majority of responders being positive for L755S, V777L, or L869R mutations. In the in vitro Ba/F3 drug screening, these mutations correlated with low IC50values. In contrast, patients with colorectal cancer did not respond to neratinib. Consistent with this clinical observation, it was found that the V842I mutation is the most common HER2 mutation in colorectal cancer cases, and this specific mutation was not sensitive to neratinib in the drug screen assays. These data suggest that differential TKI sensitivities between malignancies may be, in part, explained by cancer-specific mutational hotspots, which directly impact drug sensitivity. However, key questions remain regarding why the distributions of HER2 mutations vary by tumor type and whether a given mutation yields a similar drug response in different tumor types. Data from the SUMMIT trial showed that while specific exon 20 insertions were associated with neratinib sensitivity in breast cancer patients, these identical mutations were associated with resistance in all other cancer types demonstrating that there may be potential mechanisms underlying these tumor-type specific differences in sensitivities that merit further investigation.

Exon 20 insertion mutations and the exon 19 L755P mutation are resistant to most HER2 TKIs. The in vitro drug screening revealed that exon 20 insertion mutations and the L755P mutation had the highest IC50values for each TKI tested. Molecular dynamic simulations revealed that these mutations induce conformational changes that affect the overall size and mobility of the drug binding pocket. Collectively, these in vitro and in silico findings are consistent with the clinical observations that patients with HER2 exon 20 insertion mutations historically have had poor responses to TKIs. In lung cancer, where exon 20 insertions frequently occur, patients harboring HER2 exon 20 insertion mutations had response rates of 0%, 11.5%, and 18.2%-18.8% to neratinib, dacomitinib, and afatinib, respectively. Moreover, while L755S mutations have been shown to respond to neratinib, L755P mutations are profoundly resistant to both TKIs, and antibody-drug conjugates.

Example 4—Materials and Methods

Analysis of HER2 Mutation Prevalence and Variant Frequency:

To determine the frequencies of each HER2 mutation reported in databases from MD Anderson Cancer Center, cBioPortal, Foundation Medicine, or Guardant Health, each database was queried individually, then frequencies were weighted by the total number of patients in each database and are reported as weighted averages. To determine the frequency of HER2 mutations across cancer types in cBioPortal, all non-overlapping studies were selected and exported. For overlapping studies, only the largest dataset was used. To determine HER2 mutation frequencies at MD Anderson Cancer Center, the Institute for Personalized Cancer Therapy database was queried for all HER2 mutations independent of cancer type. To determine the frequency of HER2 exon 20 mutations from Foundation Medicine, de-identified data of the number of patients with HER2 deletions, frame shifts, insertions, and point mutation were tabulated, and cancer types with less than 5 mutations were excluded. Lastly, to determine the frequency of HER2 exon 20 mutations at Guardant Health, the Guardant360 clinical database was queried for samples tested between October 2015 and May 2018 (70 and 73 gene panels) with an ERBB2 exon 20 mutation. Guardant360® is a CLIA—certified, CAP/NYSDOH accredited comprehensive cfDNA NGS test that reports out SNVs, indels, fusions, and SNVs in up to 73 genes. Frequencies reported from Guardant Health were then normalized to correct for clinical sensitivity as reported in Odegaard et al 2018. Specifically, frequencies were divided by the percent clinical sensitivity, 85.9%.

Ba/F3 Cell Line Generation and IL-3 Deprivation:

Ba/F3 cell lines were established as previously described. Briefly, stable Ba/F3 cell lines were generated by retroviral transduction of Ba/F3 cell line for 12 hours. Retroviruses were generated by transfecting pBabe-Puro based vectors summarized in Table 1 (Addgene and Bioinnovatise) into Phoenix 293T-ampho cells (Orbigen) using Lipofectamine 2000 (Invitrogen). Three days after transduction, 2 μg/ml puromycin (Invitrogen) was added to the RPMI media. After 5 days of selection, cells were stained with FITC-HER2 (Biolegend) sorted by FACS. Cell lines were then grown in the absence of IL-3 for two weeks and cell viability was assessed every three days using the Cell Titer Glo assay (Progema). Resulting stable cell lines were maintained in RPMI-1640 media containing 10% FBS without IL-3.

Cell Viability Assay and IC50Estimation:

Cell viability was determined using the Cell Titer Glo assay (Promega) as previously described (Robichaux et al., 2018). Briefly, 2000-3000 cells per well were plated in 384-well plates (Greiner Bio-One) in technical triplicate. Cells were treated with seven different concentrations of tyrosine kinase inhibitors or vehicle alone at a final volume of 404, per well. After 3 days, 11 μL of Cell Titer Glo was added to each well. Plates were shaken for 15 minutes, and bioluminescence was determined using a FLUOstar OPTIMA multi-mode micro-plate reader (BMG LABTECH). Bioluminescence values were normalized to DMSO treated cells, and normalized values were plotted in GraphPad Prism using non-linear regression fit to normalized data with a variable slope. IC50 values were calculated by GraphPad Prism at 50% inhibition.

ELISA for Phospho- and Total-HER2 and Correlation with IC50 Values:

Protein was harvested from the parental Ba/F3 cell line and each of the Ba/F3 cell lines expressing HER2 mutations as described above. 5 μg/ml of protein was added to each ELISA plate and ELISA was performed as described by the manufacture instructions for phosphorylated HER2 Cell signaling, (#7968) and total HER2 (Cell Signaling, #7310). Relative p-HER2 expression was determined by taking the ratio of p-HER2 over total HER2 as determined by ELISA. The relative p-HER2 ratio was plotted against poziotoinib IC50 values calculated as described above. Pearson correlations and p-values were determined by GraphPad Prism.

Tyrosine Kinase Inhibitors and T-DM1:

All inhibitors were purchased from Selleck Chemical with the exception of EGF816 and pyrotinib which were purchased from MedChem Express. All inhibitors were dissolved in DMSO at a concentration of 10 mM and stored at −80° C. Inhibitors were limited to two freeze thaw/cycle before being discarded. T-DM1 was purchased reconstituted from the M.D. Anderson Cancer Center institutional pharmacy.

Protein structural models of the HER2 mutants were constructed using the MOE computer program (Chemical Computing Group) by introducing in silico mutations to the PDB 3PP0 X-ray structure. Classical and accelerated molecular dynamics simulations were performed using the NAMD simulation package. Additional detail is provided in the Supplemental Information section.

Human Cell Lines:

MCF10A cells were purchased from ATCC and were cultured in DMEM/F12 media supplemented with 1% penicillin/streptomycin, 5% horse serum (sigma), 20 ng/ml EGF, 0.5 mg/ml hydrocortisone, and 10 μg/ml insulin. Stable cell lines were created by retroviral transduction, and retroviruses were generated by transfecting pBabe-Puro based vectors summarized in Table 1 (Addgene and Bioinnovatise) into Phoenix 293T-ampho cells (Orbigen) using Lipofectamine 2000 (Invitrogen). Two days after transduction, 0.5 μg/ml puromycin (Invitrogen) was added to the RPMI media. After 14 days of selection, cells were tested in cell viability assays as described above. CW-2 cells were provided by the Riken cell line database under MTA, and were maintained in RPMI containing 10% FBS and 1% penicillin/streptomycin.

In vivo xenograft studies: CW-2 cell line xenografts were created by injecting 1×106cells in 50% matrigel into 6 week old female nu/nu nude mice. When tumors reached 350 mm3mice were randomized into 4 groups: 20 mg/kg afatinib, 5 mg/kg poziotinib, 30 mg/kg neratinib, or vehicle control (0.5% Methylcellulose, 2% Tween-80 in dH2O). Tumor volumes were measured three times per week. Mice received drug Monday-Friday (5 days per week), but began dosing on Wednesday allowing for a 2 day holiday after the first 3 days of dosing.

Y772dupYVMA PDX mice were purchased from Jax Labs (Model #TM01446). Fragments from tumors expressing HER2 Y772dupYVMA were inoculated into 5- to 6-week old female NSG mice (Jax Labs #005557). Mice were measured three times per week, and when tumors reached a volume of 200-300 mm3mice were randomized into four treatment groups: vehicle control (0.5% Methylcellulose, 0.05% Tween-80 in dH2O), 2.5 mg/kg poziotinib, 10 mg/kg T-DM1, or combination of 2.5 mg/kg poziotinib and 10 mg/kg T-DM1. Tumor volumes and body weight were measured three times per week. Mice treated with 2.5 mg/kg poziotinib received drug orally Monday-Friday (5 days per week). Mice treated with 10 mg/kg T-DM1 received one intravenous (IV) dose of T-DM1 on the day of randomization. Mice treated with combination poziotinib and T-DM1 received one IV dose of T-DM1 and began 2.5 mg/kg poziotinib five days per week, 3 days after the dose of T-DM1. Mice received a holiday from dosing if the mouse dropped in body weight by greater than 10% or if body weight dropped below 20 grams. Progression free survival was defined as tumor doubling from best response for two consecutive measurements. Complete regression was defined as greater than 95% reduction in tumor burden, and for mice with complete regression, tumor doubling was defined greater than 75 mm3for more than two consecutive measurements. Experiments were completed in agreement with Good Animal Practices and with approval from MD Anderson Cancer Center Institutional Animal Care and Use Committee (Houston, Tex.).

TABLE 5Patient Characteristics and number of prior lines of therapy.# ofpriorAgeSexlinesMutation57F1Y772_A775dupYVMA64F6Y772_A775dupYVMA54F1A775_G776insYVMA59F0Y772_A775dupYVMA58F3Y772_A775dupYVMA60F1G778_P780dupGSP61F3G778_P780dupGSP62F0A775_G776insYVMA55F2G778_P780dupGSP61M4Y772_A775dupYVMA63M1Y772_A775dupYVMA60F3Y772_A775dupYVMA

MCF10A cells overexpressing HER2 mutations were plated overnight in a 6-well plate, then treated with 10 nM poziotinib. After 24 hours, cells were washed twice with PBS, and trypsinized. Cells were then resuspended in 0.5% FBS in PBS, and stained with anti-HER2-FITC antibody from Biolegend (#324404) for 45 minutes on ice. Cells were washed with 0.5% FBS in PBS twice, and analyzed by flow cytometry. IgG and unstained controls were used for gating.

For Western blotting, cells were washed in PBS and lysed in RIPPA lysis buffer (ThermoFisher) and protease inhibitor cocktail tablets (Roche). Protein (30-40 μg) was loaded into gels purchased from BioRad. BioRad semi-dry transfer was used and then probed with antibodies against, pHER2, HER2, pPI3K, PI3K, p-AKT, AKT, p-ERK1/2, and ERK1/2 (1:1000; Cell Signaling). Blots were probed with antibodies against vinculin or β-actin (Sigma-Aldrich) as a loading control, and exposed using ECL Western Blotting substrate (Promega).

HER2 Expression Level and Correlation with Ba/F3 Mutant IC50:

Protein was harvested from Ba/F cell lines, and ELISAs were performed as described by the manufacture instructions for total HER2 (Cell Signaling, #7310). Relative expression determined by ELISA was plotted against IC50 values calculated as described above. Pearson correlations and p-values were determined by GraphPad Prism.

Clinical Trial and CIND Identifiers:

Patients provided written informed consent for treatment with poziotinib on either compassionate use protocol (MD Anderson Cancer Center CIND-18-0014) or clinical trial NCT03066206. The protocols are approved by both the MD Anderson Cancer Center institutional review board and the Food and Drug Administration.

REFERENCES