ABCB1 is a member of the ATP-binding cassette (ABC) superfamily of proteins. Also known as P-glycoprotein (P-gp) or MDR1, it is a 170 kDa glycosylated membrane protein expressed in various locations including the liver, intestines, kidney, brain, and testis [39]. Generally speaking, ABCB1 is located on the membrane of cells in these locations and serves to eliminate metabolites and a wide range of hydrophobic foreign substances, including drugs, from cells by acting as an efflux transporter [40, 41]. Due to the localization of ABCB1 on specific cells, ABCB1 aids in eliminating drugs into the urine or bile and helps maintain the blood–brain barrier.

Like other eukaryotic ABC proteins, the ABCB1 protein is composed of two similar halves, each half containing a hydrophobic membrane-binding domain and a nucleotide-binding domain ([39]. The membrane-binding domains are each composed of six hydrophobic transmembrane helices and the two hydrophilic nucleotide-binding domains are located on the intracellular side of the membrane where they bind ATP. ABCB1 was first identified in cancer cells that had developed a resistance to several anticancer drugs because of an overexpression of the transporter. When expressed at normal levels in noncancerous cells, ABCB1 has been shown to transport other classes of drugs out of cells including cardiac drugs (digoxin), antibiotics, steroids, HIV protease inhibitors, and immunosuppressants (cyclosporin A).

Genetic variations in the ABCB1 gene expressed in normal cells have been shown to have a role in interindividual variability in drug response [39]. Although many polymorphisms have been detected in the ABCB1 gene, correlations between genotype and either protein expression or function have only been described for a few of the genetic variants. Most notable among these is the 3435 C > T polymorphism, found in exon 26, which has been found to result in decreased expression of ABCB1 in individuals homozygous for the T allele. The possible importance of the 3435 C > T is particularly interesting considering the mRNA levels are not affected by this polymorphism which is found within a coding exon. Although the correlation between the 3435 C > T polymorphism and ABCB1 protein levels may be due to linkage of this polymorphism to others in the ABCB1 gene, a recent study showed that this polymorphism alone does not affect ABCB1 mRNA or protein levels but does result in ABCB1 protein with an altered configuration. The altered configuration due to 3435 C > T is hypothesized to be caused by the usage of a rare codon which may affect proper folding or insertion of the protein into the membrane, affecting the function, but not the level of ABCB1 [42]. Genetic variations affecting the expression or function of drug transporter proteins, such as ABCB1, could drastically alter the pharmacokinetics and pharmacodynamics of a given drug.

FLT3 is a receptor tyrosine kinase expressed and activated in most cases of acute myeloid leukemia (AML) which has a relatively high relapse rate due to acquired resistance to traditional chemotherapies. An internal tandem duplication (ITD) mutation in the FLT3 gene is found in up to 30 % of AML patients while a point mutation at D835 has been shown to account for approximately 5 % of refractory AML [43, 44]. The FLT3-ITD induces activation of this receptor and results in downstream constitutive phosphorylation in STAT5, AKT, and ERK pathways. This mutation in FLT3 is a negative prognostic factor in AML.

FLT3-ITD-positive AML has become a clinical dilemma due to the poor results obtained with standard chemotherapy. One potential therapeutic option for patients who are at risk for relapse is allogeneic stem cell transplant [45]. In addition, randomized phase III trials using FLT3 inhibitors in combination with chemotherapy in patients with FLT3-positive AML are ongoing. Two promising multitargeted receptor tyrosine kinase inhibitors (TKIs), sorafenib and ABT-869, have been developed to suppress signal transduction from constitutively expressed kinases such as a mutated FLT3 [46]. The investigational FLT3-specific TKIs, quizartinib (AC220) and crenolanib, have also shown some recent success in a phase II trial in patients with FLT3-ITD+ AML with some evidence for increased activity against the D835 resistance mutation [47].

The fusion of the anaplastic lymphoma kinase (ALK) gene with the echinoderm microtubule-associated protein-like 4 (EML4) gene was first identified in 2007 in Japanese non-small-cell lung cancers (NSCLCs) [48]. The EML4-ALK fusion gene is the result of an inversion on the short arm of chromosome 2 that joins exons 1–13 of EML4 to exons 20–29 of ALK [49]. The fusion gene can be detected by use of break-apart probes and FISH technology (Fig. 43.5).

The EML4-ALK fusion gene represents a novel biomarker and potential molecular target in NSCLC and translocations or rearrangements of the ALK gene with other genes have been reported in several other human cancers [49, 50]. Approximately 3–5 % of NSCLCs found in North America harbor the EML4-ALK fusions. The fusion of these two genes results in constitutive ALK tyrosine kinase activity which has significant oncogenic function. Because of its oncogenic role, the EML4-ALK fusion product has been a target for tyrosine kinase inhibitors. Several ALK kinase inhibitors have been developed and FDA-approved for treatment of NSCLC, such as crizotinib (Xalkori) and certitnib (Zykadia) [49, 51]. Crizotinib is a first-line oral inhibitor of ALK tyrosine kinase activity which has shown high response rates in patients with EML4-ALK-positive NSCLC [52]. However, a large number of patients treated with crizotinib develop resistance to treatment, many by acquiring secondary mutations in the ALK tyrosine kinase domain, driving relapse [53]. These patients are now eligible for treatment with a newly approved ALK TKI, ceritinib, which has exhibited a response rate of greater than 70 % in those patients resistant to crizotinib [54]. In addition, there are numerous phase II trials investigating the efficacy of heat shock protein 90 (HSP-90) inhibitors to treat patient who are positive for ALK fusions. Early results suggest a significant response to treatment with these HSP-90-targeted inhibitors [55]. The identification of these resistance mutations and the successful development of second- and third-generation therapies to combat them exhibit the utility in fully characterizing the genotypes of therapy-resistant tumors.