Pharmacokinetic Methods Samples were periodically obtained from patients enrolled in both arms of the study to monitor the steady-state minimum concentration of hydroxychloroquine (HCQ) in whole blood and plasma. Patients were instructed to take the HCQ dosage at approximately the same time every day, at a time in the morning that would allow them to arrive at the outpatient clinic for collection of a predose sample. Blood specimens were obtained before initiating treatment, at the beginning of weeks 2, 3, and 4 of cycle 1, and once a month during regularly scheduled visits to the clinic for study evaluations as long as the patient was receiving treatment. Sampling was also performed during cycle 1 to define the plasma concentration-time profile of erlotinib over a single 24-h dosing interval after steady-state conditions had been achieved when given alone and together with HCQ. Blood specimens were obtained before initiating treatment, immediately before taking the seventh daily dose of single agent erlotinib, at 0.5, 1, 2, 3, 4, 6 and 8-h after dosing, and before dosing on the following day. Sampling was also performed according to this same schedule after six days of combined treatment with erlotinib and HCQ. Blood samples (6-mL) were drawn from a peripheral arm vein into collection tubes containing sodium heparin and placed in crushed ice until processed for storage within 15 min. Actual sample collection times were recorded. For the HCQ pharmacokinetic samples, 2-mL of whole blood was transferred from the collection tube, after inverting it several times to disperse the blood cells, directly into a polypropylene cryotube. The remaining blood was centrifuged (1,100-1,300 g, 4°C, 10 min) to afford plasma which was transferred into a cryotube. Plasma was similarly harvested from the erlotinib samples. The blood and plasma samples were stored at -70ºC until assayed. HCQ in whole blood and plasma was determined by liquid chromatography/mass spectrometry. Study samples were thawed at room temperature and mixed by vortexing before removing a 100-µL aliquot for analysis. After spiking with 5-µL of internal standard (IS) working solution (10-µg/mL chloroquine in acetonitrile), the sample was vigorously mixed with 300-µL of acetonitrile, then centrifuged (10,000-g, 5-min) to pellet the lysed cellular fragments and precipitated protein. The supernatant (250-µL) was combined with 200-mM triethylamine/272 mM-formic acid in water (25-µL) and 100-µL of this solution was injected onto a 150 x 4.6-mm Luna 5-µm CN HPLC column (Phenomenex, Torrance, CA) eluted with a binary mobile phase composed of 30% acetonitrile and 70% 10-mM triethylamine/13.6-mM formic acid in water (pH 4.0) delivered at 1.0-mL/min. An Agilent 1100 Series LC/MSD system with an electrospray ionization interface (Agilent Technologies, Palo Alto, CA) was used for detection. Nitrogen was used as the nebulizing gas (60-p.s.i.) and as the drying gas (10-L/min, 350°C). The single-quadrupole mass spectrometer was operated in the selected-ion monitoring mode to measure positive ions corresponding to [M+H]+ ions of HCQ and the IS at m/z 336.2 and 320.2, respectively. Additional operating parameters were: capillary voltage, 1,500-V; fragmentor voltage, 150-V; peak width, 0.1-min; dwell time, 114-msec. Extracted ion chromatograms were integrated to provide peak areas. Erlotinib in plasma was determined by liquid chromatography-tandem mass spectrometry, as previously reported, with minor modifications (1). Plasma (100-µL) was spiked with 5-µL of IS working solution (2.4-µg/mL N-ethylerlotinib in acetonitrile) and vigorously mixed with 300-µL of acetonitrile. The mixture was centrifuged (10,000g, 5-min) and the resulting supernantant (100-µL) was diluted with an equivalent volume of 0.1% (v/v) formic acid in water. The final sample solution (10-µL) was injected onto a 150 x 4.6-mm Luna 5-µm C18(2) HPLC column (Phenomenex, Torrance, CA) eluted with a mobile phase composed of methanol/0.1% (v/v) formic acid in water (47:53, v/v) at 1.0-mL/min. Upon completing the run at 6.0-min, the column was flushed with methanol/0.1% (v/v) formic acid in water (95:5, v/v) for 5-min and reequilibrated with the original composition for 3-min. An Agilent 1100 series XCT ion trap mass spectrometer with an atmospheric pressure ionization-electrospray interface (Agilent Technologies, Palo Alto, CA) was used for detection. Operating parameters were established to individually maximize the response for the most abundant product ions resulting from isolation and fragmentation of the [M+H]+ ions for the IS (m/z 422.2) and erlotinib (m/z 394.2), which were monitored in separate time segments of 2.0-4.0-min and 4.0-6.0-min, respectively. Nitrogen was used as the nebulizing gas (50-psi) and drying gas (12-L/min, 350°C). Time programmed parameters for ion transport and focusing were as follows (2.0-4.0 min/4.0-6.0 min): capillary potential (V), -1,598/-2,366; skimmer (V), 16.4/19.2; capillary exit offset (V), 50.0/50.0; octopole 1 DC (V), 13.4/16.1; octopole 2 DC (V), 2.5/2.8; trap drive (rel %), 51.3/52.1; octopole rf (Vpp), 181.2/193.4; lens 1 (V), -6.7/-3.5; lens 2 (V), -100.0/-67.5. Ion Charge Control was used with a 250-ms maximum accumulation time and maximum abundance of 200,000 ions. Helium was used as the collision gas to fragment the parent ions with an amplitude of 1.02-V and m/z 155.0 cutoff for the IS and an amplitude of 1.00-V and m/z 140.9 cutoff for erlotinib. Product ions were monitored by scanning from m/z 250-450 with data averaging over every 5 scans. Extracted ion chromatograms for the m/z 422.2→364.2 and m/z 394.2→336.1 transitions for the IS and erlotinib, respectively, were integrated to provide peak areas. The analytical methods were validated according to current recommendations (2). Peaks that interfered with detection of either drug or IS were not evident in chromatograms of pretreatment plasma or blood samples obtained from patients participating in this clinical trial. Calibration standards of HCQ in human donor plasma or whole blood and erlotinib in plasma had concentrations ranging from 10-1,000 ng/mL. Study samples were independently assayed in duplicate, on different days, together with a set calibration standards, drug-free plasma or blood prepared for analysis with and without addition of the IS, and quality control samples. In each case, the calibration curves were best described by the equation, y = a + bxc, where y is the analyte/IS peak area ratio and x is the known analyte concentration in each calibration standard. Nonlinear regression was performed using WinNonlin Professional version 5.0 software (Pharsight Corp., Cary, NC), with weighting in proportion to the reciprocal of the drug concentration, normalized to the number of calibration standards, to determine the y-intercept (a), coefficient (b) and exponent (c), of the best-fit curve. Values of the parameters describing the best-fit line were used to calculate the analyte concentration in study samples. Specimens with concentrations exceeding the upper range of the standard curve were reassayed upon appropriate dilution with drug-free human plasma or whole blood. The average of the two initial determinations of each study sample was calculated. Samples were reassayed in cases where the individual determinations differed from their average by more than 15%. During the analysis of samples from this study, the calibration curves exhibited correlation coefficients ranging from 0.995 to 1.000 and the interday accuracy was within ±11.1% of the known concentration of the calibration standards and quality control solutions with a precision ≤10.5%. Actual sample times were calculated relative to the time that the prior dose of either drug was taken. Observations were excluded for samples collected after the daily dose had already been taken, if the sample was not collected within 24 ± 2 h of taking the prior dose, or determined to be an outlier by application of Dixon's test. Cminss was not calculated if there were fewer than three acceptable determinations. References 1. Zhao M, He P, Rudek MA, Hidalgo M, Baker SD. Specific method for determination of OSI-774 and its metabolite OSI-420 in human plasma by using liquid chromatography-tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci. 2003 Aug 15;793(2):413-20. 2. Shah VP, Midha KK, Findlay JW, Hill HM, Hulse JD, McGilveray IJ, et al. Bioanalytical method validation--a revisit with a decade of progress. Pharm Res. 2000 Dec;17(12):1551-7.