J.L. and T.V. are supported by the National Institute of Allergy and Infectious Diseases (NIAID) of the National Institutes of Health (R01 AI111965). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institute of Allergy and Infectious Diseases or the National Institutes of Health. MC is an Australian NHMRC Principal Research Fellow. J. L. is an Australian National Health and Medical Research Council (NHMRC) Senior Research Fellow, and T.V. is an Australian NHMRC Industry Career Development Level 2 Research Fellow. E.K.S is an appointed Young Ambassador 2017 for ASM (American Society for Microbiology) and is supported by the Australian Postgraduate Award. 
Parts of this work was presented at the 12th Australiasian Conference on Cystic Fibrosis In Melbourne (5-8th of August 2017).

Approval for ethics was obtained from Monash University Human Research Ethics Committee (MUHREC).
1. Application of the Assay: Patient Sample Collection
<ol>
	<li>Record the time when the patient takes their standard dose of either 150 mg ivacaftor or ivacaftor 125 mg /lumacaftor 200 mg.</li>
	<li>Note down the exact time when the patient blood sample is collected. 
	NOTE: We recommend collecting 4-5 samples over a 24 h time course. If the collection of only one sample is possible, the indicated time point is 2.5-4 h post ivacaftor or ivacaftor-lumacaftor combination dosing as Cmax concentrations at steady state will be achievable after &#62;5 days of consecutive treatment.</li>
	<li>Collect 4-5 mL of blood in commercially available untreated blue tubes.</li>
	<li>After collection of the whole blood, allow the blood to clot by leaving it undisturbed at room temperature. 
	NOTE: This usually takes 15-30 min.</li>
	<li>Remove the clot by centrifuging at 1,000-2,000 x g for 10 min at 4 &#176;C in a refrigerated centrifuge. Designate the resulting supernatant as plasma.</li>
	<li>Following centrifugation, immediately transfer the supernatant (plasma) into a clean polypropylene tube using a Pasteur pipette. Label the plasma tube with the Patient ID (e.g., Patient 1), the administered drug (e.g., ivacaftor-lumacaftor combination), and time the patient sample was collected (e.g., 2.5 h post-dosage).</li>
	<li>Maintain samples at 2-8 &#176;C during handling. Once handling is completed, store samples at &#8211;20 &#176;C.</li>
	<li>If necessary, ship samples with an approved courier to the analyzing institute. 
	NOTE: Samples are to be shipped on dry ice until arrival and should be kept at &#8211;80&#176;C until analysis.</li>
</ol>
2. Preparation and Processing of Incurred Samples and Standards
NOTE: Plasma from healthy donors na&#239;ve to ivacaftor/lumacaftor therapy was obtained from the Australian Red Cross. To ensure the integrity, all samples/standards should be kept at 2-8 &#176;C during collection and processing. Once handling is completed, store samples at &#8211;20 &#176;C.
<ol>
	<li>Weigh out IVA, IVA-carboxylate, hydroxymethyl-IVA, and LUMA which will serve as a reference for the internal standards.</li>
	<li>Prepare two independent stock solutions of each analyte (IVA, M1, M6 and LUMA) in LC-MS grade methanol at 100 &#181;g/mL and at 10 &#181;g/mL. 
	Note: Compounds will expire after 10 days on the benchtop.</li>
	<li>Freshly prepare LC-MS calibration standards prior to each analytical run by dilution of the calibration standards stock solutions into human plasma to achieve following concentrations: 0.01, 0.025, 0.05, 0.1, 0.2, 0.5, 1.0, 2.5, 5.0, and 10.0 &#181;g/mL. These samples are referred to as standards.</li>
	<li>To precipitate proteins, prepare 0.1% formic acid (FA) in acetonitrile (ACN, LC-MS grade) and leave in the refrigerator until needed.</li>
</ol>
3. Pre-treatment of Incurred Samples and Standards
<ol>
	<li>Allow both patient and blank plasma samples to equilibrate to room temperature.</li>
	<li>Vortex to mix each plasma sample for 15 s per sample.</li>
	<li>Transfer a 100 &#181;L aliquot of either blank plasma for standards or patient samples for analysis into a 1.5-mL polypropylene microcentrifuge tube.</li>
	<li>Add the internal standard IVA into each of the standard tubes (e.g., 0.01, 0.025, 0.05, 0.1, 0.2, 0.5, 1.0, 2.5, 5.0, and 10.0 &#181;g/mL to cover the potential concentration range), close the lid, and vortex for 2-3 s. Note that internal standard is only added to the blank plasma and no internal standard is added to the patient samples.</li>
	<li>Repeat step 3.4. for the other internal standards M1, M6, and LUMA.</li>
	<li>Spin down each tube briefly to ensure that there are no droplets on the lid.</li>
	<li>Add 200 &#181;L of the mix of 0.1% FA in ACN into each tube to precipitate plasma proteins.</li>
	<li>Vortex the mixture vigorously for about 15 s.</li>
	<li>Allow tubes to stand for 10 min in the refrigerator.</li>
	<li>Centrifuge at 10,000 x g for 10 min at 4 &#176;C, if possible.</li>
	<li>Filter a 200 &#181;L aliquot of the supernatant through a 13 mm syringe filter into a 1.5 mL HPLC vial.</li>
	<li>Transfer 100 &#181;L of the supernatant into the LC-MS vial for the HPLC-MS analysis.</li>
</ol>
4. HPLC-MS Analysis
NOTE: The HPLC-MS analysis was performed on an LC-MS system coupled with the triple quadrupole mass spectrometer (Table 1).
<ol>
	<li>Turn on the LC-MS system, place the tray with the samples in the auto-sampler.</li>
	<li>Attach the column to a guard column and connect to the LC-MS system.</li>
	<li>Attach both bottles of mobile phases (bottle A: 100% ACN; bottle B: 0.1% formic acid in water) and equilibrate the LC-MS system.</li>
	<li>Incorporate the following parameters into the LC-MS protocol.
	<ol>
		<li>Split the mobile phase flow before entering the mass spectrometer in a 2:1 ratio (waste: MS inlet).</li>
		<li>Perform a gradient elution at a flow rate of 0.5 mL/min using a mobile phase consisting of 100% ACN and 0.1% formic acid in water (starting point at 40:60, v/v). Note that the volume percent of the mobile phase changes throughout analysis.</li>
		<li>Operate the mass spectrometer in a positive electrospray ionization mode.</li>
		<li>Make sure that the LC-MS settings are as follows: ion spray voltage 4.5 kV, collision energy 295.9 V, nebulizing gas: nitrogen at 3 L/min; collision gas: argon; drying gas flow 20 L/min, lens voltage Q3: - 22 V, desolvation temperature 250 &#176;C with a heat block temperature of 400 &#176;C.</li>
		<li>Inject 10 &#181;L volume per sample.</li>
		<li>Detect analytes using multiple reaction monitoring (MRM). Monitor the ion transitions of m/z 392.49 &#8594; 393, m/z 408.49 &#8594; 409, m/z 422.47 &#8594; 423 and m/z 452.40 &#8594; 453 for IVA, IVA-M1, IVA-M6 and LUMA, respectively. 
		NOTE: The newly optimized method has yet to be fully validated according to FDA standards.</li>
	</ol>
	</li>
</ol>
5. Calibration Curves
<ol>
	<li>Construct the LC-MS calibration curves before each analytical run using the relationship between the peak area ratios of each of the four analytes to internal standard and the calibration standard nominal concentrations of ivacaftor (IVA-M1, IVA-M6 or LUMA) within the LC-MS settings program. 
	NOTE: The exact steps for the construction of the calibration curve is dependent on the model of LC-MS equipment being used. This information may be available in the equipment manual.</li>
	<li>Perform linear least-squares regression analysis by weighting 1/C2 according to the reciprocal of concentrations.</li>
</ol>

<ol>
	<li>Schneider, E. K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Drug-drug+plasma+protein+binding+interactions+of+ivacaftor.">Drug-drug plasma protein binding interactions of ivacaftor.</a> J Mol Recognit. 28 (6), 339-348 (2015).</li><li>Solomon, M., Leatte, P. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Treatments for Cystic fibrosis. , (2009).</li><li>O'Sullivan, B. P., Flume, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+clinical+approach+to+lung+disease+in+patients+with+cystic+fibrosis.">The clinical approach to lung disease in patients with cystic fibrosis.</a> Semin Respir Crit Care Med. 30 (5), 505-513 (2009).</li><li>Ramsey, B. W., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+CFTR+potentiator+in+patients+with+cystic+fibrosis+and+the+G551D+mutation.">A CFTR potentiator in patients with cystic fibrosis and the G551D mutation.</a> N Engl J Med. 365 (18), 1663-1672 (2011).</li><li>Wainwright, C. E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Lumacaftor-Ivacaftor+in+Patients+with+Cystic+Fibrosis+Homozygous+for+Phe508del+CFTR.">Lumacaftor-Ivacaftor in Patients with Cystic Fibrosis Homozygous for Phe508del CFTR.</a> N Engl J Med. 373 (3), 220-231 (2015).</li><li>Hadida, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Discovery+of+N-(2,4-di-tert-butyl-5-hydroxyphenyl)-4-oxo-1,4-dihydroquinoline-3-carboxamide+(VX-770,+ivacaftor),+a+potent+and+orally+bioavailable+CFTR+potentiator.">Discovery of N-(2,4-di-tert-butyl-5-hydroxyphenyl)-4-oxo-1,4-dihydroquinoline-3-carboxamide (VX-770, ivacaftor), a potent and orally bioavailable CFTR potentiator.</a> J Med Chem. 57 (23), 9776-9795 (2014).</li><li>FDA. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> FDA Advisory Commitee Briefing Material VERTEX-FDA Pulmonary-Allergy drugs advisory commitee. 98 , (2015).</li><li>Holmes, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=False+dawn+for+cystic+fibrosis+disease+modifiers?.">False dawn for cystic fibrosis disease modifiers?.</a> Nat Rev Drug Discov. 13 (10), 713-714 (2014).</li><li>Veit, G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Some+gating+potentiators,+including+VX-770,+diminish+DeltaF508-CFTR+functional+expression.">Some gating potentiators, including VX-770, diminish DeltaF508-CFTR functional expression.</a> Sci Transl Med. 6 (246), 246ra297 (2014).</li><li>Cholon, D. M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Potentiator+ivacaftor+abrogates+pharmacological+correction+of+DeltaF508+CFTR+in+cystic+fibrosis.">Potentiator ivacaftor abrogates pharmacological correction of DeltaF508 CFTR in cystic fibrosis.</a> Sci Transl Med. 6 (246), 246ra297 (2014).</li><li>EMA, <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Assessment report ORKAMBI (ivacaftor/lumacaftor) European medicines agency. , (2015).</li><li>VERTEX. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Vertex prescribing infomation. , (2015).</li><li>Matthes, E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Low+free+drug+concentration+prevents+inhibition+of+F508del+CFTR+functional+expression+by+the+potentiator+VX-770+(ivacaftor).">Low free drug concentration prevents inhibition of F508del CFTR functional expression by the potentiator VX-770 (ivacaftor).</a> Br J Pharmacol. 173 (3), 459-470 (2016).</li><li>Schneider, E. K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Development+of+HPLC+and+LC-MS/MS+methods+for+the+analysis+of+ivacaftor,+its+major+metabolites+and+lumacaftor+in+plasma+and+sputum+of+cystic+fibrosis+patients+treated+with+ORKAMBI+or+KALYDECO.">Development of HPLC and LC-MS/MS methods for the analysis of ivacaftor, its major metabolites and lumacaftor in plasma and sputum of cystic fibrosis patients treated with ORKAMBI or KALYDECO.</a> J Chrom B Analyt Technol Biomed Life Sci. 1038, 57-62 (2016).</li><li>Su, Q., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+LC-MS/MS+method+for+the+quantitation+of+cabozantinib+in+rat+plasma:+application+to+a+pharmacokinetic+study.">An LC-MS/MS method for the quantitation of cabozantinib in rat plasma: application to a pharmacokinetic study.</a> J Chromatogr B Analyt Technol Biomed Life Sci. 985, 119-123 (2015).</li></ol>

The authors have nothing to disclose.

As previously reported, our group has for the first time developed and validated a HPLC and LC-MS method for rapid detection and quantification of ivacaftor and its major metabolites hydroxymethyl-IVA M1 (active) and IVA-carboxylate M6 (inactive); and lumacaftor in the plasma and sputum of CF patients14. The assay reported by our group previously was successfully used to quantify the concentration of LUMA, IVA, IVA-M1, and IVA-M6 in the plasma and sputum of CF patients undergoing steady state standard therapy with IVA 150 mg /q12 h (Latin terminology: quaque 12 h; once every 12 h) or 200 mg /q12 h LUMA-125 mg /q12 h IVA combination14. For the high-throughput analysis of large amounts of patient samples, we have optimized the reported method by using a smaller pore size reverse-phase chromatography column C8 (2.6 &#181;m; 100 &#197;; 50 x 2.1 mm2) and a gradient solvent system instead of the current isocratic elution. This reduces the running time to 6 min per sample.
This reliable and novel method offers a simple, sensitive and rapid approach for therapeutic drug monitoring of ivacaftor and ivacaftor-lumacaftor combination in biological fluids. Given the need to develop exposure-response relationships to maximize drug efficacy as well as contain health care costs, more sensitive tools need to be developed and validated to assist clinicians in using evidence-based therapies and high-throughput analytical techniques for patients suffering from CF. Our group has previously reported a partially validated HPLC-MS for simultaneously analyzing IVA, IVA-M1, IVA-M6, and LUMA in the plasma and sputum of CF patients14. Establishing a common and easy-to-use analytical protocol for the analysis of patients receiving ivacaftor or ivacaftor-lumacaftor combination would facilitate data comparison and interpretation of results of future pharmacokinetic studies. Measuring IVA, IVA-M1, IVA-M6, and LUMA in biological fluids using LC-MS techniques might embody a powerful tool for exploring the exposure-response relationship in relation to therapeutic outcomes.
More generally, HPLC-MS analysis of ivacaftor or ivacaftor-lumacaftor combination in biological fluids might provide a molecular basis for the implementation of individualized pharmacotherapeutic strategies with patients suffering from CF and may prove useful on the grounds of making the expensive ivacaftor or ivacaftor-lumacaftor combination therapy more cost effective, by potentially indicating the need for less frequent dosing. By applying the proposed analytical method to clinical pharmacokinetic/pharmacodynamic studies, the opportunity has arisen to further investigate the pharmacokinetic parameters of ivacaftor or ivacaftor-lumacaftor combination on a larger patient collective.

Cystic fibrosis (CF) is a common genetic disease involving the exocrine mucus glands of the lung, liver, pancreas, and intestines causing progressive multi-organ failure, such as a decline in lung function and pancreatic insufficiency1,2,3. Ivacaftor (IVA) is the first Food and Drug Administration (FDA-US) and European Medicines Agency (EMA) approved cystic fibrosis trans-membrane conductance regulator (CFTR) potentiator drug, with evidenced clinical efficacy producing a significant improvement in the lung function over placebo in a small subset of CF patients bearing the G551D-CFTR [glycine (G) in position 551 is replaced by aspartic acid (D)]&#160;missense mutation (~4-5% of the CF population)4,5. This orally administered drug increases the CFTR channel opening, thus increasing the chloride ion flow and acting on the primary defect that leads to the clinical manifestations of CF4,6. Unfortunately, IVA monotherapy is not effective in patients with the more common homozygous F508del mutation [in frame deletion of the CFTR gene which results in the loss of phenylalanine (F) at position 508]&#160;which results in misfolded CFTR, which is seen in ~50% of the CF population7,8.
Recently, the FDA has granted approval for combining IVA with the CFTR corrector drug lumacaftor. The clever strategy of combining a CFTR corrector (lumacaftor, LUMA) which rescues F508del-CFTR to the cell surface with a modulator (IVA) which potentiates CFTR channel activity, effectively expands the treatment window to most of the CF population5. Questions remain over whether these drugs will fulfill their promise as a number of conflicting reports have emerged that cast doubt upon their clinical efficacy9,10. Additionally, improvements in lung function were only modest (2.6-4% for ivacaftor-lumacaftor combination) compared to the success achieved with IVA monotherapy in patients bearing a G551D mutation (10.6-12.5%)8. Potential antagonistic drug-drug interactions between IVA and LUMA that potentially limit the clinical efficacy of ivacaftor-lumacaftor combination come from its less than ideal pharmacokinetic properties7,11. IVA is extensively metabolized by cytochrome P450 enzymes (CYP), primarily to an active metabolite hydroxymethyl-IVA (IVA-M1, M1) and an inactive form IVA-carboxylate (IVA-M6, M6)7,12. The CYP3A4 inducer LUMA, on the other hand, is not extensively metabolized and is largely excreted unchanged in the feces11. As CYP3A4 inducers induce cytochrome metabolism, ivacaftor (CYP3A4 substrate) concentrations could be reduced. Moreover, both IVA and LUMA are very hydrophobic molecules and are ~99% bound to plasma proteins, which significantly limits the free (active) drug concentration1,13.
Collectively, these factors may be coming together to limit the clinical efficacy of ivacaftor-lumacaftor combination. It is not known whether optimal plasma concentrations are achieved under the current dosage regimen for ivacaftor-lumacaftor combination or if the therapeutic threshold is maintained8. Presently, there is a paucity of information regarding pharmacokinetic parameters such as the peak and steady-state plasma concentrations of ivacaftor or ivacaftor-lumacaftor. Given the noted metabolism of ivacaftor and lumacaftor, monitoring of exposure-response relationships is requisite to achieve optimal dosage regimens for ivacaftor or ivacaftor-lumacaftor therapy. Our group recently published the first HPLC/LC-MS method for the monitoring of exposure-response relationships of IVA and LUMA14. No alternative techniques of measuring the concentrations of ivacaftor, its metabolites, and lumacaftor have been reported to date. To allow the high-throughput analysis of a larger patient collective and to dramatically reduce analysis time, our group has optimized the reported method through the use of a smaller pore size reverse-phase chromatography column and a gradient solvent system that reduces cost and running times.

<table border="0" cellpadding="0" cellspacing="0" width="915">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:480px;">IVA (Cat#S114)&#160;</td>
			<td style="width:229px;">SelleckChem (USA).&#160;</td>
			<td style="width:143px;"></td>
			<td style="width:64px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">LUMA (Cat#S1565)&#160;</td>
			<td>SelleckChem (USA).&#160;</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">IVA-carboxylate (Cat# 510242247CS)&#160;</td>
			<td>Clearsynth (Canada).&#160;</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">hydroxymethyl-IVA (Cat# 510240849CS)&#160;</td>
			<td>Clearsynth (Canada).&#160;</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Methanol (MeOH, LC-MS grade),&#160;</td>
			<td>Sigma-Aldrich</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">acetonitrile (ACN, LC-MS grade)&#160;</td>
			<td>Sigma-Aldrich</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">formic acid (FA)&#160;</td>
			<td>Sigma-Aldrich</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">triple-quadrupole Shimadzu 8030 LC-MS&#160;</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Phenomenex Kinetex (2.6 &#181;m C8 100 &#197;; 50 &#215; 2.1mm)</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">(KrudKatcher Ultrea HPLC In-Line Filter 0.5 m Depth Filter x 0.004inID).&#160;</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">1.5 mL polypropylene microcentrifuge tube (VWR).&#160;</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Eppendorf Centrifuge 5430</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">13-mm syringe filter (0.45 &#181;m nylon, GRACE, USA)&#160;</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">[Phenomenex VEREX, 9 mm, PP, 300 &#181;L, PTFE/Silicone septa].&#160;</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
	</tbody>
</table>

optimized lc-ms/ms method for the high-throughput analysis of clinical samples of ivacaftor, its major metabolites, and lumacaftor in biological fluids of cystic fibrosis patients

Defects in the cystic fibrosis trans-membrane conductance regulator (CFTR) are the cause of cystic fibrosis (CF), a disease with life-threatening pulmonary manifestations. Ivacaftor (IVA) and ivacaftor-lumacaftor (LUMA) combination are two new breakthrough CF drugs that directly modulate the activity and trafficking of the defective CFTR-protein. However, there is still a dearth of understanding on pharmacokinetic/pharmacodynamic parameters and the pharmacology of ivacaftor and lumacaftor. The HPLC-MS technique for the simultaneous analysis of the concentrations of ivacaftor, hydroxymethyl-ivacaftor, ivacaftor-carboxylate, and lumacaftor in biological fluids in patients receiving standard ivacaftor or ivacaftor-lumacaftor combination therapy has previously been developed by our group and partially validated to FDA standards. However, to allow the high-throughput analysis of a larger number of patient samples, our group has optimized the reported method through the use of a smaller pore size reverse-phase chromatography column (2.6 &#181;m, C8 100 &#197;; 50 x 2.1 mm) and a gradient solvent system (0-1 min: 40% B; 1-2 min: 40-70% B; 2-2.7 min: held at 70% B; 2.7-2.8 min: 70-90% B; 2.8-4.0 min: 90% B washing; 4.0-4.1 min: 90-40% B; 4.1-6.0 min: held at 40% B) instead of an isocratic elution. The goal of this study was to reduce the HPLC-MS analysis time per sample dramatically from ~15 min to only 6 min per sample, which is essential for the analysis of a large amount of patient samples. This expedient method will be of considerable utility for studies into the exposure-response relationships of these breakthrough CF drugs.

We have recently reported a method, partially validated to FDA standards, on a triple-quadrupole LC-MS and an HPLC detector system, using a C8 column (5 &#181;m, 3.9 mm x 50 mm i.d.) with the mobile phase consisting of 100% ACN and 0.1% formic acid in water (40:60, v/v) at a flow rate of 1 mL/min. A linear correlation of the peaks was observed over a concentration range from 0.01 to 10 &#181;g/mL in human plasma for all metabolites, ivacaftor, Iva-M1, Iva-M6, and lumacaftor14. Here this method has been optimized to allow dramatically reduced LC retention times and, therefore, the complete running time of the assay, which is essential for the high-throughput analysis of a large amount of clinical samples. The assay was optimized through the use of a smaller pore size reverse-phase chromatography column and a gradient solvent system instead of an isocratic elution, reducing the time per sample from ~15 min to only 6 min. The analytes are determined in electrospray positive mode using multiple reaction monitoring (MRM). The procedure should be validated in-house prior to use, as we have previously detailed14.
The accuracy of the method was 94.2% &#177; 4.53% to 97.5% &#177; 2.94%, depending on the analyte14. The calibration range from 0.01 to 10 &#181;g/mL is applicable for use in the clinical setting, in particular given that under ivacaftor-lumacaftor therapy, very low concentrations of active IVA and M1 were reported by our group previously, in plasma potentially due to the induction of CYP3A4 by LUMA, which results in extensive IVA metabolism14. The intra-day accuracy of each analyte was assessed with six independently prepared quality control (QC) samples on the same day at concentrations of 0.05, 0.5, and 8 &#181;g/mL. The inter-day accuracy was assessed with six independently prepared QC samples on three consecutive days. Accuracy and precision were calculated via relative standard deviation (RSD). For each QC sample, the RSD values should be less than 15%15. All four analytes showed RSD values of less than 15%14. The lower limit of detection (LOD) and quantification (LOQ) were established: for IVA LOD 2.50 x 10-3 &#181;g/mL and LOQ 7.57 x 10-3 &#181;g/mL; for M1, LOD 4.57 x 10-4 &#181;g/mL and LOQ 1.38 x 10-3 &#181;g/mL; for M6 LOD 5.86 x 10-4 &#181;g/mL and LOQ 1.78 x 10-3 &#181;g/mL; for LUMA LOD was 6.08 x 10-4 &#181;g/mL and LOQ 1.84 x 10-3 &#181;g/mL14. A typical chromatogram is shown in Figure 1. An optimized chromatographic resolution was obtained using a mobile phase of 100% ACN and 0.1% formic acid in water (starting point at 40:60, v/v) with a gradient elution on a C8 column (2.6 &#181;m; 100 &#197;; 50 mm x 2.1 mm). The gradient separation was used with 40% of mobile phase B from 0 to 1 min; then 40%-70% of mobile phase B from 1 min to 2 min; holding 70% of mobile phase B from 2 min to 2.7 min; increasing from 70% to 90% of mobile phase B from 2.7 min to 2.8 min; holding 90% of mobile phase B from 2.8 min to 4.0 min for washing purposes; finally returning from 90% to 40% of mobile B from 4.0 min to 4.1 min; then holding 40% of mobile phase B from 4.1 min to 6.0 min for initial conditions (Figure 1). The LC retention times were as follows for M6 1.0 min; for M1 1.3 min; for IVA: 1.55 min; for LUMA: 2.3 min (Figure 1). In all blank plasma samples, no interference with the retention time of either of the analytes was observed, nor was interference detected from the combination of ivacaftor with lumacaftor.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/56084/56084fig1.jpg" /> 
Figure 1: Representative LC-MS chromatogram of human plasma spiked with 10 &#181;g/mL of IVA-M6, IVA-M1, lumacaftor, and ivacaftor in relation to the gradient elution of pump. A 0.1% formic acid in water and pump B 100% acetonitrile (0-1 min: 40% B; 1-2 min: 40%-70% B; 2-2.7 min: held at 70% B; 2.7-2.8 min: 70%-90% B; 3.8-4.0 min: 90% B washing; 4.0-4.1 min: 90%-40% B; 4.1-6.0 min: held at 40% B). The ion transitions of m/z 392.49 &#8594; 393, m/z 408.49 &#8594; 409, m/z 422.47 &#8594; 423 and m/z 452.40 &#8594; 453 were used for MS/MS monitoring of ivacaftor, IVA- M1, IVA-M6 and lumacaftor, respectively. <a href="https://cloudflare-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/56084/56084fig1large.jpg" target="_blank"> Please click here to view a larger version of this figure.</a>
<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td colspan="2">HPLC Conditions</td>
		</tr>
		<tr>
			<td colspan="2"></td>
		</tr>
		<tr>
			<td>Column</td>
			<td>C8; 2.6 &#181;m; 100 &#197;; 50 x 2.1 mm</td>
		</tr>
		<tr>
			<td rowspan="2">Guard column</td>
			<td>HPLC In-Line Filter 0.5 &#181;m; Depth Filter x 0.004 inID</td>
		</tr>
		<tr>
			<td>Filter x 0.004 inID</td>
		</tr>
		<tr>
			<td>Column temperature:</td>
			<td>30 &#176;C</td>
		</tr>
		<tr>
			<td>Mobile phase A:</td>
			<td>0.1 % FA in water</td>
		</tr>
		<tr>
			<td>Mobile phase B:</td>
			<td>100 % ACN</td>
		</tr>
		<tr>
			<td>Mobile Phase composition at starting point</td>
			<td>60 / 40 (v/v)</td>
		</tr>
		<tr>
			<td>Sample temperature:</td>
			<td>4 &#176;C</td>
		</tr>
		<tr>
			<td>Injection volume:</td>
			<td>5 &#181;L</td>
		</tr>
		<tr>
			<td>Needle wash</td>
			<td>80 % methanol, 20 % water 300 &#181;L</td>
		</tr>
		<tr>
			<td>Flow rate:</td>
			<td>0.5 mL/min</td>
		</tr>
		<tr>
			<td rowspan="7">Gradient:</td>
			<td>-&#160;&#160;&#160;&#160;&#160;&#160;&#160; 1 min: 40 % B</td>
		</tr>
		<tr>
			<td>-&#160;&#160;&#160;&#160;&#160;&#160;&#160; 1 - 2 min: 40 % - 70 % B</td>
		</tr>
		<tr>
			<td>-&#160;&#160;&#160;&#160;&#160;&#160;&#160; 2 - 2.7 min: held at 70 % B</td>
		</tr>
		<tr>
			<td>-&#160;&#160;&#160;&#160;&#160;&#160;&#160; 2.7 - 2.8 min: 70 % - 90 % B</td>
		</tr>
		<tr>
			<td>-&#160;&#160;&#160;&#160;&#160;&#160;&#160; 2.8 - 4.0 min: 90 % B washing</td>
		</tr>
		<tr>
			<td>-&#160;&#160;&#160;&#160;&#160;&#160;&#160; 4.0 - 4.1 min: 90 % - 40 %</td>
		</tr>
		<tr>
			<td>-&#160;&#160;&#160;&#160;&#160;&#160;&#160; 4.1 - 6.0 min: held at 40 %,</td>
		</tr>
		<tr>
			<td>Total run:</td>
			<td>6 mins</td>
		</tr>
		<tr>
			<td rowspan="5">Retention times:</td>
			<td>Retention time for M6: 1.0 min</td>
		</tr>
		<tr>
			<td>Retention time for M1: 1.3 min</td>
		</tr>
		<tr>
			<td>Retention time for IVA: 1.55 min</td>
		</tr>
		<tr>
			<td>Retention time for LUMA: 2.3 min</td>
		</tr>
		<tr>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td colspan="2">MS Conditions</td>
		</tr>
		<tr>
			<td>Detection mode:</td>
			<td>electrospray positive ESI +</td>
		</tr>
		<tr>
			<td>Ion spray voltage:</td>
			<td>4.5 kV</td>
		</tr>
		<tr>
			<td>Collision Energy:</td>
			<td>295.9 V</td>
		</tr>
		<tr>
			<td>Nebulizing Gas (nitrogen):</td>
			<td>3 L/min</td>
		</tr>
		<tr>
			<td>CID Gas:</td>
			<td>230 kPa</td>
		</tr>
		<tr>
			<td>Drying gas (nitrogen) flow:</td>
			<td>20 L/min</td>
		</tr>
		<tr>
			<td>Q1 Pre-rod bias:</td>
			<td>-&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160; 5 V</td>
		</tr>
		<tr>
			<td>CE:</td>
			<td>-&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160; 25 V</td>
		</tr>
		<tr>
			<td>Q3 pre-rod bias:</td>
			<td>-&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160; 5 V</td>
		</tr>
		<tr>
			<td>Interface current:</td>
			<td>0.1 UA</td>
		</tr>
		<tr>
			<td>Desolvation temperature:</td>
			<td>250 &#176;C</td>
		</tr>
		<tr>
			<td>Heat block temperature:</td>
			<td>400 &#176;C</td>
		</tr>
		<tr>
			<td>IVA m/z</td>
			<td>392.49 &#8594; 393</td>
		</tr>
		<tr>
			<td>M1 m/z</td>
			<td>408.49 &#8594; 409</td>
		</tr>
		<tr>
			<td>M6 m/z</td>
			<td>422.47 &#8594; 423</td>
		</tr>
		<tr>
			<td>LUMA m/z</td>
			<td>452.40 &#8594; 453</td>
		</tr>
	</tbody>
</table>
Table 1: Details of the HPLC-MS conditions.

Watch this Scientific Journal Video about Optimized LC-MS/MS Method for the High-throughput Analysis of Clinical Samples of Ivacaftor, Its Major Metabolites, and Lumacaftor in Biological Fluids of Cys

Optimized LC-MS/MS Method for the High-throughput Analysis of Clinical Samples of Ivacaftor, Its Major Metabolites, and Lumacaftor in Biological Fluids of Cystic Fibrosis Patients

Ivacaftor and ivacaftor-lumacaftor combination are two new CF drugs. However, there is still a dearth of understanding on their PK/PD and pharmacology. We present an optimized HPLC-MS technique for the simultaneous analysis of ivacaftor and its major metabolites, and lumacaftor.

Defects in the cystic fibrosis trans-membrane conductance regulator (CFTR) are the cause of cystic fibrosis (CF), a disease with life-threatening ...

optimized-lc-msms-method-for-high-throughput-analysis-clinical

Nanyang Technological University

Research

JoVE Journal

Medicine

8.2K Views.  Monash University. Ivacaftor and ivacaftor-lumacaftor combination are two new CF drugs. However, there is still a dearth of understanding on their PK/PD and pharmacology. We present an optimized HPLC-MS technique for the simultaneous analysis of ivacaftor and its major metabolites, and lumacaftor.

Video: Optimized LC-MS/MS Method for the High-throughput Analysis of Clinical Samples of Ivacaftor, Its Major Metabolites, and Lumacaftor in Biological Fluids of Cystic Fibrosis Patients

Quantification of the Immunosuppressant Tacrolimus on Dried Blood Spots Using LC-MS/MS

The calcineurin inhibitor tacrolimus is the cornerstone of most immunosuppressive treatment protocols after solid organ transplantation in the United States. Tacrolimus is a narrow therapeutic index drug and as such requires therapeutic drug monitoring and dose adjustment based on its whole blood trough concentrations. To facilitate home therapeutic drug and adherence monitoring, the collection of dried blood spots is an attractive concept. After a finger stick, the patient collects a blood drop on filter paper at home. After the blood is dried, it is mailed to the analytical laboratory where tacrolimus is quantified using high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) in combination with a simple manual protein precipitation step and online column extraction.
For tacrolimus analysis, a 6-mm disc is punched from the saturated center of the blood spot. The blood spot is homogenized using a bullet blender and then proteins are precipitated with methanol/0.2 M ZnSO4 containing the internal standard D2,13C-tacrolimus. After vortexing and centrifugation, 100 &#181;l of supernatant is injected into an online extraction column and washed with 5 ml/min of 0.1 formic acid/acetonitrile (7:3, v:v) for 1 min. Hereafter, the switching valve is activated and the analytes are back-flushed onto the analytical column (and separated using a 0.1% formic acid/acetonitrile gradient). Tacrolimus is quantified in the positive multi reaction mode (MRM) using a tandem mass spectrometer.
The assay is linear from 1 to 50 ng/ml. Inter-assay variability (3.6%-6.1%) and accuracy (91.7%-101.6%) as assessed over 20 days meet acceptance criteria. Average extraction recovery is 95.5%. There are no relevant carry-over, matrix interferences and matrix effects. Tacrolimus is stable in dried blood spots at RT and at +4 &#176;C for 1 week. Extracted samples in the autosampler are stable at +4 &#176;C for at least 72 hr.

Here we describe a high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) assay to quantify the immunosuppressant tacrolimus in dried blood spots using a simple manual protein precipitation step and online column extraction.

The calcineurin inhibitor tacrolimus is the cornerstone of most immunosuppressive treatment protocols after solid organ transplantation in the United ...

Network Analysis of Foramen Ovale Electrode Recordings in Drug-resistant Temporal Lobe Epilepsy Patients

Approximately 30% of epilepsy patients are refractory to antiepileptic drugs. In these cases, surgery is the only alternative to eliminate/control seizures. However, a significant minority of patients continues to exhibit post-operative seizures, even in those cases in which the suspected source of seizures has been correctly localized and resected. The protocol presented here combines a clinical procedure routinely employed during the pre-operative evaluation of temporal lobe epilepsy (TLE) patients with a novel technique for network analysis. The method allows for the evaluation of the temporal evolution of mesial network parameters. The bilateral insertion of foramen ovale electrodes (FOE) into the ambient cistern simultaneously records electrocortical activity at several mesial areas in the temporal lobe. Furthermore, network methodology applied to the recorded time series tracks the temporal evolution of the mesial networks both interictally and during the seizures. In this way, the presented protocol offers a unique way to visualize and quantify measures that considers the relationships between several mesial areas instead of a single area.

This protocol describes a procedure to track the evolution of mesial network measures in temporal lobe epilepsy (TLE) patients. It is based on the combination of intracranial recordings with a novel numerical technique for data analysis. Specifically, we present a protocol for network analyses of foramen ovale recordings.

Approximately 30% of epilepsy patients are refractory to antiepileptic drugs. In these cases, surgery is the only alternative to eliminate/control ...

Forskolin-induced Swelling in Intestinal Organoids: An In Vitro Assay for Assessing Drug Response in Cystic Fibrosis Patients

Recently-developed cystic fibrosis transmembrane conductance regulator (CFTR)-modulating drugs correct surface expression and/or function of the mutant CFTR channel in subjects with cystic fibrosis (CF). Identification of subjects that may benefit from these drugs is challenging because of the extensive heterogeneity of CFTR mutations, as well as other unknown factors that contribute to individual drug efficacy. Here, we describe a simple and relatively rapid assay for measuring individual CFTR function and response to CFTR modulators in vitro. Three dimensional (3D) epithelial organoids are grown from rectal biopsies in standard organoid medium. Once established, the organoids can be bio-banked for future analysis. For the assay, 30-80 organoids are seeded in 96-well plates in basement membrane matrix and are then exposed to drugs. One day later, the organoids are stained with calcein green, and forskolin-induced swelling is monitored by confocal live cell microscopy at 37 &#176;C. Forskolin-induced swelling is fully CFTR-dependent and is sufficiently sensitive and precise to allow for discrimination between the drug responses of individuals with different and even identical CFTR mutations. In vitro swell responses correlate with the clinical response to therapy. This assay provides a cost-effective approach for the identification of drug-responsive individuals, independent of their CFTR mutations. It may also be instrumental in the development of future CFTR modulators.

Forskolin-induced Swelling in Intestinal Organoids: An In Vitro Assay for Assessing Drug Response in Cystic Fibrosis Patients

This protocol describes an assay for measuring CFTR function and CFTR modulator responses in cultured tissue from subjects with cystic fibrosis (CF). Biopsy-derived intestinal organoids swell in a cAMP-driven fashion, a response that is defective (or strongly reduced) in CF organoids and can be restored by exposure to CFTR modulators.

Recently-developed cystic fibrosis transmembrane conductance regulator (CFTR)-modulating drugs correct surface expression and/or function of the mutant ...

Optimized Analysis of In Vivo and In Vitro Hepatic Steatosis

Establishing a system of procedures to qualitatively and quantitatively characterize in vivo and in vitro hepatic steatosis is important for metabolic study in the liver. Here, numerous assays are described to comprehensively measure the phenotype and parameters of hepatic steatosis in mouse and hepatocyte models. 
Combining the physiological, histological, and biochemical methods, this system can be used to assess the progress of hepatic steatosis. In vivo, the measurements of body weight and nuclear magnetic resonance (NMR) provide a general understanding of mice in a non-invasive manner. Hematoxylin and Eosin (H&amp;E) and Oil Red O staining determine the histological morphology and lipid deposition of liver tissue under nutrient overload conditions, such as high-fat diet feeding. Next, the total lipid contents are isolated by chloroform/methanol extraction, which are followed by a biochemical analysis for triglyceride and cholesterol. Moreover, mouse primary hepatocytes are treated with high glucose plus insulin to stimulate lipid accumulation, an efficient in vitro model to mimic diet-induced hyperglycemia and hyperinsulinemia in vivo. Then, the lipid deposition is measured by Oil Red O staining and chloroform/methanol extraction. Oil Red O staining determines intuitive hepatic steatotic phenotypes, while the lipid extraction analysis determines the parameters that can be analyzed statistically. The present protocols are of interest to scientists in the fields of fatty liver diseases, insulin resistance, and type 2 diabetes.

Optimized Analysis of In Vivo and In Vitro Hepatic Steatosis

Here, optimized methods to generate in vivo and in vitro models of hepatic steatosis and to analyze the steatotic phenotypes and related physiological parameters are described.

Establishing a system of procedures to qualitatively and quantitatively characterize in vivo and in vitro hepatic steatosis is important for metabolic ...

Sampling Strategies and Processing of Biobank Tissue Samples from Porcine Biomedical Models

In translational medical research, porcine models have steadily become more popular. Considering the high value of individual animals, particularly of genetically modified pig models, and the often-limited number of available animals of these models, establishment of (biobank) collections of adequately processed tissue samples suited for a broad spectrum of subsequent analyses methods, including analyses not specified at the time point of sampling, represent meaningful approaches to take full advantage of the translational value of the model. With respect to the peculiarities of porcine anatomy, comprehensive guidelines have recently been established for standardized generation of representative, high-quality samples from different porcine organs and tissues. These guidelines are essential prerequisites for the reproducibility of results and their comparability between different studies and investigators. The recording of basic data, such as organ weights and volumes, the determination of the sampling locations and of the numbers of tissue samples to be generated, as well as their orientation, size, processing and trimming directions, are relevant factors determining the generalizability and usability of the specimen for molecular, qualitative, and quantitative morphological analyses. Here, an illustrative, practical, step-by-step demonstration of the most important techniques for generation of representative, multi-purpose biobank specimen from porcine tissues is presented. The methods described here include determination of organ/tissue volumes and densities, the application of a volume-weighted systematic random sampling procedure for parenchymal organs by point-counting, determination of the extent of tissue shrinkage related to histological embedding of samples, and generation of randomly oriented samples for quantitative stereological analyses, such as isotropic uniform random (IUR) sections generated by the &#34;Orientator&#34; and &#34;Isector&#34; methods, and vertical uniform random (VUR) sections.

The practical application and performance of methods for generation of representative tissue samples of porcine animal models for a broad spectrum of downstream analyses in biobank projects are demonstrated, including volumetry, systematic random sampling, and differential processing of tissue samples for qualitative and quantitative morphologic and molecular analyses types.

In translational medical research, porcine models have steadily become more popular. Considering the high value of individual animals, particularly of ...

Collecting Hair Samples for Hair Cortisol Analysis in African Americans

The hormone cortisol is typically assessed in saliva, serum, or urine samples. More recently, cortisol has been successfully extracted from hair, including humans. The advantage of hair cortisol concentration is that it reflects a retrospective representation of hypothalamic-pituitary-adrenal (HPA) axis function over time, much like hemoglobin A1C represents glycemic control. However, obtaining hair samples can be challenging, due to the cultural beliefs and hair care practices of minority participants. For example, African Americans may be reluctant to provide samples. Additionally, few researchers are trained to collect hair samples from African Americans. The purpose of this paper is to present a culturally informed protocol to help researchers obtain hair samples from African Americans. To illustrate the representative results of this protocol implementation, de-identified data from African Americans that participated in a community-based study on chronic stress are provided. Hair practice preferences are assessed. The participants are made comfortable by showing pictures of hair samples prior to cutting their hair. The single strain twist and gently pull method is used to collect approximately 30 - 50 strands of hair from the posterior vertex region of the scalp. This protocol will significantly improve collection of hair samples from African Americans.

Hair cortisol concentration analysis provides an alternative to traditional measures of cortisol; however, to collect hair samples from African Americans, scientists need to be culturally informed and competent. The purpose of this protocol is to demonstrate a culturally informed technique to collect hair samples for cortisol analysis from African Americans.

The hormone cortisol is typically assessed in saliva, serum, or urine samples. More recently, cortisol has been successfully extracted from hair, ...

High-Throughput Analysis of Optical Mapping Data Using ElectroMap

Optical mapping is an established technique for high spatio-temporal resolution study of cardiac electrophysiology in multi-cellular preparations. Here we present, in a step-by-step guide, the use of ElectroMap for analysis, quantification, and mapping of high-resolution voltage and calcium datasets acquired by optical mapping. ElectroMap analysis options cover a wide variety of key electrophysiological parameters, and the graphical user interface allows straightforward modification of pre-processing and parameter definitions, making ElectroMap applicable to a wide range of experimental models. We show how built-in pacing frequency detection and signal segmentation allows high-throughput analysis of entire experimental recordings, acute responses, and single beat-to-beat variability. Additionally, ElectroMap incorporates automated multi-beat averaging to improve signal quality of noisy datasets, and here we demonstrate how this feature can help elucidate electrophysiological changes that might otherwise go undetected when using single beat analysis. Custom modules are included within the software for detailed investigation of conduction, single file analysis, and alternans, as demonstrated here. This software platform can be used to enable and accelerate the processing, analysis, and mapping of complex cardiac electrophysiology.

This protocol describes the setup and use of ElectroMap, a MATLAB-based open-source software platform for analysis of cardiac optical mapping data. ElectroMap provides a versatile high-throughput tool for analysis of optical mapping voltage and calcium datasets across a wide range of cardiac experimental models.

Optical mapping is an established technique for high spatio-temporal resolution study of cardiac electrophysiology in multi-cellular preparations. Here we ...

A High-Throughput In Situ Method for Estimation of Hepatocyte Nuclear Ploidy in Mice

When the liver is injured, hepatocyte numbers decrease, while cell size, nuclear size and ploidy increase. The expansion of non-parenchymal cells such as cholangiocytes, myofibroblasts, progenitors and inflammatory cells also indicate chronic liver damage, tissue remodeling and disease progression. In this protocol, we describe a simple high-throughput approach for calculating changes in the cellular composition of the liver that are associated with injury, chronic disease and cancer. We show how information extracted from two-dimensional (2D) tissue sections can be used to quantify and calibrate hepatocyte nuclear ploidy within a sample and enable the user to locate specific ploidy subsets within the liver in situ. Our method requires access to fixed/frozen liver material, basic immunocytochemistry reagents and any standard high-content imaging platform. It serves as a powerful alternative to standard flow cytometry techniques, which require disruption of freshly collected tissue, loss of spatial information and potential disaggregation bias.

We present a robust, cost-effective, and flexible method for measuring changes in hepatocyte number and nuclear ploidy within fixed/cryopreserved tissue samples that does not require flow cytometry. Our approach provides a powerful sample-wide signature of liver cytology ideal for tracking the progression of liver injury and disease.

When the liver is injured, hepatocyte numbers decrease, while cell size, nuclear size and ploidy increase. The expansion of non-parenchymal cells such as ...

Validated LC-MS/MS Panel for Quantifying 11 Drug-Resistant TB Medications in Small Hair Samples

Drug resistant-tuberculosis (DR-TB) is a growing public health threat, and assessment of therapeutic drug levels may have important clinical benefits. Plasma drug levels are the current gold standard assessment, but require phlebotomy and a cold chain, and capture only very recent adherence. Our method uses hair, a matrix that is easily collected and reflective of long-term adherence, to test for 11 anti-TB medications. Previous work by our group shows that antiretroviral drug levels in hair are associated with HIV outcomes. Our method for DR-TB drugs uses 2 mg of hair (3 cm proximal to the root), which is pulverized and extracted in methanol. Samples are analyzed with a single LC-MS/MS method, quantifying 11 drugs in a 16 min run. Lower limits of quantification (LLOQs) for the 11 drugs range from 0.01 ng/mg to 1 ng/mg. Drug presence is confirmed by comparing ratios of two mass spectrometry transitions. Samples are quantified using the area ratio of the drug to the deuterated, 15N-, or 13C-labeled drug isotopologue. We used a calibration curve ranging from 0.001-100 ng/mg. Application of the method to a convenience sample of hair samples collected from DR-TB patients on directly observed therapy (DOT) indicated drug levels in hair within the linear dynamic range of nine of the eleven drugs (isoniazid, pyrazinamide, ethambutol, linezolid, levofloxacin, moxifloxacin, clofazimine, bedaquiline, pretomanid). No patient was on prothionamide, and the measured levels for ethionamide were close to its LLOQ (with further work instead examining the suitability of ethionamide&#8217;s metabolite for monitoring exposure). In summary, we describe the development of a multi-analyte panel for DR-TB drugs in hair as a technique for therapeutic drug monitoring during drug-resistant TB treatment.

Current methods of analyzing patients&#8217; adherence to complex drug resistant-tuberculosis (DR-TB) regimens can be inaccurate and resource-intensive. Our method analyzes hair, an easily collected and stored matrix, for concentrations of 11 DR-TB medications. Using LC-MS/MS, we can determine sub-nanogram drug levels that can be utilized to better understand drug adherence.

Drug resistant-tuberculosis (DR-TB) is a growing public health threat, and assessment of therapeutic drug levels may have important clinical benefits. ...

Design and Development of a Model to Study the Effect of Supplemental Oxygen on the Cystic Fibrosis Airway Microbiome

Airway microbial communities are thought to play an important role in the progression of cystic fibrosis (CF) and other chronic pulmonary diseases. Microbes have traditionally been classified based on their ability to use or tolerate oxygen. Supplemental oxygen is a common medical therapy administered to people with cystic fibrosis (pwCF); however, existing studies on oxygen and the airway microbiome have focused on how hypoxia (low oxygen) rather than hyperoxia (high oxygen) affects the predominantly aerobic and facultative anaerobic lung microbial communities. To address this critical knowledge gap, this protocol was developed using an artificial sputum medium that mimics the composition of sputum from pwCF. The use of filter sterilization, which yields a transparent medium, allows optical methods to follow the growth of single-celled microbes in suspension cultures. To create hyperoxic conditions, this model system takes advantage of established anaerobic culturing techniques to study hyperoxic conditions; instead of removing oxygen, oxygen is added to cultures by daily sparging of serum bottles with a mixture of compressed oxygen and air. Sputum from 50 pwCF underwent daily sparging for a 72-h period to verify the ability of this model to maintain differential oxygen conditions. Shotgun metagenomic sequencing was performed on cultured and uncultured sputum samples from 11 pwCF to verify the ability of this medium to support the growth of commensal and pathogenic microbes commonly found in cystic fibrosis sputum. Growth curves were obtained from 112 isolates obtained from pwCF to verify the ability of this artificial sputum medium to support the growth of common cystic fibrosis pathogens. We find that this model can culture a wide variety of pathogens and commensals in CF sputum, recovers a community highly similar to uncultured sputum under normoxic conditions, and creates different culture phenotypes under varying oxygen conditions. This new approach might lead to a better understanding of unanticipated effects induced by the use of oxygen in pwCF on airway microbial communities and common respiratory pathogens.

The goal of this protocol is to develop a model system for the effect of hyperoxia on cystic fibrosis airway microbial communities. Artificial sputum medium emulates the composition of sputum, and hyperoxic culture conditions model the effects of supplemental oxygen on lung microbial communities.

Airway microbial communities are thought to play an important role in the progression of cystic fibrosis (CF) and other chronic pulmonary diseases. ...

Optimized LC-MS/MS Method for the High-throughput Analysis of Clinical Samples of Ivacaftor, Its Major Metabolites, and Lumacaftor in Biological Fluids of Cystic Fibrosis Patients

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Design and Development of a Model to Study the Effect of Supplemental Oxygen on the Cystic Fibrosis Airway Microbiome