William Clarke, PhD, MBA, DABCC Associate Professor, Pathology Johns Hopkins University School of Medicine

1. High Throughput Screening for ARV
Drugs in HIV Prevention Studies
William Clarke, PhD, MBA, DABCC
Associate Professor, Pathology
Johns Hopkins University School of
Medicine

2. Disclosures
• Research funding: NIH, FDA, Thermo Fisher
Scientific, Nova Biomedical, Saladax
Biomedical, Instrumentation Laboratories
• Consulting/Advisory Boards: Thermo Fisher
Scientific, Nova Biomedical, Roche
Diagnostics, Instrumentation Laboratories

3. HIGH RESOLUTION MASS SPECTROMETRY
SCREENING AND ANTIRETROVIRAL
ADHERENCE MONITORING

4. Use of ARVs in HIV Prevention
• HIV Prevention Trials Network (HPTN) is a global collaborative
network focused on non-vaccine interventions of HIV transmission
prevention
• Data suggest a correlation between HIV viral load and HIV
transmission (increased viral load leads to an increased likelihood of
HIV transmission)
- ART as Prevention
• Studies have demonstrated that administration of ARVs at birth
(and prenatally) prevent HIV transmission
- Pre-exposure Prophylaxis (PrEP)
• Additional studies are focused on preventative treatment with ARVs
as pre-exposure prophylaxis in high-risk populations

5. Big Problems?
• For PrEP and ART as Prevention studies,
interpretation dependent on adherence to protocol
• Partners in Prevention HSV/HIV study observed
undisclosed ARV use in 46% of infected participants
• HPTN 052 study found that in 96 index participants
(reported no ARV treatment) with viral suppression,
45 had detectable ARVs in blood
• Causes great concern:
– Self-report is unreliable
– Cost of objective testing in large sets of participants
would be very high ($200-250/sample for 1,000s of
subjects)
Fogel et al. JID 208 (2013) 1624-28.
Celum et al. N Engl J Med 362 (2010) 427-39.
Kahle et al. Proceedings of the Int Microbicides Conf; April 2012; Sydney, Australia. Abstract 347.

6. Total Ion Chromatogram
Marzinke et al. Clin Chim Acta 433 (2014) 157-68. For research use only. Not for use in diagnostic procedures.

7. Lamuvidine Extracted Ion
Chromatogram
Marzinke et al. Clin Chim Acta 433 (2014) 157-68.

8. Challenges and Goals
• Must have faster methods
– >10K specimens in the queue; ~50K to come
• Automated data analysis – remove subjective
interpretation
• Confirmatory testing selected specimens

14. Courtesy of Thermo Fisher Scientific

15. Preliminary work on TSQ Endura MS
1.33 minute method
With .4 minute data
Collection window. Using
0.5*50 Cyclone P column
With 2.1*10 Hypersil gold
Javelin cartridge @ source
Courtesy, Francois Espourteille – Thermo Fisher Scientific

16. 24 second data window (SRM)
Courtesy, Francois Espourteille – Thermo Fisher Scientific
Warfarin - IS
Nevirapine
Saquinavir

17. Full Scan Data with Rapid Separation

18. Rapid Analysis with Q Exactive MS
• Targeted MS2 using quadrupole for nominal
precursor mass; exact mass for analysis of
fragments
– All positive mode; Resolution = 17.5K at m/z of 200
• Utilize 1-3 product ions per compound, maintain
ability to view the exact mass of the precursor
• Use ‘de-tuned’ chromatography to optimize
number of scans across the peaks
– Target: 2 retention time groups in <60 seconds

19. SPE Preparation
• Phenomenex Strata-X 96-well plates
– 33 mm particle size; 10 mg sorbent mass
• Precondition with 200 mL MeOH
• Add 200 mL of internal standard (abacavir-d4
and lopinavir-d8) in 1%TFA/0.025 formic acid
• 100 mL sample (wait 2 min)
• 200 mL H2O (wait 3 min)
• 2x elution with 200 mL MeOH + 0.025% formic
acid

23. Chromatography
• Starting LC Conditions:
– Mobile Phase A: 10mM ammonium formate + 0.05%
formic acid
– Mobile Phase B: Methanol + 0.05 % formic acid
– Mobile Phase C: 2:2:1 IPA:Acetone:Acetonitrile
– Analytical column: Hypersil Gold PFP, 50 x 2.1; 5um
particle size
• Elution: Step gradient from 100%A to 100% B
• Wash: Mobile Phase C & Re-equilibrate
• Total program time = 3.1 minutes

25. RT: 0.00 - 1.50 SM: 11G
0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.1 1.2 1.3 1.4 1.5
Time (min)
0
50
100
0
50
100
0
50
100
0
50
100
0
50
100
0
50
100
0
50
100
Lamuvidine
0.28
0.42
Emtricitabine
0.24
0.44
Nevirapine
0.26
Abacavir
0.30
Tenofovir
0.27
Zidovudine
0.25
Efavirenz
0.80
NL: 9.33E5
m/z= 112.0502-112.0514 F: FTMS + p ESI
Full ms2 230.06@hcd32.00 [60.00-255.00]
MS Sys_Suit_3
NL: 1.33E6
m/z=
130.0404-130.0418+248.0488-248.0512 F:
FTMS + p ESI Full ms2 248.05@hcd70.00
[60.00-270.00] MS Sys_Suit_3
NL: 2.89E6
m/z=
107.0603-107.0613+226.0837-226.0859 F:
FTMS + p ESI Full ms2 267.12@hcd57.00
[60.00-290.00] MS Sys_Suit_3
NL: 5.71E7
m/z= 191.1025-191.1045 F: FTMS + p ESI
Full ms2 287.16@hcd29.00 [60.00-310.00]
MS Sys_Suit_3
NL: 2.89E4
m/z=
136.0613-136.0627+176.0922-176.0940 F:
FTMS + p ESI Full ms2 288.09@hcd42.00
[60.00-310.00] MS Sys_Suit_3
NL: 1.02E5
m/z=
127.0496-127.0508+142.0603-142.0617 F:
FTMS + p ESI Full ms2 268.10@hcd10.00
[60.00-290.00] MS Sys_Suit_3
NL: 2.12E4
m/z=
244.0114-244.0138+272.0424-272.0452 F:
FTMS + p ESI Full ms2 316.03@hcd12.00
[60.00-340.00] MS Sys_Suit_3

26. RT: 0.00 - 1.50 SM: 9G
0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4
Time (min)
0
50
100
0
50
100
0
50
100
0
50
100
0
50
100
0
50
100
0
50
100
0
50
100 Raltegravir
0.75
1.03 1.431.26
Amprenavir
0.75
Maraviroc
0.90
Darunavir
0.73
Nelfinavir
0.98
Tipranavir
0.87
Indinavir
0.90
Lopinavir
0.84
NL: 2.44E6
m/z= 109.0947-109.0957+361.1290-361.1326 F:
FTMS + p ESI Full ms2 445.16@hcd20.00
[60.00-470.00] MS Sys_Suit_3
NL: 3.22E6
m/z= 245.1630-245.1654+418.1768-418.1810 F:
FTMS + p ESI Full ms2 506.23@hcd13.00
[60.00-535.00] MS Sys_Suit_3
NL: 5.79E6
m/z= 280.1582-280.1610+389.2375-389.2413 F:
FTMS + p ESI Full ms2 514.34@hcd17.00
[60.00-540.00] MS Sys_Suit_3
NL: 2.64E6
m/z=
69.0338-69.0344+113.0593-113.0605+
392.1977-392.2017 F: FTMS + p ESI Full ms2
548.24@hcd10.00 [60.00-575.00] MS Sys_Suit_3
NL: 2.07E6
m/z= 330.1140-330.1174+467.2338-467.2384 F:
FTMS + p ESI Full ms2 568.32@hcd25.00
[60.00-600.00] MS Sys_Suit_3
NL: 3.23E5
m/z=
375.2170-375.2208+411.0596-411.0638+
585.1994-585.2052 F: FTMS + p ESI Full ms2
603.21@hcd13.00 [60.00-635.00] MS Sys_Suit_3
NL: 1.65E6
m/z=
421.2330-421.2372+465.2829-465.2875+
513.2825-513.2877 F: FTMS + p ESI Full ms2
614.37@hcd24.00 [60.00-645.00] MS Sys_Suit_3
NL: 2.98E6
m/z= 183.1118-183.1136+447.2617-447.2661 F:
FTMS + p ESI Full ms2 629.37@hcd10.00
[60.00-660.00] MS Sys_Suit_3

27. RT: 0.00 - 1.50 SM: 13G
0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.1 1.2 1.3 1.4 1.5
Time (min)
0
50
100
0
50
100
0
50
100
0
50
100
0
50
100
0
50
100
Saquinavir
1.11
Atazanavir
0.79
Ritonavir
0.83
Rilpivirine
0.89
Abacavir d4
0.30
Lopinavir d8
0.85
1.42
NL: 2.18E6
m/z= 433.1845-433.1889+570.3042-570.3100
F: FTMS + p ESI Full ms2 671.39@hcd26.00
[60.00-705.00] MS Sys_Suit_3
NL: 2.71E6
m/z=
168.0799-168.0815+335.1946-335.1980+
534.3049-534.3103 F: FTMS + p ESI Full ms2
705.40@hcd22.00 [60.00-735.00] MS
Sys_Suit_3
NL: 1.67E6
m/z= 296.1413-296.1443+426.1825-426.1867
F: FTMS + p ESI Full ms2 721.32@hcd11.00
[60.00-755.00] MS Sys_Suit_3
NL: 2.96E3
m/z= 182.0831-182.0849+195.0908-195.0928
F: FTMS + p ESI Full ms2 367.17@hcd57.00
[60.00-390.00] MS Sys_Suit_3
NL: 5.24E6
m/z= 78.0544-78.0552+195.1282-195.1302 F:
FTMS + p ESI Full ms2 291.19@hcd29.00
[60.00-315.00] MS Sys_Suit_3
NL: 6.07E5
m/z= 191.1621-191.1641+447.2616-447.2660
F: FTMS + p ESI Full ms2 637.42@hcd10.00
[60.00-670.00] MS Sys_Suit_3

28. Do We Have a High Throughput Assay?

29. Do We Have a High Throughput Assay?
• Automated sample preparation
– 50-60 min/plate; 0.6-0.7 min/sample
• 1.6 min to first result by LC-MS
– 1.5 min sample to sample
• Approx. 2 hr/plate (130 min for subjects + QC)
• ~ 12 hours/day  6 plates  80 subjects/plate
• 2 instruments = 960 specimens/day
• LOD = 5-10 ng/mL for all assay components

30. Things are not always that easy …

31. Things are not always that easy …
• Some specimens clog wells
– Need dilution or manual extraction
• Processing is a bottleneck
• Must keep 8 channels going
• Column degradation monitoring
• Re-analysis management
• Reagent management

32. Ongoing and Planned Studies
• Programming for automated data review and
compilation
• Ongoing studies in HIV Prevention
– ART as Prevention
– PrEP in IDU and SOA settings
• Additional screening from same extracted
plate
– Hormonal contraceptives
– Substances of abuse

33. WHAT IS CLIA AND WHY DOES IT MATTER?

34. CLIA ‘67
CLIA ‘88

35. CLIA
CMS
FDACDC

36. CLIA
CMS
FDACDC
Clinical Laboratory Oversight
Test CategorizationScientific Consultation

37. Test Complexity
• 7 categories considered for scoring
– Knowledge, training/experience,
reagent/materials preparation, operational steps,
calibration/QC, troubleshooting/maintenance,
interpretation & judgement
• Complexity = waived, moderate, high
• Moderate and high complexity tests require
site inspection
• As complexity increases, regulatory
requirements become more stringent

38. Accepted Accreditation Organizations
• College of American Pathologists (CAP)
• The Joint Commission (JC)
• Commission on Laboratory Accreditation
(COLA)
• American Association of Blood Banks (AABB)
• American Osteopathic Association (AOA)
• American Society for Histocompatibility and
Immunogenetics (ASHI)

39. Acknowledgements
• Johns Hopkins School of
Medicine
– Mark Marzinke, PhD
– Sue Eshleman, MD, PhD
– Craig Hendrix, MD
– Teresa Parsons, PhD
– Matthew Olson, MD
– Athena Petrides, PhD
• Clinical Mass Spec Lab
– Autumn Breaud
– Sabitha Schools
– Veronica Gantert
– Josh Moskowitz
• Funding
– NIH (UM1-AI068613)
– NIAID, NIDA, NIMH under
Cooperative Agreement #
UM1 AI068619
– Thermo Fisher Scientific

40. QUESTIONS??
wclarke@jhmi.edu