The Identification and Quantification of Residual Host Cell Proteins (HCPs) Steve Taylor ©2009 Waters Corporation | COMPANY CONFIDENTIAL Overview In purified product there is a high concentration of ‘product’ ‘p od ct’ proteins low concentration of ‘host’ proteins Waters can Identify and Quantify these with UPLC-MSE ©2009 Waters Corporation | COMPANY CONFIDENTIAL 2 HCP Background to HCPs and the Guidelines of the EU Regulatory Authority ©2009 Waters Corporation | COMPANY CONFIDENTIAL Host Cell Proteins ( (HCPs) ) Recombinant Proteins produced in host cells Proteins from cells can co-purify with therapeutic protein of interest —e.g. Chinese Chi Hamster H t Ovary O (CHO) cell ll proteins in recombinant monoclonal antibody therapeutics Purification steps should remove contaminants. Low levels can remain because of —Poor process control Process changes: can affect HCP —Process pattern and abundances Biopharm International, Volume 13, Number 6, pp. 38-45, May 2008 ©2009 Waters Corporation | COMPANY CONFIDENTIAL 4 Guidelines Governing g HCPs Safety drives the need for removal/minimization —Link Link between HCPs and immunogenicity European regulations in effect since 2007 —‘6 6.2 2 Validation of the purification procedure - …. The ability of the purification process to remove other specific p p contaminants such as host-cell proteins … should also be demonstrated’ —ICH Guidelines: 2009 review in progress (http://www.emea.europa.eu/pdfs/human/bwp/BWPworkprogramme.pdf) ©2009 Waters Corporation | COMPANY CONFIDENTIAL 5 Importance p of HCPs – approval pp 2008: approval of follow-on biologic/ biosimilar (EU; USA) Diagramatic representation of amino acid sequence of human growth hormone — Initially the application was turned down due to a potential immunogenetic effect due to HCPs — Issue was resolved before drug release – positive opinion given — ‘The cause of immunogenicity was linked to excess host cell protein contamination, which was resolved by the manufacturer f t with ith additional dditi l purification steps’. (http://www.pubmedcentral.nih.gov/articlerender.fcgi? artid=2638545) artid 2638545) Image source: http://www.rxlist.com/omnitrope-drug.htm ©2009 Waters Corporation | COMPANY CONFIDENTIAL 6 Importance p of HCPs – failure HCPs and approval problems for some Biosimilars: — Application pp cat o by biosimilar b os a company co pa y for o Interferon te e o Alfa a 2a a (HepC) ( epC) — Marketing permission rejected 2006: — “The reasons for the rejection by the EMEA included quality and clinical differences between [the biosimilar product] and the reference product, … inadequate validation of the process for the finished process and insufficient validation of immunogenicity testing.” testing ” Liver Damage from Hepatitis Image Source : Copyright © 1996, 1997 University of Pittsburgh http://tpis.upmc.edu/tpis/HB/H00030m.html ©2009 Waters Corporation | COMPANY CONFIDENTIAL 7 Challenges g of HCP Analysis y Thousands of possible protein contaminants HCPs can be present at extremely low levels o Typically ppt to ppm (relative to biotherapeutic) o Guidelines suggest monitoring to ppm (1-100ppm) Developing methods is expensive and time consuming Business Impacts of Failure to identify and remove contaminants: o Can reduce drug efficacy o May lead to adverse events o Drug development and introduction delays o Longer cycle to introduce process improvements o Perceived product quality issue = competitive disadvantage o Kill a promising candidate ©2009 Waters Corporation | COMPANY CONFIDENTIAL 8 Main Goals of Waters Host Cell Protein Analysis y Develop a method — To identify, — Quantify and — Monitor HCPs from recombinant means Results must have a means of validating the results (e.g. peptide sequence; concentration confirmation) Needs to be complementary/ compatible with existing methods Needs to provide improvements compared to existing methods (generality; efficiency; speed) Needs to provide cost-effective benefits for process improvements for Waters customers ©2009 Waters Corporation | COMPANY CONFIDENTIAL 9 HCP Current Methods for Host Cell Protein Analysis ©2009 Waters Corporation | COMPANY CONFIDENTIAL Comparison p of current HCP Methods Narrow dynamic range (<100) Biopharm International, Volume 13, Number 6, pp. 38-45, May 2008 ©2009 Waters Corporation | COMPANY CONFIDENTIAL 11 EFFICIENCY Simultaneous i.d. and Quan of proteins Efficient assay and use of resources SPEED Significantly shorter development time for assay Ability to provide high throughput/ flexible monitoring assay Why h UPLC/MS C/ SE off HCPs? C ? ACCURACY Accurate quan of HCPs in complex mixture Quan over > 4 orders of magnitude ©2009 Waters Corporation | COMPANY CONFIDENTIAL GENERALLY APPLICABLE HCPs do not need to be known prior to analysis Can be widely applied and easily modified Attributes Needed for Analysis of HCPs – User Expertise p User Expertise Needed for Routine Use LC/MS Tof High LC/UV Low ELISA: Very Low Gel and Blot: Low LC/MS Quad Reasonably Low ©2009 Waters Corporation | COMPANY CONFIDENTIAL 13 Attributes Needed for Analysis of HCPs - Quantitation Q Ability to Quantify over wide dynamic range ELISA: Poor LC/UV 2 - 3 orders Good LC/MS 4 orders Good Gel and Bl t Blot: Poor ©2009 Waters Corporation | COMPANY CONFIDENTIAL 14 Attributes Needed for Analysis of HCPs - Sensitivity y Ability to Detect at very low levels LC/UV: Acceptable (high ppm) LC/MS Good (ppm) ELISA: Excellent (ppt) Gel and Blot: Variable ©2009 Waters Corporation | COMPANY CONFIDENTIAL 15 Attributes Needed for Analysis of HCPs - Interpretation p User Interpretation required for Analysis LC/UV Objective by RT ELISA: Subjective LC/MS Highly Objective Gel and Blot: Subjective ©2009 Waters Corporation | COMPANY CONFIDENTIAL 16 Attributes Needed for Analysis of HCPs - Certainty y Unambiguous Identification of HCPs LC/UV: High with SOP ELISA: Low LC/MS Extremely High Gel and Blot: Acceptable ©2009 Waters Corporation | COMPANY CONFIDENTIAL 17 Attributes Needed for Analysis of HCPs - Certainty y Method Flexibility LC/UV: Flexible ELISA: Very Inflexible LC/MS Extremely Flexible Gel and Blot: Flexible ©2009 Waters Corporation | COMPANY CONFIDENTIAL 18 HCP Summary of Waters Host Cell Protein Methodology ©2009 Waters Corporation | COMPANY CONFIDENTIAL Comparison p to Proteomics Similarity to proteomics applications - Similar tools can be used with minor changes - Complex Samples by tryptic digest g and rules for identifying y g - Same data mining - Databases used - MSE acquisition Differences: - Greater need for dynamic range (>4) - Need d to cope with h high h h product d concentration and da small amount of HCP (ppm) - Not normally sample limited - Databases can be tailored because Host is known ©2009 Waters Corporation | COMPANY CONFIDENTIAL 20 Tools Available for HCP Analysis y Informatics PLGS and IdentityE: validated protein identification reducing d i ffalse-positive l iti space. BiopharmaLynx 1.2 for automated sequence coverage and confirmation of primary structure of biomolecules (intact mass; peptide mapping) VerifyE for the determination of the most appropriate peptides for quantification (by MRM) Instrumentation NanoUPLC with 2D RP-RP – more reproducible chromatography (greater sensitivity) Synapt/ XevoQtof – accurate mass MSMS TQD/ Xevo TQ – high dynamic range quantitation Chemistry Rapigest: aids tryptic digestion PST/ BEH: Peptide Separation Columns HILIC (‚normal phase‘); Glycan columns ©2009 Waters Corporation | COMPANY CONFIDENTIAL 21 General Methodologies g IdentityE to discover proteins - Peptide sequences matched (dB) - Confidence ranking of identification BiopharmaLynx to - Compare samples vs control - Monitor/ M it / quan modifications difi ti - ExpressionE to quantify proteins - Measure of amount - Established E t bli h d protocol t l - Generally applicable - (e.g. glycoforms) Confirm peptide sequence with MSE VerifyE for ‘signature’ signature peptides - Relevant Peptides obtained for MRMs - Output of MRM method for Tandem Quad ©2009 Waters Corporation | COMPANY CONFIDENTIAL 22 HCP The Application of 2D nanoAcquity Chromatography ©2009 Waters Corporation | COMPANY CONFIDENTIAL Optimisation p of 2D Chromatography g p y FIRST DIMENSION: 1 mm x 0.5 cm X X-Bridge Bridge packed with BEH130, 5 µm; 10 µL/min at pH 10 to elute all peptides. — HIGH RESISTANCE to extreme pH Trap column col mn fo for this research esea ch project p oject 500 µm mx 2 cm packed with Symmetry C18, 5 µm — High loading capacity SECOND DIMENSION: 300 µm x 15 cm with BEH130 BEH130, 1.7 1 7 µm; 4 µL/min Standard ESI probe with narrow bore capillary ©2009 Waters Corporation | COMPANY CONFIDENTIAL 24 MSE Alternating High/Low Energy gy Acquisition q MS Precursor MSE Fragments Retention Time ©2009 Waters Corporation | COMPANY CONFIDENTIAL 25 Yeast Enolase MS TIME MSE ©2009 Waters Corporation | COMPANY CONFIDENTIAL 26 15 Seconds Chromatographic Window Product Mass Prec cursor Mass Time-Aligned TimePrecursor/Product / Ion list retention time MH+ Ret.Time Volume ChargeStat e 1189.5802 46.71 78430 1.98 765.3742 46.67 449 1 522.2606 46.67 554 1 800.4481 46.67 3754 1 963.5187 46.69 3658 1 515.3250 46.70 2325 1 687.3742 46.70 2351 1 1100.5773 46.71 1112 1 822.4154 46.71 436 1 781.4823 46.71 163 1 896 5183 896.5183 46 72 46.72 675 1 685.3210 46.72 862 1 1009.6112 46.74 125 1 498.3296 46.75 709 1 432.2357 46.75 356 1 906.5477 46.76 364 1 Precursor/Product Ion List ©2009 Waters Corporation | COMPANY CONFIDENTIAL 27 Waters IdentityE High Definition Proteomics System y ‘C il ‘Capilary’ ’ scale l Chromatography Ch t h nanoAcquity UPLC system Mass Spectrometry SynaptTM HDMSTM with 2D Technology Informatics IdentityE Software ProteinLynx Global Server ©2009 Waters Corporation | COMPANY CONFIDENTIAL 28 Comprehensive Peptide Ion Accounting g 1 2 3 4 5 ©2009 Waters Corporation | COMPANY CONFIDENTIAL 29 HCP Methodology h d l ffor Host Cell ll Protein i Monitoring by Tandem Quadrupole Once HCPs have been established a high high-throughput throughput method can be developed for process monitoring. ©2009 Waters Corporation | COMPANY CONFIDENTIAL VerifyE y flow diagram g 2 3 .8 0 4 1 8 .7 100 2 2 .4 5 4 5 8 .7 Discovery phase LC-MSE data Acquisition as above 3 3 .1 3 4 8 4 .7 2 7 .3 7 4 2 2 .2 2 6 .9 9 5 4 0 .2 2 4 .9 3 4 5 9 .7 VerifyE data processing (N) proteotypic pep (X) trans per peptide 2 9 .1 2 2 9 .9 3 6 2 6 .3 4 0 7 .7 3 0 .7 3 5 8 2 .3 1 9 .4 0 4 0 6 .2 % 3 3 .2 4 7 2 4 .3 2 4 .5 4 4 6 1 .7 2 0 .8 7 4 1 1 .7 1 8 .7 4 5 5 1 .2 2 6 .7 7 4 1 6 .7 2 6 .2 6 4 3 5 .2 2 1 .6 0 7 2 2 .2 2 6 .1 6 5 3 1 .7 2 2 .8 6 4 4 7 .2 2 5 .8 9 5 5 9 .2 3 1 .3 5 5 2 7 .2 2 8 .2 2 4 0 7 .7 2 8 .2 9 5 3 6 .7 3 1 .9 0 7 2 1 .8 3 3 .4 4 5 9 8 .3 1 6 .9 3 4 8 8 .5 1 7 .4 7 5 7 5 .2 2 0 .2 2 3 7 3 .2 3 2 .2 8 6 6 9 .7 3 0 .3 5 6 2 5 .3 1 7 .9 6 4 1 9 .9 3 5 .8 4 7 9 0 .9 3 3 .7 6 7 4 0 .3 3 6 .9 90 7 0 0 .3 3 5 .7 0 7 8 9 .8 3 9 .1 1 4 9 9 .2 4 1 .7 9 7 8 2 .3 0 T im e 1 6 .0 0 1 8 .0 0 2 0 .0 0 2 2 .0 0 2 4 .0 0 2 6 .0 0 2 8 .0 0 3 0 .0 0 3 2 .0 0 3 4 .0 0 3 6 .0 0 3 8 .0 0 4 0 .0 0 4 2 .0 0 Automatically generated Xevo TQ MRM exp file Verification- MRM transition monitoring ©2009 Waters Corporation | COMPANY CONFIDENTIAL 31 MRM development for Targeted Monitoring g Use MSE data to develop MRM assay Use in high-throughput monitoring and absolute quantification of HCPs Xevo TQMSTM MS1 Static Xevo TQ with selected MRMs Collision Cell MS2 Static ©2009 Waters Corporation | COMPANY CONFIDENTIAL 32 Applying Proteomics Workflows to HCP Analysis y Workflow Overview: —Shotgun enzymatic digestion of sample into peptides —1D 1D or 2D LC/MSE with IdentityE to DISCOVER contaminant proteins —2D 2D for more loading capacity —Develop proprietary host cell protein database —(Hi3 (Hi3 for absolute quantitation, label label-free) free) —Data mined for MRMs Quad for absolute —Transfer to Tandem Q quantitation (e.g. labeled peptides) ©2009 Waters Corporation | COMPANY CONFIDENTIAL 33 2D Chromatography g p y Factors 2D Chromatography requires optimisation because: Column loading is non non-linear linear (more loading —Column does not equate to more dynamic range) —Product is present in much higher concentrations - 2D app approach oa h means low-level lo le el imp impurities ities Gilar M. et. al, J. Sep. Sci. 2005, quantifiable despite disparity in 28, 1694-1703 concentrations Chemistries specifically selected for RP/RP 2D approach: —Retention Retention time models applied (based on hydrophobicity scale of tryptic peptides) —All Chemistries readily available (but dimensions adapted) ©2009 Waters Corporation | COMPANY CONFIDENTIAL 34 Host Cell Protein Analysis of Biopharmaceutical p Product 1D Chromatography (75 um scale) —0 0.05 05 ug of o product p oduct digest d gest loaded oaded for o peptide pept de mapping app g — 90 min gradient (5-40% acetonitrile) 2D RP-RP (High/Low pH) Chromatography Gilar M. et. al, J. Sep. Sci. 2005, 28, 1694-1703 — 5 ug (80 pmol) l) off product d t digest di t (over)loaded ( )l d d + 100 fmol f l ADH + 1 fmol BSA — 1st Dimension (pH 10): 5 or 10 step gradient (0 - 45% acetonitrile) — 2nd Dimension (pH 2.6): 90 min gradient (5 - 40% acetonitrile) UPLC: nanoACQUITY® 2D UPLC® QTof: SYNAPT MS (MSE mode) D t Data: PLGS 2 2.4 4 (Identity (Id tit E) ©2009 Waters Corporation | COMPANY CONFIDENTIAL 35 Diagram g of 2D setup p at higher g scale Online dilution of 1D flow to Trap column – change pH a p and d therefore t e e o e selectivity se ect ty 1D pH=10. flow 10 µL/min. XBridge high resistance to pH regime. Mobile phase 20 mM ammonium formate in water (Solvent A) and ACN (Solvent B). Five Fractions (to 50.0% B). 2D pH=2.4. 0.3 mm x 150 mm BEH C18 1.7 µm, Flow at 4 µL/min. 90 min gradient from 3 to 40% acetonitrile t it il (0 (0.1% 1% FA-formic FA f i acid). id) Trap: 5-µm Symmetry C18 trap peptides washed on to 2D column. ©2009 Waters Corporation | COMPANY CONFIDENTIAL 36 2D HPLC using High/Low pH RPLC pH 10.0 20 mM ammonium formate 0-42% 0 42% acetonitrile in 5 or 10 steps of 15 min TIC 4.37e8 100 pH 10 18 95 18.95 41.26 25.68 % 35.85 14.03 13.21 10.38 5.70 6.77 4.10 5.21 16.41 11.73 9.64 37.65 29.41 15.79 8.53 25.92 22.39 18.58 18 21 18.21 41.92 29.00 39.58 35.48 21.04 19.89 24.20 0-56% 1 B in 70 minutes 20 mM NH4OH pH 10 2.50 5.00 7.50 10.00 Bovine_Hemoglobin_Digest_Stored_091803_1 12.50 15.00 17.50 neutral 100 20.00 22.50 25.00 acidic 30.00 32.50 35.00 37.50 28.55 acidic basic pH 2.6 27.50 40.00 Time 42.50 1: Scan 45.00ES+ TIC 4.51e9 basic 18 75 18.75 23.86 27.00 26.68 % 17.36 26.51 8.91 16.30 10.99 22.79 13.24 4.70 31.41 pH 2.6 0.2% Formic acid 0-42% acetonitrile in 90 min 22.39 11.40 4.29 35.05 30.68 6.29 11.93 19.61 19.93 14.09 26.06 34.27 36.19 1 Gilar M. et. al, J. Sep. Sci. 2005, 28, 1694-1703 ©2009 Waters Corporation | COMPANY CONFIDENTIAL 37 2D Chromatograms 10 Fractions,, 5 μg Loaded One peptide may appear in multiple Ch Chromatographic hi steps - ‘merge’ step to create coherent fractions 45% ACN 23.6% ACN 20 8% ACN 20.8% 18.9% ACN 17.4% ACN 15.9% ACN 14.5% ACN 13.0% ACN 11.7% ACN 8.2% ACN ©2009 Waters Corporation | COMPANY CONFIDENTIAL 38 HCP Example Results from Biosimilar of Trastuzumab ©2009 Waters Corporation | COMPANY CONFIDENTIAL HCPs from Biosimilar of Trastuzumab (Non ( European p Production) ) Methodology for Greater Confidence: R Random d peptide id sequences added dd d as Decoy D strategy to ensure identified peptides real = Total 27,216 entries in database created — 13,600 entries from Swissprot for Golden Hamster and Mouse (homologs) — 6 protein sequences from spiked in proteins: LA, ADH, PHO, BSA, ENL, porcine trypsin, — 2 sequences from TrastuzumAb (heavy and light chains) q number of random sequences q as known entries ((13,608)) — Equal False Positive Rate of Protein Return: 5% (user adjustable) Concentration range found here was 10 to 50 ppm relative to therapeutic Lower confidence hits (nearing random) not reported ©2009 Waters Corporation | COMPANY CONFIDENTIAL 40 HCPs from Biosimilar of Trastuzumab (Non ( European p Production) ) Host cell: Chinese Hamster Ovary (CHO) Database with combination of all the mouse and hamster protein sequences listed in the SwissProt database (http://www.expasy.ch/sprot/) —Chinese Hamster database held privately so homology database used (Golden hamster; M Mouse) ) ©2009 Waters Corporation | COMPANY CONFIDENTIAL 41 HCPs from Biosimilar of Trastuzumab – confident assignments, g , 1010-50ppm pp range g ©2009 Waters Corporation | COMPANY CONFIDENTIAL 42 PLGS Project j view of proteins p id’d Listing of Proteins — Accession details — Names and sequences generated — Confidence ranking Spectral overview (can be zoomed) Sequence information for identified protein ©2009 Waters Corporation | COMPANY CONFIDENTIAL 43 Comprehensive p Info from PLGS Sequence Information available even on low level proteins ©2009 Waters Corporation | COMPANY CONFIDENTIAL 44 VERIFYE …Data WorkWork-Flow IDENTITYE (Discovery Data) Input .csv/.txt Proteotypic Peptide Filters Efficient Transition Filters Retention Time Optimization Scouting Run UPLC/MRM UPLC/MRM (& TargetLynx) Method File Creation Targeted (MRM) Quanpedia dB Targeted (DDA) .exp File OPTIMISED TARGET PROTEIN ANALYSIS UPLC/MRM ©2009 Waters Corporation | COMPANY CONFIDENTIAL 45 VERIFYE …Proteotypic Peptide Review …Generation of MRM Methods ©2009 Waters Corporation | COMPANY CONFIDENTIAL 46 Verify yE to find appropriate pp p p peptides p ©2009 Waters Corporation | COMPANY CONFIDENTIAL 47 Reproducibility of the MRM assay: MIX-5 p protein digest g RSD = 3% 1 picomole BSA digest on column Reproducible Chromatography Reproducible R d ibl RT RTs ©2009 Waters Corporation | COMPANY CONFIDENTIAL 48 Reproducibility of MRM assay: MIX-5 proteins spiked p in Trastuzumab and digested g RSD = 3% 1 picomole BSA digest on column Reproducible R d ibl Ch Chromatography t h Reproducible RTs ©2009 Waters Corporation | COMPANY CONFIDENTIAL 49 Reproducibility of the MRM assay: MIX-5 protein digest RSD = 8% 200 fmoles ENL digest on column Reproducible Chromatography Reproducible RTs ©2009 Waters Corporation | COMPANY CONFIDENTIAL Reproducibility of MRM assay: MIX-5 proteins spiked in Trastuzumab and digested g RSD = 13% 200 fmoles ENL digest on column Reproducible Chromatography Reproducible R d ibl RT RTs ©2009 Waters Corporation | COMPANY CONFIDENTIAL 51 Summary of Workflow advantages for HCP Analysis y Workflow Models: — UPLC-MSE is well-established — Proteomics tools already exist and are developing (e.g. HDMSE) Applications Benefits: — Confident Identification of individual HCPs – with ranking of confidence — Quantitation of each identified HCP o Label-free Label free with discovery stage (Synapt/ XevoQT) o Using isotopically labelled peptides (XevoTQ/ TQD) — Much faster development time than immunoassay — Provide a multi-purpose platform for many other tasks — Sensitivity levels comparable to ELISA (low ppm) — Also applicable to subunit (recombinant) Vaccines ©2009 Waters Corporation | COMPANY CONFIDENTIAL 52 Conclusions The 2D-LC/MSE setup is able to identify low abundance protein contaminants p p present in biopharmaceuticals p over more than 4 order of magnitude The 2D-LC 2D LC setup using the second chromatographic dimension provides the sensitivity and robustness required for HCP analysis A high-throughput MRM assay on the Xevo TQ MS can quantify q y these protein p impurities p (absolute ( quantification q can be done using isotopically labeled peptides) The combination of 2D-LC/MS 2D LC/MSE and Xevo TQ MS provides a total system solution for HCP analysis ©2009 Waters Corporation | COMPANY CONFIDENTIAL 53 Acknowledgments g Waters Biopharmaceutical Development: Catalin Doneanu Hongwei Xie Keith Fadgen Martha Stapels Jim Kehoe Weibin Chen Scott Berger ©2009 Waters Corporation | COMPANY CONFIDENTIAL 54