A Unique LC-MS Assay for Host Cell Proteins(HCPs) ) in Biologics

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1 A Unique LC-MS Assay for Host Cell Proteins(HCPs) ) in Biologics Catalin Doneanu,, Ph.D. Biopharmaceutical Sciences, Waters September 16, 2009 Mass Spec Waters Corporation

2 Host Cell Proteins (HCPs( HCPs) Recombinant Proteins produced in host cells Proteins from cells can co-purify with therapeutic protein of interest e.g. Chinese Hamster Ovary (CHO) cell 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 pattern and abundances Biopharm International 2008, 13, Number 6, 38-45

3 Guidelines Governing HCPs Safety drives the need for removal/minimization Link between HCPs and immunogenicity European regulations in effect since Validation of the purification procedure -. The ability of the purification process to remove other specific contaminants such as host-cell proteins should also be demonstrated ICH Guidelines: 2009 review in progress (

4 Importance of HCPs: Drug Approval or Failure 2008: a human growth hormone was approved by FDA, after initial denial The cause of immunogenicity was linked to excess host cell protein contamination, which was resolved by the manufacturer with additional purification steps. ( 2006: an interferon biosimilar was rejected by EMEA 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.

5 Challenges of HCP Analysis Thousands of possible protein contaminants HCPs can be present at extremely low levels Typically ppt to ppm (relative to biotherapeutic) Guidelines suggest monitoring to ppm (1-100ppm) Developing methods is expensive and time consuming

6 Comparison of Current HCP Methods Narrow dynamic range (<100) Biopharm International 2008, 13, Number 6, 38-45

7 Requirements for HCP Identification and Quantification Assay Ability to detect protein impurities down to 0.001% (5 orders of magnitude) A non-targeted, unbiased approach for HCP identification and monitoring Fast, high-throughput measurements

8 HCP Analysis Workflow Workflow Overview: Enzymatic digestion of sample into peptides 2D-LC/MS E with IDENTITY E to DISCOVER contaminant proteins 2D-LC allows more sample loading Develop specific host cell protein databases (Top3 peptides for absolute quantitation, label-free *) Data mined for MRMs using VERIFY E Transfer to Tandem Quad for targeted quantitation (e.g. using isotopically labeled peptides) * Silva et al. Moll Cell Proteomics, 2006, 5,

9 MS E Acquisition : Alternating Low/High Energy Scans MS Precursor MS E Fragments Retention Time

10 Comprehensive Peptide Ion Accounting: IDENTITY E Geromanos et al. Proteomics 2009, 9,

11 2D-LC Separation using High/Low ph Reversed Phases 100 ph 10 ph mm ammonium formate 0-42% acetonitrile in 15 min TIC 4.37e8 % 0-56% 1 B in 70 minutes 20 mm NH4OH ph 10 Bovine_Hemoglobin_Digest_Stored_091803_ : Scan Time ES TIC neutral acidic 4.51e9 % ph basic acidic basic ph % Formic acid 0-42% acetonitrile in 90 min Gilar M. et. al, J. Sep. Sci. 2005, 28,

12 Fluidic Configuration for 2D- Chromatography and Online Dilution: Sample Loading Injection Valve 0.1% TFA, ph = 2.1 ASM 100 µl/min 1.0 x 50 mm TEE HTM Valve 5 µm XBridge TRAP 0.5 x 20 mm 0.3 x 150 mm 1.7 µm BEH MS BSM1 10 µl/min WASTE A: 20 mm Amm Formate, ph = 10.0 BSM2 4 µl/min B: ACN A: 0.1% FA, ph = 2.4 B: 0.1% FA in ACN

13 Fluidic Configuration for 2Dchromatography and Online Dilution: Peptide Elution Injection Valve 0.1% TFA, ph = 2.1 ASM 100 µl/min 1.0 x 50 mm TEE HTM Valve BSM1 5 µm XBridge 10 µl/min WASTE TRAP 0.5 x 20 mm 0.3 x 150 mm 1.7 µm BEH MS A: 20 mm Amm Formate, ph = 10.0 B: ACN BSM2 4 µl/min A: 0.1% FA, ph = 2.4 B: 0.1% FA in ACN

14 Chromatographic Performance A Same Chromatographic Performance B All separations were performed using a 30 min gradient (3-40% ACN, 0.1% FA) C A direct injection of 1 picomole of ENL digest on a 300 µm x 150 mm BEH column B simulated 1D run using a single elution step (50% Eluent B) 1 picomole ENL digest C Fraction 3 of the 2D-LC run 60 fmoles ENL digest on column

15 Reproducibility of 2D Chromatography 24 h later 48 h later Mass chromatograms of T43 peptide from ENL digest; 60 fmoles of digest were loaded in each 2 D-LC experiment. This peptide (VNQIGTLSESIK) eluted only in Fraction 3.

16 1D Chromatography No Fractionation,60 μg g Sample Loaded

17 2D Chromatograms 5 Fractions, 60 μg g Sample Loaded 10.8 % ACN 14.0 % ACN 16.7 % ACN 20.4 % ACN 50 % ACN

18 MIX-5 5 proteins spiked in a mab Protein Name Species Accession No. MW (kda) Protein Conc. in Sample mab Humanized n/a ,000 n/a Dynamic Range (DR) (fmol/ul) (ppm) (Ratio) [log (DR)] LA Bovine P ,000 3, ADH Yeast P , PHO Rabbit P , BSA Bovine P , ENL Yeast P ,

19 Controlling False Positive Identifications Random peptide sequences added as Decoy strategy to ensure that identified peptides are real 13,600 entries from Swissprot (mouse and hamster proteins) 6 protein sequences from LA, ADH, PHO, BSA, ENL, porcine trypsin, 2 sequences from heavy and light chain sequences of MAB Equal number of random sequences (13,608) Total number of protein sequences: 27,216 False Positive Rate of Protein Return: 5% (user adjustable) Concentration range 10 to 100 ppm Lower confidence hits (nearing random) not reported

20 HCP s can be identified over 5 orders of magnitude in concentration ENL was detected in all three 2D-LC/MSE replicates when present at a concentration of 40 ppm.

21 MS Spectrum of T43 ENL peptide in the mab digest T43

22 HCP s Identified in the mab Biosimilar (A) direct injection of 1 pmole of ENL digest on a 300 µm x 150 mm BEH column Simultaneous protein identification and quantitation

23 Reproducibility of the MRM assay RSD = 8 % Reproducible Chromatography TGNPTVEVELTTEK LC Conditions: Column: 2.1 x 150 mm BEH130 C18, 1.7 µm particles Flow rate: 300 µl/min Gradient: 3% to 40% ACN in 10 min Sample: 200 fmoles ENL digest on column

24 Example of MRM Interference Two MRM transitions from the same peptide

25 Summary on the Advantages of the HCP Assay Confident Identification of individual HCPs Quantitation of each identified HCP o Label-free in the discovery stage o Using isotopically labeled peptides (Tandem Quadrupole) Much faster development time than immunoassays Provide a multi-purpose platform for many other tasks Sensitivity comparable to ELISA assays Applicable to subunit (recombinant) vaccines

26 Conclusions and Future Directions The 2D-LC/MS E setup is able to identify low abundance protein contaminants present in biopharmaceuticals over 5 orders of magnitude A high-throughput MRM assay on a tandem quadrupole can quantify these protein impurities (absolute quantification can be done using isotopically labeled peptides) The combination of 2D-LC/MS E and tandem quadrupole MS provides a total system solution for HCP analyses

27 Acknowledgments Keith Fadgen Martha Stapels Weibin Chen St John Skilton Jim Kehoe Scott Berger Jeff Mazzeo

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