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Fall 2012 • Volume 11 / Issue 3 • ISSN 1538-8786

BioProcessing
J O U R N A L
Trends & Developments in BioProcess Technology

A Production of BioProcess
Winter 2010/2011 BioProcessing Journal • 3 Technology Network
• www.bioprocessingjournal.com
TRENDS & DEVELOPMENTS IN BIOPROCESS TECHNOLOGY

Cell-Based Potency Assays:


Expectations and Realities
By ROBERT D. SCHROCK

activity based on the attribute of the product that is

A
mong the battery of assays linked to the relevant biological properties...”
needed to release viral-based A potency assay should be designed to:
gene therapy biologics products, • Measure a relevant biological activity of the product
the potency assay is typically the • Measure a property specific to the product
most customized and unique • Be quantitative
of all the tests found on a Certificate of Analysis • Include use of a reference standard (RS) for
(COA). Where many safety, purity, and to some comparison
extent, identity assays can be applied with little Potency assays should be intended for use in lot release, to
to no custom modifications, the potency assay demonstrate lot-to-lot consistency, and indicate stability.
should be directly related to the biological activity Finally, the assay should be robust enough that it can be
validated.
of the construct. This aspect of the potency assay
The demonstration of potency can range from animal
requires that development, characterization, and
models to cell-based assay systems that incorporate direct
validation efforts be started early in the lifecycle
measurement of a biological activity. In vivo animal
of the product, and adequate resources should models that measure, for example, weight gain/loss or
be allocated to this end. This article will cover a antibody titer, can be a direct measure of biological
brief overview of available regulatory guidances, activity in a dose-dependent response. However, this
discuss hallmarks of a good cell-based potency type of assay is very difficult to validate. Ex vivo assays
assay, and provide a case study of an assay that was utilize cultures of primary cells from a specific tissue
developed for a Phase 3 gene therapy product. upon which the product has activity. Examples of this
approach are signaling pathways and activities of growth
factors or hormones. Due to a lack of a consistent and
Introduction well-characterized cell bank, these assays can have
Potency is typically thought of as “the capacity of a considerable variability. In vitro cell-based assays include
product to produce an expected biological activity.” In well-characterized cell banks and often incorporate
more formal language, the International Conference biochemical methods such as protein kinase activation,
on Harmonization (ICH) (section Q6B, Guidance for transgene expression, or reporter gene expression. Based
Industry: Specifications: Test Procedures and Acceptance on considerations of variability, reproducibility, and cost,
Criteria for Biotechnological/Biological Products)[1] defines the goal should be to develop a cell-based potency assay
potency as “…the quantitative measure of biological with a measurable, quantitative endpoint.

ABOUT THE AUTHOR


Robert D. Schrock, PhD (robert.schrock@lonza.com), Head of Quality Control
Lonza Viral-Based Therapeutics, 8066 El Rio St., Houston, Texas USA | Phone: 713-568-6190
Website: www.lonza.com/custom-manufacturing/biological-manufacturing/viral-based-therapeutics.aspx
This article is based on Dr. Schrock’s presentation at the ISBioTech 2nd Annual Meeting held in Rosslyn, Virginia, April 2-4, 2012.

Fall 2012 BioProcessing Journal • 4 • www.bioprocessingjournal.com


The primary regulatory guidances are listed in this point, the assay method should be pretty well locked
Table 1. The United States Pharmacopeial Convention down, although refinements that improve efficiency,
(USP) <111>[2] is applicable primarily toward the use repeatability, and robustness can be implemented. It
of in vivo potency assays — typically animal models or is important that no fundamental changes to the assay
microbiological assays. Recent publications, USP <1032>[3], are made at this point unless the intent is to perform
<1033>[4], and <1034>[5] have much more information comparison studies to demonstrate clear advantages in
applicable to cell-based potency assays. These guidances the method. By the time the product enters Phase 2 trials,
expand on expected attributes of potency assays and specifications should be set. The specification range can
describe various types of assays and parameters that are be wide, perhaps stating a minimum value, with the
to be included during validation. intention of narrowing this range based on data from
multiple production lots (Table 2).
Lifecycle of Potency Assay Development
Development of the potency assay should be initiated In Vitro Cell-Based Potency Assay Approaches
early in the product lifecycle, during pre-clinical stages. As mentioned earlier, the overarching premise behind
Potency assays are typically the most challenging to cell-based potency assays is to demonstrate that a product
implement as the molecular mechanisms of therapy need has the expected biological activity. This is typically
to be understood to some extent. The basic requirements customized based on the product. For example, infection
of the assay should be demonstrated: (a) quantitative; of a tumor cell line with an adenoviral product that
(b) specific to the product; and (c) stability-indicating. delivers an important tumor suppressor gene would
By Phase 1 stage, important parameters (i.e., temperatures, cause growth inhibition and cell death. When compared
range, incubation limits, curve fit reliability) should be to an “ad-empty” vector that does not contain the tumor
defined (as part of the general qualification assay). It suppressor, the therapeutic vector concentration that
may be acceptable for the assay specification to be “report inhibits cell growth (IC50) for this cell line is much lower
results” at this stage until enough data points are collected than for the control vector.[10] Another example is an
to determine an acceptable range. Once these parameters enzyme delivered by a recombinant virus that activates
are known, pre-validation (planning of validation an inert pro-drug given in trans. The activated drug then
strategy) activities should be underway by the time the inhibits growth in a specific cell line.[11] In all cases, the
product is in Phase 2 trials. Full validation work should activity measured is calculated and statistical analysis can
be underway by late Phase 2 and early Phase 3 stages. At be applied to the data. It is advantageous to identify a

TABLE 1. Regulatory publications.

TABLE 2. Lifecycle of potency assay development and validation.

Fall 2012 BioProcessing Journal • 5 • www.bioprocessingjournal.com


RS (in these examples, a well-characterized virus lot) to of performance over time after thaw will help reduce
be used to show assay comparability, determine system variability, so a maximum number of passages after thaw
suitability parameters, and to follow assay trending. should be established, typically as part of the validation.

Matrix Approach Assay Design: Mitigating Variability


A suite of assays can be used to demonstrate a cascade Variability is one of the biggest challenges one faces in
of activities that are essential for biological activity. establishing a potency assay and in cell-based assays in
This approach is illustrated by using the case study of general. Variability is inherent in cell-based assays. A high
a gene therapy vector that provides a functional tumor number of replicates per data point help mitigate variability;
suppressor gene that, when expressed in susceptible cells, therefore 96-well plate formats are often used. Well-to-
induces apoptosis. Four separate assays measure the steps well variability should be explored during development,
to true biological activity: (1) the virus particle (VP) including positional variability, such as edge effects. Other
concentration is measured by absorbance at 260 nm parameters that affect variability are cell health, confluency,
although this is more a measure of strength; (2) the passage number, and incubator conditions (including
infectious titer measures the ability of the virus to infect temperature gradients).[12, 13] In our experience, cell health
cells; (3) the Western blot or (preferably) ELISA assay is the largest single contributor to variability and risk of
measures expression of transgene-encoding protein; and invalid assays. Therefore, analysts should be well-trained
(4) the IC50 assay most directly measures the biological to assess cell health by appearance, and be enabled to abort
activity on susceptible cells. Taken together, this series of the assay if obvious cell stress is observed at early stages.
assays is a powerful measure of the potency of the lot.[8] It is advisable, that standard operating procedures (SOPs)
The matrix approach is shown schematically in Figure 1. include specific instructions on how to carry and maintain
cell lines. In addition, the assay protocol should have a
Cell Line Attributes good balance of data points, replicates, and range without
Any cell line used in a quality control (QC) assay increasing the number of plates used past the point where
needs to be well-characterized and tested.[8] Cell line the assay is too onerous to perform.
origin and history should be well-documented. Sterility,
Mycoplasma, percent viability, growth characteristics, Case Study: Potency Assay
and some performance information from the potency for a Gene Therapy Adenovirus
assay should be documented. A tiered cell bank system The remainder of this article will describe our experience
(master and working cell bank) should be used to ensure in developing and validating a bioactivity assay to assess
consistency in assays over time.[3] In addition, knowledge the potency of a gene therapy recombinant adenovirus.

FIGURE 1. Matrix approach to demonstrating potency.

Fall 2012 BioProcessing Journal • 6 • www.bioprocessingjournal.com


This project was undertaken well before any detailed were included to accumulate data for future revisions of
guidances were available for cell-based potency assays, the assay. Further assay development was carried out to
though it is a good general example of the development ensure the quantifiable nature of the assay. This included
and validation process for assay development. This adding additional data points to generate a more accurate
replication-deficient adenovirus was engineered to and precise curve fit and to verify that the four-parameter
express a tumor suppressor gene that is either deficient sigmoidal curve fit model was appropriate. During the
or mutated in many cancer cells. Upon infection, the pre-validation phase in developing this assay, various
expressed tumor suppressor induced apoptosis in parameters were examined as sources of variability.
susceptible cells. By adding increasing amounts of VP/cell Results are shown in Table 3.
(multiplicity of infection [MOI]), growth inhibition could Overall, the two major factors contributing to
be quantified and an IC50 calculated (expressed in VP/ variability were cell health (minimizing cell stress) and
cell). A schematic of the assay setup is in Figure 2. analyst training. The method was revised to minimize
The bioactivity measured in this assay has been cell stress by not removing media from the cells before
linked to the ability of the tumor suppressor-containing infection. Concentrated virus dilutions were simply
adenovirus to shrink tumors in animal models. Apoptosis added to the existing media in the 96-well plates. There
of tumor cells in vivo and in vitro has been demonstrated was little variance (amongst experienced analysts)
through in situ staining for apoptotic markers. Tumor whether the virus dilution series was prepared in tubes or
shrinkage and in vitro growth inhibition of cells were plates. However, using a 96-well serial dilution plate and
shown to be dependent on the presence of the tumor- transferring the fluid from this plate to the cell-containing
suppressor transgene, as opposed to ad-empty vectors that plate accelerated this step considerably, reducing time
did not contain this transgene. spent during the infection step and making the assay
Early versions of the assay were not quantifiable less sensitive to analyst experience. Finally, results from
and assay results were expressed as pass/fail. Cells were analysts not experienced in this type of cell-based assay
infected at MOIs of 100, 500, and 1000 VP/cell. The test varied considerably. Further training usually rectified this.
article passed if the growth of the cells were reduced In addition, results were most consistent at four days post-
≥ 50% (compared to no infection) at 1000 VP/cell after infection. Once these improvements were implemented,
four days of incubation. MOI data at 100 and 500 VP/cell the assay was consistent, with a good signal that detected

FIGURE 2. Assay design for increasing amounts of adenovirus-expressed tumor suppressor induces cell death.

TABLE 3. Developing a process to identify parameters that affect variability.

Fall 2012 BioProcessing Journal • 7 • www.bioprocessingjournal.com


to cell-based potency
assay validation. Detailed
statistical analyses that can
be applied to this type of
assay will not be covered
in this article. Discussions
of statistical analysis as it
applies to biological assays
can be found in USP 35-
NF 30 chapters <1032>[3],
<1033>[4], <1034>[5] and
in EP chapter 5.3.[9]
According to USP
<1033>[4], the validation
parameters that should be
addressed in a cell-based
potency assay are: linearity,
relative accuracy, and
FIGURE 3. Determination of bioactivity for adenoviral gene therapy product. intermediate precision (IP)
which includes repeatability,
growth inhibition and four-parameter sigmoidal curve fit range, and specificity. Linearity is used to verify the
R2 values that were typically ≥ 0.9. An example of the data relative accuracy and effective range of the dilutional
output from the quantitative assay is shown in Figure 3. linearity method. Each potency assay typically measures
In this experiment, the test article and a reference control a unique activity. Therefore, the term “relative accuracy”
were prepared on separate plates in parallel. applies as there is often no way to confirm absolute
After improving the assay, the curves from 35 assays accuracy using an accepted alternative method. The
were analyzed (Figure 4). The minimum asymptote range is defined by the user and needs to be optimized
is small and represents the part of the curve where to cover values that are to be expected from the product.
there is 100% cell death. This parameter was the most IP is performed by evaluating intra-laboratory (different
variable. The primary indicator of potency is the curve fit analysts/days within a laboratory) and inter-laboratory
parameter, C, the IC50. Only one test of
35 was outside two standard deviations
of the mean value of 251 VP/cell. Based
on this assessment, the preliminary
specification for this viral construct
was set at an IC50 of 100 -500 VP/cell.
The specification would later evolve to
express the result as a ratio of sample
IC50 to reference IC50 that was run in
the same assay. The example in Figure 3
shows that this ratio would be 0.9.

Validation of Potency Assay:


Expectations
USP 35-NF 30: <1033>[4] (Biological
Assay Validation) describes general goals
in validation of relative potency assays.
This chapter is a guidance although
it does outline current expectations
for validation of cell-based potency
assays. The case study presented is
intended to illustrate a basic approach FIGURE 4. Curve fit statistics.

Fall 2012 BioProcessing Journal • 8 • www.bioprocessingjournal.com


TABLE 4. Dilutional linearity of potency assay for adenoviral gene therapy vector.

(variation between laboratories) results. Specificity of an various VP/cell concentrations, the limit of quantitation
assay is used to demonstrate a lack of interference from was shown to be 480 VP/cell as higher VP/cell values
components that are likely to be present in the sample resulted in ~100% cell death. Based on the linear portion
matrix. While not specifically required per USP <1033>[4], of the curve, the range of the method was shown to be
robustness may be added to assess whether such things as 77- 480 VP/cell.
plate manufacturers, cell passage, and slight temperature To determine relative accuracy, the approach was to
variations affect the outcome of the assay. prepare a standard curve in the manner of the assays
shown in Figure 3. In addition, two samples within the
Validation of Potency Assay for linear range of the curve (200 and 400 VP/cell) were tested
Gene Therapy Adenoviral Product as unknowns within the same experiment. The values
Data from the aforementioned adenoviral gene therapy from these samples were calculated from the standard
product is shown below. Dilutional linearity was shown curve and then compared to the theoretical values of
by the analysis of three different lots, run in duplicate, 200 and 400 VP/cell. A % recovery was determined
with the assays performed on three different days. Virus ([calculated value ÷ theoretical value] × 100). This was
concentrations from 12-3000 VP/cell were added to repeated using three different lots, in duplicate, for each
wells containing 10,000 cells/well. After addition of lot. The acceptance criterion for % recovery was 50 -150%.
alamarBlue® (Life Technologies Corp.), which indicates The results from these experiments are contained in
the extent of cell metabolism based on decreasing Table 5. The relative accuracy acceptance criterion for all
absorbance at 570 nm, the plate is read for absorbance in a experiments was met. The mean % recovery for the 400 VP/
plate reader. The results are shown in Table 4. cell sample was 87% and 80% for the 200 VP/cell sample.
The expected correlation of determination (R2) was Repeatability of the assay was determined by testing ten
≥ 0.9 for a four-parameter sigmoidal curve. For these replicates from one lot at three different concentrations
assays, the mean R2 value was 0.999, demonstrating (77, 192, and 480 VP/cell). As for relative accuracy, the %
excellent curve fit. Based on the % relative standard recovery was calculated by comparing the calculated value
deviation (% RSD) values of the absorbance values at the to the theoretical values. The mean and % RSD of the ten

TABLE 5. Relative accuracy of potency


assay for adenoviral gene therapy vector.

Fall 2012 BioProcessing Journal • 9 • www.bioprocessingjournal.com


replicates were calculated. The acceptance criterion for transfers from lab-to-lab, including different analysts,
% recovery was 50-150%, and the criterion for % RSD on different days and with different instruments. It
was ≤ 40%. The results from these experiments are in demonstrates how resistant an assay is to intangibles
Table 6. Both acceptance criteria for this experiment were that are not defined in the protocol. To demonstrate
met, demonstrating that the assay gives consistent values inter-assay precision, the IC50 of a single lot of product
within the usable part of the standard curve. was determined three times each by two laboratories
To assess intra-laboratory precision, the assay was (using different analysts, equipment, and on different
performed on three different days using two analysts, and days). The mean IC50 values and % RSD of the three
two concentrations (200 and 400 VP/cell) were tested runs from each laboratory were compared. Results from
within each experiment. Six replicates were assayed each the internal laboratory were an IC50 of 227 VP/cell and a
day, along with a standard curve run in the same plate % RSD of 16.7%, and results from the outside laboratory
each day. For each day, the calculated VP/cell value was were an IC50 of 185 VP/cell and a % RSD of 6.8%. The
averaged and the % RSD and % recovery calculated for the variability of the results was found to be within the
six replicates. The % recovery acceptance criterion over the expected range of the assay (± 50%). These results are
three days of the test was 50-150% which was met (91% shown in Table 8.
for 400 VP/cell and 89% for 200 VP/cell concentrations). For cell-based potency assays, specificity involves
The % RSD values were acceptable at < 10% for each day. demonstrating certain components that may be expected
These results are summarized in Table 7. to be present in the sample do not interfere with the assay.
Inter-laboratory precision measures how well an assay In this example, it was reasoned the most likely source of

TABLE 6. Repeatability of potency assay


for adenoviral gene therapy vector.

TABLE 7. Intra-laboratory precision of potency


assay for adenoviral gene therapy vector.

TABLE 8. Inter-laboratory precision of potency


assay for adenoviral gene therapy vector.

Fall 2012 BioProcessing Journal • 10 • www.bioprocessingjournal.com


interference would be inactive virus. Empty adenoviral IC50 values were variable between assays for some of these
capsids could also contribute to specificity loss, but the variances. However, the relative accuracy within each
presence of unstable inactive virus was thought to be assay was more consistent. When two concentrations of
the most probable and abundant source of interference, sample (200 VP/cell and 400 VP/cell) were compared to
especially during forced degradation stability studies. The a standard curve within the same assay (as in Table 5),
inactivated virus could then be used to spike active virus % recovery ranged from 73-117%, well within the
and the IC50 values compared ± the spike. To produce acceptance criterion of 50-150% for relative accuracy.
inactive virus, purified final product was heat-inactivated These results (Table 10) indicated that, although absolute
(56 °C for one hour) and used as the challenge compound. IC50 values might change in some cases, relative accuracy
As shown in Table 9, inactivation was complete. Heat was not meaningfully compromised nor was the R2
inactivation resulted in an IC50 value of > 3000 VP/cell correlation coefficient for the four-parameter sigmoidal
for the inactivated virus alone. In a preparation of equal curve fit. In other words, a product tested relative to a RS
parts active and inactive virus, the measured activity of would be expected to yield the same IC50 ratio as long as
the active virus was essentially the same as when measured the test article and reference were tested under the same
alone (IC50 values of 205 and 180 VP/cell, respectively). conditions.
These results demonstrated that the assay could effectively The use of a RS is important throughout development,
measure potency in the presence of inactive product, thus validation, and trending of assay performance. During
the assay had acceptable specificity. development, a standard may be a process development
In addition to the assay specificity experiment, the lot or Phase 1 material and can be used for early system
specificity of the system was explored by comparing suitability testing. As long as it is (approximately)
IC50 values obtained from the cells typically used in the representative of the manufacturing process for future
assay compared to non-susceptible cells. The IC50 values good manufacturing practices (GMP) lots, this approach
indicated that the non-susceptible cells required over can help elucidate the true variability of the assay. Once
three times more virus to achieve an equivalent reduction the product is in late-phase clinical development, an
in cell metabolism than when compared to the cells used official RS should be well-characterized (e.g., from part of
in the assay (data not shown). a GMP clinical trial lot). As part of this characterization,
It is advantageous to demonstrate the robustness of an external RS (if available) should be tested side-by-
the potency assay. In this case, robustness was tested by side as part of internal RS release. This provides a good
assessing different cell culture plate suppliers, media reference point between internal RS lots. For example,
source, cell passage number, as well as the effects of a even if the adenoviral reference material cannot be
lower incubator temperature (it is known that higher tested for transgene bioactivity, the comparisons from
incubator temperatures severely reduce infectivity). The other tests such as infectious titer and virus particle

TABLE 9. Specificity of potency assay


for adenoviral gene therapy vector.

TABLE 10. Robustness of potency assay for adenoviral gene therapy vector.

Fall 2012 BioProcessing Journal • 11 • www.bioprocessingjournal.com


enumeration give more confidence that the internal potency assay development early in a product’s lifecycle.
RS is representative of the product that will be tested. It is essential to understand some of the molecular
Internal RS should be stored in stable conditions. mechanisms of the product’s therapeutic effect and
Trend analysis of RS is the ideal way to assess assay narrow down the assay to a single, measurable biological
drift, QC cell bank comparability, analyst to analyst activity. The capabilities and limits of the assay should be
comparability, and changes in assay variability. understood before validation begins, with plans to validate
the assay once the product is in Phase 3 clinical trials.
Conclusion
The cell-based potency assay is usually the most
customized assay on a biological product’s COA, and ACKNOWLEDGEMENT
it typically requires a higher commitment of time The author would like to thank Ricardo Jimenez, Dr. Jessica Carmen,
and resources to develop. It is, therefore, wise to start and Kim Yang for assistance and critical review of this manuscript.

REFERENCES

[1] International Conference on Harmonization. ICH Topics Q6B- [8] Center for Biologics Evaluation and Research (CBER). Guidance
Guidance for Industry: Specifications: Test Procedures and Acceptance for Industry: Potency Tests for Cellular and Gene Therapy Products.
Criteria for Biotechnological/Biological Products. 18 August 1999, Rockville (MD): CBER. Jan 2011, http://www.fda.gov/downloads/
vol 64, p 44928, http://www.ich.org/products/guidelines/quality/ BiologicsBloodVaccines/GuidanceComplianceRegulatoryInformation/
article/quality-guidelines.html. Guidances/CellularandGeneTherapy/UCM243392.pdf.
[2] USP <111> Design and Analysis of Biological Assays. USP 35– [9] Statistical Analysis of Results of Biological Assays and Tests:
NF 30:106, http://www.usp.org/meetings-courses/workshops/past-usp- European Pharmacopoeia 7th Edition. July 2012, http://online6.edqm.
workshops/usp-bioassay-guidance-chapters. eu/ep705/.
[3] USP <1032> Development and Design of Biological Assays. [10] Peng Z. Current Status of Gendicine in China: Recombinant
USP 35–NF 30: 162, http://www.usp.org/sites/default/files/usp_pdf/ Human Ad-p53 Agent for Treatment of Cancers. Human Gene Therapy,
EN/2010-03-25_1032_PF36(4)_w_line_numbers.pdf. 2005; 16 (9): 1016-1027.
[4] USP <1033> Biological Assay Validation. USP 35–NF 30: 5174, [11] Trask TW, Trask RP, Aguilar-Cordova E, Shine HD, Wyde PR,
http://www.usp.org/sites/default/files/usp_pdf/EN/2010-03-25_1033_ Goodman JC, Hamilton WJ, Rojas-Martinez A, Chen SH, Woo SLC,
PF36(4)_w_line_numbers.pdf. Grossman RG. Phase I Study of Adenoviral Delivery of the HSV-tk Gene
[5] USP <1034> Analysis of Biological Assays. USP 35–NF 30: 5186, and Ganciclovir Administration in Patients with Recurrent Malignant
http://www.usp.org/sites/default/files/usp_pdf/EN/2010-03-25_1034_ Brain Tumors. Molecular Therapy, 2000; 1 (2): 196-203.
PF36(4)_w_line_numbers.pdf. [12] Rieder N, Gazzano-Santoro H, Schenerman M, Strause R, Fuchs C,
[6] USP First Supplement. Design and Analysis of Biological Mire-Sluis A, McLeod LD. The Roles of Bioactivity Assays in Lot Release
Assays. USP 35–NF 30, http://www.uspnf.com/uspnf/ and Stability Testing. BioProcess International, 2010; 8 (6): 33-42.
display?cmd=jsp&page=chooser. [13] Joelsson D. A Practical Guide to Design of Experiments (DOE) for
[7] USP Second Supplement (not yet official). USP Bioassay Guidance Assay Developers, 2010, http://www.potencyassay.com/wp-content/
Chapters, 2012, http://www.usp.org/es/node/595. uploads/2010/06/DOE_for_assay_developers_Chp1_Rev-1.0.pdf.

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