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Allogeneic Cell Therapy Manufacturing - Process Modeling and Techno-

Economic Assessment (TEA) with SuperPro Designer

Preprint · April 2020

DOI: 10.13140/RG.2.2.17364.55681

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 Allogeneic Cell Therapy
Manufacturing
Modeling and Evaluation with
SuperPro Designer®

by

Doug Carmichael, Rafael da Gama and Demetri Petrides

This is the ReadMe file of a SuperPro Designer example that deals with process modeling, cost analysis
and optimization of Allogeneic Stem Cell Production. The flowsheet of the process is appended to the
bottom of this document. You may test-drive this model by downloading the functional evaluation edition
of SuperPro Designer from the downloads page of our website (www.intelligen.com). The files of this
example can be found in the Examples \ Pharmaceuticals \ AllogeneicCellTherapy folder. The default
installation path of the SuperPro Designer Examples folder follows below.

C:\ Users \ Public \ Public Documents \ Intelligen \ SuperPro Designer \ v# \ Process Library \ Examples

If you have any questions about this example and SuperPro Designer in general, please send an email
message to dpetrides@intelligen.com

INTELLIGEN, INC.
Simulation, Design, and Scheduling Tools
For the Process Manufacturing Industries
www.intelligen.com

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Introduction
Stem cell therapy is a nascent but fast-growing field within the pharmaceutical industry. Stem cells are
undifferentiated cells which are capable of transforming into different cell types. Human mesenchymal stem
cells (MSCs) are one of several varieties of human stem cells. They are capable of transforming into bone
cells, muscle cells, cartilage cells, etc. As a result, MSCs have potential to be used in regenerative medicine
to repair injured tissues and restore their lost functions. Furthermore, the usefulness of MSCs can be greatly
expanded through genetic modification of the cells in order to provide new functions or improve existing
ones.

Although only 13 MSC-based products had gained marketing authorization by the end of 2017,
approximately 190 clinical trials with MSCs were being conducted at that time [1], and there were over 600
cell therapy clinical trials overall in 2017 [2]. This is because stem cells have the potential to combat many
serious diseases which currently lack satisfactory treatments, including cardiac, neurological, and metabolic
disorders [3]. Genetically modified MSCs also have the potential to be used as targeted anticancer drug
carriers [4], and to treat genetic diseases for which there currently is no cure [5].

Therapeutic stem cells may be produced through either allogeneic or autologous processes. The main
difference between allogeneic and autologous production methods are the source of the cells. Allogeneic
therapies are manufactured in large batches from unrelated donor tissues (such as bone marrow). In this
manner, a single donor’s cells may be used to provide treatments for many different patients. In contrast,
autologous therapies are manufactured as a single lot from the patient being treated. In other words, a
patient’s own stem cells are harvested, culture-expanded, and then returned to the patient. For more
information on autologous cell therapy processes, please consult the Cell and Gene Therapy example
located in the Examples \ Pharmaceuticals \ CellAndGeneTherapy folder.

Although autologous production methods eliminate the possibility of a patient contracting a disease from
cells that originated from another person’s body, the cost of therapies based on autologous production is
exceptionally high. One analysis estimated that the cost to produce cells by autologous manufacturing
methods is more than double that to produce the same therapy allogeneically [3].

One reason for the additional expense is that autologous therapies currently require that every single patient
undergoes donor screening and testing, and every individual person’s final therapeutic dose of product is
subject to release testing. In contrast, with allogeneic production only a small number of donors will need
to be screened and tested to find a high-quality stem-cell sample to produce a cell-bank system (which
could provide therapeutic doses to many people), and release testing will be limited to each batch of the
final product, rather than each individual dose. In addition, autologous production methods are not as
efficient as allogeneic production since autologous production requires many individual cell culture
operations to be performed during the production of every individual dose of product at a very small scale,
whereas allogeneic production allows many doses to be produced from a single batch of product. These

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are some of the reasons why the autologous cell therapies which are currently approved for sale (as of
early 2019) cost hundreds of thousands of dollars per dose, which is prohibitively expensive for widespread
adoption [6]. Although cell therapy is a relatively new field, and manufacturing costs are expected to decline
as production methods improve, the high current cost of autologous cell production is a compelling reason
to use allogeneic production instead (where possible). It is estimated that in the future, the cost of cell
therapies produced through allogeneic methods may decline to thousands of dollars per dose rather than
hundreds of thousands of dollars per dose [4].

In addition to the financial benefits, there are various other advantages to allogeneic production. For
instance, allogeneic therapy can be standardized and optimized because all doses may be produced from
a single cell bank from a young and healthy donor. In contrast, autologous production is highly variable
because cells from different patients (especially patients of different ages) can multiply at different rates [7].
This variability necessitates greater manufacturing flexibility. It also results in variable media requirements
(and associated costs), less-efficient facility use, logistical difficulties, etc. As a result, even though
autologous therapies account for most of the cell therapies currently undergoing clinical trials, there is
substantial interest in eventually producing most therapeutic MSCs using allogeneic production methods.
Therefore, this example evaluates the allogeneic production of an MSC product. Key details of the
production process are described in the following section.

Process Description
This example includes the following SuperPro file:

• AllogeneicCellTherapy.spf

This file models the manufacturing of an allogeneic mesenchymal stem cell therapy product. The
development of this model was based on data from the technical literature, supported by our experience
with related processes and our engineering judgment. Note that cell therapy is a very new field and therefore
there is a great deal of variation in the cell production and purification processes that are currently in use
by various organizations. The process description which follows represents just one example of how a cell
therapy model could be represented.

Although some rare diseases might only require hundreds of doses per year, the potential market for some
cell therapies is tens of thousands of doses or more per year. The process which is modelled in this example
is assumed to produce approximately 7,800 doses per year. For production quantities such as this,
allogeneic production is far more cost-effective than autologous production.

For reporting and analysis purposes, the process flowsheet has been divided into three sections: Upstream,
Downstream, and Fill/Finish. Flowsheet sections in SuperPro are simply sets of related unit procedures
(processing steps). Each section has been assigned a different color on the flowsheet (black for Upstream,

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green for Downstream, and purple for Fill/Finish). For information on how to specify flowsheet sections and
edit their properties, please consult Chapter 8.1 of the SuperPro manual.

Upstream cultivation of stem cells can be performed in equipment similar to what is used for Chinese
Hamster Ovary (CHO) cell production. Downstream processing is substantially different, though, because
the cells themselves are the product. The live cells must therefore be recovered, washed, frozen, and stored
while maintaining high viability and potency. The key details associated with each section of this process
model are described below.

Upstream Section

The production process begins with a small amount (5 ml) of concentrated “seed” cells which are removed
from cryogenic storage (procedure P-101). These cells are thawed (P-102) and then washed with serum-
enriched media (P-103) in order to remove the cryopreservation solution. In reality, the cells may be washed
and centrifuged multiple times. However, for simplicity, this step was modelled with a batch (bulk flow)
Generic Box unit procedure containing a Transfer In operation, a Hold operation, and a Load/Split operation
(to represent the media washes).

Meanwhile, a set of four 250 ml spinner flasks (P-104) are prepared with sterile media. The media that is
added to these flasks contains a mixture of amino acids, vitamins, inorganic salts, glucose, and other
components. The number of flasks that this procedure icon represents can be seen by right-clicking P-104,
selecting Equipment Data, and looking at the “Number of Containers (per Unit/Skid/Rack)” listed in the
upper right quadrant of first tab (see Figure 1). This value is calculated by SuperPro based on the working
volume of each flask and the total amount of material which is added to the flasks.

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Figure 1: Number of units in the shake flask rack

Note that within P-104 and various subsequent procedures, “Pull In” operations are used for many of the
material additions. Charge operations could have alternatively been used for these material additions. Like
a Charge operation, a Pull In operation allows you to bring material into a vessel using a process input
stream (assuming the amount and composition of the material stream is known). However, Pull In
operations also allow you to bring materials into a vessel from another unit procedure using an intermediate
stream (this is similar to the functionality of a Transfer In operation). The Pull In operation’s ability to draw
in materials from either an input stream or an intermediate stream is convenient if a flowsheet might be
modified in the future to incorporate additional unit procedures which will feed units that already exist on
the flowsheet. For instance, the first operation in the P-104 procedure within this flowsheet draws 0.5 L of

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media into the flasks. However, a “dead end filtration” unit procedure could be added upstream of P-104
later, and the intermediate stream which would flow out of that new filtration procedure could still be drawn
into the flasks (by switching the Amount specification from the user-defined “Volume” specification to the
“Available in Pull In Stream” specification – see Figure 2). In contrast, if a Charge operation had been used
for this media addition in P-104, and then a filtration procedure was subsequently added to the flowsheet
upstream of P-104, that Charge operation would need to be deleted and replaced with a Transfer In
operation (since a Charge operation cannot draw in materials from intermediate streams; it can only draw
in materials from input streams). In contrast, since the Pull In operation provides a superset of the
capabilities of Charge and Transfer In operations, there is no need to delete and replace this operation if
its associated stream is later changed from an input stream to an intermediate stream.

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Figure 2: Use of a Pull In operation to bring materials in from an intermediate stream

Another reason why Pull In operations can be useful is that they allow an input stream’s flow to be
automatically calculated based on certain process specifications. For instance, the “Add microbeads” Pull
In operation in P-106 automatically adds enough microbeads so that they are equivalent to 2% of the mass
of solution which was in the vessel prior to the microbead addition. This was done by selecting the “Set by

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Other Specification” option in the Amount section of Figure 2, clicking the Setup button, and then specifying
a Mass Ratio of 0.02 relative to the initial amount in the vessel at the beginning of the “Add microbeads”
operation (see Figure 3). Not only does this allow the microbead addition amount to be calculated
automatically, but it also ensures that if the solution volume in the bioreactor prior to the microbead addition
is later modified, the microbead addition will automatically be scaled up or down by an appropriate factor
as well.

Figure 3: Advanced options for a Pull In operation’s material input specifications

After the media is added to the 250 ml flasks using a Pull In operation, the flasks are inoculated with the
washed cells (using a standard Transfer In operation). Then the cells undergo viral transduction in order to
introduce a desired genetic modification into the cells. This activity is represented with a simple “Hold”
operation in P-104. Afterward, the cell expansion begins. In this model, the expansion is modelled as a
series of Ferment operations in unit procedures of increasing size (first the 250 ml flasks, then a set of
rocking bioreactors, then a 70 L cell culture bag, then a 280 L cell culture bag). The Ferment operations
within the 250 ml flasks are simplified to only account for key components that would be consumed /
produced during this operation. For instance, a simple mass stoichiometry relationship was specified to

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account for the consumption of glucose and oxygen, and generation of carbon dioxide, cells, metabolic
impurities, and some water (see Figure 4). The fermentation operations in the larger-scale bioreactors (P-
106 and P-107) are similar, although those operations also account for consumption of fetal bovine serum
(FBS). Note that the oxygen associated with each of these fermentations is supplied by checking-on broth
aeration on the Oper.Cond’s tab of each Ferment operation (see Figure 5) and by specifying the associated
inlet and outlet streams (e.g., the inlet is the stream labelled “Air”, which is initialized to the composition of
the stock mixture named Air, and the outlet vent stream is S-116, which is the default stream on the
Vent/Emissions tab of this operation).

Figure 4: Stoichiometry of Ferment operations in P-104

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Figure 5: Specification of the aeration stream in P-104

In P-104 and the subsequent (larger) bioreaction units, roughly half of the media is exchanged every three
days. This is done in order to replenish consumed components and remove toxic metabolic by-products
and other wastes. To model this, 3 days after the cell expansion begins, a Batch Component Splitting
operation is used to remove 50% of each of the soluble media components (see Figure 6). Then a Pull In
operation is used to add fresh media to the flasks. A second Ferment operation is used to represent days
4-6 of the cell expansion. The subsequent cell expansion procedures (in P-105, P-106, and P-107) follow
a similar structure of multiple Ferment operations coupled with media exchanges.

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Figure 6: Use of a Batch Component Splitting operation to remove 50% of each soluble material

As the fermentation in the 250 ml flasks is nearing completion, two rocking bioreactors (P-105) are prepared

for the next step of the cell expansion. The flowsheet displays a special sub-icon ( ) below P-105 in order
to highlight the fact that two parallel units are required to accommodate the volume of material at this step.
This could also be seen by right-clicking P-105, choosing Equipment Data, and viewing the “Number of
Units” value listed on the first tab of the dialog which appears. The reason two rocking bioreactors is needed
is that although each of them has a 2 L capacity, the bags can only be filled to a maximum level of 50% of
that capacity (i.e., a maximum of 1 L of solution per bag). Furthermore, this procedure requires more than
1 L of solution capacity (1 L of fresh media is added to the bags initially, and another 0.6 L of solution is

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then transferred in from the flasks). As with P-104, P-105 includes two 3-day Ferment operations separated
by a media exchange. The second media exchange brings the final solution volume up to about 1.7 L.

As the second Ferment operation in P-105 nears completion, 8 L of media and 0.2 L of fetal bovine serum
are added to the “N-1” disposable seed bioreactor unit (P-106). Approximately 0.2 kg of microcarrier beads
are also added to P-106. The beads provide extensive surface area on which the cells can grow. Bioreactors
containing microcarrier beads are currently the most cost-effective cell culture equipment at scales of
several hundred liters (which is the size of the production bioreactor in this example), whereas multiplate
(planar) units are more cost-effective at very small scales. Numerous types of microcarrier beads are
available. The microcarrier beads are typically incubated in a solution of vitronectin and phosphate-buffered
saline (PBS) in order to coat them prior to their addition to the bioreactor.

Next, the “N-1” bioreactor is inoculated with the cells from the rocking bioreactors (P-105), and the cells
begin to adhere to the microcarrier beads. This process lasts for about 8 hours. As with the previous
procedures, there are two 3-day Ferment operations separated by a 50% solution exchange in P-106.
However, the Ferment operations in P-106 (and P-107) also include consumption of serum (FBS). Since
serum is extremely expensive, very little is used. This is especially the case for the initial 3 days of
fermentation, since the cell density is very low and therefore consumption of the serum is also low. The
second fermentation operation in P-106 (representing days 4-6 of that procedure’s fermentation) requires
more serum than the first fermentation operation since there are more cells by that point in the procedure.
Therefore, 0.5 L of additional serum is added during the second serum addition in order to provide sufficient
nourishment to the multiplying cells. The cell count roughly doubles every 3 days within this unit, so the
total cell mass at the end of the procedure is roughly 4 times the initial cell mass transferred into it from P-
105.

Note that the majority of cell therapy expansions utilize single-use (a.k.a., “disposable”) equipment. These
units are preferred partially because they are pre-sterilized, so there is no need to sterilize or clean them
during a production batch. Single-use systems also decrease the risk of cross-contamination from one
batch to the next.

The final procedure in the Upstream section of the flowsheet is the production-scale bioreaction (P-107),
which takes place in a 280 L disposable bioreactor (with a working volume of about 200 L). This represents
the approximate upper limit of bioreactor sizes for gene/cell therapy processes, as of 2019 (when this
example was created). It is expected that larger production bioreactors may be possible in the future with
continued developments in this field.

After fresh sterile media and serum are added to this unit, and additional microcarrier beads are added, the
contents of the seed bioreactor unit are transferred into it. This is followed by three separate ferment
operations (lasting for a total of nine days) which are separated by 50% solution exchanges. As with P-106,
the serum addition volumes in procedure P-107 increase as the cell culture progresses. The Ferment

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operations in this unit use the same stoichiometry as the Ferment operations in P-106, and the cell count
roughly doubles every 3 days within this unit as well.

After Day 9 of the fermentation, the cells are detached from the microcarrier beads using a proteolytic
enzyme. This allows the microcarrier beads to be separated from the cells (based on their size differential)
in the subsequent step. At this point, there are about 0.4 kg of cells (dry cell mass), which is equivalent to
approximately 0.5% of the fermentor broth.

Downstream Purification Section

After the fermentation operations in the production bioreactor are complete, the bioreactor contents are
transferred through a filter (P-108) in order to remove the microcarrier beads (which are much larger than
the cells). The yield of cells through this unit is about 94%.

Next, the cells are concentrated using a tangential flow filtration (TFF) unit (P-109). TFF units are also
commonly used for the purification of therapeutic proteins from mammalian cell culture. In this example,
the TFF (ultrafiltration-diafiltration) unit concentrates the whole cells 10-fold, to a dry cell mass concentration
of around 53 g/L. The concentrated cells are subsequently washed with 8 volumes of diafiltration buffer
composed of phosphate buffered saline (PBS) in order to remove any unwanted components such as FBS
residues, enzymes, etc. During the concentration and washing, it was assumed that 4% of the cells would
be lost or die, so the yield of cells through P-109 is 96%. The 4% loss was specified with the “product
denaturation” setting on the Diafilter operation’s Oper.Cond’s tab. The overall yield through the Downstream
portion of the process is approximately 90%. This is higher than current typical yields, but it is expected that
yields will improve in the future due to ongoing research and development activities for this type of process.

Fill/Finish Section

After filtration, the concentrated-and-washed cells are combined with a cryopreservation solution (P-110)
in preparation for the filling (P-111) and freezing (P-112) steps. There is a short window of time available
to transfer the cells from the culture medium into the cryopreserved state, so the operations in the
downstream section must be completed quickly. In addition, although the DMSO component within the
cryopreservation solution is cryoprotective, it also has a toxic effect on the cells. Therefore, the mixture
must be filled into containers and frozen as soon as possible after the cryo-solution is added.

The Filling procedure (P-111) fills empty plastic vials with the solution from P-110. To set this up, the
component “plastic” was created within this project’s Pure Components database. Then the Fill operation
was initialized by specifying that 50 ml of solution should be added per vial (see Figure 7). The name and
composition of the vial (container) was specified by clicking the Container Line button in Figure 7, specifying

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the type of container (e.g., “vials”, see Figure 8), specifying the amount of material per container (e.g., the
vials are each made of 1 g of material), then clicking the Composition tab and specifying the material itself
(e.g., plastic). In this way, the S-112 “bulk” intermediate stream (which is measured in mass or volume
units) is transformed into a discrete stream (measured by the number of filled entities). Note that by default,
discrete streams on a SuperPro flowsheet are shown in blue rather than black.

Figure 7: Specifying the filled amount per container (per vial)

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Figure 8: Specifying the mass and composition of each vial

Based on the amount of solution per batch after the cryopreservation solution is added, and the volume of
solution per vial, approximately 242 vials would be produced per batch (based on this model’s assumptions
regarding cell expansion productivity, purification yield, scale of operations, and patient dose size). The
cell-filled vials are then quickly frozen and stored under liquid nitrogen. Since liquid nitrogen is not included
in the default SuperPro Designer databanks, it was added to the Heat Transfer Agents databank (under the
Databanks menu of the main SuperPro interface). Then it was available to be selected as the cooling agent
within procedure P-112’s Freeze operation. For information on modifying SuperPro’s Heat Transfer Agent
databank, please refer to that section of the SuperPro Help file.

Once frozen, the cells can remain viable for years or even decades. They are supplied as-needed to the
medical facilities where cell therapy treatments or clinical trials occur.

Material Balances
Table 1: Material Balance Results for this ExampleTable 1 displays the material requirements in kg/year,
kg/batch, and kg/MP Entity (where “MP Entity” is the “main product entity”, i.e., each 10 ml product vial in
this case). Since this plant produces approximately 242 vials per batch and runs 32 batches per year,
approximately 7,744 vials of product are produced each year. The table below was extracted from the RTF
version of the Materials & Streams report of this example file. Note – reports in SuperPro are generated

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through the Reports menu of the main menu bar. The format and contents of the reports can be customized
by selecting Reports \ Options from the main menu bar.

Table 1: Material Balance Results for this Example

BULK MATERIALS (Entire Process)

Material kg/yr kg/batch kg/MP Entity
Air 7,141 223.17 0.92
Carb. Dioxide 144 4.51 0.02
Cells 0 0.00 0.00
Cryopreservatio 42 1.32 0.01
EDTA Disodium 0 0.00 0.00
Media 9,613 300.39 1.24
Microcarrier Be 52 1.61 0.01
PBS 333 10.40 0.04
Plastic 8 0.24 0.00
Serum 152 4.76 0.02
Trypsin 0 0.01 0.00
WFI 64 1.99 0.01
TOTAL 17,549 548.40 2.26

Scheduling Results
A portion of the Equipment Occupancy Chart (EOC) is displayed in Figure 9. The equipment names are
shown on the vertical axis and the timeline is shown on the horizontal axis. To generate this chart, select
Charts \ Equipment Occupancy \ Multiple Batches from the main menu of SuperPro. Figure 9 shows
the equipment usage for each batch in a different color (light blue for the first batch, orange for the second
batch, etc.). If you would like to change the number of displayed batches, right-click on an empty area of
the EOC and select “Set Number of Batches”.

Based on Figure 9, it is clear the production bioreactor (“N BRX”) is the cycle time bottleneck. If additional
annual throughput was needed for this product, a second production bioreactor could be added. The second
production bioreactor would be run in “staggered” mode relative to the first unit (i.e., the first batch would
be run in the first production bioreactor, the second batch would be run in the second production bioreactor,
the third batch would be run in the first production bioreactor, etc.) In this way, the batch-to-batch cycle time
could be substantially reduced. Therefore, more batches could be run each year.

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Figure 9: A portion of the Equipment Occupancy Chart

In addition to the EOC, SuperPro generates Gantt charts for the various operations and their unit
procedures (through Charts \ Gantt Charts \ Operations GC). Figure 10 shows a portion of the Gantt chart
for this process. In this chart, the tan bar at the top represents the time required for one full batch. The dark
blue bars represent the time required for each unit procedure, and the light blue (cyan) bars represent
individual operations. The Gantt chart is highly customizable. For instance, to modify the bar properties
(such as their colors, labels for duration, etc.), right-click on an empty area of the chart and select Styles
from the drop-down list. Then choose a bar type to edit. If you wish to modify the time scale at the top of
the chart, select Styles \ Chart & Grid and then click the “Time Line” tab on the dialog that appears. There
you can customize the timeline with your own desired minor and major units.

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Charts such as the Gantt chart and the Equipment Occupancy chart are useful tools for cycle time analysis,
debottlenecking, scheduling, and technology transfer. Note that SuperPro recipes may also be exported to
SchedulePro for additional plant scheduling and debottlenecking activities. SchedulePro is a tool from
Intelligen which is complimentary to SuperPro Designer, and which focuses on multiproduct plant planning,
scheduling, and debottlenecking.

Figure 10: Operations Gantt Chart

Economic Evaluation
In addition to the mass and energy balances, SuperPro Designer performs thorough cost calculations
related to the capital expenses (CAPEX) and operating expenses (OPEX), as well as the production cost
and the profitability of the project. The results can be found in the Economic Evaluation (EER), Cash Flow
Analysis (CFR), Itemized Cost (ICR), and Excel Custom reports (accessed through the Reports menu).

In this example, various assumptions were made for the costs of raw materials, heat transfer agents, facility
cost factors, labor rates, etc. Table 2 displays the key economic results for the process, based on these
inputs and the other simulation results (e.g., material requirements, labor hours, etc.). Table 2 was extracted
from the Economic Evaluation Report (generated in RTF format). For a facility of this capacity, the total
capital investment is around $20 million. The estimated operating cost is $8.6 million per year, which
translates to a unit production cost of roughly $1,100 per vial (dose) of this allogeneic cell therapy product.

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By way of comparison, the unit production cost for an autologous cell therapy product was estimated at
approximately $20,000 per dose in the Cell and Gene Therapy example (…Examples \ Pharmaceuticals \
CGT). The numbers for the calculation of the Return-On-Investment, Payback Time, etc. are based on a
selling price of $10,000 per vial (i.e., $10,000 per dose) of the product. This selling price is much lower than
the price of the very few currently approved autologous cell therapy treatments. However, as stated earlier,
cell therapy is a very young field. It is very likely that costs for large-scale human cell culture and cell
purification technologies will decrease dramatically in the future as this market expands and matures (due
to increased competition, scaling, technological improvements, etc). In addition, allogeneic cell therapy
production processes (such as this one) are expected to be much less expensive than autologous cell
therapy production. Also note that the unit production cost for a given cell therapy product is extremely
dependent on the dose size, which may vary by several orders of magnitude. Clearly, a very high dose size
will tend to greatly increase the unit cost, since many more batches will be required annually (at a particular
scale) in order to treat a given number of patients.

Table 2: Key Economic Results

EXECUTIVE SUMMARY (2019 prices)

Total Capital Investment 20,156,000 $
Operating Cost 8,622,000 $/yr
Revenues 77,815,000 $/yr
Batch Size 243.19 MP Entities
Cost Basis Annual Rate 7,782 MP
Unit Production Cost 1,107.98Entities/yr
$/MP Entity
Unit Production Revenue 10,000.00 $/MP Entity
Gross Margin 88.92 %
Return On Investment 214.84 %
Payback Time 0.47 years
IRR (After Taxes) 107.58 %
NPV (at 7.0% Interest) 287,128,000 $
MP = Flow of Discrete Entity ‘Filled Entity’ in Stream ‘To storage’

Figure 11 displays the annual operating cost breakdown for this process. This is a chart that was
automatically generated with the Economic Evaluation Report. To include such charts in the reports, visit
Reports \ Options and select Include Charts (lower right corner of the dialog). In this example, the facility-
dependent costs, labor costs, and raw material costs are the most important items, accounting for 40%,
28%, and 23% of the overall operating cost, respectively. Lab/QC/QA costs for this type of process are also
quite substantial, at roughly 6% of the operating cost. This is equivalent to approximately $15,000 per batch.
The Lab/QC/QA costs for this example were set at 20% of the total operator labor cost for each of the three

flowsheet sections. This was done by clicking the Section Operating Cost Adjustments button ( ) for a

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given section, clicking the Lab/QC/QA tab, and setting these costs equal to 20% of the total labor cost (see
Figure 12).

Figure 11: Annual Operating Cost Breakdown

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Figure 12: Setting the Lab/QC/QA cost factor for the Upstream section of the process

The facility-dependent cost in Figure 11 accounts for the depreciation and maintenance of the facility and
other overhead expenses. Since stem cell products cannot be sterilized at the end of production, the entire
production process must be aseptic. This typically requires processes to be run in clean rooms or in closed
systems, which increases the facility expenses relative to many other types of pharmaceutical products. To
account for this, the “buildings” capital cost factor for each section of the process in this model was

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increased from its default value of 0.45 to a value of 4.00. This was done by clicking the Section Capital

Cost Adjustments button ( ) and entering the new “buildings” cost factor for each of the three flowsheet
sections (see Figure 13).

Figure 13: Capital cost adjustment factors for the Upstream section

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Table 3 displays the operating cost breakdown per flowsheet section for this example. The table was copied
from the Itemized Cost Report (RTF format), which can be generated by selecting Reports \ Itemized Cost
(ICR).
Table 3: Operating costs for each process section

SUMMARY PER SECTION

Section $/MP Entity $/batch $/year %
Upstream 931.14 226,428 7,245,685 84.04
Downstream 32.88 7,996 255,880 2.97
Fill/Finish 143.96 35,007 1,120,220 12.99
TOTAL 1,107.98 269,431 8,621,784 100.00

Table 3 shows that most of the costs associated with cell therapy products are associated with the Upstream
portion of the process. This is consistent with various economic studies in the literature. The high Upstream
cost is due to the fact that most of the raw material, labor, and facility costs occur with the Upstream
production.

The raw material costs for the overall process are displayed in Table 4. This table was extracted from the
RTF version of the Economic Evaluation Report. Notice that microcarrier beads, media, and serum are by
far the largest contributors to the total material cost. In particular, the microcarrier beads are almost two
thirds of the total material cost. In this model, a cost of $25/g was assigned to the microcarrier beads. There
are a variety of beads available for this type of process, with a wide range of prices (including proprietary
beads which cost well over $100/g). However, some popular bead types are in the $25/g range currently,
and prices are expected to decline in the future.

Table 4: Raw Material Costs for this Process

Bulk Material Unit Cost Annual Annual Cost %

Cryopreservatio ($)
100.00 Amount
42 kg ($)
4,213 0.21
EDTA Disodium 0.01 13 g 0 0.00
Media 50.00 9,613 kg 480,625 24.25
Microcarrier Be 25.00 51,590 g 1,289,758 65.08
PBS 50.00 333 kg 16,648 0.84
Serum 1,200.00 152 kg 182,725 9.22
Trypsin 1.00 160 g 160 0.01
WFI 0.20 64 kg 13 0.00

Unit Cost Annual

Discrete Material Annual Cost($) %
($/Entity) Amount
Vials 1.00 (Entities)
7,782 7,782 0.39

TOTAL 1,981,923 100.00

Intelligen, Inc. Page 23

Table 5, which was also extracted from the Economic Evaluation Report, provides information on equipment
sizes for this process and the associated equipment purchase costs. The total estimated processing
equipment cost for this small-scale facility is roughly $1.5 million.

Table 5: Equipment Capacities and Costs (2019 Prices in US$)

Quantity Name Description Unit Cost ($) Cost ($)

1 N BRX Disposable Bioreactor Skid 116,000 116,000
Container Volume = 280.00 L
1 FT-101 Freeze-Thaw Module 356,000 356,000
Vessel Volume = 10.00 mL
1 N-1 BRX Disposable Seed Bioreactor Skid 102,000 102,000
Container Volume = 70.00 L
1 DF-101 Diafilter 27,000 27,000
Membrane Area = 2.46 m2
1 DE-101 Dead-End Filter 39,000 39,000
Filter Area = 10.00 m2
1 SDLB-101 Skid for Disposable Large Bag 37,000 37,000
Container Volume = 100.00 L
1 DFT-101 Discrete Freeze-Thaw Module 356,000 356,000
Vessel Volume = 3.42 L
2 RBS-101 Rocking Bioreactor Skid 70,000 140,000
Container Volume = 2.00 L
Unlisted Equipment 293,000
TOTAL 1,466,000

Table 6, which was also extracted from the Economic Evaluation Report, provides a breakdown of the direct
fixed capital investment, which is around $19 million for a plant of this capacity. This cost is based on a
variety of multipliers (associated with piping, instrumentation, etc.) that are process and region specific.
Note that SuperPro’s default capital cost multipliers may not be appropriate for your particular location,
process scale, or industry (e.g., cell therapy vs. monoclonal antibody production vs. synthetic chemistry vs.
food industry, etc). As mentioned previously, these multipliers may be edited to improve the accuracy of
the cost estimate. For detailed information on how to access and modify the capital cost multipliers, please
consult the Economic Evaluation chapter of the manual and the corresponding topic in the Help Facility
of SuperPro.

Note: Most of the multipliers used in cost analyses such as the one shown in Table 6 can be stored in the
User Database of SuperPro and retrieved for future work on similar projects. This facilitates standardization
and improves the accuracy of cost estimation. For information on how to take advantage of the database
capabilities of SuperPro, please consult the SynPharmDB document in the …Examples \
Pharmaceuticals \ SynPharm directory.

Intelligen, Inc. Page 24

 Table 6: Fixed Capital Costs (2019 Prices in US$)

Total Plant Direct Cost (TPDC) (physical cost)

1. Equipment Purchase Cost 1,466,000
2. Installation 792,000
3. Process Piping 513,000
4. Instrumentation 587,000
5. Insulation 44,000
6. Electrical 147,000
7. Buildings 5,865,000
8. Yard Improvement 220,000
9. Auxiliary Facilities 587,000
TPDC 10,220,000

Total Plant Indirect Cost (TPIC)

10. Engineering 2,555,000
11. Construction 3,577,000
TPIC 6,132,000

Total Plant Cost (TPC = TPDC+TPIC)

TPC 16,351,000

Contractor’s Fee & Contingency (CFC)

12. Contractor’s Fee 818,000
13. Contingency 1,635,000
CFC = 12+13 2,453,000

Direct Fixed Capital Cost (DFC = TPC+CFC)

DFC 18,804,000

Additional tables associated with labor, utilities, consumables, etc., may be extracted from the Economic
Evaluation Report and the Itemized Cost report as well.

Intelligen, Inc. Page 25

Summary
Our objective with this example was to present a conceptual model for an allogeneic cell therapy production
process. As mentioned previously, cell therapy is a comparatively new field. In particular, allogeneic
production of cell therapies for humans is essentially at its inception. As a result, there is currently a great
deal of variability in potential production methods, and the field is evolving rapidly. Research studies are
being conducted with various feed materials (e.g., different types of media, different types of microcarrier
beads, etc.), different equipment types (e.g., stirred tank bioreactors vs. planar units), different purification
steps (e.g., with or without diafiltration), etc. Furthermore, dose sizes may end up varying by several orders
of magnitude depending on the treatment being developed. As a result, the flowsheet setup, operational
parameters, cost calculations, and other analyses in this example should be viewed as merely one possible
outcome for an allogeneic cell therapy product, based on current technologies and processing methods.

REFERENCES

1] Jossen, V., van den Bos, C., Eibl, R., and Eibl, D. “Manufacturing human mesenchymal stem cells at
clinical scale: process and regulatory challenges”. Applied Microbiology Biotechnology, 102(9): 3981–
3994. 2018. DOI: 10.1007/s00253-018-8912-x

2] Pigeau, G., Csaszar, E., and Dulgar-Tulloch, A. “Commercial Scale Manufacturing of Allogeneic Cell
Therapy”. Frontiers in Medicine, 5:233. 2018. DOI 10.3389/fmed.2018.00233.

3] Malik, N. “Allogeneic Versus Autologous Stem-Cell Therapy”. BioPharm International, Volume 25,
Issue 7. Jul 01, 2012.

4] Satyanarayana, M. “Immunotherapy turns to natural killers”. Chemical & Engineering News, Volume
97, Issue 30. July 28, 2019.

5] Lin, P., Lin, Y., Lennon, D., Correa, D., Schluchter, M., and Caplan, A. “Efficient Lentiviral Transduction
of Human Mesenchymal Stem Cells That Preserves Proliferation and Differentiation Capabilities”. Stem
Cells Translational Medicine, 1(12). December 2012. DOI 10.5966/sctm.2012-0086.

6] Stanton, D. “Cost of Goods Is Crucial for the Future of Regenerative Medicine: CAR-T Cell Therapy
Provides a Case Study in Perspective”. BioProcess International. 18 April 2019.

7] Malik, N. “Allogeneic Versus Autologous Stem-Cell Therapy”. BioPharm International, Volume 25,
Issue 7. July 2012.

Intelligen, Inc. Page 26

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