Monoliths in Bioprocess Technology

Monolithic columns are a special type of chromatography column, which can be used for the purification of different biomolecules. They have become popular due to their high mass transfer properties and short purification times. Several articles have already discussed monolith manufacturing, as well as monolith characteristics. In contrast, this review focuses on the applied aspect of monoliths and discusses the most relevant biomolecules that can be successfully purified by them. We describe success stories for viruses, nucleic acids and proteins and compare them to conventional purification methods. Furthermore, the advantages of monolithic columns over particle-based resins, as well as the limitations of monoliths are discussed. With a compilation of commercially available monolithic columns, this review aims at serving as a ‘yellow pages’ for bioprocess engineers who face the challenge of purifying a certain biomolecule using monoliths.


Introduction
The Centre for Chemical Process Safety (CCPS) defines a bioprocess as a process that makes use of microorganisms, cell culture or enzymes to manufacture a product or to complete a chemical transformation [1].In other words, a bioprocess envelops production and purification of a biomolecule that can be of therapeutic (e.g., protein-based therapeutic drugs) or economic importance (e.g., food industry, waste water treatment).As shown in Figure 1, a typical bioprocess is comprised of upstream (strain engineering, production of target biomolecule) and downstream processes (clarification, separation, purification).In a typical downstream process, the product undergoes capture, purification and/or polishing steps to yield the final, purified preparation.Of course, these steps and their execution depend on the purity of the starting material; e.g., the purification of an intracellular biomolecule from E. coli might require more purification steps than the purification of a secreted product from yeast.During the last decade, production titers in the upstream dramatically increased due to strain engineering, media optimization and bioprocess engineering approaches.However, the downstream process did not develop at the same pace, which is why product purification actually describes the bottleneck of a typical bioprocess.To date, conventional downstream methods, like centrifugation and filtration, are not able to handle the high product titers coming from the upstream process [2], which is why alternative, fast and efficient separation techniques are needed.Chromatography with particle-based resins has become the backbone of downstream processing for biomolecules, such as viruses, nucleic acids and proteins.However, mass transfer in particle-based resins occurs through diffusion, which is why purification of large biomolecules, such as glyco-proteins and immunoglobulins, takes a long time.This can be critical for unstable products, which is why faster purification methods are needed.In the past twenty years, monolithic columns have become popular as an efficient tool for the purification of large biomolecules due to their high mass transfer properties and short purification times [3].Monoliths are a special type of chromatographic column having a single block of a homogenous stationary phase with many interconnected channels [4].The stationary phase of the monolith can be of various chemistries, allowing the purification of different kinds of biomolecules with different characteristics.Monoliths are the fourth generation chromatography material [3], succeeding beads, porous particle-based columns and membrane adsorbers.In the last two decades, numerous articles describing preparation, properties and applications of monolithic columns were published [4][5][6][7][8][9][10][11][12][13][14][15][16][17][18].In contrast, this review focuses on the applied aspect of monoliths and describes recent applications of monoliths for the purification of biomolecules.Thus, this review serves as a 'yellow pages' for bioprocess engineers who want to purify a certain biomolecule by monoliths.

Advantages and Limitations of Monoliths
The complexity of any purification process is finding the optimal balance between surface area, porosity, pore size and distribution and other physical and chemical properties of the chromatographic support, such as mass transfer properties and flow distribution.In this respect, monoliths show several advantages over particle-based resins.

Convective Flow
In particle-based resins, separation processes happen by diffusion into pores.The longitudinal diffusion of the target analyte declines with increasing flow rate.Furthermore, the diffusion coefficient, which is comprised of both diffusive and convective components, is predominantly dependent on convection for higher flow velocities, which, in turn, is dependent on the pore size [20].In contrast to particle-based resins, in monoliths, the separation of biomolecules dominantly happens by convective flow through channels having a diameter of more than 1,000 nm.This allows high flow velocity and, therefore, high throughput purifications [16].

Porosity
Monolithic columns have high porosity due to their large interconnected channels.Optimization of pore size and pore distribution can be done over a wide range by changing the porogen composition, porogen to monomer ratio and polymerization temperature [21][22][23][24][25]. Owing to their high bed porosity, the pressure drop in monoliths is much lower in comparison to particle-based resins.

Adsorption Area and Dynamic Binding Capacity
Monolithic columns have a low absolute surface area, but a high adsorption area due to their porous structure [3], allowing a high dynamic binding capacity (DBC).Another main advantage of monoliths is their flow-independent DBC allowing straight-forward scalability [3,[26][27][28].A direct comparison between monoliths and particle-based resins for the purification of virus-like particles from yeast homogenate has been conducted by Burden et al.The authors concluded that the monoliths are three-fold superior in terms of DBC with equivalent recovery in yield (90%) compared to particle-based resins [29].

Separation Time
Due to the high flow velocity and low pressure drop, the overall process time using monoliths is much lower compared to particle-based resins [30].For example, Rupar et al. were able to purify potato virus Y with the help of monolithic columns in half the separation time in comparison to classical methods.Even though the yield achieved by monolithic columns was slightly lower than by classical methods, the possibility for easy scale-up offered valuable compensation for subsequent industrial-scale purification [31].In another study, a direct performance comparison between conventional and monolithic C-18 columns was conducted, and it was shown that separation time was decreased five-fold by using monolithic columns [32].

Stationary Phase
Monoliths allow a high degree of freedom for the operator, since they can be manufactured from various raw materials (such as polymethacrylate, polyacrylamide, polystyrene, silica and cryogels) with different morphologies and channel diameters [33].In general, the monolithic media can be classified into two categories, namely organic, polymer-based and inorganic, silica-based media.The main advantages of organic, polymer-based media are pH stability and customizability, but the columns are mechanically not very stable, which shortens the column life-time.On the other hand, inorganic, silica-based monoliths show excellent stability and separation efficiency.However, manufacturing is sophisticated and time consuming [34].Recently, also organic-inorganic hybrid monoliths have been prepared combining the advantages of both [34][35][36].

Customizability
Monoliths can be customized to the needs of the user, since there are various stationary phase chemistries, active binding sites and shapes and sizes (disks, tubes) available.Although the shape of the monolith per se does not present a significant advantage, a minor advantage to be noted is that monolithic disks (0.34 mL) do not have a specific flow direction, enabling back-flush to encounter clogging problems.BIA separations, Slovenia, offers small 0.34-mL monolithic disk columns comprising a wide variety of stationary phases [19].Since monolithic columns do not lose resolution with scale-up, preliminary, less expensive characterization and screening studies using analytical-scale disks are possible.

Scalability
Monolithic supports are easy to scale up without the need for column modifications [3,26].Monolithic disks can be stacked up to four disks in the same housing, increasing efficiency and capacity without compromising resolution [3].Monoliths have overcome the mass transfer problems posed by particle-based columns, and commercial monolithic columns up to 8 L are available [3].

Limitations of Monolithic Columns
Mass transfer in monoliths is based on convection and, hence, cannot be used for size exclusion chromatography (SEC), since SEC is based on the difference in diffusivity of individual molecules into pores.Recently, it was shown that biomolecules can still be separated by size by using friction in the monolithic support, called slalom chromatography [37][38][39].However, monolithic columns for slalom chromatography have to be further optimized and have not been utilized in industry yet [3].
Fouling and clogging is another major limitation in most chromatographic columns, as it results in the reduction of DBC and an increase in the pressure drop across the column, which decreases the life span of the column significantly.As mentioned before, back-flush is possible only in smaller monolithic disks (with axial flow) to reverse fouling and clogging and is not possible in tubular monolithic columns (with radial flow).
Lipids are a major class of biological foulants, as they bind irreversibly and are hard to remove from the column.Burden et al. tackled lipid fouling by sample pretreatment, using Amberlite/XAD-4 beads for lipid removal, which doubled the dynamic binding capacity of a monolithic disk column [29].

Applications of Monoliths
Monolithic supports have been extensively used for the purification of different biomolecules.Boehringer Ingelheim (Austria) established the first industrial process for pDNA purification using monolithic supports [16].Here, we want to sum up recent studies describing monolithic purifications of the three major biomolecule classes: (1) viruses; (2) nucleic acids; and (3) proteins.We describe one success story for each biomolecule in more detail and compare it with conventional downstream strategies.We want to present the review as a yellow pages for bioprocess engineers, who face the challenge of purifying either of these biomolecules.

Virus Purification
Viruses can be used for the production of recombinant proteins and for gene therapy applications [40,41] and describe a major class of biomolecules in industry.Today, conventional virus purification includes centrifugation, filtration and chromatography, which either returns low yields (e.g., only 1% for ultracentrifugation [42]) or is time consuming and tedious.For several years, ion exchange monolithic supports have been extensively used for the purification of viruses.In 2013, Rupar et al. purified the potato virus Y (PVY) by conventional methods and by monoliths and compared both strategies (Figure 2; [31]).The authors used a CIM ® QA (quaternary amine) monolith column and achieved product recovery and purity comparable to conventional purification methods involving ultracentrifugation.However, they could reduce the overall process time by more than half.
In another study, baculovirus from cell culture supernatant was successfully purified using the anion exchange monolithic column CIM ® QA [30].The authors were able to reduce the volume 82-fold, increase activity 51-fold and remove 99% of the contaminants.More successful applications of monolithic columns for the purification of viruses are summarized in Table 1.

Nucleic Acid Purification
Since the introduction of plasmid-based DNA (pDNA) therapeutics in the 1990s [57], they have been extensively used in medical diagnostics.In 2003, the first DNA vaccine for human therapy was approved [58].These therapeutic applications require high amounts of highly pure pDNA.There is a variety of purification strategies available for the purification of pDNA using conventional methods, including tangential flow filtration (TFF) [59][60][61], membrane adsorption [62][63][64] and chromatography [65,66].Monolithic columns with different functionalities have also been tested for the purification of pDNA.In the past few years, several studies described the successful grafting of a weak anion exchange monolithic column (CIM ® DEAE) with different functionalities, such as hydrophobic and ion exchange moieties, to allow pDNA purification in only a single step [67][68][69].This concept, called conjoint liquid chromatography (CLC), allows the formation of mixed mode monoliths.This provides a much faster, but still a very efficient alternative to the conventional multi-step procedure (Figure 3).The one-step strategy proved efficient for removal of over 99% of gDNA, RNA and host cell proteins and was able to achieve highly pure pDNA from cell culture.Theoretically, this strategy can easily be scaled up, giving a total amount of 15 g of pDNA, which can be purified with an 8-L column in only one single loading step [67].However, monolithic columns have not only been employed for the purification of pDNA, but also for other nucleic acids (Table 2).

Protein Purification
In conventional particle-based chromatography, different protein properties, like the isoelectric point and hydrophobicity, can be used to purify the product.Typical purification strategies comprise ion-exchange (IEX) and hydrophobic interaction (HIC) approaches, as well as the use of affinity tags.Since different raw materials and, thus, chemistries can be used for monoliths, the same purification principles can be applied there (Table 3).To mention only a few examples, ion-exchange monoliths have been successfully used for the purification of coagulation factors and recombinant proteins [78,79]; myoglobin, lysozyme [80] and bovine serum albumin [81] were purified by HIC monoliths; and affinity chromatography was employed for the purification of immunoglobulin G using a CIM ® r-Protein A monolithic column [82,83].More applications of monoliths for the purification of proteins are shown in Table 3.A prominent example for the use of a monolith for protein purification is the downstream process for Factor IX (FIX), which plays an important role in blood coagulation.Ribeiro et al. tested different particle-based and monolithic anion exchange resins for the purification of recombinant FIX (rFIX) from cell culture supernatant (Figure 4; [78]).Four different supports, namely monolith CIM ® QA, Sartobind ® Q, Q Sepharose ® and Fractogel ® TMAE (trimethylamino ethyl), were used for screening, and a pseudo-affinity elution with calcium chloride was developed.CIM ® QA rendered the highest dynamic binding capacity in comparison to the other resins, namely 4.6 mg/mL of monolithic support.The authors conducted a design of experiments to optimize elution conditions and finally obtained a recovery yield of 83%, a purification factor of 304, 99.99% removal of DNA and 1,256-fold removal of host cell proteins in only one purification step.Upon up-scaling from a 1-mL to an 8-mL CIM ® QA monolithic tube column, similar results were obtained [78].

Commercially Available Monoliths
As shown above, monoliths are a powerful alternative to particle-based resins for the purification of biomolecules, and the first industrial processes employing monoliths have been launched.Thus, several providers offer monoliths of different chemistries, shapes and sizes.Polymethacrylate-based monolithic columns are currently produced and distributed by BIA separations (Ljubljana, Slovenia) under the trade name CIM ® (convective interaction media), CIMac ® (CIM analytical columns) and CIMmultus ® .They also offer custom-made columns with different column chemistry to suit the needs of the end user.Dionex (CA, USA) also produces polymethacrylate monolithic columns under the trade name ProSwift ® .Phenomenex (CA, USA) markets silica-based monolithic columns under the trade name Onyx ® .Agilent technologies (CA, USA) markets poly-(glycidyl methacrylate-co ethylene dimethacrylate) monoliths, made by BIA separations, under the trade name Bio-monolith ® [91].Merck Millipore (MA, USA) has the trade name Chromolith ® for marketing their silica-based monolithic columns.Bio-Rad (CA, USA) produces polymer-based monolithic columns under the trade name Uno ® .A summary of commercially available monoliths, their underlying purification principle and respective distributors is given in Table 4.

Concluding Remarks and Outlook
In terms of resolution and separation speed, monolithic columns outperform particle-based resins.Furthermore, scale-up does not affect the resolution of monolithic purification processes.It was shown that the dynamic binding capacity of monoliths, which is comparable to particle-based resins, actually increases with increasing product size.Furthermore, the possibility of using different raw materials, chemistries, pore sizes and grafting, which allows a high degree of freedom for the operator, causes an overwhelming interest in monoliths today.Our research group is currently conducting experiments to implement monolith technology as an impurity monitoring process analytical technology (PAT) tool across unit operations.In a similar approach, Smrekar et al. already implemented the monolith technology as a PAT tool to monitor a virus production process [97].
Another highly interesting approach was recently given by Fee et al., who used a 3D printer to manufacture monoliths with hexagonal channels from computer-aided design (CAD) models [98].This allows more control in pore formation and distribution and might further boost the performance and applicability of monolith technology in the future.

Table 1 .
Applications of monolithic columns for purification and concentration of viruses.

Table 2 .
Applications of monolithic columns for the purification of nucleic acids.

Table 3 .
Applications of monolithic columns for the purification of proteins.