Week 1 HW: Final Project Ideas

description: “Biomanufacturing recombinant fibrous proteins for large-area wound coverage”

🧬 Programmable Wound Scaffolds

Rapid biomanufacturing of an off-the-shelf scaffold for major burns

1. What do I want to make, and why?

During my medical training, I developed a particular interest in surgery, reconstructive procedures and wound healing. One problem I want to explore through biomanufacturing is how to make large quantities of wound-covering material available to patients with extensive burns.

The clinical problem: major burns can require coverage of large areas of skin while leaving patients with limited healthy donor sites. Patient-specific cultured skin products, such as Epicel, can expand the available skin but require a biopsy and approximately 17 days of cell culture.

Other technologies, including RECELL and STRATAGRAFT, address parts of this problem. However, they do not eliminate the need for autografting in every type of major burn.

My goal is to explore a complementary approach: manufacture standardized wound scaffolds before patients need them, rather than manufacturing each scaffold after a patient arrives.

The proposed material

My first-generation scaffold would be an acellular sheet made from a recombinant hybrid protein containing three components:

Unlike naturally extracted collagen, recombinant proteins can be engineered at the amino-acid level.

Future versions could incorporate cell-adhesion motifs, enzyme-sensitive sequences and other functional domains that influence how the material interacts with regenerating tissue.

Collagen-like/ELP fusion proteins have already been investigated experimentally for wound healing. My proposed research would focus on whether such proteins can be manufactured efficiently and converted into standardized, large-area scaffolds.

2. What living system would make it?

Primary chassis: engineered E. coli

I would initially use engineered Escherichia coli to manufacture the recombinant hybrid protein.

Producing native human collagen in bacteria is challenging because its structure normally requires post-translational modifications, including proline hydroxylation.

Certain bacterial collagen-like proteins, however, can form collagen-type triple helices without requiring hydroxyproline. These provide a potentially simpler starting point for microbial production.

The collagen-like domain would be fused to an elastin-like polypeptide to create a single genetically encoded building block.

Proposed manufacturing process

flowchart TD
    A["Design recombinant DNA"] --> B["Engineered E. coli"]
    B --> C["Automated fermentation"]
    C --> D["Recombinant hybrid protein"]
    D --> E["Recovery and purification"]
    E --> F["Scaffold fabrication"]
    F --> G["Sterilization and quality control"]
    G --> H["Off-the-shelf wound sheets"]

Inputs: recombinant DNA, bacterial production strain, carbon source, nitrogen, water, salts and oxygen.

Biological process: bacterial growth and expression of the collagen-like/ELP fusion protein.

Output: purified recombinant protein that can be formulated into a porous wound scaffold.

The protein-manufacturing step and the scaffold-fabrication step are separate processes. Producing the protein does not automatically guarantee that it can form a suitable wound sheet.

3. How would I use automation?

I would use different automation technologies during early development and manufacturing.

Prototype development

A liquid-handling robot, such as Opentrons, could help me screen different versions of the recombinant protein.

For example, I could compare:

• 3 collagen-like architectures
• 4 elastin-like polypeptide designs
• 2 cell-adhesion motif conditions

This would produce 24 protein variants, or 72 experimental cultures if tested in triplicate.

Automation could assist with media preparation, inoculation, induction, sampling and protein quantification.

The most promising candidates would then undergo testing for protein stability, scaffold formation, mechanical properties, degradation and cell compatibility.

Manufacturing

At larger scale, I would use an automated fed-batch bioreactor.

The system could continuously control temperature, pH, dissolved oxygen, agitation and nutrient feeding.

Downstream automation could assist with protein recovery, purification, formulation, sheet fabrication and quality control.

The purpose of this two-stage approach is to use small-scale automation to identify a suitable protein before committing to a larger manufacturing process.

4. How much would I need to make, and how long would it take?

I will use 1 m² of wound scaffold as my initial manufacturing target. This is an engineering benchmark, not a recommended clinical dose.

The scaffold would be manufactured as modular 10 × 10 cm sheets.

Back-of-the-envelope calculation

The protein concentration and thickness are initial assumptions. The final dry or hydrated scaffold dimensions would depend on the fabrication process.

The assumed purified yield of 2 g/L is a working estimate for my proposed fusion protein. It is not an experimentally demonstrated yield for this exact construct. Published studies have achieved gram-per-liter production of recombinant bacterial collagen-like proteins under optimized fermentation conditions.

Manufacturing time

The timeline is an engineering assumption. Medical-grade manufacturing, sterilization validation and product release testing may require additional time.

Crucially, the patient would not wait for this process. The goal is to manufacture and store the scaffold in advance so that approved, released material is immediately available when needed.

5. What don’t I know yet?

Three technical questions would determine whether this idea can become a viable manufacturing platform.

1. Can the hybrid protein form a clinically useful scaffold?

Producing a recombinant protein does not guarantee that it can form a large, porous and mechanically stable sheet.

I would need to determine which fabrication process achieves suitable wet strength, elasticity, fluid handling and wound conformity.

Early experiments would compare material properties and cell compatibility before progressing to more complex biological testing.

2. What is the optimal protein architecture?

Changing the collagen-like or elastin-like domains could affect folding, expression yield, mechanical properties and degradation.

I would need to determine which combinations of structural domains and functional motifs provide useful material properties without compromising manufacturability.

This is where automated design-build-test screening would be most valuable.

3. Can it be manufactured safely and economically at scale?

A recombinant protein intended for large open wounds would require rigorous purification, particularly if produced in E. coli.

Major concerns include endotoxin removal, residual bacterial proteins and DNA, batch consistency, sterilization and shelf stability.

I would eventually need to evaluate production cost and throughput using a more meaningful metric than protein yield alone:

Square meters of acceptable scaffold manufactured per batch, per dollar and per day.

Long-Term Vision

The initial product would be a standardized structural scaffold. If the manufacturing platform proves viable, later versions could progressively introduce cell-adhesion motifs, controlled degradation and regenerative signaling.

My long-term interest is to explore whether programmable biomaterials could eventually improve tissue regeneration and reduce fibrosis in extensive wounds.

The immediate goal, however, is much simpler: determine whether recombinant protein biomanufacturing can provide a scalable source of clinically useful wound-scaffold material.