A Closer Look at EV-Based Therapeutics: Purification, Scalability, and GMP Compatibility

Dr. Yu Fujita is spearheading a transformative approach to treating lung diseases through extracellular vesicle-based therapeutics, a novel modality poised to redefine therapeutic strategies for conditions such as idiopathic pulmonary fibrosis (IPF) and chronic obstructive pulmonary disease (COPD). Trained as a medical doctor in Japan and driven by the limitations of existing respiratory treatments, Fujita transitioned into research, earning a PhD at the National Cancer Center in Tokyo and completing postdoctoral work at UC San Diego. His pioneering efforts focus on harnessing extracellular vesicles (EVs) to address critical unmet medical needs. In an exclusive interview with GeneOnline, Fujita elucidates the potential of EVs, the complexities of scaling production, and strategic insights for achieving market success.

EVs: A Multi-Pronged Weapon Against Lung Disease

Fujita’s research targets lung-specific EVs derived from bronchial epithelial basal cells to combat intricate diseases like IPF. “Conventional therapies address single molecular targets, but IPF involves multiple signaling pathways. EVs, enriched with microRNAs and proteins, modulate several pathways simultaneously,” he explains. Since beginning his research in 2012 at the National Cancer Center, Fujita discovered that EVs from diseased cells exacerbate IPF, whereas those from healthy cells offer therapeutic benefits. “Our focus on lung resident cells, rather than generic EVs, enhances treatment specificity,” he asserts.

This strategy underpins Fujita’s initial pipeline targeting IPF, a rare yet severe lung disease with limited therapeutic options. “IPF is our primary focus, but we plan to address COPD, which impacts a significantly larger population,” he states. Fujita’s hypothesis posits that EVs’ multifaceted mechanisms can surpass the efficacy of single-target therapies, such as small molecules, which frequently fail in IPF’s complex pathological environment. “Our preclinical data suggest that EVs from healthy lung cells can arrest IPF progression,” he notes, signaling a future where EVs address both rare and prevalent lung conditions.

Evolving EV Therapeutics: From Broad to Precision Targeting

Building on this foundation, Fujita envisions EV-based therapeutics evolving across multiple generations, each refining specificity and expanding applications, with cancer as a key target for advanced stages. “First- and second-generation EVs, like those from mesenchymal stem cells or our lung-specific EVs, target broad mechanisms—anti-inflammatory, anti-fibrotic, or anti-senescence effects—suitable for diseases like IPF,” he explains. These native EVs, while potent, lack precise targeting. In contrast, third- and fourth-generation EVs employ advanced engineering—chemical modifications, peptide ligands, and post-loading of siRNA or microRNAs—to enable active targeting of organs like the lungs or brain. “These later generations are tailored for specific diseases, with cancer as a primary focus due to its urgent medical need,” Fujita says. He sees cancer as a springboard, paving the way for EVs to address other complex conditions, such as neurological disorders or untreated rare diseases, through refined drug delivery systems for precise cellular uptake. “The transition from broad to specialized EVs will broaden their therapeutic scope, tackling both common and niche diseases,” he predicts, underscoring their potential for scalable, precision-driven treatments.

Given the competitive landscape of EV research, Fujita emphasizes the importance of strategic focus for emerging researchers.  “Don’t chase generic EVs. Pick a cell source tied to your target organ for better efficacy,” Fujita urges. “And validate your hypothesis early—test diseased versus healthy EVs to understand their role in pathogenesis.”

Scaling Up: Cracking the Mass Production Puzzle

Scaling EV production presents formidable challenges, which Fujita’s team is addressing with innovative solutions. “Mass production is essential, particularly for engineered EVs, but it is both costly and technically demanding,” he acknowledges. His group has developed robust processes for producing native EVs using primary cells, yet engineering EVs—modified for precise delivery to organs such as the lungs or brain—requires advanced techniques. “We are investigating chemical modifications, peptide ligands, and post-loading methods to incorporate siRNA or microRNAs into EVs,” he details, highlighting efforts to optimize drug delivery systems (DDS).

A critical starting point is the supernatant, or conditioned media, which poses unique production challenges. Unlike conditioned media treatments, which include growth factors, cytokines, and potential contaminants, EVs deliver superior therapeutic potency. “Our research shows EVs significantly outperform conditioned media, but their purification demands precision,” Fujita explains. Current purification methods, like ultracentrifugation, are a bottleneck. “They’re slow and yield only a fraction of EVs,” Fujita laments. To address this, Fujita’s team has transitioned to combining tangential flow filtration (TFF) with chromatography. “This approach removes nearly 100% of impurities, bringing us closer to GMP-grade EVs, though it remains labor-intensive,” he notes. Streamlining purification is vital for scalability, as current methods strain time and resource budgets.

Then, the challenge of tracking EV biodistribution further complicates production. Labeling EVs with lipid-based dyes like PKH or DIR enables imaging but risks altering their function. “Free dyes can distort data, and labeling reagents may compromiseFaq1 may compromise EV integrity,” Fujita warns. His team is exploring genetic tags, such as CD63 or GFP, which are expressed within cells for more reliable labeling. “Genetic tags show promise, but we must rigorously validate them to ensure labeled EVs behave like native ones,” he emphasizes, underscoring the need for precision in biodistribution studies.

Crafting GMP-Ready, High-Purity EV Solutions

To guide researchers in optimizing purification, Fujita stresses innovation in technology and process design. “Develop high-yield, low-impurity purification methods that are GMP-compatible,” he advises. “Combining TFF with chromatography is a strong start, but explore automated systems to reduce labor and enhance scalability.”

Looking ahead, Fujita predicts a shift to immortalized cell lines for engineered EVs. “Primary cells are great for native EVs, but immortalized cells offer uniform quality and larger yields,” he says. Automation is another game-changer. “We’re developing self-driving EV production systems—think automated bioreactors with AI monitoring,” he enthuses. These could slash costs and boost scalability, making EVs viable for global markets.

To support researchers navigating these technical hurdles, Fujita offers practical guidance. “Invest in TFF and chromatography early, as they are scalable and compatible with GMP standards,” he advises. “For engineered EVs, prioritize immortalized cell lines and automate upstream processes. Ensure labeling methods are validated to preserve native EV functionality.”

Market Entry: Aligning Stakeholders and Securing Funding

Getting EVs to market is as much about strategy as science. Fujita, who earned his PhD in 2019 and completed a postdoc at UC San Diego, stresses the need to align stakeholders. “In Japan, we’re working with AMED to shape EV guidelines, as this is the country’s first EV pipeline,” he says. His team collaborates with clinicians, regulatory experts, and pharmaceutical companies to navigate Japan’s stringent regulatory landscape. “You need a diverse team—scientists alone won’t cut it,” he asserts.

Funding is another hurdle. “Large-scale production isn’t cheap, and investors want proof of concept,” Fujita notes. His team secured grants from Japan’s Agency for Medical Research and Development (AMED) by aligning their IPF project with national priorities like regenerative medicine. “We used AMED funding to generate proof-of-concept data, which attracted manufacturing and pharma partners,” he says. Last year, Fujita co-founded a venture company to commercialize his IPF pipeline, a bold step toward market entry. “You need a dedicated entity to handle funding and scale-up,” he explains.

For global markets, Fujita sees Asia as a hotspot. “Taiwan’s biotech ecosystem is robust—academia, ventures, and government work seamlessly,” he says. He predicts EV therapeutics will gain traction in Asia first, with Japan and Taiwan leading due to their regulatory agility. “FDA approval might come in a year or two, but Asia could move faster,” he speculates.

To navigate the path to market successfully, Fujita advises researchers to strategically align their projects with national health priorities to secure government funding. “Build a multidisciplinary team with regulatory and industry expertise from the outset,” he recommends, “and consider establishing a venture to attract investors. Targeting markets like Japan or Taiwan can expedite regulatory approvals.”

Patient Safety and AI: Cornerstones of Innovation

Patient safety is the cornerstone of Fujita’s mission. “As a clinician, I have witnessed the suffering of IPF patients with no viable treatments. Safety is paramount,” he affirms. Unlike conditioned media treatments, which pose risks due to unknown contaminants, EVs offer a safer, cleaner profile. “Properly purified EVs outperform conditioned media in both efficacy and safety,” he states. His team conducts comprehensive safety assessments, including rodent studies, to ensure GMP-grade EVs. “CDMOs must prioritize upstream cell health, as healthy cells produce high-potency EVs,” he adds.

Artificial intelligence (AI) is revolutionizing Fujita’s research. “EVs contain complex cargos, including microRNAs and proteins. AI enables comprehensive biomarker profiling and production optimization,” he explains. His team employs AI to monitor cell morphology and culture conditions, ensuring consistent EV quality. “In downstream processes, AI can enhance purification efficiency, reducing costs,” he predicts. Fujita envisions AI-driven “quality by design” systems that optimize every production stage, making EVs accessible to millions.

For researchers leveraging AI and prioritizing safety, Fujita offers targeted insights. “Utilize AI to monitor cell health and streamline purification—it significantly enhances efficiency,” he advises.  “For safety, test EVs in animal models early and partner with CDMOs experienced in biologics.”

The Road Ahead: A Patient-First Future

Fujita’s vision is clear: deliver EV therapeutics to patients. “My dream is to see IPF patients treated with our pipeline,” he says. His venture company is pushing for clinical trials, with COPD and engineered EV pipelines in the works. “Engineered EVs could target cancer or neurological diseases in five to ten years,” he predicts. Collaboration is key—Fujita’s team partners with academia, industry, and regulators across Japan and Asia. “This modality could change medicine, but it takes a village,” he says.

For Fujita, it’s personal. “Patients visit my hospital hoping for new treatments. I want to give them that hope,” he shares. His work, showcased at global conferences like the JPM Healthcare Conference, signals a new era for lung disease treatment. As EVs move closer to market, Fujita’s patient-first ethos and strategic savvy are lighting the way.

Dr. Fujita actively supports global collaboration to advance EV-based therapies, targeting idiopathic pulmonary fibrosis, COPD, and beyond, with a vision to transform patient health across Asia and worldwide. Image: GeneOnline

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Author

Bernice Lottering