Innovation that Matters


Delivering on the Promise of New Modalities: An Interview with Zachary Hornby, President & CEO, Boundless Bio

As part of WuXi AppTec’s ongoing efforts to collaboratively foster new thinking and actionable approaches in advancing breakthroughs for patients, we have launched a new interview series in 2022 – “Delivering on the Promise of New Modalities” – so leading voices of R&D can share how their approaches are addressing the barriers standing in the way of breakthroughs. We’re joined for our latest interview by Zachary Hornby, President and CEO of Boundless Bio, a next-generation precision oncology company who raised an oversubscribed $105 million in Series B Financing last year to develop innovative therapeutics directed against extrachromosomal DNA (ecDNA) in aggressive cancers. Earlier this month, Boundless Bio announced a partnership with Sophia Genetics to further develop Boundless’s proprietary precision diagnostic method called ECHO (ecDNA Harboring Oncogenes) to detect ecDNA in a patient’s routine tumor sequencing data to select appropriate patients for treatment in the in clinical trials of the first ecDNA-directed therapies (ecDTx). Greetings Zachary! In your opinion, what are the top therapeutic challenges in the field of oncology? Zachary: Within the field of oncology, the top therapeutic challenge is the fact that patients with oncogene amplified tumors, which account for 400,000 new patients per year in the US, have no standard of care therapies and have significantly worse survival than the cancer population at large. The underlying biology that accounts for this poor prognosis of patients with oncogene amplified tumors is the phenomenon that oncogene amplifications, in contrast to other types of oncogenic alterations, frequently do not occur on linear chromosomal DNA and instead occur on circular extrachromosomal DNA (ecDNA). ecDNA are large (1-3 mega base pair), circular units of nuclear DNA that are physically distinct from chromosomes, highly transcriptionally active, and do not adhere to Mendelian principles of genomic inheritance. They are the primary site of high copy number focal oncogene amplifications, and they propel primary tumor oncogenesis and secondary tumor resistance through rapid amplification and genetic evolution. ecDNA are observed only in cancer cells and not in healthy cells. Until now, the industry has not previously understood ecDNA biology and its role in cancer nor how to appropriately treat cancers that leverage this biology for growth and resistance. Indeed, ecDNA is becoming a new focus of the cancer field. How might your approaches lead to better cancer therapeutics? Zachary: Boundless Bio’s novel technological approach to treating patients with oncogene amplified cancers is to therapeutically exploit the unique cellular vulnerabilities associated with cancer cells’ reliance on ecDNA. Boundless has built an only-in-class platform called Spyglass that allows us to exquisitely characterize oncogene amplified cancer models and determine how, when, and why they rely on ecDNA for growth and survival. In thoroughly interrogating ecDNA’s role in these cancer cells, we have learned the lifecycle of ecDNA—how they form, replicate, transcribe, segregate, and degrade. Through our understanding of the ecDNA lifecycle, we have identified nodes of vulnerability that represent pharmacological intervention points where we can develop small molecule inhibitors that disrupt the formation and function of ecDNA and render them inaccessible to cancer cells’ benefit. No other company in the biopharma industry is dedicated to improving and extending the lives of patients with oncogene amplified cancers, and no other company is exploiting ecDNA biology to develop novel therapeutics. To realize the full potential of your ecDNA platform, do you anticipate any critical challenges? What about recent milestones? Zachary: One key challenge is that ecDNA represents novel biology that has not previously been therapeutically targeted. Most of the targets that Boundless is pursuing are novel or have not been successfully drugged to date. A second challenge is that ecDNA is a novel biomarker for which no clinical detection methods exist. Boundless is developing a novel companion diagnostic clinical trial assay (CTA) called ECHO (ecDNA Harboring Oncogenes) that uses routine clinical NGS (next generation sequencing) data to detect ecDNA in patient tumor specimens. A key milestone for Boundless will be to demonstrate clinical proof of concept with our first ecDNA directed therapy (ecDTx), BBI-355, in its first in human (FIH) clinical study, due to begin in Q1:2023, which will be a precision oncology trial leveraging ECHO to select appropriate patients for treatment. If we were to gather here again in 10 or 15 years’ time, what do you think we’re going to be talking about in terms of what we have already achieved in the industry? Zachary: In 10-15 years, we will be discussing the first drugs ever designed specifically for, and approved and commercialized for, patients with high unmet need oncogene amplified cancers. We will talk about how an advanced understanding of the underlying molecular biology, not just the genetic driver (e.g., EGFR amplification), but the genetic topology (i.e., circular extrachromosomal DNA) afforded insight into cancer specific synthetic lethality. We will eagerly look forward to the additional indications, possibly beyond cancer, that our new understanding of topology-dependent synthetic lethality enables for targeted treatment. In your opinion, what will be the next big scientific breakthrough in life science industry? Zachary: The next big scientific breakthrough is the concept of topology-dependent synthetic lethality (i.e., where genes are architecturally located in the nuclear genome); this concept is in contrast to genomic synthetic lethality (i.e., what genes encode). Topology-dependent synthetic lethality is an utterly new concept and is based on the observation that circular ecDNA creates profound accessibility of the DNA encoded on the circle and those DNA remain accessible throughout the cell cycle. Open accessible DNA is available to the cellular machinery for DNA replication and for RNA transcription. Normally, these processes are tightly coordinated so that cells don’t try to replicate and transcribe regions of DNA at the same time. When they do occur at the same time, transcription-replication collisions also occur. These collisions damage the DNA and cause a shortage of precursors for synthesizing new DNA. Consequently, tumor cells that have ecDNA are under a great deal of replication stress, which creates a unique, druggable, cancer-specific liability.     Zachary Hornby President & CEO, Boundless Bio Zachary (“Zach”) Hornby has served in executive and director roles for multiple private and public biotechnology companies. He is currently a Director at Aardvark Therapeutics, Novome Biotechnologies, and Radionetics Oncology. Prior to joining Boundless Bio, Zach was Chief Operating Officer at Ignyta, where he oversaw development of the company’s portfolio of four clinical stage therapeutics and was the team leader for the company’s lead program, RozlytrekTM (entrectinib), which was the first drug in pharmaceutical history to garner the coveted BTD (FDA), PRIME (EMA). and Sakigake (PMDA) designations. In that role, he also led the business development process that resulted in Ignyta’s acquisition by Roche for $2 billion; after the Roche acquisition, Zach served as the Ignyta site head where he was responsible for overseeing the integration into Roche. Before assuming the COO role, Zach was Ignyta’s Chief Financial Officer, helping the company go public and raise $120 million in capital. Prior to joining Ignyta, Zach served in roles of increasing responsibility across business development, marketing, new product planning, finance, and regulatory affairs at Fate Therapeutics, Halozyme Therapeutics, Neurocrine Biosciences and Transkaryotic Therapeutics (“TKT;” now the Human Genetic Therapies division within Takeda/Shire) and was a life sciences consultant at L.E.K. Consulting. Zach holds B.S. and M.S. degrees in biology, with a concentration in neuroscience, from Stanford University and an MBA from Harvard Business School

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Delivering on the Promise of New Modalities: An Interview with Nikole Kimes, CEO & Co-Founder, Siolta Therapeutics

As part of WuXi AppTec’s ongoing efforts to collaboratively foster new thinking and actionable approaches in advancing breakthroughs for patients, we have launched a new interview series in 2022 – “Delivering on the Promise of New Modalities” – so leading voices of R&D can share how their approaches are addressing the barriers standing in the way of breakthroughs. In our latest interview, we’re joined by Nikole Kimes, CEO & Co-Founder of Siolta Therapeutics, a clinical-stage biotech company that was awarded an NIH grant earlier this year and has raised $35 million to date for the development of live biotherapeutic products (LBPs) for the prevention and treatment of diseases of high unmet medical need. Siolta’s proprietary Precision Symbiotics platform has allowed the company to build a robust pipeline of potential first-in-class microbiome-based medicines and diagnostics for allergic diseases, women’s health, and rare pediatric indications. Congratulations on your recent NIH grant funding and thank you for joining us, Nikole. For drug discovery & development related to allergic diseases, what are the challenges in current therapeutic intervention, or current modality solutions? Nikole: Current medicines are exceptionally good at alleviating the symptoms of diseases; however, most approaches fail to address the underlying causes of disease and do not provide long-term benefits, particularly when dealing with complex multifactorial diseases that dominate modern society. Traditional pharmaceuticals typically involve a single molecule that targets a well-defined pathway and results in the alleviation of a specific symptom. Although the pharmaceutical industry’s investments in this approach have been successful in many ways, it leaves a lot to be desired if our ultimate goal is to cure diseases with modalities that do not require lifelong chronic treatments or better yet to prevent diseases from happening in the first place. To address these more challenging goals, we are currently witnessing a shift towards more dynamic approaches in the world of biologics. At Siolta Therapeutics, we aim to utilize the vast repertoire of genes and functionality that the human microbiome contributes toward maintaining human health to develop a new class of biologics, called live biotherapeutic products (LBPs), that offer long-term clinical benefit in disease areas where existing modalities have failed. What is your new modality or technological approach helping to address the challenges? How is it different from existing approaches? Nikole: We are embracing the dynamic and complex nature of human biology to develop next-generation microbiome-based medicines capable of addressing difficult diseases driven by multiple mechanisms of action. Improving upon food-grade probiotics and donor-derived fecal microbiota for transplantation (FMT) approaches, we are developing LBPs that contain defined bacterial consortia. To do this we isolate beneficial microbes from the human microbiome (i.e., fecal, vaginal, and other sample types) and combine synergistic organisms capable of reshaping and redirecting human physiology to maintain the metabolic and immunological balance required to support human health. Our approach initially incorporates human clinical data to direct early product design and requires an in-depth understanding of each microbe’s functionality (e.g., barrier function, pathogen inhibition, and immune modulation) and their complex downstream metabolic signaling to select the ones that provide the greatest therapeutic benefit for a given patient population. What are some critical challenges in realizing the full potential of your new modality or technologies? What are the solutions and do you anticipate any recent milestones? Nikole: Integrating the complexity of systems biology into more traditional drug development processes presents a number of challenges, including novel regulatory considerations, complex manufacturing, and unique clinical trial approaches. To address these challenges, we had to be creative throughout the entire R&D continuum to expand the in-house expertise needed to develop this novel treatment modality. From a regulatory perspective, we continue to work with the FDA to align expectations around the unique aspects of LBP development that make traditional toxicology, pharmacokinetic, and pharmacodynamic measures irrelevant. Our internal expertise was also essential from a manufacturing perspective, allowing us to overcome the difficulties associated with large-scale manufacturing of strict anaerobic organisms. Having overcome the many challenges of this exciting emerging field, we have safely and efficiently advanced our lead program STMC-103H into Phase 2, a proof-of-concept study in the US and Australia, for the prevention of allergic diseases (atopic dermatitis, food allergy, asthma, and allergic rhinitis) in at-risk newborns. Do you see novel technologies, AI or machine learning being used in the next couple of years? Nikole: Absolutely, machine learning is an important tool we use to identify and predict key features of a given system, and it plays an important role in our platform by supporting diagnostic development and informing patient stratification methods. This is an area that we believe will continue to have important contributions in our design of new consortia for a wide range of indications. Progressing beyond current machine learning methods to even more advanced AI-driven drug design (e.g., deep learning) will require incredible amounts of data across various populations and longitudinal timepoints. As we strive to move towards a precision medicine model in our healthcare system, we believe that developing diagnostic tests associated with the diseases we are targeting and recognizing factors that drive patient response are essential components of this equation, and core to our strategy. This approach can be iterative and allows us to identify new consortia combinations that could improve patient responses in distinct subsets of the population in order to have the most profound therapeutic impact. What do you think we will achieve as an industry in the next 10-15 years? What do you think are going to be some game changers in the future? Nikole: I would like to think that we will look back and appreciate a multitude of advances, including the incorporation of precision medicine concepts to improve efficacy standards and a focus on early intervention and prevention. Going from a symptomatic relief approach to disease-modifying will likely be one of the biggest changes we will observe. In addition, targeted approaches, such as gene editing (whether human or microbial) to treat genetic disorders, cell therapies for the management and potential cure of cancer, and microbes designed to prevent diseases before they start will transform our understanding of the human health. Interestingly, as we continue to embrace more complex approaches to drug development as evidenced in the world of biologics, I also believe we will begin to see even more transformative approaches through the combination of emerging modalities. There is a lot to be excited about!   Nikole Kimes, Ph.D. CEO & Co-Founder, Siolta Therapeutics Nikole E. Kimes, Ph.D., is Chief Executive Officer and co-founder of Siolta Therapeutics, a clinical-stage biotech company developing targeted live biotherapeutic products (LBPs) for the prevention and treatment of diseases of high unmet medical need. Siolta’s growing pipeline of first-in-class LBPs focuses on inflammatory conditions, women’s health, rare pediatric indications, and more. Dr. Kimes leads a talented and passionate team of researchers and clinicians with expertise in microbiology, immunology, bioinformatics, clinical operations, diagnostics, and manufacturing. An inventor of Siolta’s technology, her research in Dr. Susan Lynch’s lab at UCSF, also a co-founder of Siolta, provided the foundational translational research for the company’s formation. In addition to her scientific and entrepreneurial pursuits at Siolta, Dr. Kimes is the chairwoman of the Microbiome Therapeutics Innovation Group (MTIG) board, an independent 501(c)(6) coalition of companies leading the research and development of FDA-approved microbiome therapeutics and microbiome-based products to address unmet medical needs, improve clinical outcomes, and reduce health care costs. Dr. Kimes was also a member of the Springboard Health Innovation Hub: Life Sciences Track 2018 and participated in the 2017 California Life Sciences Institute’s FAST Program. She has over a decade of research experience in microbial ecology and host/microbe interactions, previously supported by a National Science Foundation (NSF) Fellowship and a postdoctoral scholar position at UCSF.

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Delivering on the Promise of New Modalities: An Interview with Geoff Hamilton, Co-Founder & CEO, Stemson Therapeutics

As part of WuXi AppTec’s ongoing efforts to collaboratively foster new thinking and actionable approaches in advancing breakthroughs for patients, we have launched a new interview series in 2022 – “Delivering on the Promise of New Modalities” – so leading voices of R&D can share how their approaches are addressing the barriers standing in the way of breakthroughs. We recently sat down with Geoff Hamilton, Co-Founder & CEO of Stemson Therapeutics, an early-stage company focused on hair regeneration using stem cells to generate healthy new follicles as part of our interview series. Last year, the company secured $15 million in Series A Financing to create a hair loss treatment that makes net-new hair follicles. Stemson’s vision is to provide a solution to all patients battling the emotional trauma or social stigma of hair loss through a novel approach using the patient’s own cells. Thank you for taking the time to join us, Geoff. For cell therapies, what are the challenges in current therapeutic intervention in general? Geoff: The primary industry-wide challenge that cell therapy companies like Stemson face is the fact that we are working with cells as the therapeutical modality. The challenge of working with cells as the actual therapy is the ability to safely and scalability control these cells for the therapeutic endpoints. Cells are alive and have their own activities with a high degree of variability, which can pose huge challenges in establishing a level of control and reproducibility to have the cells perform the functions that we need on a consistent basis. Having tools, processes, and methods for making those cells more uniform, controllable and reproducible are probably the biggest challenges that not only face us here at Stemson, but also folks across the industry working on cell therapy solutions which are now widely in development across the whole industry. A large number of big pharma and biotechs are developing cell therapy-based solutions in their pipeline. What is your new modality approach helping to address these challenges? How is it different from existing approaches? Geoff: Stemson’s new modality uses a cell therapy approach to address the broad problem of hair loss across the human population. Hair loss affects all races, ethnicities, nationalities and genders; it’s very widespread, and has a tremendously negative effect on mental health, self-confidence and well-being. Until now, the therapeutic products brought forward to treat this condition were all small molecule or biologics-based approaches. Hair loss is a degenerative disease in the skin. Much like other degenerative diseases across the body, a cell therapy approach makes a lot of sense in terms of regenerating the tissue that’s been lost in hair. So, the uniqueness of our approach is that we are capable of making the cell types required to regenerate hair follicles. We leverage these cells as the starting materials to bioengineer a new supply of hair follicles to treat folks who have lost their hair. That’s novel. And there is no therapeutic solution available today capable of generating de novo hair follicles. What are critical challenges in realizing the full potential of your regenerative cell therapy? Key milestones anticipated? Geoff: The biggest challenge for Stemson in realizing the full potential of cell therapy to treat hair loss is how we use cells as the building blocks to engineer a functionable, durable hair follicle tissue that can survive once transplanted into the skin. Engineering cells is hard enough but directing that population of cells to work together to form a functional tissue that’s capable of engrafting successfully into a patient’s skin and surviving over the long term is the next big challenge. So, the key milestone driving Stemson’s focus will be the first-in-human clinical trial which we expect to begin following successful completion of our pre-clinical trials. Our initial animal data shows tremendous promise, but we need that first-in-human proof of concept to prove that this is possible and reproducible in humans. With many new modalities advancing into the clinic and getting closer to patients, how will the 2030 class of FDA new approvals look compared to those of today? Geoff: With many new modalities advancing into the clinic, there is a strong push forward across the cell therapy front. Cell therapy, rather than other types of biologics or other drug molecules, is going to prove to be a better approach to treating a number of degenerative diseases. With a robust pharma pipeline of cell therapies in development across many indications, I would expect the 2030 class of FDA new approvals to have a much larger share of these cell therapies making their way out into commercialization to treat broader patient populations. This will be true not just for companies targeting degenerative diseases but for companies attempting to modulate and tune immune cells to unleash the immune system on certain types of diseases such as cancer. For cell therapy development, do you see novel data technologies, AI, or machine learning being used in the next couple of years? Geoff: I do see machine learning and AI being put to heavy use specifically on cell therapies. The challenge of understanding the basic biological mechanisms with which we need to control broad populations of cells is a daunting challenge of biological variability. The complex genetic and proteomic interactions driving cellular behavior is such an enormous amount of data to consume even for a single individual cell. Typical analytical approaches to understand the drivers of cell function and behavior cannot be addressed effectively without the use of big data tools like machine learning and Artificial Intelligence. At Stemson, we collect large amounts of molecular data to tell us what is happening in the cells that we are engineering and what is happening in the tissues that we are engineering. The complexity of this data requires that we write and leverage algorithms with machine learning and AI to pick out patterns and correlations and statistical significance to help us understand what is going on across a broad population of cells and across many molecular mechanisms existing within those cells.   Geoff Hamilton Co-Founder & CEO, Stemson Therapeutics Geoff Hamilton is co-founder and Chief Executive Officer of Stemson Therapeutics. He brings 20 years of product commercialization and business executive experience in life science and biotech companies. Prior to founding Stemson Therapeutics, Geoff spent five years at Illumina, a Fortune 500 company and world leader in DNA sequencing technology, where he held leadership positions in marketing, product management, and strategic partnerships. During his time at Illumina, Geoff launched three instrument platforms and helped the company grow from $1.4B to $3.8B in annual sales. Prior to Illumina, Geoff spent ten years at Life Technologies (now a part of ThermoFisher Scientific) where he held various leadership roles in marketing, global commercial operations, and acquisition integration. He helped build the company from $1.2B to $3.6B in annual sales before the ThermoFisher Scientific acquisition. Geoff earned a Bachelor of Science in Business Administration from the University of North Carolina, Chapel Hill.

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