Team:British Columbia/Human Practices
HUMAN PRACTICES
Integrated Human Practices
REFLECTIONS
At each stage of project development, from initial ideation to the incorporation of expert feedback, we believe that it is essential to consider the societal and environmental context to which our proposed solution is geared. As cancer treatment can be a sensitive issue for many people, it is important for us to communicate our project information and knowledge in a way that is respectful and considerate.
As young scientists, it is our responsibility to communicate our research and scientific knowledge about cancer in a way that is transparent and understandable by everyone. Our Outreach page outlines the educational outreach work that we conducted with people of different ages, ethnicities, learning abilities, and educational backgrounds to explain our project and ensure that our intent and scientific information was conveyed in the most comprehensible and accessible manner.
We have taken various steps to ensure that the solution that we are currently developing for predicting immunotherapy outcomes is appropriate and tailored for the people for whom it is intended. Through our Integrated Human Practices interviews, our team members learned that there is indeed a need for a solution to the problem that we hope to address; the different cancer immunologists and medical doctors we spoke to confirmed that DetecTME has the potential to complement traditional biopsy procedures in meaningful ways.
As our project is still in development, our team decided that it was best to seek feedback about project feasibility and end-user opinions from cancer researchers and oncologists even though our biosensor tool is designed for use by both cancer patients and physicians providing care to them.
INFORMING OUR DECISIONS
Informed decisions are at the core of any successful research project. Through review of literature we attempt to paint the most accurate picture of some necessary context in our heads - for example, the ideal assay for characterizing our system as a proof of concept in mammalian cells or a mouse model. However, often a personal interaction with an expert in this topic would be able to answer questions that papers cannot, and offer personalized insight into the approaches you are pitching. For this reason, we believed it was critical for us to integrate insight obtained from experts through interviews throughout the year to our design process.
OVERVIEW
Throughout the development of our project, at each stage, we have engaged with cancer researchers as well as oncologists studying various types of cancer. We have taken their feedback and suggestions into account to further develop our project in a way that would make our biosensor tool more suitable to potential end users such as physicians and cancer patients. Over the past months, our team members have interviewed a wide range of research and medical specialists to receive insight and feedback on our project design. These interviews have enabled us to continue expanding upon our project in a direction that would make DetecTME suitable for patient needs. Through these interactions, we were able to find out more about safety concerns regarding Salmonella in clinical settings and these insights have formed a vital part of our proposed real-world implementation.
After speaking with a cancer immunologist, we found out that current research has not been able to pinpoint any one biomarker that is sufficient to predict treatment outcome. As a proof of concept of immune activity detection, with the help of the cancer researchers we spoke to, we chose to focus on TNFa, a protein associated with inflammatory response, and lactate, a molecule that can regulate tumour immune activity.
Additionally, at the start of our project, we proposed 3 pillars which would include a diagnostic, a prognostic, and a therapeutic component. Based on our interviews with Dr. Saltzman, we realized that focusing on the diagnostic and prognostic components would be more suitable and relevant at this stage in our project.
1. UNDERSTANDING THE PROBLEM
To make sure our proposed design is most accurately solving the issue at hand, we must first understand the problem from different angles. The perspectives obtained from literature search cannot do justice to the knowledge that experts in the field hold regarding biopsies and exploration of alternatives. Having directly interacted with affected patients, they have seen first-hand accounts of the satisfaction of end users when being screened for immune activity. We have therefore interviewed certain experts to weigh in on what they believe is the issue.
Dr. Daniel Saltzman | Salspera LLC.
Dr. Daniel Saltzman is the Chief Medical Officer of the medical biotech company Salspera, which aims to develop novel tumour microbiome immunotherapies for solid tumour cancers. Given that he has a background in microbial immunotherapy, we felt he could guide our project and answer some of our questions including how to best administer Salmonella, and how we can best enhance colonization ability.
Our conversation with Dr. Saltzman revealed some tangible ways of choosing administration routes. He suggested that some of the benefits of the intravenous route are more robust colonization, while an oral route can avoid toxicity. To further assess toxicity, he encouraged us to perform experiments on mouse models and measure their weight loss as an indication of toxic effects.
Finally, he pointed out that Salmonella colonization often peaks around 20 days, after which point we assume the host immune system kills the bacteria. This can help inform how we approach colonization for our project and optimize how our Salmonella strain interacts with the tumour microenvironment to achieve the goals of our tool.
Dr. Morgan Roberts | Vancouver Prostate Centre
Dr. Morgan Roberts is a postdoctoral fellow at the Vancouver Prostate Centre in British Columbia, Canada. Her research focuses on investigating the mechanisms of immune evasion in bladder cancer.
Dr. Roberts affirmed that using TNFa would work and all our biomarkers currently make sense. She also confirmed that there is a need for predicting the outcome of immunotherapy treatment. Biopsies, in which a small amount of tissue is collected from the cancer site using a biopsy needle, are imperative for cancer diagnosis and cannot be replaced by another tool such as ours. However, we learned that if we are able to develop our tool such that we can monitor the tumour microenvironment long-term, which cannot be done through a tissue needle biopsy, we would be able to address that limitation and develop a biosensor that can be used as a supplement to biopsies. She advised that it may not be very useful to categorize tumour immune responses as hot or cold, unless we include monitoring of immunosuppressive responses. She noted that biopsies for specific cancers (bladder, melanoma, and ovarian cancer) are more dangerous than others. The type of specific immunotherapy may also influence our results.
2. EVALUATING OUR APPROACH
As described on our Design page, our AND-gate biosensing system for immune activity in tumours depends on the induction of two promoters, each inducible by a different immune marker. In the search for our optimal two markers to compose the AND-gate, we consulted with various professionals in immunology and pathology to confirm that TNFa and lactate, our proposed markers obtained from literature search, were the most accurate to detect immune activity in an in vivo context.
Dr. Tracy Kion | UBC
Dr. Tracy Kion is an immunology professor at The University of British Columbia in the Department of Microbiology and Immunology.
Dr. Kion informed us that since TNFa is already present in the body, TNFa could flow into the TME. Although TNFa is expressed throughout the body, she noted that using an AND-gate would make our detection method credible. She also suggested utilizing different Salmonella strains to develop different sensors, to further equip our diagnostic tool with the potential to detect the tumour microenvironment broadly.
Dr. James Lim | BC Children's Hospital Research Institute
Dr. James Lim is a cancer researcher at the BC Children’s Hospital Research Institute in Vancouver, Canada. His research is aimed at understanding cellular signalling mechanisms and protein function in diseases of the immune system, such as leukemia, lymphoma, and autoimmunity.
We interviewed Dr. Lim during the early stages of our project development. We discussed the feasibility of utilizing TNFa and lactate as our primary biomarkers and affirmed that there is a need for a solution to the problem of patient response to tumour immunotherapy. He suggested that we incorporate a 3D tumour microenvironment model into our project design; to accomplish this, we would need to perfuse hydrogel with a specific cancer cell line, stromal cells, and immune cells to replicate the TME. Dr. Lim brought up the issue of controlling the effect of Salmonella in the human body and urged us to look into how Salmonella could potentially change the TME and immune response. He also recommended that we use microfluidics chambers, organoid cultures, and mouse models in the future to benchmark our biosensor tool.
Dr. Anne-Marie Fortier | McGill University
Dr. Anne-Marie Fortier is a research associate at the Goodman Cancer Research Centre at McGIll University, Canada. She has expertise in 3D cell culture and using tumour organoids for precision oncology.
To follow up on Dr. Lim’s advice on 3D modelling of the tumour microenvironment, we spoke with Dr. Fortier about how we could implement a hydrogel model to simulate the tumour microenvironment. Dr. Fortier kindly walked us through the protocols for perfusing hydrogel with a specific cancer cell line, immune cells, fibroblasts, as well as our engineered Salmonella strain, to construct a 3D model with which we can further investigate how the different components of the TME will interact with our biosensor. Dr. Fortier recommended that we focus on further developing the diagnostic and prognostic pillars of our project, rather than focus on the therapeutic pillar at this time. After discussing the details of the hydrogel model further, our team decided that given our wet-lab timeline and access to resources, it was not feasible at the time to proceed with it. However, now that we have this valuable knowledge about hydrogel model implementation, we hope to put this to use in the near future.
Dr. Brad Nelson | BC Cancer
Dr. Brad Nelson is the Scientific Co-Director of BC Cancer’s Immunotherapy Program. His laboratory focuses on exploring the development of innovative immunotherapies for cancer. His current research focus includes using genetic engineering to create more potent immune cells for immunotherapy use.
We have competition with other research including imaging proxies for immune activity, so we need to prove that our project has a significant advantage. He thinks our product would work best as a theranostics tool that would both sense immune activity and increase the response to immunotherapy. Since, the US medical system tends towards giving immunotherapy in order to avoid denying someone a possible life-saving treatment. While that process in Canada is more selective, Dr Nelson emphasized that if you are denying treatment to those who do not pass your test, it better be a good test. Dr. Nelson suggested we look for a similar predictive biomarker that could be used across different cancers like anti-PDL1 antibodies are currently used for all MMR cancers. Moreover, Dr. Nelson brought up a couple viable concerns. One is we need to demonstrate if there is any difference in how Salmonella behaves within the same patient depending on differing expression of natural antibodies. Also, Dr. Nelson brought up a potential safety concern regarding Salmonella: even though our Salmonella strain is highly attenuated, what is our plan if the strain mutates? While our team found this unlikely, putting in additional measures to prevent possible harmful mutations would be a great fail safe.
3. FINETUNING OUR DESIGN
Once our biomarkers were chosen upon cross-validation, we sought help in carrying out our circuit construction and characterization. Given that we chose an attenuated strain from another UBC-based lab, this presented an opportunity for further consultation on culturing Salmonella — a feat our team had not done before, as well as characterization of our inducible promoters. For more details on this process, please refer to our Experimental Design page.
Katelyn Knuff-Janzen | UBC
She gave insight into our understanding of the Sip A promoter for our construct. She said that using SipA as our promoter might work but SipA might be upregulated so it might not be the best possible regulator. She also said that Salmonella follows the normal growth curve and does well in nutrient deficient environments. Moreover, she suggested an experimental design to test for endotoxins (known to be harmful to the human body) for our attenuated strain: this would remove a potential limitation to our project. She suggested some troubleshooting steps for the colony PCR. She thinks that it would be helpful to visualize Salmonella gene segments using Snapgene. She said that cloning operons can be difficult as they have one promoter so she suggested we clone a big chunk of DNA upstream of sicA. Lastly, she recommended we insert our pieces into a chromosome if plasmid insertions do not work.
Dr. Kevin Bennewith | BC Cancer
Dr. Kevin Bennewith suggested some key points to address regarding potential TME modulators and 3D modeling. For potential TME modulators, he said using MMP inhibitors could make things worse and that no individual cytokine will selectively target antitumor immune cells. That said, collagenases - compounds to increase blood perfusion or modulate vasculature to decrease hypoxia and increase immune cell infiltration - are a potential modulation candidate. As for 3D TME modeling, Dr. Bennewith suggested potential modeling aspects including gradients of hypoxia and necrosis surrounding vasculature, fluid exchange, pH, the localization of different immune cell populations within the tumour, and cancer associated fibroblasts. Moreover, he suggested the modulation of macrophage phenotype could be promising to explore since the LPS and immunogenic proteins in Salmonella may already help skew towards M1. If our team was to perform in vivo experimentation, it would take about 2 weeks to grow to a pea-size cancer spheroid with the right cell lines.
Dr. Bennewith’s feedback is significant for the software aspect of our project as we are working on 3D simulations of the TME. We would like to capture features like blood vessel networks, oxygenation levels, blood and interstitial fluid flow, and major cell composition, and it is beneficial to learn from Dr. Bennewith about the various elements that we would need to incorporate into our 3D TME model.
4. CONSIDERING DOWNSTREAM IMPLEMENTATION
As part of the diagnostics track, the proposed clinical implementation of our system must be carefully considered, even if we leave the project as a proof-of-concept. Using Salmonella as our chassis could evoke hesitation in the target audience, hence speaking to individuals who are more proficient in cancer therapeutics, medicinal industry, and policies could help foresee downstream clinical applications.
Dr. Brad Nelson | BC Cancer
After speaking with cancer research experts such as Dr. Morgan Roberts, we realized that there is a need to address this problem through our proposed solution, we connected with Dr. Brad Nelson, Scientific Co-Director of BC Cancer's Immunotherapy Program, to further discuss the usefulness and benefits of our biosensor tool and how we may be able to develop it to suit patient needs.
We have competition with other research including imaging proxies for immune activity, so we need to prove that our project has a significant advantage. He thinks our product would work best as a theranostics tool that would both sense immune activity and increase the response to immunotherapy. Since, the US medical system tends towards giving immunotherapy in order to avoid denying someone a possible life-saving treatment. While that process in Canada is more selective, Dr Nelson emphasized that if you are denying treatment to those who do not pass your test, it better be a good test. Dr. Nelson suggested we look for a similar predictive biomarker that could be used across different cancers like anti-PDL1 antibodies are currently used for all MMR cancers. Moreover, Dr. Nelson brought up a couple viable concerns. One is we need to demonstrate if there is any difference in how Salmonella behaves within the same patient depending on differing expression of natural antibodies. Also, Dr. Nelson brought up a potential safety concern regarding Salmonella: even though our Salmonella strain is highly attenuated, what is our plan if the strain mutates? While our team found this unlikely, putting in additional measures to prevent possible harmful mutations would be a great fail safe.
Dr. Daniel Saltzman | Salspera LLC.
He reminded us of how important our work is by recognizing that our tool has the potential to help clinicians perform cancer diagnosis and treatment with enhanced efficiency. While he acknowledged that it is unlikely this project could replace biopsies entirely, he mentioned that it could serve as a great complementary tool. He also noted that our tool may actually be more sensitive to tissue localization and movement than traditional radiology procedures. One potential application of our project he could foresee was in aiding clinicians with localization/identification of tumour areas during pre-operative planning, and possibly during surgical/radiology procedures as well. In advancing our project further, he noted that we may want to determine the advantages/disadvantages of delivering the attenuated Salmonella orally or intravenously, suggesting that intravenous administration could result in a higher colonization rate to the tumour. As a result of this interview, we chose our proposed route of administration to be intravenously as described in our Implementation page. He also suggested we look into performing in vivo experimentation with subcutaneously implanted tumours in mice to determine clinical efficacy further.
Dr. Mathieu Roumiguié | Hospital Center University De Toulouse
Our interview with Dr. Roumiguié helped our project by aiding us in planning our timeline. He suggested that there is a need for biomarkers to predict immunotherapy response, and inflamed tumours may have an increased likelihood of responding to immunotherapies, and our tool would be useful in detecting that. Additionally, he suggested to us that our tool could also be used to monitor progress and response to ongoing immunotherapy treatment. In this way, if the tumour become resistant to the immunotherapy, we can monitor changes in the TME using our reporter system to learn more and probe why. He also acknowledged that there is indeed a need for non-invasive ways to learn about tumours through biomarkers - especially when patients may find repeated invasive diagnostic procedures inconvenient or uncomfortable. Our interview with him highlighted how tools like ours can help i) improve our ability to monitor immunotherapy results, and ii) increase accessibility for non-invasive diagnostic/prognostic tumour characterization tools. Lastly, Dr. Mathieu Roumiguié suggested some ideas on the downstream in vivo experiments and clinical implementation of our project, which is discussed in the Implementation page.