Impetus:
Our motivation for this project stemmed from the urgent need to address the limitations of the current TNBC diagnostics. If cancer is detected at a later stage, treatment must be more aggressive. Treatment options for TNBC are frequently restricted to aggressive chemotherapy, which has serious side effects and limited efficacy, because TNBC lacks the hormonal receptors that oncologists rely on to treat other breast cancers with targeted therapy. To guarantee our project addressed actual gaps in care, we felt compelled to contact oncologists, researchers, patients, and advocacy groups after realizing these difficulties. The “Description” and “Feelings” phases of Gibbs' cycle are reflected in this motivation, and we started with a well-defined issue and a sympathetic understanding of its effects on people with TNBC.
Two Way Communication:
The foundation of our project's stakeholder engagement was two-way communication. We invited patients to share their experiences, advocacy groups to voice concerns about communication, safety, and accessibility, and oncologists to question the viability of our methods, rather than just sharing what we were developing. For example, clinicians encouraged us to consider scalability and integration into existing treatment protocols, while patients stressed the significance of treatments that minimize side effects and maintain quality of life. The "Evaluation Phase" of Gibbs' cycle states that this reciprocal communication enabled goals and concerns from various viewpoints to actively influence the course of our project. The specific information that we learned and how we incorporated it is described below.
Analysis:
After collecting feedback, our team shifted to the analysis stage. We examined recurring themes like affordability, accessibility, and safety, and contrasted the input from stakeholders with our current project framework. For example, after stakeholders raised the issue of ensuring equitable access to innovative cancer treatments, we found that our design needed to consider biological efficacy and the project’s potential for implementation in various healthcare contexts. This reflective analysis helped us see the broader implications of our work: a successful TNBC therapy must be both innovative and beneficial for patients and healthcare providers.
Implementation:
Converting insights into real change was the last stage of reflection. We modified parts of our design and communication plan in accordance with Gibbs' "Conclusion" and "Action Plan" phases. We considered pathways to make the therapy scalable and accessible, and improved our suggested model to highlight specificity in targeting TNBC cells. Regarding human practices, we created educational resources that directly addressed patient concerns and explained complicated science in an understandable manner. These adjustments demonstrate our dedication to developing the project in light of reflection, guaranteeing that our TNBC initiative is both a scientific breakthrough and a socially responsible solution.
Identification of Stakeholders: Our main stakeholders were Triple Negative Breast Cancer doctors, patients and survivors, researchers, and current medical manufacturing companies.
Dr. Cesar Augusto Santa-Maria, a medical oncologist and Associate Professor of Oncology at the Johns Hopkins University School of Medicine, specializes in treating and researching breast cancer. The goal of his research and clinical work, which is supported by the Breast Cancer Research Foundation, is to develop more specialized treatments for breast cancer, particularly immunotherapy and strategies for triple-negative breast cancer (TNBC). During our meeting, Dr. Santa-Maria provided our iGEM team with valuable information regarding the clinical and translational aspects of our TNBC diagnostic project. In reference to the uniqueness of our approach, he emphasized the importance of identifying clear gaps in current diagnostics and modifying our work to fill them, particularly in the areas of accessibility and patient-centered care. He pointed out that patients are concerned about breast cancer biopsies and that advancements in detection and diagnostic effectiveness could have a big impact on patient satisfaction and doctor-patient relationships. Technically speaking, Dr. Santa-Maria suggested that we deepen our comprehension of toehold switch-based diagnostics by directing us to particular studies on cell-free systems, like the Zika virus detection model. He urged us to examine more specialized literature on the subject and posed the question of whether post-transcriptional changes to miRNAs, such as 3’ methylation, could obstruct their binding to toehold switches. Additionally, he suggested that we carefully evaluate whether it would be more efficient to start with DNA transcription in the mixture or to rehydrate freeze-dried toehold systems for direct blood sample input, keeping in mind that this decision would have an impact on our kit’s design. He also emphasized how crucial it is to comprehend the advantages and disadvantages of cell-free systems in comparison to cell-based systems, guiding us to read reviews that dissect any potential benefits and drawbacks.
Dr. Santa-Maria offered ways to improve the quantitativeity of our
system’s execution, like equipping plate readers with colorimetric or
fluorescent outputs for accurate measurements. Regarding implementation,
Dr. Santa-Maria recommended ways to increase the quantitative nature of
our system, like incorporating colorimetric or fluorescent outputs into
plate readers to ensure accurate measurements. Additionally, he offered
a practical viewpoint on the cost of scaling up, reminding us that
although reagents might be cheap, labor, packaging, branding, and
distribution are significant obstacles to product development. He
illustrated how collaborating with well-established businesses can aid
in overcoming these obstacles by using his experience with BioBits. All
things considered, his criticism pushed our group to strengthen the
project’s technical underpinnings while maintaining patient needs,
budget, and viability as our top priorities.
You can find Dr. Santa-Maria's interview/questions here.
Dr. Jackie Zimmerman, MD, PhD, is a physician and Assistant Professor of Medical Oncology at Johns Hopkins School of Medicine. She is a practicing oncologist and leads research projects developing new models for drug testing to create more personalized cancer treatments.
Impetus
Finding a specific clinical niche for our project is crucial, according to Dr. Zimmerman, a specialist consultant for our TNBC miRNA diagnostic. She suggested focusing on patients who already had a confirmed diagnosis of TNBC rather than promoting the test as a general screening tool. The diagnostic would be most helpful in this situation for monitoring minimal residual disease (MRD) and recurrence. The test could more effectively integrate into longitudinal patient care and assist doctors in making well-informed treatment decisions if it is prescribed at regular intervals (every three to six months).
Two-way Communication
The goal of our intensely interactive conversations with Dr. Zimmerman was to match clinical priorities with our technical design. Inquiring about timing, patient baselines, and longitudinal tracking, she urged us to consider our test's practical application. She also pushed us to improve the way we choose biomarkers, emphasizing that some miRNAs, like miR-21, may not be very specific because they increase when inflammation occurs. Her comments forced us to think about the biological dependability of our selected targets in addition to the clinical context of use, making sure our project is both technically sound and clinically significant. She also told us that a binary answer to the question “do I have breast cancer?” was the best possible output for easy interpretation.
Analysis
Dr. Zimmerman listed a number of technical obstacles that need to be overcome. She proposed that pre-amplification and careful probe design may be required due to miRNA’s short length, low abundance, and potential for post-transcriptional modifications that could impact toehold binding.
To prevent an excessively broad marker panel and guarantee adequate diagnostic coverage, she advised prioritizing specificity to TNBC and confirming the universality of the selected miRNAs across TNBC subtypes. She encouraged us to use colorimetric or fluorescent readouts for output measurement, pointing out that these could be read by conventional plate readers or even calibrated smartphone apps that could be used to set thresholds and monitor trends over time. Her critical perspective helped us concentrate more intently on the dependability and technical viability of our detection technique.
Implementation
Dr. Zimmerman suggested a methodical approach for implementation and validation. To directly compare test results with current diagnostic standards, she suggested that testing be synchronized with imaging and clinical follow-ups. To set detection thresholds, she recommended conducting validation tests using samples of mixed stage and/or recurrence, negative controls, samples from healthy controls, and graded TNBC-level samples. Crucially, she advised us to put more emphasis on proving the scientific validity of particular miRNAs than on developing new hardware. Lastly, she recommended emphasizing the non-invasive nature and early detection potential of our project in its branding since these attributes amply convey patient value.Her suggestions offered a path forward for transforming our diagnostic idea into a patient-centered, clinically applicable instrument.
You can find Dr. Zimmerman's interview/questions here.
Research Scientist: Dr. Ally Huang
Dr. Ally Huang is a Lead Research Scientist and co-developer of the BioBits, a synthetic biology system that harnesses freeze-dried cell-free technology to make it possible to run biological experiments without living cells.
Impetus
Ally Huang, an expert in the area of cell-free devices, pointed out that although the general idea behind our TNBC diagnostic is encouraging, further information regarding the experimental setup is required before the viability of the test can be completely evaluated. To gain a better understanding of the sequential validation process and the advantages and disadvantages of cell-free versus cell-based systems, she suggested examining current toehold switch-based diagnostics, such as Zika virus detection in cell-free systems. On the technical side, she pointed out a crucial design decision between using freeze-dried toehold switches for direct blood sample testing or adding DNA transcription machinery to the mix, and she recommended looking into whether post-transcriptional modifications of miRNAs (like 3′ methylation) could affect toehold binding. For quantification, she advised using colorimetric or fluorescent outputs measured with plate readers to provide standardized, accurate results. In closing, she underlined that although reagents might seem cheap, labor, plastics, packaging, distribution, and marketing are the real implementation costs. Based on her own experience with BioBits, she suggested collaborations with well-established businesses as a means of scaling and practical application.
Two-way Communication
We had a very cooperative and educational conversation with Ally Huang. Ally Huang provided our iGEM team with valuable information regarding the clinical and translational aspects of our TNBC diagnostic project. In reference to the uniqueness of our approach, she emphasized the importance of identifying clear gaps in current diagnostics and modifying our work to fill them, particularly in the areas of accessibility and patient-centered care. She pointed out that patients are concerned about breast cancer biopsies and that advancements in detection and diagnostic effectiveness could have a big impact on patient satisfaction and doctor-patient relationships. She also discussed the technical facets of our synthetic biology approach while offering clinical and translational insights. She encouraged us to learn more about cell-free systems, for example, by pointing our team to research on the Zika virus detection model and toehold switch-based diagnostics. She also raised important questions for us to investigate, like whether toehold binding could be hampered by post-transcriptional changes to miRNAs (like 3′ methylation). Our viewpoint was influenced by this discussion, which highlighted the clinical importance of our work as well as its scientific difficulties.
Analysis
With Ally Huang’s assistance, we were able to weigh the benefits and drawbacks of our project. She advised us to research the benefits and drawbacks of both cell-free and cell-based systems, emphasizing the importance of doing so. She also challenged us to consider design tradeoffs in system execution, such as whether to begin with DNA transcription in the mixture or to use freeze-dried toehold systems for direct blood input. She also highlighted potential scaling bottlenecks, reminding us that while reagents may be inexpensive, problems with labor, packaging, and distribution make implementation extremely difficult. This analysis motivated our team to base our design choices on practicality, cost-effectiveness, and clinical relevance.
Implementation
Ally Huang offered useful implementation techniques to ensure the accuracy and viability of our diagnostic tool. In order to make sure that our results are quantifiable, standardized, and repeatable, she suggested adding colorimetric or fluorescent outputs to plate readers to increase the quantitative nature of our system. Additionally, Ally Huang emphasized the value of working with well-established biotech businesses, using her experience with BioBits to show how alliances can help get past obstacles in distribution, branding, and scaling. Her counsel has influenced our system's technical design as well as our long-term goals for how it might actually transition from the lab to clinical and patient settings.
You can find Dr. Santa-Maria's interview/questions here.
TNBC Survivor: Emily Hernstein
Emily Hernstein is a breast cancer advocate in the Triple Negative Breast Cancer Foundation. Last fall, the Baltimore community had a dance fundraiser for her, and this spring, the Baltimore Biocrew contacted her about her willingness to engage in the project. We met in person and discussed her experience as a survivor and how to improve the TNBC treatment process.
Impetus
During our research about TNBC, we did not find many survivor stories in our area that include future improvements to diagnosis. As a result, we did not know how people in our area felt about their diagnosis experience and recurrence checkups. We decided to interview a local survivor, Emily Hernstein, to hear her experience and how our test could improve the TNBC journey.
Two-Way Communication
Emily Hernstein told us her story; she went to biyearly checkups, knowing that she was predisposed to TNBC, but the breast cancer was caught after it had developed. She went through surgery, chemotherapy, and remission. The experience was mentally and physically exhausting. When asked, she said that if a test like ours had been available for her, she would have used it every month.
Analysis
From our discussion with Emily Hernstein, we learned about the patient side of Triple Negative Breast Cancer: grueling, tiresome, and tough. We also learned that if our project could provide an accurate test for former TNBC patients at any time, they could regain control of their lives.
Implementation
Speaking with a survivor made us realize that we would need to be very clear when explaining the project, as she originally thought the project was for diagnosis, instead of recurrence. Meanwhile, Emily Hernstein’s experience made us reflect on the accuracy needed to publicize the test. The experience also made us speak with more patients and create a patient survey to connect with all parts of the TNBC community.
You can find Emily Hernstein's interview/questions here.
TNBC Survivor: Mary Passini
After speaking with Emily Hernstein, she offered to ask her Facebook cancer support group if anyone was willing to speak with us about their experiences. Mary Passini responded to the message, and we met over Zoom to discuss her experiences and her opinion of the project.
Impetus
During our research about TNBC, we did not find many survivor stories in our area that included future improvements to diagnosis. As a result, we did not know how people in our area felt about their diagnosis experience and recurrence checkups. We interviewed a woman currently in remission to understand her current emotions throughout the process and to understand what she would prefer for her future recurrence tests.
Two-way Communication
During our talk, Mary Passini candidly shared with us what patients want most from diagnostic tools. She described our project as a "good idea," highlighting the importance of accuracy and simplicity, and stated that she would feel at ease using a straightforward blood-prick test. She also reassured us that patients like herself won't have significant privacy concerns if the test is accurate and beneficial. By expressing her perspective, she emphasized the importance of researchers actively involving patients in the design process to ensure that new technologies satisfy their needs and expectations in the real world.
Analysis
We were able to examine the discrepancy between patient expectations and current clinical practices thanks to Mary's reflections. Current diagnostics are accurate, but they are also slow, invasive, and stressful, leaving patients with constant uncertainty. She stressed that providing comfort and certainty regarding remission status or recurrence is the most significant contribution a diagnostic tool could make. Her comments reaffirmed the need for our test to function both technically and in a way that minimizes anxiety and maximizes clarity while integrating into patient care.
Implementation
Mary's suggestions influenced our approach to designing our diagnostic system. She urged us to develop a simple, minimally invasive test that people could rely on. She also encouraged us to keep involving patients in the development process so that their opinions can have a direct impact on design choices. In practice, this entails giving top priority to features such as non-invasive sampling (blood input via finger prick), accuracy that engenders confidence, and usability that necessitates little to no specialized training. By putting patients like Mary at the center of our implementation strategy, we hope to provide the TNBC community with a diagnostic tool that is both genuinely useful and scientifically sound.
You can find Mary Passini's interview/questions here.
TNBC Survivor: Ana Lohrmann
Ana Lohrmann is a patient who has had metastatic breast cancer for years; she was given 4 months to live six years ago. She runs the YouTube channel Ana’s Cancer Journey, where she catalogs her own struggles against breast cancer for others.
Impetus
As part of our effort to learn more from the patient perspective, we had shared a survey with our contacts. We reached out to Ana because we thought that we might be getting as few answers to our survey as we were because a survey was too impersonal. From talking with Ana, we gained much deeper insights.
Two-way Communication and Analysis
She gave us the two following valuable insights:
Implementation
We did not have time to implement what we learned from Ana for this survey round, but for future rounds we would look for ways to make the text more user-friendly for vision-impaired people. This could include larger font size, considering the contrast between text and background, and perhaps even creating an audio version. We shared what we learned about the CEA and CA27.29 tests with the Entrepreneurship subteam, and they will look into what would be required to potentially add these use cases to our test.
Project Summary: TNBC Diagnostic
Our project's objective is to develop a toehold switch-based diagnostic for Triple-Negative Breast Cancer (TNBC), one of the most aggressive and difficult subtypes of breast cancer to treat due to its high recurrence rate and lack of receptor targets. Though modern diagnostic methods, including fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC), are helpful in identifying receptors, they are still invasive, costly, and not generally accessible, often requiring uncomfortable and stressful biopsies.
Among others, Dr. Cesar Augusto Santa-Maria and Ally Huang stressed the importance of developing patient-centered, non-invasive, and easily accessible tools that are backed by strong technical validation. Their suggestions prompted us to concentrate on issues related to scalability, quantification techniques, and experimental design, guaranteeing that our system is not only novel but also feasible for real-world use.
Theoretically, our diagnostic scans for miRNAs associated with TNBC using cell-free toehold switches. Expert consultants guided us on how to deal with problems such as the short length, low abundance, and modifications of miRNAs, which may necessitate pre-amplification and careful probe design. They also underscored the importance of balancing specificity to TNBC subtypes with the necessity of maintaining a manageable marker panel.
Quantification methods, such as colorimetric or fluorescent outputs that could be measured by plate readers or calibrated apps, were recommended for accuracy and repeatability. Scalability issues—labor, packaging, and distribution costs—were also brought to light, and suggestions were made to work with reputable biotech companies to overcome infrastructure barriers. Our project's technical foundation was formed by these realizations, ensuring that we approached design with a focus on both practical implementation and scientific rigor.
Patient interviews reaffirmed the importance of TNBC diagnostics from the community's viewpoint. Emily Hernstein, a survivor, highlighted the fear of recurrence, and Mary Passini, a current patient, described how her treatment experience was affected by delayed detection because of dense breast tissue. Both voiced strong support for a straightforward, non-invasive test that could provide peace of mind and accurately track remission or recurrence, like a finger-prick blood assay.
Their comments emphasized that the benefits of diagnostics go beyond simple detection, including patient comfort, clarity, and an enhanced quality of life. Our project aims to provide a diagnostic that is not only scientifically sound but also easily accessible, reasonably priced, and significant to the TNBC community by combining patient input with professional technical advice.
The Baltimore Biocrew’s project was shaped by our goals to improve accessibility and reduce inequality in healthcare by creating an improved remission detection technology for Triple Negative Breast Cancer (TNBC). We aimed to help support post-breast cancer individuals, promote early, non-invasive cancer diagnostics, and ensure accuracy in tests using ethical and sustainable methods with our project. Our project is based on the fact that there are limited opportunities for recurrence monitoring as women receive very expensive standard mammograms every year after treatment. Oftentimes, because of how infrequent the mammograms are, the breast cancer has time to develop and become severe without the patient’s notice. This was our call to action and why we chose this project–we support the development of a rapid test meant to identify breast cancer mRNA that is cheap and can be done at home. Then we needed to inform the community about our project for support, so our human practices group surveyed and interviewed doctors, researchers, and patients to guarantee a positive impact produced by our project. The results were widely supportive, and past and current patients, as well as doctors and experts, gave us suggestions about how we might improve our project to meet its full potential.
The highly aggressive subtype of breast cancer known as triple-negative breast cancer (TNBC) is distinguished by the lack of HER2, progesterone receptor (PR), and estrogen receptor (ER) expression. The two main diagnostic techniques used today for TNBC are fluorescence in situ hybridization (FISH) testing and immunohistochemistry (IHC). Although these methods work well for determining receptor status, they have a number of drawbacks:
By creating a faster, affordable, and potentially more accurate recurrence detection system, our project avoids these restrictions. Our approach capitalizes on the fact that miRNA expression is changed in TNBC cells. This makes it possible for:
By addressing the shortcomings of current diagnostic methods and expanding upon them to identify TNBC more quickly and precisely, our project could increase patients’ survival rates.