Dr. Chiara Luberto

Dr. Luberto is an Oncology researcher affiliated with the Stony Brook Cancer Center. One of her research specializations involves the progression of certain cancers such as leukemia and lung cancer. Dr. Luberto is an Oncology researcher affiliated with the Stony Brook Cancer Center. One of her research specializations involves the progression of certain cancers such as leukemia and lung cancer.

Dr. Luberto gave the perspective of a clinical research scientist. She further affirmed the need for a faster and easier B-cell lymphoma diagnostic, as patients usually find out in advanced stages of this cancer because symptoms at early stages are not very distinct from the common cold. She thinks that our system would provide a good screening test and has a competitive edge over biopsies due to time and cost; but, she recommended that we work on the sensitivity of our system. We will be working on this in our cell free system by amplifying the fluorescent signal given off in different conditions (control, GFP, GFP with repression). Having our system being able to detect more subtle changes to miRNA concentrations within the patient’s blood would allow earlier diagnosis and better treatment outcomes. She also suggested that we should look into other strong miRNA candidates for other diseases that might be difficult to diagnose.

https://cancer.stonybrookmedicine.edu/tlc/investigators/luberto

Dr. Suhu Liu

Dr. Liu is a hematologist and medical oncologist that specializes in the diagnosis and treatment of hematologic malignancies as well as a Clinical Assistant Professor in Medicine & Physiology. Dr. Liu provided an alternate Clinician perspective, especially on the diagnostics side. Dr. Liu brought up qt-PCR as an golden standard for identifying RNA molecules in the blood, but she expressed interest in our novel method. She echoed what Dr. Luberto mentioned about sensitivity, and for us to work on our system so that it can be on-par with qt-PCR. She also told us that MicroRNA that can differentiate between malignant and benign tumors can provide very useful information for health care providers.

https://doctors.stonybrookmedicine.edu/provider/suhu-liu/2603242

Dr. Jingfiang Ju

Dr. Ju is an Oncology Research Scientist affiliated with the Stony Brook Cancer Center and the Renaissance School of Medicine who studies the role of non-coding RNAs (such as miRNAs) in cancer development as well as how they can be used clinically for cancer diagnosis and therapy. His research is focused on how miRNAs are involved in tumor cell growth and how miRNAs can be a biomarker for cancer diagnosis and prognosis. Dr. Ju is a research scientists affiliated with the NIH, the National Cancer Institute Study Section, the Cancer Genomics and Proteomics, the American Association for Cancer Research, the Society of Chinese Bioscientists in America, and the RNA institute and is a leading researcher studying the role of miRNAs as biomarkers for cancer as well as their role in cancer development. He provided significant feedback to implementations of our project.

Due to his expertise with RNA, Dr. Ju discussed existing RNA detection methods, specifically RT-qPCR. He said it can detect up to 1fM differences and discriminate between similar miRNA of just 1 base pair difference. With these strengths in RT-qPCR, he encouraged us to explore and emphasize the clinical friendliness of our project. Dr.Ju emphasizes the importance of having a test that does not require any trained lab personnel. We are implementing this feedback by moving to a cell free system where heat shock into bacteria and other extraneous steps will be reduced, which also minimizes the need for speciality training.

https://renaissance.stonybrookmedicine.edu/pathology/faculty/ju

Department of Health New York State Cancer Registry

The New York State Registry reached out redirecting us saying as they are a population based registry and do not have the capacity to engage in biological research. They redirected us to cancer research centers that are actively engaged in such research at which point we got in contact with the Stony Brook University Cancer Center.

https://www.health.ny.gov/statistics/cancer/registry/

Landon Finkel (NMDP)

Landon Finkel is a recruiter for the National Marrow Donor Program (NMDP). He helps recruit people for the NMDP registry at their events. Finkel has gone to campuses and hosted NMDP events where he helps clear misconceptions about the donation process and helps educate the public about it. Discussed collaborative events that can be done between the Stony Brook iGEM team and NMDP, such as the NMDP Unite event in Brooklyn and outreach events on the Stony Brook Campus. After meeting him, we learned about ways to educate the public about blood cancer awareness and how our project ties into the mission of NMDP. The events that were done in collaboration with NMDP both added people to the bone marrow donation registry and helped people understand our project.

https://network.nmdp.org/locations/new-york

Dr. Ron Jacob, MD

Dr. Jacob is a Physician associated with the National Marrow Donor Program (NMDP) and is their Director of Member Recruitment. He has held NMDP outreach events on the Stony Brook Campus as well as been a speaker at other NMDP events in NYS such as Unite. We discussed the possible clinical perspectives of our project with him. We first connected with him at the NMDP Unite Event at Brooklyn, and further at a blood cancer awareness event hosted by him at Stony Brook. He gave us insight into how the goals of NMDP and the 2024 project are intertwined, and how this research project could be clinically adapted as a cheaper and more accessible method of detecting non-Hodgkin’s B-cell Lymphoma.

Linda Bily EdD, CSA, OPN-CG

Dr. Bily is a professional at the Community Outreach and Engagement program held at the Stony Brook Cancer Center that invited us to present and gain feedback on our project.

Linda Mermelstein, MD, MPH

Dr. Mermelstein is a professional at the Community Outreach and Engagement program held at the Stony Brook Cancer Center that invited us to present and gain feedback on our project.

Patrick J. Dineen, MD, MBA

Dr. Dineen is a professional at the Community Outreach and Engagement program held at the Stony Brook Cancer Center that invited us to present and gain feedback on our project.

Natalie Lo MD/PhD Student

Background in DNA repair pathways and their connection with cancer tumorigenesis to potentially develop cancer therapeutics that target these repair pathways. Current MD/PhD student at Renaissance School of Medicine. 2018 Stony Brook iGEM Team alum.

Natalie discussed her experience with lymphoma patients during her clinical rotations with Dr. Christina Lee, a hematologist and medical oncologist. One of the tests that she observed in the clinic was an antibodies test that showed peaks of immunoglobulin levels, which may be indicative of cancer. Another test she mentioned was flow cytometry of blood to detect markers on white blood cells.

We discussed our implementation plans of a yearly test/screening for earlier diagnosis. However, yearly blood tests are already a common occurrence, so she urged us to look into what makes our system special. She affirmed that fluorescence is a good indicator for the general public and we could look into quantifying the fluorescence for a more advanced product. She also suggested that a mock product or marketing for our final theorized biosensor will also help relay the project to the general public.

Another point she emphasized is the lack of education on lymphoma and miRNA detection, so she encouraged outreach about this. Since then, we have hosted more events, such as our collaboration with NMDP and NYBC for the Blood Cancer Awareness Month Event.

https://renaissance.stonybrookmedicine.edu/mstp/people/lo

Lizzie Hernandez (NMDP)

Lizzie Hernandez is the account manager for the New York chapter of the National Marrow Donor Program. She assisted in connecting us with NMDP recruiter Landon Finkel and Dr. Ron Jacob. She helped facilitate meetings between the iGEM team and NMDP by first connecting us with Landon Finkel, who is an NMDP representative for Stony Brook. Secondly, she worked to connect us with Dr. Ron Jacob at the NMDP Unite event, allowing us to speak to him personally regarding our project.

Maureen Marcello (NYBC)

Maureen is the account manager for the New York Blood Center (NYBC) and she helps run blood drives in the NYC-Long Island area. We set up a meeting with her in order to learn more about blood donation programs and organizations in our local area. We engaged in a discussion with her about the work carried out by the New York Blood Center (NYBC) and the critical need for blood donations that the organization facilitates. We emphasized the importance of blood donations and explored how the iGEM team can support the NYBC’s goals. Additionally, we discussed how our project represents a multilayered approach, serving as an early detection tool for non-Hodgkin's B-cell lymphoma, which can ultimately lead to more effective treatments of the cancer.

Zachary Don

Zachary was the Outreach Team Leader of the 2023 SBU iGEM Team and he is currently a Blood cancer student researcher at Stony Brook Medicine. Zachary has a vested interest in blood cancer research due to a family history of the debilitating disease. He assisted us throughout our research journey by helping us connect with relevant organizations and figures such as the NYBC, NMDP, and the Leukemia and Lymphoma Society.

Dr. Simon d'Oelsnitz

Dr. d'Oelsnitz is a Synthetic Biology Fellow at Harvard Medical School - Wyss Institute - with interests in biosensors and enzyme engineering. 2015 Stony Brook iGEM Team alum. Dr. Simon d’Oelsnitz provided feedback on our presentation, specifically the models on our brochure. He relayed that our models for our genetic circuit were difficult to understand. In response, we revised our schematics to improve clarity and make the information more accessible to the general public.

Northwell Health Oncology-Hematology Cancer Trials Office

Spoke with professionals in the Oncology-Hematology Department regarding our research project. From there, they offered us valuable feedback regarding how our project would benefit from clinical advice as we plan to develop a diagnostic tool with clinical application. This advice led us to seek further assistance from medical professionals located at Stony Brook Medicine.

Andrew Sillato

Andrew participated in weekly hour-long meetings where he reviewed our wet lab results and addressed any unexpected outcomes or failures. He contributed valuable feedback to our initial project proposal, significantly influencing its direction. Firstly, he recommended utilizing a GST-Tag to improve the solubility of Ago2. Secondly, he assisted us with the protocols, as well as supplied us reagents for TEDA and other general lab materials. Additionally, he was the first to propose using a cell-free system instead of a bacterial one. These suggestions demonstrate a commitment to continually optimizing and improving experimental design for more effective and practical outcomes in a clinical setting. Andrew guided us in creating a research plan that prioritized responsibility in the lab as well as ethical conduct. He helped relay our wet lab research findings to outside stakeholders

Abhishek Cherath

Abhishek is a 2020 and 2021 Stony Brook iGEM alum. We met with Abhishek to gain feedback on the modeling of our system. He suggested modeling binding between Ago2 and miRNA binding to further understand this interaction. We created and recorded a simulation in GROMACS. This will help with public understanding of our research. Additionally, understanding the development of RISC will assist with improving clinical practices for miRNA detection.

Melanie Cragan

One concern with our project was that miRNA would break down inside of the bacteria because of RNAses, prior to detection. This was a design constraint that was largely influential to our project development. Melanie suggested the use of MRE600 because it is an RNase free strain, so miRNA should not be degraded. Her suggestions ensure that our miRNA detection system is accurate and reliable, promoting integrity in our findings.

Janice Xu

Our iGEM mentor, Janice Xu, who was assigned to us upon application for a mentor gave us crucial advice on our project. Janice discussed our parts and spoke about ensuring they are compatible with RFC 10 and Type IIS standards, they must include the specified prefixes and suffixes while avoiding illegal restriction enzyme sites like EcoR1, Xba1, Spe1, and Pst1 within the sequence She gave us advice on real-world application when naming engineered genes – it's less critical to attach these prefixes and suffixes, as we can test them as they are and later document any necessary modifications. She informed us that if our parts do contain illegal recognition sites, it's best to perform site-directed mutagenesis to remove them before testing; however, we can still proceed with testing while addressing any potential impacts in our write-up. Additionally, if an illegal site appears within important codons, we should consider whether a silent mutation is necessary. Finally, she informed us that submitting full plasmids may provide exemptions from RFC 10/Type IIS requirements, but we should clarify if any formal applications for exemptions are needed, especially for complex constructs that include multiple components like promoters and coding sequences. This understanding will help us navigate the technical standards while promoting best practices in our synthetic biology projects.

Explorations in STEM

Leanne Demay, Karen Kernan, Jessica Roman, and Amie Cohen lead workshops for the Explorations in STEM program by URECA and the Career Center. This program aims to provide research and professional guidance to undergraduates in the STEM field. Along with funding from this organization, members on our team were given the opportunity to attend weekly workshops to learn how to communicate their scientific findings, design posters about their research, ethical standards, publishing, reading scientific literature, applying to graduate school, and more.