Article by Caroline McMahon and Cleta D’Sa
Before working in the Immune Oncology department at Bristol Meyers-Squibb, where she developed immuno-oncology therapies for first-in-human (FIH) clinical trials and worked with teams to genetically engineer T-cells to treat cancers, Dr. Lillian Seu was a National Institute of Health (NIH) Fogarty Fellow at the Centre for Infectious Disease Control, Zambia (CIDRZ). Fogarty fellowships provide funding for American clinician scientists to promote research and train researchers in a variety of global health areas in low- and middle-income countries in regions such as Sub-Saharan Africa, South America and Southeast Asia.
Seu, a graduate of Barnard College with a PhD in Biopharmaceutical Sciences from the University of California, San Francisco, is passionate about expanding quality health care everywhere in the world and embraced her Fogarty fellowship, viewing it as an opportunity to pursue that passion. From 2011 to 2014, Seu researched HIV in Lusaka, Zambia, as a continuation of her PhD. Zambia is among the countries most affected by the HIV and AIDS epidemic, which has become part of a national health priority. Inspired by her training to solve complex problems in systematic and sustainable ways, Seu hoped her work through the fellowship would help in an overall effort to strengthen health care systems abroad.
Using Sanger Sequencing
At the time of Seu’s fellowship, Zambia had an 11%-12% HIV prevalence rate and benefitted from the influx of funding for antiretroviral drugs. However, as a result of more patients receiving therapy, a high level of drug resistance emerged. Initially trained by the CIDRZ laboratory management team into a supervisory role with the antiretroviral resistance genotyping laboratory at the CIDRZ central lab, Seu was later responsible for coordinating antiretrovial resistance testing for patients at the Zambian Ministry of Health HIV clinic as well as private hospitals. There, Seu applied her knowledge of Sanger sequencing; prior CIDRZ laboratory scientists had shown that it was an effective method for drug resistance mutation discovery and easily adapted from the alternative Sanger-based diagnostic at the time (Viroseq).
Seu stresses that as technology moves forward at such a rapid rate, researchers shouldn’t be so quick to dismiss existing technology as “being old.” “Sanger sequencing can accomplish what some other new platforms can’t,” says Seu. “It’s thought that next-gen sequencing and high throughput sequencing methods, and now even long-read sequencing methods, are pulling past the ‘older ways’ of doing DNA sequencing, which involved the Sanger dideoxynucleotide chain terminating method.” Seu believes that Sanger sequencing continues to be relevant and has become an advocate “especially when you want to look at minor allele frequency haplotypes from contiguous viral genes that might not get captured in some of the higher-throughput platforms.” Additionally, the ability to quickly turn around small volumes of samples, to hone in on a predefined genetic locus such as the HIV pol gene, and to analyze complex gene structures makes Sanger sequencing flexible enough to use for other diagnostic testing.
Seu’s team used Sanger sequencing at the CIDRZ HIV Drug Resistance lab, the HIV reference lab for Zambia, where all 14 million patients who need tertiary care for HIV drug resistance mutation received care. Patients were sequenced for HIV drug resistance mutation for both major as well as minor allele variants. Sanger sequencing allowed the team to obtain deep coverage of all the different nucleotides, reverse transciptase inhibitors, non-nucleotide reverse transcriptase inhibitors, protease inhibitors, and integrase inhibitors — genes that, when mutated, can contribute to drug resistance [1,2]
The team captured details internally and deposited them to the Stanford drug resistance database (HIVdb), the foremost international collection used by WHO as a reference, which then enabled the comparison of drug resistance mutations for the Clade C virus on an international stage. Stanford conducted a meta-analysis of drug resistance mutations from all over the world, including the research being done in Zambia, and published it to E-Bio . Seu credits this international recognition of the research being done in Zambia to Sanger sequencing “because we were able to capture minor allele frequency haplotypes from contiguous viral genes and because we were able to input into a format that was compatible with the HIV drug resistance platform at Stanford.”
The Right Tools Make a Difference
Seu works in a field where precision medicine is at the center and has true meaning; it’s not just a buzzword. In Zambia, Sanger sequencing enabled her to perform precision medicine, which Seu states is very gratifying. “We would get the Sanger-based sequencing sample, we would get the panel of drug resistance mutations, and then we would print that sheet out, put in in a manila envelope and have it delivered to the tertiary care hospital down the road within an hour. With that, the doctor would call up the patient and tell them to switch medication the very next day.”
Seu explains, “Laboratory diagnostics are critical to making clinically impactful decisions, and technologies such as Sanger sequencing can allow the laboratory scientists to build and improve upon critical assays needed in the clinical diagnostic lab.”
In her spare time, Seu is a student and career mentor, finding great joy in training and learning from the next generation of scientific leaders. She is dedicated to mentoring students in high school and beyond. She currently serves on the Board of Directors for the Stuyvesant High School Alumni Association, where she works closely with faculty to increase interest in and awareness of independent research in an effort to place students in the best labs in the New York City area. Passionate about working with teams to solve complex problems, Seu firmly believes in equipping people with the right tools to be able to make a difference.
- Seu, L., Melenga, L.B., Siwingwa, M., et al. (2015) Characterization of HIV Drug Resistance Mutations Among Patients Failing First-Line Antiretroviral Therapy From a Tertiary Referral Center in Lusaka, Zambia. J Med Virol 87(7):1149-1157.
- Seu, L., Mwape, I., Guffey Bradford, M. (2014) Single genome amplification of proviral HIV-1 DNA from dried blood spot specimens collected during early infant screening programs in Lusaka, Zambia. J Med Virol 203:97-101.
- Rhee, S.Y., et al. (2017) EBioMedicine. Apr; 18: 225–235.