Exciting Advantages to Single-Cell Sequencing of Parasites: Researchers Walzer and Chi Explain

Jen-Tsan Ashley Chi:

I was born and grew up in Taiwan. I obtained my MD from National Taiwan University and PhD from Stanford University. From my post-doctoral training with Dr. Patrick Brown at Stanford, I have been using genomic analysis and gene expression to dissect the influences of various tumor microenvironmental stresses in human cancer and tumor heterogeneity. Since arriving at Duke University, we discovered the presence of abundant and diverse species of RNAs in mature erythrocyte, a cell type long thought to lack any DNA or RNA. Since then we have pioneered the efforts to apply the genomic analysis of erythrocyte microRNAs to dissect the phenotypic variations among sickle cell diseases and blood storage. From the investigation of erythrocytes, we have been interested in the role of erythrocyte RNA in the malaria parasites, including the recent adoption of single cell RNA-Seq technology of malaria parasite pioneered by Dr. Katie Walzer during her thesis work in my lab.

Katelyn Walzer:

For over ten years, Dr. Katelyn Walzer has studied the genetics and genomics of multiple apicomplexan parasites, including Toxoplasma gondii, Plasmodium falciparum, and now Cryptosporidium parvum. She completed her PhD in 2018 under the guidance of Dr. Jen-Tsan Ashley Chi at Duke University, where she studied the malaria-causing parasite P. falciparum using high-throughput genomic technologies, including single-cell RNA sequencing. Her work, published in multiple journals including mSphere and PLoS Genetics, identified distinct gene expression differences between male and female parasites during the transmissible sexual stage and uncovered unexpected transcription of genes during multiple times in the P. falciparum life cycle. These findings imply that significant transcriptional diversity allows the P. falciparum parasite to survive its dynamic host environment. Now a post-doctoral fellow in Dr. Boris Striepen's lab at the University of Pennsylvania, Dr. Walzer studies the transcriptional regulators of the C. parvum life cycle and has used single-cell RNA sequencing to determine the genes expressed during the asexual and sexual stages. Further work will focus on functionally characterizing stage-specific regulators and determining single-cell gene expression of the host immune response.

Walzer KA, Fradin H, Emerson LY, Corcoran DL, Chi JT (2019) Latent transcriptional variations of individual Plasmodium falciparum uncovered by single-cell RNA-seq and fluorescence imaging. PLOS Genetics 15(12): e1008506. https://doi.org/10.1371/journal.pgen.1008506

Walzer KA, Kubicki DM, Tang X, Chi JT. Single-Cell Analysis Reveals Distinct Gene Expression and Heterogeneity in Male and Female Plasmodium falciparum Gametocytes. mSphere. 2018;3(2):e00130-18. Published 2018 Apr 11. doi:10.1128/mSphere.00130-18

Researcher Katelyn Walzer and her Ph.D. mentor Dr. Jen-Tsan Ashley Chi used single-cell analysis to study the malaria-causing parasite, Plasmodium. Dr. Walzer is now studying another parasite called Cryptosporidium. In this podcast, they discuss

• How Cryptosporidium infects hosts and the dangers it poses, especially for children,
• Past bulk-sequencing techniques for parasites and what they missed in analysis,
• The mechanics for single-cell genomics analysis, what it offers microbiology, and advantages specific to fighting Cryptosporidium.

Jen-Tsan Ashley Chi, MD, PhD, is an associate professor at the Center for Genomic and Computational Biology at Duke University School of Medicine. His former microbiology student, Katelyn Ann Walzer, PhD, is currently working on her post-doc at the University of Pennsylvania with single-cell analysis. They tell listeners about their specific findings on Plasmodium and Dr. Walzer's current focus on Cryptosporidium, a parasite that causes a diarrheal disease, and what else she hopes to study regarding the parasite.

She gives some background on the parasite, describing how detrimental it can be for children in some countries of Africa who've already suffered from other diseases. Cryptosporidium can actually reactivate and cause chronic infection in these children, affecting their general health and quality of life. Dr. Walzer explains how single-cell genomics analysis has allowed her to identify which genes are expressed in the two different matting types (sexual and asexual). Dr. Chi explains how this technique also helped in Plasmodium research because mating is the only way to achieve intrapersonal human transmission, and identifying males and understanding the stages of development in both parasites may offer ways to block their development. Dr. Walzer explains additional findings, plans for upcoming research, and her goals to discover information that will help develop better treatments for infection by Cryptosporidium.

For more information, search these researchers in Google Scholar. Available on Apple Podcasts: apple.co/2Os0myK