BME52300 - Stem Cell Technologies
This course provides an in-depth exploration of advanced stem cell engineering technologies and bioinformatics approaches such as single-cell RNA sequencing (scRNA-seq). The course emphasizes the practical application of these tools in the development of tissue engineered models for basic research and translational medicine.
Credit Hours: 3
Instructor(s): Estelle Park
Email: park1713@purdue.edu
Learning Objective:
- Design experimental approaches for developing tissue models and analyzing their structural and functional properties.
- Apply technologies using stem cells for disease modeling and precision medicine.
- Utilize advanced bioinformatics approaches such as scRNA-seq to investigate the molecular mechanisms underlying tissue development and disease.
- Integrate experimental and computational tools for multi-scale analysis of engineered tissue constructs.
- Critically evaluate recent advancements in stem cell technologies for their applications.
Description:
This course provides an in-depth exploration of advanced stem cell engineering technologies and bioinformatics approaches such as single-cell RNA sequencing (scRNA-seq). The course emphasizes the practical application of these tools in the development of tissue engineered models for basic research and translational medicine.
Topics Covered:
| Week | Topics |
|---|---|
| 1 |
Syllabus review & overview of stem cell technologies Single-cell and high-dimensional analysis of stem cells Paper discussion instruction |
| 2 |
Adult stem cell niches & homeostasis Download & install the software |
| 3 |
Induced pluripotency and reprogramming technologies Loading scRNA-seq data into R/Creating Seurat objects Quiz 1 Paper discussion - iPSC technology |
| 4 |
Directed differentiation & lineage specification Merging Seurat objects/Quality control & selecting cells for further analysis Paper discussion - organoids |
| 5 |
Organoids & 3D stem cell cultures Data normalization, feature selection & data scaling Paper discussion - stem cell based organ chips |
| 6 |
Organs-on-chips & microphysiological systems Dimensional reduction & cell clustering Quiz 2 Paper discussion - genome editing in stem cell engineering |
| 7 |
Genome editing in stem cells scRNA-seq data integration Paper discussion - biomaterials for stem cells |
| 8 |
Find markers and differentially expressed genes Paper discussion - stem cell therapies |
| 9 |
Biomaterials & synthetic niches Rename cell clusters/The subset function Quiz 3 Paper discussion - disease modeling using stem cells |
| 10 | Spring Break |
| 11 |
Immunomodulation & stem cell-derived therapies Azimuth annotation in R Paper discussion - stem cells for developmental biology |
| 12 |
Stem cells in disease modeling Calculating cluster frequencies/Seurat plot functions Paper discussion - stem cells in drug screening |
| 13 |
Drug screening & toxicology with stem cell-derived models Integrate datasets between control & disease samples Quiz 4 Paper discussion - stem cells in immunotherapies |
| 14 |
Manufacturing & scaling of stem cell technologies Identify conserved and differentially expressed genes across conditions Paper discussion - scaling and manufacturing of stem cell engineered tissues |
| 15 |
Regulatory, ethical, and societal considerations Biological interpretation of analyzed datasets Paper discussion - organoid intelligence (Stem research with AI) |
| 16 |
Emerging frontiers and future directions Applying concepts to understand scRNA-seq data in published studies Quiz 5 Paper discussion - stem cell engineering in precision medicine |
Web Address:
https://purdue.brightspace.com
Homework:
Homework will be due in Brightspace every 3 weeks. Homework may consist of definition/short answer/multiple choice questions or online activities. Each assignment is worth 7 points (35%)
Projects:
(20%):
- Analyze a provided scRNA-seq dataset (normal vs diseased human lungs) using a bioinformatics tool (e.g. Seurat)
- Identify at least three major cell populations in the normal lung and generate labeled UMAP/t-SNE plots. Write a short paragraph describing each cell population's function in lung physiology and attach the corresponding plots. One-page limit, including figures and up to 5 reerences. (10 pts)
- Identify at least three differentially expressed genes or markers associated with lung disease and generate corresponding plots (e.g., violin, dot, heatmap). Briefly discuss the potential biological roles of those gnees in lung disease. Attach the corresponding plots. One-page limit, including figures and up to 5 references. (10 pts)
Paper presentation (20%):
Students will participate in a mock NIH study section-style journal club, following the review structure and scoring criteria outlined in the provided instructions. The goal is to build skills in critically evaluating scientific manuscripts, identifying strengths and weaknesses, and understanding how research proposals are judged for impact.
-
Each student will be assigned a research paper related to stem cell technologies. Presentation will include:
- [Slide 1] Title slide (paper title, authors, journal)
- [Slide 2] Investigator(s)/Corresponding author, their background, research focus areas
- [Slides 3-5] Background/Introduction/Significance
- [Slides 6-9] Approach/Major results and key figures
- [Slide 10] Innovation
- [Slide 11] Discussion (strengths & weaknesses) and Score
- Give a 20 min in-class presentation moderated by the TA or instructor
Exams:
There will be 5 in class quizzes at the beginning of class. Quiz will cover the materials discussed in previous weeks (not cumulative). Closed books and closed notes. (25%)
Textbooks:
No required textbooks. Handouts prepared by the instructor will be made available for download from Brightspace prior to each lecture and used as the course material.