Genomics case study

Biology 420 Case Study 2 Name:____________________________ 4/1/2024 Additional notes: Remember that some questions will ask you to design questions and experiments. You do not have to answer every possible related question. Choose Occam’s razor – the simplest solution is typically the best. Context: HIV infects certain immune cells by binding to a receptor called CCR5. Individuals that have mutations or deletions in CCR5 are immune to many variations of HIV. A proposed treatment for HIV would remove cells from patient bone marrow, modify CCR5 to an uninfectable variation, differentiate those cells into specific immune cell types (like CD34+ T-cells in the picture below), and infuse the modified cells back to the patient. A variation on this method removes stem cells from the patient, modifies the genome to be CCR5-deficient, and then differentiates those cells into immune pre-cursor cells. After infusion, the pre-cursor cells continue to differentiate into many different immune cell types. We will follow the method of removing stem cells, modifying them, starting differentiation, then infusing the cells back to finish differentiation in the patient. Q1: Assume that stem cells were removed and the CCR5 modification was verified. Now, you can differentiate the cells to immune precursors. In the process of differentiation, what changes to you expect are happening at the molecular level? Be as specific as you can, but don’t worry about the true markers (protein names, etc) of immune cells. (5 points) Q2: Assuming you could only choose one (budgets are tight!), what molecules would you look at to confirm cell identity (DNA, RNA, protein, something else)? Justify your choice. (5 points) Q3: Given your answer in Q2, how would you set-up your experiment to determine if the cells you’ve grown share features with immune cell types? Explain the techniques you would use and how you would control the experiment by choosing appropriate cells or datasets for comparison. (10 points) Q4: In vitro differentiation of the stem cells typically depends on transcription factor binding and regulating genes. The efficiency of differentiation is low. Give a hypothesis for why efficiency of transcription factor binding or activity might be low. (5 points) Q5: Given your answer in Q4, propose an experiment that would allow you to test this hypothesis. Remember that the transcription factor has many targets – use an omics approach to ensure that you are testing multiple sites at once. (7 points) Biology 420 Case Study 2 Name:____________________________ 4/1/2024 Q6: Imagine that you find some modified cells are still susceptible to (infected by) HIV. You compare the genomes of the resistant and susceptible cells and find that there is a mutation in a proposed gene of unknown function. Propose an experimental method to determine a possible function of that gene. (Note – you may take biochemical, genetic, or genomic approaches to this question. Play to your strengths!) (8 points) Bonus: This is a true story. Community member (CM): Do you teach Biology? Like molecules and cells and stuff? DHL: I do. CM: How come they’re always teaching that all people are the same, when some groups have animal DNA and other groups don’t? So obviously, we aren’t all the same group. DHL: I’m not sure what you mean. All humans are animals, mammals specifically, and share parts of their DNA with animals. CM: Yea, but you are like 65% mouse and 99% chimpanzee, but I’m not. DHL: ????? What information would you share with this individual to address their questions?