Lecture Summaries

• Introductions: Instructors and students
• Overview of the syllabus and expectations
• Overview of primary research papers and how to find them
• Introduction to the field
  • How biology defines cell "identity" and "fate"—what constitutes a cell's identity?
  • Regulation of gene expression (transcriptional, post-transcriptional, translational)

Week 1 handout (PDF)

Following the discovery and initial characterization of pluripotent stem cells, several open questions remained on how pluripotent stem cells are derived and maintain their potency. Some of these mechanisms have been elucidated through functional characterization of specific pluripotency factors, such as the core transcription factor Nanog and the histone methyltransferase Wdr5. The two papers we will read this week focus on these essential factors, which work to maintain a specific transcriptional state and chromatin environment (i.e., the spatial organization of the genome within the nucleus) that is conducive for pluripotency.

Week 3 handout (PDF)

In contrast to pluripotent stem cells, which are undifferentiated cells that maintain the capability to give rise to any cell type, germ cells are specialized cells that develop either as eggs or sperm. There are major differences between germ cells and somatic cells (haploid as opposed to diploid, for example), and germ cell identity and differentiation is massively distinct from the identity and differentiation of either pluripotent stem cells or differentiated somatic cells. However, like pluripotent stem cells, germ cells must maintain their developmental potential to give rise to an entirely new organism. This week, we will read papers that discuss how cells within the early embryo are guided toward a germ cell fate rather than a somatic fate, using both intrinsic and extrinsic mechanisms. We will study examples of the two prevailing models of germ cell formation: 1) preformation via inheritance of maternally supplied germ plasm in flies and 2) induction via signaling from extraembryonic tissue in mice.

While it is generally thought that a cell's developmental potential becomes restricted as it commits to a somatic fate, forced expression of specific transcription factors can induce fate-switching in somatic cells. Termed pioneer transcription factors, these factors are thought to activate certain transcriptional programs by binding the promoters of genes necessary for somatic development. This week we will read a classic paper that identified the first pioneer transcription factor, MyoD, the expression of which causes fibroblasts to switch to a muscle cell fate. We will then explore the molecular events that follow the expression of pioneer transcription factors and lead to reprogramming of fibroblasts to neurons.

Week 7 handout (PDF)

With the advance of high-throughput sequencing of RNA from single cells, researchers have been able to characterize genome-wide transcriptional differences between cell types, rather than the differential expression of only a few genes. Current transcriptional profiling methods have allowed for expanded and more precise categorizations of hematopoietic cells and thus refinement in how cell identity is defined. This week's reading highlights more recent research that demonstrates the greater resolution with which we can classify cell types via genome-wide transcriptional profiling and single-cell sequencing. The first paper utilizes single-cell RNA sequencing to identify novel subsets of differentiated hematopoietic cells. The second paper more closely examines the transcriptional profiles of early progenitor cells, including hematopoietic stem cells, and challenges earlier paradigms of hematopoietic differentiation.

In addition to internal changes within cells that influence cell fate (such as master regulator transcription factors and chromatin remodeling), external signals also play an important role in guiding cell fate and identity. These signals are often small proteins secreted by other immune cells called cytokines. This week we will read different examples of how cell signaling is able to guide cell identity. Both of the papers this week focus on hematopoietic cells from the adaptive immune system: B cells, which recognize antibodies, and T cells, which bind to other immune cells that have identified pathogens in the body. In the first example, we will read about how B cells require signaling from the cytokine interleukin-7 to properly develop. In the second example, we will read about how naive CD4+ T cell differentiation is influenced by the surrounding cytokine environment.

Genes that play important roles in the differentiation of hematopoietic lineages are often mutated in blood cancers, i.e., forms of leukemia. This week we will examine two variations of leukemia that result from mutations in crucial B cell or T cell differentiation genes. By analyzing the specific phenotypes that arise from these oncogenic mutations, researchers can characterize the roles that different genes play in immune cell differentiation. While both papers focus on oncogenes, i.e., genes that contribute to cancer when mutated, each study utilizes a different approach. The first paper identifies this genes through a genome-wide screen of patients with acute lymphoblastic leukemia, while the second paper targets specific oncogenes and demonstrates their importance in T cell differentiation in mouse models.

Students will give their final presentations, complete course evaluations, and discuss the course (good and bad).