Lecture Summaries

1 Class introduction
  • Introductions: instructor and students
  • Overview of the syllabus and expectations
  • Overview of primary research papers and how to find them (demo of literature search on PubMed).
  • Introduction to cellular immunology: functions and cellular components of the immune system; development of immune cells during embryogenesis and postnatal development; overview of some commonly used methods in immunology: flow cytometry, immunofluorescence, immunoblotting, genetic approaches to generate engineered cells or animals, transplantation assays to reconstitute immune system (mostly in recipient mice).
  • Introduction of papers to be discussed in week 2.
2 Development of immune cells

In mammals, immune cells include numerous specialized hematopoietic blood cells that are differentiated from hematopoietic stem cells (HSCs) located mostly in the bone marrow of adult animals. HSCs were one of the first well-characterized classes of somatic stem cells: they can self-renew in the bone marrow, and through a process of multi-step differentiation, generate all types of hematopoietic blood cells. In addition to the immune cells circulating in blood, a different group of cells collectively referred to as resident myeloid cells is thought to arise through a different developmental history. These cells are formed from precursors in the yolk sac during early embryogenesis and then migrate to developing organs to maintain the homeostasis of resident myeloid cells independently of HSCs.

This week we will read one classic paper that contributed to our fundamental knowledge about lymphoid progenitors that give rise to lymphoid cells during hematopoiesis and a more recent paper focusing on a completely different development paradigm/model of resident myeloid cells.

3 DNA rearrangements in adaptive immune cells

The innate immune system consists of the cells and mechanisms that provide the first line of defense from infection in a non-specific manner. However, if a pathogen overwhelms innate immunity, an adaptive immune response is initiated in a pathogen-specific manner. B cells and T cells mediate the adaptive immune response thorough antigen-specific antibodies and pathogenspecific effector T cells (various types of T cells that exert different functions in adaptive immune response against particular pathogens), respectively. The capability of B cells and T cells to specifically recognize enormously diverse antigens relies on V(D)J recombination (recombination of immunoglobulin (Igs) and T cell receptor (TCRs) variable (V), diversity (D), and joining (J) segments), a fundamental process that occurs during the early developmental stages of T and B cell maturation.

This week we will read a classic paper identifying the Recombination Activating Gene 1 (Rag1) genes that encodes a critical endonuclease instrumental to V(D)J recombination. Additionally, we will read a recent study examining the chromosomal mechanism controlling this locus-specific recombination frequency. Higher frequency of recombination is achieved through CTCF-binding elements (DNA sequences that are bound by the transcription factor CCCTC-binding factor (CTCF), which acts as a regulator of chromatin architecture). CTCF-binding elements slow the chromatin-scanning movements of the RAG complex (composed of both Rag1 and Rag2), thereby improving the recombination frequency for recombination sites close to CTCT-binding elements.

4 T cells: Th2 and cytotoxic T cells T cells are critical mediators of the adaptive immune response. This week we focus on two classes of T cells: CD4+ helper T cells (Th) and CD8+ cytotoxic T cells. We will read a classic paper about a master regulator that is necessary and sufficient to specify a particular set of helper T cells (Th cells), Th2 cells that induce humoral immunity. Additionally, we will examine how the immune checkpoint pathway (regulations of immune activation to prevent autoimmune disorders) in cytotoxic T cells contributes to immune evasion (strategies used by pathogens and cancer cells to evade immune responses) of HIV-infected cells.
5 Cell death and immune processes

Programmed cell death is critical for homeostasis and immunity. This week we read a fundamental paper in the field of the cell death that describe how C. elegans developmental genetics identified critical players in the programmed cell death (apoptosis) pathway that subsequently proved to also be used when immune cells eliminate virus-infected cells.

The second paper describes pyroptosis, a relatively new mode of cell death that is generally inflammatory, in contrast to the generally non-inflammatory process of apoptotic cell death.

6 Lymphocytes in disease

The mechanisms immune cells employ to protect against pathogens can backfire and instead contribute to disease progression. We examine two examples this week.

First, recombination of DNA is critical for the diversity of immunoglobulins and TCRs. However, this process of recombining DNA can contribute to leukemia as discovered in Erikson et al.: the Igh (Immunoglobulin heavy chain) locus experiences a high frequency of double-stranded DNA breaks and error-prone non-homologous end-joining repair, and this process can lead to translocation (chromosome abnormality caused by rearrangement of parts between nonhomologous chromosomes) of the c-Myc locus to Igh locus. Cis-regulatory elements of the Igh locus then will drive high expression of c-Myc and leukemogenesis. Doitsh et al. described how pyroptotic cell death, a process thought to function in antimicrobial defense, contributes to cell death of HIV-infected CD4 T cells, thereby facilitating AIDS pathogenesis.

7 Th17 cells

T helper (Th) cells are critical components of the immune system, and different Th cell types respond to different stimuli. Th1 produces INF-gamma and mediates the response to intracellular infection by killing infected cells. Th2 produces the cytokines IL4, IL5, and IL13, which are thought to mediate a “weep-and-sweep” response to remove extracellular pathogens by regulating smooth muscles cells and mucus-secreting cells. IL17-producing Th17 cells constitute a proinflammatory group of T helper cells that mediate inflammation and are implicated in autoimmune disease and other chronic inflammatory conditions.

This week we read a paper describing RORgt as a master regulator of Th17 cells. The second paper examines how Th17 cytokines accelerate initiation and progression of one of the most deadly of human malignancies, pancreatic ductal adenocarcinoma (PDAC).

8 T cells (adoptive immune transfer)

Immune checkpoints act to maintain self-tolerance (the ability of the immune system to recognize the body’s own cells or products as non-harmful and not mount immune responses). Cancer cells can hijack this process to evade immune surveillance.

This week we read one of the early papers testing the hypothesis that the Programmed Cell Death Protein 1 (PD1)-mediated immune checkpoint plays a role in tumor survival and might serve as a target of immune checkpoint inhibition. Then we examine how CRISPR/Cas9-mediated genome editing of T cells generated chimeric antigen T cells (or CAR-T cells, T cells engineered to recognize a particular antigen) for adopted immune transfer to treat certain blood malignancies.

9 Autoimmunity

Multiple immune cell types function in preventing autoimmune disease. Regulatory T cells or T-regs are a class of anti-inflammatory T helper cells critical for suppressing autoimmunity.

This week we discuss a paper in developmental immunology that discovered that the critical transcription factor FoxP3 specifies T-reg cell fate. Loss of FoxP3 function in mice resulted in a lethal autoimmune syndrome. The second paper showed that loss of MyD88 (a critical signaling component in innate immune cells) protected autoimmune diabetes in pathogenfree mice but not germ-free mice (mice without commensal microbiota). This is one of the first studies that examined the contributions of the microbiota and innate immune cells in autoimmune diabetes in mice.

10 Innate lymphoid cells (ILC)

Type 2 innate lymphoid cells (ILC2) function in type 2 responses (“weep-and-sweep” protective immune response against helminth parasites) that stimulate secretion of mucus and hypercontractility of smooth muscles. ILCs play important roles in responses to parasites and allergens. This week we read two papers about the role of ILCs in the intestine and in the airway.

The first paper shows interactions between tuft cells, a type of gut epithelial cells, and ILC2 through IL12. In turn, ILC2 functions by secreting IL13, which orchestrates the “weep-andsweep” response from the gut epithelia. The second paper demonstrates that in the airway pulmonary neuroendocrine cells (PNESs), a rare type of airway epithelial cells, activate ILC2s by secreting calcitonin gene-related peptide (CGRP) and gamma-aminobutyric acid (GABA). ILC2s then activate the immune response in allergies by stimulating mucus secretion from airway epithelia.

11 Macrophages

Macrophages are a type of innate immune cells that engulf and digest microbes and cellular debris, and regulate local and global inflammation. However, excess inflammation operates at the cost of regular tissue function and can cause damage and reduce fitness during infection. Immune tolerance (a state of unresponsiveness of the immune system to substances that generally elicit an immune response) is another coping mechanism and is hypothesized to be more advantageous than extreme inflammation.

The first paper describes the impact of heme, a metabolite increased upon lysis of red blood cells (such as in severe bacterial infection), and how heme oxygenase protects endothelial cells from apoptosis by producing carbon monoxide (CO). The second paper describes how regular HSCs upregulate the macrophage “don’t eat me” signal CD47 during migration/mobilization to improve HSCs survival during migration, and how leukemic stem cells mimic normal physiological function to reduce phagocytosis by macrophages, thereby promoting leukemia progression.

12 Trained immunity

Innate immune cells were long thought to be of no or very limited adaptation/memory. This week we read some recent papers suggesting that the innate immune response could show features of memory, a process termed trained immunity.

The first paper maps epigenetic (DNA methylations or histone modifications that regulate gene expression without altering DNA sequences) mechanisms underlying trained immunity in the process of monocyte (a precursor cell type that can differentiate into a macrophage or a dendritic cell) to macrophage differentiation. The second paper explores the trained immunity of HSCs during the immune responses to tuberculosis bacteria infection after Bacille Calmette-Guérin (BCG) vaccination.

13 Emerging technologies in immunology

Powerful technologies have been instrumental for the field of immunology. This week we read some emerging methods in the field.

The first paper shows simultaneous measurements of 34 parameters (including multiple cell-surface and interacellular signaling components) at the single-cell level by combining flow cytometry and mass spectrometry. The second paper applies single-cell RNA-sequencing (RNA-seq) analysis for the discovery of potential new types of innate immune cells.

14 Field trip No lecture
15 Oral presentations No lecture