T-Cells Flashcards
what is innate immunity?
- every organism has an innate response (animals, plants, bacteria etc)
- includes barriers (i.e skin, mucus membrane) to form first line of defence
- also includes phagocytes (macrophages, neutrophils etc) as backup to destroy pathogens if it enters the body
what is adaptive immunity?
- only present in animals with a backbone and a jaw
- can mount a specific immune response against anything (diverse)
- a type of immunity that develops after an initial response to a pathogen and leads to an enhanced response to future encounters with it
3 characteristics of adaptive immunity
1) Specificity = incredibly specific, combats one specific pathogen
2) Diversity = mounts an immune response to almost anything
3) Memory = responds to a reinfection faster and stronger than a first exposure (escalating response)
what are the cells of the adaptive immune system? what are their roles?
2 types of cells:
1) T- cells (CD4 and CD8 t-cell)
2) B-cells
- B-cells produce antibodies for a long range, distance site of infection
- CD4+ t-cell are helper cells that orchestrate an immune response
- CD8+ t-cell are cytotoxic that move to the infected tissue and physically destroy infected cells
what are antigen-presenting cells?
- dendritic cells, macrophages, b-cells are all APC’s
- they are immune cells that have detected and internalized a pathogen then digested it into various antigen fragments
- these fragments (proteins) are placed onto MHC class I or MHC class II molecules on the surface of the immune cell
- the APC may now interact with t-cell receptors (TCRs) on CD4 or CD8 t-cells
- this presentation is essential for initiating and coordinating a targeted immune response against the infection.
how do B-cells and T-cells recognize pathogens?
there are 2 adaptive immune receptors
1) TCRs = t-cell receptor
2) BCRs = b-cell receptor
- they work by recognizing pathogens (antigens) and initiating adaptive immune responses within the body
- receptors are randomly generated through the random receptor arrangement
why are b-cells and t-cells so important?
- without the ability to produce b-cells and t-cells, we couldn’t use our adaptive immunity
- the randomized generation of receptors provides diversity, meaning it can be prepared for any new threats
what are naive t-cells and b-cells?
- naive cells are mature (completed selection)
- when a lymphocyte has never been activated and is still searching for its unique antigen
–> naive t-cells circulate through the bloodstream and move through secondary lymph organs (spleen, lymph nodes) to search for matching antigen
–> naive b-cells reside in b-cell areas of lymph nodes awaiting their matching antigen and activation by t-cells
what is the structure of t-cell receptors?
- there is only one “arm” (antigen binding domain) that contain two chains
- most TCRs have alpha and beta chains that recognize antigens on the outside; some TCRs have gamma and delta chains
- TCRs function as part of a complex with CD3 chains (gamma, delta, epsilon and zeta) to help produce good receptors and signal effectively
- receptors can only recognize the primary structure (chopped up peptides) of antigens that are presented by MHC
what do T-cell receptors bind to?
- TCRs cannot bind to the pathogen directly, they requires MHC to present the peptides
- they bind to the short fragments of peptides (primary structure) presented in a peptide receptor called MHC (major histocompatibility complex)
what is the Major Histocompatibility Complex (MHC)?
- MHC is a set of molecules expressed on the surface host cells (typically thymic cells)
- it presents antigen fragments (proteins)
- t-cell receptors binding to MHC determine if it can become activated or not
- without MHC, you wouldn’t activate a single t-cell
what are the 2 types of MHC?
1) class 1 MHC = expressed on every cell in the body and present intracellular pathogen peptides to TCRs
–> present to CD8+ t-cells
2) class 2 MHC = expressed on specialized antigen presenting cells (APCs; macrophages, dendritic cells) and present extracellular pathogen peptides to TCRs
–> present to CD4+ t-cells
how are lymphocyte receptors so diverse?
- b-cells and t-cells don’t have receptors when they’re first produced
- lymphocyte receptors (TCRs and BCRs) are produced by random rearrangement of their DNA
- this process is celled SOMATIC RECOMBINATION
–> if changes are made to DNA of cells = change in mRNA and protein produced
only occurs in lymphocytes, most cells DNA don’t change
how does the process of somatic combination work for t-cells and b-cells?
- receptors are encoded by variable (V), diversity (D), joining (J) and constant (C) gene segments
- there are many possible combinations of V(D) and J
- V(D) J recombination randomly selects and joins segments from the V, D, J gene pool and connects to a C domain to produce a functional receptor
- lymphocytes do not express functional antigen receptors (BCRs or TCRs) until somatic recombination occurs
- this process occurs early in lymphocyte development
what are RAG-1 and RAG-2 enzymes
- RAG-1 and RAG-2 are recombinase enzymes (recombination activating genes)
- these enzymes are expressed exclusively in immature B and T-cells only (because we don’t DNA rearrangement in other cells)
- RAG-1 and RAG-2 form a recombinase complex that mediates the cutting and joining of single gene segments of each V(D)J and connect it to a C domain to produce a functional gene receptor
how does the process of somatic combination lead to diversity?
- lymphocyte receptor rearrangement is a RANDOM process which resulting in every individual generating a large and unique TCR and BCR repertoire
–> T-cell diversity takes place in thymus
–> B-cell diversity takes place in bone marrow - diversity ensures that the b-cells and t-cells can recognize a wide variety of antigens/pathogens
what are the genes involved TCR rearrangement?
- TCR genes are typically made up of alpha and beta chains (found on chromosome 14)
- Sometimes TCR genes are made up of gamma and delta chains (found on chromosome 7)
- Mature T-cells express either ⍺β or ɣδ TCRs, which are critical for antigen recognition
- TCR β and ɣ genes contain only V and J exons (no D exons)*
what are the primary and second lymphoid organs?
1) primary lymphoid organs
- bone marrow and thymus
- sites of leukocyte production and maturation
- where hematopoiesis occurs
2) secondary lymphoid organs
- lymph nodes, spleen, Peyer’s patches, mucosal tissues
- the sites of leukocyte activation
what is the importance of the bone marrow?
- bone marrow is the site for hematopoiesis = production of leukocytes (including b-cell, t-cells)
-the site for B-cell development and maturation
what is the importance of the thymus?
- the site of T-cell development and maturation
- immature t-cells produced in the bone marrow move to the thymus for maturation
what would happen without t-cell selection in the thymus?
without maturation in thymus, the body would be deficient in t-cells = no activation of b-cells = inability to fight infections
1) autoimmunity
- if negative selection didn’t occur, T cells that bind too strongly to self-antigens would not be eliminated = self-reactive T cells could attack the body’s own tissues, leading to autoimmune diseases.
what happens after immature t-cells are formed during hematopoiesis?
- immature t-cells (aka thymocytes) are produced in the bone marrow through hematopoeisis, where they migrate to the thymus for maturation
- immature T-cells do NOT express a TCR so they undergo random receptor rearrangement when they reach the subcapsular region of the thymus
- upon receptor production, they must pass positive/negative selection process to remove self-reactive cells
what are the steps to t-cell selection
there are 2 checkpoints
1) positive selection: is the rearranged TCR useful?
- lymphocytes expressing TCRs that can bind to self MHC with low affinity receive a survival signal
- TCRs that cannot bind to self MHC die because they’re useless
2) negative selection: is the rearranged TCR dangerous?
- lymphocytes expressing TCRs that bind to self MHC with high affinity receive a signal to die (apoptosis)
- if they bind with low affinity, they survive
- if the t-cell pass their selection processes they move to the secondary lymphoid organs for activation
- however, the majority of thymocytes die during the selection process (95%)
what is central tolerance?
the process of eliminating any developing t-cells or b-cells that are auto reactive, preventing the immune system from attacking itself (negative selection)
what happens when a thymocyte passes selection?
- the remaining 5% of lymphocytes express TCR with low affinity for self MHC can recognize self and aren’t auto-reactive
- this contains an individuals unique t-cell repertoire and is highly diverse
- now they are ready to be activated and detect invading pathogens
–> all have the potential to be useful but only few are actually useful to things in body (i.e some may be effective to things found in fish so it’ll never be used)
why is it important that multiple TCRs can recognize different parts of the same pathogen?
- a single pathogen can be recognized by many t-cells, which each one targeting different parts (epitopes) of the pathogen
- it is not a 1:1 relationship between a pathogen epitope and TCR
- TCRs have varying binding strengths (affinities) for epitopes of a pathogen (stronger = more effective response)
this is important because it ensures the immune system can build a robust and diverse response to a pathogen. it also increases the chances of eliminating a pathogen even if not all TCRs bind strongly to the epitope of the pathogen
what are the main t-cell types of the adaptive immune system?
- helper t-cells = express accessory molecule CD4 which binds to MHC class II
- cytotoxic (killer) t-cells = express accessory molecule CD8 which binds to MHC class I
- Tregs = regulatory t-cells that suppress the activity of CD4 and CD8 t-cells and control immune responses
–> they all work in tandem and know what to do because of cytokines (communication)
how are antigens presented to t-cells?
- t-cells are only activated in the presence of antigen-presenting cells (APCs) such as dendritic cells, macrophages or B-cells
- the APCs internalize and digest pathogens into small antigen fragments, which are loaded into their MHC class I or MHC class II molecules on the surface
- it can then be recognized by t-cells, leading to activation
how do dendritic cells present antigens?
- dendritic cells exist within tissues in an immature state
- immature dendritic cells have the high ability to internalize antigens, such as pathogens
- dendritic cells drain from the tissue to the lymph nodes at a steady rate, particularly increasing during inflammation or infection
- as the dendritic cells migrate to the lymph nodes, they mature and cannot pick up any more antigens; they can only present them
- mature dendritic cells exist in the lymph nodes
- in the lymph nodes, mature dendritic cells present processed antigens using MHC (Class I and class II) to T-cells, leading to activation and a target immune response
why are dendritic cells important?
- dendritic cells are part of the innate immune system, but they also bridge the gap to the adaptive immune system by activating T-cells
- this antigen presentation process occurs at high rates during infection, helping to initiate an immune response.
if no dendritic cell present = no t-cell activation = no adaptive immune response = PROBLEM
what is MHC?
- called the major histocompatibility complex (MHC)
–> called a ‘complex’ because all the MHC genes are found in a single location on this chromosome - MHC molecules are essentially peptide receptors because they bind to peptides (short chains of amino acids) in order to present them to t-cells
- these peptides are derived from pathogen or host-derived proteins that have bene broken down by antigen-presenting cells
how does the structure for MHC class I and MHC class II compare?
1) class I MHC = comprised of alpha chain non-covalently attached to a beta-2 macroglobulin
2) class II MHC = comprised of an alpha and beta chain
–> both MHC have a peptide binding groove
–> however, MHC class I and class II have different pathways for loading peptides into their peptide-binding grooves
what are MHC molecules in humans, and how are they expressed?
- in humans, the genes that code for MHC is known as HLA (human leukocyte antigens)
–> genes coding for class I MHC are HLA-A, HLA-B HLA-C
–> genes coding for class II MHC are HLA-DR, HLA-DP, HLR-DQ - MHC molecules are co-dominantly expressed, meaning that both maternal and paternal genes are expressed simultaneously in the same cells
–> each cell in your body expresses 2 copies of HLA-A, HLA-B, HLA-C resulting in 6 different classes of class I MHC
–> specialized APCs express 2 copies of HLA-DR alpha/beta, 2 copies of HLA-DP alpha/beta, 2 copies of HLA-DQ alpha/beta = 12 classes of MHC class II
why are MHC genes considered polymorphic?
- polymorphic means that there are many different alleles (versions) of the same gene found within the population
–> for MHC genes, this means that the gene exists in many different forms among people, creating a great deal of genetic diversity - MHC genes are the most polymorphic genes in the human population = the chance you have the same MHC genotype as someone else is extremely rare unless you’re twins
how does polymorphism relate to MHC bindng and presentation?
- the polymorphic region is the peptide binding groove (most diversity occurs here)
- different MHC alleles can bind to different sets of peptides (small parts of pathogens like viruses or bacteria).
- the more different MHC alleles you have, the broader the range of peptides (from various pathogens) your immune system can present.
- the diversity in MHC molecules means that each individual can present a unique set of pathogen-derived peptides, allowing for a wide-ranging and more effective immune response.
what does polymorphic, oligomorphic and monomorphic mean?
- polymorphic = many different alleles (for the same gene) within a population
- oligomorphic = few different alleles found within a population
- monomorphic = only one allele found within a population
what is MHC haplotype?
A haplotype refers to the combination of all MHC genes (HLA alleles in humans) inherited from each parent
- these genes are co-dominantly expressed, meaning that alleles from both maternal and paternal chromosomes are present on the individual’s cells
- although your haplotypes are inherited from your parents, recombination during meiosis (cell division creating sex cells) can shuffle the MHC genes, creating unique haplotypes in offspring.
- this results in variation across generations and among siblings = genetic diversity in immune responses
how does an individuals haplotype impact antigen presentation?
- an individuals MHC haplotypes dictates what peptides your MHC can bind best to
–> this means that some cells MHC may be great at presenting some antigens to your T-cells and others will be bad at presenting other antigens to your T-cells
how does the process of MHC restriction work?
when t-cells interact with antigen-presenting cells (APCs), they need to check 2 things:
1) does my receptor bind the ligand
2) is the MHC self-MHC?
- mismatch haplotype = t-cell doesn’t recognize MHC
- mismatch antigen affinity = t-cell will not recognize antigen because theres insufficient binding affinity even if MHC is correct
- MHC haplotype and antigen affinity must match
what is the pathway to MHC class I peptide loading?
1) Within the rough endoplasmic reticulum (RER), the MHC class I alpha chain binds to calnexin (a chaperone) and ERp57, ensuring proper folding and stabilization.
2) The binding of beta-2-microglobulin to the alpha chain displaces calnexin. This enables the MHC class I molecule to interact with other chaperones like calreticulin and tapasin, which is connected to the peptide transporter TAP (Transporter Associated with Antigen Processing).
3) Meanwhile, immunoproteasome is actively cleaving and breaking down intracellular proteins into peptides that will be transported into the ER by TAP
4) The association of calreticulin, tapasin, and TAP forms the protein loading complex (PLC), which promotes the binding of antigenic peptides to the MHC class I molecule.
5) Antigenic peptides transported into the RER by TAP can be further trimmed and modified by ERAP to optimize their length for binding to MHC class I molecules.
6) The binding of a suitable antigenic peptide stabilizes the MHC class I molecule-peptide complex, allowing it to exit the RER and be transported to the plasma membrane for presentation to cytotoxic T cells (CD8+ T cells).
what is the pathway to MHC class II peptide loading?
1) newly synthesized MHC class II alpha and beta chains bind to protein called invariant chain while still in the endoplasmic reticulum (ER)
–> the invariant chain (li) prevents intracellular peptides from entering and bindings MHC class II prematurely/by mistake
2) meanwhile, extracellular pathogens/antigens are taken into the cell via phagocytosis or endocytosis by antigen-presenting cells (APCs)
3) as the antigen travels away from the surface, the phagosome/endosome acidifies, merges with lysosomes, and the pathogen is degraded into peptides
4) the MHC class II + li complex goes through the golgi and will eventually merge with a late endosome
5) the invariant chain (li) is degraded by proteases inside the vesicle, leaving a small portion remaining in the MHC class II peptide groove, called CLIP (class II associated invariant chain peptide)
6) HLA-DM catalyzes and mediates the release of CLIP from the peptide binding groove which is replaced by a pathogen-derived/antigenic peptide
–> HLA-DO acts a negative regulator of this pathway, binding HLA-DM and blocking its function
7) the MHC class II peptide complex is then transported to the plasma membrane where it is presented to CD4+ t-cells
what is the pathway of cross-presentation?
1) activation of CD4+ t-cell
- the dendritic cell (typically residing in tissues) phagocytoses extracellular pathogens and processes them into smaller peptides
- as it migrates to the lymph node, they mature and presents these processed pieces on MHC class II to activate CD4+ t-cells
2) dendritic cell licensing by the CD4+ t-cells
- the activation of CD4+ t-cell leads to the release of IL-2
- IL-2 contributes to the activation of CD8+ t-cells
- IL-2 also triggers dendritic cells through proper signalling to begin cross presentation, which is the process of presenting extracellular antigens on MHC class I molecules
3) activation of CD8+ t-cells
- CD8+ t-cells with TCRs that match the antigen presented in MHC class I become activated
- activated CD8+ t-cell leave the lymph node and travel to infected tissue, where they bind infected cells by MHC class I
what are the 3 signals required for t-cell activation?
1st signal:
- the T-cell receptor (TCR) must recognize and bind a specific peptide antigen presented by the MHC molecule on the antigen-presenting cell (APC). the MHC must be recognized as self.
2nd signal:
- a co-stimulatory signal is also required for activation
-together these trigger a signalling cascade that results in production of cytokines
3rd signal:
- cytokines trigger t-cell proliferation (IL-2) and differentiation into functional subtypes (polarizing cytokines)
what is the role of signal 3 in t-cell activation?
CYTOKINES are the 3rd signal and are responsible for the type of CD4+ t-cell it will become
- PRRs on the surface of the APC and other cells will sense PAMPs from the pathogen
- this PRR/PAMP binding triggers cytokine production
- the cytokines produced depends on which PRRs are activated
- cytokines are sensed by the CD4+ t-cells and will change how the t-cell responds to infection
what is Th1 response? how does it work?
Th1 response combats intracellular pathogens by inducing cell-mediated immune responses (i.e activating phagocyte) and activating CD8+ t-cells for killing infected cells
- PAMPs from intracellular pathogens are detected by PRRs on APCs, triggering production of polarizing cytokines like IL-12
- the APC presents the pathogen’s antigen on its MHC class II molecule, and co-stimulatory molecules (CD80/86) on the APC binds to CD28 on the CD4+ T cell, leading to activation.
- upon activation, the APC releases Th1-polarizing cytokines such as IL-12, which acts as Signal 3 in T cell activation. This ensures that the CD4+ T cell will proliferate and differentiate into a Th1 helper T cell
- the Th1 CD4+ T cell produces IFN-gamma and TNF, which have several important effects such as activating CD8+ t-cells and promoting inflammation (macrophages)
what is Th2 response how does it work?
Th2 response combats extracellular pathogens by recruit and activate inflammatory cells (i.e. mast cells, basophils)
- extracellular pathogens (PAMPS) are sensed by PRRs on the surface of the APC, triggering production of polarizing cytokines like IL-4
- The APC presents the pathogen’s antigen on its MHC class II molecule, and co-stimulatory signals (CD80/86 binding to CD28) activate the CD4+ T cell.
- upon activation, the APC releases Th1-polarizing cytokines such as IL-4, which acts as Signal 3 in T cell activation. This ensures that the CD4+ T cell will proliferate and differentiate into a Th2 helper T cell.
- Th2 CD4+ T cells produce IL-4, IL-5 and IL-13 which encourages production of IgE antibodies from b-cells (basophils and mast cells) all helpful to control worm infections
how does Th1 CD4+ T-cells help activate CD8+ t-cells?
Th1 CD4+ T cell produces effector cytokines that:
- Encourage cross-presentation of antigens in MHC class I = allowing CD8+ T cells to recognize antigens
- Can provide co-stimulatory molecules
(CD40L) to bind CD40 on CD8+ T cells to help with CD8+ T cell activation = provide 2nd signal to promote activation
- Produce IL-2 to cause CD8+ proliferation
- Produce IFN-gamma that aids in CD8+ T cell differentiation into cytotoxic T cells
*CD8+ t-cell can activate in the absence of CD4 helper cell, but efficiency would be dramatically reduced
what is the timeline for antiviral immune responses?
1) type 1 IFNs are produced within minutes to hours after infection = FASTEST
- production of interferon stimulated genes (ISGs) produce an antiviral state
- they also recruit NK cells
2) NK cells recognize virus infected cells and kill by apoptosis (capable of killing low level infection)
- NK cells control the virus until cytotoxic t lymphocytes (CTLs) are generated.
Virus infections can be managed by IFNs and NK cells alone in some cases, without CTLs
what is the activation step of CD8+ t-cell killing? (SEQUENTIAL)
1) The CD4+ (helper) T cell binds to the APC first, which licenses (activates) the APC to cross present antigens in MHC class I for CD8+ T cell recognition.
2) The APC then binds to the naive CD8+ T cell, providing:
- antigen in MHC class I for the TCR binding (Signal 1)
- CD80/86 binding to CD28 for co-stimulation (Signal 2)
- Cytokines to support activation (Signal 3)
3) The activated CD8+ T cell undergoes clonal expansion (rapid mitosis) and differentiates into a mature CTL or memory cell
what is the activation step of CD8+ t-cell killing? (SIMULTANEOUS)
1) CD4+ t-cell and naive CD8+ t-cell bind to the APC at the same time
- The CD4+ T cell is not directly stimulated by the APC at this point. Instead, it assists in the activation of the CD8+ T cell
2) CD4+ T cell licenses the APC to present antigens in MHC class I via the release of cytokines. the remaining 2 signals occur:
- CD80/86 binding to CD28 for co-stimulation (Signal 2)
- the CD4+ T cell releases IL-2 (signal 3)
3) the CD8+ t-cell undergoes clonal expansion (rapid mitosis) and differentiates into a mature CTL or memory cell
APCs can express multiple MHC (class I and class II) and can interact with various immune cells at the same time
