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Lecture 2 – Intro to Immunology
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Angiten: chemical substances that elicit a specific immune response
Components of Innate Sys: phagocytes, NK cells, serum proteins (complement,
CRP, MBP)
Innate System recognizes
well-conserved structures s/a LPS, PepG, dsRNA,
etc
Adaptive Sys made up of
T cells and B cells. These cells express “clonally
restricted, antigen-specific cell surface receptors”. (TcR and BcR). These receptors
recognize antigen and activate their respective cells.
While both B and T lymphocytes have Ag receptors, the mechanism by which they
recognize Ag differs. BcR is similar in structure to antibody (Ig) and can recognize
any chemical structure that is floating around. TcR requires Ag to be presented by
MHC located on APCs.
“Naïve” Lymphocyte: lymphocyte which has never seen Ag. (As opposed to
memory lymphocyte)
Cardinal features of adaptive response: specificity, diversity, memory. Memory =
the 2nd time a T/B sees Ag, its response is both faster and stronger. Due to 1: clonal
expansion during initial Ag exposure & 2)differences in functional responses between
naïve lymphocytes and memory lymphocytes.
Adaptive System is divided into humoral and cell-mediated immunity.
 Humoral: mediated by antibody (the secreted product of B cells). Largely
directed against extracellular pathogens (eg bact, parasites)
 Cell-Mediated: mediated by T cells either directly or through action of secreted
cytokines. Largely directed against intracellular pathogens (some bact, viruses).
There are 2 types of T cells: helper T cells (TH, CD4+) and cytotoxic T cells
(CTLs, CD8+). In response to antigen, CD4s secrete cytokines, while CD8s kill
the cells directly.
Primary Lymphoid Organs: where leukocytes develop and mature. For all
leukocytes except T cells, this is the bone marrow. For T cells it is the thymus.
FC: What are the secondary lymphoid organs? Ans: Lymph nodes, spleen,
mucosal immune system, cutaneous immune system. It is to these secondary
lymphoid organs that the naïve B and T lymphocytes home once they have matured.
It is in these secondary lymphoid organs that the B and T initially encounter Ag and
where the immune responses are generated.
 All secondary lymphoid organs are highly organized into specialized B and T
areas. B areas are called follicles while T areas are known as interfollicular zones.
 T cells traffic through the secondary lymphoid organs using the blood and
lymphatic system.
Adjuvant: A vehicle used to enhance antigenicity. Generally speaking, adjuvants
activate macrophages and dendritic cells in the tissues activating them to present Ag
to T cells in the secondary lymphoid organs. Most microbes contains one or more
natural adjuvants.
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Lymphocyte Recirculation: Lymphocytes, particularly naïve Ts, constantly
recirculate through the secondary lymphoid organs. Naïve lymphocytes leave the
blood through HEV and enter the T cell area. (B cells migrate to the follicle). If the
lymphocytes don’t encounter Ag, they leave through the efferent lymphatics. They
then either go to other lymph nodes via afferent lymphatics, or reenter circulation via
the thoracic duct. Each T cell hits one lymph node each day (estimate). Ie: A given
specific T cell does not remain in its one lymph node forever. It moves around to
other lymph nodes too.
Lecture 3 – Antibody and TcR
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Assembly of Antibody: The variable region of IgH is made up of V,D,J gene
segments. Once the VDJ region is formed, it is spliced together to the constant region
to form a mature IgH. A similar process takes place with IgL, but there are only V
and J (no D) gene segments.
Somatic Gene Rearrangement: Antibody molecules are assembled from a large
number of individual gene segments. This process is known as somatic gene
rearrangement. It occurs during B development in the bone marrow. Gene segments
are known as V, D, J.
During the course of an immune response (c/o!!) antibody molecules undergo
changes in their variable regions to increase affinity, and in their constant regions to
change effector functions.
TcR: Similar to antibody.  chain is analogous to IgL ( looks like L) while  chain
is analogous to IgH ( looks like ‘H’). Like Ig molecules, the TcR is assembled from
numerous gene segments by somatic gene rearrangement.  chain has V,D,J while 
chain has only V and J.
CDR1 and CDR2 are primarily responsible for interacting with MHC while CDR3 is
responsible for interacting with peptide antigen.
Unlike Ig, TcR does not undergo structural changes during the immune response.
Defects in RAG Genes/Proteins: Somatic Gene Recombination is controlled by
lymphocyte specific proteins known as RAG-1 (recombinase activating gene) and
RAG-2. Defects in RAG genes prevent recombination which means that no mature B
or T cells can be formed.
D and J are joined first. Then V. The variable region is then spliced to the constant
region (which is also variable—determines which Ig in B cells. Not as important in T
cells).
If for any reason rearrangement is unable to generate a functional BcR or TcR, the
cell dies. (see previous bullet).
Once a mature receptor has been generated, they still must go through some final
checkpoints to eliminate those B and T that do things like recognize self-antigen
(negative selection). TcR undergo additional selection to ensure that only those
receptors that require MHCs can go on.
Mecanisms of Generating Diversity: 1)Combinatorial association of VDJ regions.
2)Pairing of the two different receptor chains (, ). 3)P-region addition 4)Nregion diversification.
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P-region addition: imprecise cleavage/splicing of the VDJ regions with
addition or deletion of nucleotides
- N-region diversification: addition of nucleotide sequences between gene
segments by the enzyme terminal transferase.
- In all cases, the major location for diversity is at the junctions. It is the
hypervariability of these junctional regions that gives rise to the CDR3
regions (principally responsible for Ag recognition).
Allelic Exclusion: Receptors can only be expressed at the cell surface in dimer form.
So the heavy chains are expressed along with pre-BcR or pre-TcR. Cell surface
expression of a functional heavy chain with a pre-receptor chain means that
successful rearrangement has occurred. A signal is sent down to the cell to inform it
to cease further rearrangement. This ensures that only a single receptor is expressed.
At this point the immature B and T cells (now expressing functional TcR/BcR) can
undergo positive and negative selection.
Negative Selection: those cells that recognize self-MHC with high affinity and
therefore are potentially autoreactive are induced to die by apoptosis.
Ig but not TcR undergo further molecular changes:
- Isotype switching: delete the intervening DNA between the VDJ and the new
isotype C region.
- Somatic hypermutation: Random mutations in the V regions. Those that
lead to lower affinity cells are induced to die.
- Switch to secreted Ab: Splice the Ig mRNA coding for the transmembrane
exon protein.
6 – MHC and Antigen Presentation
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The principal function of MHC is presentation of protein antigen to TcR.
MHC-I is present on nearly all cells (except RBCs). – antiviral immunity
MHC-II is present only on pro-APCs (Bs, dendritic cells, Macrophages).DTH/humoral immunity
They are also responsible for self/non-self discrimination. (the principal cause of
graft rejection)
Awos: MHC alleles control immune responsiveness and graft rejection.
MHC Restriction: T cells can only recognize antigen when presneted in
combination with self-MHCs.
Only MHC I (2 microglobulin) chain is not polymorphic. I, II and II are all
polymorphic. (Ie: The 2 chain on MHC-I is identical for all MHC-Is).
- Each variant MHC-I allele is encoded by a single  chain.
- Each variant MHC-II allele is encoded by both an  and a  chain.
- This means that you have 6 different MHC-I molecules (genes) in your
halotype (eg: HLA-A13, HLA-A299, HLA-B27 (ankSpond), HLA-B5301 (resistance
to malaria), HLA-C2, HLA-C348). Because MHC-II has two chains, you have
12 different possible molecules for that one.
Certain polymorphic MHC alleles are linked to resistance for disease (eg HLAB*5301 for malaria) as well as for autoimmunity (HLA-B27 – ankylosing spondylitis)
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In order for MHC-Ag to be presented, the Ag must first be “presented” to a T by an
APC. ??
Dendritic cells tend to capture antigen at initial site of infection. They then run off to
a lymph node so they can present it to a naïve T cell.
FC: What is the purpose (other than ID!) of CD4/8? The CD4/CD8 co-receptor
interacts with the non-polymorphic chains during activation. Ie: CD4 interacts with 3 domain of
MHCII and CD8 interacts with 2 chain of MHC-I. The Lck on the CD4/8 phosphorylates
the ITAMs on CD3 copmlex allowing ZAP70 to come in and bind.
MHCI presents to CD8+ and MHCII presents to CD4+.
Each MHC molecule (I and II) are coded for by three different gene loci. MHC-I is
coded for by HLA-A, HLA-B, HLA-C on chromosome 6. Each of those loci has
many different possible alleles. Similarly, MHC-II is coded for by HLA-DP, HLADQ, HLA-DR also on chromosome 6.
 Each person has a specific HLA-A allele, HLA-B allele, HLA-C allele. If there
were 5 different alleles of each, each halotype has a 1/125 chance of being
identical. However, recall that there are 2 chromosomes… (MHC genes are
expressed codominantly).
Halotype: the entire set of MHC genes on each chromosome.
Anchor Residues vs TcR Contact Residues: the part of the peptide that binds to the
MHC is called the anchor residue. The part that binds to the TcR is called the contact
residue.
Only MHCs bound to peptide are stably expressed at the cell surface. (If inside the
ER a peptide does not get bound, the MHC will be destroyed).
MHCs are unable to discriminate between self and foreign peptides.
IFN  (eg by NK, CD4) increases MHC expression and Ag presentation.(in addition
to activating macrophages, etc)
MHC Class I Pathway (cytosolic proteins):
1. cytosolic proteins are degraded by the proteosome
2. residues are transported into ER by TAP
3. protein is bound to MHC and sent off to the surface
- if a person is deficient in TAP, they are  susceptible to viral infections
MHC Class II Pathway (proteins in endosomes/phagosomes)
1. phago/endosome fuses with lysosome to form phagolysosome which degrades
peptides and transported into the ER.
2. Meanwhile, inside the ER, class II MHCs are bound to invariant chain protein
(occludes the peptide groove)
3. MHCII-Ii and peptide are transported into a vesicle called ‘MHC class II
compartment’ (MIIC) where Ii is attacked by proteases leaving only a peptide
called CLIP. Another protein called HLA-DM catalyzes removal of CLIP
allowing the peptide to bind to the MHC.
- Question: what keeps these peptides from binding to MHC-I?
- “II = Ii”
7 – T Lymphocyte Activation
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TcR/CD3 Complex: The TcR dimer is expressed along with other molecules, most
importantly, the CD3 complex. Because the TcR cytoplasmic tails are so short, the T
cell needs the CD3 to delve into the cytoplasm to deliver the message.
Signal Transduction in T activation: The CD3 complex has ITAM(s) attached to each
chain. Phosphorylation of ITAM allows molecules containing SH-2 domains to bind.
The most important of these molecules in T activation is ZAP70.
 When a T cell encounters Ag (with MHC, of course!), TcR and CD3 are
recruited to the site of interaction. CD4/8 is recruited as well. On the
cytoplasmic tail of CD4/8 is a tyrosine kinase called p561ck or Lck. It is Lck
that phosphorylates the ITAMs on the CD3 which then allows ZAP70 to bind.
 Activated ZAP70 triggers a variety of events such as:  Ca; activation of
MAPK pathway; activation of calcineurin; Also transcription factors that
promote cytokine gene expression. Eg: NFAT, AP-1, etc
 IOW: 1)T/Ag interact. 2)Recruit CD3, CD4/8. 3)Lck on CD4/8
phosphorylates ITAMs on CD3. 4)ZAP70 binds and is activated by ITAMs.
5)ZAP70 exerts effects by phosphorylating multiple substrates (eg RasMAPK).
CD4/CD8 Coreceptors: see above…
Adhesion Molecules: Provide adhesion of the TcR to the APC. (Requires > 4-6
hours for full activation). Eg The integrin LFA-1 (ICAM-1); CD2 (LFA-3).
Adhesion molecules are not activated until the TcR is bound to an antigen.
Costimulatory Molecules: Eg: CD28, CD40L. Also known as the second signal.
Essential for proper activation of T cells. Without 2nd signal  anergy.
 CD28 is present on essentially all T cells and binds to B7 found on APCs.
 FC: Functions of CD40L (nreg of B7; Induce IL-12; isotype switching) is
upregulated on activated Ts. Interacts with CD40 found on a variety of APC.
CD40 activation on macrophages causes upregulation of costimulatory B7s,
activates macorphages, induces IL-12, etc. CD40 activation on B cells
upregulates B7 co-stimulation and induces B cells to undergo isotype switching.
 FC: Deficiency of CD40L? Note how CD40 signalling is important for both
CMI and humoral immunity. Patients with deficiencies in CD40L (hyper-IgM)
exhibit profound defects in both cell-mediated and humoral immunity.
 A “resting” APC is co-stimulator deficient. Initially, the APCs (eg macrophage)
do NOT have B7, CD40, etc. However, if they are activated (eg by innate
immune system), they will upregulate their co-stimulator molecules.
 FC: How is CD40 induced? Ans: By TcR signalling (following activation from
an antigen).
Role of IL-2: IL-2 causes clonal expansion of T cells When a T cell becomes fully
activated it upregulates expression of IL-2 (“T cell growth factor”). It also
upregulates expression of the high-affinity IL-2 receptor. (Ie: Autocrine action).
ITAMs: found in a wide variety of cell-surface signalling molecules involved in
signal transduction in the immune system.
FC: Phases of the T cell immune response (from naïve T): Ans: 1)Ag is presented to
naïve T by APC. 2)T (CD4 or CD8) is activated and secretes IL-2 and upregulates IL-2R. This causes
proliferation 3) IL-2 also causes differentiation: CD4 into CD4 effectors and CD4 memory cells.
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Same thing with CD8. 4)CD4 effectors activate Bs/Ts; activate macrophages; inflammation. CD8
effectors lyse target cells and activate macrophages.
Signal 1 vs Signal 2: The TcR provides signal 1. The costimulatory molecules are
known as signal 2. Signal 2 is essential to achieve full activation. In fact, without
signal 2, you get anergy.
FC 3 Mechanisms for turning off T immune response: (no Ag,   Ag, CTLA-4)
1. No Antigen: As antigen is reduced, TcR stimulation is decreased, and so therefore
is IL-2. Absent IL-2, T cells will die by apoptosis.
2. Too Much Antigen: In the presence of very high concentration of antigens, T
cells can be induced to undergo apoptosis via Fas/FasL pathway.
3. Time: >96 hours after stimulation, T cells upregulate CTLA-4. CTLA-4 binds
B7 with twenty-fold higher affinity (removes costimulation). Also, CTLA-4
dephosphorylates the ITAMs and ZAP70.
APPON: Classes of Lymphocytes:
1. B Lymphocytes  secretion of antibodies
2. CD4 Lymphocytes  secretion of cytokines  activation and proliferation of B
(into plasma cells) and CD8 lymphocytes (into cytotoxic effectors) ; Activation
of macrophages; Inflammation
3. CTL  target cell lysis
4. NK  target cell lysis
10- B Lymphocyte Activation
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Humoral Response (general features)
BcR and signal transduction
Role of complement in augmenting B specific antigen responses
Early signals following BcR
Role of T cells and CD40L in humoral responses
Role of cytokines in isotype switching (Eg: IFN-gamma  IgG)
Germinal Center reaction and affinity maturation
Role of Ig in feedback inhibition of humoral response
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Plasma Cells: The B cells that secrete antibody. (Some plasma cells end up in bone
marrow where they differentiate into plasma cells and secrete basal levels of antibody
giving continuous protection.) Another few B cells will become memory cells.
Germinal Center Reaction: affinity maturation, isotype switching and generation of
memory B cells
Once activated Bs differentiate into antibody-secreting cells, they typically still
remain in the peripheral lymphoid organ (in which they were activated). Their
antibodies enter the circulation.
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Question: Why is it that the secondary response can only be induced by protein antigens?
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FC: What is meant by “Thymus-dependent humoral response”? Ans: Humoral
response to protein antigen requires Ts in addition Bs. These are referred to as “Thymusdependent humoral responses” (TD). The T cells are needed to help by secreting cytokines and
expressing CD40L which together help with isotype switching and affinity maturation.
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Humoral response to non-protein antigens does not require T cells and are referred to
as “Thymus-independent humoral responses” (TI). Ie: Thymus dependent vs
independent refers to the requirement of T cells.
Question: Exactly which processes take place in the germinal centers?
FC: What are some of the functions carried out by antibodies? Ans:
neutralization, opsonization, ADCC, complement activation (NOAC)
BcR and initiation of Signalling: The BcR of naïve B cells is IgM. (Of course, this
can/will change if isotype switching occurs later). IgM is associated with two other
chains called Ig-alpha and Ig-beta (analogous to CD3 complex in T cells). These two
chains contain the ITAM motifs which, when phosphorylated, attract Syk (analogous
to ZAP70). Note: If the antigen is also attached to complement product C3d, this
will complex with CD21 on the B cell and enhance activation about 1000 times!
FC Role of CD40 on B cells: CD40, located on B cells needs to interact with CD40L
found on T cells. Engagement of the B cell’s CD40 allows: isotype switching,
affinity maturation, secretion, generation of B memory cells. Also upregulation of B7.
FC: Describe the process for B Activation beginning with a naïve B cell in a
peripheral lymphoid organ. List the main effectors. Activation usually occurs in
the lymph node. A filtered antigen binds the BcR. Activation leads to changes that
are essential for effective interaction with CD4s. These include: processing of
antigen and subsequent presentation along with MHCII. Upregulation of B7 and
other costimulatory molecules. Upregulation of cytokine receptors (in preparation for
the Cyk’s to be obtained from the T cells). AWOS: Upregulation of B7 and Cyk
receptors. Migration into T-cell rich area.
- Antigen activated B cells then enter the T region to present their antigens. The Ts
have recently been activated by the same antigen presented by dendritic cells.
Both the B and T cells receive stimuli from each other. The T gets Ag/MHC and
costimulation. The B gets cytokines for growth and differentiation and CD40L
for germinal center reactions.
- FC: Describe the process of B/T bidirectional interaction from the point that
the B first presents antigen to the T: The B cell presents antigen to the T. The
T responds by expressing CD40L and secreting cytokines. The B cell is now
induced to proliferate and differentiate.
Isotype Switching: changing the IgH from one Ig type to another. Because the
switch is always “downstream” (i.e. via deletion of intervening DNA), they can never
revert to IgM. Similarly, they can never go from a downstream type to an upstream
one. Isotype switching is defective in certain types of immunity. Isotope switching
requires T cells. For cytokines and CD40 engagement.(IFN-gamma for IgG; IL-4
for IgE; TGF-beta for IgA. No signal, of course, will result in remaining IgM).
FC: Which cytokines cause switching to IgE, IgA, IgM, IgG? IgG: IFN-. IgE:
IL-4; IgA: TGF-; IgM: no signal…
Affinity Maturation: During the course of an immune response, the average affinity
of an antibody for an antigen changes. This is due to point mutations taking place in
the CDRs of V regions of both light and heavy chains. Because activated B cells
need continual feedback from BcR to survive, those receptors with higher affinity
will bind antigen and survive, while those that have low affinity will not. Again, be
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aware that affinity maturation requires CD40L. Therefore, this is limited to thymicdependent antigens.
Thymic In/Dependent: Affinity maturation only occurs for thymic-dependent
agents” (ie proteins, AA?) because in thymic-independent antigens, no CD40 or
Cytokine are produced. Thymic independent produce only low affinity IgM.
Switch to Secretion: occurs by splicing out part of the Ig mRNA coding for
transmembrane and cytoplasmic regions.
Generation of Memory Cells: Even once the response is over, a small fraction of
antibodies will be found to have gone on to become memory cells. The mechanism is
not known. However, CD40 is essential. Another few will become plasma cells.
Germinal Center: All of the reactions take place in the germinal center, aka
secondary follicle. This is a specialized region that forms in the primary follicles in
an absolutely T-cell dependent way. Germinal center formation fades after the Ag
stimulus is removed.
FC: How is B activation ended? Late during the humoral response, antigen-ab
complexes crosslink the BcR with Fc receptors on B cells. This inhibits further B activation.
11 – Cytokines and Cytokine Receptors
1. General properties of cytokines
2. Function of cytokines during the innate immune response
3. Role of TNF, IL1, chemokines in regulation of inflammation and leukocyte
recruitment.
4. Cytokines produced in response to viral infection
5. Function of cytokines during the adaptive response
6. Differentiation and function of Th1 vs Th2
think….
 IFN-γ: think macrophage activation; isotope switch to IgG;  expression of MHC
 TNF: think inflammation
 Helper T cells: think production of cytokines
 Cytokines: think “the means by which cells of the immune system communicate.
 Function of TNF, IL-1: think inflammation via recruitment of luekocytes (via
upregulation of endothelial adhesion molecules and chemokines).
 IL-12: think potent activator of Th1 pathway;  cytolytic activity of CTLs and NKs
(potent inducer of IFN- secretion by these cells).  Th1;  IFN-
 Type I Interferon: (IFN-, IFN-) think anti-viral
 IL-4: Th2 pathway; isotope switch to IgE; inhibit macrophages
Flashcards:
 FC: Give 2 examples by which prolonged cytokine production can be deleterious:
TNF-alpha  sepsis; IFN-gamma  autoimmunity
 FC: Give an example of pleitropy and redundancy in cytokines: Pleiotropy: IL-4
 IgE antibody production, Th2 differentiation; inhibition of macrophages.
Redundancy: IL-2, IL-4, IL-5 all stimulate B proliferation.
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FC: Main cytokines produced during innate response. Who secretes them.
Primary Function. TNF-α, IL-1, IL-12, Chemokines. Secreted by macrophages and
NK cells. Modulation of innate immunity; Inflammation; Leukocyte recruitment;
Induction of adaptive response.
FC: Main cytokines produced during adaptive response. Who secretes them.
Primary Function. IL-2, IL-4, IL-5, IFN-γ. Secreted by T cells. Regulation of
adaptive response; Regulate lymphocyte growth/differentiation; Activation of
effector cells.
FC: Main functions of IL-12: 1. Potent activator of Th1 pathway (IL-4 is activator of
Th2); 2. Enhancement of cytolytic activity of CTL and NK cells.
FC: IFN-α and IFN-γ. What do they do and How do they do it? aka type I
interferons. Important in anti-viral immunity. Inhibits viral replication. Increases the
number of MHC molecules on infected and neighboring cells (thereby enhancing
presentation of viral peptides).
Notes
 Cytokines work by altering the pattern of gene expression on the target cell.
 All cells produce and respond to cytokines
 Expression of cytokine receptors is also tightly regulated.
 Unlike hormones, cytokines do not usually act at a distance. Rather they are shortacting, often on the cell with which the secreting cell is interacting.
 Some functions of cytokines: Proliferation of activated lymphocytes; Isotype
switching; Plasma cell development; Lineage commitment of CD4s to Th1/2;
Macrophage activation; Hematopoiesis aspects
 SEE SLIDE 6… INNATE VS ADAPTIVE CYTOKINES…
 Cytokines of innate: TNF-α, IL-1, IL-12, IFN-α, IFN-β.
 FC: What is the principal function of TNF and IL1? Activate endothelial cells
causing them to upregulate adhesion molecules and chemokines in order to recruit
leukocytes. Ie; Promotion of the inflammatory response. (TNF/IL1/IL6 also act on the
liver to secrete acute phase proteins for anti-microbial affinity).
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TNF/IL1/IL6 act on the liver to induce the acute phase response which greatly
enhances anti-microbial immunity.
What do acute phase proteins specialize in doing? [??]: bind specifically to
bacteria and opsonize them.
FC: Give an overview of the innate response of a macrophage to bacterial
infection: Nearby macrophage responds to the LPS on the bacterial wall by quickly
secreting TNF and IL1 and IL-12. (Note: we have not yet activated the macrophage). This
causes recruitment of leukocytes to the site of infection. A little while after, the IL-12
kicks in and causes CD4 to differentiate into Th1 which secretes IFN-γ. The IL-12
also activates NK cells which also secrete IFN-γ. The IFN-γ now activates the
macrophages so that they have phagocytic activity.
TNF in septic shock: systemic release of TNF results in systemic inflammation
(edema, etc)
Cytokines in the adaptive response: Once a T cell (both CD4 and CD8) has been
presented with antigen, it begins to secrete IL-2. It also upregulates IL-2R. IL-2 is
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the principal growth factor for T cells. This autocrine loop drives T proliferation and
activation. Now that activated T cell can begin secreting its other cytokines.
Question: what are other functions of IL-2? [proliferation of Ts, Bs, and NKs??—I
think so…]
Phases of CD4 activation: Recognition: The CD4 responds to an APC. Activation:
It responds by secreting IL-2 which causes expansion into many CD4s. Effector:
The various CD4s secrete their various cytokines…
FC: List the cytokines secreted by the Th1 and Th2 pathways: Th1: IFN-γ, IL2. Th2: IL-4, IL-5, IL-10, IL-13.
FC: Which of the Th pathways are concerned with humoral immunity? Broadly
speaking, Th1 cytokines regulate cell-mediated immunity. Th2 cytokines regulate
humoral immunity.
FC: Give the innate cytokines that influence the choice of CD4 pathway. List
which antigens typically stimulate production of those cytokines. IL-12 produced
by the innate response to bacteria induces Th1. IL-4 produced by the innate response
to parasites/nematodes, induces Th2.
Question: the innate response produces IL-4???
FC: Actions of IFN-γ: macrophage activation; isotype switching to opsonizing
bodies (IgG); development of Th1[???]; increased MHC expression/presentation.
FC: Actions of IL-4: induction of Th2; isotype switching to IgE; inhibition of
macrophage activation.
Overview of cytokine receptors: Most are heterodimers with an α chain and a β (or
γ) chain. The α chain is the binding while the β (or γ) is the signalling unit.
Remember that these chains are shared (which explains both pleitropy and
redundancy).
FC: Mechanism for cytokine receptor signalling: The mechanism is
phosphorylation of JAK kinases (analogous to ITAMs) which allows STAT (SH-2
protein—analogous to Syk and ZAP70) to bind. Phosphorylation of STAT causes
gene transcription. NOTE: This is only for type I and type II cytokine receptors.
Things like TNF and IL-1 each have different receptors. (Eg: TNF has a cell death
pathway via caspases).
X-Linked SCID: IL2, 4, 7, 13, 15 all share a common γ chain which is defective in this disease. This
means lots of problems in generation and regulation of immune response. “Bubble Boy Syndrome”.
Question: What about ADA deficiency???
Lecture 14 – Effector Functions of Cell-Mediated Immunity:
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FC: What are effector functions of humoral immunity? NOAC
FC: CMI principally takes two forms: 1)activation of macrophages (by IFN-
secreted by Th1 ) and 2) lysis of infected cells (by CD8 CTLs)
First we’ll talk about CD4s in CMI, then we’ll talk about CTLs in CMI.
Delayed Type Hypersensitivity: Once a Th1 &/ CTL has been activated, they
1)downregulate CD62L (their lymph-node homing receptors) and 2)upregulate
ligands for endothelial selectins & chemokines.
 When a Th1 encounters local Ag, it activates local macrophages by secretion
of IFN-. (IFN- is the most important mediator of DTH).
 Appon: CD4 Th1s mediate DTH.
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DTH Sequence:
1. Ag is recognized (for the first time) by macrophage which presents it to CD4.
2. CD4 generates lots of Th1 memory cells which exist for years. (Why
preferentially Th1 is not clear).
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3. Subsequent expoure preferentially induce a Th1 response.
What does it mean to activate a macrophage? Express more MHC-II on surface;
 microcidal activity;  ability to kill tumor cells; secretion of several growth
factors (PDGF, TGF)
How do macrophages kill microbes? Prodction of ROS, NO, lysosomal enzymes
CTLs in CMI
 Cross Priming: Pro-APC ingests a cell that has been infected (eg with virus). The
APC then presents the cell via an MHC-I (one!). The mechanism for doing so is not
well understood. (Key Pt: APC displays MHC-I).
 HSC as a pssible mechanism: Ag complexes with HSP (heat shcok protein)
on APC membrane. This Ag-HSC complex binds to CD91. The Ag-HSCCD91 complex is taken into the cytosol and taken into the ER by TAP and
placed onto MHC-I.
 Mechanisms of CTL killing: 1. perforin/granzyme 2. Fas/FasL
 Perforin Method: CTLs contain granules with perforin and granzymes. They
release these granules onto the target cell. The perforins make holes in the targetcell’s membrane, so that the granzymes can enter. The granzymes activate caspases
triggering apoptosis.
 Fas/FasL: Antigen stimulation of a CD8 triggers expression of FasL. This protein
interacts with Fas on the target cell also triggering apoptosis.
Lecture 15 – Effector Functions of Humoral Immunity:
Methods by which Ab enhance immune response: (NOAC)
1. Neutralize a toxin/pathogen by binding/blocking imp site
2. Opsonize (make phag more efficient; the Ag/path with bound Ab is gulped down
by phags expressing receptors for Fc portion of the Ab attached to the Ag. )
3. ADCC (target pathogen for direct killing by phagocytes or NKs)
4. Activate complement “LIP” ( opsonization;  inflammation; lysis via MAC)
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Secretion of antibodies: In response to a specific antigen, activated B cells will
secrete antibody specific for that antigen.
An antibody can bind an Fc receptor only once the Ab has bound an antigen.
Where are Fc receptors mainly found? Phagocytes, NKs, selective others
Effector functions of the different Ig isotypes:
 IgG: most important Ig for most infections; IgG is good at: opsonization; activating
classical complement pway; ADCC; being transferred across placenta ( neonatal
immunity); feedback inhibition of B response (crosslink BcR together with an
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inhibitory FcR on B cells) OCANI: IgG as the eager beaver, wanting (and good
at) to do everything. Saying to mom/teacher “Oh Can I? Oh can I???”
IgA: primarily involved in mucosal immunity; secreted across mucosal
epithelium (lumen of gut, tears, breast milk ie also neonatal immunity)
IgM: BcR on naïve B cells; However, in their secreted form, IgM are very good
at being fixed by complement;  affinity since no affinity maturation has
occurred; pentamer (  avidy for Ag)
IgD: BcR on naïve cells but no secreted form
IgE: mediating ADCC by eosinophils (against parasites); regulation of mast cell
responses (eg secretion of histamine, etc)
What’s so great about opsonization? Phagocytes can and do ingest particles at a
low basal rate. However, if the particles are opsonized (Ab or complement), the rate
of uptake is much greater (eg 1000X).
Describe Ab and ADCC: If a target cell is bound by antibody (especially IgG – or,
in the case of parasites, IgE), the FcR of those antibodies will bind NKs, macrophages,
and eosinophils.
Overview of complement (3 steps): 1. generation of C3 convertase; 2. generation
of C5 convertase; 3. generation of MAC
Details of complement formation:
1. Generation of C3 convertase: can be generated in 3 ways. Classical: Ab
binds to Ag. This generates a conformational change in serum C1QRS. This
new form of C1QRS splits C4 and C2 to generate C4bC2a (aka C3 convertase).
Lectin: A serum protein, MBP binds to (microbial-specific) mannose residues
on bacteria and split C4 and C2 to make C3 convertase from C4 and C2.
Alternative: Low constant turnover of C3 on the microbial surface. This is
stabilized by Bb (a product of cleavage of protein B). C3bBb is also a C3
convertase.
2. Generation of C5 Convertase: These C3 convertases (C3bBb, C4b2a) split
C3 to form C4b2a3b and C3bBb3b. These are both C5 convertases. (Note:
because C3 convertase uses one of its products in generating C5 convertase,
there is much amplification)
3. C5 Convertase can go on to generate the MAC.
Fate of C3b: C3b can be used to generate C5 convertase, or it can function as an
opsonin (by binding to Ag-Ab complexes, or directly to antigen >1000X).
Regulation of Complement - Inhibition:
- List: C1 Inh, Factor I, Factor H, CD46, DAF, CD59
- C1 INH: inhibits C1qrs.
- Factor I: splits C3b into iC3b, C3d, C3g. These do not activate complement but
do bind receptors.
- Factor H: Inhibits function of alternative C3-Convertase by displacing Bb. (“H
looks like B”. Ie: “fools” its way into replacing C3b).
- CD46: Because of the potential severe damage of complement, mammalian cells
have evolved protective molecules. CD46 acts as a potent co-factor for Factor I.
Found on leuks, endoth, epith.
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DAF & CD59: inhibit formation of C3 convertase by dissociating C4b2a and
C3bBb thus preventing generation of MAC. Found on blood, endoth, epith cells.
(Recall,  CD59 or DAF  PNH)
More regulation of complement:
 Low C3 level in serum Indicative of chronic complement activation. Eg:
autoimmune or immune-complex DZ.
 Deficiency of C2 or C4: symptoms resembling SLE (ie. immune-complex-like
disease)
 Deficiency of C3: very serious infections with pyogenic bacteria
 Deficiency of C5-C9: infections with Nisseria
 Deficiency of C1-INH: Hereditary Angioneurotic Edema (HANE)
 Deficiency of DAF/CD59: unregulated complement activation on RBCs, therefore,
PNH (paroxysmal nocturnal hemaglobinuria)
How does complement promote inflammation? C3a and C5a are potent chemoattractants
Lecture 16 – INNATE IMMUNITY
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Components of Innate Immunity: Phagocytes (macrophages, neutrophils), NKs,
serum proteins, epithelial barriers
Important Cytokines secreted in innate immunity: TNF, IL-1, IL-12
Timing: occurs within minutes to hours as opposed to several days for adaptive
response
Innate system alerts the body to the presence of invading pathogens and then tries to
delay them with a variety of non-specific effector functions.
While these defenses may sometimes be enough, one of the most important functions
of innate system is to get the adaptive system going. Still, innate system does work!
Eg: Even during adaptive response, mechanisms of innate system are working too (eg
phagocytosis, complement activation).
Triggers of Innate Response: structural features of microbial pathogens that are not
found on mammals (LPS, pepG, dsRNA, etc)
Innate Receptors: k/a “Toll-like receptors” (TLRs). Interaction of pathogenspecific structures with TLRs on host cells triggers secretion of things like: antimicrobial peptides, inflammatory cytokines, chemokines,  efficiency of
phagocytosis, upregulation of costimulatory molecules on APCs.
Sequence when a microbe binds to a TLR on a phagocyte: Signal transduction
cascade  production of anti-microbial products; -reg of costimulatory molecules;
secretion of cytokines and chemokines. IE: Neuts and Mo ingest microbes into
phagolysosomes where it is destroyed by proteolytic enzymes and ROIs. The
phagocytes also produce cytokines and chemokines (inflammation, and recruitment of
leuks). Eg: TNF, IL-1
Describe the important serum factors in the innate response: Complement
(discussed elsewhere). MBP: Resembles C1q. Therefore, it can be bound by C1q
receptor found on macrophages. CRP: binds to microbes and can also bind C1q.
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This means that it can also be phagocytosed by macrophages (and trigger
complement).
NK Cells (function, stimuli for activation): Function: kills two kinds of cells:
those coated by antibody (ADCC), those lacking MHC-I. NKs are not activated by
antibody-receptor interaction. Rather, they are activated by competing activating and
inhibitory stimuli. Foe example, an (activating) host-stress protein is connected to a
tyrosine kinase, while an (inhibitory) MHC-I molecule receptor is connected to a
tyrosine phosphatase.
What do activated NKs do? Kill cells by perforin-mediated pathway. Secrete IFN which causes macrophages to imrprove on presenting to T cells ( adaptive
immunity).
Why the “natural” in Natural Killer? Because they can lyse cells without any prior
sensitization.
What is the most important method by which the innate system stimulates the
adaptive system? Activation of TLRs causes, among other things, upregulation of
costimulatory molecules (eg B7) on APCs. Secretion of IL-12. Recruitment of
additional inflammatory mediators. If pathogens fail to elicit an innate response, they
are much less effective at eliciting an adaptive response.
In what way does the innate system play an important role in humoral response?
During alternative complement cascade, a breakdown product of C3 called C3d is
deposited on Ag or microbial surfaces. Receptors for C3d (called CR2 or CD21) are
present on B cells. These receptors associate with CD19 which results in a greatly
amplified B cell response. (C3d  CR2/CD21  CD21   B response)
33 – AUTOIMMUNE DISORDERS
1. Factors influencing tolerance
2. Mechanisms of certain autoimmune diseases
3. Autoimmune diseases relating to: 1 Ab  >= 1 organ; or many Abs  1 organ
system
AI (autoimmunity) may be modified by several mechanisms:
1. Antigens: Modified (eg infection, inflmammation, drugs); Isolated (eg
thyroglobulin, lens protein, spermatazoa); Similar (foreign Ag which are similar
enough to provoke AI Abs) [“MIS”]
2. Antibodies: many (but not all) autoimmune diseases are characterized by the
presence of autoantibodies.
3. Disordered Immunoregulation:  CD4 function;  Tsuppressor activity; non-specific
B activation (eg EBV triggering polyclonal Ab formtion); Thymic defects; B cell
defects
4. Genetic: Predisposition (several AI disorders s/a HT,IDDM are associated with
increased incidence of other disorders). HLA Antigens: are associated with 
incidence of certain AI disorders (eg  IDDM in HLA-DR3 & HLA-DR4 individuals)
5. Environmental Factors: Infection (esp viral) or other environmental agents may
initiate AI reactions in genetically susceptible individuals. Some viruses trigger AI
islet inflammation resulting in IDDM.
Tolerance
 Definition: specific inhibition of the immune response at its inception. Controls are
at central or peripheral level.
 Central: clonal deletion: T/Bs with receptors for self-antigen are deleted
 Peripheral: Clonal Anergy: lack of costimulation in first presentation triggers
anergy. Sustained Activation: of Ts by repeated antigen exposure. Or, by activation
of FasL. Both of these trigger apoptosis. Suppresor cell (TH2):
35 – AMYLOIDOSIS p. 89-91 in BRS
Amyloidosis: A group of disorders characterized by the deposition of amyloid.
Workup of Pt with amyloidosis:
1. + Congo-red or green birefringence under polarized light  consider AL
2. If either IMF (IMmunoFixation electrophoresis) or BMB (bone marrow biopsy) is
+,  AL amyloidosis
3. If both negative, check: IF (Isoelectric Focusing) & RFLP. If either positive 
AA. If both negative, consider secondary, hereditary, rare types of amyloidosis.
1. IMM/BMB;
2. IE/RFLP
36,37 – CONNECTIVE TISSUE DISORDERS - BRS: p. 86-89
CT Disorder: immune-mediated pathological alterations in ECM and/or ground
substance.
- In most cases, the cellular changes are secondary to the entrapment of either
Ab or immune-complex in the ECM. (Eg: trapping of Ab or immune complex
in the blood vessel wall leading to fibrinoid necrosis).
- May be (often) of autoimmune origin. Antinuclear antibodies (ANAs) often
present. These nucleolar antigens have certain patterns of
immunoflourescence: (Speckled: MCTD & anti-Sm; Nucleolar:
polymyositis; Peripheral: SLE)
SLE: All kinds of lesions (joints, skin, serous membranes, lungs, spleen, kidneys).
- Clinical: Arthralgias(joints are most common prob in SLE), Butterfly
rash/Raynaud, pleuritis/endocarditis (Libmann-Sacks: vegetations on both sides
of the mitral valve), Pulmonary fibrosis; Splenic arterioles  onion skin
appearnce; Glomerular changes (varying from minimal involvement to
membranous glomerulonephritis).
- Antigen: anti-dsDNA; anti-Sm are most specific; Peripheral staining on IMF
- Biological false positive for syphylis (often earliest detected abnormality)…
“Lorilee has syphylis???”
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Crithidia luciliae test: a routinely-used staining test for anti-dsDNA antibodies
Antiphospholipid antibodies: Include lupus coagulant and anti-cardiolipin
sometimes present in SLE
Kidney Problems in SLE: Lupus Glomerulonephritis:
- Normal, Minimal change, Mesangial proliferative, Focal proliferative, Diffuse
proliferative, Membranous Nephritis, Tubulo-interstitial nephritis.
- I: Normal Kidney (no deposits, no proliferation of cells)
- IIA: Minimal Change: occasional immune-complex deposit , minimal
proliferation
- IIB: Mesangial Proliferative: immune deposits containing IgG, C3; mesangial
cell proliferation
- III: Focal Proliferative: segmental partial proliferation with involvement of
mesangium and endothelium [deposits?]
- IV: Diffuse Proliferative: severe form; PMNs influx, crescents, wire loops,
hematoxylin bodies, thumbprints-like elements in subendothelial depost,
proteinuria, hematuria (nephrItic state)
- V: Membranous Nephritis: supbepithelial and mesangial deposits containing IgG
and C3; thickened basement membranes (GBMs); patients are usually heavily
proteinuric
- Tubulo-Interstitial Nephritis: immune-deposits in tubular and vascular
membranes with inflammatory response
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Nephritics vs Nephrotics: Minimal  Diffuse Proliferative = nephrItics.
Membranous Nephritis: nephrOtics. Nephritic: Hematuria, Oligria (these are
not found in nephrotic syndrome)
Diffuse vs Membranous: Membranous has thickened bmt membranes & is
heavily proteinuric. Diffuse has everything else! (Nephritic, karryorhexis, wire
loops, hematoxylin bodies, thumprint-like element, etc)
Wire loops: one of the feared consequences is renal failure. When you see
glomerular loops that are thickened (pink smudgy loops), strongly consider SLE.
Drug-Induced Lupus Erythematosus (DILE): Drugs (antihypertensives,
anticonvulsants, antiarrythmics, etc); Antibodies: ssDNA, antihistone; Etiology: Nacetyltransferase deficiency (“slow-acetylators”), HLA-DR4 “DR 4 DRugs!!”
association
Chronic Discoid LE: limited to skin (surrounded by zone of erythema and edema);
Ig’s present at dermo-epidermal junction but only at involved areas (as opposed to SLE
where it is more widespread).
PSS: Think widespread fibrosis and degeneration; skin, gi, lung, kidney, ht; Antigen:
anti-Scl (Antigen: anti-centromere in CREST); Nucleolar pattern of staining on IMF
Skin (sclerodactyly, maskface); GI: reflux esophagitis, rubber-hose deformity;
Lungs: honeycomb lung & pulmonary hypertension; Kidney: systemic
hypertension from intimal proliferation of BVs
SS: Think triad (dry eye, mouth, CT dz esp RA); Antigen: anti-SSb; Etiology: some
think EBV is causative.
Polymyositis: Chronic inflammatory process involving muscles of the extremities.
- Often associated with malignancy.
- Antigen: Associated with increased creatine kinase. Anti-Jo-1.
- No characteristic IMF pattern (as obvious as the others…)
- Can be confirmed by muscle biopsy (necrotic cells & lymphocytic infiltrate).
MCTD: (MCTD = “MARE”): myositis, arthralgias, Raynaud, esophogeal hypomotility.
- shares clinical features of other CT disorders h/e no renal involvement
- Antigen: anti-nRNP; speckled nuclear appearance on immunoflourescence
- female35-50
PAN: A multi-organ disease (Ht, Liv, Kid, Alimentary tract) causing necrotizing
vasculitis, etc
- predominantly in men
- Antigen: anti-HBsAg/Ab; drugs (haptens); P-ANCA
- Clinical: Panarteritis (everything!)  fibrinoid necrosis; PAN is one of the
vasculitides
Wegener’s Granulomatosis: TRIAD: “GVG”: necrotizing nasopharyngeal granulomas;
vasculitis; crescenteric necrotizing glomerulonephritis
- Antigen: C-ANCA ( sensitive;  specific)
- Usually fatal (infections, hemorrhage, renal failure)
VIROLOGY NOTES
INTRODUCTION TO VIRUSES
MORPHOLOGY
 Energy-less: they float around until they come in contact with an appropriate cell
 Composed of nucleic acid and a protein coat (capsid). Some have lipid envelopes
(from membranes).
 Contain all the genetic information to build replicas—but not the enzymes.
 Nucleic Acid: single vs double stranded; linear vs loop; segmented vs nonsegmented; one simple message vs hundreds of proteins
 Capsids: two types: icosahedral vs helical
 Envelope: can get from cell membrane, golgi, nuclear membrane (as the viruse
leaves the cell).
RNA VIRUSES
 3 types of RNA: single-stranded (most common), double-stranded (one), retrograde
(one)
 + means just like mRNA and thus, can be translated right away by the host’s
ribosomes
 - means it must be converted to + RNA prior to translation
 Retrovirus: must be converted to DNA which must then be transcribed to +RNA. To
convert RNA to DNA (!) these viruses carry a unique enzyme called reverse
transcriptase.
 RNA Dependent RNA Polymerase: Because a negative-stranded RNA needs to be
transcribed into a + strand, -RNA viruses must carry in their capsid this enzyme.
(Human cells do not have this enzyme).
 DNA VIRUSES: DNA must first be transcribed into mRNA (by using the + strand
as a template). The – strand is simply ignored.
 CAPSIDS Two types: icosahedral (polypeptide chains  capsomer  triangle 
icosahedron).
 Helical: capsomers bound to DNA which coil.
DNA VIRUSES: (HHAPPPy)
 Double stranded; Icosahedrals; Nuclear replication
 Herpes, Hepadna, Aeno, Papova, Parvo, Pox
 EXCEPTION: Parvo: single-stranded “PAR One”
 EXCEPTION: Pox: ‘Pox in a Box’ i.e. complicated DNA (hundreds of proteins),
complicated capsid structure
 ENVELOPES: (Half—the middle 3) hhAPPpy)
RNA VIRUSES (PC-CRaFT-FARBOP-Reo)
 Most: Single stranded; Cytoplasmic replication; Enveloped; Helical
 4 Groups: +Naked; +Enveloped; -Enveloped; (no + env); ds naked
 Picorna, Calici; Corona, Retro, Flavi, Toga; Filo, Rhabdo, Adeno, Bunya,
Orthomyxo, Paramyxo; Reo)
 picorna (small i.e. comes first); Flavius’s Toga;
 most are enveloped (middle 2 of the 4 groups)
 EXCEPTION: replicate in nucleus: Retro, Orthomyxo
 EXCPEPTION: Icosahedral: picorna, calici, flavi, toga, reo
Transcription, Translation, Replication
 + RNA: Adsorption, Penetration, Uncoating sans probleme. +RNA (since it is
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identical to mRNA) is translated directly using cell ribosomes, proteins, enzymes.
For replication, the +RNA must be transcribed into –RNA which is what is needed to
have as a template for replication of new +RNA progeny. Finally you get assembly
and release.
- RNA: Adsorption, Penetration as normal. In the uncoating process, the RNA
Dependent RNA Polymerase enzyme is released into the cytoplasm. Immediately,
+RNA strands are generated using the RNA Dependent RNA Polymerase.
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Translation: Translation begins. Replication: The +RNAs can be used to make
many –RNA progeny.
DNA Viruses: transcription and replication typically occur in the nucleus;
translation occurs in the cytoplasm.
DNA Transcription is divided into three phases: Immediate early; Early; Late.
Immediate early and Early is when 1)enzymes are encoded for replication and for
2)transcription of late mRNA.
Late Transcription:Late is when capsids are made. Late mRNA is usually transcribed
after DNA replication has begun. Late mRNA is transcribed from progeny mRNA.
Late mRNA is used to make capsids.
Assembly and Release and Host Outcome
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Naked Virions: released via lysis or exocytosis
Enveloped: get their membranes by budding through nuclear membrane, golgi,
cell membrane
Host outcome either death (cell loses its functions when virus takes over); or
transformation: Infection introduces or activates oncogenes.
32 – DNA/RNA Viruses in Latency
GOAL: Understand properties of viruses that allow them to establish latent infections
and that determine their site of latency. Know characteristic features of the diseases.
HERPESVIRIDAE
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We all probably have at least 1 of herpes family right now living in latent state in our
bodies. (Antibodies to HSV1 are in 90% of people by 40 y.o. IE: latent!)
Herpes viruses are held at bay by cell-mediated immunity. Patients with
compromised CMI are more likely to suffer from severe herpes infections. (eg: CMV
frequently causes disease in AIDS patients)
8 different herpes viruses have been isolated from humans: HSV1, HSV2, VZV
(alphaviruses) / CMV, HHV6, HHV7 (betaviruses) / HHV8, EBV (gammaviruses)
Alphaviruses: broad host range; highly lytic in culture; neurotropic
Betaviruses: more limited host range; slower growing in nature; cells infected with
this subclass often show enlargement.
Gammaviruses: lymphotropic
LATENCY: Hallmark of herpes viruses is ability to establish latent infections during
primary encounter. This encounter may or may not result in clinical disease. This
infection can reactivate long after to cause secondary disease. During latency, viruse
is invisible to immune system.
 What determines latency in a cell? The cell factors that determine whether
an infection will be productive of latent are not known for any herpes virus.
Herpes viruses are antigenically stable. (Vaccines should theoretically be possible).
Cell Surface Receptors: heparan sulfate for most herpesviruses.
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All herpesviridae: can develop latent state. Alpha family cause multinucleated
syncticial cells with intranuclear inclusion bodies.
- alpha subgroup cause cell destruction; results in separation of epithelium causing
blisters (vesicles)
- biopsies/scrapings show multinucleated giant cells (viral proteins inserted into
host cell membranes resulting in cell fusion) with intranuclear inclusion-bodies
(proably areas of viral assembly)
- Beta and gamma subgroup have less cytopathic effects
Neonatal Herpes
HSV infection during pregnancy can get transmitted across the placenta. (Also
during delivery if active genital herpes). Herpes is one of the TORCHES
(toxoplasmosis, rubella, CMV, herpes, HIV, syphilis)
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Virus replicates in epithelial cells with destruction of the cells
Rarely during reactivation, virus moves up neuron to CNS  encephalitis.
(usually HSV1) Neural or hematogenous spread may also result in meningitis.
(usually HSV2).
Latency
Virus enters endings of adjacent neurons; circularization of genome; no expression of
genome except for LAT (latency-associated transcript). LAT is a stable intron that
accumulates in the nuclei of some latently-infected cells. B/c neurons are postmitotic, viral genome does not have to be replicated.
Reactivation:
HSV: recurrent lesions (immunocompetent)
VZV: zoster
EBV: B cell lymphomas (immunocompromised)
CMV: various s/a retinitis (AIDS), pneumonia (BM tplant): (immunocompromised)
APPON: MONONUCLEAR CELLS; refers to macrophage cells (progeny of
monocytes[?]. Eg: regular macrophages; Kuppfer cells (liver); Alveolar macrophages
(lung); Microglia (NS)
HSV-1
Clinical Symptoms: KERG
- Gingivostomatitis: painful swollen gums and mucus membranes with multiple
vesicles; disease will resolve in about 2 weeks; Vesicles can also appear on
areas of skin where viral entry occurred
- Reactivation: About 25% of people will have reactivation in stressed states.
Mucocutaneous lesions (cold sores, fever blisters); Keratitis, Encephalitis (rare)
- Herpetic Keratitis: most common (infectious) cause of corneal blindness in US
- Encephalitis: HSV1 is the most common cause of viral encephalitis in US.
Infection occurs with cell death and brain tissue swelling. Patients present with
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sudden onset fever and focal neurologic abnormalities. Always consider HSV-1
b/c this is one of the few treatable causes of viral encephalitis.
Site of Latency: sensory or autonomic ganglia
HSV-2
- Commonly causes genital disease. (However, can also cause oral/eye/skin disease
just as HSV1 can cause genital herpes). Difference is unimportant b/c symptoms
and treatment are same.
- Genital Herpes: vesicles on vagina, cervix, vulva, perineum, glans/shaft of penis.
Vesicles are painful with burning and itching, often with urination.
VZV
Systemic Disease: In constrast to HSV, VZV causes systemic primary disease, not
localized disease.
Transfer: Respiratory secretions can be transmitted through air or ventilation
systems. In contrast, HSV requires close person-to-person contact and transfer of
secretions.
Varicella (chicken-pox)  children; Highly contagious; About 90% have had in
childhood.
- Infects respiratory tract  2 week incubation (replication?)  Viremia
- Clinical: Fever, malaise, headache followed by characteristic rash. Begins on
face and trunk and spreads to rest of body including mucous membranes.
- Vesicles: dew on a rose petal (red base with fluid vesicle on top)
- “Crops” of vesicles will scab over in about 1 week and patient ceases to be
contagious.
Zoster
Reactivation = zoster (shingles). In zoster, vesicles appear in a dermatomal
distribution, almost always unilaterally.
Burning, painful skin lesions develop over area supplied by the sensory nerve.
Dx of zoster is likely when Pt develops skin rash over a specific sensory dermatome.
CMV
 CMV disease is primarily seen only in the immunocompromised.
 Causes 4 infectious states:
- Asymptomatic infection (about 80% of adults in world have).
- Congenital Dz: one of the “TORCHES”. CMV is the most common cause of
viral mental retardation. Also: microcephaly, deafness, seizures, other birth
defects.
- CMV Mono: similar to EBV mono
- Reactivation Dz: in immunocompromised to cause blindness (AIDS),
pneumonia (BM tplant), disseminated infection, even death.
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In immunocompromised, CMV causes different diseases in different people. AIDS:
CMV retinitis (blindness). Bone Marrow Trnsplant: CMV pneumonia. (AIDS 
eye; Marrow  lung)
Eg: In febrile BMar tplant patients and in AIDS patients, you will often order blood
cultures for CMV. (CMV invades WBCs, so be sure to culture the buffy coat).
Therapy: gancIclovir (acyclovir does not work on CMV)
EBV
 Target cells are B lmphocytes (not neurons)
 Transfer: requires close person-to-person contact and transfer of oral secretions
(kissing disease)
 Infection of B cells requires interaction with 2 receptors: CD21 (a complement
receptor) and MHCII. (Receptors on epithelial cells have not been identified).
 Latent vs Productive: How/Whether a given B cell will become productively or
latently infected is not clear yet.
 Primary Disease = infections mononucleosis;
Infectious Mononucleosis
Latent B cells can be of different types (i.e. express different viral proteins).
Those that express all three (EBNA1, LMP2, LMP1) will provoke brisk T cell
response. (It is the LMP1…) It is this response and released cytokines that
cause the symptoms of the disease. The response kills off the cells, and the only
B’s remaining in latency are those with only EBNA1.
Classic feature of mono is lymph node swelling.
Reactivation: Usually not in immunocompetent. In immunocompromised, poor
T response  lymphoproliferative disease. Oral hairy leukoplakia can also
develop in immunocompromised. Cancers: NPC, Burkitt’s, Hodgkin’s
lymphoma.
Diseases caused by EBV:
Children: infection often not apparent
Young Adults: mono
Immunosuppressed: lymphoproliferative disease; oral hairy leukoplakia
Cancers: Burkitt’s, Nasopharyngeal carcinoma
HIV
 Infection  Latent virus  assault on imune system cells (CD4)  AIDS 
opportunistic infections  death
 As with all retroviruses, a DNA copy of the HIV genome is integrated into the cell’s
DNA. This means that proviral DNA is transmitted to all daughter cells.
- Under some conditions, proviral DNA is transcribed by cell polymerase III
- Under other conditions, proviral genome is not transcribed and no viral antigens
are produced. These latently infected cells are invisible to the immune system.
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Inexorable progression to AIDS: due to inability of immune system to keep up with
virus. Several reasons including: latent infections; extreme variability of viral
proteins; virus attacks immune cells directly.
FC: Give one important explanation for the high variability of HIV: error-prone
reverse transcriptase
Mode of Infection
- parenteral including sexual and perinatal
- receptors are CD4R and chemokine receptors CCR5, CXCR4. Mutations in
CCR5 means that you are immune to HIV!
Sequence of events following infection:
1. Primary Infection: acute mono-like syndrome (or asymptomatic)
2. Latent Phase: long period; HIV is repicating in lymphoid tissues and CD4s are
being turned over at a high rate (without aggressive treatment).
- HIV infected T-cells die within 48 hours. Eventually balance shifts
and T-cell cound is reduced.
- Asymptomatic infection: 2e11 CD4 T cells
3. Later: Appearance of HIV in blood; gradual loss of CD4; opportunistic
infections
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HIV and other lentiviruses are “souped-up” forms of retrovirus that encode several
proteins in addition to those neede for replication (eg gag, pol, env, etc)
HAART: highly active anti-retroviral therapy: a combination of drugs for therapy.
Often includes 2 nucleoside analogs and 1 protease inhibitor. This combination
strongly reduces the frequency of emergence of drug-resistant mutants.
 Inhibits HIV production
 Keeps plasma levels of HIV low
  drug resistant mutants
 reverse-transcriptase inhibitors are important too
Viremia and CD4 Counts (graph): As CD4 drops towards the end of the disease,
viremia goes up.
34 – VIRAL ONCOGENESIS
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3 major concepts to retroviruses: Retro (DNARNA); Grow (cancer); Blow
(lytic to some cells e.g. HIV “blows” CD4s)
Oncogene: Genes alled oncogenes can cause malignant transformation of normal
cells into cancer cels. (Some retroviruses carry oncogenes).
Proto-Oncogene (define/how are they activated?): Inactive oncogenes are called
proto-oncogenes. These are “genetic time-bombs waiting for activation”. Activation:
carcinogen-induced mutations; retrovirus infection
How do oncogenes cause cancer? Normal cell has membrane receptors that regulate
growth (eg PDGF-rec, EGF-rec, Insulin-rec, etc). Mitogen (ie growth factor)
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stimulation of these receptors causes phosphorylation of intracellular tyrosine.
Phosphotyrosine acts as an intracellular growth messenger.
- ‘src’ (Rous sarcoma virus oncogene) encodes a membrane receptor that
phorphorylates tyrosine—but at 10 times the normal rate!
- erb-B oncogene (causes cancer in chickens) encodes a protein that is similar to
EGF receptor. Other oncogenes mimic other receptors.
- Other oncogenes encode proteins that act at the nuclear level to promote
uncontrolled expression of various growth genes.
How do retroviruses cause cancer? Some cause cancer directly (acute) by
integrating an oncogene into the host DNA. Others cause cancer indirectly (nonacute)
by activating a host proto-oncogene.
List the most important oncogenic viruses and their associated cancers: “b,c,Eh,p,t) HBV,HCV: primary hepatocellular carcinoma; EBV: Burkitt’s, NPC, B
lymphomas in immunodeficient individuals; HHV8: Kasposi’s; HPV:
carcinomas—especially cervical and other genital carcinomas; HTLV-8: adult T-cell
lymphoma.
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38 – ANTIVIRAL DRUGS
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Think of the steps in viral attack and then you can see where the drugs try to work.
(Adsorption, Penetration, Uncoating, Sythesis of early regulatory proteins, Synthesis
of genomic or DNA/RNA, Synthesis of late structural proteins, Reassembly, Release
of virion from cell)
Most antivirals target the step of viral DNA/RNA (inhibit DNA/RNA synthesis)
Most of these drugs are nucleotide analogs. That is, they resemble nucleotides but are
more like monkey-wrenches. They inhibit DNA polymerase or reverse transcriptase,
and also, are incorporated into the growing DNa strand resulting in premature chain
termination.
Absorption/Penetration
 Enfuvirtide (en-fyu-veer’-tide): An analogue of one of the domains of gp41
inhibits uncoiling of this glycoprotein. This means that the virion can’t enter the
cell.
 Pleconaril: investigational; active against picornavirus; binds to a pocket on
the viral capsid preventing attachment or uncoating.
Uncoating
 Amantadine & Rimantadine: Inhibits uncoating of influenza A. “Amantadine =
Influ A) Rimantadine has less CNS side effects (anxiety, confusion) making it
more suited to elderly. (Rimantadine = Retired);
 A-Man-to-Dine with: ie date with a guy who takes off his coat; has a
nasty cold
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ANTI-HERPES
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Acyclovir & Ganciclovir. To become active, acyclovir must be phosphorylated by a
virus-specific thymidine kinase. Most herpesviridae have this (not CMV) while
human cells do not. So acyclovir is good for HSV, VZV (not CMV, EBV).
Acyclovir Clinical: Acyclovir is good for HSV,VZV. However it is not
recommended unless the disease is severe (eg eye, genital, encephalitis) or if the
patient is immunocompromised.
Acyclovir Adverse: A-CYCLE crystalizing in the renal tubule (renal toxicity).
About 1% have CNS effects s/a confusion or seizures.
Ganciclovir does not need to be phosphorylated by thymidine kinase. The downside
is toxic to some rapidly replicating human cells such as neutrophils, platelets
(neutropenia, thrombocytopenia). Because of its toxicity, it is only used for CMV
infections in the immunocompromised.
Ganciclovir Clinical: used only for CMV in immunocompromised (eg: retinits in
AIDS, pneumonia in BMTplant)
Ganciclovir Adverse: Neutropenia and thrombocytopenia. Since zidovudine (AZT)
also causes neutropenia, carefully monitor neutrophil counts in patients taking both
ganciclovir and zidovudine.
Foscarnet: Inhibits DNA polmerase and reverse transcriptase. Still, not strong
enough for anti-HIV. However, used in AIDS patients with CMV retinitis. Also used
for herpes viruses that are resistant to acyclovir.
Foscarnet Adverse: reversible nephrotoxicity; increased seizure potential (so don’t
give to people with prior history of seizure or on meds that  seizure potential).
Some of these drugs have versions that are more bioavailable following oral
administration:
Valacyclovir  Acyclovir
Famciclovir  Penciclovir
Valganciclovir  Ganciclovir
Ribavarin
 only used for severe RSV
 also measles, HCV
 inhibits capping of mRNAs of certain viruses