Module 1

Basic Oncology (Hallmarks of Cancer) - To Inhibit/To activate

1. Self-Sufficiency in growth signals
a. A mutant hyperactive Ras in cancers = no ligand binding needed for cell division
b. Amplified Epidermal Growth Factor Receptors (EGFR) = very little ligand needed
c. HER1-4 amplification: acts on
i. RAS-GDP pathway, PI3K-Akt, and RAF-MEK-MAPK
2. Insensitivity to Anti-Growth Signals
a. At G0 in cell cycle, normally Rb protein binds to DNA to stop cell division and
allows cell division by being phosphorylated
i. Cancer = mutated Rb so ‘always inactive’ even w/ phosphorylation = cell
division
b. Mutated/loss of p53
i. Controls: apoptosis, cycle arrest, DNA repair, differentiation, senescence
ii. Loss or mutation = cancer formation
3. Evading Apoptosis
a. IGF-1R/IGF-1 and Ras upregulate survival pathway to evade apoptosis
4. Limitless Replicative Potential
a. Usually, telomerase activity is turned off and the telomeres shorten =
senescence, cancer cells reactivate telomerase
5. Sustained Angiogenesis
a. Tumor secretes VEGF => VEGF increases blood vessel mvmt to tumor =>
increased blood supply
6. Tissue Invasion and Metastasis
a. Cells in primary tumor reduce E-cadherins (cell-cell) and increase integrins
(connect to ECM)
7. Deregulating Cellular energetics
a. Warburg Effect
i. Tumors produce large amount of lactate = aerobic glycolysis even if there
is oxygen, but it means rapid cell proliferation
8. Avoiding immune destruction
9. Enabling characteristics: Genome instability and mutation, Tumor-promoting
inflammation

Tumor angiogenesis and lymphangiogenesis

1. Areas of low O2 (hypoxia) = high HIF (Hypoxia inducible factor) [HIF1-alpha] = secreted
VEGF and then parycytes help stabilize the new vessel
2. VEGF:
a. A binds to R-2 = blood vessel formation
b. R-1 = Negative and decoy detector
c. C and D bind to R-3 = lymphanogiogenesis
3. Tumor angio = abnormal blood vessels
a. Can renormalize vasculature
4. Inhibition of tumor angionenesis
 a. Bevacizumab, VEGF-trap, Pegaptinib, Anti-VEGF-2 antibodies
5. Tumor Interstitial Fluid Pressure (IFP)
a. Keeps T cells from infiltrating, when IHP is low - there is good drainage for LEC
and a barrier for BEC. at high IHP - opposite
6. Microfluidic tools for angiogenesis/vasculogenesis:
a. Source channel and parent channel with gap inbetween
b. Use endothelial cell progenitors = primitive vascular plexus
c. 3D printing network and encapsulate network in fibrin, collagen etc
7. Engineering Lymphatic vessels
a. Lymph molllecules able to diffuse on collagen toward a VEGF-3 factor?

Tumor Invasion and Metastasis I

1. What is Metastasis?
a. Tumor Vascularization
i. VEGF sprouting due to hypoxia and HIF
b. Intravasation
i. MMP (matrix metalloproteinase)- activated by cleavage of a propeptide
1. MMP2 and MMP9 cleave type 4 collagen which is part of
basement membrane of BV
ii. Integrins: cell-ECM (cell migration)
1. Alpha and beta subunits, signaling = mechanotransduction after
conformation change
iii. E-cadherin: cell-cell (EMT)
1. Single cells, can become mesenchymal
c. Circulating Tumor Cells
d. Extravasation and Colonization (in distant organ)
2. Molecular Mechanisms of metastasis (EMT vs MET)
a. EMT = decreased E-cadherin during intravasation
b. MET = increased E-cad during Extravasation and colonization
3. Engineering approaches studying metastasis
a. Tubes of blood vessel and cancer cells with space to cross inbetween
i. Cancer cells literally replace the blood vessels
b. TGF-beta receptor inhibitor blocks EC replacement by PDAC in vitro
c. Reversing vessel leakiness = blocking metastasis

Tumor Invasion and Metastasis II

1. Metastatic colonization
a. Seed and Soil hypothesis

i.
 ii.
2. Organ-specific metastasis
a. Organotropism
i. The attraction of microorganisms/chemicals to specific parts of the body
b. 50-80% of patients with breast cancer are predicted to have bone and lung
metastases
i. Study with channel and media reservoir
3. Case Study: how do lymphatics affect tumor metastasis?
a. Lymphatic AND blood vessels as routes of metastasis (up to 60% of breast
cancer cases)
b. Organ-residing LEC promote metastasis
i. Prepare a metastatic niche (may give off VEGF, IL6, and CCL5 which can
promote metastasis or angiogenesis)
ii. Maraviroc: CCR5 inhibitor - can block tumor cell migration
c. LEC secreted CCL5 recruits tumor cells to lymph nodes and lungs, secret
VEGF
i. So use Maraviroc AND anti-VEGF

Biomechanics and cancer mechanobiology

1. Physics of Cancer
a. Solid stress
b. Fluid pression
c. Stiffness
d. Microarchitecture
2. Key terms and equations in solid mechanics
a. E = stress/strain [Pa = N/m2 = NM/m3 = J/m3]
b. Stress = F/A
c. Strain = deltaL/L0
d. The higher the Young’s modulus, the stiffer the material property

e.
i. Area under curve = Stress*strain = Strain energy (J/m3)
 ii. Under same strain: greater E stores most energy, under same stress:
smaller E stores most energy
3. Problem set for solid mechanics
4. Stiffness and cancer
a. Netrin4 knock out increases metastasis in vivo (NTN4 softens basement
membrane) = Stiffer ECM shows more tumor invasion because there are
more places for the Cell-ECM interactions and adhesion, more stress fibers
5. Solid Stress and Cancer
a. Solid stress impairs lymphocyte infiltration into lymph-node metastases
b. Solid stress (or tumor IFP) is determined by blood pressure (blood vessel
leakage) and lymphatic drainage
c. Losartan, angiotensin inhibitor helps to increase T cells within LN lesions
6. Fluid shear stress and cancer
a. Fluid shear stress activates YAP1 to promote cancer cell motility
b. Shear stress is a “pressure” that cells on the wall experience against luminal flow

i. with Q: flow rate; R: radius of channel

c. WSS increases filopodia formation in cancer cells = migration, and
vasculogenesis etc

Biomaterials and tissue engineering in cancer research

1. ECM
a. Tumor Microenvironment
i. Crosstalk b/n BMDSCs and cancer cells stumulates growth factor
secretion
ii. Macrophage recruitment and growth factor secretion
iii. Hypoxic induction of collagen-modifying enzymes (LOX and P4HA)
iv. Invasion and intravasation
v. Fribillar collagen production and remodeling
vi. Fibroblast recruitment
b. ECM
i. Lies under epithelia, produced oriented and modified by cells
ii. Saffolding, anchorage, signaling
c. Composition
i. Proteins and polysaccharides (glycoproteins, proteoglycans,
glycosaminoglycans)
ii. Structural proteins, amorphous components, adhesive proteins
2. Collagen (Fibrillar ECM)
a. Most abundant protein - only type I,II, and III are fibrillar
b. Steps: preprocollagen - procollagen - connect the chains and cleave peptides -
collagen fibril - multiple fibrils = 1 fiber
i. Is assembled outside of cells
ii. Cross-linking via lysine side chains
c. Stiffer ECM shows more tumor invasion
 3. GAG (Space filling ECM)
a. Functions: space filling, binding cells and localizing proteins, regulate transport
b. Resistance to compressive forces
i. High swelling pressure, forms a gel, attract osmotically active Na+ ions
ii. Hyaluronic acid increases solid stress in tumors by swelling and
taking up space so people used hyaluronidase to degrad the HA and
lower tumor stress
c. GAG gets growth factor to cells
4. Adhesive ECM
a. Fibronectin
i. Cell adhesion to surfaces
ii. Integrin subunits: a5b1 , avb3
iii. Arginylylycylaspartic acid (RGD) is the analog that binds integrins
5. Case Studies
a. Top-down Approach: natural ECM
i. Tumor derived decellularized ECM is pro-tumorigenic
ii. Overlap b/n obesity and cancer etc: COL 12, COL6, FN, VTN etc
iii. Collagen VI was key component in tumor-derived deceullularized ECM
1. Perilipin: lipid associated protein, expressed on the surface
of lipid droplets
2. Crosstalk between EGFR and NG2 mediated by Collagen VI
b. Bottom-up approach: synthetic materials to mimic natural ECM
i. Peptide amphiphiles (PA) - scaffold fibers - when mized with ECM is
similar to primary tumor ECM
1. PDAC: pancreatic ductal adenocarcinoma
2. PSCs: pancreatic stomal cells
3. EPCAM: epithelial cellular adhesion molecule
4. CD 68: macrophage marker

Drug Delivery Systems in Cancer Research

1. About Polymers
a. Terminology:
i. Monomer, residue, Chain length -or- degree of polymerization (DP)
1. DP = n+m
ii. Molecular weight: MWp = n* MWr
1. Number average: Mn = E(NiMi)/E(Ni)
2. Weight average: Mw = E(NiMi2)(ENiMi)
3. PDI = Mw/Mn
4. Low (softer); high (harder)
iii. GPC: smaller analytes can enter the pores and spend more time in
the pores so they will elute last
2. Basics of drug delivery systems
a. Theraputic index
 b. How to increase drug effectiveness?: ID targets, increase longevity, decrease
elimination rate
c. Reservoir System
i. Fick’s Law: Flux = -D*gradientCdrug
1. D: diffusion coefficient: 1.10-9 for small macro and 1.10-12 for big
3. Cancer drug delivery systems
a. PEGylation based systems
i. Water soluble, reduce immune reaction, incrase biocomp, reduce phago
b. Passive targeting (EPR: enhanced permeability and retention effect) - lymph
targeting
i. Varied: in general - more vascularized = stronger EPR effect
ii. Except in breast cancer: lymph vessels in breast cancer tend to be
hyperactive and have less retention and poorer EPR effect
c. Active Targeting
i. Antibody based targeting
ii. Aptamer based targeting
iii. Ligand based targeting
4. What do you deliver for treating cancer?
a. DNA, RNA - small molecule drug
b. RNAi (RNA interference): represses the translation of the RNA, not permanent
c. CRISPR-Cas9: used in T cell engineering, not as active in vivo for oncogenes
(replaces the dna)
d. Protein inhibition: not long-term, more safe, less reproduceable
e. DNA/RNA inhibition: more long-term, less safe, more reproduceable

Module 2
Innate Immunity
1. Introduction to the innate immune system
a. Second line of defence (physical barriers like skin is first defense)
b. Very Fast activation and function bc microbes multiply quickly (2^n)
2. The complement system
i. 20 different proteins that work together to destroy invaders and signal to
other immune cells
a. Complement protein C3
i. C3 produced by liver -> breaks into C3a and C3b (Slow Reaction,
spontaneous). C3b binds to animo/hydroxyl group on bacterium.
ii. B binds to C3b and protein D = C3bBb (‘Convertase = converting
enzyme)
iii. C3bBb cuts other C3 to make C3b = Dont wait for the spontaneous
reaction and can make more C3b more efficiently
iv. C3Bb + C3b = C5a & C5b: C5b +(C6-9) = Membrane attack complex on
the invader’s surface (20-30nm) - C9 proteins open a channel hole in the
bacterium = ded
b. Lectin activation
 i. Mannose-binding lectin (MBL): binds to mannose (carbohydrate) found on
common pathogens
ii. MBL binds to MASP and MASP is convertase and clips C3 to make C3b
= goes to complement protein pathway
c. Other Roles
i. iC3b-mediated opsonization
1. iC3b bound cannot make MAC so it is tagged so phagocytes can
eat it (Opsonization)
ii. C3a and C5a mediated chemoattraction - freely secreted
1. Chemoattractants of macrophages and neutrophils to the site
of infection which gets them attacked
3. The professional phagocytes (macrophages, neutrophils)
a. Macrophages
i. 1)Resting; 2)Activated(Primed); 3)Hyperactivated
1. Resting: “garbage collector” clean off dead cells through DAMPs
(Damage associated molecular patterns). No MHC II
expression during resting.
2. Activated (An antigen presenter) become activated by IFN-
gamma (sec by NK cells) - Innate
a. Upregulate MHC II molecules and present to CD4 T cells -
adaptive
b. Activated bridges innate and adaptive
3. Hyperactivated: induced by LPS (direct contact) = focus on killing
and secret tumor-necrosis factor (TNF)
ii. Recognizing other invaders:
1. Pattern-recogntion receptors: TLRs for structural features = secret
TNF
a. TLR2: Gram Positive
b. TLR4: Gram Negative (LPS)
c. TLR7: RNA
d. TLR9: DNA
b. Neutrophils
i. Professional killers, are summoned by macrophafes, secrete TNF; Only
live for 5 days
ii. Extravasation of Neutrophils
1. Neutrophils have SLIG (selectin ligand). Hyperactivated
macrophages produce TNF
2. TNF recruits E-selectin receptors to bind SLIG, IL-1 released by
inflamed tissue
3. Inflammed tissue releases C5a and LPS- C5a promots beta2
integrin binding to ICAM = now neutrophil is bound to ICAM
4. Extravasation: exists blood and follows concentration of f-met and
C5a
iii. Why need 3 signals? Fail safe
 iv. 6 hrs? Too slow? No, want to be sure we need it

Adaptive Immunity I (B cells and Antibodies)

1. Why adaptive immunity?
a. Immune system must adapt by producing counter-weapons
2. B cell and B cell receptor (BCR)
a. B Cells
i. Primarily produce antibodies (antibodies do not have the anchoring
sequence so they can be ‘exported’)
b. B Cell Receptor
i. Recognition part (Hc+Lc) + a signaling part (accessory proteins)
1. Select gene segments coding for 2 proteins (Hc and Lc):
accessory proteins are conserved
2. Genes located on chromosome 14: can make diff BCRs to
recognize diff organic molecules (VDJ)
ii. Once decided on gene segment to express = only one kind of BCR and
antibody
c. How BCR signals?
i. Recognizes its cognate antigen Epitope
ii. Once bound, signal is transduced through accessory protein Igalpha
and Igbeta which interact with the Heavy Chain
iii. Signal transduction = secrete antibodies
iv. B Cell immunity (humoral immunity)
3. B cell activation
a. Naive (never been activated); Experienced (activated)
b. To activate
i. BCR epitope binding must be clustered: multiple BCRs bind to multiple
epitopes at a time -> crosslinked -> B cell activation
ii. Also need other thing to activate
c. Two Types of B cell activation
i. T cell-dependent
1. BCR-epitope + Helper T cell (CD40L-T binds to CD40-B)
a. Protein antigens do not have repeated antigen units =
need Th Cells
2. Only focused on protein antigens
ii. T cell-independent
1. BCR-epitope to repeated epitopes + danger signal (carbohydrates
of bacteria)
2. It is faster than T-dependent (Protection from diverse antigens)
3. Secreting Pneymolysin: a toxic cytokine giving a danger
signal
d. Polyclonal B cell activation: (unusual and indicate immune issues)
i. Polyclonal antibodies are not antigen-specific, so they are NOT
effective killing invaders
 1. When antigens are LPS that can bind TLR4 on BCR, TLR4 recruit
accessory proteins Igalpha and Igbeta. Produces antibodies
without a regular mechanism
ii. Polyclonal B cell activation is unnatural and tells your immune
system goes wrong
4. B cell maturation and antibody types
a. Class switching
i. Change the class of the antibody (switches constant Fc region) [IgM
=>IgG, IgE, IgA]
1. igM: produced by B cells in response to a pathogen that has not
been enounter
a. One IgM has 5 IgGs = very good opsonizer (5-10
invaders to 1 macrophage)
2. IgG: regular antibody shape (Lc+Hc), amost abundant in blood,
opsonizer neutralizer = “gamma globulin”
3. IgA: sideways structure; protects mucosal surfaces; has a ‘clip’
and can go through the intestinal barrier 80% of B cells in the
mucosal surf produce IgA antibodies
4. IgE: cytokine storm, fc region binds to receptor in mast cells
a. Cascade increases the risk of systemic shock
b. Somatic hypermutation
i. Changing antigen binding or variable (Fab) region
ii. Binding and proliferation theory**
1. Requites helper cells to do
2. Important for making Memory B cells
c. Career Decision
i. Decides if plasma B cell (an antibody factory) or a memory B cell
1. Plasma B cell: antibody factory, leaves lymph node, goes to
spleen and bone marrow ~ few days
2. Memory cells: lover life
ii. CD40-CD40L needed for memory B cells T cell dependent somatic
hypermutation

Adaptive Immunity II (Antigen Presentation)

1. Major Histocompatibility Complex (MHC) Molecules
a. Class I = killer T cells (CD8+ T cells or cytotoxic T lymphocytes: CTL)
b. Class II = helper Y cells (CD4+ T cells)
2. Class I MHC molecules & Class II MHC Molecules
a. Class I Molecules
i. From chromosome 6
ii. MHC made up of HLA pair(polymorphic) + Beta2-microglobulin
(monomorphic)
b. Class II Molecules
i. Only HLA-D encodes for II (polymorphic)
3. Antigen presentation by MHC I molecules and & MHC II molecules
a. MHC I Steps: Express invader proteins in host cell: endogenously expressed
invader antigen
i. Viral proteins degraded by proteasomes
ii. Go to ER by TAP transporters
iii. Bind to MHC I in ER
iv. Move to surface and present antigens
1. Killer T cells inspect viral peptides presented by MHC I
molecules to see if they should be destroyed
b. MHC II Steps: 3 proteins (Alpha-chain (ribosome), beta-chain(ribosome), and
invariant chain (in ER))
i. In ER, invariant binds to grove of MHC and acts as a chaperone to
make sure it doesn’t pick up other peptides
ii. Guided out through golgi to endosomes without capturing peptides
iii. Meets up with phagosome with exogenous protein, merge to make
exogenous peptides
iv. Invariant chain is destroyed except for CLIP (Loading is in the
endosome)
v. Goes to surfaces of cell
c. MHC I & II Compare
i. I: killer T cels, CD8 co-receptor, expressed in almost all cells
ii. II: helper, CD4 co-receptor, only expressed on professional APCs
(dendritic, activated macrophages, activated B)
4. Antigen-presenting cells (APCs):
a. Activated dendritic cells: Activate virgin T cells, sentinel cells
i. Resting: taste extracellular fluids
ii. Activation causes (would be good diagram to have)
1. TNF
2. Dead cells killed by invaders (DAMPs?)
3. TLR to recognize certain patterns (ex: LPS)
iii. Activated = travel to lymph node, only move when activated
iv. Short life cycle of DCs (ensures updated view of surroundings)
v. Recruit monocytes from blood to become dendritic cells
b. Activated macrophages: bridge between innate and adaptive
i. When activated by INF-gamma or LPS, then will express enough MHC
and co-stim proteins to activate T cells
ii. Help to re-stimulate the experienced T cells by additionally
presenting antigens (keeps the fight going)[Gives bardic inspo to T
cells]
c. Activated B cells
i. Once activated by helper T cells will enhance expression of MHC I
and B7… Order: DCs active = Th active = B Active
ii. B cells can concentrate antigen for presentation and act as a magnet to
capture antigens: activate T cells better
 d. Times and Locations
i. DC: antigens in lymph nodes in early infection
ii. Macrophages: infected lesion at later stage
iii. B cells: antigens in lymph nodes at later stage or re-infection
5. Biological meaning of MHC I and MHC II presentation
a. MHC I: focus on only infected host cells, not other viruses or pathogens,
endogeneous proteins presented
b. MHC II: exogenous proteins presented, pathogens in tissues or blood

Adaptive Immunity III

1. T cells in general
a. Two Types
i. Killer T cells: kill infected cells
ii. Helper T cells: remain in blood and help B cells and killer T cells to go to
site and help innate and adaptive immune system
b. Why is activation important
i. Specificity
ii. Needs: 1)recognition of invader by T cell receptors - required; 2)co-
receptors focus attention of TCRs on MHC I/II - helpful; 3)co-
stimulation provided by activated APCs - required
c. Receptors, co-receptors, and co-stimulation
i. TCR:
1. TCR coupled with CD3 which can dictate: cell death (prevent
autoimmunity), T cell anergy (if it doesn’t have co-stimulatory
signals then won’t function), T cell activation
ii. Co-Receptor
1. Help to stabilize the TCR-MHC-peptide complex and strengthen
the signal
2. Originally CD4 and CD8 are both expressed by all T cells
iii. Co-Stimulator
1. B7 on AMP binding to CD28 in Naive T cells
2. Lowers the threshold number of TCRs
2. Helper T cells
a. Helper T cells: immunological synapse formation
i. Adhesion molecule (ICAM-1) on the DC bind to their adhesion partners
(LFA-1)
ii. CD4 co-receptor molecules on the T cell clip onto the MHC II molecule on
DC
iii. Engagement of TCRs upregulates the adhesion partners (LFA-1) on
Th cell surface: initial binding must be weak to allow for scanning
b. Immunological Synapse
i. Formed between T cells and APCs
ii. Central supramolecular activation complex (cSMAC)
 iii. Peripheral SMAC (pSMAC) formed between ICAM-1 on APC and LFA-1
on T cells which bring the cells in close proximity [Leukocyte associated
antigen-1]
c. CD40L on helper T cells
i. Expression of MHC II and B7 is enhanced with CD40L bings CD40 on DC
ii. CD life span prolonged when CD40L bound to CD40
iii. Th cells are fully activated and express more CD40L = B cell activation
iv. Only activated Th cells can express both IL-2 and IL-2R in large
amount which makes them proliferate and have clone selection
3. Killer T cells
a. How killer T cells are activated
i. Activated by encountering an activated DC but need IL-2 for
continued proliferation which comes from activated Th cells
ii. Memory killer T cells are only made through Th cell help
b. How do killer T cells kill
i. Killing by contact between CTL and target cell
ii. Perforin:
1. Delivers granzyme B into target’s cytoplasm to kill
a. Similar to C9 complement protein (perforin) = drills holes to
insert granzyme B = apoptosis
iii. Fas Ligand (FasL):
1. Binds to Fas protein (death receptor) on target cell, triggers
apoptosis through Caspase 8/3 pathway

Adaptive Immunity IV (T cells at Work) & Secondary Lymphoid Organ I

1. T cells at work and Helper T cells
a. Two types of T cells
i. Killer (CD8)
ii. Helper (CD4)
1. Remain in blood and circulation and provide help to B cells and
killer T cells
2. Go to site and help soldiers with innate and adaptive immune
system
b. How is the dendritic cell’s decision conveyed to the helper T cells
i. Helper T cells are cytokine producers, which are coached by
dendritic cells (DCs)
ii. Secrete TNF, INF-gamma, IL-2,4,5,6 etc
iii. Three Th cells: Th1, Th2, Th17 - have own cytokine profile
1. Cytokines produced depends on: what types of invaders, where in
body invaders are located
iv. Two Types of Inputs:
1. Pattern-recognition receptors on DCs: TLRs
a. 2: gram positive
b. 4: gram negative
 c. 3: viral RNA
d. 9: bacterial DNA
2. Cytokine receptors on DCs: sense cytokine environments to
learn
3. DCs decode inputs to discern type of invader and location
and to decide which weapons mobilized
c. Th1/Th2/Th17 helper T cells
i. Th1: viruses and bacteria which infect human cells (skin), DCs alerted via
TLRs and secrete IL-12 when meet virgin Th cells
1. Th1 cytokines: TNF, INF-gamma, IL-2
ii. Th2: parasites and pathogenic bacteria via GI tract
1. DCs present parasites and bacteria antigens to Th cells
2. Th2 cytokines: IL-4, IL-5, IL-13
3. Related to allergies/anaphylaxis
a. IL-4: against parasites IgE antibodies - Richet’s experiment
b. IL-5: IgA antibodies, against gut bacteria
iii. Th17: fungi and extracellular bacteria
1. TGF-beta and IL6 secreted by DCs on contact
2. Th17 cytokines: IL-17 and IL-21
d. Th0 helper T cells
i. Unbiased, not virgin, DCs tell where to go but not what to do
ii. Will commit to differentiation at the battlefield
e.

2. Secondary Lymphoid Organs

a. Introduction
i. Primary lymphoid organs: bone marrow (B and T cells made),
thymus(T cell early training)
 ii. Secondary organs: spleen, lymph nodes, mucosal associated
lymphoid tissue (MALT or Peyers patches)
1. APCs, T cells, and B cells meet which favors activation
2. Lymphoid follicles produce antibodies
b. Lymphoid follicles
i. Start as primary lymph follicles which has follicular dendritic cells
(FDCs) within a sea of B cells
ii. Follicular Dendritic Cells (FDCs) present antigens to B cells with no
help of MHC molecules/ DCs present antigens to T cells via MHCs
iii. How FDCs present antigens to B cells:
1. Complement-opsonized antigens deliver to second lymph organs
2. FDCs bind complements with receptors
3. FDCs get tons of antigens and can crosslink to B cell
receptors
4. B cells can later produce antibodies
iv. Active lymphoid follicles = B cells proliferate “germinal center”
1. Helper T cell’s CD40L keep B cells proliferating
2. Then B cells become either plasma B or undergo somatic
hypermutation to make antibodies or become memory B cells
c. High endothelial venules (HEV)
i. Common to second lymph organs (except spleen)
ii. Where B and T cells enter lymph organs
1. RelA and RelB are NF-xB transcription factor family
iii. HEVs have less tight junctions = T/B lymphocytes circulating can
enter
iv. Antigen presenting DCs enter a lymph node through the afferent
lymphatic vessel

Secondary Lymphoid Organs II

1. Lymph nodes
a. Fluid transport:
i. Afferent vessels bring lymph in and leaves through efferent
ii. Arterioles being blood and leave through venules
b. Immune cell trafficking
i. HEVs for enter and efferent LVs for exit
ii. T cells can enter the lymph node through LV when come from
peripheral tissues
c. Multi-layered node structure
i. Enters node, Passes through holes in marginal sinus, then cortex,
paracortex, and into medullary sinus
ii. Walls of marginal sinus are lined with macrophages - capture and
devour non-opsonized pathogens: Lymph filter (lower number of
invaders in area)
d. T cell area (paracortex) & B cell area (cortex)
 i. T cells have integrins, bind to paracortex and accume there
ii. B cells more to cortex and accume there. There are FDCs in cortex
which show antigens to B cells
e. Roles of chemokine (CXCL13) & chemokine receptor CXCR5 in B cell zone
i. FDCs have CXCL13 and B cells have CXCR5
ii. If naive antigen finds cognate antigen then takes FDC
1. Antigen bound the the receptor is internalized and processed
to display antigen via MHC II molecule
Q: T cell-dependent B cell activation is critical for antibody maturation,
How can B cells and Th cells meet with each other in the lymph node to
allow T cell-dependent B cell activation?
A: Antigen-bound B cells downreg CXCR5 and upreg CCR7 then move
toward CCL21 rich areas to meet Th cells. Th upreg CXCR5 to move toward
B cells. Follicular helper T cells (Tfh)

2. Peyer’s patches
a. MALT (muscosal-associated lymphoid tissues), has efferent lymphatic vessels
only
b. M cells transport antigens from lumen of small intestine into the tissues beneath
the M cell using endosomes
c. Antibody-opsonized antigens collected by M cells go to the FDCs, non-opsonized
antigens can leave. Macrophages in marginal sinus capture and devour non-
opsonized
d. M cell = concentrating on only the potential pathogens
3. The spleen
a. Blood filter, screens all blood. Does not have HEV
b. Made medium is blood not lymph
c. The marginal sinus is lines with macrophages that clean up the pathogens
and cell debris
d. Spleen has leaky walls for T/B cells to enter. T cell accumulate in periarteriolar
lymphocyte sheath (PALS). B cells between PALS and marginal sinuses
e. Blood-circulating DCs initially residing in marginal sinuses capture antigens that
pass through spleen
4. Anatomical comparisons
5. The logic of secondary lymphoid organs
a. Each secondary lymphoid organ is strategically positioned to intercept
invaders that enter the body via different routes
i. Skin: lymph node drain tissue antigens
1. Th1 cells and B cells secrete IgG antibodies
ii. Eat contaminated foods: peyer’s patches that line small intestine
1. Th2 cells and IgA antibodies
iii. Blood-borne pathogens: spleen filters out
iv. Respiratory tract, tonsils defend