Slide 1 15.09.2015 Ref: VPS-0036-DOC-A CONFIDENTIAL CONFIDENTIAL tie Part 3: immunology & metabolomics Basics of biology – Verhaert lunch lectures Jef Aernouts
Slide 115.09.2015Ref: VPS-0036-DOC-A
CONFIDENTIAL
CONFIDENTIAL
TEM
P-0
010-
DO
T-D
-Ver
haer
t Pre
sent
atie
Part 3: immunology & metabolomics
Basics of biology – Verhaert lunch lectures
Jef Aernouts
Slide 215.09.2015Ref: VPS-0036-DOC-A
CONFIDENTIAL
Chapters• Building blocks of life• Genomics• Proteomics• Immunology• Metabolomics
Slide 315.09.2015Ref: VPS-0036-DOC-A
CONFIDENTIAL
Part 1: building blocks of life
CONFIDENTIAL
Biomolecules
Backbone slideLife
Living organisms
forming
viruses bacteria fungi plants animals
Made up of cell(s):
Prokaryotic Eukaryotic
classes
Single vs. multicellular organisms
Unicellular Multicellular
• Organisms composed of only 1 cell
• Examples:Bacteria (prokaryotic)
Yeast (fungi, eukaryotic)
Protosoa (eukaryotic), e.g. plasmodium causingmalaria
• Organisms consisting of many cells (always eukaryotic)
• Examples:Plants (autotroph)
Animals (heterotroph)
Fungi (heterotroph)e.g. mushrooms
Virus - definitions
Parasitism: viruses are dependent on specific host cells; they cannot reproduce on their own but have to reside in a specific host.
A virus consists of:• Nucleic acids (DNA or RNA)• Covered by a protein coat• Sometimes enclosed by a membrane (= enveloped)
Various hosts:• Bacteriophages (host = bacterium)• Animal virus (host = animal), e.g. influenza virus (flu)• Plant virus (host = plant), e.g. tobacco mosaic virus
Size: 20 - 300 nm
Source: http://www.biology-online.org/dictionary
Virus replication
Example of influenza infection:
Result: viruses take over the normal cell metabolism infected
Part 3: immunology
Slide 915.09.2015Ref: VPS-0036-DOC-A
CONFIDENTIALCONFIDENTIAL
Backbone slide
Immunity: definitions & role
Innate immunity(=natural, =native)• First line of defense• Basic/generic resistance
Adaptive immunity(=specific, = acquired)• Induced by invaders
time
Humoral Cell-mediated
extracellular intracellular
interplay
Immunity – intro video
Video: https://youtu.be/8EEJsu3NjQU
Immunity - definitions
Immunity: resistance to infectious disease
Immune (defense) system: collection of cells, tissues and molecules that mediate resistance
Immune response: coordinated reaction to microbes
Pathogen (microbe): infectious agent that can cause disease• Viruses (e.g. HIV causing AIDS)• Bacteria (e.g. Anthrax causing)• Fungi (e.g. Ringworm skin infection)• Protosoa (e.g. Plasmodium causing Malaria)
Immunity – involved cells
Cell differentiation from stem cells:
White blood cells (leukocytes): cells of the immune system that are involved in protecting the body against both infectious disease and foreign invaders
Slide 1315.09.2015Ref: VPS-0036-DOC-A
CONFIDENTIAL
Immunity - overview
• Also called natural or native • Always present in healthy individuals
(present before infection)• Immediate response (first line of defense)• Basic resistance to disease
• Also called specific or acquired • Stimulated/induced by microbes• Lag time between exposure and maximal
response• Exposure results in immunologic memory
(base for vaccines)
Innate immunity Adaptive immunityinterplay
Slide 1415.09.2015Ref: VPS-0036-DOC-A
CONFIDENTIALCONFIDENTIAL
Backbone slide
Immunity: definitions & role
Innate immunity(=natural, =native)• First line of defense• Basic/generic resistance
Adaptive immunity(=specific, = acquired)• Induced by invaders
time
Humoral Cell-mediated
extracellular intracellular
interplay
Slide 1515.09.2015Ref: VPS-0036-DOC-A
CONFIDENTIAL
Innate immunity
1. Physical components
• Anatomic/physical: • Skin (barrier)• Mucous membranes• Tears (washing effect)
• Physiological:• Temperature
e.g. chicken (41 °C) are resistant to anthrax (37-39 °C)• pH• Variety of chemicals
2. Phagocytosis: ‘eating invaders’
Ingestion and digestion of foreign cells/molecules through phagocytosis
• Macrophages• Neutrophils• Natural Killer (NK) cells• Complement system
Slide 1615.09.2015Ref: VPS-0036-DOC-A
CONFIDENTIAL
Innate immunity – video phagocytosis
Video: https://youtu.be/r4-g6tVyUAU
Slide 1715.09.2015Ref: VPS-0036-DOC-A
CONFIDENTIALCONFIDENTIAL
Backbone slide
Immunity: definitions & role
Innate immunity(=natural, =native)• First line of defense• Basic/generic resistance
Adaptive immunity(=specific, = acquired)• Induced by invaders
time
Humoral Cell-mediated
extracellular intracellular
interplay
Adaptive immunity: intro video
Video: https://youtu.be/Bf2t8n1ibwQ
Adaptive immunity
Although innate immunity can effectively combat infections many microbes have evolved to resist innate immunity adaptive immunity
Adaptive immune system consists of lymphocytes (class of white blood cells) and their products (e.g. antibodies):• B lymphocytes• T lymphocytes
Slide 2015.09.2015Ref: VPS-0036-DOC-A
CONFIDENTIAL
Adaptive immunity: humoral vs. cell-mediated
Extracellular microbes(e.g. bacterium in blood)
Invaders have antigens on its outer surface (antibody generators): they are recognized as foreign by B-cells that attach to it
B-cells differentiate to plasma cells that produce antibodies
Antibodies bind temporarily to the pathogen: Temporarily inactivate Mark for digestion by phagocytes
Also, some B cells differentiate to memory cells: respond to secondary encounter
Intracellular microbes (e.g. a virus in a host cell)
Defense mediated by T-cells (T-Lymphocytes)
T-cells recognizes antigens
T-cells transform to antigen-specific cells, and differentiate into effector cells
Effector cells act against target cell Directly by killing infected cells
(phagocytic) Indirectly by releasing chemicals
(cytotoxic)
Humoral immunity Cell-mediated immunity
Slide 2115.09.2015Ref: VPS-0036-DOC-A
CONFIDENTIAL
Adaptive immunity: humoral vs. cell-mediated
Also cross-talk between 2 pathways:
Slide 2215.09.2015Ref: VPS-0036-DOC-A
CONFIDENTIAL
Immunity: active vs. passive & natural vs. artificial
Video: https://youtu.be/njNdANeRK3A
Slide 2315.09.2015Ref: VPS-0036-DOC-A
CONFIDENTIAL
Immunity: active vs. passive & natural vs. artificial
Slide 2415.09.2015Ref: VPS-0036-DOC-A
CONFIDENTIAL
Immunity: active vs. passive & natural vs. artificial
Slide 2515.09.2015Ref: VPS-0036-DOC-A
CONFIDENTIALCONFIDENTIAL
Example: immuno-assay
05.03.2014Slide 26
CONFIDENTIAL
Immunometry
• Definition:
The measurement of amounts of substances by the use of specific antigen‐antibody reactions.
05.03.2014Slide 27
CONFIDENTIAL
Immunometry
• Definition:
The measurement of amounts of substances by the use of specific antigen‐antibody reactions.
Substances are biomarkers
• Proteins that are present in the blood, urine … The amount is an indicator of a disease, risk …
• e.g. the use of PSA (prostate specific antigen) in the screening of prostate cancer
• Also possible to measure markers that reflect the concentration of active drugs in the blood circulation, i.e. therapeutic drug monitoring (TDM)
• e.g. monitoring Everolimus, drug to prevent rejection of organ transplants
05.03.2014Slide 28
CONFIDENTIAL
Immunometry
• Definition:
The measurement of amounts of substances by the use of specific antigen‐antibody reactions.
Basics of immunity:
1. A foreign object enters the bloodstream. The outer surface contains proteins that are not recognized by the host. These little portions of proteins are called antigens (coming from ANTIbody GENerator)
2. The white blood cells recognize the antigens as foreign, and specific white blood cells initialize the production of antibodies (which typically takes a couple of days). For each antigen, a specific antibody!
3. The produced antibodies are able to bind very specifically to the antigen. This results in a coating of the foreign objectwith antibody(ies). This will initiate the destruction of the object.
4. After infection is eradicated, the specific white blood cells will hide in the bone marrow and will go in a standby modus. Immunity is build up in this way.
antigen B
antigen A
antibody B
antibody A
05.03.2014Slide 29
CONFIDENTIAL
Immunometry – making assays
1. Extracting the protein of interest
Collect human blood samples Extract and purify protein of interest (e.g. PSA)
PSA
PSA
PSA
PSA
PSA
PSA: biomarker for prostate cancer
05.03.2014Slide 30
CONFIDENTIAL
Immunometry – making assays
2. Generate mouse antibodies
Insert the human proteins ofinterest (e.g. PSA) in amouse. Since these proteinsare foreign, mouse white blood cells initiate the formation of mouse antibodies.
The specific white blood cells are extracted, andused as fabrics for the formation of mouse antibodies for human PSA.
PSAPSA
PSA
PSA
WBC for antibody A
WBC for antibody B
humanantigen A
mouseantibody B
white blood cellmouseantibody A
humanantigen BPSA
05.03.2014Slide 31
CONFIDENTIAL
Immunometry – making assays
3. Typical lab assay that is a measure of the specific human protein (e.g. PSA)
Strip with mouse “capture”antibodies A for human PSA
Blood sample with protein
of interest (e.g. PSA)
PSA
PSA
PSA
PSA
PSA
PSA
PSA
PSA
PSA
+
Mix with “label” anti-bodies B with a colorparticle attached
After washing the strip:the more the strip is filled, the more color is produced
05.03.2014Slide 32
CONFIDENTIAL
Immunometry – making assays
3. Typical lab assay that is a measure of the specific human protein
This principle is also used in a pregnancy test (detection of HCG):
Slide 3315.09.2015Ref: VPS-0036-DOC-A
CONFIDENTIAL
Part 3: metabolism
Slide 3415.09.2015Ref: VPS-0036-DOC-A
CONFIDENTIAL
Metabolism
Video: https://youtu.be/yiuPCSYBdJk
Slide 3515.09.2015Ref: VPS-0036-DOC-A
CONFIDENTIAL
Definitions
Metabolism: the sum of all chemical interactions inside a cell• Catabolic: degrade into smaller compounds
release of energye.g. proteins (food, muscles) to amino-acids
• Anabolic: linking smaller compounds to a bigger molecule (synthesis) requires energye.g. protein synthesis
Metabolomics: study of metabolism (includes techniques…)
Cf.: genetics vs. genomics
Catabolic Anabolic
Anabolic steroids:excessive muscle buildup
Starvation
Slide 3615.09.2015Ref: VPS-0036-DOC-A
CONFIDENTIAL
Metabolic pathways
To study in life sciences …
Slide 3715.09.2015Ref: VPS-0036-DOC-A
CONFIDENTIAL
Chapters• Building blocks of life• Genomics• Proteomics• Immunology• Metabolomics
Slide 3815.09.2015Ref: VPS-0036-DOC-A
CONFIDENTIAL