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Part 3: immunology & metabolomics

Basics of biology – Verhaert lunch lectures

Jef Aernouts

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Chapters• Building blocks of life• Genomics• Proteomics• Immunology• Metabolomics

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Part 1: building blocks of life

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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

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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

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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

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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

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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

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Innate immunity – video phagocytosis

Video: https://youtu.be/r4-g6tVyUAU

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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

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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

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Adaptive immunity: humoral vs. cell-mediated

Also cross-talk between 2 pathways:

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Immunity: active vs. passive & natural vs. artificial

Video: https://youtu.be/njNdANeRK3A

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Immunity: active vs. passive & natural vs. artificial

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Immunity: active vs. passive & natural vs. artificial

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Example: immuno-assay

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Immunometry

• Definition:

The measurement of amounts of substances by the use of specific antigen‐antibody reactions.

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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

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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

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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

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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

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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

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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):

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Part 3: metabolism

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Metabolism

Video: https://youtu.be/yiuPCSYBdJk

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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

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Metabolic pathways

To study in life sciences …

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Chapters• Building blocks of life• Genomics• Proteomics• Immunology• Metabolomics

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