1. Molecular basis of disease

Question 1

What does pathos mean?

Answer 1

Pathos= Suffering

Question 2

Define pathology

Answer 2

• Pathology: Study of different aspects of disease, including:

1. etiology
2. development
3. structural & functional changes in cells/tissues/organs

Question 3

Define etiology

Answer 3

• Etiology:
  
  1. Study of underlying causes & modifying factors
  2. WHY disease arises?

Many factors single or combined (inherited genetic susceptibility & various environmental triggers).

Question 4

Define pathogenesis

Answer 4

• Pathogenesis:
  
  1. Study of the steps in the development of a disease.
  2. ​How a disease develops?
     
     • Study how etiologic factors trigger cellular & molecular changes that give rise to the specific functional & structural abnormalities characterizing the disease.

Question 5

Why understanding disease development is so important?

Answer 5

Understanding disease development is the

basis for accurate diagnosis & rational treatments.

Question 6

What are the levels that disease operates in?

Answer 6

1. Molecular
2. Cellular/Tissue/Organ
3. Organism

Question 7

What do you know about the molecular level of the disease?

Answer 7

• Molecular:
  
  1. Change at the level of DNA, RNA, & protein (Mutation of genes, changes at the transcriptional, translational or post translational levels leading to changes in proteins quality, quantity or function).
  2. Changes at DNA level will be translated into abnormalities in cells, tissues, & organs.

Question 8

What do you know about the Cellular/Tissue/Organ level of disease?

Answer 8

• Cellular/Tissue/organ: Gross or microscopic change of:
  
  1. structure
  2. organization
  3. function of cells & tissues (Morphology)
  4. biochemical alterations in body fluids
     
     • blood
     • urine

Question 9

What do you know about the organism level of disease?

Answer 9

Clinical expression (signs & symptoms)

Question 10

Define Molecular Pathology

Answer 10

• Molecular Pathology:
  
  1. Study of diseases at molecular level.
  2. Study of changes in gene structure or expression underlying certain diseases.
     
     • Gene abnormalities affect the structure & function of proteins:
       
       1. → disrupts cellular homeostasis
       2. → contributes to disease development
     • Gene abnormalities occur in inherited & acquired human diseases.
       (genetic changes ≠ hereditary)

1. Genetic changes in germ cells are transmitted to the progeny & give rise to inherited diseases (Hereditary disorders); these changes are transmitted through generations (familial). The term congenital simply implies “present at birth”.
2. Genetic changes in somatic cells are not transmitted to the progeny but are responsible of the causation of diseases.

Question 11

List the 2 types of genetic abnormalities.

Answer 11

1. DNA changes
2. Epigenetic changes

Question 12

What do you know about the

two types of genetic abnormalities?

(DNA Changes)

Answer 12

• DNA changes:

1. • Mutation: (permanent changes in the DNA sequence).
2. • Chromosomal alterations:

• Amplifications
• Deletions
• Translocations

Question 13

What do you know about the

two types of genetic abnormalities?

(Epigenetic changes)

Answer 13

• Epigenetic changes: Modulation of gene/protein expression in the absence of alterations in DNA sequence or structure.
  
  1. DNA methylation of cytosine residues at the gene promoters: -heavily methylated promoters become inaccessible to RNA polymerase, leading to transcriptional silencing.
  2. Histone modifications: Methylation & acetylation
     
     • affect 2* & 3* DNA structures
     • regulate gene transcription
  3. Non-coding RNAs: miRNA & lncRNA
     
     • ​miRNAs: do not encode proteins but inhibit the translation of target mRNAs into their corresponding proteins.
     • lncRNAs: modulate gene expression by binding to regions of chromatin & restricting access of RNA polymerase to the coding genes.
  4. Protein modification:
     
     • Folding
     • Phosphorylation

Question 14

Tell me more about epigenetic changes.

Answer 14

• There’s a change in transcription or translation of protein expression, resulting in:

1. abnormalities of protein quantity/quality
2. abnormalities in cells/tissues/organs

Question 15

Chromosomal changes in diseases

Answer 15

1. Deletion
2. Duplication
3. Inversion
4. Translocation
5. Aneuploidy

Question 16

Explain chromosomal changes in diseases

Answer 16

1. Deletion:
   
   • ​loss of a chromosomal fragment, which results in gene loss or deficiency.
2. Duplication:
   
   • Create fusion proteins or amplification of genes. ​
3. Inversion:
   
   • ​a segment of chromosome is reversed end by end.
4. Translocation:
   
   • ​exchange of two chromosome segments.
   • generation of novel fusion proteins with
     altered gene expression.
5. Aneuploidy:
   
   • ​​Whole chromosome gain or loss.

Question 17

Epigenetic

Answer 17

1. DNA Methylation:
   
   • “Silences” genes so they can’t be expressed.
2. Histone Modification:
   
   • “Alters” the expression of DNA wrapped around it.
3. MicroRNA:
   
   • Binds to mRNA & then
   • Blocks protein assembly
4. Protein Phosphorelation:
   
   • “Modulates” protein activity

Question 18

True or False: acetylation & deacetylation of histones change gene expression.

Answer 18

• True.
• Acetylation & Deacetylation of histones change gene expression.​

Question 19

What do you know about MicroRNA?

Answer 19

• MicroRNA
  
  1. are being involved in many diseases now.
  2. are small non-coding RNA fragments.
  3. just regulatory
  4. no protein expression
  5. bind to the mRNA
  6. block protein translation

Question 20

What does Molecular Pathogenesis starts & ends with?

Answer 20

• Starts ➡️ molecular pathogenesis
• Ends ➡️ clinical presentation

Question 21

Sickle cell disease (SCD) - abnormality of hemoglobin

Answer 21

• Point mutation: CTC in normal β-globin (βA) chain is changed to CAC, leading to the change of the sixth amino acid of the normal β- hemoglobin (βA) chain (glutamine) to another amino acid (valine).
• This change converts the β-globin (βA) chain to sickle β-globin (βS).
• Remember: Hemoglobin consists of two chains (α&β), and the point mutation appears in the β.

Question 22

Change of hemoglobin structure and function (SCD)

Answer 22

• The point mutation valine for glutamic acid at the sixth amino acid in the beta-globin chain generates a structurally abnormal molecule (hemoglobin S) that polymerizes under conditions of deoxygenation.
• Polymerization of hemoglobin S
  
  1. transforms the cytoplasm into a rigid filamentous gel
  2. leads to the formation of less deformable sickled erythrocytes
• The rigidity of sickled erythrocytes:
  
  1. results in obstruction of the microcirculation
  2. with subsequent tissue hypoxia & ischemic injury in many organs
• The inflexible nature of sickle cells also renders them susceptible to destruction (hemolysis) during circulation through the spleen.
• [That’s why those people are anemic]
• The two primary manifestations of sickle cell disease are
  
  1. Recurrent ischemic events
  2. Hemolytic anemia
• Sickle cell anemia is the most common familial hemolytic anemia in the world.

Question 23

List the SCD clinical manifestations.

Answer 23

1. Normally, RBCs are round (concave) containing hemoglobin that carry O2.
2. People with SCD don’t have the normal HbA, instead they have the abnormal HbS, and due to the change in the AA into Valine, there will be a change in the folding.
3. The abnormal HbS:
   
   • tend to polymerize
   • form rigid filaments
   • are continuously oxygenated & deoxygenated
4. When they become rigid, they change the structure of the RBC to the sickle shape.
5. The sickling problem destroys the rearrangement of the RBC’s membrane (the membrane is damaged), so when circulating in the body especially in small BV, they attach to the BV & damage its wall (cuz they have pointy ends & they’re no longer flexible due to the rigid Hb).
6. Coagulation & Thrombosis are triggered (clots blocking blood supply)
   
   • (that’s why it’s a davestating disease that affect all body parts)

Question 24

Molecular pathogenesis

Chronic myeloid leukemia (CML)

Answer 24

Question 25

Molecular pathogenesis - **CML**

Answer 25

* **CML**: is associated with the presence of a BCR-ABL fusion gene. * **The _BCR-ABL_ gene is the product of a _balanced (9;22) translocation (Philadelphia chromosome)_** that moves ABL from chromosome 9 to a position on chromosome 22 adjacent to BCR. * Normal myeloid progenitors depend on: 1. ***_signals_*** generated by hematopoietic *growth factors* 2. and their ***_receptors_*** for growth & survival * **The BCR-ABL fusion protein generates constitutive signals that mimic the effects of growth factor receptor activation.** *[* *It'll have a continuous tyrosine kinase activity (phosphorylation & activation of cell signaling)]* * This constitutive growth signal enables _CML cells to grow & reproduce out of control_. * **This translocation is important for _diagnosis_** since its is available in most CML patients. * **It is important for therapy** because of the availability of **tyrosine kinase inhibitors. Treatment by tyrosine kinase inhibitor (Imatinib) achieves long term survival.**

Question 26

No need to know everything in that pic

Answer 26

* _It is just to show you that the:_ 1. **Fusion protein** is activating multiple signaling pathways that all end up in cell proliferation cuz cancer or leukemia is an abnormality of growth, so there'll be *uncontrolled cell growth & proliferation*. 2. **BCR-ABL** has a: * conti. **tyrosine activity** = conti. **phosphorylation** = conti. **proliferation** of many pathways

Question 27

Targeting signaling pathways of **BCR-ABL**

Answer 27

The **BCR-ABL** new protein ***activates*** many signaling pathways involved in transformation of _hematopoietic cells_ to _cancer cells_.

Question 28

What do you know about Acute promyelocytic leukemia (**PML**)?

Answer 28

* PML is the most aggressive type of leukemia * PML is caused by a **balanced reciprocal translocation** between chromosomes **15&17** [t(15;17)(q21;q21)]. * **Translocation (15;17)** in PML, results in the fusion of the retinoic acid receptor α **_(RARA) gene & PML gene_**. The **PML/RARα** fusion protein blocks myeloid differentiation at the promyelocytic stage. This disease is the _most malignant form of acute leukemia_. * **PML with t(15;17) is _treated with all-trans retinoic acid (ATRA)_** that binds to the fusion protein & antagonizes its effect. 1. **ATRA** causes the neoplastic promyelocytes to rapidly differentiate into neutrophils. Because neutrophils die after an average lifespan of 6 hours 2. **ATRA** treatment rapidly clears the tumor 3. **AMLs** without translocations involving (RARA) do not respond to **ATRA** * In the past, **cytotoxic chemotherapy** was the primary modality for treatment of **APL**. Only 35% of the patients were cured. **With ATRA treatment the 5-year disease-free survival improved to 74%**.

Question 29

* Name me one **multiple genes abnormalities** disease? * Name me one **multifactorial disease**?

Answer 29

Cancer

Question 30

Name me a **cell signaling disorder**.

Answer 30

Diabetes

Question 31

What do you know about **insulin**?

Answer 31

* It's a **very active molecule** & is responsible for many things including **diabetes**. * It _**binds** to its receptor_ & _**activates** many signaling pathways_.

Question 32

What do you know about **GLUT-4 Vesicle**?

Answer 32

1. It _allows glucose to **pass** & be **stored** inside_. 2. ​So, when there's no insulin or it's present but not functional, * GLUT- 4 won't pass glucose inside to be stored or used in cellular respiration; therefore, glucose level will increase in the blood → hyperglycemia

Question 33

**IMPORTANT** graph about **Cell signaling disorder - Diabetes**

Answer 33

Question 34

Pathogenesis- diabetes mellitus

Answer 34

* **_Type 1 diabetes_ is an autoimmune disease** caused by progressive **destruction** of **islet beta cells leading to absolute insulin deficiency**. Pathogenesis is linked to genes involved in immune tolerance and regulation (HLA, CTLA4). * **_Type 2 diabetes_ is caused by insulin resistance** & beta cell dysfunction resulting in **relative insulin deficiency**. Autoimmunity is not involved. * **_Insulin resistance_** is defined as the failure of target tissues to respond normally to insulin. This is mainly caused by reduced phosphorylation dependent activation of the insulin receptor & its downstream components, which **attenuate signal transduction**. * Since **insulin is a major anabolic hormone** in the body, lack of functional insulin results in a catabolic state that affects not only glucose metabolism but also fat & protein metabolism. **Storage of glucose is diminished resulting in _hyperglycemia_**. * **Obesity** has an important relationship with **insulin resistance**. Cytokines released from adipose tissues (**adipocytokines) & other molecules such as FFAs & [PPARγ] receptor** contribute to insulin resistance by affecting the activity of key **insulin-signaling proteins**. → causing **hyperglycemia**

Question 35

PPARγ

Answer 35

* PPARγ: **P**eroxisomes **P**roliferator-**A**ctivated **R**eceptor **Gamma** 1. Nowadays, there are drugs that target these _receptors_. 2. Those _receptors_ contribute to abnormalities in cell *signaling* & of insulin *resistance*.

Question 36

Pathogenesis - diabetes mellitus What **converge to cause insulin resistance**?

Answer 36

* What converge to cause **insulin resistance**? 1. **Genetic predisposition** (diabetogenic & obesity-related genes) 2. **Environmental influences** (obesity & sedentary life style) * What does **Free fatty acids** do? 1. cause **_beta cell dysfunction_** 2. induce **_insulin resistance_** in target tissues 3. induce the **_secretion of pro-inflammatory cytokines_** that cause more damage

Question 37

Activation of Cell signaling pathways & Transcription Factors

Answer 37

1. **Hyperglycemia** alter gene expression by epigenetic mechanisms leading to diabetes-associated complications. 2. **Hyperglycemia** induces metabolic changes including: * activation of the mitogen activated protein kinase (MAPK) pathway * formation of **AGE** - advanced glycation end products * oxidative stress 3. The resulting **signaling pathways activation** & **nuclear translocation** of transcription factors influences gene expression leading to: * clinical presentation * complications of the disease 4. ​The **long-term complications of diabetes** affect mainly: * blood vessels * kidneys * nerves * eyes

Question 38

**MAP Kinase** signaling pathway is responsible for?

Answer 38

* Cell Growth * Gene Expression

Question 39

**PI-3K** signaling pathway is responsible for?

Answer 39

1. **Synthesis** of: * lipids * proteins * glycogens 2. **Cell survival: Proliferation**

Question 40

What do you know about **Cystic fibrosis**?

Answer 40

* **_Cystic Fibrosis_**: is an autosomal (recessive) disease caused by mutations in the CF Transmembrane Conductance Regulator (CFTR) gene. → results in abnormal folding in the protein expressed by this gene * **_CFTR_**: is an anion channel that regulates the transmembrane ion transport. CFTR → Cystic Fibrosis Transporter Regulator * **CFTR gene mutation causes defective electrolyte transport (chloride ion)** in epithelial cells which affects: 1. salt absorption 2. fluid absorption 3. anion-mediated fluid secretion * This abnormality _results in_ a complex multisystem disease & **occurs in**: 1. respiratory tract 2. pancreas 3. intestine 4. liver 5. exocrine glands * The pathogenesis of respiratory & intestinal complications in CF results from the **low-volume of surface fluid layer**. In the lungs, this dehydration leads to: 1. defective mucociliary action 2. accumulation of concentrated & viscid secretions that obstruct the air passages & predispose to recurrent pulmonary infections. * **Bronchial mucous plugging** facilitates colonization by microorganisms. **Lung infection** is the leading cause of morbidity and mortality in CF. * **Morbidity** is mainly associated with: 1. infections 2. exacerbated inflammatory response causing tissue damage

Question 41

Graph about "**Cystic Fibrosis**"

Answer 41

1. CFTR defect in the **sweat duct** causes **increased** chloride & sodium _concentration_ in sweat * (increased sweat chloride concentration is a diagnostic criteria). 2. ​CFTR defect in the **lung** causes **decreased** chloride _secretion_ & **increased** sodium + water _reabsorption_ in the airways, leading to: * dehydration of the mucus layer coating epithelial cells * defective mucociliary action * mucous plugging

Question 42

Lungs of a **"Cystic Fibrosis"** patient (Graph)

Answer 42

* Lungs of a CF patient show **mucous plugging & dilation** of the tracheobronchial tree. * The **pulmonary parenchyma is consolidated by pneumonia** (greenish discoloration due to _bacterial infection_).

Question 43

**Pancreatic abnormalities** in CF patient. | (graph)

Answer 43

* Pancreatic abnormalities occur in most **85% to 90%** of CF patients. * ​The _ducts_ are dilated & plugged with eosinophilic mucin, and the _parenchymal glands_ are atrophic & **replaced** by **fibrous tissue**.

Question 44

Mechanisms of disease - viruses

Answer 44

Question 45

Molecular Medicine | (Read Slide)

Answer 45

Question 46

Biomarkers- Breast cancer | (A)

Answer 46

Question 47

Biomarkers- Breast cancer | (B)

Answer 47