1. Biology of Neurodegenerative Diseases BIOS E-108
Harvard Extension School Spring 2013
Lucia Pastorino, Ph.D.
Contact:
office

2. Policy of the course Class Location and Time
Tuesday, 7:40-9:40 pm, Sever Hall 103
Office Hours
Mondays 77 Ave. Louis Pasteur, New Research Building NRB, Longwood Medical Area, Boston. Green Line T stop Longwood. Students who want to meet for office hours have to contact the instructor with an ahead of time.
Sections
Required/mandatory for graduate-credit students, optional for undergraduate-credit students Tuesday, 6:30-7:30 pm. Sections are lead by TAs and are meant to further discuss the topics covered during the previous class, to stimulate discussion about scientific approaches, techniques and methodologies in the field of the molecular and cellular biology of neurodegenerative diseases. A research article inherent to the topic covered in the previous class will be presented by rotating graduate students.

3. Prerequisites
BIOS E-1A, or the equivalent in cell biology and molecular biology; BIOS E-12 or equivalent in molecular biology; BIOS E-16/W or equivalent in cell biology are recommended. These prerequisites indicate the background the students should have to follow this course.
Material for the course:
This course does not use a textbook, but detailed handouts which will be provided by the instructor ahead of time as powerpoint presentations and pdf files uploaded on the course’s website. Students will be notified with an when each class is available to be downloaded.
Website
Assignments, research articles, titles of the reviews relevant to the topics covered during the class (available through Hollis Harvard Library online) and handouts will be posted here ahead of time.

4. Grading Policy:
Exams
There will be two midterm exams and one final exam.
No make-up or re-take exam will be allowed for any of the exams.
Assignments
Both undergraduate and graduate students will submit one assignment by the date of the final exam. The instructor will assign it 3 to 4 weeks from the date due to turn it in.
Performance in Section (only for graduate students)
During section, graduate students will present a research article inherent to the topics covered during the previous class. Graduate students will be evaluated for their overall performance in the section. This will include quality of the paper presentation, level of participation during the section, attendance and punctuality. Special issues related to difficulties in attending the section on time should be discussed with the Instructor and with the TA ahead of time.
 Final grade components:
Undergraduate:
Midterm exam 1: 25%
Midterm exam 2: 25%
Final exam: 30%
Assignment: 20%
The score in all the exams and assignment will be assigned to a maximum of 100 points. The final grade will be calculated as the average between the scores obtained in each exam, assignment and performance in section (this only for graduate students). The cutoffs for the evaluation of the final grade will be calculated at the end of the course and will be different for graduates and undergraduates, as undergraduates will have a larger window to discriminate between the grades.
Graduate:
Midterm exam 1: 20%
Midterm exam 2: 20%
Final exam: 25%
Assignment: 15%
Performance in section: 20%

5. Program of the Lectures
Part 1
January 29th. Introduction to the course. Neurodegenerative diseases: common features and risk factors. Mechanisms of protein oxidation, protein aggregation and cell death (apoptosis). Proteostasis and autophagy. Part 1.
February 5th. Introduction to the course. Neurodegenerative diseases: common features and risk factors. Mechanisms of protein oxidation, protein aggregation and cell death (apoptosis). Proteostasis and autophagy. Part 2.
February 12th. Parkinson’s disease (PD)
Pathological features in PD: Lewy bodies. Molecular mechanisms in PD: role of Parkin1, PINK1, a-synuclein and other factors that lead to Lewy bodies formation and neuronal death. Mitophagy. Genetics of PD: inherited mutations on human genes. Diagnosis and treatment. Part 1.
February 19th. Parkinson’s disease (PD)
Pathological features in PD: Lewy bodies. Molecular mechanisms in PD: role of Parkin1, PINK1, a-synuclein and other factors that lead to Lewy bodies formation and neuronal death. Mitophagy. Genetics of PD: inherited mutations on human genes. Diagnosis and treatment. Part 2.
February 26th. Midterm exam 1

6. Part 2
March 5th. Huntington disease (HD)
Genetic of HD: the triplet repeat expansion disease. Huntingtin in protein aggregation and apoptosis. Animal models. Mechanisms of cell death in HD.
March 12th. Creutzfeldt Jacob disease (CJD)
The prion disease or Transmissible Spongiform Encephalopathy (TSE).
Pathological features: amyloid-like deposit in the brain. Molecular mechanisms in CJD: from cellular prion protein (Prpc) to the misfolded form scrapie (Prpsc). Prion protein intracellular trafficking. Diagnosis of CJD: neuro-imaging techniques. Epidemiology of Prion disease: ovine scrapie and transmission of prions. The vCJD variant. Animal models of CJD.
March 19th. Spring Break
March 26th. Multiple Sclerosis (MS)
Pathological features and molecular mechanisms: inflammatory disease, demyelination. Genetic of MS. Animal models. Diagnosis and treatment: neuro-imaging, biological markers, interferon.
April 2nd. Amyotrophic Lateral Sclerosis (ALS)
Motorneuron Disease: pathological features. Molecular mechanisms: apoptosis, oxidative stress, the protein SOD1 and other factors that induce neuronal death. Genetic of ALS. Animal models. Therapeutic approaches.
April 9th. Midterm exam 2

7. PART 3
April 16th. Alzheimer’s Disease (AD)
Pathological features: b-amyloid plaques and tangles. APP pathology and tau pathology/taupaties. Diagnosis. Biological markers. The amyloid precursor protein APP and the generation of b-amyloid peptide.
April 23rd. Alzheimer’s disease (AD)
Molecular basis of APP pathology: the protein APP, role of the secretases (a, b and g) and cholesterol in AD. b-amyloid peptide: monomers and oligomers function in modulating the neuronal function. Part 1.
April 30th. Alzheimer’s disease (AD)
Molecular basis of APP pathology: the protein APP, role of the secretases (a, b and g) and cholesterol in AD. b-amyloid peptide: monomers and oligomers function in modulating the neuronal function. Part 2. Therapeutic approaches.
May 7th. Alzheimer’s disease (AD).
Tau pathology in AD. Tau hyperphosphorylation, tangle formation and neurodegeneration.
May 14th. Final Exam.

8. Common features and molecular pathways in Neurodegenerative diseases
January 29th 2013
Common features and molecular pathways
in Neurodegenerative diseases

9. Characteristics -Irreversible neuronal death
-No treatment that can revert the disease

10. Degeneration in cortical neurons
Normal
Degenerating
Dead Neuron
Journal of Cerebral Blood Flow & Metabolism (2011) 31, 328–338

11. advantages and disadvantages
Methods of diagnosis:
advantages and disadvantages
-Identification of biological markers: particularly advantageous for early detection. However, for this approach it is crucial to know which are the molecular pathways that become pathologic in the early stages of the disease.
-Behavioural/Neurological tests (PD, ALS, MS) Cognitive tests (AD)
-PET Scan:
Visualization of the damage. Use of radio-labeled molecules reaching brain areas specifically affected in a particular disease. For example L-DOPA, a precursor of Dopamin, is used for PET in Parkinson’s disease; b-amyloid binding molecules are used for PET of Alzheimer’ diseases, etc. However, when the damage can be detected by PET, it might be already too late for therapeutic intervention.
-MRI
X-rays of the all brain, evaluating changes in brain volume in specific areas, phenomena that occur late in the development of the disease.

12. MRI in Alzheimer’s disease (AD)
Normal
Alzheimer’s diseases
MRI
Computer graphic

13. Different imaging techniques could detect different stages of the disease
The example of AD
CurrOpinNeurol 2012, 25:410–420

14. Amyloid-binding molecules are used in PET to follow the progression of amyloid deposition in AD

15. Radio-labeled molecules can be used in PET
to study biological mechanisms affected in a disease
Potential for the development of imaging techniques for early diagnosis in AD
CurrOpinNeurol 2012, 25:410–420

16. The example of amyloid-binding molecules in AD
Radio-labeled molecules to assess the efficacy of a therapeutic approach
The example of amyloid-binding molecules in AD
APOEe4 AD
CurrOpinNeurol 2012, 25:410–420

17. PET scan in Parkinsons’s disease (PD)
L-DOPA treatment

18. PET analysis to follow the disease progression also in PD

19. PET analysis to evaluate neuronal integrity and functionality
The example of PD

20. MRI analysis in Huntington’s disease (HD)
Nuclei
Cortex
Cerebellum
Huntington’s disease
Normal

21. Creutzfeldt-Jacob Disease (Mad cow disease, BSE or Prion disease)

22. MRI evidences progressive cortical degeneration in sporadic CJD
July
November

23. MRI in Amytrophic Lateral Sclerosis (ALS)
Normal
ALS

24. MRI in Multiple Sclerosis (MS)
Image courtesy of Siemens Medical Solutions.

25. The development of early and specific diagnostic approaches is crucial to impact the success of a therapy for neurodegenerative diseases
Study of the BIOLOGY of these diseases to unravel the mechanisms that are responsible for the diseases and could be targeted for diagnosis and therapy

26. Common factors in neurodegenerative phenomena
1-Deposition of fibrillar proteinacious material in the intracellular or extracellular matrix
2- Mitochondrial dysfunction, increased oxidative stress and production of ROS
3- Increased apoptosis
4- Decreased proteasomal degradation due to proteasome impairment (ubiquitin is present in all the lesions)
5-Decreased autophagy and lysosomal degradation of proteins
6-Excitotoxicity
7-Alterations in the integrity of the cell membrane: implications for altered levels of intracellular cholesterol

27. PROTEIN MISFOLDING, AGGREGATION AND NEURODEGENERATION

28. Deposition of fibrillar proteinacious material
in the intracellular or extracellular matrix
Amyloid: amyloid fibrils are filamentous, hydrophobic structures, width ~10nm, length between mM. Ribbon-like b-sheets motifs are formed by b-strands and b-turns. These kind of fibrils are common to different neurodegenerative diseases, from Alzheimer’s to Huntington’s disease.
NH2
COOH
Ross CA, Poirier MA. Nat Med Jul;10 Suppl:S10-7. Review.

29. How proteins aggregate and form amyloid/insoluble fibrils
Several factors may induce
protein aggregation:
1-Protein oxidation (a-synuclein in PD)
2-Metal chelation (Prion disease and AD)
3-Specific protein cleavage (AD)
4-Inefficient protein degradation of
b-sheet proteins/proteasome impairment
(PD, AD, ALS, Prion Disease, HD)
5-Change in intracellular pH (AD)
Early
Late
Ross CA, Poirier MA. Nat Med Jul;10 Suppl:S10-7. Review.

30. Different hypotheses in the different neurodegenerative diseases
Aggregates
Toxic or protective? 100,000,000 $$$$$ question!!!
Different hypotheses in the different neurodegenerative diseases
AD: plaques, soluble Ab, correlate with progression of the disease. However, Ab oligomers seem to be the more toxic species.
PD: inclusion bodies do not follow the progression of the disease.
HD: aggregates may be present ONLY in surviving neurons.

31. Representation of structural components of protein structure

32. Protein folding: a folding funnel to change the structure and the energy of proteins. Only folded, native proteins are functionally active.
Unfolded states: characterized by higher degree of conformational entropy and free energy than native states. This leads to “unstableness” of proteins when in the unfolded state. As the folding funnel proceeds, conformational entropy decreases as proteins have lower number of conformational states, as well as the free energy decreases. The minimum of the energy level of a protein is reached when it’s in its native/folded state.

33. Thermodynamics of protein folding/misfolding
“The energy of the different conformations decreases with the development of organized, native-like proteins”.

34. Protein misfolding
A common and continuously happening phenomenon in the life of a protein
Denaturation: the process by which the native structure of proteins is disrupted. It results in the unfolding of the protein, which then loses the state of lower energy level.
The protein is then in a highly disorganized structure and tends to form aggregates to reduce the state of high energy, in a word to stabilize.

35. Steps that lead to formation of aggregates
Unfolding
Nucleation: when proteins attach REVERSIBLY to a growing core.
Aggregation: when proteins attach IRREVERSIBLY to the core forming larger aggregates. Aggregation can be triggered by hydrophobic residues in the sequence of the protein and by b-sheet structure. Amyloid is one of the forms of protein aggregates that occurs in nature, is very stable but its formation can be still reversible. This is not true, unfortunately, for most of the protein aggregates that are responsible of neurodegenerative diseases.

36. Factors that might influence protein denaturation and misfolding
-Mutations
-Glucose levels
-Oxidation
-changes in the physiological pH
-Binding to ions
-Levels/concentration of monomers: if low the protein tends not to aggregate, if high the protein tends to form aggregates

37. Schematic representation of protein misfolding

38. Summary of protein folding diseases

39. Both mechanisms contribute to the development of pathologic conditions
When in the form of aggregates, proteins can lose their physiological function and gain a toxic function
Both mechanisms contribute to the development of pathologic conditions
Winklhofer et al.,

40. How the cell tries to “cope” with the presence of aggregates

41. Can the cell effectively “win” over the presence of the aggregates?
N O T A L W A Y S
Aggregates will eventually form lesions in the brain or in neuronal cells, causing the disease.

42. Deposition of fibrillar proteinacious material in Alzheimer’s disease
Alzheimer’s disease: characterized by extracellular depositions, the b-amyloid plaque, and intracellular depositions, the Neurofibrillary Tangles (NFT) comprised of Paired Helical Filaments (PHF), aggregates of hyperphosphorylated protein tau.
Bossy-Wetzel E, et al., Nat Med Jul;10 Suppl:S2-9. Review.

43. Origin of b-amyloid and plaques:
Amyloid Precursor protein APP
APP
NH2
TMD
Ab Oligomers Fibrils Plaques
Ab levels as well as number and size of plaques increase with the progression of the disease
Origin of tau
Microtubule-associated protein that regulates cytoskeleton structure. When highly phosphorylated, tau is sequestered into PHF, and causes disruption of microtubules, leading to cell death.
ptau
PHF
Paired Helical Filaments
NFTs
Neurofibrillary tangles

44. Deposition of fibrillar proteinacious material in Parkinson’s disease
Parkinson’s disease: characterized by dopaminergic neuronal loss and by intracellular depositions, the Lewy bodies, comprised of a-synuclein and ubiquitin, as the major components. Other components are proteasome and cytoskeletal proteins and other proteins that interact with a-synuclein.
Bossy-Wetzel E, et al., Nat Med Jul;10 Suppl:S2-9. Review.

45. How a-synuclein is involved in Lewy bodies formation
Oxidation of Dopamine and subsequent interaction with a-synuclein or with Cys residues on different substrates: first step to the formation of
protofibrils O2
a-synuclein
on Tyr, Met or Lys
Long-lived protofibrillar intermediate
+ H2O2 + O2-

46. Deposition of fibrillar proteinacious material in Huntington’s disease
Huntington’s disease: a progressive neurodegenerative disease characterized by CAG repeats causing glutamine expansion motifs (polyQ) in the N-terminal region of the protein huntingtin. Onset of the disease inversely correlates with the number of CAG repeats. In the HD, huntingtin forms intracellular inclusion bodies, containing material of cellular origin.
Ross CA, Poirier MA. Nat Med Jul;10 Suppl:S10-7. Review.

47. Deposition of fibrillar proteinacious material
in Creutzfeldt-Jakob’s disease (Prion’s disease)
Prion’s disease: neurodegenerative disorder caused by prions, via environmental stimuli or genetic mutations. Alterations in the prion protein lead to both intracellular and extracellular accumulation of amyloid aggregates, plaques, similar to those characteristic of AD, and positive to prion protein staining. Probably, replication and accumulation of the protease insensitive PrPsc results in fibril formation and plaque deposition.
Alzheimer’s
Creutzfeldt-Jakob’s

48. Pathogenic mechanism of prion protein
Prion: the transmissible principle that causes Transmissible Spongiform Encephalopaties (TSE), also called Mad Cow disease or Prion’s disease or Creutzfeldt-Jakob disease
It is caused by the replication of a protease-resistant modified form of the cellular prion protein.
Cellular prion protein PrPc is converted to Scrapie prion protein PrPsc. The infectious principle may consist of i) PrPsc subspecies, ii) unstable intermediate of PrPc, iii) or a complex with PrPsc and other host-derived proteins

49. Deposition of fibrillar proteinacious material
in Amyotrophic Lateral Sclerosis (ALS)
ALS: a progressive fatal disease caused by the degeneration of lower motor neurons in the lateral horn of the spinal cord and the upper motor neurons of the cortex. Insoluble cytoplasmic inclusions are observed in the brain of ALS patients. These inclusions are composed also of SOD1 protein and ubiquitin.
Ross CA, Poirier MA. Nat Med Jul;10 Suppl:S10-7. Review.

50. In conclusions:
Most of the neurodegenerative diseases are characterized by intracellular or extracellular deposition of insoluble material.
Whether this is a cause or a consequence of the diseases is not known yet.
It is speculated that the early species in this process might be most toxic, by being involved in abnormal interactions with other cellular proteins.
However, the fact that all these diseases are characterized by the same common factors, and the observation that inherited forms of these diseases cause a massive increase in the production of b-sheet related proteins lead to hypothesize that these b-sheet proteins and the subsequent formation of the insoluble lesions may be upstream the cascade of events that lead to neurodegeneration.

52. Common cellular pathways involved in the formation of insoluble aggregates
Many of them are related to aging, or can be triggered by particular toxins or by loss-of-function or gain-of-function protein mutants.
1- Mitochondrial dysfunction and increased oxidative stress, increased production of ROS
2-Increased apoptosis
3-Decreased chaperones and proteasomal activity
4-Alterations in the integrity of the cell membrane: implications for altered levels of intracellular cholesterol

53. Mitochondrial dysfunction and oxidative stress

54. The neuron
The Synapse

55. The mitochondrion

56. Mitochondria Dysfunction
Hypoxic
Damaged
Normal
Pharmaceuticals 2010, 3(1),

57. Mitochondrial dynamics in neurodegeneration
Physiologic Fission and Fusion
Balance or disease
Itoh et al., Trends in Cell Biology 2012

58. Mitochondrial activity
The role of the mitochondria is to produce ATP through a process called Oxidative Phosphorylation. This process occurs thanks to a complex system of redox reactions that moves H+ and e- between the inner membrane and the inter space of the mitochondrion, generating H+ gradient that moves the reactions.
H2O is a product of this reaction
oxidase
O2 + e O2-. Superoxide ion
dismutase
O2-. + e- + 2H H2O2 Hydrogen peroxide
catalase
H2O2 + e- + H OH. + H2O Hydroxyl radical
OH. + e- + H H2O
This is the last step, last reaction of the cellular respiration upon the action of cytochrome c oxidase, aka Complex IV.

59. Cellular Respiration
1- This process occurs thank to a H+ gradient generated through the transport of electrons between the two sides of the inner membrane. Many proteins are involved in this process, which is based on a chain of redox reactions. Among these, the NADH dehydrogenase, also called Complex I, is a proton pump, crucially involved in the transport of 4 H+, creating a strong H+ gradient. Lack or loss of function of Complex I leads to e- leakage in the intermembrane space, and in the cytosol, initiating the process that leads to the formation of Reactive Oxygen Species, ROS.
2- e- are transported to proteins thank to e- transporters like Fe-S and cytochrome c, involved in different moments of the mitochondrial respiration. The succinate dehydrogenase, also called Complex II, moves e- from intermediate species, and cytochrome bc complex, also called Complex III, move e- to the cytochrome c and pumps back 4 H+ from the inter-space to the inner-space, creating a strong H+ gradient.
3- Cytochrome c oxidase, also called Complex IV, removes the e- from cytochrome c molecules and transfer them to molecular oxygen O2, creating H2O. It also moves 4 H+ back out of the inner space of the mitochondrion, re-initiating the H+ gradient.

61. O2-. Superoxide ion and e-
During synthesis of molecules of water, numerous Reactive Oxygen Species (ROS) are generated
mitochondrial deficit related to either aging or protein dysfunction may lead to leakage of reactive species out of the mitochondrion into the cytosol through Voltage Dependent Anion Channel (VDAC), in particular
O2-. Superoxide ion and e-
This phenomenon increases oxidative stress and promotes the generation of other ROS within the cell, being toxic for the cell.

62. Loss of function, impaired cellular activity and death
How oxidative stress is toxic?
By promoting oxidation of
1- proteins
2-lipids
3-cathecolamine (adrenaline, noradrenaline, dopamine)
4-DNA
Loss of function, impaired cellular activity and death

63. Antioxidant proteins and enzymes
Superoxide Dismutase SOD: dismutes ion supeeroxide O2-. to hydrogen peroxide H2O2
- 3 different types, SOD1, SOD2, SOD3 localized in different intracellular compartments
-SOD1 (CuZnSOD): localized mainly in cytosol and nucleus and in the intermembrane space of the mitochondria. Abundantly expressed ubiquitously, in the brain, and high levels of expression in the spinal cord. More than 100 mutations are found in genetic ALS, motor neuron disease in which SOD1 shows a gain of toxic function (SOD1 KO mice have no motorneuron degeneration)
-SOD2 (MnSOD): essential for mitochondrial integrity. When nitrosylated by peroxinitrate, SOD2 loses its function.
-SOD3: low expression profile in brain.