Our body, including our brain, is constantly changing. Within each of the 37 trillion cells [1] there is a constant dynamic activity. A relentlessly hive of activity maintaining, coordinating and enhancing functioning. All of this activity is based on four major molecules—macromolecules—essential for all known forms of life. These are fats, carbohydrates, nucleic acids and proteins.
Fats and carbohydrates are the source of all energy for the body, while nucleic acids (meaning from the nucleus) and proteins (meaning primary or first) constitute the components of the body.
Nucleic acids hold our genetic material our DNA—Deoxyribonucleic Acid—whose sole purpose is to make and coordinate the production of proteins. DNA is stored in the nucleus while a replica of this DNA called RNA—Ribonucleic Acid—is a working copy of the many parts—called genes—of the DNA. The sole purpose of the DNA and RNA is to hold information that make up all the proteins that our body needs.
RNAs are thought to be earlier versions of DNA, our genetic templates. At some point the strand of information that contains the four nucleotides—chemical codes—must have combined with another RNA strand to form a DNA helix, a more stable and accurate structure. This structure is more stable because each nucleotide, piece of information, is matched on the other side of the double helix—like double entry book keeping, resulting in less chance of making mistakes. This robustness is a necessary feature if you aim to become immortal, as genes are.
Because the DNA is a stable structure, it must however be unwound and transcribed to form copies of RNAs which can then be translated to proteins. Proteins—which are made up of amino acids—function as enzymes, hormones and body tissues. The importance of proteins is expressed by the recent ambition to map all human proteins in the Human Proteome Project. Just because we mapped the genome does not mean very much if you do not know what those codes mean. Proteins are the deciphering tool.
As there are more proteins than genes, the aim to map all proteins is ambitious and much larger than mapping the genome. It is also very complex. The proteome has two additional levels of complexity. While the genome is defined by the sequence of four nucleotides, the proteome is determined by the same genome but then involving the permutations of 20 different amino acids. Each amino acid is defined by a set of three nucleotides on the RNA—a codon. A chain of amino acid is defined as a protein, having varying sequence and lengths. Each variation defines the physical structure, and the structure determines its function. This complexity resides within nearly each of our 37 trillion cells. Cells within specific organs produce specific proteins, although all cells have the capacity to synthesize all proteins.
In our body, most of our cells have a nucleus and a membrane around it—Eukaryotic Cell as apposed to Prokaryotic Cell. Within these eukaryotic cells is a complex factory of activity. Not only have eukaryotic cells evolved to include alien small organs— organelle such as mitochondria which have their own genetic material separate from the cell’s DNA—each cell has a copy of all of our genetic material, our body’s complete template. How our genes virtually replace or maintain each and every cell as we live, is one of the most intriguing enigmas in science.
The DNA is like a musical record that is being played constantly. Instead of sound, the player—an enzyme, another protein, called ribozyme—makes negative copies of one strand of the DNA. Through a process known as transcription—it produces a negative copy called the RNA. As the DNA is transcribed, a strand of RNA is created within the nucleus of the cell. This RNA strand migrates out of the nucleus wall into the cytoplasm, the main part of the cell. This small negative replica is composed of a string of nucleotides which are “read” three nucleotides at a time—these keys are called codons. To produce protein, the DNA transcribes three types of RNA.
One part defines the type of protein to build, this is the messenger RNA—mRNA. The second RNA strand is a transfer RNA—tRNA—which attaches to a specific amino acid. Like a shopping trolley, it selects individual amino acids as the building blocks of protein. The final structure —rRNA—is the two-part machine called a ribosome, that builds the protein itself. Ribosomes combine the messenger and the transfer RNA according to the code, the codon. As it matches them together it then steals their amino acids. Ribosomes join one amino acid with the subsequent amino acid, creating chains of amino acids. This is the birth of a protein.
A protein starts life in the cell as a long chain of, on average, 300 of these amino acids. There are 20 different types of amino acids—nine are called essential that we need to get from our diet and cannot be manufactured. The sequence and number of amino acids determines how the protein chain will fold upon itself once completed. Some proteins provide structure, others transport molecules, while others help cells to divide and grow. The function of a protein is dependent on their folding structure. It is an origami dictated by the sequences of amino acids and the length of the chain.[2]
Back to Alzheimer’s disease
The Amyloid Cascade hypothesis was first articulated in 1992 [3] and became enshrined in the guidelines published by the National Institute on Aging and Alzheimer’s Association (Jack et al., 2011). The amyloid cascade hypothesis posits that the deposition of the amyloid-β peptide in the brain is a crucial step that ultimately leads to Alzheimer's disease. Amyloid-β peptide is a small protein called a beta (β) that has misfolded and became an amyloid. [4] Amyloid refers to how small proteins interact together by combining and forming a solid insoluble mass—they become hydrophobic, shy of water, because of how they fold. This type of interaction has its own designation as a disease called amyloidosis. These misfolded proteins combine together to create plaques of a million or so amyloid beta molecules. According to the National Institute on Aging and Alzheimer’s Association, these amyloid beta molecules grow until they interfere with the normal functioning of the brain. This is the cause of Alzheimer’s disease. And they have tested and substantiated this theory with mice models. But there is a problem.
The problem
The Amyloid Cascade hypothesis has not been supported by the data on humans. To date most of the treatments tested in human clinical trials are amyloid-β-based drugs, including those that remove amyloid-β. Despite the success of these drugs in removing the plaques from the brains of Alzheimer’s disease patients, the effect on behavior and thinking was negative. [5] Patients who had the misfolded proteins removes chemically did worse in tests than before the intervention. [6]
It seems that the clinical expression, the behavior, is not solely determined by increases in misfolded protein. A longitudinal study reported that eight percent of participants who behaved and acted free from dementia—when they died and had their brain examined—were found to have the most severe neuropathology. [7] Despite having abundant and severe disease—neurofibrillary tangles and senile plaques—they had normal functioning.
Approximately half of clinically demented oldest-old have insufficient neuropathology to account for their dementia. [8] While approximately thirty to fifty percent of older adults without dementia meet the neuropathological criteria for Alzheimer’s disease. [9]
The reality
The story of errors in making proteins which end up in the brain, as the cause of neurological disease, is incomplete. The repetitive story about the biology is also intentionally simplistic. In reality, science is still too naïve to understand the molecular biology of cells and therefore the biology of Alzheimer’s disease. Although geneticists play with genes and create amazing results, we still do not understand the fundamental nature of biology. And we cannot understand the biology of Alzheimer’s disease before we can understand the molecular biology of cells.
Scientists make simplified determination despite knowing only a very small proportion of the biology of cell functioning. We might have traced most of the dance moves, but we still do not know the music. That symphony that all our cells are all dancing to remains mute. With a complex choreography of steps there remains new ones to identify. We are missing the poetry because of the words, and we are missing the music because of the steps.
Each DNA sequence that contains instructions to make proteins is known as a gene. There are two variants of the same type of gene called alleles. Consider these as the paired dancers, with one being “dominant” over the other. There might be many (more than two) alleles for the same gene. How alleles communicate each other’s protein is unknown, especially how they communicate with alleles from a different gene. Unless we know the music of the dance, all that we can see is that there is communication and we can predict the outcome using a mathematical model. [10] However, prediction does not mean that we understand the mechanism.
Another perplexity is that the size of a gene may vary greatly, ranging from about 1,000 individual nucleotides (bases) to 1 million bases. Genes that make protein—defined by unique start and stop codons—only make up about 1 percent of the DNA sequence. The rest is—we think—involved in the regulation. Around 99 percent of all genetic material is devoted to coordination.
Coordination of protein production—-how and how much of a protein is made; distribution, equilibrium and maintenance, including protection from viruses, bacteria, aberrant cells and malformations. This is the dance music and it seems that DNA is more invested in the music than the dance.
Regulation is the music of this dance that we see in protein synthesis. The transcription—DNA to RNA—and translation—RNA to protein synthesis—involves constant feedback, ensuring an equilibrium within the whole body. So far we are still mapping steps in the dance. It is a mystery how DNA self-polices itself, but it does. It edits code and monitors outcomes. [11] For example in gene splicing, the initial messenger RNA is edited by removing introns--and joining exons together. And it does this as a dance. First it identifies the beginning and the end of the intron by its nucleotides. Small proteins (snRNPs), bind to these ends of the intron and forms a loop. The loop is then removed leaving the two remaining exons to link together. In addition to this method, there are alternate splicing methods which create many different variations from the same gene. In 2000 S. Lawrence Zipursky and his colleagues at the University of California, Los Angeles (UCLA) identified that this alternate splicing resulted in "one gene–many polypeptides." From one template (gene) there are multiple ways of generating different proteins. How this is done is a mystery. But we know it is not a simple mechanistic process. This is a rhapsody that constantly repeats itself 37 trillion times in each of our cells.
And looking at this fathomless universe, you have to wonder, where does this leave the Amyloid Cascade hypothesis? If the music becomes faulty, then the dance becomes erratic. And we can see this not in one or two steps, but in a series of steps across the body.
Imbalance
Protein mis-folding is continuous and “normal.” The ribosome which reads the DNA to make the proteins makes mistakes in as many as 1 in every 7 proteins. The gene splicing seems variable. Proteins can misfold through other mechanisms. For example, one of the amino acid might be deformed and eventually effect the whole protein. Or the protein is formed perfect but the conditions inside the cell—e.g. temperature or acidity—make it fold unconventionally. Sometimes the misfold is a required fold. Perhaps the gene itself is dictating a misfold. We have to be careful with this concept of misfold and errors. These are moral judgments. Especially when some combination of misfolded proteins--amyloids--are naturally produced to carry out necessary functions in the body.
Neal Hammer with the University of Michigan Medical school, and his colleagues, [12] reviewed cases where the amyloid has been shown to be a necessary feature. The authors conclude that “Despite over twenty years of [Alzheimer’s disease] AD research the nature of the toxic species of Aβ has yet to be conclusively identified and little is known about how Aβ polypeptide aggregation begins in vivo.“
We still do not know for certainty how many proteins there are in the body. The Human Proteone Project has so far identified 30,057 proteins. [13] This figure might be revised to 100,000 unique types of proteins in humans. We also do not know the full extent, how often, and the overall consequence of misfolded proteins. Aβ can be formed from 18 inappropriately folded versions of proteins naturally present in the body. But there are many more misfolded proteins that we have already identified, more remain to be identified. [14] One thing that we have learned from nature is that errors are the salvation to immortality. Humans are the product of errors and the immortality of genes relies on the continuation of errors. Perhaps we should refrain from judging nature too early in our knowledge.
Amyloidosis in Alzheimer's disease.
The problem, we are told, is that when proteins fold incorrectly some become amyloids. And this happens so frequently that it becomes a disease all by itself called Amyloidosis. This physical expressions of the disease is determined by the type of protein that is misfolded and the organ or tissue it resides in. [15] By studying amyloidosis it is now believed that certain misfolded small proteins called “seeds” can induce other proteins to fold—known as the study of proteopathy. This is exactly what happens with the prion misfolded protein which causes a cascade of prion disease— Creutzfeldt–Jakob disease disease in humans. As with music that orchestrates the dance, the wrong tune will cause multiple wrong steps, and they are related to the same sheet of music. So that, as an example, Alzheimer’s disease is related, both clinically and also statistically, with type 2 diabetes, both seen as diseases of amyloidosis. The other protein implicated in Alzheimer's disease, tau protein, also forms such prion-like misfolds. There is some evidence that misfolded Aβ can induce tau to misfold, although this might be a symbiotic relationship, one promotes the other.
So the question is why—if the National Institute on Aging and Alzheimer’s Association truly believe in the Amyloid Cascade hypothesis—are they not looking at all of these other diseases of amyloidosis together rather than in silos?
And we know the answer to that question already. [16]
The second question that follows is more fundamental. If all these diseases share a common process, if by addressing the known cause of one can we delay or stop the cause of a secondary disease? Perhaps then, a public health approach to Alzheimer’s disease is warranted. [17]
There is a third and more radical question. If these misfolded proteins are in fact there for a reason and not as a result of error, then what are they protecting us from?
Perhaps we do not know the underlying disease of Alzheimer's yet. There is increasing evidence suggesting that the large amyloid plaques are developed to protect. [18] And science is bearing this out. It could be that although the small misfolds are dangerous because they are small enough to interfere with the workings of synapsis—-by clamping together they become too big to interfere with the small synaptic transmissions. They are likely protecting the brain. Like a scab on a wound.
A research cul de sac might remain as long as we remain in our silos of research. We need to venture out and explore. “Man cannot discover new oceans unless he has the courage to lose sight of the shore.”―André Gide. We need such intellectual honesty to understand the complexity of Alzheimer’s disease and to dig ourselves out of this research cul de sac.
Citations
[1] Bianconi, E., Piovesan, A., Facchin, F., Beraudi, A., Casadei, R., Frabetti, F., ... & Perez-Amodio, S. (2013). An estimation of the number of cells in the human body. Annals of human biology, 40(6), 463-471.
[2] . With two common structures called “alpha helices,” like a slinky and “beta sheets” like folded paper fan–α-helices have 21 amino acids while β-sheets have 30 amino acids. There are many other types of shapes and varying levels of complexity of the final structure.
[3] Hardy, J. A. & Higgins, G. A. Alzheimer's disease: the amyloid cascade hypothesis. Science 256, 184–185 (1992).
[4] Peptides are small proteins consisting of 2 or more amino acids. Oligopeptides have 10 or fewer amino acids. Polypeptides are chains of 10 or more amino acids, while polypeptides having more than 50 amino acids are classified as proteins.
[5] Iqbal K., Liu, F. & Gong, C.X. (2014). Alzheimer disease therapeutics: focus on the disease and not just plaques and tangles. Biochemical pharmacology, 88(4): 631-639.
[6] Boche D., Donald J., Love S., Harris S., Neal J.W., Holmes C., et al. (2010). Reduction of aggregated tau in neuronal processes but not in the cell bodies after Abeta42 immunisation in Alzheimer’s disease. Acta Neuropathol, 120: 13–20.
Gilman S., Koller M., Black R.S., Jenkins L., Griffith S.G., Fox N.C, et al. (2005). Clinical effects of Abeta immunization (AN1792) in patients with AD in an interrupted trial. Neurology, 64:1553–62.
[7] as defined by Braak & Braak stages:
Snowdon D. (1997). Aging and Alzheimer's Disease: Lessons From the Nun Study. The Gerontologist, 37(2):150-156
Snowdon D.A. (2003).Healthy aging and dementia: findings from the Nun Study. Annals of Internal Medicine, 139(5,2): 450–454.
Snowdon DA, Greiner LH, Mortimer JA, et al. Brain infarction and the clinical expression of Alzheimer disease. The Nun Study. JAMA. 1997;277:813-817.
[8] (Crystal et al 2000; Polvikoski et al 2001)
[9] (Crystal et al, 1988; Polvikoski et al, 2001; Katzman et al, 1988; Tomlinson, Blessed & Roth 1970; Dickson et al, 1997).
[10] Hardy-Weinberg principle
[11] Some of these are:
Antisense RNA—asRNA, piRNA, micRNA—inhibits translation of mRNA by physically obstructing the translation of some of the nucleoids, germ cell and stem cell development, sperm production, and epigenetic process.
Natural antisense transcripts (NATs) are regulatory RNA involved in interference and inhibit gene expression (RNAi), alternative splicing, genomic imprinting, and X-chromosome inactivation
Long and Short non-coding RNA—ncRNA— perform multiple tasks related non protein transcription for four-fifths of all genome. The FANTOM3 project identified ~35,000 non-coding transcripts from ~10,000 distinct loci.
There are also parasitic RNA that we inherited from other retroviruses (in most cases.) But the most interesting are those RNAs involved in post-transcription. The message within each mRNA is edited—known as gene splicing—by other types of RNA. How they know what to delete and edit is a mystery. There are also some RNA that modifies our DNA replication. Not just through epigenetic switches—which does not change the DNA—but through modification of our DNA itself.
[12] Hammer, N. D., Wang, X., McGuffie, B. A., & Chapman, M. R. (2008). Amyloids: friend or foe?. Journal of Alzheimer's Disease, 13(4), 407-419.
[13] Kim et al. A draft map of the human proteome. 2014. Nature. 509, 575-581.
[14] Misfolded proteins:
1. ABri
2. ADan
3. Amyloid A protein
4. Amyloid β peptide
5. Apolipoprotein AI
6. Apolipoprotein AII
7. Apolipoprotein AIV
8. Atrial natriuretic factor
9. Beta-2 microglobulin
10. Calcitonin
11. Crystallins
12. Cystatin C
13. Fibrinogen
14. Fused in sarcoma (FUS) protein
15. Gelsolin
16. Glial fibrillary acidic protein (GFAP)
17. Immunoglobulin heavy chains
18. Islet amyloid polypeptide (IAPP; amylin)
19. Keratoepithelin
20. Lysozyme
21. Medin (lactadherin)
22. Monoclonal immunoglobulin light chains
23. Notch3
24. Prion protein
25. Prolactin
26. Proteins with tandem glutamine expansions
27. rhodopsin
28. Seipin
29. Serpins
30. Superoxide dismutase,
31. Tau protein
32. TDP-43
33. Transthyretin
34. α-Synuclein
[15] Amyloidosis Disease:
Amyloidosis—systemic
Primary systemic amyloidosis
Ig heavy-chain-associated amyloidosis
Secondary (reactive) systemic amyloidosis
Senile systemic amyloidosis
Hemodialysis-related amyloidosis
Hereditary systemic ApoAI amyloidosis
Hereditary systemic ApoAII amyloidosis
Finnish hereditary amyloidosis
Hereditary lysozyme amyloidosis
Hereditary cystatin C amyloid angiopathy
Amyloidosis—localized
Injection-localized amyloidosis
Hereditary renal amyloidosis
Senile seminal vesicle amyloid
Familial subepithelial corneal amyloidosis
Cataract
Medullary thyroid carcinoma
Neurodegenerative diseases
Alzheimer’s disease
Parkinson’s disease
Lewy-body dementia
Huntington’s disease
Spongiform encephalopathies
Hereditary cerebral hemorrhage with amyloidosis
Amyotrophic lateral sclerosis
Familial British dementia
Familial Danish dementia
Familial amyloidotic polyneuropathy
Frontotemporal dementias
Other diseases
Diabetes mellitus
Atherosclerosis
Sickle cell anemia
[16] Garrett MD (2015) Politics of Anguish: How Alzheimer's disease become the malady of the 21st century. Createspace. USA
[17] Garrett MD, & Valle R (2015) A New Public Health Paradigm for Alzheimer’s Disease Research. SOJ Neurol 2(1), 1-9.
Garrett MD &Valle RJ (2016).A Methodological Critique of The National Institute of Aging and Alzheimer’s Association Guidelines for Alzheimer’s disease, Dementia and Mild Cognitive Impairment. Dementia: The International Journal of Social Research and Practice,15(2) 239–254. DOI: 10.1177/1471301214525166
[18] D.M. Walsh, I. Klyubin, J.V. Fadeeva, et al.Naturally secreted oligomers of amyloid beta protein potently inhibit hippocampal long-term potentiation in vivo Nature, 416 (2002), pp. 535–539
P.M. Douglas, S. Treusch, H.Y. Ren, et al. Chaperone-dependent amyloid assembly protects cells from prion toxicity. Proc Natl Acad Sci USA, 105 (2008), pp. 7206–7211
© USA Copyrighted 2016 Mario D. Garrett
