Filter out significantly differential expression genesMethodApply two methods to filter out the candidates of AD genes that hold significant expression differences.
The method of fold change analysis (Fig. 4). The genes whose expression levels are higher or lower than average expression levels significantly are selected, where the criteria of significance are that Fold_Change ≥ 1.5. The method acts on two independent datasets GSE84422 and GSE1297 respectively, candidate genes are selected into two sets, then their intersection is the output.
The method of Volcano plot (Fig. 5). For every gene, the difference between two states AD and control is used as the input of the Limma differential expression method, then the genes with a significant difference are selected, where the criteria of significance were set as P-value ≤ 0.05, |log2FC|≥ 0.5. The method acts on two independent datasets GSE84422 and GSE1297 respectively, candidate genes are selected into two sets, then their intersection is the output.
Figure 4The identification of AD genes using the method of fold change. The genes of hemoglobin subunits are included in the intersection.Figure 5The identification of AD genes using expression difference. The genes of hemoglobin subunits are included in the intersection.Input dataAll data were from GSE84422 and GSE1297 datasets, NCBI website. GSE84422 includes four states, Normal, Possible AD, Probable AD, and Definite AD. GSE1297 includes four stages of AD, Control, Incipient, Moderate, and Severe. All raw data were logarithmized and normalized, and their exponents were used for size comparison. In this way, only the magnitude of each number was compared, minimizing the impact of noise as much as possible.Output dataFigures 4 and 5 illustrate the output.The special feature of outputUsing two independent datasets and two different methods, still, the hemoglobin subunits are filtered out. That is, hemoglobin subunits hold significant abnormal expression as AD progression, it is very possible that they are related to AD.Hemoglobin subunits are key nodes in the PPI networkMethodConstruct a protein–protein interaction network (PPI network) using the STRING website (version11.string-db.org).Input dataThe 106 genes from the fold change analysis (Fig. 4) and the 12 genes identified from the Limma analysis (Fig. 5) were grouped and subjected to the PPI network.Output dataFigure 6 is the output of the PPI network.Figure 6PPI Network. Hemoglobin subunits form a minimized closed loop.The special feature of outputThe hemoglobin subunits HBB, HBA1 and HBA2 hold high confidence associated with AD (The thicker the line, the more confident it is.). Hemoglobin subunits form a closed loop in PPI, demonstrating a marked correlation between these three genes.The expression feature of hemoglobin subunits on the visual information transmission pathwayMethodList the expression levels of hemoglobin subunits on the pathway that transmits visual information (V–H pathway), and observe the feature of change as AD progresses.Input dataThe different brain regions of the V–H pathway and the gene expression levels in these regions. The brain regions consist of the Occipital visual cortex, Middle temporal gyrus, Inferior temporal gyrus, Parahippocampal gyrus, and Hippocampus. The original data are from GSE84422.Output (Fig. 7)Figure 7Expression levels of hemoglobin subunits on V–H Pathway. The expression levels exhibited a decreasing trend with the onset of AD.The expression levels of hemoglobin subunits in different brain regions are visualized and displayed using box-and-whisker plots, based on mean expression values.The special feature of the output
On the brain regions of the V–H pathway, the hemoglobin subunits are down-regulated overall with AD progression.
On the regions of the Inferior temporal gyrus and Hippocampus, the subunits are consistently down-regulated with AD progression.
Guess: The down-regulation feature suggests that, as AD progresses, on the pathway of visual information transmitted, the number of hemoglobin decreases gradually overall, the oxygen supply becomes weaker, the energy supply becomes weaker, and then dysfunction on the V–H pathway happens. That is, dementia not only comes from memory loss of the hippocampus but also from damage to the information transmission pathway. The following work of this paper is all based on the argumentation of this hypothesis.
Hemoglobin system becomes disordered at early stage of ADMethodThe hemoglobin system consists of subunits HBB, HBA1, and HBA2. Under the disturbing of toxic substances, their expression becomes disorder possibly, and the coordination of the three subunits becomes weak. That is, the entropy of the hemoglobin system will change as AD progresses and toxic substances accumulate.In this section, the entropy of the hemoglobin system was calculated. AD progression passes through four stages, Normal, Possible AD, Probable AD, and Definite AD. So, there are four values of entropy. The trend of entropy changing reflects the disorder of the system with AD progression.V–H pathway includes five brain tissue regions. At each region, the entropy was calculated in this section. If the entropy at some region becomes significantly high and more disordered, then the pathway has the risk of dysfunction.Input dataThe original data are from GSE84422. The expression levels of the subunits of hemoglobin HBB, HBA1, and HBA2, are sampled from the brain tissue regions of the V–H pathway. The entropy of every region is calculated, which measures the disorder of the region. The entropies at the four stages are calculated, which are Normal, Possible AD, Probable AD, and Definite AD respectively.OutputFor each brain tissue region, the trend of entropy with AD progression is described visually by curves and presented in Fig. 8.Figure 8The trend of entropy of the hemoglobin system in the V–H pathway. At early AD stage, brain regions MTG and HC hold increased entropy and hemoglobin expression becomes more disordered.The special feature of the output
At the stage of Possible AD, the entropy of most brain regions markedly increased.
In the Middle Temporal Gyrus (MTG) and Hippocampus (HC) regions, entropy increase is significant at early stage of Possible AD.
At early stage, the hemoglobin system becomes disordered, and the oxygen supply on the V–H pathway becomes inadequate.
MTG is responsible for spatial orientation, so the disorder leads to orientation disorder.
The entropy in HC becomes high, the disorder of HC increases, V–H pathway holds a high risk of dysfunction at early stage. So, at early stage, the patient holds a high risk of spatial orientation disorder and object recognition disorder.
Gibbs free energy analysisPreliminary: Gibbs free energyGibbs free energy, GGibbs free energy expresses the amount of energy capable of doing work during a reaction at constant temperature and pressure. When a reaction proceeds with the release of free energy (that is when the system changes to possess less free energy), the free-energy change, ΔG, has a negative value and the reaction is said to be exergonic. In endergonic reactions, the system gains free energy and ΔG is positive56.Enthalpy, HEnthalpy is the heat content of the reacting system. It reflects the number and kinds of chemical bonds in the reactants and products. When a chemical reaction releases heat, it is said to be exothermic; the heat content of the products is less than that of the reactants, and the change in enthalpy, ΔH, has, by convention, a negative value. Reacting systems that take up heat from their surroundings are endothermic and have positive values of ΔH56.Entropy, SEntropy is a quantitative expression of the randomness or disorder in a system. When the products of a reaction are less complex and more disordered than the reactants, the reaction is said to proceed with a gain in entropy56.The relationship between energy and entropyUnder the conditions existing in biological systems (including constant temperature and pressure), changes in free energy, enthalpy, and entropy are related to each other quantitatively by the equation56.$$\Delta G=\Delta H-T \Delta S,$$
(1)
in which ΔG is the change in Gibbs free energy of the reacting system, ΔH is the change in enthalpy of the system, T is the absolute temperature, and ΔS is the change in entropy of the system.Living organisms preserve their internal order by taking from the surroundings free energy in the form of nutrients or sunlight, and returning to their surroundings an equal amount of energy as heat and entropy56.The energy supply of hemoglobin becomes weaker at early stage of ADAccording to Fig. 7, it is known that, at early stage, and at most of brain tissue regions of the V–H pathway, the expressions of hemoglobin subunits are disordered. The disorder interferes with the biochemical processes in which hemoglobin is involved, affecting oxygen transport. This disorder will increase the entropy ΔS of the reacting system in which hemoglobin is involved.Under ideal conditions, such as constant temperature and pressure, enthalpy ΔH is constant, because enthalpy refers to the energy saved in the chemical bond and the energy of system to do work on the outside which is a constant under the ideal condition.So according to formula (1), we have the following differential expression$$d\left(\Delta G\right)=-T d(\Delta S)$$
(2)
To understand formula (2), we give the following example: If the entropy increases by 0.02 units (i.e., \(d\left(\Delta S\right)=0.02\)), the free energy will decrease by 0.02T (i.e., \(d\left(\Delta G\right)=-0.02T\)). That is to say, the energy involved in the biochemical reactions of hemoglobin will decrease by 0.02T, which will reduce its oxygen transport capacity.Therefore, the following conclusions can be drawn: During early stage of AD, at the brain tissue regions of the V–H pathway, the hemoglobin system holds increased entropy, and then the system becomes more disordered. This disorder dissipates energy saved in hemoglobin, then the capacity of hemoglobin to transport oxygen becomes weak, the energy supply of the V–H pathway becomes weak, and at last, the dysfunction risk of the V–H pathway increases. Ultimately, patient holds a high risk of spatial orientation disorder and object recognition disorder at early stage.The correlation between different brain regions becomes weaker at early stage of ADMethodCalculate the Pearson correlation coefficients between different brain tissue regions of the V–H pathway.For example, along the V–H pathway, MTG is neighbor to PHG (Fig. 2), and MTG–PHG is one of a section of the pathway. The hemoglobin expression at the two neighboring brain regions should be correlated if the patient is at normal state. The correlation between the two neighboring regions was calculated.When the expression levels of three subunits of hemoglobin form a 3-dimensional vector on MTG, it was denoted as$$\overrightarrow{{x}_{MTG}}=\left(HBB, HBA1, HBA2\right)$$
(3)
The vector \(\overrightarrow{{x}_{MTG}}\) is called as the hemoglobin expression on brain region MTG.As a same, hemoglobin expression at region PHG is denoted by \(\overrightarrow{{x}_{PHG}}\).The correlation between the two vectors is defined as the Pearson correlation coefficient of two unit vectors:$${R}_{MTG-PHG}=\frac{\sum (\overrightarrow{{x}_{i}}-\overline{x })(\overrightarrow{{y}_{i}}-\overline{y })}{\sqrt{\sum {\left(\overrightarrow{{x}_{i}}-\overline{x }\right)}^{2}\sum {\left({\overrightarrow{{y}_{i}}}-\overline{y }\right)}^{2}}},$$
(4)
where \(\overrightarrow{{x}_{i}}\) presents a 3-dimensional vector from a sample in MTG, and \({y}_{i}\) presents vector from PHG.If the value \({R}_{MTG-PHG}\) is close to zero at AD stage, the correlation of the two regions is meager, it is not coordinated that the hemoglobin expression on the two regions. That is, the oxygen supply in the two neighboring regions is not coordinated, and this coordination will lead to the dysfunction of visual information transmission.Input dataThe raw data are from dataset GSE84422. The input data is logarithmically transformed and only the exponential is compared, which eliminates noise pollution. Then all data are standardized, making data from different brain regions and different samples comparable.OutputThe correlations between different regions are listed in Fig. 9.Figure 9The correlation between different brain regions along the V–H pathway. The correlation MTG–PHG becomes weak significantly, the information transmission becomes weak, where the information is responsible for spatial orientation. So, the earliest symptom is spatial orientation disorder, and the symptom is high risk. At early stage, PHG–HC becomes weak significantly, and saving information becomes weak. So, the two symptoms are high-risk spatial orientation disorder and object recognition disorder.The special feature of the output
At the earliest stage (Possible AD), the correlation between MTG and PHG is close to zero (i.e., \({R}_{MTG-PHG}\approx 0\)). Section MTG–PHG of the V–H pathway is responsible for transmitting the information of spatial orientation. So it is a high risk that the patient holds weak spatial orientation at the earliest stage.
At early stage (Probable AD), the correlation between PHG and HC is close to zero. Section PHG–HC is responsible for saving information in the hippocampus, and the information includes spatial orientation and object recognition. So, it is a high risk that the patient holds weak spatial orientation and face recognition at early stage.
At early stage (Possible AD and Probable AD), the correlation between brain regions becomes weak, and the dysfunction of the V–H pathway is possible. So, it is a high risk that the patient holds weak spatial orientation and face recognition.
The discoordination of the V–H pathway is related to neurofibrillary tanglesConceptions to measure correlation between two brain regionsHemoglobin consists of three subunits HBB, HBA1, HBA2.Hemoglobin expression is defined as the vector (HBB, HBA1, HBA2), where the expression level of the three subunits is abstracted as the three components of the vector respectively.If the vector is measured at brain region OVC, it is denoted by \(\overrightarrow{{x}_{OVG}}\). V–H pathway consists of five brain regions, OVC, MTG, ITG, PHG, HC. So, for a sample, there five vectors, \(\overrightarrow{{x}_{OVG}}\), \(\overrightarrow{{x}_{MTG}}\), \(\overrightarrow{{x}_{ITG}}\), \(\overrightarrow{{x}_{PHG}}\), \(\overrightarrow{{x}_{HC}}\).For n samples, there are 5n vectors, every region has n vectors.The size of Hemoglobin expression is defined as the length of vector, such as \(| \overrightarrow{{x}_{OVG}}|\). The length \(| \overrightarrow{{x}_{OVG}}|\) reflects the total expression of the three subunits on region OVC. If region OVC contains many molecular hemoglobin, the hemoglobin expression on the region is high, the three subunits hold high expression also, then the size of hemoglobin on OVC is big (i.e., \(| \overrightarrow{{x}_{OVG}}|\) is big).Size correlation between two brain regions is defined as the product of two sizes of hemoglobin expressions. For example, \(\left|\overrightarrow{{x}_{OVG}}\right|\cdot |\overrightarrow{{x}_{MTG}}|\) is the size correlation between region OVC and MTG. The bigger the size correlation, the richer hemoglobin in these two neighbor regions in general. At least, it is not possible that any of the two regions contains very little molecular hemoglobin. Size correlation reflects the coordination of hemoglobin supply on the two neighbor regions of the V–H pathway. If the size correlation becomes very small as AD progresses, the coordination of oxygen supply on the V–H pathway is impaired.Proportion correlation between two brain regions is defined as the cosine of the angle between two vectors of the two regions. For example, for the two neighbor regions MTG and PHG, there are two vectors \(\overrightarrow{{x}_{MTG}}\) and \(\overrightarrow{{x}_{\text{PHG}}}\). And the proportion correlation is \({R}_{MTG-PHG}=cos\theta\), where \(\theta\) denotes the angle between the two vectors. i.e.,$${R}_{MTG-PHG}=\frac{\overrightarrow{{x}_{MTG}}}{|\overrightarrow{{x}_{MTG}}|}.\frac{\overrightarrow{{x}_{\text{PHG}}}}{|\overrightarrow{{x}_{\text{PHG}}}|}$$Every molecular hemoglobin contains two HBB, one HBA1, and one HBA2, so the proportion is HBB: HBA1: HBA2 = 2:1:1. In an ideal model, every region holds the ideal proportion 2:1:1. So, the vector of every region is proportional to vector (2, 1, 1). Then, if any proportion correlation is \(cos\theta =1\) the correlation is perfect. However, under the impact of toxic substances, the standard proportion 2:1:1 is damaged. For example, in the MTG region, the hemoglobin expression is proportional to vector (0.3, 0.2, 0.3). That is, toxic substances make HBB expression decrease severely (from 2 units to 0.3 units. On the PHG region, the hemoglobin expression is proportional to vector (0.2, 0.4, 0.4). Thus \(cos\theta =0.26\), suggests that it is not coordinated hemoglobin expressions on the neighbor regions of the V–H pathway, the oxygen supply on the two regions is not coordinated, and the dysfunction of energy supply on the two regions holds high risk.Synthesized correlation between two regions is defined as the inner product of between two vectors of two regions. For example, for the two neighbor regions MTG and PHG, there are two vectors \(\overrightarrow{{x}_{MTG}}\) and \(\overrightarrow{{x}_{\text{PHG}}}\). The inner product is \(\overrightarrow{{x}_{MTG} }. \overrightarrow{{x}_{\text{PHG}}}\).If the inner product becomes very small as AD progresses, either the size of hemoglobin expression on the two neighbor regions is not coordinated, or the proportion of hemoglobin subunits is not coordinated. Any discoordination will impact on V–H pathway and damage the oxygen supply on the pathway, resulting in dysfunction of the energy supply on the pathway. At last, the visual information transmission along the V–H pathway is impaired, and this impairment will lead to spatial orientation disorder and object recognition disorder.In the following third level sections 2, 3, and 4, it will be analyzed that the relationship between neurofibrillary tangles (NFTs) and the correlation among different brain regions. In “The relationship between NFTs and the size correlation of two neighbor brain regions”, it was discussed that the relationship between NFTs and the size correlation of hemoglobin. In “The relationship between NFTs and the proportion correlation of two neighbor regions”, the relationship between NFTs and the proportion correlation of hemoglobin was discussed. In “The relationship between NFTs and synthesized correlation of neighbor regions”, the relationship between NFTs and the synthesized correlation was discussed.The relationship between NFTs and the size correlation of two neighbor brain regionsMethodThere is the following one-to-one correspondence in the data structure of this paper: For a given sample (or patient), a brain region ~ a NFT value ~ a vector of hemoglobin expression (HBB, HBA1, HBA2).So, we have that,Sample 1: region OVC~\(m\) (NFT value) ~ \(|\overrightarrow{{x}_{OVG}}|\) (size of hemoglobin expression).Sample 2: region MTG~\(n\) (NFT value) ~ \(|\overrightarrow{{x}_{MTG}}|\)Then, the size correlation between OVC and MTG is a pair of orders: \((\sqrt{\text{mn}}, \left|\overrightarrow{{x}_{OVG}}\right|\cdot |\overrightarrow{{x}_{MTG}}|\)), where \(\sqrt{\text{mn}}\) presents the geometric mean. In essence, it is still NFTs.All of the correlations between two neighbor regions can be calculated as above, and a set of 2-dimensional points can be plotted.Input dataThe raw data are from dataset GSE84422. The input data is logarithmically transformed and only the exponential is compared, which eliminates noise pollution. Then all data are standardized, making data from different brain regions and different samples comparable.OutputAll points are plotted in Fig. 10.Figure 10The relationship between NFTs and the size correlation of hemoglobin expression at two neighbor regions.The special feature of output
The average of all data of size correlations decreases with the increase of NFTs. That is the more dis-coordinated hemoglobin expression on neighbor regions, the bigger the NFTs, the more severe AD, and the weaker spatial orientation recognition and object recognition.
The variance of size correlation increases with the increase of NFTs. That is, hemoglobin expression loses control gradually on the V–H pathway and becomes more disordered, the more disorder spatial orientation recognition and object recognition.
The relationship between NFTs and the proportion correlation of two neighbor regionsMethodAccording to Sect. 2, we have a similar example,Sample 1: region OVC ~ \(m\) (NFT value) ~ \(\overrightarrow{{x}_{OVG}}\)Sample 2: region MTG ~ \(n\) (NFT value) ~ \(\overrightarrow{{x}_{MTG}}\)Then, the proportion correlation between OVC and MTG is a pair of orders: \((\sqrt{\text{mn}}, cos\theta\)), where$$cos\theta =\frac{\overrightarrow{{x}_{\text{OVC}}}}{|\overrightarrow{{x}_{\text{OVC}}}|}.\frac{\overrightarrow{{x}_{MTG}}}{|\overrightarrow{{x}_{MTG}}|}.$$All of the proportion correlation between two neighbor regions can be calculated as above, and a set of 2-dimensional points can be plotted.Input dataSee Section 2.OutputFigure 11.Figure 11The relationship between NFTs and the proportion correlation of two neighbor regions.The special features of outputAs AD occurs, the data distribution becomes more disordered, and the correlation of the proportion of the three subunits becomes disordered. That is, the hemoglobin expression on a region cannot stimulate the response of adjacent brain regions or stimulation becomes weak and disorder. The disorder leads to the dysfunction risk of the V–H pathway, and spatial orientation and object recognition become disorders.The relationship between NFTs and synthesized correlation of neighbor regionsMethodCalculate the inner product between two vectors of hemoglobin expression at two neighbor brain regions along the V–H pathway. At the same time, the corresponding NFTs value is obtained by multiplying the corresponding NFTs values of the two samples by the square root.According to Sect. 2, we have similar example,Sample 1: region OVC ~ \(m\) (NFT value) ~ \(\overrightarrow{{x}_{OVG}}\)Sample 2: region MTG ~ \(n\) (NFT value) ~ \(\overrightarrow{{x}_{MTG}}\)Then, the synthesized correlation between OVC and MTG is a pair of orders: \((\sqrt{\text{mn}}, \overrightarrow{{x}_{OVG}}.\overrightarrow{{x}_{MTG}}\)), where \(\overrightarrow{{x}_{OVG}}.\overrightarrow{{x}_{MTG}}\) presents inner product.All of the synthesized correlations between two neighbor regions can be calculated as above, and a set of 2-dimensional points can be plotted.Input dataSee section 1.OutputFigure 12.Figure 12The relationship between NFTs and synthesized correlation of neighbor regions.The features of the output
As NFTs increase, synthesized correlation decreases significantly.
As NFTs increase, synthesizedc correlation becomes more disordered significantly.
The feature of isolation of islands: Hemoglobin expression in one brain region is not synchronized with its expression in neighboring regions, and tends to be independent. So, the coordination of the V–H pathway becomes weak, the oxygen supply becomes disorder, and the energy supply becomes disorder. Then, visual information transmission is impaired. And this impairment impacts spatial orientation recognition and object recognition. At last, the early symptoms appear as spatial orientation recognition disorder and object recognition disorder.
HypothesisThe features of the V–H pathwayThe V–H pathway is the pathway of visual information transmission, which transmits information from the retina to the hippocampus. It consists of five brain tissue regions (Figs. 1, 2): OVC, MTG, ITG, PHG, and HC.V–H pathway includes two sub-pathways. And one is OVC–MTG–PHG–HC (Fig. 2), named dorsal stream (Fig. 1). Dorsal stream mainly conducts visual information related to spatial perception, target positioning, and motion observation. The other sub-pathway is OVC–ITG–PHG–HC, named ventral stream (Fig. 1). Ventral stream is mainly related to the processing of visual information such as recognition, shape, and color of visual stimuli.Visual information transmission goes through three stages (Fig. 2): obtaining and organizing information (Stage 1), transmitting information (Stage 2), and storing information (Stage 3). Section OVC–MTG and OVC–ITG belong to the first stage, MTG–PHG and ITG–PHG belong to the second stage, and PHG–HC is the third stage.To transmit visual information, along the V–H pathway, a brain region should coordinate with its neighboring region. Especially, it is necessary that the energy supply of different brain regions should be coordinated. The release of most energy is determined by the oxygen supply. To release more energy, more oxygen is needed. The oxygen supply is determined by the expression level of hemoglobin. More hemoglobin expression determines more oxygen supply. Therefore, the hemoglobin expression in each brain region reflects the state of energy supply of each brain region like a mirror. More importantly, studying the correlation between hemoglobin expression in various brain regions can detect the coordination of the energy supply of the V–H pathway.Molecular hemoglobin consists of three subunits, HBB, HBA1, and HBA2. So, the expression levels of the three subunits form a vector (HBB, HBA1, HBA2), and this vector is the hemoglobin expression. For a given sample (patient) and a given brain, the expression levels of the three subunits can be measured, and then the hemoglobin expression is known. Studying the correlation among the vectors of hemoglobin expression will detect the coordination of different brain regions along the V–H pathway.After studying the correlation among brain regions along the V–H pathway, the following features were observed:
Hemoglobin expression is significantly abnormal as AD occurs (Figs. 4, 5 and 6).
This feature suggests that hemoglobin is related to AD very possibly.
Expression feature: Hemoglobin expression in different brain regions is down-regulated gradually as AD progresses overall (Fig. 7).
This feature suggests that there is not enough molecular hemoglobin to transport oxygen along the V–H pathway and not enough energy to transport visual information.
Entropy feature: At the earliest stage of AD, possibly AD, the entropy of the hemoglobin system on brain region MTG and HC increases by more than twice (Fig. 8).
This feature suggests that significant disorder happens on the V–H pathway. The disorder affects oxygen transportation and energy supply and, at last, affects the transmission of visual information. Especially, the degree of disorder in the MTG region increases by nearly threefold, with spatial orientation disorder symptoms posing a high risk at the earliest stage of AD.
Gibbs free energy feature: The Gibbs free feature of the hemoglobin system decreases.
This feature suggests that entropy increases and significant disorder dissipates energy, and reduces the ordered energy to transport oxygen molecules.
The feature of correlation among brain regions: At early stage of AD (possibly AD or probably AD), the correlation between different brain regions becomes weak, especially for MTG–PHG and PHG–HC (Fig. 9).
This suggests that the coordination of the V–H pathway becomes weak at early stage. The section MTG–PHG of the pathway holds a very weak correlation, declining more than twice. And this suggests that there is a high risk of spatial orientation disorder at the earliest stage of AD. MTG–PHG holds a very weak correlation too, declining more than twice. And this suggests that there is a high risk of spatial orientation disorder, object recognition disorder, and motion barrier at early stage.
The relationship between the dis-coordination of the V–H pathway and NFTs: As NFTs increases, the V–H pathway loses coordination gradually (Figs. 10, 11, 12), every brain region of the pathway loses correlation with its neighbor region gradually and becomes independent. This feature is called the isolation of islands in this paper. That is, every brain region loses or weakens connections with its neighbor region, resulting in each region acting like an isolated island.
This suggests that the dis-coordination of the V–H pathway damages visual information transmission obtained from the retina. Then, the early symptoms appear–spatial orientation disorder and face recognition disorder.
The structure features of tau protein and NFTsThe features of tau protein
It is a small molecule with highly hydrophilic. Abnormal tau can easily permeate into the bloodstream and bind to hemoglobin. (Fig. 13A–C).
It has no fixed conformation, and residues exposed (Fig. 13A,B).
Enrichment of lysine and arginine, which are easily to combine with ions in heme (Fig. 13A).
A significant quantity of tau is needed to maintain microtubules. And their residues are exposed, resulting in strong activity. Then, there is a high risk of generating abnormal tau (Fig. 13D,E).
Its residues are easily bound to ions in heme, disrupting the oxygen transport function of hemoglobin (Fig. 13A,B).
Its mechanism of toxicity is similar to carbon monoxide (CO). Both involve the binding of iron in the heme of hemoglobin to its residues, preventing oxygen from binding to the iron (Fig. 13A,B).
The toxicity of abnormal tau is stronger than CO because tau contains more residues than the CO molecule (Fig. 13A,B).
Figure 13The structure of tau protein (A) Distribution of alkali amino acid in a single tau. (B) Distribution of acidic amino acid in a single tau. (C) The amino acids in a single tau. (D) Tau proteins in tubulin. (E) Charge distribution (red: negative, blue: positive) (Note: Subfigures (A) and (B) are generated from website: https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?&mmdbid=183918&bu=1&showanno=1&source=full-feature Subfigures (C–E) are generated from website: https://swissmodel.expasy.org/repository/uniprot/P10636).The features of NFTsThe formation of NFTs is due to the aggregation of proteins within neurons. Specifically, NFTs are formed by the abnormal aggregation of a protein tau. These abnormally aggregated tau proteins form irregular fiber structures and form tangled clumps within neurons. These clumps ultimately lead to the loss of normal function and the eventual death of neurons.The structure features of hemoglobinThe features of ironThe electron configuration of an iron atom (Fe) in its outer shell is 3d64s2. The two electrons on the outermost layer (i.e., in the 4 s orbital) can be easily lost, resulting in a + 2 valence (Fe2+). However, the six electrons on the next outer layer (i.e., in the 3d orbitals) are in an unstable unfilled state, making it susceptible for one additional electron to be lost from the 3d orbitals, resulting in + 3 valence (Fe3+). Fe3+ is a stable structure with half-filling, so it is more stable than Fe2+. The conversion between Fe2+ and Fe3+ enables hemoglobin to both bind and release oxygen molecules, thus fulfilling its role in oxygen transport, thus achieving the purpose of transporting oxygen by hemoglobin.The features of HemeTo control Fe2+ and Fe3+, Heme (iron porphyrin) is needed (Fig. 14A). Heme consists of a complex organic ring structure, protoporphyrin IX, featuring a bound iron atom in its ferrous (Fe2+) state56. The iron atom of heme has six coordination bonds: four in the plane of heme, and bonded to the flat porphyrin ring system, and two are perpendicular to the porphyrin ring (Fig. 14B). And one of the perpendicular coordination bonds to an oxygen molecule, and the other perpendicular coordination is occupied by a His residue56. Under the control of Heme, Fe2+ combines with oxygen molecules in an orderly manner, and releasing oxygen molecules is ordered too. It should be noted that, because Fe2+ is very active, bonding to toxic substances, such as abnormal tau, is very easy, where the infiltration of abnormal tau exists in brain blood as AD occurs because tau is small and holds hydrophilic property (Fig. 13A).Figure 14The structure of hemoglobin. (A) Heme (iron porphyrin). (B) Heme captures oxygen. (C) Heme locates in hemoglobin. (D) Sphere of Hemoglobin. (Note: Subfigures (A, B) are downloaded from David et al.56 Subfigures (C, D) are downloaded from website: https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?&mmdbid=7599&bu=1&showanno=1&source=full-feature).The features of haemoglobinTo regulate Heme orderly and send oxygen to other proteins, hemoglobin protein is needed. Four polypeptide subunits are packed together and form a hemoglobin molecule (Fig. 14C). Interactions between the subunits can permit a highly sensitive response to small changes in ligand concentration. Interactions among the subunits in hemoglobin cause conformational changes that alter the affinity of the protein for oxygen. The modulation of oxygen binding allows the O2-transport protein to respond to changes in oxygen demand by tissues56. In addition, the wavelength of light absorbed by hemoglobin is 400–450 nm, which is a high-energy photon in body. That is, when the residues of hemoglobin are exposed disorderly and its chemical bonds are opened, they are easily combined with toxic substances, such as CO or toxic tau protein.HypothesisThe above discussion includes three types of features, structure features of NFTs, structure features of hemoglobin, and pathway features of the V–H pathway. The three types of features are related to each other, and their coherence impacts visual information transmission from the retina. Synthesizing the three types of features, the following hypothesis was induced.As AD occurs, abnormal tau proteins accumulate, some tau proteins package together disorderly and form NFTs, and some penetrate various brain regions. The abnormal tau molecule penetrates brain regions of the V–H pathway. The abnormal tau is more active than CO and O2. Then, it combines with the iron of heme of hemoglobin molecule. And this case is similar to CO poisoning, with molecular CO occupying the position of O2. So, the hemoglobin expression on the brain regions of the V–H pathway becomes dysregulated, such as down-regulation, and expression disorder (entropy increases). And this dysregulation leads to the disorder of the V–H pathway, such as the correlation among brain regions of the V–H pathway becoming weak, the pathway being blocked, and every region becoming an isolated island. The disorder of the V–H pathway leads to dysfunction of visual information transmission, such as insufficient oxygen supply and insufficient energy supply.Therefore, the more NFTs, the more abnormal tau existing in the brain regions of V–H pathway, the higher the risk of hemoglobin being attacked by abnormal tau, the more disorder hemoglobin expression, the more discoordination of V–H pathway, the less oxygen supply and energy supply on V–H pathway, the more dysfunctional V–H pathway.At last, this dysfunction has an impact on the early symptoms of AD, such as spatial orientation disorder and object recognition disorder, where the V–H pathway is responsible for motion and spatial orientation, object recognition, etc.