**6. Presenilin interactome: implementation in AD and PA**

Numerous studies have been conducted in order to identify proteins interacting with PS1 and PS2. Majority of these studies have focused on the key signalling cascades specific for AD, as well as for PA, that is, oxidative stress, generation of free radicals or inflammatory processes. The best studied presenilin partners are components of γ-secretase complex (nicastrin, APH-1 and PEN-2), presenilin substrates (APP, Notch) and proteins involved in a regulation of cell death, calcium homeostasis and cell adhesion. It should be stressed that the knowledge on full PS interactome is crucial for more detailed definition of the pathomechanisms of AD and PA, and further studies are needed to complement this image.

#### **6.1. The γ-secretase complex partners**

Direct partners of presenilins are the components of the γ-secretase complex, namely nicastrin, APH-1 and PEN-2 [44]. Nicastrin associates with the complex comprising PS1-C′ terminal and APH-1 [45]. Nicastrin is required for the assembly of presenilin complexes to mediate Notch signalling and for processing and trafficking of β-amyloid precursor protein and thus plays a role in amyloid plaque formation [46]. Proper signalling between presenilin and nicastrin is important not only for processing of APP and accumulation of Aβ peptides but also for synaptic plasticity [47]. The next component of γ-secretase complex is PEN-2, a membrane protein with two predicted transmembrane domains, both N′ and C′ terminals are in extracellular space and with hydrophilic cytosolic loop [48]. PEN-2 binds to the fourth transmembrane domain of PS and helps to stabilize the γ-secretase complex after PS endoproteolysis [49]. Together with APH-1, PEN-2 is indispensable for Notch signalling [50], exhibiting thus similar properties like nicastrin. Importantly, mutations in TM4 reduced PS1-PEN-2 interaction which was further accompanied by an increased Aβ42 production and disrupted the endoplasmic reticulum calcium homeostasis [51]. The final component of γ-secretase complex is APH-1, a protein composed of seven transmembranes with N-terminus and large loops at cytosolic side [52]. APH-1 contains a conserved GXXXG motif that may be involved in interactions with other subunits of the complex [53]. APH-1 together with nicastrin forms a stable complex that constitutes a scaffold prior to the generation of the full presenilin complex [54]. APH-1 directly interacts with both immature and mature forms of the presenilins and nicastrin and this is indispensable for γ-secretase activity [55]. According to that described above, presenilin biological functions are regulated by complex assembly.

#### **6.2. Mitochondrial interactome of presenilins**

The γ-secretase complex was found in mitochondria [56]. Since Aβ is not a substrate for mitochondrial γ-secretase complex, its mitochondrial implication may be related to cell death signalling, switching between necrosis and apoptosis depending on ATP levels [56]. Moreover, PS2 was found to modulate ER-mitochondria juxtaposition and interactions, and that was enhanced in the case of PS2 mutations [57]. In detail, the components of γ-secretase complex were found in mitochondria-associated ER membranes (MAMs) with lipid raft-like domain [58]. Mutations in presenilin 1 were found to impair the IP3 receptor- and voltage-dependent calcium transport, as well as Ca2+-dependent mitochondrial proteins transport, and this was followed by a mitochondrial dysfunction, reduced patients' motor coordination and Aβ aggregation with ultimate dementia [59]. Presenilin 1 was found to interact with mitochondrial intramembrane cleaving protease, called presenilin-associated rhomboid-like protein (PARL), which could promote changes in mitochondrial morphology [60]. Next to mitochondrial membrane residing proteins, presenilins interact with immunophilin FKBP38 forming macromolecular complexes, which promoted anti-apoptotic protein Bcl-2 sequestration into endoplasmic reticulum and Golgi apparatus compartments [61]. Importantly, AD-linked presenilin mutants enhanced the pro-apoptotic activity by reducing levels of mitochondrial Bcl-2 [62]. In the light of above, presenilins and other elements of the γ-secretase complex located in mitochondria establish a novel type of cellular signalling and interacting network.

#### **6.3. Hif-1α interaction**

**6. Presenilin interactome: implementation in AD and PA**

and further studies are needed to complement this image.

presenilin biological functions are regulated by complex assembly.

**6.2. Mitochondrial interactome of presenilins**

**6.1. The γ-secretase complex partners**

100 Senescence - Physiology or Pathology

Numerous studies have been conducted in order to identify proteins interacting with PS1 and PS2. Majority of these studies have focused on the key signalling cascades specific for AD, as well as for PA, that is, oxidative stress, generation of free radicals or inflammatory processes. The best studied presenilin partners are components of γ-secretase complex (nicastrin, APH-1 and PEN-2), presenilin substrates (APP, Notch) and proteins involved in a regulation of cell death, calcium homeostasis and cell adhesion. It should be stressed that the knowledge on full PS interactome is crucial for more detailed definition of the pathomechanisms of AD and PA,

Direct partners of presenilins are the components of the γ-secretase complex, namely nicastrin, APH-1 and PEN-2 [44]. Nicastrin associates with the complex comprising PS1-C′ terminal and APH-1 [45]. Nicastrin is required for the assembly of presenilin complexes to mediate Notch signalling and for processing and trafficking of β-amyloid precursor protein and thus plays a role in amyloid plaque formation [46]. Proper signalling between presenilin and nicastrin is important not only for processing of APP and accumulation of Aβ peptides but also for synaptic plasticity [47]. The next component of γ-secretase complex is PEN-2, a membrane protein with two predicted transmembrane domains, both N′ and C′ terminals are in extracellular space and with hydrophilic cytosolic loop [48]. PEN-2 binds to the fourth transmembrane domain of PS and helps to stabilize the γ-secretase complex after PS endoproteolysis [49]. Together with APH-1, PEN-2 is indispensable for Notch signalling [50], exhibiting thus similar properties like nicastrin. Importantly, mutations in TM4 reduced PS1-PEN-2 interaction which was further accompanied by an increased Aβ42 production and disrupted the endoplasmic reticulum calcium homeostasis [51]. The final component of γ-secretase complex is APH-1, a protein composed of seven transmembranes with N-terminus and large loops at cytosolic side [52]. APH-1 contains a conserved GXXXG motif that may be involved in interactions with other subunits of the complex [53]. APH-1 together with nicastrin forms a stable complex that constitutes a scaffold prior to the generation of the full presenilin complex [54]. APH-1 directly interacts with both immature and mature forms of the presenilins and nicastrin and this is indispensable for γ-secretase activity [55]. According to that described above,

The γ-secretase complex was found in mitochondria [56]. Since Aβ is not a substrate for mitochondrial γ-secretase complex, its mitochondrial implication may be related to cell death signalling, switching between necrosis and apoptosis depending on ATP levels [56]. Moreover, PS2 was found to modulate ER-mitochondria juxtaposition and interactions, and that was enhanced in the case of PS2 mutations [57]. In detail, the components of γ-secretase complex were found in mitochondria-associated ER membranes (MAMs) with lipid raft-like domain [58]. Mutations in presenilin 1 were found to impair the IP3 receptor- and voltage-dependent calcium Hypoxia-inducible factor 1α (Hif-1α), which upregulates γ-secretase activity, was recently identified as PSs partner [63]. Hif-1α is related to ubiquitin-mediated proteolysis, induction of angiogenesis, inflammation or increase of vascular tone. Villa et al. [63] showed that Hif-1α acts as a subunit of γ-secretase activity, which is distinct from its canonical role as a transcription factor. Moreover, hypoxia-induced cell invasion and metastasis were improved by either γ-secretase inhibitors or a dominant-negative Notch coactivator, indicating essential role of γ-secretase/Notch signalling [63]. These data provided the molecular mechanism for an increased incidence of AD and PA following cerebral ischaemic injuries and strokes [64]. In addition, cells lacking presenilin 1 were characterized by an impaired induction of HIF-1α in response to hypoxia. Furthermore, presenilin 1 and HIF-1α physical interaction may protect HIF-1α from degradation through proteasome. Additionally, M146V Psen1 mutation impaired metabolic induction of HIF-1α [65]. These data suggest that PS1 regulates the induction of HIF-1α.

#### **6.4. Presenilin interactome of tetraspanin-enriched microdomains (TEMs)**

Tetraspanin-enriched microdomains (TEMs) consist of proteins and lipids crucial for coordination of many biological processes, including cell adhesion, proteolysis, cell motility or sorting to exosomes [66]. A series of proteins transiently interacting with the γ-secretase complex were found in TEM network. Moreover, the disruption of TEM inhibited Aβ production [67]. The study of Wakabayashi and co-workers showed an interaction of γ-secretase complex with tetraspanin proteins, that is, CD81, Upk1b and CD9 and cell surface immunoglobulin superfamily proteins EWI-2 and EWI-F [67]. Another research evidenced that the association of TEM with γ-secretase complex is needed for an enhancement of its proteolytic activity [68]. These data also confirmed a localization of γ-secretase in the raft-like domains [69]. All the above studies revealed that the integrity of tetraspanin microdomains is crucial for presenilins and γ-secretase signalling. In addition to TEM, presenilin complex and its interactive network were shown to be located predominantly in a specialized sub-compartment of ER, spatially and biochemically connected to mitochondria, called mitochondria-associated ER membranes (MAMs). MAM is a lipid raft-like structure, enriched in anionic phospholipids, cholesterol and sphingomyelin. MAM is involved in cholesterol and phospholipid metabolism, calcium homeostasis and in mitochondrial function and dynamics. MAM function was altered and ER–mitochondrial connectivity is significantly increased in AD. The authors of these findings proposed the "MAM-AD hypothesis" with a central role of ER–mitochondrial-presenilin network in AD pathogenesis [70]. Schon and Area-Gomez [71] reported a large list of genes encoded in MAM, including genes involved in the regulation of apoptosis process, maintenance of calcium signalling, inflammatory response (formation of inflammasomes) or protein ubiquitination. In addition, they discovered that a MAM function in cholesteryl ester and phospholipid synthesis was overactive in AD. According to Schon and Area-Gomez [71], MAM is an unexplored research area, and its importance is vastly underestimated in brain pathology, both AD and PA.

#### **6.5. Recent findings on presenilin interactome**

The large list of molecular partners of presenilins supports their extended significance in AD and PA. Testing whole presenilin interactome, instead of selected signalling pathway, is highly recommended due to the fact that any brain pathologies are extremely complex diseases, where causative and susceptibility genes are highly interconnected [72]. Novel PSEN-related genes were discovered through high-throughput immunoaffinity (co-IP and pull-down) studies [73, 74]. Novel findings on PS1 partners involved ST13, GCDH, ECSIT and CDC37 proteins, and novel PS2 partners were PDCD4, DYNC1H1 and ECSIT. These interactions together with the already known might provide a novel and holistic insight into the molecular pathways interconnection underlying various brain pathologies. Soler-López and co-workers also indicated and confirmed a physical connection between apolipoprotein E (APOE) and PS1 [73, 74]. Direct evidence on APOE and PS1 binding provided a novel insight into the pathogenic role of APOE as a regulator of PS1 in APP cleavage. Furthermore, Soler-López et al. also confirmed an interaction between PS1 and PS2, previously suggested to cooperate as part of the γ-secretase complex in APP cleavage [73, 74]. The direct binding of APP with both PS1 and PS2, confirmed by co-IP, had been previously suggested [75]. These results provided a fresh perspective on the possible functions of presenilin in the process of brain degeneration in AD or PA.

Furthermore, the interaction of presenilin with ECSIT components (evolutionarily conserved signalling intermediates in Toll pathway) could constitute a molecular link between oxidative stress, inflammation and mitochondrial dysfunction in AD. Supporting the idea of the implication of presenilins' interactome in oxidative stress response, another component of redox signalling, glutaryl-CoA dehydrogenase (GCDH), also interacts with PS. Moreover, the association of ECSIT with APOE was shown to bind Aβ in its oxidized form Ref. [76]. Another novel example of presenilin interaction partners is the member of the tumour necrosis factor receptor-associated factor (TRAF) family. More precisely, presenilin full-length holo-proteins were suggested to be novel substrates of TRAF6-mediated Lysine-63-linked ubiquitination. Furthermore, TRAF6 induced PS1 gene transcription in a JNK-dependent manner. Notably, TRAF6-mediated ubiquitination of presenilin did not affect γ-secretase enzyme activity, but likely regulated presenilin function in calcium signalling. TRAF6 deficiency coincided with reduced PS1 ubiquitination, protein levels and Ca2+ leakage from ER, suggesting that ubiquitination may be an important regulatory post-translational modification of presenilin function [77]. On the other hand, TRAF6 is involved in nerve growth factor (NGF)-dependent phosphorylation, ubiquitination and association of tropomyosin receptor kinase A (TrkA) with p75NTR, thereby promoting cell survival and differentiation. Under pathological conditions in AD or PA, pro-NGF stimulation can lead to nitrosylation of TrkA, thereby impairing its ubiquitination and downstream signalling which results in apoptosis [78]. In addition, presenilin ubiquitination was shown to be controlled by ubiquilin 1. In detail, ubiquilin 1 promoted the formation of PS1-positive aggregosomes [79, 80]. Furthermore, PS1 ubiquitination was found to demand Cdc4 component of the SCF ubiquitin E2-E3 ligase complex (Skp1-Cdc53/CUL1-F-box protein) and formation of this complex was followed by an increase in Aβ production [81]. Overall, the above-described scientific reports present a large spectrum and different aspects of presenilin interactome, important for brain functions thus implemented in brain pathological ageing or degeneration.

#### **6.6. Presenilins and synaptic transmission**

and sphingomyelin. MAM is involved in cholesterol and phospholipid metabolism, calcium homeostasis and in mitochondrial function and dynamics. MAM function was altered and ER–mitochondrial connectivity is significantly increased in AD. The authors of these findings proposed the "MAM-AD hypothesis" with a central role of ER–mitochondrial-presenilin network in AD pathogenesis [70]. Schon and Area-Gomez [71] reported a large list of genes encoded in MAM, including genes involved in the regulation of apoptosis process, maintenance of calcium signalling, inflammatory response (formation of inflammasomes) or protein ubiquitination. In addition, they discovered that a MAM function in cholesteryl ester and phospholipid synthesis was overactive in AD. According to Schon and Area-Gomez [71], MAM is an unexplored research area, and its importance is vastly underestimated in brain pathology,

The large list of molecular partners of presenilins supports their extended significance in AD and PA. Testing whole presenilin interactome, instead of selected signalling pathway, is highly recommended due to the fact that any brain pathologies are extremely complex diseases, where causative and susceptibility genes are highly interconnected [72]. Novel PSEN-related genes were discovered through high-throughput immunoaffinity (co-IP and pull-down) studies [73, 74]. Novel findings on PS1 partners involved ST13, GCDH, ECSIT and CDC37 proteins, and novel PS2 partners were PDCD4, DYNC1H1 and ECSIT. These interactions together with the already known might provide a novel and holistic insight into the molecular pathways interconnection underlying various brain pathologies. Soler-López and co-workers also indicated and confirmed a physical connection between apolipoprotein E (APOE) and PS1 [73, 74]. Direct evidence on APOE and PS1 binding provided a novel insight into the pathogenic role of APOE as a regulator of PS1 in APP cleavage. Furthermore, Soler-López et al. also confirmed an interaction between PS1 and PS2, previously suggested to cooperate as part of the γ-secretase complex in APP cleavage [73, 74]. The direct binding of APP with both PS1 and PS2, confirmed by co-IP, had been previously suggested [75]. These results provided a fresh perspective on the possible functions of presenilin in the process of

Furthermore, the interaction of presenilin with ECSIT components (evolutionarily conserved signalling intermediates in Toll pathway) could constitute a molecular link between oxidative stress, inflammation and mitochondrial dysfunction in AD. Supporting the idea of the implication of presenilins' interactome in oxidative stress response, another component of redox signalling, glutaryl-CoA dehydrogenase (GCDH), also interacts with PS. Moreover, the association of ECSIT with APOE was shown to bind Aβ in its oxidized form Ref. [76]. Another novel example of presenilin interaction partners is the member of the tumour necrosis factor receptor-associated factor (TRAF) family. More precisely, presenilin full-length holo-proteins were suggested to be novel substrates of TRAF6-mediated Lysine-63-linked ubiquitination. Furthermore, TRAF6 induced PS1 gene transcription in a JNK-dependent manner. Notably, TRAF6-mediated ubiquitination of presenilin did not affect γ-secretase enzyme activity, but likely regulated presenilin function in calcium signalling. TRAF6 deficiency coincided with reduced PS1 ubiquitination,

both AD and PA.

102 Senescence - Physiology or Pathology

**6.5. Recent findings on presenilin interactome**

brain degeneration in AD or PA.

One of the most important pathologies of brain degeneration or pathological ageing is disturbed synaptic transmission. It is believed that the impairment of synaptic function accounts for pathological ageing or degeneration independently on SP deposition. Recently, presenilins were proposed to participate in neurotransmitter release in the γ-secretase function-independent manner. It was reported that presenilins are essential for regulating neurotransmitter release like glutamate, and its inhibition is mediated by a depletion of ER Ca2+ storage and a block of intracellular Ca2+ release [82]. Importantly, PS1 knockout and PS1-M146V neurons did not exhibit synaptic strengths. On the other hand, synaptic activity was found to modulate PS1 activity and Aβ40/42 ratio via altering PS1 conformation [83]. Additionally, it has recently been demonstrated that the interaction of PS1 with synaptic vesicle-associated protein, synaptotagmin 1 (Syt1), implicated novel synaptic functions of PS1, and both proteins modulated each other's functions in neurons via direct activity-triggered interaction, and the PS1-Syt1 complexes were crucial for exocytosis at the synapses and safeguarding of PS1 conformation [84]. Overall, mounting evidence points to a role of presenilins in synaptic transmission. It is clear that the interplay between presenilins and synaptic activity could originate from presenilins γ-secretase activity.

#### **6.7. Other aspects of interactomes of presenilins 1 and 2**

PS1 and PS2 can exhibit distinct from γ-secretase activities [85]. For instance, it has been demonstrated that autophagy and lysosomal proteolysis required presenilin 1 [86], as well as presenilin 2 through a γ-secretase-independent mechanism [87]. Further detailed analyses revealed novel interactions of the γ-secretase core complex with a molecular machinery targeting synaptic vesicles to cellular membranes, and with the H+ -transporting lysosomal ATPase macrocomplex [88]. Importantly, lysosomal dysfunction is also associated with many age-related pathologies like Parkinson's and Alzheimer's disease, as well as with a decline in lifespan. Conversely, targeting lysosomal functional capacity is emerging as a means to promote longevity [89]. Another example of γ-secretase-independent interaction is the catenin/

cadherin network that was almost exclusively found associated with PS1. In detail, catenin α2, catenin β1 and plakophilin 4, as well as the cadherins 2 and 11, were repeatedly and strongly enriched in the PS1-specific sample [90]. On the other hand, an intramembrane protease, signal peptide peptidase (SPP), predominantly co-purified with PS2-containing γ-secretase complexes and was observed to influence Aβ production [90]. Another interesting interaction was found between PS2 and DREAM protein [91]. The Ca2+-binding protein DREAM regulates gene transcription and activity of potassium channels in neurons. DREAM interaction with PS2 might have implication in the regulation of the Ca2+ content in endoplasmic reticulum. The transient co-expression of DREAM and presenilin 2 potentiated the decrease of endoplasmic reticulum Ca2+ observed in presenilin-overexpressing cells. This could be due to a direct effect of DREAM on presenilin 2 as the two proteins interacted in a Ca2+-independent fashion. Finally, an example of an interaction unique to PS2 is the DRAL protein. DRAL is an LIM-only protein containing four LIM domains and an N-terminal half LIM domain. The PS2-DRAL interaction was confirmed using yeast two-hybrid and immunoaffinity studies, suggesting that DRAL functioned as an adaptor protein that links PS2 to an intracellular signalling [92]. This paragraph outlines the differences between PS1 and PS2, and cautions against correct attributing of a given interactome with disease phenotype.

### **7. Pathological ageing and Alzheimer's disease in the** *omic* **era**

The above-presented insight on the presenilins' interactome provides important information about the background of pathological ageing and neurodegeneration. Nevertheless, the protein interactome is still only a small fragment recognized by the systemic biology. Thus, there is a need to integrate interactome data with other high-throughput data. The importance of integration of different parts of biological systems is stressed by the fact of becoming an ageing society. Undoubtedly, the ageing is one of the major risk factors for various diseases, ranging from cancer, cardiovascular diseases, type 2 diabetes (T2D) and ending with Alzheimer's disease. This creates a long list of ageing-related diseases (ARDs). In this regard, a recognition of the whole functional network linking ageing and ARD becomes one of the key tasks of current medical science. In the era of *omics* research, publicly available domains allow comparison of genomics, transcriptomics, proteomics, metabolomics, miRomics, epigenomics, regulomics (regulatory genomics), microbiomics, and lipidomics with particular diseasome [93]. These criteria are met by the 'GeroNet' research model, an approach that is targeting the relationship between ageing and hundreds of ARD [94]. These studies indicated several subnetworks associated with ageing, including 'response to reduced oxygen levels' or 'cell cycle checkpoints'. Importantly, the GeroNet model has helped to identify several genes that may play a key role combining pathological ageing and Alzheimer's disease, including the top five most significant STAT3, P53, FOS, BCL2 and NFKB1. The next example of integration of several omics research is analysis of the genes associated with longevity and ageing, collected in Ageing Gene/Interventions database (http://www.kaeberleinlab.org/ageid) and in GenAge database, which can be useful for the research on different interactome networks in AD or PA. Another recent *omic* approach was presented in the studies on inflammaging with propagation of pro- and anti-inflammatory mediators in a dynamic manner from cell to cell and from organ to organ, supplemented by glycomics data [95]. Additionally, other widegenomic studies revealed longevity and age-related functional biological networks, underlining the importance of neuronal development, autophagy and other processes associated with Alzheimer's diseases [96]. Furthermore, the integration of various systemic biology data has revealed common mechanisms associated with genomic instability and reduced capacity to DNA repair for both ageing and neurodegeneration. [97, 98]. Genomic instability is also influenced by a number of epigenetic changes that can be associated with both ageing and AD. These epigenetic changes occur at different levels, for example, histone methylation pattern, replacement of the canonical histones by rare variants of histones or regulated by an altered expression of non-coding RNA [99]. Indeed, there are studies confirming a decrease in genome-wide DNA methylation occurring in both ageing and AD patients [100]. Significantly, epigenetic regulation of the presenilins 1 and 2 was found to be pivotal in the development of the cerebral cortex of mice [101]. This epigenetic regulation of PS1 and PS2 was controlled by the acetylation and methylation of histone H3K9/14 and this was associated with further differential expression of PS1 and PS2, as well as their interacting protein partners. These data indicated that multiple levels of epigenetic regulation may be involved in controlling the formation of amyloid beta. Given epigenetic context, interestingly, dietary supplementation with B group vitamins restored methylation of promoters of presenilin 1, APP and BACE1 and slowed down the progression of AD [102]. In addition, this was associated with a decrease in oxidative stress and a delay in the accumulation of neurological symptoms in transgenic mice with beta amyloid pathology [102]. Generally, the methylation status of all the elements of presenilins' interactome may be suitable for future research on ageing and AD. Supplementing the above data, an important matter in the era of omics research is the use of appropriate computational and mathematical models. One example is weighted gene co-expression network analysis method (WGCNA), which by the use of large omics data may predict genegene, protein-protein, or gene-miRNA interaction nature [103]. In particular, the WGCNA method was used to organize gene expression data into a functionally significant structure, in order to indicate the modules of co-expressed genes and novel gene signatures associated with Alzheimer's disease [104].

cadherin network that was almost exclusively found associated with PS1. In detail, catenin α2, catenin β1 and plakophilin 4, as well as the cadherins 2 and 11, were repeatedly and strongly enriched in the PS1-specific sample [90]. On the other hand, an intramembrane protease, signal peptide peptidase (SPP), predominantly co-purified with PS2-containing γ-secretase complexes and was observed to influence Aβ production [90]. Another interesting interaction was found between PS2 and DREAM protein [91]. The Ca2+-binding protein DREAM regulates gene transcription and activity of potassium channels in neurons. DREAM interaction with PS2 might have implication in the regulation of the Ca2+ content in endoplasmic reticulum. The transient co-expression of DREAM and presenilin 2 potentiated the decrease of endoplasmic reticulum Ca2+ observed in presenilin-overexpressing cells. This could be due to a direct effect of DREAM on presenilin 2 as the two proteins interacted in a Ca2+-independent fashion. Finally, an example of an interaction unique to PS2 is the DRAL protein. DRAL is an LIM-only protein containing four LIM domains and an N-terminal half LIM domain. The PS2-DRAL interaction was confirmed using yeast two-hybrid and immunoaffinity studies, suggesting that DRAL functioned as an adaptor protein that links PS2 to an intracellular signalling [92]. This paragraph outlines the differences between PS1 and PS2, and cautions against correct

attributing of a given interactome with disease phenotype.

104 Senescence - Physiology or Pathology

**7. Pathological ageing and Alzheimer's disease in the** *omic* **era**

The above-presented insight on the presenilins' interactome provides important information about the background of pathological ageing and neurodegeneration. Nevertheless, the protein interactome is still only a small fragment recognized by the systemic biology. Thus, there is a need to integrate interactome data with other high-throughput data. The importance of integration of different parts of biological systems is stressed by the fact of becoming an ageing society. Undoubtedly, the ageing is one of the major risk factors for various diseases, ranging from cancer, cardiovascular diseases, type 2 diabetes (T2D) and ending with Alzheimer's disease. This creates a long list of ageing-related diseases (ARDs). In this regard, a recognition of the whole functional network linking ageing and ARD becomes one of the key tasks of current medical science. In the era of *omics* research, publicly available domains allow comparison of genomics, transcriptomics, proteomics, metabolomics, miRomics, epigenomics, regulomics (regulatory genomics), microbiomics, and lipidomics with particular diseasome [93]. These criteria are met by the 'GeroNet' research model, an approach that is targeting the relationship between ageing and hundreds of ARD [94]. These studies indicated several subnetworks associated with ageing, including 'response to reduced oxygen levels' or 'cell cycle checkpoints'. Importantly, the GeroNet model has helped to identify several genes that may play a key role combining pathological ageing and Alzheimer's disease, including the top five most significant STAT3, P53, FOS, BCL2 and NFKB1. The next example of integration of several omics research is analysis of the genes associated with longevity and ageing, collected in Ageing Gene/Interventions database (http://www.kaeberleinlab.org/ageid) and in GenAge database, which can be useful for the research on different interactome networks in AD or PA. Another recent *omic* approach was presented in the studies on inflammaging with

Overall, ADs or PAs are systemic diseases based on the interplay of several cellular networks. Thus, it should be noted that conducting the research only on individual protein factors, as the studies on presenilins and processing of APP, is only a part of the holistic homeostatic insight on these pathological states and such comprehensive approach is still missing in the discussion. Due to wide-range nature of ageing and degeneration process, the conducted studies should be more non-deterministic, without a concrete causation and particular trigger (gene, protein pathway). The holistic approach should include the response to DNA repair with cell cycle and genome integrity checkpoints, proteostasis, unfolded protein response, proteinfolding chaperone networks, ER-associated degradation/ubiquitin proteasome system, endolysosomal network, autophagy, inflammatory response and other stress-response networks. This can be accomplished by integration of various omics data and can be fulfilled when supported by latest methods and research approaches including next-generation sequencing, modern neuroimaging or high-throughput computational bioinformatic studies. Complexity and multi-level nature of the network of genes, proteins, their interactomes and relationships with ageing-related disease processes present in both AD and PA have been reported in several recent review papers [94, 98, 105–107]. This and other reviews underline the importance of the integration of different biological data provided for the process of brain degeneration, in both PA and AD, and other neurodegeneration disorders with dementia.
