Biological mechanisms of aging predict age‐related disease co‐occurrence in patients

Abstract Genetic, environmental, and pharmacological interventions into the aging process can confer resistance to multiple age‐related diseases in laboratory animals, including rhesus monkeys. These findings imply that individual mechanisms of aging might contribute to the co‐occurrence of age‐related diseases in humans and could be targeted to prevent these conditions simultaneously. To address this question, we text mined 917,645 literature abstracts followed by manual curation and found strong, non‐random associations between age‐related diseases and aging mechanisms in humans, confirmed by gene set enrichment analysis of GWAS data. Integration of these associations with clinical data from 3.01 million patients showed that age‐related diseases associated with each of five aging mechanisms were more likely than chance to be present together in patients. Genetic evidence revealed that innate and adaptive immunity, the intrinsic apoptotic signaling pathway and activity of the ERK1/2 pathway were associated with multiple aging mechanisms and diverse age‐related diseases. Mechanisms of aging hence contribute both together and individually to age‐related disease co‐occurrence in humans and could potentially be targeted accordingly to prevent multimorbidity.


(e) DNS, (f) MD and (g) CS GO Terms
response to glucose regulation of lipid metabolic process glucose homeostasis regulation of insulin secretion (glucose stimulus) CAMKK−AMPK signaling cascade glucose mediated signaling pathway regulation of glucose transmembrane transport response to nutrient regulation of lipid storage regulation of insulin secretion regulation of TORC1 signaling positive regulation of insulin secretion cellular response to insulin stimulus negative regulation of insulin secretion (glucose stimulus) positive regulation of glucose transmembrane transport neutral lipid metabolic process negative regulation of lipid storage regulation of protein lipidation response to nutrient levels regulation of mitochondrial fission intracellular distribution of mitochondria establishment of mitochondrion localization protein insertion into mitochondrial membrane (apoptosis) negative regulation of reactive oxygen species biosynthetic process positive regulation of release of cytochrome c from mitochondria negative regulation of protein targeting to mitochondrion dynamin family protein polymerization involved in mitochondrial fission protein import into mitochondrial outer membrane positive regulation of protein insertion into mitochondrial membrane (apoptosis) positive regulation of autophagy of mitochondrion reactive oxygen species metabolic process positive regulation of reactive oxygen species metabolic process replicative senescence negative regulation of cellular senescence replicative cell aging cell aging positive regulation of cellular senescence

(h) SCE and (i) AIC GO Terms
regulation of somatic stem cell population maintenance stem cell differentiation somatic stem cell division somatic stem cell population maintenance positive regulation of stem cell population maintenance stem cell proliferation hematopoietic stem cell proliferation negative regulation of stem cell proliferation positive regulation of stem cell proliferation negative regulation of inflammatory response hormone biosynthetic process thyroid hormone generation negative regulation of neurotransmitter secretion inflammatory response to antigenic stimulus response to growth hormone regulation of hormone secretion inflammatory response wound healing negative regulation of neurotransmitter uptake follicle−stimulating hormone secretion negative regulation of acute inflammatory response synaptic transmission, cholinergic neuromuscular synaptic transmission regulation of synaptic transmission, GABAergic positive regulation of transmission of nerve impulse positive regulation of neurotransmitter secretion peptide hormone processing steroid hormone mediated signaling pathway growth hormone receptor signaling pathway regulation of growth hormone receptor signaling pathway cellular response to corticotropin−releasing hormone stimulus positive regulation of peptide hormone secretion response to thyroid hormone cellular response to thyroid hormone stimulus  Figure S2. Subnetworks of top 30 ranked ARDs after network propagation for (a) mitochondrial dysfunction (60-69 years) and (b) deregulated nutrient sensing (60-69 years). Nodes are coloured by ARD ranking after network propagation for a given aging hallmark. The 1 st to 10 th ranked ARDs for a given aging hallmark are red, the 11 th to 20 th ranked ARD for a given aging hallmark are in orange and the 21 st to 30 th ranked ARDs for a given aging hallmark are yellow. The abbreviations are listed in Table S9.  Tables   Table S1. The 65 aging hallmark taxonomy terms derived from "The Hallmarks of Aging" paper. The table shows quotations from "The Hallmarks of Aging" paper by Lopez-Otin et al. (2013), which support the selection of taxonomy terms. Occasionally, taxonomy terms are inferred rather than being directly mentioned in "The Hallmarks of Aging" , which is indicated with (i).

Original Aging Hallmark
Taxonomy Term(s) Supporting quotations from "The Hallmarks of Aging" (Lopez-Otin et al., 2013) or rationale Genomic Instability Genomic instability "Genomic Instability" (Hallmark of Aging) Somatic mutations "Somatic mutations accumulate within cells from aged humans." DNA damage, Chromosomal breakage "Other forms of DNA damage, such as chromosomal aneuploidies and copy number variations, have also been found associated with aging." Transposable elements "The genetic lesions arising from extrinsic or intrinsic damage are highly diverse and include … gene disruption caused by the integration of viruses or transposons". DNA repair deficiencies "Deficiencies in DNA repair mechanisms cause accelerated aging." mtDNA mutations "Mutations and deletions in aged mtDNA may also contribute to aging." mtDNA damage "The first evidence that mtDNA damage might be important for aging and ARDs derived from the identification of human multisystem disorders caused by mtDNA mutations." Double strand (ds)-DNA breaks "Note that both nuclear DNA and mitochondrial DNA are subjected to age-associated genomic alterations … double strand breaks." DNA breaks (i), Single strand (ss)-DNA breaks (i) "The genetic lesions arising from intrinsic and extrinsic damages are highly diverse and include point mutations … ". Additional examples include single-strand DNA breaks or, more generally, DNA breaks 1 .

Telomere Attrition
Telomere attrition "Telomere Attrition" (Hallmark of Aging) Decreased telomere length, Decreased leukocyte telomere length (i) "In humans, recent meta-analyses have indicated a strong relation between short telomeres and mortality risk, particularly at younger ages." Leukocyte telomere length is a more specific subcategory of decreased telomere length 2 .

Epigenetic Alterations
Epigenetic alterations "Epigenetic Alterations" (Hallmark of Aging) Gene transcription, coding-RNAs "Aging is associated with an increase in transcriptional noise, and an aberrant production and maturation of many mRNAs." microRNAs, non-coding RNAs "The aging-associated transcriptional signatures also affect non-coding RNAs, including a class of miRNAs that is associated with the aging process". Histone modifications, histone acetylation, histone methylation, DNA methylation "Alterations in the acetylation and methylation of DNA or histones, as well as of other chromatinassociated proteins, can induce epigenetic changes that contribute to the aging process."

Loss of Proteostasis
Loss of proteostasis "Loss of Proteostasis" (Hallmark of Aging) Proteolysis, autophagy, proteasome "The activities of the two principal proteolytic systems implicated in protein quality control, namely, the autophagy-lysosomal system and the ubiquitin-proteasome system, decline with aging." Protein aggregation "Failure to refold or degrade unfolded proteins can lead to their accumulation and aggregation, resulting in proteotoxic effects." ER stress, unfolded protein response (UPR) "Endogenous and exogenous stress causes the unfolding of proteins … ER Stress. Unfolded proteins are usually refolded by heat-shock proteins (HSP) or targeted to destruction by the ubiquitin-proteasome or lysosomal (autophagic) pathways." Chaperone "The stress-induced synthesis of cytosolic and organelle-specific chaperones is significantly impaired in aging."

Deregulated Nutrient Sensing
Deregulated nutrient sensing "Deregulated Nutrient Sensing" (Hallmark of Aging) Insulin resistance, dyslipidaemia (i) "Thus, a decreased IIS is a common characteristic of both physiological and accelerated aging, while a constitutively decreased IIS extends longevity." Dyslipidaemia is also associated with deregulated nutrient sensing 3 . IIS pathway, nutrient-sensing pathways "In addition to the IIS pathway that participates in glucose-sensing, three additional related and interconnected nutrient-sensing systems are the focus of intense investigation…" mTORC1 "These observations, together with those involving the IIS pathway, indicate that intense trophic and anabolic activity, signalled through the IIS or the mTORC1 pathways, are major accelerators of aging." AMPK, sirtuin 1 "The other two nutrient sensors, AMPK and sirtuins, act in the opposite direction to IIS and mTOR, meaning that they signal nutrient scarcity and catabolism instead of nutrient abundance and anabolism. Accordingly, their up-regulation favours healthy aging. Moreover, SIRT1 and AMPK can engage in a positive feedback loop, thus connecting both sensors of low-energy states into a unified response."

Mitochondrial Dysfunction
Mitochondrial dysfunction "Mitochondrial Dysfunction" (Hallmark of Aging) Mitochondrial toxicity (i) "Mitochondrial function becomes perturbed by aging-associated mtDNA mutations …". Another cause of perturbed mitochondrial function is toxin exposure, such as from alcohol, termed mitochondrial toxicity 4 . Reactive oxygen species (ROS) "As chronological age advances, the levels of ROS increase in an attempt to maintain survival until they betray their original purpose and eventually aggravate, rather than alleviate, the ageassociated damage." Mitochondrial bioenergetics, mitochondrial biogenesis "The reduced efficiency of mitochondrial bioenergetics with aging may result from multiple converging mechanisms including reduced biogenesis of mitochondria." Mitochondrial turnover, mitochondrial degradation "The combination of increased damage and reduced turnover in mitochondria, due to lower biogenesis and reduced clearance, may contribute to the aging process." Electron transport chain (ETC), mitochondrial dynamics, Krebs cycle (i) "Mitochondrial function becomes perturbed by aging-associated mtDNA mutations, reduced mitochondriogenesis, destabilization of the electron transport chain (ETC) complexes, altered mitochondrial dynamics or defective quality control by mitophagy." The Krebs cycle produces electron carriers that pass electrons to the electron transport chain (ETC).

Cellular Senescence
Cellular senescence "Cellular Senescence" (Hallmark of Aging) Senescence markers "The accumulation of senescent cells in aged tissues has been often inferred using surrogate markers, such as DNA damage. Some studies have directly used senescence-associated βgalactosidase (SABG) to identify senescence in tissues." Senescence-associated secretory phenotype (SASP) "Senescent cells manifest dramatic alterations in their secretome, which … is referred to as the 'senescence-associated secretory phenotype'." Immunosenescence (i) Immunosenescence describes age-related alterations in the function of the immune system 5 and is partly explained by cellular senescence 6 .

Stem Cell Exhaustion
Stem cell exhaustion "Stem Cell Exhaustion" (Hallmark of Aging) Progenitor cell, stem cell "Although deficient proliferation of stem and progenitor cells is obviously detrimental for the long-term maintenance of the organism." Stem cell self-renewal "Studies on aged mice have revealed an overall decrease in cell cycle activity of hematopoietic stem cells (HSCs), with old HSCs undergoing fewer cell divisions than young HSCs." Altered Intercellular Comm.

Altered intercellular communication
"Altered Intercellular Communication" (Hallmark of Aging) Endocrine signalling, neuronal signalling, hormone (i), neurotransmitters (i) "Aging also involves changes at the level of intercellular communication, be it endocrine, neuroendocrine or neuronal." In endocrine signalling, the signalling molecules are hormones. In neuronal signalling, the signalling molecules neurotransmitters.
Inflammaging "A prominent aging-associated alteration in intercellular communication is 'inflammaging'." Inflammatory signalling "Inflammaging may result from multiple causes such as the accumulation of pro-inflammatory tissue damage." Inflammation "Inflammation" (Subheading)  • generation or presence of reactive oxygen species (ROS) or active oxygen • mitochondrial dysfunction or degeneration • altered mitochondrial dynamics or bioenergetics • mitochondrial damage • impaired mitochondrial turnover including mitochondrial biogenesis or mitophagy Cellular Senescence • accelerated, early or enhanced cellular senescence, replicative senescence or immunosenescence • activation of cellular senescence or cellular aging • association with the senescence-associated secretory phenotype (SASP)

• increased senescent cells or expression of senescence markers Stem Cell Exhaustion
• reduced number, impaired proliferative capacity or increased destruction of stem cells or progenitor cells • impaired function, mobilization or exhaustion of stem cells or progenitor cells • aging or senescence of stem cells or progenitor cells • decreased number of circulating stem cells or progenitor cells • decreased stem cell or progenitor cell differentiation • stem cell disorder Altered Intercellular Communication • increased inflammation • decreased levels of specific hormones, e.g. oestradiol, testosterone • decreased synaptic transmission • increased levels of specific hormones, e.g. parathyroid hormone Table S4. Examples of sentences correctly reporting that an aging hallmark (yellow) has a role in the development or disordered physiology of an ARD (grey). Sentences such as these were labelled as a "confirmed association" between an aging hallmark and an ARD on manual curation. Those aging hallmark-ARD combinations with insufficient evidence were set to zero.  Table S7. Network density of subnetworks of the top 30 ranking ARD nodes after network propagation for age categories 50-59 years, 60-69 years, 70-79 years and ≥80 years. The number of times the network density from permutations (n = 20,000) was greater than or equal to the true network density for that aging hallmark was used to calculate the pvalue. The p-value was corrected for multiple testing across the 4 age categories per aging hallmark using the Benjamini-Hochberg procedure (*p < 0.05, ** p <0.01, *** p <0.001, ****p<0.0001). Articles were required to be indexed with the "journal article" publication type. Publication date Journal articles published between the date of the landmark paper on lifespan extension, "A C. elegans mutant lives twice as long as wildtype", on 2 nd December 1993 to 31 st December 2017 were included.

English language
Abstracts were required to be in English.

Humans
We confined our search to the literature on humans because certain mechanisms of aging are only found in particular evolutionary lineages 16 . Therefore, articles were required to be indexed with the humans Medical Subject Heading (MeSH) term, as certain mechanisms of aging are private.

Aging synonyms
Articles were required to be associated with one of 43 aging terms. b) Exclusion Criteria Rationale Specific publication types Reviews, introductory journal articles, retractions of publication, letters to the editor and comments were excluded in order to retrieve high quality original research rather than data from secondary sources. We excluded review articles to avoid re-using content within the scientific literature.

Germline mutation
Abstracts mentioning, or indexed with, 'germline mutations' or related terms were excluded. Germline mutations can be a consequence of the maternal or paternal aging process. Thus, germline mutations were excluded to maximize retrieval of articles focused on the effects of the individual's own aging process.

Telomerase activation and inhibition
Abstracts mentioning 'telomerase activation', 'telomerase inhibition' or related terms were excluded. Telomerase activation is a consequence of cancer progression, as opposed to aging, and leads to telomere lengthening. Therefore, telomerase activation and inhibition were excluded to reduce selection of irrelevant abstracts under the telomere attrition aging hallmark. Adverse drug effects Abstracts reporting adverse drug effects, such as DNA damage from chemotherapy for cancer, were excluded to reduce selection of irrelevant abstracts. Hormone preparations and anti-inflammatory drugs Abstracts mentioning 'hormone preparations', 'anti-inflammatory drugs' or related terms, were excluded to reduce selection of irrelevant abstracts under the altered intercellular communication aging hallmark. Stem cell transplant Abstracts mentioning 'stem cell transplant', or related terms, were excluded to reduce selection of irrelevant abstracts under the stem cell exhaustion aging hallmark.

Induced Pluripotent stem cells (iPSC)
Abstracts mentioning, or indexed with, induced pluripotent stem cells (iPSC) or related terms were excluded. iPSC are used experimentally to treat ARDs, which can result in incorrect selection of abstracts under the stem cell exhaustion aging hallmark. Neoplastic stem cells Abstracts mentioning, or indexed with, 'neoplastic stem cells' or related terms were excluded. According to the cancer stem-cell hypothesis, neoplastic stem cells are responsible for cancer tumour growth. This contrasts with stem cell exhaustion, where loss of stem cells leads to ARD development. Therefore, neoplastic stem cells were excluded to avoid incorrect selection of abstracts under the stem cell exhaustion aging hallmark.

GWAS catalog
We excluded PMIDs that were linked to studies included from the GWAS catalog. Thus, the genetic approach to verifying aging hallmark-ARD associations was independent of the literature-based method.