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This study presents a comprehensive multiomics ana This study presents a comprehensive multiomics analysis of an extraordinary human subject, M116, the world’s oldest verified living person from January 2023 until her death in August 2024 at the age of 117 years and 168 days. Born in 1907 in San Francisco to Spanish parents, M116 spent most of her life in Spain. Despite surpassing the average female life expectancy in Catalonia by over 30 years, she maintained an overall good health profile until her final months. The research aimed to dissect the molecular and cellular factors contributing to her extreme longevity by integrating genomic, epigenomic, transcriptomic, proteomic, metabolomic, and microbiomic data derived primarily from blood, saliva, urine, and stool samples.
Key Insights and Findings
Longevity is multifactorial, with no single genetic or molecular determinant but rather a complex interplay of rare genetic variants, preserved molecular functions, and adaptive physiological traits.
Extreme age and poor health are decoupled; M116 exhibited biological markers of advanced age alongside molecular features indicative of healthy aging.
Molecular assessments reveal preserved and robust biological functions that likely contributed to her extended lifespan.
Genomic Landscape
Telomere Length:
M116 exhibited extremely short telomeres (~8 kb), shorter than all healthy volunteers studied, with 40% of her telomeres below the 20th percentile.
This suggests telomere attrition acts more as a biological aging clock rather than a predictor of age-associated diseases in this context.
The short telomeres may have contributed to cancer resistance by limiting malignant cell replication.
Structural Variants (SVs):
Ten rare SVs identified via Optical Genome Mapping, including a large 3.3 Mb deletion on chromosome 4 and a 93.5 kb deletion on chromosome 17.
These SVs may play unknown roles but were not associated with detrimental gross chromosomal alterations.
Rare Genetic Variants:
Whole Genome Sequencing identified ~3.8 million SNVs; after filtering, 91,666 variants of interest (VOI) affecting 25,146 genes were analyzed.
Seven homozygous rare variants unique to M116 were found in genes linked to immune function, cognitive retention, longevity, pulmonary function, neuroprotection, and DNA repair (e.g., DSCAML1, MAP4K3, TSPYL4, NT5DC1, PCDHA cluster, TIMELESS).
Functional enrichment highlighted pathways involving:
Immune system regulation (e.g., T cell differentiation, response to pathogens, antigen receptor signaling)
Neuroprotection and brain health
Cardioprotection and heart development
Cholesterol metabolism and insulin signaling
Mitochondrial function and oxidative phosphorylation
Mitochondrial function assays showed robust mitochondrial membrane potential and superoxide ion levels in M116’s PBMCs, surpassing those in younger controls, indicating preserved mitochondrial health.
Burden Tests:
Identified genes with significantly higher rare variant load related to neuroprotection and longevity (e.g., EPHA2, MAL, CLU, HAPLN4).
No single gene or pathway explained longevity; rather, multiple pathways acted synergistically.
Blood Cellular and Molecular Characteristics
Clonal Hematopoiesis of Indeterminate Potential (CHIP):
M116 harbored CHIP-associated mutations: one in SF3B1 (RNA splicing factor) and two in TET2 (DNA demethylase) with variant allele frequency >2%.
Despite this, she did not develop malignancies or cardiovascular disease, suggesting CHIP presence does not necessarily translate to disease.
Single-cell RNA Sequencing (scRNA-seq) of PBMCs:
Identified a diverse immune cell repertoire including naive and memory B cells, NK cells, monocytes, and T cell subpopulations.
Notably, M116 exhibited an expanded population of age-associated B cells (ABCs), expressing markers SOX5 and FCRL2, a feature unique compared to other supercentenarians.
The T cell compartment was dominated by effector and memory cytotoxic T cells, consistent with prior observations in supercentenarians.
Metabolomic and Proteomic Profiles
Metabolomics (1H-NMR Analysis):
Compared with 6,022 Spanish individuals, M116’s plasma showed:
Extremely efficient lipid metabolism:
Very low VLDL-cholesterol and triglycerides
Very high HDL-cholesterol (“good cholesterol”)
High numbers of medium and large HDL and LDL particles, indicating effective lipoprotein maturation.
Low levels of lipid biomarkers associated with poor health (saturated fatty acids, esterified cholesterol, linoleic acid, acetone).
High free cholesterol levels linked to good health and survival.
Low glycoproteins A and B, suggesting a low systemic inflammatory state (“anti-inflammaging”).
Cardiovascular risk-associated metabolites supported excellent cardiovascular health.
Some amino acid levels (glycine, histidine, valine, leucine) were low, and lactate and creatinine were high, consistent with very advanced chronological age and imminent mortality.
Proteomics of Extracellular Vesicles (ECVs):
Compared to younger post-menopausal women, 231 proteins were differentially expressed.
GO enrichment revealed eight functional clusters: coagulation, immune system, lipid metabolism, apoptosis, protein processing, detoxification, cellular adhesion, and mRNA regulation.
Proteomic signatures indicated:
Increased complement activation and B cell immunity
Enhanced lipid/cholesterol transport and lipoprotein remodeling
Elevated oxidative stress response and detoxification mechanisms
The most elevated protein was serum amyloid A-1 (SAA1), linked to Alzheimer’s disease, yet M116 showed no neurodegeneration.
Gut Microbiome Composition
16S rDNA sequencing compared M116’s stool microbiome to 445 healthy controls (61-91 years old).
M116’s microbiome showed:
Higher alpha diversity (Shannon index 6.78 vs. 3.05 controls), indicating richer microbial diversity.
Distinct beta diversity, clearly separating her microbiome from controls.
Markedly elevated Actinobacteriota phylum, primarily due to Bifidobacteriaceae family and Bifidobacterium genus, which typically decline with age but are elevated in centenarians.
Bifidobacterium is associated with anti-inflammatory effects, production of short-chain fatty acids, and conjugated linoleic acid, linking to her efficient lipid metabolism.
Lower relative abundance of pro-inflammatory genera such as Clostridium and phyla Proteobacteria and Verrucomicrobiota, associated with frailty and inflammation in older adults.
Diet likely influenced microbiome composition; M116 consumed a Mediterranean diet and daily yogurts containing Streptococcus thermophilus and Lactobacillus delbrueckii, which promote Bifidobacterium growth.
Epigenetic and Biological Age Analysis
DNA Methylation Profiling (Infinium MethylationEPIC BeadChip):
Identified 69 CpG sites with differential methylation (β-value difference >50%) compared to controls aged 21-78 years.
Majority (68%) showed hypomethylation, consistent with known aging-associated DNA methylation changes.
Differential CpGs were more often outside CpG islands and enriched in gene bodies or regulatory regions.
Hypomethylation correlated with altered expression of genes involved in:
Vascular stemness (EGFL7)
Body mass index regulation (ADCY3)
Macular degeneration (PLEKHA1)
Bone turnover (VASN)
Repetitive DNA Elements:
Unlike typical age-associated global hypomethylation, M116 retained hypermethylation in repetitive elements (LINE-1, ALU, ERV), suggesting preserved genomic stability.
Epigenetic Clocks:
Six different DNA methylation-based epigenetic clocks and an independent rDNA methylation clock (using Whole Genome Bisulfite Sequencing) consistently estimated M116’s biological age to be significantly younger than her chronological age (~117 years).
This indicates a decelerated epigenetic aging process in M116’s cells, which may contribute to her longevity.
Integration and Conclusions
Coexistence of Advanced Age Biomarkers and Healthy Aging Traits:
M116 simultaneously exhibited biological signatures indicative of very old age (short telomeres, CHIP mutations, aged B cell populations) and preserved healthy molecular and functional profiles (genetic variants protective against diseases, efficient lipid metabolism, anti-inflammatory gut microbiome, epigenome stability, robust mitochondrial function).
Decoupling of Aging and Disease:
These findings challenge the assumption that aging and disease are inseparably linked, showing that extreme longevity can occur with a healthy functional tissue environment despite advanced biological age markers.
Multidimensional and Multifactorial Basis of Longevity:
The supercentenarian’s extended lifespan likely resulted from the synergistic effects of rare genetic variants, favorable epigenetic patterns, preserved mitochondrial and immune function, healthy metabolism, and a beneficial microbiome, rather than any single factor.
Potential Implications:
Understanding the interplay of these factors could open avenues for promoting healthy aging and preventing age-related diseases in the general population.
Timeline and Demographics of M116
Event Date / Age Notes
Birth March 4, 1907 San Francisco, USA
Moved to Spain 1915 (age 8) Following father’s death
Lived in elderly residence 2001 - 2024 Olot, Catalonia, Spain
COVID-19 Infection Not specified Survived
Death August 19, 2024 (age 117y, 168d) While sleeping, no major neurodegeneration or cancer recorded
Summary Table of Key Molecular Features in M116
Feature Status in M116 Interpretation/Significance
Telomere length Extremely short (~8 kb) Aging clock marker; may limit cancer risk
Structural variants 10 rare SVs, including large deletions Unknown effect; no gross chromosomal abnormalities
Rare homozygous variants 7 unique variants in longevity/immune-related genes Suggest combined genetic contribution to longevity
CHIP mutations Present (SF3B1, TET2 mutations) No malignancy or cardiovascular disease
Mitochondrial function Robust membrane potential & superoxide levels Preserved energy metabolism
Immune cell composition Expanded ABCs, enriched cytotoxic T cells Unique immune profile linked to longevity
Lipid metabolism Very efficient (high HDL, low VLDL) Cardiovascular protection
Inflammation Low glycoproteins A & B levels Reduced inflammaging
Gut microbiome High Bifidobacterium abundance Anti-inflammatory, supports metabolism
DNA methylation Predominantly hypomethylated CpGs with preserved methylation in repeats Epigenetic stability and decelerated aging
Biological age (epigenetic clocks) Significantly younger than chronological age Indicative of healthy aging
Proteomic profile Upregulated immune and lipid metabolism proteins; elevated SAA1 Protective mechanisms with unexplained elevated SAA1
Keywords
Supercentenarian, Extreme Longevity, Multiomics, Telomere Attrition, Rare Genetic Variants, Clonal Hematopoiesis (CHIP), Immune Cell Profiling, Mitochondrial Function, Metabolomics, Proteomics, Gut Microbiome, DNA Methylation, Epigenetic Clock, Biological Age, Inflammaging, Lipid Metabolism
Conclusion
This landmark study of M116 provides the first extensive multiomics blueprint of extreme human lifespan, revealing that exceptional longevity arises from a balance of advanced biological aging markers coupled with preserved and enhanced molecular functions across multiple systems. The results underscore the importance of immune competence, metabolic health, epigenetic stability, and microbiome composition in sustaining health during extreme aging, offering valuable insights into the biological underpinnings of healthy human longevity.
Smart Summary
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