Rounds of TPE diminish DNA damage and senescence of PBMCs

To investigate the effect of TPE, we examined blood samples before and after rounds of this clinical procedure (Fig. 1A and Supplementary Fig. 1). The samples were de-identified and used as per the approved IRB (see “Materials and methods”). Each sample was separated into plasma/serum and cells, as published [21]. Our focus was on assaying the effects of TPE rounds on such hallmarks of aging, as DNA damage and cellular senescence. Samples 1, 2, 4, 6, 7, and 8 were from old individuals (77, 67, 72, 68, 60, and 72 years of age), while samples 3 and 5 were from middle-aged people (46 and 52 years of age) (Supplementary Table 1).

Fig. 1

The remodeling effect of TPE treatment on aged blood. A Schematic depicting the study; R0 is before TPE, R1 is 1 month afterwards and before the next round of TPE, and so on. B. Changes in 8-OHdG levels after TPE. S is the subject or patient number. Oxidative DNA damage gradually decreases and becomes statistically lower by the last round, in all patients. 8-OHdG ELISA was performed on each sample in triplicates. C TPE decreases p16 levels in PBMCs of old and middle-aged people, as assayed by qRT-PCR. D TPE upregulates the markers of lymphoid genes (T cells, B cells, NK cells) in old PBMCs. E The lymphoid:myeloid ratio is increased by the rounds of TPE. The myeloid:NK ratio is downregulated by TPE. The ratios of lymphoid:CD68 and NK:CD68 are elevated by the rounds of TPE. These data show a rejuvenation of the lymphoid/myeloid balance, suggesting an improved capacity for productive immune responses. Each gene profiling is performed by qRT-PCR in 3 replicates for each sample. *p < 0.05, **p < 0.01, ***p < 0.001, ns = not significant

DNA damage can be caused by exogenous and endogenous sources, exemplified by X-rays, UV, and ROS [24, 25]. Accumulated DNA damage triggers genetic aberrations, senescence [26], and loss of cell function and leads to age-related diseases [24].

Oxidative DNA damage was assayed in PBMCs with the 8OH-dg kit (IT7974, G-Biosciences) (Fig. 1B). The relative level of 8-OHdG was high before TPE, and although there is a difference in the fold change among the samples, the DNA damage was significantly decreased by the rounds of TPE (Fig. 1B).

For assaying senescence, messenger RNA (mRNA) was isolated from the PBMCs and profiled with qRT-PCR for p16, using GAPDH as the control (Fig. 1C). Expression of the p16 senescence marker was high in the PBMCs before TPE and was reduced by subsequent rounds of TPE (Fig. 1C).

Tumor-related genes were also profiled by qRT-PCR on PBMCs. There was no significant change in the expression of c-Myc, a known oncogene, while the expression of tumor suppressor genes such as P21 and p53 increased after TPE treatment in most patients (Supplementary Fig. 2).

These results demonstrate that repetitive plasmapheresis reduces the markers of senescence and DNA damage in human PBMCs.

Rounds of TPE gradually restore youthful lymphoid/myeloid markers to old PBMCs

To determine the effects of repeated TPE on the age-imposed myeloid skewing, we performed qRT-PCR on the gene expression pattern that reflects the lymphoid cell fates and macrophage-linked inflammaging (Fig. 1D). Lymphoid and natural killer cells decrease with aging, while macrophages, and particularly inflammatory CD68 + macrophages, increase [11, 26,27,28], explaining the age-related deficiency in combatting viral infections and the tendency to easily develop hyper-inflammation [27].

As shown in Fig. 1D and E, rounds of TPE increased the CD3, CD4, and CD8 markers in PBMCs. For the B cell markers, there was a large sample-specific range, but CD19 and B220 were generally induced by the rounds of TPE (Fig. 1D, E). CD94, a NK cell–specific marker, was low in the old PBMCs, but rebounded after the rounds of TPE (Fig. 1D, E).

Further suggesting a rejuvenation of the leukocyte subsets, the expression of macrophage-specific markers, CD11b and CD68, was generally reduced by the rounds of TPE (Fig. 1D, E). Interestingly, these transitions were clearly longitudinal and gradual, becoming more statistically significant with more rounds of the procedure and stably improving overall for several months. And importantly, the positive effects of TPE were maintained for at least 1 month, the time from one round to another. In agreement with the increase in lymphoid gene markers and diminished inflammatory markers, the ratios of lymphoid to myeloid markers showed a sharp increase through the rounds of TPE, suggesting that this procedure re-balances adaptive immunity and that it diminishes the cellular signatures of inflammation (Fig. 1E). In addition to the net change in the lymphoid/myeloid markers, which is shown in Fig. 1D and E, the direct comparison between the R0 and Rlast rounds for each marker is shown in Supplementary Fig. 3.

These results demonstrate that repetitive TPE diminishes the pro-inflammatory leukocyte skewing and upregulates the lymphoid markers of old and middle-aged human PBMCs.

Stable and significant longitudinal rejuvenation of systemic proteome by TPE

Next, we profiled the serum samples from young and old control donors (young, 28–32 years of age; old 70–79 years of age, Supplementary Table 1) and the longitudinal samples from TPE patients, using RayBiotech antibody arrays (Fig. 2A and Supplementary Fig. 4A). Out of 507 proteins, 72 proteins were significantly different in their levels between the old and the young groups (> 1.75 fold change, p < 0.05). These 72 proteins were analyzed further in the longitudinal TPE datasets by heat mapping, which revealed a gradual rejuvenation of the age-specific systemic proteome by subsequent rounds of TPE (Fig. 2B and Supplementary Fig. 4B). PCA confirmed that each R0 proteome (before the first TPE) was closer to the old control group than to the young control group and shifted from the old toward the young group with the rounds of TPE (Fig. 2C).

Fig. 2

Proteomic profiling of TPE serum using antibody array. A Schematic of the study. B Heat mapping of the 72 proteins that are significantly different (> 1.75 fold change) between the young and the old cohorts. C Principal component analysis (PCA) of the antibody array data of the young, old, and TPE groups for all rounds. Young, N = 5; old, N = 5; TPE, N = 8 (e.g., 8 patients in each TPE round). Arrow tails are R0, and heads are the last round for each group. D The top 30 Gene Ontology terms of biological processes. E The heat map of inflammatory response protein levels (p = 4.10E − 14). F The heat map of apoptosis protein levels (p = 3.60E − 07). Most proteins in the three different terms were close to old before TPE treatment and became close to the young group over monthly rounds of TPE

The Gene Ontology (GO) analysis through DAVID (version 6.8, https://david.ncifcrf.gov) with the 72 selected proteins revealed that 226 terms were in biological processes (BPs), 29 terms were related to cellular components, and 40 groups belonged to molecular functions (Fig. 2 and Supplementary Fig. 5).

With respect to BPs, the top 30 GO terms are presented in Fig. 2D and Supplementary Fig. 5, and many of these participate in signal transduction (p = 1.50E − 17); regulate the inflammatory response (p = 4.10E − 14); positively regulate the ERK/ERK2 cascade (p = 5.50E − 14) and the cytokine-mediated signaling pathways (p = 4.00E − 13); positively regulate the cell proliferation (p = 5.20E − 10), chemokine-mediated signaling pathways (p = 5.40E − 09), immune response (p = 1.20E − 08), and chemotaxis (p = 5.00E − 06); and negatively regulate the apoptotic process (p = 3.60E − 07).

The inflammatory response is both an essential defensive system and a hallmark of age-related dysfunctions [29]. We identified 19 proteins which were upregulated before the first TPE treatment or in the control old group, as compared to the young group (Fig. 2E). Notably, many of these proteins, including CCL20, CCL25, MIF, TLR3, TLR4, IL-2RA, and IL-16, were gradually downregulated by the rounds of TPE, with the expression levels measured just before the final round being close to the young levels (Fig. 2E).

Some difference in the levels of specific proteins was observed within the old cohort and between the old and TPE R0 cohorts, which could be explained, for example, by the differences in the ages, lifestyles, genetics, etc., parameters of the donors of commercial blood samples and those who were undergoing the TPE (Fig. 2E).

We also determined whether repetitive TPE may regulate the complement system including C3 and C1q, which play a key role in immune responses and also participate in non-immune crosstalks of cell–cell signaling pathways [30,31,32]. When we examined 15 commercial human serum samples across young (21–26), middle (46–52), and old (70–74) ages, we found that C1q and C3 levels were significantly elevated with age (Supplementary Fig. 6A). Mean levels of C3 and C1q complement proteins were significantly reduced by roughly half immediately following a TPE procedure, as expected from the immediate dilution of plasma, but on average, they returned to the initial levels by the next round ~ 1 month later. Even three TPE rounds had no significant lasting effects on the serum levels of C3 or C1q (Supplementary Fig. 6B and C).

Lastly, we analyzed the systemic regulators of apoptosis. Apoptosis plays an important role in immune responses and tissue homeostasis [33, 34]. However, with advancing age, resistance to apoptosis is increased through an enhanced negative loop of anti-apoptotic signaling, leading to senescence, inflammation, fibrosis, and a propensity for cancer [35,36,37]. In our BP analysis, 13 proteins were related to the negative regulation of apoptosis and the levels of these proteins were higher in the old group than in the young (Fig. 2F) [35,36,37]. Consistent with better tissue homeostasis, the levels of these apoptotic inhibitors diminished over rounds of TPE, becoming closer to the young cohort (Fig. 2F).

Therefore, rounds of TPE gradually reset the circulating protein markers of key cellular responses to their younger levels.

Pathway interaction String analysis defines the rejuvenation interactome

Although TPE treatment has been in clinic for decades, its impact on the process of aging and specifically the links to rejuvenation remain unstudied. To address this limitation, we first applied Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway bioinformatics analysis to the dataset of our comparative proteomics. Forty-three pathways were identified including cytokine–cytokine receptor interaction (p = 1.60E − 28), rheumatoid arthritis (p = 6.80E − 06), pathways in cancer (p = 9.30E − 06), intestinal immune network for IgA production (p = 3.50E − 05), JAK-STAT signaling pathway (p = 2.40E − 04), MAPK signaling pathway (p = 4.00E − 04), TGF-beta signaling pathway (p = 7.80E − 04), Toll-like receptor signaling pathway (p = 1.20E − 03), and nuclear factor (NF)-κB signaling pathway (p = 5.80E − 03) (Fig. 3A).

Fig. 3

Profiling-relevant mechanisms of TPE using selected 72 proteins. A Top 30 KEGG pathways. B Heat map with designations of the key functions of the groups of proteins. C The protein–protein interaction (PPI) network analysis of the canonical signaling pathways identifies TLR4 as the crosstalk node. D The PPI network analysis of the pathways in cancer identifies six designated nodal points of their interaction. E TLR4 gene expression levels in 349 young vs. old individuals (120.5 vs. 162.9, *p < 0.05). Nyoung = 181, N.old = 168

Interestingly, we also found KEGG terms related to cancer (Fig. 3B), e.g., a disease with a well-known age-elevated risk [38]. There are many reasons as to why cancers occur more frequently with aging, including the decline in productive immune responses, inflammation, the overall aging of immune cells [38], and the accumulation of senescent cells [39]. In agreement with the age-related etiology of cancers, most KEGG cancer terms, including pancreatic cancer, and proteoglycans in cancer were upregulated in the control old groups, as compared to the control young group (Fig. 3B). Notably, these excessive cancer pathway proteins were downregulated by the rounds of TPE (Fig. 3B).

Based on the broad multitissue rejuvenation by the old plasma dilution, we noted those pathways among the 43, which are known to be altered with aging in ways that interfere with the maintenance and repair of multiple tissues: the JAK-STAT [40], MAPK/ERK1/2 [41], TGF-beta [35], NF-κB [42], and Toll-like receptor signaling [43] (Fig. 3B and Supplementary Fig. 7).

To analyze the pathway interactions and the crosstalks between key proteins, we used a protein–protein interaction (PPI) network, the String [44] (Fig. 3C, D). The String consists of known and predicted PPIs including physical and functional associations from many data sources spanning more than 14,000 organisms [44, 45]. Moreover, String allows the display of various functional studies simultaneously with PPIs including GO, KEGG, and InterPro, facilitating the search for nodal proteins [44, 45]. With selected 72 proteins, PPI enrichment p values were less than 1.0E − 16, demonstrating that their interactions were significantly meaningful (Fig. 3C, D).

Through String analysis, we found that only one protein (TLR4) was linked to all the age-specific TPE-rejuvenated networks (Fig. 3C). Notably, the levels of TLR4 protein were significantly decreased after TPE, as compared to before this procedure (Supplementary Fig. 8). In addition, String pathway interaction analysis identified six proteins (TGFBR2, TGFA, FGF21, SMAD4, TGFBR1, and FZD3) that were at the intersection of the cancer-associated pathways and, importantly, which were restored to their younger crosstalks by the rounds of TPE (Fig. 3D).

To test and expand the significance of the findings that TLR4 is a nodal point of the age-altered and TPE-normalized pathway interactions, we analyzed the age-specific levels of TLR4 gene expression in 349 individuals (young [20–29 years] and aged [65–75 years]), using data mining of publicly available datasets [46,47,48,49,50,51,52,53,54].

TLR4 expression increases with age, in agreement with our proteomics and confirming the significance of the long-term attenuation of TLR4 by TPE (Fig. 3E).

These data demonstrate that rounds of TPE normalize the interactions between several key pathways, which, at their young signaling intensity, are known to be responsible for the homeostatic health of multiple organ systems, including the immune system. TLR4 was identified as a potential nodal point of the age-specific TPE-balanced signaling crosstalks.

Age and neurological disease–specific clustering of systemic proteomes and the reduction of a circulating biomarker of neurodegeneration, TDP43, by TPE

Aging is accompanied by various diseases with neurological disorders being a prominent class [55]. The blood biomarkers of brain diseases remain unknown, but promisingly, the Uniform Manifold Approximation and Projection (UMAP) analysis of our comparative blood proteomics defined distinct clustering of old people with Alzheimer’s disease (AD) and AD-related diseases (ADRDs), as compared to the healthy age-matched and younger cohorts (Fig. 4A and Supplementary Table 1). In agreement with the data on rejuvenation of the systemic proteome which we described above, the rounds of TPE moved the old blood proteome cluster of this AD/ADRD dataset toward the younger age cohort (Fig. 4A). Further substantiating the robustness of our results, the healthy old proteome of the age-matched controls of the AD/ADRD samples clustered close to the pre-TPE proteome, an independent dataset of healthy old blood donors (Fig. 4A).

Fig. 4

Age and dementia–specific blood proteome clustering and reduction of blood TDP43 by TPE. A Distinct UMAP clustering of the 72 proteins that differ between Y and O, for the six age and disease groups showing that the population of the R0 is close to the old group. However, the R last cluster is closer to the middle-aged group. B Circulating TDP43 levels are higher in old than in young individuals (12,024 ± 399 vs. 7732 ± 346.8). Values are mean picograms/milliliters ± SEM. C TDP43 levels diminished right after TPE (R1: 0.99 ± 0.01 vs. 0.66 ± 0.03, R2: 0.82 ± 0.04 vs. 0.58 ± 0.04) and remained significantly low for 1 month until the next round (0.99 ± 0.01 vs. 0.82 ± 0.04). **p < 0.01, ***p < 0.001

Considering these observations, we decided to analyze systemic levels of TDP43, which is the trigger of several neurological pathologies and becomes increased in the blood of patients with ALS, Parkinson’s disease (PD), frontotemporal dementia (FTD), and AD [56,57,58,59,60,61].

We analyzed the levels of this protein in young, old, pre-TPE, and after TPE serum samples. Interestingly, a TDP43-specific enzyme-linked immunosorbent assay (ELISA) demonstrated a robust age-specific increase in this determinant of neurological diseases in the serum of old, relatively healthy adults, as compared to the young cohort (Fig. 4B). Moreover, the longitudinal studies on the plasma before vs. after the rounds of TPE demonstrated that systemic TDP43 was stably attenuated by plasmapheresis (Fig. 4C). Notably, the overall levels of TDP43 in older adults were not just transiently diluted by the procedure, which is expected, but remained lower for at least a month after TPE (Fig. 4C).

These results suggest that the selected proteins enable the identification of AD/ADRD through UMAP analysis of blood plasma and confirm that TPE promotes a younger systemic proteome. Additionally, we show that TPE stably attenuates a known biomarker of neurological diseases, TDP43.

A novel biomarker of protein level noise provides a direct molecular measurement of human biological age and shows that it is reduced by TPE

Biological noise is the variation of a given biological parameter in an otherwise assumed constant or steady state. Several papers suggest that biological noise increases with age [62, 63], and noise of gene expression and protein levels is an independent age-related parameter that is relatively less studied, as compared with total levels of the genes, proteins, and other cellular and tissue metrics. An unmet need remains in identifying reliable molecular biomarkers that allow measuring biological age, in contrast to predicting it by data selection and adjustment, such as machine learning models of population statistics. We approached this problem by comparing not just young vs. old samples, as typically done, but also the rejuvenated cohort, and moreover, in the longitudinal studies of the same older individuals whose blood compartments became more like those of young people after TPE, based on the cellular and humoral blood assays.

To test if not just the protein levels but also their noise became more youthful through TPE, we compared the standard deviations (SDs) of protein levels, using our comparative proteomics datasets: the control young and old cohorts, round 0 vs. the last round of TPE, and of the old cohort with the cognitive disorders (progressive AD and ADRD). As the measurement uncertainty is similar between populations, any change in SD should reflect biological variation; here, biological variation is the levels of protein expression. A change in this variation could mean many things, from a loss of transcription regulation to stochasticity in protein quality checking to changes in turnover, but the end result is that protein levels are either more heavily controlled for lower SD or less heavily controlled for a greater SD.

To find statistically significant changes in biological noise, we looked at the difference in variance with Levene’s test. Levene’s test has various possible shortcomings in both power and significance when dealing with small sample sizes and asymmetric distributions [64]. To deal with this, we increased significance through the Benjamini–Hochberg procedure, selecting only proteins with significant changes in multiple populations and selecting proteins with other measures of substantial change in variance, albeit only larger sample size ultimately increases power. We found only 6 proteins showing increased SD in the young-to-old transition and decreased SD in the pre-to-after TPE transition: TRAIL R1, IL-16, TIMP-1, IL-15R alpha, CD27, and APJ (Fig. 5A). Interestingly, when we considered proteins which were significantly different in their SD between the healthy old and the old with cognitive disease and between the healthy young and healthy old, there were just 4 such proteins: Smad5, uPAR, FADD, and TGFBR1 (Fig. 5B). Namely for these 4 proteins, the SD increased in a young-to-old transition and in an old-to-disease transition but decreased in the R0-to-Rlast TPE transition (Fig. 5B).

Fig. 5

Profiling changes in biological noise using standard deviation (SD) among young, old, TPE, and disease cohorts. A The change in the SD of the 507 proteins (antibody array proteomics) between young and old people and between people before TPE and people after TPE, in proteins which had a Benjamini–Hochberg procedure false discovery rate of 10% regarding the significance of variance changes with age. B The change in SD between young and old people, between people with a neurodegenerative disorder and healthy people of the same age, and between people before and after TPE, in proteins which have significantly different variances in the aging and disease comparisons. C The change in SD between young and old people and between people before TPE and people after TPE, in proteins which had significantly different variances between age groups and which had their SD change by a factor of 5 or greater with TPE treatment. D The change in SD between young and old people, between people with a neurodegenerative disorder and healthy people of the same age, between people before TPE and people after TPE, and between middle-aged and old people, in proteins which have significantly different variances in the aging and disease comparisons and which had their SD change by a factor of 5 or greater with TPE treatment. In each case, significance was determined with the mean based Levene’s test. E Comparison of mean SDs of the mRNA levels of 8 genes between young and old groups, for each SD value of each gene (left), expressed as a fold increase of young (right, **p = 0.003). F The change in SD of the 5 genes between young and old people, in proteins which had a Benjamini–Hochberg procedure (see “Materials and methods”) false discovery rate of 10% regarding the significance of variance changes with age. G The biological noise was calculated using the SD of 10 selected proteins, divided by age. The biological noise of 10 proteins increases in the old group, compared with the young group. Interestingly, there is a clear and significant decrease of protein noise levels after rounds of TPE for all noise-detectors. H Plot of biological age calculated as the SD of the uncovered noise detectors versus chronological age. I The distribution of MCI, based on the 10 noise biomarkers. J Biological age shifts after repeated TPE treatment. Compared to before TPE treatment, all patients show a decrease in biological age in the last round of TPE, demonstrating significant rejuvenation by TPE

We next profiled the proteins which had not just a statistically significant change in the young-to-old transition, but also had a substantial change (greater than fivefold) in SD with TPE. We found 5 such proteins: APJ, TNFRSF27, uPAR, CCL25, and TGFBR2 (Fig. 5C). Very interestingly, when the field was further narrowed to only those proteins which also have significant SD changes in the healthy-to-disease transition, there was only one protein showing increased SD in young-to-old transition and old-to-disease transition, but decreased SD in pre-to-post-TPE transition, uPAR (Fig. 5D). And for this best noise detector protein, the middle-aged individuals lay right between the young and old individuals (Fig. 5D).

To confirm and extrapolate the significance of the identified protein determinants of age-related biological noise, their mRNA expression was analyzed in 349 individuals from publicly available datasets [46,47,48,49,50,51,52,53,54]. Interestingly and in agreement with our comparative proteomics data, the mean SD values, e.g., the noise, of all these genes increased with age, albeit to a different degree for the different transcripts (Fig. 5E).

Their mRNA levels were also age-elevated (Fig. 3E [for TLR4] and Supplementary Fig. 9 [for other transcripts]). These results agree with the proteomics data and expand the significance of TLR4 as a nodal point of the age-altered, signal transduction networks (Fig. 3B, C).

Supplementary Fig. 10 arranges the data by the size of SD of protein levels in a healthy population, which gives further credence to the idea that the changes in SD are the consequence of the age/disease-imposed biological noise. Namely, the proteins that are most tightly controlled initially were also those most likely to have a significant change in SD (deregulation) with age and disease. Supplementary Fig. 10 also shows that TPE is indeed returning the SDs to their younger lower states, e.g., the noise dampening effects of TPE are manifested more on the proteins that become less controlled or noisier with age. Of note, there is no uniform change in variance in noise with age; instead, those proteins which are least controlled change most and vice versa.

Our next goal was to apply the discovered biomarkers of proteome noise toward a novel measurement of person’s biological age. There is an unmet need for unambiguous molecular quantification of biological age based on experimentally defined biomarkers, without machine learning (ML) methods, large data statistics, and data adjustments and with improved resilience to batch effects [65, 66]. Typical ML models are trained on chronological age and predict