Ken Raj - Academia.edu (original) (raw)

Papers by Ken Raj

Maximum lifespan is an intrinsic characteristic of a biological species and is defined as the lon... more Maximum lifespan is an intrinsic characteristic of a biological species and is defined as the longest time an individual of a species has been reported to survive. By analyzing 15K samples derived from 348 mammalian species representing 25 taxonomic orders we previously identified CpG methylation sites associated with maximum lifespan. Here we present accurate DNA methylation-based (DNAm) predictors of maximum lifespan (r=0.89), average gestation time (r=0.96), and age at sexual maturity (r=0.85). Our DNAm maximum lifespan predictor indicates a potential innate longevity advantage for females over males in 17 mammalian species such as humans, red deer, and cattle. The DNAm maximum lifespan predictions do not vary significantly by caloric restriction and partial reprogramming. Genetic disruptions in the somatotropic axis, which includes growth hormone, IGF-1, and their related receptors, have an impact on DNAm maximum lifespan only in select mouse tissues. Cancer mortality rates in m...

Research Square (Research Square), Jan 19, 2022

bioRxiv (Cold Spring Harbor Laboratory), Sep 11, 2020

Cattle are an attractive animal model of fertility in women due to their high degree of similarit... more Cattle are an attractive animal model of fertility in women due to their high degree of similarity relative to follicle selection, embryo cleavage, blastocyst formation, and gestation length. To facilitate future studies of the epigenetic underpinnings of aging effects in the female reproductive axis, several DNA methylation-based biomarkers of aging (epigenetic clocks) for bovine oocytes are presented. One such clock was germane to only oocytes, while a dual-tissue clock was highly predictive of age in both oocytes and blood. Dual species clocks that apply to both humans and cattle were also developed and evaluated. These epigenetic clocks can be used to accurately estimate the chronological age of the oocyte donor. Both epigenetic clock studies and epigenome wide association studies revealed that blood and oocytes differ substantially with respect aging and the underlying epigenetic signatures that potentially influence the aging process. The rate of epigenetic aging was found to be slower in oocytes compared to blood, however, oocytes appeared to begin at an older epigenetic age. The epigenetic clocks for oocytes are expected to address questions in the field of reproductive aging, including the central question: how to slow aging of oocytes.

bioRxiv (Cold Spring Harbor Laboratory), Nov 22, 2020

Human DNA methylation data have previously been used to develop highly accurate biomarkers of agi... more Human DNA methylation data have previously been used to develop highly accurate biomarkers of aging ("epigenetic clocks"). Subsequent studies demonstrate that similar epigenetic clocks can also be developed for mice and many other mammals. Here, we describe epigenetic clocks for common marmosets (Callithrix jacchus) based on novel DNA methylation data generated from highly conserved mammalian CpGs that were profiled using a custom Infinium array (HorvathMammalMethylChip40). From these, we developed and present here, two epigenetic clocks for marmosets that are applicable to whole blood samples. We find that the human-marmoset clock for relative age exhibits moderately high age correlations in two other non-human primate species: vervet monkeys and rhesus macaques. In a separate cohort of marmosets, we tested whether intervention with rapamycin, a drug shown to extend lifespan in mice, would alter the epigenetic age of marmosets, as measured by the marmoset epigenetic clocks. These clocks did not detect significant effects of rapamycin on the epigenetic age of marmoset blood. The common marmoset stands out from other mammals in that it is not possible to build accurate estimators of sex based on DNA methylation data: the accuracy of a random forest predictor of sex (66%) was substantially lower than that observed for other mammals (which is close to 100%). Overall, the epigenetic clocks developed here for the common marmoset are expected to be useful for age estimation of wild-born animals and for anti-aging studies in this species.

International journal of radiation biology, 2012

The target cells for radiation carcinogenesis are widely held to be stem or stem-like cells. Clas... more The target cells for radiation carcinogenesis are widely held to be stem or stem-like cells. Classically, stem cells are considered to be those capable of renewing tissues while differentiated cells lose the potential to replicate. More recently it has become apparent that greater developmental plasticity exists and that cells can be reprogrammed to form induced pluripotent stem cells. Modelling of radiation cancer-risk requires understanding of the characteristics, numbers and responses of target stem cells to radiation. Therefore progress in understanding mechanisms of radiation-induced carcinogenesis is dependent on knowledge of stem cell radiobiology. In this context, the European Community's network of excellence on low dose radiation risk called, 'Low Dose Research towards Multidisciplinary Integration (DoReMi)' ( www.doremi-noe.net ) and the United Kingdom's Health Protection Agency organised a workshop on Stem Cells and DNA damage in Oxfordshire on 7/8 Decemb...

Journal of Molecular Biology, 1998

Human papillomavirus type 18 (HPV18) capsid proteins L1 and L2, synthesised in mammalian cells us... more Human papillomavirus type 18 (HPV18) capsid proteins L1 and L2, synthesised in mammalian cells using recombinant vaccinia viral expression vectors, are transported to the nucleus and assembled into virus-like particles. When 293T cells, which express SV40 T antigen, were transfected with plasmid DNAs containing an SV40 origin of replication then infected with vaccinia viral vectors encoding L1 and L2, plasmid DNA was encapsidated into the particles. The DNAs ranged in size from 5.4 to 7.9 kb. By encapsidating plasmids containing either the b-galactosidase gene or the puromycin-resistance gene, the pseudovirions were shown to be infectious in that they could transfer b-galactosidase activity or confer resistance to puromycin to a number of cell types, indicating that the uptake and decapsidation of HPV particles are not the main determinants of cell type speci®city of HPV. Episomal HPV16 DNA in a cervical keratinocyte line could also be encapsidated. Further investigation showed that DNA encapsidation is independent of HPV DNA sequences and of T antigen-mediated plasmid DNA replication. Instead, the minor capsid protein, L2, was found to be attached to plasmid mini-chromosomes extracted from these cells, suggesting a role for L2 in encapsidation. Consistent with this, the L1 protein alone was unable to encapsidate DNA, although it was able to form virus-like particles. The results suggest that intracellular episomal DNAs of suitable size can be encapsidated by the HPV18 L1 and L2 proteins without the need of any HPV packaging signal, and reintroduced into cells.

Journal of General Virology, 1995

The E1 protein of human papillomavirus (HPV) type 16 is the only known papillomavirus E1 which do... more The E1 protein of human papillomavirus (HPV) type 16 is the only known papillomavirus E1 which does not contain any proline residues in the phosphate-loop (P-loop) of its ATP-binding site. To ascertain whether this feature influences the activities of HPV-16 E1, we generated a mutant HPV-16 E1 (E1Pro) in which prolines are inserted in place of alanines in this site, making the P-loop identical to its bovine papillomavirus type 1 counterpart. Glutathione S-transferase (GST) fusion proteins (GSTE1wt and GSTE1Pro) were produced, purified and used to assay for ATP-binding ability, ATPase activity and ability to complex with the HPV-16 E2 protein. The results show that the lack of prolines in the P-loop, which is unique to HPV-16 E1, significantly weakens its ATP-binding and ATPase activities without affecting its ability to complex with the HPV-16 E2 protein.

Nature communications, Jan 26, 2018

DNA methylation age is an accurate biomarker of chronological age and predicts lifespan, but its ... more DNA methylation age is an accurate biomarker of chronological age and predicts lifespan, but its underlying molecular mechanisms are unknown. In this genome-wide association study of 9907 individuals, we find gene variants mapping to five loci associated with intrinsic epigenetic age acceleration (IEAA) and gene variants in three loci associated with extrinsic epigenetic age acceleration (EEAA). Mendelian randomization analysis suggests causal influences of menarche and menopause on IEAA and lipoproteins on IEAA and EEAA. Variants associated with longer leukocyte telomere length (LTL) in the telomerase reverse transcriptase gene (TERT) paradoxically confer higher IEAA (P < 2.7 × 10-11). Causal modeling indicates TERT-specific and independent effects on LTL and IEAA. Experimental hTERT-expression in primary human fibroblasts engenders a linear increase in DNA methylation age with cell population doubling number. Together, these findings indicate a critical role for hTERT in regula...

International Journal of Radiation Biology, 2017

Epidemiological studies indicate that radiation doses as low as 0.5 Gy increase the risk of cardi... more Epidemiological studies indicate that radiation doses as low as 0.5 Gy increase the risk of cardiovascular disease decades after the exposure. The aim of the present study was to investigate whether this radiation dose causes late molecular alterations in endothelial cells that could support the population-based data. Human coronary artery endothelial cells were irradiated at 0.5 Gy (X-ray) and radiation-induced changes in the proteome were investigated after different time intervals (1, 7 and 14 d) using ICPL technology. Key changes identified by proteomics and bioinformatics were validated by immunoblotting and ELISA. The radiation-induced alteration of the endothelial proteome was characterized by sustained perturbation of Rho GDP-dissociation inhibitor (RhoGDI) and nitric oxide (NO) signalling pathways. At later time-points, this was accompanied by reduced proteasome activity, enhanced protein carbonylation indicating augmented oxidative stress, and senescence. These molecular changes are indicative of long-term premature endothelial dysfunction and provide a mechanistic framework to the epidemiological data showing increased risk of cardiovascular disease at 0.5 Gy.

Proceedings of the National Academy of Sciences

Significance Epigenetic estimators of age (known as clocks) allow one to identify interventions t... more Significance Epigenetic estimators of age (known as clocks) allow one to identify interventions that slow or reverse aging. Previous epigenetic clocks only applied to one species at a time. Here, we describe epigenetic clocks that apply to both dogs and humans. These clocks, which measure methylation levels in highly conserved stretches of the DNA, promise to increase the likelihood that interventions that reverse epigenetic age in one species will have the same effect in the other.

Epigenetics of Aging and Longevity, 2018

The power of mathematical analyses that are brought to bear on large DNA methylation data sets is... more The power of mathematical analyses that are brought to bear on large DNA methylation data sets is uncovering previously unknown aspects of aging. By far, the most significant discovery is the specificity by which the methylation status of some cytosine-guanine dinucleotides changes with age. Although changes to DNA methylation state were known to occur with age, it is nevertheless a surprise to behold the remarkable precision of this change and that it can lend itself as a measuring stick of biological age. With it, many surprises have been uncovered, including the uniformity of age from diverse tissues of a body, influences of internal and external factors on aging, and the distinctiveness of epigenetic aging from current understanding of aging. Very rapidly, the epigenetic clock has uncovered many novel aspects of aging and most excitingly it is challenging concepts of aging that we have long held to be correct or complete.

ABSTRACTAge-related changes to cytosine methylation have been extensively characterized across th... more ABSTRACTAge-related changes to cytosine methylation have been extensively characterized across the mammalian family. Some cytosines that are conserved across mammals exhibit age-related methylation changes that are so consistent that they were used to successfully develop cross-species age predictors. In a similar vein, methylation levels of some conserved cytosines correlate highly with species lifespan, leading to the development of highly accurate lifespan predictors. Surprisingly, little to no commonality is found between these two sets of cytosines even though the relationship between aging and lifespan is by most measures linked. We ventured to address this conundrum by first identifying age-related cytosines whose methylation levels change in opposite directions between short and long-lived species. We hypothesized that age-related CpGs that are also associated with species lifespan would tap into biological processes that simultaneously impact aging and lifespan. To this end...

support the notion that, in the event of DNA damage, thep53 tumour-suppressor protein is able to ... more support the notion that, in the event of DNA damage, thep53 tumour-suppressor protein is able to prevent cell death bysustaining an arrest of the cell cycle at the G2 phase. We reporthere that adeno-associated virus (AAV) selectively induces apop-tosis in cells that lack active p53. Cells with intact p53 activity arenot killed but undergo arrest in the G2 phase of the cell cycle. Thisarrest is characterized by an increase in p53 activity and p21 levelsand by the targeted destruction of CDC25C. Neither cell killingnor arrest depends upon AAV-encoded proteins. Rather, AAVDNA, which is single-stranded with hairpin structures at bothends

Oncotarget, 2017

The association between ionising radiation (IR) exposure and risk of cardiovascular diseases (CVD... more The association between ionising radiation (IR) exposure and risk of cardiovascular diseases (CVD) is well documented, but the underlying mechanism is still poorly understood. As atherosclerotic plaques are the most common cause of CVD, we investigated the effects of IR on one of the critical parameters for atherosclerotic plaque formation-endothelium permeability to macromolecules. We used endothelial cells from human coronary artery as a model of the endothelial layer. Our results show that exposure of this endothelial layer to IR increased its permeability to macromolecules of various sizes in a dose-dependent manner. Immunofluorescence analysis revealed disruption of cell junctions caused by decreased amounts of two junction proteins, one of which is vascular endothelial cadherin (VE-cadherin). The reduction in the level of this protein was not due to diminished transcription but to protein processing instead. We observed a radiation dose-dependent increase in the cleavage of VE-cadherin by ADAM10. This was not mediated through the canonical VEGF route but was instead accompanied by intra-cellular calcium release. Importantly, inhibition of ADAM10 activity rescued IR-induced permeability. Our observations demonstrate that exposure to IR activates ADAM10 to cleave VEcadherin leading to augmented endothelium permeability; a feature that can lead to the development of atherosclerotic plaques and increase the risk of cardiovascular disease.

Journal of Proteome Research, 2017

Radiation is the most common treatment of cancer. Minimizing the normal tissue injury, especially... more Radiation is the most common treatment of cancer. Minimizing the normal tissue injury, especially the damage to vascular endothelium, remains a challenge. This study aimed to analyze direct and indirect radiation effects on the endothelium by investigating mechanisms of signal transfer from irradiated to non-irradiated endothelial cells by means of secreted proteins. Human coronary artery endothelial cells (HCAECest2) undergo radiation-induced senescence in vitro 14 days after exposure to 10 Gy X-rays. Proteomics analysis was performed on HCAECest2 14 days after irradiation with X-ray doses of 0 Gy (control) or 10 Gy using label-free technology. Additionally, the proteomes of control and radiation-induced secretomes, and those of non-irradiated HCAECest2 exposed for 24 hours to secreted proteins of either condition were measured. Key changes identified by proteomics and bioinformatics were validated by immunoblotting, ELISA, bead-based multiplex assays, and targeted transcriptomics. The irradiated cells, their secretome and the non-irradiated recipient cells showed similar inflammatory response, characterized by induction of interferon type I-related proteins and activation of the STAT3 pathway. These data indicate that irradiated endothelial cells may adversely affect nonirradiated surrounding cells via senescence-associated secretory phenotype. This study adds to our knowledge of the pathological background of radiation-induced cardiovascular disease.

International Journal of Radiation Biology, 2016

Low-dose radiation differentially regulates protein acetylation and histone deacetylase expressio... more Low-dose radiation differentially regulates protein acetylation and histone deacetylase expression in human coronary artery endothelial cells

Journal of Visualized Experiments, 2015

One of the cardinal processes of inflammation is the infiltration of immune cells from the lumen ... more One of the cardinal processes of inflammation is the infiltration of immune cells from the lumen of the blood vessel to the surrounding tissue. This occurs when endothelial cells, which line blood vessels, become adhesive to circulating immune cells such as monocytes. In vitro measurement of this adhesiveness has until now been done by quantifying the total number of monocytes that adhere to an endothelial layer either as a direct count or by indirect measurement of the fluorescence of adherent monocytes. While such measurements do indicate the average adhesiveness of the endothelial cell population, they are confounded by a number of factors, such as cell number, and do not reveal the proportion of endothelial cells that are actually adhesive. Here we describe and demonstrate a method which allows the enumeration of adhesive cells within a tested population of endothelial monolayer. Endothelial cells are grown on glass coverslips and following desired treatment are challenged with monocytes (that may be fluorescently labeled). After incubation, a rinsing procedure, involving multiple rounds of immersion and draining, the cells are fixed. Adhesive endothelial cells, which are surrounded by monocytes are readily identified and enumerated, giving an adhesion index that reveals the actual proportion of endothelial cells within the population that are adhesive.

Mutation Research/Reviews in Mutation Research, 2015