Biology subjects

Cawthon, R. M.

Publications and source records attributed to Cawthon, R. M..

4 recordsLinked to original sources

bioRxiv2018

Matrilineal Transmission of Familial Excess Longevity (mtFEL): Effects on Cause-specific Mortality in Utah, 1904-2002

The heritable component to a long and healthy life is likely to involve the actions and interactions of both nuclear and mitochondrial genetic variants. Using computerized genealogical records with accompanying cause of death information from the Utah population, we previously reported cause-specific mortality rate distributions associated with the nuclear genetic component of familial exceptional longevity. Here we identify Utah matrilineages (mitochondrial lineages) in which overall survival is better than expected, and compare cause-specific mortality rates in those matrilineages to cause-specific mortality rates in the general population. We also examine the effects on cause-specific mortality of interactions between the nuclear and mitochondrial components of familial excess longevity (nuclear FEL and mtFEL). Among individuals from the bottom quartile of nuclear FEL, those who were also in the top quartile for mtFEL had lower all-cause, heart disease, cancer, stroke, and diabetes mortality rates than those in the bottom quartile of mtFEL. In contrast, among individuals from the top quartile of nuclear FEL, the mortality rates from these diseases were similar for those also in the top quartile of mtFEL vs. those also in the bottom quartile of mtFEL, with the exception of diabetes mortality, which was dramatically suppressed in the high nuclear FEL + high mtFEL group as compared to the high nuclear FEL + low mtFEL group. Moreover, the highest mortality rates from diabetes were found in individuals aged 90 years or older who were members of both the high nuclear FEL and low mtFEL quartiles. These results support the hypothesis that some nuclear genetic variants contributing to long life carry an increased risk of dying from diabetes that is strongly ameliorated by some mitochondrial DNA variants.

epidemiology↗

bioRxiv2018

Monochrome multiplex qPCR of 18S and 5.8S human rDNA

Ribosomal DNA encodes the structural RNAs of the ribosomes. Ribosomal DNA instability is a major contributor to aging in yeast, but its role in human aging and longevity is largely unknown. Human 45S rDNA encodes the 18S, 5.8S, and 28S ribosomal RNAs; ranges in copy number from 60 to > 800 per cell, distributed as tandem repeats along the short arms of the five acrocentric chromosomes (p13, p14, p15, p21, and p22); and is prone to frequent homologous and non-homologous recombination. Here we present two multiplex quantitative PCR assays, one for 18S rDNA normalized to the single copy gene beta-globin (HBB), and the other for 5.8S rDNA normalized to the single copy gene albumin (ALB). Longitudinally-collected pairs of DNAs from bloods drawn approximately 16 years apart from 40 females and 39 males, aged < 1 to 77 years at first blood draw, from the Utah CEPH families were assayed. Ribosomal DNA copy number varied over a four-fold range between subjects and increased approximately 14% across the lifespan. Longitudinal within-individual gains in copy number up to +68% and losses down to -25% were observed, while repeated assays of single DNA samples varied approximately +/- 10%. While 18S and 5.8S rDNA tended to be gained and lost together, the 18S:5.8S ratio was also unstable longitudinally, with increases up to +19% and decreases down to -15% observed. The 18S:5.8S ratio at second draw, relative to that at first draw, increased significantly across the lifespan in males, but not in females. To our knowledge this is the first report of within-individual longitudinal changes in the human 18S and 5.8S rDNA copy numbers. These assays will facilitate investigations of the biology of ribosomal RNA genes and their roles in health and disease across the human lifespan.

genomics↗

bioRxiv2018

Mitochondrial genetics of exceptional longevity in multigeneration matrilineages

Some heritable mitochondrial DNA (mtDNA) sequence variants may slow the rate of aging. The European mitochondrial haplogroup K has previously been reported to be increased in frequency in centenarians and nonagenarians relative to its frequency in younger individuals, by standard case/control study designs. To select for mitochondrial genomes likely to carry beneficial genetic variants, we screened a large genealogical database (the Utah Population Database, UPDB) for mitochondrial lineages in which the frequency of survival past 90 years was significantly higher than in the general population, and also significantly higher than in close non-matrilineal relatives. We ranked 14,900 distinct matrilineages by the strength of their association with longevity. Full sequencing of the mtDNAs from a single individual from each of 53 matrilineages in the top longevity ranks and each of 374 control matrilineages from the general Utah population, followed by analyses of the mtDNA haplogroup frequencies, identified haplogroup K2 as the haplogroup most enriched in frequency by the longevity selection (Odds Ratio = 23.05). We then analyzed overall survival and cause-specific mortality in the several thousand individuals aged 40 years or older whose mtDNA genotypes could be imputed from the 374 fully sequenced control mtDNAs. In these control matrilineages Haplogroup K2 individuals (n=332) enjoyed a significantly lower all-cause mortality risk than the general population (HR=0.81), attributable in part to a significantly lower risk of dying from heart disease (HR=0.50), as well as lower (though not significantly lower) risks of dying from cancer (HR=0.72) and diabetes (HR=0.74). Furthermore, K2 was the only haplogroup in which mortality was reduced for all three of these common causes of death.

genetics↗

bioRxiv2018

A novel PCR method directly quantifies sequence features that block primer extension

Many quantitative polymerase chain reaction (qPCR) assays indirectly quantify a target of interest as a drop in amplification signal relative to a larger total signal. The targeted sequence features include: DNA strand breaks introduced by enzymes that cleave at specific sequences or modifications, or caused by ionizing radiation or other DNA-damaging agents; DNA damage that does not break the DNA but blocks the DNA polymerase; and deletions of various sizes that prevent one or both primers from annealing. All of these loss of signal (a.k.a. negative) assays share the drawback of low sensitivity, as compared to positive assays, which generate an amplification signal that directly reflects the copy numbers of the sequence feature. Here we present a novel qPCR strategy that converts all of the above negative assays into positive ones. A mixture of three primers is added to genomic DNA, one primer pair that targets a sequence for strand-specific PCR, and a third, longer primer that prevents initiation of that PCR, by annealing at high temperature and extending across the target sequence, rendering it doublestranded and inaccessible for priming. Any sequence feature that blocks the third primers annealing or extension, while leaving the target sequence intact, allows the PCR to proceed and quantify the copy number of the sequence feature. This Primer Extension Blockade Enabled qPCR (PEBE-qPCR) method will facilitate many high-throughput, low-cost qPCR-based investigations in biology and medicine. As a first example, we present direct qPCR of the unmethylated allele at a MspI/HpaII site in the promoter of the human 45S rDNA gene.

genomics↗