John C Newman

UCSF University of California, San Francisco | UCSF · Division of Geriatrics

Beta-hydroxybutyrate (BHB) is a ketone body synthesized during fasting or strenuous exercise. Our previous study demonstrated that a cyclic ketogenic diet (KD), which induces BHB levels similar to fasting every other week, reduces midlife mortality and improves memory in aging mice. BHB actively regulates gene expression and inflammatory activation...

Diet can protect from autoimmune disease; however, whether diet acts via the host and/or microbiome remains unclear. Here, we use a ketogenic diet (KD) as a model to dissect these complex interactions. A KD rescued the experimental autoimmune encephalomyelitis (EAE) mouse model of multiple sclerosis in a microbiota-dependent fashion. Dietary supple...

Background: Frailty is a geriatric syndrome characterized by chronic inflammation and metabolic insufficiency that creates vulnerability to poor outcomes with aging. We hypothesize that geroscience interventions, which target mechanisms of aging, could ameliorate frailty. Metabolites such as ketone bodies are candidate geroscience interventions, ha...

Aging is a complex biological process that compromises brain function and neuronal network activity, leading to cognitive decline and synaptic dysregulation. In recent years, a cyclic Ketogenic Diet (KD) has emerged as a potential treatment to ameliorate cognitive decline by improving memory in aged mice after long term administration. However, the...

Loss of proteostasis is a hallmark of aging and Alzheimer disease (AD). Here, we identify β-hydroxybutyrate (βHB), a ketone body, as a regulator of protein solubility in the aging brain. βHB is a small molecule metabolite which primarily provides an oxidative substrate for ATP during hypoglycemic conditions, and also regulates other cellular proces...

Understanding how our cells maintain energy homeostasis has long been a focus of aging biology. A decline in energy metabolism is central to many age-related diseases such as Alzheimer's disease, heart failure, frailty, and delirium. Intervening on pathways involved in energy homeostasis can extend healthy lifespan. When the primary energy substrat...

Altered brain network activity and the resulting hypersynchrony are important for the pathogenesis of cognitive decline in Alzheimer's disease (AD) mouse models. Treatments that reduce epileptiform discharges (EDs) or network hyperactivity improve cognition in AD models and humans. We first show that ketogenic diet, but not fasting, rapidly and per...

Background: Ketosis has been reported to benefit healthspan and resilience, which has driven considerable interest in development of exogenous ketones to induce ketosis without dietary changes. Bis hexanoyl (R)-1,3-butanediol (BH-BD) is a novel ketone di-ester that can be used as a food ingredient that increases hepatic ketogenesis and blood beta-...

Nutritional ketosis is a state of mildly elevated blood ketone concentrations resulting from dietary changes (e.g., fasting or reduced carbohydrate intake) or exogenous ketone consumption. In this study, we determined the tolerability and safety of a novel exogenous ketone diester, bis-hexanoyl-(R)-1,3-butanediol (BH-BD), in a 28-day, randomized, d...

A series of studies was conducted to assess the genetic toxicity of a novel ketone ester, bis hexanoyl (R)-1,3-butanediol (herein referred to as BH-BD), according to Organization for Economic Co-operation and Development testing guidelines under the standards of Good Laboratory Practices. In bacterial reverse mutation tests, there was no evidence o...

Bis-hexanoyl (R)-1,3-butanediol (BH-BD) is novel ketone ester undergoing development as a food ingredient to achieve nutritional ketosis in humans. Male and female Crl:CD(SD) rats were administered BH-BD twice daily at 9,000, 12,000 or 15,000 mg/kg/day, by oral gavage in a 90-day toxicity study with 28-day recovery period; and an interim 28-day pha...

Background Accumulating evidence suggests that the failing heart reprograms fuel metabolism toward increased utilization of ketone bodies and that increasing cardiac ketone delivery ameliorates cardiac dysfunction. As an initial step toward development of ketone therapies, we investigated the effect of chronic oral ketone ester (KE) supplementation...

Mitochondrial acyl-coenzyme A species are emerging as important sources of protein modification and damage. Succinyl-CoA ligase (SCL) deficiency causes a mitochondrial encephalomyopathy of unknown pathomechanism. Here, we show that succinyl-CoA accumulates in cells derived from patients with recessive mutations in the tricarboxylic acid cycle (TCA)...

A novel ketone ester, bis hexanoyl (R)-1,3-butanediol (BH-BD), has been developed as a means to elevate blood ketones, for use as an energy substrate and a signaling metabolite. The metabolism of BH-BD and its effects on blood beta-hydroxybutyrate (BHB) levels was evaluated in various in vitro matrices and through analysis of plasma collected from...

Reversible posttranslational modifications are emerging as critical regulators of mitochondrial proteins and metabolism. Here, we use a label-free quantitative proteomic approach to characterize the lysine succinylome in liver mitochondria and its regulation by the desuccinylase SIRT5. A total of 1,190 unique sites were identified as succinylated,...

Traditionally, the ketone body β-hydroxybutyrate (βOHB) has been looked upon as a carrier of energy from liver to peripheral tissues during fasting or exercise. However, βOHB also signals via extracellular receptors and acts as an endogenous inhibitor of histone deacetylases (HDACs). These recent findings support a model in which βOHB functions to...

Large-scale proteomic approaches have identified numerous mitochondrial acetylated proteins; however in most cases, their regulation by acetyltransferases and deacetylases remains unclear. Sirtuin 3 (SIRT3) is an NAD(+)-dependent mitochondrial protein deacetylase that has been shown to regulate a limited number of enzymes in key metabolic pathways....

The sirtuins are a family of NAD+-dependent protein deacetylases that regulate cell survival, metabolism, and longevity. Three sirtuins, SIRT3, 4 and 5, localize to mitochondria. Expression of SIRT3 is selectively activated during fasting and calorie restriction. SIRT3 regulates the acetylation level and enzymatic activity of key metabolic enzymes,...

Sirtuins are NAD(+)-dependent protein deacetylases and have been implicated in the regulation of metabolism, stress responses, and aging. Three sirtuins are located in mitochondria: SIRT3, 4, and 5. SIRT3 deacetylates and regulates the enzymatic activity of many metabolic enzymes in mitochondria, whereas SIRT5 removes two novel post-translational m...

Cockayne syndrome is a segmental progeria most often caused by mutations in the CSB gene encoding a SWI/SNF-like ATPase required for transcription-coupled DNA repair (TCR). Over 43Mya before marmosets diverged from humans, a piggyBac3 (PGBD3) transposable element integrated into intron 5 of the CSB gene. As a result, primate CSB genes now generate...

Moves to protect the copyright of the Mini–Mental State Examination, the standard of care for cognitive screening, have left clinicians at risk of legal action for infringement and distribution and made a new tool, apparently seen as derivative, unavailable.

Cockayne syndrome (CS) is a devastating progeria most often caused by mutations in the CSB gene encoding a SWI/SNF family chromatin remodeling protein. Although all CSB mutations that cause CS are recessive, the complete absence of CSB protein does not cause CS. In addition, most CSB mutations are located beyond exon 5 and are thought to generate o...

CSB mutations associated with human disease. (0.06 MB DOC)

Comparison of galago PGBD3-like sequences with human PGBD3. (0.06 MB DOC)

L2L results comparing MER85-associated genes to the L2L microarray database, with P values corrected by random-data simulation. (0.17 MB XLS)

Quantitation of the relative abundance of CSB and CSB-PGBD3 fusion transcripts in HeLa cDNA. (A) Ratio of abundance between similarly sized CSB and fusion PCR products, assayed by real time RT-PCR. The average ratio of all eighteen fusion:CSB comparisons is 2.0:1. (B) Expected sizes of all PCR products. (1.07 MB TIF)

Additional Western blots for CSB and the fusion protein. (A) Western blot using a Cterminal antibody against CSB reveals only the expected major band for full length CSB(filled arrowhead) in MRC5 (SV40-immortalized human fetal lung fibroblast), E61ANd(GM00739B fibroblasts from compound heterozygote CS1AN, immortalized by SV40 and rescued by wt CSB...

Sequence identity between PGBD3 and pseudogenes. (0.04 MB DOC)

L2L microarray database results analyzed by groups of similar database lists. (0.02 MB XLS)

Conservation of the 3′ splice site in PGBD3. (A) Conserved 3′ splice site in the genomic sequence of PGBD3 and pseudogenes for human (Hs, Homo sapiens), chimpanzee (Pt, Pan troglodytes), Rhesus (Mm, Macaca mulatta), marmoset (Ct, Callithrix jacchus) and orangutan (Pa, Pongo abelli), organized by gene. Uppercase letters represent exon sequence; ATG...

Conservation of the polyadenylation signal in PGBD3. (A) Conserved polyadenylation signals in the genomic sequence of PGBD3 and pseudogenes for human (Hs), chimpanzee (Pt), Rhesus (Mm), marmoset (Ct) and orangutan (Pa), organized by gene. Uppercase letters represent the AAUAAA motif. Dashes indicate pseudogenes for which the 3′ end (including the p...

Locations of human MER85 elements and MER85-associated genes. (0.09 MB XLS)

L2L results comparing MER85-associated genes to Gene Ontology Molecular Function terms, with P values corrected by random-data simulation. (0.17 MB XLS)

Fusion mRNA is more abundant than CSB in other cell lines. Three pairs of primer combinations (A1–D1, A2–D2 and B1–E1) were tested on cDNA from CSB-null, CSB-wt and WI38/hTERT cell lines. In all cases, the fusion PCR products were substantially more abundant than the corresponding CSB products as quantified by real time RT-PCR. (0.65 MB TIF)

Schematic of PGBD3 element and the relationship with PGBD3 pseudogenes. The 5′ and 3′ ends of PGBD3 correspond to the 5′ arm (100 nt) and 3′ arm (40 nt) of a MER85 element (140 nt). The 13 nt inverted repeats of MER85 define the boundaries of the element, which is flanked by a TTAA target site duplication. Only two pseudogenes span the entire eleme...

The putative catalytic motif is DDD in all pseudogenes, but DND in all PGBD3s. PiggyBac transposases share a DDD motif [1] that may be analogous to the metalcoordinating DDE motif common to other transposase families [2]. The most likely candidates for this motif in human PGBD3 are D270, N352 and D467. N352 is the result of a G to A mutation that o...

Consensus sequence of putative catalytic motif is DDD in galago PGBD3-related sequences. Six of seven sequences encode D at position 270, and six of seven encode D at 467. At position 352, four encode D while three encode K, G or N. Numbers designtating the PGBD3-like sequences represent the galago (Otolemur garnetti, Og) genomic contig on which th...

Microarray profiling of gene expression is a powerful tool for discovery, but the ability to manage and compare the resulting data can be problematic. Biological, experimental, and technical variations between studies of the same phenotype/phenomena create substantial differences in results. The application of conventional meta-analysis to raw micr...

Cockayne syndrome (CS) is an inherited neurodevelopmental disorder with progeroid features. Although the genes responsible for CS have been implicated in a variety of DNA repair- and transcription-related pathways, the nature of the molecular defect in CS remains mysterious. Using expression microarrays and a unique method for comparative expressio...

L2L is a database consisting of lists of differentially expressed genes compiled from published mammalian microarray studies, along with an easy-to-use application for mining the database with the user's own microarray data. As illustrated by re-analysis of a recent study of diabetic nephropathy, L2L identifies novel biological patterns in microarr...

Many bacterial pathogens turn on virulence genes at host body temperature. In the September 6, 2002, issue of Cell, Johansson et al. show that the Listeria monocytogenes thermosensor is an RNA structure in the 5' untranslated region of the mRNA for the virulence-activating transcription factor PrfA. The stem-loop structure blocks translation initia...