Tracing the Diverse Paths of One-Carbon Metabolism in Cancer and Beyond

One-carbon (1C) metabolism is a network of biochemical reactions distributed across organelles that delivers folate-activated 1C units to support macromolecule synthesis, methylation, and reductive homeostasis. Fluxes through these pathways are up-regulated in highly proliferative cancer cells, and anti-folates, which target enzymes within the 1C pathway, have long been used in the treatment of cancer. In this work, we review fundamental aspects of 1C metabolism and place it in context with other biosynthetic and redox pathways, such that 1C metabolism acts to bridge pathways across compartments. We further discuss the importance of stable-isotope-tracing techniques combined with mass spectrometry analysis to study 1C metabolism and conclude by highlighting therapeutic approaches that could exploit cancer cells' dependency on 1C metabolism.

Serine biosynthesis as a novel therapeutic target for dilated cardiomyopathy

AIMS

Genetic dilated cardiomyopathy (DCM) is a leading cause of heart failure. Despite significant progress in understanding the genetic aetiologies of DCM, the molecular mechanisms underlying the pathogenesis of familial DCM remain unknown, translating to a lack of disease-specific therapies. The discovery of novel targets for the treatment of DCM was sought using phenotypic sceening assays in induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) that recapitulate the disease phenotypes in vitro.

METHODS AND RESULTS

Using patient-specific iPSCs carrying a pathogenic TNNT2 gene mutation (p.R183W) and CRISPR-based genome editing, a faithful DCM model in vitro was developed. An unbiased phenotypic screening in TNNT2 mutant iPSC-derived cardiomyocytes (iPSC-CMs) with small molecule kinase inhibitors (SMKIs) was performed to identify novel therapeutic targets. Two SMKIs, Gö 6976 and SB 203580, were discovered whose combinatorial treatment rescued contractile dysfunction in DCM iPSC-CMs carrying gene mutations of various ontologies (TNNT2, TTN, LMNA, PLN, TPM1, LAMA2). The combinatorial SMKI treatment upregulated the expression of genes that encode serine, glycine, and one-carbon metabolism enzymes and significantly increased the intracellular levels of glucose-derived serine and glycine in DCM iPSC-CMs. Furthermore, the treatment rescued the mitochondrial respiration defects and increased the levels of the tricarboxylic acid cycle metabolites and ATP in DCM iPSC-CMs. Finally, the rescue of the DCM phenotypes was mediated by the activating transcription factor 4 (ATF4) and its downstream effector genes, phosphoglycerate dehydrogenase (PHGDH), which encodes a critical enzyme of the serine biosynthesis pathway, and Tribbles 3 (TRIB3), a pseudokinase with pleiotropic cellular functions.

CONCLUSIONS

A phenotypic screening platform using DCM iPSC-CMs was established for therapeutic target discovery. A combination of SMKIs ameliorated contractile and metabolic dysfunction in DCM iPSC-CMs mediated via the ATF4-dependent serine biosynthesis pathway. Together, these findings suggest that modulation of serine biosynthesis signalling may represent a novel genotype-agnostic therapeutic strategy for genetic DCM.

Progressive alterations in amino acid and lipid metabolism correlate with peripheral neuropathy in PolgD257A mice

Mitochondria are central to metabolic homeostasis, and progressive mitochondrial defects have diverse metabolic consequences that could drive distinct pathophysiological states. Here, we comprehensively characterized metabolic alterations in PolgD257A mice. Plasma alanine increased markedly with time, with other organic acids accumulating to a lesser extent. These changes were reflective of increased Cori and Cahill cycling in PolgD257A mice and subsequent hypoglycemia, which did not occur during normal mouse aging. Tracing with [15N]ammonium further supported this shift in amino acid metabolism with mild impairment of the urea cycle. We also measured alterations in the lipidome, observing a reduction in canonical lipids and accumulation of 1-deoxysphingolipids, which are synthesized from alanine via promiscuous serine palmitoyltransferase activity and correlate with peripheral neuropathy. Consistent with this metabolic link, PolgD257A mice exhibited thermal hypoalgesia. These results highlight the longitudinal changes that occur in intermediary metabolism upon mitochondrial impairment and identify a contributing mechanism to mitochondria-associated neuropathy.

Serine biosynthesis defect due to haploinsufficiency of PHGDH causes retinal disease

Macular telangiectasia type 2 (MacTel) is a progressive, late-onset retinal degenerative disease linked to decreased serum levels of serine that elevate circulating levels of a toxic ceramide species, deoxysphingolipids (deoxySLs); however, causal genetic variants that reduce serine levels in patients have not been identified. Here we identify rare, functional variants in the gene encoding the rate-limiting serine biosynthetic enzyme, phosphoglycerate dehydrogenase (PHGDH), as the single locus accounting for a significant fraction of MacTel. Under a dominant collapsing analysis model of a genome-wide enrichment analysis of rare variants predicted to impact protein function in 793 MacTel cases and 17,610 matched controls, the PHGDH gene achieves genome-wide significance (P = 1.2 × 10^-13) with variants explaining ~3.2% of affected individuals. We further show that the resulting functional defects in PHGDH cause decreased serine biosynthesis and accumulation of deoxySLs in retinal pigmented epithelial cells. PHGDH is a significant locus for MacTel that explains the typical disease phenotype and suggests a number of potential treatment options.

Extracellular serine and glycine are required for mouse and human skeletal muscle stem and progenitor cell function

OBJECTIVE

Skeletal muscle regeneration relies on muscle-specific adult stem cells (MuSCs), MuSC progeny, muscle progenitor cells (MPCs), and a coordinated myogenic program that is influenced by the extracellular environment. Following injury, MPCs undergo a transient and rapid period of population expansion, which is necessary to repair damaged myofibers and restore muscle homeostasis. Certain pathologies (e.g., metabolic diseases and muscle dystrophies) and advanced age are associated with dysregulated muscle regeneration. The availability of serine and glycine, two nutritionally non-essential amino acids, is altered in humans with these pathologies, and these amino acids have been shown to influence the proliferative state of non-muscle cells. Our objective was to determine the role of serine/glycine in MuSC/MPC function.

METHODS

Primary human MPCs (hMPCs) were used for in vitro experiments, and young (4-6 mo) and old (>20 mo) mice were used for in vivo experiments. Serine/glycine availability was manipulated using specially formulated media in vitro or dietary restriction in vivo followed by downstream metabolic and cell proliferation analyses.

RESULTS

We identified that serine/glycine are essential for hMPC proliferation. Dietary restriction of serine/glycine in a mouse model of skeletal muscle regeneration lowered the abundance of MuSCs 3 days post-injury. Stable isotope-tracing studies showed that hMPCs rely on extracellular serine/glycine for population expansion because they exhibit a limited capacity for de novo serine/glycine biosynthesis. Restriction of serine/glycine to hMPCs resulted in cell cycle arrest in G0/G1. Extracellular serine/glycine was necessary to support glutathione and global protein synthesis in hMPCs. Using an aged mouse model, we found that reduced serine/glycine availability augmented intermyocellular adipocytes 28 days post-injury.

CONCLUSIONS

These studies demonstrated that despite an absolute serine/glycine requirement for MuSC/MPC proliferation, de novo synthesis was inadequate to support these demands, making extracellular serine and glycine conditionally essential for efficient skeletal muscle regeneration.

Deuterium Tracing to Interrogate Compartment-Specific NAD(P)H Metabolism in Cultured Mammalian Cells

Oxidation-reduction (redox) reactions are ubiquitous in biology and typically occur in specific subcellular compartments. In cells, the electron transfer between molecules and organelles is commonly facilitated by pyridine nucleotides such as nicotinamide adenine dinucleotide phosphate (NADPH) and nicotinamide adenine dinucleotide (NADH). While often taken for granted, these metabolic reactions are critically important for maintaining redox homeostasis and biochemical potentials across membranes. While ¹³C tracing and metabolic flux analysis (MFA) have emerged as powerful tools to study intracellular metabolism, this approach is limited when applied to pathways catalyzed in multiple cellular compartments. To address this issue, we and others have applied ²H (deuterium) tracers to observe transfer of labeled hydride anions, which accompanies electron transfer. Furthermore, we have developed a reporter system for indirectly quantifying NADPH enrichment in specific subcellular compartments. Here, we provide a detailed description of ²H tracing applications and the interrogation of mitochondrial versus cytosolic NAD(P)H metabolism in cultured mammalian cells. Specifically, we describe the generation of reporter cell lines that express epitope-tagged R132H-IDH1 or R172K-IDH2 and produce (D)2-hydroxyglutarate in a doxycycline-dependent manner. These tools and methods allow for quantitation of reducing equivalent turnover rates, the directionality of pathways present in multiple compartments, and the estimation of pathway contributions to NADPH pools.

Serine restriction alters sphingolipid diversity to constrain tumour growth

Serine, glycine, and other non-essential amino acids are critical for tumor progression, and strategies to limit their availability are emerging as potential cancer therapies^1–3. However, the molecular mechanisms driving this response remain unclear, and the impact on lipid metabolism is relatively unexplored. Serine palmitoyltransferase (SPT) catalyzes the de novo biosynthesis of sphingolipids but also produces non-canonical 1-deoxysphingolipids (doxSLs) when using alanine as a substrate^4,5. DoxSLs accumulate in the context of SPTLC1 or SPTLC2 mutations^6,7 or low serine availability^8,9 to drive neuropathy, and deoxysphinganine (doxSA) has been investigated as an anti-cancer agent¹⁰. Here we exploit amino acid metabolism and SPT promiscuity to modulate the endogenous synthesis of toxic doxSLs and slow tumor progression. Anchorage-independent growth reprograms a metabolic network involving serine, alanine, and pyruvate resulting in increased susceptibility to endogenous doxSL synthesis. Targeting the mitochondrial pyruvate carrier (MPC) promotes alanine oxidation to mitigate doxSL synthesis and improves spheroid growth, while direct inhibition of doxSL synthesis drives similar phenotypes. Restriction of dietary serine/glycine potently induces accumulation of doxSLs in xenografts while decreasing tumor growth. Pharmacological modulation of SPT rescues xenograft growth on serine/glycine-restricted diets, while reduction of circulating serine by inhibition of phosphoglycerate dehydrogenase (PHGDH) leads to doxSL accumulation and mitigates tumor growth. SPT promiscuity therefore links serine and mitochondrial alanine metabolism to membrane lipid diversity, which sensitizes tumors to metabolic stress.

3D collagen architecture regulates cell adhesion through degradability, thereby controlling metabolic and oxidative stress

The collagen-rich tumor microenvironment plays a critical role in directing the migration behavior of cancer cells. 3D collagen architectures with small pores have been shown to confine cells and induce aggressive collective migration, irrespective of matrix stiffness and density. However, it remains unclear how cells sense collagen architecture and transduce this information to initiate collective migration. Here, we tune collagen architecture and analyze its effect on four core cell-ECM interactions: cytoskeletal polymerization, adhesion, contractility, and matrix degradation. From this comprehensive analysis, we deduce that matrix architecture initially modulates cancer cell adhesion strength, and that this results from architecture-induced changes to matrix degradability. That is, architectures with smaller pores are less degradable, and degradability is required for cancer cell adhesion to 3D fibrilar collagen. The biochemical consequences of this 3D low-attachment state are similar to those induced by suspension culture, including metabolic and oxidative stress. One distinction from suspension culture is the induction of collagen catabolism that occurs in 3D low-attachment conditions. Cells also upregulate Snail1 and Notch signaling in response to 3D low-attachment, which suggests a mechanism for the emergence of collective behaviors.

Robotic transperineal prostate biopsy: pilot clinical study

OBJECTIVE

To develope a robot (BioXbot) that performs mapping transperineal prostate biopsy (PB) with two perineal skin punctures under ultrasound guidance. Our pilot study's clinical endpoints were complications and its technical endpoints were the duration for each phase.

METHODS

This institution review board-approved prospective clinical trial included patients with indications for PB. Two urologists performed these PBs. In the lithotomy position and under general anesthesia, the transrectal biplane ultrasound probe acquired transverse images of the prostate gland. The urologist defined its boundaries and planned the biopsy. It guided the PB in 3 axes, passing through a single perineal skin puncture for each prostate side. After each biopsy, it automatically moved to the next position. The steps were repeated on the contralateral side.

RESULTS

Our 20 patients had a mean prostate-specific antigen of 8.4 ± 4.9 ng/mL. Two patients had 2 previous biopsies, whereas the rest had one. The mean number of biopsies taken was 28.5 ± 6.2 in a mean total procedure time of 32.5 ± 3.2 minutes. We detected 3 patients with prostate cancer with Gleason score 3 + 3. Two patients required brief bladder catheterization after their biopsy. Their prostate volumes were >50 mL and the number of biopsies taken was >30 cores. There was no mechanical failure, sepsis, bleeding per-rectal, or perineal hematoma.

CONCLUSION

This pilot study demonstrated BioXbot's safety and feasibility as a biopsy platform. It can potentially be used for image-guided PB and focal therapy.

Endogenous source of bacteria in tracheal tube and proximal ventilator breathing system in intensive care patients

Although bacteria from both the ventilator breathing system and the gastrointestinal tract have been implicated in the pathogenesis of ventilator-associated pneumonia, an endogenous source of bacteria in the proximal respiratory breathing system has yet to be demonstrated conclusively. We investigated a potential route of bacterial colonization from the stomach contents to the efferent limb of the ventilator breathing system by bacterial culture of daily specimens from six sites in 20 surgical intensive care patients. Gram-negative bacilli were isolated in a progressively increasing proportion of samples at successive sampling points, consistent with an endogenous-to-external route of spread (patients, chi-square = 14.12, P < 0.02; samples, chi-square = 106.15, P < 0.001). Identical strains of gram-negative bacilli, confirmed by REPS typing, were found at two or more sites in seven patients. In all seven, gram-negative bacilli were first isolated from a site in the patient. In none of the 20 patients was there evidence of a sequence of colonization from the ventilator tubing or Y-piece connector towards the patient. Probable colonization sequences plotted from the time of first isolation supported the proposed sequence in six patients, and in five began with the stomach contents. Isolation sequences contrary to the proposed direction of colonization involved four bacterial species and two patients, and did not extend beyond two sample sites. These findings imply that the retrograde route of bacterial colonization of the ventilated lung extends into the proximal respiratory breathing system and may help to identify additional targets for preventive intervention.

Bacteria, viruses, yeasts and protozoans associated with diarrheal disease in Singapore

Labile toxin producing enterotoxic E. coli (ETEC) were the commonest pathogen isolated from diarrheal stools of hospitalized children (21%) and adults (26%) in Singapore. Salmonellas ranked a close second in children (19%). Other bacterial pathogens were isolated from less than 5% of subjects. Blastocystis hominis was detected in 4.3% of diarrheal stools when a simple sedimentation technique was used. Cryptosporidium was not detected at all. An analysis of yeast counts in smears of diarrheal and non-diarrheal stools suggested they were etiologically associated with at least 6% of diarrhea in children and 19% in adults. Testing for rotaviruses by Latex agglutination and for adenovirus by electronmicroscopy showed an association with 6 per cent and 3 per cent diarrhea respectively. The study highlighted a need for: case control studies on ETEC and B. hominis; studies on the epidemiology of diarrhea by yeasts; establishing the true incidence of adenovirus diarrhea; studies on the prevalence and seasonality of rotavirus infection in Singapore.

The specificity of a rapid method of assay for the presence of Legionella species in water

A rapid method of assay, using a monoclonal antibody linked to alkaline phosphatase, was used for the detection of the Pontiac subgroup of Legionella pneumophila serogroup 1. It was tested for its specificity against 53 strains of Legionella recently isolated from the environment in Singapore and Malaysia. The specificity and sensitivity of this method of assay was confirmed, though there is some concern that the specificity was too narrow, and there are reservations about the criteria suggested for interpreting the results.

Legionella species, serogroups and subgroups found in the environment in Singapore

Over a period of seven months, 87 samples of water collected from 48 air-conditioning cooling-towers on 15 sites in Singapore yielded 19 strains of Legionella. Legionellas were found in 7 of the 15 sites. The strains isolated fell into 7 species, serogroups or subgroups of the genus Legionella. Only 11% of them belonged to the more pathogenic Pontiac subgroup of Legionella pneumophila serogroup 1.

Intestinal bacterial flora of the household lizard, Gecko gecko

A total of 114 isolates was recovered from the intestines of 43 househould lizards, Gecko gecko. Among the important ones were Staphylococcus aureus, Salmonella typhimurium, Pseudomonas aeruginosa, Proteus mirabilis and Edwardsiella tarda.

Ecology of mycoplasmas in clinically healthy cats

Mycoplasmas were isolated from various sites and organs of a series of 319 clinically healthy cats. They include M. felis, M. gateae, M. Arginini, A. laidlawii, feline ureaplasmas, M. pulmonis, M. arthritidis, and M. gallisepticum. In addition, there were 10 strains of mycoplasmas which could not be identified with the specific antiserums by growth inhibition tests. Antibody against M. felis was demonstrated by haemagglutination-inhibition and complement-fixation tests in cats which were over 6 months of age. However, no such antibody against M. felis was detected in animals which were less than 6 months old. No antibody against A. laidlawii, M. gateae, M. arginini and feline ureaplasmas was demonstrated by the same serological methods. The significance of these mycoplasmas in cats is described.

Significance and pathogenic role of Mycoplasma arginini in cat diseases

Eighty-one strans of Mycoplasma arginini were isolated from swabs and tissues cultured from a series of 555 cats. The majority of these strains (84%) were recovered from the oropharyngeal regions. M. arginini was experimentally inoculated into young kittens. No clinical disease was produced. However, there was rapid colonization in the inoculated sites.

Torulopsis glabrata infections in Singapore: a 4-year study

During the period 1971-4, Torulopsis glabrata formed 42% of yeasts isolated from 5677 clinical specimens from patients with cancers, diabetes mellitus, chronic renal failure, pregnacy or major surgical operations complicated by mycotic infections. The significance of T. glabrata in these patients is discussed.

Torulopsis glabrata--urinary tract infections in diabetic patients in Singapore

Urinary tract infections result mostly from ascending infection by micro-organisms introduced by way of the urethra. Bacteria are the usual causative agents. Occasionally, yeasts notably Candida albicans, are involved. Females are more prone to acute infections than males because of shorter urethra and the higher risks of contamination in the females.