1
|
Paz-Ruza J, Freitas AA, Alonso-Betanzos A, Guijarro-Berdiñas B. Positive-Unlabelled learning for identifying new candidate Dietary Restriction-related genes among ageing-related genes. Comput Biol Med 2024; 180:108999. [PMID: 39137672 DOI: 10.1016/j.compbiomed.2024.108999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 07/25/2024] [Accepted: 08/05/2024] [Indexed: 08/15/2024]
Abstract
Dietary Restriction (DR) is one of the most popular anti-ageing interventions; recently, Machine Learning (ML) has been explored to identify potential DR-related genes among ageing-related genes, aiming to minimize costly wet lab experiments needed to expand our knowledge on DR. However, to train a model from positive (DR-related) and negative (non-DR-related) examples, the existing ML approach naively labels genes without known DR relation as negative examples, assuming that lack of DR-related annotation for a gene represents evidence of absence of DR-relatedness, rather than absence of evidence. This hinders the reliability of the negative examples (non-DR-related genes) and the method's ability to identify novel DR-related genes. This work introduces a novel gene prioritization method based on the two-step Positive-Unlabelled (PU) Learning paradigm: using a similarity-based, KNN-inspired approach, our method first selects reliable negative examples among the genes without known DR associations. Then, these reliable negatives and all known positives are used to train a classifier that effectively differentiates DR-related and non-DR-related genes, which is finally employed to generate a more reliable ranking of promising genes for novel DR-relatedness. Our method significantly outperforms (p<0.05) the existing state-of-the-art approach in three predictive accuracy metrics with up to ∼40% lower computational cost in the best case, and we identify 4 new promising DR-related genes (PRKAB1, PRKAB2, IRS2, PRKAG1), all with evidence from the existing literature supporting their potential DR-related role.
Collapse
Affiliation(s)
- Jorge Paz-Ruza
- LIDIA Group, CITIC, Universidade da Coruña, Campus de Elviña s/n, A Coruña 15071, Spain.
| | - Alex A Freitas
- School of Computing, University of Kent, Canterbury CT2 7FS, United Kingdom.
| | - Amparo Alonso-Betanzos
- LIDIA Group, CITIC, Universidade da Coruña, Campus de Elviña s/n, A Coruña 15071, Spain.
| | | |
Collapse
|
2
|
Jamerson LE, Bradshaw PC. The Roles of White Adipose Tissue and Liver NADPH in Dietary Restriction-Induced Longevity. Antioxidants (Basel) 2024; 13:820. [PMID: 39061889 PMCID: PMC11273496 DOI: 10.3390/antiox13070820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/01/2024] [Accepted: 07/03/2024] [Indexed: 07/28/2024] Open
Abstract
Dietary restriction (DR) protocols frequently employ intermittent fasting. Following a period of fasting, meal consumption increases lipogenic gene expression, including that of NADPH-generating enzymes that fuel lipogenesis in white adipose tissue (WAT) through the induction of transcriptional regulators SREBP-1c and CHREBP. SREBP-1c knockout mice, unlike controls, did not show an extended lifespan on the DR diet. WAT cytoplasmic NADPH is generated by both malic enzyme 1 (ME1) and the pentose phosphate pathway (PPP), while liver cytoplasmic NADPH is primarily synthesized by folate cycle enzymes provided one-carbon units through serine catabolism. During the daily fasting period of the DR diet, fatty acids are released from WAT and are transported to peripheral tissues, where they are used for beta-oxidation and for phospholipid and lipid droplet synthesis, where monounsaturated fatty acids (MUFAs) may activate Nrf1 and inhibit ferroptosis to promote longevity. Decreased WAT NADPH from PPP gene knockout stimulated the browning of WAT and protected from a high-fat diet, while high levels of NADPH-generating enzymes in WAT and macrophages are linked to obesity. But oscillations in WAT [NADPH]/[NADP+] from feeding and fasting cycles may play an important role in maintaining metabolic plasticity to drive longevity. Studies measuring the WAT malate/pyruvate as a proxy for the cytoplasmic [NADPH]/[NADP+], as well as studies using fluorescent biosensors expressed in the WAT of animal models to monitor the changes in cytoplasmic [NADPH]/[NADP+], are needed during ad libitum and DR diets to determine the changes that are associated with longevity.
Collapse
Affiliation(s)
| | - Patrick C. Bradshaw
- Department of Biomedical Sciences, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| |
Collapse
|
3
|
Gutierrez E, Mitchell S, Hambly C, Sayle KL, von Kriegsheim A, Speakman JR, Britton K. Carbon, nitrogen, and sulfur elemental and isotopic variations in mouse hair and bone collagen during short-term graded calorie restriction. iScience 2024; 27:110059. [PMID: 38947513 PMCID: PMC11214416 DOI: 10.1016/j.isci.2024.110059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 03/19/2024] [Accepted: 05/17/2024] [Indexed: 07/02/2024] Open
Abstract
This study characterized the effect of calorie restriction (CR) on elemental content and stable isotope ratio measurements of bone "collagen" and hair keratin. Adult mice on graded CR (10-40%; 84 days) showed decreased hair δ 15N, δ 13C, and δ 34S values (significantly for δ 15N) with increasing CR, alongside a significant increase in bone "collagen" δ 15N values and a decrease in "collagen" δ 13C values. We propose this was likely due to the intensified mobilization of endogenous proteins, as well as lipids in newly synthesized "collagen". Elemental analysis of bone "collagen" revealed decreased carbon, nitrogen, and sulfur % content with increasing CR which is attributed to a change in the in vivo bone "collagen" structure with extent of CR. This complexity challenges the use of elemental indicators in the assessment of collagen quality in archaeological studies where nutritional stress may be a factor.
Collapse
Affiliation(s)
- Eléa Gutierrez
- Department of Archaeology, University of Aberdeen, Aberdeen, Scotland AB39 2PN, UK
- School of Biological Sciences, University of Aberdeen, Aberdeen, Scotland AB24 2TZ, UK
- AASPE “Archéozoologie, Archéobotanique: Sociétés, Pratiques, Environnements”, Muséum national d’Histoire naturelle, 75005 Paris, France
| | - Sharon Mitchell
- School of Biological Sciences, University of Aberdeen, Aberdeen, Scotland AB24 2TZ, UK
| | - Catherine Hambly
- School of Biological Sciences, University of Aberdeen, Aberdeen, Scotland AB24 2TZ, UK
| | - Kerry L. Sayle
- Scottish Universities Environmental Research Centre, University of Glasgow, Scotland G75 0QF, UK
| | - Alex von Kriegsheim
- Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh Scotland EH4 2XR, UK
| | - John R. Speakman
- School of Biological Sciences, University of Aberdeen, Aberdeen, Scotland AB24 2TZ, UK
- Shenzhen Key Laboratory of Metabolic Health, Centre for Energy Metabolism and Reproduction, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, PRC
- Centre of Excellence in Animal Evolution and Genetics, Kunming, PRC
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, PRC
| | - Kate Britton
- Department of Archaeology, University of Aberdeen, Aberdeen, Scotland AB39 2PN, UK
| |
Collapse
|
4
|
Vatashchuk MV, Hurza VV, Stefanyshyn N, Bayliak MM, Gospodaryov DV, Garaschuk O, Lushchak VI. Impact of caloric restriction on oxidative stress and key glycolytic enzymes in the cerebral cortex, liver and kidney of old and middle-aged mice. Neuropharmacology 2024; 247:109859. [PMID: 38340956 DOI: 10.1016/j.neuropharm.2024.109859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 12/28/2023] [Accepted: 01/25/2024] [Indexed: 02/12/2024]
Abstract
Caloric restriction (CR) is proposed as a strategy to prevent age-related alterations like impaired glucose metabolism and intensification of oxidative stress. In this study, we examined effects of aging and CR on the activities of glycolytic enzymes and parameters of oxidative stress in the cerebral cortex, liver, and kidney of middle-aged (9 months old) and old (18 months old) C57BL6/N mice. Control middle-aged and old mice were fed ad libitum (AL groups), whereas age-matched CR groups were subjected to CR (70% of individual ad libitum food intake) for 6 and 12 months, respectively. There were no significant differences in the activities of key glycolytic and antioxidant enzymes and oxidative stress indices between the cortices of middle-aged and old AL mice. The livers and kidneys of old AL mice showed higher activity of glucose-6-phosphate dehydrogenase, an enzyme that produces NADPH in the pentose phosphate pathway, compared to those of middle-aged mice. CR regimen modulated some biochemical parameters in middle-aged but not in old mice. In particular, CR decreased oxidative stress intensity in the liver and kidney but had no effects on those parameters in the cerebral cortex. In the liver, CR led to lower activities of glycolytic enzymes, whereas its effect was the opposite in the kidney. The results suggest that during physiological aging there is no significant intensification of oxidative stress and glycolysis decline in mouse tissues during the transition from middle to old age. The CR regimen has tissue-specific effects and improves the metabolic state of middle-aged mice. This article is part of the Special Issue on "Ukrainian Neuroscience".
Collapse
Affiliation(s)
- Myroslava V Vatashchuk
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, 57 Shevchenko Str., Ivano-Frankivsk, 76018, Ukraine
| | - Viktoriia V Hurza
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, 57 Shevchenko Str., Ivano-Frankivsk, 76018, Ukraine
| | - Nadiia Stefanyshyn
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, 57 Shevchenko Str., Ivano-Frankivsk, 76018, Ukraine
| | - Maria M Bayliak
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, 57 Shevchenko Str., Ivano-Frankivsk, 76018, Ukraine
| | - Dmytro V Gospodaryov
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, 57 Shevchenko Str., Ivano-Frankivsk, 76018, Ukraine
| | - Olga Garaschuk
- Department of Neurophysiology, University of Tübingen, Tübingen, 72074, Germany.
| | - Volodymyr I Lushchak
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, 57 Shevchenko Str., Ivano-Frankivsk, 76018, Ukraine; Research and Development University, 13a Shota Rustaveli Str., Ivano-Frankivsk, 76018, Ukraine.
| |
Collapse
|
5
|
Qian X, Klatt S, Bennewitz K, Wohlfart DP, Lou B, Meng Y, Buettner M, Poschet G, Morgenstern J, Fleming T, Sticht C, Hausser I, Fleming I, Szendroedi J, Nawroth PP, Kroll J. Impaired Detoxification of Trans, Trans-2,4-Decadienal, an Oxidation Product from Omega-6 Fatty Acids, Alters Insulin Signaling, Gluconeogenesis and Promotes Microvascular Disease. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2302325. [PMID: 38059818 PMCID: PMC10811472 DOI: 10.1002/advs.202302325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 11/22/2023] [Indexed: 12/08/2023]
Abstract
Omega-6 fatty acids are the primary polyunsaturated fatty acids in most Western diets, while their role in diabetes remains controversial. Exposure of omega-6 fatty acids to an oxidative environment results in the generation of a highly reactive carbonyl species known as trans, trans-2,4-decadienal (tt-DDE). The timely and efficient detoxification of this metabolite, which has actions comparable to other reactive carbonyl species, such as 4-hydroxynonenal, acrolein, acetaldehyde, and methylglyoxal, is essential for disease prevention. However, the detoxification mechanism for tt-DDE remains elusive. In this study, the enzyme Aldh9a1b is identified as having a key role in the detoxification of tt-DDE. Loss of Aldh9a1b increased tt-DDE levels and resulted in an abnormal retinal vasculature and glucose intolerance in aldh9a1b-/- zebrafish. Transcriptomic and metabolomic analyses revealed that tt-DDE and aldh9a1b deficiency in larval and adult zebrafish induced insulin resistance and impaired glucose homeostasis. Moreover, alterations in hyaloid vasculature is induced by aldh9a1b knockout or by tt-DDE treatment can be rescued by the insulin receptor sensitizers metformin and rosiglitazone. Collectively, these results demonstrated that tt-DDE is the substrate of Aldh9a1b which causes microvascular damage and impaired glucose metabolism through insulin resistance.
Collapse
Affiliation(s)
- Xin Qian
- Department of Vascular BiologyEuropean Center for Angioscience (ECAS)Medical Faculty MannheimHeidelberg University68167MannheimGermany
| | - Stephan Klatt
- Institute for Vascular SignalingCentre for Molecular MedicineGoethe‐Universityam Main60590FrankfurtGermany
- The German Centre for Cardiovascular Research (DZHK)Partner site RheinMain60590FrankfurtGermany
| | - Katrin Bennewitz
- Department of Vascular BiologyEuropean Center for Angioscience (ECAS)Medical Faculty MannheimHeidelberg University68167MannheimGermany
| | - David Philipp Wohlfart
- Department of Vascular BiologyEuropean Center for Angioscience (ECAS)Medical Faculty MannheimHeidelberg University68167MannheimGermany
| | - Bowen Lou
- Department of Vascular BiologyEuropean Center for Angioscience (ECAS)Medical Faculty MannheimHeidelberg University68167MannheimGermany
- Present address:
Cardiovascular Department, the First Affiliated Hospital of Xi'an Jiaotong University277 West Yanta RoadXi'an710061China
| | - Ye Meng
- Bone Marrow Transplantation CenterThe First Affiliated HospitalZhejiang University School of MedicineHangzhou310003China
| | - Michael Buettner
- Metabolomics Core Technology PlatformCentre for Organismal StudiesHeidelberg University69120HeidelbergGermany
| | - Gernot Poschet
- Metabolomics Core Technology PlatformCentre for Organismal StudiesHeidelberg University69120HeidelbergGermany
| | - Jakob Morgenstern
- Department of Internal Medicine I and Clinical ChemistryHeidelberg University Hospital69120HeidelbergGermany
| | - Thomas Fleming
- Department of Internal Medicine I and Clinical ChemistryHeidelberg University Hospital69120HeidelbergGermany
| | - Carsten Sticht
- NGS Core FacilityMedical Faculty MannheimHeidelberg University68167MannheimGermany
| | - Ingrid Hausser
- Institute of Pathology IPHEM LabHeidelberg University Hospital69120HeidelbergGermany
| | - Ingrid Fleming
- Institute for Vascular SignalingCentre for Molecular MedicineGoethe‐Universityam Main60590FrankfurtGermany
- The German Centre for Cardiovascular Research (DZHK)Partner site RheinMain60590FrankfurtGermany
| | - Julia Szendroedi
- Department of Internal Medicine I and Clinical ChemistryHeidelberg University Hospital69120HeidelbergGermany
| | - Peter Paul Nawroth
- Department of Internal Medicine I and Clinical ChemistryHeidelberg University Hospital69120HeidelbergGermany
| | - Jens Kroll
- Department of Vascular BiologyEuropean Center for Angioscience (ECAS)Medical Faculty MannheimHeidelberg University68167MannheimGermany
| |
Collapse
|
6
|
Sun H, Zhang Q, Xu C, Mao A, Zhao H, Chen M, Sun W, Li G, Zhang T. Different Diet Energy Levels Alter Body Condition, Glucolipid Metabolism, Fecal Microbiota and Metabolites in Adult Beagle Dogs. Metabolites 2023; 13:metabo13040554. [PMID: 37110212 PMCID: PMC10143615 DOI: 10.3390/metabo13040554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/31/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Diet energy is a key component of pet food, but it is usually ignored during pet food development and pet owners also have limited knowledge of its importance. This study aimed to explore the effect of diet energy on the body condition, glucolipid metabolism, fecal microbiota and metabolites of adult beagles and analyze the relation between diet and host and gut microbiota. Eighteen healthy adult neutered male beagles were selected and randomly divided into three groups. Diets were formulated with three metabolizable energy (ME) levels: the low-energy (Le) group consumed a diet of 13.88 MJ/kg ME; the medium-energy (Me) group consumed a diet of 15.04 MJ/kg ME; and the high-energy (He) group consumed a diet of 17.05 MJ/kg ME. Moreover, the protein content of all these three diets was 29%. The experiment lasted 10 weeks, with a two-week acclimation period and an eight-week test phase. Body weight, body condition score (BCS), muscle condition score (MCS) and body fat index (BFI) decreased in the Le group, and the changes in these factors in the Le group were significantly higher than in the other groups (p < 0.05). The serum glucose and lipid levels of the Le and He groups changed over time (p < 0.05), but those of the Me group were stable (p > 0.05). The fecal pH of the Le and He groups decreased at the end of the trial (p < 0.05) and we found that the profiles of short-chain fatty acids (SCFAs) and bile acids (BAs) changed greatly, especially secondary BAs (p < 0.05). As SCFAs and secondary BAs are metabolites of the gut microbiota, the fecal microbiota was also measured. Fecal 16S rRNA gene sequencing found that the Me group had higher α-diversity indices (p < 0.05). The Me group had notably higher levels of gut probiotics, such as Faecalibacterium prausnitzii, Bacteroides plebeius and Blautia producta (p < 0.05). The diet-host-fecal microbiota interactions were determined by network analysis, and fecal metabolites may help to determine the best physical condition of dogs, assisting pet food development. Overall, feeding dogs low- or high-energy diets was harmful for glucostasis and promoted the relative abundance of pathogenic bacteria in the gut, while a medium-energy diet maintained an ideal body condition. We concluded that dogs that are fed a low-energy diet for an extended period may become lean and lose muscle mass, but diets with low energy levels and 29% protein may not supply enough protein for dogs losing weight.
Collapse
Affiliation(s)
- Haoran Sun
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Qiaoru Zhang
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao 066004, China
| | - Chao Xu
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Aipeng Mao
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao 066004, China
| | - Hui Zhao
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Miao Chen
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Weili Sun
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266000, China
| | - Guangyu Li
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266000, China
| | - Tietao Zhang
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| |
Collapse
|