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Parenti M, Schmidt RJ, Tancredi DJ, Hertz-Picciotto I, Walker CK, Slupsky CM. Neurodevelopment and Metabolism in the Maternal-Placental-Fetal Unit. JAMA Netw Open 2024; 7:e2413399. [PMID: 38805224 PMCID: PMC11134213 DOI: 10.1001/jamanetworkopen.2024.13399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/26/2024] [Indexed: 05/29/2024] Open
Abstract
Importance Disturbances in maternal, placental, and fetal metabolism are associated with developmental outcomes. Associations of maternal, placental, and fetal metabolism with subsequent neurodevelopmental outcomes in the child are understudied. Objective To investigate the metabolic associations within the maternal-placental-fetal unit and subsequent neurodevelopmental outcomes in younger siblings of children with autism spectrum disorder (ASD). Design, Setting, and Participants This cohort study was conducted within a subset of the Markers of Autism Risk in Babies, Learning Early Signs (MARBLES) cohort. MARBLES is a prospective birth cohort of younger siblings of children with ASD assessed for neurodevelopmental outcomes at approximately age 36 months. Participants in MARBLES were recruited through the UC Davis MIND Institute. This subset of the MARBLES cohort included younger siblings born between 2009 and 2015. Maternal third trimester serum, placental tissue, and umbilical cord serum samples were collected from participants. Only pregnancies with at least 2 of these sample types were included in this analysis. Data analysis was conducted from March 1, 2023, to March 15, 2024. Exposures Quantitative metabolomics analysis was conducted on maternal third trimester serum, as well as placental tissue and umbilical cord serum collected at delivery. Main Outcomes and Measures Using the Autism Diagnostic Observation Schedule and Mullen Scales of Early Learning, outcomes were classified as ASD, other nontypical development (non-TD), and typical development (TD). Results This analysis included 100 maternal serum samples, 141 placental samples, and 124 umbilical cord serum samples from 152 pregnancies (median [IQR] maternal age, 34.6 [30.8-38.3] years; median [IQR] gestational age, 39.0 [38.6-39.7] weeks; 87 [57.2%] male infants). There was no evidence that the maternal third trimester serum metabolome was significantly associated with the other metabolomes. The placental and cord serum metabolomes were highly correlated (first latent variate pair: R2 = 0.75; P < .001) and the variate scores for each tissue were significantly associated with reduced risk of non-TD (placenta: relative risk [RR], 0.13; 95% CI, 0.02-0.71; cord: RR, 0.13; 95% CI, 0.03-0.70) but not ASD (placenta: RR, 1.09; 95% CI, 0.42-2.81; cord: RR, 0.63; 95% CI, 0.23-1.73) compared with the TD reference group. Conclusions and Relevance In this cohort study of children with high familial risk of ASD, placental and cord serum metabolism at delivery were highly correlated. Furthermore, placental and cord serum metabolic profiles were associated with risk of non-TD.
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Affiliation(s)
- Mariana Parenti
- Department of Nutrition, University of California, Davis
- Now with Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, Seattle, Washington
| | - Rebecca J. Schmidt
- Department of Public Health Sciences, University of California, Davis
- MIND Institute, University of California, Davis, Sacramento
| | - Daniel J. Tancredi
- Department of Pediatrics, School of Medicine, University of California, Davis
| | - Irva Hertz-Picciotto
- Department of Public Health Sciences, University of California, Davis
- MIND Institute, University of California, Davis, Sacramento
| | - Cheryl K. Walker
- MIND Institute, University of California, Davis, Sacramento
- Department of Obstetrics & Gynecology, School of Medicine, University of California, Davis, Sacramento
| | - Carolyn M. Slupsky
- Department of Nutrition, University of California, Davis
- Department of Food Science and Technology, University of California, Davis
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Hasegawa Y, Kim DHJ, Zhang Z, Taha AY, Capitanio JP, Hogrefe CE, Bauman MD, Golub MS, Van de Water J, VandeVoort CA, Walker CK, Slupsky CM. Calorie restriction and pravastatin administration during pregnancy in obese rhesus macaques modulates maternal and infant metabolism and infant brain and behavioral development. Front Nutr 2023; 10:1146804. [PMID: 37255938 PMCID: PMC10225656 DOI: 10.3389/fnut.2023.1146804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/26/2023] [Indexed: 06/01/2023] Open
Abstract
Background Maternal obesity has been associated with a higher risk of pregnancy-related complications in mothers and offspring; however, effective interventions have not yet been developed. We tested two interventions, calorie restriction and pravastatin administration, during pregnancy in a rhesus macaque model with the hypothesis that these interventions would normalize metabolic dysregulation in pregnant mothers leading to an improvement in infant metabolic and cognitive/social development. Methods A total of 19 obese mothers were assigned to either one of the two intervention groups (n = 5 for calorie restriction; n = 7 for pravastatin) or an obese control group (n = 7) with no intervention, and maternal gestational samples and postnatal infant samples were compared with lean control mothers (n = 6) using metabolomics methods. Results Gestational calorie restriction normalized one-carbon metabolism dysregulation in obese mothers, but altered energy metabolism in her offspring. Although administration of pravastatin during pregnancy tended to normalize blood cholesterol in the mothers, it potentially impacted the gut microbiome and kidney function of their offspring. In the offspring, both calorie restriction and pravastatin administration during pregnancy tended to normalize the activity of AMPK in the brain at 6 months, and while results of the Visual Paired-Comparison test, which measures infant recognition memory, was not significantly impacted by either of the interventions, gestational pravastatin administration, but not calorie restriction, tended to normalize anxiety assessed by the Human Intruder test. Conclusions Although the two interventions tested in a non-human primate model led to some improvements in metabolism and/or infant brain development, negative impacts were also found in both mothers and infants. Our study emphasizes the importance of assessing gestational interventions for maternal obesity on both maternal and offspring long-term outcomes.
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Affiliation(s)
- Yu Hasegawa
- Department of Food Science and Technology, University of California-Davis, Davis, CA, United States
| | - Danielle H J Kim
- Department of Internal Medicine, Division of Rheumatology, Allergy, and Clinical Immunology, University of California-Davis, Davis, CA, United States
| | - Zhichao Zhang
- Department of Food Science and Technology, University of California-Davis, Davis, CA, United States
| | - Ameer Y Taha
- Department of Food Science and Technology, University of California-Davis, Davis, CA, United States
| | - John P Capitanio
- California National Primate Research Center, University of California-Davis, Davis, CA, United States
| | - Casey E Hogrefe
- California National Primate Research Center, University of California-Davis, Davis, CA, United States
| | - Melissa D Bauman
- California National Primate Research Center, University of California-Davis, Davis, CA, United States
- The UC Davis MIND Institute, University of California-Davis, Sacramento, CA, United States
- Department of Psychiatry and Behavioral Sciences, University of California-Davis, Sacramento, CA, United States
| | - Mari S Golub
- California National Primate Research Center, University of California-Davis, Davis, CA, United States
| | - Judy Van de Water
- The UC Davis MIND Institute, University of California-Davis, Sacramento, CA, United States
- Department of Internal Medicine, University of California-Davis, Sacramento, CA, United States
| | - Catherine A VandeVoort
- California National Primate Research Center, University of California-Davis, Davis, CA, United States
- Department of Obstetrics and Gynecology, University of California-Davis, Davis, CA, United States
| | - Cheryl K Walker
- California National Primate Research Center, University of California-Davis, Davis, CA, United States
- The UC Davis MIND Institute, University of California-Davis, Sacramento, CA, United States
- Department of Obstetrics and Gynecology, University of California-Davis, Davis, CA, United States
| | - Carolyn M Slupsky
- Department of Food Science and Technology, University of California-Davis, Davis, CA, United States
- Department of Nutrition, University of California-Davis, Davis, CA, United States
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Laufer BI, Hasegawa Y, Zhang Z, Hogrefe CE, Del Rosso LA, Haapanen L, Hwang H, Bauman MD, Van de Water J, Taha AY, Slupsky CM, Golub MS, Capitanio JP, VandeVoort CA, Walker CK, LaSalle JM. Multi-omic brain and behavioral correlates of cell-free fetal DNA methylation in macaque maternal obesity models. Nat Commun 2022; 13:5538. [PMID: 36130949 PMCID: PMC9492781 DOI: 10.1038/s41467-022-33162-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 09/06/2022] [Indexed: 11/28/2022] Open
Abstract
Maternal obesity during pregnancy is associated with neurodevelopmental disorder (NDD) risk. We utilized integrative multi-omics to examine maternal obesity effects on offspring neurodevelopment in rhesus macaques by comparison to lean controls and two interventions. Differentially methylated regions (DMRs) from longitudinal maternal blood-derived cell-free fetal DNA (cffDNA) significantly overlapped with DMRs from infant brain. The DMRs were enriched for neurodevelopmental functions, methylation-sensitive developmental transcription factor motifs, and human NDD DMRs identified from brain and placenta. Brain and cffDNA methylation levels from a large region overlapping mir-663 correlated with maternal obesity, metabolic and immune markers, and infant behavior. A DUX4 hippocampal co-methylation network correlated with maternal obesity, infant behavior, infant hippocampal lipidomic and metabolomic profiles, and maternal blood measurements of DUX4 cffDNA methylation, cytokines, and metabolites. We conclude that in this model, maternal obesity was associated with changes in the infant brain and behavior, and these differences were detectable in pregnancy through integrative analyses of cffDNA methylation with immune and metabolic factors.
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Affiliation(s)
- Benjamin I Laufer
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, 95616, USA
- UC Davis Genome Center, University of California, Davis, CA, 95616, USA
- MIND Institute, School of Medicine, University of California Davis, Sacramento, CA, 95817, USA
- Department of OMNI Bioinformatics, Genentech, Inc., South San Francisco, CA, 94080, USA
| | - Yu Hasegawa
- Department of Food Science and Technology, University of California Davis, Davis, CA, 95616, USA
| | - Zhichao Zhang
- Department of Food Science and Technology, University of California Davis, Davis, CA, 95616, USA
| | - Casey E Hogrefe
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
| | - Laura A Del Rosso
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
| | - Lori Haapanen
- MIND Institute, School of Medicine, University of California Davis, Sacramento, CA, 95817, USA
| | - Hyeyeon Hwang
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, 95616, USA
- UC Davis Genome Center, University of California, Davis, CA, 95616, USA
- MIND Institute, School of Medicine, University of California Davis, Sacramento, CA, 95817, USA
| | - Melissa D Bauman
- MIND Institute, School of Medicine, University of California Davis, Sacramento, CA, 95817, USA
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
- Department of Psychiatry and Behavioral Sciences, School of Medicine, University of California Davis, Davis, CA, 95616, USA
- Perinatal Origins of Disparities Center, University of California Davis, Davis, CA, 95616, USA
| | - Judy Van de Water
- Perinatal Origins of Disparities Center, University of California Davis, Davis, CA, 95616, USA
- Department of Internal Medicine, University of California Davis, Davis, CA, 95616, USA
| | - Ameer Y Taha
- Department of Food Science and Technology, University of California Davis, Davis, CA, 95616, USA
| | - Carolyn M Slupsky
- Department of Food Science and Technology, University of California Davis, Davis, CA, 95616, USA
- Perinatal Origins of Disparities Center, University of California Davis, Davis, CA, 95616, USA
- Department of Nutrition, University of California Davis, Davis, CA, 95616, USA
| | - Mari S Golub
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
| | - John P Capitanio
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
- Department of Psychology, University of California Davis, Davis, CA, 95616, USA
| | - Catherine A VandeVoort
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
- Department of Obstetrics and Gynecology, School of Medicine, University of California Davis, Davis, CA, 95616, USA
| | - Cheryl K Walker
- MIND Institute, School of Medicine, University of California Davis, Sacramento, CA, 95817, USA
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
- Perinatal Origins of Disparities Center, University of California Davis, Davis, CA, 95616, USA
- Department of Obstetrics and Gynecology, School of Medicine, University of California Davis, Davis, CA, 95616, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, 95616, USA.
- UC Davis Genome Center, University of California, Davis, CA, 95616, USA.
- MIND Institute, School of Medicine, University of California Davis, Sacramento, CA, 95817, USA.
- Perinatal Origins of Disparities Center, University of California Davis, Davis, CA, 95616, USA.
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Parenti M, Schmidt RJ, Ozonoff S, Shin HM, Tancredi DJ, Krakowiak P, Hertz-Picciotto I, Walker CK, Slupsky CM. Maternal Serum and Placental Metabolomes in Association with Prenatal Phthalate Exposure and Neurodevelopmental Outcomes in the MARBLES Cohort. Metabolites 2022; 12:829. [PMID: 36144233 PMCID: PMC9500898 DOI: 10.3390/metabo12090829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 01/16/2023] Open
Abstract
Prenatal exposure to phthalates, a family of endocrine-disrupting plasticizers, is associated with disruption of maternal metabolism and impaired neurodevelopment. We investigated associations between prenatal phthalate exposure and alterations of both the maternal third trimester serum metabolome and the placental metabolome at birth, and associations of these with child neurodevelopmental outcomes using data and samples from the Markers of Autism Risk in Babies Learning Early Signs (MARBLES) cohort. The third trimester serum (n = 106) and placental (n = 132) metabolomes were investigated using 1H nuclear magnetic resonance spectroscopy. Children were assessed clinically for autism spectrum disorder (ASD) and cognitive development. Although none of the urinary phthalate metabolite concentrations were associated with maternal serum metabolites after adjustment for covariates, mixture analysis using quantile g-computation revealed alterations in placental metabolites with increasing concentrations of phthalate metabolites that included reduced concentrations of 2-hydoxybutyrate, carnitine, O-acetylcarnitine, glucitol, and N-acetylneuraminate. Child neurodevelopmental outcome was not associated with the third trimester serum metabolome, but it was correlated with the placental metabolome in male children only. Maternal phthalate exposure during pregnancy is associated with differences in the placental metabolome at delivery, and the placental metabolome is associated with neurodevelopmental outcomes in males in a cohort with high familial ASD risk.
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Affiliation(s)
- Mariana Parenti
- Department of Nutrition, University of California, Davis, CA 95616, USA
| | - Rebecca J. Schmidt
- Department of Public Health Sciences, University of California, Davis, CA 95616, USA
- Medical Investigation of Neurodevelopmental Disorders (MIND) Institute, University of California, Davis, CA 95616, USA
| | - Sally Ozonoff
- Medical Investigation of Neurodevelopmental Disorders (MIND) Institute, University of California, Davis, CA 95616, USA
- Department of Psychiatry and Behavioral Sciences, University of California, Davis, CA 95616, USA
| | - Hyeong-Moo Shin
- Department of Environmental Science, Baylor University, Waco, TX 76798, USA
| | - Daniel J. Tancredi
- Department of Pediatrics, School of Medicine, University of California, Davis, CA 95616, USA
| | - Paula Krakowiak
- Department of Public Health Sciences, University of California, Davis, CA 95616, USA
| | - Irva Hertz-Picciotto
- Department of Public Health Sciences, University of California, Davis, CA 95616, USA
- Medical Investigation of Neurodevelopmental Disorders (MIND) Institute, University of California, Davis, CA 95616, USA
| | - Cheryl K. Walker
- Medical Investigation of Neurodevelopmental Disorders (MIND) Institute, University of California, Davis, CA 95616, USA
- Department of Obstetrics & Gynecology, School of Medicine, University of California, Davis, CA 95616, USA
| | - Carolyn M. Slupsky
- Department of Nutrition, University of California, Davis, CA 95616, USA
- Department of Food Science and Technology, University of California, Davis, CA 95616, USA
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Hasegawa Y, Zhang Z, Taha AY, Capitanio JP, Bauman MD, Golub MS, Van de Water J, VandeVoort CA, Walker CK, Slupsky CM. Impact of Maternal Obesity on the Gestational Metabolome and Infant Metabolome, Brain, and Behavioral Development in Rhesus Macaques. Metabolites 2022; 12:764. [PMID: 36005637 PMCID: PMC9415340 DOI: 10.3390/metabo12080764] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/13/2022] [Accepted: 08/14/2022] [Indexed: 01/16/2023] Open
Abstract
Maternal gestational obesity is associated with elevated risks for neurodevelopmental disorder, including autism spectrum disorder. However, the mechanisms by which maternal adiposity influences fetal developmental programming remain to be elucidated. We aimed to understand the impact of maternal obesity on the metabolism of both pregnant mothers and their offspring, as well as on metabolic, brain, and behavioral development of offspring by utilizing metabolomics, protein, and behavioral assays in a non-human primate model. We found that maternal obesity was associated with elevated inflammation and significant alterations in metabolites of energy metabolism and one-carbon metabolism in maternal plasma and urine, as well as in the placenta. Infants that were born to obese mothers were significantly larger at birth compared to those that were born to lean mothers. Additionally, they exhibited significantly reduced novelty preference and significant alterations in their emotional response to stress situations. These changes coincided with differences in the phosphorylation of enzymes in the brain mTOR signaling pathway between infants that were born to obese and lean mothers and correlated with the concentration of maternal plasma betaine during pregnancy. In summary, gestational obesity significantly impacted the infant systemic and brain metabolome and adaptive behaviors.
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Affiliation(s)
- Yu Hasegawa
- Department of Food Science and Technology, University of California-Davis, Davis, CA 95616, USA
| | - Zhichao Zhang
- Department of Food Science and Technology, University of California-Davis, Davis, CA 95616, USA
| | - Ameer Y. Taha
- Department of Food Science and Technology, University of California-Davis, Davis, CA 95616, USA
| | - John P. Capitanio
- California National Primate Research Center, University of California-Davis, Davis, CA 95616, USA
| | - Melissa D. Bauman
- California National Primate Research Center, University of California-Davis, Davis, CA 95616, USA
- The UC Davis MIND Institute, University of California-Davis, Sacramento, CA 95817, USA
- Department of Psychiatry and Behavioral Sciences, University of California-Davis, Sacramento, CA 95817, USA
| | - Mari S. Golub
- California National Primate Research Center, University of California-Davis, Davis, CA 95616, USA
| | - Judy Van de Water
- The UC Davis MIND Institute, University of California-Davis, Sacramento, CA 95817, USA
- Department of Internal Medicine, University of California-Davis, Sacramento, CA 95817, USA
| | - Catherine A. VandeVoort
- California National Primate Research Center, University of California-Davis, Davis, CA 95616, USA
- Department of Obstetrics and Gynecology, University of California-Davis, Davis, CA 95616, USA
| | - Cheryl K. Walker
- California National Primate Research Center, University of California-Davis, Davis, CA 95616, USA
- Department of Obstetrics and Gynecology, University of California-Davis, Davis, CA 95616, USA
| | - Carolyn M. Slupsky
- Department of Food Science and Technology, University of California-Davis, Davis, CA 95616, USA
- Department of Nutrition, University of California-Davis, Davis, CA 95616, USA
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Lim SY, Ng BH, Vermulapalli D, Lau H, Carrasco Laserna AK, Yang X, Tan SH, Chan MY, Li SFY. Simultaneous Polar Metabolite and N-Glycan Extraction Workflow for Joint-Omics Analysis: A Synergistic Approach for Novel Insights into Diseases. J Proteome Res 2022; 21:643-653. [DOI: 10.1021/acs.jproteome.1c00676] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Si Ying Lim
- NUS Graduate School for Integrative Sciences & Engineering (NGS), National University of Singapore, University Hall, Tan Chin Tuan Wing, Singapore 119077
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Bao Hui Ng
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Dhruti Vermulapalli
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Hazel Lau
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), Fusionopolis Way, Innovis, #08-03, Singapore 138634
| | - Anna Karen Carrasco Laserna
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
- Central Instrumentation Facility (Laguna Campus), Office of the Vice Chancellor for Research and Innovation, De La Salle University, 2041 Taft Avenue, Manila 1004, Philippines
| | - Xiaoxun Yang
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599
| | - Sock Hwee Tan
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599
| | - Mark Y. Chan
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599
| | - Sam Fong Yau Li
- NUS Graduate School for Integrative Sciences & Engineering (NGS), National University of Singapore, University Hall, Tan Chin Tuan Wing, Singapore 119077
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
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Integrated Metabolomics and Transcriptomics Using an Optimised Dual Extraction Process to Study Human Brain Cancer Cells and Tissues. Metabolites 2021; 11:metabo11040240. [PMID: 33919944 PMCID: PMC8070957 DOI: 10.3390/metabo11040240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/12/2021] [Accepted: 04/12/2021] [Indexed: 11/18/2022] Open
Abstract
The integration of untargeted metabolomics and transcriptomics from the same population of cells or tissue enhances the confidence in the identified metabolic pathways and understanding of the enzyme–metabolite relationship. Here, we optimised a simultaneous extraction method of metabolites/lipids and RNA from ependymoma cells (BXD-1425). Relative to established RNA (mirVana kit) or metabolite (sequential solvent addition and shaking) single extraction methods, four dual-extraction techniques were evaluated and compared (methanol:water:chloroform ratios): cryomill/mirVana (1:1:2); cryomill-wash/Econospin (5:1:2); rotation/phenol-chloroform (9:10:1); Sequential/mirVana (1:1:3). All methods extracted the same metabolites, yet rotation/phenol-chloroform did not extract lipids. Cryomill/mirVana and sequential/mirVana recovered the highest amounts of RNA, at 70 and 68% of that recovered with mirVana kit alone. sequential/mirVana, involving RNA extraction from the interphase of our established sequential solvent addition and shaking metabolomics-lipidomics extraction method, was the most efficient approach overall. Sequential/mirVana was applied to study a) the biological effect caused by acute serum starvation in BXD-1425 cells and b) primary ependymoma tumour tissue. We found (a) 64 differentially abundant metabolites and 28 differentially expressed metabolic genes, discovering four gene-metabolite interactions, and (b) all metabolites and 62% lipids were above the limit of detection, and RNA yield was sufficient for transcriptomics, in just 10 mg of tissue.
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