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Tian Q, Chung H, Wen D. The role of lipids in genome integrity and pluripotency. Biochem Soc Trans 2024; 52:639-650. [PMID: 38506536 PMCID: PMC11088914 DOI: 10.1042/bst20230479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 03/05/2024] [Accepted: 03/11/2024] [Indexed: 03/21/2024]
Abstract
Pluripotent stem cells (PSCs), comprising embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), offer immense potential for regenerative medicine due to their ability to differentiate into all cell types of the adult body. A critical aspect of harnessing this potential is understanding their metabolic requirements during derivation, maintenance, and differentiation in vitro. Traditional culture methods using fetal bovine serum often lead to issues such as heterogeneous cell populations and diminished pluripotency. Although the chemically-defined 2i/LIF medium has provided solutions to some of these challenges, prolonged culturing of these cells, especially female ESCs, raises concerns related to genome integrity. This review discusses the pivotal role of lipids in genome stability and pluripotency of stem cells. Notably, the introduction of lipid-rich albumin, AlbuMAX, into the 2i/LIF culture medium offers a promising avenue for enhancing the genomic stability and pluripotency of cultured ESCs. We further explore the unique characteristics of lipid-induced pluripotent stem cells (LIP-ESCs), emphasizing their potential in regenerative medicine and pluripotency research.
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Affiliation(s)
- Qiyu Tian
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10065, U.S.A
| | - Hoyoung Chung
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10065, U.S.A
| | - Duancheng Wen
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10065, U.S.A
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Yilmaz A, Liraz-Zaltsman S, Shohami E, Gordevičius J, Kerševičiūtė I, Sherman E, Bahado-Singh RO, Graham SF. The longitudinal biochemical profiling of TBI in a drop weight model of TBI. Sci Rep 2023; 13:22260. [PMID: 38097614 PMCID: PMC10721861 DOI: 10.1038/s41598-023-48539-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/28/2023] [Indexed: 12/17/2023] Open
Abstract
Traumatic brain injury (TBI) is a major cause of mortality and disability worldwide, particularly among individuals under the age of 45. It is a complex, and heterogeneous disease with a multifaceted pathophysiology that remains to be elucidated. Metabolomics has the potential to identify metabolic pathways and unique biochemical profiles associated with TBI. Herein, we employed a longitudinal metabolomics approach to study TBI in a weight drop mouse model to reveal metabolic changes associated with TBI pathogenesis, severity, and secondary injury. Using proton nuclear magnetic resonance (1H NMR) spectroscopy, we biochemically profiled post-mortem brain from mice that suffered mild TBI (N = 25; 13 male and 12 female), severe TBI (N = 24; 11 male and 13 female) and sham controls (N = 16; 11 male and 5 female) at baseline, day 1 and day 7 following the injury. 1H NMR-based metabolomics, in combination with bioinformatic analyses, highlights a few significant metabolites associated with TBI severity and perturbed metabolism related to the injury. We report that the concentrations of taurine, creatinine, adenine, dimethylamine, histidine, N-Acetyl aspartate, and glucose 1-phosphate are all associated with TBI severity. Longitudinal metabolic observation of brain tissue revealed that mild TBI and severe TBI lead distinct metabolic profile changes. A multi-class model was able to classify the severity of injury as well as time after TBI with estimated 86% accuracy. Further, we identified a high degree of correlation between respective hemisphere metabolic profiles (r > 0.84, p < 0.05, Pearson correlation). This study highlights the metabolic changes associated with underlying TBI severity and secondary injury. While comprehensive, future studies should investigate whether: (a) the biochemical pathways highlighted here are recapitulated in the brain of TBI sufferers and (b) if the panel of biomarkers are also as effective in less invasively harvested biomatrices, for objective and rapid identification of TBI severity and prognosis.
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Affiliation(s)
- Ali Yilmaz
- Metabolomics Department, Beaumont Research Institute, Beaumont Health, Royal Oak, MI, 48073, USA
- Oakland University-William Beaumont School of Medicine, Rochester, MI, 48073, USA
| | - Sigal Liraz-Zaltsman
- Department of Pharmacology, The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Ramat-Gan, Israel
- Department of Sports Therapy, Institute for Health and Medical Professions, Ono Academic College, Qiryat Ono, Israel
| | - Esther Shohami
- Department of Pharmacology, The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Juozas Gordevičius
- VUGENE LLC, 625 EKenmoor Avenue Southeast, Suite 301, PMB 96578, Grand Rapids, MI, 49546, USA
| | - Ieva Kerševičiūtė
- VUGENE LLC, 625 EKenmoor Avenue Southeast, Suite 301, PMB 96578, Grand Rapids, MI, 49546, USA
| | - Eric Sherman
- Wayne State University School of Medicine, Detroit, MI, 48202, USA
| | - Ray O Bahado-Singh
- Oakland University-William Beaumont School of Medicine, Rochester, MI, 48073, USA
| | - Stewart F Graham
- Metabolomics Department, Beaumont Research Institute, Beaumont Health, Royal Oak, MI, 48073, USA.
- Oakland University-William Beaumont School of Medicine, Rochester, MI, 48073, USA.
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Vernì F. DNA Damage Response (DDR) and DNA Repair. Int J Mol Sci 2022; 23:ijms23137204. [PMID: 35806207 PMCID: PMC9266642 DOI: 10.3390/ijms23137204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 02/04/2023] Open
Affiliation(s)
- Fiammetta Vernì
- Department Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
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Wang YH, Sheetz MP. When PIP 2 Meets p53: Nuclear Phosphoinositide Signaling in the DNA Damage Response. Front Cell Dev Biol 2022; 10:903994. [PMID: 35646908 PMCID: PMC9136457 DOI: 10.3389/fcell.2022.903994] [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: 03/25/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
The mechanisms that maintain genome stability are critical for preventing tumor progression. In the past decades, many strategies were developed for cancer treatment to disrupt the DNA repair machinery or alter repair pathway selection. Evidence indicates that alterations in nuclear phosphoinositide lipids occur rapidly in response to genotoxic stresses. This implies that nuclear phosphoinositides are an upstream element involved in DNA damage signaling. Phosphoinositides constitute a new signaling interface for DNA repair pathway selection and hence a new opportunity for developing cancer treatment strategies. However, our understanding of the underlying mechanisms by which nuclear phosphoinositides regulate DNA damage repair, and particularly the dynamics of those processes, is rather limited. This is partly because there are a limited number of techniques that can monitor changes in the location and/or abundance of nuclear phosphoinositide lipids in real time and in live cells. This review summarizes our current knowledge regarding the roles of nuclear phosphoinositides in DNA damage response with an emphasis on the dynamics of these processes. Based upon recent findings, there is a novel model for p53's role with nuclear phosphoinositides in DNA damage response that provides new targets for synthetic lethality of tumors.
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Affiliation(s)
| | - Michael P. Sheetz
- Biochemistry and Molecular Biology Dept., University of Texas Medical Branch, Galveston, TX, United States
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Nuclear Lipid Droplet Birth during Replicative Stress. Cells 2022; 11:cells11091390. [PMID: 35563696 PMCID: PMC9105094 DOI: 10.3390/cells11091390] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/14/2022] [Accepted: 04/14/2022] [Indexed: 12/18/2022] Open
Abstract
The nuclear membrane defines the boundaries that confine, protect and shape the genome. As such, its blebbing, ruptures and deformations are known to compromise the integrity of genetic material. Yet, drastic transitions of the nuclear membrane such as its invagination towards the nucleoplasm or its capacity to emit nuclear lipid droplets (nLD) have not been evaluated with respect to their impact on genome dynamics. To begin assessing this, in this work we used Saccharomyces cerevisiae as a model to ask whether a selection of genotoxins can trigger the formation of nLD. We report that nLD formation is not a general feature of all genotoxins, but of those engendering replication stress. Exacerbation of endogenous replication stress by genetic tools also elicited nLD formation. When exploring the lipid features of the nuclear membrane at the base of this emission, we revealed a link with the unsaturation profile of its phospholipids and, for the first time, of its sterol content. We propose that stressed replication forks may stimulate nLD birth by anchoring to the inner nuclear membrane, provided that the lipid context is adequate. Further, we point to a transcriptional feed-back process that counteracts the membrane’s proneness to emit nLD. With nLD representing platforms onto which genome-modifying reactions can occur, our findings highlight them as important players in the response to replication stress.
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