HRMAS 1H-NMR measured changes of the metabolite profile as mesenchymal stem cells differentiate to targeted fat cells in vitro: implications for non-invasive monitoring of stem cell differentiation in vivo

In-cell NMR: Why and how?

NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.

NMR Metabolomics Assessment of Osteogenic Differentiation of Adipose-Tissue-Derived Mesenchymal Stem Cells

This Article presents, for the first time to our knowledge, an untargeted nuclear magnetic resonance (NMR) metabolomic characterization of the polar intracellular metabolic adaptations of human adipose-derived mesenchymal stem cells during osteogenic differentiation. The use of mesenchymal stem cells (MSCs) for bone regeneration is a promising alternative to conventional bone grafts, and untargeted metabolomics may unveil novel metabolic information on the osteogenic differentiation of MSCs, allowing their behavior to be understood and monitored/guided toward effective therapies. Our results unveiled statistically relevant changes in the levels of just over 30 identified metabolites, illustrating a highly dynamic process with significant variations throughout the whole 21-day period of osteogenic differentiation, mainly involving amino acid metabolism and protein synthesis; energy metabolism and the roles of glycolysis, the tricarboxylic acid cycle, and oxidative phosphorylation; cell membrane metabolism; nucleotide metabolism (including the specific involvement of O-glycosylation intermediates and NAD⁺); and metabolic players in protective antioxidative mechanisms (such as glutathione and specific amino acids). Different metabolic stages are proposed and are supported by putative biochemical explanations for the metabolite changes observed. This work lays the groundwork for the use of untargeted NMR metabolomics to find potential metabolic markers of osteogenic differentiation efficacy.

Metabolomic Applications in Stem Cell Research: a Review

This review describes the use of metabolomics to study stem cell (SC) characteristics and function, excluding SCs in cancer research, suited to a fully dedicated text. The interest in employing metabolomics in SC research has consistently grown and emphasis is, here, given to developments reported in the past five years. This text informs on the existing methodologies and their complementarity regarding the information provided, comprising untargeted/targeted approaches, which couple mass spectrometry or nuclear magnetic resonance spectroscopy with multivariate analysis (and, in some cases, pathway analysis and integration with other omics), and more specific analytical approaches, namely isotope tracing to highlight particular metabolic pathways, or in tandem microscopic strategies to pinpoint characteristics within a single cell. The bulk of this review covers the existing applications in various aspects of mesenchymal SC behavior, followed by pluripotent and neural SCs, with a few reports addressing other SC types. Some of the central ideas investigated comprise the metabolic/biological impacts of different tissue/donor sources and differentiation conditions, including the importance of considering 3D culture environments, mechanical cues and/or media enrichment to guide differentiation into specific lineages. Metabolomic analysis has considered cell endometabolomes and exometabolomes (fingerprinting and footprinting, respectively), having measured both lipid species and polar metabolites involved in a variety of metabolic pathways. This review clearly demonstrates the current enticing promise of metabolomics in significantly contributing towards a deeper knowledge on SC behavior, and the discovery of new biomarkers of SC function with potential translation to in vivo clinical practice.

Challenges in Studying Stem Cell Metabolism

The expanding field of stem cell metabolism has been supported by technical advances in metabolite profiling and novel functional analyses. While use of these methodologies has been fruitful, many challenges are posed by the intricacies of culturing stem cells in vitro, along with the distinctive scarcity of adult tissue stem cells and the complexities of their niches in vivo. This review provides an examination of the methodologies used to characterize stem cell metabolism, highlighting their utility while placing a sharper focus on their limitations and hurdles the field needs to overcome for the optimal study of stem cell metabolic networks.

Rationale for the design of 3D-printable bioresorbable tissue-engineering chambers to promote the growth of adipose tissue

Tissue engineering chambers (TECs) bring great hope in regenerative medicine as they allow the growth of adipose tissue for soft tissue reconstruction. To date, a wide range of TEC prototypes are available with different conceptions and volumes. Here, we addressed the influence of TEC design on fat flap growth in vivo as well as the possibility of using bioresorbable polymers for optimum TEC conception. In rats, adipose tissue growth is quicker under perforated TEC printed in polylactic acid than non-perforated ones (growth difference 3 to 5 times greater within 90 days). Histological analysis reveals the presence of viable adipocytes under a moderate (less than 15% of the flap volume) fibrous capsule infiltrated with CD68⁺ inflammatory cells. CD31-positive vascular cells are more abundant at the peripheral zone than in the central part of the fat flap. Cells in the TEC exhibit a specific metabolic profile of functional adipocytes identified by ¹H-NMR. Regardless of the percentage of TEC porosity, the presence of a flat base allowed the growth of a larger fat volume (p < 0.05) as evidenced by MRI images. In pigs, bioresorbable TEC in poly[1,4-dioxane-2,5-dione] (polyglycolic acid) PURASORB PGS allows fat flap growth up to 75 000 mm³ at day 90, (corresponding to more than a 140% volume increase) while at the same time the TEC is largely resorbed. No systemic inflammatory response was observed. Histologically, the expansion of adipose tissue resulted mainly from an increase in the number of adipocytes rather than cell hypertrophy. Adipose tissue is surrounded by perfused blood vessels and encased in a thin fibrous connective tissue containing patches of CD163⁺ inflammatory cells. Our large preclinical evaluation defined the appropriate design for 3D-printable bioresorbable TECs and thus opens perspectives for further clinical applications.

Multi-platform NMR Study of Pluripotent Stem Cells Unveils Complementary Metabolic Signatures towards Differentiation

Stem cells, poised to revolutionize current medicine, stand as major workhorses for monitoring changes in cell fate. Characterizing metabolic phenotypes is key to monitor in differentiating cells transcriptional and epigenetic shifts at a functional level and provides a non-genetic means to control cell specification. Expanding the arsenal of analytical tools for metabolic profiling of cell differentiation is therefore of importance. Here, we describe the metabolome of whole pluripotent stem cells (PSCs) using high‐resolution magic angle spinning (HR-MAS), a non-destructive approach for Nuclear Magnetic Resonance (NMR) analysis. The integrated ¹H NMR analysis results in detection of metabolites of various groups, including energy metabolites, amino acids, choline derivatives and short chain fatty acids. It unveils new metabolites that discriminate PSCs from differentiated counterparts and directly measures substrates and co-factors of histone modifying enzymes, suggesting that NMR stands as a strategic technique for deciphering metabolic regulations of histone post-translational modifications. HR-MAS NMR analysis of whole PSCs complements the much used solution NMR of cell extracts. Altogether, our multi-platform NMR investigation provides a consolidated picture of PSC metabolic signatures and of metabolic pathways involved in differentiation.

Applications of high-resolution magic angle spinning MRS in biomedical studies I-cell line and animal models

High-resolution magic angle spinning (HRMAS) MRS allows for direct measurements of non-liquid tissue and cell specimens to present valuable insights into the cellular metabolisms of physiological and pathological processes. HRMAS produces high-resolution spectra comparable to those obtained from solutions of specimen extracts but without complex metabolite extraction processes, and preserves the tissue cellular structure in a form suitable for pathological examinations following spectroscopic analysis. The technique has been applied in a wide variety of biomedical and biochemical studies and become one of the major platforms of metabolomic studies. By quantifying single metabolites, metabolite ratios, or metabolic profiles in their entirety, HRMAS presents promising possibilities for diagnosis and prediction of clinical outcomes for various diseases, as well as deciphering of metabolic changes resulting from drug therapies or xenobiotic interactions. In this review, we evaluate HRMAS MRS results on animal models and cell lines reported in the literature, and present the diverse applications of the method for the understanding of pathological processes and the effectiveness of therapies, development of disease animal models, and new progress in HRMAS methodology.

Distinguishing tendon and ligament fibroblasts based on 1H nuclear magnetic resonance spectroscopy

Tendon and ligament (T/L) have been known to be obviously different from each other in tissue level. However, due to the overlapping gene markers, distinction in cellular level has not been clearly verified yet. Recently, the use of nuclear magnetic resonance (NMR) spectroscopy has shown the potential to detect biological markers in cellular level. Therefore, in this study we applied a non-invasive technique based on NMR spectroscopy to establish biomarkers to distinguish between T/L fibroblasts. In addition the cellular morphologies and gene expression patterns were also investigated for comparison through optical microscopy and real-time polymerase chain reaction (PCR). No difference was observed from morphology and real-time PCR results, either as expected. However, we found clear differences in their metabolomic spectra using 1H NMR spectroscopy. The calculated integral values of fatty acids (with chemical shifts at ~0.9, 1.26, 1.59, 2.05, 2.25, and 2.81 ppm), lactate (~1.33 ppm), and leucine (~2.72 ppm) were significantly different between the two types of fibroblasts. To be specific tendon group exhibited higher level of the metabolite than ligament group. In conclusion, in-cell metabolomic evaluation by NMR technique used in this study is believed to provide a promising tool in distinguishing cell types, especially T/L cells, which cannot be classified by conventional biological assays.

Bone Marrow Lipid Profiles from Peripheral Skeleton as Potential Biomarkers for Osteoporosis: A 1H-MR Spectroscopy Study

RATIONALE AND OBJECTIVES

To characterize the lipidic profile of bone marrow in the calcaneus and femoral neck of healthy, osteopenic, and osteoporotic women, by using magnetic resonance spectroscopy (MRS) at 3T. The final goal was to identify specific metabolites with the potential ability to discriminate between healthy, osteopenic, and osteoporotic subjects.

MATERIALS AND METHODS

Sixty-two and thirty three postmenopausal women recruited to investigate calcaneus and femoral neck, respectively, underwent a bone mineral density (BMD) measurement to be classified as healthy subjects (n = 22), osteopenic (n = 45), or osteoporotic (n = 28) patients. MRS spectra were used to quantify and compare bone marrow fat resonances between the three BMD groups. Between-group differences were tested using a Welch analysis of variance. Multiple comparisons were made with the Games-Howell correction. Relationships between pairs of variables were assessed with linear correlation analysis. Reproducibility analysis was performed for all the lipid resonances in both sites.

RESULTS

The reproducibility was satisfactory. In femoral neck, methylene (L13), glycerol (L41, L43), and total lipid resonances were significantly lower in healthy as compared to osteoporotic subjects. On the other hand, in calcaneus, L13/glycerol significantly discriminated between osteopenic and osteoporotic subjects whereas L13/(unsaturated lipid) discriminated between healthy and osteopenic group. However, the reproducibility of both unsaturated lipid and glycerol resonances were less optimal.

CONCLUSIONS

MRS of bone marrow lipid profiles from peripheral skeletal sites may be a promising tool for screening of large population to identify individuals with or at risk for developing osteoporosis. Moreover, it provides information about the metabolic changes occurring in bone marrow with the development of osteoporosis, which are skeletal site dependent.

MSCs conditioned media and umbilical cord blood plasma metabolomics and composition

Human mesenchymal stem cells (hMSCs) from umbilical cord (UC) blood (UCB) and matrix are tested clinically for a variety of pathologies but in vitro expansion using culture media containing fetal bovine serum (FBS) is essential to achieve appropriate cell numbers for clinical use. Human UCB plasma (hUCBP) can be used as a supplement for hMSCs culture, since UCB is rich in soluble growth factors and due to worldwide increased number of cryopreserved UCB units in public and private banks, without the disadvantages listed for FBS. On the other hand, the culture media enriched in growth factors produced by these hMSCs in expansion (Conditioned medium--CM) can be an alternative to hMSCs application. The CM of the hMSCs from the UC might be a better therapeutic option compared to cell transplantation, as it can benefit from the local tissue response to the secreted molecules without the difficulties and complications associated to the engraftment of the allo- or xeno-transplanted cells. These facts drove us to know the detailed composition of the hUCBP and CM, by 1H-NMR and Multiplexing LASER Bead Technology. hUCBP is an adequate alternative for the FBS and the CM and hUCBP are important sources of growth factors, which can be used in MSCs-based therapies. Some of the major proliferative, chemotactic and immunomodulatory soluble factors (TGF-β, G-CSF, GM-CSF, MCP-1, IL-6, IL-8) were detected in high concentrations in CM and even higher in hUCBP. The results from 1H-NMR spectroscopic analysis of CM endorsed a better understanding of hMSCs metabolism during in vitro culture, and the relative composition of several metabolites present in CM and hUCBP was obtained. The data reinforces the potential use of hUCBP and CM in tissue regeneration and focus the possible use of hUCBP as a substitute for the FBS used in hMSCs in vitro culture.

Antidiabetic property of Symplocos cochinchinensis is mediated by inhibition of alpha glucosidase and enhanced insulin sensitivity

The study is designed to find out the biochemical basis of antidiabetic property of Symplocos cochinchinensis (SC), the main ingredient of ‘Nisakathakadi’ an Ayurvedic decoction for diabetes. Since diabetes is a multifactorial disease, ethanolic extract of the bark (SCE) and its fractions (hexane, dichloromethane, ethyl acetate and 90% ethanol) were evaluated by in vitro methods against multiple targets relevant to diabetes such as the alpha glucosidase inhibition, glucose uptake, adipogenic potential, oxidative stress, pancreatic beta cell proliferation, inhibition of protein glycation, protein tyrosine phosphatase-1B (PTP-1B) and dipeptidyl peptidase-IV (DPP-IV). Among the extracts, SCE exhibited comparatively better activity like alpha glucosidase inhibition (IC₅₀ value-82.07±2.10 µg/mL), insulin dependent glucose uptake (3 fold increase) in L6 myotubes, pancreatic beta cell regeneration in RIN-m5F (3.5 fold increase) and reduced triglyceride accumulation (22% decrease) in 3T3L1 cells, protection from hyperglycemia induced generation of reactive oxygen species in HepG2 cells (59.57% decrease) with moderate antiglycation and PTP-1B inhibition. Chemical characterization by HPLC revealed the superiority of SCE over other extracts due to presence and quantity of bioactives (beta-sitosterol, phloretin 2′glucoside, oleanolic acid) in addition to minerals like magnesium, calcium, potassium, sodium, zinc and manganese. So SCE has been subjected to oral sucrose tolerance test to evaluate its antihyperglycemic property in mild diabetic and diabetic animal models. SCE showed significant antihyperglycemic activity in in vivo diabetic models. We conclude that SC mediates the antidiabetic activity mainly via alpha glucosidase inhibition, improved insulin sensitivity, with moderate antiglycation and antioxidant activity.

Metabolism under hypoxia in Tm1 murine melanoma cells is affected by the presence of galectin-3, a metabolomics approach

Metabolomics has proven an useful tool for systems biology. Here we have used a metabolomics approach to identify conditions in which de novo expression of an established tumor marker, galectin-3, would confer a potential selective advantage for melanoma growth and survival. A murine melanoma cell line (Tm1) that lacks galectin-3 was modified to express it or not (Tm1.G2 and Tm1.N3, respectively). These variant cell line were then exposed to conditions of controlled oxygen tensions and glucose levels. Metabolic profiling of intracellular metabolites of cells exposed to these conditions was obtained in steady state using high resolution ¹H Magnetic Resonance Spectroscopy (¹H-MRS) and multivariate statistical analysis. The Nuclear Magnetic Resonance (NMR) spectra contained a large number of absorption lines from which we were able to distinguish 20 metabolites, 3 fatty acids and some absorption lines and clusters were not identified. Principal Components Analysis (PCA) allowed for the discrimination of 2 experimental conditions in which expression of the tumor marker galectin-3 may play a significant role, namely exposure of cells to hypoxia under high glucose. Interestingly, under all other experimental conditions tested, the cellular system was quite robust. Our results suggest that the Metabolomics approach can be used to access information about changes in many metabolic pathways induced in tumorigenic cells and to allow the evaluation of their behavior in controlled environmental conditions or selective pressures.

Evaluation of metabolomic changes as a biomarker of chondrogenic differentiation in 3D-cultured human mesenchymal stem cells using proton (1H) nuclear magnetic resonance spectroscopy

PURPOSE

The purpose of this study was to evaluate the metabolomic changes in 3D-cultured human mesenchymal stem cells (hMSCs) in alginate beads, so as to identify biomarkers during chondrogenesis using (1)H nuclear magnetic resonance (NMR) spectroscopy.

MATERIALS AND METHODS

hMSCs (2×10(6) cells/mL) were seeded into alginate beads, and chondrogenesis was allowed to progress for 15 days. NMR spectra of the chondrogenic hMSCs were obtained at 4, 7, 11, and 15 days using a 14.1-T (600-MHz) NMR with the water suppression sequence, zgpr. Real-Time polymerase chain reaction (PCR) was performed to confirm that that the hMSCs differentiated into chondrocytes and to analyze the metabolomic changes indicated by the NMR spectra.

RESULTS

During chondrogenesis, changes were detected in several metabolomes as hMSC chondrogenesis biomarkers, e.g., fatty acids, alanine, glutamate, and phosphocholine. The metabolomic changes were compared with the Real-Time PCR results, and significant differences were determined using statistical analysis. We found that changes in metabolomes were closely related to biological reactions that occurred during the chondrogenesis of hMSCs.

CONCLUSIONS

In this study, we confirm that metabolomic changes detected by (1)H-NMR spectroscopy during chondrogenic differentiation of 3D-cultured hMSCs in alginate beads can be considered as biomarkers of stem cell differentiation.

Nuclear magnetic resonance spectroscopy is highly sensitive for lipid-soluble metabolites

Although the water-soluble metabolite profile of human mesenchymal stem cells is known, the lipid profile still needs further investigation. In this study, methanol-chloroform was used to extract pid-soluble metabolites and perchloric acid was used to extract water-soluble metabolites. Furthermore, a dual phase extraction method using methanol-chloroform and water was used to obtain both water and lipid fractions simultaneously. All metabolite extractions were analyzed on a 9.4T high-resolution nuclear magnetic resonance spectrometer. Metabolite resonance peaks were assigned in the acquired spectra according to the chemical shift, and the extraction efficiency of ferent methods was compared. Results showed that in the spectra of water-soluble extracts, major metabolites comprised low molecular weight metabolites, including lactate, acetic acid, fatty acids, threonine, glutamic acid, creatine, choline and its derivatives, while in the spectra of lipid-soluble extracts, most metabolites were assigned to fatty acids. Among the different extraction procedures, perchloric acid was more efficient in extracting water-soluble metabolites and methanol-chloroform was efficient in extracting organic components compared with the dual phase extraction method. Nuclear magnetic resonance spectroscopy showed that as low as 0.7 mg organic yield was enough to obtain clear resonance peaks, while about 6.0 mg water-soluble yield was needed to obtain relatively favorable spectral lines. These results show that the efficiency of extracting water and lipid fractions is higher using perchloric acid and methanol-chloroform compared with dual phase extraction and that nuclear magnetic resonance spectroscopy is highly sensitive for analyzing lipid-soluble extracts.

Human umbilical mesenchymal stem cell and its adipogenic differentiation: Profiling by nuclear magnetic resonance spectroscopy

AIM

To study the metabolic profile of human umbilical mesenchymal stem cells (HUMSC) and adipogenic differentiation by nuclear magnetic resonance (NMR) spectroscopy.

METHODS

HUMSC isolated from human umbilical cord stroma were induced to adipocytes over 2 wk by adding dexamethasone, 3-isobutyl-1-methylxanthine, indomethacin, and insulin to the culture medium. Adipogenic differentiation was confirmed by Red O staining and transcription-polymerase chain reaction. Perchloric acid extracts of the HUMSCs and adipocytes (about 7 × 10(6)) were characterized for metabolites by using in vitro high resolution 9.4T NMR spectroscopy.

RESULTS

Several major metabolites, such as: choline, creatine, glutamate and myo-inositol, acetate, and some fatty acids/triglycerides, were observed in the MR spectroscopic pattern of HUMSCs and their adipogenic differentiation. HUMSCs are characterized by an unusually low number of NMR-detectable metabolites, high choline, acetate, glutamate and creatine content. However, the metabolic profiles of adipogenic differentiation demonstrated considerably higher methionine and fatty acids, and non-detectable creatine.

CONCLUSION

The biomarkers of HUMSCS and adipocytes were obtained and assigned. NMR spectroscopy will be a promising tool for monitoring stem cell differentiation.

Detection of "oncometabolite" 2-hydroxyglutarate by magnetic resonance analysis as a biomarker of IDH1/2 mutations in glioma

Somatic mutations in isocitrate dehydrogenase (IDH)1 and 2 have been identified in a subset of gliomas, rendering these tumors with elevated levels of "oncometabolite," D-2-hydroxyglutarate (2HG). Herein, we report that 2HG can be precisely detected by magnetic resonance (MR) in human glioma specimens and used as a reliable biomarker to identify this subset of tumors. Specifically, we developed a two-dimensional correlation spectroscopy resonance method to reveal the distinctive cross-peak pattern of 2HG in the complex metabolite nuclear MR spectra of brain tumor tissues. This study demonstrates the feasibility, specificity, and selectivity of using MR detection and quantification of 2HG for the diagnosis and classification of IDH1/2 mutation-positive brain tumors. It further opens up the possibility of developing analogous non-invasive MR-based imaging and spectroscopy studies directly in humans in the neuro-oncology clinic.

NMR metabonomics for mammalian cell metabolism studies

The detailed knowledge of mammalian cell metabolism and its adjustments to different cell properties and perturbations, such as disease and drug exposure, is of enormous value in the deeper understanding of pathological processes and drug mechanisms, as well as in the development of new and improved methods for diagnosis, follow-up of disease progression and treatment response. This review covers recent developments in the use of NMR-based metabonomics to characterize cellular metabolomes and interpret them in terms of metabolic changes taking place in a wide range of situations. The analytical methodology available is briefly presented and the applications developed so far are reviewed. These include differences in cell properties (e.g., drug resistance, cell cycle stage, specific growth conditions and genetic characteristics) and changes induced in response to different perturbations (e.g., disease, drug exposure and irradiation).