A robust clustering approach for NMR spectra of natural product extracts

Pierens, Gregory K.; Palframan, Meredith Elizabeth; Tranter, Carolyn J.; Carroll, Anthony Richard; Quinn, Ronald J.

doi:10.1002/mrc.1562

Cited by 21 publications

(9 citation statements)

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“…Thus, study of the metabolome has become a powerful tool in the fields of biotechnology (Oksman-Caldentey and Saito 2005), natural compounds (Pierens et al 2005;Yang et al 2004;Ott et al 2003), nutrition (Trujillo et al 2006), biomedicine (van der Greef et al 2006;German et al 2005), and especially in cancer studies (Malyankar 2007;Morvan and Demidem 2007;Jordan and Cheng 2007;Claudino et al 2007;Denkert et al 2006;Boros et al 2002).…”

Section: Introductionmentioning

confidence: 99%

Robust metabolic adaptation underlying tumor progression

2008

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Tumor metabolism represents the end point of many signal cascades recruited by oncogenic activation. Energy metabolism of cancer cells attracted the attention of biochemists over eight decades ago. For example, high consume of glucose and high lactate production under aerobic conditions make up one of the most fundamental characteristics of cancer cells and has been exploited for diagnosis. At the same time, study of the metabolic status of tumor cells during tumor progression reveals characteristic adaptations during carcinogenesis. Although these metabolic adaptations are not the main defects that cause cancer, they may confer advantages to survive. In this review, we discuss the main metabolic hot spots and their relationship with main tumor progression events. An accurate metabolic map of the many tumor phenotypes could offer new options in the treatment of cancer.Keywords Tumor metabolism Á Warburg effect Á Regulation of glucose metabolism in tumors Á Acidosis and tumor progression Á Biosynthetic pathways in tumoral metabolism Á Alternative to glycolytic energy conversion Á Isoenzyme expression in tumor cells Á Tumor metabolism and apoptosis1 Introduction

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Section: Introductionmentioning

confidence: 99%

Robust metabolic adaptation underlying tumor progression

2008

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“…This kind of analytical method combined with multivariate statistical data analysis has already been successfully used to identify, discriminate and classify samples of terrestrial plants (Xie et al 2008;Yang et al 2007) but never to discriminate between marine species. A robust clustering of NMR spectra from partially purified extracts was only once applied to select marine sponges that produce the same bioactive compound or family of compounds (Pierens et al 2005).…”

Section: Introductionmentioning

confidence: 99%

Metabolic fingerprinting as an indicator of biodiversity: towards understanding inter-specific relationships among Homoscleromorpha sponges

et al. 2010

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Sponges are an important source of secondary metabolites showing a great diversity of structures and biological activities. Secondary metabolites can display specificity on different taxonomic levels, from species to phylum, which can make them good taxonomic biomarkers. However, the knowledge available on the metabolome of non-model organisms is often poor. In this study, we demonstrate that sponge chemical diversity may be useful for fundamental issues in systematics or evolutionary biology, by using metabolic fingerprints as indicators of metabolomic diversity in order to assess interspecific relationships. The sponge clade Homoscleromorpha is particularly challenging because its chemistry has been little studied and its phylogeny is still debated. Identification at species level is often troublesome, especially for the highly diversified Oscarella genus which lacks the fundamental characters of sponge taxonomy. An HPLC-DAD-ELSD-MS metabolic fingerprinting approach was developed and applied to 10 Mediterranean Homoscleromorpha species as a rapid assessment of their chemical diversity. A first validation of our approach was to measure intraspecific variability, which was found significantly lower than interspecific variability obtained between two Oscarella sister-species. Interspecific relationships among Homoscleromorpha species were then inferred from the alignment of their metabolic fingerprints. The resulting classification is congruent with phylogenetic trees obtained for a DNA marker (mitochondrial COI) and demonstrates the existence of two distinct groups within Homoscleromorpha. Metabolic fingerprinting proves a useful complementary tool in sponge systematics. Our case study calls for a revision of Homoscleromorpha with further phylogenetic studies and identification of additional chemical synapomorphic characters.

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“…PCA is the prevailing method for reducing data dimensionality, though other data-mining techniques such as clustering algorithms (hierarchical clustering, tree clustering, K-means, etc.) are routinely used [57, 58]. With PCA, major sample components are structured to represent the data variance in a two-/three-dimensional coordinate scheme.…”

Section: Instrumentation and Toolsmentioning

confidence: 99%

“…However combinatorial chromatographic and spectroscopic techniques such as gas and liquid chromatography, infrared (IR) spectroscopy, mass spectrometry (MS), nuclear magnetic resonance (NMR) spectroscopy and ultraviolet absorption (UV) spectroscopy are proven efficient methods at achieving the most comprehensive analysis of complex extracts [58, 87, 88]. Hyphenated mass spectrometry techniques are routinely used to detect hundreds of metabolites within a single extract.…”

Section: Utility In Natural Products De-replication and Drug Discomentioning

confidence: 99%

The utility of metabolomics in natural product and biomarker characterization

Cox

Keasling

et al. 2014

Biochimica et Biophysica Acta (BBA) - General Subjects

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Background Metabolomics is a well-established rapidly developing research field involving quantitative and qualitative metabolite assessment within biological systems. Recent improvements in metabolomics technologies reveal the unequivocal value of metabolomics tools in natural products discovery, gene-function analysis, systems biology and diagnostic platforms. Scope of review We review of some of the prominent metabolomics methodologies employed in data acquisition and analysis of natural products and disease-related biomarkers. Major conclusions This review demonstrates that metabolomics represents a highly adaptable technology with diverse applications ranging from environmental toxicology to disease diagnosis. Metabolomic analysis is shown to provide a unique snapshot of the functional genetic status of an organism by examining its biochemical profile, with relevance toward resolving phylogenetic associations involving horizontal gene transfer and distinguishing subgroups of genera possessing high genetic homology, as well as an increasing role in both elucidating biosynthetic transformations of natural products and detecting preclinical biomarkers of numerous disease states. General significance This review expands the interest in multiplatform combinatorial metabolomic analysis. The applications reviewed range from phylogenetic assignment, biosynthetic transformations of natural products, and the detection of preclinical biomarkers.

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A robust clustering approach for NMR spectra of natural product extracts

Cited by 21 publications

References 50 publications

Robust metabolic adaptation underlying tumor progression

Robust metabolic adaptation underlying tumor progression

Metabolic fingerprinting as an indicator of biodiversity: towards understanding inter-specific relationships among Homoscleromorpha sponges

The utility of metabolomics in natural product and biomarker characterization

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