Targeting proteomics to investigate metastasis-associated mitochondrial proteins

Comprehensive analysis of tissue proteomics in patients with papillary thyroid microcarcinoma uncovers the underlying mechanism of lymph node metastasis and its significant sex disparities

Background

Lymph node metastasis (LNM) in papillary thyroid microcarcinoma (PTMC) is associated with an increased risk of recurrence and poor prognosis. Sex has been regarded as a critical risk factor for LNM. The present study aimed to investigate the molecular mechanisms underlying LNM and its significant sex disparities in PTMC development.

Methods

A direct data-independent acquisition (DIA) proteomics approach was used to identify differentially expressed proteins (DEPs) in PTMC tumorous tissues with or without LNM and from male and female patients with LNM. The functional annotation of DEPs was performed using bioinformatics methods. Furthermore, The Cancer Genome Atlas Thyroid Carcinoma (TCGA-THCA) dataset and immunohistochemistry (IHC) were used to validate selected DEPs.

Results

The proteomics profile in PTMC with LNM differed from that of PTMC without LNM. The metastasis-related DEPs were primarily enriched in categories associated with mitochondrial dysfunction and may promote tumor progression by activating oxidative phosphorylation and PI3K/AKT signaling pathways. Comparative analyses of these DEPs revealed downregulated expression of specific proteins with well-established links to tumor metastasis, such as SLC25A15, DIRAS2, PLA2R1, and MTARC1. Additionally, the proteomics profiles of male and female PTMC patients with LNM were dramatically distinguishable. An elevated level of ECM-associated proteins might be related to more LNM in male PTMC than in female PTMC patients. The upregulated expression levels of MMRN2 and NID2 correlated with sex disparities and showed a positive relationship with unfavorable variables, such as LNMs and poor prognosis.

Conclusions

The proteomics profiles of PTMC show significant differences associated with LNM and its sex disparities, which further expands our understanding of the functional networks and signaling pathways related to PTMC with LNM.

Comparative mitochondrial proteomic analysis of human large cell lung cancer cell lines with different metastasis potential

Background

Lung cancer is a highly aggressive cancer with a poor prognosis and is associated with distant metastasis; however, there are no clinically recognized biomarkers for the early diagnosis and prediction of lung cancer metastasis. We sought to identify the differential mitochondrial protein profiles and understand the molecular mechanisms governing lung cancer metastasis.

Methods

Mitochondrial proteomic analysis was performed to screen and identify the differential mitochondrial protein profiles between human large cell lung cancer cell lines with high (L‐9981) and low (NL‐9980) metastatic potential by two‐dimensional differential gel electrophoresis. Western blot was used to validate the differential mitochondrial proteins from the two cells. Bioinformatic proteome analysis was performed using the Mascot search engine and messenger RNA expression of the 37 genes of the differential mitochondrial proteins were detected by real‐time PCR.

Results

Two hundred and seventeen mitochondrial proteins were differentially expressed between L‐9981 and NL‐9980 cells (P < 0.05). Sixty‐four analyzed proteins were identified by matrix‐assisted laser desorption/ionization‐time of flight mass spectrometry coupled with database interrogation. Ontology analysis revealed that these proteins were mainly involved in the regulation of translation, amino acid metabolism, tricarboxylic acid cycle, cancer invasion and metastasis, oxidative phosphorylation, intracellular signaling pathway, cell cycle, and apoptosis.

Conclusion

Our results suggest that the incorporation of more samples and new datasets will permit the definition of a collection of proteins as potential biomarkers for the prediction and diagnosis of lung cancer metastasis.

Targeted Proteomics to Study Mitochondrial Biology

Targeted mass spectrometry in the selected or parallel reaction monitoring (SRM or PRM) mode is a widely used methodology to quantify proteins based on so-called signature or proteotypic peptides. SRM has the advantage of being able to quantify a range of proteins in a single analysis, for example, to measure the level of enzymes comprising a biochemical pathway. In this chapter, we will detail how to set up an SRM assay on the example of the mitochondrial protein succinate dehydrogenase [ubiquinone] flavoprotein subunit (mouse UniProt-code Q8K2B3). First, we will outline the in silico assay design including the choice of peptides based on a range of properties. We will further delineate different quantification strategies and introduce the reader to LC-MS assay development including the selection of the optimal peptide charge state and fragment ions as well as a discussion of the dynamic range of detection. The chapter will close with an application from the area of mitochondrial biology related to the quantification of a set of proteins isolated from mouse liver mitochondria in a study on mitochondrial respiratory flux decline in aging mouse muscle.

Traditional and novel tools to probe the mitochondrial metabolism in health and disease

Mitochondrial metabolism links energy production to other essential cellular processes such as signaling, cellular differentiation, and apoptosis. In addition to producing adenosine triphosphate (ATP) as an energy source, mitochondria are responsible for the synthesis of a myriad of important metabolites and cofactors such as tetrahydrofolate, α-ketoacids, steroids, aminolevulinic acid, biotin, lipoic acid, acetyl-CoA, iron-sulfur clusters, heme, and ubiquinone. Furthermore, mitochondria and their metabolism have been implicated in aging and several human diseases, including inherited mitochondrial disorders, cardiac dysfunction, heart failure, neurodegenerative diseases, diabetes, and cancer. Therefore, there is great interest in understanding mitochondrial metabolism and the complex relationship it has with other cellular processes. A large number of studies on mitochondrial metabolism have been conducted in the last 50 years, taking a broad range of approaches. In this review, we summarize and discuss the most commonly used tools that have been used to study different aspects of the metabolism of mitochondria: ranging from dyes that monitor changes in the mitochondrial membrane potential and pharmacological tools to study respiration or ATP synthesis, to more modern tools such as genetically encoded biosensors and trans-omic approaches enabled by recent advances in mass spectrometry, computation, and other technologies. These tools have allowed the large number of studies that have shaped our current understanding of mitochondrial metabolism. WIREs Syst Biol Med 2017, 9:e1373. doi: 10.1002/wsbm.1373 For further resources related to this article, please visit the WIREs website.

Application of metabolomics in drug resistant breast cancer research

The metabolic profiles of breast cancer cells are different from normal mammary epithelial cells. Breast cancer cells that gain resistance to therapeutic interventions can reprogram their endogenous metabolism in order to adapt and proliferate despite high oxidative stress and hypoxic conditions. Drug resistance in breast cancer, regardless of subgroups, is a major clinical setback. Although recent advances in genomics and proteomics research has given us a glimpse into the heterogeneity that exists even within subgroups, the ability to precisely predict a tumor’s response to therapy remains elusive. Metabolomics as a quantitative, high through put technology offers promise towards devising new strategies to establish predictive, diagnostic and prognostic markers of breast cancer. Along with other “omics” technologies that include genomics, transcriptomics, and proteomics, metabolomics fits into the puzzle of a comprehensive systems biology approach to understand drug resistance in breast cancer. In this review, we highlight the challenges facing successful therapeutic treatment of breast cancer and the innovative approaches that metabolomics offers to better understand drug resistance in cancer.

Mitochondria in relation to cancer metastasis: introduction to a mini-review series

This introductory article and those that follow focus on the roles that mitochondria may have in cancer metastasis (spreading) that all too frequently leads to death of cancer patients. The history of cancer dates back in time to several thousand years BC and continues to this day. Although billions of dollars have been invested, numerous cancer researchers/scientists and oncologist located at universities, hospitals, cancer centers, commercial entities (companies), and government agencies have been unable to discover "magic bullets" to quickly silence most cancers. That is, agents that are effective not only in eradicating the primary tumor at its site of origin, but eradicating also distant tumors that have arisen therefrom via metastatic cells. Fortunately, in recent years some researchers have obtained evidence that the mitochondria of cancer cells are involved not only in providing in part the necessary energy (ATP) to fuel their growth, but hold the secrets to their immortality, and propensity to metastasize (spread) from their original site of origin to other body locations. This introductory article, as well as those that follow, focus on the possible roles of mitochondria in cancer metastasis as well as strategies to arrest cancer metastasis based on this knowledge. Ideally, for a patient to become "cancer free" the anticancer agent/agents used must 1) eradicate the primary tumor at its site of origin, 2) eradicate any tumors at other body locations that have arisen via metastasis, and 3) eradicate any tumor cells that remain in the blood, i.e., circulating tumor cells. One such agent that holds promise for doing all three is the small molecule 3-bromopyruvate (3BP) discovered in the author's laboratory by Dr. Young H. Ko near the turn of the century to be a potent anti-cancer agent [Ko et al.(2001) Can Lett 173:83-91].