Identification of diagnostic metabolic signatures in clear cell renal cell carcinoma using mass spectrometry imaging

Abstract

Clear cell renal cell carcinoma (ccRCC) is the most common and lethal subtype of kidney cancer. Intraoperative frozen section (IFS) analysis is used to confirm the diagnosis during partial nephrectomy. However, surgical margin evaluation using IFS analysis is time consuming and unreliable, leading to relatively low utilization. In our study, we demonstrated the use of desorption electrospray ionization mass spectrometry imaging (DESI-MSI) as a molecular diagnostic and prognostic tool for ccRCC. DESI-MSI was conducted on fresh-frozen 23 normal tumor paired nephrectomy specimens of ccRCC. An independent validation cohort of 17 normal tumor pairs was analyzed. DESI-MSI provides two-dimensional molecular images of tissues with mass spectra representing small metabolites, fatty acids and lipids. These tissues were subjected to histopathologic evaluation. A set of metabolites that distinguish ccRCC from normal kidney were identified by performing least absolute shrinkage and selection operator (Lasso) and log-ratio Lasso analysis. Lasso analysis with leave-one-patient-out crossvalidation selected 57 peaks from over 27,000 metabolic features across 37,608 pixels obtained using DESI-MSI of ccRCC and normal tissues. Baseline Lasso of metabolites predicted the class of each tissue to be normal or cancerous tissue with an accuracy of 94 and 76%, respectively. Combining the baseline Lasso with the ratio of glucose to arachidonic acid could potentially reduce scan time and improve accuracy to identify normal (82%) and ccRCC (88%) tissue. DESI-MSI allows rapid detection of metabolites associated with normal and ccRCC with high accuracy. As this technology advances, it could be used for rapid intraoperative assessment of surgical margin status.K.V.L. and V.S. contributed equally to this work Ryan M. Bain's current address is: Dow Chemical Co., Midland, MI 48674 Additional Supporting Information may be found in the online version of this article.

SU086, an inhibitor of HSP90, impairs glycolysis and represents a treatment strategy for advanced prostate cancer

“…Experimental details of tissue imaging by desorption electrospray ionization mass spectrometry imaging (DESI) have been described. 30 , 58 , 59 Briefly, DESI-MSI was performed in the negative ion mode (−5 kV) from m/z 50–1000, using LTQ-Orbitrap XL mass spectrometer (Thermo Fisher Scientific) coupled to a home-built DESI-source and a two-dimensional (2D) motorized stage. C4-2 and DU145 xenograft tissues, from mice treated with vehicle or SU086 (from Figure 3 experiment), were flash frozen at time of harvest and later embedded in OCT.…”

“…Cells were then pelleted, counted, and resuspended in PBS into ten tubes of 1x10 6 cells (in 100 ml PBS). Tubes were exposed to respective temperatures (37,41,44,47,50,53,56,59, 63, 67 C) for 3 min using a thermal cycler, followed by two minutes at room temperature, and subsequently snap frozen with liquid nitrogen. Cells were lysed by freeze thaw cycling three times, then centrifuged at 14000 RPM for 30 min at 4 C. Equal amounts of cell lysate from each temperature group was labeled with Tandem mass Tag (TMT) using manufacturers protocol (TMT10plex TM Isobaric Label Reagent Set #90110, Thermo Fisher Scientific).…”

Recent Advances of Ambient Mass Spectrometry Imaging and Its Applications in Lipid and Metabolite Analysis

“…In addition, understanding the molecular spatial information of cancer tissues will help us to further study the molecular pathological mechanism of cancer and find possible treatment methods [82]. AMSI has been used to investigate the lipid profiles of human serous ovarian tumors [83], breast cancer [84], brain tumors [85], lung cancer [86], prostate cancer [87], human basal cell carcinomas [14], diabetic kidney disease [88], epithelial ovarian carcinomas [89], cerebral ischaemia [90], epithelial ovarian carcinomas [89], pancreatic cancer [80], clear renal cell carcinomas [91] and muscle invasive bladder cancer [92]. In 2016, the Eberlin group utilized DESI AMSI to investigate the lipid profile of mitochondria-rich thyroid oncocytic tumors and the distribution of cardiolipins (CLs) overlapped with regions of mitochondria-rich oncocytic cells [93].…”

In situ mass spectrometry analysis of intact proteins and protein complexes from biological substrates

“…DESI is now routinely applied to the analysis of lipids and metabolites, with recent studies investigating lipidosis within rodent lungs [62], and lipidomic and metabolic profiling of kidney cancers [63,64]. Few studies have focused on the analysis of intact proteins by DESI ( Figure 1D) suggesting it remains a considerable challenge.…”