NECTAR: A New Algorithm for Characterizing and Correcting Noise in QToF-Mass Spectrometry Imaging Data.

A typical mass spectrometry imaging experiment yields a very high number of detected peaks, many of which are noise and thus unwanted. To select only peaks of interest, data preprocessing tasks are applied to raw data. A statistical study to characterize three types of noise in MSI QToF data (random, chemical, and background noise) is presented through NECTAR, a new NoisE CorrecTion AlgoRithm. Random noise is confirmed to be dominant at lower m/z values (∼50-400 Da) while systematic chemical noise dominates at higher m/z values (>400 Da). A statistical approach is presented to demonstrate that chemical noise can be corrected to reduce its presence by a factor of ∼3. Reducing this effect helps to determine a more reliable baseline in the spectrum and therefore a more reliable noise level. Peaks are classified according to their spatial S/N on the single ion images, and background noise is thus removed from the list of peaks of interest. This new algorithm was applied to MALDI and DESI QToF data generated from the analysis of a mouse pancreatic tissue section to demonstrate its applicability and ability to filter out these types of noise in a relevant data set. PCA and t-SNE multivariate analysis reviews of the top 4000 peaks and the final 744 and 299 denoised peak list for MALDI and DESI, respectively, suggests an effective removal of uninformative peaks and proper selection of relevant peaks.

Metabolic profiling stratifies colorectal cancer and reveals adenosylhomocysteinase as a therapeutic target.

The genomic landscape of colorectal cancer (CRC) is shaped by inactivating mutations in tumour suppressors such as APC, and oncogenic mutations such as mutant KRAS. Here we used genetically engineered mouse models, and multimodal mass spectrometry-based metabolomics to study the impact of common genetic drivers of CRC on the metabolic landscape of the intestine. We show that untargeted metabolic profiling can be applied to stratify intestinal tissues according to underlying genetic alterations, and use mass spectrometry imaging to identify tumour, stromal and normal adjacent tissues. By identifying ions that drive variation between normal and transformed tissues, we found dysregulation of the methionine cycle to be a hallmark of APC-deficient CRC. Loss of Apc in the mouse intestine was found to be sufficient to drive expression of one of its enzymes, adenosylhomocysteinase (AHCY), which was also found to be transcriptionally upregulated in human CRC. Targeting of AHCY function impaired growth of APC-deficient organoids in vitro, and prevented the characteristic hyperproliferative/crypt progenitor phenotype driven by acute deletion of Apc in vivo, even in the context of mutant Kras. Finally, pharmacological inhibition of AHCY reduced intestinal tumour burden in ApcMin/+ mice indicating its potential as a metabolic drug target in CRC.