Automated annotation and visualisation of high-resolution spatial proteomic mass spectrometry imaging data using HIT-MAP

Spatial proteomics has the potential to significantly advance our understanding of biology, physiology and medicine. Matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) is a powerful tool in the spatial proteomics field, enabling direct detection and registration of protein abundance and distribution across tissues. MALDI-MSI preserves spatial distribution and histology allowing unbiased analysis of complex, heterogeneous tissues. However, MALDI-MSI faces the challenge of simultaneous peptide quantification and identification. To overcome this, we develop and validate HIT-MAP (High-resolution Informatics Toolbox in MALDI-MSI Proteomics), an open-source bioinformatics workflow using peptide mass fingerprint analysis and a dual scoring system to computationally assign peptide and protein annotations to high mass resolution MSI datasets and generate customisable spatial distribution maps. HIT-MAP will be a valuable resource for the spatial proteomics community for analysing newly generated and retrospective datasets, enabling robust peptide and protein annotation and visualisation in a wide array of normal and disease contexts.

Lysyl oxidase enzymatic function increases stiffness to drive colorectal cancer progression through FAK

The extracellular, matrix-modifying enzyme lysyl oxidase (LOX) has recently been linked to colorectal cancer (CRC) progression, in particular to the stages of invasion and metastasis. In this report, we use cell lines expressing a catalytically inactive mutant form of LOX to show that catalytic activity is required for LOX-mediated effects on proliferation and invasion in both in vitro and in vivo models of CRC. Furthermore, we use rheology to measure the relative stiffness of modified collagen matrices and subcutaneous tumors, and show that LOX-induced collagen cross-linking results in stiffening of the matrix both in vitro and in vivo. We observe a strong association between matrix stiffness and activation of the FAK (focal adhesion kinase)/SRC-signaling pathway, with a stiffer environment resulting in increased FAK/SRC phosphorylation and a more proliferative and invasive phenotype. We are the first to show a direct relationship between LOX enzymatic activity and tissue stiffness, and to demonstrate a role for stiffness in driving CRC progression. Our findings provide significant evidence to suggest that therapeutic inhibition of LOX activity may provide a novel effective treatment option for patients with metastatic CRC.

Ventilator-related Acinetobacter outbreak in an intensive care unit

An outbreak of 16 cases of ciprofloxacin-resistant Acinetobacter baumannii (calcoaceticus subspecies anitratus) infections occurred during a 7-month period in a medical intensive care unit. Fifteen of the patients developed pneumonia associated with ventilator support. Possible sources considered in the outbreak investigation were sinks, ice, personnel, patients on multiple antibiotic therapy, reusable ventilator circuits, and hemodialysis. The equipment and environment associated with the outbreak were cultured. Patients on ventilators were significantly more susceptible to Acinetobacter nosocomial infection compared with the rest of the patients in the medical intensive care unit (p < 0.05). Sputum cultures were only 5% sensitive to ciprofloxacin and gentamicin, but they were 100% sensitive to imipenem (p < 0.0001). Uncloaking imipenem was a significant contributing factor in controlling this outbreak. Once outbreak control measures were instituted, Acinetobacter isolates dropped from 77 (during the outbreak year) to 9 (during the subsequent year) and no new pneumonia cases occurred.

Vascular infections: exceeding the threshold

During fiscal year 1988, our hospital infection control practitioner identified a 400% increase in the incidence of vascular surgery nosocomial infections. The six graft and six amputation infections were validated as nosocomial against hospital definitions adopted from the Centers for Disease Control. Our Infection Control Committee mandated an audit of the infected vascular surgery patients using a case/control design to identify and examine associated variables that may need attention. The significant finding was microbial resistance to prophylactic antibiotics used during surgery (p > 0.0001, Fisher's exact). The use of vancomycin as a prophylactic antimicrobial agent for all major vascular cases was recommended to the surgeons.