Deep learning for the prediction of the chemotherapy response of metastatic colorectal cancer: comparing and combining H&E staining histopathology and infrared spectral histopathology.

Colorectal cancer is a global public health problem with one of the highest death rates. It is the second most deadly type of cancer and the third most frequently diagnosed in the world. The present study focused on metastatic colorectal cancer (mCRC) patients who had been treated with chemotherapy-based regimen for which it remains uncertainty about the efficacy for all eligible patients. This is a major problem, as it is not yet possible to test different therapies in view of the consequences on the health of the patients and the risk of progression. Here, we propose a method to predict the efficacy of an anticancer treatment in an individualized way, using a deep learning model constructed on the retrospective analysis of the primary tumor of several patients. Histological sections from tumors were imaged by standard hematoxylin and eosin (HE) staining and infrared spectroscopy (IR). Images obtained were then processed by a convolutional neural network (CNN) to extract features and correlate them with the subsequent progression-free survival (PFS) of each patient. Separately, HE and IR imaging resulted in a PFS prediction with an error of 6.6 and 6.3 months respectively (28% and 26% of the average PFS). Combining both modalities allowed to decrease the error to 5.0 months (21%). The inflammatory state of the stroma seemed to be one of the main features detected by the CNN. Our pilot study suggests that multimodal imaging analyzed with deep learning methods allow to give an indication of the effectiveness of a treatment when choosing.

Identification of circulating biomarkers of Crohn's disease and spondyloarthritis using Fourier transform infrared spectroscopy.

Crohn's disease (CD) and spondyloarthritis (SpA) are two inflammatory diseases sharing many common features (genetic polymorphism, armamentarium). Both diseases lack diagnostic markers of certainty. While the diagnosis of CD is made by a combination of clinical, and biological criteria, the diagnosis of SpA may take several years to be confirmed. Based on the hypothesis that CD and SpA alter the biochemical profile of plasma, the objective of this study was to evaluate the analytical capability of Fourier transform infrared spectroscopy (FTIR) in identifying spectral biomarkers. Plasma from 104 patients was analyzed. After data processing of the spectra by Extended Multiplicative Signal Correction and linear discriminant analysis, we demonstrated that it was possible to distinguish CD and SpA from controls with an accuracy of 97% and 85% respectively. Spectral differences were mainly associated with proteins and lipids. This study showed that FTIR analysis is efficient to identify plasma biosignatures specific to CD or SpA.

Biopolymers-calcium phosphate antibacterial coating reduces the pathogenicity of internalized bacteria by mesenchymal stromal cells.

A multifunctional material system that kills bacteria and drives bone healing is urgently sought to improve bone prosthesis. Herein, the osteoinductive coating made of calcium phosphate/chitosan/hyaluronic acid, named Hybrid, was proposed as an antibacterial substrate for stromal cell adhesion. This Hybrid coating possesses a contact-killing effect reducing by 90% the viability of Gram-positive Staphylococcus aureus (S. aureus) and Gram-negative Pseudomonas aeruginosa (P. aeruginosa) strains after 48 h of contact. In addition to the production of immunomodulatory mediators, Wharton's jelly (WJ-SCs), dental pulp (DPSCs) and bone marrow (BM-MSCs) derived stromal cells were able to release antibacterial and antibiofilm agents effective against S. aureus and P. aeruginosa strains, respectively. Studying the effect of the Hybrid coating on the internalization of S. aureus by the stromal cells, in acute-mimicking bone infection, highlighted an increase in the bacteria internalization by DPSCs and BM-MSCs when cultured on the Hybrid coating versus uncoated glass. Despite the internalization, Hybrid coating showed a beneficial effect by reducing the pathogenicity of the internalized bacteria. The formation of biofilm was reduced by at least 50% in comparison to internalized bacteria by stromal cells on uncoated glass. This work opens the route for the development of innovative antibacterial coatings by taking into account the internalization of bacteria by stromal cells.

Serum bikunin isoforms in congenital disorders of glycosylation and linkeropathies.

Bikunin (Bkn) isoforms are serum chondroitin sulfate (CS) proteoglycans synthesized by the liver. They include two light forms, that is, the Bkn core protein and the Bkn linked to the CS chain (urinary trypsin inhibitor [UTI]), and two heavy forms, that is, pro-α-trypsin inhibitor and inter-α-trypsin inhibitor, corresponding to UTI esterified by one or two heavy chains glycoproteins, respectively. We previously showed that the Western-blot analysis of the light forms could allow the fast and easy detection of patients with linkeropathy, deficient in enzymes involved in the synthesis of the initial common tetrasaccharide linker of glycosaminoglycans. Here, we analyzed all serum Bkn isoforms in a context of congenital disorders of glycosylation (CDG) and showed very specific abnormal patterns suggesting potential interests for their screening and diagnosis. In particular, genetic deficiencies in V-ATPase (ATP6V0A2-CDG, CCDC115-CDG, ATP6AP1-CDG), in Golgi manganese homeostasis (TMEM165-CDG) and in the N-acetyl-glucosamine Golgi transport (SLC35A3-CDG) all share specific abnormal Bkn patterns. Furthermore, for each studied linkeropathy, we show that the light abnormal Bkn could be further in-depth characterized by two-dimensional electrophoresis. Moreover, besides being interesting as a specific biomarker of both CDG and linkeropathies, Bkn isoforms' analyses can provide new insights into the pathophysiology of the aforementioned diseases.

Anaerobic degradation of anionic surfactants by indigenous microorganisms from sediments of a tropical polluted river in Brazil.

Linear alkylbenzene sulfonate (LAS) is widely used in the formulation of domestic and industrial cleaning products, the most synthetic surfactants used worldwide. These products can reach water bodies through the discharge of untreated sewage or non-effective treatments. This study evaluates the ability of the microorganisms found in the Tiete river sediment to degrade this synthetic surfactant. The experiment was conducted in a bioreactor, operated in batch sequences under denitrifying conditions, with cycles of 24 hours and stirring at 150rpm, using 430 mL of sediments and 1 070mL of a synthetic substrate consisting of yeast extract, soluble starch, sodium bicarbonate and sucrose. LAS was added at different concentrations of l5mg/L and 30mg/L. The reactor operation was divided into the biomass adaptation to the synthetic substrate without LAS and three experimental conditions: a) addition of l5mg/L of LAS; b) 50% reduction the co-substrate concentration and 15 mg/L of LAS, and c) addition of 30mg/L of LAS and 100% co-substrate concentration. The results showed that the degradation efficiency of LAS was directly related to the addition of co-substrates and the population of denitrifying bacteria. The removal of LAS and nitrate can be achieved simultaneously in wastewater with low organic loads. The reduction in the co-substrates concentration was directly influenced by the number of denitrifying bacteria (2.2x10(13) to 1.0 x 10(8) MPN/gTVS), and consequently, LAS degradation (60.1 to 55.4%). The sediment microorganisms in the Tiete river can be used as an alternative inoculum in the treatment of wastewater with nitrate and LAS contamination.