N-glycosylation Regulates Intrinsic IFN-γ Resistance in Colorectal Cancer: Implications for Immunotherapy.

BACKGROUND & AIMS: Advanced colorectal carcinoma (CRC) is characterized by a high frequency of primary immune evasion and refractoriness to immunotherapy. Given the importance of interferon (IFN)-γ in CRC immunosurveillance, we investigated whether and how acquired IFN-γ resistance in tumor cells would promote tumor growth, and whether IFN-γ sensitivity could be restored. METHODS: Spontaneous and colitis-associated CRC development was induced in mice with a specific IFN-γ pathway inhibition in intestinal epithelial cells. The influence of IFN-γ pathway gene status and expression on survival was assessed in patients with CRC. The mechanisms underlying IFN-γ resistance were investigated in CRC cell lines. RESULTS: The conditional knockout of the IFN-γ receptor in intestinal epithelial cells enhanced spontaneous and colitis-associated colon tumorigenesis in mice, and the loss of IFN-γ receptor α (IFNγRα) expression by tumor cells predicted poor prognosis in patients with CRC. IFNγRα expression was repressed in human CRC cells through changes in N-glycosylation, which decreased protein stability via proteasome-dependent degradation, inhibiting IFNγR-signaling. Downregulation of the bisecting N-acetylglucosaminyltransferase III (MGAT3) expression was associated with IFN-γ resistance in all IFN-γ-resistant cells, and highly correlated with low IFNγRα expression in CRC tissues. Both ectopic and pharmacological reconstitution of MGAT3 expression with all-trans retinoic acid increased bisecting N-glycosylation, as well as IFNγRα protein stability and signaling. CONCLUSIONS: Together, our results demonstrated that tumor-associated changes in N-glycosylation destabilize IFNγRα, causing IFN-γ resistance in CRC. IFN-γ sensitivity could be reestablished through the increase in MGAT3 expression, notably via all-trans retinoic acid treatment, providing new prospects for the treatment of immune-resistant CRC.

Neutrophil extracellular traps drive epithelial-mesenchymal transition of human colon cancer.

Neutrophil extracellular traps (NETs) are extracellular structures, composed of nuclear DNA and various proteins released from neutrophils. Evidence is growing that NETs exert manifold functions in infection, immunity and cancer. Recently, NETs have been detected in colorectal cancer (CRC) tissues, but their association with disease progression and putative functional impact on tumourigenesis remained elusive. Using high-resolution stimulated emission depletion (STED) microscopy, we showed that citrullinated histone H3 (H3cit) is sufficient to specifically detect citrullinated NETs in colon cancer tissues. Among other evidence, this was supported by the close association of H3cit with de-condensed extracellular DNA, the hallmark of NETs. Extracellular DNA was reliably differentiated from nuclear condensed DNA by staining with an anti-DNA antibody, providing a novel and valuable tool to detect NETs in formalin-fixed paraffin-embedded tissues. Using these markers, the clinical association of NETs was investigated in a cohort of 85 patients with colon cancer. NETs were frequently detected (37/85, 44%) in colon cancer tissue sections and preferentially localised either only in the tumour centre or both in the tumour centre and the invasive front. Of note, citrullinated NETs were significantly associated with high histopathological tumour grades and lymph node metastasis. In vitro, purified NETs induced filopodia formation and cell motility in CRC cell lines. This was associated with increased expression of mesenchymal marker mRNAs (vimentin [VIM], fibronectin [FN1]) and epithelial-mesenchymal transition promoting transcription factors (ZEB1, Slug [SNAI2]), as well as decreased expression of the epithelial markers E-cadherin (CDH1) and epithelial cell adhesion molecule (EPCAM). These findings indicated that NETs activate an epithelial-mesenchymal transition-like process in CRC cells and may contribute to the metastatic progression of CRC. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

MRM Microcoil Performance Calibration and Usage Demonstrated on Medicago truncatula Roots at 22 T.

This protocol describes a signal-to-noise ratio (SNR) calibration and sample preparation method for solenoidal microcoils combined with biological samples, designed for high-resolution magnetic resonance imaging (MRI), also referred to as MR microscopy (MRM). It may be used at pre-clinical MRI spectrometers, demonstrated on Medicago truncatula root samples. Microcoils increase sensitivity by matching the size of the RF resonator to the size of the sample of interest, thereby enabling higher image resolutions in a given data acquisition time. Due to the relatively simple design, solenoidal microcoils are straightforward and cheap to construct and can be easily adapted to the sample requirements. Systematically, we explain how to calibrate new or home-built microcoils, using a reference solution. The calibration steps include: pulse power determination using a nutation curve; estimation of RF-field homogeneity; and calculating a volume-normalized signal-to-noise ratio (SNR) using standard pulse sequences. Important steps in sample preparation for small biological samples are discussed, as well as possible mitigating factors such as magnetic susceptibility differences. The applications of an optimized solenoid coil are demonstrated by high-resolution (13 x 13 x 13 µm3, 2.2 pL) 3D imaging of a root sample.

Characterizing the structure of aerobic granular sludge using ultra-high field magnetic resonance.

Despite aerobic granular sludge wastewater treatment plants operating around the world, our understanding of internal granule structure and its relation to treatment efficiency remains limited. This can be attributed in part to the drawbacks of time-consuming, labor-intensive, and invasive microscopy protocols which effectively restrict samples sizes and may introduce artefacts. Time-domain nuclear magnetic resonance (NMR) allows non-invasive measurements which describe internal structural features of opaque, complex materials like biofilms. NMR was used to image aerobic granules collected from five full-scale wastewater treatment plants in the Netherlands and United States, as well as laboratory granules and control beads. T1 and T2 relaxation-weighted images reveal heterogeneous structures that include high- and low-density biofilm regions, water-like voids, and solid-like inclusions. Channels larger than approximately 50 µm and connected to the bulk fluid were not visible. Both cluster and ring-like structures were observed with each granule source having a characteristic structural type. These structures, and their NMR relaxation behavior, were stable over several months of storage. These observations reveal the complex structures within aerobic granules from a range of sources and highlight the need for non-invasive characterization methods like NMR to be applied in the ongoing effort to correlate structure and function.

Assessing spatial resolution, acquisition time and signal-to-noise ratio for commercial microimaging systems at 14.1, 17.6 and 22.3 T.

This work provides a systematic comparison of the signal-to-noise ratio (SNR), spatial resolution, acquisition time and metabolite limits-of-detection for magnetic resonance microscopy and spectroscopy at three different magnetic field strengths of 14.1 T, 17.6 T and 22.3 T (the highest currently available for imaging), utilizing commercially available hardware. We find an SNR increase of a factor 5.9 going from 14.1 T to 22.3 T using 5 mm radiofrequency (saddle and birdcage) coils, which results in a 24-fold acceleration in acquisition time and deviates from the theoretically expected increase of factor 2.2 due to differences in hardware. This underlines the importance of not only the magnetic field strengths but also hardware optimization. In addition, using a home-built 1.5 mm solenoid coil, we can achieve an isotropic resolution of (5.5 µm)3 over a field-of-view of 1.58 mm × 1.05 mm × 1.05 mm with an SNR of 12:1 using 44 signal averages in 58 h 34 min acquisition time at 22.3 T. In light of these results, we discuss future perspectives for ultra-high field Magnetic Resonance Microscopy and Spectroscopy.

Magnetic Resonance Microscopy at Cellular Resolution and Localised Spectroscopy of Medicago truncatula at 22.3 Tesla.

Interactions between plants and the soil's microbial & fungal flora are crucial for the health of soil ecosystems and food production. Microbe-plant interactions are difficult to investigate in situ due to their intertwined relationship involving morphology and metabolism. Here, we describe an approach to overcome this challenge by elucidating morphology and the metabolic profile of Medicago truncatula root nodules using Magnetic Resonance (MR) Microscopy, at the highest magnetic field strength (22.3 T) currently available for imaging. A home-built solenoid RF coil with an inner diameter of 1.5 mm was used to study individual root nodules. A 3D imaging sequence with an isotropic resolution of (7 µm)3 was able to resolve individual cells, and distinguish between cells infected with rhizobia and uninfected cells. Furthermore, we studied the metabolic profile of cells in different sections of the root nodule using localised MR spectroscopy and showed that several metabolites, including betaine, asparagine/aspartate and choline, have different concentrations across nodule zones. The metabolite spatial distribution was visualised using chemical shift imaging. Finally, we describe the technical challenges and outlook towards future in vivo MR microscopy of nodules and the plant root system.

3D biofilm visualization and quantification on granular bioanodes with magnetic resonance imaging.

The use of microbial fuel cells (MFCs) for wastewater treatment fits in a circular economy context, as they can produce electricity by the removal of organic matter in the wastewater. Activated carbon (AC) granules are an attractive electrode material for bioanodes in MFCs, as they are cheap and provide electroactive bacteria with a large surface area for attachment. The characterization of biofilm growth on AC granules, however, is challenging due to their high roughness and three-dimensional structure. In this research, we show that 3D magnetic resonance imaging (MRI) can be used to visualize biofilm distribution and determine its volume on irregular-shaped single AC granules in a non-destructive way, while being combined with electrochemical and biomass analyses. Ten AC granules with electroactive biofilm (i.e. granular bioanodes) were collected at different growth stages (3 to 21 days after microbial inoculation) from a multi-anode MFC and T1-weighted 3D-MRI experiments were performed for three-dimensional biofilm visualization. With time, a more homogeneous biofilm distribution and an increased biofilm thickness could be observed in the 3D-MRI images. Biofilm volumes varied from 0.4 µL (day 4) to 2 µL (day 21) and were linearly correlated (R2 = 0.9) to the total produced electric charge and total nitrogen content of the granular bioanodes, with values of 66.4 C µL-1 and 17 µg N µL-1, respectively. In future, in situ MRI measurements could be used to monitor biofilm growth and distribution on AC granules.

Bacterially driven cadmium sulfide precipitation on porous membranes: Toward platforms for photocatalytic applications.

The emerging field of biofabrication capitalizes on nature's ability to create materials with a wide range of well-defined physical and electronic properties. Particularly, there is a current push to utilize programmed, self-organization of living cells for material fabrication. However, much research is still necessary at the interface of synthetic biology and materials engineering to make biofabrication a viable technique to develop functional devices. Here, the authors exploit the ability of Escherichia coli to contribute to material fabrication by designing and optimizing growth platforms to direct inorganic nanoparticle (NP) synthesis, specifically cadmium sulfide (CdS) NPs, onto porous polycarbonate membranes. Additionally, current, nonbiological, chemical synthesis methods for CdS NPs are typically energy intensive and use high concentrations of hazardous cadmium precursors. Using biosynthesis methods through microorganisms could potentially alleviate these issues by precipitating NPs with less energy and lower concentrations of toxic precursors. The authors adopted extracellular precipitation strategies to form CdS NPs on the membranes as bacterial/membrane composites and characterized them by spectroscopic and imaging methods, including energy dispersive spectroscopy, and scanning and transmission electron microscopy. This method allowed us to control the localization of NP precipitation throughout the layered bacterial/membrane composite, by varying the timing of the cadmium precursor addition. Additionally, the authors demonstrated the photodegradation of methyl orange using the CdS functionalized porous membranes, thus confirming the photocatalytic properties of these composites for eventual translation to device development. If combined with the genetically programmed self-organization of cells, this approach promises to directly pattern CdS nanostructures on solid supports.