STAT6 mutations enriched at diffuse large B-cell lymphoma relapse reshape the tumor microenvironment.

Diffuse large B-cell lymphoma (DLBCL) relapses in approximately 40% of patients following frontline therapy. We reported that STAT6D419 mutations are enriched in relapsed/refractory DLBCL (rrDLBCL) samples, suggesting that JAK/STAT signaling plays a role in therapeutic resistance. We hypothesized that STAT6D419 mutations can improve DLBCL cell survival by reprogramming the microenvironment to sustain STAT6 activation. Thus, we investigated the role of STAT6D419 mutations on DLBCL cell growth and its microenvironment. We found that phospho-STAT6D419N was retained in the nucleus longer than phospho-STAT6WT following IL-4 stimulation, and STAT6D419N recognized a more restricted DNA-consensus sequence than STAT6WT. Upon IL-4 induction, STAT6D419N expression led to a higher magnitude of gene expression changes, but in a more selective list of gene targets compared with STATWT. The most significantly expressed genes induced by STAT6D419N were those implicated in survival, proliferation, migration, and chemotaxis, in particular CCL17. This chemokine, also known as TARC, attracts helper T-cells to the tumor microenvironment, especially in Hodgkin's lymphoma. To this end, in DLBCL, phospho-STAT6+ rrDLBCL cells had a greater proportion of infiltrating CD4+ T-cells than phospho-STAT6- tumors. Our findings suggest that STAT6D419 mutations in DLBCL lead to cell autonomous changes, enhanced signaling, and altered composition of the tumor microenvironment.

Mutated RAS-associating proteins and ERK activation in relapse/refractory diffuse large B cell lymphoma.

Diffuse large B cell lymphoma (DLBCL) is successfully treated with combination immuno-chemotherapy, but relapse with resistant disease occurs in ~ 40% of patients. However, little is known regarding relapsed/refractory DLBCL (rrDLBCL) genetics and alternative therapies. Based on findings from other tumors, we hypothesized that RAS-MEK-ERK signaling would be upregulated in resistant tumors, potentially correlating with mutations in RAS, RAF, or associated proteins. We analyzed mutations and phospho-ERK levels in tumor samples from rrDLBCL patients. Unlike other tumor types, rrDLBCL is not mutated in any Ras or Raf family members, despite having increased expression of p-ERK. In paired biopsies comparing diagnostic and relapsed specimens, 33% of tumors gained p-ERK expression, suggesting a role in promoting survival. We did find mutations in several Ras-associating proteins, including GEFs, GAPs, and downstream effectors that could account for increased ERK activation. We further investigated mutations in one such protein, RASGRP4. In silico modeling indicated an increased interaction between H-Ras and mutant RASGRP4. In cell lines, mutant RASGRP4 increased basal p-ERK expression and lead to a growth advantage in colony forming assays when challenged with doxorubicin. Relapsed/refractory DLBCL is often associated with increased survival signals downstream of ERK, potentially corresponding with mutations in protein controlling RAS/MEK/ERK signaling.

Sedimentary structure discrimination with hyperspectral imaging in sediment cores.

Hyperspectral imaging (HSI) is a non-destructive, high-resolution imaging technique that is currently under significant development for analyzing geological areas with remote devices or natural samples in a laboratory. In both cases, the hyperspectral image provides several sedimentary structures that must be separated to temporally and spatially describe the sample. Sediment sequences are composed of successive deposits (strata, homogenite, flood) that are visible depending on sample properties. The classical methods to identify them are time-consuming, have a low spatial resolution (millimeters) and are generally based on naked-eye counting. In this study, we compare several supervised classification algorithms to discriminate sedimentological structures in lake sediments. Instantaneous events in lake sediments are generally linked to extreme geodynamical events (e.g., floods, earthquakes), so their identification and counting are essential to understand long-term fluctuations and improve hazard assessments. Identification and counting are done by reconstructing a chronicle of event layer occurrence, including estimation of deposit thicknesses. Here, we applied two hyperspectral imaging sensors (Visible Near-Infrared, VNIR, 60 µm, 400-1000 nm; Short Wave Infrared, SWIR, 200 µm, 1000-2500 nm) on three sediment cores from different lake systems. We highlight that the SWIR sensor is the optimal one for creating robust classification models with discriminant analyses (prediction accuracies of 0.87-0.98). Indeed, the VNIR sensor is impacted by the surface reliefs and structures that are not in the learning set, which causes mis-classification. These observations are also valid for the combined sensor (VNIR-SWIR) and the RGB images. Several spatial and spectral pre-processing were also compared and enabled one to highlight discriminant information specific to a sample and a sensor. These works show that the combined use of hyperspectral imaging and machine learning improves the characterization of sedimentary structures compared to conventional methods.

Inhibiting the MNK1/2-eIF4E axis impairs melanoma phenotype switching and potentiates antitumor immune responses.

Melanomas commonly undergo a phenotype switch, from a proliferative to an invasive state. Such tumor cell plasticity contributes to immunotherapy resistance; however, the mechanisms are not completely understood and thus are therapeutically unexploited. Using melanoma mouse models, we demonstrated that blocking the MNK1/2-eIF4E axis inhibited melanoma phenotype switching and sensitized melanoma to anti-PD-1 immunotherapy. We showed that phospho-eIF4E-deficient murine melanomas expressed high levels of melanocytic antigens, with similar results verified in patient melanomas. Mechanistically, we identified phospho-eIF4E-mediated translational control of NGFR, a critical effector of phenotype switching. Genetic ablation of phospho-eIF4E reprogrammed the immunosuppressive microenvironment, exemplified by lowered production of inflammatory factors, decreased PD-L1 expression on dendritic cells and myeloid-derived suppressor cells, and increased CD8+ T cell infiltrates. Finally, dual blockade of the MNK1/2-eIF4E axis and the PD-1/PD-L1 immune checkpoint demonstrated efficacy in multiple melanoma models regardless of their genomic classification. An increase in the presence of intratumoral stem-like TCF1+PD-1+CD8+ T cells, a characteristic essential for durable antitumor immunity, was detected in mice given a MNK1/2 inhibitor and anti-PD-1 therapy. Using MNK1/2 inhibitors to repress phospho-eIF4E thus offers a strategy to inhibit melanoma plasticity and improve response to anti-PD-1 immunotherapy.

Cross-Sectional Evaluation of Humoral Responses against SARS-CoV-2 Spike.

SARS-CoV-2 is responsible for the coronavirus disease 2019 (COVID-19) pandemic, infecting millions of people and causing hundreds of thousands of deaths. The Spike glycoproteins of SARS-CoV-2 mediate viral entry and are the main targets for neutralizing antibodies. Understanding the antibody response directed against SARS-CoV-2 is crucial for the development of vaccine, therapeutic, and public health interventions. Here, we perform a cross-sectional study on 106 SARS-CoV-2-infected individuals to evaluate humoral responses against SARS-CoV-2 Spike. Most infected individuals elicit anti-Spike antibodies within 2 weeks of the onset of symptoms. The levels of receptor binding domain (RBD)-specific immunoglobulin G (IgG) persist over time, and the levels of anti-RBD IgM decrease after symptom resolution. Although most individuals develop neutralizing antibodies within 2 weeks of infection, the level of neutralizing activity is significantly decreased over time. Our results highlight the importance of studying the persistence of neutralizing activity upon natural SARS-CoV-2 infection.

Cross-sectional evaluation of humoral responses against SARS-CoV-2 Spike.

The SARS-CoV-2 virus is responsible for the current worldwide coronavirus disease 2019 (COVID-19) pandemic, infecting millions of people and causing hundreds of thousands of deaths. The Spike glycoprotein of SARS-CoV-2 mediates viral entry and is the main target for neutralizing antibodies. Understanding the antibody response directed against SARS-CoV-2 is crucial for the development of vaccine, therapeutic and public health interventions. Here we performed a cross-sectional study on 106 SARS-CoV-2-infected individuals to evaluate humoral responses against the SARS-CoV-2 Spike. The vast majority of infected individuals elicited anti-Spike antibodies within 2 weeks after the onset of symptoms. The levels of receptor-binding domain (RBD)-specific IgG persisted overtime, while the levels of anti-RBD IgM decreased after symptoms resolution. Some of the elicited antibodies cross-reacted with other human coronaviruses in a genus-restrictive manner. While most of individuals developed neutralizing antibodies within the first two weeks of infection, the level of neutralizing activity was significantly decreased over time. Our results highlight the importance of studying the persistence of neutralizing activity upon natural SARS-CoV-2 infection.

Sponges against miR-19 and miR-155 reactivate the p53-Socs1 axis in hematopoietic cancers.

Normal cell proliferation is controlled by a balance between signals that promote or halt cell proliferation. Micro RNAs are emerging as key elements in providing fine signal balance in different physiological situations. Here we report that STAT5 signaling induces the miRNAs miR-19 and miR-155, which potentially antagonize the tumor suppressor axis composed by the STAT5 target gene SOCS1 (suppressor of cytokine signaling-1) and its downstream effector p53. MiRNA sponges against miR-19 or miR-155 inhibit the functions of these miRNAs and potentiate the induction of SOCS1 and p53 in mouse leukemia cells and in human myeloma cells. Adding a catalytic RNA motif of the hammerhead type within miRNA sponges against miR-155 leads to decreased miR-155 levels and increased their ability of inhibiting cell growth and cell migration in myeloma cells. The results indicate that antagonizing miRNA activity can reactivate tumor suppressor pathways downstream cytokine stimulation in tumor cells.

PDE-based enhancement of color images in RGB space.

A novel method for color image enhancement is proposed as an extension of the scalar-diffusion-shock-filter coupling model, where noisy and blurred images are denoised and sharpened. The proposed model is based on using the single vectors of the gradient magnitude and the second derivatives as a manner to relate different color components of the image. This model can be viewed as a generalization of the Bettahar-Stambouli filter to multivalued images. The proposed algorithm is more efficient than the mentioned filter and some previous works at color images denoising and deblurring without creating false colors.

Endothelin-converting enzyme-like 1 (ECEL1) is present both in the plasma membrane and in the endoplasmic reticulum.

Enzymes of the M13 family of zinc-containing endopeptidases are recognized as important regulators of neuropeptide and peptide hormone activity. Peptidases of this family are type II integral-membrane proteins characterized by short cytosolic domains and large extracellular domains containing the active site. The M13 family has, at present, seven members, including ECEL1 (endothelin-converting enzyme-like 1), one of the newest members. ECEL1 is expressed predominantly in the central nervous system. It has been proposed that the enzyme has a role in the nervous regulation of the respiratory system. No physiological substrate has been identified yet. To better understand the function(s) of this enzyme, we have expressed human ECEL1 in cultured cells and monitored its biosynthesis and subcellular localization. Immunoblot and cell-surface biotinylation analysis of transfected cells expressing ECEL1 showed that only a fraction of the protein travelled to the cell surface, while most of the enzyme was present in an intracellular compartment identified by confocal immunofluorescence microscopy and cell fractionation as the ER (endoplasmic reticulum). Pulse-chase experiments showed that ER-localized ECEL1 was stable, with a half-life of more than 3 h. Endogenous ECEL1 from mouse pituitary gland had a similar distribution between the cell surface and the ER. Finally, using domain-swapping experiments with neprilysin, another member of the M13 family, we showed that localization of ECEL1 to the ER requires both the transmembrane and cytoplasmic domains. It thus appears that ECEL1 may have functions both at the cell surface and in the ER.