Toward Precision Diagnosis: Machine Learning in Identifying Malignant Orbital Tumors With Multiparametric 3 T MRI.

BACKGROUND: Orbital tumors present a diagnostic challenge due to their varied locations and histopathological differences. Although recent advancements in imaging have improved diagnosis, classification remains a challenge. The integration of artificial intelligence in radiology and ophthalmology has demonstrated promising outcomes. PURPOSE: This study aimed to evaluate the performance of machine learning models in accurately distinguishing malignant orbital tumors from benign ones using multiparametric 3 T magnetic resonance imaging (MRI) data. MATERIALS AND METHODS: In this single-center prospective study, patients with orbital masses underwent presurgery 3 T MRI scans between December 2015 and May 2021. The MRI protocol comprised multiparametric imaging including dynamic contrast-enhanced (DCE), diffusion-weighted imaging (DWI), intravoxel incoherent motion (IVIM), as well as morphological imaging acquisitions. A repeated nested cross-validation strategy using random forest classifiers was used for model training and evaluation, considering 8 combinations of explanatory features. Shapley additive explanations (SHAP) values were used to assess feature contributions, and the model performance was evaluated using multiple metrics. RESULTS: One hundred thirteen patients were analyzed (57/113 [50.4%] were women; average age was 51.5 ± 17.5 years, range: 19-88 years). Among the 8 combinations of explanatory features assessed, the performance on predicting malignancy when using the most comprehensive model, which is the most exhaustive one incorporating all 46 explanatory features-including morphology, DWI, DCE, and IVIM, achieved an area under the curve of 0.9 [0.73-0.99]. When using the streamlined "10-feature signature" model, performance reached an area under the curve of 0.88 [0.71-0.99]. Random forest feature importance graphs measured by the mean of SHAP values pinpointed the 10 most impactful features, which comprised 3 quantitative IVIM features, 4 quantitative DCE features, 1 quantitative DWI feature, 1 qualitative DWI feature, and age. CONCLUSIONS: Our findings demonstrate that a machine learning approach, integrating multiparametric MRI data such as DCE, DWI, IVIM, and morphological imaging, offers high-performing models for differentiating malignant from benign orbital tumors. The streamlined 10-feature signature, with a performance close to the comprehensive model, may be more suitable for clinical application.

Incidence and Outcomes of Eye Trauma Associated With Recreative Use of Nonpowder Toy Guns: A 12-Year Retrospective Study.

PURPOSE: Nonpowder toy guns (NPTGs) are responsible for many ocular traumas. This study aims to detail the outcomes of these injuries depending on the causative NPTG. DESIGN: Retrospective, observational case series. METHODS: Cases of NPTG-associated ocular trauma managed in a Parisian eye emergency department between August 1, 2010, and January 1, 2023, were reviewed. The date of trauma, causative NPTG, patient demographics, initial and follow-up eye examinations, any surgical procedure, and visual outcomes for each ocular trauma were analyzed. RESULTS: Over 12 years, NPTGs were responsible for 324 eye injuries and 980 visits. Patients were mostly male (77.5%), and mean age at trauma was 16.2 years. Foam bullets or foam dart blasters accounted for 54.9% of traumas and were mainly responsible for corneal injuries and hyphema (30.9% and 27%, respectively). BB guns and airsoft guns were frequently responsible for anterior segment lesions, as well as intravitreal hemorrhages (14.7%) and commotio retinae (21.1%). Paintball guns accounted for the largest proportion of posterior segment lesions (eg, intraretinal or subretinal hemorrhages leading to macular atrophy/contusion maculopathy), and one-third of casualties had undergone ocular surgery. Among all traumas, final visual acuity was lower than 20/200 in 6.5% of cases. Phthisis occurred in 8 cases: Two were related to foam bullets or foam dart blaster injuries (1 contusion and 1 rupture), 2 other cases followed a rupture due to BB guns/airsoft guns, 1 case occurred after a rupture related to a paintball gunshot, and 3 others were due to other types of compressed air guns (1 rupture, 1 intraocular foreign body, and 1 total retinal detachment). CONCLUSIONS: NPTG-related ocular trauma outcomes differ according to the causative toy. Paintball guns and BB guns/airsoft gun-related traumas were more likely to be associated with severe lesions, but an increasing number of ocular injuries related to the use of foam bullets or foam dart blasters are reported in younger and younger children. Public health policies should promote the use of protective eyewear.

Solid-state NMR study of structural heterogeneity of the apo WT mouse TSPO reconstituted in liposomes.

In the last decades, ligand binding to human TSPO has been largely used in clinical neuroimaging, but little is known about the interaction mechanism. Protein conformational mobility plays a key role in the ligand recognition and both, ligand-free and ligand-bound structures, are mandatory for characterizing the molecular binding mechanism. In the absence of crystals for mammalian TSPO, we have exploited solid-state nuclear magnetic resonance (ssNMR) spectroscopy under magic-angle spinning (MAS) to study the apo form of recombinant mouse TSPO (mTSPO) reconstituted in lipids. This environment has been previously described to permit binding of its high-affinity drug ligand PK11195 and appears therefore favourable for the study of molecular dynamics. We have optimized the physical conditions to get the best resolution for MAS ssNMR spectra of the ligand-free mTSPO. We have compared and combined various ssNMR spectra to get dynamical information either for the lipids or for the mTSPO. Partial assignment of residue types suggests few agreements with the published solution NMR assignment of the PK11195-bound mTSPO in DPC detergent. Moreover, we were able to observe some lateral chains of aromatic residues that were not assigned in solution. 13C double-quantum NMR spectroscopy shows remarkable dynamics for ligand-free mTSPO in lipids which may have significant implications on the recognition of the ligand and/or other protein partners.

Structural Insights into the Interaction of the Intrinsically Disordered Co-activator TIF2 with Retinoic Acid Receptor Heterodimer (RXR/RAR).

Retinoic acid receptors (RARs) and retinoid X receptors (RXRs) form heterodimers that activate target gene transcription by recruiting co-activator complexes in response to ligand binding. The nuclear receptor (NR) co-activator TIF2 mediates this recruitment by interacting with the ligand-binding domain (LBD) of NRs trough the nuclear receptor interaction domain (TIF2NRID) containing three highly conserved α-helical LxxLL motifs (NR-boxes). The precise binding mode of this domain to RXR/RAR is not clear due to the disordered nature of TIF2. Here we present the structural characterization of TIF2NRID by integrating several experimental (NMR, SAXS, Far-UV CD, SEC-MALS) and computational data. Collectively, the data are in agreement with a largely disordered protein with partially structured regions, including the NR-boxes and their flanking regions, which are evolutionary conserved. NMR and X-ray crystallographic data on TIF2NRID in complex with RXR/RAR reveal a multisite binding of the three NR-boxes as well as an active role of their flanking regions in the interaction.

A Plant-Specific N-terminal Extension Reveals Evolutionary Functional Divergence within Translocator Proteins.

Conserved translocator proteins (TSPOs) mediate cell stress responses possibly in a cell-type-specific manner. This work reports on the molecular function of plant TSPO and their possible evolutionary divergence. Arabidopsis thaliana TSPO (AtTSPO) is stress induced and has a conserved polybasic, plant-specific N-terminal extension. AtTSPO reduces water loss by depleting aquaporin PIP2;7 in the plasma membrane. Herein, AtTSPO was found to bind phosphoinositides in vitro, but only full-length AtTSPO or chimeric mouse TSPO with an AtTSPO N-terminus bound PI(4,5)P2in vitro and modified PIP2;7 levels in vivo. Expression of AtTSPO but not its N-terminally truncated variant enhanced phospholipase C activity and depleted PI(4,5)P2 from the plasma membrane and its enrichment in Golgi membranes. Deletion or point mutations within the AtTSPO N-terminus affected PI(4,5)P2 binding and almost prevented AtTSPO-PIP2;7 interaction in vivo. The findings imply functional divergence of plant TSPOs from bacterial and animal counterparts via evolutionary acquisition of the phospholipid-interacting N-terminus.

Characterization of the High-Affinity Drug Ligand Binding Site of Mouse Recombinant TSPO.

The optimization of translocator protein (TSPO) ligands for Positron Emission Tomography as well as for the modulation of neurosteroids is a critical necessity for the development of TSPO-based diagnostics and therapeutics of neuropsychiatrics and neurodegenerative disorders. Structural hints on the interaction site and ligand binding mechanism are essential for the development of efficient TSPO ligands. Recently published atomic structures of recombinant mammalian and bacterial TSPO1, bound with either the high-affinity drug ligand PK 11195 or protoporphyrin IX, have revealed the membrane protein topology and the ligand binding pocket. The ligand is surrounded by amino acids from the five transmembrane helices as well as the cytosolic loops. However, the precise mechanism of ligand binding remains unknown. Previous biochemical studies had suggested that ligand selectivity and binding was governed by these loops. We performed site-directed mutagenesis to further test this hypothesis and measured the binding affinities. We show that aromatic residues (Y34 and F100) from the cytosolic loops contribute to PK 11195 access to its binding site. Limited proteolytic digestion, circular dichroism and solution two-dimensional (2-D) NMR using selective amino acid labelling provide information on the intramolecular flexibility and conformational changes in the TSPO structure upon PK 11195 binding. We also discuss the differences in the PK 11195 binding affinities and the primary structure between TSPO (TSPO1) and its paralogous gene product TSPO2.

Recombinant Overexpression of Mammalian TSPO Isoforms 1 and 2.

TSPO is a 18 kDa membrane protein that exists in mammalian as two isoforms 1 and 2. They are involved in different functions and are located in different membranes. TSPO1 is mainly located in outer mitochondrial membrane, whereas TSPO2 is encountered in plasma membrane of red blood cells. Determination of their structures is a milestone to understand their function. Their natural abundance is not sufficient to get large amounts usually required for structural studies. We described heterologous overexpression in both bacterial and cell-free system and purification on immobilized-metal affinity chromatography (IMAC) of both proteins. Using the same vector, TSPO1 is mostly recovered in bacterial inclusion bodies whereas TSPO2 is found in both bacterial cytosol and inclusion bodies, but in low amounts. Cell-free expression was the best system to overexpress pure TSPO2.

Solid-State NMR of Membrane Protein Reconstituted in Proteoliposomes, the Case of TSPO.

Structural studies of membrane proteins (MP) in a native or native-like environment remain a challenge. X-ray crystallography of three-dimensional crystals of MP in lipids and cryo-electron microscopy of two-dimensional crystals also in lipids have given atomic structures of several MP. Recent developments of solid-state NMR (ssNMR) provided structural data of MP in lipids and should give access to the dynamic behavior of MP's in a native-like environment. Preparation of samples for ssNMR is not trivial with overexpressed proteins since purified recombinant MP have to be reincorporated in proteoliposomes and concentrated in the small volume of the rotor used for ssNMR studies. We present here the protocol that we have used to study the recombinant mouse TSPO1, an integral membrane protein of 20 kDa mostly found in the outer membrane of mitochondria and overexpressed in E. coli bacteria.

Probing the gel to liquid-crystalline phase transition and relevant conformation changes in liposomes by (13)C magic-angle spinning NMR spectroscopy.

A straightforward way to visualize gel to liquid-crystalline phase transition in phospholipid membranes is presented by using ¹³C magic-angle spinning NMR. The changes in the 13C isotropic chemical shifts with increasing temperature are shown to be a sensitive probe of the main thermotropic phase transition related to lipid hydrocarbon chain dynamics and relevant conformational changes. The average value of the energy difference between trans and gauche states in the central C4­11 fragment of the DMPC acyl chain was estimated to be 4.02 ± 0.2 kJ mol⁻¹ in the liquid crystalline phase. The reported spectral features will be useful in 13C solid state NMR studies for direct monitoring of the effective lipid chain melting allowing rapid uniaxial rotation of membrane proteins in the biologically relevant liquid-crystalline phase.