Human leucine-rich repeat proteins: a genome-wide bioinformatic categorization and functional analysis in innate immunity.

In innate immune sensing, the detection of pathogen-associated molecular patterns by recognition receptors typically involve leucine-rich repeats (LRRs). We provide a categorization of 375 human LRR-containing proteins, almost half of which lack other identifiable functional domains. We clustered human LRR proteins by first assigning LRRs to LRR classes and then grouping the proteins based on these class assignments, revealing several of the resulting protein groups containing a large number of proteins with certain non-LRR functional domains. In particular, a statistically significant number of LRR proteins in the typical (T) and bacterial + typical (S+T) categories have transmembrane domains, whereas most of the LRR proteins in the cysteine-containing (CC) category contain an F-box domain (which mediates interactions with the E3 ubiquitin ligase complex). Furthermore, by examining the evolutionary profiles of the LRR proteins, we identified a subset of LRR proteins exhibiting strong conservation in fungi and an enrichment for "nucleic acid-binding" function. Expression analysis of LRR genes identifies a subset of pathogen-responsive genes in human primary macrophages infected with pathogenic bacteria. Using functional RNAi, we show that MFHAS1 regulates Toll-like receptor (TLR)-dependent signaling. By using protein interaction network analysis followed by functional RNAi, we identified LRSAM1 as a component of the antibacterial autophagic response.

Comparison of contrast-enhanced digital mammography and contrast-enhanced digital breast tomosynthesis for lesion assessment.

Contrast-enhanced digital mammography (CEDM) reveals neovasculature of breast lesions in a two-dimensional contrast enhancement map. Contrast-enhanced digital breast tomosynthesis (CEDBT) provides contrast enhancement in three dimensions, which may improve lesion characterization and localization. We aim to compare CEDM and CEDBT for lesion assessment. Women with breast imaging-reporting and data system 4 or 5 suspicious breast lesion(s) were recruited in our study and were imaged with CEDM and CEDBT in succession under one breast compression. Two radiologists assessed CEDM and CEDBT with both images displayed side-by-side and compared (1) contrast enhancement of lesions and (2) lesion margin using a five-point scale ranging from - 2 (CEDM much better) to + 2 (CEDBT much better). Biopsy identified 19 malignant lesions with contrast enhancement. Our results show that CEDBT provides better lesion margins than CEDM with limited reduction in contrast enhancement. CEDBT delivers less radiation dose compared to CEDM + DBT. Synthetic CEDM can be generated from CEDBT data and provides lesion contrast enhancement comparable to CEDM. CEDBT has potential for clinical applications, such as treatment response monitoring and guidance for biopsy.

Reevaluating the Utility of Maxillary Sinus Opacification as a Screening Tool for Facial Bone Fracture a Decade After Its Original Analysis.

In 1997, Lambert and colleagues demonstrated that the absence of sinus fluid on head CT essentially excludes a fracture involving the sinus walls. Our purpose is to reevaluate this association utilizing the current standard of imaging technology. With improved image resolution, we aim to reassess whether the sensitivity and specificity of the "clear sinus sign" are improved or worsened. Furthermore, the current standard of care is to obtain a CT of the facial bones along with a head CT when facial trauma is suspected, so we also analyzed the association of the "clear sinus sign" with nasal bone and mandible fractures. We identified 629 facial bone CT scans performed on adult patients in the emergency department between July 2012 and May 2013. They were retrospectively analyzed by three reviewers for the presence of facial bone fracture and/or fluid opacification of at least one paranasal sinus (as defined by either complete sinus opacification or an air-fluid level - circumferential mucosal thickening was considered the absence of fluid). We found that sinus opacification was 98.8% specific for facial bone fracture but only 44.7% sensitive. However, for complex facial fractures, such as zygomaticomaxillary complex, orbital, and sinus fractures, the lack of sinus fluid is significantly more sensitive at 91%. Therefore, our results for complex facial fractures are congruent with those of the previous studies conducted by Lambert, et al. and Lewandowski, et al. However, we also demonstrate that sinus opacification is not specific for nasal bone or mandibular fractures.

A genome-wide siRNA screen reveals multiple mTORC1 independent signaling pathways regulating autophagy under normal nutritional conditions.

Autophagy is a cellular catabolic mechanism that plays an essential function in protecting multicellular eukaryotes from neurodegeneration, cancer, and other diseases. However, we still know very little about mechanisms regulating autophagy under normal homeostatic conditions when nutrients are not limiting. In a genome-wide human siRNA screen, we demonstrate that under normal nutrient conditions upregulation of autophagy requires the type III PI3 kinase, but not inhibition of mTORC1, the essential negative regulator of starvation-induced autophagy. We show that a group of growth factors and cytokines inhibit the type III PI3 kinase through multiple pathways, including the MAPK-ERK1/2, Stat3, Akt/Foxo3, and CXCR4/GPCR, which are all known to positively regulate cell growth and proliferation. Our study suggests that the type III PI3 kinase integrates diverse signals to regulate cellular levels of autophagy, and that autophagy and cell proliferation may represent two alternative cell fates that are regulated in a mutually exclusive manner.

Identification of Atg5-dependent transcriptional changes and increases in mitochondrial mass in Atg5-deficient T lymphocytes.

Autophagy is implicated in many functions of mammalian cells such as organelle recycling, survival and differentiation, and is essential for the maintenance of T and B lymphocytes. Here, we demonstrate that autophagy is a constitutive process during T cell development. Deletion of the essential autophagy genes Atg5 or Atg7 in T cells resulted in decreased thymocyte and peripheral T cell numbers, and Atg5-deficient T cells had a decrease in cell survival. We employed functional-genetic and integrative computational analyses to elucidate specific functions of the autophagic process in developing T-lineage lymphocytes. Our whole-genome transcriptional profiling identified a set of 699 genes differentially expressed in Atg5-deficient and Atg5-sufficient thymocytes (Atg5-dependent gene set). Strikingly, the Atg5-dependent gene set was dramatically enriched in genes encoding proteins associated with the mitochondrion. In support of a role for autophagy in mitochondrial maintenance in T lineage cells, the deletion of Atg5 led to increased mitochondrial mass in peripheral T cells. We also observed a correlation between mitochondrial mass and Annexin-V staining in peripheral T cells. We propose that autophagy is critical for mitochondrial maintenance and T cell survival. We speculate that, similar to its role in yeast or mammalian liver cells, autophagy is required in T cells for the removal of damaged or aging mitochondria and that this contributes to the cell death of autophagy-deficient T cells.