An automated pattern recognition system for classifying indirect immunofluorescence images for HEp-2 cells and specimens

AbstractImmunofluorescence antinuclear antibody tests are important for diagnosis and management of autoimmune conditions; a key step that would benefit from reliable automation is the recognition of subcellular patterns suggestive of different diseases. We present a system to recognize such patterns, at cellular and specimen levels, in images of HEp-2 cells. Ensembles of SVMs were trained to classify cells into six classes based on sparse encoding of texture features with cell pyramids, capturing spatial, multi-scale structure. A similar approach was used to classify specimens into seven classes. Software implementations were submitted to an international contest hosted by ICPR 2014 (Performance Evaluation of Indirect Immunofluorescence Image Analysis Systems). Mean class accuracies obtained on heldout test data sets were 87.1% and 88.5% for cell and specimen classification respectively. These were the highest achieved in the competition, suggesting that our methods are state-of-the-art. We provide detailed descriptions and extensive experiments with various features and encoding methods

Purification of GFRα1+ and GFRα1– Spermatogonial Stem Cells Reveals a Niche-Dependent Mechanism for Fate Determination

Summary: Undifferentiated spermatogonia comprise a pool of stem cells and progenitor cells that show heterogeneous expression of markers, including the cell surface receptor GFRα1. Technical challenges in isolation of GFRα1+ versus GFRα1– undifferentiated spermatogonia have precluded the comparative molecular characterization of these subpopulations and their functional evaluation as stem cells. Here, we develop a method to purify these subpopulations by fluorescence-activated cell sorting and show that GFRα1+ and GFRα1– undifferentiated spermatogonia both demonstrate elevated transplantation activity, while differing principally in receptor tyrosine kinase signaling and cell cycle. We identify the cell surface molecule melanocyte cell adhesion molecule (MCAM) as differentially expressed in these populations and show that antibodies to MCAM allow isolation of highly enriched populations of GFRα1+ and GFRα1– spermatogonia from adult, wild-type mice. In germ cell culture, GFRα1– cells upregulate MCAM expression in response to glial cell line-derived neurotrophic factor (GDNF)/fibroblast growth factor (FGF) stimulation. In transplanted hosts, GFRα1– spermatogonia yield GFRα1+ spermatogonia and restore spermatogenesis, albeit at lower rates than their GFRα1+ counterparts. Together, these data provide support for a model of a stem cell pool in which the GFRα1+ and GFRα1– cells are closely related but show key cell-intrinsic differences and can interconvert between the two states based, in part, on access to niche factors. : In this article, Garbuzov and colleagues devise a new strategy for isolating pure populations of GFRα1+ and GFRα1– undifferentiated spermatogonia from adult testis of TertTomato reporter mice based on expression of telomerase and GFRα1. Transcriptional profiling showed a remarkable similarity between GFRα1+ and GFRα1– cells, and both populations showed elevated stem cell activity by transplantation. Keywords: spermatogonial stem cells, germ cells, telomerase, germ line, stem cells, niche, transplantation, RNA-seq, FAC

Single cell RNA sequencing unravels mechanisms underlying senescence-like phenotypes of alveolar macrophages

Summary: Alveolar macrophages (AMs) are resident innate immune cells that play vital roles in maintaining lung physiological functions. However, the effects of aging on their dynamics, heterogeneity, and transcriptional profiles remain to be fully elucidated. Through single cell RNA sequencing (scRNA-seq), we identified CBFβ as an indispensable transcription factor that ensures AM self-renewal. Intriguingly, despite transcriptome similarities of proliferating cells, AMs from aged mice exhibited reduced embryonic stem cell–like features. Aged AMs also displayed compromised DNA repair abilities, potentially leading to obstructed cell cycle progression and an elevation of senescence markers. Consistently, AMs from aged mice exhibited impaired self-renewal ability and reduced sensitivity to GM-CSF. Decreased CBFβ was observed in the cytosol of AMs from aged mice. Similar senescence-like phenotypes were also found in human AMs. Taken together, these findings suggest that AMs in aged hosts demonstrate senescence-like phenotypes, potentially facilitated by the abrogated CBF β activity