A case of eccrine porocarcinoma: A treacherous mimic and diagnostic challenge.

Eccrine porocarcinoma is a rare malignant dermal appendageal tumor notorious for its varied morphology, both clinically and histologically; and it can pose a considerable diagnostic dilemma to both the dermatologist and the pathologist. Herein, we present a case of a 74-year-old woman with slow-growing nodular masses on both buttocks, reaching a fairly large size over a course of 3 years. Although atypical morphologic features posed significant diagnostic difficulty to both the surgeon and the pathologists, it was eventually diagnosed as eccrine porocarcinoma with focal squamoid features, using immunostains. To our knowledge, this is the second reported case of bilateral eccrine porocarcinoma which highlights the need for awareness of the morphological variations that this entity is capable of producing.

Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia.

Altered olfactory function is a common symptom of COVID-19, but its etiology is unknown. A key question is whether SARS-CoV-2 (CoV-2) - the causal agent in COVID-19 - affects olfaction directly, by infecting olfactory sensory neurons or their targets in the olfactory bulb, or indirectly, through perturbation of supporting cells. Here we identify cell types in the olfactory epithelium and olfactory bulb that express SARS-CoV-2 cell entry molecules. Bulk sequencing demonstrated that mouse, non-human primate and human olfactory mucosa expresses two key genes involved in CoV-2 entry, ACE2 and TMPRSS2. However, single cell sequencing revealed that ACE2 is expressed in support cells, stem cells, and perivascular cells, rather than in neurons. Immunostaining confirmed these results and revealed pervasive expression of ACE2 protein in dorsally-located olfactory epithelial sustentacular cells and olfactory bulb pericytes in the mouse. These findings suggest that CoV-2 infection of non-neuronal cell types leads to anosmia and related disturbances in odor perception in COVID-19 patients.

Cellular mechanisms of epithelial stem cell self-renewal and differentiation during homeostasis and repair.

Epithelia in adult mammals exhibit remarkable regenerative capacities owing to the presence of adult stem cells, which self-renew and differentiate to replace cells lost to normal turnover or injury. The mechanisms supporting tissue homeostasis and injury-induced repair often differ from each other as well as from those used in embryonic development. Recent studies have also highlighted the phenomenon of cellular plasticity in adult tissues, in which differentiated cells can change fate and even give rise to new stem cell populations to complement the canonical stem cells in promoting repair following injury. Signaling pathways such as WNT, bone morphogenetic protein, and Sonic Hedgehog play critical roles in stem cell maintenance and cell fate decisions across diverse epithelia and conditions, suggesting that conserved mechanisms underlie the regenerative capacity of adult epithelial structures. This article is categorized under: Gene Expression and Transcriptional Hierarchies > Regulatory Mechanisms Adult Stem Cells, Tissue Renewal, and Regeneration > Tissue Stem Cells and Niches Adult Stem Cells, Tissue Renewal, and Regeneration > Stem Cell Differentiation and Reversion Adult Stem Cells, Tissue Renewal, and Regeneration > Regeneration.

clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets.

Clustering of genes and/or samples is a common task in gene expression analysis. The goals in clustering can vary, but an important scenario is that of finding biologically meaningful subtypes within the samples. This is an application that is particularly appropriate when there are large numbers of samples, as in many human disease studies. With the increasing popularity of single-cell transcriptome sequencing (RNA-Seq), many more controlled experiments on model organisms are similarly creating large gene expression datasets with the goal of detecting previously unknown heterogeneity within cells. It is common in the detection of novel subtypes to run many clustering algorithms, as well as rely on subsampling and ensemble methods to improve robustness. We introduce a Bioconductor R package, clusterExperiment, that implements a general and flexible strategy we entitle Resampling-based Sequential Ensemble Clustering (RSEC). RSEC enables the user to easily create multiple, competing clusterings of the data based on different techniques and associated tuning parameters, including easy integration of resampling and sequential clustering, and then provides methods for consolidating the multiple clusterings into a final consensus clustering. The package is modular and allows the user to separately apply the individual components of the RSEC procedure, i.e., apply multiple clustering algorithms, create a consensus clustering or choose tuning parameters, and merge clusters. Additionally, clusterExperiment provides a variety of visualization tools for the clustering process, as well as methods for the identification of possible cluster signatures or biomarkers. The R package clusterExperiment is publicly available through the Bioconductor Project, with a detailed manual (vignette) as well as well documented help pages for each function.

Role of p16/Ki-67 Dual Immunostaining in Detection of Cervical Cancer Precursors.

BACKGROUND: Pap-smears-based cytology and human papilloma virus testing have their own limitations in detecting cervical precancerous lesions, and still need further standardization. Co-expression of p16ink4a and Ki-67 can be used as additional biomarker. AIMS: To study the role of liquid-based cytology and the dual immunostaining for p16/Ki-67 in predicting the presence of significant lesion in cases of mild cytological atypia. MATERIALS AND METHODS: A prospective, cross-sectional study was performed in the Department of Pathology, in collaboration with Department of Obstetrics and Gynecology over 15 months including 545 patients. Immunocytochemistry followed by colposcopy-guided biopsy were performed in 52 cases with epithelial abnormalities. RESULTS: Thirty-five cases (67%) were dual-stain positive among the cases with epithelial abnormalities. In the ASC-US and LSIL group, the sensitivity and specificity of the immunostaining in diagnosing CIN2+ lesions were 100 and 70% and 87.5 and 100%, respectively. p16/Ki-67 positivity also increased with cytological severity which in turn corresponded with histological findings: it reached from 33% in ASC-US to 100% in both HSIL and SCC categories. CONCLUSION: This dual immunostaining may potentially be a useful tool in the triage of the ASC-US and the LSIL group, considering the high sensitivity and specificity values.

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics.

BACKGROUND: Single-cell transcriptomics allows researchers to investigate complex communities of heterogeneous cells. It can be applied to stem cells and their descendants in order to chart the progression from multipotent progenitors to fully differentiated cells. While a variety of statistical and computational methods have been proposed for inferring cell lineages, the problem of accurately characterizing multiple branching lineages remains difficult to solve. RESULTS: We introduce Slingshot, a novel method for inferring cell lineages and pseudotimes from single-cell gene expression data. In previously published datasets, Slingshot correctly identifies the biological signal for one to three branching trajectories. Additionally, our simulation study shows that Slingshot infers more accurate pseudotimes than other leading methods. CONCLUSIONS: Slingshot is a uniquely robust and flexible tool which combines the highly stable techniques necessary for noisy single-cell data with the ability to identify multiple trajectories. Accurate lineage inference is a critical step in the identification of dynamic temporal gene expression.

Creating Lineage Trajectory Maps Via Integration of Single-Cell RNA-Sequencing and Lineage Tracing: Integrating transgenic lineage tracing and single-cell RNA-sequencing is a robust approach for mapping developmental lineage trajectories and cell fate changes.

Mapping the paths that stem and progenitor cells take en route to differentiate and elucidating the underlying molecular controls are key goals in developmental and stem cell biology. However, with population level analyses it is difficult - if not impossible - to define the transition states and lineage trajectory branch points within complex developmental lineages. Single-cell RNA-sequencing analysis can discriminate heterogeneity in a population of cells and even identify rare or transient intermediates. In this review, we propose that using these data, one can infer the lineage trajectories of individual stem cells and identify putative branch points. Clonal lineage tracing of stem cells allows one to define the outcome of differentiation. Integrating these single cell-based approaches provides a robust strategy for establishing and testing models of how an individual stem cell changes through time to differentiate and self-renew.

Injury Activates Transient Olfactory Stem Cell States with Diverse Lineage Capacities.

Tissue homeostasis and regeneration are mediated by programs of adult stem cell renewal and differentiation. However, the mechanisms that regulate stem cell fates under such widely varying conditions are not fully understood. Using single-cell techniques, we assessed the transcriptional changes associated with stem cell self-renewal and differentiation and followed the maturation of stem cell-derived clones using sparse lineage tracing in the regenerating mouse olfactory epithelium. Following injury, quiescent olfactory stem cells rapidly shift to activated, transient states unique to regeneration and tailored to meet the demands of injury-induced repair, including barrier formation and proliferation. Multiple cell fates, including renewed stem cells and committed differentiating progenitors, are specified during this early window of activation. We further show that Sox2 is essential for cells to transition from the activated to neuronal progenitor states. Our study highlights strategies for stem cell-mediated regeneration that may be conserved in other adult stem cell niches.

Deconstructing Olfactory Stem Cell Trajectories at Single-Cell Resolution.

A detailed understanding of the paths that stem cells traverse to generate mature progeny is vital for elucidating the mechanisms governing cell fate decisions and tissue homeostasis. Adult stem cells maintain and regenerate multiple mature cell lineages in the olfactory epithelium. Here we integrate single-cell RNA sequencing and robust statistical analyses with in vivo lineage tracing to define a detailed map of the postnatal olfactory epithelium, revealing cell fate potentials and branchpoints in olfactory stem cell lineage trajectories. Olfactory stem cells produce support cells via direct fate conversion in the absence of cell division, and their multipotency at the population level reflects collective unipotent cell fate decisions by single stem cells. We further demonstrate that Wnt signaling regulates stem cell fate by promoting neuronal fate choices. This integrated approach reveals the mechanisms guiding olfactory lineage trajectories and provides a model for deconstructing similar hierarchies in other stem cell niches.