The spatial landscape of lung pathology during COVID-19 progression

Recent studies have provided insights into the pathology of and immune response to COVID-191-8. However, a thorough investigation of the interplay between infected cells and the immune system at sites of infection has been lacking. Here we use high-parameter imaging mass cytometry9 that targets the expression of 36 proteins to investigate the cellular composition and spatial architecture of acute lung injury in humans (including injuries derived from SARS-CoV-2 infection) at single-cell resolution. These spatially resolved single-cell data unravel the disordered structure of the infected and injured lung, alongside the distribution of extensive immune infiltration. Neutrophil and macrophage infiltration are hallmarks of bacterial pneumonia and COVID-19, respectively. We provide evidence that SARS-CoV-2 infects predominantly alveolar epithelial cells and induces a localized hyperinflammatory cell state that is associated with lung damage. We leverage the temporal range of fatal outcomes of COVID-19 in relation to the onset of symptoms, which reveals increased macrophage extravasation and increased numbers of mesenchymal cells and fibroblasts concomitant with increased proximity between these cell types as the disease progresses-possibly as a result of attempts to repair the damaged lung tissue. Our data enable us to develop a biologically interpretable landscape of lung pathology from a structural, immunological and clinical standpoint. We use this landscape to characterize the pathophysiology of the human lung from its macroscopic presentation to the single-cell level, which provides an important basis for understanding COVID-19 and lung pathology in general.

Optical coherence tomography for the investigation of skin adaptation to mechanical stress

BACKGROUND

Skin breakdown due to limb-socket interface stress is a significant problem for lower limb prosthesis users. While it is known that skin can adapt to stress to become more resistant to breakdown, little is understood about skin adaptation and few methods exist to noninvasively investigate it. In this study, we present novel, noninvasive imaging methods using Optical Coherence Tomography (OCT) to assess key features of the cutaneous microvasculature that may be involved in skin adaptation.

MATERIALS AND METHODS

Eight able-bodied participants wore a modified below-knee prosthetic socket for two weeks to stress the skin of their lower limb. Two OCT-based imaging tests were used to assess the function and structure, respectively, of the cutaneous microvasculature at multiple time points throughout the socket wear protocol.

RESULTS

A measurable reactive hyperemia response was reliably induced in the skin of study participants in the vascular function assessment test. The vascular structure assessment demonstrated excellent field-of-view repeatability, providing rich data sets of vessel structure. No statistically significant differences were found in any of the measurements when compared between time points of the adaptation protocol. The participants' limbs were likely not stressed enough by the able-bodied socket to induce measurable skin adaptation.

CONCLUSION

This study introduced new techniques to investigate skin adaptation to mechanical stress. If the key limitations are addressed, these methods have the potential to provide insight into the function and structure of the cutaneous microvasculature that previously could not be attained noninvasively.

The landscape of myeloid and astrocyte phenotypes in acute multiple sclerosis lesions

Activated myeloid cells and astrocytes are the predominant cell types in active multiple sclerosis (MS) lesions. Both cell types can adopt diverse functional states that play critical roles in lesion formation and resolution. In order to identify phenotypic subsets of myeloid cells and astrocytes, we profiled two active MS lesions with thirteen glial activation markers using imaging mass cytometry (IMC), a method for multiplexed labeling of histological sections. In the acutely demyelinating lesion, we found multiple distinct myeloid and astrocyte phenotypes that populated separate lesion zones. In the post-demyelinating lesion, phenotypes were less distinct and more uniformly distributed. In both lesions cell-to-cell interactions were not random, but occurred between specific glial subpopulations and lymphocytes. Finally, we demonstrated that myeloid, but not astrocyte phenotypes were activated along a lesion rim-to-center gradient, and that marker expression in glial cells at the lesion rim was driven more by cell-extrinsic factors than in cells at the center. This proof-of-concept study demonstrates that highly multiplexed tissue imaging, combined with the appropriate computational tools, is a powerful approach to study heterogeneity, spatial distribution and cellular interactions in the context of MS lesions. Identifying glial phenotypes and their interactions at different lesion stages may provide novel therapeutic targets for inhibiting acute demyelination and low-grade, chronic inflammation.

Multiplexed imaging of immune cells in staged multiple sclerosis lesions by mass cytometry

Multiple sclerosis (MS) is characterized by demyelinated and inflammatory lesions in the brain and spinal cord that are highly variable in terms of cellular content. Here, we used imaging mass cytometry (IMC) to enable the simultaneous imaging of 15+ proteins within staged MS lesions. To test the potential for IMC to discriminate between different types of lesions, we selected a case with severe rebound MS disease activity after natalizumab cessation. With post-acquisition analysis pipelines we were able to: (1) Discriminate demyelinating macrophages from the resident microglial pool; (2) Determine which types of lymphocytes reside closest to blood vessels; (3) Identify multiple subsets of T and B cells, and (4) Ascertain dynamics of T cell phenotypes vis-à-vis lesion type and location. We propose that IMC will enable a comprehensive analysis of single-cell phenotypes, their functional states and cell-cell interactions in relation to lesion morphometry and demyelinating activity in MS patients.

It takes an army of immune cells to defend the body against infection. But sometimes the body’s immune system mistakenly attacks its own cells and chronic inflammatory conditions develop. In multiple sclerosis – also known as “MS” – a horde of immune cells infiltrate the brain and spinal cord, forming lesions which strip nerve cells of their insultation, a protective fatty material called myelin. Nerve cells become damaged, scarred and exposed, and this interferes with messages between the brain and other parts of the body.

Advanced imaging techniques have revolutionized the diagnosis of multiple sclerosis by capturing lesions as they develop in the brain and spinal cord. Researchers have also focused their efforts on understanding how immune cells activated in the blood stream invade the central nervous system. To better understand how a mistaken immune response leads to nerve damage in multiple sclerosis, a forensic examination of which immune cells accumulate in brain tissue to form lesions is needed. Standard techniques for analyzing whole tissue samples are however limited by design, capable of detecting only a few cell markers in one section of tissue.

Ramaglia et al. have now validated a new imaging technique for looking at an array of cell types in brain tissue in a single sample. The technique – called imaging mass cytometry (or IMC for short) – was used to look at post-mortem brain tissue from a multiple sclerosis patient with an acute form of the illness. The tissue examined had multiple sclerosis lesions present. Different types of immune cells were simultaneously identified and characterized using a panel of antibodies which recognize the signature proteins each immune cell makes when active. The state of the underlying myelin content of the tissue was also characterized.

The imaging approach could distinguish between the immune cells of the brain (known as resident microglia) and a type of white blood cell summoned as part of the immune response (infiltrating macrophages). The analysis showed that, in the particular patient examined, microglia are abundant in active lesions in multiple sclerosis; also, different subsets of white blood cells were detected. Measuring how far different immune cells had migrated from nearby blood vessels added insights as to how immune cells move through the brain and which cells may have arrived first.

Altogether, Ramaglia et al. have shown that IMC can be used as a discovery tool to gain a deeper understanding of multiple sclerosis lesions and immune cells active in the inflamed brain. Further work will apply this now validated imaging approach to large cohorts of multiple sclerosis patients.

Instrumented socket inserts for sensing interaction at the limb-socket interface

The objective of this research was to investigate a strategy for designing and fabricating computer-manufactured socket inserts that were embedded with sensors for field monitoring of limb-socket interactions of prosthetic users. An instrumented insert was fabricated for a single trans-tibial prosthesis user that contained three sensor types (proximity sensor, force sensing resistor, and inductive sensor), and the system was evaluated through a sequence of laboratory clinical tests and two days of field use. During in-lab tests 3 proximity sensors accurately distinguish between don and doff states; 3 of 4 force sensing resistors measured gradual pressure increases as weight-bearing increased; and the inductive sensor indicated that as prosthetic socks were added the limb moved farther out of the socket and pistoning amplitude decreased. Multiple sensor types were necessary in analysis of field collected data to interpret how sock changes affected limb-socket interactions. Instrumented socket inserts, with sensors selected to match clinical questions of interest, have the potential to provide important insights to improve patient care.

Unfolding the story of chromatin organization in senescent cells

Cell senescence, the permanent withdrawal of a cell from the cell cycle, is characterized by dramatic, cytological scale changes to DNA condensation throughout the genome. While prior emphasis has been placed on increases in heterochromatin, such as the formation of compact Senescent Associated Heterochromatin Foci (SAHF) structures, our recent findings showed that SAHF formation is preceded by the unravelling of constitutive heterochromatin into visibly extended structures, which we have termed Senescent Associated Distension of Satellites or SADS. Interestingly, neither of these marked changes in DNA condensation appear to be mediated by changes in canonical, heterochromatin-associated histone modifications. Rather, several observations suggest that these events may be facilitated by changes in LaminB1 levels and/or other factors that control higher-order chromatin architecture. Here, we review what is known about senescence-associated chromatin reorganization and present preliminary results using high-resolution microscopy techniques to show that each peri/centromeric satellite in senescent cells is comprised of several condensed domains connected by thin fibrils of satellite DNA. We then discuss the potential importance of these striking changes in chromatin condensation for cell senescence, and also as a model to provide a needed window into the higher-order packaging of the genome.

Higher-order unfolding of satellite heterochromatin is a consistent and early event in cell senescence

Higher-order unfolding of peri/centromeric satellite DNA is a consistent and early event in senescence of cultured normal human and mouse cells, progeria cells, and a senescent tumor.

Epigenetic changes to chromatin are thought to be essential to cell senescence, which is key to tumorigenesis and aging. Although many studies focus on heterochromatin gain, this work demonstrates large-scale unraveling of peri/centromeric satellites, which occurs in all models of human and mouse senescence examined. This was not seen in cancer cells, except in a benign senescent tumor in vivo. Senescence-associated distension of satellites (SADS) occurs earlier and more consistently than heterochromatin foci formation, and SADS is not exclusive to either the p16 or p21 pathways. Because Hutchinson Guilford progeria syndrome patient cells do not form excess heterochromatin, the question remained whether or not proliferative arrest in this aging syndrome involved distinct epigenetic mechanisms. Here, we show that SADS provides a unifying event in both progeria and normal senescence. Additionally, SADS represents a novel, cytological-scale unfolding of chromatin, which is not concomitant with change to several canonical histone marks nor a result of DNA hypomethylation. Rather, SADS is likely mediated by changes to higher-order nuclear structural proteins, such as LaminB1.

Defining the roots of cementum formation

Significant progress has been seen in research aimed at regeneration of the disease-damaged periodontium. Our own strategy has been to approach periodontal tissue development (i.e. root, cementum, periodontal ligament, and bone) as a source for the identification of key regulators of cellular processes that may be applicable to periodontal tissue repair. Specifically, enamel-like molecules, bone morphogenetic proteins (BMPs), and phosphates have been investigated for their role in altering gene expression and cell functions in follicle cells, periodontal ligament cells, and cementoblasts. Amelogenin, leucine-rich amelogenin peptide, and tyrosine-rich amelogenin peptide have been found to similarly affect cementoblast gene expression and cementoblast-mediated mineralization in vitro; however, these enamel-like factors do not increase cell proliferation as has been observed in cells treated with Emdogain (Biora AB, Malmö, Sweden), an enamel matrix derivative. BMP-2 has been found to promote differentiation of follicle cells into a cementoblast/osteoblast phenotype, and BMP-3 is being investigated as a negative regulator of mineralization. The increased ratio of phosphate to pyrophosphate in the local region during root development has been found to significantly enhance the extent of cementum formation in animal models. Furthermore, phosphate has been identified as a regulator of cementoblast SIBLING (small integrin-binding ligand N-linked glycoprotein) gene expression in vitro. These investigations of candidate factors for periodontal regeneration have uncovered mechanisms regulating gene expression and cell function in cells controlling the behavior of periodontal tissues (i.e. follicle cells, periodontal cells, and cementoblasts) and offer new directions to consider for clinical repair of periodontal defects.

Regulation of cementoblast gene expression by inorganic phosphate in vitro

Examination of mutant and knockout phenotypes with altered phosphate/pyrophosphate distribution has demonstrated that cementum, the mineralized tissue that sheathes the tooth root, is very sensitive to local levels of phosphate and pyrophosphate. The aim of this study was to examine the potential regulation of cementoblast cell behavior by inorganic phosphate (P(i)). Immortalized murine cementoblasts were treated with P(i) in vitro, and effects on gene expression (by quantitative real-time reverse-transcriptase polymerase chain reaction [RT-PCR]) and cell proliferation (by hemacytometer count) were observed. Dose-response (0.1-10 mM) and time-course (1-48 hours) assays were performed, as well as studies including the Na-P(i) uptake inhibitor phosphonoformic acid. Real-time RT-PCR indicated regulation by phosphate of several genes associated with differentiation/mineralization. A dose of 5 mM P(i) upregulated genes including the SIBLING family genes osteopontin (Opn, >300% of control) and dentin matrix protein-1 (Dmp-1, >3,000% of control). Another SIBLING family member, bone sialoprotein (Bsp), was downregulated, as were osteocalcin (Ocn) and type I collagen (Col1). Time-course experiments indicated that these genes responded within 6-24 hours. Time-course experiments also indicated rapid regulation (by 6 hours) of genes concerned with phosphate/pyrophosphate homeostasis, including the mouse progressive ankylosis gene (Ank), plasma cell membrane glycoprotein-1 (Pc-1), tissue nonspecific alkaline phosphatase (Tnap), and the Pit1 Na-P(i) cotransporter. Phosphate effects on cementoblasts were further shown to be uptake-dependent and proliferation-independent. These data suggest regulation by phosphate of multiple genes in cementoblasts in vitro. During formation, phosphate and pyrophosphate may be important regulators of cementoblast functions including maturation and regulation of matrix mineralization.

Characterization of calcitonin- and adrenocorticotropin-producing human cloned cell lines

We have developed three human cloned cell lines that produce immunoreactive human calcitonin (ihCT) and ACTH (iACTH) as well as exhibit characteristics of cultured neural cells. Clones HMS-41/I, -78/2, and -98/2 were developed from cell lines HeLa AV3, MBA 9812 (bronchogenic carcinoma), and SW 267 (pheochromocytoma), respectively. Karyological analysis of both the parent and the cloned cell lines confirmed the identity of HeLa AV3 and MBA 9812. When grown in serum-free media designed for culturing neural cells, the patterns of production for both ihCT and iACTH varied among the clones. The multiple patterns of hormone production suggest that the mechanisms involved in the biosynthesis, processing, and secretion of these hormones differ among the clones. The clones contain neuron-specific enolase and the putative neurotransmitters beta-alanine and gamma-amino butyric acid, and they respond to cAMP analogs by differentiating, as noted by the extension of neurites (except the HeLa-derived HMS-41/I). The iACTH extracted from cells and synthetic ACTH exhibited equivalent profiles upon isoelectric focusing. The forms of ihCT noted in cell extracts were similar to those observed in extracts of human tumor tissue. Our rabbit antiserum to hCT failed to detect ihCT in those cell extracts prepared for ACTH determination or in extracts of rat pituitaries, but it did detect CT in rat thyroids by both RIA and immunofluorescent procedures. We concluded that our antisera to hCT do not detect the precursor form of ACTH. The availability of these cloned cell lines provides model systems for examining the production of these peptide hormones and the concomitant expression of neural and endocrine characteristics.

Use of the API 20E system to identify non-Enterobacteriaceae from veterinary medical sources

The capability of the API 20E system to identify gram-negative nonfermenters and nonenteric fermenters was evaluated for 272 isolates from veterinary sources. Two different methods were used for interpreting the carbohydrate fermentation reactions on the strip. In method I, weakly fermented (yellow-green) carbohydrates were considered positive for all oxidase-positive organisms, and in method II, yellow-green carbohydrates were considered positive for all organisms requiring incubation for 48 hours. By both methods, the API system correctly identified 62% of the isolates. With method I, 31% of the isolates were misidentified and 6% were not identified. With method II, 21% of the isolates were misidentified and 17% received no identification. Organisms most affected by these 2 methods of interpretation were Pasteurella and Actinobacillus. Identifications reached by the API system were also compared with identifications made by veterinary diagnostic laboratories. The frequency of identifications agreements was not significantly affected by the method of API carbohydrate fermentation reaction interpretation. Generally, 30% of the identifications agreed (diagnostic laboratories vs API) when using only the API Index, whereas 51% agreed when the entire API computer data base identifications were included. The type of identification disagreements between diagnostic laboratories and the API system, however, was significantly affected by the method of API strip interpretation. With method I, 42% of the identifications were different and 6% were not in the API data base. With method II, 33% of the identifications were different and 17% were not in the API data base. Biotype differences between human and veterinary isolates were also compared. Significant differences between the predicted and actual reactions were noted for Pseudomonas aeruginosa and Bordetella bronchiseptica; however, these differences did not affect their correct identification to the API Index. For Pasteurella multocida, most profile numbers were not listed in the API Index because of differences in the actual vs predicted oxidase and nitrate reduction reactions; however, they were correctly identified with the total computer data base.

Use of the API 20E system to identify veterinary Enterobacteriaceae

A total of 503 veterinary enteric bacterial pathogens obtained from state veterinary diagnostic laboratories were tested on API 20E strips to determine whether this rapid microidentification system could be utilized for veterinary clinical microbiology. The API 20E strip accurately identified 96% of the veterinary isolates and misidentified 3%. Identifications by the API system and the diagnostic laboratories were in agreement in 85% of the isolates, disagreement on 16% of the isolates, and 1% were not identified by the API strip. Differences in identification occurred primarily in distinguishing between Klebsiella and Enterobacter and between Enterobacter and Escherichia coli. These disagreements were most often due to incorrect identifications by the diagnostic laboratory rather than by the API system. Biotype differences between human and veterinary isolates were compared. Significant differences were noted in several biochemical reactions. The main differences observed for E. coli isolates were in ornithine decarboxylase production and melibiose fermentation. The largest differences for Salmonella occurred in arginine dihydrolase production, citrate utilization, and inositol fermentation, whereas for Klebsiella pneumoniae the main differences were noted in urease production and nitrate reduction. These biotype differences, however, did not affect the accurate identification of organisms on the API strip.

Genetic translocation in Staphylococcus aureus

A 5.2-kilobase pair transposon, Tn551, has been found in Staphylococcus aureus, a Gram-positive bacterium. Initially detected on plasmid pI258, it undergoes rec-independent transposition to multiple chromosomal and plasmid sites, sometimes causing insertional inactivation. Unlike most other transposons, Tn551 undergoes apparently precise excision as a rule. The initial observation of Tn551 transition involved UV inactivation of the carrier plasmid; this would appear to be a general means of detecting transposable elements.