Probes for INS

Purpose: As skeletal maturity is approached, long bone elongation draws to a close and the cartilaginous growth plate (GP) ossifies and fuses as bone bridges form. This is likely a pivotal moment for the appendicular skeleton, but our mechanistic appreciation of how this process is orchestrated is limited. We have been studying how chondrocytes integrate biological cues, such as growth factor signalling, and mechanical forces, and have investigated the mechanosensitivity of epiphyseal fusion and roles for putative mechanotransduction machinery, including the primary cilium, in these contexts. Here we asked whether primary cilia have a mechanotransduction role in the juvenile GP and adolescent epiphyseal fusion. Methods: We used an inducible aggrecan (ACAN) Cre mouse model, enabling temporal deletion of the core ciliary protein IFT88 in cartilage to investigate GP narrowing dynamics and closure from 4 - 10 weeks of age. Both control (Ift88fl/fl) and cKO (Ift88fl/fl;ACANCreERT2) were injected with tamoxifen (I.P.). Cre activity was validated using a ROSA26TdTomato reporter line. Animals were exposed to (i) sciatic and femoral double neurectomy (DN) to off-load the right hind limb (immobilised DN) whilst the left bears full weight (contralateral DN) at 8 weeks of age, or (ii) voluntary wheel exercise between 8 and 10 weeks of age. Joints were scanned by μCT before histomorphometric analyses of tibial GP using Safranin-O/fast green, TUNEL, Collagen type X (ColX) immunohistochemistry, Von Kossa and TRAP. Cryosections of mouse GPs were analysed by confocal microscopy to investigate primary cilia prevalence and RNA scope was used to identify molecular mechanisms in situ. Medians +/- 95% confidence intervals quoted throughout below, Two-way ANOVA statistical comparisons. Results: We have, for the first time, investigated the role of cilia beyond 4 weeks of age. μCT analysis showed GP length in wild-type mice reduces from ∼260 μm to 130 μm between 4 and 10 weeks of age. Deletion of IFT88 in juvenile mice at 4 or 6 weeks of age resulted in longer GPs in cKO mice at every timepoint compared with control mice (Fig. 1A, 1st and 2nd panel and 1B). Thus, two weeks after tamoxifen, cKO GP lengths were not statistically significantly different to controls at time of treatment, indicating inhibition of GP closure. Deleting IFT88 at 8 weeks of age also resulted in longer GPs (p< 0.0001, n=12 controls, n=23 cKO). Interestingly, some cKO mice exhibited extremely elongated GPs at the edges of the tibia, which appeared as large holes by μCT (Fig. 1A), whilst the centre of the GP appeared less affected. Histology confirmed longer GPs were predominantly characterised by increases in hypertrophic chondrocyte populations. The large, often bi-lateral “holes”, observed by μCT were largely filled with disorganised hypertrophic chondrocytes, as indicated by IHC labelling for ColX. Interestingly limb immobilisation, (DN), at 8 weeks of age, rescued the GP phenotype observed in IFT88 cKO mice (Fig. 1A, 2nd and 3rd panels, and 1C), whilst the contralateral, unoperated (increased load-bearing) limb exhibited bi-lateral failure of ossification, similar to that observed in IFT88 cKO mice. Compared with naïve controls, wheel-exercised mice also displayed elongated GP (p< 0.0001, n=12 controls, n=10 wheel exercised) (Fig. 1A, 4th panel, and 1C) at 10 weeks of age. These expanded GP were, again, most pronounced at the edges of the tibia, whilst the centre of the GP appeared less affected and again was largely filled with disorganised, differentiated, ColX positive hypertrophic chondrocytes. In both wheel exercised and IFT88 cKO mice, regions of failed ossification, but not middle regions, were associated with loss of osteoclast activity. Confocal imaging and analysis revealed a statistically significant (p< 0.001) decrease in cilia positive cells in wheel exercised mice (32.9%, n=5) compared with control (40.7%, n=4) and IFT88cKO mice (p< 0.0001, (23.4%, n=4) compared with controls (40.7% n=4) at 10 weeks of age. Ongoing experiments are investigating 3D spatial analysis of fusion mechanisms, and the status of ciliary Hh signalling (Gli1, by RNAscope) within GP from control, DN, exercised, and cKO mice to dissect the apparently negative, regulatory role IFT88 is plays in the mechanical regulation of epiphyseal fusion. Conclusions: We conclude that IFT88 unequivocally plays a role in GP closure, its removal resulting in failed ossification of the GP, without disruption to chondrocytic lineage differentiation. This phenomenon, observed in cKO animals, is mechanosensitive with limb immobilisation rescuing the phenotype, suggesting, paradoxically, that IFT88 is dampening a mechanically-induced signal in the GP. Wheel exercise also resulted in impaired ossification thus these data collectively unveil both the acute response of the adolescent mouse GP to exercise and, through Ift88 deletion (cKO), a novel mechanoregulatory mechanism orchestrated by ciliary IFT. The effects of altered mechanics and mechanotransduction are most pronounced in the hypertrophic zone where cells are apparently trapped short of transdifferentiation. Osteoclast recruitment and/or activity is impaired, and bone formation inhibited. These Results may have implications for our understanding of hypertrophic chondrocyte biology in articular cartilage in OA. Moreover, it has been proposed that changes to mechanical inputs during adolescence and associated cam morphology contribute to hip OA development. In adolescent patient cohorts, high levels of exercise lead to cartilaginous hypertrophy, epiphyseal extension, cam development, and reduced rates of GP closure. Femoral and tibial epiphyseal extension has also been observed in adolescent athletes that sustain repetitive trauma through high intensity exercise. This research is crucial to a holistic understanding of skeletal mechano-biological health, and the effects of exercise, on the maturing appendicular skeleton

Objectives: Up to 20% and 15% of critically ill influenza and coronavirus disease 2019 (COVID-19) patients are affected by influenza- and COVID-19-associated pulmonary aspergillosis (IAPA and CAPA) respectively. These viral-fungal coinfections are difficult to diagnose and are associated with increased mortality. Mechanistic insights into the development of IAPA and CAPA are a prerequisite for the development of new biomarkers and novel immunomodulatory therapeutic targets. However, data on the pathophysiology are scarce. With this study, we aimed at expanding our knowledge of IAPA and CAPA pathophysiology in an explorative way, resorting to lower respiratory tract samples and focusing on the epithelial and myeloid innate immunity components of the antifungal host response. Methods: We performed nCounter gene expression analyses of 755 genes linked to innate immunity, and determined protein levels of 47 cytokines, chemokines, growth factors, and other inflammatory mediators on bronchoalveolar lavage (BAL) fluid samples from 166 ICU-admitted influenza and COVID-19-patients with or without aspergillosis. Additionally, we performed spatial transcriptomics and RNAscope on in vivo tracheobronchial biopsies from four IAPA and CAPA patients. Results: Several genes encoding proteins with important effector functions in antifungal immunity are downregulated in BAL fluid of IAPA and CAPA patients compared with influenza-only or COVID-19-only patients. Cellular deconvolution of the gene expression data reveals a significantly lower BAL neutrophil fraction in CAPA patients compared to COVID-19-only patients. IAPA and CAPA patients have high BAL fluid levels of pro-inflammatory cytokines, but these are not significantly different from the levels seen in influenza-only and COVID-19-only patients. By integrating the BAL fluid cytokine levels with their respective transcriptional responses, we show that IAPA patients, and to a lesser extent CAPA patients, have an aberrant transcriptional response to pro-inflammatory cytokines as well as type I and type II interferons, which may result in poor cellular effector functions (Fig. 1a). Interferon-gamma signaling is abrogated in both IAPA and CAPA patients when compared with influenza-only and COVID-19-only patients. We observe significantly higher levels of growth factors associated with lung fibrosis in both IAPA and CAPA BAL fluid, which may contribute to the higher mortality seen in these coinfections (Fig. 1b). Using spatial transcriptomics, we show that different epithelial defense mechanisms are at play in IAPA and CAPA (Fig. 2a). Finally, using RNAscope ultrasensitive single-molecule RNA in situ hybridization, we visualize fungal and viral colocalization in CAPA tracheobronchial tissue, proving that virus-induced epithelial barrier disruption paves the way for tissueinvasive aspergillosis (Fig. 2b). Conclusion: Using state-of-the-art techniques in lower respiratory tract samples obtained from a large representative patient cohort, we provide arguments for a three-level breach in antifungal immunity in IAPA and CAPA. A hampered ability to phagocytize and kill fungal spores enables Aspergillus germination and growth, leading to hyphae that are not contained because of restrained extracellular defense mechanisms. These hyphae may easily become tissue-invasive through an epithelium that is weakened by the viral infection, causing detrimental damage to the respiratory system. Functional studies will be necessary to further unravel the pathophysiology of IAPA and CAPA.

Introduction: Four randomized controlled trials studying fecal microbiota transplantation (FMT) in active ulcerative colitis (UC) patients showed variable success rates. The efficacy of FMT appears to be influenced by various factors including donor- and procedure-specific characteristics. Aim: We hypothesized that the outcome of FMT in patients with active UC could be improved by donor preselection on microbiota level, by using a strict anaerobic approach, and by repeated FMT administration. Methods: The RESTORE-UC trial (NCT03110289) was a national, multi-centric double-blind, sham-controlled randomized trial. Active UC patients (Total Mayo score 4-10 with endoscopic sub-score > or = 2) were randomly allocated (1:1) to receive 4 anaerobic-prepared superdonor (S) FMT or autologous (A) FMT by permutated blocks (2- 4) and stratified for weight, concomitant steroid use, and therapy refractoriness. S-FMTs were selected after a rigorous screening excluding samples with Bacteroides 2 enterotype, high abundances of Fusobacterium, Escherichia coli and Veillonella and the lowest microbial loads (Q1). A futility analysis after 66% (n=72) of inclusions was planned per protocol including a modified intention-to-treat (mITT) analysis using non-responder imputation (NRI) for patients receiving at least one FMT. The primary endpoint was steroid-free clinical remission (Total Mayo ≤ 2, with no subscore >1) at week 8. Secondary outcomes included steroid-free PRO-2 remission (Combined Mayo subscores of ≤1 for rectal bleeding plus stool frequency) and response (≥3 points or/and ≥50% reduction from baseline in combined Mayo subscores for rectal bleeding plus stool frequency) and steroid-free endoscopic remission (Mayo endoscopic subscore ≤1) and response (Mayo endoscopy subscore ≤1 and ≥1 point reduction from baseline). Results: Between March 2017-2021, 72 patients signed the ICF and 66 were randomly allocated to S-FMT (n=30) or A-FMT (N=36) and received at least one FMT. Both study arms were matched for baseline characteristics, yet a trend (p= 0,07) towards higher concomitant biological use in the S-FMT arm was observed. A remarkably high proportion of patients were previously exposed to biologicals (58.3% and 60.0% for the A-FMT and S-FMT group respectively). In the S-FMT and the A-FMT respectively 4 and 5 patients terminated the trial early due to worsening of colitis (4 in both arms) or FMT enema intolerance (1 A-FMT). They were included in the mITT analysis using NRI, showing after 66% of intended inclusions, the primary endpoint was reached in 3/30 (mITT with NRI 10.0%) S-FMT and 5/31 (13.9%) patients randomized to A-FMT (p=0.72). As the predefined minimum difference of 5% between both treatment arms was not attained, the study was stopped due to futility. Steroid-free PRO-2 remission was achieved in 7/30 (23,3%) patients on S-FMT and 10/36 (27,8%) on A-FMT (p= 0,78). Steroid-free PRO-2 response was attained by respectively 9/30 (30,0%) patients in the S-FMT arm and 12/36 (33,3%) patients in the A-FMT arm (p= 0,80). Steroid-free endoscopic response and remission were noted in 5/30 (16,7%) assigned to the S-FMT arm compared with 7/36 (19,4%) allocated to the A-FMT arm (p= 1.0). Of note, no patients on concomitant biologicals reached the primary endpoint, and there were 2 serious adverse events in the A-FMT arm: dysuria requiring hospitalization and worsening of UC requiring colectomy. Conclusions: In this double-blind sham-controlled trial comparing repeated administrations of anaerobic-prepared S-FMT with A-FMT in patients with active UC, no significant difference in steroid-free remission rates at week 8 were observed. The FMT procedure was generally well tolerated, and no new safety signals were observed.

Introduction: Four randomized controlled trials studying fecal microbiota transplantation (FMT) in active ulcerative colitis (UC) patients showed variable success rates. The efficacy of FMT appears to be influenced by various factors including donor- and procedure-specific characteristics. Aim: We hypothesized that the outcome of FMT in patients with active UC could be improved by donor preselection on microbiota level, by using a strict anaerobic approach, and by repeated FMT administration. Methods: The RESTORE-UC trial (NCT03110289) was a national, multi-centric double-blind, sham-controlled randomized trial. Active UC patients (Total Mayo score 4-10 with endoscopic sub-score > or = 2) were randomly allocated (1:1) to receive 4 anaerobic-prepared superdonor (S) FMT or autologous (A) FMT by permutated blocks (2- 4) and stratified for weight, concomitant steroid use, and therapy refractoriness. S-FMTs were selected after a rigorous screening excluding samples with Bacteroides 2 enterotype, high abundances of Fusobacterium, Escherichia coli and Veillonella and the lowest microbial loads (Q1). A futility analysis after 66% (n=72) of inclusions was planned per protocol including a modified intention-to-treat (mITT) analysis using non-responder imputation (NRI) for patients receiving at least one FMT. The primary endpoint was steroid-free clinical remission (Total Mayo ≤ 2, with no subscore >1) at week 8. Secondary outcomes included steroid-free PRO-2 remission (Combined Mayo subscores of ≤1 for rectal bleeding plus stool frequency) and response (≥3 points or/and ≥50% reduction from baseline in combined Mayo subscores for rectal bleeding plus stool frequency) and steroid-free endoscopic remission (Mayo endoscopic subscore ≤1) and response (Mayo endoscopy subscore ≤1 and ≥1 point reduction from baseline). Results: Between March 2017-2021, 72 patients signed the ICF and 66 were randomly allocated to S-FMT (n=30) or A-FMT (N=36) and received at least one FMT. Both study arms were matched for baseline characteristics, yet a trend (p= 0,07) towards higher concomitant biological use in the S-FMT arm was observed. A remarkably high proportion of patients were previously exposed to biologicals (58.3% and 60.0% for the A-FMT and S-FMT group respectively). In the S-FMT and the A-FMT respectively 4 and 5 patients terminated the trial early due to worsening of colitis (4 in both arms) or FMT enema intolerance (1 A-FMT). They were included in the mITT analysis using NRI, showing after 66% of intended inclusions, the primary endpoint was reached in 3/30 (mITT with NRI 10.0%) S-FMT and 5/31 (13.9%) patients randomized to A-FMT (p=0.72). As the predefined minimum difference of 5% between both treatment arms was not attained, the study was stopped due to futility. Steroid-free PRO-2 remission was achieved in 7/30 (23,3%) patients on S-FMT and 10/36 (27,8%) on A-FMT (p= 0,78). Steroid-free PRO-2 response was attained by respectively 9/30 (30,0%) patients in the S-FMT arm and 12/36 (33,3%) patients in the A-FMT arm (p= 0,80). Steroid-free endoscopic response and remission were noted in 5/30 (16,7%) assigned to the S-FMT arm compared with 7/36 (19,4%) allocated to the A-FMT arm (p= 1.0). Of note, no patients on concomitant biologicals reached the primary endpoint, and there were 2 serious adverse events in the A-FMT arm: dysuria requiring hospitalization and worsening of UC requiring colectomy. Conclusions: In this double-blind sham-controlled trial comparing repeated administrations of anaerobic-prepared S-FMT with A-FMT in patients with active UC, no significant difference in steroid-free remission rates at week 8 were observed. The FMT procedure was generally well tolerated, and no new safety signals were observed.

Background: Mucus buildup in multiple mucin-producing organs, including the lungs and the intestine, is the hallmark of CF. In the gastrointestinal (GI) tract, aberrant mucus properties may play a critical role in bowel obstruction, inflammation, and bacterial overgrowth, as well as reduced nutrient absorption. Interestingly, all animal models of CF (e.g., mice, rats, ferrets, pigs) experience gastrointestinal complications, with poor growth and intestinal obstruction, as a result of excessive mucus accumulation. However, the precise biochemical change(s) within the CF gut mucus is still undetermined. Disrupted transepithelial Cl− and HCO3 − secretions due to CFTR malfunction affect the viscoelastic properties of airway mucus and may affect gut mucus similarly. Using WT and F508delCftr (CF) mice, we explored how interactions between Cftr and Muc2, the dominant GI mucin, resulted in the intestinal obstructive phenotype observed in CF mice. Methods: CF mice were weaned from laxative for 48 h prior to experiments. Intestinal sections (duodenum, jejunum, ileum, and colon) from WT and F508del-cftr CF mice were analyzed using H&E and AB-PAS staining to examine tissue structure, cell morphology, and mucus accumulation. RNAScope and qRT-PCR were used to determine Muc2 and Cftr mRNA expression along the proximal-to-distal and crypt-villus axes of the murine gut. IHC was used to determine the mucin compositions of gut sections, and fluorescent in-situ hybridization (FISH) was used to observe bacterial penetration of the mucus layer in the mouse intestine. Comparing WT and CF mice, we measured % solids of the luminal content and relative changes in gut mucus concentration via Western blotting on intestinal lavages. Results: Gross pathology revealed that intestinal blockage frequently emerged from the distal ileum. In parallel, we demonstrated that Muc2 expression increased from proximal to distal, while Cftr expression remained uniform throughout the GI tract of WT animals. However, Cftr expression changed gradually along the crypt-villus axis, with a homogenous signal distribution in the duodenum that progressively concentrated to the crypts in the ileum. FISH confirmed that a layer of mucus devoid of bacteria protected the WT murine epithelium from pathogen invasion. Histological and IHC examinations of obstructed ileal regions revealed that distal regions of intestinal plugs were mainly composed of mucus and inflammatory cells, while more proximal regions of the blockages were contaminated by feces and other luminal debris. Luminal content % solids was significantly increased in the CF (32.7%) compared to the WT ileum (22.3%), with concentrations approaching that of the WT colon (37.3%). Western blot analysis of intestinal lavages revealed that highmolecular-weight Muc2 was more concentrated (fold increase ∼2) in the small intestine of CF compared to WT mice. Conclusion: In CF mice, elevated mucus concentrations are caused by the combination of high Muc2 expression and lack of fluid secretion due to defective Cftr protein in the distal ileum, which creates optimal conditions for bowel obstruction in this particular region. Unlike the colon, the ileum is not adapted to high friction and is prone to villi sloughing, further exacerbating the gut phenotype in CF animals.

The intergeniculate leaflet and ventral lateral geniculate nucleus (IGL/VLG) of the rodent thalamus process various signals and participate in circadian entrainment In both structures, cells exhibiting infra-slow oscillatory activity as well as non-rhythmically firing neurons can be observed Here, we reveal that only one of these two groups of cells responds to anorexigenic (CCK, GLP-1 and OXM) and orexigenic (Ghrl and OXA) peptides. Neuronal responses vary depending on the time of day (day vs. night) and on the diet (standard vs. high-fat diet) Additionally, we visualized receptors to the tested peptides in the IGL/VLG using in situ hybridisation Our results suggest that two electrophysiologically different subpopulations of IGL/VLG neurons are involved in two separate functions: the one related to body's energy homeostasis and the one associated with the subcortical visual system ABSTRACT: The intergeniculate leaflet and ventral lateral geniculate nucleus (IGL/VLG) are subcortical structures involved in entrainment of the brain's circadian system to photic and non-photic (e.g. metabolic and arousal) cues. Both receive information about environmental light from photoreceptors, exhibit an infra-slow oscillations (ISO) in vivo, and connect to the master circadian clock. Although current evidence demonstrates that the IGL/VLG communicate metabolic information and are crucial for entrainment of circadian rhythms to time-restricted feeding, their sensitivity to food-intake-related peptides has not been investigated yet. We examined the effect of metabolically relevant peptides on the spontaneous activity of IGL/VLG neurons. Using ex vivo and in vivo electrophysiological recordings as well as in situ hybridisation, we tested potential sensitivity of the IGL/VLG to anorexigenic and orexigenic peptides, such as cholecystokinin, glucagon-like peptide 1, oxyntomodulin, peptide YY, orexin A, and ghrelin. We explored neuronal responses to these drugs during day and night, and in standard vs. high-fat diet conditions. We found that IGL/VLG neurons response to all the substances tested, except peptide YY. Moreover, more neurons responded to anorexigenic drugs at night, while a high-fat diet affected the IGL/VLG sensitivity to orexigenic peptides. Interestingly, ISO neurons responded to light and orexin A, but did not respond to the other food-intake-related peptides.. In contrast, non-ISO cells were activated by metabolic peptides, with only some being responsive to light. Our results show for the first time that peptides involved in the body's energy homeostasis stimulate the thalamus and suggest functional separation of the IGL/VLG cells. Abstract figure legend (1) Sprague Dawley rats were fed ad libitum with control (CD) or a high-fat (HFD) chow in a 12:12 h light-dark cycle. (2) The subject of the study was a thalamic intergeniculate leaflet (IGL) and ventral lateral geniculate nucleus (VLG) showing spontaneous infra-slow oscillatory (ISO) or nonâ¿¿oscillatory (nonâ¿¿ISO) activity. (3) Neuronal activity of the IGL and VLG was recorded using ex vivo and in vivo electrophysiological techniques. (4) Anorexigenic (in green) and orexigenic (in red) peptides such as cholecystokinin (CCK), glucagon-like peptide 1 (GLPâ¿¿1), oxyntomodulin (OXM), peptide YY (pYY), orexin A (OXA) and ghrelin (Ghrl) were administered during IGL/VLG recordings. (5) We found that non-ISO neurons of the IGL/VLG responded with an increase in firing rate to all the substances tested, except peptide YY. The amplitude (marked with arrows) and frequency of responses (marked with <, >) varied depending on the diet and the phase of the day. (6) In situ hybridization was performed on IGL/VLGâ¿¿containing brain sections to visualise receptors to the tested peptides. This article is protected by

First Person is a series of interviews with the first authors of a selection of papers published in Disease Models & Mechanisms, helping researchers promote themselves alongside their papers. Xuming Zhu is first author on ‘ FZD2 regulates limb development by mediating β-catenin-dependent and -independent Wnt signaling pathways’, published in DMM. Xuming is an instructor in the lab of Sarah E. Millar at Icahn School of Medicine at Mount Sinai, New York, NY, USA, investigating the molecular mechanisms that underlie the development of appendages, epithelial homeostasis and diseases.

Mike May, is a freelance writer and editor with more than 30 years of experience. He earned an MS in biological engineering from the University of Connecticut and a PhD in neurobiology and behavior from Cornell University. He worked as an associate editor at American Scientist, and he is the author of more than 1,000 articles for clients that include GEN, Nature, Science, Scientific American and many others. In addition, he served as the editorial director of many publications, including several Nature Outlooks and Scientific American Worldview.

Models of heart disease and drug responses are increasingly based on human pluripotent stem cells (hPSCs) since their ability to capture human heart (dys-)function is often better than animal models. Simple monolayer cultures of hPSC-derived cardiomyocytes, however, have shortcomings. Some of these can be overcome using more complex, multi cell-type models in 3D. Here we review modalities that address this, describe efforts to tailor readouts and sensors for monitoring tissue- and cell physiology (exogenously and in situ) and discuss perspectives for implementation in industry and academia.

The widespread Coronavirus Disease 2019 (COVID-19) is caused by infection with the novel coronavirus SARS-CoV-2. Currently, we have a limited toolset available for visualizing SARS-CoV-2 in cells and tissues, particularly in tissues from patients who died from COVID-19. Generally, single-molecule RNA FISH techniques have shown mixed results in formalin fixed paraffin embedded tissues such as those preserved from human autopsies. Here, we present a platform for preparing autopsy tissue for visualizing SARS-CoV-2 RNA using RNA FISH with amplification by hybridization chain reaction (HCR). We developed probe sets that target different regions of SARS-CoV-2 (including ORF1a and N) as well as probe sets that specifically target SARS-CoV-2 subgenomic mRNAs. We validated these probe sets in cell culture and tissues (lung, lymph node, and placenta) from infected patients. Using this technology, we observe distinct subcellular localization patterns of the ORF1a and N regions, with the ORF1a concentrated around the nucleus and the N showing a diffuse distribution across the cytoplasm. In human lung tissue, we performed multiplexed RNA FISH HCR for SARS-CoV-2 and cell-type specific marker genes. We found viral RNA in cells containing the alveolar type 2 (AT2) cell marker gene ( SFTPC ) and the alveolar macrophage marker gene ( MARCO ), but did not identify viral RNA in cells containing the alveolar type 1 (AT1) cell marker gene ( AGER ). Moreover, we observed distinct subcellular localization patterns of viral RNA in AT2 cells and alveolar macrophages, consistent with phagocytosis of infected cells. In sum, we demonstrate the use of RNA FISH HCR for visualizing different RNA species from SARS-CoV-2 in cell lines and FFPE autopsy specimens. Furthermore, we multiplex this assay with probes for cellular genes to determine what cell-types are infected within the lung. We anticipate that this platform could be broadly useful for studying SARS-CoV-2 pathology in tissues as well as extended for other applications including investigating the viral life cycle, viral diagnostics, and drug screening.

Kidney failure is common in patients with Coronavirus Disease-19 (COVID-19) resulting in increased morbidity and mortality. In an international collaboration, 284 kidney biopsies were evaluated to improve understanding of kidney disease in COVID-19. Diagnoses were compared to five years of 63,575 native biopsies prior to the pandemic and 13,955 allograft biopsies to identify diseases increased in patients with COVID-19. Genotyping for APOL1 G1 and G2 alleles was performed in 107 African American and Hispanic patients. Immunohistochemistry for SARS-CoV-2 was utilized to assess direct viral infection in 273 cases along with clinical information at the time of biopsy. The leading indication for native biopsy was acute kidney injury (45.4%), followed by proteinuria with or without concurrent acute kidney injury (42.6%). There were more African American patients (44.6%) than patients of other ethnicities. The most common diagnosis in native biopsies was collapsing glomerulopathy (25.8%) which associated with high-risk APOL1 genotypes in 91.7% of cases. Compared to the five-year biopsy database, the frequency of myoglobin cast nephropathy and proliferative glomerulonephritis with monoclonal IgG deposits was also increased in patients with COVID-19 (3.3% and 1.7%, respectively), while there was a reduced frequency of chronic conditions (including diabetes mellitus, IgA nephropathy, and arterionephrosclerosis) as the primary diagnosis. In transplants, the leading indication was acute kidney injury (86.4%), for which rejection was the predominant diagnosis (61.4%). Direct SARS-CoV-2 viral infection was not identified. Thus, our multi-center large case series identified kidney diseases that disproportionately affect patients with COVID-19, demonstrated a high frequency of APOL1 high-risk genotypes within this group, with no evidence of direct viral infection within the kidney.