SIRT6 loss causes intervertebral disc degeneration in mice by promoting senescence and SASP status.

Intervertebral disc degeneration is a major risk factor contributing to chronic low back and neck pain. While the etiological factors for disc degeneration vary, age is still one of the most important risk factors. Recent studies have shown the promising role of SIRT6 in mammalian aging and skeletal tissue health, however its role in the intervertebral disc health remains unexplored. We investigated the contribution of SIRT6 to disc health by studying the age-dependent spinal phenotype of mice with conditional deletion of Sirt6 in the disc (Acan CreERT2 ; Sirt6 fl/fl ). Histological studies showed a degenerative phenotype in knockout mice compared to Sirt6 fl/fl control mice at 12 months which became pronounced at 24 months. RNA-Seq analysis of NP and AF tissues, quantitative histone analysis, and in vitro multiomics employing RNA-seq with ATAC-seq revealed that SIRT6-loss resulted in changes in acetylation and methylation status of specific Histone 3 lysine residues, thereby affecting DNA accessibility and transcriptomic landscape. A decrease in autophagy and an increase in DNA damage were also noted in Sirt6-deficient cells. Further mechanistic insights revealed that loss of SIRT6 increased senescence and SASP burden in the disc characterized by increased p21, γH2AX, IL-6, and TGF-ß abundance. Taken together our study highlights the contribution of SIRT6 in modulating DNA damage, autophagy and cell senescence, and its importance in maintaining disc health during aging thereby underscoring it as a potential therapeutic target to treat intervertebral disc degeneration.

Polymorph driven diversification of photosalient responses in a zinc(II) coordination complex.

A novel crystallographic form of a Zn(II) coordination complex [Zn(4-ohbz)2(4-nvp)2] (1-Form-III) (H4-ohbz = 4-hydroxybenzoic acid and 4-nvp = (E)-4-(1-naphthylvinyl)pyridine), undergoes a solid-state photochemical [2+2] cycloaddition reaction accompanied by a moderate photosalient effect, whereby single-crystals show cracking and splitting. This UV-induced cycloaddition accompanies a single-crystal to single-crystal transformation, allowing for continuous monitoring of the unit cell parameters. The new polymorph represents an intermediate form of the two previously reported crystallographic forms of [Zn(4-ohbz)2(4-nvp)2], and provides novel insight into moderating the magnitude of photosalient responses across polymorphic materials.

Space Flight Enhances Stress Pathways in Human Neural Stem Cells.

Mammalian cells have evolved to function under Earth's gravity, but how they respond to microgravity remains largely unknown. Neural stem cells (NSCs) are essential for the maintenance of central nervous system (CNS) functions during development and the regeneration of all CNS cell populations. Here, we examined the behavior of space (SPC)-flown NSCs as they readapted to Earth's gravity. We found that most of these cells survived the space flight and self-renewed. Yet, some showed enhanced stress responses as well as autophagy-like behavior. To ascertain if the secretome from SPC-flown NSCs contained molecules inducing these responses, we incubated naïve, non-starved NSCs in a medium containing SPC-NSC secretome. We found a four-fold increase in stress responses. Proteomic analysis of the secretome revealed that the protein of the highest content produced by SPC-NSCs was secreted protein acidic and rich in cysteine (SPARC), which induces endoplasmic reticulum (ER) stress, resulting in the cell's demise. These results offer novel knowledge on the response of neural cells, particularly NSCs, subjected to space microgravity. Moreover, some secreted proteins have been identified as microgravity sensing, paving a new venue for future research aiming at targeting the SPARC metabolism. Although we did not establish a direct relationship between microgravity-induced stress and SPARC as a potential marker, these results represent the first step in the identification of gravity sensing molecules as targets to be modulated and to design effective countermeasures to mitigate intracranial hypertension in astronauts using structure-based protein design.

Ohio School Nurses´ Perceptions of School Absences for Dental Care.

Purpose: To evaluate the knowledge, practices and attitudes of Ohio school nurses regarding school absenteeism (SA) for dental treatment. Methods: A 40-item questionnaire was generated and distributed to 246 attendees at an annual conference for Ohio school nurses in December 2019. Results: The response rate was 65.9 percent (n=162 out of 246 attendees) and 136 surveys were eligible for inclusion. The sample was female (100 percent), worked at public schools (86.0 percent, n=117) and trained as registered nurses (83.8 percent, n=114). Nurses reported no change in concerns over children missing school for dental appointments in the last five years (69.9 percent, n=95) and most agreed that SA for dental visits "almost never" negatively impacted the educational needs of children. The medical history of the patient was the most common factor when determining the duration of a school excuse (81.6 percent, n=111) and the potential for pain was the most common dental consideration (93.4 percent, n=127). Nurses reported that they "sometimes" had problems with a child after a dental visit (44.9 percent, n=61) and pain was the most reported problem (83.8 percent, n=114). Conclusion: Nurses did not feel that SA for dental treatment negatively impacted the educational needs of children.

Commensal myeloid crosstalk in neonatal skin regulates long-term cutaneous type 17 inflammation.

Early life microbe-immune interactions at barrier surfaces have lasting impacts on the trajectory towards health versus disease. Monocytes, macrophages and dendritic cells are primary sentinels in barrier tissues, yet the salient contributions of commensal-myeloid crosstalk during tissue development remain poorly understood. Here, we identify that commensal microbes facilitate accumulation of a population of monocytes in neonatal skin. Transient postnatal depletion of these monocytes resulted in heightened IL-17A production by skin T cells, which was particularly sustained among CD4+ T cells into adulthood and sufficient to exacerbate inflammatory skin pathologies. Neonatal skin monocytes were enriched in expression of negative regulators of the IL-1 pathway. Functional in vivo experiments confirmed a key role for excessive IL-1R1 signaling in T cells as contributing to the dysregulated type 17 response in neonatal monocyte-depleted mice. Thus, a commensal-driven wave of monocytes into neonatal skin critically facilitates long-term immune homeostasis in this prominent barrier tissue.

Correction: Tran et al. Delayed Maturation of Oligodendrocyte Progenitors by Microgravity: Implications for Multiple Sclerosis and Space Flight. Life 2022, 12, 797.

The authors wish to make the following corrections to Figure 10 of this paper [...].

Loss of function mutation in Ank causes aberrant mineralization and acquisition of osteoblast-like-phenotype by the cells of the intervertebral disc.

Pathological mineralization of intervertebral disc is debilitating and painful and linked to disc degeneration in a subset of human patients. An adenosine triphosphate efflux transporter, progressive ankylosis (ANK) is a regulator of extracellular inorganic pyrophosphate levels and plays an important role in tissue mineralization. However, the function of ANK in intervertebral disc has not been fully explored. Herein we analyzed the spinal phenotype of Ank mutant mice (ank/ank) with attenuated ANK function. Micro-computed tomography and histological analysis showed that loss of ANK function results in the aberrant annulus fibrosus mineralization and peripheral disc fusions with cranial to caudal progression in the spine. Vertebrae in ank mice exhibit elevated cortical bone mass and increased tissue non-specific alkaline phosphatase-positive endplate chondrocytes with decreased subchondral endplate porosity. The acellular dystrophic mineral inclusions in the annulus fibrosus were localized adjacent to apoptotic cells and cells that acquired osteoblast-like phenotype. Fourier transform infrared spectral imaging showed that the apatite mineral in the outer annulus fibrosus had similar chemical composition to that of vertebral bone. Transcriptomic analysis of annulus fibrosus and nucleus pulposus tissues showed changes in several biological themes with a prominent dysregulation of BMAL1/CLOCK circadian regulation. The present study provides new insights into the role of ANK in the disc tissue compartments and highlights the importance of local inorganic pyrophosphate metabolism in inhibiting the mineralization of this important connective tissue.

Long-term tolerance to skin commensals is established neonatally through a specialized dendritic cell subgroup.

Early-life establishment of tolerance to commensal bacteria at barrier surfaces carries enduring implications for immune health but remains poorly understood. Here, we showed that tolerance in skin was controlled by microbial interaction with a specialized subset of antigen-presenting cells. More particularly, CD301b+ type 2 conventional dendritic cells (DCs) in neonatal skin were specifically capable of uptake and presentation of commensal antigens for the generation of regulatory T (Treg) cells. CD301b+ DC2 were enriched for phagocytosis and maturation programs, while also expressing tolerogenic markers. In both human and murine skin, these signatures were reinforced by microbial uptake. In contrast to their adult counterparts or other early-life DC subsets, neonatal CD301b+ DC2 highly expressed the retinoic-acid-producing enzyme, RALDH2, the deletion of which limited commensal-specific Treg cell generation. Thus, synergistic interactions between bacteria and a specialized DC subset critically support early-life tolerance at the cutaneous interface.

High-Throughput Neutralization and Serology Assays Reveal Correlated but Highly Variable Humoral Immune Responses in a Large Population of Individuals Infected with SARS-CoV-2 in the US between March and August 2020.

The ability to measure neutralizing antibodies on large scale can be important for understanding features of the natural history and epidemiology of infection, as well as an aid in determining the efficacy of interventions, particularly in outbreaks such as the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Because of the assay's rapid scalability and high efficiency, serology measurements that quantify the presence rather than function of serum antibodies often serve as proxies of immune protection. Here, we report the development of a high-throughput, automated fluorescence-based neutralization assay using SARS-CoV-2 virus to quantify neutralizing antibody activity in patient specimens. We performed large-scale testing of over 19,000 COVID-19 convalescent plasma (CCP) samples from patients who had been infected with SARS-CoV-2 between March and August 2020 across the United States. The neutralization capacity of the samples was moderately correlated with serological measurements of anti-receptor-binding domain (RBD) IgG levels. The neutralizing antibody levels within these convalescent-phase serum samples were highly variable against the original USA-WA1/2020 strain with almost 10% of individuals who had had PCR-confirmed SARS-CoV-2 infection having no detectable antibodies either by serology or neutralization, and ~1/3 having no or low neutralizing activity. Discordance between neutralization and serology measurements was mainly due to the presence of non-IgG RBD isotypes. Meanwhile, natural infection with the earliest SARS-CoV-2 strain USA-WA1/2020 resulted in weaker neutralization of subsequent B.1.1.7 (alpha) and the B.1.351 (beta) variants, with 88% of samples having no activity against the BA.1 (omicron) variant. IMPORTANCE The ability to directly measure neutralizing antibodies on live SARS-CoV-2 virus in individuals can play an important role in understanding the efficacy of therapeutic interventions or vaccines. In contrast to functional neutralization assays, serological assays only quantify the presence of antibodies as a proxy of immune protection. Here, we have developed a high-throughput, automated neutralization assay for SARS-CoV-2 and measured the neutralizing activity of ~19,000 COVID-19 convalescent plasma (CCP) samples collected across the United States between March and August of 2020. These data were used to support the FDA's interpretation of CCP efficacy in patients with SARS-CoV-2 infection and their issuance of emergency use authorization of CCP in 2020.

Oligodendrocyte Progenitors Display Enhanced Proliferation and Autophagy after Space Flight.

Intracranial hypertension (ICP) and visual impairment intracranial pressure (VIIP) are some of the consequences of long-term space missions. Here we examined the behavior of oligodendrocyte progenitors (OLPs) after space flight using time-lapse microscopy. We show that most OLPs divided more than ground control (GC) counterparts did. Nonetheless, a subpopulation of OLPs flown to space presented a significant increase in autophagic cell death. Examination of the proteomic profile of the secretome of space flown OLPs (SPC-OLPs) revealed that the stress protein heat shock protein-90 beta "HSP-90ß" was the 5th most enriched (6.8 times) and the secreted protein acidic and rich in cysteine "SPARC" was the 7th most enriched (5.2 times), with respect to ground control cells. SPARC induces endoplasmic reticulum stress, which leads to autophagy. Given the roles and importance of these two proteins in mammalian cells' metabolism, their upregulation may hold the key to modulating cell proliferation and autophagy, in order to mitigate ICP and VIIP during and after space missions.

FLG Deficiency in Mice Alters the Early-Life CD4+ T-Cell Response to Skin Commensal Bacteria.

FLG variants underlie ichthyosis vulgaris and increased risk of atopic dermatitis, conditions typified by disruption of the skin microbiome and cutaneous immune response. Yet, it remains unclear whether neonatal skin barrier compromise because of FLG deficiency alters the quality of commensal-specific T cells and the functional impact of such responses. To address these questions, we profiled changes in the skin barrier and early cutaneous immune response of neonatal C57BL/6 Flg‒/‒ and wild-type mice using single-cell RNA sequencing, flow cytometry, and other modalities. Flg‒/‒ neonates showed little alteration in transepidermal water loss or lipid- or corneocyte-related gene expression. However, they showed increases in barrier disruption genes, epidermal dye penetration, and numbers of skin CD4+ T cells. Using an engineered strain of Staphylococcus epidermidis (S. epidermidis 2W) to study the response to neonatal skin colonization, we found that commensal-specific CD4+ T cells were skewed in Flg‒/‒ pups toward effector rather than regulatory T cells. This altered response persisted into adulthood, where it was typified by T helper 17 (Th17) cells and associated with increased susceptibility to imiquimod-induced skin inflammation. Thus, subtle but impactful differences in neonatal barrier function in Flg‒/‒ mice are accompanied by a skewed commensal-specific CD4+ response, with enduring consequences for skin immune homeostasis.

Barriers and facilitators to exclusive breastfeeding among Black mothers: A qualitative study utilizing a modified Barrier Analysis approach.

Breastfeeding has health benefits for both infants and mothers, yet Black mothers and infants are less likely to receive these benefits. Despite research showing no difference in breastfeeding intentions by race or ethnicity, inequities in breastfeeding rates persist, suggesting that Black mothers face unique barriers to meeting their breastfeeding intentions. The aim of this study is to identify barriers and facilitators that Black women perceive as important determinants of exclusively breastfeeding their children for at least 3 months after birth. Utilizing a Barrier Analysis approach, we conducted six focus group discussions, hearing from Black mothers who exclusively breastfed for 3 months and those who did not. Transcripts were coded starting with a priori parent codes based on theory-derived determinants mapped onto the Socioecological Model; themes were analysed for differences between groups. Facilitators found to be important specifically for women who exclusively breastfed for 3 months include self-efficacy, lactation support, appropriate lactation supplies, support of mothers and partners, prior knowledge of breastfeeding, strong intention before birth and perceptions of breastfeeding as money-saving. Barriers that arose more often among those who did not exclusively breastfeed for 3 months include inaccessible lactation support and supplies, difficulties with pumping, latching issues and perceptions of breastfeeding as time-consuming. Lack of access to and knowledge of breastfeeding laws and policies, as well as negative cultural norms or stigma, were important barriers across groups. This study supports the use of the Socioecological Model to design multicomponent interventions to increase exclusive breastfeeding outcomes for Black women.

Space Microgravity Alters Neural Stem Cell Division: Implications for Brain Cancer Research on Earth and in Space.

Considering the imminence of long-term space travel, it is necessary to investigate the impact of space microgravity (SPC-µG) in order to determine if this environment has consequences on the astronauts' health, in particular, neural and cognitive functions. Neural stem cells (NSCs) are the basis for the regeneration of the central nervous system (CNS) cell populations and learning how weightlessness impacts NSCs in health and disease provides a critical tool for the potential mitigation of specific mechanisms leading to neurological disorders. In previous studies, we found that exposure to SPC-µG resulted in enhanced proliferation, a shortened cell cycle, and a larger cell diameter of NSCs compared to control cells. Here, we report the frequent occurrence of abnormal cell division (ACD) including incomplete cell division (ICD), where cytokinesis is not successfully completed, and multi-daughter cell division (MDCD) of NSCs following SPC-µG as well as secretome exposure compared to ground control (1G) NSCs. These findings provide new insights into the potential health implications of space travel and have far-reaching implications for understanding the mechanisms leading to the deleterious effects of long-term space travel as well as potential carcinogenic susceptibility. Knowledge of these mechanisms could help to develop preventive or corrective measures for successful long-term SPC-µG exposure.

A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients.

The molecular underpinnings of organ dysfunction in acute COVID-19 and its potential long-term sequelae are under intense investigation. To shed light on these in the context of liver function, we performed single-nucleus RNA-seq and spatial transcriptomic profiling of livers from 17 COVID-19 decedents. We identified hepatocytes positive for SARS-CoV-2 RNA with an expression phenotype resembling infected lung epithelial cells. Integrated analysis and comparisons with healthy controls revealed extensive changes in the cellular composition and expression states in COVID-19 liver, reflecting hepatocellular injury, ductular reaction, pathologic vascular expansion, and fibrogenesis. We also observed Kupffer cell proliferation and erythrocyte progenitors for the first time in a human liver single-cell atlas, resembling similar responses in liver injury in mice and in sepsis, respectively. Despite the absence of a clinical acute liver injury phenotype, endothelial cell composition was dramatically impacted in COVID-19, concomitantly with extensive alterations and profibrogenic activation of reactive cholangiocytes and mesenchymal cells. Our atlas provides novel insights into liver physiology and pathology in COVID-19 and forms a foundational resource for its investigation and understanding.

Delayed Maturation of Oligodendrocyte Progenitors by Microgravity: Implications for Multiple Sclerosis and Space Flight.

In previous studies, we examined the effects of space microgravity on human neural stem cells. To date, there are no studies on a different type of cell that is critical for myelination and electrical signals transmission, oligodendrocyte progenitors (OLPs). The purpose of the present study was to examine the behavior of space-flown OLPs (SPC-OLPs) as they were adapting to Earth's gravity. We found that SPC-OLPs survived, and most of them proliferated normally. Nonetheless, some of them displayed incomplete cytokinesis. Both morphological and ontogenetic analyses showed that they remained healthy and expressed the immature OLP markers Sox2, PDGFR-α, and transferrin (Tf) after space flight, which confirmed that SPC-OLPs displayed a more immature phenotype than their ground control (GC) counterparts. In contrast, GC OLPs expressed markers that usually appear later (GPDH, O4, and ferritin), indicating a delay in SPC-OLPs' development. These cells remained immature even after treatment with culture media designed to support oligodendrocyte (OL) maturation. The most remarkable and surprising finding was that the iron carrier glycoprotein Tf, previously described as an early marker for OLPs, was expressed ectopically in the nucleus of all SPC-OLPs. In contrast, their GC counterparts expressed it exclusively in the cytoplasm, as previously described. In addition, analysis of the secretome demonstrated that SPC-OLPs contained 3.5 times more Tf than that of GC cells, indicating that Tf is gravitationally regulated, opening two main fields of study to understand the upregulation of the Tf gene and secretion of the protein that keep OLPs at a progenitor stage rather than moving forward to more mature phenotypes. Alternatively, because Tf is an autocrine and paracrine factor in the central nervous system (CNS), in the absence of neurons, it accumulated in the secretome collected after space flight. We conclude that microgravity is becoming a novel platform to study why in some myelin disorders OLPs are present but do not mature.

Identifying Social Media Competencies for Health Professionals: An International Modified Delphi Study to Determine Consensus for Curricular Design.

STUDY OBJECTIVE: The use of social media by health professionals is widespread. However, there is a lack of training to support the effective use of these novel platforms that account for the nuances of an effective health and research communication. We sought to identify the competencies needed by health care professionals to develop an effective social media presence as a medical professional, with the goal of building a social media curriculum. METHODS: We conducted a modified Delphi study, utilizing Kraiger's Knowledge, Skills, and Attitudes framework to identify appropriate items for inclusion in a social media curriculum targeted at health care professionals. Experts in this space were defined as health care professionals who had delivered workshops, published papers, or developed prominent social media tools/accounts. They were recruited through a multimodal campaign to complete a series of 3 survey rounds designed to build consensus. In keeping with prior studies, a threshold of 80% endorsement was used for inclusion in the final list of items. RESULTS: Ninety-eight participants met the expert criteria and were invited to participate in the study. Of the 98 participants, 92 (94%) experts completed the first round; of the 92 experts who completed the first round, 83 (90%) completed the second round; and of the 83 experts who completed the second round, 81 (98%) completed the third round of the Delphi study. Eighteen new items were suggested in the first survey and incorporated into the study. A total of 46 items met the 80% inclusion threshold. CONCLUSION: We identified 46 items that were believed to be important for health care professionals using social media. This list should inform the development of curricular activities and objectives.

Ohio Dentists' Perceptions on Children School Absenteeism for Dental Care Appointments.

Purpose: This cross-sectional study evaluated knowledge, practices, and beliefs of Ohio dentists treating school-aged children regarding school absenteeism in relation to compliance with dental appointments.
Methods: A 26-item questionnaire was distributed to 7,274 dentists licensed in the state of Ohio in 2019. Eligible participants were pediatric dentists (PDs) and general dentists (GDs) who treated individuals younger than 16 years of age.
Results: A return rate of 13.5 percent (958 total participants) provided a sample consisting of approximately 90 percent of GDs, a mean age of 48.5 years and primarily practicing in suburban locations. Respondents felt parental attitudes had changed over the past five years, with a significantly higher proportion of PDs reporting increased parental concerns about school absences than GDs (59.5 percent versus 31.5 percent; P <0.001). Length of excused absence increased with treatment complexity. PDs were more likely to permit longer absences than GDs and to allow parents to decide the length of absence, particularly for children with special health care needs. PDs were 6.6 times more likely to report that concerns about school absences often negatively affected oral health (P <0.001).
Conclusion: Dentists acknowledged that school absences and school policy affected parental choices regarding dental visits, with PDs consistently stating a greater effect than GDs.

Long-term treatment with senolytic drugs Dasatinib and Quercetin ameliorates age-dependent intervertebral disc degeneration in mice.

Intervertebral disc degeneration is highly prevalent within the elderly population and is a leading cause of chronic back pain and disability. Due to the link between disc degeneration and senescence, we explored the ability of the Dasatinib and Quercetin drug combination (D + Q) to prevent an age-dependent progression of disc degeneration in mice. We treated C57BL/6 mice beginning at 6, 14, and 18 months of age, and analyzed them at 23 months of age. Interestingly, 6- and 14-month D + Q cohorts show lower incidences of degeneration, and the treatment results in a significant decrease in senescence markers p16INK4a, p19ARF, and SASP molecules IL-6 and MMP13. Treatment also preserves cell viability, phenotype, and matrix content. Although transcriptomic analysis shows disc compartment-specific effects of the treatment, cell death and cytokine response pathways are commonly modulated across tissue types. Results suggest that senolytics may provide an attractive strategy to mitigating age-dependent disc degeneration.

How do breastfeeding workplace interventions work?: a realist review.

BACKGROUND: Women are representing an increasing share of the labor force, thus, raising the need to accommodate breastfeeding working mothers at the workplace. While there is an emerging body of evidence supporting the positive influence of workplace lactation programs on breastfeeding outcomes, there is a lack of literature on the mechanisms underlying those interventions. Aims of this realist review were three-fold: to uncover underlying mechanisms, determine who benefits the most from such interventions and important contextual factors influencing uptake. METHODS: Purposive bibliographic searches on Medline, Web of Science Core Collection, CINAHL, Global Health, LILACS, Global Index Medicus, Business Source Complete, Proquest Dissertations and Theses and Open Access Theses and Dissertations were conducted to identify relevant publications. Included publications (qualitative and quantitative) described interventions aiming to improve the breastfeeding behavior of working mothers, that were initiated by the employer, reported on breastfeeding outcomes and had a clearly defined workplace. Publications only focusing on maternity leave or that were not published in English, Spanish, Portuguese or German were excluded. A realist approach was followed to identify how workplace interventions work, who benefits the most and the important contextual factors. RESULTS: The bibliographic search yielded a total of 4985 possible publications of which 37 publications were included in the realist analysis. Effective workplace breastfeeding interventions activate three mechanisms: 1) awareness of the intervention, 2) changes in workplace culture, manager/supervisor support, co-worker support and physical environments, and 3) provision of time. Contextual factors such as the distance between the workplace and the infant and the type of workplace may influence the degree of activation of the underlying mechanisms for programs to positively impact breastfeeding outcomes. CONCLUSIONS: In order to be effective, workplace breastfeeding interventions need to: raise awareness of the intervention(s) available among working mothers as well as their work environment, change the workplace culture, foster manager/supervisor support and co-workers support, provide enough time and adequate space and facilities for women to breastfeed or express breastmilk during the workday.

COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets.

COVID-19, which is caused by SARS-CoV-2, can result in acute respiratory distress syndrome and multiple organ failure1-4, but little is known about its pathophysiology. Here we generated single-cell atlases of 24 lung, 16 kidney, 16 liver and 19 heart autopsy tissue samples and spatial atlases of 14 lung samples from donors who died of COVID-19. Integrated computational analysis uncovered substantial remodelling in the lung epithelial, immune and stromal compartments, with evidence of multiple paths of failed tissue regeneration, including defective alveolar type 2 differentiation and expansion of fibroblasts and putative TP63+ intrapulmonary basal-like progenitor cells. Viral RNAs were enriched in mononuclear phagocytic and endothelial lung cells, which induced specific host programs. Spatial analysis in lung distinguished inflammatory host responses in lung regions with and without viral RNA. Analysis of the other tissue atlases showed transcriptional alterations in multiple cell types in heart tissue from donors with COVID-19, and mapped cell types and genes implicated with disease severity based on COVID-19 genome-wide association studies. Our foundational dataset elucidates the biological effect of severe SARS-CoV-2 infection across the body, a key step towards new treatments.