Cells of the human intestinal tract mapped across space and time.

The cellular landscape of the human intestinal tract is dynamic throughout life, developing in utero and changing in response to functional requirements and environmental exposures. Here, to comprehensively map cell lineages, we use single-cell RNA sequencing and antigen receptor analysis of almost half a million cells from up to 5 anatomical regions in the developing and up to 11 distinct anatomical regions in the healthy paediatric and adult human gut. This reveals the existence of transcriptionally distinct BEST4 epithelial cells throughout the human intestinal tract. Furthermore, we implicate IgG sensing as a function of intestinal tuft cells. We describe neural cell populations in the developing enteric nervous system, and predict cell-type-specific expression of genes associated with Hirschsprung's disease. Finally, using a systems approach, we identify key cell players that drive the formation of secondary lymphoid tissue in early human development. We show that these programs are adopted in inflammatory bowel disease to recruit and retain immune cells at the site of inflammation. This catalogue of intestinal cells will provide new insights into cellular programs in development, homeostasis and disease.

Longitudinal analysis reveals that delayed bystander CD8+ T cell activation and early immune pathology distinguish severe COVID-19 from mild disease.

The kinetics of the immune changes in COVID-19 across severity groups have not been rigorously assessed. Using immunophenotyping, RNA sequencing, and serum cytokine analysis, we analyzed serial samples from 207 SARS-CoV2-infected individuals with a range of disease severities over 12 weeks from symptom onset. An early robust bystander CD8+ T cell immune response, without systemic inflammation, characterized asymptomatic or mild disease. Hospitalized individuals had delayed bystander responses and systemic inflammation that was already evident near symptom onset, indicating that immunopathology may be inevitable in some individuals. Viral load did not correlate with this early pathological response but did correlate with subsequent disease severity. Immune recovery is complex, with profound persistent cellular abnormalities in severe disease correlating with altered inflammatory responses, with signatures associated with increased oxidative phosphorylation replacing those driven by cytokines tumor necrosis factor (TNF) and interleukin (IL)-6. These late immunometabolic and immune defects may have clinical implications.

Single-cell multi-omics analysis of the immune response in COVID-19.

Analysis of human blood immune cells provides insights into the coordinated response to viral infections such as severe acute respiratory syndrome coronavirus 2, which causes coronavirus disease 2019 (COVID-19). We performed single-cell transcriptome, surface proteome and T and B lymphocyte antigen receptor analyses of over 780,000 peripheral blood mononuclear cells from a cross-sectional cohort of 130 patients with varying severities of COVID-19. We identified expansion of nonclassical monocytes expressing complement transcripts (CD16+C1QA/B/C+) that sequester platelets and were predicted to replenish the alveolar macrophage pool in COVID-19. Early, uncommitted CD34+ hematopoietic stem/progenitor cells were primed toward megakaryopoiesis, accompanied by expanded megakaryocyte-committed progenitors and increased platelet activation. Clonally expanded CD8+ T cells and an increased ratio of CD8+ effector T cells to effector memory T cells characterized severe disease, while circulating follicular helper T cells accompanied mild disease. We observed a relative loss of IgA2 in symptomatic disease despite an overall expansion of plasmablasts and plasma cells. Our study highlights the coordinated immune response that contributes to COVID-19 pathogenesis and reveals discrete cellular components that can be targeted for therapy.

Ageing compromises mouse thymus function and remodels epithelial cell differentiation.

Ageing is characterised by cellular senescence, leading to imbalanced tissue maintenance, cell death and compromised organ function. This is first observed in the thymus, the primary lymphoid organ that generates and selects T cells. However, the molecular and cellular mechanisms underpinning these ageing processes remain unclear. Here, we show that mouse ageing leads to less efficient T cell selection, decreased self-antigen representation and increased T cell receptor repertoire diversity. Using a combination of single-cell RNA-seq and lineage-tracing, we find that progenitor cells are the principal targets of ageing, whereas the function of individual mature thymic epithelial cells is compromised only modestly. Specifically, an early-life precursor cell population, retained in the mouse cortex postnatally, is virtually extinguished at puberty. Concomitantly, a medullary precursor cell quiesces, thereby impairing maintenance of the medullary epithelium. Thus, ageing disrupts thymic progenitor differentiation and impairs the core immunological functions of the thymus.

Work productivity loss and fatigue in psoriatic arthritis.

OBJECTIVE: To explore the relationship between fatigue and work productivity loss (WPL) in people with psoriatic arthritis (PsA). METHODS: Data were collected from participants in the Utah Psoriasis Initiative Arthritis registry between January 2010 and May 2013. WPL was measured with the 8-item Work Limitations Questionnaire. Fatigue was assessed with question 1 from the Bath Ankylosing Spondylitis Disease Activity Index (BASDAI#1), "How would you describe the overall level of fatigue/tiredness you have experienced?" and with question 1 from the Psoriatic Arthritis Quality of Life Questionnaire (PsAQOL#1) "I feel tired whatever I do." Psoriatic activity was evaluated with tender joint count (TJC), swollen joint count (SJC), dactylitis count, enthesitis count, inflammatory back pain (IBP), physician global assessment, body surface area, and psoriasis pain and itch. RESULTS: Among 107 participants, work productivity was reduced by 6.7%, compared to benchmark employees without limitations. Fatigue was reported by 54 patients (50.5%) on PsAQOL#1, and 64 (60.0%) were classified as high fatigue by BASDAI#1. TJC, SJC, enthesitis count, IBP, and depressed mood were highest or most frequent in participants reporting fatigue. After adjustments for psoriatic activity and depressed mood, WPL was associated with fatigue, as measured by PsAQOL#1 (p = 0.01) and BASDAI#1 (p = 0.002). CONCLUSION: WPL was associated with fatigue, and the association was not entirely explained by the evaluated musculoskeletal, cutaneous, or psychiatric manifestations of PsA.

Skeletal muscle molecular responses to resistance training and dietary supplementation in COPD.

BACKGROUND: Skeletal muscle dysfunction is a systemic feature of chronic obstructive pulmonary disease (COPD), contributing to morbidity and mortality. Physical training improves muscle mass and function in COPD, but the molecular regulation therein is poorly understood. METHODS: Candidate genes and proteins regulating muscle protein breakdown (ubiquitin proteasome pathway), muscle protein synthesis (phosphatidylinositol 3 kinase/Akt/mammalian target of rapamycin pathway), myogenesis (MyoD, myogenin and myostatin) and transcription (FOXO1, FOXO3 and RUNX1) were determined in quadriceps muscle samples taken at four time points over 8 weeks of knee extensor resistance training (RT) in patients with COPD and healthy controls (HCs). Patients with COPD were randomly allocated to receive protein/carbohydrate or placebo supplements during RT. RESULTS: 59 patients with COPD (mean (SD) age 68.0 (9.3) years, forced expiratory volume in 1 s (FEV1) 46.9 (17.8) % predicted) and 21 HCs (66.1 (4.8) years, 105.0 (21.6) % predicted) were enrolled. RT increased lean mass (~5%) and strength (~20%) in all groups. Absolute work done during RT was lower throughout in patients with COPD compared with HCs. RT resulted in increases (from basal) in catabolic, anabolic, myogenic and transcription factor protein expression at 24 h, 4 weeks and 8 weeks of exercise in HCs. This response was blunted in patients with COPD, except for myogenic signalling, which was similar. Nutritional supplementation did not augment functional or molecular responses to RT. CONCLUSIONS: The potential for muscle rehabilitation in response to RT is preserved in COPD. Except for markers of myogenesis, molecular responses to RT are not tightly coupled to lean mass gains but reflect the lower work done during RT, suggesting some caution when identifying molecular targets for intervention. Increasing post-exercise protein and carbohydrate intake is not a prerequisite for a normal training response in COPD.

Inflammatory and satellite cells in the quadriceps of patients with COPD and response to resistance training.

BACKGROUND: Quadriceps dysfunction in COPD may be mediated by inflammatory mechanisms or impaired satellite cell function. Resistance training is of proven efficacy in these patients, but data on muscle inflammatory and satellite cell response to resistance exercise in COPD are lacking.We aimed to examine the inflammatory and satellite cell profile of the quadriceps in patients with COPD and healthy control subjects at rest and after acute and chronic resistance exercise. METHODS: Seventeen patients with COPD and 10 healthy control subjects underwent 8 weeks ofbilateral lower-limb, high-intensity resistance training, thrice weekly, on an isokinetic dynamometer.Quadriceps muscle biopsy specimens from the dominant thigh were obtained at baseline,24 h following the fi rst exercise bout, and after 8 weeks 24 h after the last exercise bout. Glycolmethacrylate-embedded muscle biopsy specimens were analyzed using immunohistochemistry to identify neutrophils, macrophages, and satellite cells. RESULTS: Neutrophils were significantly elevated in the quadriceps of patients with COPD at baseline compared with healthy control subjects ( P 5 .03). Inflammatory cells were increased significantly at 24 h in both groups but were similar to baseline values at week 8, with no difference detectable between healthy control subjects and patients with COPD. Satellite cell numbers were comparable between patients and control subjects at baseline, tended to increase at 24 h, and remained elevated at week 8. CONCLUSIONS: Inflammatory cells are elevated in the resting quadriceps of patients with COPD. Acute resistance exercise leads to an inflammatory myositis, which is attenuated with regular training. Satellite cells in patients and control subjects are comparable and are increased in response to exercise. TRIAL REGISTRY: ISRCTN Register ; No.: ISRCTN22764439; URL: www.controlled-trials.com.

Staged bilateral lung volume reduction surgery - the benefits of a patient-led strategy.

OBJECTIVE: Lung volume reduction surgery (LVRS) is conventionally a one-staged bilateral operation. We hypothesised that a more conservative staged bilateral approach determined by the patient not the surgeon would reduce operative risk and prolong the overall benefit. METHODS: In a population of 114 consecutive patients who were identified as suitable for bilateral LVRS an initial cohort of 26 patients (15 male; 11 female, median age: 58 years) underwent one-staged bilateral surgery: 18 by median sternotomy and eight by video-assisted thoracoscopic surgery (VATS) (group OB). A subsequent cohort of 88 patients had unilateral VATS LVRS with the contralateral operation not scheduled until the patient requested this. Longitudinal follow-up included analysis of lung function, health status (SF 36) and survival. RESULTS: At a median follow-up of 2.8 (range: 0-9.9) years, staged bilateral LVRS was performed in 16 patients (10 male; 6 female, median age: 59 years) (group SB) at a median interval of 3.9 (range: 0.7-5.9) years after the first operation. Unilateral LVRS has been performed in 73 patients (43 male; 30 female, median age: 60 years) (group U). There were significant improvements in forced expiratory volume in 1s (FEV1) for 6 months in groups OB and U; in group SB there was a second improvement at 4 years (p<0.05). There were significant reductions in residual volume (RV) and total lung capacity (TLC) in groups OB and U for 2 years; in group SB there was a further significant reduction lasting up to 6 years in TLC (p<0.05) and RV (p<0.01). There were significant improvements in health status lasting up to 1 year in groups OB and U. However, in group SB these improvements lasted for 4 years in the domain of physical functioning and 6 years in the domains of social functioning and energy/vitality. There was no significant difference (p=0.07) in 30-day mortality among groups OB (7.7%), SB (13%) and U (4.1%). Similarly, there was no difference between groups OB and SB/U in 3-year survival (81% vs 77%) or 5-year survival (54% vs 66%). CONCLUSION: A staged bilateral approach to LVRS dictated by patients' perception of their condition appears to lead to a more prolonged overall benefit than one-staged LVRS without compromising survival.

The increase in body mass index observed after lung volume reduction may act as surrogate marker of improved health status.

OBJECTIVE: To assess the effects of lung volume reduction surgery (LVRS) on body mass index (BMI). METHODS: Prospective data was collected on a series of 63 patients undergoing LVRS (bilateral in 22 patients, unilateral in 41 patients). Median age was 58 (41-70) years. The peri-operative effects of LVRS on BMI, lung function and health status (assessed by SF 36 questionnaire) were recorded at 3, 6, 12 and 24 months. RESULTS: We found an overall increase in BMI after LVRS, which was significant up to 2 years. These changes correlated with the changes in FEV1 (R = 0.3, P < 0.01 6 months after LVRS) and diffusing capacity for carbon monoxide (DLCO) (R = 0.5, P < 0.01 6 months after LVRS). At 6 months, when the best results in health status were found, the patients were divided in a responders group (improved SF 36 score) and a non-responders group (same or worse SF 36 score) for each of the 8 domains of the SF 36. In 6 domains the non-responders showed no increase in BMI. In 6 domains the responders showed a significant increase in BMI. CONCLUSION: LVRS significantly improves postoperative BMI, which correlates with improvements in DLCO and reflects changes in health status.

The long-term health status improvements seen after lung volume reduction surgery.

OBJECTIVES: To correlate the long-term changes in respiratory physiology, body mass index (BMI) and health status after lung volume reduction surgery (LVRS). PATIENTS/METHODS: From 1995 to 2002 77 patients; 48 male: 29 female, median age 59 (41-72) years, have undergone LVRS (simultaneous bilateral in 27; staged bilateral in 3; unilateral in 47). FEV(1), total lung capacity (TLC), residual volume (RV) and RV/TLC ratio were measured preoperatively and at 3 months, 6 months, 1 year, 2 years, 3 years and 4 years post surgery. At the same time interval health status was assessed by Euroquol and Short Form 36 (SF 36) questionnaires. Seventeen patients have died within 4 years of their operation (30 day mortality 5%). RESULTS: The changes in FEV(1) are only significantly improved for 1 year post LVRS, while the improvements in TLC and RV remain significant up to 3 years postoperatively. The improvements in BMI also persist for 3 years. The best scores in Euroquol and SF 36 are obtained 6 months after LVRS but are only significantly improved up to 1 year. CONCLUSION: The physiological effects of volume LVRS are lasting but initial improvements in health status decline more rapidly.