Imperial College London

DrDavidThomas

Faculty of MedicineDepartment of Immunology and Inflammation

Reader in Immunology and Inflammation (Clinical)
 
 
 
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Contact

 

+44 (0)20 3313 8506david.thomas1

 
 
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Location

 

9NCCommonwealth BuildingHammersmith Campus

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Summary

 

Publications

Publication Type
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41 results found

Svetitsky S, Shuaib R, McAdoo S, Thomas DCet al., 2021, Commentary: Long-Term Effects of Covid-19 on the kidney., QJM

Journal article

Mortimer PM, Mc Intyre SA, Thomas DC, 2021, Beyond the Extra Respiration of Phagocytosis: NADPH Oxidase 2 in Adaptive Immunity and Inflammation, FRONTIERS IN IMMUNOLOGY, Vol: 12, ISSN: 1664-3224

Journal article

Medjeral-Thomas N, Troldborg A, Hansen A, Pihl R, Clarke C, Peters J, Thomas D, Willicombe M, Palarasah Y, Botto M, Pickering M, Thiel Set al., 2021, Protease inhibitor plasma concentrations associate with COVID-19 infection, Oxford Open Immunology, Vol: 2, ISSN: 2633-6960

Protease inhibitors influence a range of innate immunity and inflammatory pathways. We quantified plasma concentrations of key anti-inflammatory protease inhibitors in chronic haemodialysis patients with COVID-19. The samples were collected early in the disease course to determine whether plasma protease inhibitor levels associated with the presence and severity of COVID-19. We used antibody-based immunoassays to measure plasma concentrations of C1 esterase inhibitor (C1-INH), alpha2-macroglobulin (α2M), antithrombin, and inter-alpha-inhibitor heavy chain 4 (ITIH4) in 100 serial samples from 27 haemodialysis patients with COVID-19. ITIH4 was tested in two assays, one measuring intact ITIH4 and another also detecting any fragmented ITIH4 (total ITIH4). Control cohorts were 32 haemodialysis patients without COVID-19 and 32 healthy controls. We compared protease inhibitor concentration based on current and future COVID-19 severity and with CRP. Results were adjusted for repeated measures and multiple comparisons. Analysis of all available samples demonstrated lower plasma C1-INH and α2M and higher total ITIH4 in COVID-19 compared to dialysis controls. These differences were also seen in the first sample collected after COVID-19 diagnosis, a median of four days from diagnostic swab. Plasma ITIH4 levels were higher in severe than non-severe COVID-19. Serum CRP correlated positively with plasma levels of antithrombin, intact ITIH4, and total ITIH4. In conclusion, plasma protease inhibitor concentrations are altered in COVID-19.

Journal article

Medjeral-Thomas N, Troldborg A, Hansen A, Gisby J, Clarke C, Prendecki M, McAdoo S, Sandhu E, Lightstone E, Thomas D, Willicombe M, Botto M, Peters J, Pickering M, Thiel Set al., 2021, Plasma lectin pathway complement proteins in patients with COVID-19 and renal disease, Frontiers in Immunology, Vol: 12, ISSN: 1664-3224

We do not understand why non-white ethnicity and chronic kidney disease increase susceptibility to COVID-19. The lectin pathway of complement activation is a key contributor to innate immunity and inflammation. Concentrations of plasma lectin pathway proteins influence pathway activity and vary with ethnicity. We measured circulating lectin proteins in a multi-ethnic cohort of chronic kidney disease patients with and without COVID19 infection to determine if lectin pathway activation was contributing to COVID19 severity.We measured 11 lectin proteins in serial samples from a cohort of 33 patients with chronic kidney impairment and COVID19. Controls were single plasma samples from 32 patients on dialysis and 32 healthy individuals. We demonstrated multiple associations between recognition molecules and associated proteases of the lectin pathway and COVID-19, including COVID-19 severity. Some of these associations were unique to patients of Asian and White ethnicity. Our novel findings demonstrate that COVID19 infection alters the concentration of plasma lectin proteins and some of these changes were linked to ethnicity. This suggests a role for the lectin pathway in the host response to COVID-19 and suggest that variability within this pathway may contribute to ethnicity-associated differences in susceptibility to severe COVID-19.

Journal article

Behmoaras J, Olona A, Hateley C, Guerrero A, Ko J-H, Johnson MR, Anand PK, Thomas D, Gil J, Behmoaras Jet al., 2021, Cardiac glycosides cause cytotoxicity in human macrophages and ameliorate white adipose tissue homeostasis, British Journal of Pharmacology, Pages: 1-1, ISSN: 0007-1188

Background and purpose: Cardiac glycosides (CGs) inhibit the Na+,K+‐ATPase and are widely prescribed medicines for chronic heart failure and cardiac arrhythmias. Recently, CGs have been described to induce inflammasome activation and pyroptosis in human macrophages, suggesting a cytotoxicity that remains to be elucidated in tissues.Experimental approach: To determine the cell type specificity of CG‐mediated cytotoxicity, we used human primary monocyte‐derived macrophages (hMDMs) and non‐adherent peripheral blood cells isolated from healthy donors. Omental white adipose tissue (WAT) and stromal vascular fraction (SVF)‐derived pre‐adipocytes and adipocytes were isolated from obese patients undergoing bariatric surgery. All these primary cells/tissues were treated with nanomolar concentrations of ouabain (50nM, 100nM and 500nM) to investigate its degree of cytotoxicity and mechanisms leading to cell death. In WAT, we further explored the consequences of ouabain‐mediated cytotoxicity by measuring insulin sensitivity, adipose tissue function and extracellular matrix (ECM) deposition ex vivo.Key results: The ouabain‐induced cell death is through pyroptosis and apoptosis, and more efficient in hMDMs compared to non‐adherent PBMC populations. This selective cytotoxicity is dependent on K+ flux, as ouabain causes an intracellular depletion of K+, while inducing accumulation of Na+ and Ca2+ levels. Consistently, the cell‐death caused by these ion imbalances can be rescued by addition of potassium chloride in hMDMs. Remarkably, when WAT explants from obese patients are cultured with nanomolar concentrations of ouabain, this causes depletion of macrophages, down‐regulation of type VI collagen levels, and amelioration of insulin sensitivity ex vivo.Conclusions and implications: These results suggest that the usage of nanomolar concentration of CGs can be an attractive therapeutic avenue in metabolic syndrome characterised by pathogenic infiltration and activation of macrophages.

Journal article

Canton J, Blees H, Henry CM, Buck MD, Schulz O, Rogers NC, Childs E, Zelenay S, Rhys H, Domart M-C, Collinson L, Alloatti A, Ellison CJ, Amigorena S, Papayannopoulos V, Thomas DC, Randow F, Sousa Cet al., 2021, The receptor DNGR-1 signals for phagosomal rupture to promote cross-presentation of dead-cell-associated antigens (vol 22, pg 140, 2021), NATURE IMMUNOLOGY, Vol: 22, Pages: 391-391, ISSN: 1529-2908

Journal article

Willicombe M, Gleeson S, Clarke C, Dor F, Prendecki M, Lightstone L, Lucisano G, McAdoo S, Thomas Det al., 2021, Identification of Patient Characteristics Associated With SARS-CoV-2 Infection and Outcome in Kidney Transplant Patients Using Serological Screening, TRANSPLANTATION, Vol: 105, Pages: 151-157, ISSN: 0041-1337

Journal article

Clarke C, Lucisano G, Prendecki M, Gleeson S, Martin P, Ali M, McAdoo SP, Lightstone L, Ashby D, Charif R, Griffith M, McLean A, Dor F, Willicombe M, ICHNT Renal COVID Groupet al., 2021, Informing the risk of kidney transplantation versus remaining on the wait list in the COVID-19 era, Kidney International Reports, Vol: 6, Pages: 46-55, ISSN: 2468-0249

Introduction: There is limited data pertaining to comparative outcomes of remaining on dialysis versus kidney transplantation as the threat of COVID-19 remains. This study aims to delineate the differential risks involved using serological methods to help define exposure rates. Methods: From a cohort of 1433 patients with ESKD, we analysed COVID-19 infection rates and outcomes in 299 wait list patients compared with 237 transplant recipients within their first year post-transplant. Patients were followed over a 68-day period from the time our transplant programme closed due to COVID-19. Results: The overall mortality rate in wait list and transplant populations were equivalent, p=0.69. However, COVID-19 infection was more commonly diagnosed in the wait list patients, p=0.001, who were more likely to be tested by RT-PCR, p=0.0004. Once infection was confirmed, mortality risk was higher in the transplant patients, p=0.015. The seroprevalence in dialysis and transplant patients with undetected infection was 18.3% and 4.6% respectively, p=0.0001. After adjusting for a potential screening bias, the relative risk of death following a diagnosis of COVID-19 remained higher in transplant recipients, HR: 3.36 (1.19-9.50), p=0.022. Conclusions: In conclusion, whilst COVID-19 infection was more common in the wait list patients, a higher COVID-19 associated mortality rate was seen in transplant recipients, resulting in comparable overall mortality rates.

Journal article

Prendecki M, Clarke C, McKinnon T, Lightstone L, Pickering MC, Thomas DC, McAdoo SP, Willicombe Met al., 2021, SARS-CoV-2 antibody point-of-care testing in dialysis and kidney transplant patients with COVID-19., Kidney Medicine, Vol: 3, Pages: 54-59.e1, ISSN: 2590-0595

Rationale & Objective: A number of serologic tests for immunoglobulin G (IgG) against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are now commercially available, including multiple lateral flow immunoassays (LFIAs), which have the advantage of being inexpensive and easy to use, without the reliance on laboratory facilities. However, data on the development of humoral immunity to SARS-CoV-2 in patients with kidney disease is limited, and the utility of an LFIA to test for antibodies in these patients has not been assessed. Study Design: Observational study. Setting & Participants: 60 patients (40 hemodialysis and 20 kidney transplant recipients) with SARS-CoV-2 infection confirmed by viral reverse transcriptase-polymerase chain reaction (RT-PCR) testing and 88 historic negative-control samples (collected before September 2019). Test: A commercially available LFIA to test for SARS-CoV-2 IgG in patients with infection confirmed by viral RT-PCR testing. Outcomes: Sensitivity and specificity of the LFIA to detect SARS-CoV-2 IgG in dialysis patients and transplant recipients. Results: 56/58 (96.6%) patients (38/39 hemodialysis and 18/19 transplant recipients) tested positive for SARS-CoV-2 IgG. 5/7 (71.4%) patients who were negative on preliminary testing had detectable IgG when retested more than 21 days postdiagnosis. Median times to first and second tests after diagnosis were 17 (interquartile range, 15-20) and 35 (interquartile range, 30-39) days, respectively. Calculation of test characteristics gave sensitivity of 96.6% (95% CI, 88.3%-99.4%) and specificity of 97.7% (95% CI, 92.0-99.6%). Limitations: Possible exposure to other beta-coronaviruses that may cross-react with the antigen used in the LFIA cannot be excluded. Conclusions: Symptomatic dialysis patients and transplant recipients commonly develop an immune response against SARS-CoV-2 infection that can be detected using an LFIA. Used diligently, an LFIA could be used to help scre

Journal article

Canton J, Blees H, Henry CM, Buck MD, Schulz O, Rogers NC, Childs E, Zelenay S, Rhys H, Domart M-C, Collinson L, Alloatti A, Ellison CJ, Amigorena S, Papayannopoulos V, Thomas DC, Randow F, Reis e Sousa Cet al., 2020, The receptor DNGR-1 signals for phagosomal rupture to promote cross-presentation of dead-cell-associated antigens, NATURE IMMUNOLOGY, Vol: 22, Pages: 140-U56, ISSN: 1529-2908

Journal article

Gisby J, Clarke C, Medjeral-Thomas N, Malik T, Papadaki A, Mortimer P, Buang N, Lewis S, Pereira M, Toulza F, Fagnano E, Mawhin M-A, Dutton E, Tapeng L, Kirk P, Behmoaras J, Sandhu E, McAdoo S, Prendecki M, Pickering M, Botto M, Willicombe M, Thomas D, Peters Jet al., 2020, Longitudinal proteomic profiling of high-risk patients with COVID-19 reveals markers of severity and predictors of fatal disease, eLife, Vol: 10, Pages: 1-30, ISSN: 2050-084X

End-stage kidney disease (ESKD) patients are at high risk of severe COVID-19. We performed dense serial blood sampling in hospitalised and non-hospitalised ESKD patients with COVID-19 (n=256 samples from 55 patients) and used Olink immunoassays to measure 436 circulating proteins. Comparison to 51 non-infected ESKD patients revealed 221 proteins differentially expressed in COVID-19, of which 69.7% replicated in an independent cohort of 46 COVID-19 patients. 203 proteins were associated with clinical severity scores, including IL6, markers of monocyte recruitment (e.g. CCL2, CCL7), neutrophil activation (e.g proteinase-3) and epithelial injury (e.g. KRT19). Random Forests machine learning identified predictors of current or future severity such as KRT19, PARP1, PADI2, CCL7, and IL1RL1 (ST2). Survival analysis with joint models revealed 69 predictors of death including IL22RA1, CCL28, and the neutrophil-derived chemotaxin AZU1 (Azurocidin). Finally, longitudinal modelling with linear mixed models uncovered 32 proteins that display different temporal profiles in severe versus non-severe disease, including integrins and adhesion molecules. Our findings point to aberrant innate immune activation and leucocyte-endothelial interactions as central to the pathology of severe COVID-19. The data from this unique cohort of high-risk individuals provide a valuable resource for identifying drug targets in COVID-19.

Journal article

Prendecki M, Clarke C, Medjeral-Thomas N, McAdoo SP, Sandhu E, Peters JE, Thomas DC, Willicombe M, Botto M, Pickering MCet al., 2020, Temporal changes in complement activation in haemodialysis patients with COVID-19 as a predictor of disease progression, Clinical Kidney Journal, Vol: 13, Pages: 889-896, ISSN: 2048-8505

Background: Complement activation may play a pathogenic role in patients with severe coronavirus disease 2019 (COVID-19) by contributing to tissue inflammation and microvascular thrombosis. Methods: Serial samples were collected from patients receiving maintenance haemodialysis (HD). Thirty-nine patients had confirmed COVID-19 and 10 patients had no evidence of COVID-19. Plasma C5a and C3a levels were measured using enzyme-linked immunosorbent assay. Results: We identified elevated levels of plasma C3a and C5a in HD patients with severe COVID-19 compared with controls. Serial sampling identified that C5a levels were elevated prior to clinical deterioration in patients who developed severe disease. C3a more closely mirrored both clinical and biochemical disease severity. Conclusions: Our findings suggest that activation of complement plays a role in the pathogenesis of COVID-19, leading to endothelial injury and lung damage. C5a may be an earlier biomarker of disease severity than conventional parameters such as C-reactive protein and this warrants further investigation in dedicated biomarker studies. Our data support the testing of complement inhibition as a therapeutic strategy for patients with severe COVID-19.

Journal article

Clarke C, Prendecki M, Dhutia A, Ali MA, Sajjad H, Shivakumar O, Lightstone L, Kelleher P, Pickering MC, Thomas D, Charif R, Griffith M, McAdoo SP, Willicombe Met al., 2020, High prevalence of asymptomatic COVID-19 infection in hemodialysis patients detected using serologic screening, Journal of the American Society of Nephrology, Vol: 31, Pages: 1969-1975, ISSN: 1046-6673

BACKGROUND: Strategies to minimize the risk of transmission and acquisition of COVID-19 infection in patients with ESKD receiving in-center hemodialysis have been rapidly implemented across the globe. Despite these interventions, confirmed COVID-19 infection rates have been high in the United Kingdom. Prevalence of asymptomatic disease in an adult hemodialysis population has not been reported. Also, to our knowledge, the development of humoral response to SARS-CoV-2 has not been previously reported in this population. Although serologic testing does not provide information on the infectivity of patients, seroprevalence studies may enable investigation of exposure within dialysis units and hence, assessment of current screening strategies. METHODS: To investigate the seroprevalence of SARS-CoV-2 antibodies in a hemodialysis population, we used the Abbott IgG assay with the Architect system to test serum samples from 356 patients receiving in-center hemodialysis for SARS-CoV-2 antibodies. RESULTS: Of 356 patients, 121 had been symptomatic when screened before a dialysis session and received an RT-PCR test; 79 (22.2% of the total study population) tested positive for COVID-19. Serologic testing of all 356 patients found 129 (36.2%) who tested positive for SARS-CoV-2 antibodies. Only two patients with PCR-confirmed infection did not seroconvert. Of the 129 patients with SARS-CoV-2 antibodies, 52 (40.3%) had asymptomatic disease or undetected disease by PCR testing alone. CONCLUSIONS: We found a high seroprevalence of SARS-CoV-2 antibodies in patients receiving in-center hemodialysis. Serologic evidence of previous infection in asymptomatic or PCR-negative patients suggests that current diagnostic screening strategies may be limited in their ability to detect acute infection.

Journal article

Schejtman A, Aragão-Filho WC, Clare S, Zinicola M, Weisser M, Burns SO, Booth C, Gaspar HB, Thomas DC, Condino-Neto A, Thrasher AJ, Santilli Get al., 2020, Lentiviral gene therapy rescues p47phox chronic granulomatous disease and the ability to fight Salmonella infection in mice, Gene Therapy (Basingstoke), Vol: 27, Pages: 459-469, ISSN: 0969-7128

Chronic granulomatous disease (CGD) is an inherited primary immunodeficiency disorder characterised by recurrent and often life-threatening infections and hyperinflammation. It is caused by defects of the phagocytic NADPH oxidase, a multicomponent enzyme system responsible for effective pathogen killing. A phase I/II clinical trial of lentiviral gene therapy is underway for the most common form of CGD, X-linked, caused by mutations in the gp91phox subunit of the NADPH oxidase. We propose to use a similar strategy to tackle p47phox-deficient CGD, caused by mutations in NCF1, which encodes the p47phox cytosolic component of the enzymatic complex. We generated a pCCLCHIM-p47phox lentiviral vector, containing the chimeric Cathepsin G/FES myeloid promoter and a codon-optimised version of the human NCF1 cDNA. Here we show that transduction with the pCCLCHIM-p47phox vector efficiently restores p47phox expression and biochemical NADPH oxidase function in p47phox-deficient human and murine cells. We also tested the ability of our gene therapy approach to control infection by challenging p47phox-null mice with Salmonella Typhimurium, a leading cause of sepsis in CGD patients, and found that mice reconstituted with lentivirus-transduced hematopoietic stem cells had a reduced bacterial load compared with untreated mice. Overall, our results potentially support the clinical development of a gene therapy approach using the pCCLCHIM-p47phox vector.

Journal article

Dattani R, Hill P, Medjeral-Thomas N, Griffith ME, Ashby D, McAdoo S, Corbett RW, Lucisano G, Beadle J, McCafferty K, Frankel A, Thomas Det al., 2020, Oral potassium binders: increasing flexibility in times of crisis, NEPHROLOGY DIALYSIS TRANSPLANTATION, Vol: 35, Pages: 1446-1448, ISSN: 0931-0509

Journal article

Corbett RW, Blakey S, Nitsch D, Loucaidou M, McLean A, Duncan N, Ashby DRet al., 2020, Epidemiology of COVID-19 in an urban dialysis center, Journal of the American Society of Nephrology, Vol: 31, Pages: 1815-1823, ISSN: 1046-6673

Background During the coronavirus disease 2019 (COVID-19) epidemic, many countries have instituted population-wide measures for social distancing. The requirement of patients on dialysis for regular treatment in settings typically not conducive to social distancing may increase their vulnerability to COVID-19.Methods Over a 6-week period, we recorded new COVID-19 infections and outcomes for all adult patients receiving dialysis in a large dialysis center. Rapidly introduced control measures included a two-stage routine screening process at dialysis entry (temperature and symptom check, with possible cases segregated within the unit and tested for SARS-CoV-2), isolated dialysis in a separate unit for patients with infection, and universal precautions that included masks for dialysis nursing staff.Results Of 1530 patients (median age 66 years; 58.2% men) receiving dialysis, 300 (19.6%) developed COVID-19 infection, creating a large demand for isolated outpatient dialysis and inpatient beds. An analysis that included 1219 patients attending satellite dialysis clinics found that older age was a risk factor for infection. COVID-19 infection was substantially more likely to occur among patients on in-center dialysis compared with those dialyzing at home. We observed clustering in specific units and on specific shifts, with possible implications for aspects of service design, and high rates of nursing staff illness. A predictive epidemic model estimated a reproduction number of 2.2; cumulative cases deviated favorably from the model from the fourth week, suggesting that the implemented measures controlled transmission.Conclusions The COVID-19 epidemic affected a large proportion of patients at this dialysis center, creating service pressures exacerbated by nursing staff illness. Details of the control strategy and characteristics of this epidemic may be useful for dialysis providers and other institutions providing patient care.

Journal article

Thaventhiran JED, Lango Allen H, Burren OS, Rae W, Greene D, Staples E, Zhang Z, Farmery JHR, Simeoni I, Rivers E, Maimaris J, Penkett CJ, Stephens J, Deevi SVV, Sanchis-Juan A, Gleadall NS, Thomas MJ, Sargur RB, Gordins P, Baxendale HE, Brown M, Tuijnenburg P, Worth A, Hanson S, Linger RJ, Buckland MS, Rayner-Matthews PJ, Gilmour KC, Samarghitean C, Seneviratne SL, Sansom DM, Lynch AG, Megy K, Ellinghaus E, Ellinghaus D, Jorgensen SF, Karlsen TH, Stirrups KE, Cutler AJ, Kumararatne DS, Chandra A, Edgar JDM, Herwadkar A, Cooper N, Grigoriadou S, Huissoon AP, Goddard S, Jolles S, Schuetz C, Boschann Fet al., 2020, Whole-genome sequencing of a sporadic primary immunodeficiency cohort (vol 583, pg 90, 2020), Nature, Vol: 584, Pages: E2-E2, ISSN: 0028-0836

Journal article

Thaventhiran JED, Lango Allen H, Burren OS, Rae W, Greene D, Staples E, Zhang Z, Farmery JHR, Simeoni I, Rivers E, Maimaris J, Penkett CJ, Stephens J, Deevi SVV, Sanchis-Juan A, Gleadall NS, Thomas MJ, Sargur RB, Gordins P, Baxendale HE, Brown M, Tuijnenburg P, Worth A, Hanson S, Linger RJ, Buckland MS, Rayner-Matthews PJ, Gilmour KC, Samarghitean C, Seneviratne SL, Sansom DM, Lynch AG, Megy K, Ellinghaus E, Ellinghaus D, Jorgensen SF, Karlsen TH, Stirrups KE, Cutler AJ, Kumararatne DS, Chandra A, Edgar JDM, Herwadkar A, Cooper N, Grigoriadou S, Huissoon AP, Goddard S, Jolles S, Schuetz C, Boschann F, Primary Immunodeficiency Consortium for the NIHR Bioresource, Lyons PA, Hurles ME, Savic S, Burns SO, Kuijpers TW, Turro E, Ouwehand WH, Thrasher AJ, Smith KGCet al., 2020, Whole-genome sequencing of a sporadic primary immunodeficiency cohort, Nature, Vol: 583, Pages: 90-95, ISSN: 0028-0836

Primary immunodeficiency (PID) is characterized by recurrent and often life-threatening infections, autoimmunity and cancer, and it poses major diagnostic and therapeutic challenges. Although the most severe forms of PID are identified in early childhood, most patients present in adulthood, typically with no apparent family history and a variable clinical phenotype of widespread immune dysregulation: about 25% of patients have autoimmune disease, allergy is prevalent and up to 10% develop lymphoid malignancies1-3. Consequently, in sporadic (or non-familial) PID genetic diagnosis is difficult and the role of genetics is not well defined. Here we address these challenges by performing whole-genome sequencing in a large PID cohort of 1,318 participants. An analysis of the coding regions of the genome in 886 index cases of PID found that disease-causing mutations in known genes that are implicated in monogenic PID occurred in 10.3% of these patients, and a Bayesian approach (BeviMed4) identified multiple new candidate PID-associated genes, including IVNS1ABP. We also examined the noncoding genome, and found deletions in regulatory regions that contribute to disease causation. In addition, we used a genome-wide association study to identify loci that are associated with PID, and found evidence for the colocalization of-and interplay between-novel high-penetrance monogenic variants and common variants (at the PTPN2 and SOCS1 loci). This begins to explain the contribution of common variants to the variable penetrance and phenotypic complexity that are observed in PID. Thus, using a cohort-based whole-genome-sequencing approach in the diagnosis of PID can increase diagnostic yield and further our understanding of the key pathways that influence immune responsiveness in humans.

Journal article

Turro E, Astle WJ, Megy K, Graef S, Greene D, Shamardina O, Allen HL, Sanchis-Juan A, Frontini M, Thys C, Stephens J, Mapeta R, Burren OS, Downes K, Haimel M, Tuna S, Deevi SVV, Aitman TJ, Bennett DL, Calleja P, Carss K, Caulfield MJ, Chinnery PF, Dixon PH, Gale DP, James R, Koziell A, Laffan MA, Levine AP, Maher ER, Markus HS, Morales J, Morrell NW, Mumford AD, Ormondroyd E, Rankin S, Rendon A, Richardson S, Roberts I, Roy NBA, Saleem MA, Smith KGC, Stark H, Tan RYY, Themistocleous AC, Thrasher AJ, Watkins H, Webster AR, Wilkins MR, Williamson C, Whitworth J, Humphray S, Bentley DR, Kingston N, Walker N, Bradley JR, Ashford S, Penkett CJ, Freson K, Stirrups KE, Raymond FL, Ouwehand WHet al., 2020, Whole-genome sequencing of patients with rare diseases in a national health system, Nature, Vol: 583, Pages: 96-102, ISSN: 0028-0836

Most patients with rare diseases do not receive a molecular diagnosis and the aetiological variants and causative genes for more than half such disorders remain to be discovered1. Here we used whole-genome sequencing (WGS) in a national health system to streamline diagnosis and to discover unknown aetiological variants in the coding and non-coding regions of the genome. We generated WGS data for 13,037 participants, of whom 9,802 had a rare disease, and provided a genetic diagnosis to 1,138 of the 7,065 extensively phenotyped participants. We identified 95 Mendelian associations between genes and rare diseases, of which 11 have been discovered since 2015 and at least 79 are confirmed to be aetiological. By generating WGS data of UK Biobank participants2, we found that rare alleles can explain the presence of some individuals in the tails of a quantitative trait for red blood cells. Finally, we identified four novel non-coding variants that cause disease through the disruption of transcription of ARPC1B, GATA1, LRBA and MPL. Our study demonstrates a synergy by using WGS for diagnosis and aetiological discovery in routine healthcare.

Journal article

Prendecki M, Clarke C, Cairns T, Cook T, Roufosse C, Thomas D, Willicombe M, Pusey CD, McAdoo SPet al., 2020, Anti-glomerular basement membrane disease during the COVID-19 pandemic, Kidney International, ISSN: 0085-2538

Journal article

Willicombe M, Thomas D, McAdoo S, 2020, COVID-19 and calcineurin inhibitors: should they get left out in the storm?, Journal of the American Society of Nephrology, Pages: ASN.2020030348-ASN.2020030348, ISSN: 1046-6673

Journal article

Mukhopadhyay S, Heinz E, Porreca I, Alasoo K, Yeung A, Yang H-T, Schwerd T, Forbester JL, Hale C, Agu CA, Choi YH, Rodrigues J, Capitani M, Jostins-Dean L, Thomas DC, Travis S, Gaffney D, Skarnes WC, Thomson N, Uhlig HH, Dougan G, Powrie Fet al., 2020, Loss of IL-10 signaling in macrophages limits bacterial killing driven by prostaglandin E2, Journal of Experimental Medicine, Vol: 217, ISSN: 0022-1007

Loss of IL-10 signaling in macrophages (Mφs) leads to inflammatory bowel disease (IBD). Induced pluripotent stem cells (iPSCs) were generated from an infantile-onset IBD patient lacking a functional IL10RB gene. Mφs differentiated from IL-10RB-/- iPSCs lacked IL-10RB mRNA expression, were unable to phosphorylate STAT3, and failed to reduce LPS induced inflammatory cytokines in the presence of exogenous IL-10. IL-10RB-/- Mφs exhibited a striking defect in their ability to kill Salmonella enterica serovar Typhimurium, which was rescuable after experimentally introducing functional copies of the IL10RB gene. Genes involved in synthesis and receptor pathways for eicosanoid prostaglandin E2 (PGE2) were more highly induced in IL-10RB-/- Mφs, and these Mφs produced higher amounts of PGE2 after LPS stimulation compared with controls. Furthermore, pharmacological inhibition of PGE2 synthesis and PGE2 receptor blockade enhanced bacterial killing in Mφs. These results identify a regulatory interaction between IL-10 and PGE2, dysregulation of which may drive aberrant Mφ activation and impaired host defense contributing to IBD pathogenesis.

Journal article

Bashford-Rogers RJM, Bergamaschi L, McKinney EF, Pombal DC, Mescia F, Lee JC, Thomas DC, Flint SM, Kellam P, Jayne DRW, Lyons PA, Smith KGCet al., 2019, Analysis of the B cell receptor repertoire in six immune-mediated diseases, Nature, Vol: 574, Pages: 122-126, ISSN: 0028-0836

B cells are important in the pathogenesis of many, and perhaps all, immune-mediated diseases. Each B cell expresses a single B cell receptor (BCR)1, and the diverse range of BCRs expressed by the total B cell population of an individual is termed the ‘BCR repertoire’. Our understanding of the BCR repertoire in the context of immune-mediated diseases is incomplete, and defining this could provide new insights into pathogenesis and therapy. Here, we compared the BCR repertoire in systemic lupus erythematosus, anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis, Crohn’s disease, Behçet’s disease, eosinophilic granulomatosis with polyangiitis, and immunoglobulin A (IgA) vasculitis by analysing BCR clonality, use of immunoglobulin heavy-chain variable region (IGHV) genes and—in particular—isotype use. An increase in clonality in systemic lupus erythematosus and Crohn’s disease that was dominated by the IgA isotype, together with skewed use of the IGHV genes in these and other diseases, suggested a microbial contribution to pathogenesis. Different immunosuppressive treatments had specific and distinct effects on the repertoire; B cells that persisted after treatment with rituximab were predominately isotype-switched and clonally expanded, whereas the inverse was true for B cells that persisted after treatment with mycophenolate mofetil. Our comparative analysis of the BCR repertoire in immune-mediated disease reveals a complex B cell architecture, providing a platform for understanding pathological mechanisms and designing treatment strategies.

Journal article

Wei W, Tuna S, Keogh MJ, Smith KR, Aitman TJ, Beales PL, Bennett DL, Gale DP, Bitner-Glindzicz MAK, Black GC, Brennan P, Elliott P, Flinter FA, Floto RA, Houlden H, Irving M, Koziell A, Maher ER, Markus HS, Morrell NW, Newman WG, Roberts I, Sayer JA, Smith KGC, Taylor JC, Watkins H, Webster AR, Wilkie AOM, Williamson C, Attwood A, Brown M, Brod NC, Crisp-Hihn A, Davis J, Deevi SVV, Dewhurst EF, Edwards K, Erwood M, Fox J, Frary AJ, Hu F, Jolley J, Kingston N, Linger R, Mapeta R, Martin J, Meacham S, Papadia S, Rayner-Matthews PJ, Samarghitean C, Shamardina O, Simeoni I, Staines S, Staples E, Stark H, Stephens J, Titterton C, Tuna S, von Ziegenweidt J, Watt C, Whitehorn D, Wood Y, Yates K, Yu P, James R, Ashford S, Penkett CJ, Stirrups KE, Bariana T, Lentaigne C, Sivapalaratnam S, Westbury SK, Allsup DJ, Bakchoul T, Biss T, Boyce S, Collins J, Collins PW, Curry NS, Downes K, Dutt T, Erber WN, Evans G, Everington T, Favier R, Gomez K, Greene D, Gresele P, Hart D, Kazmi R, Kelly AM, Lambert M, Madan B, Mangles S, Mathias M, Millar C, Obaji S, Peerlinck K, Roughley C, Schulman S, Scully M, Shapiro SE, Sibson K, Simeoni I, Sims MC, Tait RC, Talks K, Thys C, Toh C-H, Van Geet C, Westwood J-P, Papadia S, Mumford AD, Ouwehand WH, Freson K, Laffan MA, Tan RYY, Harkness K, Mehta S, Muir KW, Hassan A, Traylor M, Drazyk AM, Markus HS, Parry D, Ahmed M, Kazkaz H, Vandersteen AM, Aitman TJ, Ormondroyd E, Thomson K, Dent T, Brennan P, Buchan RJ, Bueser T, Carr-White G, Cook S, Daniels MJ, Harper AR, Ware JS, Watkins H, Dixon PH, Chambers J, Cheng F, Estiu MC, Hague WM, Marschall H-U, Vazquez-Lopez M, Williamson C, Arno G, Dewhurst EF, Erwood M, French CE, Michaelides M, Moore AT, Sanchis-Juan A, Carss K, Webster AR, Raymond FL, Chinnery PF, Griffiths P, Horvath R, Hudson G, Jurkute N, Pyle A, Wei W, Yu-Wai-Man P, Whitworth J, Adlard J, Ahmed M, Armstrong R, Brewer C, Casey R, Cole TRP, Evans DG, Greenhalgh L, Hanson HL, Hoffman J, Izatt L, Kumar A, Lalloo F, Ong KR, Park S-M, Searet al., 2019, Germline selection shapes human mitochondrial DNA diversity, Science, Vol: 364, ISSN: 0036-8075

INTRODUCTIONOnly 2.4% of the 16.5-kb mitochondrial DNA (mtDNA) genome shows homoplasmic variation at >1% frequency in humans. Migration patterns have contributed to geographic differences in the frequency of common genetic variants, but population genetic evidence indicates that selection shapes the evolving mtDNA phylogeny. The mechanism and timing of this process are not clear.Unlike the nuclear genome, mtDNA is maternally transmitted and there are many copies in each cell. Initially, a new genetic variant affects only a proportion of the mtDNA (heteroplasmy). During female germ cell development, a reduction in the amount of mtDNA per cell causes a “genetic bottleneck,” which leads to rapid segregation of mtDNA molecules and different levels of heteroplasmy between siblings. Although heteroplasmy is primarily governed by random genetic drift, there is evidence of selection occurring during this process in animals. Yet it has been difficult to demonstrate this convincingly in humans.RATIONALETo determine whether there is selection for or against heteroplasmic mtDNA variants during transmission, we studied 12,975 whole-genome sequences, including 1526 mother–offspring pairs of which 45.1% had heteroplasmy affecting >1% of mtDNA molecules. Harnessing both the mtDNA and nuclear genome sequences, we then determined whether the nuclear genetic background influenced mtDNA heteroplasmy, validating our findings in another 40,325 individuals.RESULTSPreviously unknown mtDNA variants were less likely to be inherited than known variants, in which the level of heteroplasmy tended to increase on transmission. Variants in the ribosomal RNA genes were less likely to be transmitted, whereas variants in the noncoding displacement (D)–loop were more likely to be transmitted. MtDNA variants predicted to affect the protein sequence tended to have lower heteroplasmy levels than synonymous variants. In 12,975 individuals, we identified a correlation between

Journal article

Thomas DC, Charbonnier L-M, Schejtman A, Aldhekri H, Coomber EL, Dufficy ER, Beenken AE, Lee JC, Clare S, Speak AO, Thrasher AJ, Santilli G, Al-Mousa H, Alkuraya FS, Chatila TA, Smith KGCet al., 2019, EROS/CYBC1 mutations: Decreased NADPH oxidase function and chronic granulomatous disease, Journal of Allergy and Clinical Immunology, Vol: 143, Pages: 782-785.e1, ISSN: 0091-6749

Journal article

Doonan J, Thomas D, Wong MH, Ramage HJ, Al-Riyami L, Lumb FE, Bell KS, Fairlie-Clarke KJ, Suckling CJ, Michelsen KS, Jiang H-R, Cooke A, Harnett MM, Harnett Wet al., 2018, Failure of the anti-inflammatory parasiticWorm product ES-62 to provide protection in mouse models of Type I diabetes, multiple sclerosis, and inflammatory bowel disease, Molecules, Vol: 23, Pages: 1-14, ISSN: 1420-3049

Parasitic helminths and their isolated secreted products show promise as novel treatments for allergic and autoimmune conditions in humans. Foremost amongst the secreted products is ES-62, a glycoprotein derived from Acanthocheilonema viteae, a filarial nematode parasite of gerbils, which is anti-inflammatory by virtue of covalently-attached phosphorylcholine (PC) moieties. ES-62 has been found to protect against disease in mouse models of rheumatoid arthritis, systemic lupus erythematosus, and airway hyper-responsiveness. Furthermore, novel PC-based synthetic small molecule analogues (SMAs) of ES-62 have recently been demonstrated to show similar anti-inflammatory properties to the parent molecule. In spite of these successes, we now show that ES-62 and its SMAs are unable to provide protection in mouse models of certain autoimmune conditions where other helminth species or their secreted products can prevent disease development, namely type I diabetes, multiple sclerosis and inflammatory bowel disease. We speculate on the reasons underlying ES-62’s failures in these conditions and how the negative data generated may help us to further understand ES-62’s mechanism of action.

Journal article

Bashford-Rogers RJM, Smith KGC, Thomas DC, 2018, Antibody repertoire analysis in polygenic autoimmune diseases, Immunology, Vol: 155, Pages: 3-17, ISSN: 0019-2805

High‐throughput sequencing of the DNA/RNA encoding antibody heavy‐ and light‐chains is rapidly transforming the field of adaptive immunity. It can address key questions, including: (i) how the B‐cell repertoire differs in health and disease; and (ii) if it does differ, the point(s) in B‐cell development at which this occurs. The advent of technologies, such as whole‐genome sequencing, offers the chance to link abnormalities in the B‐cell antibody repertoire to specific genomic variants and polymorphisms. Here, we discuss the current research using B‐cell antibody repertoire sequencing in three polygenic autoimmune diseases where there is good evidence for a pathological role for B‐cells, namely systemic lupus erythematosus, multiple sclerosis and rheumatoid arthritis. These autoimmune diseases exhibit significantly skewed B‐cell receptor repertoires compared with healthy controls. Interestingly, some common repertoire defects are shared between diseases, such as elevated IGHV4‐34 gene usage. B‐cell clones have effectively been characterized and tracked between different tissues and blood in autoimmune disease. It has been hypothesized that these differences may signify differences in B‐cell tolerance; however, the mechanisms and implications of these defects are not clear.

Journal article

Thomas DC, 2018, How the phagocyte NADPH oxidase regulates innate immunity, Free Radical Biology and Medicine, Vol: 125, Pages: 44-52, ISSN: 0891-5849

The phagocyte NADPH oxidase is a multi subunit protein complex that generates reactive oxygen species at cell membranes and within phagosomes. It is essential for host defence as evidenced by the severe immunodeficiency syndrome caused by a loss of one of the subunits. This is known as chronic granulomatous disease (CGD). However, the phagocyte NADPH oxidase also has a key role to play in regulating immunity and it is notable that chronic granulomatous disease is also characterised by autoimmune and autoinflammatory manifestations. This is because reactive oxygen species play a role in regulating signalling through their ability to post-translationally modify amino acid residues such as cysteine and methionine. In this review, I will outline the major aspects of innate immunity that are regulated by the phagocyte NADPH oxidase, including control of transcription, autophagy, the inflammasome and type 1 interferon signalling.

Journal article

Thomas DC, 2017, The phagocyte respiratory burst: Historical perspectives and recent advances, Immunology Letters, Vol: 192, Pages: 88-96, ISSN: 0165-2478

When exposed to certain stimuli, phagocytes (including neutrophils, macrophages and eosinophils) undergo marked changes in the way they handle oxygen. Firstly, their rate of oxygen uptake increases greatly. This is accompanied by (i) the production of large amounts of superoxide and hydrogen peroxide and (ii) the metabolism of large quantities of glucose through the hexose monophosphate shunt. We now know that the oxygen used is not for respiration but for the production of powerful microbiocidal agents downstream of the initial production of superoxide. Concomitantly, glucose is oxidised through the hexose monophosphate shunt to re-generate the NADPH that has been consumed through the reduction of molecular oxygen to generate superoxide.This phagocyte respiratory burst is generated by an NADPH oxidase multi-protein complex that has a catalytic core consisting of membrane-bound gp91phox (CYBB) and p22phox (CYBA) sub-units and cytosolic components p47phox (NCF1), p67phox (NCF2) and p40phox (NCF4). Finally, another cytosolic component, the small G-protein Rac (Rac2 in neutrophils and Rac1 in macrophages) is also required for full activation. The importance of the complex in host defence is underlined by chronic granulomatous disease, a severe life-limiting immunodeficiency caused by mutations in the genes encoding the individual subunits.In this review, I will discuss the experimental evidence that underlies our knowledge of the respiratory burst, outlining how elegant biochemical analysis, coupled with study of patients deficient in the various subunits has helped elucidate the function of this essential part of innate immunity. I will also discuss some exciting recent studies that shed new light on how the abundance of the various components is controlled. Finally, I will explore the emerging role of reactive oxygen species such as superoxide and hydrogen peroxide in the pathogenesis of major human diseases including auto-inflammatory diseases.

Journal article

Sowerby JM, Thomas DC, Clare S, Espeli M, Guerrero JA, Hoenderdos K, Harcourt K, Marsden M, Abdul-Karim J, Clement M, Antrobus R, Umrania Y, Barton PR, Flint SM, Juss JK, Condliffe AM, Lyons PA, Humphreys IR, Chilvers ER, Ouwehand WH, Dougan G, Smith KGCet al., 2017, NBEAL2 is required for neutrophil and NK cell function and pathogen defense, Journal of Clinical Investigation, Vol: 127, Pages: 3259-3264, ISSN: 0021-9738

Mutations in the human NBEAL2 gene cause gray platelet syndrome (GPS), a bleeding diathesis characterized by a lack of α granules in platelets. The functions of the NBEAL2 protein have not been explored outside platelet biology, but there are reports of increased frequency of infection and abnormal neutrophil morphology in patients with GPS. We therefore investigated the role of NBEAL2 in immunity by analyzing the phenotype of Nbeal2-deficient mice. We found profound abnormalities in the Nbeal2-deficient immune system, particularly in the function of neutrophils and NK cells. Phenotyping of Nbeal2-deficient neutrophils showed a severe reduction in granule contents across all granule subsets. Despite this, Nbeal2-deficient neutrophils had an enhanced phagocyte respiratory burst relative to Nbeal2-expressing neutrophils. This respiratory burst was associated with increased expression of cytosolic components of the NADPH oxidase complex. Nbeal2-deficient NK cells were also dysfunctional and showed reduced degranulation. These abnormalities were associated with increased susceptibility to both bacterial (Staphylococcus aureus) and viral (murine CMV) infection in vivo. These results define an essential role for NBEAL2 in mammalian immunity.

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