Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease.Department of Health and Social Care (DHSC), Illumina, LifeArc, the Medical Research Council (MRC), UKRI, Sepsis Research (the Fiona Elizabeth Agnew Trust), the Intensive Care Society, a Wellcome Trust Senior Research Fellowship (J.K.B., 223164/Z/21/Z) a BBSRC Institute Program Support Grant to the Roslin Institute (BBS/E/D/20002172, BBS/E/D/10002070 and BBS/E/D/30002275) and UKRI grants MC_PC_20004, MC_PC_19025, MC_PC_1905 and MRNO2995X/1. WGS was performed by Illumina at Illumina Laboratory Services and was overseen by Genomics England. We would like to thank all at Genomics England who have contributed to the sequencing, clinical and genomic data analysis. This research is supported in part by the Data and Connectivity National Core Study, led by Health Data Research UK in partnership with the Office for National Statistics and funded by UK Research and Innovation (grant ref. MC_PC_20029). A.D.B. would like to acknowledge funding from the Wellcome PhD training fellowship for clinicians (204979/Z/16/Z) and the Edinburgh Clinical Academic Track (ECAT) programme. We thank the research participants and employees of 23andMe for making this work possible. Genomics England and the 100,000 Genomes Project were funded by the National Institute for Health Research, the Wellcome Trust, the MRC, Cancer Research UK, the DHSC and NHS England. We are grateful for the support from S. Hill and the team in NHS England and the 13 Genomic Medicine Centres that delivered the 100,000 Genomes Project, which provided most of the control genome sequences for this study. We thank the participants in the 100,000 Genomes Project, who made this study possible, and the Genomics England Participant Panel for their strategic advice, involvement and engagement. We acknowledge NHS Digital, Public Health England and the Intensive Care National Audit and Research Centre, who provided life-course longitudinal clinical data on the participants. This work forms part of the portfolio of research of the National Institute for Health Research Barts Biomedical Research Centre. Mark Caulfield is an NIHR Senior Investigator. This study owes a great deal to the National Institute for Healthcare Research Clinical Research Network (NIHR CRN) and the Chief Scientist’s Office (Scotland), who facilitate recruitment into research studies in NHS hospitals, and to the global ISARIC and InFACT consortia. Additional replication was conducted using the UK Biobank Resource (project 26041). The Penn Medicine BioBank is funded by a gift from the Smilow family; the National Center for Advancing Translational Sciences of the National Institutes of Health under CTSA award number UL1TR001878; and the Perelman School of Medicine at the University of Pennsylvania. We thank the AncestryDNA customers who voluntarily contributed information in the COVID-19 survey. HRS (dbGaP accession: phs000428.v1.p1): HRS was supported by the National Institute on Aging (NIA U01AG009740). The genotyping was funded separately by the National Institute on Aging (RC2 AG036495, RC4 AG039029). Genotyping was conducted by the NIH Center for Inherited Disease Research (CIDR) at Johns Hopkins University. Genotyping quality control and final preparation of the data were performed by the Genetics Coordinating Center at the University of Washington. The Genotype-Tissue Expression (GTEx) Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health, and by the NCI, NHGRI, NHLBI, NIDA, NIMH and NINDS. The data used for the analyses described in this manuscript were obtained from the GTEx Portal on 22 August 2021 (GTEx Analysis Release v.8 (dbGaP Accession phs000424.v8.p2). We thank the research participants and employees of 23andMe for making this work possible. A full list of contributors who have provided data that were collated in the HGI project, including previous iterations, is available at https://www.covid19hg.org/acknowledgements. The views expressed are those of the authors and not necessarily those of the DHSC, NHS, Department for International Development (DID), NIHR, MRC, Wellcome Trust or Public Health England

Spermatozoal sensitive biomarkers to defective protaminosis and fragmented DNA

Human sperm DNA damage may have adverse effects on reproductive outcome. Infertile men possess substantially more spermatozoa with damaged DNA compared to fertile donors. Although the extent of this abnormality is closely related to sperm function, the underlying etiology of ensuing male infertility is still largely controversial. Both intra-testicular and post-testicular events have been postulated and different mechanisms have been proposed to explain the presence of damaged DNA in human spermatozoa. Three among them, i.e. abnormal chromatin packaging, oxidative stress and apoptosis, are the most studied and discussed in the present review. Furthermore, results from numerous investigations are presented, including our own findings on these pathological conditions, as well as the techniques applied for their evaluation. The crucial points of each methodology on the successful detection of DNA damage and their validity on the appraisal of infertile patients are also discussed. Along with the conventional parameters examined in the standard semen analysis, evaluation of damaged sperm DNA seems to complement the investigation of factors affecting male fertility and may prove an efficient diagnostic tool in the prediction of pregnancy outcome

Susceptibility of sperm chromatin to acid denaturation in situ: A study in endogenous FSH-deprived adult male bonnet monkeys (Macaca radiata)

Acid denaturation of calf thymus DNA in vitro followed by acridine orange (AO) binding induced a 112% increase in the emission of red, a 58% decrease in green, and a consequential decrease in the ratio of green:red fluorescences from 1.7 to 0.9. This metachromatic property of AO on binding to DNA following acid denaturation was utilized to study the susceptibility of normal and ovine follicle-stimulating hormone (oFSH) actively immunized bonnet monkey spermatozoa voided throughout the year. For analyses, the scattergram generated by the emission of red and green fluorescences by 10,000 AO-bound sperm from each semen sample was divided into 4 quadrant zones representing percentage cells fluorescing high green-low red (Q1), high green-high red (Q2), low green-low red (Q3) and low green-high red. (Q4). Normal monkey sperm obtained during the months of July-December exhibited 76, 13, and 11% cells in Q2, Q3, and Q4 quadrants, respectively. However, during January-June, when the females of the species are markedly subfertile, noncycling, and amenorrhoeic, the spermatozoa ejaculated by the male monkeys exhibited 38, 39, and 23% sperm in Q2, Q3, and Q4, respectively, the differences being highly significant (p < .01-.001). FSH deprivation induced significant shifts in fluorescence emissions, from respective controls, with 39, 33, and 28% cells in Q2, Q3, and Q4, respectively, during July-December, and 15, 48, and 37% sperm in Q2, Q3, and Q4 quadrants, respectively, during January-June. It is postulated that the altered kinetics of germ cell transformations and the deficient spermiogenesis observed earlier following FSH deprivation in these monkeys may have induced the enhanced susceptibility to acid denaturation in sperm

Enhanced susceptibility of follicle-stimulating-hormone-deprived infertile bonnet monkey (Macaca radiata) spermatozoa to dithiothreitol-induced DNA decondensation in situ

Immunoneutralization of endogenous follicle-stimulating hormone (FSH) of adult male monkeys leads to oligospermia and infertility despite unchanged testosterone levels, The inability of these monkeys to impregnate despite repeated exposures to cycling females appeared to be due to abnormal alterations in the kinetics of germ cell transformations and deficient spermiogenesis. Here we investigated the stability of sperm chromatin in oFSH-immunized monkeys as a marker for spermiogenesis. The susceptibility of spermatozoa to in vitro decondensation induced by dithiothreitol (DTT, 0.05-50 mM) was studied by measuring the nuclear fluorescence of DTT-treated, ethidium bromide (EB)-stained sperm using flow cytometry. Changes in sperm morphology and binding of thiol-specific C-14-iodoacetamide (C-14-IA) were also monitored under the same conditions. Sperm from the immunized monkeys decondensed at a lower concentration of DTT, bound more EB, and decondensed more extensively than those from control animals. The difference was apparent in sperm from all regions of the epididymis. Immunized monkey sperm also bound significantly more C-14-IA at all concentrations of DTT. Overall, the effective concentration of DTT required to elicit 50% of maximal decondensation (ED50) of epididymal and ejaculated sperm was significantly lower for the immunized monkeys than even the caput sperm of controls. These results suggest that FSH deprivation in monkeys results in production of sperm with limited potential for disulfide formation and reduced chromatin stability

DNA flow-cytometric analysis of testicular germ cell populations of the bonnet monkey (Macaca radiata) as a function of sexual maturity

Testicular germ cell populations of biopsies from 32 male bonnet monkeys in 5 different age groups were quantitated in a flow cytometer after labelling of germ cell DNA with the specific fluorochrome, 4,6-diamidino phenyl indole. The 5 quantifiable populations were spermatogonia (2C), preleptotene spermatocytes (S phase), primary spermatocytes (4C), round spermatids (1C) and elongate spermatids (HC). The seminiferous tubules of immature 3-4-year-old monkey had only Sertoli cells and spermatogonia (2C). At 5-6 years, germ cells in S-phase (9.5%), 4C (11.1%), 1C (41.8%) and HC (17.1%) stages of maturation appeared for the first time but at 7-8 years of age and beyond all cell types except HC decreased while 1C remained relatively constant. Histometric analysis correlated well with the flow-cytometric data. The decrease in cells of 2C, S-phase and 4C stages was associated with an increase in mitotic index, signifying acceleration in the kinetics of germ cell transformation into subsequent cell types. The total turnover in cell transformation (1C:2C) was significantly (P less than 0.01) increased at and beyond 7-8 years. Maximum transition from 2C to 4C occurred at 5-6 years (4C:2C ratio 0.8 at 5-6 years and 0.6 at 7-8 years). The ratio HC:1C (kinetics of cell transformation during spermiogenesis) attained near total efficiency only by 10 years of age (1.08 at 10-14 years; 0.9 at 18-20 years). Also, the cell associations within the seminiferous tubules of monkeys greater than or equal to 10 years of age were better defined than those of younger animals. The changes in germ cell ratios correlated well with alterations in testicular volume, sperm numbers in the ejaculate and surges of testosterone and increments in FSH in the serum, characteristic of development of sexual maturity. It is apparent from this study that DNA flow cytometry of testicular germ cell populations reveals subtle changes in spermatogenic status of bonnet monkeys with a high degree of sensitivity

Identification, isolation, and characterization of a 41-kilodalton protein from rat germ cell-conditioned medium exhibiting concentration- dependent dual biological activities

In this report, we describe the purification of a novel protease with dual biological actions from germ cell-conditioned medium (GCCM) where germ cells were isolated from adult rat testes using a mechanical procedure. Using multiple HPLC columns and two sequential high performance electrophoresis chromatography steps in association with an [125I]-collagen film assay to detect protease activity, a 41-kDa polypeptide (41-kDa-P) was purified to apparent homogeneity from GCCM. Partial N-terminal amino acid sequence analysis of the purified protein revealed a sequence of NH2-KYEFYEIXLL that, when compared with the existing database at Protein Identification Resource (PIR), GenBank, and BLAST revealed that this is a unique protein. The purified protein, when incubated with [125I]-testin, a Sertoli cell secretary product that is localized at the intertesticular cell junction and is resistant to tryptic digest, was found capable of hydrolyzing testin dose dependently. The proteolysis of [125I]-testin by this 41-kDa protein was inhibited by α2-macroglobulin (a Sertoli cell secretary product) also in a dose-dependent manner. A study on the interactions between different classes of protease inhibitors and the purified 41-kDa protein revealed that it is a serine protease. At doses ranging between 0.5 and 50 ng/ml, 41-kDa-P induced a dose-dependent inhibition of Sertoli cell secretory function using testin and clusterin as markers without any apparent proteolytic activity. However, at doses greater than 0.5 μg/ml, 41-kDa-P was found to cleave [125I]- collagen and [125I]-testin at physiological pH, indicating that this 41- kDa protein has dual biological activities whose primary action is concentration dependent. In view of the biological activities of this protease, it is postulated that this protein may be involved in facilitating germ cell migration in the epithelium.published_or_final_versio

DNA flow-cytometric analysis of testicular germ cell populations of the bonnet monkey (Macaca radiata) as a function of sexual maturity

Testicular germ cell populations of biopsies from 32 male bonnet monkeys in 5 different age groups were quantitated in a flow cytometer after labelling of germ cell DNA with the specific fluorochrome, 4,6-diamidino phenyl indole. The 5 quantifiable populations were spermatogonia (2C), preleptotene spermatocytes (S phase), primary spermatocytes (4C), round spermatids (1C) and elongate spermatids (HC). The seminiferous tubules of immature 3-4-year-old monkey had only Sertoli cells and spermatogonia (2C). At 5-6 years, germ cells in S-phase (9.5%), 4C (11.1%), 1C (41.8%) and HC (17.1%) stages of maturation appeared for the first time but at 7-8 years of age and beyond all cell types except HC decreased while 1C remained relatively constant. Histometric analysis correlated well with the flow-cytometric data. The decrease in cells of 2C, S-phase and 4C stages was associated with an increase in mitotic index, signifying acceleration in the kinetics of germ cell transformation into subsequent cell types. The total turnover in cell transformation (1C:2C) was significantly (P less than 0.01) increased at and beyond 7-8 years. Maximum transition from 2C to 4C occurred at 5-6 years (4C:2C ratio 0.8 at 5-6 years and 0.6 at 7-8 years). The ratio HC:1C (kinetics of cell transformation during spermiogenesis) attained near total efficiency only by 10 years of age (1.08 at 10-14 years; 0.9 at 18-20 years). Also, the cell associations within the seminiferous tubules of monkeys greater than or equal to 10 years of age were better defined than those of younger animals. The changes in germ cell ratios correlated well with alterations in testicular volume, sperm numbers in the ejaculate and surges of testosterone and increments in FSH in the serum, characteristic of development of sexual maturity. It is apparent from this study that DNA flow cytometry of testicular germ cell populations reveals subtle changes in spermatogenic status of bonnet monkeys with a high degree of sensitivity

Long-term contraceptive efficacy of vaccine of ovine follicle-stimulating hormone in male bonnet monkeys (Macaca radiata)

A group of ten healthy fertile adult male bonnet monkeys were actively immunized using procedures acceptable for human use with pure follicle-stimulating hormone (oFSH) isolated from sheep pituitaries. The vaccine elicited an immunogenic response in all ten monkeys; the antibody-binding capacity, determined by Scatchard analysis, varied from 3 to 18 micrograms $oFSH ml^{-1}$, the binding affinity ranging from $0.13 to 2.0 \times 10(10) mol^{-1}$. A substantial population of antibodies against oFSH crossreacted with 125I-labelled human (h) FSH, used here as a representative ligand of primate FSH. The bioneutralization activity of the antisera assessed by a specific bioassay in vitro, when the antibody titre was high, was 6.9 $\pm$ 0.18 micrograms $hFSH ml^{-1}$. Immunization for 4.7-5.7 years did not affect the health and libido of the animals. Concentration of testosterone in serum remained normal throughout the study, but, within 150 days of immunization, there was a marked decrease (75-100%) in the number of spermatozoa in seminal ejaculates. Oligospermic status interspersed with azoospermia was maintained by periodic boosting. The fertility of these animals was monitored between 6 months and 2 years after primary immunization. All the ten animals proved infertile in repeated mating experiments with females of proven fertility. After stopping booster injections, nine of ten animals regained fertility, but the time taken for this depended upon the rate of decline of antibody titres. Re-boosting these monkeys with 100 micrograms oFSH after confirming that recovery had occurred revealed prompt increases in antibody titres followed once again by onset of oligo-azoospermia and infertility, underscoring the specificity of immunization effect. The immunized monkeys, apart from being acutely oligospermic, ejaculated spermatozoa that were markedly deficient in key acrosomal enzymes, such as acrosin and hyaluronidase, and motility as well as in their ability to penetrate a gel in vitro, suggesting that the infertility observed was due to gross reductions in the numbers of spermatozoa that could effectively interact with the oocyte and cause successful fertilization

Long-term contraceptive efficacy of vaccine of ovine follicle-stimulating hormone in male bonnet monkeys (Macaca radiata)

A group of ten healthy fertile adult male bonnet monkeys were actively immunized using procedures acceptable for human use with pure follicle-stimulating hormone (oFSH) isolated from sheep pituitaries. The vaccine elicited an immunogenic response in all ten monkeys; the antibody-binding capacity, determined by Scatchard analysis, varied from 3 to 18 micrograms $oFSH ml^{-1}$, the binding affinity ranging from $0.13 to 2.0 \times 10(10) mol^{-1}$. A substantial population of antibodies against oFSH crossreacted with 125I-labelled human (h) FSH, used here as a representative ligand of primate FSH. The bioneutralization activity of the antisera assessed by a specific bioassay in vitro, when the antibody titre was high, was 6.9 $\pm$ 0.18 micrograms $hFSH ml^{-1}$. Immunization for 4.7-5.7 years did not affect the health and libido of the animals. Concentration of testosterone in serum remained normal throughout the study, but, within 150 days of immunization, there was a marked decrease (75-100%) in the number of spermatozoa in seminal ejaculates. Oligospermic status interspersed with azoospermia was maintained by periodic boosting. The fertility of these animals was monitored between 6 months and 2 years after primary immunization. All the ten animals proved infertile in repeated mating experiments with females of proven fertility. After stopping booster injections, nine of ten animals regained fertility, but the time taken for this depended upon the rate of decline of antibody titres. Re-boosting these monkeys with 100 micrograms oFSH after confirming that recovery had occurred revealed prompt increases in antibody titres followed once again by onset of oligo-azoospermia and infertility, underscoring the specificity of immunization effect. The immunized monkeys, apart from being acutely oligospermic, ejaculated spermatozoa that were markedly deficient in key acrosomal enzymes, such as acrosin and hyaluronidase, and motility as well as in their ability to penetrate a gel in vitro, suggesting that the infertility observed was due to gross reductions in the numbers of spermatozoa that could effectively interact with the oocyte and cause successful fertilization