HostSeq: a Canadian whole genome sequencing and clinical data resource

HostSeq was launched in April 2020 as a national initiative to integrate whole genome sequencing data from 10,000 Canadians infected with SARS-CoV-2 with clinical information related to their disease experience. The mandate of HostSeq is to support the Canadian and international research communities in their efforts to understand the risk factors for disease and associated health outcomes and support the development of interventions such as vaccines and therapeutics. HostSeq is a collaboration among 13 independent epidemiological studies of SARS-CoV-2 across five provinces in Canada. Aggregated data collected by HostSeq are made available to the public through two data portals: a phenotype portal showing summaries of major variables and their distributions, and a variant search portal enabling queries in a genomic region. Individual-level data is available to the global research community for health research through a Data Access Agreement and Data Access Compliance Office approval. Here we provide an overview of the collective project design along with summary level information for HostSeq. We highlight several statistical considerations for researchers using the HostSeq platform regarding data aggregation, sampling mechanism, covariate adjustment, and X chromosome analysis. In addition to serving as a rich data source, the diversity of study designs, sample sizes, and research objectives among the participating studies provides unique opportunities for the research community.

Impact of maternal pre-pregnancy overweight on infant overweight at 1 year of age: associations and sex-specific differences

BACKGROUND

Maternal overweight or obesity (OWOB) is linked to gestational diabetes, fetal macrosomia and higher rates of caesarean delivery.

OBJECTIVES

The study aims to assess whether maternal pre-pregnancy OWOB is associated with infant overweight in a sex-dependent manner, independent of microbiota-altering variables.

METHODS

Weight and length measurements of 955 mother-infant pairs were obtained from the Canadian Healthy Infant Longitudinal Development cohort. Maternal pre-pregnancy weight was defined as follows: normal, overweight (25 ≤ body mass index < 30) and obese (body mass index ≥ 30). Age and sex-adjusted weight-for-length z-scores >97th percentile were classified as infant overweight at age 1 year. Associations between pre-pregnancy and infant overweight were determined by linear and logistic regression, adjusting for covariates.

RESULTS

Maternal pre-pregnancy OWOB were associated with infant weight-for-length and overweight risk at 1 year. Except for pre-pregnancy obesity, these associations were not attenuated appreciably after adjustment for birth mode, exclusivity of breastfeeding, exposure to antibiotics and infant sex. Yet only boys born to mothers with obesity were three times more likely to become overweight at age 1 independent of microbiota-altering variables. Pre-pregnancy obesity was associated with weight-for-length in male and female infants.

CONCLUSIONS

Maternal pre-pregnancy OWOB increases the risk of infant overweight, and this association is more evident in male infants.

Impact of maternal intrapartum antibiotics, method of birth and breastfeeding on gut microbiota during the first year of life: a prospective cohort study

OBJECTIVE

Dysbiosis of the infant gut microbiota may have long-term health consequences. This study aimed to determine the impact of maternal intrapartum antibiotic prophylaxis (IAP) on infant gut microbiota, and to explore whether breastfeeding modifies these effects.

DESIGN

Prospective pregnancy cohort of Canadian infants born in 2010-2012: the Canadian Healthy Infant Longitudinal Development (CHILD) Study.

SETTING

General community.

SAMPLE

Representative sub-sample of 198 healthy term infants from the CHILD Study.

METHODS

Maternal IAP exposures and birth method were documented from hospital records and breastfeeding was reported by mothers. Infant gut microbiota was characterised by Illumina 16S rRNA sequencing of faecal samples at 3 and 12 months.

MAIN OUTCOME MEASURES

Infant gut microbiota profiles.

RESULTS

In this cohort, 21% of mothers received IAP for Group B Streptococcus prophylaxis or pre-labour rupture of membranes; another 23% received IAP for elective or emergency caesarean section (CS). Infant gut microbiota community structures at 3 months differed significantly with all IAP exposures, and differences persisted to 12 months for infants delivered by emergency CS. Taxon-specific composition also differed, with the genera Bacteroides and Parabacteroides under-represented, and Enterococcus and Clostridium over-represented at 3 months following maternal IAP. Microbiota differences were especially evident following IAP with emergency CS, with some changes (increased Clostridiales and decreased Bacteroidaceae) persisting to 12 months, particularly among non-breastfed infants.

CONCLUSIONS

Intrapartum antibiotics in caesarean and vaginal delivery are associated with infant gut microbiota dysbiosis, and breastfeeding modifies some of these effects. Further research is warranted to explore the health consequences of these associations.

TWEETABLE ABSTRACT

Maternal #antibiotics during childbirth alter the infant gut #microbiome.

The Canadian healthy infant longitudinal development birth cohort study: biological samples and biobanking

BACKGROUND

It is hypothesised that complex interactions between genetic and environmental factors give rise to allergy and asthma in childhood. The Canadian Healthy Infant Longitudinal Development (CHILD) study was designed to explore these factors.

METHODS

CHILD is a longitudinal, general population birth cohort study following infants from mid-pregnancy to age 5 years. Over this time period, biological samples, questionnaires, clinical measures and environmental data are collected.

RESULTS

A total of 3624 families have been recruited, and many thousands of samples and questionnaires have been collected, annotated, and archived. This report outlines the rationale and methodology for collecting and storing diverse biological samples from parents and children in this study, and the mechanisms for their release for analyses.

CONCLUSIONS

The CHILD sample and data repository is a tremendous current and future resource and will provide a wealth of information not only informing studies of asthma and allergy, but also potentially in many other aspects of health relevant for Canadian infants and children.

Primary immunodeficiency diseases: a practical guide for clinicians

Primary immunodeficiency diseases (PIDs) are genetically determined disorders of the immune system resulting in greatly enhanced susceptibility to infectious disease, autoimmunity and malignancy. While individual PIDs are rare, as a group, it is estimated that between 1:2000 and 1:10 000 live births are affected by a PID. Moreover, PIDs can present at any age from birth to adulthood, posing a considerable challenge for the practising physician to know when and how to work-up a patient for a possible immune defect. In this review, we outline the basic organisation of the human immune system and the types of infections that occur when elements of the immune system are dysfunctional. Importantly, we provide practical guidelines for identifying patients who should be referred for assessment of possible immunodeficiency and an overview of screening investigations and effective therapeutic options available for these patients.

Toll-like receptor 4 polymorphisms and idiopathic chromosomally normal miscarriage

BACKGROUND

Lipopolysaccharide (LPS or endotoxin) exposure resulting from microbial invasion of the endometrium disturbs the Th1/Th2 balance at the feto-maternal interface and has been linked to the risk of idiopathic miscarriage in a range of human and animal studies. Toll-like receptor 4 (TLR4) mediates LPS signalling, and the human TLR4 gene harbours two single-nucleotide polymorphisms (SNPs) known to reduce LPS responsiveness. We hypothesized that genetic variation altering TLR4 function may influence the risk of idiopathic pregnancy loss.

METHODS AND RESULTS

We examined fetal TLR4 genotypes in a case-control cohort of chromosomally normal miscarriages (n=96) and healthy term newborns (n=113). The allele frequencies of the Asp299Gly and Thr399Ile TLR4 SNPs were determined by quantitative PCR using DNA extracted from extraembryonic tissues and umbilical cord blood, respectively. TLR4 genotype frequencies were not significantly different between cases and controls.

CONCLUSIONS

There was no association between fetal TLR4 polymorphisms, Asp299Gly and Thr399Ile, known to blunt LPS responsiveness, and the risk of idiopathic, chromosomally normal miscarriage. Nevertheless, TLR4 or perhaps other LPS-binding chaperone molecules are biologically plausible candidate genes that may alter the risk of idiopathic miscarriage.

The Wiskott-Aldrich syndrome

The Wiskott-Aldrich Syndrome (WAS) is an inherited immunodeficiency caused by a variety of mutations in the gene encoding the WAS protein (WASp). WASp is expressed in hematopoetic cells and facilitates the reorganization of the actin cytoskeleton in response to many important cell stimuli. Extensive study of WAS and more recently WASp has given great insight into the relevance of this molecule and related molecules to both basic cell biology and human immune defenses.

IL-10 is required for regulatory T cells to mediate tolerance to alloantigens in vivo

We present evidence that donor-reactive CD4(+) T cells present in mice tolerant to donor alloantigens are phenotypically and functionally heterogeneous. CD4(+) T cells contained within the CD45RB(high) fraction remained capable of mediating graft rejection when transferred to donor alloantigen-grafted T cell-depleted mice. In contrast, the CD45RB(low) CD4(+) and CD25(+)CD4(+) populations failed to induce rejection, but rather, were able to inhibit rejection initiated by naive CD45RB(high) CD4(+) T cells. Analysis of the mechanism of immunoregulation transferred by CD45RB(low) CD4(+) T cells in vivo revealed that it was donor Ag specific and could be inhibited by neutralizing Abs reactive with IL-10, but not IL-4. CD45RB(low) CD4(+) T cells from tolerant mice were also immune suppressive in vitro, as coculture of these cells with naive CD45RB(high) CD4(+) T cells inhibited proliferation and Th1 cytokine production in response to donor alloantigens presented via the indirect pathway. These results demonstrate that alloantigen-specific regulatory T cells contained within the CD45RB(low) CD4(+) T cell population are responsible for the maintenance of tolerance to donor alloantigens in vivo and require IL-10 for functional activity.

Differential susceptibility of heart, skin, and islet allografts to T cell-mediated rejection

Although it is widely accepted that there is a hierarchy in the susceptibility of different allografts to rejection, the mechanisms responsible are unknown. We show that the increased susceptibility of H-2K(b+) skin and islet allografts to rejection is not based on their ability to activate more H-2K(b)-specific T cells in vivo; heart allografts stimulate the activation and proliferation of many more H-2K(b)-specific T cells than either skin or islet allografts. Rejection of all three types of graft generate memory cells by 25 days posttransplant. These data provide evidence that neither tissue-specific Ags nor, surprisingly, the number of APCs carried in the graft dictate their susceptibility to T cell-mediated rejection and suggest that the graft microenvironment and size may play a more important role in determining the susceptibility of an allograft to rejection and resistance to tolerance induction.

Islet allograft rejection can be mediated by CD4+, alloantigen experienced, direct pathway T cells of TH1 and TH2 cytokine phenotype

BACKGROUND

It is widely believed that Thl cells that secrete interferon-gamma are primarily involved in the rejection of allografts whereas Th2 cells [interleukin(IL) 4 and IL-10] are thought to be protective of this process. However, the exact role and specificity of these helper T lymphocytes in mediating allograft damage is presently unknown.

METHODS

Th0, Th1, and Th2 cell lines specific for the class II MHC molecule H2IAb were adoptively transferred into T cell deficient, syngeneic, diabetic mice before transplantation of fully allogeneic C57BL/10 (H2b) or (CBKxBALB/c)F1 (H2k/d+Kb) islet grafts. T cells were 5-(and-6-)-carboxyfluorescein diacetate succinimidyl ester- (CFSE) labeled to allow detection, immunohistochemistry was performed, and IL-4 transcripts within the rejected islet grafts were quantified by reverse transcriptase polymerase chain reaction (RT-PCR).

RESULTS

Adoptive transfer (IV) of Th0-, Th1-, and Th2 IAb-specific T cells resulted in rejection of H2b islet allografts. CFSE-labeling demonstrated that these T cells were able to home to the graft site. CD4+ T cells and CD11b+ macrophages were present within the graft after adoptive transfer of both Thl and Th2 cells. Interestingly, CD8+ T cells and B cells were absent from these rejecting grafts. Even when Th2 cells were introduced directly at the graft site, prompt rejection was still observed despite the presence of increased IL-4 mRNA expression within the islet allografts.

CONCLUSIONS

Th2 and Th0 alloreactive CD4+ T helper cells can reject islet grafts with similar efficiency to Th1 cells. These results suggest that deviation of the immune response from a Th1 to Th2 phenotype will not be sufficient to allow successful engraftment of allogeneic organs or tissues.

Fas ligand-transfected myoblasts and islet cell transplantation

BACKGROUND

Expression of Fas ligand (FasL, CD95L) within the local environment of an allograft may protect from rejection by inducing apoptosis of infiltrating T cells. However, there is mounting evidence that ectopic expression of FasL stimulates an inflammatory response and targets the FasL-expressing tissue for destruction. Given the potential therapeutic applicability of FasL-based immune protection, we sought to determine whether ectopic FasL expression was detrimental and to analyze the inflammatory response induced by ectopic FasL expression in the absence of any confounding allo-immune responses.

METHODS AND RESULTS

Two myoblast cell lines expressing different levels of functional FasL were produced. Co-implantation of FasL-expressing myoblasts with syngeneic islets allowed examination of the inflammatory response induced by ectopic FasL expression. In contrast to the suggested benefits of localized FasL expression, islets co-implanted with FasL-expressing myoblasts were destroyed in a vigorous inflammatory response predominated by neutrophils. Interestingly, FasL expression also had a marked anti-tumor effect.

CONCLUSIONS

Unless FasL-dependent neutrophil-mediated inflammation can be prevented, it is unlikely that this strategy will be useful for preventing allograft rejection.

Immunobiology of solid organ transplantation

The field of organ transplantation is entering a very exciting phase in which tolerance induction may become a therapeutic possibility. The induction of tolerance would allow patients to enjoy the benefits of their transplanted organ without risking the mortality and morbidity associated with long-term pharmacological immunosuppression. In this review, we explore the immunobiology of solid organ transplantation, discussing the immunological mechanisms responsible for allograft rejection, and outlining the rational behind a range of successful experimental tolerance induction strategies.

Mechanisms of tolerance induction after intrathymic islet injection: determination of the fate of alloreactive thymocytes

BACKGROUND

Intrathymic (IT) administration of antigen when combined with peripheral T-cell depletion has been shown to induce operational tolerance in a wide range of experimental protocols. IT injection of pancreatic islets has been demonstrated not only to induce tolerance to alloantigen but also to prevent the development of autoimmune beta-cell destruction in models of type I diabetes. However, little is known about the mechanisms involved in tolerance induction after IT islet injection.

METHODS AND RESULTS

A protocol for the induction of tolerance to fully allogeneic (C57BL/10; H2b) peripheral islet allografts was developed in CBA/Ca (H2k) recipients by the IT injection of allogeneic islets combined with depletion of peripheral CD4+ T cells. This protocol was based upon our own data and those of others showing that CD4+ T cells play a critical role in islet allograft rejection. Using this regimen, donor-type peripheral islet allografts survived indefinitely whereas third-party grafts were rejected. To determine the fate of alloreactive thymocytes that recognize donor major histocompatibility complex antigens via the direct pathway, T-cell receptor transgenic mice specific for the major histocompatibility complex class I molecule Kb (BM3 and DES) were used as recipients. IT injection of islets expressing the specific alloantigen Kb resulted in clonal deletion of alloreactive thymocytes in T-cell receptor transgenic recipients. No evidence of clonal inactivation in the residual peripheral alloreactive population was observed in this system.

CONCLUSIONS

IT injection of allogeneic islets and concomitant CD4+ T-cell depletion is able to induce donor-specific unresponsiveness. One mechanism responsible for this unresponsiveness is the clonal deletion of thymocytes that recognize alloantigen via the direct pathway.

The visualization of T cell responses

Transplanting allogeneic grafts is still significantly hampered by the rejection process, despite the use of powerful immunosuppressive agents. The T cell is recognized as playing a central role in the process of rejection, and it is believed that graft tolerance will ultimately be achieved by immunological manipulation of this cell (1, 2). As immunologists strive to define the role of the T cell in the fundamental processes of immunity and tolerance, new methods are emerging that will facilitate visualization of the T cells directly involved in the rejection response (3, 4). This overview addresses the visualization of T cell responses as made possible by these technological developments.

Changes in myoplasmic sodium concentration during exposure to lactate in perfused rat heart

OBJECTIVE

The free myoplasmic sodium concentration ([Na+]i) is thought to change during acidosis and ischaemia in the mammalian heart. Although there are methods available for measuring [Na+]i in isolated cells or small preparations, none is very effective in the isolated heart, which is one of the best models for studying ischaemia. The use of a fluorescent sodium indicator, sodium binding benzofuran isophthalate (SBFI), to measure [Na+]i in the isolated, perfused rat heart is described. This method was used to estimate the activity of the Na/H exchanger under conditions resembling some aspects of ischaemia.

METHODS

The acetoxymethyl ester of SBFI was loaded into the perfused rat heart via the perfusate. Fluorescence signals developed on loading and were shown to be [Na+]i sensitive. An in vivo calibration technique allowed the fluorescence signals to be converted to [Na+]i.

RESULTS

The [Na+]i under control conditions was 6.4 mM. When the hearts were exposed to 20 mM lactate at the normal extracellular pH (pHo = 7.4) for 10 min, developed pressure fell abruptly and then slowly recovered [Na+]i rose slowly by 1.5 mM during lactate exposure and paralleled the recovery of pressure. Exposure to lactate at reduced extracellular pH (pHo = 6.4) produced a larger rise in [Na+]i. In the presence of the Na/H exchange inhibitor 5-(N-methyl-N-isobutyl)-amiloride exposure to lactate caused a small fall in [Na+]i at pHo 7.4 and 6.4.

CONCLUSIONS

The advantages and disadvantages of SBFI as an [Na+]i indicator in the perfused heart are described. The Na/H exchanger is an important regulator of [Na+]i during lactate induced intracellular acidosis, and it remains active in the presence of a substantial extracellular acidosis. This shows that low pHo does not necessarily inhibit the Na/H exchanger. The use of SBFI to estimate [Na+]i in the perfused heart is novel and has considerable potential for studies of ischaemia and related conditions.

Intracellular calcium and myocardial function during ischemia

Cardiac ischemia causes a rapid decline in mechanical performance and, if prolonged, myocardial cell death occurs on reperfusion. The early decline in mechanical performance could, in principle, be caused either by reduced intracellular calcium release or by reduced responsiveness of the myofibrillar proteins to calcium. It is now known that intracellular calcium rises during ischemia and that the early decline in mechanical performance is caused largely by the inhibitory effects of phosphate and protons on the myofibrillar proteins. The rise of intracellular calcium during ischemia is related to the acidosis and is probably caused by calcium influx on the Na/Ca exchanger. This is triggered by a rise in intracellular sodium which enter the cell in exchange for protons on the Na/H exchanger. Intracellular calcium rises still further on reperfusion the elevation of calcium and the degree of muscle damage are closely correlated.

Three Cases of Endometriosis

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