New Genetic Loci Associated With Chronic Kidney Disease in an Indigenous Australian Population

Association of Integrated Proteomic and Metabolomic Modules with Risk of Kidney Disease Progression

Key Points

Background

Proteins and metabolites play crucial roles in various biological functions and are frequently interconnected through enzymatic or transport processes.

Methods

We present an integrated analysis of 4091 proteins and 630 metabolites in the Chronic Renal Insufficiency Cohort study (N=1708; average follow-up for kidney failure, 9.5 years, with 537 events). Proteins and metabolites were integrated using an unsupervised clustering method, and we assessed associations between clusters and CKD progression and kidney failure using Cox proportional hazards models. Analyses were adjusted for demographics and risk factors, including the eGFR and urine protein–creatinine ratio. Associations were identified in a discovery sample (random two thirds, n=1139) and then evaluated in a replication sample (one third, n=569).

Results

We identified 139 modules of correlated proteins and metabolites, which were represented by their principal components. Modules and principal component loadings were projected onto the replication sample, which demonstrated a consistent network structure. Two modules, representing a total of 236 proteins and 82 metabolites, were robustly associated with both CKD progression and kidney failure in both discovery and validation samples. Using gene set enrichment, several transmembrane-related terms were identified as overrepresented in these modules. Transmembrane–ephrin receptor activity displayed the largest odds (odds ratio=13.2, P value = 5.5×10−5). A module containing CRIM1 and NPNT expressed in podocytes demonstrated particularly strong associations with kidney failure (P value = 2.6×10−5).

Conclusions

This study demonstrates that integration of the proteome and metabolome can identify functions of pathophysiologic importance in kidney disease.

Novel genetic markers for chronic kidney disease in a geographically isolated population of Indigenous Australians: Individual and multiple phenotype genome-wide association study

BACKGROUND

Chronic kidney disease (CKD) is highly prevalent among Indigenous Australians, especially those in remote regions. The Tiwi population has been isolated from mainland Australia for millennia and exhibits unique genetic characteristics that distinguish them from other Indigenous and non-Indigenous populations. Notably, the rate of end-stage renal disease is up to 20 times greater in this population compared to non-Indigenous populations. Despite the identification of numerous genetic loci associated with kidney disease through GWAS, the Indigenous population such as Tiwi remains severely underrepresented and the increased prevalence of CKD in this population may be due to unique disease-causing alleles/genes.

METHODS

We used albumin-to-creatinine ratio (ACR) and estimated glomerular filtration rate (eGFR) to estimate the prevalence of kidney disease in the Tiwi population (N = 492) in comparison to the UK Biobank (UKBB) (N = 134,724) database. We then performed an exploratory factor analysis to identify correlations among 10 CKD-related phenotypes and identify new multi-phenotype factors. We subsequently conducted a genome-wide association study (GWAS) on all single and multiple phenotype factors using mixed linear regression models, adjusted for age, sex, population stratification, and genetic relatedness between individuals.

RESULTS

Based on ACR, 20.3% of the population was at severely increased risk of CKD progression and showed elevated levels of ACR compared to the UKBB population independent of HbA1c. A GWAS of ACR revealed novel association loci in the genes MEG3 (chr14:100812018:T:A), RAB36 (rs11704318), and TIAM2 (rs9689640). Additionally, multiple phenotypes GWAS of ACR, eGFR, urine albumin, and serum creatinine identified a novel variant that mapped to the gene MEIS2 (chr15:37218869:A:G). Most of the identified variants were found to be either absent or rare in the UKBB population.

CONCLUSIONS

Our study highlights the Tiwi population's predisposition towards elevated ACR, and the collection of novel genetic variants associated with kidney function. These associations may prove valuable in the early diagnosis and treatment of renal disease in this underrepresented population. Additionally, further research is needed to comprehensively validate the functions of the identified variants/genes.

From biocolonialism to emancipation: considerations on ethical and culturally respectful omics research with indigenous Australians

As part of a (bio)colonial project, the biological information of Indigenous Peoples has historically been under scientific scrutiny, with very limited benefits for communities and donors. Negative past experiences have contributed to further exclude Indigenous communities from novel developments in the field of omics research. Over the past decade, new guidelines, reflections, and projects of genetic research with Indigenous Peoples have flourished in Australia, providing opportunities to move the field into a place of respect and ethical relationships. This review explores the ethical and cultural implications of the use of biological samples from Indigenous communities in biomedical research. A structured framework outlining emerging topics of interest for the development of respectful omics research partnerships with Indigenous Australians is presented. This paper highlights aspects related to Indigenous governance, community and individual consent, respectful handling of biological samples, data management, and communication in order to protect Indigenous interests and rights and to promote communities' autonomy.

The pharmacogenomic landscape of an Indigenous Australian population

Background: Population genomic studies of individuals of Indigenous ancestry have been extremely limited comprising <0.5% of participants in international genetic databases and genome-wide association studies, contributing to a "genomic gap" that limits their access to personalised medicine. While Indigenous Australians face a high burden of chronic disease and associated medication exposure, corresponding genomic and drug safety datasets are sorely lacking. Methods: To address this, we conducted a pharmacogenomic study of almost 500 individuals from a founder Indigenous Tiwi population. Whole genome sequencing was performed using short-read Illumina Novaseq6000 technology. We characterised the pharmacogenomics (PGx) landscape of this population by analysing sequencing results and associated pharmacological treatment data. Results: We observed that every individual in the cohort carry at least one actionable genotype and 77% of them carry at least three clinically actionable genotypes across 19 pharmacogenes. Overall, 41% of the Tiwi cohort were predicted to exhibit impaired CYP2D6 metabolism, with this frequency being much higher than that for other global populations. Over half of the population predicted an impaired CYP2C9, CYP2C19, and CYP2B6 metabolism with implications for the processing of commonly used analgesics, statins, anticoagulants, antiretrovirals, antidepressants, and antipsychotics. Moreover, we identified 31 potentially actionable novel variants within Very Important Pharmacogenes (VIPs), five of which were common among the Tiwi. We further detected important clinical implications for the drugs involved with cancer pharmacogenomics such as thiopurines and tamoxifen, immunosuppressants like tacrolimus and certain antivirals used in the hepatitis C treatment due to potential differences in their metabolic processing. Conclusion: The pharmacogenomic profiles generated in our study demonstrate the utility of pre-emptive PGx testing and have the potential to help guide the development and application of precision therapeutic strategies tailored to Tiwi Indigenous patients. Our research provides valuable insights on pre-emptive PGx testing and the feasibility of its use in ancestrally diverse populations, emphasizing the need for increased diversity and inclusivity in PGx investigations.

The genomic landscape of blood groups in Indigenous Australians in remote communities

Background

Methods and materials

Results

Conclusion

Pharmacogenomic analysis of a genetically distinct Indigenous population

Indigenous Australians face a disproportionately severe burden of chronic disease relative to other Australians, with elevated rates of morbidity and mortality. While genomics technologies are slowly gaining momentum in personalised treatments for many, a lack of pharmacogenomic research in Indigenous peoples could delay adoption. Appropriately implementing pharmacogenomics in clinical care necessitates an understanding of the frequencies of pharmacologically relevant genetic variants within Indigenous populations. We analysed whole-genome sequence data from 187 individuals from the Tiwi Islands and characterised the pharmacogenomic landscape of this population. Specifically, we compared variant profiles and allelic distributions of previously described pharmacologically significant genes and variants with other population groups. We identified 22 translationally relevant pharmacogenomic variants and 18 clinically actionable guidelines with implications for drug dosing and treatment of conditions including heart disease, diabetes and cancer. We specifically observed increased poor and intermediate metabolizer phenotypes in the CYP2C9 (PM:19%, IM:44%) and CYP2C19 (PM:18%, IM:44%) genes.

Sociodemographic determinants of chronic kidney disease in Indigenous children

Rates of chronic kidney disease (CKD) are disproportionately increased in Indigenous peoples. The focus has traditionally been on adults, as they experience the highest rates of kidney failure requiring kidney replacement therapy. The impacts of colonization, systemic racism, and sociodemographic marginalization however impact the health of Indigenous peoples across the lifespan. This review presents the social context within which Indigenous children develop and the impact relevant to kidney health across the developmental stages. In utero exposures impact nephron endowment which can manifest in glomerular hyperfiltration and sclerosis as well as an increased risk of congenital anomalies of the kidney and urinary tract. Young children are at increased risk of autoimmune conditions, secondary to infectious and environmental exposures, and are also exposed to the impacts of a Western lifestyle manifesting early onset overweight/obesity. Adolescents begin to manifest more severe metabolic complications such as type 2 diabetes. The impacts of early onset diabetes are associated with aggressive kidney complications and high rates of kidney failure in young adulthood. Finally, the key elements of successful prevention and treatment strategies are discussed including the importance of screening for asymptomatic, modifiable early disease, linked with clinical primary and tertiary care follow-up, and culturally relevant and safe care.

A roadmap to increase diversity in genomic studies

Two decades ago, the sequence of the first human genome was published. Since then, advances in genome technologies have resulted in whole-genome sequencing and microarray-based genotyping of millions of human genomes. However, genetic and genomic studies are predominantly based on populations of European ancestry. As a result, the potential benefits of genomic research-including better understanding of disease etiology, early detection and diagnosis, rational drug design and improved clinical care-may elude the many underrepresented populations. Here, we describe factors that have contributed to the imbalance in representation of different populations and, leveraging our experiences in setting up genomic studies in diverse global populations, we propose a roadmap to enhancing inclusion and ensuring equal health benefits of genomics advances. Our Perspective highlights the importance of sincere, concerted global efforts toward genomic equity to ensure the benefits of genomic medicine are accessible to all.

Deletions in VANGL1 are a risk factor for antibody-mediated kidney disease

We identify an intronic deletion in VANGL1 that predisposes to renal injury in high risk populations through a kidney-intrinsic process. Half of all SLE patients develop nephritis, yet the predisposing mechanisms to kidney damage remain poorly understood. There is limited evidence of genetic contribution to specific organ involvement in SLE.1,2 We identify a large deletion in intron 7 of Van Gogh Like 1 (VANGL1), which associates with nephritis in SLE patients. The same deletion occurs at increased frequency in an indigenous population (Tiwi Islanders) with 10-fold higher rates of kidney disease compared with non-indigenous populations. Vangl1 hemizygosity in mice results in spontaneous IgA and IgG deposition within the glomerular mesangium in the absence of autoimmune nephritis. Serum transfer into B cell-deficient Vangl1+/- mice results in mesangial IgG deposition indicating that Ig deposits occur in a kidney-intrinsic fashion in the absence of Vangl1. These results suggest that Vangl1 acts in the kidney to prevent Ig deposits and its deficiency may trigger nephritis in individuals with SLE.

Birthweight and the Prevalence, Progression, and Incidence of CKD in a Multideterminant Model in a High-Risk Australian Aboriginal Community

INTRODUCTION

We have previously showed that albuminuria was associated with low birthweight in young adults in a remote Australian Aboriginal community that has high rates of kidney disease. Here we describe the association of birthweight with incidence and progression of kidney disease over time.

METHODS

Among 695 members of an Aboriginal community with recorded birthweights, urine albumin creatinine ratio (ACR) and estimated glomerular filtration rate (eGFR) were measured at ages 5 to 40 years, and follow-up values were measured or imputed again a median of 11.6 years later. Prevalence of markers on each occasion and change over time were evaluated in the context of birthweights and other potentially significant factors.

RESULTS

On the second screen, ACR was inversely and significantly correlated with birthweight and eGFR was directly correlated with birthweight. Increases in ACR and in proportions of persons who developed new-onset (incident) albuminuria between screens were higher in those of lower birthweights (<2.5 kg). Proportions of persons who lost ≥20% of their baseline eGFR were higher in the lower birthweight groups. Lower birthweights also amplified elevations of ACR associated with other risk factors, specifically higher body mass indexes (BMIs) and a prior history of poststreptococcal glomerulonephritis (PSGN). At both screens, progressively higher levels of ACR beyond the mid-microalbuminuria range were correlated with lower levels of eGFR.

CONCLUSIONS

Lower birthweight contributes to an excess of kidney disease and its progression in this population. Because an excess of low birthweight and episodes of PSGN are eminently preventable, substantial containment of kidney disease is feasible.

Diabetic kidney disease: Are the reported associations with single-nucleotide polymorphisms disease-specific?

BACKGROUND

The genetic backgrounds of diabetic kidney disease (DKD) and end-stage kidney disease (ESKD) have not been fully elucidated.

AIM

To examine the individual and cumulative effects of single-nucleotide polymorphisms (SNPs) previously associated with DKD on the risk for ESKD of diabetic etiology and to determine if any associations observed were specific for DKD.

METHODS

Fourteen SNPs were genotyped in hemodialyzed 136 patients with diabetic ESKD (DKD group) and 121 patients with non-diabetic ESKD (NDKD group). Patients were also re-classified on the basis of the primary cause of chronic kidney disease (CKD). The distribution of alleles was compared between diabetic and non-diabetic groups as well as between different sub-phenotypes. The weighted multilocus genetic risk score (GRS) was calculated to estimate the cumulative risk conferred by all SNPs. The GRS distribution was then compared between the DKD and NDKD groups as well as in the groups according to the primary cause of CKD.

RESULTS

One SNP (rs841853; SLC2A1) showed a nominal association with DKD (P = 0.048; P > 0.05 after Bonferroni correction). The GRS was higher in the DKD group (0.615 ± 0.260) than in the NDKD group (0.590 ± 0.253), but the difference was not significant (P = 0.46). The analysis of associations between GRS and individual factors did not show any significant correlation. However, the GRS was significantly higher in patients with glomerular disease than in those with tubulointerstitial disease (P = 0.014) and in those with a combined group (tubulointerstitial, vascular, and cystic and congenital disease) (P = 0.018).

CONCLUSION

Our results suggest that selected SNPs that were previously associated with DKD may not be specific for DKD and may confer risk for CKD of different etiology, particularly those affecting renal glomeruli.

The Gene-Drug Duality: Exploring the Pharmacogenomics of Indigenous Populations

While pharmacogenomic studies have facilitated the rapid expansion of personalized medicine, the benefits of these findings have not been evenly distributed. Genomic datasets pertaining to Indigenous populations are sorely lacking, leaving members of these communities at a higher risk of adverse drug reactions (ADRs), and associated negative outcomes. Australia has one of the largest Indigenous populations in the world. Pharmacogenomic studies of these diverse Indigenous Australian populations have been hampered by a paucity of data. In this article, we discuss the history of pharmacogenomics and highlight the inequalities that must be addressed to ensure equal access to pharmacogenomic-based healthcare. We also review efforts to conduct the pharmacogenomic profiling of chronic diseases among Australian Indigenous populations and survey the impact of the lack of drug safety-related information on potential ADRs among individuals in these communities.

Reported sources of health inequities in Indigenous Peoples with chronic kidney disease: a systematic review of quantitative studies

BACKGROUND

To summarise the evidentiary basis related to causes of inequities in chronic kidney disease among Indigenous Peoples.

METHODS

We conducted a Kaupapa Māori meta-synthesis evaluating the epidemiology of chronic kidney diseases in Indigenous Peoples. Systematic searching of MEDLINE, Google Scholar, OVID Nursing, CENTRAL and Embase was conducted to 31 December 2019. Eligible studies were quantitative analyses (case series, case-control, cross-sectional or cohort study) including the following Indigenous Peoples: Māori, Aboriginal and Torres Strait Islander, Métis, First Nations Peoples of Canada, First Nations Peoples of the United States of America, Native Hawaiian and Indigenous Peoples of Taiwan. In the first cycle of coding, a descriptive synthesis of the study research aims, methods and outcomes was used to categorise findings inductively based on similarity in meaning using the David R Williams framework headings and subheadings. In the second cycle of analysis, the numbers of studies contributing to each category were summarised by frequency analysis. Completeness of reporting related to health research involving Indigenous Peoples was evaluated using the CONSIDER checklist.

RESULTS

Four thousand three hundred seventy-two unique study reports were screened and 180 studies proved eligible. The key finding was that epidemiological investigators most frequently reported biological processes of chronic kidney disease, particularly type 2 diabetes and cardiovascular disease as the principal causes of inequities in the burden of chronic kidney disease for colonised Indigenous Peoples. Social and basic causes of unequal health including the influences of economic, political and legal structures on chronic kidney disease burden were infrequently reported or absent in existing literature.

CONCLUSIONS

In this systematic review with meta-synthesis, a Kaupapa Māori methodology and the David R Williams framework was used to evaluate reported causes of health differences in chronic kidney disease in Indigenous Peoples. Current epidemiological practice is focussed on biological processes and surface causes of inequity, with limited reporting of the basic and social causes of disparities such as racism, economic and political/legal structures and socioeconomic status as sources of inequities.

Association Between Indigenous Status and Severity of Coronary Artery Disease: A Comparison of Coronary Angiogram Findings in Patients With Chest Pain Presenting to a Regional Hospital Emergency Department

BACKGROUND

Coronary artery disease (CAD) remains the leading cause of death amongst Indigenous Australians accounting for 12.1% of all deaths in this population. However, there is little evidence to suggest that Indigenous status is an independent risk factor for the development of coronary artery disease. This study assessed the association between Indigenous status and the severity of CAD in patients presenting with chest pain at a regional hospital emergency department.

METHODS

This was a retrospective single-centre audit over 12 months from January to December 2017. Charts were reviewed for both Indigenous and non-Indigenous patients 18 years and older who presented with chest pain and subsequently underwent an invasive coronary angiogram. Multivariable logistic regression was performed to examine the association of Indigenous status with the severity of CAD.

RESULTS

Indigenous patients are 2.7 times more likely to experience significant CAD compared to non-Indigenous patients (Adjusted odds ratio [AOR]=2.73, 95% CI [1.38, 5.39], p≤0.001) even after adjusting for other risk factors. Those aged 65 years and older are more prone to significant CAD (AOR=2.96, 95% CI [1.12, 7.78], p=0.03), while women were less likely to have significant CAD compared to men, (AOR=0.46, 95% CI [0.27, 0.78], p<0.01).

CONCLUSION

In this study cohort, our analysis indicates that there is a strong association between Indigenous status and significant coronary artery disease, independent of the increased burden of traditional cardiovascular risk factors among Indigenous Australians.

Health Disparities among Australia's Remote-Dwelling Aboriginal People: A Report from 2020

BACKGROUND

Australia has 2 distinct indigenous groups, Torres Strait Islanders and Aborigines. The Aborigines, described in this report, first colonized the continent 65 millennia ago. Those still living in the Northern Territory (NT) retain much ancestrally derived genetic complement but also are the most health-challenged by environment and lifestyle in 21st century. Reports providing overviews of these disparities are, as yet, rare.

CONTENT

This review defines the studied population and then describes and attempts to explain contemporary clinical findings among Australia's remote-dwelling Aborigines, principally in the NT. The report is structured by life stage and then by organ system. Finally, a brief synthesis is advanced concerning the disparities that Australia's Aboriginals face.

SUMMARY

In 2015-2017, NT aboriginal life expectancy for people then born was 66.6 years for men and 69.9 years for women compared with 78.1 and 82.7 years, respectively, among nonindigenous Territorians. Principal causes of the reduced longevity, with nonindigenous comparisons, include adolescent pregnancy, with maternal use of alcohol and tobacco (each 7-fold greater); fetal alcohol spectrum disorder and attention deficit hyperactivity disorder; skin infections, both scabies and impetigo (50-fold greater); rheumatic heart disease (260-fold greater); premature acute myocardial infarction (9-fold greater); bronchiectasis (40-fold greater); lung cancer (2-fold greater); diabetes mellitus (10-fold greater); renal failure (30-fold greater); and suicide (2-fold greater). Some disease has genetic roots, secondary to prolonged genetic drift. Much arises from avoidable stressors and from contemporary environmental disparities in housing. The Europid diet is also not helpful.

Analysis of the F2LR3 (PAR4) Single Nucleotide Polymorphism (rs773902) in an Indigenous Australian Population

The F2RL3 gene encoding protease activated receptor 4 (PAR4) contains a single nucleotide variant, rs773902, that is functional. The resulting PAR4 variants, Thr120, and Ala120, are known to differently affect platelet reactivity to thrombin. Significant population differences in the frequency of the allele indicate it may be an important determinant in the ethnic differences that exist in thrombosis and hemostasis, and for patient outcomes to PAR antagonist anti-platelet therapies. Here we determined the frequency of rs773902 in an Indigenous Australian group comprising 467 individuals from the Tiwi Islands. These people experience high rates of renal disease that may be related to platelet and PAR4 function and are potential recipients of PAR-antagonist treatments. The rs773902 minor allele frequency (Thr120) in the Tiwi Islanders was 0.32, which is similar to European and Asian groups and substantially lower than Melanesians and some African groups. Logistic regression and allele distortion testing revealed no significant associations between the variant and several markers of renal function, as well as blood glucose and blood pressure. These findings suggest that rs773902 is not an important determinant for renal disease in this Indigenous Australian group. However, the relationships between rs773902 genotype and platelet and drug responsiveness in the Tiwi, and the allele frequency in other Indigenous Australian groups should be evaluated.