The Evolving Story Of Apolipoprotein L1 Nephropathy: The End Of The Beginning

Abstract | Genetic coding variants in APOL1, which encodes apolipoprotein L1 (APOL1), were identified in 2010 and are relatively common among individuals of sub-Saharan African ancestry. Approximately 13% of African Americans carry two APOL1 risk alleles. These variants, termed G1 and G2, are a frequent cause of kidney disease - termed APOL1 nephropathy - that typically manifests as focal segmental glomerulosclerosis and the clinical syndrome of hypertension and arterionephrosclerosis. Cell culture studies suggest that APOL1 variants cause cell dysfunction through several processes, including alterations in cation channel activity, inflammasome activation, increased endoplasmic reticulum stress, activation of protein kinase R, mitochondrial dysfunction, and disruption of APOL1 ubiquitinylation. The risk of APOL1 nephropathy is mostly confined to individuals with two APOL1 risk variants. However, only a minority of individuals with two APOL1 risk alleles develop kidney disease, suggesting the need for a 'second hit'. The best-recognized factor responsible for this 'second hit' is a chronic viral infection, particularly HIV-1, resulting in interferon-mediated activation of the APOL1 promoter, although most individuals with APOL1 nephropathy do not have an obvious cofactor. Current therapies for APOL1 nephropathies are not adequate to halt the progression of chronic kidney disease, and new targeted molecular therapies are in clinical trials.

NEW HERBAL FORMULATION FOR KIDNEY DISEASE

Since its discovery in 1997, research efforts have revealed the multifaceted nature of apolipoprotein L1 (APOL1) and, most notably, its implications for adaptation to parasitic diseases and the pathogenesis of kidney diseases. The discovery of variants in APOL1 in 2010 improved our understanding of the disproportionate prevalence of non-diabetic kidney diseases in individuals with sub-Saharan African ancestry1,2. Following the Allied victory at El Alamein in 1942, Winston Churchill said "It is not the end. It is not even the beginning of the end. But it is, perhaps, the end of the beginning". Now, around a decade after the discovery of APOL1 risk variants, we have perhaps reached the end of the beginning in our task to understand the spectrum and mechanisms of APOL1 nephropathies. However, we are only now beginning the search for effective treatments.

The APOL1 risk genotypes, defined by the G1 and G2 risk alleles, are absent in populations without African ancestry and likely evolved to protect carriers in West Africa from African sleeping sickness. The dispersion of people from West and Central Africa to the Americas and the Caribbean islands as a consequence of the trans-Atlantic slave trade and more recent migration has led to the global distribution of APOL1 variants4,5. The alleles are therefore common among African Americans, with a combined allele frequency of approximately 34%6,7. The association between APOL1 variants and kidney function is incompletely understood. The observation that a functional (non-pseudogenized) APOL1 gene exists in only a few African primate species and the identification of an APOL1-null individual with normal kidney function suggests that this gene is not required for normal kidney function8,9. From this perspective, the APOL1 coding variants associated with kidney disease seem to represent "gain of dysfunction" variants8,10. Thus, natural selection in sub-Saharan African populations likely shaped this locus by balancing the beneficial effects of the variants on trypanosomal immunity with detrimental effects on kidney function11. In addition to effects on primary glomerular diseases, these genetic variants might also modify outcomes in other renal and extrarenal conditions, such as kidney allografts, coronary artery disease, cardiomyopathies, and preeclampsia12–15.

This Review summarizes insights gained from research over the past decade into the role of APOL1 variants in kidney disease and provides context for findings that are expected to emerge in the coming years. We describe principal aspects of the APOL1 knowledge base, in particular focusing on findings most relevant to nephrology with an emphasis on our understanding of the genetics, protein structure, and biological functions of APOL1 variants and their associations with cardiorenal disease.

Key points

• In contrast to other APOL family members, which are primarily intracellular, APOL1 contains a unique secretory signal peptide, resulting in its secretion into plasma.

• APOL1 renal risk alleles protect African human trypanosomiasis but are a risk factor for progressive kidney disease in those carrying two risk alleles. 

• APOL1 risk allele frequency is ~35% in the African American population in the United States, with ~13% of individuals having two risk alleles; the highest allele frequencies are found in West African populations and their descendants. 

• Cell and mouse models implicate endolysosomal and mitochondrial dysfunction, altered ion channel activity, altered autophagy, and activation of protein kinase R in the pathogenesis of APOL1-associated kidney disease; however, the relevance of these injury pathways to human disease has not been resolved. 

• APOL1 kidney disease tends to be progressive, and current standard therapies are generally ineffective; targeted therapeutic strategies hold the most promise.

The APOL1 protein 

In 1997, researchers seeking to identify the protein components of ApoA1-containing lipoproteins - which are present in high-density lipoprotein (HDL) particles - isolated a novel protein, which was termed ApoL16. Four years later, they described three additional APOL family members, ApoL I–IV (now termed APOL 1–4). The APOL family expanded further in 2001 when two groups cloned the APOL gene cluster on chromosome 22, which also encodes APOL5 and APOL6 (refs17,18). Although some researchers continue to use "ApoL", consistent with protein terminology from the lipoprotein field, in this Review we use the HUGO Gene Nomenclature Committee-recommended nomenclature and style for human proteins (APOL) and genes (APOL) 17.

APOL1 RNA is expressed in many tissues18. APOL1 is unique among the APOL genes in encoding a secretory signal peptide, resulting in the secretion of APOL1 into plasma (Fig. 1a). However, APOL1 is present in humans and several Old World primates, but is otherwise absent in other mammals, indicating that APOL1 likely arose by tandem gene duplication during primate evolution around 30 million years ago19.

In 2009, studies of APOL family members showed that APOL1–6 are present in humans and that rapid evolution among simian primates occurred in domains involved in host-parasite interactions. In APOL1 for example, sequences with evidence of rapid evolution are present in or adjacent to the domain of APOL1, which interacts with the serum resistance antigen (SRA) in trypanosomes, likely reflecting a prolonged period of host-parasite interactions20.

Evolution of APOL1 variants 

The high burden of CKD and kidney failure - in particular, the strikingly high frequency of focal segmental glomerulosclerosis (FSGS) and HIV-associated nephropathy (HIVAN) - among African Americans suggested that particular risk variants were likely responsible and that such variants might be enriched on Africaninherited haplotypes. In 2008, two studies employed an admixture-mapping strategy to identify chromosomal segments of African origin enriched in patients with biopsy-confirmed FSGS and non-diabetic kidney failure. One group identified a region on chromosome 22, centered on MYH9, which was strongly associated with FSGS and HIVAN; this finding was replicated in patients with hypertensive nephrosclerosis and non-diabetic kidney failure, but not in patients with diabetes-associated kidney failure21. Another group identified the same African ancestry linkage region on chromosome 22 with non-diabetic kidney failure but similarly, not in patients with diabetes-associated kidney failure22. These findings led to the discovery 2 years later of African-specific variants in the APOL1 gene, which is adjacent to MYH9. The two studies identified three APOL1 variants nearby in the C-terminal SRA-binding domain of APOL1 (Fig. 1a) as being primarily responsible for the association with kidney disease1. The two variant haplotypes were termed G1 and G2, with G1 (rs73885319 and rs60910145) comprising two non-synonymous coding variants (Ser342Gly, Ile384Met), and G2 (rs71785313) consisting of a six-base-pair deletion resulting in two amino acid deletions: del Asn388 and del Tyr3891. In West Africans and their recent descendants, the two alleles (G1 and G2) form two common variant haplotypes and one infrequent haplotype (Fig. 1b) 13. The ancestral haplotype is termed G0 and does not carry G1 or G2 variants1,13. In the absence of G0, the risk variants showed a strong association with FSGS, non-diabetic kidney failure, and HIVAN, leading to the conclusion that they contribute to the overall higher risk of these kidney disorders in African Americans1,2,13 (Fig. 1c).

Loss of function or gain of dysfunction 

Except for one South African study, which showed a dominant association of G1 with HIVAN23, overwhelming evidence from case-control and cohort studies suggests that the APOL1 risk variants follow a recessive model of inheritance. Most recessive alleles are associated with a loss of gene function; however, some evidence suggests that APOL1 variants might counter this paradigm. Although at least one in vitro study did not observe toxicity following the expression of APOL1 risk variants in kidney cells, supporting a loss-of-function mechanism24, most studies suggest that APOL1 risk alleles follow a gain-of-dysfunction mechanism8,9. One model suggests that multimerization of APOL1 enables a recessive mode of inheritance with gain-of-dysfunction effects for G1 and G2 and suppression of toxicity by G0 (ref.25). Another study26 reported that G0 rescues G1 and G2 toxicity by transporting the variant proteins from the endoplasmic reticulum to the cytoplasm on lipid droplets; this model suggests that G0 may act as a dominant suppressor of toxicity by oligomerizing with the variant proteins and serving as a chaperone. Others have found that G1 and G2, but not G0, form multimers in the mitochondrial matrix and induce cell death by activating the mitochondrial permeability transition pore27. More recently, researchers have proposed a model in which risk alleles are associated with enhanced cation permease activity compared with the reference genotype28.

Fig. 1 | APOL1 domains and variants. a | The APOL1 protein has four functional domains and a signal peptide, which is required for secretion of liver-produced APOL1 into plasma. Forms of APOL1 that lack the signal peptide owing to alternative splicing are retained as intracellular proteins. The G1 and G2 variant isoforms are the primary drivers of APOL1-mediated chronic kidney disease (CKD). The presence of two missense mutations (Ser342Gly and Ile384Met) in the nucleotide sequence encoding the serum resistance-associated protein-binding domain of APOL1 generates the G1 variant, whereas a 6 base-pair deletion that results in the loss of two amino acids (delAsn388 and delTry389) generates the G2 variant. b | The three kidney risk variants form only four observed haplotypes. Owing to the close physical proximity of the three disease-associated alleles, recombination events have not been observed and therefore the G1 and G2 alleles are mutually exclusive and do not occur together on the same chromosome. The G1 and G2 haplotypes are unique to individuals with sub-Saharan ancestry whereas the ancestral G0 haplotype is found in all global populations. Haplotype frequencies are shown for a healthy African American population7. c | Susceptibility and resistance (indicated by red and blue shading, respectively) to acute human African trypanosomiasis (HAT) caused by Trypanosoma brucei rhodesiense and chronic HAT caused by T.b. gambiense, and risk of APOL1-associated CKD, vary as a function of APOL1 haplotype. Heterozygous or homozygous carriers of the G0 allele are not at increased risk of kidney disease. Carriers of 1 or 2 copies of the G1 allele are susceptible to infection by T.b. gambiense but are less likely to develop symptoms of HAT; the mechanism of this protective association is unknown. The G2 variant protein efficiently lyses T.b. rhodesiense in vitro, thereby limiting infection in G2 carriers. People with G1/G1, G2/G2, and G1/G2 genotypes are at an increased risk of CKD. In certain uncommon settings (for example, in individuals with untreated HIV infection), G1/G0 individuals may also be at an increased risk of CKD.

Of note, a comparison of naturally occurring G1 and G2 haplotypes with the artificial haplotypes used in experimental models showed the existence of amino acid changes in other domains of the naturally occurringring G1 and G2 haplotypes that were not present in the commonly used artificial, reference haplotype29. These naturally occurring, linked variants affect the properties of the expressed protein and modify the degree of risk allele-mediated toxicity. These findings support the gain-of-toxicity hypothesis and further explain why some studies do not observe enhanced toxicity with the risk variants29. A 2020 study found that APOL1 risk alleles have dose-dependent toxic effects in human embryonic kidney HEK293 cells, resulting in loss of cell viability, cell swelling, and dysregulation of energy metabolism30. These effects were not attenuated by co-expression of G0, supporting the notion that the APOL1 risk alleles acquire toxicity in a gain-of-function manner.