Genetics, pathogenesis, and pathology of Alport syndrome (hereditary nephritis)

INTRODUCTION — Alport syndrome (previously referred to as hereditary nephritis) is an inherited progressive form of glomerular disease that is often associated with sensorineural hearing loss and ocular abnormalities [1].

The pathogenesis, genetics, and pathology of Alport syndrome will be reviewed here. The clinical manifestations and course, diagnosis, and treatment of Alport syndrome are discussed separately. (See "Clinical manifestations, diagnosis, and treatment of Alport syndrome (hereditary nephritis)".)

GENETICS

Overview — Alport syndrome is a primary basement membrane disorder arising from pathogenic variants in genes encoding several members of the collagen IV protein family [1].

Collagen IV molecules are composed of three alpha chains that form triple-helical structures through specific interactions of C-terminal noncollagenous domains [2]. Six distinct type IV collagen chains are encoded by six different genes that are distributed in head-to-head pairs (figure 1) on three chromosomes.

The genes include:

●COL4A1 and COL4A2 at 13q34

●COL4A3 and COL4A4 at 2q35-37

●COL4A5 and COL4A6 on chromosome X

The six alpha chains of collagen IV form three triple helical protomers: alpha-1-1-2, alpha-3-4-5, and alpha-5-5-6. These protomers are further organized into networks by end-to-end connections via C-terminal and N-terminal interactions.

Genetic analyses of affected families have identified the affected genes for the four different modes of transmission seen in patients with Alport syndrome, which are discussed in the following sections [1]:

●X-linked

●Autosomal recessive

●Autosomal dominant

●Digenic

Pathogenic variants in the COL4A3, COL4A4, and COL4A5 genes disrupt the synthesis and/or the formation of collagen IV alpha-3-4-5 protomers and networks. Based on pedigree studies, linkage analysis, and Sanger sequencing, the relative frequencies of the four genetic types were estimated at 80 percent for X-linked disease, 15 percent for autosomal recessive disease, less than 5 percent for autosomal dominant disease, and case reports for digenic inheritance. However, studies using next-generation sequencing in Alport families suggest that autosomal dominant Alport syndrome may occur more frequently (20 to 30 percent of patients) than previously thought [3,4].

X-linked inheritance — X-linked Alport syndrome accounts for of the majority of Alport syndrome cases. It arises from pathogenic variants in the COL4A5 gene on the X chromosome, which codes for the alpha-5(IV) chain of collagen IV [5-12].

Confirmation of the direct pathogenetic role of these mutations was provided by an animal model in which a specific known human nonsense mutation was introduced into the mouse COL4A5 gene [13]. The primary clinical and pathologic findings of human X-linked disease were recapitulated in this animal model.

This mode of inheritance leads to important clinical characteristics in affected families:

●Father-to-son transmission does not occur, since the father passes only the unaffected Y chromosome to the son.

●Females with X-linked Alport syndrome are heterozygous for disease-causing COL4A5 variants. Almost all heterozygotes have some degree of hematuria, and a significant minority develop kidney failure [14]. The variable course in females is probably due to lyonization, by which only one X chromosome is active per cell. As a result, in most females with X-linked Alport syndrome, roughly one-half of the cells will express the variant COL4A5 allele and the remaining cells the normal COL4A5 allele, leading to a variable phenotype that is generally less severe than in affected males. The influence of X-inactivation on kidney outcomes in heterozygotes has been confirmed in the X-linked Alport syndrome mouse model [15]. (See "Clinical manifestations, diagnosis, and treatment of Alport syndrome (hereditary nephritis)", section on 'Phenotype-genotype correlation'.)

Autosomal recessive inheritance — Autosomal recessive inheritance accounts for approximately 10 to 15 percent of patients with Alport syndrome [10]. It arises from genetic defects in either the COL4A3 or COL4A4 genes. The COL4A3 and COL4A4 genes encode the alpha-3(IV) chain (which contains the Goodpasture antigen) and the alpha-4(IV) chain, respectively.

Females are as severely affected as males [7,16,17], and the clinical manifestations in both sexes are virtually identical to those of classic X-linked Alport syndrome in males [14,16]. (See "Clinical manifestations, diagnosis, and treatment of Alport syndrome (hereditary nephritis)", section on 'Clinical manifestations and course'.)

Autosomal dominant inheritance — Studies utilizing next-generation sequencing have reported approximately 20 to 30 percent of patients with Alport syndrome have autosomal dominant disease, which arises from heterozygous variants in the COL4A3 or COL4A4 genes [3,4,18-20]. The clinical features of autosomal dominant genotype are variable, ranging from isolated microscopic hematuria to some individuals who progress to end-stage kidney disease. In a large case series of 82 families with 252 patients, pathogenic variants were identified for both the COL4A3 (107 patients from 35 families) and COL4A4 (133 patients from 43 families) genes [21]. In this cohort, microhematuria was the most common manifestations (92 percent), followed by proteinuria (65 percent), and extrarenal findings (eg, sensorineural hearing loss and ocular abnormalities) were rare. Approximately one-third of the cohort (n = 61) had progressive disease requiring kidney replacement therapy, all of whom had proteinuria.

It is unclear why some patients with heterozygous variants in the COL4A3 or COL4A4 genes exhibit progressive kidney disease (ie, autosomal dominant Alport syndrome), while others have nonprogressive or very slowly progressive kidney disease (historically called "thin basement membrane nephropathy," although some consider this condition to be a form of Alport syndrome) [1,19,20,22]. Some evidence suggests that genetic factors other than mutations in these genes may affect underlying clinical features [20]. (See "Thin basement membrane nephropathy (benign familial hematuria)".)

Digenic inheritance — Rarely, patients with coexisting mutations in COL4A3, COL4A4, and COL4A5 with digenic inheritance have been reported [23].

PATHOGENESIS — Elucidation of the pathogenesis of Alport syndrome was facilitated by the chance observation that the glomerular basement membrane (GBM) of most affected patients did not bind antibodies from patients with anti-GBM antibody disease (including Goodpasture syndrome) [2,24-26]. This finding suggested an abnormality in collagen IV, the protein target of anti-GBM antibodies. The alpha-3, alpha-4, and alpha-5(IV) chains are highly expressed and co-distributed within the normal GBM [27]. They form a collagen IV network within the GBM that is distinct from that formed by alpha-1(IV) and alpha-2(IV) chains (figure 1) [5,28]. Pathogenic genetic variants affecting the alpha-3, alpha-4, and alpha-5(IV) chains impair their deposition into this collagen network, leading to secondary changes in GBM and resident glomerular cells that predispose to the development of glomerulosclerosis. Abnormal expression of collagen IV alpha-3-4-5 networks in basement membranes of the eye and cochlea result in specific ocular anomalies and sensorineural hearing loss.

Monoclonal antibody probes have been used to determine the tissue distribution of the alpha-3, alpha-4, and alpha-5(IV) chains in normal tissues and tissues from Alport patients.

●Collagen IV chains are normally located in Bowman capsule and the basement membranes of the glomerulus, distal and collecting tubules, and basement membranes of the cochlea and eye [29,30]. Thus, an abnormality in any of these chains can impair the integrity of basement membranes in these sites, leading to the various clinical findings of Alport syndrome. In most patients with alpha-5(IV) variants, the alpha-3, alpha-4 chains, and alpha-5(IV) chains are all absent from the GBM [12,31]. However, transcription of the alpha-3(IV) and alpha-4(IV) genes is not turned off in the kidney cortex, suggesting that failure of incorporation of these chains is responsible for the lack of glomerular expression and not failure of synthesis [32]. (See 'Kidney' below.)

●In normal individuals, the alpha-5(IV) chain is present in the basement membrane underlying the epidermis as a component of alpha-5-5-6 networks. In individuals with variants in the COL4A5 gene on the X chromosome (ie, X-linked inheritance), there is complete absence of alpha-5(IV) chain within epidermal basement membranes in most affected males. (See 'Skin' below.)

PATHOLOGY

Kidney

Immunostaining — Immunostaining of kidney biopsy specimens for collagen IV can be diagnostic for patients with suspected Alport syndrome (figure 2).

●X-linked disease – Males with X-linked Alport syndrome typically show complete absence of immunostaining for the alpha-3, alpha-4, and alpha-5(IV) chains in their kidneys, while heterozygous females exhibit patchy loss of staining in GBM and tubular basement membranes. (See 'Pathogenesis' above.)

As with skin staining for the alpha-5(IV) chain, approximately 20 percent of males with X-linked Alport syndrome have normal staining of kidney basement membranes for the alpha-3, alpha-4, and alpha-5(IV) chains. Further quantitative analysis reveals lower amounts of the alpha-3, alpha-4, and/or alpha-5(IV) chains in these cases compared with healthy controls [33]. Some of these patients have missense variants of COL4A5, which may explain the detection of alpha IV chains with immunostaining, albeit with decreased intensity [34].

●Autosomal recessive disease – Individuals with autosomal recessive Alport syndrome have abnormalities of collagen IV expression that differ from those of patients with X-linked disease. These patients typically exhibit complete absence of staining for the alpha-3 and alpha-4(IV) chains. However, while their glomerular basement membranes (GBMs) show no staining for the alpha-5(IV) chain, there is staining of Bowman capsules and distal tubular basement membranes for the alpha-5(IV) chain. This observation can be interpreted as failure of the alpha-5(IV) chain to be deposited in the GBM due to the absence of the alpha-3 and alpha-4(IV) chains, but the alpha-5(IV) chain, in conjunction with the alpha-6(IV) chain, is deposited in the basement membranes of the distal tubule, Bowman capsules, and epidermis.

Histologic changes — The changes on light microscopy are nonspecific and include focal increases in glomerular cellularity, progressing to glomerulosclerosis and interstitial fibrosis-tubular atrophy over time, and an interstitial infiltrate containing lipid-laden foam cells. Histologic changes in Alport syndrome typically increase in severity with age.

The earliest ultrastructural lesion is thinning of the GBM [5,35]. With time, there is development of longitudinal splitting of the lamina densa of the GBM, producing a laminated appearance that is diagnostic of Alport syndrome (picture 1A-B). In males with X-linked Alport syndrome, the proportion of GBM showing splitting increases from approximately 30 percent by age 10 to more than 90 percent by age 30 [35]. A similar progression likely occurs in patients with autosomal recessive Alport syndrome. Females with X-linked Alport syndrome, and males and females with autosomal dominant Alport syndrome, may have thin GBM or a mix of thin and lamellated GBM. (See "Thin basement membrane nephropathy (benign familial hematuria)".)

Kidney biopsy of affected individuals at a young age may manifest only nonspecific light microscopic changes and no definitive electron microscopic findings. However, results of immunostaining for collagen IV alpha chains are frequently diagnostic even in the absence of specific ultrastructural changes. In some patients, less invasive skin biopsy with appropriate immunohistochemical analysis may be the preferred diagnostic study. (See "Clinical manifestations, diagnosis, and treatment of Alport syndrome (hereditary nephritis)", section on 'Diagnosis' and 'Skin' below.)

Skin — Immunohistochemical studies with a monoclonal antibody directed against the alpha-5(IV) chain demonstrates complete absence of alpha-5(IV) chain within epidermal basement membranes in most males with X-linked Alport syndrome, while female carriers have discontinuous staining (picture 2) [29]. The latter observation is compatible with lyonization in female carriers, in whom it would be expected that one-half of their cells would express a normal alpha-5(IV) chain.

However, conventional immunofluorescence microscopy will detect alpha-5(IV) chain of the skin in approximately 20 percent of males with X-linked Alport syndrome and 30 to 40 percent of heterozygous females. All patients with autosomal recessive and autosomal dominant Alport syndrome have normal skin reactivity for alpha-5(IV) (picture 2). Thus, the presence of epidermal basement membrane staining for alpha-5(IV) does not exclude a diagnosis of X-linked or autosomal Alport syndrome. However, the absence of alpha-5(IV) chain in a skin biopsy is diagnostic of X-linked Alport syndrome.

Eye — Anterior lenticonus, which is associated with thinning of the lens capsule, occurs in 20 to 30 percent of males with X-linked Alport syndrome as well as in patients with autosomal recessive Alport syndrome. If present, anterior lenticonus is pathognomonic for Alport syndrome. The lens capsule normally contains alpha-3, alpha-4, and alpha-5(IV) chains. In some patients with anterior lenticonus, these chains are absent from the lens capsule basement membrane [36]. Other ocular findings in patients with Alport syndrome include a distinctive dot-fleck retinopathy and, rarely, macular holes, likely related to the abnormal collagen IV composition of retinal basement membranes.

Cochlea — Hearing loss in Alport syndrome likely reflects abnormal function of cochlear basement membranes due to the absence of the alpha-3-4-5 collagen IV network [37]. The precise mechanism for hearing loss in Alport syndrome remains under investigation.

Aorta and intracranial arteries — A growing number of case reports have described premature thoracoabdominal aortic aneurysm and dissection, as well as aneurysms of intracranial arteries, in patients, typically male, with X-linked Alport syndrome [38,39]. The collagen IV alpha-5-5-6 network is a normal component of arterial media, and its absence may predispose to aneurysm formation [40]. (See "Clinical manifestations, diagnosis, and treatment of Alport syndrome (hereditary nephritis)", section on 'Arterial disease'.)

Leiomyomas — Leiomyomas are benign tumors characterized by visceral smooth muscle overgrowth within the respiratory, gastrointestinal, and female reproductive tracts. Rarely, X-linked Alport syndrome is associated with leiomyomas. (See "Clinical manifestations, diagnosis, and treatment of Alport syndrome (hereditary nephritis)", section on 'Leiomyomatosis'.)

Individuals who develop leiomyomas carry deletions that involve COL4A5 and extend into the adjacent COL4A6 gene [41]. Of note, defects in the alpha-6 chain gene alone do not appear to cause Alport syndrome [5]. The pathogenetic relationship between deletions of the 5' end of the COL4A6 gene and the formation of leiomyomas is not understood. One hypothesis suggests that deletions that encompass both the COL4A5 and COL4A6 genes cause misregulation of neighboring genes, which contribute to smooth muscle overgrowth [41].

SUMMARY

●Introduction – Alport syndrome (hereditary nephritis) is a progressive inherited form of glomerular disease that is often associated with sensorineural hearing loss and ocular abnormalities. (See 'Introduction' above.)

●Genetics – Alport syndrome is a primary basement membrane disorder arising from mutations in genes encoding several members of the collagen IV protein family. It is a genetically heterogeneous disease with X-linked, autosomal recessive, and autosomal dominant variants. (See 'Genetics' above.)

•The X-linked form accounts for the majority of affected patients. It arises from variants in the COL4A5 gene on the X chromosome, which encodes alpha-5(IV) chains. (See 'X-linked inheritance' above.)

•The autosomal recessive form accounts for approximately 15 percent of patients with Alport syndrome. It arises from genetic defects in either the COL4A3 or COL4A4 genes, which encodes the alpha-3 and alpha-4(IV) chains, respectively. The clinical manifestations of affected patients regardless of sex are very similar to those of male patients with X-linked Alport syndrome. (See 'Autosomal recessive inheritance' above and "Clinical manifestations, diagnosis, and treatment of Alport syndrome (hereditary nephritis)".)

•Autosomal dominant disease appears to account for 20 to 30 percent of patients with Alport syndrome, based on results of next-generation sequencing studies. It arises from heterozygous variants in the COL4A3 or COL4A4 genes. The clinical and pathologic features of this form of Alport syndrome are similar to those of X-linked disease, although deterioration of kidney function tends to occur more slowly and sensorineural hearing loss and ocular abnormalities are unusual. (See 'Autosomal dominant inheritance' above.)

●Pathogenesis – Pathogenic variants in genes that encode the alpha-3, alpha-4, and alpha-5(IV) chains cause disruption of the normal collagen network (figure 1) found in the basement membrane of the cochlea; eye; and the kidney's Bowman capsule, glomerulus, and distal and collecting tubules. These abnormalities impair the integrity of basement membranes in these sites, leading to the various clinical findings of Alport syndrome. (See "Clinical manifestations, diagnosis, and treatment of Alport syndrome (hereditary nephritis)", section on 'Clinical manifestations and course' and 'Pathogenesis' above.)

●Pathology

•Immunostaining – In patients with Alport syndrome, immunostaining of kidney tissue is usually diagnostic demonstrating absence of alpha-3, alpha-4, and alpha-5(IV) chains. In addition, immunostaining of skin tissue directed against the alpha-5(IV) chain demonstrates complete absence of alpha-5(IV) chain within epidermal basement membranes in most males with X-linked Alport syndrome. (See 'Immunostaining' above and 'Skin' above.)

•Histology – Histologic changes in the kidney increase in severity with age. The earliest finding is thinning of the glomerular basement membrane (GBM). With increasing age, longitudinal splitting of the lamina densa of the GBM produces a laminated appearance that is diagnostic of Alport syndrome and is present in 90 percent of male patients by 30 years of age (picture 1A-B). (See 'Histologic changes' above.)