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CD46

CD46, also known as membrane cofactor protein (MCP), is a type I transmembrane encoded by the CD46 on 1q32 that functions as a key regulator of the . It acts as a cofactor for the factor I, facilitating the proteolytic inactivation of complement components C3b and C4b deposited on host cell surfaces, thereby protecting autologous cells from complement-mediated and . This regulatory role is essential for maintaining immune , as deficiencies or mutations in CD46 can lead to uncontrolled complement activation and associated pathologies. Structurally, CD46 consists of four extracellular complement control protein (CCP) modules, an O-glycosylated serine-threonine-proline-rich domain, a transmembrane region, and a short cytoplasmic tail, with multiple isoforms arising from that affect the cytoplasmic domain length and patterns. The protein is ubiquitously expressed on the surface of nearly all nucleated cells, with particularly high levels in tissues such as the , testis, and , enabling broad protection against complement attack. Its extracellular CCP domains bind C3b and C4b with high affinity, while the cytoplasmic tails interact with intracellular signaling molecules, linking complement regulation to broader cellular responses. Beyond complement regulation, CD46 serves as a cellular receptor for several pathogens, including measles virus, Neisseria species, and , earning it the moniker "pathogen magnet" due to its exploitation by microbial invaders for host cell entry. It also modulates adaptive immunity by influencing T-cell differentiation, promoting a switch from pro-inflammatory Th1 responses to regulatory T cells (Tregs) that suppress . Clinically, genetic variants in CD46, including missense mutations in the CCP domains, are implicated in diseases such as (aHUS), where they impair complement control and contribute to , affecting approximately 10-20% of aHUS cases. Other associations include systemic lupus erythematosus, , and pregnancy complications like , underscoring CD46's multifaceted role in immune-related disorders.

Gene

Location and organization

The CD46 gene is located on the long arm of human chromosome 1 at cytogenetic band 1q32.2, within the regulators of complement activation (RCA) gene cluster. It spans approximately 43 kb and consists of 14 exons and 13 introns, with exons 2 through 5 encoding the four complement control protein (CCP) domains characteristic of the protein product. The gene was first identified in 1986 as a complement regulatory protein, initially termed membrane cofactor protein (MCP), through affinity purification of C3b-binding molecules from human peripheral blood cells. This discovery highlighted its role in protecting host cells from autologous complement attack. The of CD46 includes a partial gene duplicate encompassing exons 1–4 upstream of the functional , though this duplicate shows no evidence of expression. The promoter region lacks a but features a GC-rich sequence, a reverse-oriented , and multiple Sp1 binding sites that drive ubiquitous yet tissue-specific transcription. Regulatory single nucleotide polymorphisms (SNPs) in the promoter, such as -366A>G (rs2796268) and -652A>G (rs2796267), form haplotypes like MCPggaac, which reduce transcriptional activity and are associated with increased risk for (aHUS). Mutations in the CD46 gene are a major genetic cause of aHUS, accounting for 10–20% of familial and sporadic cases, with over 50 distinct variants reported to date. These are predominantly heterozygous loss-of-function mutations, including missense (most common, ~70%), nonsense, frameshift, and splice-site alterations, with approximately 95% localized to the exons encoding the extracellular CCP domains (13 in CCP1, 9 in CCP2, 14 in CCP3, and 13 in CCP4). About 75% of these mutations result in absent protein expression due to instability or trafficking defects, while the remainder impair cofactor activity for complement factor I; recurrence after transplantation is high (up to 60%) due to the biallelic expression requirement in renal endothelium. The gene undergoes alternative splicing to produce multiple isoforms, including four major transmembrane variants.

Isoforms and expression

CD46 is produced through alternative splicing of its pre-mRNA, resulting in four major isoforms that differ primarily in their O-glycosylation sites and cytoplasmic tails. The isoforms vary in the serine-threonine-proline (STP)-rich region, where β1 isoforms contain a single O-glycosylation site and β2 isoforms contain four sites, while the cytoplasmic tails are either 16 amino acids long (cyt-1) or 23 amino acids long (cyt-2). These variations arise from the inclusion or exclusion of exons 7-9 for the STP region and exon 13 for the cytoplasmic tail, generating the combinations β1-cyt-1, β1-cyt-2, β2-cyt-1, and β2-cyt-2. CD46 exhibits ubiquitous expression on the surface of nearly all nucleated human cells, serving as a broad protector against complement-mediated damage. Expression levels are particularly elevated in epithelial cells, the , and , where it plays specialized roles in tissue protection and reproductive processes. For instance, in the , CD46 levels are notably increased to safeguard the from maternal complement attack during . The regulation of CD46 expression involves both transcriptional and post-transcriptional mechanisms, including modulation by s and developmental factors. Interferon-γ (IFN-γ), a key , upregulates CD46 surface expression on various types, enhancing its complement regulatory capacity and supporting immune functions such as T regulatory type 1 (Tr1) . Developmental factors also influence expression, particularly in reproductive tissues like the testis and , where CD46 is tightly controlled to facilitate processes such as sperm-egg fusion. Quantitative expression data from the Genotype-Tissue Expression (GTEx) database reveal consistent median transcripts per million (TPM) values across tissues, underscoring its ubiquitous nature, with variations highlighting tissue-specific patterns. For example, median TPM exceeds 100 in epithelial-rich tissues like the and , around 50-70 in , and 20-40 in immune tissues such as and , indicating relatively higher expression in non-immune epithelial and reproductive sites compared to hematopoietic ones.

Structure

Extracellular domains

The extracellular region of CD46, also known as membrane cofactor protein (MCP), is primarily composed of four tandem short consensus repeats (SCRs), also referred to as domains or complement control protein (CCP) modules, located at the . Each SCR domain spans approximately 60 amino acids and features four conserved cysteine residues that form two intramolecular disulfide bonds, stabilizing the characteristic beta-sheet-rich fold typical of CCP modules. These domains are connected by short linker regions, resulting in an overall rod-like architecture that extends about 115 Å in length, with a slight bend between SCR3 and SCR4. Following the SCR domains, the extracellular portion includes a serine/threonine-proline-rich (STP) region, which is heavily O-glycosylated and serves as a flexible stem or spacer between the ligand-binding SCRs and the . The STP region's length and glycosylation extent vary due to in different CD46 isoforms, influencing the overall spacing and mobility of the extracellular domain. The SCR2-4 domains mediate binding to complement components C3b and C4b, with SCR3-4 playing a primary role in both interactions. Crystal structures of the CD46 extracellular , such as those derived from PDB entry 3O8E (in with adenovirus knob, revealing the full SCR1-4 arrangement) and PDB entry 1CKL (focusing on the N-terminal SCR1-2), demonstrate an extended conformation suitable for access. These structures also indicate potential for dimerization, as observed in packing where SCR1 of one interfaces with SCR4 of another, suggesting possible oligomeric states under physiological conditions.

Membrane and intracellular regions

CD46 is integrated into the plasma membrane via a single hydrophobic transmembrane , spanning approximately 20 , which spans residues 281–300 in the isoform and anchors the protein as a type I transmembrane . This helical segment facilitates the orientation of the extracellular domains outward and the cytoplasmic tail inward, enabling the protein's dual role in membrane association and without reliance on lipid modifications. Alternative splicing of the CD46 produces two distinct cytoplasmic tail isoforms, designated Cyt-1 and Cyt-2, which differ in length and functional motifs. Cyt-1 consists of 16 and includes sites targeted by casein kinase II and , supporting specific intracellular interactions. In contrast, Cyt-2 is longer at 23 and incorporates additional serine, , and residues that serve as substrates for by various kinases, such as family members during interactions. These isoform-specific tails share a common membrane-proximal sequence but diverge in their C-terminal regions, influencing protein trafficking and signaling specificity. Unlike GPI-anchored complement regulators such as (DAF/CD55), CD46 entirely lacks a (GPI) , distinguishing its membrane topology and localization patterns. This transmembrane configuration promotes basolateral distribution in polarized cells and supports dynamic internalization upon ligand binding. The cytoplasmic tails of CD46 demonstrate notable evolutionary conservation across vertebrates, particularly in the signaling motifs that mediate interactions with intracellular adaptors and kinases, underscoring their role in adapting complement regulation to diverse physiological contexts. This preservation highlights the tails' importance beyond structural ing, facilitating conserved pathways for cellular responses to environmental cues.

Function

Complement regulation

CD46, also known as membrane cofactor protein (MCP), serves as a key regulator of the by protecting host cells from autologous complement activation. It functions primarily as a cofactor for the factor I, which cleaves the opsonins b into iC3b and b into C4d, thereby inactivating these fragments and preventing the amplification of complement cascades that could lead to cell damage. This activity limits the formation of and convertases, ultimately inhibiting the assembly of the membrane attack complex (). The regulatory function of CD46 is mediated through its extracellular complement control protein (CCP) domains, also termed short consensus repeats (SCRs). The four SCR domains exhibit binding affinity for C3b and C4b, with SCR1 contributing specifically to C4b binding, SCR2 and SCR3 to both ligands, and SCR4 showing involvement particularly in C3b interactions. These interactions occur on the surface of self-cells, where CD46 restricts complement activation initiated via both the classical and pathways, ensuring that complement-mediated responses target foreign surfaces rather than host tissues. Experimental evidence from transfected cells demonstrates the potency of CD46 in complement inhibition; expression of CD46 in cells significantly reduces MAC formation, providing dose-dependent protection against complement-mediated lysis compared to non-expressing controls. This protective effect correlates directly with CD46 surface density and underscores its role in maintaining immune by confining complement activity to appropriate targets.

Cellular signaling and other roles

CD46 engages in diverse intracellular signaling pathways that extend beyond complement inhibition, influencing cellular processes such as cytoskeletal dynamics and immune modulation. The Cyt-1 isoform, characterized by its specific cytoplasmic tail, is particularly involved in these signaling events. In T lymphocytes, CD46 costimulation with CD3 triggers the relocalization of actin filaments, leading to profound morphological changes that enhance T cell activation and potentially regulate motility by reorganizing the cytoskeleton. A key function of CD46 signaling involves the promotion of immunosuppressive responses through regulatory T cells (Tregs). Ligation of CD46 on human CD4+ T cells induces the differentiation of type 1 regulatory T cells (Tr1), which secrete interleukin-10 (IL-10) and thereby suppress effector T cell proliferation and cytokine production, fostering peripheral immune tolerance. This IL-10-dependent mechanism is mediated primarily by the Cyt-1 tail and is essential for dampening inflammatory responses in various tissues. In , CD46 contributes to fertilization and early embryonic development. On human , CD46 localizes to the inner acrosomal membrane and serves as a marker for acrosome-reacted spermatozoa, facilitating their binding to the of the during gamete fusion. Additionally, CD46 expression on cells contributes to immune protection against complement-mediated damage during their invasion of the maternal , aiding in the establishment of the and successful implantation. Recent investigations have uncovered CD46's role in metabolic regulation within epithelial cells, particularly through induction. In respiratory epithelial cells, CD46 engagement by pathogens or activates the Cyt-1 tail to recruit GOPC and initiate formation, thereby modulating cellular metabolism to protect against and maintain . Studies as of 2025 have further elucidated how this pathway links complement sensing to autophagy-mediated nutrient recycling and energy balance during in epithelial barriers, with emerging evidence of its involvement in oncologic metabolic reprogramming.

Interactions

With complement proteins

CD46 primarily binds to the complement activation fragments C3b and C4b, which are deposited on surfaces during complement activation, with a (K_d) of approximately 1 μM for each. These interactions occur via the complement control protein (CCP) domains 2 and 3 (also known as short consensus repeats SCR2 and SCR3) in the extracellular region of CD46, enabling it to recognize and engage covalently bound C3b and C4b specifically on self-tissues. In addition to direct ligand binding, CD46 associates with the serine protease factor I to form a multimolecular proteolytic complex on the cell surface. This association facilitates the cleavage of bound C3b into inactive iC3b and C4b into C4d, thereby limiting amplification of the complement cascade. The cofactor function requires the presence of intact CCP2 and CCP3 domains, as mutations or deletions in these regions abolish the association and subsequent proteolysis. CD46 exhibits weak interactions with C3d, a downstream degradation product of C3b generated after factor I cleavage, as well as with , a positive regulator that stabilizes alternative pathway convertases; however, these bindings are of significantly lower affinity than those to C3b and C4b. In contrast, CD46 does not bind C1q, the recognition molecule of the classical pathway, nor the membrane attack complex C5b-9, setting it apart from regulators like and that target those components.

With pathogens and other molecules

CD46 serves as a cellular receptor for several pathogens, facilitating their attachment and entry into host cells. Measles virus (MV) binds to the short consensus repeats 1 and 2 (SCR1-2) of the CD46 extracellular domain, enabling viral hemagglutinin attachment and subsequent membrane fusion for infection. This interaction is specific to primate CD46 and is essential for laboratory-adapted MV strains, though wild-type isolates primarily use SLAM (CD150) as the primary receptor, with CD46 acting as a secondary entry point. Similarly, CD46 serves as the primary receptor for human herpesvirus 6A (HHV-6A) through its glycoprotein complex (gH-gL-gQ1-gQ2), promoting viral fusion and entry, particularly in CD46-expressing cells like T lymphocytes and monocytes. CD46 can also facilitate entry for HHV-6B in some cell types, though HHV-6B primarily uses CD134. CD46 isoforms influence the efficiency of HHV-6 entry, with certain cytoplasmic tails modulating post-binding signaling. Bacterial pathogens also exploit CD46 for adhesion and invasion. and bind to CD46 via their type IV pili, which recognize SCR3-4 domains, allowing pilus-mediated attachment to epithelial cells and facilitating bacterial colonization of mucosal surfaces. This binding can lead to CD46 downregulation on host cells, potentially aiding immune evasion. Group A Streptococcus () interacts with CD46 on through its M protein, particularly the C-terminal repeat domains, enabling bacterial adherence and contributing to skin and soft tissue infections. CD46's role as a "pathogen magnet" includes its exploitation by for enhanced virulence in human infections. Beyond pathogens, CD46 engages with cellular molecules to regulate adhesion and membrane organization. It associates directly with β1 integrins, such as α3β1 and α5β1, forming complexes that support cell-matrix interactions and cytoskeletal rearrangements during processes like sperm-egg fusion or epithelial invasion by pathogens. For instance, in group A Streptococcus infection, coordinated engagement of CD46 and α5β1 integrin is required for efficient bacterial entry into lung epithelial cells. Additionally, CD46 interacts with tetraspanins CD9 and CD81 within membrane microdomains, stabilizing these proteins in tetraspanin-enriched microdomains (TEMs) that facilitate signaling and pathogen entry. These associations with CD9 enhance HHV-6 infection by promoting CD46 clustering, while CD81 modulates broader membrane dynamics involving CD46.

Clinical significance

Complement-mediated diseases

Atypical hemolytic uremic syndrome (aHUS) is a complement-mediated characterized by , , and , where dysfunction in CD46 leads to uncontrolled activation on endothelial cells, promoting and vascular damage. in the CD46 gene, encoding membrane cofactor protein (MCP), account for 10-15% of aHUS cases, often resulting in reduced CD46 surface expression and impaired C3b/C4b cofactor activity. These are typically heterozygous and inherited in an autosomal dominant manner with incomplete , meaning not all carriers develop the disease, likely due to environmental triggers or modifier genes. A 2025 study identified a novel homozygous CD46 (c.1127 + 2T > A) in a family with aHUS, causing aberrant splicing, , and a frameshift that reduced mRNA expression to 0.78-fold and protein levels to approximately 47% of normal in patient-derived cells, thereby exacerbating complement dysregulation. CD46 dysfunction also contributes to glomerulopathies, a group of renal disorders driven by persistent C3 deposition in glomeruli due to defective complement regulation; mutations in CD46 are included in genetic screening panels for these conditions alongside other regulators like CFH and CFI. Similarly, in age-related (AMD), particularly the dry form, CD46 dysregulation allows excessive complement activation in the , leading to and degeneration; CD46-deficient mouse models spontaneously develop AMD-like phenotypes with drusen-like deposits and photoreceptor loss. CD46 variants have also been implicated in , a severe complication characterized by , elevated liver enzymes, and low platelet count, often overlapping with . Heterozygous in CD46, such as the S13F variant, impair complement regulation and increase susceptibility to endothelial damage during , contributing to disease pathogenesis in affected individuals. Therapeutic management of CD46-associated aHUS focuses on complement inhibition, with —a targeting —demonstrating efficacy in preventing relapse and improving renal outcomes in patients with CD46 , though lifelong may be required in some cases due to high recurrence rates post-transplantation.

Infectious diseases

CD46 functions as a key cellular receptor for several pathogens, enabling their entry into host cells and contributing to dynamics. In the case of measles (MeV), CD46 serves as the primary receptor for and laboratory-adapted strains, such as the Edmonston , where the hemagglutinin protein binds to the short repeats (SCR1 and SCR2) domains of CD46 to facilitate attachment and membrane fusion. This interaction not only supports entry into diverse cell types, including immune cells, but also triggers intracellular signaling that promotes , a hallmark of MeV responsible for secondary complications like and increased susceptibility to other . Specifically, CD46 cross-linking by MeV inhibits interleukin-12 (IL-12) production in monocytes and dendritic cells, dampening Th1 immune responses and secretion essential for antiviral defense. Although wild-type clinical isolates primarily utilize signaling lymphocyte activation molecule (/CD150) for entry, many retain the ability to engage CD46, particularly after adaptation in culture, underscoring its role in persistent . Vaccine evasion through mutations altering CD46 binding affinity is rare, with most failures attributed to host factors like polymorphisms in the CD46 gene rather than widespread resistance. Human herpesvirus 6 (HHV-6), encompassing variants A and B, also exploits CD46 as its principal receptor, binding via the viral glycoprotein complex to mediate and of T lymphocytes, glial cells, and other targets. This receptor usage is critical for HHV-6 , as evidenced by selective downregulation of surface CD46 during active replication, which evades complement-mediated clearance and allows viral spread. In immunocompromised individuals, such as transplant recipients or those with , HHV-6 reactivation via CD46 can lead to severe neurological complications, including and , characterized by brain inflammation, seizures, and long-term cognitive deficits. Experimental models, including CD46-transgenic mice, demonstrate persistent HHV-6 DNA in the following , mirroring and highlighting CD46's role in facilitating neurotropism. Neisseria gonorrhoeae, the causative agent of , leverages to invade mucosal epithelial cells, initiating infection in the genital tract. The bacterium's type IV pili bind directly to , recruiting the c-Yes to the invasion site, which rapidly phosphorylates at 354 within minutes of attachment. This activates downstream signaling cascades, including cortical plaque formation beneath adherent bacteria, enhancing adhesion, cytoskeletal rearrangements, and bacterial internalization while suppressing autophagic killing mechanisms. Inhibition of this pathway, such as through kinase blockers, significantly reduces invasion efficiency, confirming 's essential contribution to gonococcal and potential . By manipulating , N. gonorrhoeae not only evades innate immunity but also promotes and tissue damage in urogenital infections. Altered CD46 expression in the otic capsule and footplate has been implicated in the of , a progressive disorder involving abnormal in the . Research indicates a unique CD46 isoform pattern in otosclerotic tissues, with upregulated expression potentially facilitating persistent by providing an optimal receptor environment for viral persistence in cells. This hypothesis aligns with evidence of paramyxovirus-like inclusions in otosclerotic lesions and suggests that dysregulated CD46 signaling disrupts osteoid turnover, leading to focal and fixation of the . Regarding , the virus responsible for , no direct receptor role for CD46 has been established, as entry primarily occurs via ACE2. However, CD46's complement regulatory functions may indirectly modify disease severity by influencing endothelial injury and inflammatory cascades in severe cases; reduced membrane CD46 expression on endothelial cells has been observed, enhancing complement-mediated damage. This potential modulatory effect highlights CD46's broader involvement in pathogen-host interactions beyond direct binding.

Cancers

CD46, a complement regulatory protein, is frequently overexpressed in various malignancies, enabling tumor cells to evade complement-mediated and immune . This overexpression contributes to tumor and progression by inhibiting the classical and alternative complement pathways, thereby protecting cancer cells from by the . In , a pediatric , CD46 is highly expressed on tumor cells, promoting through complement evasion and correlating with aggressive disease phenotypes. Studies have demonstrated that medulloblastoma specimens exhibit elevated CD46 levels, which facilitate resistance to complement-dependent immune attacks and support the rationale for CD46-targeted oncolytic virotherapies. In , CD46 upregulation is associated with advanced disease and , as highlighted in a 2025 review detailing the "" of CD46's oncologic interactions. This review synthesizes evidence linking elevated CD46 expression to and increased metastasizing potential, particularly in castration-resistant where CD46 shields tumors from complement activation. CD46's role extends to immune escape mechanisms, preventing effective antitumor responses and contributing to poor in metastatic settings. CD46 also plays a role in and s by facilitating immune escape. In , high CD46 expression serves as an unfavorable prognostic factor, protecting tumor cells from host immune responses, including , and is linked to worse clinical outcomes. Similarly, in , tumoral CD46 promotes immune evasion by activating regulatory T cell-mediated suppression through interactions with lymphocyte cytosolic protein 1, thereby dampening antitumor immunity and supporting tumor progression. Therapeutically, CD46's overexpression in solid tumors has spurred the development of targeted agents, including in phase I trials. FOR46, a CD46-targeted conjugated to , has shown preliminary activity in metastatic castration-resistant and other solid tumors, with acceptable safety profiles in early clinical testing. These approaches exploit CD46's tumor-selective expression to deliver cytotoxic payloads, bypassing normal tissue toxicity and enhancing antitumor efficacy.

Autoimmune and inflammatory diseases

CD46 has been implicated in the pathogenesis of (MS) through genetic polymorphisms that influence disease susceptibility and altered expression patterns on immune cells. Specific variants in the CD46 gene have been associated with increased risk of , including MS, by disrupting complement regulation and T-cell signaling pathways. In patients with MS, CD46 expression is reduced on T cells, particularly affecting the generation of regulatory Tr1 cells that secrete interleukin-10 (IL-10), leading to impaired immune suppression and enhanced inflammation. This reduction correlates with a shift toward pro-inflammatory Cyt2 isoform dominance, exacerbating T-cell effector functions in the . In (RA), soluble CD46 (sCD46) levels are elevated in and , serving as a potential for activity and inflammation. Decreased membrane-bound CD46 expression on peripheral blood mononuclear cells and synovial tissues in RA patients contributes to unchecked complement activation, promoting synovial fibroblast proliferation and leukocyte infiltration. Dysregulated CD46 signaling in T cells from RA individuals impairs IL-10 production, sustaining chronic synovial inflammation and autoantibody-driven pathology. These alterations highlight CD46's role in balancing complement-mediated damage in arthritic s. Systemic lupus erythematosus (SLE) involves dysregulated CD46 signaling that promotes B-cell hyperactivity and production. In SLE patients, excessive shedding of membrane CD46 into its soluble form interferes with Th1 cell contraction, leading to persistent T-helper cell activation and enhanced B-cell stimulation. This dysregulation, often linked to CD46 genetic variants, results in hyperactive B cells that fail to undergo proper , contributing to immune complex deposition and tissue damage. CD46's interaction with complement fragments like C3b further amplifies IFN-α-driven B-cell responses in active disease. Recent 2025 studies have strengthened associations between CD46 and (IBD), particularly through its expression in gut epithelial cells. CD46 is constitutively expressed on the basolateral surface of , maintaining barrier integrity and modulating inflammation during IBD flares such as in and . Stable CD46 levels in inflamed mucosa support repair and limit complement-mediated epithelial damage, with reduced function linked to and chronic gut inflammation. These findings underscore CD46's protective role in epithelial , offering potential therapeutic targets for IBD management.

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