EDEM3-CDG (CDG-IIv)

Disorders of N-linked Protein Glycosylation / EDEM3-CDG (CDG-IIv)

Lay Summary

EDEM3-CDG is a rare inherited condition that affects many parts of the body. It is a recently discovered CDG, first being reported in 2021 with 12 patients from 7 families. EDEM3-CDG is classified as a disorder of N-linked protein glycosylation. EDEM3-CDG arises from an individual having mutations in both copies of their EDEM3 gene, which provides instructions for making an enzyme that helps ensure misfolded N-linked glycoproteins are broken down. Mutations in the EDEM3 gene cause proteins to have altered patterns in the sugar chains on N-linked glycoproteins and allows misfolded proteins to accumulate instead of being degraded. Symptoms of EDEM3-CDG begin in infancy and affect multiple systems. The most common symptoms are developmental delay, feeding/growth problems, abnormal features, and behavioural problems. Screening tests that assess abnormal sugars on N-linked glycoproteins are available for EDEM3-CDG, but a definitive diagnosis is achieved through genetic testing. There are currently no approved treatments for EDEM3-CDG, and treatment is focused on the management of specific symptoms and preventing disease complications.

Overview

Endoplasmic reticulum (ER) degradation enhancing alpha-mannosidase like protein 3 congenital disorder of glycosylation (EDEM3-CDG) is a rare autosomal recessive genetic disorder. The first cases of EDEM3-CDG were reported in 2021, with 12 patients from 7 families¹.

The EDEM3 gene encodes a protein (EDEM3) that is thought to play a role in N-glycoprotein quality control. EDEM3 has mannosidase activity and can catalyze the removal of specific mannose sugars from the glycan chain of N-glycoproteins that are improperly folded. Removal of mannose residues aids glycoprotein degradation through ER-associated degradation (ERAD)—a complex process that begins in the ER and monitors, identifies, and degrades proteins². Deficiency in EDEM3 results in decreased removal of mannose residues and accumulation of misfolded proteins. Further studies are needed to understand the precise disease mechanism of EDEM3-CDG^1,3.

Symptoms of EDEM3-CDG begin in infancy and typically include developmental delay, feeding/growth problems, abnormal features, and behavioural problems. Definitive diagnosis can only be achieved through genetic testing, but total N-glycan analysis may aid in diagnosis. Currently, there is no cure or treatment for EDEM3-CDG, and treatment is based on managing symptoms^1,4.

Synonyms

ER Degradation Enhancing Alpha-Mannosidase Like Protein 3 congenital disorder of glycosylation
Congenital disorder of glycosylation Type 2v
CDG2V
CDG-IIv
CDG-2v

Inheritance

EDEM3-CDG is an autosomal recessive disorder, meaning an affected individual inherits one defective copy of the gene from each asymptomatic parent.

Gene Function

The EDEM3 gene encodes the enzyme ER degradation enhancing alpha-mannosidase like protein 3 (EDEM3). EDEM3 is a part of a group of proteins (ER-1,2-alpha mannosidases or EDEMs) that possess mannosidase activity and can catalyze the removal of mannose sugar residues from the glycan chain of improperly folded N-glycoproteins. The removal of mannose residues by EDEM3, along with EDEM1 and EDEM2, accelerates the degradation of misfolded glycoproteins through ERAD (Figure 1)^1,3.

ER-Associated Degradation (ERAD)

N-linked glycosylation is the process by which a glycan chain is added to the amino acid asparagine on a recently synthesized protein. N-glycoprotein synthesis is split into three main phases:

Construction of a 14-sugar glycan chain on the lipid dolichol (also known as the lipid-linked oligosaccharide or LLO) in the cytoplasm and ER
Transfer of this glycan onto an asparagine residue of a newly synthesized protein in the ER to form an N-glycoprotein
Further trimming of the now N-linked glycan chain occurs as the protein moves from the ER and through to the Golgi to create a mature N-glycoprotein.

The third step of glycosylation also incorporates a quality control process. After attachment of the glycan to the polypeptide (step 2), the three glucose residues are sequentially removed from the glycan chain by glycosidases, and the resultant N-glycoprotein undergoes additional folding with the help of chaperones⁵. If the protein is folded correctly, removal of the terminal glucose is a signal for the N-glycoprotein to be transported to the Golgi. However, if the protein is not folded correctly, the enzyme UDP-glucose: glycoprotein glucosyltransferase (UGGT) will re-add a glucose molecule to the glycan chain⁶. Next, two chaperones, calreticulin and calnexin, bind to the misfolded protein and prevent it from leaving the ER—giving the misfolded protein more time to become properly folded^7–9. If an N-glycoprotein is unable to fold correctly, it will eventually be marked for degradation through ERAD.

Figure 1. Role of EDEM3 in glycosylation.
EDEM3 is involved in ERAD/non-lysosomal degradation of misfolded N-glycoproteins. EDEM3 removes mannose residues from the Man₈GlcNAc₂ glycan, which is needed for the misfolded protein to be able to move to the cytosol for degradation.

The first step of ERAD is the removal of the middle mannose residue from the glycan chain (M9) of a misfolded N-glycoprotein by MAN1B1. This allows other mannosidases (EDEMs 1-3 and MAN1A1) to trim additional mannoses from the glycan (M8). EDEM3 removes one to three mannose residues from the Man₈GlcNAc₂(M8) glycan chain, generating Man₇GlcNAc₂(M7), Man₆GlcNAc₂(M6), or Man₅GlcNAc₂(M5) (Figure 2). EDEM3 may also play a role in generating further truncated N-glycans, such as Man₄GlcNAc₂(M4) and Man₃GlcNAc₂(M3)¹. This now-truncated N-glycoprotein can then be recognized by lectin OS-9 and is translocated into the cytosol and has multiple ubiquitin molecules added to the protein, a process called polyubiquitination³. The ubiquitination marks the misfolded glycoprotein for transport to the proteasome, where it is chemically broken apart.

Figure 2. N-glycan products after EDEM-3 action.
For ERAD glycoprotein degradation, certain mannoses need to be removed from the N-glycan chain: Man9GlcNAc2 (M9). MAN1B1 removes the first mannose residue, generating Man8GlcNAc2 glycan (M8), EDEM-3 can then remove additional mannose residues, generating Man7GlcNAc2 (M7), Man6GlcNAc2 (M6) or Man5GlcNAc2 (M5).

Disease Mechanism

Impaired EDEM3 activity may lead to reduced trimming of Man₈GlcNAc₂, causing an accumulation of abnormal glycans in cells. Further studies are necessary to better understand the pathophysiological mechanism of EDEM3-CDG1.

Mutations

The EDEM3 gene is located on chromosome 1 (1q25.3) and 8 mutations have been reported for the EDEMB3 gene including 2 biallelic frameshift deletions, 2 frameshift variants, 1 biallelic nonsense variants, 1 splice site variant, 1 nonsense variant, and a compound heterozygous change¹.

Signs & Symptoms

Clinical Presentation

Individuals with EDEM3-CDG typically develop signs and symptoms during infancy. EDEM3-CDG is primarily characterized by developmental delay, speech delay, and mild facial abnormalities. The characteristic clinical presentations of EDEM3-CDG include^1,4:

Neurological – developmental delay, intellectual deficiency, brain abnormalities, delayed speech development, low muscle tone (hypotonia), breathing apnea that resolves with age, and loss of smell (anosmia)
Musculoskeletal – delayed bone age and one case of Poland sequence, with low muscle tone (hypotonia), impaired wrist movement, underdeveloped muscles (arm and pectoral), thinning/loss of muscle (atrophy) in the palm, and shortened bones in the fingers
Ophthalmological – astigmatism, refractive error, and strabismus
Growth/feeding problems – gastroesophageal reflux and early feeding difficulties requiring a nasogastric tube which may lead to failure to thrive and constipation
Behavioural – hyperactivity, attention deficit, slow response in social situations, and anxiety
Dysmorphic features – abnormal features can affect the skull, spine, shoulders, feet, and face, such as down-slanting opening between the eyelids (palpebral fissures), thickened ear skin (thickened helix), increased nasal height, bulbous nose, thin upper lip, abnormal position of the lower jaw (retrognathia), drooping eyelids (ptosis), shoulder webbing, narrow temporal skull, low posterior hairline, short stature, thin skin, abnormal hair growth, club feet, and abnormal position or shape of the ear

Biochemical Abnormalities

Some affected individuals have displayed elevated levels of transaminases, thyroid-stimulating hormones and blood cholesterol (hypercholesterolemia), reduced blood albumin (hypoalbuminemia) and morning cortisol levels, iron deficiency, and diabetes¹.

Diagnosis

EDEM3-CDG should be suspected in any multisystem disorder, especially when developmental delay, speech delay, and facial dysmorphism is present. Screening in suspected patients typically begins with a blood test to analyze serum transferrin, however, patients tested to date have shown normal transferrin glycosylation. Profiling of total N-glycans in the serum by mass spectrometry can also be performed and may show global glycosylation abnormalities. Direct molecular genetic testing is the only way to definitively diagnose EDEM3-CDG^1,4.

Total Serum N-Glycan Analysis

N-glycan profiling in affected patients showed abnormal levels of various small high-mannose species. Profiling patterns from patient fibroblasts showed normal M8 glycan levels but reduced M3, M4, M5, M6, and M7 glycan levels compared to control samples¹.

Biomarkers

Through N-glycan analysis of EDEM3-CDG patient fibroblasts, an increased M9:M3 ratio may serve as a biomarker to aid diagnosis¹.

Classification

EDEM3-CDG is classified as a disorder of N-linked protein glycosylation.

Under the former CDG classification system, EDEM3-CDG is classified as a Type II CDG, which arise due to defects in the processing of N-glycans attached to proteins.

Prognosis

With EDEM3-CDG being a recently-discovered CDG and the few cases currently reported in the medical literature, information on long-term outcomes for EDEM3-CDG patients is unclear. As of 2021, a patient has been reported to be 33 years old⁴.

Management

Management of EDEM3-CDG requires a multidisciplinary team and may include combinations of physical therapy, occupational therapy, oral motor and speech therapy, and psychiatry.

Therapies

There are currently no treatment options available for EDEM3-CDG. Treatment is focused on management of symptoms and prevention of complications.

Research Models

Several mouse models for EDEM3 have been generated.

Mouse (M.musculus)

Edem3 ^-/-knockout mice
Edem3 knockout mice were used to analyze glycan profiles in plasma protein and brain lysate assays. Like affected humans, mice have decreased ratios of M5: M9, M6: M9, and M7: M9 glycans and increased abundance of M8 and M9 glycans in both plasma and brain profiles. It is noted that Edem3 knockout mice did not have any obvious phenotypic characteristics, but subtle changes such as reduced weight of brain and body and skewed ratios of pups were observed¹.

Edem3 knockout embryonic stem cells
Edem3^{tmb1(EUCOMM)Hmgu}embryonic stem cells generate mice that lack Edem3. Behaviour, nervous system, skeletal system, pigmentation, and mortality/aging are significantly affected. Heterozygous mutants are unresponsive to stimuli, have decreased bone mineral content and density, abnormal coat pigmentation, show no spontaneous movement, and live to stage E18.5 up to early adulthood. Homozygous mutants are also unresponsive to stimuli, show no spontaneous movement, and have pre-weaning lethality with complete penetrance, living to stage E18.5 up to early adulthood (MGI).

Clinical Studies

Active

Clinical and Basic Investigations into Congenital Disorders of Glycosylation (NCT04199000)
The Frontiers in Congenital Disorder of Glycosylation Disorders Consortium (FCDGC) is conducting a 5-year natural history study on all CDG types, including EDEM3-CDG. The purpose of this study is to define the natural history and clinical symptoms of CDG, develop new diagnostic techniques, identify clinical biomarkers that can be used in future clinical trials and evaluate whether dietary treatments improve clinical symptoms and quality of life.

Publications

EDEM-CDG Scientific Articles on PubMed

Additional Resources

EDEM3-CDG on FCDGC
IEMbase
EDEM3-CDG: Austin, Savannah and Lily’s story | Children's Hospital of Philadelphia (chop.edu)
OMIM
Genetic Testing Registry
ClinVar
NIH
GeneCards

References

Polla, D. L. et al. Bi-allelic variants in the ER quality-control mannosidase gene EDEM3 cause a congenital disorder of glycosylation. American journal of human genetics 108, 1342–1349 (2021).
Gariballa, N. & Ali, B. R. Endoplasmic Reticulum Associated Protein Degradation (ERAD) in the Pathology of Diseases Related to TGFβ Signaling Pathway: Future Therapeutic Perspectives. Frontiers in Molecular Biosciencesvol. 7 (2020).
Hirao, K. et al. EDEM3, a soluble EDEM homolog, enhances glycoprotein endoplasmic reticulum-associated degradation and mannose trimming. Journal of Biological Chemistry 281, 9650–9658 (2006).
EDEM3 (ER Degradation Enhancing Alpha-Mannosidase Like Protein 3) - congenital disorder of glycosylation (EDEM3-CDG) | Rare Diseases Clinical Research Network. https://www.rarediseasesnetwork.org/index.php/fcdgc/edem3.
Taylor, M. E. & Drickamer, K. Introduction to Glycobiology. (OUP Oxford, 2011).
Dejgaard, S., Nicolay, J., Taheri, M., Thomas, D. Y. & Bergeron, J. J. M. The ER glycoprotein quality control system. Current Issues in Molecular Biology 6, 29–42 (2004).
Ganan, S., Cazzulo, J. J. & Parodi, A. J. A major proportion of N-glycoproteins are transiently glucosylated in the endoplasmic reticulum. Biochemistry 30, 3098–3104 (2002).
Gelebart, P., Opas, M. & Michalak, M. Calreticulin, a Ca2+-binding chaperone of the endoplasmic reticulum. The International Journal of Biochemistry & Cell Biology 37, 260–266 (2005).
Hammond, C., Braakman, I. & Helenius, A. Role of N-linked oligosaccharide recognition, glucose trimming, and calnexin in glycoprotein folding and quality control. Proceedings of the National Academy of Sciences 91, 913–917 (1994).
Polla, D. L. et al. Bi-allelic variants in the ER quality-control mannosidase gene EDEM3 cause a congenital disorder of glycosylation. American Journal of Human Genetics 108, (2021).