TMEM106B protein is an independent receptor for SARS-CoV-2 entry into ACE2-negative host cells

In their recent study, a group of researchers led by Belgian scientists demonstrated that TMEM106B, a lysosomal transmembrane protein, can serve as an alternative receptor for the entry of SARS-CoV-2 into the angiotensin-converting enzyme 2 (ACE2)-negative cells. In addition, they showed that TMEM106B directly engages the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein and promotes spike-mediated syncytium formation.

ACE2 is thought to be the main entry receptor for SARS-CoV-2. Also, virus entry was found to depend on transmembrane protease serine 2 (TMPRSS2) or endo/lysosomal cathepsins. ACE2 is highly expressed in some organs, but it is very low in others, such as the liver and the brain.

The lysosomal transmembrane protein TMEM106B is expressed in a large variety of cell types, with the highest levels observed in the brain, heart, thyroid, adrenal, and testis. TMEM106B is linked with brain aging, myelination disorders and several neurodegenerative diseases, such as frontotemporal lobar degeneration, amyotrophic lateral sclerosis, Alzheimer’s disease, and Parkinson’s disease.

About the study

In order to confirm that TMEM106B can support ACE2-independent infection, scientists generated ACE2 and TMEM106B knockout NCI-H1975 cells. They discovered that TMEM106B can serve as receptor for SARS-CoV-2 entry into ACE2-negative cells. In addition, SARS-CoV-2 infection was neutralized with TMEM106B-specific monoclonal antibodies. The authors proposed that SARS-CoV-2 either engages TMEM106B on the cell surface, or that the virus and (antibody-bound) TMEM106B are co-internalized, after which binding occurs inside endocytic vesicles.

The findings also revealed that TMEM106B directly engages with the RBD of SARS-CoV-2 spike protein. Cryogenic electron microscopy and hydrogen-deuterium exchange mass spectrometry identified the RBD region 443–495 as the binding site for TMEM106B. The authors suggested that the striking overlapping of the footprints of ACE2 and TMEM106B on the RBD indicates that these receptors cannot simultaneously bind the spike protein, as demonstrated by a competition assay.

Furthermore, the findings showed that TMEM106B directly promoted spike-mediated syncytium formation, indicating a possible involvement of TMEM106B in viral fusion. Previous studies have shown that SARS-CoV-2 infection induces fusion between neurons and between neurons and glia in vitro, disrupting their communication.

The spike-TMEM106B interaction had a lower affinity of 10 to 20μM than the spike-ACE2 interaction (∼10–100nM). However, the affinity was similar to the affinity of SARS-CoV-2 spike binding to neuropilin-1 (10–20μM).

Researchers also demonstrated that spike substitution E484D facilitated viral entry via the TMEM106B-dependent route. They noted that several studies have reported that E484D enables the SARS-CoV-2 infection of ACE2-negative cell lines, but the underlying mechanism is still unknown.

In conclusion, this study found that SARS-CoV-2 can enter ACE2-deficient host cells through a TMEM106B-dependent entry mechanism. It implies that TMEM106B and ACE2 can support separate infection mechanisms. These findings could explain the multi-organ pathology seen in COVID-19 and the infection of cells with low or undetectable expression of ACE2, like intestine and brain cells. However, the mechanism by which TMEM106B promotes SARS-CoV-2 infection remains unclear.

The findings also demonstrated that TMEM106B-specific monoclonal antibodies can effectively block SARS-CoV-2 infection. Consequently, the scientists speculated that potent and specific antibodies may have scientific and therapeutic applications in the future. Due to its relevance in multiple neurodegenerative disorders and cancer metastasis, it may be useful to develop modulators of TMEM106B activity for therapeutic applications.

This article was published in Cell.

Journal Reference

Baggen et al., TMEM106B is a receptor mediating ACE2-independent SARS-CoV-2 cell entry, Cell (2023).