A recent collaborative study found rare variants in the YKT6 gene as a cause of a new neurological disorder characterized by developmental delays along with severe progressive liver disease and a potential risk of liver cancer. The study was led by Dr. Hugo Bellen, professor emeritus at Baylor College of Medicine and principal investigator at the Duncan Neurological Research Institute at Texas Children’s Hospital; and Dr. Wendy Chung, chief of the Department of Pediatrics at Boston Children’s Hospital. In collaboration with Dr. Mythily Ganapathi at Columbia University Irving Medical Center, Drs. Paula Hertel and Davut Pehlivan of Texas Children’s Hospital and Dr. James Lupski of Baylor College of Medicine. Using the GeneMatcher tool and the Baylor Genetics Clinical Diagnostics Laboratory, this team of researchers and clinicians found three unrelated individuals with missense variants in both copies of the YKT6 gene.
All three individuals had early onset of the disease (four to six months of age) with growth retardation. Two of them had one missense variant identical due to which the amino acid tyrosine at position 185 was changed to cysteine (Y185C). On the other hand, the third child carried a variant that caused the same amino acid change but in a different position (Y64C) of the YKT6 protein. Interestingly, in addition to the developmental delays and neurological defects observed in all three children, only the two individuals with the Y185C variant had liver dysfunction and a potential risk of developing liver cancer. Both individuals with the Y185C variant belong to the Syrian/St. Thomas Christians of Kerala, India, a group currently estimated to number approximately 5 million individuals worldwide. Genetic lineage analysis suggests that this variant likely originated from a common ancestor before the community split.
To evaluate how YKT6 variants drive the observed pathologies, Bellen’s team studied the fruit fly version of this gene that is quite similar to its human counterpart. They found that the fly version of this protein is expressed in body fat and brain, which are analogous to human liver and brain, respectively. Furthermore, fly strains with loss-of-function mutations in this gene were lethal, and Ykt6 mutant flies expressing the normal version of the Ykt6 gene had an average lifespan. However, transgenic flies expressing versions of the disease variants were less effective at restoring lifespan and other symptoms. While Ykt6 mutant flies expressing Y65C (same as human Y64C) had normal lifespan and locomotion, those expressing Y186C (same as human Y185C) had severely reduced lifespan and locomotor defects.
This means that the corresponding human YKT6 Y185C is a more severe variant of Y64C. To understand why these variants behaved differently, scientists delved into their biology. YKT6 belongs to the family of SNARE proteins that regulate the flow of vesicular protein trafficking towards various cellular compartments. It is an isoprenylated membrane-associated protein that functions in the endoplasmic reticulum-Golgi transport phase, forming a “priming” complex with syntaxin-17 and SNAP29 to facilitate fusion between the lysosome and autofagosoma. As an additional partner it has the protein BET1L, involved in vesicular traffic in the Golgi apparatus. This, in turn, interacts with partners such as GOSR1 and syntaxin-5, which serve for the correct assembly of the vesicles. Furthermore, in mammalian cells, YKT6 mediates the fusion of autophagosomes and lysosomes to form autolysosomes, within which “used” molecules are recycled.
This process called autophagy it is essential for the correct functioning and health of cells. The team found that loss of fly Ykt6 led to an abnormal accumulation of proteins involved in the formation of the autophagosome and the autophagic cargo receptor, indicating a block in the autophagy pathway. Further studies revealed that, much like lethality and other defects, the fly’s Y186C (same as human Y185C) was less efficient at reversing symptoms than a normal copy of the Ykt6 gene. Furthermore, they observed that while the initiation of autophagy was normal, steps involved in the breakdown of cellular waste were impaired in the absence of Ykt6. The team’s work suggests they may be facing a new neurological disease with a major component in brain development. And that children diagnosed with YKT6 liver disease will also need to be screened for the HCC.
But it is not the only clinical option to exploit. Lysosomal dysfunction has been implicated in a number of neurodegenerative diseases such as Parkinson’s disease. Various molecular, clinical and genetic studies have highlighted a central role of lysosomal pathways and proteins in the pathogenesis of the disease. In its pathology the synaptic protein alpha-synuclein (α-Syn) converts from a soluble monomer to oligomeric structures and insoluble amyloid fibrils. These structures can cause difficulties for lysosomal proteases greater (the cathepsins) in being able to be degraded. Using patient-derived induced pluripotent stem cells and a transgenic mouse model of Parkinson’s, a German team last year examined the effect of intracellular α-Syn conformers on cellular homeostasis and lysosomal function in dopaminergic neurons by biochemical analyses. Indeed, lysosomal cathepsins had the aforementioned difficulty in attaching synuclein aggregates.
And this is where YKT6 came into play, as it uses an inhibitor of farnesil-transferasi (which allows the protein to anchor to the membranes to do its job), which enhances hydrolase transport through the activation of the YKT6 protein, the researchers improved the maturation and proteolytic activity of cathepsins and therefore reduced the levels of pathological α-Syn protein. Just last year, a team at Northwestern University Feinberg School of Medicine, Chicago, demonstrated that pathological alpha-synuclein targets the YKT6 protein, preventing it from forming contacts with the SNAP29 component. In their wild-type (WT) cell culture experiments, depletion of YKT6 caused an almost complete block of autophagic flux, highlighting its critical role for autophagy in human neurons derived from neuronal progenitors. This defect, once again, was corrected by blocking farfalle transferase leading to restoration of macro-autophagic flux in cultured diseased neurons.
Autophagy could be a cellular pathway to be encouraged in Parkinson’s therapy, as it would allow the elimination of abnormal proteins and extend the life of diseased dopaminergic neurons. It should be remembered, in fact, that the death of the affected brain cells is not only responsible for the worsening of the disease over time, but also for the progressive loss of effectiveness of pharmacological therapies. Wanting to extend the horizon where we can look, this information could be used to correct other very serious neurological diseases such as multiple system atrophy and the dementia with Lewy bodies. For these conditions, which are based on α-Syn defects, there are no corrective or disease-modifying drugs but only symptomatic and palliative ones. If it could be demonstrated that acting on the state of YKT6 improved cell viability and the clinical outcome of these conditions, we could be faced with the first therapies that modify their course.
By Dr. Gianfrancesco Cormaci, PhD, specialist in Clinical Biochemistry.
Scientific publications
Ma M, Ganapathi M et al. Genet Med. 2024 Mar 21:101125.
Zheng D, Tong M et al. Cell Rep. 2024 Feb; 43(2):113760.
Graves NJ et al. Int J Mol Sci. 2023 Jul 28; 24(15):12134.
Pitcairn C et al. J Neurosci. 2023 Apr 5; 43(14):2615-2629.
Prieto Huarcaya S et al. Autophagy. 2022; 18(5):1127-1151.
Sakata N, Shirakawa R et al. J Biochem. 2021; 169(3):363.
Bellomo G, Paciotti S et al. Movement Disord. 2020; 35(1):34-44.