Ciliogenesis associated kinase 1: targets and functions in various organ systems

Ciliogenesis associated kinase 1 (CILK1) was previously known as intestinal cell kinase because it was cloned from that origin. However, CILK1 is now recognized as a widely expressed and highly conserved serine/threonine protein kinase.

In this review, we summarize what is known about CILK1 functions and targets, and discuss gaps in current knowledge that motivate further experimentation to fully understand the role of CILK1 in organ development in humans.

Regulation of CILK1 by phosphorylation

Little else is known about the mechanism and the effect of the T¹⁴Y¹⁵ motif phosphorylation in CILK1 and MAK.

Intrinsically disordered but functionally critical non‐catalytic domain

intrinsically disordered proteins (IDPs)

Although IDPs lack well‐defined three‐dimensional structures, they are known to rely on short linear motifs to interact with folded protein domains and facilitate key protein functions

Better understanding of the basis for CTD functions merits further investigation.

CILK1 substrate phosphorylation consensus

To date, there are still major gaps in our knowledge about how primary cilia are formed, maintained and function in signal transduction, and the mechanisms associated with ciliary dysfunction are yet to be fully elucidated.

Further studies are required to find out how CILK1 supports ‘catch‐up’ growth of intestinal epithelium in response to nutrient deficiency and impacts the pathophysiological outcomes induced by the vicious cycle of malnutrition and infection.

Surprisingly, loss of CILK1 function in brain affects ciliogenesis only in neural progenitor cells, not in mature neurons, suggesting a neuronal cell type‐specific effect of CILK1 in ciliogenesis.

CILK1 in lung morphogenesis and primitive alveoli formation

The mechanism by which CILK1 regulates lung morphogenesis and sacculation through ciliary signaling and autophagy is still unclear and awaits future investigation.

CILK1 in skeletal development

the mechanisms underlying these skeletal phenotypes are not fully understood

CILK1 in inner ear development and auditory function

The cochlea in the inner ear is the hearing organ. The planar cell polarity (PCP) signalling pathway plays a critical role in the establishment of cellular asymmetry within the plane of a sheet of inner ear sensory hair cells.

The mechanism by which CILK1 controls cilia morphology and function and the establishment of PCP in the cochlea remains to be elucidated.

CILK1 in cardiac development

Conditional KO mouse models will be needed to interrogate the role of CILK1 in the heart under both normal and pathophysiological conditions.

CILK1 in kidney and adrenal glands

CILK1 has a highly conserved role in regulating cilia function

CILK1 may be involved in the development of adrenal glands through regulating various ciliary signalling pathways.

CILK1 targets in signalling pathways

Further studies are required to address how CILK1 phosphorylation of KIF3A‐Thr672 affects IFT and ciliogenesis, and whether deregulation of this phosphorylation event is required for the ciliopathy phenotypes caused by CILK1 dysfunction.

Targeting Raptor in mTORC1 signalling

CILK1 could regulate ciliogenesis and IFT through phosphorylation of Raptor and activation of mTORC1.

Targeting Scythe in autophagy

These observations raise the question whether CILK1 loss‐of‐function increased autophagy for the elongation of primary cilia in ECO ciliopathy.

Whether CILK1 controls ciliogenesis in part through regulating autophagy via phosphorylation of Scythe awaits further investigation.

Targeting GSK3β in hedgehog signalling

These results raise the hypothesis that CILK1 negatively regulates GSK3β activity through inhibitory Thr7 phosphorylation to suppress cilia formation and Hh signalling.

Conclusions and perspectives

Ciliogenesis associated kinase 1 has an essential role in human development.

Several candidate substrates for CILK1 have been identified, such as KIF3A, Raptor and Scythe but how they mediate CILK1 effects on cilia morphology and function is still poorly defined.

How the phosphorylation of these substrates relates to mutant CILK1 ciliopathies and epilepsy is completely unknown.

Although remarkable progress has been made within the past two decades, many significant questions remain to be addressed in future research.

Does CILK1 have cellular functions separate from the primary cilium?

It is likely that CILK1 interacts with distinct pools of substrates and signalling proteins in its various locations within cells. Biochemical isolation and characterization of these mutation‐specific CILK1 complexes may expose other, new targets for the diversity of CILK1 signalling.

What are the environmental stimuli that activate or inactivate CILK1?

Primary cilium offers a unique signalling environment. The primary cilium contains many cell surface receptors, including GPCR, RTK, Hh, PDGFRα, TGFβ, and WNT. The cilium provides highly efficient signal processing, with a remarkably large ratio of sensing surface to internal volume. This restricted intracellular environment favours generation of high concentrations of second messengers such as calcium and cyclic AMP and protein‐protein interactions. How CILK1 is regulated in this unique signalling environment is largely unknown. What extracellular signals impact CILK1 activity? Is CILK1 intracellular localization regulated? We need to move beyond establishing a requirement for CILK1 in ciliary‐dependent functions and define with more precision what CILK1 does, and how. The answers to these questions will require tools to track CILK1 activity in time and space under different cellular conditions. Plus, we need to understand how ciliopathy‐associated mutations affect CILK1 activation and inactivation, as well as association with and phosphorylation of different substrates, and the effects on these targets.

Do CILK1, MAK, and MOK have similar or distinct functions and mechanisms of action?

The effects of CILK1 and MOK on cilium length both require mTORC1 signalling, but identification of their individual downstream targets and effectors require further investigation.

A key question that remains to be addressed in our future study is whether the ciliary functions of CILK1 and MAK are distinct or redundant, and whether these kinases utilize different targets and pathways to regulate ciliary length and ciliary transport machinery.