PTEN proteoforms in biology and disease

Abstract

Proteoforms are specific molecular forms of protein products arising from a single gene that possess different structures and different functions. Therefore, a single gene can produce a large repertoire of proteoforms by means of allelic variations (mutations, indels, SNPs), alternative splicing and other pre-translational mechanisms, post-translational modifications (PTMs), conformational dynamics, and functioning. Resulting proteoforms that have different sizes, alternative splicing patterns, sets of post-translational modifications, protein-protein interactions, and protein-ligand interactions, might dramatically increase the functionality of the encoded protein. Herein, we have interrogated the tumor suppressor PTEN for its proteoforms and find that this protein exists in multiple forms with distinct functions and sub-cellular localizations. Furthermore, the levels of each PTEN proteoform in a given cell may affect its biological function. Indeed, the paradigm of the continuum model of tumor suppression by PTEN can be better explained by the presence of a continuum of PTEN proteoforms, diversity, and levels of which are associated with pathological outcomes than simply by the different roles of mutations in the PTEN gene. Consequently, understanding the mechanisms underlying the dysregulation of PTEN proteoforms by several genomic and non-genomic mechanisms in cancer and other diseases is imperative. We have identified different PTEN proteoforms, which control various aspects of cellular function and grouped them into three categories of intrinsic, function-induced, and inducible proteoforms. A special emphasis is given to the inducible PTEN proteoforms that are produced due to alternative translational initiation. The novel finding that PTEN forms dimers with biological implications supports the notion that PTEN proteoform-proteoform interactions may play hitherto unknown roles in cellular homeostasis and in pathogenic settings, including cancer. These PTEN proteoforms with unique properties and functionalities offer potential novel therapeutic opportunities in the treatment of various cancers and other diseases.

Keywords: Alternative translational initiation; PTEN; Post-translational modifications; Proteoforms.

Fig. 1

The continuum model of tumor suppression. The tumor-suppressive functions of PTEN can be best explained by the continuum model of tumor suppression, wherein the levels of the PTEN protein dictate disease severity and tissue selectivity rather than mutations in the PTEN gene itself. Subtle reductions in PTEN protein levels, due to post-translational modifications, transcriptional repression, promoter methylation, and sub-cellular mislocalization, have a profound impact on oncogenic signaling pathways. Further, experiments in hypomorphic Pten transgenic mouse models have revealed that certain organs, such as the mammary glands, are particularly sensitive to small changes in the total PTEN levels. This is in contrast to the prostate gland, wherein a dramatic reduction in PTEN levels is required to initiate oncogenic transformation

Fig. 2

Protein complexes of PTEN generate new PTEN proteoforms. a The co-crystal structure of the PTEN–PDZ-binding domain with the PDZ-binding domain of MAST2 demonstrates that the disordered PTEN–PDZ-binding domain adopts a secondary structure primarily comprising a β-strand, a turn, and a bend. b In contrast, the PTEN–PDZ-binding domain adopts a slightly different secondary structure, comprising a β-strand and a bend, in complex with Par3

Fig. 3

Post-translational modifications of PTEN generates a set of PTEN proteoforms. PTEN undergoes several post-translational modifications that control its catalytic activity, stability, sub-cellular localization, and ability to engage in protein–protein interactions. (Ub ubiquitination, P phosphorylation, O oxidation, N nitrosylation, Rib ribosylation, Su sumoylation, Me methylation, Ac acetylation). Each of these modified PTEN proteins is considered a novel proteoform

Fig. 4

Mutations in the PTEN protein generate novel proteoforms with distinct functions. Different PTEN mutations have a varying impact on its function and the resulting phenotype. Point mutations in PTEN, which are outside of the catalytic core, usually have slightly reduced phosphatase activity and/or stability resulting in a mild activation of downstream oncogenic pathways compared to wild-type PTEN. In contrast, mutations in the PTEN catalytic core region result in the production of proteins that are oncogenic (i.e., PTEN C124S or PTEN G129E) or result in the production of PTEN protein with altered enzyme activity (PTEN A126G). Consequently, these point mutations have a worse phenotype compared to PTEN loss perpetuating the concept that PTEN mutations and loss are not synonymous. Truncating mutations in PTEN usually cause a decrease in stability of the PTEN protein, resulting in lower total PTEN levels (indicated in a lighter shade of green). An exception to this is the PTEN C-tail truncated mutant which behaves like an oncogene. Thus, each type of mutation in PTEN gives rise to a functionally and perhaps structurally distinct proteoform

Fig. 5

Translational variants of PTEN. PTEN has four reported translational variants, PTEN-L, -M, -N, and -O that are produced due to alternative translational initiation. Translation begins from an upstream non-AUG codon resulting in N-terminal extensions for each of the variants. It is likely that each of these proteoforms may behave differently in terms of their function and sub-cellular routing, trafficking, and localization

Fig. 6

PTEN-L and PTEN-M have a putative nuclear and nucleolar localization sequence, indicating their distinct sub-cellular functions. The sequence indicates the positions of the nuclear and nucleolar localization sequence as predicted by NLStradamus, NucPred, and the NoDsoftwares, respectively

Fig. 7

Functional relevance of PTEN and its proteoforms. PTEN and its translational variants give rise to various proteoforms that localize to various sub-cellular compartments to regulate cell signaling. PTEN exerts its effects on the cell cycle, ribosome biogenesis, DNA damage, and repair processes in the nucleus and nucleolus. PTEN-L and -M have putative nuclear and nucleolar localization sequences and their unique roles in these compartments remain to be determined. PTEN and PTEN-L also localize to the mitochondria where they regulate apoptosis and mitochondrial energetics, respectively. Both PTEN and PTEN-L associate with the membrane and PTEN-L has an additional membrane-binding helix that facilitates this association. The other PTEN translational variants, PTEN-M, -N, and -O also possess the membrane-binding helix and whether they truly localize to the plasma membrane is unknown. PTEN-L has also been found in extracellular tissues and in circulation in the blood stream. PTEN-L, by virtue of a cell-penetrating polyarginine peptide, re-enters the cells to inhibit PI3K signaling and has been shown to be therapeutically effective in mouse models. Whether, PTEN-L is truly secretory remains controversial. However, the biochemical process underlying its secretion represents an active area of research