Reverse Engineering Gene Network Identifies New Dysferlin-interacting Proteins

Abstract

Dysferlin (DYSF) is a type II transmembrane protein implicated in surface membrane repair of muscle. Mutations in dysferlin lead to Limb Girdle Muscular Dystrophy 2B (LGMD2B), Miyoshi Myopathy (MM), and Distal Myopathy with Anterior Tibialis onset (DMAT). The DYSF protein complex is not well understood, and only a few protein-binding partners have been identified thus far. To increase the set of interacting protein partners for DYSF we recovered a list of predicted interacting protein through a systems biology approach. The predictions are part of a “reverse-engineered” genome-wide human gene regulatory network obtained from experimental data by computational analysis. The reverse-engineering algorithm behind the analysis relates genes to each other based on changes in their expression patterns. DYSF and AHNAK were used to query the system and extract lists of potential interacting proteins. Among the 32 predictions the two genes share, we validated the physical interaction between DYSF protein with moesin (MSN) and polymerase I and transcript release factor (PTRF) in mouse heart lysate, thus identifying two novel Dysferlin-interacting proteins. Our strategy could be useful to clarify Dysferlin function in intracellular vesicles and its implication in muscle membrane resealing.

Proper Voltage-Dependent Ion Channel Function in Dysferlin-Deficient Cardiomyocytes

“…We had expected a regulatory effect because the dysferlin interaction partner AHNAK [19,20] associates with regulatory β-subunits of Ca v 1.2 channels [21,22], and the α 2 δ 1 calcium channel subunit, which modulates the channel's function [23], is significantly downregulated in the dysferlin-deficient heart [24]. In this regard it is worthwhile to consider recent work dealing with dysferlin regulation of calcium signaling and homeostasis in skeletal muscle cells [25,26].…”

“…The following lines of evidence point to a potential regulatory effect of dysferlin on Ca v 1.2 channels: First, in skeletal muscle, dysferlin colocalizes with the L-type calcium channel [16,17], and muscle membrane repair requires an interplay between these two proteins [18]. Secondly, the dysferlin interaction partner AHNAK [19,20] associates with regulatory β-subunits of Ca v 1.2 channels [21,22], and thirdly, the α 2 δ 1 calcium channel subunit, which modulates the channel's function [23], is significantly downregulated in the dysferlin-deficient heart (NCBI GEO profile: http://www.ncbi.nlm.nih.gov/geoprofiles?term=GDS1247[ACCN]+cacna2d1, ref. [24]).…”

Structure of a C-terminal AHNAK peptide in a 1:2:2 complex with S100A10 and an acetylated N-terminal peptide of annexin A2

“…Depletion of AnxA2 by siRNA causes release of AHNAK into the cytoplasm, suggesting that (p11) 2 (AnxA2) 2 may recruit AHNAK to the plasma membrane and act as a scaffold, locating it nearby for cell membrane-repair activities and possibly regulation of membrane cyto-architecture (Benaud et al, 2004). Both AHNAK and annexins A1 and A2 have been shown to interact with dysferlin, a 230 kDa muscle membrane protein with roles in skeletal muscle regeneration and wound healing (Huang et al, 2007;Lennon et al, 2003;Cacciottolo et al, 2011). Furthermore, AHNAK-deficient mice were highly susceptible to Leishmania major infection owing to the proposed role of AHNAK in T-cell Ca 2+ signaling mediated by Ca v 1 channels based on loss-of-function experiments, the expression characteristics of AHNAK in T cells and the requirement of AHNAK for the expression of L-type calcium channels (Matza et al, 2008).…”

Plasma membrane and cytoskeleton dynamics during single-cell wound healing

“…Several observations also suggest that enlargeosome-and dysferlin-mediated plasmalemma repair may be closely related. Indeed, dysferlin have been shown to interact with AHNAK through its C2A domain [117,[141][142][143], and both proteins co-localize to the sarcolemmal membrane and T-tubles of normal skeletal muscle [143]. Reduction or absence of dysferlin observed in the muscle of dysferlinopahties such as LGMD2B and Miyoshi myopathy correlates with a secondary muscle-specific loss of AHNAK [143].…”

“…20 Indeed, dysferlin has been shown to bind or be associated with many proteins such as MG53 [114], caveolin-3 [115], annexin I [116], annexin V [74], as well as many others [117]. Dysferlin has even been shown to associated with the annexin II:S100A10: AHNAK complex, which is involved in enlargeosome exocytosis.…”