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Article

The Autophagic Process Occurs in Human Bone Metastasis and Implicates Molecular Mechanisms Differently Affected by Rab5a in the Early and Late Stages

1
Istituto Ortopedico Galeazzi, Scientific Institute for Research, Hospitalization and Health Care (IRCCS), Milano 20161, Italy
2
Dipartimento di Scienze Biomediche per la Salute, Molecular Pathology Laboratory, Università degli Studi di Milano, Milano 20133, Italy
3
San Raffaele Scientific Institute, Division of Genetics and Cell Biology, Milano 20133, Italy
*
Author to whom correspondence should be addressed.
Academic Editor: Johannes Haybaeck
Int. J. Mol. Sci. 2016, 17(4), 443; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms17040443
Received: 18 February 2016 / Revised: 9 March 2016 / Accepted: 9 March 2016 / Published: 25 March 2016
(This article belongs to the Special Issue Cellular and Molecular Mechanisms of Bone Metastasis)

Abstract

Autophagy favours metastatic growth through fuelling energy and nutrients and resistance to anoikis, typical of disseminated-tumour cells. The autophagic process, mediated by a unique organelle, the autophagosome, which fuses with lysosomes, is divided into three steps. Several stages, especially early omegasome formation and isolation-membrane initiation, remain controversial; molecular mechanisms involve the small-GTPase Rab5a, which regulates vesicle traffic for autophagosome formation. We examined Rab5a involvement in the function of key members of ubiquitin-conjugation systems, Atg7 and LC3-lipidated, interacting with the scaffold-protein p62. Immunohistochemistry of Rab5a was performed in human specimens of bone metastasis and pair-matched breast carcinoma; the autophagic-molecular mechanisms affected by Rab5a were evaluated in human 1833 bone metastatic cells, derived from breast-carcinoma MDA-MB231 cells. To clarify the role of Rab5a, 1833 cells were transfected transiently with Rab5a-dominant negative, and/or stably with the short-hairpin RNA Atg7, were exposed to two inhibitors of autolysosome function, and LC3II and p62 expression was measured. We showed basal autophagy in bone-metastatic cells and the pivotal role of Rab5a together with Beclin 1 between the early stages, elongation of isolation membrane/closed autophagosome mediated by Atg7, and the late-degradative stages. This regulatory network might occur in bone-metastasis and in high-grade dysplastic lesions, preceding invasive-breast carcinoma and conferring phenotypic characteristics for dissemination.
Keywords: Rab5a; autophagy; bone metastasis Rab5a; autophagy; bone metastasis

1. Introduction

The catabolic process of autophagy (macroautophagy) performs the degradation of cytoplasmic material. After sequestration in the autophagosome―a double membrane vesicle―long-lived proteins, damaged organelles, lipids and glycogens are delivered to lysosomes [1]. Autophagy occurs in three steps: autophagosome formation, autophagosome-lysososme/late endosome fusion (autophagosome maturation) and degradation. The molecular mechanisms underlying several stages (especially in the initial steps of omegasome formation and isolation membrane initiation) remain controversial. Multiple autophagosomal assembly sites, including endoplasmic reticulum (ER), Golgi, and mitochondria, have been detected. Omegasomes are formed from ER-associated membrane compartments enriched in phosphatidylinositol 3-phosphate-product of phosphatidyl-inositol 3-kinase catalytic subunit type 3 (PIK3C3)- and in the zinc-finger FYVE domain-containing protein 1, including EEA1, which is necessary for endosomal trafficking [1,2].
In mammalian cells the role of autophagy-related proteins (Atg) and their interaction with Rab5a, in the various steps of the autophagic process, remain largely unknown. Atg proteins are classified according to the function in four groups [3]. Atg14 recruits PIK3C3 and the Atg18 homolog in the omegasome [1]. Rab5a, a small GTPase localized to early endosomes, regulates the fusion between endocytic vesicles and early endosomes, as well as the homotypic fusion between early endosomes [4]. It has been reported that both PIK3C3 and the regulatory subunit PIK3R4 are Rab5a effectors: Rab5a binds directly to PIK3R4, and regulates the localization of the PIK3C3–PIK3R4 complex. Rab5a is also associated with the Beclin 1–PIK3C3 complex, promoting the early stages of autophagosome formation [5,6]. ER membrane protein complex subunit 6 (ECM6) is an ER-localized protein interacting with Beclin 1–PIK3C3 complex, facilitating ER localization of Rab5a and modulating omegasome formation [1].
Human diseases including cancer are attributable to a dysfunction of protein degradation. Autophagy in cancer is an intensely debated concept because of its double nature, and of the possibility to modulate pro-survival and pro-death mechanisms in tumour initiation and progression [7]. Cancer cells may use autophagy as a survival strategy to provide essential biomolecules required for cell viability under metabolic stress [8], partly via degradation of pro-apoptotic proteins [3]. In contrast, the impaired function of mitochondria produces reactive oxygen species, leading to DNA mutations and genomic instability, with protein misfolding: this suggests the relationship between autophagy failure and tumorigenesis. By controlling necrosis, autophagy may favour inflammation counteracting metastasis. On the other end, autophagy provides a survival advantage to detached, dormant metastatic cells through nutrient fuelling by tumour-associated stromal cells [7].
Notably, the role of the autophagic process in bone metastasis is scarcely known. We have shown in the xenograft model of bone metastasis, prepared with 1833 clones derived from human MDA-MB231 breast carcinoma cells, that autophagy failure reduces metastatic growth: this effect occurs after the co-treatment with two inhibitors, i.e., NK4, a competitive inhibitor of HGF that prevents the binding to Met receptor, and dasatinib, a specific inhibitor of Src activity [9]. Rab5a signal is very faint in a large percentage of primary breast carcinomas, increasing in the invaded lymph nodes [10].
In the present paper we examined the expression of Rab5a in human bone metastasis in comparison with dysplastic lesions, adjacent to primary ductal breast carcinoma, to identify a prognostic marker of tumour progression. In vitro, we studied the underlying molecular mechanisms of Rab5a involvement in skeletal metastasis. Our purpose was to evaluate whether a functional interaction between Rab5a and Atg7 occurred, using 1833 cells silenced with short-hairpin RNA Atg7 (shRNA Atg7), and whether Rab5a interacted with Beclin 1 and p62, by blocking the autophagic process at the late stages. To this end, we used two inhibitors: ammonium chloride (NH4Cl), which halts lysosomal enzymes and autolysosomal function, and Bafilomycin A1, which inhibits the fusion between autophagosome and lysosome by blocking vacuolar ATPase activity [8,11]. Atg7 seems critical for elongation of the isolation membrane and conversion to a nascent closed autophagosome, which is mediated by two ubiquitin-like protein conjugated systems [7]. The influence of Rab5a on these systems in bone metastasis has never been investigated.
The ubiquitin-like Atg12 is activated by the E1-like enzyme Atg7, and binds to the E2-like enzyme Atg10 before being transferred to Atg5. After interaction with Atg16L, the complex is directed to the outer autophagosomal membrane. The second ubiquitin-like pathway involves LC3 lipidation, which plays an essential role in membrane dynamics during autophagy. LC3 is synthesized as a precursor protein, pro-LC3, and is cleaved at its C-terminus by the protease Atg4B, resulting in the cytosolic LC3I. LC3I is conjugated to phosphatidylethanolamine in a reaction involving Atg7 and Atg3 to form membrane-bound LC3II. The latter is recruited to both the inner and outer surfaces of the autophagosomal membrane and is degraded and recycled, respectively [7]. The p62 is an adaptor between autophagic machinery and ubiquinated proteins via its Ubiquitin Associated Binding Domain (UBA) and the LC3-interacting region (LTR) [12]. The interaction between p62 and LC3II is required for the autophagy-mediated elimination of unfolded ubiquinated long-half-life proteins. The p62 level may be considered an index of autophagy flux since it is degraded by active autophagosome, but p62 may play also an essential role in the regulation of NF-κB pathway. Thus, p62 is a scaffold protein at the crossroad between pro-oncogenic signalling pathways—NF-κB, MAPK, mammalian target of rapamycin (mTOR)- and autophagic degradative pathway. Although p62 is by itself a significant participant in cellular transformation and tumour propagation, it is also regulated by autophagy, which can target some pathways or key proteins involved in tumour development [12].
We found a constitutively active autophagy in 1833-bone metastatic cells probably dependent on the high expression of Rab5a, similar to the findings in human specimens of bone metastasis. The elevated Rab5a expression in high grade dysplasia might be used as a predictive index of bone metastatization. Atg7 seemed involved in early and late steps of the autophagic process, interacting with Rab5a.

2. Results and Discussion

2.1. Expression of Rab5a during Breast Carcinoma Progression until Bone Metastasis, and in 1833 Bone Metastatic Cells

The present paper deals with some molecular mechanisms critical for the autophagic process in bone metastasis. In particular, we considered the expression of Rab5a GTPase, and its involvement in the function of key players of autophagy.
Initially, we assayed by immunohistochemistry the Rab5a signal during breast carcinoma progression using pair-matched specimens of invasive ductal carcinoma and bone metastasis (Figure 1 and Figure 2). As shown in Figure 1, the Rab5a expression was evaluated in the normal mammary gland and in dysplastic lesions of various grades, adjacent to the carcinoma (Patient 1). Rab5a signal was practically absent (−) in epithelial cells lining the normal duct, and increased progressively in mild-grade dysplastic duct (++) and in the pseudostratified high-grade dysplastic epithelium where it was strongly expressed (+++++) at cytosolic level. Invasive ductal breast carcinoma was negative for Rab5a in Patient 1. Negative control did not show a specific signal. In addition, Rab5a was evaluated in dysplastic lesions and in ductal breast carcinomas of other five Patients (Pt 2–6). In these Patients, the results for normal mammary gland and for dysplasia of various grade were similar to those of Patient 1 (data not shown). Figure 1 (lower panels) shows the data for Rab5a in breast carcinomas. In Patient 4 a scarce positivity (+) in neoplastic epithelium was shown; in Patient 6 the signal was estimated as (++). The other three patients were negative. Our data in invasive ductal breast carcinoma were in agreement with those of Frittoli et al. [10], showing low Rab5a in about 70% of primary breast cancers, while the Rab5a signal increased in lymph node invaded by the tumours.
Thus, we decided to evaluate whether Rab5a was present not only in axillary lymph nodes of breast cancer patients, but also at distant sites in bone metastasis. We hypothesize that Rab5a might have key roles in bone metastasis, not limited to invasion and migration of neoplastic cells [10,13,14], and might be an index of the worst outcome.
In Figure 2A we report Rab5a immunohistochemistry in bone metastases of the six Patients: Pt 1–6. The semiquantitative evaluation of Rab5a signal, and its localization in cytosol and nuclei, is shown in Figure 2B. A strong nuclear Rab5a signal was observed in Pt 2, 4 and 6, and a lower nuclear expression occurred in the other Pts. This nuclear localization of Rab5a seemed typical of bone metastasis, and was consistent with its involvement in a process with isolation membrane and vesicular formation like autophagy [2]. In 1833-bone metastatic cells, the steady-state protein level of Rab5a was three-fold higher than that of parental MDA-MB231 cells, known to be invasive but scarcely metastatic and with tropism for various organs [15].
The high-grade dysplasia corresponds to the ductal breast carcinoma in situ (DCIS), a biologically and clinically heterogeneous disease [16]. Even if not all DCISs progress to invasive carcinoma, this histological pattern may represent a late stage of cell deregulation. The natural history is influenced by both tumour- and host-related factors. In DCIS patients, the postoperative radiation therapy approximately halves local recurrence, both in situ and invasive. However, it might be an “overtreatment” for the subgroup of patients with low risk of progression to invasive breast cancer, for whom local surgery would be sufficient. For an appropriate treatment of DCIS, it would be important to clarify the predictivity of risk factors used in statistical analysis, to prevent discrepancies between prospective and observational studies. In an attempt to identify biological factors with predictive value for worst outcome related to bone metastasis formation, in our papers a number of biomarkers are currently under intensive investigation. All these biomarkers are characterized to be markedly expressed in high-grade dysplasia (DCIS) and in bone metastasis, even if the expression is low in invasive ductal carcinoma. Thus, Rab5a expression patterns here reported, may be analysed together with those of Endothelin 1 (ET-1) and secreted protein acidic and rich in cysteine (SPARC) to evaluate the risk of long-term outgrowth of skeletal metastases [17].
We thought it important to understand why Rab5a was highly expressed in established bone metastasis as well as in DCIS cells: this pattern was probably related to the acquisition of characteristics to disseminate from the primary tumour. There is evidence to support the protective nature of autophagy in anoikis [18]. By inhibiting mTOR, the AMP-activated protein kinase (AMPK), a stress response pathway, is involved in mediating anoikis resistance, typical of disseminating cells. In addition, the PI3K-Akt-mTOR signalling pathway when inhibited causes autophagy stimulation [7]. This might be our scenario, since we have demonstrated AMPK activity in 1833 bone metastatic cells (data not shown). Based on recent data [19], it would be interesting to verify whether under our experimental conditions protein translation and mitochondrial function are dependent or not on mTOR signalling.

2.2. Involvement of Beclin 1, p62 and Atg7 in Autophagy of Bone Metastatic Cells

Autophagy is an evolutionary conserved catabolic process, and it is a critical adaptive response that recycles energy and nutrients during starvation or stress. Autophagy is inhibited in tumorigenesis, indicating that it is a tumour-suppressor mechanism. However, it may be active during the metastatic process [7]. Since the complex Beclin 1-PIK3C3/Vps34 (vacuolar sorting protein34)-Vps35 (vacuolar sorting protein35) is a positive regulator of initiation and nucleation of autophagy, Beclin 1 is often mutated in breast and ovarian carcinomas [7].
Of note, in 1833 cells we observed Beclin 1 expression under basal conditions (Figure 3A), as shown in the 1833-xenograft model of bone metastasis [9]. Reduction of the steady-state protein level of Beclin 1 took place between 8 and 16 h after NH4Cl, and 4 h after Bafilomycin A1 followed by a return to control value (Figure 3A). Thus, under the blockade of the autophagy flux Beclin 1 downregulation occurred with different time-courses depending on the inhibitor used, that blocks lysosomal enzymes (NH4Cl) or autophagosome-lysosome fusion (Bafilomycin A1) [8,11]. Similar patterns were shown for p62, even if the inhibitory effects of NH4Cl and Bafilomycin A1 on this scaffold protein were slightly anticipated in respect to those on Beclin 1.
First, the effects observed with the inhibitors of the late stages of the autophagy indicated that Beclin 1 might be important also in the final degradative steps; Second, the rapid downregulation of Beclin 1 and p62 after autophagy blockade suggested a possible interaction with another degradative process. Eukaryotic cells have two major protein degradation pathways. One is the ubiquitin-proteasome pathway, which is responsible for the selective degradation of most short-lived and misfolded proteins. The other is the autophagy/lysosomal pathway, that consists in the delivery of intracellular and endocytosed proteins to the lysosomes. p62 is known to be degraded by lysosomes and proteasome, while the degradative pathways are unknown for Beclin 1. Our data indicated the interaction of the two degradative pathways with possible functional significance for the outgrowth of bone metastasis, and the beneficial adaptation to the microenvironment [12]. Ubiquinated proteasomal substrates may be induced via the inhibition of autophagy, which has been proved by increased proteasomal activities and upregulation of proteasomal subunits [20]; Third, the downregulation of p62 under autophagy blockade in 1833 cells indicated that this protein probably was not substrate of the autophagic process, but might exert specific roles in metastatic cell signalling [12]. Also, p62 may be a receptor that recognizes ubiquinated proteins, which helps to include them in the macroautophagy cascade [12]. We cannot exclude that p62 was degraded in the proteasome under autophagy blockade [3]. The functionality of the inhibitors was controlled by analyzing LC3II formation from LC3I. The two LC3 forms were present under basal conditions. Both under NH4Cl and Bafilomycin A1, LC3II progressively increased, while the LC3I protein level was lower than that of control during the entire observation period (Figure 3A).
In Figure 3B, we show the results obtained with 1833 cells exposed to the specific proteasome inhibitor clasto-lactacystin-β-lactone (LLnL) [21,22], in the presence or the absence of NH4Cl. Beclin 1 protein level almost tripled under LLnL alone, and under LLnL associated with the autophagy inhibitor. The p62 protein doubled in 1833 cells exposed concomitantly to proteasome and autophagy blockade. Thus, autophagy and proteasome pathways may work complementarily to degrade proteins in bone metastatic cells.
To evaluate the role of Atg7 in metastatic cells, we prepared and used 1833 cells silenced with shRNA Atg7 (Figure 3C). The transfection of shRNA Atg7, strongly reduced the expression of Atg7 protein in respect to MOCK-transfected cells, and the effect depended on the construct dilution. The shRNA Atg7 dilution 1:50 was the most effective by reducing of 90% Atg7 protein level. Thus, this dilution was used in the next experiments. In 1833 cells, silenced with shRNA Atg7, p62-steady state protein level increased about 1.5-fold after normalization with the respective actin signal (Figure 3C). As shown in Figure 3D, LC3I and II were present in MOCK cells; after NH4Cl exposure LC3I largely decreased (−85%) while LC3II doubled. In shRNA Atg7 cells, the formation of LC3II was prevented in the presence (−80%) and in the absence (−40%) of NH4Cl (all the data were normalized for actin). For transduction efficiency in MOCK and shRNA Atg7 cells see Figure S1 (Supplementary Material). The shRNA Atg7-1833 cells showed very low necrosis similar to 1833 cells (MOCK); in any case, the transduced cells proliferated as 1833 cells.
Altogether our findings indicate that in 1833 cells autophagy occurred under basal conditions with expression of Atg7, Beclin 1, p62 and LC3II. In further experiments, the functional interaction of Rab5a with these proteins was studied to evaluate its involvement in molecular events of early and late steps of autophagy.

2.3. Role of Rab5a Together with Atg7 in LC3 Lipidation

LC3 plays a central role in the autophagy process; it is directly incorporated into the autophagosome membrane, and it is crucial for autophagosome formation, expansion and cargo recruitment. These functions of LC3 are built on by an ubiquitination-like system by which soluble LC3 is converted to the membrane-bound form via conjugation with phosphatidylethanolamine, with the assistance of Atg7 and Atg3 [23].
Figure 4A shows that the I and II forms of LC3 decreased in 1833 cells transiently transfected with the dominant negative of Rab5a (ΔRab5a), or stably transfected with shRNA Atg7. In the latter cells, a partial recovery of the expression of the I and II forms of LC3 was observed after ΔRab5a co-transfection. These results indicated that Rab5a was involved as Atg7 in basal autophagy of 1833 cells, because ΔRab5a prevented the LC3 lipidation as occurred under Atg7 knockdown. The two molecular events might be also correlated in the formation of the membrane conjugated LC3. However, shAtg7 and ΔRab5a co-transfection determined in the 1833 cells a partial return towards basal conditions with the re-expression of LC3I. Acetylation might stabilize LC3 preventing lysosome-independent degradation into the 20S proteasome [24]. Nonlipidated LC3I is selectively involved in the formation of complexes mediating ER-associated degradation [25].
The accumulation of LC3II under the blockade of the autophagy flux with NH4Cl was enhanced by ΔRab5a. The data suggested that the function of autophagolysome was completely prevented, with consequent impairment of LC3II degradation (Figure 4B). This finding was in agreement with the reported role of activated Rab5a in the inhibition of autophagosome-lysosome fusion [26]. In fact, under our conditions the blockade of lysosome enzymes, together with impairment of Rab5a, enhanced autophagy function as indicated by LC3II formation.
As shown in Figure 4C, the LC3II form is detectable as puncta by immunofluorescence. We observed that in 1833 cells the puncta increased under 16 h NH4Cl, as well as under 16 h NH4Cl plus ΔRab5a. In shRNA Atg7-transfected 1833 cells, the 16 h NH4Cl and 16 h NH4Cl plus ΔRab5a strongly reduced puncta accumulation, because of the impairment of the autophagic process (Figure 4C). In fact, the initial molecular events controlled by Rab5a and Atg7 were hampered, making the cells insensitive to the inhibitory treatment with NH4Cl, that blocks later events in the autophagic process.

2.4. Rab5a Influenced Beclin 1 and p62 Functions in the Autophagic Process

We decided to clarify whether other molecular events were affected by Rab5a in the autophagic process of bone-metastatic cells (Figure 5A); the elongation of the isolation membrane and the conversion to a nascent closed autophagosome is mediated by two ubiquitin-like protein conjugated systems with the key players Atg7 and LC3II [7]. After transfection of ΔRab5a, the steady-state protein level of Beclin 1 doubled, suggesting that this protein was not utilized for vesicle induction/nucleation. Interestingly, Beclin 1 decreased under ΔRab5a and shRNA Atg7 co-transfection, since it likely underwent proteolysis in the proteasoma in the absence of functional autophagic process. In contrast, the knocking down of Atg7 augmented p62 without ΔRab5a, because the early stages of the autophagosome formation were hampered preventing p62 utilization.
In disseminated breast carcinoma cells with bone tropism, basal autophagy seemed to occur. A homeostatic degradation of proteins and organelles by basal autophagy might be important for cellular quality control in metastatic cells, as before reported for neurons [27]. Our findings support the notion that autophagy and protasome pathways work complementarily to degrade proteins under some circumstances [3].
As shown in Figure 5B, the blockade of the lysosome function with NH4Cl in 1833 cells transfected with ΔRab5a, increased Beclin 1 suggesting that the proteasome degradation of Beclin 1 16 h after NH4Cl treatment was impaired by unfunctional GTPase. The knocking down of Atg7 together with ΔRab5a made the cells transiently insensitive to 16 h NH4Cl. Thus, Beclin 1 might also be implicated in later steps, related to the function of autolysosomes, which were strongly dependent on the initial steps regulated by Rab5a-Atg7 interaction (Figure 5C). Under the shRNA Atg7 transfection, p62 accumulated in the presence of NH4Cl, because it was not utilized in the autophagosome function as a scaffold protein: a rapid down-regulation occurred when Rab5a was made nonfunctional. Rab5a GTPase seemed actually critical for autolysosome formation and function (Figure 5B,C), and also for redirecting degradation towards the proteasome. The present data were in agreement with the results obtained with the xenograft model, in which p62 was low under basal conditions increasing after the therapeutic treatment with NK4 plus dasatinib, that causes autophagy failure [9].
Numerous stimuli that trigger autophagy might be present in bone metastatic tissue (Figure 5C): autophagy is up-regulated when the cells need to generate intracellular nutrients and energy. It is known that bursts of oxygen radicals are activated downstream of growth factor/receptors couples in the bone marrow, a dynamic microenvironment of metastasis [15,28,29], and defective tumour mitochondria might release oxygen radicals [30,31]. Areas of hypoxia are known to occur also in bone metastasis [32]. AMPK directly regulates autophagy by phosphorylating and thereby activating ULK1 with consequent Beclin 1 expression; AMPK may act a sensor of the overall cellular energy level. Conversely, ULK activity is inhibited by mTOR-dependent phosphorylation [33].

3. Experimental Section

3.1. Patient Recruitment and Immunohistochemistry Assay

Immunohistochemistry assays were performed in invasive ductal breast carcinoma and in pair-matched bone metastasis from six patients. The samples of bone metastasis were collected during surgical interventions at Istituto Ortopedico Galeazzi, Milano, Italy. In accordance with the Declaration of Helsinki, all the patients with metastasis provided informed consent; we also obtained patient consent for the experimental use of the slices of primary carcinoma, furnished by the Hospital where the intervention had been done. The human bone specimens were fixed, decalcified, and embedded in paraffin; five serial sections were prepared and analysed by immunohistochemistry [34]. The anti-Rab5 (S-19) antibody was used (1:100, Santa Cruz Biotechnology, Santa Cruz, CA, USA). Negative controls were assayed without the specific antibody. We made a semiquantitative evaluation of the samples after immunostaining, and the scores were: no staining = −; very weak staining = +; weak staining = ++; moderate staining = +++; strong staining = ++++; very strong staining = +++++.

3.2. Cell Lines and RNA Interference with Lentiviral Vector

Invasive parental MDA-MB231 breast carcinoma cells and the derived 1833-bone metastatic clone were kindly given by J. Massagué (Memorial Sloan-Kettering Cancer Center, New York, NY, USA), and were cultured as reported before [34]. The comparative study of transcriptomic profile of MDA-MB231 and 1833 cell lines identifies a gene set whose expression pattern is associated with, and promotes the formation of, metastasis to bone [35]. MDA-MB231 and 1833 cells were authenticated with the method of short-tandem repeat profiling (STR) of nine highly polymorphic STR loci plus amelogenin on September 2014 (Cell Service from IRCCS-Azienda Ospedaliera Universitaria San Martino-IST-Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy). The 1833 cells were stably transfected with the shRNA for Atg7 (1833-shRNA Atg7). Plasmid constructs expressing shRNA Atg7 and control shRNA were obtained with Mission shRNAs pLKO.1-puro (Non-Target shRNA: SHC002; shATG7: TRCN0000007584; Sigma-Aldrich, Saint Louis, MO, USA). Lentiviral vectors were packaged with Sigma-Aldrich Mission shRNAs, pMD2-VSV-G, pMDLg/pRRE and pRSV-Rev plasmids in HEK 293T cells for 14 h; then, the medium was replaced, and 1 mM Na-butirrate added. 48 h later, the cell supernatants were collected, ultra-centrifuged, filtered and administered to 1833 cells with polybrene (8 μg/mL) for 16 h. Transduced cells were selected for 1 week with 2 μg/mL puromycin. For cytofluorimetric analysis, the puromycin resistance was replaced with GFP.
shRNA Atg7 sequence: CCGGGCCTGCTGAGGAGCTCTCCATCTCGAGATGGAGAGCTCCTCAGCAGGCTTTTT.

3.3. Western Blot Analysis

Total extracts were prepared from control MDA-MB231 and 1833 cells. Some 1833 cells were treated for various times with 50 mM NH4Cl, also after 4-h pre-treatment with 10 μM LLnL [20,21], or with 1 μM Bafilomycin A1 [11]. In some experiments, the 1833 or 1833-shRNA Atg7 cells, seeded in 6 multiwell, were transiently transfected with 0.5 μg/mL ΔRab5a (Rab5S34N). The transfection of the expression vector was performed for 24 h with a mixture (3:1) of DNA and Fugene 6 (Roche Applied Science, Basel, Switzerland). During the last 2 or 16 h of the transfection period with ΔRab5a, the cells were added NH4Cl. After Western blot analysis, immunoblots were performed with anti-Rab5a (1 μg/mL, Santa Cruz Biotechnology), anti-Beclin 1 or anti-LC3 (1:1000, Novus Biologicals, Littleton, CO, USA), anti-p62 (1:500, Abcam, Cambridge, UK), anti-Atg7 (1:1000, Sigma-Aldrich). The densitometric analysis was performed after reaction with an ECL plus chemiluminescence kit from Thermo Fisher Scientific (RockFord, IL, USA).

3.4. Immunofluorescence Assay

1833 and 1833-shRNA Atg7 cells (4 × 104) on coverslips were transfected with ΔRab5a and exposed to NH4Cl for 16 h. The cells were probed with anti-human LC3β2 (F14) antibody (1:50, Santa Cruz Biotechnology), and the formation of LC3II was evidenced by secondary anti-goat AlexaFluor 568 (1:800) antibody. The images were collected under Eclipse 80i Fluorescence microscope (Nikon, Milano, Italy) [36].

3.5. Statistical Analysis

The data of Western blots after densitometric evaluation were analysed by analysis of variance, with p < 0.05 considered significant.

4. Conclusions

We have clarified some molecular mechanisms implicated in the function of Rab5a in the different steps of the autophagic process. First of all, we showed the favouring role of Rab5a in the functional interaction of Atg7 with LC3, which is necessary for the formation of LC3II becoming able to bind membranes. Thus, Rab5a is involved in critical events not only at the beginning of the autophagy process with endosomal formation (initiation), but also later on, being important for autophagosome sealing and fusion with lysosomes through an interplay with Beclin 1. Thus, Rab5a seems to interact with Beclin 1 in two stages of the autophagic process, one of which involves Rab5a-Beclin 1-PIK3C3 complex promoting the early stages of autophagosome formation. The other network observed by us involving Rab5a-Atg7 complex was responsible for LC3 lipidation and autophagosome function (Figure 5C), that regulated the protein levels of Beclin 1 and p62 together with proteasome. This network might counteract the negative role of Rubicon (RUN domain Beclin 1-interacting and cysteine-rich containing protein) [37].
The significance of Rab5a in bone metastasis might be related to cell survival during dormancy and the following outgrowth through fuelling of energy and nutrients via the triggering of autophagy and also autophagosome sealing. In DCIS of high grade, autophagy signalling pathways might be correlated to anoikis resistance, which is a phenotype necessary for cell dissemination. The evaluation of Rab5a overexpression in breast cancer grading would predict worst prognosis, related to bone metastatization. Our findings expand the knowledge of biological features, which include concomitant overexpression of Rab5a, ET-1/ETAR receptor and SPARC, to identify the group of breast cancer patients with high risk of bone metastasis [17,38], who are suitable for local postoperative radiation therapy and for observational studies. The importance of testing the response to treatments depends on the unfavourable outcome consequent to the occurrence of an invasive local recurrence. As a future clinical perspective, new anti-metastatic therapies should benefit from the pivotal function of p62 between tumorigenesis and autophagy to prevent tumour progression.

Supplementary Materials

Supplementary materials can be found at https://0-www-mdpi-com.brum.beds.ac.uk/1422-0067/17/4/443/s1.

Acknowledgments

We thank Alessandro Luzzati and Giuseppe Perrucchini (Department of Surgery, Istituto Ortopedico Galeazzi) for the human samples. We thank Alessandro Fulgenzi for the graphical display of the file. This work was supported by the following Grants: UNIMI, Piano di Sostegno alla Ricerca 2015, Linea 2, Azione B, and Ministero della Salute, Ricerca Corrente (L4069, L4071 and L4077) Italy.

Author Contributions

Maria Alfonsina Desiderio, Paola Bendinelli and Paola Maroni conceived and designed the experiments; Paola Maroni prepared the tissue specimens and performed the immunohistochemistry; Paola Maroni and Emanuela Matteucci carried out the immunofluorescence assay; Emanuela Matteucci performed cell cultures, transient transfections and Western blot analysis; Paola Bendinelli performed the statistical analysis of the data; Massimo Resnati and Enrico Milan performed stable transfection of 1833 cells with shRNA Atg7 and cytofluorimetric analysis; Maria Alfonsina Desiderio wrote the paper. All the authors approved the final version of the article.

Conflicts of Interest

The authors declare no conflict of interest.

Abbreviations

ERendoplasmic reticulum
PIK3C3Phosphatidylinositol 3-kinase catalytic subunit type 3
AtgAutophagy related proteins
ECM6ER membrane protein complex subunit 6
shRNA Atg7Short hairpin RNA for Atg7
NH4Clammonium chloride
UBAUbiquitin associated binding
LTRLC3-interacting region
mTORmammalian target of rapamycin
DCISDuctal carcinoma in situ
ET-1Endothelin 1
SPARCSecreted protein acidic and rich in cysteine
AMPKAMP-activated protein kinase
LLnLclasto-lactacystin-β-lactone
ΔRab5adominant negative of Rab5a

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Figure 1. Rab5a expression in human dysplastic lesions and in invasive ductal breast carcinoma. Representative images of immunohistochemical staining for Rab5a were shown. The upper panels reported Rab5a signals for Patient 1 (Pt 1) throughout all the progression stages from normal mammary gland to mild and high grade dysplasia, and invasive ductal breast carcinoma. The lower panels reported the Rab5a signals for Pt 2–6 in invasive ductal breast carcinoma. Magnification of details is shown. Bar = 240 µm. Negative control was assayed without the specific antibody. We analysed by immunohistochemistry five serial sections prepared from each human specimen; ca, breast carcinoma.
Figure 1. Rab5a expression in human dysplastic lesions and in invasive ductal breast carcinoma. Representative images of immunohistochemical staining for Rab5a were shown. The upper panels reported Rab5a signals for Patient 1 (Pt 1) throughout all the progression stages from normal mammary gland to mild and high grade dysplasia, and invasive ductal breast carcinoma. The lower panels reported the Rab5a signals for Pt 2–6 in invasive ductal breast carcinoma. Magnification of details is shown. Bar = 240 µm. Negative control was assayed without the specific antibody. We analysed by immunohistochemistry five serial sections prepared from each human specimen; ca, breast carcinoma.
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Figure 2. Rab5a expression in human bone metastasis from breast carcinoma. (A) For Pts 1–6, we show representative images of immunohistochemical staining for Rab5a in bone metastases pair matched with primary carcinoma. Magnification of details is shown. Bar = 240 µm. Negative control was assayed without the specific antibody. We analysed by immunohistochemistry five serial sections prepared from each human specimen. me, bone metastasis; bo, bone; (B) For the six Patients, we performed a semi-quantitative evaluation of Rab5a intracellular distribution; the evaluation was performed on the five serial sections for each specimen analysed by immunohistochemistry; (C) Samples of total protein extracts (100 µg) were used for Western blot analysis of Rab5a. Actin was used for normalization. The experiments were repeated three times with similar results.
Figure 2. Rab5a expression in human bone metastasis from breast carcinoma. (A) For Pts 1–6, we show representative images of immunohistochemical staining for Rab5a in bone metastases pair matched with primary carcinoma. Magnification of details is shown. Bar = 240 µm. Negative control was assayed without the specific antibody. We analysed by immunohistochemistry five serial sections prepared from each human specimen. me, bone metastasis; bo, bone; (B) For the six Patients, we performed a semi-quantitative evaluation of Rab5a intracellular distribution; the evaluation was performed on the five serial sections for each specimen analysed by immunohistochemistry; (C) Samples of total protein extracts (100 µg) were used for Western blot analysis of Rab5a. Actin was used for normalization. The experiments were repeated three times with similar results.
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Figure 3. Markers of autophagy in 1833 cells, and effect of Atg7 knock down. (A) Samples of total protein extracts (100 µg) were analysed by Western blot. Actin was used for normalization. The experiments were repeated three times with similar results. * p < 0.05; ** p < 0.005 versus control; (B) Samples of total protein extracts (100 µg) from cells pre-treated with the proteasome inhibitor LLnL were analysed by Western blot. Actin was used for normalization. The experiments were repeated three times with similar results * p < 0.05; ** p < 0.005 versus control; Δ p < 0.05 versus 16-h NH4Cl treated cells; (C) Samples of total protein extracts (100 µg) were analysed by Western blot. Two dilutions of shRNA Atg7 were tested. Actin was used for normalization. The experiments were repeated three times with similar results; (D) Samples of total protein extracts (100 µg) were analysed by Western blot. Actin was used for normalization. The experiments were repeated three times with similar results.
Figure 3. Markers of autophagy in 1833 cells, and effect of Atg7 knock down. (A) Samples of total protein extracts (100 µg) were analysed by Western blot. Actin was used for normalization. The experiments were repeated three times with similar results. * p < 0.05; ** p < 0.005 versus control; (B) Samples of total protein extracts (100 µg) from cells pre-treated with the proteasome inhibitor LLnL were analysed by Western blot. Actin was used for normalization. The experiments were repeated three times with similar results * p < 0.05; ** p < 0.005 versus control; Δ p < 0.05 versus 16-h NH4Cl treated cells; (C) Samples of total protein extracts (100 µg) were analysed by Western blot. Two dilutions of shRNA Atg7 were tested. Actin was used for normalization. The experiments were repeated three times with similar results; (D) Samples of total protein extracts (100 µg) were analysed by Western blot. Actin was used for normalization. The experiments were repeated three times with similar results.
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Figure 4. Effect of ΔRab5a on LC3 forms in 1833 and in 1833-shRNA Atg7 cells. (A) Samples of total protein extracts (100 µg) were analysed by Western blot. Actin was used for normalization. The experiments were repeated three times with similar results. ** p < 0.005 versus the first lane; Δ p < 0.05 versus 1833-shRNA Atg7 cells; (B) Samples of total protein extracts (100 µg) were analysed by Western blot. Actin was used for normalization. The experiments were repeated three times with similar results. * p < 0.05 versus the first lane; Δ p < 0.05 and ° p < 0.05 versus 1833 cells exposed to NH4Cl for 2 and 16 h, respectively; (C) 1833 and 1833-shRNA Atg7 cells on coverslips were transfected or not with ΔRab5a, and were exposed to NH4Cl. The immunofluorescence experiment was performed in triplicate. LC3II, red; DAPI, blue. The images were collected at 400× magnification under fluorescence microscope. Size bar = 120 μm.
Figure 4. Effect of ΔRab5a on LC3 forms in 1833 and in 1833-shRNA Atg7 cells. (A) Samples of total protein extracts (100 µg) were analysed by Western blot. Actin was used for normalization. The experiments were repeated three times with similar results. ** p < 0.005 versus the first lane; Δ p < 0.05 versus 1833-shRNA Atg7 cells; (B) Samples of total protein extracts (100 µg) were analysed by Western blot. Actin was used for normalization. The experiments were repeated three times with similar results. * p < 0.05 versus the first lane; Δ p < 0.05 and ° p < 0.05 versus 1833 cells exposed to NH4Cl for 2 and 16 h, respectively; (C) 1833 and 1833-shRNA Atg7 cells on coverslips were transfected or not with ΔRab5a, and were exposed to NH4Cl. The immunofluorescence experiment was performed in triplicate. LC3II, red; DAPI, blue. The images were collected at 400× magnification under fluorescence microscope. Size bar = 120 μm.
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Figure 5. Effect of ΔRab5a on Beclin 1 and p62 in 1833 and in 1833-shRNA Atg7 cells. (A) Samples of total protein extracts (100 µg) were analysed by Western blot. Actin was used for normalization. The experiments were repeated three times with similar results. * p < 0.05 versus 1833-untransfected cells; Δ p < 0.05 versus 1833-shRNA Atg7 cells; (B) Samples of total protein extracts (100 µg) were analysed by Western blot. Actin was used for normalization. The experiments were repeated three times with similar results. * p < 0.05 versus the first lane; Δ p < 0.05 and ° p < 0.05 versus cells exposed to NH4Cl for 2 and 16 h, respectively; (C) Schematic representation of the experimental approach and of the results obtained by us, in the context of autophagy triggering by a plethora of stimuli, which might be active in bone metastatic tissue, influencing basal autophagic process observed in the bone-metastatic 1833 cells.
Figure 5. Effect of ΔRab5a on Beclin 1 and p62 in 1833 and in 1833-shRNA Atg7 cells. (A) Samples of total protein extracts (100 µg) were analysed by Western blot. Actin was used for normalization. The experiments were repeated three times with similar results. * p < 0.05 versus 1833-untransfected cells; Δ p < 0.05 versus 1833-shRNA Atg7 cells; (B) Samples of total protein extracts (100 µg) were analysed by Western blot. Actin was used for normalization. The experiments were repeated three times with similar results. * p < 0.05 versus the first lane; Δ p < 0.05 and ° p < 0.05 versus cells exposed to NH4Cl for 2 and 16 h, respectively; (C) Schematic representation of the experimental approach and of the results obtained by us, in the context of autophagy triggering by a plethora of stimuli, which might be active in bone metastatic tissue, influencing basal autophagic process observed in the bone-metastatic 1833 cells.
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