Comprehensive Genomic Analysis Reveals the Prognostic Role of LRRK2 Copy-Number Variations in Human Malignancies

Abstract

Genetic alterations of leucine-rich repeat kinase 2 (LRRK2), one of the most important contributors to familial Parkinson’s disease (PD), have been hypothesized to play a role in cancer development due to demographical and preclinical data. Here, we sought to define the prevalence and prognostic significance of LRRK2 somatic mutations across all types of human malignancies by querying the publicly available online genomic database cBioPortal. Ninety-six different studies with 14,041 cases were included in the analysis, and 761/14,041 (5.4%) showed genetic alterations in LRRK2. Among these, 585 (76.9%) were point mutations, indels or fusions, 168 (22.1%) were copy number variations (CNVs), and 8 (1.0%) showed both types of alterations. One case showed the somatic mutation R1441C. A significant difference in terms of overall survival (OS) was noted between cases harboring somatic LRRK2 whole deletions, amplifications, and CNV-unaltered cases (median OS: 20.09, 57.40, and 106.57 months, respectively; p = 0.0008). These results suggest that both LRRK2 amplifications and whole gene deletions could play a role in cancer development, paving the way for future research in terms of potential treatment with LRRK2 small molecule inhibitors for LRRK2-amplified cases.

1. Introduction

Identification of the PARK8 locus [1] and mutations in the leucine-rich repeat kinase 2 (LRRK2) gene [2,3], located on chromosome 12 (12q12) in familial cases of Parkinson’s disease (PD), more than fifteen years ago is considered a game-changing discovery in our knowledge of this yet incurable neurodegenerative disorder. Today, single LRRK2 mutations represent one of the most frequently known genetic determinants of PD [4].

The LRRK2 gene consists of 51 exons, and it encodes a large protein of 2527 amino acids, retaining two catalytic domains with kinase (MAPKKK domain) and GTPase (ROC, Ras in Complex domain) function and other protein–protein interaction domains (armadillo-like, leucine-rich repeats, WD40) [5]. All PD-associated mutations identified until now are single nucleotide substitutions, the most relevant being G2019S, which accounts for approximately half of LRRK2 mutation in Caucasian populations, underlying approximately 5% of PD cases of autosomal dominant PD and approximately 2% of PD cases with no known family history [6,7,8], and R1441C/G/H. Interestingly, these mutations cluster in the two aforementioned enzymatic domains. The gene encodes for the LRRK2 protein, also known as dardarin, which is widely expressed in different tissues, namely the brain, heart, kidney, and lungs [9], but also in peripheral blood mononuclear cells (PBMCs), including lymphocytes and monocytes [10].

The physiological role of LRRK2 is still not completely understood, despite the enormous amount of research conducted on this protein in the last years. LRRK2 has been hypothesized to have a role in several fundamental cellular processes, primarily autophagy, endocytosis, and mitochondrial and cytoskeletal function [11,12,13,14]. Notably, disruptions in all these processes have been implicated in the neurodegeneration leading to PD [15,16,17,18]. Furthermore, as predictable from the expression of the protein in PBMCs, LRRK2 alterations have also been implicated in dysfunction of immune pathways [19]. Interestingly, genome-wide association studies have linked LRRK2 to at least three chronic inflammatory conditions, namely Crohn’s Disease [20,21,22], leprosy [23], and tuberculosis [24]. Taken together, current evidence strongly suggests a role of LRRK2 misfunction in the pathogenesis of PD, possibly mediated by a role in neuroinflammation [25].

Current evidence in the literature may suggest a negative association between certain neurological diseases like PD or Alzheimer’s disease and cancer [26]. Interestingly, demographical data suggest an increased incidence of cancer in individuals with a germline G2019S LRRK2 mutation, in particular, melanoma [27,28,29,30]; however, findings are not consistent across all studies [31,32]. Moreover, in vitro models recently demonstrated that downregulation of LRRK2 suppresses cholangiocarcinoma cell growth [33] and decreases proliferation of papillary thyroid carcinoma [34]; on the other hand, overexpression of LRRK2 activates survival and proliferation signals in melanocytes and melanoma cells [35]. A series of molecular studies have linked the abnormal activity of this protein to autophagic pathways, inflammation, and mitochondrial dysfunction [11,12,13,14,19], but a defined role in cancer pathogenesis needs yet to be elucidated. Several mechanisms for which LRRK2 could display a tumor-suppressor function have been described, most notably p53 phosphorylation and p21 induction [36], JNK activation [37], and RCAN1 phosphorylation [38]. In contrast, LRRK2 has also a potentially oncogenic role in MET signaling activation [39]. Using multigene testing panels, LRRK2 demonstrated a prognostic significance in different types of cancers, including oral squamous cell carcinomas [40], intrahepatic cholangiocarcinoma [33], non-small-cell lung cancer [41,42], and colon cancer [43]. Recently, great efforts to develop small molecule inhibitors of LRRK2 have been made, hoping for a disease-modifying role in the setting of PD [44,45,46,47]. If an oncogenic role of LRRK2 is confirmed, those drugs are of potential use in the field of cancer-targeted therapy as well.

The current study aims to establish the prevalence of LRRK2 point mutations, indels or fusions (hereby MUTs) and copy-number variations (CNVs) in a large cohort of human malignancies, as well to investigate the potential prognostic value of such genetic alterations.

2. Materials and Methods

A curated set of 176 non-redundant studies publicly available in the online cancer genomic database cBioPortal [48,49,50], comprising 46,595 samples from all types of human malignancies, was initially screened, assessing whether LRRK2 was profiled across those publications; 96 studies endured the screening (full list available in Table S1), encompassing 23,796 different samples from all human cancers excluding those of the eye, the peripheral nervous system, and the thymus. Cases without both MUTs and CNVs data were excluded; a total of 14,286 samples from 14,041 patients remained. The dataset was also queried for MUTs alone, comprising 17,454 patients from 94 studies (2 studies excluded for not profiling LRRK2 MUTs), and for CNVs alone, comprising 15,183 patients from 93 studies (3 studies excluded for not profiling LRRK2 CNVs). For survival analysis of the different types of CNVs, (i.e., amplifications and whole gene deletions), the raw data were downloaded from the cBioPortal database and processed with MedCalc Statistical Software version 19.1.3 (MedCalc Software, Ostend, Belgium). Overall survival was calculated using the Kaplan–Meier Estimate; statistical significance was calculated with a Log-rank Test. Statistical significance of co-occurrence of alterations of LRRK2 and other genes was calculated with Fisher Exact test for p-values and with the Benjamini–Hochberg procedure for q-values.

3. Results

Among 96 non-redundant studies publicly available in the online cancer genomic database cBioPortal [48,49,50], comprising 46,595 samples from all types of human malignancies, the overall observed prevalence of LRRK2 genetic alterations was 761/14041 (5.4%), with MUTs accounting for 585 cases (76.9%; 426 missense, 155 truncating, 3 inframe indels, 1 fusion) and CNVs accounting for 168 cases (22.1%; 123 amplifications and 45 whole gene deletions); eight cases (1.0%) showed both MUTs and CNVs (5 missense and amplification, 1 fusion and amplification, 1 missense and whole gene deletion, 1 inframe indel and amplification), as shown in Figure 1. All these were somatic alterations, and no germinal LRRK2 mutations were present in the dataset.

Figure 1.

Prevalence and distribution of LRRK2 genetic alterations across the analyzed studies. The 5% of the first and second row is expanded to better visualize the data [48,49,50].

When considering studies with at least 50 patients profiled, alterations across different cancer types ranged from 18.06% (bladder/urinary tract cancer) to 0.0% (seminoma), as shown in Figure 2.

Figure 2.

LRRK2 alteration frequency across cancer types. The types of alterations are color-coded as shown in the legend above [48,49,50].

The distribution of missense, truncating, and inframe mutations across the LRRK2 protein is shown in the lollipop plot in Figure 3. Of note, one case of endometrial carcinoma displayed the missense mutation R1441C; one case of stomach adenocarcinoma showed the missense mutation G2019D.

Figure 3.

LRRK2 missense, truncating, and inframe mutations in the studies analyzed. A scattered mutational distribution is evident. The alterations are color-coded as shown in the legend above [48,49,50].

Overall survival (OS) analysis of all cancer types pooled together demonstrated a worse prognosis for cases with LRRK2 alterations (207/613 deceased, median OS: 94.03 months) in comparison to cases with unaltered LRRK2 (4123/11,356 deceased, median OS: 103.26 months) as shown in Figure 4; this result was statistically significant, with p = 0.0280.

Figure 4.

Overall survival of LRRK2 altered (MUT and/or CNV) vs. LRRK2 non-altered cases. A slightly worse prognosis can be observed for altered cases [48,49,50]. MUT: point mutations, indels and fusions; CNV: copy-number variations.

By stratifying for organ sites, a similar result was observed for prostate adenocarcinoma (LRRK2 altered: 6/16 deceased, median OS months: 120, vs. LRRK non-altered: 127/649 deceased, median OS: 115.13 months; p = 0.037); interestingly, an opposite, statistically significant trend was noted for endometrial carcinoma (LRRK2 altered: 6/85 deceased, median OS: NA, vs. LRRK non-altered: 110/479 deceased, median OS: 110.10 months; p = 0.0001481; Figure 5). No other significant results for other organ sites were noted, with trends pointing toward a better/worse prognosis in different settings (Figure S1).

Figure 5.

Overall survival of LRRK2 altered (MUT and/or CNV) vs. LRRK2 non-altered cases in prostatic adenocarcinoma (A) and endometrial carcinoma (B). The prognostic significance of LRRK2 altered cases is negative for prostatic cancer and positive for endometrial cancer [48,49,50]. MUT: point mutations, indels and fusions; CNV: copy-number variations.

When analyzing MUTs and CNVs alone, a significant (p = 0.0005102) worse survival was noted within the CNV-altered cases (52/111 deceased, median OS: 55.47 months) in contrast to CNV-unaltered ones (4799/13198 deceased, mean OS: 106.57 months); no difference was noted in the cohort analyzed for MUTs only (827/17454; mutated cases: 210/597 deceased, mean OS: 84 months; non-mutated cases: 3711/10945, median OS: 78.8 months; p = 0.870; Figure 6). The majority of CNV-altered cases included in the survival analysis are composed of LRRK2 amplifications (85 amplifications and 26 deep deletions).

Figure 6.

Prognostic significance of LRRK2 CNV-altered vs. CNV-unaltered cases (A) and in MUT-altered vs. MUT-unaltered cases (B). A significant difference is noted for cases analyzed for CNVs, but not for cases profiled for MUTs [48,49,50]. MUT: point mutations, indels and fusions; CNV: copy-number variations.

By stratifying for amplifications and deletions, survival analysis shows a significantly (p = 0.0008) worse prognosis in terms of OS for whole gene deleted cases (13/26 deceased, median OS: 20.09 months) in comparison to amplified cases (39/85 deceased, median OS: 57.40 months) and unaltered cases (4799/13,198 deceased, median OS: 106.57 months; Figure 7).

Figure 7.

Survival of cases showing LRRK2 whole gene deletions (DEL, orange curve), amplifications (AMP, green curve), and no copy-number alterations (0, blue curve).

The co-occurrence of CNV alterations of LRRK2 and other genes located at 12q12 is shown in Table 1. The co-occurrence of CNV-alterations of LRRK2 and other genes involved in cancer pathogenesis located at 12q13-12q15 is shown in Table 2.

Table 1.

Co-occurrence of amplifications and whole gene deletions of genes located at 12q12 and LRRK2.

Gene	Alteration	Altered Group	Unaltered Group	Log Ratio	p-Value	q-Value	Enriched in
SLC2A13	Amp	99 (57.56%)	26 (0.17%)	8.40	5.76 × 10−183	2.83 × 10−178	Altered group
CNTN1	Amp	95 (55.23%)	32 (0.21%)	8.04	2.10 × 10−170	5.16 × 10−166	Altered group
C12ORF40	Amp	88 (51.16%)	27 (0.18%)	8.18	2.46 × 10−158	4.02 × 10−154	Altered group
ABCD2	Amp	85 (49.42%)	30 (0.20%)	7.98	3.71 × 10−150	4.55 × 10−146	Altered group
KIF21A	Amp	84 (48.84%)	35 (0.23%)	7.74	2.61 × 10−145	2.56 × 10−141	Altered group
PDZRN4	Amp	82 (47.67%)	35 (0.23%)	7.70	3.80 × 10−141	3.11 × 10−137	Altered group
MUC19	Amp	74 (43.02%)	21 (0.14%)	8.29	1.52 × 10−132	1.06 × 10−128	Altered group
CPNE8	Amp	82 (47.67%)	132 (0.86%)	5.79	1.09 × 10−110	6.65 × 10−107	Altered group
ALG10B	Amp	76 (44.19%)	137 (0.90%)	5.62	5.19 × 10−99	2.83 × 10−95	Altered group
PPHLN1	Amp	63 (36.63%)	54 (0.35%)	6.70	1.25 × 10−95	6.15 × 10−92	Altered group
YAF2	Amp	62 (36.05%)	50 (0.33%)	6.78	4.27 × 10−95	1.91 × 10−91	Altered group
GXYLT1	Amp	60 (34.88%)	45 (0.29%)	6.89	4.42 × 10−93	1.81 × 10−89	Altered group
ZCRB1	Amp	60 (34.88%)	46 (0.30%)	6.86	1.01 × 10−92	3.81 × 10−89	Altered group
PRICKLE1	Amp	61 (35.47%)	53 (0.35%)	6.68	3.28 × 10−92	1.15 × 10−88	Altered group
ADAMTS20	Amp	59 (34.30%)	61 (0.40%)	6.42	4.67 × 10−86	1.53 × 10−82	Altered group
PUS7L	Amp	55 (31.98%)	52 (0.34%)	6.55	1.96 × 10−81	6.00 × 10−78	Altered group
IRAK4	Amp	54 (31.40%)	53 (0.35%)	6.50	2.62 × 10−79	7.15 × 10−76	Altered group
TWF1	Amp	53 (30.81%)	57 (0.37%)	6.37	2.42 × 10−76	5.93 × 10−73	Altered group
TMEM117	Amp	54 (31.40%)	82 (0.54%)	5.87	5.64 × 10−72	1.32 × 10−68	Altered group
NELL2	Amp	53 (30.81%)	80 (0.52%)	5.88	1.08 × 10−70	2.40 × 10−67	Altered group
CNTN1	DeepDel	38 (22.09%)	15 (0.10%)	7.81	4.09 × 10−64	8.73 × 10−61	Altered group
DBX2	Amp	44 (25.58%)	62 (0.41%)	5.98	2.37 × 10−59	4.85 × 10−56	Altered group
C12ORF40	DeepDel	31 (18.02%)	5 (0.03%)	9.11	5.82 × 10−57	1.14 × 10−53	Altered group
ANO6	Amp	44 (25.58%)	76 (0.50%)	5.68	2.06 × 10−56	3.89 × 10−53	Altered group
SLC2A13	DeepDel	35 (20.35%)	20 (0.13%)	7.28	4.60 × 10−56	8.35 × 10−53	Altered group
KIF21A	DeepDel	30 (17.44%)	6 (0.04%)	8.79	3.24 × 10−54	5.67 × 10−51	Altered group
PLEKHA8P1	Amp	41 (23.84%)	66 (0.43%)	5.79	1.86 × 10−53	3.14 × 10−50	Altered group
ABCD2	DeepDel	29 (16.86%)	5 (0.03%)	9.01	5.03 × 10−53	8.23 × 10−50	Altered group
PDZRN4	DeepDel	32 (18.60%)	19 (0.12%)	7.22	6.05 × 10−51	9.57 × 10−48	Altered group
SCAF11	Amp	38 (22.09%)	77 (0.50%)	5.45	1.49 × 10−46	2.08 × 10−43	Altered group
ADAMTS20	DeepDel	31 (18.02%)	26 (0.17%)	6.73	1.57 × 10−46	2.13 × 10−43	Altered group
GXYLT1	DeepDel	28 (16.28%)	13 (0.09%)	7.58	3.17 × 10−46	4.15 × 10−43	Altered group
ARID2	Amp	38 (22.09%)	79 (0.52%)	5.42	3.22 × 10−46	4.15 × 10−43	Altered group
CPNE8	DeepDel	27 (15.70%)	10 (0.07%)	7.91	6.85 × 10−46	8.62 × 10−43	Altered group
ALG10B	DeepDel	25 (14.53%)	10 (0.07%)	7.79	4.00 × 10−42	4.90 × 10−39	Altered group
LINC02402	Amp	29 (16.86%)	31 (0.20%)	6.38	1.64 × 10−41	1.96 × 10−38	Altered group
YAF2	DeepDel	26 (15.12%)	16 (0.10%)	7.17	3.27 × 10−41	3.82 × 10−38	Altered group
ZCRB1	DeepDel	25 (14.53%)	12 (0.08%)	7.53	3.96 × 10−41	4.52 × 10−38	Altered group
PPHLN1	DeepDel	25 (14.53%)	14 (0.09%)	7.31	3.17 × 10−40	3.53 × 10−37	Altered group
PRICKLE1	DeepDel	26 (15.12%)	19 (0.12%)	6.93	4.66 × 10−40	5.08 × 10−37	Altered group
PUS7L	DeepDel	26 (15.12%)	22 (0.14%)	6.71	5.09 × 10−39	5.43 × 10−36	Altered group
IRAK4	DeepDel	25 (14.53%)	22 (0.14%)	6.66	2.89 × 10−37	2.78 × 10−34	Altered group
NELL2	DeepDel	24 (13.95%)	25 (0.16%)	6.41	1.25 × 10−34	9.57 × 10−32	Altered group
RACGAP1P	Amp	27 (15.70%)	47 (0.31%)	5.67	1.65 × 10−34	1.24 × 10−31	Altered group
TWF1	DeepDel	22 (12.79%)	21 (0.14%)	6.54	2.29 × 10−32	1.29 × 10−29	Altered group
MUC19	DeepDel	17 (9.88%)	2 (0.01%)	9.56	4.64 × 10−32	2.50 × 10−29	Altered group
SCAF11	DeepDel	24 (13.95%)	36 (0.24%)	5.89	6.43 × 10−32	3.43 × 10−29	Altered group
TMEM117	DeepDel	23 (13.37%)	30 (0.20%)	6.09	1.21 × 10−31	6.27 × 10−29	Altered group
LINC00938	Amp	27 (15.70%)	65 (0.43%)	5.21	1.65 × 10−31	8.34 × 10−29	Altered group
DBX2	DeepDel	21 (12.21%)	21 (0.14%)	6.47	1.20 × 10−30	5.75 × 10−28	Altered group
ARID2	DeepDel	25 (14.53%)	54 (0.35%)	5.36	3.63 × 10−30	1.65 × 10−27	Altered group
PLEKHA8P1	DeepDel	21 (12.21%)	25 (0.16%)	6.22	1.49 × 10−29	6.63 × 10−27	Altered group
ANO6	DeepDel	21 (12.21%)	27 (0.18%)	6.11	4.69 × 10−29	2.00 × 10−26	Altered group
LINC00938	DeepDel	21 (12.21%)	27 (0.18%)	6.11	4.69 × 10−29	2.00 × 10−26	Altered group
RACGAP1P	DeepDel	20 (11.63%)	21 (0.14%)	6.40	6.07 × 10−29	2.57 × 10−26	Altered group
LINC02402	DeepDel	10 (5.81%)	7 (0.05%)	6.99	4.09 × 10−16	3.74 × 10−14	Altered group

Table 2.

Genes located in 12q12-12q15 for which CNVs are associated with cancer, and correlation with LRRK2 CNVs.

Gene	Cytoband	Alteration	Altered Group	Unaltered Group	Log Ratio	p-Value	q-Value	Enriched in
MDM2	12q15	Amp	36 (20.93%)	480 (3.14%)	2.74	5.05 × 10−19	7.37 x 10−17	Altered group
MDM2	12q15	DeepDel	1 (0.58%)	4 (0.03%)	4.47	0.0544	0.0963	Altered group
CDK4	12q14.1	Amp	26 (15.12%)	350 (2.29%)	2.72	8.28 × 10−14	5.38 × 10−12	Altered group
ERBB3	12q13.2	Amp	22 (12.79%)	133 (0.87%)	3.88	2.18 × 10−18	2.81 × 10−16	Altered group
ERBB3	12q13.2	DeepDel	9 (5.23%)	14 (0.09%)	5.84	1.52 × 10−12	7.93 × 10−11	Altered group
KMT2D	12q13.12	Amp	11 (6.40%)	38 (0.25%)	4.68	4.77 × 10−12	2.32 × 10−10	Altered group
KMT2D	12q13.12	DeepDel	7 (4.07%)	21 (0.14%)	4.89	1.82 × 10−8	3.28 × 10−7	Altered group

No significant clustering of LRRK2 CNV-altered versus LRRK2 CNV-unaltered cases was observed in terms of neoplasm staging (Figure S2). Sex and age at diagnosis distribution for LRRK2 CNV-altered and LRRK2 CNV-unaltered cases are shown in Figure S3; both results were statistically non-significant (p > 0.05).

4. Discussion

To our knowledge, this is the first study to assess the prevalence, characteristics, and prognostic implications of LRRK2 alterations in a large cohort of human malignancies. A significant proportion of cancers (5%, Figure 1) across the majority of tumor subtypes (Figure 2) harbor MUTs and/or CNVs of this gene involved in the pathogenesis of PD; however, the role of LRRK2 in cancer development remains to be elucidated, and the possible driver or passenger role of LRRK2 alterations in cancer needs yet to be established.

The mutational landscape of LRRK2 in this cohort suggests a passenger role of MUTs, given their scattered distribution and absence of clustering in specific domains such as Pkinase and Roc (Figure 3). It is also worth noting that the two most commonly encountered mutations of LRRK2 in PD (and therefore pathogenic, albeit in a different setting of human disease), i.e., G2019S and R1441C, are seldom encountered (R1441C: n = 1, G2019S: n = 0, with a case showing a somatic mutation at the same codon: G2019D). An explanation could be represented by a hypothetical tumor-suppressor role of LRRK2 in normal cellular development, for which a multitude of different inactivating mutations could result in a decrease of LRRK2 levels and activity; however, this hypothesis is not supported by previously published data [33] and our subsequent analysis.

The negative prognostic implications of LRRK2 alterations in the studies analyzed (Figure 4) seem to suggest, on the other hand, that LRRK2 does not simply represent a bystander during the process of cancer pathogenesis; the conflicting results for prostate adenocarcinoma and endometrial carcinoma also seem to indicate a site-specific biological meaning of such alterations. By querying for MUTs and CNVs alone, the two different Kaplan–Meier plots unravel the negative prognostic role of CNV-altered cases, while the curves for mutated/nonmutated cases almost completely overlap.

By stratifying for the type of copy-number alteration, in comparison to unaltered cases, both whole gene deleted cases (CNV = −2) and amplified cases (CNV = 2) show a worse prognosis, the former being more marked. Notably, LRRK2 amplification has been observed to be of indirect oncogenic potential in papillary renal cell carcinoma and thyroid carcinomas trough MET signaling [39].

Given the nature of the alterations which confer a negative prognostic value to LRRK2, i.e., amplifications and deletions, other genes located within or near the locus 12q12 need to be taken into account when trying to explain a putative role of LRRK2 in cancer development, since duplications and deletions can involve large segments of DNA strands. The list of genes located at 12q12 and their frequency of CNV alterations in LRRK2 CNV-altered and CNV unaltered cases is shown in Table 1; notably, all genes are significantly co-altered along with LRRK2 (percentage of co-alterations range: 5.81–57.56%; percentage of alterations in LRRK2 unaltered cases range: 0.07-0.54%; Log ratio range: 5.21–9.56). By querying the OncoKB database [51,52] for genes located at 12q12, only ARID2 deletion was found to be likely oncogenic, specifically in non-small cell lung cancer [53] and hepatocellular carcinoma [54]; in our analysis, ARID2 whole gene deletion co-occurred in 14.53% of LRRK2 CNV-altered cases.

CNVs of other genes located at 12q12-12q15 are known to be oncogenic, such as KMT2D deletions [55], ERRB3 amplifications [56], CDK4 amplifications [57], and MDM2 amplifications [58]. Correlations between CNV of those genes and LRRK2 in our analysis are presented in Table 2. Notably, amplifications of MDM2 and CDK4 are both associated with liposarcoma [57,58]. Given the oncogenic role of amplification of ERRB3, CDK4, and MDM2, it could be speculated that LRRK2 represents only a passenger of 12q amplification; it must be noted, though, that the major impact on prognosis is observed in LRRK2 whole gene deleted cases, and the concordance between LRRK2 and KMT2D whole gene deletions is 4.07% in our analysis, and a significant proportion of LRRK2-amplified cases lack amplification of MDM2, CDK4, and ERBB3. Besides, MDM2 acts as a down-regulator of p53 by initiating its ubiquitination which leads to proteasomal degradation [59], and LRRK2 has been described to phosphorylate p53 [36], therefore protecting it from MDM2-induced degradation; in this view, the 20.93% of cases harboring both LRRK2 and MDM2 amplifications could not rely on the latter as a driver of tumor progression. The same applies to the 15.12% of CKD4-amplified cases, as LRRK2 induces p21, a known CKD4 inhibitor [60], via p53 phosphorylation [36].

The hypothesized role of an increase in kinase activity of LRRK2 in cancer development, if confirmed via in vitro studies, potentially paves the way for the use of small molecule LRRK2 inhibitors beyond PD: LRRK2-amplificated cases are putative candidates for such treatment. Our analysis indeed shows that LRRK2 amplification, given its negative prognostic significance, could play a role in cancer development and may be clinically actionable. And yet, we also note a dismal prognosis for LRRK2 whole gene deleted cases. In this view, an inhibition of LRRK2 activity could prove to be more harmful than beneficial. However, when considering that both amplifications (gain of function) and whole gene deletions (loss of function) of LRRK2 are associated with a worse prognosis in cancer, it must be acknowledged that the modulation of the kinase activity by LRRK2 small molecule inhibitors in G2019S-mutated PD patients might lead to a normal kinase function rather than a loss of kinase activity. However, given the complex interplay between the different domains of LRRK2, an inhibition of its kinase domain could have pleiotropic effects on the function of the whole protein [61,62]. Further research is needed, both in vitro and in vivo, in order to better characterize the potential anticancer effects of LRRK2 small molecule inhibitors.

Our analysis provides insights on the potential biological balancing role of LRRK2, a fact hinted at by the different biological processes in which this gene is involved. A number of other genes have been described to possess both oncogenic and tumor-suppressor functions [63]. A subset of these genes possesses kinase activity (e.g., MAP2K4, MAP3K4, PRKAR1A, PRKCB), similarly to LRRK2. In this view, any CNV alteration could play a role in the disruption of normal cellular homeostasis which ultimately leads to cancer. Notably, a small molecule LRRK2 inhibitor, LRRK2-IN-1, demonstrated activity in colorectal and pancreatic cancer via direct inhibition of DCLK1 [64]; the clinical utility of such therapeutic agents could also spawn further from LRRK2-overexpressed cases.

5. Conclusions

Herein, we demonstrated that a significant subset of human malignancies shows LRRK2 genetic alterations. The most frequently encountered mutations in PD, G2019S, and R1441C are almost nonexistent in sporadic human malignancies. LRRK2 CNV, both amplifications and whole gene deletions, confer a poorer prognosis in terms of OS in comparison to unaltered cases; the latter cases show the worse prognosis. In contrast, LRRK2 somatic MUTs show no prognostic significance. These data support the fact that both LRRK2 overexpression and complete loss-of-function could play a role in cancer development, and potentially pave the way for future research to investigate the potential treatment of amplified cases with LRRK2 small molecule inhibitors; the dismal prognosis of LRRK2 whole gene deleted cases also needs further research. In contrast, LRRK2 non-activating MUTs are of probable passenger significance.

Supplementary Materials

The following are available online at https://www.mdpi.com/2073-4425/11/8/846/s1, Table S1. Studies included in the analysis using cBioPortal. Figure S1. Kaplan–Meier survival estimates of LRRK2-altered vs. LRRK2-wild-type cases in (A) urothelial cancer, (B) esophagogastric cancer, (C) melanoma, (D) non-small cell lung cancer, (E) colorectal cancer, and (F) pancreatic cancer [48,49,50]. Figure S2. Neoplasm staging for LRRK2 CNV-altered and LRRK2 CNV-unaltered cases. No significant clustering can be observed [48,49,50]. Figure S3. Sex (A) and age at diagnosis (B) distribution for LRRK2 CNV-altered and LRRK2 CNV-unaltered cases (A, p > 0.05, Chi-squared test; B, altered group: median 61.2, interquartile range 52.1-65.0; unaltered group, median 61.16, interquartile range 52.0-69.6; p > 0.05, Kruskal–Wallis Test) [48,49,50].

Author Contributions

Conceptualization, G.L. (Gianluca Lopez) and G.L. (Giulia Lazzeri); formal analysis, G.L. (Gianluca Lopez) and A.R.; investigation, G.L. (Gianluca Lopez) and G.L. (Giulia Lazzeri); methodology, A.R., E.G.-R., and V.V.; supervision, G.I., F.M.C., E.G.-R., S.F., V.V., and A.D.F.; validation, G.L. (Gianluca Lopez), A.R., V.V., and A.D.F.; visualization, G.L. (Gianluca Lopez) and A.R.; writing – original draft, G.L. (Gianluca Lopez) and G.L. (Giulia Lazzeri); writing – review & editing, G.L. (Giuseppe Isimbaldi), F.M.C., S.F., V.V., and A.D.F. All authors have read and agreed to the published version of the manuscript.

Funding

The APC was funded by by the Italian Ministry of Health “Ricerca Corrente 2020” program to S.F.

Conflicts of Interest

The authors declare no conflict of interest.