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. 2021 Nov 23;12(12):1851. doi: 10.3390/genes12121851

X-Linked Osteogenesis Imperfecta Possibly Caused by a Novel Variant in PLS3

Petar Brlek 1,2,*, Darko Antičević 1,3, Vilim Molnar 1, Vid Matišić 1, Kristina Robinson 4, Swaroop Aradhya 4, Dalibor Krpan 5, Dragan Primorac 1,3,6,7,8,9,10,11,12,*
Editors: Susanna Balcells Comas, Daniel Grinberg, Natalia Garcia-Giralt
PMCID: PMC8701009  PMID: 34946798

Abstract

Osteogenesis imperfecta (OI) represents a complex spectrum of genetic bone diseases that occur primarily due to mutations and deletions of the COL1A1 and COL1A2 genes. Recent molecular studies of the network of signaling pathways have contributed to a better understanding of bone remodeling and the pathogenesis of OI caused by mutations in many other genes associated with normal bone mineralization. In this paper, a case of a rare X-linked variant of OI with a change in the gene encoding plastin 3—a protein important for the regulation of the actin cytoskeleton, is presented. A 16-year-old patient developed ten bone fractures caused by minor trauma or injury, including a compression fracture of the second lumbar vertebra during his lifetime. Next-generation sequencing analysis did not show pathologically relevant deviations in the COL1A1 and COL1A2 genes. Targeted gene analyses (Skeletal disorder panel) of the patient, his father, mother and sister were then performed, detecting variants of uncertain significance (VUS) for genes PLS3, FN1 and COL11A2. A variant in the PLS3 gene were identified in the patient, his mother and sister. Since the PLS3 gene is located on the X chromosome, the mother and sister showed no signs of the disease. Although the variant in the PLS3 gene (c.685G>A (p.Gly229Arg)) has not yet been described in the literature, nor is its pathogenicity known, clinical findings combined with genetic testing showed that this variant may explain the cause of X-linked OI in our patient. This rare case of the PLS3 variant of X-linked OI might point to a novel target for personalized therapy in patients with this severe disease.

Keywords: osteogenesis imperfecta, X-linked osteoporosis, pathological fracture, PLS3, FN1, COL11A2

1. Introduction

Osteogenesis imperfecta (OI) is a clinically and genetically heterogeneous group of diseases that is inherited in an autosomal dominant, autosomal recessive, and X-linked manner [1,2]. This hereditary skeletal dysplasia manifests with three main clinical hallmarks: bone fragility ("brittle bone disease"), skeletal deformities and growth deficiency [2,3]. The clinical presentation of OI is variable in its severity. In addition to the skeletal findings, it can affect multiple organ systems and cause secondary complications. The most common secondary features include macrocephaly and dental abnormalities, blue sclerae, hearing loss, respiratory and cardiopulmonary complications [4]. The traditional types of OI (types I-IV) are inherited in an autosomal dominant manner and encompass about 80–85% of OI cases [2]. These cases are caused by pathogenic variants in exons of the genes that encode type I collagen, which is essential for normal extracellular matrix (ECM) function [5]. Previous studies have shown that in addition to pathogenic variants within exons, intronic region variants can cause splice-defective COL1A1 transcripts that also manifest with symptoms of OI [6,7]. Dysfunction of the molecular mechanisms that regulate bone mineralization, formation of ECM and normal osteoblast differentiation plays a key role in the pathogenesis of OI [2,8]. Osteocytes control bone turnover by regulating the activity of both osteoclasts and osteoblasts, and they enable constant remodeling of the extracellular matrix. The imbalance of osteoclast-mediated bone resorption and osteoblast-mediated bone formation can result in either loss or gain of bone mass [9]. In recent years, it has become clear that bone remodeling is regulated by several signaling pathways. The main pathways included in the regulation of bone formation are the Hedgehog (HH), parathyroid hormone-related peptide (PTHrP), fibroblast growth factor (FGF), C-type natriuretic peptide (CNP), transforming growth factor-beta (TGFβ), bone morphogenetic protein (BMP), Notch, WNT and osteocyte mechanosensing pathway [10,11,12]. Any disruption of genes whose protein products are involved in the molecular network of these signaling pathways can cause changes in bone remodeling and poor mineralization. Dysregulation of these pathways disrupts the mechanisms that control skeletal strength and integrity, leading to bone fragility associated with reduced bone mass [11].

Due to the discovery of a large number of new genes involved in the pathogenesis of OI, new classifications of this disease have been made based not only on the clinical but also on the molecular characteristics of OI. A classification by Marini et al. based on the molecular etiopathogenesis of the disease classifies OI by defects in collagen synthesis, bone mineralization, collagen modification and processing, and defects in osteoblast differentiation [2]. The majority of OI cases (type I-IV) are associated with reduced production of normal type I collagen or the synthesis of abnormal collagen as a result of pathogenic variants in COL1A1 and COL1A2 genes [3]. Pathogenic variants in the IFITM5 (OI type V) and SERPINF1 (OI type VI) genes are responsible for deficiencies in bone mineralization [13]. Among the genes responsible for OI with deficits in collagen modification and processing are CRTAP (type VII), LEPREI (type VIII), PPIB (type IX), SERPINH1 (type X), FKBP10 (type XI) and BMP1 (type XII). Pathogenic variants in genes SP7 (type XIII), TMEM38B (type XIV), WNT1 (type XV), CREB3L1 (type XVI), SPARC (type XVII) and MBTPS2 (type XVIII) cause defects in osteoblast differentiation [2].

Recently discovered cases of OI have been associated with pathogenic variants in an X-chromosome gene coding for plastin 3 (PLS3). The clinical presentation in hemizygous men matched the presentation of classical OI and was variable in heterozygous women [14]. The main role of PLS3 is in F-actin-binding, which consequently suggests that PLS3 participates in all processes dependent on F-actin dynamics, such as cell motility, cell division, focal adhesion, endocytosis, neurotransmission, vesicle trafficking, axonal local translation, and intracellular calcium PLS3-dependent processes [15,16]. Plastins are proteins with a single polypeptide chain composed of two tandem repeats of actin-binding domains (ABD1 and ABD2). Each ABD is assembled from two tandem calponin-homology (CH) domains (CH1 and CH2 in ABD1, and CH3 and CH4 in ABD2) [17]. The binding of each ABD to two separate actin filaments promotes the formation of a bundle resulting in distinct F-actin organization [16].

In the present study, a novel PLS3 variant in a nonconsanguineous family of a proband with X-linked OI was detected and potential link between this variant of plastin 3 and osteogenesis imperfecta was reviewed.

2. Materials and Methods

2.1. Subjects

A 16-year-old patient (proband), who complained of pain, pathological fractures and patellar subluxations that arose due to a moderate valgus of the distal femur, was admitted to St. Catherine’s Special Hospital. The patient was accompanied by his father, mother and sister, who had no symptoms related to diseases of the locomotor system and who were all included in the study. All participants involved in this study signed an informed consent form.

2.2. Clinical Examination

Clinical data were collected, including fracture history, height, weight, growth speed and family history. Additionally, the sclera, teeth, hearing and musculoskeletal system were checked upon clinical examination. Blood analysis was performed to determine serum calcium, inorganic phosphates, osteocalcin and vitamin D (25-OH) in all patients. Moreover, biochemical findings of creatinine and deoxypyridinoline were obtained from urine. The results of the analysis were interpreted according to the reference intervals of the Laboratory of the Special Hospital St. Catherine. Bone densitometry was performed in the whole family, which included the measurement of bone density of the proximal femur and spine, whose reference values were validated according to the Croatian population. The proband received high-dose vitamin D therapy (25,000 IU/day) for three months. To evaluate the effect of the therapy, we measured markers of bone remodeling and bone mineral density (BMD) measured by densitometry.

2.3. Genetic Testing

Genomic DNA was isolated from the patient’s blood sample and subjected to clinical next-generation sequencing using a multi-gene panel. Invitae Skeletal Disorders Panel includes sequence analysis and deletion/duplication testing of 320 genes was conducted (Table 1). All target genes were sequenced to a minimum depth of ≥50× and an average of 350×. Sequence reads were aligned with the reference genome (GRCh37) and single nucleotide variants (SNVs) were called from coding sequences and 20 bp of flanking intronic sequences. Promoters and other non-coding regions were not included. Exon-level copy number (deletions and duplications) and other types of non-SNV variants were identified using validated algorithms [18,19].

Table 1.

A complete list of genes analyzed, including the relevant gene transcripts.

GENE TRANSCRIPT GENE TRANSCRIPT GENE TRANSCRIPT GENE TRANSCRIPT
ACAN NM_013227.3 CDKN1C NM_000076.2 DHCR24 NM_014762.3 C2CD3 NM_015531.5
ACP5 NM_001111035.2 CDT1 NM_030928.3 DIP2C NM_014974.2 CA2 NM_000067.2
ACVR1 NM_001105.4 CENPJ NM_018451.4 DLL3 NM_016941.3 CANT1 NM_138793.3
ADAMTS10 NM_030957.3 CEP120 NM_153223.3 DLX3 NM_005220.2 CASR NM_000388.3
ADAMTS17 NM_139057.3 CEP135 NM_025009.4 DMRT2 NM_006557.6 CCDC8 NM_032040.4
AFF4 NM_014423.3 CEP152 NM_014985.3 DNA2 NM_001080449.2 CDC45 NM_001178010.2
AGA NM_000027.3 CEP63 NM_025180.3 DONSON NM_017613.3 CDC6 NM_001254.3
AGPS NM_003659.3 CFAP410 NM_004928.2 DVL1 NM_004421.2 FN1 NM_212482.2
AIFM1 NM_004208.3 CHST14 NM_130468.3 DVL3 NM_004423.3 FTO NM_001080432.2
ALPL NM_000478.5 CHST3 NM_004273.4 DYM NM_017653.3 FUCA1 NM_000147.4
AMER1 NM_152424.3 CHUK NM_001278.4 DYNC2H1 NM_001080463.1 FZD2 NM_001466.3
ANKH NM_054027.4 CLCN7 NM_001287.5 DYNC2LI1 NM_016008.3 GALNS NM_000512.4
ANO5 NM_213599.2 COG1 NM_018714.2 EBP NM_006579.2 GALNT3 NM_004482.3
ARCN1 NM_001655.4 COL10A1 NM_000493.3 EIF2AK3 NM_004836.6 GDF5 NM_000557.4
ARSB NM_000046.3 COL11A1 NM_001854.3 ESCO2 NM_001017420.2 GDF6 NM_001001557.2
ARSE NM_000047.2 COL11A2 NM_080680.2 EVC NM_153717.2 GHR NM_000163.4
ASCC1 NM_001198800.2 COL1A1 NM_000088.3 EVC2 NM_147127.4 GHRHR NM_000823.3
ASPM NM_018136.4 COL1A2 NM_000089.3 EXOC6B NM_001321729.1 GHSR NM_198407.2
ATR NM_001184.3 COL27A1 NM_032888.3 EXOSC2 NM_014285.6 CSGALNACT1 NM_001130518.1
B3GALT6 NM_080605.3 COL2A1 NM_001844.4 EXT1 NM_000127.2 CSPP1 NM_024790.6
B3GAT3 NM_012200.3 COL9A1 NM_001851.4 EXT2 NM_207122.1 CTSA NM_000308.3
B4GALT7 NM_007255.2 COL9A2 NM_001852.3 EXTL3 NM_001440.3 CTSK NM_000396.3
BGN NM_001711.5 COL9A3 NM_001853.3 FAM20C NM_020223.3 CUL7 NM_014780.4
BMP1 NM_006129.4 COMP NM_000095.2 FAM46A NM_017633.2 CWC27 NM_005869.3
BMP2 NM_001200.3 CREB3L1 NM_052854.3 FAR1 NM_032228.5 DDR2 NM_006182.2
BMPER NM_133468.4 CRTAP NM_006371.4 FBN1 NM_000138.4 DDRGK1 NM_023935.2
BMPR1B NM_001203.2 CSF1R NM_005211.3 FGF23 NM_020638.2 IFT43 NM_052873.2
IFT52 NM_001303458.2 IFT122 NM_052985.3 LIG4 NM_002312.3 MYH3 NM_002470.3
IFT57 NM_018010.3 IFT140 NM_014714.3 LMNA NM_170707.3 MYO18B NM_032608.6
IFT74 NM_001099222.1 IFT172 NM_015662.2 LMX1B NM_002316.3 NAGLU NM_000263.3
IFT80 NM_020800.2 IDUA NM_000203.4 LONP1 NM_004793.3 NANS NM_018946.3
IFT81 NM_014055.3 IFITM5 NM_001025295.2 LOXL3 NM_032603.3 NBAS NM_015909.3
IGF1 NM_000618.4 IFT122 NM_052985.3 LRP4 NM_002334.3 NEK1 NM_012224.2
IGF2 NM_000612.5 IFT140 NM_014714.3 LRP5 NM_002335.3 NEU1 NM_000434.3
IHH NM_002181.3 IFT172 NM_015662.2 LRRK1 NM_024652.4 NKX3-2 NM_001189.3
IMPAD1 NM_017813.4 IDUA NM_000203.4 LTBP2 NM_000428.2 NOG NM_005450.4
FGF9 NM_002010.2 IFITM5 NM_001025295.2 LTBP3 NM_001130144.2 NOTCH2 NM_024408.3
FGFR1 NM_023110.2 PCYT1A NM_005017.3 MAFB NM_005461.4 NPPC NM_024409.3
FGFR2 NM_000141.4 PDE4D NM_001104631.1 MAN2B1 NM_000528.3 NPR2 NM_003995.3
FGFR3 NM_000142.4 PEX5 NM_001131025.1 MANBA NM_005908.3 NPR3 NM_000908.3
FIG4 NM_014845.5 PEX7 NM_000288.3 MAP3K7 NM_145331.2 NSDHL NM_015922.2
FKBP10 NM_021939.3 PGM3 NM_001199917.1 MATN3 NM_002381.4 NSMCE2 NM_173685.2
FLNA NM_001456.3 PISD NM_001326411.1 MBTPS2 NM_015884.3 NXN NM_022463.4
FLNB NM_001457.3 PKDCC NM_138370.2 SH3PXD2B NM_001017995.2 OBSL1 NM_015311.2
MCM5 NM_006739.3 PLK4 NM_014264.4 SLC17A5 NM_012434.4 OCRL NM_000276.3
MCPH1 NM_024596.4 PLOD2 NM_182943.2 SLC26A2 NM_000112.3 ORC1 NM_004153.3
MEOX1 NM_004527.3 PLS3 NM_005032.6 SLC35D1 NM_015139.2 ORC4 NM_002552.4
MESP2 NM_001039958.1 POC1A NM_015426.4 SLC39A13 NM_152264.4 ORC6 NM_014321.3
MGP NM_000900.3 POLR1A NM_015425.4 SLCO2A1 NM_005630.2 OSTM1 NM_014028.3
MMP13 NM_002427.3 POP1 NM_015029.2 SLCO5A1 NM_030958.2 P3H1 NM_022356.3
MMP14 NM_004995.3 POR NM_000941.2 SMAD4 NM_005359.5 P4HB NM_000918.3
MMP2 NM_004530.5 PPIB NM_000942.4 SMARCAL1 NM_014140.3 PAM16 NM_016069.9
MMP9 NM_004994.2 PPP3CA NM_000944.4 SNRPB NM_198216.1 PAPSS2 NM_001015880.1
MNX1 NM_005515.3 PRKAR1A NM_002734.4 SNX10 NM_001199835.1 PCGF2 NM_007144.2
GJA1 NM_000165.4 PTDSS1 NM_014754.2 SOX9 NM_000346.3 PCNT NM_006031.5
GLB1 NM_000404.2 PTH1R NM_000316.2 SP7 NM_001173467.2 TRMT10A NM_152292.4
GMNN NM_015895.4 PTHLH NM_198965.1 SPARC NM_003118.3 TRPS1 NM_014112.4
GNAS NM_000516.5 PTPN11 NM_002834.3 SQSTM1 NM_003900.4 TRPV4 NM_021625.4
GNE NM_001128227.2 PYCR1 NM_006907.3 SRCAP NM_006662.2 TTC21B NM_024753.4
GNPAT NM_014236.3 RAB33B NM_031296.2 SUCO NM_014283.4 TUBGCP6 NM_020461.3
GNPTAB NM_024312.4 RBBP8 NM_002894.2 SULF1 NM_001128205.1 TYROBP NM_003332.3
GNPTG NM_032520.4 RECQL4 NM_004260.3 TAB2 NM_015093.5 VAC14 NM_018052.3
GNS NM_002076.3 RIPPLY2 NM_001009994.2 TAPT1 NM_153365.2 VPS33A NM_022916.4
GORAB NM_152281.2 RMRP NR_003051.3 TBCE NM_003193.4 WDR19 NM_025132.3
GPC6 NM_005708.3 RNU4ATAC NR_023343.1 TBX15 NM_152380.2 WDR34 NM_052844.3
GPX4 NM_001039848.2 SFRP4 NM_003014.3 TBX3 NM_005996.3 WDR35 NM_001006657.1
GSC NM_173849.2 INPPL1 NM_001567.3 TBX5 NM_000192.3 WDR60 NM_018051.4
GUSB NM_000181.3 JAG1 NM_000214.2 TBX6 NM_004608.3 WISP3 NM_003880.3
GZF1 NM_022482.4 KAT6B NM_012330.3 TBXAS1 NM_001061.4 WNT1 NM_005430.3
HES7 NM_032580.3 KIAA0586 NM_001244189.1 TCIRG1 NM_006019.3 WNT3 NM_030753.4
HGSNAT NM_152419.2 KIAA0753 NM_014804.2 TCTEX1D2 NM_152773.4 WNT3A NM_033131.3
HPGD NM_000860.5 KIF22 NM_007317.2 TCTN3 NM_015631.5 WNT5A NM_003392.4
HSPG2 NM_005529.6 KL NM_004795.3 TGFB1 NM_000660.5 XRCC4 NM_022406.3
HYAL1 NM_153281.1 KMT2A NM_001197104.1 TMEM165 NM_018475.4 XYLT1 NM_022166.3
IARS2 NM_018060.3 LARP7 NM_016648.3 TMEM38B NM_018112.2 XYLT2 NM_022167.3
ICK NM_016513.4 LBR NM_002296.3 TNFRSF11A NM_003839.3 SGSH NM_000199.3
IDS NM_000202.6 LEMD3 NM_014319.4 TNFRSF11B NM_002546.3 ROR2 NM_004560.3
IDUA NM_000203.4 LFNG NM_001040167.1 TNFSF11 NM_003701.3 RSPRY1 NM_133368.2
IFITM5 NM_001025295.2 LIFR NM_002310.5 MSX2 NM_002449.4 RTTN NM_173630.3
SEC24D NM_014822.3 TRAPPC2 NM_001011658.3 SERPINH1 NM_001235.3 RUNX2 NM_001024630.3
TRIP11 NM_004239.4 TREM2 NM_018965.3 SERPINF1 NM_002615.6 SC5D NM_006918.4
SETBP1 NM_015559.2 TRIM37 NM_015294.4 ZMPSTE24 NM_005857.4

2.4. Bioinformatics Analysis of Gene Variants of Unknown Significance

Bioinformatics software Sorting Intolerant to Tolerant (SIFT), Polymorphism Phenotyping v2 (PolyPhen-2) and Align-GVGD were used to predict the possible pathogenicity of the gene variants found in proband’s sample. SIFT (https://sift.bii.a-star.edu.sg/) is a tool that predicts the possible impact of an amino acid substitution based on sequence homology and the physical properties of amino acids. PolyPhen-2 (http://genetics.bwh.harvard.edu/pph2/) predicts whether an amino acid substitution affects protein function by comparing the physical and chemical properties of amino acids. Align-GVGD (http://agvgd.hci.utah.edu/) is a freely available program that combines the biophysical characteristics of amino acids and protein multiple sequence alignment to predict possible pathogenicity of gene variants.

3. Results

3.1. Phenotypes of the Patients

The proband, a 15-year-old boy (164 cm, 65 kg, BMI = 24.2 kg/m2), was the first child of a nonconsanguineous family. He was delivered vaginally at term with a birth weight of 3500 g. In the maternity ward, he had neonatal jaundice and phototherapy was performed. His psychomotor development was normal. He suffered his first low-trauma fracture (fifth metatarsal bone of his right foot) at the age of 2 years and ten months. Since then, he had experienced a total of 10 fractures, including a fracture of the neck of the left humerus, the radius metaphysis and a compression fracture of the L2 vertebra (Figure 1).

Figure 1.

Figure 1

(a) Profile lumbar spine radiograph showing a compression fracture of the L2 vertebral body. The superior endplate is compressed posteriorly, with minor loss of vertebral body height corresponding to grade 1 by Genant classification. (b) Anteroposterior radiograph of the left upper arm showing a spiral fracture of the proximal third of the humerus.

During the physical examination, impaired growth was determined (3rd–15th percentile), while sclerae, dentition and joint laxity were normal. Although the hearing loss was initially observed at age 3, the most recent hearing test showed a normal tympanogram and tonal audiogram. Radiographic images showed inadequate bone mineralization, while densitometry revealed reduced bone density in favor of osteoporosis. Laboratory findings showed decreased levels of vitamin D (25-OH). The serum concentration was normalized after administering an increased dose of vitamin D (25,000 IU). The proband had normal inorganic phosphates, creatinine, ALP, ALT and deoxypyridinoline concentrations with an increased serum concentration of osteocalcin and calcium. He had low BDMs at the lumbar spine of 0.587 g/cm2 (L1-L4 T score −4.3) and left hip of 0.604 g/cm2 (T score −2.8). The proband’s 14-year-old sister from the same parents was healthy (163 cm, 89 kg, BMI = 33.5 kg/m2) with normal hearing, sclerae, dentition and joint laxity. Laboratory findings showed normal serum calcium and osteocalcin levels with significantly reduced inorganic phosphates and vitamin D (25-OH). She had BDMs at the lumbar spine of 0.990 g/cm2 (L1-L4 T score −0.5) and left hip of 0.971 g/cm2 (T score 0.2), which indicate initial osteoporotic changes. The mother of the proband was healthy (155 cm, 70 kg, BMI = 29.1kg/m2). She had normal hearing, sclerae, dentition and joint laxity. Laboratory findings showed normal serum calcium levels, osteocalcin and inorganic phosphates with significantly reduced vitamin D (25-OH). She had BDMs at the lumbar spine of 0.897 g/cm2 (L1-L4 T score −1.4) and left hip of 0.903 g/cm2 (T score −0.3), which indicate initial osteoporotic changes. The mother and her siblings had not yet experienced bone fractures. The proband’s father and his parents were healthy with no history of fractures. More clinical features of the whole family with results of bone remodeling markers measured on 1 September 2021, are shown in Table 2.

Table 2.

A complete list of clinical features of the whole family.

Proband Sister Mother Father
Age (years) 15 14 42 41
Height (cm) 164 163 155 177
Weight (kg) 65 89 70 107
Vertebral compression fractures 1 No No No
Long-bone fractures 10 No No No
Sclerae White White White White
Subluxation of the joints 3 No No No
Dentinogenesis imperfecta No No No No
Hearing loss No No No No
F1 BDM (g/cm2) 0.604 / / /
F1 BDM T-score −2.8 / / /
F2 BDM (g/cm2) 0.689 0.971 0.903 1.163
F2 BDM T-score −2.3 0.2 −0.3 0.9
S1 BDM (g/cm2) 0.587 / / /
S1 BDM T-score −4.6 / / /
S2 BDM (g/cm2) 0.622 0.990 0.897 0.916
S2 BDM T-score −4.3 −0.5 −1.4 −1.6
Ca (mmol/L) 2.67 * 2.61 2.43 2.58 *
Inorganic phosphates (mmol/L) 1.39 0.84 * 1.22 1.07
Osteocalcin (µg/L) 34.0 * 18.3 7.91 3.92
vitamin D (25-OH) (nmol/L) 83 36 * 39 * 75
Creatinine (mmol/L) 12.3 4.9 13.4 15.6
Deoxypyridinoline (nM/mM of creatinine) 9.1 9.9 4.4 5.0

F1—proximal femur densitometry finding on May 20, 2021; F2—proximal femur densitometry finding on 1 September 2021; S1—spine densitometry finding on May 20, 2021; S2—spine densitometry finding on 1 September 2021; *—values outside the reference interval.

3.2. Genetic Findings

Multiplex ligation-dependent probe amplification (MLPA) analysis and next-generation sequencing analysis performed on the COL1A1 and COL1A2 genes excluded pathogenic variants. Subsequent analysis performed using a multi-gene skeletal disorder panel on the proband’s blood sample identified variants of uncertain significance (VUS) in PLS3, FN1 and COL11A2 (Figure 2). These variants were not present in the Genome Aggregation Database (gnomAD), the Exome Aggregation Consortium (ExAC), or Invitae’s in-house variant database.

Figure 2.

Figure 2

The pedigree of the family with X-linked osteogenesis imperfecta (OI) and variants of unknown significance (VUS) for the PLS3, NF1, and COL11A2 genes. The proband is marked with an arrow. The proband’s sister, mother and her siblings had no history of fractures. Created with BioRender.com (accessed on 10 November 2021).

The c.4418G>A (p.Arg1473Gln) variant in exon 28 of the FN1 gene was heterozygous in both the mother and the patient, thus reducing the likelihood that it is the cause of the disease. Additionally, we found an amplification of exons 41–66 of the COL11A2 gene in the proband and his healthy father. The exact location of this copy-number change is unknown. The analysis from Invitae suggests that the 5’ breakpoint is likely in intron 40, but the 3’ boundary is difficult to determine as it likely exists beyond the end of the gene.

A c.685G>A (p.Gly229Arg) variant in the X-linked PLS3 gene was identified in the patient, his mother and his sister. This variant has not yet been described in the literature, nor is its pathogenicity known. Furthermore, we confirmed the absence of this variant in the proband’s maternal grandfather, suggesting that the variant either occurred de novo in the proband’s mother or she may have inherited it from the proband’s grandmother.

Along with these observations, our clinical findings indicate that this variant may explain the X-linked OI in the proband. Since the PLS3 gene is located on the X chromosome, the mother and sister were not expected to show pathological fractures if this variant were definitively pathogenic. The results of the genetic analysis performed in this family has led to the discovery of an apparently novel variant in the PLS3 gene, for which the available evidence indicates a favorable likelihood of pathogenicity (Figure 2).

3.3. Bioinformatics Analysis

Algorithms developed to predict the effect of missense changes on protein structure and function showed results in favor of the pathogenicity of the newly discovered variant of the PLS3 gene (Figure 3).

Figure 3.

Figure 3

Molecular structure of the PLS3 protein with an indicated mutation in exon 7, which is a part of the CH1 (calponin-homology 1) domain. Created with BioRender.com (accessed on 10 November 2021).

The new variant in the PLS3 gene was characterized as “deleterious” by SIFT software, which predicts whether amino acid substitution affects protein function. A similar result was shown by the bioinformatics tool PolyPhen-2, which classified the change of PLS3 gene (c.685G>A (p.Gly229Arg)) as “probably harmful”.

Align-GVGD, a web-based program that combines the biophysical characteristics of amino acids and protein multiple sequence alignments, classified the new variant of the PLS3 gene as “Class C15”. Prediction groups form a spectrum from C0 to C65, with C0 least likely to interfere with protein function and C65 most likely.

3.4. The Effect of Vitamin D Treatment

Hypovitaminosis was successfully corrected, and there was an improvement in bone density after three months of therapy with increased doses of vitamin D (25,000 IU/day). Bone densitometry confirmed the increase in BMD measured on 1 September 2021, compared to BMD on 20 May 2021 on both the femur (F1 BDM = 0.604; F2 BDM = 0.689) and the spine (S1 BDM = 0.587; S2 BDM = 0.622) (Table 2).

4. Discussion

We identified a Croatian family with X-linked OI caused by a novel missense variant in the PLS3 gene (c.685G>A (p.Gly229Arg)). The proband presented with low bone mass, frequent pathological fractures and occasional subluxations of the patella. His mother and sister were healthy without previous fractures; however, the densitometry findings revealed initial osteoporotic changes. All of the family members had normal hearing, sclerae, dentition and joint laxity. These findings suggest that the variant in PLS3, described now for the first time, may have an impact on the process of bone formation or mineralization, while its role in odontogenesis and the processes associated with the formation of other connective tissue is not clinically noticeable. Interestingly, Hu et al. in their case of X-linked OI showed an entire family that had characteristic blue sclera, while the proband and his family did not have the stated characteristic. Additionally, in their study, it was stated that the mother, as the carrier of the mutation, had normal BMD, while in this case the proband’s sister and mother had reduced BMD [14]. Densitometric findings indicated initial osteoporotic changes visible on the bones of the spine and proximal femur. Such findings suggest a diverse range of clinical phenotypes in women as the process of X chromosome inactivation is random and leads to mosaicism [20].

Studies indicate that pathogenic variants in the PLS3 gene, which encodes plastin 3, play a major role in bone metabolism and lead to severe early osteoporosis [21]. Different variants in PLS3, which is ubiquitously expressed in solid tissues, lead to decreased bone mineral density [22]. Previous findings suggest that the majority of the OI-linked PLS3 pathogenic variants are either loss-of-function changes (nonsense or frameshift varaints) which rarely result in translated protein products due to nonsense-mediated mRNA decay [16,23]. Separately, a rare single nucleotide polymorphism of the PLS3 gene was reported in association with osteoporosis in postmenopausal women [24]. The current identified X-linked PLS3 actin bundling-deficient mutation (L478P) that produces a full-length protein disables actin-binding in the ABD2 and thus prevents F-actin bundling. The bundling-deficient PLS3 fails to co-localize with any F-actin structures in cells despite preserved F-actin binding through a non-mutation-bearing ABD [25]. Our results indicate that the Gly229Arg missense change in exon 7, which encodes a CH1 domain that is a key part of ABD1, may thus cause actin-binding disorders. Based on literature reports, we believe that disease-causing variants in the PLS3 gene are generally loss-of-function. However, there is currently not enough evidence available to determine whether p.Gly229Arg is a loss-of-function variant.

Different variants in PLS3 have shown differences in distribution between lamellipodia and focal adhesions [16]. Studies on the chicken homolog of the PLS3 gene have shown that the function of its protein product can be linked to mechanosensitivity of osteocytes [26]. Dendrites are the most mechanosensitive part of the osteocyte and they are indicators of overall osteocyte mechanosensitivity [27]. Increased PLS3 expression was observed during osteoblast maturation and within osteocyte dendritic processes indicating its role in bone morphogenesis and remodeling [25]. Although other examined mutations that produce a full-length protein have fully retained F-actin bundling ability, it is shown that they have defects in Ca2+ sensitivity. While wild-type PLS3 was distributed equally in lamellipodia and focal adhesions, the Ca2+-hyposensitive PLS3 was localized exclusively at focal adhesions. On the other hand, the Ca2+-hypersensitive PLS3 mutants were bound to lamellipodia. These findings unveiled that severe osteoporosis can be caused by a mutational disruption of the Ca2+-controlled PLS3’s cycling between lamellipodia and focal adhesions [16]. Additionally, it is possible that the PLS3 mutation we found in exon 7 (c.685G>A), which replaces the amino acid glycine with arginine, changes the conformation of PLS3 itself and consequently leads to hypersensitivity or hyposensitivity of the PLS3 protein to calcium. Such a change in calcium sensitivity would lead to misregulation of actin cytoskeleton remodeling and consequently to OI symptoms as found in our patient. Although the exact mechanism of pathogenesis of the novel PLS3 variant we have described here remains unknown, the genetic analysis in the family, absence in population genomic databases, and the in silico predictions suggest that it is very likely a pathogenic variant that causes X-linked OI unrelated to collagenopathies.

Discoveries in the field of bone development and actin cytoskeleton reorganization provide a better understanding of mechanisms by which plastin 3 causes OI [28]. The leading hypotheses include insufficient mineralization by osteoblasts, dysregulation of osteocyte mechanosensing, and increased bone resorption by osteoclasts [16,23,27,29,30]. Previous findings showed that PLS3 actin-bundling activity, as well as finely tuned Ca2+ regulation, are essential for proper bone formation [16]. Different localization of PLS3 within cells is altered by sensitivity to Ca2+, which suggests that fine regulation of PLS3 by Ca2+ is critical for bone formation, as its imbalance in either direction results in OI [25]. Studies on animal models have indicated the importance of PLS3 in bone tissue development and preservation of bone architecture [26]. The mouse knockout model for PLS3 showed decreased bone strength and osteoporosis, while PLS3 knockdown in zebrafish manifests in muscular and skeletal abnormalities [28,30]. In contrast to classical OI caused by COL1A1 and COL1A2 variants or a mutation in the IFITM5 gene (OI type V), which result in hypermineralized bone matrix, defects in PLS3 cause significant hypomineralization of the bone matrix [31,32,33]. Such findings were confirmed by densitometry in our patients (mother, sister and proband), whose bones showed a loss of bone density in support of the diagnosis of osteoporosis. A recent study has proposed a role for PLS3 in osteoclast activity through the regulation of podosomes by nuclear factor κB (NFκB) signaling [30]. Receptor activator of nuclear factor κB ligand (RANKL) signaling inhibits osteoblastic differentiation mainly through activating NFκB as well as inhibiting the β-catenin synthesis and promoting osteoclastogenesis [12]. Since PLS3 represents the major plastin isoform in osteocytes, it could contribute to both osteogenesis and osteolysis [34]. The findings that Ca2+ is involved in the redistribution of PLS3 from focal adhesions to the leading edge represent a strong link between the activities of PLS3 and the machinery thought to drive bone mechanosensing and reorganization [25].

In recent years, the genetic range of diseases associated with osteoporosis has expanded widely and, so far, at least 24 genes have been identified to cause OI [11]. Mechanistic studies in vitro and preclinical mouse models have demonstrated defects in type I collagen processing and crosslinking, post-translational modifications, folding, procollagen transport from rough ER to the Golgi or collagen secretion and structure [11,35]. Moreover, some forms of OI associated with collagen type I deposition and mineralization are caused by mutations in SERPINF1 or IFITM5, while mutations in WNT1 or SP7 are linked to inhibition of chondrocyte differentiation and stimulation of osteoblast differentiation [36,37,38,39]. Other diseases associated with disordered bone formation, in which collagen processing is not affected, have disrupted cellular signaling via the WNT, the RANKL-RANK and the NOTCH2 signaling pathways, which are important in the regulation of bone resorption and formation [11,40,41,42]. The understanding of these pathways through the study of rare bone diseases has opened up new possibilities of specific therapeutic agents for the treatment of common osteoporosis. Many rare fragility disorders remain insufficiently understood and hence drug targets remain undiscovered for future drug development. Acquired bone fragility conditions such as cytokine and glucocorticoid-induced as well as postmenopausal osteoporosis are far more common and new, pathway-specific treatments are still needed [11].

Today, there are numerous therapeutic options for the treatment of OI, including bisphosphonates, denosumab, teriparatide, sclerostin inhibitory antibody, transforming growth factor-beta inhibition, orthopedic management of OI and, among the latest therapies, the use of stem cells [4,43]. Bisphosphonates are the basis of pharmacological treatment and act by inhibiting osteoclast activity and enhancing bone resorption. Current evidence demonstrates that bisphosphonates increase bone mineral density in children and adults with OI and also reduce the risk of fractures [44]. They are most commonly used in pediatric patients because, during growth, they favorably affect the fusion of the vertebrae after compression fractures. However, when using them, care should be taken to avoid side effects that include the acute phase of the infusion reaction and transient hypocalcemia [4,45]. In our case, we showed that high doses of vitamin D improved bone density after three months as evidenced by densitometry findings performed on the proximal femur and lumbar spine. Among the drugs for OI, biological drugs like denosumab are being investigated today. This drug is an antibody for RANKL and inhibits osteoclast differentiation and function [46]. Additionally, like bisphosphonates, it acts on osteoclasts in order to inhibit bone resorption. Several studies have shown that denosumab treatment improves bone mineral density in patients with OI [4]. Another inhibitory antibody (sclerostin) has an inhibitory effect on bone formation via the canonical WNT signaling pathway. Dysregulation of sclerostin expression causes skeletal disorders characterized by loss of bone mass [47]. Romosozumab is a humanized monoclonal antibody that inhibits bone resorption by inhibiting sclerostin and promoting bone formation [48]. The parathyroid hormone analog (teriparatide) induces bone anabolism and stimulates bone formation before it enhances bone resorption in adults with type I OI [49]. Drugs that inhibit transforming growth factor-beta (TGFβ) act on TGFβ signaling, which is extremely important for the formation of the skeleton [50]. Fresolimumab is one of the TGFβ inhibitors and is currently being studied in adult patients with OI [4]. By performing a complex two-part operation in the severe form of OI type III, Jeleč et al. demonstrated that, aside from drug therapy, personalized surgical treatment has an important role in treating OI patients [51]. Recently, mesenchymal stem cells (MSCs) have been suggested as an ideal tool for bone and cartilage regeneration [52]. Research on the treatment of OI is also developing in the direction of MSC transplants. This form of therapy is a personalized treatment that starts before birth or as soon as possible after birth. In this way, it is possible to prevent fractures, which is not possible with any other therapy available today [29].

The limitation of the study was the small number of people we could test for this variant of the PLS3 gene and relate to the clinical phenotype since we found a novel variant never before described in the literature.

5. Conclusions

The normal process of bone remodeling and mineralization is extremely important for the formation of sufficiently strong bones. To improve the treatment of patients with bone dysplasia, further studies of the molecular substrate involved in the regulation of signaling pathways that control bone remodeling are needed. Our discovery of a novel missense variant in the PLS3 gene that is segregating with disease in a Croatian family and present in a hemizygous state in an affected male proband suggests a link to X-linked OI. The protein product of PLS3 participates in the reorganization of the actin cytoskeleton contributes to a better understanding of the involvement of this gene in the pathogenesis of X-linked OI. Future research of the role of plastin 3 in the function of bone remodeling regulation by osteoblasts and osteoclasts will shed light on potential molecular targets in personalized therapy.

Acknowledgments

We would like to thank the International Society for Applied Biological Sciences for their support.

Author Contributions

Conceptualization, P.B. and D.P.; methodology, P.B., D.A., K.R., S.A., D.K. and D.P.; software, K.R. and S.A.; validation, D.A., V.M. (Vid Matišić) and D.P.; formal analysis, P.B., D.A., D.K. and D.P.; investigation, P.B., V.M. (Vid Matišić) and D.P.; writing—original draft preparation, P.B.; writing—review and editing, P.B., D.A., D.K., V.M. (Vilim Molnar), V.M. (Vid Matišić) and D.P.; visualization, P.B. and V.M. (Vilim Molnar); supervision, D.P.; project administration, D.P. All authors have read and agreed to the published version of the manuscript.

Funding

This research received no external funding.

Institutional Review Board Statement

The study was conducted according to the guidelines of the Declaration of Helsinki and approved by the Ethics committee of St. Catherine Specialty Hospital.

Informed Consent Statement

Informed consent was obtained from all subjects involved in the study. Written informed consent has been obtained from the patients to publish this paper with case details and accompanying images.

Data Availability Statement

The data presented in this study are available on request from the corresponding author.

Conflicts of Interest

The authors declare no conflict of interest.

Footnotes

Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Availability Statement

The data presented in this study are available on request from the corresponding author.


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