Hermansky-Pudlak Syndrome: Identification of Novel Variants in the Genes HPS3, HPS5, and DTNBP1 (HPS-7)

Hermansky-Pudlak syndrome (HPS), a rare heterogeneous autosomal recessive disorder, is characterized by oculocutaneous albinism (OCA) and a bleeding diathesis due to a defect regarding melanosomes and platelet delta (δ)-granule secretion. Interestingly, patients with HPS type 2 (HPS-2) or HPS type 10 (HPS-10) present additionally with an immunological defect. We investigated three patients (IP1, IP2, and IP3) who suffer from a bleeding diathesis. Platelet aggregometry showed impaired platelet function and flow cytometry revealed a severely reduced platelet CD63 expression hinting to either a defect of platelet delta granule secretion or a decreased number of delta granules in these patients. However, only IP3 presents with an apparent OCA. We performed panel sequencing and identified a homozygous deletion of exon 6 in DTNBP1 for IP3. Western analysis confirmed the absence of the encoded protein dysbindin confirming the diagnosis of HPS-7. Interestingly, this patient reported additionally recurrent bacterial infections. Analysis of lymphocyte cytotoxicity showed a slightly reduced NK-degranulation previously documented in a more severe form in patients with HPS-2 or HPS-10. IP1 is carrier of two compound heterozygous variants in the HPS3 gene (c.65C > G and c.1193G > A). A homozygous variant in HPS5 (c.760G > T) was identified in IP2. The novel missense variants were classified as VUS (variant of uncertain significance) according to ACMG guidelines. For IP1 with the compound heterozygous variants in HPS3 a specialized ophthalmological examination showed ocular albinism. HPS3 and HPS5 encode subunits of the BLOC-2 complex and patients with HPS-3 or HPS-5 are known to present with variable/mild hypopigmentation.

BLOC-3 encompasses the gene products of HPS1 and HPS4 (Wei 2006). Deficiencies in these proteins are associated with a more severe bleeding diathesis, OCA, and serious complications such as pulmonary fibrosis and granulomatous colitis (Huizing et al., 2020;Nurden et al., 2020).
Here, we report novel genetic alterations in HPS3, HPS5, and DTNBP1 (HPS-7) in patients with a platelet delta granule secretion defect and differently pronounced OCA. Interestingly, we also document a mild NK cell degranulation defect in HPS-7, potentially implicating BLOC-1 also in immune functions.

Index Patient 1
The six-year-old girl (ethnic origin: European) presented with frequent epistaxis (once a month) and bruising. Previous surgery had not been performed. Cutaneous albinism was not apparent. After the molecular genetic analysis had identified compound heterozygous variants in the gene HPS3, a specialized ophthalmological examination was initiated and showed ocular albinism (atypical albino-VEP) with normal visual acuity (no nystagmus). The girl's mother exhibits prolonged menstrual bleeding. Her father and older sister did not show any bleeding symptoms. The parents are not consanguine.

Index Patient 2
The 45-year-old woman (ethnic origin: Arabic) had a history of extensive bruising, epistaxis, menorrhagia, postoperative bleeding (teeth extraction, liposuction), bleeding after deliveries, joint hemorrhages, microhematuria, and impaired wound healing/ increased scarring after surgery. She has eight children and suffered from increased bleeding during childbirth. Therefore, she had received red blood cell and platelet concentrates each time. The symptoms of menorrhagia improved significantly after therapy with tranexamic acid and desmopressin. Cutaneous albinism was not apparent. She and her husband are consanguine, however, her husband does not present any bleeding symptoms. Some of their 8 children seem to exhibit only very mild bleeding symptoms, none of them is clinically as severely affected as their mother. We performed panel sequencing for IP2 and two of her children (daughter and son).

Index Patient 3
The 60-year-old woman (ethnic origin: European, Portuguese descent) presented with OCA and frequent gingival bleeding. Furthermore, she had experienced prolonged bleeding after skin excision and adenoma resection. She did not show signs of colitis.
She suffers from asthma. She reported that she has always suffered from severe respiratory infections and recurrent skin furuncles. The patient does not have children. Her consanguine parents are deceased. Her brother had OCA and recurring epistaxis. At the age of 54 ears, he died due to liver cirrhosis (caused by a hepatitis B infection) and due to internal bleeding.

Molecular Genetic Analyses
Informed consent for molecular genetic analysis was obtained for each patient and the investigated family members. To extract genomic DNA from EDTA blood, we used standard procedures and the Blood and Cell Kit by Qiagen (Qiagen GmbH, Hilden, Germany). For index patients panel sequencing (95 genes including all 11 HPS genes; Supplementary Material S1 gene list) was performed using a custom-designed Nextera Rapid Enrichment Kit (Illumina) followed by sequencing on a MiSeq (Illumina). The average sequencing depth overall genes for the 3 patients investigated was 98% for 20x and 91% for 100x, respectively. SeqPilot (JSI medical systems) was used for data analyses. The variants were exported and filtered by allele frequency and serious consequences. We utilized supporting software ALAMUT ® (v.2.15), pathogenicity prediction (SIFT, MutTaster, PolyPhen2, and CADD), occurrence in population and disease databases (HGMD public version, Huizing HPS Mutation update (Huizing et al., 2020)) in order to classify the variants. These analyses were performed in accordance with the ACMG (American College of Medical Genetics) guidelines (Richards et al., 2015). For segregation analysis Sanger sequencing was conducted.
cDNA Sequencing Using Reverse Transcripted Platelet-Derived mRNA (for IP3) Total RNA was isolated from washed human platelets using 2 ml TRIzol ® reagent (Thermo Fisher Scientific). Single strand cDNA synthesis was generated with SuperScript ® III Reverse Transcriptase (Thermo Fisher Scientific). Amplification was performed using specific primers (fw: TGCAGCAGGATTTCA CCTCC; rev: ATCTGCTCCAGCATGTCCAC) covering the coding region from exon 1 to exon 9 of DTNBP1.

Analysis of NK Cell and CTL Degranulation (for IP3)
NK cell degranulation was analyzed as described (Bryceson et al., 2012). Briefly, fresh NK cell degranulation was assessed by

Platelet Count, In-Vivo Bleeding Time, and Platelet Function Analysis
All three index patients presented with normal platelet counts (234 × 10 9 /L, 173 × 10 9 /L, and 189 × 10 9 /L, respectively). The in-vivo bleeding time (Ivy) was severely prolonged (IP1 and IP3 > 15 min, IP2 > 8 min (norm < 6 min)). Platelet aggregation was severely impaired after stimulation with collagen (2 μg/ml) and epinephrine (8 μmol/L) for all index patients. Impaired aggregation after stimulation with low dose ADP (4 μmol/L) was seen in IP1 and IP2. Agglutination after stimulation with ristocetin (1.2 mg/ml) was normal ( Table 1). Flow cytometry analysis revealed severely reduced CD63 expression for all index patients ( Figure 1). All of them showed normal values for expression of CD62, CD42a, CD42b, CD41, fibrinogen binding, and VWF-binding (data not shown). IP1's sister presented with only slightly reduced CD63 expression, while her mother`s expression was borderline low. Flow cytometry was not performed for the father. Six of IP2`s children presented with borderline low and two with a slightly reduced CD63 expression.
In IP2 a novel homozygous missense variant (c.760G > T; p.Val254Phe) in HPS5 (NM_181507.1) was identified. The patient's husband showed wild type sequence at this position. NGS and Sanger sequencing revealed that all of her eight children were heterozygous carriers for this HPS5 variant as expected. The variant c.760G > T is reported six times in the GnomAD database in a heterozygous state (all counts in South Asian population) and absent from EVS (ACMG Classification: uncertain significance [PM1, PM2, PP3]). In silico PP is concordant disease causing and CADD score is 28.1. Additionally we identified a variant (NM_018668.5:c.1780A > G) in the gene VPS33B in a heterozygous state. This variant was also detected in the NGS analysis of her daughter. According to OMIM alterations in the gene VPS33P are autosomal recessive associated with ARC (Arthrogryposis, renal dysfunction, and cholestasis) and α-granule deficiency.
IP3 showed a novel homozygous deletion of exon 6 in DTNBP1 ( Figure 2B). Exon 6 could not be amplified from genomic DNA using PCR analysis. We performed cDNA sequencing out of platelet derived mRNA and confirmed the absence of exon 6. Interestingly, the small exon 7 was spliced out. It seems that the spliceosome used the acceptor splice site of exon 8. This would result in an in-frame loss of 52 amino acids in the middle of the expected protein (p.H120_A171del). ( Figure 2C). To investigate if the aberrant mRNA is leading to detectable dysbindin we performed Western blot analysis. Dysbindin, which is encoded by DTNBP1, was not detectable in platelets ( Figure 2D). The antibody used recognizes the C-terminal sequence within human dysbindin (aa 251-301). However, it is possible that the protein will fold incorrectly and in addition protein degradation will occur. Genetic alterations of all patients are summarized in Table 2.

Analysis of Lymphocyte Cytotoxicity
We analyzed the degranulation capacity of NK cells and cytotoxic T lymphocytes (CTL) from IP3 using CD107 degranulation assays. "Fresh" NK cell degranulation in response to K562 target cell stimulation was slightly impaired compared to more than 30 historical controls and additional day controls in two independent experiments ( Figure 3A). Following IL-2 stimulation for 48h, the degranulation of patient NK cells increased to normal values. Moreover, degranulation of PHA/IL-2 blasts following stimulation with anti-CD3/28 was in the normal range ( Figure 3B).

DISCUSSION
We report three patients with a severely impaired δ-granule secretion. NGS identified genetic alterations in three genes associated with different types of HPS. For IP3 the diagnosis of the rare HPS-7 was made after extensive investigations (cDNA sequencing, Western blot). The patient presented with an apparent OCA. Missense variants identified in HPS3 (IP1) and HPS5 (IP2) have to be classified as variant of uncertain significance (VUS), however we think it is valuable to report the findings of these variants in our patients.

Mild Phenotype in BLOC-2 Deficiencies
For IP1 (HPS-3) two compound heterozygous missense variants in HPS3 with predominantly and concordant disease-causing prediction were identified. Both variants are classified as VUS according to ACMG guidelines. The patient presented without cutaneous albinism, however, significantly hypopigmentation of the retina was detected in a specialized ophthalmological investigation. So far, the young girl exhibits mild bleeding symptoms. Taking these findings together these compound heterozygous variants most probably cause the patient's mild phenotype. Such a mild phenotype has been described also in other patients with HPS-3 (Liu et al., 2021). IP2 (HPS-5) carries a homozygous missense variant in HPS5 (c.760G > T). The PP is concordant disease-causing. According to the ACMG criteria the variant classifies VUS. The patient does not exhibit apparent albinism, however, a life-long history of bleeding diathesis. None of her 8 children (all heterozygous carriers) are clinically affected as severely as their mother (IP2), although some show very minor bleeding symptoms, such as gingival bleeding and easy bruising. Because the patient lives outside of Germany, a specialized opthalmological investigation has not been performed to date. IP2 suffered from a cystic lesion of her gall bladder, therefore the gall bladder was removed. Clinically, she did not show any symptoms of colitis and the ultrasound investigations did not reveal any signs of colitis. Besides the HPS5 variant, which we detected homozygous in the severely affected mother (IP2), we identified a heterozygous VUS in the gene VPS33B. According to OMIM alterations in the gene VPS33B are autosomal recessive associated with ARC (Arthrogryposis, renal dysfunction, and cholestasis). IP2 and the daughter who we investigated with NGS are carrier of the VPS33B variant; however, they do not show any symptoms of ARC. The son investigated with NGS presented wild type at the position. We did not investigate the other siblings for occurrence of the VPS33B variant. VPS33B is a protein essential for alpha granule biogenesis (Lo et al., 2005). Thrombin induced alpha-granule specific membrane protein P-selectin (CD62) exposure measured by flow cytometry was normal compared to healthy controls. However, a synergistic effect along with the homozygous HPS5 variant, which is also classified as VUS is conceivable. We excluded Chediak-Higashi syndrome an autosomal recessive disease associated with alterations in the gene LYST. One of the features is a partial or severe reduction of dense-granules. LYST is included in our NGS gene panel and the analysis did not show any pathological findings. Inclusions in polymorph nuclear leukocytes have typically been reported in the blood smear of patients with Chediak-Higashi syndrome. IP2 did not show any inclusions in polymorph nuclear leukocytes and no signs of immunodeficiency. Both HPS3 and HPS5 gene products are part of the BLOC-2 complex and patients primarily present with mild bleeding symptoms (Huizing et al., 2020;Nurden et al., 2020) and not necessarily with noticeable hypopigmentation (Liu et al., 2021). Complications usually did not include pulmonary fibrosis and immunodeficiency. Granulomatous colitis has been reported in about 10-20% of patients (Hussain et al., 2006). Most of the reported variants in HPS3 and HPS5 are variants with serious consequences like deletions, duplications, and variants affecting splicing (Huizing et al., 2020;Liu et al., 2021), only a few missense variants have been described (Huizing et al., 2004;Michaud et al., 2017;Lasseaux et al., 2018). It has also been described that two different nonsense variants in HPS3 lead to different degrees of severities of OCA, suggesting a wide spectrum. One patient presented with a mild and two brothers exhibited a clear OCA (Sandrock-Lang et al., 2017;Lecchi et al., 2020). Both IP1 and IP2 show a mild phenotype, especially concerning the albinism. No further complications, like pulmonary fibrosis or immunodeficiency, were clinically observed in IP1 and IP2, so far.

BLOC-1 Deficiency
The homozygous deletion of exon 6 in DTNBP1, found in IP3, has not been previously described. This deletion is pathogenic according to the ACMG guidelines due to the serious consequence. In addition, we showed the absence of dysbindin in platelet lysate. Although this patient has exhibited the characteristic HPS symptoms since birth, the genetic defect was detected rather late in life. Even if the symptoms of OCA are obvious, the diagnosis of HPS can be delayed if the bleeding diathesis is not recognized as part of the disease: the patient was 60 years old at the time when HPS-7 was diagnosed. To our knowledge only seven patients with HPS-7 have been reported worldwide comprising 4 nonsense or frameshift variants in DTNBP1 Lowe et al., 2013;Bryan et al., 2017;Bastida et al., 2019). Due to the small number of patients, a definite statement regarding additional complications cannot be made. So far, only one patient has been reported developing granulomatous colitis (Lowe et al., 2013). The DTNBP1 encoded Dysbindin-1 is involved in neurotransmission regulation and neurodevelopment (Tang et al., 2009;Ghiani et al., 2010) and seems to be involved in the etiology of Schizophrenia (Cheah et al., 2015;Wang et al., 2017). IP3 showed no symptoms of schizophrenia or other psychiatric disorders, however mild deficits in social interaction or depressive-like emotion are difficult to identify.
IP3 shows a history of severe and recurring airway infections which may possibly hint to immunodeficiency. The most obvious immune defect in lysosomal trafficking disorders is impaired NK cell and CTL cytotoxicity (Fischer et al., 2007). Strong degranulation defects predispose to hemophagocytic lymphohistiocytosis (HLH), a severe disorder of hyperinflammation, while the clinical consequences of milder defects are poorly characterized. A previous report has concluded that CTL cytotoxicity is normal in "sandy" mice (a model of HPS-7) (Bossi et al., 2005), which we could confirm in our patient. However, as previously documented in patients and mice with Chediak-Higashi-Syndrome (Jessen et al., 2011) the fresh NK cell degranulation assay is more sensitive than the CTL assay in detecting subtle impairments of the lytic machinery. Moreover, the degranulation defect could also affect other immune cells such as neutrophils or mast cells (Ramadass and Catz 2016), which could make an additional contribution to the observed infection susceptibility.
Two patients with HPS-9 (subunit of BLOC-1) have been reported presenting immunodeficiency (Badolato et al., 2012;Okamura et al., 2019). This might point to a possible complication in patients with BLOC-1 variants. However, only a few patients with BLOC-1 deficiencies have been described at all. More data are required to understand the role of BLOC-1 proteins in the immune system.

CONCLUSION
Patients with variants of the BLOC-2 complex may not show the characteristic phenotype of a severe bleeding diathesis and oculocutaneous albinism; therefore, molecular genetic analysis including all HPS genes is needed for patients with a platelet delta granule secretion defect. Only a few patients with BLOC-1 deficiencies have been described so far and more data are needed to predict the phenotype and possible additional consequences. NGS can facilitate and accelerate the process of identifying the genetic defects regarding the different HPSsubtypes, especially if the patient presents with only a mild phenotype. Identification of a larger cohort for each subtype of HPS is important for the precise prediction of possible complications. This also offers new opportunities for further understanding the pathophysiology of HPS.

DATA AVAILABILITY STATEMENT
The original contributions presented in the study are included in the article/Supplementary Materials, further inquiries can be directed to the corresponding author.

ETHICS STATEMENT
The studies involving human participants were reviewed and approved by the Ethics Committee of the Albert Ludwig University of Freiburg. Written informed consent to participate in this study was provided by the participants' legal guardian/next of kin. Written informed consent was obtained from the individual(s), and