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Li Y, Zhang C, Peng G. Ap4s1 truncation leads to axonal defects in a zebrafish model of spastic paraplegia 52. Int J Dev Neurosci 2023; 83:753-764. [PMID: 37767851 DOI: 10.1002/jdn.10303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 08/11/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Biallelic mutations in AP4S1, the σ4 subunit of the adaptor protein complex 4 (AP-4), lead to autosomal recessive spastic paraplegia 52 (SPG52). It is a subtype of AP-4-associated hereditary spastic paraplegia (AP-4-HSP), a complex childhood-onset neurogenetic disease characterized by progressive spastic paraplegia of the lower limbs. This disease has so far lacked effective treatment, in part due to a lack of suitable animal models. Here, we used CRISPR/Cas9 technology to generate a truncation mutation in the ap4s1 gene in zebrafish. The ap4s1 truncation led to motor impairment, delayed neurodevelopment, and distal axonal degeneration. This animal model is useful for further research into AP-4 and AP-4-HSP.
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Affiliation(s)
- Yiduo Li
- State Key Laboratory of Medical Neurobiology, Ministry of Education Frontiers Center for Brain Science, and Institutes of Brain Science, Fudan University, Shanghai, China
| | - Cuizhen Zhang
- State Key Laboratory of Medical Neurobiology, Ministry of Education Frontiers Center for Brain Science, and Institutes of Brain Science, Fudan University, Shanghai, China
| | - Gang Peng
- State Key Laboratory of Medical Neurobiology, Ministry of Education Frontiers Center for Brain Science, and Institutes of Brain Science, Fudan University, Shanghai, China
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Postel MD, Darabi S, Howe JR, Liang WS, Craig DW, Demeure MJ. Multiomic sequencing of paired primary and metastatic small bowel carcinoids. F1000Res 2023; 12:417. [PMID: 37954063 PMCID: PMC10632590 DOI: 10.12688/f1000research.130251.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/15/2023] [Indexed: 11/14/2023] Open
Abstract
Background: Small bowel carcinoids are insidious tumors that are often metastatic when diagnosed. Limited mutation landscape studies of carcinoids indicate that these tumors have a relatively low mutational burden. The development of targeted therapies will depend upon the identification of mutations that drive the pathogenesis and metastasis of carcinoid tumors. Methods: Whole exome and RNA sequencing of 5 matched sets of normal tissue, primary small intestine carcinoid tumors, and liver metastases were investigated. Germline and somatic variants included: single nucleotide variants (SNVs), insertions/deletions (indels), structural variants, and copy number alterations (CNAs). The functional impact of mutations was predicted using Ensembl Variant Effect Predictor. Results: Large-scale CNAs were observed including the loss of chromosome 18 in all 5 metastases and 3/5 primary tumors. Certain somatic SNVs were metastasis-specific; including mutations in ATRX, CDKN1B, MXRA5 (leading to the activation of a cryptic splice site and loss of mRNA), SMARCA2, and the loss of UBE4B. Additional mutations in ATRX, and splice site loss of PYGL, leading to intron retention observed in primary and metastatic tumors. Conclusions: We observed novel mutations in primary/metastatic carcinoid tumor pairs, and some have been observed in other types of neuroendocrine tumors. We confirmed a previously observed loss of chromosome 18 and CDKN1B. Transcriptome sequencing added relevant information that would not have been appreciated with DNA sequencing alone. The detection of several splicing mutations on the DNA level and their consequences at the RNA level suggests that RNA splicing aberrations may be an important mechanism underlying carcinoid tumors.
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Affiliation(s)
- Mackenzie D. Postel
- Institute of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Sourat Darabi
- Precision Medicine, Hoag Family Cancer Institute, Newport Beach, CA, 92663, USA
| | - James R. Howe
- Department of Surgery, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | | | - David W. Craig
- Institute of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Michael J. Demeure
- Precision Medicine, Hoag Family Cancer Institute, Newport Beach, CA, 92663, USA
- Translational Genomics Research Institute, Phoenix, AZ, USA
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Postel MD, Culver JO, Ricker C, Craig DW. Transcriptome analysis provides critical answers to the "variants of uncertain significance" conundrum. Hum Mutat 2022; 43:1590-1608. [PMID: 35510381 PMCID: PMC9560997 DOI: 10.1002/humu.24394] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/16/2022] [Accepted: 04/26/2022] [Indexed: 12/30/2022]
Abstract
While whole-genome and exome sequencing have transformed our collective understanding of genetics' role in disease pathogenesis, there are certain conditions and populations for whom DNA-level data fails to identify the underlying genetic etiology. Specifically, patients of non-White race and non-European ancestry are disproportionately affected by "variants of unknown/uncertain significance" (VUS), limiting the scope of precision medicine for minority patients and perpetuating health disparities. VUS often include deep intronic and splicing variants which are difficult to interpret from DNA data alone. RNA analysis can illuminate the consequences of VUS, thereby allowing for their reclassification as pathogenic versus benign. Here we review the critical role transcriptome analysis plays in clarifying VUS in both neoplastic and non-neoplastic diseases.
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Affiliation(s)
- Mackenzie D. Postel
- Department of Translational GenomicsUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
- Keck School of Medicine of USCUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Julie O. Culver
- Keck School of Medicine of USCUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Charité Ricker
- Keck School of Medicine of USCUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - David W. Craig
- Department of Translational GenomicsUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
- Keck School of Medicine of USCUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
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Panza E, Meyyazhagan A, Orlacchio A. Hereditary spastic paraplegia: Genetic heterogeneity and common pathways. Exp Neurol 2022; 357:114203. [PMID: 35970204 DOI: 10.1016/j.expneurol.2022.114203] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 07/11/2022] [Accepted: 08/09/2022] [Indexed: 02/07/2023]
Abstract
Hereditary Spastic Paraplegias (HSPs) are a heterogeneous group of disease, mainly characterized by progressive spasticity and weakness of the lower limbs resulting from distal degeneration of corticospinal tract axons. Although HSPs represent rare or ultra-rare conditions, with reported cases of mutated genes found in single families, overall, with 87 forms described, they are an important health and economic problem for society and patients. In fact, they are chronic and life-hindering conditions, still lacking a specific therapy. Notwithstanding the number of forms described, and 73 causative genes identified, overall, the molecular diagnostic rate varies among 29% to 61.8%, based on recent published analysis, suggesting that more genes are involved in HSP and/or that different molecular diagnostic approaches are necessary. The accumulating data in this field highlight several peculiar features of HSPs, such as genetic heterogeneity, the discovery that different mutations in a single gene can be transmitted in dominant and recessive trait in families and allelic heterogeneity, resulting in the involvement of HSP-genes in other conditions. Based on the observation of protein functions, the activity of many different proteins encoded by HSP-related genes converges into some distinct pathophysiological mechanisms. This suggests that common pathways could be a potential target for a therapy, possibly addressing several forms at once. Furthermore, the overlap of HSP genes with other neurological conditions can further expand this concept.
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Affiliation(s)
- Emanuele Panza
- Dipartimento di Scienze Mediche e Chirurgiche, Università di Bologna, Bologna, Italy
| | - Arun Meyyazhagan
- Dipartimento di Medicina e Chirurgia, Università di Perugia, Perugia, Italy
| | - Antonio Orlacchio
- Dipartimento di Medicina e Chirurgia, Università di Perugia, Perugia, Italy; Laboratorio di Neurogenetica, Centro Europeo di Ricerca sul Cervello (CERC), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione Santa Lucia, Rome, Italy.
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Gómez-González C, Pizarro-Sánchez C, Rodríguez-Antolín C, Pascual-Pascual I, Garcia-Romero M, Rodriguez-Jiménez C, de Sancho-Martín R, Del Pozo-Mate Á, Solís-López M, Prior-de Castro C, Torres RJ. Hereditary spastic paraplegia associated with a novel homozygous intronic noncanonical splice site variant in the AP4B1 gene. Ann Hum Genet 2021; 86:109-118. [PMID: 34927723 DOI: 10.1111/ahg.12455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 11/15/2021] [Accepted: 12/02/2021] [Indexed: 11/27/2022]
Abstract
Pathogenic variants in the AP4B1 gene lead to a rare form of hereditary spastic paraplegia (HSP) known as SPG47. We report on a patient with a clinical suspicion of complicated HSP of the lower limbs with intellectual disability, as well as a novel homozygous noncanonical splice site variant in the AP4B1 gene, in which the effect on splicing was validated by RNA analysis. We sequenced 152 genes associated with HSP using Next-Generation Sequencing (NGS). We isolated total RNA from peripheral blood and generated cDNA using reverse transcription-polymerase chain reaction (RT-PCR). A region of AP4B1 mRNA was amplified by PCR and the fragments obtained were purified from the agarose gel and sequenced. We found a homozygous variant of uncertain significance in the AP4B1 gene NM_006594.4: c.1511-6C>G in the proband. Two different AP4B1 mRNA fragments were obtained in the patient and his carrier parents. The shorter fragment was the predominant fragment in the patient and revealed a deletion with skipping of the AP4B1 exon 10. The patient's longer fragment corresponded to an insertion of the last five nucleotides of AP4B1 intron 9. We confirmed that this variant affects the normal splicing of RNA, sustaining the molecular diagnosis of SPG47 in the patient.
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Affiliation(s)
- Clara Gómez-González
- Department of Molecular Genetics, INGEMM, La Paz University Hospital, Madrid, Spain
| | | | - Carlos Rodríguez-Antolín
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Madrid, Spain.,Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain
| | | | - Mar Garcia-Romero
- Department of Paediatric Neurology, La Paz University Hospital, Madrid, Spain
| | | | | | | | - Mario Solís-López
- Department of Bioinformatics, INGEMM, La Paz University Hospital, Madrid, Spain
| | | | - Rosa J Torres
- Biochemistry Laboratory, La Paz University Hospital Health Research Institute (FIBHULP), IdiPAZ, Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Spain
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The role of AP-4 in cargo export from the trans-Golgi network and hereditary spastic paraplegia. Biochem Soc Trans 2020; 48:1877-1888. [PMID: 33084855 DOI: 10.1042/bst20190664] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/22/2020] [Accepted: 09/29/2020] [Indexed: 01/02/2023]
Abstract
Heterotetrameric adaptor protein (AP) complexes play key roles in protein sorting and transport vesicle formation in the endomembrane system of eukaryotic cells. One of these complexes, AP-4, was identified over 20 years ago but, up until recently, its function remained unclear. AP-4 associates with the trans-Golgi network (TGN) through interaction with small GTPases of the ARF family and recognizes transmembrane proteins (i.e. cargos) having specific sorting signals in their cytosolic domains. Recent studies identified accessory proteins (tepsin, RUSC2 and the FHF complex) that co-operate with AP-4, and cargos (amyloid precursor protein, ATG9A and SERINC3/5) that are exported from the TGN in an AP-4-dependent manner. Defective export of ATG9A from the TGN in AP-4-deficient cells was shown to reduce ATG9A delivery to pre-autophagosomal structures, impairing autophagosome formation and/or maturation. In addition, mutations in AP-4-subunit genes were found to cause neurological dysfunction in mice and a form of complicated hereditary spastic paraplegia referred to as 'AP-4-deficiency syndrome' in humans. These findings demonstrated that mammalian AP-4 is required for the development and function of the central nervous system, possibly through its role in the sorting of ATG9A for the maintenance of autophagic homeostasis. In this article, we review the properties and functions of AP-4, and discuss how they might explain the clinical features of AP-4 deficiency.
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