1
|
de J López-Rodríguez VR, Arce-González R, Navas-Pérez A, Graue-Hernández E, García-Martínez F, Montes-Almanza L, Chacón-Camacho OF, Zenteno JC. Familial fleck corneal dystrophy caused by complete deletion of the PIKFYVE gene. Ophthalmic Genet 2024:1-5. [PMID: 38956867 DOI: 10.1080/13816810.2024.2365737] [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: 04/06/2023] [Accepted: 06/04/2024] [Indexed: 07/04/2024]
Abstract
BACKGROUND Fleck corneal dystrophy (FCD) is a rare autosomal dominant disease that affects exclusively the corneal stroma. The disease is caused by heterozygous variants in PIKFYVE, a gene encoding a lipid kinase involved in multiple cellular pathways, primarily participating in membrane dynamics and signaling. This report describes a familial case of FCD caused by a complete deletion of the PIKFYVE gene. MATERIAL AND METHODS A clinical ophthalmic examination was performed on the proband and family members. Genetic testing included next-generation sequencing (multigene panel), and chromosomal microarray analysis. A quantitative PCR assay was designed in order to segregate the deletion. RESULTS A 19-year-old male, with no family or personal history of ocular disease, presented for evaluation due to an acute illness consisting of burning, foreign body sensation, and red eye. Slit lamp biomicroscopy revealed bilateral small pterygia and scattered bilateral white opacities in the corneal stroma, a very similar corneal phenotype was found in the 47-year-old father, who was asymptomatic. NGS detected a heterozygous deletion of the entire PIKFYVE coding sequence. CMA in DNA from the propositus indicated a 543 kb deletion in 2q33.3q34 spanning the entire PIKFYVE gene. The deletion was confirmed in the father. CONCLUSIONS We add to the molecular spectrum of FCD by describing a familial case of a whole PIKFYVE gene deletion in affected subjects. Our findings support that normal expression of PIKFYVE is necessary for corneal keratocytes homeostasis and normal corneal appearance. We conclude that PIKFYVE haploinsufficiency is the molecular mechanism underlying this familial case of FCD.
Collapse
Affiliation(s)
| | - Rocío Arce-González
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
| | - Alejandro Navas-Pérez
- Department of Cornea, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
| | | | - Froylán García-Martínez
- Research Unit-Genetics Department, Institute of Ophthalmology, "Conde de Valenciana", Mexico City, Mexico
| | - Luis Montes-Almanza
- Research Unit-Genetics Department, Institute of Ophthalmology, "Conde de Valenciana", Mexico City, Mexico
| | - Oscar F Chacón-Camacho
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
| | - Juan C Zenteno
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
- Department of Biochemistry, Faculty of Medicine, National Autonomous University of Mexico, Mexico City, Mexico
| |
Collapse
|
2
|
Shiels A. Through the Cat-Map Gateway: A Brief History of Cataract Genetics. Genes (Basel) 2024; 15:785. [PMID: 38927721 PMCID: PMC11202810 DOI: 10.3390/genes15060785] [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: 05/21/2024] [Revised: 06/06/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
Clouding of the transparent eye lens, or cataract(s), is a leading cause of visual impairment that requires surgical replacement with a synthetic intraocular lens to effectively restore clear vision. Most frequently, cataract is acquired with aging as a multifactorial or complex trait. Cataract may also be inherited as a classic Mendelian trait-often with an early or pediatric onset-with or without other ocular and/or systemic features. Since the early 1990s, over 85 genes and loci have been genetically associated with inherited and/or age-related forms of cataract. While many of these underlying genes-including those for lens crystallins, connexins, and transcription factors-recapitulate signature features of lens development and differentiation, an increasing cohort of unpredicted genes, including those involved in cell-signaling, membrane remodeling, and autophagy, has emerged-providing new insights regarding lens homeostasis and aging. This review provides a brief history of gene discovery for inherited and age-related forms of cataract compiled in the Cat-Map database and highlights potential gene-based therapeutic approaches to delay, reverse, or even prevent cataract formation that may help to reduce the increasing demand for cataract surgery.
Collapse
Affiliation(s)
- Alan Shiels
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA
| |
Collapse
|
3
|
Xia J, Wang H, Zhong Z, Jiang J. Inhibition of PIKfyve Leads to Lysosomal Disorders via Dysregulation of mTOR Signaling. Cells 2024; 13:953. [PMID: 38891085 PMCID: PMC11171791 DOI: 10.3390/cells13110953] [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: 04/24/2024] [Revised: 05/23/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
PIKfyve is an endosomal lipid kinase that synthesizes phosphatidylinositol 3,5-biphosphate from phosphatidylinositol 3-phsphate. Inhibition of PIKfyve activity leads to lysosomal enlargement and cytoplasmic vacuolation, attributed to impaired lysosomal fission processes and homeostasis. However, the precise molecular mechanisms underlying these effects remain a topic of debate. In this study, we present findings from PIKfyve-deficient zebrafish embryos, revealing enlarged macrophages with giant vacuoles reminiscent of lysosomal storage disorders. Treatment with mTOR inhibitors or effective knockout of mTOR partially reverses these abnormalities and extend the lifespan of mutant larvae. Further in vivo and in vitro mechanistic investigations provide evidence that PIKfyve activity is essential for mTOR shutdown during early zebrafish development and in cells cultured under serum-deprived conditions. These findings underscore the critical role of PIKfyve activity in regulating mTOR signaling and suggest potential therapeutic applications of PIKfyve inhibitors for the treatment of lysosomal storage disorders.
Collapse
Affiliation(s)
- Jianhong Xia
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (J.X.); (H.W.)
| | - Haiyun Wang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (J.X.); (H.W.)
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong SAR, China
| | - Zhihang Zhong
- State Key Laboratory of Swine and Poultry Breeding Industry, South China Agricultural University, Guangzhou 510642, China;
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Jun Jiang
- State Key Laboratory of Swine and Poultry Breeding Industry, South China Agricultural University, Guangzhou 510642, China;
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| |
Collapse
|
4
|
Olszewska M, Malcher A, Stokowy T, Pollock N, Berman AJ, Budkiewicz S, Kamieniczna M, Jackowiak H, Suszynska-Zajczyk J, Jedrzejczak P, Yatsenko AN, Kurpisz M. Effects of Tcte1 knockout on energy chain transportation and spermatogenesis: implications for male infertility. Hum Reprod Open 2024; 2024:hoae020. [PMID: 38650655 PMCID: PMC11035007 DOI: 10.1093/hropen/hoae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 03/08/2024] [Indexed: 04/25/2024] Open
Abstract
STUDY QUESTION Is the Tcte1 mutation causative for male infertility? SUMMARY ANSWER Our collected data underline the complex and devastating effect of the single-gene mutation on the testicular molecular network, leading to male reproductive failure. WHAT IS KNOWN ALREADY Recent data have revealed mutations in genes related to axonemal dynein arms as causative for morphology and motility abnormalities in spermatozoa of infertile males, including dysplasia of fibrous sheath (DFS) and multiple morphological abnormalities in the sperm flagella (MMAF). The nexin-dynein regulatory complex (N-DRC) coordinates the dynein arm activity and is built from the DRC1-DRC7 proteins. DRC5 (TCTE1), one of the N-DRC elements, has already been reported as a candidate for abnormal sperm flagella beating; however, only in a restricted manner with no clear explanation of respective observations. STUDY DESIGN SIZE DURATION Using the CRISPR/Cas9 genome editing technique, a mouse Tcte1 gene knockout line was created on the basis of the C57Bl/6J strain. The mouse reproductive potential, semen characteristics, testicular gene expression levels, sperm ATP, and testis apoptosis level measurements were then assessed, followed by visualization of N-DRC proteins in sperm, and protein modeling in silico. Also, a pilot genomic sequencing study of samples from human infertile males (n = 248) was applied for screening of TCTE1 variants. PARTICIPANTS/MATERIALS SETTING METHODS To check the reproductive potential of KO mice, adult animals were crossed for delivery of three litters per caged pair, but for no longer than for 6 months, in various combinations of zygosity. All experiments were performed for wild-type (WT, control group), heterozygous Tcte1+/- and homozygous Tcte1-/- male mice. Gross anatomy was performed on testis and epididymis samples, followed by semen analysis. Sequencing of RNA (RNAseq; Illumina) was done for mice testis tissues. STRING interactions were checked for protein-protein interactions, based on changed expression levels of corresponding genes identified in the mouse testis RNAseq experiments. Immunofluorescence in situ staining was performed to detect the N-DRC complex proteins: Tcte1 (Drc5), Drc7, Fbxl13 (Drc6), and Eps8l1 (Drc3) in mouse spermatozoa. To determine the amount of ATP in spermatozoa, the luminescence level was measured. In addition, immunofluorescence in situ staining was performed to check the level of apoptosis via caspase 3 visualization on mouse testis samples. DNA from whole blood samples of infertile males (n = 137 with non-obstructive azoospermia or cryptozoospermia, n = 111 samples with a spectrum of oligoasthenoteratozoospermia, including n = 47 with asthenozoospermia) was extracted to perform genomic sequencing (WGS, WES, or Sanger). Protein prediction modeling of human-identified variants and the exon 3 structure deleted in the mouse knockout was also performed. MAIN RESULTS AND THE ROLE OF CHANCE No progeny at all was found for the homozygous males which were revealed to have oligoasthenoteratozoospermia, while heterozygous animals were fertile but manifested oligozoospermia, suggesting haploinsufficiency. RNA-sequencing of the testicular tissue showed the influence of Tcte1 mutations on the expression pattern of 21 genes responsible for mitochondrial ATP processing or linked with apoptosis or spermatogenesis. In Tcte1-/- males, the protein was revealed in only residual amounts in the sperm head nucleus and was not transported to the sperm flagella, as were other N-DRC components. Decreased ATP levels (2.4-fold lower) were found in the spermatozoa of homozygous mice, together with disturbed tail:midpiece ratios, leading to abnormal sperm tail beating. Casp3-positive signals (indicating apoptosis) were observed in spermatogonia only, at a similar level in all three mouse genotypes. Mutation screening of human infertile males revealed one novel and five ultra-rare heterogeneous variants (predicted as disease-causing) in 6.05% of the patients studied. Protein prediction modeling of identified variants revealed changes in the protein surface charge potential, leading to disruption in helix flexibility or its dynamics, thus suggesting disrupted interactions of TCTE1 with its binding partners located within the axoneme. LARGE SCALE DATA All data generated or analyzed during this study are included in this published article and its supplementary information files. RNAseq data are available in the GEO database (https://www.ncbi.nlm.nih.gov/geo/) under the accession number GSE207805. The results described in the publication are based on whole-genome or exome sequencing data which includes sensitive information in the form of patient-specific germline variants. Information regarding such variants must not be shared publicly following European Union legislation, therefore access to raw data that support the findings of this study are available from the corresponding author upon reasonable request. LIMITATIONS REASONS FOR CAUTION In the study, the in vitro fertilization performance of sperm from homozygous male mice was not checked. WIDER IMPLICATIONS OF THE FINDINGS This study contains novel and comprehensive data concerning the role of TCTE1 in male infertility. The TCTE1 gene is the next one that should be added to the 'male infertility list' because of its crucial role in spermatogenesis and proper sperm functioning. STUDY FUNDING/COMPETING INTERESTS This work was supported by National Science Centre in Poland, grants no.: 2015/17/B/NZ2/01157 and 2020/37/B/NZ5/00549 (to M.K.), 2017/26/D/NZ5/00789 (to A.M.), and HD096723, GM127569-03, NIH SAP #4100085736 PA DoH (to A.N.Y.). The authors declare that there is no conflict of interest that could be perceived as prejudicing the impartiality of the research reported.
Collapse
Affiliation(s)
- Marta Olszewska
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Agnieszka Malcher
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Tomasz Stokowy
- Scientific Computing Group, IT Division, University of Bergen, Bergen, Norway
| | - Nijole Pollock
- Department of OB/GYN and Reproductive Sciences, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Andrea J Berman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sylwia Budkiewicz
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | | | - Hanna Jackowiak
- Department of Histology and Embryology, Poznan University of Life Sciences, Poznan, Poland
| | | | - Piotr Jedrzejczak
- Division of Infertility and Reproductive Endocrinology, Department of Gynecology, Obstetrics and Gynecological Oncology, Poznan University of Medical Sciences, Poznan, Poland
| | - Alexander N Yatsenko
- Department of OB/GYN and Reproductive Sciences, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Maciej Kurpisz
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| |
Collapse
|
5
|
Zubkova E, Kalinin A, Bolotskaya A, Beloglazova I, Menshikov M. Autophagy-Dependent Secretion: Crosstalk between Autophagy and Exosome Biogenesis. Curr Issues Mol Biol 2024; 46:2209-2235. [PMID: 38534758 DOI: 10.3390/cimb46030142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 03/28/2024] Open
Abstract
The cellular secretome is pivotal in mediating intercellular communication and coordinating responses to stressors. Exosomes, initially recognized for their role in waste disposal, have now emerged as key intercellular messengers with significant therapeutic and diagnostic potential. Similarly, autophagy has transcended its traditional role as a waste removal mechanism, emerging as a regulator of intracellular communication pathways and a contributor to a unique autophagy-dependent secretome. Secretory authophagy, initiated by various stress stimuli, prompts the selective release of proteins implicated in inflammation, including leaderless proteins that bypass the conventional endoplasmic reticulum-Golgi secretory pathway. This reflects the significant impact of stress-induced autophagy on cellular secretion profiles, including the modulation of exosome release. The convergence of exosome biogenesis and autophagy is exemplified by the formation of amphisomes, vesicles that integrate autophagic and endosomal pathways, indicating their synergistic interplay. Regulatory proteins common to both pathways, particularly mTORC1, emerge as potential therapeutic targets to alter cellular secretion profiles involved in various diseases. This review explores the dynamic interplay between autophagy and exosome formation, highlighting the potential to influence the secretome composition. While the modulation of exosome secretion and cytokine preconditioning is well-established in regenerative medicine, the strategic manipulation of autophagy is still underexplored, presenting a promising but uncharted therapeutic landscape.
Collapse
Affiliation(s)
- Ekaterina Zubkova
- National Medical Research Centre of Cardiology Named after Academician E.I. Chazov, 121552 Moscow, Russia
| | - Alexander Kalinin
- National Medical Research Centre of Cardiology Named after Academician E.I. Chazov, 121552 Moscow, Russia
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Anastasya Bolotskaya
- National Medical Research Centre of Cardiology Named after Academician E.I. Chazov, 121552 Moscow, Russia
- Institute of Clinical Medicine, Sechenov University, 119435 Moscow, Russia
| | - Irina Beloglazova
- National Medical Research Centre of Cardiology Named after Academician E.I. Chazov, 121552 Moscow, Russia
| | - Mikhail Menshikov
- National Medical Research Centre of Cardiology Named after Academician E.I. Chazov, 121552 Moscow, Russia
| |
Collapse
|
6
|
Rodríguez-Solana P, Arruti N, Nieves-Moreno M, Mena R, Rodríguez-Jiménez C, Guerrero-Carretero M, Acal JC, Blasco J, Peralta JM, Del Pozo Á, Montaño VEF, Dios-Blázquez LD, Fernández-Alcalde C, González-Atienza C, Sánchez-Cazorla E, Gómez-Cano MDLÁ, Delgado-Mora L, Noval S, Vallespín E. Whole Exome Sequencing of 20 Spanish Families: Candidate Genes for Non-Syndromic Pediatric Cataracts. Int J Mol Sci 2023; 24:11429. [PMID: 37511188 PMCID: PMC10380485 DOI: 10.3390/ijms241411429] [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: 05/25/2023] [Revised: 06/23/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Non-syndromic pediatric cataracts are defined as opacification of the crystalline lens that occurs during the first years of life without affecting other organs. Given that this disease is one of the most frequent causes of reversible blindness in childhood, the main objective of this study was to propose new responsible gene candidates that would allow a more targeted genetic approach and expand our genetic knowledge about the disease. We present a whole exome sequencing (WES) study of 20 Spanish families with non-syndromic pediatric cataracts and a previous negative result on an ophthalmology next-generation sequencing panel. After ophthalmological evaluation and collection of peripheral blood samples from these families, WES was performed. We were able to reach a genetic diagnosis in 10% of the families analyzed and found genes that could cause pediatric cataracts in 35% of the cohort. Of the variants found, 18.2% were classified as pathogenic, 9% as likely pathogenic, and 72.8% as variants of uncertain significance. However, we did not find conclusive results in 55% of the families studied, which suggests further studies are needed. The results of this WES study allow us to propose LONP1, ACACA, TRPM1, CLIC5, HSPE1, ODF1, PIKFYVE, and CHMP4A as potential candidates to further investigate for their role in pediatric cataracts, and AQP5 and locus 2q37 as causal genes.
Collapse
Affiliation(s)
- Patricia Rodríguez-Solana
- Molecular Ophthalmology Section, Institute of Medical and Molecular Genetics (INGEMM), IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (P.R.-S.); (R.M.); (C.R.-J.); (V.E.F.M.); (C.G.-A.); (E.S.-C.)
| | - Natalia Arruti
- Department of Pediatric Ophthalmology, IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (N.A.); (M.N.-M.); (M.G.-C.); (J.C.A.); (J.B.); (J.M.P.); (C.F.-A.); (S.N.)
- European Reference Network on Eye Diseases (ERN-EYE), La Paz University Hospital, 28046 Madrid, Spain
| | - María Nieves-Moreno
- Department of Pediatric Ophthalmology, IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (N.A.); (M.N.-M.); (M.G.-C.); (J.C.A.); (J.B.); (J.M.P.); (C.F.-A.); (S.N.)
- European Reference Network on Eye Diseases (ERN-EYE), La Paz University Hospital, 28046 Madrid, Spain
| | - Rocío Mena
- Molecular Ophthalmology Section, Institute of Medical and Molecular Genetics (INGEMM), IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (P.R.-S.); (R.M.); (C.R.-J.); (V.E.F.M.); (C.G.-A.); (E.S.-C.)
- Biomedical Research Center in the Rare Diseases Network (CIBERER), Carlos II Health Institute (ISCIII), 28029 Madrid, Spain; (Á.D.P.); (M.d.L.Á.G.-C.); (L.D.-M.)
| | - Carmen Rodríguez-Jiménez
- Molecular Ophthalmology Section, Institute of Medical and Molecular Genetics (INGEMM), IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (P.R.-S.); (R.M.); (C.R.-J.); (V.E.F.M.); (C.G.-A.); (E.S.-C.)
| | - Marta Guerrero-Carretero
- Department of Pediatric Ophthalmology, IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (N.A.); (M.N.-M.); (M.G.-C.); (J.C.A.); (J.B.); (J.M.P.); (C.F.-A.); (S.N.)
| | - Juan Carlos Acal
- Department of Pediatric Ophthalmology, IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (N.A.); (M.N.-M.); (M.G.-C.); (J.C.A.); (J.B.); (J.M.P.); (C.F.-A.); (S.N.)
| | - Joana Blasco
- Department of Pediatric Ophthalmology, IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (N.A.); (M.N.-M.); (M.G.-C.); (J.C.A.); (J.B.); (J.M.P.); (C.F.-A.); (S.N.)
| | - Jesús M. Peralta
- Department of Pediatric Ophthalmology, IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (N.A.); (M.N.-M.); (M.G.-C.); (J.C.A.); (J.B.); (J.M.P.); (C.F.-A.); (S.N.)
| | - Ángela Del Pozo
- Biomedical Research Center in the Rare Diseases Network (CIBERER), Carlos II Health Institute (ISCIII), 28029 Madrid, Spain; (Á.D.P.); (M.d.L.Á.G.-C.); (L.D.-M.)
- Clinical Bioinformatics Section, Institute of Medical and Molecular Genetics (INGEMM), IdiPaz, CIBERER, La Paz University Hospital, 28046 Madrid, Spain;
| | - Victoria E. F. Montaño
- Molecular Ophthalmology Section, Institute of Medical and Molecular Genetics (INGEMM), IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (P.R.-S.); (R.M.); (C.R.-J.); (V.E.F.M.); (C.G.-A.); (E.S.-C.)
- Biomedical Research Center in the Rare Diseases Network (CIBERER), Carlos II Health Institute (ISCIII), 28029 Madrid, Spain; (Á.D.P.); (M.d.L.Á.G.-C.); (L.D.-M.)
| | - Lucía De Dios-Blázquez
- Clinical Bioinformatics Section, Institute of Medical and Molecular Genetics (INGEMM), IdiPaz, CIBERER, La Paz University Hospital, 28046 Madrid, Spain;
| | - Celia Fernández-Alcalde
- Department of Pediatric Ophthalmology, IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (N.A.); (M.N.-M.); (M.G.-C.); (J.C.A.); (J.B.); (J.M.P.); (C.F.-A.); (S.N.)
| | - Carmen González-Atienza
- Molecular Ophthalmology Section, Institute of Medical and Molecular Genetics (INGEMM), IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (P.R.-S.); (R.M.); (C.R.-J.); (V.E.F.M.); (C.G.-A.); (E.S.-C.)
| | - Eloísa Sánchez-Cazorla
- Molecular Ophthalmology Section, Institute of Medical and Molecular Genetics (INGEMM), IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (P.R.-S.); (R.M.); (C.R.-J.); (V.E.F.M.); (C.G.-A.); (E.S.-C.)
| | - María de Los Ángeles Gómez-Cano
- Biomedical Research Center in the Rare Diseases Network (CIBERER), Carlos II Health Institute (ISCIII), 28029 Madrid, Spain; (Á.D.P.); (M.d.L.Á.G.-C.); (L.D.-M.)
- Clinical Genetics Section, Institute of Medical and Molecular Genetics (INGEMM), IdiPaz, CIBERER, La Paz University Hospital, 28046 Madrid, Spain
| | - Luna Delgado-Mora
- Biomedical Research Center in the Rare Diseases Network (CIBERER), Carlos II Health Institute (ISCIII), 28029 Madrid, Spain; (Á.D.P.); (M.d.L.Á.G.-C.); (L.D.-M.)
- Clinical Genetics Section, Institute of Medical and Molecular Genetics (INGEMM), IdiPaz, CIBERER, La Paz University Hospital, 28046 Madrid, Spain
| | - Susana Noval
- Department of Pediatric Ophthalmology, IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (N.A.); (M.N.-M.); (M.G.-C.); (J.C.A.); (J.B.); (J.M.P.); (C.F.-A.); (S.N.)
- European Reference Network on Eye Diseases (ERN-EYE), La Paz University Hospital, 28046 Madrid, Spain
| | - Elena Vallespín
- Molecular Ophthalmology Section, Institute of Medical and Molecular Genetics (INGEMM), IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (P.R.-S.); (R.M.); (C.R.-J.); (V.E.F.M.); (C.G.-A.); (E.S.-C.)
- European Reference Network on Eye Diseases (ERN-EYE), La Paz University Hospital, 28046 Madrid, Spain
- Biomedical Research Center in the Rare Diseases Network (CIBERER), Carlos II Health Institute (ISCIII), 28029 Madrid, Spain; (Á.D.P.); (M.d.L.Á.G.-C.); (L.D.-M.)
| |
Collapse
|
7
|
Rajala A, Rajala R, Gopinadhan Nair GK, Rajala RVS. Atlas of phosphoinositide signatures in the retina identifies heterogeneity between cell types. PNAS NEXUS 2023; 2:pgad063. [PMID: 37007713 PMCID: PMC10062291 DOI: 10.1093/pnasnexus/pgad063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/11/2023] [Accepted: 02/17/2023] [Indexed: 03/06/2023]
Abstract
Phosphoinositides (PIPs) are a family of minor acidic phospholipids in the cell membrane. Phosphoinositide (PI) kinases and phosphatases can rapidly convert one PIP product into another resulting in the generation of seven distinct PIPs. The retina is a heterogeneous tissue composed of several cell types. In the mammalian genome, around 50 genes encode PI kinases and PI phosphatases; however, there are no studies describing the distribution of these enzymes in the various retinal cell types. Using translating ribosome affinity purification, we have identified the in vivo distribution of PI-converting enzymes from the rod, cone, retinal pigment epithelium (RPE), Müller glia, and retinal ganglion cells, generating a physiological atlas for PI-converting enzyme expression in the retina. The retinal neurons, rods, cones, and RGCs, are characterized by the enrichment of PI-converting enzymes, whereas the Müller glia and RPE are characterized by the depletion of these enzymes. We also found distinct differences between the expression of PI kinases and PI phosphatases in each retinal cell type. Since mutations in PI-converting enzymes are linked to human diseases including retinal diseases, the results of this study will provide a guide for what cell types are likely to be affected by retinal degenerative diseases brought on by changes in PI metabolism.
Collapse
Affiliation(s)
- Ammaji Rajala
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, 608 Stanton L. Young Blvd, Oklahoma City, OK 73104, USA
- Dean McGee Eye Institute, 608 Stanton L. Young Blvd, Oklahoma City, OK 73104, USA
| | - Rahul Rajala
- Department of Cell Biology, University of Oklahoma Health Sciences Center, 608 Stanton L. Young Blvd, Oklahoma City, OK 73104, USA
- Cardiovascular Biology Program, Oklahoma Medical Research Foundation, 825 NE 13th St, Oklahoma City, OK 73104, USA
| | - Gopa Kumar Gopinadhan Nair
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, 608 Stanton L. Young Blvd, Oklahoma City, OK 73104, USA
- Dean McGee Eye Institute, 608 Stanton L. Young Blvd, Oklahoma City, OK 73104, USA
| | - Raju V S Rajala
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, 608 Stanton L. Young Blvd, Oklahoma City, OK 73104, USA
- Dean McGee Eye Institute, 608 Stanton L. Young Blvd, Oklahoma City, OK 73104, USA
- Department of Cell Biology, University of Oklahoma Health Sciences Center, 608 Stanton L. Young Blvd, Oklahoma City, OK 73104, USA
- Department of Physiology, University of Oklahoma Health Sciences Center, 608 Stanton L. Young Blvd, Oklahoma City, OK 73104, USA
| |
Collapse
|
8
|
Llorente A, Arora GK, Grenier SF, Emerling BM. PIP kinases: A versatile family that demands further therapeutic attention. Adv Biol Regul 2023; 87:100939. [PMID: 36517396 PMCID: PMC9992244 DOI: 10.1016/j.jbior.2022.100939] [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: 11/21/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
Phosphoinositides are membrane-localized phospholipids that regulate a plethora of essential cellular processes. These lipid signaling molecules are critical for cell homeostasis and therefore their levels are strictly regulated by the coordinated action of several families of lipid kinases and phosphatases. In this review, we provide a focused perspective on the phosphatidylinositol phosphate kinase (PIPK) family and the three subfamilies that compose it: Type I PIPKs or phosphatidylinositol-4-phosphate 5-kinases (PI4P5Ks), Type II PIPKs or phosphatidylinositol-5-phosphate 4-kinases (PI5P4Ks), and Type III PIPKs or phosphatidylinositol-3-phosphate 5-kinases (PIKfyve). Each subfamily is responsible for catalyzing a hydroxyl phosphorylation on specific phosphoinositide species to generate a double phosphorylated lipid, therefore regulating the levels of both substrate and product. Here, we summarize our current knowledge about the functions and regulation of each PIPK subfamily. Further, we highlight the roles of these kinases in various in vivo genetic models and give an overview of their involvement in multiple pathological conditions. The phosphoinositide field has been long focused on targeting PI3K signaling, but growing evidence suggests that it is time to draw attention to the other phosphoinositide kinases. The discovery of the involvement of PIPKs in the pathogenesis of multiple diseases has prompted substantial efforts to turn these enzymes into pharmacological targets. An increasingly refined knowledge of the biology of PIPKs in a variety of in vitro and in vivo models will facilitate the development of effective approaches for therapeutic intervention with the potential to translate into meaningful clinical benefits for patients suffering from cancer, immunological and infectious diseases, and neurodegenerative disorders.
Collapse
Affiliation(s)
- Alicia Llorente
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, 92037, USA
| | - Gurpreet K Arora
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, 92037, USA
| | - Shea F Grenier
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, 92037, USA
| | - Brooke M Emerling
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, 92037, USA.
| |
Collapse
|
9
|
Nanayakkara R, Gurung R, Rodgers SJ, Eramo MJ, Ramm G, Mitchell CA, McGrath MJ. Autophagic lysosome reformation in health and disease. Autophagy 2022:1-18. [DOI: 10.1080/15548627.2022.2128019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Randini Nanayakkara
- Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- Monash Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, Victoria, Australia
| | - Rajendra Gurung
- Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Samuel J. Rodgers
- Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Matthew J. Eramo
- Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Georg Ramm
- Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- Monash Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, Victoria, Australia
| | - Christina A. Mitchell
- Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Meagan J. McGrath
- Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| |
Collapse
|
10
|
|
11
|
Rivero-Ríos P, Weisman LS. Roles of PIKfyve in multiple cellular pathways. Curr Opin Cell Biol 2022; 76:102086. [PMID: 35584589 PMCID: PMC9108489 DOI: 10.1016/j.ceb.2022.102086] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/27/2022] [Accepted: 04/02/2022] [Indexed: 02/01/2023]
Abstract
Phosphoinositide signaling lipids are crucial for eukaryotes and regulate many aspects of cell function. These signaling molecules are difficult to study because they are extremely low abundance. Here, we focus on two of the lowest abundance phosphoinositides, PI(3,5)P2 and PI(5)P, which play critical roles in cellular homeostasis, membrane trafficking and transcription. Their levels are tightly regulated by a protein complex that includes PIKfyve, Fig4 and Vac14. Importantly, mutations in this complex that decrease PI(3,5)P2 and PI(5)P are linked to human diseases, especially those of the nervous system. Paradoxically, PIKfyve inhibitors which decrease PI(3,5)P2 and PI(5)P, are currently being tested for some neurodegenerative diseases, as well as other diverse diseases including some cancers, and as a treatment for SARS-CoV2 infection. A more comprehensive picture of the pathways that are regulated by PIKfyve will be critical to understand the roles of PI(3,5)P2 and PI(5)P in normal human physiology and in disease.
Collapse
Affiliation(s)
- Pilar Rivero-Ríos
- Life Sciences Institute and Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Lois S Weisman
- Life Sciences Institute and Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
| |
Collapse
|