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Asfaw E, Lin AY, Huffman A, Li S, George M, Darancou C, Kalter M, Wehbi N, Bartels D, Fleck E, Tran N, Faghihnia D, Berke K, Sutariya R, Reyal F, Tammam Y, Zhao B, Ong E, Xiang Z, He V, Song J, Seleznev A, Guo J, Pan Y, Zheng J, He Y. CanVaxKB: a web-based cancer vaccine knowledgebase. NAR Cancer 2024; 6:zcad060. [PMID: 38204924 PMCID: PMC10776203 DOI: 10.1093/narcan/zcad060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/01/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Cancer vaccines have been increasingly studied and developed to prevent or treat various types of cancers. To systematically survey and analyze different reported cancer vaccines, we developed CanVaxKB (https://violinet.org/canvaxkb), the first web-based cancer vaccine knowledgebase that compiles over 670 therapeutic or preventive cancer vaccines that have been experimentally verified to be effective at various stages. Vaccine construction and host response data are also included. These cancer vaccines are developed against various cancer types such as melanoma, hematological cancer, and prostate cancer. CanVaxKB has stored 263 genes or proteins that serve as cancer vaccine antigen genes, which we have collectively termed 'canvaxgens'. Top three mostly used canvaxgens are PMEL, MLANA and CTAG1B, often targeting multiple cancer types. A total of 193 canvaxgens are also reported in cancer-related ONGene, Network of Cancer Genes and/or Sanger Cancer Gene Consensus databases. Enriched functional annotations and clusters of canvaxgens were identified and analyzed. User-friendly web interfaces are searchable for querying and comparing cancer vaccines. CanVaxKB cancer vaccines are also semantically represented by the community-based Vaccine Ontology to support data exchange. Overall, CanVaxKB is a timely and vital cancer vaccine source that facilitates efficient collection and analysis, further helping researchers and physicians to better understand cancer mechanisms.
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Affiliation(s)
- Eliyas Asfaw
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA
- School of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Asiyah Yu Lin
- Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Anthony Huffman
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Siqi Li
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA
| | - Madison George
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chloe Darancou
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA
| | - Madison Kalter
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nader Wehbi
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA
| | - Davis Bartels
- College of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA
| | - Elyse Fleck
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nancy Tran
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniel Faghihnia
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kimberly Berke
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ronak Sutariya
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA
| | - Farah Reyal
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Youssef Tammam
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Bin Zhao
- Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Edison Ong
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Zuoshuang Xiang
- Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Virginia He
- The College of Brown University, Brown University, Providence, RI 02912, USA
| | - Justin Song
- College of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA
| | - Andrey I Seleznev
- Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Jinjing Guo
- Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- School of Information Management, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yuanyi Pan
- Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- School of Medicine, Guizhou University, Guiyang, Guizhou 550025, China
| | - Jie Zheng
- Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Yongqun He
- Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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Kawahara R, Usami T, Arakawa S, Kamo H, Suzuki T, Komatsu R, Hara H, Niwa Y, Shimizu E, Dohmae N, Shimizu S, Simizu S. Biogenesis of fibrils requires C-mannosylation of PMEL. FEBS J 2023; 290:5373-5394. [PMID: 37552474 DOI: 10.1111/febs.16927] [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: 01/24/2023] [Revised: 07/22/2023] [Accepted: 08/07/2023] [Indexed: 08/09/2023]
Abstract
Premelanosome protein (PMEL), a melanocyte-specific glycoprotein, has an essential role in melanosome maturation, assembling amyloid fibrils for melanin deposition. PMEL undergoes several post-translational modifications, including N- and O-glycosylations, which are associated with proper melanosome development. C-mannosylation is a rare type of protein glycosylation at a tryptophan residue that might regulate the secretion and localization of proteins. PMEL has one putative C-mannosylation site in its core amyloid fragment (CAF); however, there is no report focusing on C-mannosylation of PMEL. To investigate this, we expressed recombinant PMEL in SK-MEL-28 human melanoma cells and purified the protein. Mass spectrometry analyses demonstrated that human PMEL is C-mannosylated at multiple tryptophan residues in its CAF and N-terminal fragment (NTF). In addition to the W153 or W156 residue (CAF), which lies in the consensus sequence for C-mannosylation, the W104 residue (NTF) was C-mannosylated without the consensus sequence. To determine the effects of the modifications, we deleted the PMEL gene by using CRISPR/Cas9 technology and re-expressed wild-type or C-mannosylation-defective mutants of PMEL, in which the C-mannosylated tryptophan was replaced with a phenylalanine residue (WF mutation), in SK-MEL-28 cells. Importantly, fibril-containing melanosomes were significantly decreased in W104F mutant PMEL-re-expressing cells compared with wild-type PMEL, observed using transmission electron microscopy. Furthermore, western blot and immunofluorescence analysis suggested that the W104F mutation may cause mild endoplasmic reticulumretention, possibly associated with early misfolding, and lysosomal misaggregation, thus reducing functional fibril formation. Our results demonstrate that C-mannosylation of PMEL is required for proper melanosome development by regulating PMEL-derived fibril formation.
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Affiliation(s)
- Ryota Kawahara
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, Yokohama, Japan
| | - Tomoko Usami
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, Yokohama, Japan
| | - Satoko Arakawa
- Department of Pathological Cell Biology, Medical Research Institute, Tokyo Medical and Dental University, Japan
- Research Core, Institute of Research, Tokyo Medical and Dental University, Japan
| | - Hiroki Kamo
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, Yokohama, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Ryosuke Komatsu
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, Yokohama, Japan
| | - Hiroyuki Hara
- Division of Anatomical Science, Department of Functional Morphology, Nihon University School of Medicine, Tokyo, Japan
| | - Yuki Niwa
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, Yokohama, Japan
| | - Erina Shimizu
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, Yokohama, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Shigeomi Shimizu
- Department of Pathological Cell Biology, Medical Research Institute, Tokyo Medical and Dental University, Japan
| | - Siro Simizu
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, Yokohama, Japan
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Buchanan JA, Varghese NR, Johnston CL, Sunde M. Functional Amyloids: Where Supramolecular Amyloid Assembly Controls Biological Activity or Generates New Functionality. J Mol Biol 2023; 435:167919. [PMID: 37330295 DOI: 10.1016/j.jmb.2022.167919] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 06/19/2023]
Abstract
Functional amyloids are a rapidly expanding class of fibrillar protein structures, with a core cross-β scaffold, where novel and advantageous biological function is generated by the assembly of the amyloid. The growing number of amyloid structures determined at high resolution reveal how this supramolecular template both accommodates a wide variety of amino acid sequences and also imposes selectivity on the assembly process. The amyloid fibril can no longer be considered a generic aggregate, even when associated with disease and loss of function. In functional amyloids the polymeric β-sheet rich structure provides multiple different examples of unique control mechanisms and structures that are finely tuned to deliver assembly or disassembly in response to physiological or environmental cues. Here we review the range of mechanisms at play in natural, functional amyloids, where tight control of amyloidogenicity is achieved by environmental triggers of conformational change, proteolytic generation of amyloidogenic fragments, or heteromeric seeding and amyloid fibril stability. In the amyloid fibril form, activity can be regulated by pH, ligand binding and higher order protofilament or fibril architectures that impact the arrangement of associated domains and amyloid stability. The growing understanding of the molecular basis for the control of structure and functionality delivered by natural amyloids in nearly all life forms should inform the development of therapies for amyloid-associated diseases and guide the design of innovative biomaterials.
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Affiliation(s)
- Jessica A Buchanan
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
| | - Nikhil R Varghese
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
| | - Caitlin L Johnston
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
| | - Margaret Sunde
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
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Beyers WC, Detry AM, Di Pietro SM. OCA7 is a melanosome membrane protein that defines pigmentation by regulating early stages of melanosome biogenesis. J Biol Chem 2022; 298:102669. [PMID: 36334630 DOI: 10.1016/j.jbc.2022.102669] [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: 06/15/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 11/11/2022] Open
Abstract
Mutations in C10orf11 (oculocutaneous albinism type 7 [OCA7]) cause OCA, a disorder that presents with hypopigmentation in skin, eyes, and hair. The OCA7 pathophysiology is unknown, and there is virtually no information on the OCA7 protein and its cellular function. Here, we discover that OCA7 localizes to the limiting membrane of melanosomes, the specialized pigment cell organelles where melanin is synthesized. We demonstrate that OCA7 is recruited through interaction with a canonical effector-binding surface of melanosome proteins Rab32 and Rab38. Using newly generated OCA7-KO MNT1 cells, we show OCA7 regulates overall melanin levels in a melanocyte autonomous manner by controlling melanosome maturation. Importantly, we found that OCA7 regulates premelanosome protein (PMEL) processing, impacting fibrillation and the striations that define transition from melanosome stage I to stage II. Furthermore, the melanosome lumen of OCA7-KO cells displays lower pH than control cells. Together, our results reveal that OCA7 regulates pigmentation through two well-established determinants of melanosome biogenesis and function, PMEL processing, and organelle pH.
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Affiliation(s)
- Wyatt C Beyers
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Anna M Detry
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Santiago M Di Pietro
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA.
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Laible G, Cole SA, Brophy B, Wei J, Leath S, Jivanji S, Littlejohn MD, Wells DN. Holstein Friesian dairy cattle edited for diluted coat color as a potential adaptation to climate change. BMC Genomics 2021; 22:856. [PMID: 34836496 PMCID: PMC8626976 DOI: 10.1186/s12864-021-08175-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/22/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND High-producing Holstein Friesian dairy cattle have a characteristic black and white coat, often with large proportions of black. Compared to a light coat color, black absorbs more solar radiation which is a contributing factor to heat stress in cattle. To better adapt dairy cattle to rapidly warming climates, we aimed to lighten their coat color by genome editing. RESULTS Using gRNA/Cas9-mediated editing, we introduced a three bp deletion in the pre-melanosomal protein 17 gene (PMEL) proposed as causative variant for the semi-dominant color dilution phenotype observed in Galloway and Highland cattle. Calves generated from cells with homozygous edits revealed a strong color dilution effect. Instead of the characteristic black and white markings of control calves generated from unedited cells, the edited calves displayed a novel grey and white coat pattern. CONCLUSION This, for the first time, verified the causative nature of the PMEL mutation for diluting the black coat color in cattle. Although only one of the calves was healthy at birth and later succumbed to a naval infection, the study showed the feasibility of generating such edited animals with the possibility to dissect the effects of the introgressed edit and other interfering allelic variants that might exist in individual cattle and accurately determine the impact of only the three bp change.
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Affiliation(s)
- G Laible
- AgResearch, Ruakura Research Centre, Hamilton, 3240, New Zealand.
- School of Medical Sciences, University of Auckland, Auckland, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand.
| | - S-A Cole
- AgResearch, Ruakura Research Centre, Hamilton, 3240, New Zealand
| | - B Brophy
- AgResearch, Ruakura Research Centre, Hamilton, 3240, New Zealand
| | - J Wei
- AgResearch, Ruakura Research Centre, Hamilton, 3240, New Zealand
| | - S Leath
- AgResearch, Ruakura Research Centre, Hamilton, 3240, New Zealand
| | - S Jivanji
- Massey University Manawatu, Palmerston North, New Zealand
| | - M D Littlejohn
- Massey University Manawatu, Palmerston North, New Zealand
- Livestock Improvement Corporation, Newstead, Hamilton, New Zealand
| | - D N Wells
- AgResearch, Ruakura Research Centre, Hamilton, 3240, New Zealand
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