Yoshihiro Ishikawa, PhD

Title(s)Assistant Professor, Ophthalmology
SchoolSchool of Medicine
Address555 Mission Bay Blvd South
San Francisco CA 94158
Phone--
ORCID ORCID Icon0000-0003-2013-0518 Additional info
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    Collapse Biography 
    Collapse Education and Training
    Ritsumeikan University, JapanBSc2005Engineering
    Kyoto University, JapanPhD2010Biochemistry
    Oregon Health & Science University , Portland, ORPostdoctoral fellow2018

    Collapse Overview 
    Collapse Overview
    Yoshihiro Ishikawa, Ph.D. has studied how collagens are produced in the endoplasmic reticulum (ER) for over 15 years. Using diverse approaches including biochemical, biophysical, and structural analysis and animal models, I have made significant contributions to the fundamental understanding of how collagen biosynthesis is orchestrated. He has functionally characterized over ten collagen-related biosynthetic molecules, including rER chaperones and enzymes required for posttranslational modifications. Furthermore, his in vitro studies identified unique patterns on collagen posttranslational modifications in different collagen types and specific molecular interactions between rER proteins, collagens and other extracellular matrix proteins. While many studies on type IV collagen and its mutations using cell biology and model organisms have been reported, it’s still challenging to investigate the details of type IV collagen molecules with biochemical and biophysical approaches. To fill this important gap in our knowledge, he is uniquely qualified to conduct type IV collagen biochemistry and biophysics at UCSF.

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    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. FK506-Binding Protein 11 Is a Novel Plasma Cell-Specific Antibody Folding Catalyst with Increased Expression in Idiopathic Pulmonary Fibrosis. Cells. 2022 04 14; 11(8). Preisendörfer S, Ishikawa Y, Hennen E, Winklmeier S, Schupp JC, Knüppel L, Fernandez IE, Binzenhöfer L, Flatley A, Juan-Guardela BM, Ruppert C, Guenther A, Frankenberger M, Hatz RA, Kneidinger N, Behr J, Feederle R, Schepers A, Hilgendorff A, Kaminski N, Meinl E, Bächinger HP, Eickelberg O, Staab-Weijnitz CA. PMID: 35456020; PMCID: PMC9027113.
      View in: PubMed   Mentions:
    2. Sequence-dependent mechanics of collagen reflect its structural and functional organization. Biophys J. 2021 09 21; 120(18):4013-4028. Al-Shaer A, Lyons A, Ishikawa Y, Hudson BG, Boudko SP, Forde NR. PMID: 34390685; PMCID: PMC8510973.
      View in: PubMed   Mentions: 1     Fields:    
    3. Type I and type V procollagen triple helix uses different subsets of the molecular ensemble for lysine posttranslational modifications in the rER. J Biol Chem. 2021 Jan-Jun; 296:100453. Ishikawa Y, Taga Y, Zientek K, Mizuno N, Salo AM, Semenova O, Tufa SF, Keene DR, Holden P, Mizuno K, Gould DB, Myllyharju J, Bächinger HP. PMID: 33631195; PMCID: PMC7988497.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    4. Aberrant binding of mutant HSP47 affects posttranslational modification of type I collagen and leads to osteogenesis imperfecta. PLoS Genet. 2021 02; 17(2):e1009339. Syx D, Ishikawa Y, Gebauer J, Boudko SP, Guillemyn B, Van Damme T, D'hondt S, Symoens S, Nampoothiri S, Gould DB, Baumann U, Bächinger HP, Malfait F. PMID: 33524049; PMCID: PMC7877763.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    5. The novel missense mutation Met48Lys in FKBP22 changes its structure and functions. Sci Rep. 2020 01 16; 10(1):497. Ishikawa Y, Mizuno N, Holden P, Lim PJ, Gould DB, Rohrbach M, Giunta C, Bächinger HP. PMID: 31949249; PMCID: PMC6965642.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    6. The HDAC3-SMARCA4-miR-27a axis promotes expression of the PAX3:FOXO1 fusion oncogene in rhabdomyosarcoma. Sci Signal. 2018 11 20; 11(557). Bharathy N, Berlow NE, Wang E, Abraham J, Settelmeyer TP, Hooper JE, Svalina MN, Ishikawa Y, Zientek K, Bajwa Z, Goros MW, Hernandez BS, Wolff JE, Rudek MA, Xu L, Anders NM, Pal R, Harrold AP, Davies AM, Ashok A, Bushby D, Mancini M, Noakes C, Goodwin NC, Ordentlich P, Keck J, Hawkins DS, Rudzinski ER, Chatterjee B, Bächinger HP, Barr FG, Liddle J, Garcia BA, Mansoor A, Perkins TJ, Vakoc CR, Michalek JE, Keller C. PMID: 30459282; PMCID: PMC6432638.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansAnimalsCells
    7. The endoplasmic reticulum-resident collagen chaperone Hsp47 interacts with and promotes the secretion of decorin, fibromodulin, and lumican. J Biol Chem. 2018 08 31; 293(35):13707-13716. Ishikawa Y, Rubin K, Bächinger HP, Kalamajski S. PMID: 30002123; PMCID: PMC6120207.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansAnimalsCells
    8. Type III collagen affects dermal and vascular collagen fibrillogenesis and tissue integrity in a mutant Col3a1 transgenic mouse model. Matrix Biol. 2018 09; 70:72-83. D'hondt S, Guillemyn B, Syx D, Symoens S, De Rycke R, Vanhoutte L, Toussaint W, Lambrecht BN, De Paepe A, Keene DR, Ishikawa Y, Bächinger HP, Janssens S, Bertrand MJM, Malfait F. PMID: 29551664.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansAnimalsCells
    9. Heat shock protein 47 and 65-kDa FK506-binding protein weakly but synergistically interact during collagen folding in the endoplasmic reticulum. J Biol Chem. 2017 10 20; 292(42):17216-17224. Ishikawa Y, Holden P, Bächinger HP. PMID: 28860186; PMCID: PMC5655501.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansAnimalsCells
    10. A Novel Antifibrotic Mechanism of Nintedanib and Pirfenidone. Inhibition of Collagen Fibril Assembly. Am J Respir Cell Mol Biol. 2017 07; 57(1):77-90. Knüppel L, Ishikawa Y, Aichler M, Heinzelmann K, Hatz R, Behr J, Walch A, Bächinger HP, Eickelberg O, Staab-Weijnitz CA. PMID: 28257580.
      View in: PubMed   Mentions: 37     Fields:    Translation:HumansCells
    11. Ziploc-ing the structure 2.0: Endoplasmic reticulum-resident peptidyl prolyl isomerases show different activities toward hydroxyproline. J Biol Chem. 2017 06 02; 292(22):9273-9282. Ishikawa Y, Mizuno K, Bächinger HP. PMID: 28385890; PMCID: PMC5454108.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    12. Intracellular mechanisms of molecular recognition and sorting for transport of large extracellular matrix molecules. Proc Natl Acad Sci U S A. 2016 10 11; 113(41):E6036-E6044. Ishikawa Y, Ito S, Nagata K, Sakai LY, Bächinger HP. PMID: 27679847; PMCID: PMC5068301.
      View in: PubMed   Mentions: 39     Fields:    Translation:HumansCells
    13. An essential receptor for adeno-associated virus infection. Nature. 2016 Feb 04; 530(7588):108-12. Pillay S, Meyer NL, Puschnik AS, Davulcu O, Diep J, Ishikawa Y, Jae LT, Wosen JE, Nagamine CM, Chapman MS, Carette JE. PMID: 26814968; PMCID: PMC4962915.
      View in: PubMed   Mentions: 142     Fields:    Translation:HumansAnimalsCells
    14. Ziploc-ing the structure: Triple helix formation is coordinated by rough endoplasmic reticulum resident PPIases. Biochim Biophys Acta. 2015 Oct; 1850(10):1983-93. Ishikawa Y, Boudko S, Bächinger HP. PMID: 25583561.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansAnimalsCells
    15. A substrate preference for the rough endoplasmic reticulum resident protein FKBP22 during collagen biosynthesis. J Biol Chem. 2014 Jun 27; 289(26):18189-201. Ishikawa Y, Bächinger HP. PMID: 24821723; PMCID: PMC4140264.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    16. Excessive transforming growth factor-β signaling is a common mechanism in osteogenesis imperfecta. Nat Med. 2014 Jun; 20(6):670-5. Grafe I, Yang T, Alexander S, Homan EP, Lietman C, Jiang MM, Bertin T, Munivez E, Chen Y, Dawson B, Ishikawa Y, Weis MA, Sampath TK, Ambrose C, Eyre D, Bächinger HP, Lee B. PMID: 24793237; PMCID: PMC4048326.
      View in: PubMed   Mentions: 112     Fields:    Translation:AnimalsCells
    17. Structure of human peptidyl-prolyl cis-trans isomerase FKBP22 containing two EF-hand motifs. Protein Sci. 2014 Jan; 23(1):67-75. Boudko SP, Ishikawa Y, Nix J, Chapman MS, Bächinger HP. PMID: 24272907; PMCID: PMC3892300.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    18. The concave face of decorin mediates reversible dimerization and collagen binding. J Biol Chem. 2013 Dec 06; 288(49):35526-33. Islam M, Gor J, Perkins SJ, Ishikawa Y, Bächinger HP, Hohenester E. PMID: 24169694; PMCID: PMC3853298.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimalsCells
    19. An additional function of the rough endoplasmic reticulum protein complex prolyl 3-hydroxylase 1·cartilage-associated protein·cyclophilin B: the CXXXC motif reveals disulfide isomerase activity in vitro. J Biol Chem. 2013 Nov 01; 288(44):31437-46. Ishikawa Y, Bächinger HP. PMID: 24043621; PMCID: PMC3814740.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    20. Posttranslational modifications in type I collagen from different tissues extracted from wild type and prolyl 3-hydroxylase 1 null mice. J Biol Chem. 2013 Aug 23; 288(34):24742-52. Pokidysheva E, Zientek KD, Ishikawa Y, Mizuno K, Vranka JA, Montgomery NT, Keene DR, Kawaguchi T, Okuyama K, Bächinger HP. PMID: 23861401; PMCID: PMC3750170.
      View in: PubMed   Mentions: 19     Fields:    Translation:AnimalsCells
    21. A molecular ensemble in the rER for procollagen maturation. Biochim Biophys Acta. 2013 Nov; 1833(11):2479-91. Ishikawa Y, Bächinger HP. PMID: 23602968.
      View in: PubMed   Mentions: 48     Fields:    Translation:HumansAnimalsCells
    22. Crystal structures of wild-type and mutated cyclophilin B that causes hyperelastosis cutis in the American quarter horse. BMC Res Notes. 2012 Nov 08; 5:626. Boudko SP, Ishikawa Y, Lerch TF, Nix J, Chapman MS, Bächinger HP. PMID: 23137129; PMCID: PMC3522003.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    23. Mutation in cyclophilin B that causes hyperelastosis cutis in American Quarter Horse does not affect peptidylprolyl cis-trans isomerase activity but shows altered cyclophilin B-protein interactions and affects collagen folding. J Biol Chem. 2012 Jun 22; 287(26):22253-65. Ishikawa Y, Vranka JA, Boudko SP, Pokidysheva E, Mizuno K, Zientek K, Keene DR, Rashmir-Raven AM, Nagata K, Winand NJ, Bächinger HP. PMID: 22556420; PMCID: PMC3381186.
      View in: PubMed   Mentions: 20     Fields:    Translation:AnimalsCells
    24. Prolyl 3-hydroxylase 1 null mice display abnormalities in fibrillar collagen-rich tissues such as tendons, skin, and bones. J Biol Chem. 2010 May 28; 285(22):17253-62. Vranka JA, Pokidysheva E, Hayashi L, Zientek K, Mizuno K, Ishikawa Y, Maddox K, Tufa S, Keene DR, Klein R, Bächinger HP. PMID: 20363744; PMCID: PMC2878055.
      View in: PubMed   Mentions: 32     Fields:    Translation:AnimalsCells
    25. Biochemical characterization of the prolyl 3-hydroxylase 1.cartilage-associated protein.cyclophilin B complex. J Biol Chem. 2009 Jun 26; 284(26):17641-7. Ishikawa Y, Wirz J, Vranka JA, Nagata K, Bächinger HP. PMID: 19419969; PMCID: PMC2719403.
      View in: PubMed   Mentions: 52     Fields:    Translation:AnimalsCells
    26. The rough endoplasmic reticulum-resident FK506-binding protein FKBP65 is a molecular chaperone that interacts with collagens. J Biol Chem. 2008 Nov 14; 283(46):31584-90. Ishikawa Y, Vranka J, Wirz J, Nagata K, Bächinger HP. PMID: 18786928.
      View in: PubMed   Mentions: 51     Fields:    Translation:AnimalsCells
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