CanVaxKB: a web-based cancer vaccine knowledgebase

Eliyas Asfaw; Asiyah Yu Lin; Anthony Huffman; Siqi Li; Madison George; Chloe Darancou; Madison Kalter; Nader Wehbi; Davis Bartels; Elyse Fleck; Nancy Tran; Daniel Faghihnia; Kimberly Berke; Ronak Sutariya; Farah Reyal; Youssef Tammam; Bin Zhao; Edison Ong; Zuoshuang Xiang; Virginia He; Justin Song; Andrey I Seleznev; Jinjing Guo; Yuanyi Pan; Jie Zheng; Yongqun He

doi:10.1093/narcan/zcad060

CanVaxKB: a web-based cancer vaccine knowledgebase

NAR Cancer. 2024 Jan 9;6(1):zcad060. doi: 10.1093/narcan/zcad060. eCollection 2024 Mar.

Authors

Eliyas Asfaw^{1

2}, Asiyah Yu Lin^{3

4}, Anthony Huffman⁵, Siqi Li¹, Madison George¹, Chloe Darancou¹, Madison Kalter¹, Nader Wehbi¹, Davis Bartels⁶, Elyse Fleck¹, Nancy Tran¹, Daniel Faghihnia¹, Kimberly Berke¹, Ronak Sutariya¹, Farah Reyal⁷, Youssef Tammam⁷, Bin Zhao³, Edison Ong⁵, Zuoshuang Xiang³, Virginia He⁸, Justin Song⁶, Andrey I Seleznev⁹, Jinjing Guo^{3

10}, Yuanyi Pan^{3

11}, Jie Zheng³, Yongqun He^{3

5

12}

Affiliations

¹ College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA.
² School of Medicine, University of Michigan, Ann Arbor, MI 48109, USA.
³ Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
⁴ National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA.
⁵ Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
⁶ College of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA.
⁷ Department of Chemical, Biochemical and Environmental Engineering, University of Maryland, Baltimore County, Baltimore, MD 21250, USA.
⁸ The College of Brown University, Brown University, Providence, RI 02912, USA.
⁹ Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
¹⁰ School of Information Management, Nanjing University, Nanjing, Jiangsu 210023, China.
¹¹ School of Medicine, Guizhou University, Guiyang, Guizhou 550025, China.
¹² Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA.

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.

Grants and funding

U24 AI171008/AI/NIAID NIH HHS/United States