MalariaSED: a deep learning framework to decipher the regulatory contributions of noncoding variants in malaria parasites.

Journal: Genome biology
PMID: 37845769

Abstract

Malaria remains one of the deadliest infectious diseases. Transcriptional regulation effects of noncoding variants in this unusual genome of malaria parasites remain elusive. We developed a sequence-based, ab initio deep learning framework, MalariaSED, for predicting chromatin profiles in malaria parasites. The MalariaSED performance was validated by published ChIP-qPCR and TF motifs results. Applying MalariaSED to ~ 1.3 million variants shows that geographically differentiated noncoding variants are associated with parasite invasion and drug resistance. Further analysis reveals chromatin accessibility changes at Plasmodium falciparum rings are partly associated with artemisinin resistance. MalariaSED illuminates the potential functional roles of noncoding variants in malaria parasites.

Authors

  • Chengqi Wang
    Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA. chengqi@usf.edu.
  • Yibo Dong
    Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA.
  • Chang Li
    Bioengineering College of Chongqing University, Chongqing University Central Hospital (Chongqing Emergency Medical Center), Chongqing, China.
  • Jenna Oberstaller
    Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA.
  • Min Zhang
    Department of Infectious Disease, The Second Xiangya Hospital of Central South University, Changsha, China.
  • Justin Gibbons
    Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA.
  • Camilla Valente Pires
    Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA.
  • Mianli Xiao
    Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA.
  • Lei Zhu
    School of Civil and Hydraulic Engineering, Ningxia University, Yinchuan, China.
  • Rays H Y Jiang
    Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA.
  • Kami Kim
    Department of Internal Medicine, Morsani College of Medicine, Tampa, FL, USA.
  • Jun Miao
    Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio 44106.
  • Thomas D Otto
    Institute of Infection, Immunity & Inflammation, MVLS, University of Glasgow, Glasgow, UK. Thomasdan.otto@glasgow.ac.uk.
  • Liwang Cui
    Department of Internal Medicine, Morsani College of Medicine, Tampa, FL, USA.
  • John H Adams
    Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA.
  • Xiaoming Liu
    College of Agriculture, Northeast Agricultural University, Harbin, China.

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