Human bronchial-pulmonary proteomics in coronavirus disease 2019 (COVID-19) pandemic: applications and implications

ABSTRACT

Introduction

The outbreak of the newly discovered human coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has disrupted the normal life of almost every civilization worldwide. Studies have shown that the coronavirus disease 2019 (COVID-19) caused by the SARS-CoV-2 can affect multiple human organs and physiological systems, but the respiratory system remains the primary location for viral infection.

Areas covered

We summarize how omics technologies are used in SARS-CoV-2 research and specifically review the current knowledge of COVID-19 from the aspect of human bronchial-pulmonary proteomics. Also, knowledge gaps in COVID-19 that can be fulfilled by proteomics are discussed.

Expert opinion

Overall, human bronchial-pulmonary proteomics plays an important role in revealing the dynamics, functions, tropism, and pathogenicity of SARS-CoV-2, which is crucial for COVID-19 biomarker and therapeutic target discoveries. To more fully understand the impact of COVID-19, research from various angles using multi-omics approaches should also be conducted on the lungs as well as other organs.

KEYWORDS:

• SARS-CoV-2
• COVID-19
• lung diseases
• multi-omics
• mass spectrometry
• organoids
• microarray
• affinity purification
• proximity labelling

Article highlights

• Human lungs are the main physiological site of SARS-CoV-2 infection.

• Various aspects and techniques of proteomics are used to study the dynamics, functions, tropism, and pathogenicity of SARS-CoV-2, these include quantitative and targeted proteomics, PTM-proteomics, metaproteomics, affinity-purification, and proximity labelling.

• Bronchial-pulmonary proteomics is an indispensable tool for COVID-19 biomarker and therapeutic target discoveries.

• In addition to the lungs, COVID-19 patients also showed diseases and complications linked to multiple organs and cell types.

• Proteomics could be used in complementary with other omics technologies (genomics, transcriptomics, and metabolomics) to combat COVID-19.

Acknowledgments

We would like to thank members of the Lau And Xu (LAX) laboratory for critical reading of this manuscript.

Declaration of interests

The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

Additional information

Funding

This work was supported by the grants from the National Natural Science Foundation of China [Nos. 31771582 and 31271445], the Guangdong Natural Science Foundation of China [No. 2017A030313131], the ‘Thousand, Hundred, and Ten’ Project of the Department of Education of Guangdong Province of China, the Basic and Applied Research Major Projects of Guangdong Province of China [2017KZDXM035 and 2018KZDXM036], the ‘Yang Fan’ Project of Guangdong Province of China (Andy T. Y. Lau-2016; Yan-Ming Xu-2015), the ‘Young Innovative Talents’ Project of Guangdong Province of China [2019KQNCX034], and the Shantou Medical Health Science and Technology Plan [200624165260857].