Relevance of enriched expression of SARS-CoV-2 binding receptor ACE2 in gastrointestinal tissue with pathogenesis of digestive symptoms, diabetes-associated mortality, and disease recurrence in COVID-19 patients

Ashutosh Kumar; Muneeb A. Faiq; Vikas Pareek; Khursheed Raza; Ravi K. Narayan; Pranav Prasoon; Pavan Kumar; Maheswari Kulandhasamy; Chiman Kumari; Kamla Kant; Himanshu N. Singh; Rizwana Qadri; Sada N. Pandey; Santosh Kumar

The Human Protein Atlas collects transcriptomic data from the three databases (HPA, GTEx and FANTOM5). HPA RNAseq was performed on human tissue samples from healthy individuals (Accession no: PRJEB4337, Ensembl: ENSG00000130234 (version 92.38). Total RNA was extracted from the tissue samples using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. The extracted RNA samples were analyzed using either an Experion automated electrophoresis system (Bio-Rad Laboratories, Hercules, CA, USA) with the standard-sensitivity RNA chip or an Agilent 2100 Bioanalyzer system (Agilent Biotechnologies, Palo Alto, USA) with the RNA 6000 Nano Labchip Kit. Only samples of high-quality RNA (RNA Integrity Number 7.5) were used for the mRNA sample preparation for sequencing. mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines (Illumina, San Diego, CA, USA) using the standard Illumina RNA-seq protocol with a read length of 2x100 bases. Transcript abundance estimation was performed using Kallisto v0.43.1 (https://pachterlab.github.io/kallisto/about). The normalized Tags Per Million (TPM) for each gene from the three databases were calculated and included in the Human Protein Atlas. Each tissue was categorized for the intensity of gene expression using a cutoff value of 1 NX as a limit for detection across all tissues. A tissue was categorized (i) enriched if it had NX level at least four times higher than other tissues, (ii) low specificity if NX ≥ 1 in at least one tissue, (iii) Not detected if NX < 1 in all tissues. Further details of the assays and annotation used by the Human Protein Atlas can be accessed at: https://www.proteinatlas.org/about/assays+annotation#ihk.