ABSTRACT
Lung squamous cell carcinoma (LUSC) is the second most common subtype of lung cancer, accounting for a majority of lung cancer-related deaths. Detection or diagnosis of cancer at an early stage is an unmet clinical need that is being actively explored. In this study, we aimed to identify potential biomarkers for LUSC, by screening expression status of all human genes against LUSC patient samples available with The Cancer Genome Atlas (TCGA). This led to the identification of several genes that are upregulated in LUSC. Further analysis revealed that many of these genes also show higher expression at the protein level not only in lung cancer but also in other cancers. Additionally, some of these genes show stage-dependent higher expression and are associated with statistically significant poor survival of LUSC patients. As per our results, more than 60 genes are overexpressed in LUSC at the level of mRNA and some at the protein level. Thus, we identified genes such as MCC1, MRPL47, CRYGS, HSP40, DNAJC19, GMPS and PARL as novel potential biomarkers for LUSC in this study. We believe that these genes hold great potential as LUSC biomarkers for early detection as the data are derived from patient samples. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-023-03489-z.
ABSTRACT
Severe acute respiratory syndrome involving corona virus-2 (SARS-CoV-2) has been implied to cause COVID-19 disease, leading to an unprecedented health emergency across the globe with a staggering figure of mortality rate. Measures to control the pandemic are pushing the economy into a tailspin, putting burden not only on the individuals but also on the nations. Despite the widespread infection rates, young people have shown better recovery rate while COVID-19 symptoms are more pronounced in elderly and people with comorbid conditions such as diabetes, cardiac and respiratory diseases. Cancer is a highly prevalent disease affecting millions of individuals. In this study, we analyzed the expression status of genes that are required for SARS-CoV-2 infectivity and its propagation to assess the susceptibility of certain cancer patients to infection and subsequent complications. Our data indicate that patients with colon, rectum, cholangiocarcinoma, lung adenoma, kidney renal papillary cell carcinoma and kidney renal clear cell carcinoma are more at risk for COVID-19. Genes that are responsible for severe COVID-19 are also highly expressed in many cancer types. We also carried out the association rule mining analysis which is helpful in predicting the expression of proviral genes in various cancers.
ABSTRACT
It was shown that the human Angiotensin-converting enzyme 2 (ACE2) is the receptor of recent coronavirus SARS-CoV-2, and variation in this gene may affect the susceptibility of a population. Therefore, we have analysed the sequence data of ACE2 among 393 samples worldwide, focusing on South Asia. Genetically, South Asians are more related to West Eurasian populations rather than to East Eurasians. In the present analyses of ACE2, we observed that the majority of South Asian haplotypes are closer to East Eurasians rather than to West Eurasians. The phylogenetic analysis suggested that the South Asian haplotypes shared with East Eurasians involved two unique event polymorphisms (rs4646120 and rs2285666). In contrast with the European/American populations, both of the SNPs have largely similar frequencies for East Eurasians and South Asians, Therefore, it is likely that among the South Asians, host susceptibility to the novel coronavirus SARS-CoV-2 will be more similar to that of East Eurasians rather than to that of Europeans.