A Multi-Omics Study of Familial Lung Cancer: Microbiome and Host Gene Expression Patterns

Abstract

BackgroundInherited susceptibility and environmental carcinogens are crucial players in lung cancer etiology. The lung microbiome is getting rising attention in carcinogenesis. The present work sought to investigate the microbiome in lung cancer patients affected by familial lung cancer (FLC) and indoor air pollution (IAP); and further, to compare host gene expression patterns with their microbiome for potential links.MethodsTissue sample pairs (cancer and adjacent nonmalignant tissue) were used for 16S rRNA (microbiome) and RNA-seq (host gene expression). Subgroup microbiome diversities and their matched gene expression patterns were analyzed. Significantly enriched taxa were screened out, based on different clinicopathologic characteristics.ResultsOur FLC microbiome seemed to be smaller, low-diversity, and inactive to change; we noted microbiome differences in gender, age, blood type, anatomy site, histology type, TNM stage as well as IAP and smoking conditions. We also found smoking and IAP dramatically decreased specific-OTU biodiversity, especially in normal lung tissue. Intriguingly, enriched microbes were in three categories: opportunistic pathogens, probiotics, and pollutant-detoxication microbes; this third category involved Sphingomonas, Sphingopyxis, etc. which help degrade pollutants, but may also cause epithelial damage and chronic inflammation. RNA-seq highlighted IL17, Ras, MAPK, and Notch pathways, which are associated with carcinogenesis and compromised immune system.ConclusionsThe lung microbiome can play vital roles in carcinogenesis. FLC and IAP subjects were affected by fragile lung epithelium, vulnerable host-microbes equilibrium, and dysregulated immune surveillance and response. Our findings provided useful information to study the triple interplay among environmental carcinogens, population genetic background, and diversified lung microbiome.

Naso-oropharyngeal microbiome from breast cancer patients diagnosed with COVID-19

“…Considering COVID-19 severity (requirement of supplemental oxygen or mechanical ventilation) in breast cancer patients, we found a direct relationship with relative abundance of 2021) also report the presence of this genus exclusively in COVID-19 patients admitted to intensive care units. For Parasegitibacter luogiensis and Thermomonas, the higher abundance is likely resulted from opportunistic infections, as Parasegitibacter is associated with soil and skin microbiome (Manus et al, 2020), and Thermomonas is common in air pollution (Chen et al, 2022). This study has some limitations as all samples consist of a mix of nasal and oropharyngeal regions obtained by swabbing.…”

“…Regarding Scardovia , Rueca et al (2021) also report the presence of this genus exclusively in COVID-19 patients admitted to intensive care units. For Parasegitibacter luogiensis and Thermomonas , the higher abundance is likely resulted from opportunistic infections, as Parasegitibacter is associated with soil and skin microbiome ( Manus et al, 2020 ), and Thermomonas is common in air pollution ( Chen et al, 2022 ).…”

Genetic differences between smokers and never-smokers with lung cancer

“…In normal situation, it should be in a healthy balance, but inhaled carcinogens or hazardous microbes may cause cell mutations and chronic inflammation, leading to cancerogenesis. Microbiome gene expression diversity seemed to be higher than that of their human hosts because individual subjects could have different microbiomes, but all patients shared the same set of human genes, albeit frequently different alleles ( 26 ).…”

Biofilms possibly harbor occult SARS-CoV-2 may explain lung cavity, re-positive and long-term positive results

“…A great number of research studies have indicated that lung microbial communities include bacteria and other non-bacterial organisms, comprising fungi and viruses. SARS-CoV-2 may diffuse in the lung as aerosols, then colonize though pulmonary mucus (Nguyen et al, 2015;Chen et al, 2022). Gherlan et al reported a case that the COVID-19 patient got the entire right lung removed, the direct microscopic detection confirmed A. baumannii, Mucorales, Candida species (Gherlan et al, 2022).…”

“…A great number of research studies have indicated that lung microbial communities include bacteria and other non-bacterial organisms, comprising fungi and viruses. SARS-CoV-2 may diffuse in the lung as aerosols, then colonize though pulmonary mucus ( Nguyen et al., 2015 ; Chen et al., 2022 ). Gherlan et al.…”