A comprehensive analysis of breast cancer microbiota and host gene expression

Study information

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

29190829

DOI Digital object identifier for electronic documents.

10.1371/journal.pone.0188873

URI

Authors

Thompson KJ, Ingle JN, Tang X, Chia N, Jeraldo PR, Walther-Antonio MR, Kandimalla KK, Johnson S, Yao JZ, Harrington SC, Suman VJ, Wang L, Weinshilboum RL, Boughey JC, Kocher JP, Nelson H, Goetz MP, Kalari KR

Journal

PloS one

Year

2017

The inflammatory tumoral-immune response alters the physiology of the tumor microenvironment, which may attenuate genomic instability. In addition to inducing inflammatory immune responses, several pathogenic bacteria produce genotoxins. However the extent of microbial contribution to the tumor microenvironment biology remains unknown. We utilized The Cancer Genome Atlas, (TCGA) breast cancer data to perform a novel experiment utilizing unmapped and mapped RNA sequencing read evidence to minimize laboratory costs and effort. Our objective was to characterize the microbiota and associate the microbiota with the tumor expression profiles, for 668 breast tumor tissues and 72 non-cancerous adjacent tissues. The prominent presence of Proteobacteria was increased in the tumor tissues and conversely Actinobacteria abundance increase in non-cancerous adjacent tissues. Further, geneset enrichment suggests Listeria spp to be associated with the expression profiles of genes involved with epithelial to mesenchymal transitions. Moreover, evidence suggests H. influenza may reside in the surrounding stromal material and was significantly associated with the proliferative pathways: G2M checkpoint, E2F transcription factors, and mitotic spindle assembly. In summary, further unraveling this complicated interplay should enable us to better diagnose and treat breast cancer patients.

Experiment 1

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Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, ChiomaBlessing

Subjects

Location of subjects: United States of America

Host species Species from which microbiome was sampled. Contact us to have more species added.: Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Breast Mamma,Mammary part of chest,Mammary region,Breast,breast

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Breast carcinoma breast cancer,breast cancer, NOS,breast carcinoma,cancer of breast,cancer of the breast,cancer, breast,carcinoma of breast,carcinoma of the breast,mammary carcinoma,Breast carcinoma

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Control

Group 1 name Corresponds to the case (exposed) group for case-control studies: Breast Cancer

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients with breast cancer

Group 0 sample size Number of subjects in the control (unexposed) group: 668

Group 1 sample size Number of subjects in the case (exposed) group: 72

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3-V5

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: raw counts

Statistical test: DESeq2

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Yes

Signature 1

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Reviewed Marked as Reviewed by Fatima on 2021/07/28

Curated date: 2021/01/10

Curator: Phyu Han

Revision editor(s): Lwaldron, WikiWorks

Source: Figure 3 +text

Description: Species compositions of the Breast Caner and Non-cancerous Adjacent tissues

Abundance in Group 1: increased abundance in Breast Cancer

NCBI	Quality Control	Links
Alkalihalobacillus alcalophilus
Brachybacterium muris
Furfurilactobacillus rossiae
Salmonella enterica
Mycolicibacterium phlei
Mycolicibacterium fortuitum

Revision editor(s): Lwaldron, WikiWorks

Signature 2

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Reviewed Marked as Reviewed by Fatima on 2021/07/28

Curated date: 2021/01/10

Curator: Phyu Han

Revision editor(s): Lwaldron, WikiWorks

Source: Figure 3 +text

Description: Species compositions of the Breast Caner and Non-cancerous Adjacent tissues

Abundance in Group 1: decreased abundance in Breast Cancer

NCBI	Quality Control	Links
Acinetobacter radioresistens
Escherichia coli
Ralstonia pickettii
Microbacterium barkeri

Revision editor(s): Lwaldron, WikiWorks