Inferring Bacterial Infiltration in Primary Colorectal Tumors From Host Whole Genome Sequencing Data
Colorectal cancer is the third most common cancer worldwide with abysmal survival, thus requiring novel therapy strategies. Numerous studies have frequently observed infiltrating bacteria within the primary tumor tissues derived from patients. These studies have implicated the relative abundance of...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-03-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2019.00213/full |
| _version_ | 1811266939242151936 |
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| author | Man Guo Er Xu Dongmei Ai Dongmei Ai |
| author_facet | Man Guo Er Xu Dongmei Ai Dongmei Ai |
| author_sort | Man Guo |
| collection | DOAJ |
| description | Colorectal cancer is the third most common cancer worldwide with abysmal survival, thus requiring novel therapy strategies. Numerous studies have frequently observed infiltrating bacteria within the primary tumor tissues derived from patients. These studies have implicated the relative abundance of these bacteria as a contributing factor in tumor progression. Infiltrating bacteria are believed to be among the major drivers of tumorigenesis, progression, and metastasis and, hence, promising targets for new treatments. However, measuring their abundance directly remains challenging. One potential approach is to use the unmapped reads of host whole genome sequencing (hWGS) data, which previous studies have considered as contaminants and discarded. Here, we developed rigorous bioinformatics and statistical procedures to identify tumor-infiltrating bacteria associated with colorectal cancer from such whole genome sequencing data. Our approach used the reads of whole genome sequencing data of colon adenocarcinoma tissues not mapped to the human reference genome, including unmapped paired-end read pairs and single-end reads, the mates of which were mapped. We assembled the unmapped read pairs, remapped all those reads to the collection of human microbiome reference, and then computed their relative abundance of microbes by maximum likelihood (ML) estimation. We analyzed and compared the relative abundance and diversity of infiltrating bacteria between primary tumor tissues and associated normal blood samples. Our results showed that primary tumor tissues contained far more diverse total infiltrating bacteria than normal blood samples. The relative abundance of Bacteroides fragilis, Bacteroides dorei, and Fusobacterium nucleatum was significantly higher in primary colorectal tumors. These three bacteria were among the top ten microbes in the primary tumor tissues, yet were rarely found in normal blood samples. As a validation step, most of these bacteria were also closely associated with colorectal cancer in previous studies with alternative approaches. In summary, our approach provides a new analytic technique for investigating the infiltrating bacterial community within tumor tissues. Our novel cloud-based bioinformatics and statistical pipelines to analyze the infiltrating bacteria in colorectal tumors using the unmapped reads of whole genome sequences can be freely accessed from GitHub at https://github.com/gutmicrobes/UMIB.git. |
| first_indexed | 2024-04-12T20:52:20Z |
| format | Article |
| id | doaj.art-50f3ef2cda544e95bc02b8c63ed0e0f8 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-12T20:52:20Z |
| publishDate | 2019-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-50f3ef2cda544e95bc02b8c63ed0e0f82022-12-22T03:17:04ZengFrontiers Media S.A.Frontiers in Genetics1664-80212019-03-011010.3389/fgene.2019.00213449233Inferring Bacterial Infiltration in Primary Colorectal Tumors From Host Whole Genome Sequencing DataMan Guo0Er Xu1Dongmei Ai2Dongmei Ai3School of Mathematics and Physics, University of Science and Technology Beijing, Beijing, ChinaSchool of Mathematics and Physics, University of Science and Technology Beijing, Beijing, ChinaBasic Experimental of Natural Science, University of Science and Technology Beijing, Beijing, ChinaSchool of Mathematics and Physics, University of Science and Technology Beijing, Beijing, ChinaColorectal cancer is the third most common cancer worldwide with abysmal survival, thus requiring novel therapy strategies. Numerous studies have frequently observed infiltrating bacteria within the primary tumor tissues derived from patients. These studies have implicated the relative abundance of these bacteria as a contributing factor in tumor progression. Infiltrating bacteria are believed to be among the major drivers of tumorigenesis, progression, and metastasis and, hence, promising targets for new treatments. However, measuring their abundance directly remains challenging. One potential approach is to use the unmapped reads of host whole genome sequencing (hWGS) data, which previous studies have considered as contaminants and discarded. Here, we developed rigorous bioinformatics and statistical procedures to identify tumor-infiltrating bacteria associated with colorectal cancer from such whole genome sequencing data. Our approach used the reads of whole genome sequencing data of colon adenocarcinoma tissues not mapped to the human reference genome, including unmapped paired-end read pairs and single-end reads, the mates of which were mapped. We assembled the unmapped read pairs, remapped all those reads to the collection of human microbiome reference, and then computed their relative abundance of microbes by maximum likelihood (ML) estimation. We analyzed and compared the relative abundance and diversity of infiltrating bacteria between primary tumor tissues and associated normal blood samples. Our results showed that primary tumor tissues contained far more diverse total infiltrating bacteria than normal blood samples. The relative abundance of Bacteroides fragilis, Bacteroides dorei, and Fusobacterium nucleatum was significantly higher in primary colorectal tumors. These three bacteria were among the top ten microbes in the primary tumor tissues, yet were rarely found in normal blood samples. As a validation step, most of these bacteria were also closely associated with colorectal cancer in previous studies with alternative approaches. In summary, our approach provides a new analytic technique for investigating the infiltrating bacterial community within tumor tissues. Our novel cloud-based bioinformatics and statistical pipelines to analyze the infiltrating bacteria in colorectal tumors using the unmapped reads of whole genome sequences can be freely accessed from GitHub at https://github.com/gutmicrobes/UMIB.git.https://www.frontiersin.org/article/10.3389/fgene.2019.00213/fullunmapped readstumor tissuecolorectal cancerinfiltrating bacteriamaximum likelihood estimation |
| spellingShingle | Man Guo Er Xu Dongmei Ai Dongmei Ai Inferring Bacterial Infiltration in Primary Colorectal Tumors From Host Whole Genome Sequencing Data Frontiers in Genetics unmapped reads tumor tissue colorectal cancer infiltrating bacteria maximum likelihood estimation |
| title | Inferring Bacterial Infiltration in Primary Colorectal Tumors From Host Whole Genome Sequencing Data |
| title_full | Inferring Bacterial Infiltration in Primary Colorectal Tumors From Host Whole Genome Sequencing Data |
| title_fullStr | Inferring Bacterial Infiltration in Primary Colorectal Tumors From Host Whole Genome Sequencing Data |
| title_full_unstemmed | Inferring Bacterial Infiltration in Primary Colorectal Tumors From Host Whole Genome Sequencing Data |
| title_short | Inferring Bacterial Infiltration in Primary Colorectal Tumors From Host Whole Genome Sequencing Data |
| title_sort | inferring bacterial infiltration in primary colorectal tumors from host whole genome sequencing data |
| topic | unmapped reads tumor tissue colorectal cancer infiltrating bacteria maximum likelihood estimation |
| url | https://www.frontiersin.org/article/10.3389/fgene.2019.00213/full |
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