| Literature DB >> 31454437 |
Ye Feng1,2, Weerachai Jaratlerdsiri3, Sean M Patrick4, Ruth J Lyons3, Anne-Maree Haynes3, Colin C Collins5,6, Phillip D Stricker7, M S Riana Bornman4, Vanessa M Hayes3,4,8,9.
Abstract
BACKGROUND: Inflammation is a hallmark of prostate cancer (PCa), yet no pathogenic agent has been identified. Men from Africa are at increased risk for both aggressive prostate disease and infection. We hypothesize that pathogenic microbes may be contributing, at least in part, to high-risk PCa presentation within Africa and in turn the observed ethnic disparity.Entities:
Keywords: Africa; bacterial burden; ethnic disparity; microbiome; prostate cancer; prostate microenvironment; tumor mutational burden
Mesh:
Year: 2019 PMID: 31454437 PMCID: PMC6790596 DOI: 10.1002/pros.23897
Source DB: PubMed Journal: Prostate ISSN: 0270-4137 Impact factor: 4.104
Sequencing statistics and bacterial content for 22 African and Australian patients
| UP2003 | UP2039 | UP2099 | UP2113 | UP2116 | UP2133 | 5545 | 13104 | 13179 | 10651 | 15917 | 5684 | 16599 | 12543 | 5287 | 5958 | 10738 | 6359 | 5656 | 11452 | 5060 | 5902 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Ethnicity/Country | African | African | African | African | African | African | Eur/Aus | Eur/Aus | Eur/Aus | Eur/Aus | Eur/Aus | Eur/Aus | Eur/Aus | Eur/Aus | Eur/Aus | Eur/Aus | Eur/Aus | Eur/Aus | Eur/Aus | Eur/Aus | Eur/Aus | Eur/Aus |
| HR/LRPCa | HRPCa | HRPCa | HRPCa | HRPCa | HRPCa | HRPCa | HRPCa | HRPCa | HRPCa | HRPCa | HRPCa | HRPCa | HRPCa | HRPCa | HRPCa | LRPCa | LRPCa | LRPCa | LRPCa | LRPCa | LRPCa | LRPCa |
| Clinical characteristics and sequencing statistics | ||||||||||||||||||||||
| Gleason score | 9 | 8 | 8 | 8 | 10 | 9 | 8 | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 6 | 6 | 6 | 6 | 6 | 6 | 6 |
| Tumor purity | 42% | 68% | 78% | 41% | 44% | 43% | 79% | 41% | 52% | 75% | 42% | 75% | 68% | 52% | 55% | 56% | 84% | 52% | 33% | 56% | 53% | 70% |
| hg38 coverage | 86× | 75× | 82× | 86× | 87× | 81× | 67× | 76× | 85× | 91× | 86× | 71× | 89× | 77× | 80× | 68× | 80× | 79× | 86× | 68× | 74× | 74× |
| TMB (Mut/Mb) | 4.6 | 3.3 | 3.4 | 55 | 3 | 4.7 | 2.2 | 1.9 | 2.2 | 2.6 | 2.1 | 1.9 | 2.8 | 1.7 | 1.8 | 1.7 | 1.6 | 1.8 | 3 | 1.1 | 1.7 | 1.3 |
| Unmapped reads | 1.16% | 0.73% | 1.07% | 1.04% | 0.74% | 1.08% | 0.92% | 1.26% | 1.17% | 0.78% | 1.31% | 0.97% | 0.82% | 0.80% | 0.90% | 0.90% | 0.71% | 0.96% | 0.64% | 1.57% | 1% | 0.65% |
| Bacterial content and load (no reads | ||||||||||||||||||||||
| Total no of genera | 23 | 39 | 18 | 55 | 24 | 47 | 10 | 17 | 7 | 5 | 21 | 13 | 7 | 16 | 10 | 9 | 18 | 17 | 10 | 22 | 18 | 7 |
|
| 32.9 | 5267.7 | 91 | 4339.7 | 221.2 | 8085.8 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
|
| 481.9 | 310.6 | 314.6 | 982.8 | 458 | 2236.9 | 281.6 | 433.8 | 391.1 | 167.3 | 310.1 | 244.5 | 199.8 | 148.3 | 200.7 | 298.8 | 259 | 297.7 | 120.5 | 530.8 | 338 | 107.6 |
|
| 8.8 | 16.9 | 10.4 | 3862.6 | 5.9 | 892.1 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
|
| 329.3 | 279.3 | 110.7 | 1569 | 193.7 | 183.8 | NA | 5.5 | NA | NA | NA | 9.1 | NA | NA | NA | NA | 18.3 | 13.2 | NA | 8.9 | NA | 1.3 |
|
| 35.7 | 57.7 | 88.1 | 84.4 | 25.4 | 65.5 | 38 | 158.5 | 120.8 | 145.1 | 441.9 | 87.4 | 57.8 | 80.2 | 31.4 | 62.9 | 51.9 | 376.3 | 90.4 | 194 | 63.8 | 50 |
|
| 172.9 | 94.1 | 33.6 | 60.7 | 17.8 | 7 | NA | 6.1 | 5 | NA | 7.1 | NA | NA | NA | 5.8 | 6.9 | 10 | 8.4 | NA | 1099.9 | 33.5 | NA |
|
| 66.4 | 45.8 | 40 | 53.5 | 49.1 | 58 | 44.4 | 79.9 | 41.4 | 25.3 | 31.2 | 26.1 | 16.8 | 29.8 | 26.2 | 71.2 | 187 | 171.7 | 134.2 | 225.4 | 24.6 | 24 |
| Total burden | 1419.2 | 6841 | 889.4 | 13 605.7 | 1294.6 | 13 404.8 | 487.9 | 948 | 653.7 | 390.4 | 1232.2 | 539.3 | 347.5 | 590 | 418.2 | 595.5 | 827.8 | 1465 | 494.1 | 2366.4 | 717.1 | 281 |
Abbreviations: Aus, Australian; Eur, European; HRPCa, high‐risk prostate cancer; LRPCa, low‐risk prostate cancer; NA, not applicable; TMB, tumor mutational burden.
Hyperduplicated tumor genome.
Percentage of reads not mapping to the human reference genome (hg38).
Normalized number of reads.
Bacterial genera shared between African and Australian prostate tumor samples (n=28)
| Genus | Phylum | Chinese prostate tissue study | Fecal‐derived core gut microbiome (34 genera) |
|---|---|---|---|
|
| Proteobacteria | Absent | Absent |
|
| Actinobacteria | Present | Absent |
|
| Proteobacteria | Present | Absent |
|
| Proteobacteria | Present | Absent |
|
| Proteobacteria | Present | Absent |
|
| Actinobacteria | Absent | Absent |
|
| Proteobacteria | Absent | Absent |
|
| Proteobacteria | Present | Absent |
|
| Actinobacteria | Present | Absent |
|
| Proteobacteria | Present | Absent |
|
| Proteobacteria | Present | Absent |
|
| Proteobacteria | Present | Present (rank 28) |
|
| Proteobacteria | Present | Present (rank 19) |
|
| Proteobacteria | Present | Absent |
|
| Proteobacteria | Present | Absent |
|
| Proteobacteria | Present | Absent |
|
| Actinobacteria | Present | Absent |
|
| Proteobacteria | Present | Absent |
|
| Deinococcus‐Thermus | Absent | Absent |
|
| Proteobacteria | Present | Absent |
|
| Firmicutes | Present | Present (rank 14) |
|
| Proteobacteria | Present | Absent |
|
| Proteobacteria | Present | Absent |
|
| Proteobacteria | Present | Absent |
|
| Proteobacteria | Present | Absent |
|
| Proteobacteria | Absent | Absent |
|
| Firmicutes | Present | Absent |
|
| Firmicutes | Present | Absent |
Figure 1Prostate microbiomes shown in this study. A, Heatmap showing the read count of the top 15 abundant bacterial genera identified in the patients in this study, with the UPGMA tree constructed based on the weighted_UniFrac distance between specimens. B, The NMDS plots in which the African and European samples are distinguishable but the high‐ and low‐risk European samples are not distinguishable. C, Comparison of the alpha‐diversity indices, ACE and chao1, between the prostate microbiomes of the African and European patients. D, Bacterial genera that are differentially abundant between the African and the European patients. NMDS, nonmetric multidimensional scaling [Color figure can be viewed at wileyonlinelibrary.com]
Figure 2Distribution of common bacterial genera within six African high‐risk prostate tumors, with Bacteroides, included (inner panel) and excluded (outer panel). Number in a chart indicates the percentage of bacterial abundance [Color figure can be viewed at wileyonlinelibrary.com]