| Literature DB >> 29404438 |
Dar-In Tai1, Wen-Juei Jeng1, Chun-Yen Lin1.
Abstract
Genome-wide association studies have indicated that human leukocyte antigen (HLA)-DP and HLA-DQ play roles in persistent hepatitis B virus (HBV) infection in Asia. To understand the evolution of HBV-related single nucleotide polymorphisms (SNPs) and to correlate these SNPs with chronic HBV infection among different populations, we conducted a global perspective study on hepatitis-related SNPs. We selected 12 HBV-related SNPs on the HLA locus and two HBV and three hepatitis C virus immune-related SNPs for analysis. Five nasopharyngeal carcinoma-related SNPs served as controls. All SNP data worldwide from 26 populations were downloaded from 1,000 genomes. We found a dramatic difference in the allele frequency in most of the HBV- and HLA-related SNPs in East Asia compared to the other continents. A sharp change in allele frequency in 8 of 12 SNPs was found between Bengali populations in Bangladesh and Chinese Dai populations in Xishuangbanna, China (P < 0.001); these areas represent the junction of South and East Asia. For the immune-related SNPs, significant changes were found after leaving Africa. Most of these genes shifted from higher expression genotypes in Africa to lower expression genotypes in either Europe or South Asia (P < 0.001). During this two-stage adaptation, immunity adjusted toward a weak immune response, which could have been a survival strategy during human migration to East Asia. The prevalence of chronic HBV infection in Africa is as high as in Asia; however, the HBV-related SNP genotypes are not present in Africa, and so the genetic mechanism of chronic HBV infection in Africa needs further exploration.Entities:
Year: 2017 PMID: 29404438 PMCID: PMC5721408 DOI: 10.1002/hep4.1113
Source DB: PubMed Journal: Hepatol Commun ISSN: 2471-254X
GENOTYPE DIFFERENCES BETWEEN GEOGRAPHIC AREAS ON HEPATITIS‐ AND IMMUNE‐RELATED SNPs
|
TSI |
ESN |
TSI Vs. | LWK (n = 103) |
GIH | LWK Vs. GIH |
BEB |
CDX |
BEB Vs. | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SNP | Genotype | No | % | No | % |
| No | % | No | % |
| No | % | No | % |
|
| rs12614 | CC | 76 | 71.0 | 37 | 37.4 | 45 | 45.5 | 74 | 71.9 | 68 | 79.1 | 90 | 96.8 | |||
| CFB | CT | 29 | 27.1 | 47 | 47.5 | 45 | 45.5 | 25 | 24.3 | 17 | 19.8 | 3 | 3.2 | |||
| TT | 2 | 1.9 | 15 | 15.1 | 1.1×10−6 | 9 | 9.0 | 4 | 3.9 | 6.25×10−6 | 1 | 1.2 | 0 | 0 | 1.1×10−3 | |
| rs12979860 | CC | 37 | 34.6 | 8 | 8.1 | 18 | 18.2 | 62 | 60.2 | 53 | 61.6 | 75 | 80.6 | |||
| IFNL4 | CT | 55 | 51.4 | 41 | 41.4 | 60 | 60.6 | 33 | 32.0 | 32 | 37.2 | 17 | 18.3 | |||
| TT | 15 | 14.0 | 50 | 50.5 | 0.0000 | 21 | 21.2 | 8 | 7.8 | 6.6×10−4 | 1 | 1.2 | 1 | 1.1 | 1.7×10−2 | |
| rs368234815 | ‐‐ | 15 | 14.0 | 52 | 52.5 | 25 | 25.3 | 8 | 7.8 | 1 | 1.2 | 1 | 1.1 | |||
| IFNL4 | ‐T | 56 | 52.3 | 38 | 38.4 | 60 | 60.6 | 33 | 32.0 | 33 | 38.4 | 17 | 18.3 | |||
| TT | 36 | 33.7 | 9 | 9.1 | 0.0000 | 14 | 14.1 | 62 | 60.2 | 0.0000 | 52 | 60.5 | 75 | 80.6 | 1.1×10−2 | |
| rs8099917 | TT | 64 | 59.8 | 95 | 96.0 | 84 | 84.8 | 72 | 69.9 | 67 | 77.9 | 75 | 80.6 | |||
|
IFNL4 | GT | 42 | 39.3 | 4 | 4.0 | 15 | 15.2 | 29 | 28.2 | 19 | 22.1 | 18 | 19.4 | |||
| GG | 1 | 0.9 | 0 | 0 | 1×10−8 | 0 | 0 | 2 | 1.9 | 2.6×10−2 | 0 | 0 | 0.0 | 0.0 | 1.0000 | |
| rs1883832 | TT | 2 | 1.9 | 0 | 0 | 0 | 0 | 6 | 5.8 | 9 | 10.5 | 29 | 31.2 | |||
| CD40 | CT | 60 | 56.1 | 0 | 0 | 8 | 8.1 | 46 | 44.7 | 36 | 41.9 | 44 | 47.3 | |||
| CC | 45 | 42.1 | 99 | 100 | 0.0000 | 91 | 91.9 | 51 | 49.5 | 0.0000 | 41 | 47.7 | 20 | 21.5 | 1.7×10−2 | |
Abbreviations: BEB, Bengali populations from Bangladesh; CDX, Chinese Dai populations in Xishuangbanna, China; ESN, Esan in Nigeria; GIH, Gujarati in India from Houston, TX; LWK, Luhya in Webuye, Kenya; MSRB1P1, methionine sulfoxide reductase B1 pseudogene 1; TSI, Toscani in Italy.
GENOTYPE DIFFERENCES BETWEEN GEOGRAPHIC AREAS ON HBV‐ AND HLA‐RELATED SNPs
|
TSI |
ESN |
TSI Vs. | LWK (n = 103) |
GIH | LWK Vs. GIH |
BEB |
CDX |
BEB Vs. | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SNP | Genotype | No | % | No | % |
| No | % | No | % |
| No | % | No | % |
|
| rs9276370 | GG | 16 | 15.0 | 53 | 53.5 | 41 | 41.4 | 6 | 5.8 | 0 | 0.0 | 0 | 0.0 | |||
| HLA‐DQA2 | GT | 42 | 39.3 | 41 | 41.4 | 43 | 43.4 | 34 | 33.0 | 22 | 25.6 | 18 | 19.4 | |||
| TT | 49 | 45.8 | 5 | 5.1 | 0.0000 | 15 | 15.2 | 63 | 61.2 | 0.0000 | 64 | 74.4 | 75 | 80.6 | 0.6071 | |
| rs7756516 | CC | 13 | 12.1 | 41 | 41.4 | 29 | 29.3 | 13 | 12.6 | 2 | 2.3 | 0 | 0.0 | |||
| HLA‐DQB2 | CT | 54 | 50.5 | 49 | 49.5 | 47 | 47.5 | 47 | 45.6 | 35 | 40.7 | 20 | 21.5 | |||
| TT | 40 | 37.4 | 9 | 9.1 | 4.0×10−8 | 23 | 23.2 | 43 | 41.7 | 2.3×10−3 | 49 | 57.0 | 73 | 78.5 | 5.1×10−3 | |
| rs7453920 | AA | 12 | 11.2 | 8 | 8.1 | 7 | 7.1 | 6 | 5.8 | 0 | 0.0 | 0 | 0.0 | |||
| HLA‐DQB2 | AG | 41 | 38.3 | 48 | 48.5 | 42 | 42.4 | 29 | 28.2 | 19 | 22.1 | 11 | 11.8 | |||
| GG | 54 | 50.5 | 43 | 43.4 | 0.3181 | 50 | 50.5 | 68 | 66.0 | 0.0771 | 67 | 77.9 | 82 | 88.2 | 0.1850 | |
| rs9277341 | TT | 44 | 41.1 | 6 | 6.1 | 18 | 18.2 | 21 | 20.4 | 14 | 16.3 | 1 | 1.1 | |||
| HLA‐DPA1 | CT | 47 | 43.9 | 41 | 41.4 | 43 | 43.4 | 57 | 55.3 | 42 | 48.8 | 23 | 24.7 | |||
| CC | 16 | 15.0 | 52 | 52.5 | 0.0000 | 38 | 38.4 | 25 | 24.3 | 0.0909 | 30 | 34.9 | 69 | 74.2 | 1.1×10−7 | |
| rs3135021 | GG | 55 | 51.4 | 45 | 45.5 | 33 | 33.3 | 26 | 25.2 | 29 | 33.7 | 65 | 69.9 | |||
| HLA‐DPA1/B1 | AG | 40 | 37.4 | 43 | 43.4 | 46 | 46.5 | 63 | 61.2 | 45 | 52.3 | 27 | 29.0 | |||
| AA | 12 | 11.2 | 11 | 11.1 | 0.6561 | 20 | 20.2 | 14 | 13.6 | 0.1074 | 12 | 14.0 | 1 | 1.1 | 1.1×10−6 | |
| rs9277535 | AA | 51 | 47.7 | 61 | 61.6 | 62 | 62.6 | 52 | 50.5 | 40 | 46.5 | 13 | 14.0 | |||
| HLA‐DPB1 | AG | 50 | 46.7 | 34 | 34.3 | 32 | 32.3 | 48 | 46.6 | 30 | 34.9 | 42 | 45.2 | |||
| GG | 6 | 5.6 | 4 | 4.0 | 0.1329 | 5 | 5.1 | 3 | 2.9 | 0.0949 | 16 | 18.6 | 38 | 40.9 | 4.8×10−6 | |
| rs10484569 | GG | 100 | 93.5 | 83 | 83.8 | 88 | 88.9 | 95 | 92.2 | 82 | 95.3 | 33 | 35.5 | |||
| HLA‐DPA2 | AG | 7 | 6.5 | 15 | 15.2 | 10 | 10.1 | 8 | 7.8 | 3 | 3.5 | 41 | 44.1 | |||
| AA | 0 | 0.0 | 1 | 1.0 | 0.0748 | 1 | 1.0 | 0 | 0.0 | 0.4939 | 1 | 1.2 | 19 | 20.4 | 0.0000 | |
| rs3128917 | TT | 54 | 50.5 | 25 | 25.3 | 28 | 28.3 | 59 | 57.3 | 44 | 51.2 | 22 | 23.7 | |||
| HLA‐DPA2 | GT | 44 | 41.1 | 48 | 48.5 | 51 | 51.5 | 39 | 37.9 | 32 | 37.2 | 42 | 45.2 | |||
| GG | 9 | 8.4 | 26 | 26.3 | 8.3×10−5 | 20 | 20.2 | 5 | 4.9 | 2.1×10−5 | 10 | 11.6 | 29 | 31.2 | 1.4×10−4 | |
| rs2281388 | GG | 103 | 96.3 | 99 | 100.0 | 99 | 100 | 96 | 93.2 | 81 | 94.2 | 33 | 35.5 | |||
| HLA‐DPA2 | AG | 4 | 3.7 | 0 | 0.0 | 0 | 0.0 | 7 | 6.8 | 4 | 4.7 | 41 | 44.1 | |||
| GG | 0 | 0.0 | 0 | 0.0 | 0.1516 | 0 | 0.0 | 0 | 0.0 | 0.0307 | 1 | 1.2 | 19 | 20.4 | 0.0000 | |
| rs3117222 | CC | 54 | 50.5 | 25 | 25.3 | 28 | 28.3 | 59 | 57.3 | 44 | 51.2 | 21 | 22.6 | |||
| HLA‐DPA2 | CT | 44 | 41.1 | 50 | 50.5 | 51 | 51.5 | 39 | 37.9 | 32 | 37.2 | 43 | 46.2 | |||
| TT | 9 | 8.4 | 24 | 24.2 | 1.5×10−4 | 20 | 20.2 | 5 | 4.9 | 2.1×10−5 | 10 | 11.6 | 29 | 31.2 | 8.4×10−5 | |
| rs9380343 | CC | 99 | 92.5 | 93 | 93.9 | 95 | 96.0 | 95 | 92.2 | 82 | 95.3 | 31 | 33.3 | |||
| HLA‐DPB2 | CT | 8 | 7.5 | 6 | 6.1 | 4 | 4.0 | 8 | 7.8 | 3 | 3.5 | 43 | 46.2 | |||
| TT | 0 | 0.0 | 0 | 0.0 | 0.9217 | 0 | 0.0 | 0 | 0.0 | 0.5339 | 1 | 1.2 | 19 | 20.4 | 0.0000 | |
| rs9366816 | TT | 65 | 60.7 | 65 | 65.7 | 64 | 64.6 | 65 | 63.1 | 58 | 67.4 | 24 | 25.8 | |||
| HLA‐DPA3 | CT | 37 | 34.6 | 29 | 29.3 | 32 | 32.3 | 35 | 34.0 | 25 | 29.1 | 47 | 50.5 | |||
| CC | 5 | 4.7 | 5 | 5.1 | 0.7189 | 3 | 3.0 | 3 | 2.9 | 0.9690 | 3 | 3.5 | 22 | 23.7 | 2.0×10−8 | |
Abbreviations: BEB, Bengali populations from Bangladesh; CDX, Chinese Dai populations in Xishuangbanna, China; ESN, Esan in Nigeria; GIH, Gujarati in India from Houston, TX; LWK, Luhya in Webuye, Kenya; MSRB1P1, methionine sulfoxide reductase B1 pseudogene 1; TSI, Toscani in Italy.
Figure 1Global HBsAg prevalence before HBV vaccination and the locations of the population groups of 1,000 genomes. The boxed groups are populations used in Tables 1 and 2. (Modified from Hou et al., Int J Med Sci 2005; 2:50‐57.) Abbreviations: ACB, African Ancestry from Barbados in the Caribbean; ASW, African ancestry in Southwest United States; BEB, Bengali in Bangladesh; CDX, Chinese Dai in Xishuangbanna, China; CEU, Utah residents with ancestry from Northern and Western Europe; CHB, Han Chinese in Beijing, China; CHS, Han Chinese South, China; CLM, Colombians in Medellin, Colombia; ESN, Esan from Nigeria; FIN, Finnish in Finland; GBR, British from England and Scotland, United Kingdom; GDW, Gambian in Western division, Gambia, GIH, Gujarati Indians in Houston, TX; IBS, Iberian populations in Spain; ITU, Indian Telugu in the United Kingdom; JPT, Japanese in Tokyo, Japan; KHV, Kinh in Hochi Minh city, Vietnam; LWK, Luhya in Webuye, Kenya; MSL, Mende in Sierra Leone; MXL, Mexican ancestry in Los Angeles, CA; PEL, Peruvian in Lima, Peru; PJL, Punjabi in Lahore, Pakistan; PUR, Puerto Ricans in Puerto Rico; STU, Sri Lankan Tamil in the United Kingdom; TSI, Toscani in Italy; YRI, Yoruba in Ibadan, Nigeria.
Figure 2Allele frequency of viral hepatitis‐ and NPC‐related SNPs in different geographic groups. (A) Allele frequency of immune‐related SNPs (CFB, CD40, IFNL4). Significant allele type differences were found between African and European populations and between African and South Asian populations in all of the immune‐related SNPs. (B) Allele frequency of HBV‐ and HLA‐related SNPs (HLA‐DP and ‐DQ). Significant allele type differences were found between South and East Asian populations in 8 of 12 HLA‐related SNPs and between African and South Asian populations in 3 of 12 SNPs. (C) Allele frequency of NPC‐related SNPs (HLA regions). There was no significant difference among different populations in five NPC‐related SNPs. Abbreviations: ACB, African Ancestry from Barbados in the Caribbean; AFR, Africa, total; ALL, global, total; AMR, America, total; ASW, African ancestry in Southwest United States; BEB, Bengali in Bangladesh; CDX, Chinese Dai in Xishuangbanna, China; CEU, Utah residents with ancestry from Northern and Western Europe; CHB, Han Chinese in Beijing, China; CHS, Han Chinese South, China; CLM, Colombians in Medellin, Colombia; EAS, East Asia, total; ESN, Esan from Nigeria; EUR, Europe, total; FIN, Finnish in Finland; GBR, British from England and Scotland, United Kingdom; GIH, Gujarati Indians in Houston, TX; IBS, Iberian populations in Spain; ITU, Indian Telugu in the United Kingdom; JPT, Japanese in Tokyo, Japan; KHV, Kinh in Hochi Minh city, Vietnam; LWK, Luhya in Webuye, Kenya; MAG, Mandinka in Gambia; MSL, Mende in Sierra Leone; MXL, Mexican ancestry in Los Angeles, CA; PEL, Peruvian in Lima, Peru; PJL, Punjabi in Lahore, Pakistan; PUR, Puerto Ricans in Puerto Rico; SAS, South Asia, total; STU, Sri Lankan Tamil in the United Kingdom; TSI, Toscani in Italy; YRI, Yoruba in Ibadan, Nigeria.
DIFFERENCES IN CHRONIC HBV INFECTION BETWEEN AFRICA AND EAST ASIA
| Africa | East Asia | |
|---|---|---|
| HBsAg prevalence | High | High |
| Host gene pattern | ||
| HBV‐ and HLA‐ related SNPs | Rare | Common |
| Immune‐related SNPs | High expression | Low expression |
| HBV genotype | A,D,E | B,C |
| Vertical transmission | Low | High |
| Early HBeAg seroconversion | Common | Low |