Pharmacogenetics, pharmacogenomics and ecogenetics

Pharmacogenetics and pharmacogenomics deal with the role of genetic factors in drug effectiveness and adverse drug reactions. The promise of a personalized medicine is beginning to be explored but requires much more clinical and translational research. Specific DNA abnormalities in some cancers already have led to effective targeted treatments. Racially determined frequency differences in pharmacogenetic traits may affect choice of treatment requiring specific testing rather than basing treatments according to racial designation. The role of genes in variable responses to foreign chemicals (xenobiotics) has been termed ecogenetics or toxicogenetics raising problems in public health and occupational medicine. Nutrigenetics refers to genetic variation in response to nutrients and may affect nutritional requirements and predisposition to chronic disease.

RAD-seq data reveals robust phylogeny and morphological evolutionary history of Rhododendron

Rhododendron is famous for its high ornamental value.However,the genus is taxonomically difficult and the relationships within Rhododendron remain unresolved.In addition,the origin of key morphological characters with high horticulture value need to be explored.Both problems largely hinder utilization of germplasm resources.Most studies attempted to disentangle the phylogeny of Rhododendron,but only used a few genomic markers and lacked large-scale sampling,resulting in low clade support and contradictory phylogenetic signals.Here,we used restriction-site associated DNA sequencing(RAD-seq)data and morphological traits for 144 species of Rhododendron,representing all subgenera and most sections and subsections of this species-rich genus,to decipher its intricate evolutionary history and reconstruct ancestral state.Our results revealed high resolutions at subgenera and section levels of Rhododendron based on RAD-seq data.Both optimal phylogenetic tree and split tree recovered five lineages among Rhododendron.Subg.Therorhodion(cladeⅠ)formed the basal lineage.Subg.Tsutsusi and Azaleastrum formed cladeⅡand had sister relationships.CladeⅢincluded all scaly rhododendron species.Subg.Pentanthera(cladeⅣ)formed a sister group to Subg.Hymenanthes(cladeⅤ).The results of ancestral state reconstruction showed that Rhododendron ancestor was a deciduous woody plant with terminal inflorescence,ten stamens,leaf blade without scales and broadly funnelform corolla with pink or purple color.This study shows significant distinguishability to resolve the evolutionary history of Rhododendron based on high clade support of phylogenetic tree constructed by RAD-seq data.It also provides an example to resolve discordant signals in phylogenetic trees and demonstrates the application feasibility of RAD-seq with large amounts of missing data in deciphering intricate evolutionary relationships.Additionally,the reconstructed ancestral state of six important characters provides insights into the innovation of key characters in Rhododendron.

BIG to CNCB:An Explorato­ry Journey from Genomics to Bioinformation

The Beijing Institute of Genomics(BIG)of the Chinese Academy of Sciences,as the leading Institute in Genomics,has walked through 20 year’s journey since being founded in November 2003.From participating in the Human Genome Project(HGP)in completing the“1%task”to independently accomplishing the super-hybrid rice genome and other several national and international genome projects,BIG has made tremendous contributions in genomics research and development in China.In 2024,bearing great ambition and responsibility,BIG is transformed to the China National Center for Bioinformation(CNCB),aiming to become a global hub in bioinformatics big data services,innovation,and entrepreneurship.With the completion of its new infrastructure in 2027,CNCB is looking into a brighter future.

中国健康人群人类白细胞抗原B27亚型频率分布

目的调查中国健康人群中人类白细胞抗原(HLA)B27亚型的频率分布状况。方法应用聚合酶链反应—直接测序分型法对825名健康无关个体进行HLA高分辨分型。结果有25名个体呈现HLA-B27阳性(包括24名B27杂合子和1名B27纯合子个体),检出的8种亚型及相应频率分别为:B*2704(30·77%)、B*2705(23·08%)、B*2707(19·23%)、B*2711(7·69%)、B*2712(7·69%)、B*2701(3·85%)、B*2713(3·85%)和B*2721(3·85%)。结论用直接测序法获得了中国健康人群中HLA-B27亚型频率分布状况,为HLA-B27与强直性脊柱炎等疾病的相关性研究提供重要参考数据。

Characterization of microRNAs in serum： a novel class of biomarkers for diagnosis of cancer and other diseases

Dysregulated expression of microRNAs （miRNAs） in various tissues has been associated with a variety of diseases, including cancers. Here we demonstrate that miRNAs are present in the serum and plasma of humans and other animals such as mice, rats, bovine fetuses, calves, and horses. The levels of miRNAs in serum are stable, reproducible, and consistent among individuals of the same species. Employing Solexa, we sequenced all serum miRNAs of healthy Chinese subjects and found over 100 and 91 serum miRNAs in male and female subjects, respectively. We also identified specific expression patterns of serum miRNAs for lung cancer, colorectal cancer, and diabetes, providing evidence that serum miRNAs contain fingerprints for various diseases. Two non-small cell lung cancer-specific serum miRNAs obtained by Solexa were further validated in an independent trial of 75 healthy donors and 152 cancer patients, using quantitative reverse transcription polymerase chain reaction assays. Through these analyses, we conclude that serum miRNAs can serve as potential biomarkers for the detection of various cancers and other diseases.

Herbal compound 861 regulates mRNA expression of collagen synthesis- and degradation-related genes in human hepatic stellate cells

AIM： To identify the role of herbal compound 861 （Cpd 861） in the regulation of mRNA expression of collagen synthesis- and degradation-related genes in human hepatic stellate cells （HSCs）. METHODS： mRNA levels of collagen types I and III, matrix metalloproteinase 1 （MMP-1）, matrix metalloproteinase 2 （MMP-2）, membrane type-1 matrix metalloproteinase （MT1-MMP）, tissue inhibitor of metalloproteinase 1 （TIMP-1）, and transforming growth factor β1 （TGF-β1） in cultured-activated HSCs treated with Cpd 861 or interferon-γ, （IFN-γ,） were determined by real-time PCR. RESULTS： Both Cpd 861 and IFN-γ reduced the mRNA levels of collagen type Ⅲ, MMP-2 and TGF-β1. Moreover, Cpd 861 significantly enhanced the MMP-1 mRNA levels while down-regulated the TIMP-1 mRNA expression, increasing the ratio of MMP-1 to TIMP-1 to （6.3 ＋ 0.3）- fold compared to the control group. CONCLUSION： The anti-fibrosis function of Cpd 861 may be mediated by both decreased interstitial collagen sythesis by inhibiting the transcription of collagen type Ⅲ and TGF-β1 and increased degradation of these collagens by up-regulating MMP-1 and down-regulating TIMP-1 mRNA levels.

Genetic polymorphism of mitochondrial DNA HVS-I and HVS-II of Chinese Tu ethnic minority group

We analyzed the two hypervariable segments HVS-I and HVS-II of 108 Chinese Tu ethnic minority group samples for forensic and population genetics purposes, Comparing with Anderson sequence, 79 polymorphic loci in HVS-I and 40 in HVS-II were found in Chinese Tu ethnic minority group mtDNA sequences, and 90 and 64 haplotypes were then defined. Haplotype diversity and the mean pairwise differences were 0.9903±0.0013 and 5.7785 in HVS-I, and 0.9777±0.0013 and 3.5819 in HVS-II, respectively. By analyzing the hypervariable domain from nucleotide 1,6180 to 1,6193 in HVS-I, we defined some new types of sequence variations. We also compared the relationship between Tu population and other populations using mtDNA HVS-I sequences. According to Rst genetic distances, the phylogenetic tree showed that the Tu population, the Xi＇an Han population, the Chinese Korean, and the Mongol ethnic group were in a clade. This indicated a close genetic relationship between them. There were far relations between the Tu population and other Chinese southern Han populations, Siberian, European, African, and other foreign populations. The results suggest that Tu population has a multi-origin and has also merged with other local populations.

Identification of susceptibility to acute mountain sickness by detecting vascular tone using a photoplethysmographic sensor

Objective: Vascular tone had shown the potential susceptibility to acute mountain sickness(AMS), however the detailed tendency has not been studied. Methods: Vascular tone, SpO_2 and Rate pressure product(RPP) were studied in seventeen healthy subjects before and after rapid ascent from sea level to 3658 m. Human acute mountain sickness was evaluated by the Lake Louise Score(LLS). Results: Nine of the seventeen participants were diagnosed with AMS. On initial exposure, there was a significant decrease in vascular tone between subjects with and without AMS. Significance was also found in the decrease of SpO_2 before and after rapid ascent but the differences between subjects with and without AMS did not reach significance during the initial phase. Conclusions: Vascular tone on initial exposure in response to rapid ascent is a possible sign of susceptibility to AMS. Conclusion: measurement of vascular tone using a wearable sensor throughout the acute phase response will provide numerical values of pathophysiology throughout the development of AMS.

Fine mapping and genetic analysis of resistance genes,Rsc18,against soybean mosaic virus

Soybean mosaic virus(SMV) affects seed quality and production of soybean(Glycine max(L.) Merr.) worldwide.SC18 is one of the dominant SMV strains in South China,and accession Zhonghuang 24 displayed resistance to SC18.The F_(1),F_(2) and 168 F_(11) recombinant inbred lines(RILs) population derived from a hybridization between Zhonghuang 24(resistant,R) and Huaxia 3(susceptible,S) were used in this study.According to the segregation ratios of the F_(2) generation(3 R:1 S) and the recombinant inbred lines(RILs) population(1 R:1 S),one dominant locus may regulate the resistance to SC18 in Zhonghuang 24.By using composite interval mapping(CIM),Rsc18 was mapped to a 415.357-kb region on chromosome 13.Three candidate genes,including one NBS-LRR type gene and two serine/threonine protein type genes,were identified according to the genetic annotations,which may be related to the resistance to SC18.The q RT-PCR demonstrated that these genes were up-regulated in the R genotype compared to the control.In conclusion,the findings of this research enhanced the understanding about the R genes at the Rsc18 locus.Moreover,our results will provide insights for designing molecular markers to improve marker-assisted selection and developing new varieties with resistance to SC18.

Preparation and Activity Identification of Recombinant Protein PACAP-PTD

[Objective] This study aimed to prepare recombinant protein PACAP-PTD and measure its activity. [Method] The gene that encodes fusion protein PACAP-PTD was cloned into the expression vector pKYB to construct recombinant expression vector pKYB-PACAP-PTD, which was then transformed into E. coli ER2566. The fusion protein consisting of PACAP-PTD, intein and chitin was expressed under the induction of IPTG. Finally, the target fusion protein PACAP-PTD was purified with IMPACT system （ Intein Mediated Purification with an Affinity of chitin-binding Tag）, and its activities to cross blood-brain barrier and to promote cell proliferation were measured. [ Result~ The molecular weight of the fusion protein PACAP-PTD determined with laser time-of-flight mass spectrometry was con- sistent with the theoretical value. In addition, the protein could effectively cross the blood-brain barrier and promote cell proliferation as well. [ Conclusion] The construction and preparation of the fusion protein PACAP-PTD not only lays foundation for further study on its biological function, but also improves the route of PACAP administration, and thus expands its scope of application.

Identification and validation of stable and novel quantitative trait loci for pod shattering in soybean[Glycine max(L.)Merr.]

Pod shattering is an important domesticated trait which can cause great economic loss of crop yield in cultivated soybean.In this study,we utilized two recombinant inbred line populations(RILs,CY,Huachun 2×Wayao;GB,Guizao 1×B13)to identify quantitative trait loci(QTLs)associated with pod shattering in soybean across multiple environments.A total of 14 QTLs for pod shattering were identified in the two RIL populations,which had LOD scores ranging from 2.64 to 44.33 with phenotypic variance explanation(PVE)ranging from 1.33 to 50.85%.One QTL qPS16-1,located on chromosome 16,included a well-known functional gene Pod dehiscence 1(Pdh1)that was reported previously.Ten new putative QTLs were validated in two RIL populations,and their LOD scores were between 2.55 and 4.24,explaining 1.33 to 2.60%of the phenotypic variation.Of which four novel QTLs(qPS01-1,qPS03-2,qPS05-1,and qPS07-1)could be detected in two environments where nine genes had specific changes in gene expression.Although the nine genes may have significant effects on pod shattering of soybean,their detailed functions still need to be further explored in the future.The results of this study will facilitate a better understanding of the genetic basis of the pod shattering-resistant trait and benefit soybean molecular breeding for improving pod shattering resistance.

Fine mapping of an adult-plant resistance gene to powdery mildew in soybean cultivar Zhonghuang 24

Powdery mildew(PM),caused by the fungus Microsphaera diffusa,causes severe yield losses in soybean[Glycine max(L.)Merr.]under suitable environmental conditions.Identifying resistance genes and developing resistant cultivars may prevent soybean PM damage.In this study,analysis of F_(1),F_(2),and F8:11 recombinant inbred line(RIL)populations derived from the cross between Zhonghuang 24(ZH24)and Huaxia 3(HX3)indicated that adult-plant resistance(APR)to powdery mildew in the soybean cultivar(cv.)ZH24 was controlled by a single dominant locus.A high-density genetic linkage map of the RIL population was used for fine mapping.The APR locus in ZH24 was mapped to a 281-kb genomic region on chromosome 16.Using 283 susceptible plants of another F2 population,the candidate region was finemapped to a 32.8-kb genomic interval flanked by the markers InDel14 and Gm16_428.The interval harbored five genes,including four disease resistance(R)-like genes,according to the Williams 82.a2.v1 reference genome.Quantitative real-time PCR assays of candidate genes revealed that the expression levels of Glyma.16g214300 and Glyma.16g214500 were changed by M.diffusa infection and might be involved in disease defense.Rmd_B13 showed all-stage resistance(ASR)to PM in soybean cv.B13.An allelism test in the F2 segregating population from the cross of ZH24 × B13 suggested that the APR locus Rmd_ZH24 and the ASR locus Rmd_B13 may be allelic or tightly linked.These results provide a reference marker-assisted selection in breeding programs.

Specific Antigens to Distinguish <i>M. tuberculosis</i>from <i>M. avium</i>

To distinguish Mycobacterium tuberculosis from Mycobacterium avium, specific M. tuberculosis antigens had been studied for improving the early differential diagnosis effect of tuberculosis caused by different Mycobacterium. The rabbit anti-M. avium sera and anti-M. tuberculosis sera were analyzed for antibody-based reactivity by matrix-assisted laser desorption-ionization mass spectrometry (MALDI-TOF Mass) against M. tuberculosis proteins. The immunoreactive spots, which were attributed to the proteins HspX, GroES and CFP-10, were mostly located at 10 - 60 kDa and PI 4 - 6, subsequently Western blotting result proved that HspX and CFP-10 were specific to M. tuberculosis and ELISA testing result of 30 M. avium positive sera showed that GroES were cross-reactive to M. avium. Lastly, positive and negative tuberculosis reference sera and based on the mechanism of indirect ELISA, the specificity and the sensitivity of the methods targeting the antibodies HspX, GroES or CFP-10 were evaluated at 37% and 26%, 12% and 97%, 81% and 98%, respectively. The combination of these three antibody detection methods allowed to reached a specificity of 42%, and of 39% without taken into account of the method targeting the GroES antibody. Using proteomics approach, we found three M. tuberculosis specific antigens showed good potential in tuberculosis diagnosis, providing basic study for serodiagnosis of tuberculosis.

Growing research and development of targeted anticancer drugs in China

Objective:To deliver a comprehensive picture of the landscape and changing trend of trials and approvals on targeted anticancer drugs in China from 2012 to 2021.Methods:Trials,investigated products,and listed drugs were acquired from national databases.The status quo,changing trend of absolute number,and proportion of targeted trials,products,and drugs,as well as the corre-sponding difference between domestic and foreign companies were analyzed.Results:A total of 2,632 trials on 1,167 targeted antitumor drugs were identified,accounting for 81.5%of all registered trials.The number and proportion of trials on targeted drugs increased steadily,with an average growth rate of 36.0%and 6.2%,respectively.A similar growth trend was observed in the number(33.7%)and proportion(13.8%)of targeted drugs.Targeted drugs and trials owned by domestic companies accounted for a higher proportion than that by foreign companies(80.5%vs.19.5%;83.2%vs.16.8%,respectively),and the growing trend for both targeted drugs(13.8%vs.5.7%)and trials(13.8%vs.33.7%)owned by domestic companies was faster.The proportion of targeted drug trials(80.5%vs.85.6%)and multicenter trials(6.0%vs.69.9%)initiated by domestic companies was lower than that by foreign companies,with the gap gradually narrowing.Among the identified 18 targets of the 126 immune drugs under development,only one globally new target was found.Conclusions:Research and development of targeted antitumor drugs in China are booming and advancing rapidly,and domestic enterprises have become the pillar.Encouraging genomics activities and establishing incentives and public-private collaboration frameworks are crucial for innovation-oriented drug development in China.

“Beijing Region” (3pter-D3S3397) of the Human Genome: Complete sequence and analysis

The goal of the Human Genome Project (HGP) is to determine a complete and high-quality sequence of the human genome. China, as one of the six member states, takes a region between 3pter and D3S3397 of the human chromosome 3 as its share of this historic project, referred as “Beijing Region”. The complete sequence of this region comprises of 17.4 megabasepairs (Mb) with an average GC content of 42% and an average recombination rate of 2.14 cM/Mb. Within Beijing Region, 122 known and 20 novel genes are identified, as well as 42607 single nucleotide polymorphisms (SNPs). Comprehensive analyses also reveal: (i) gene density and GC-content of Beijing Region are in agreement with human cytogenetic maps, i.e. G-minus bands are GC-rich and of a high gene density, whereas G-plus bands are GC-poor and of a relatively low gene density; (ii) the average recombination rate within Beijing Region is rela-tively high compared with other regions of chromosome 3, with the highest recombination rate of 6.06 cM/Mb in the subtelomeric area; (iii) it is most likely that a large gene, associated with the mammary gland, may reside in the 1.1 Mb gene-poor area near the telomere; (iv) many dis-ease-related genes are genetically mapped to Beijing Region, including those associated with cancers and metabolic syndromes. All make Beijing Region an important target for in-depth mo-lecular investigations with a purpose of medical applications.

Computational Identification of 99 Insect MicroRNAs Using Comparative Genomics

In recent years, much effort has been made in identifying microRNA （miRNA） genes from mammals insects, worms, plants, and viruses. Continuing the search for more miRNA genes is still important but difficult. This paper presents a computational strategy based on comparative genomics analysis. The algorithm was used to scan four invertebrate genomes, Drosophila melangoster, Bombyx mori, Apis mellifera, and Anopheles gambiae, which are either model organisms or medically/economically important insects. 99 new miRNA genes were predicted from the four insect species which can be grouped into 17 miRNA gene families, of which 10 of the miRNA families are insect-specific. Sequence similarity analysis showed that 16 of the newly predicted insect miRNAs belong to the K-box, GY-box, and Brd-box miRNA families which are important participators in Notch-related pathways. To test the validity of the algorithm, 39 predicted insect miRNA genes from D. melangoster and A. mellifera were selected for further biological validation. 34 （87%） predicted miRNA genes＇ transcripts were successfully detected by reverse transcription-polymerase chain reaction experiments. Thus, this strategy can be used to efficiently screen for miRNA genes conserved cross species.

A complete sequence and comparative analysis of a SARS-associated virus(Isolate BJ01)

The genome sequence of the Severe Acute Respiratory Syndrome (SARS)-associated virus provides essential information for the identification of pathogen(s), exploration of etiology and evolution, interpretation of transmission and pathogenesis, development of diagnostics, prevention by future vaccination, and treatment by developing new drugs. We report the complete genome sequence and comparative analysis of an isolate (BJ01) of the coronavirus that has been recognized as a pathogen for SARS. The genome is 29725 nt in size and has 11 ORFs (Open Reading Frames). It is composed of a stable region encoding an RNA-dependent RNA polymerase (composed of 2 ORFs) and a variable region representing 4 CDSs (coding sequences) for viral structural genes (the S, E, M, N proteins) and 5 PUPs (putative uncharacterized proteins). Its gene order is identical to that of other known coronaviruses. The sequence alignment with all known RNA viruses places this virus as a member in the family of Coronaviridae. Thirty putative substitutions have been identified by comparative analysis of the 5 SARS- associated virus genome sequences in GenBank. Fifteen of them lead to possible amino acid changes (non-synonymous mutations) in the proteins. Three amino acid changes, with predicted alteration of physical and chemical features, have been detected in the S protein that is postulated to beinvolved in the immunoreactions between the virus and its host. Two amino acid changes have been detected in the Mprotein, which could be related to viral envelope formation. Phylogenetic analysis suggests the possibility of non-human origin of the SARS-associated viruses but provides noevidence that they are man-made. Further efforts should focus on identifying the etiology of the SARS-associated virus and ruling out conclusively the existence of otherpossible SARS-related pathogen(s).

A Mitochondrial Genome Sequence of the Tibetan Antelope(Pantholops hodgsonii)

To investigate genetic mechanisms of high altitude adaptations of native mammals on the Tibetan Plateau, we compared mitochondrial sequences of the endangered Pantholops hodgsonii with its lowland distant relatives Ovis ames and Capra hircus, as well as other mammals. The complete mitochondrial genome of P. hodgsonii （16,498 bp） revealed a similar gene order as of other mammals. Because of tandem duplications, the control region of P. hodgsonii mitochondrial genome is shorter than those of O. ames and C. hircus, but longer than those of Bos species. Phylogenetic analysis based on alignments of the entire cytochrome b genes suggested that P. hodgsonii is more closely related to O. ames and C. hircus, rather than to species of the Antilopinae subfamily. The estimated divergence time between P. hodgsonii and O. ames is about 2.25 million years ago. Eutther analysis on natural selection indicated that the COXI （cytochrome c oxidase subunit I） gene was under positive selection in P. hodgsonii and Bos grunniens. Considering the same climates and environments shared by these two mammalian species, we proposed that the mitochondrial COXI gene is probably relevant for these native mammals to adapt the high altitude environment unique to the Tibetan Plateau.

Molecular phylogeny of coronaviruses including human SARS-CoV

Phylogenetic tree of coronaviruses (CoVs) in-cluding the human SARS-associated virus is reconstructed from complete genomes by using our newly developed K- string composition approach. The relation of the human SARS-CoV to other coronaviruses, i.e. the rooting of the tree is suggested by choosing an appropriate outgroup. SARS-CoV makes a separate group closer but still distant from G2 (CoVs in mammalian host). The relation between different isolates of the human SARS virus is inferred by first constructing an ultrametric distance matrix from counting sequence variations in the genomes. The resulting tree is consistent with clinic relations between the SARS-CoV isolates. In addition to a larger variety of coronavirus ge-nomes these results provide phylogenetic knowledge based on independent novel methodology as compared to recent phylogenetic studies on SARS-CoV.

Critical role of bioinformatics in translating huge amounts of next-generation sequencing data into personalized medicine

Realizing personalized medicine requires integrating diverse data types with bioinformatics.The most vital data are genomic information for individuals that are from advanced next-generation sequencing(NGS) technologies at present.The technologies continue to advance in terms of both decreasing cost and sequencing speed with concomitant increase in the amount and complexity of the data.The prodigious data together with the requisite computational pipelines for data analysis and interpretation are stressors to IT infrastructure and the scientists conducting the work alike.Bioinformatics is increasingly becoming the rate-limiting step with numerous challenges to be overcome for translating NGS data for personalized medicine.We review some key bioinformatics tasks,issues,and challenges in contexts of IT requirements,data quality,analysis tools and pipelines,and validation of biomarkers.