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| 2. |
- Campbell, PJ, et al.
(author)
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Pan-cancer analysis of whole genomes
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Journal article (peer-reviewed)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 3. |
- Li, Constance H., et al.
(author)
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Sex differences in oncogenic mutational processes
- 2020
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11
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Journal article (peer-reviewed)abstract
- Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.
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| 5. |
- Cheng, Shi-Ping, et al.
(author)
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Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger
- 2021
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In: Horticulture Research. - : Springer Nature. - 2052-7276. ; 8:1
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Journal article (peer-reviewed)abstract
- Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger.
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| 6. |
- Jiao, Zhejing, et al.
(author)
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Effect of Ridge Width on the Lasing Characteristics of Triangular and Rectangular InAs/In 0.53 Ga 0.47 As Quantum Well Lasers
- 2022
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In: Frontiers in Materials. - : Frontiers Media SA. - 2296-8016. ; 9
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Journal article (peer-reviewed)abstract
- The lasing characteristics of InP-based InAs/In0.53Ga0.47As quantum well (QW) lasers with different ridge widths are investigated. Two groups of lasers are grown for comparison, one with active triangular QW regions and the other with rectangular QW regions. Their output powers, characteristic temperatures (T0), external differential quantum efficiencies (ηd) and junction temperatures (Tj) are analyzed and compared. The parameter of ridge width is found to play an important role in the performance of the lasers. In triangular QW lasers, by broadening the ridge width from 8 to 12 μm, output power and ηd of the lasers are decreased for the temperature range of 100–320 K due to heating effect. But by broadening the ridge width from 8 to 100 μm in rectangular QW lasers, output power has about 3.5 time increase at 100 K and ηd also has a little increase for temperatures from 100 to 180 K due to much larger emission area and much faster heat dissipation. Tj, the real temperature of the active region, is also found to have accelerated increase at high injection current and heat sink temperature. Besides, compared to the rectangular QW laser of the same ridge width, the improved thermal performance of triangular QW laser is also demonstrated.
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| 7. |
- Li, Qishuang, et al.
(author)
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Identification of the cytochrome P450s responsible for the biosynthesis of two types of aporphine alkaloids and their de novo biosynthesis in yeast
- 2024
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In: Journal of Integrative Plant Biology. - 1672-9072 .- 1744-7909. ; 66:8, s. 1703-1717
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Journal article (peer-reviewed)abstract
- Aporphine alkaloids have diverse pharmacological activities; however, our understanding of their biosynthesis is relatively limited. Previous studies have classified aporphine alkaloids into two categories based on the configuration and number of substituents of the D-ring and have proposed preliminary biosynthetic pathways for each category. In this study, we identified two specific cytochrome P450 enzymes (CYP80G6 and CYP80Q5) with distinct activities toward (S)-configured and (R)-configured substrates from the herbaceous perennial vine Stephania tetrandra, shedding light on the biosynthetic mechanisms and stereochemical features of these two aporphine alkaloid categories. Additionally, we characterized two CYP719C enzymes (CYP719C3 and CYP719C4) that catalyzed the formation of the methylenedioxy bridge, an essential pharmacophoric group, on the A- and D-rings, respectively, of aporphine alkaloids. Leveraging the functional characterization of these crucial cytochrome P450 enzymes, we reconstructed the biosynthetic pathways for the two types of aporphine alkaloids in budding yeast (Saccharomyces cerevisiae) for the de novo production of compounds such as (R)-glaziovine, (S)-glaziovine, and magnoflorine. This study provides key insight into the biosynthesis of aporphine alkaloids and lays a foundation for producing these valuable compounds through synthetic biology.
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| 9. |
- Li, Xinyi, et al.
(author)
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Phylogenetic analysis and functional characterization of norcoclaurine synthase involved in benzylisoquinoline alkaloids biosynthesis in Stephania tetrandra
- 2023
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In: Journal of Cellular Physiology. - 1097-4652 .- 0021-9541. ; In Press
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Journal article (peer-reviewed)abstract
- Benzylisoquinoline alkaloids (BIAs) are a class of secondary metabolites that possess diverse pharmaceutical properties and are exclusively accumulated in specific plant genera. The Pictet–Spengler condensation, catalyzed by norcoclaurine synthase (NCS), represents a key enzymatic reaction in the biosynthetic pathway of BIAs. While NCS genes have been identified in several plant families such as Papaveraceae, Berberidaceae, and Ranunculaceae, no NCS genes have been reported in Menispermaceae, which is another genus known to accumulate BIAs. Here, NCSs were isolated and functionally characterized from the Menispermaceae family plant Stephania tetrandra. In vitro enzyme assay identified two functional StNCSs which could catalyze the formation of (S)-norcoclaurine. These functionally characterized genes were then integrated into engineered yeast to enable the production of norcoclaurine. Phylogenetic analysis of the NCS enzymes revealed that the StNCSs predominantly clustered into two clades. The functional StNCSs clustered with known NCSs, highlighting the presence of a specific NCS catalytic domain. This study not only provides additional genetic components for the synthetic biology-based production of BIAs in yeast but also contributes to the understanding of the phylogenetic relationships and structure–function relationship of NCS genes involved in the origin and production of BIAs.
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| 10. |
- Li, Zhuwei, et al.
(author)
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Atomically dispersed Ni active sites on covalent organic frameworks for heterogeneous metallaphotocatalytic C–N cross-coupling
- 2024
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In: Applied Catalysis B. - : Elsevier BV. - 0926-3373 .- 1873-3883. ; 345
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Journal article (peer-reviewed)abstract
- Covalent organic frameworks (COFs) have been acknowledged as a potential platform for heterogeneous photoredox cross-coupling due to their excellent chemical stability, admirable controllability, and extremely prominent surface area. However, synthesizing COFs with bidentate ligand units and utilizing active sites remain a grand challenge. Herein, we report a promising new family of 2,6-pyridinedicarboxaldehyde-bis-(p-aminophenylimine)-based two-dimensional (2D) COFs (PP-COF) using an amine monomer and classic tri-aldehydes. On this basis, dispersed Ni single-atom sites were immobilized on three-types imine-based bi-coordinated 2D COFs (Ni SAS-PP-COF) as heterogeneous dual photoredox catalysts for photo/Ni dual-catalyzed C–N cross-coupling between aryl bromides and alkyl/sulfo amines. Under solar energy irradiation, PP-COF could absorb light to generate electrons and holes, then the photogenerated electrons are transferred to Ni sites to reduce divalent nickel to monovalent nickel. Monovalent nickel is necessary to drive the nickel catalytic cycle. Due to the increased charge separation and abundant active sites, the state-of-the-art Ni SAS-PP-COFs catalyst achieves excellent catalytic performance in comparison of pristine PP-COF. The heterogeneous Ni SAS-PP-COF catalytic system not only confirms the prospect of COFs as potential photoredox/transition-metal dual catalysts, but also provides in-depth insights into the synthesis of functional COFs toward practical metallaphotocatalytic application.
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