1
|
Kuo WH, Small LL, Olsen KM. Variable expression of cyanide detoxification and tolerance genes in cyanogenic and acyanogenic white clover (Trifolium repens). Am J Bot 2023; 110:e16233. [PMID: 37661820 DOI: 10.1002/ajb2.16233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/04/2023] [Accepted: 08/04/2023] [Indexed: 09/05/2023]
Abstract
PREMISE β-Cyanoalanine synthase (β-CAS) and alternative oxidase (AOX) play important roles in the ability of plants to detoxify and tolerate hydrogen cyanide (HCN). These functions are critical for all plants because HCN is produced at low levels during basic metabolic processes, and especially for cyanogenic species, which release high levels of HCN following tissue damage. However, expression of β-CAS and Aox genes has not been examined in cyanogenic species, nor compared between cyanogenic and acyanogenic genotypes within a species. METHODS We used a natural polymorphism for cyanogenesis in white clover to examine β-CAS and Aox gene expression in relation to cyanogenesis-associated HCN exposure. We identified all β-CAS and Aox gene copies present in the genome, including members of the Aox1, Aox2a, and Aox2d subfamilies previously reported in legumes. Expression levels were compared between cyanogenic and acyanogenic genotypes and between damaged and undamaged leaf tissue. RESULTS β-CAS and Aox2a expression was differentially elevated in cyanogenic genotypes, and tissue damage was not required to induce this increased expression. Aox2d, in contrast, appeared to be upregulated as a generalized wounding response. CONCLUSIONS These findings suggest a heightened constitutive role for HCN detoxification (via elevated β-CAS expression) and HCN-toxicity mitigation (via elevated Aox2a expression) in plants that are capable of cyanogenesis. As such, freezing-induced cyanide autotoxicity is unlikely to be the primary selective factor in the evolution of climate-associated cyanogenesis clines.
Collapse
Affiliation(s)
- Wen-Hsi Kuo
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Linda L Small
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Kenneth M Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| |
Collapse
|
2
|
Santangelo JS, Battlay P, Hendrickson BT, Kuo WH, Olsen KM, Kooyers NJ, Johnson MTJ, Hodgins KA, Ness RW. Haplotype-Resolved, Chromosome-Level Assembly of White Clover (Trifolium repens L., Fabaceae). Genome Biol Evol 2023; 15:evad146. [PMID: 37542471 PMCID: PMC10433932 DOI: 10.1093/gbe/evad146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/24/2023] [Accepted: 07/29/2023] [Indexed: 08/07/2023] Open
Abstract
White clover (Trifolium repens L.; Fabaceae) is an important forage and cover crop in agricultural pastures around the world and is increasingly used in evolutionary ecology and genetics to understand the genetic basis of adaptation. Historically, improvements in white clover breeding practices and assessments of genetic variation in nature have been hampered by a lack of high-quality genomic resources for this species, owing in part to its high heterozygosity and allotetraploid hybrid origin. Here, we use PacBio HiFi and chromosome conformation capture (Omni-C) technologies to generate a chromosome-level, haplotype-resolved genome assembly for white clover totaling 998 Mbp (scaffold N50 = 59.3 Mbp) and 1 Gbp (scaffold N50 = 58.6 Mbp) for haplotypes 1 and 2, respectively, with each haplotype arranged into 16 chromosomes (8 per subgenome). We additionally provide a functionally annotated haploid mapping assembly (968 Mbp, scaffold N50 = 59.9 Mbp), which drastically improves on the existing reference assembly in both contiguity and assembly accuracy. We annotated 78,174 protein-coding genes, resulting in protein BUSCO completeness scores of 99.6% and 99.3% against the embryophyta_odb10 and fabales_odb10 lineage datasets, respectively.
Collapse
Affiliation(s)
- James S Santangelo
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Paul Battlay
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | | | - Wen-Hsi Kuo
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Kenneth M Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Nicholas J Kooyers
- Department of Biology, University of Louisiana, Lafayette, Louisiana, USA
| | - Marc T J Johnson
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Rob W Ness
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| |
Collapse
|
3
|
Kuo WH, Liu SH, Chang CC, Hsieh CL, Li YH, Ito T, Won H, Kokubugata G, Chung KF. Correction to: Plastome phylogenomics of Allaeanthus, Broussonetia and Malaisia (Dorstenieae, Moraceae) and the origin of B. × kazinoki. J Plant Res 2022; 135:531. [PMID: 35278153 DOI: 10.1007/s10265-022-01382-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Wen-Hsi Kuo
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, Taipei, 115201, Taiwan
- Department of Biology, Washington University, St. Louis, MO, USA
| | - Shih-Hui Liu
- Department of Biological Sciences, National Sun Yat- sen University, Kaohsiung, Taiwan
| | - Chiung-Chih Chang
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, Taipei, 115201, Taiwan
| | - Chia-Lun Hsieh
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, Taipei, 115201, Taiwan
| | - Yi-Hsuan Li
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, Taipei, 115201, Taiwan
| | - Takuro Ito
- The Center for Academic Resources and Archives/Botanical Gardens, Tohoku University, Sendai, Miyagi, Japan
| | - Hyosig Won
- Department of Biological Science and Institute of Natural Sciences, Daegu University, Gyungsan, Gyungbuk, South Korea
| | - Goro Kokubugata
- Department of Botany, National Museum of Nature and Science, Tsukuba, Ibaraki, Japan
| | - Kuo-Fang Chung
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, Taipei, 115201, Taiwan.
| |
Collapse
|
4
|
Kuo WH, Liu SH, Chang CC, Hsieh CL, Li YH, Ito T, Won H, Kokubugata G, Chung KF. Plastome phylogenomics of Allaeanthus, Broussonetia and Malaisia (Dorstenieae, Moraceae) and the origin of B. × kazinoki. J Plant Res 2022; 135:203-220. [PMID: 35080694 DOI: 10.1007/s10265-022-01369-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Species of Broussonetia have been essential in the development of papermaking technology. In Japan and Korea, a hybrid between B. monoica and B. papyrifera (= B. × kazinoki) known as kōzo and daknamu is still the major source of raw materials for making traditional paper washi and hanji, respectively. Despite their cultural and practical significance, however, the origin and taxonomy of kōzo and daknamu remain controversial. Additionally, the long-held generic concept of Broussonetia s.l., which included Sect. Allaeanthus and Sect. Broussonetia, was challenged as phylogenetic analyses showed Malaisia is sister to the latter section. To re-examine the taxonomic proposition that recognizes Allaeanthus, Broussonetia, and Malaisia (i.e., Broussonetia alliance), plastome and nuclear ribosomal DNA (nrDNA) sequences of six species of the alliance were assembled. Characterized by the canonical quadripartite structure, genome alignments and contents of the six plastomes (160,121-162,594 bp) are highly conserved, except for the pseudogenization and/or loss of the rpl22 gene. Relationships of the Broussonetia alliance are identical between plastome and nrDNA trees, supporting the maintenance of Malaisia and the resurrection of Allaeanthus. The phylogenomic relationships also indicate that the monoecy in B. monoica is a derived state, possibly resulting from hybridization between the dioecious B. kaempferi (♀) and B. papyrifera (♂). Based on the hypervariable ndhF-rpl32 intergenic spacer selected by sliding window analysis, phylogeographic analysis indicates that B. monoica is the sole maternal parent of B. × kazinoki and that daknamu carries multiple haplotypes, while only one haplotype was detected in kōzo. Because hybridizations between B. monoica and B. papyrifera are unidirectional and have occurred rarely in nature, our data suggest that daknamu might have originated via deliberate hybrid breeding selected for making hanji in Korea. On the contrary, kōzo appears to have a single origin and the possibility of a Korean origin cannot be ruled out.
Collapse
Affiliation(s)
- Wen-Hsi Kuo
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, Taipei, 115201, Taiwan
- Department of Biology, Washington University, St. Louis, MO, USA
| | - Shih-Hui Liu
- Department of Biological Sciences, National Sun Yat- sen University, Kaohsiung, Taiwan
| | - Chiung-Chih Chang
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, Taipei, 115201, Taiwan
| | - Chia-Lun Hsieh
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, Taipei, 115201, Taiwan
| | - Yi-Hsuan Li
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, Taipei, 115201, Taiwan
| | - Takuro Ito
- The Center for Academic Resources and Archives/Botanical Gardens, Tohoku University, Sendai, Miyagi, Japan
| | - Hyosig Won
- Department of Biological Science and Institute of Natural Sciences, Daegu University, Gyungsan, Gyungbuk, South Korea
| | - Goro Kokubugata
- Department of Botany, National Museum of Nature and Science, Tsukuba, Ibaraki, Japan
| | - Kuo-Fang Chung
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, Taipei, 115201, Taiwan.
| |
Collapse
|
5
|
Pan ZJ, Nien YC, Shih YA, Chen TY, Lin WD, Kuo WH, Hsu HC, Tu SL, Chen JC, Wang CN. Transcriptomic Analysis Suggests Auxin Regulation in Dorsal-Ventral Petal Asymmetry of Wild Progenitor Sinningia speciosa. Int J Mol Sci 2022; 23:2073. [PMID: 35216188 PMCID: PMC8876764 DOI: 10.3390/ijms23042073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/22/2022] [Accepted: 02/11/2022] [Indexed: 01/27/2023] Open
Abstract
The establishment of dorsal-ventral (DV) petal asymmetry is accompanied by differential growth of DV petal size, shape, and color differences, which enhance ornamental values. Genes involved in flower symmetry in Sinningia speciosa have been identified as CYCLOIDEA (SsCYC), but which gene regulatory network (GRN) is associated with SsCYC to establish DV petal asymmetry is still unknown. To uncover the GRN of DV petal asymmetry, we identified 630 DV differentially expressed genes (DV-DEGs) from the RNA-Seq of dorsal and ventral petals in the wild progenitor, S. speciosa 'ES'. Validated by qRT-PCR, genes in the auxin signaling transduction pathway, SsCYC, and a major regulator of anthocyanin biosynthesis were upregulated in dorsal petals. These genes correlated with a higher endogenous auxin level in dorsal petals, with longer tube length growth through cell expansion and a purple dorsal color. Over-expression of SsCYC in Nicotiana reduced petal size by regulating cell growth, suggesting that SsCYC also controls cell expansion. This suggests that auxin and SsCYC both regulate DV petal asymmetry. Transiently over-expressed SsCYC, however, could not activate most major auxin signaling genes, suggesting that SsCYC may not trigger auxin regulation. Whether auxin can activate SsCYC or whether they act independently to regulate DV petal asymmetry remains to be explored in the future.
Collapse
Affiliation(s)
- Zhao-Jun Pan
- Department of Life Science, National Taiwan University, Taipei 10617, Taiwan; (Z.-J.P.); (Y.-C.N.); (Y.-A.S.); (T.-Y.C.)
| | - Ya-Chi Nien
- Department of Life Science, National Taiwan University, Taipei 10617, Taiwan; (Z.-J.P.); (Y.-C.N.); (Y.-A.S.); (T.-Y.C.)
| | - Yu-An Shih
- Department of Life Science, National Taiwan University, Taipei 10617, Taiwan; (Z.-J.P.); (Y.-C.N.); (Y.-A.S.); (T.-Y.C.)
| | - Tsun-Ying Chen
- Department of Life Science, National Taiwan University, Taipei 10617, Taiwan; (Z.-J.P.); (Y.-C.N.); (Y.-A.S.); (T.-Y.C.)
| | - Wen-Dar Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan; (W.-D.L.); (S.-L.T.)
| | - Wen-Hsi Kuo
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei 10617, Taiwan; (W.-H.K.); (H.-C.H.)
| | - Hao-Chun Hsu
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei 10617, Taiwan; (W.-H.K.); (H.-C.H.)
| | - Shih-Long Tu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan; (W.-D.L.); (S.-L.T.)
| | - Jen-Chih Chen
- Institute of Biotechnology, National Taiwan University, Taipei 10617, Taiwan
| | - Chun-Neng Wang
- Department of Life Science, National Taiwan University, Taipei 10617, Taiwan; (Z.-J.P.); (Y.-C.N.); (Y.-A.S.); (T.-Y.C.)
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei 10617, Taiwan; (W.-H.K.); (H.-C.H.)
| |
Collapse
|
6
|
Hsu HJ, He CW, Kuo WH, Hsin KT, Lu JY, Pan ZJ, Wang CN. Genetic Analysis of Floral Symmetry Transition in African Violet Suggests the Involvement of Trans-acting Factor for CYCLOIDEA Expression Shifts. Front Plant Sci 2018; 9:1008. [PMID: 30158940 PMCID: PMC6104639 DOI: 10.3389/fpls.2018.01008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/21/2018] [Indexed: 05/29/2023]
Abstract
With the growing demand for its ornamental uses, the African violet (Saintpaulia ionantha) has been popular owing to its variations in color, shape and its rapid responses to artificial selection. Wild type African violet (WT) is characterized by flowers with bilateral symmetry yet reversals showing radially symmetrical flowers such as dorsalized actinomorphic (DA) and ventralized actinomorphic (VA) peloria are common. Genetic crosses among WT, DA, and VA revealed that these floral symmetry transitions are likely to be controlled by three alleles at a single locus in which the levels of dominance are in a hierarchical fashion. To investigate whether the floral symmetry gene was responsible for these reversals, orthologs of CYCLOIDEA (CYC) were isolated and their expressions correlated to floral symmetry transitions. Quantitative RT-PCR and in situ results indicated that dorsal-specific CYCs expression in WT S. ionantha (SiCYC and SiCYC1B) shifted in DA with a heterotopically extended expression to all petals, but in VA, SiCYC1s' dorsally specific expressions were greatly reduced. Selection signature analysis revealed that the major high-expressed copy of SiCYC had been constrained under purifying selection, whereas the low-expressed helper SiCYC1B appeared to be relaxed under purifying selection after the duplication into SiCYC and SiCYC1B. Heterologous expression of SiCYC in Arabdiopsis showed petal growth retardation which was attributed to limited cell proliferation. While expression shifts of SiCYC and SiCYC1B correlate perfectly to the resulting symmetry phenotype transitions in F1s of WT and DA, there is no certain allelic combination of inherited SiCYC1s associated with specific symmetry phenotypes. This floral transition indicates that although the expression shifts of SiCYC/1B are responsible for the two contrasting actinomorphic reversals in African violet, they are likely to be controlled by upstream trans-acting factors or epigenetic regulations.
Collapse
Affiliation(s)
- Hui-Ju Hsu
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Cheng-Wen He
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Wen-Hsi Kuo
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Kuan-Ting Hsin
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Jing-Yi Lu
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Zhao-Jun Pan
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Chun-Neng Wang
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| |
Collapse
|
7
|
Chung KF, Kuo WH, Hsu YH, Li YH, Rubite RR, Xu WB. Molecular recircumscription of Broussonetia (Moraceae) and the identity and taxonomic status of B. kaempferi var. australis. Bot Stud 2017; 58:11. [PMID: 28510194 PMCID: PMC5432938 DOI: 10.1186/s40529-017-0165-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 02/13/2017] [Indexed: 05/23/2023]
Abstract
BACKGROUND Despite being a relatively small genus, the taxonomy of the paper mulberry genus Broussonetia remains problematic. Much of the controversy is related to the identity and taxonomic status of Broussonetia kaempferi var. australis, a name treated as a synonym in the floras of Taiwan and yet accepted in the floras of China. At the generic level, the monophyly of Corner (Gard Bull Singap 19:187-252, 1962)'s concept of Broussonetia has not been tested. In recent studies of Broussonetia of Japan, lectotypes of the genus were designated and three species (B. kaempferi, Broussonetia monoica, and Broussonetia papyrifera) and a hybrid (B. ×kazinoki) were recognized. Based on the revision and molecular phylogenetic analyses, this article aims to clarify these issues. RESULTS Herbarium studies, field work, and molecular phylogenetic analyses indicate that all Taiwanese materials identifiable to B. kaempferi var. australis are conspecific with B. monoica of Japan and China. Molecular phylogenetic analyses showed that Broussonetia sensu Corner (Gard Bull Singap 19:187-252, 1962) contains two clades corresponding to sect. Broussonetia and sect. Allaeanthus, with Malaisia scandens sister to sect. Broussonetia. CONCLUSIONS Based on our analyses, B. kaempferi var. australis is treated as a synonym of B. monoica and that B. kaempferi is not distributed in Taiwan. To correct the non-monophyly of Broussonetia sensu Corner (Gard Bull Singap 19:187-252, 1962), Broussonetia is recircumscribed to contain only sect. Broussonetia and the generic status of Allaeanthus is reinstated.
Collapse
Affiliation(s)
- Kuo-Fang Chung
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, 128 Academia Road, Section 2, Nangang, Taipei, 11529 Taiwan
- School of Forestry and Resource Conservation, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617 Taiwan
| | - Wen-Hsi Kuo
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, 128 Academia Road, Section 2, Nangang, Taipei, 11529 Taiwan
| | - Yi-Hsuan Hsu
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, 128 Academia Road, Section 2, Nangang, Taipei, 11529 Taiwan
- School of Forestry and Resource Conservation, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617 Taiwan
| | - Yi-Hsuan Li
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, 128 Academia Road, Section 2, Nangang, Taipei, 11529 Taiwan
- School of Forestry and Resource Conservation, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617 Taiwan
| | - Rosario Rivera Rubite
- Department of Biology, College of Arts and Sciences, University of the Philippines Manila, Padre Faura, 1000 Manila, Philippines
| | - Wei-Bin Xu
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006 China
| |
Collapse
|
8
|
Chen IC, Lin CH, Huang CS, Lien HC, Hsu C, Kuo WH, Lu YS, Cheng AL. Lack of efficacy to systemic chemotherapy for treatment of metaplastic carcinoma of the breast in the modern era. Breast Cancer Res Treat 2011; 130:345-51. [PMID: 21792625 DOI: 10.1007/s10549-011-1686-9] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Accepted: 07/14/2011] [Indexed: 12/20/2022]
Abstract
Metaplastic carcinoma of the breast (MCB) is a rare subtype of breast cancer. Anecdotal reports are available regarding its response to systemic chemotherapy. We reviewed the records of patients diagnosed with MCB at National Taiwan University Hospital between 1988 and 2009. A total of 46 MCB cases were identified from 8,695 breast tumor patients who underwent biopsy or resection. About 11 of 25 patients with initial bulky disease (T3-4) received neoadjuvant chemotherapy before surgery, and 2 (18.2%) exhibited a partial response. About 12 of 18 patients who developed distant metastasis received palliative systemic chemotherapy. Of them, only 1 (8.3%), 1 (10%), and none (0%) responded to first-, second-, or third- and beyond line chemotherapy, respectively. None of the patients who received anthracyline- (n = 13), vinorelbine- (n = 7), or cyclophosphamide-based (n = 18) chemotherapy responded, whereas 3 (17.6%) of 17 patients who received taxane-based chemotherapy exhibited a partial response. Tumor response to systemic chemotherapy remains generally poor for MCB patients. Taxanes may have modest activity, but need to be validated in further studies.
Collapse
Affiliation(s)
- I C Chen
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
| | | | | | | | | | | | | | | |
Collapse
|
9
|
Kuo WH, Chen HL, Hsiao CK, Chuang EY, Chang KJ. Abstract P6-04-03: Unique Recurrent Signature and Signaling Pathway of Asian Triple Negative Breast Cancer. Cancer Res 2010. [DOI: 10.1158/0008-5472.sabcs10-p6-04-03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Triple-negative (TN) breast cancer, a lack of understanding of the driving oncogenic mechanisms and thus therapeutic targets has left this an understudied ‘Cinderella’ in breast cancer phase III trials. No publication has been addressed on recurrent signature and pathway signaling of Asia TN breast cancer. The gene expression difference between Eastern and Western breast cancer is also unknown.
Material and Methods: 185 represent breast cancer cases including 43 Luminal A, 31 Luminal B, 35 Her-2 type, 51 TN and remaining 25 unclassified were selected from our tissue bank. Using Agilent microarray chip, we explored gene expression profile of these patients. For direct western and eastern comparison, 195 Caucasian breast cancer gene expression profile using the same Agilent platform were downloaded wedsite. In TN breast cancers, excluding 3 cases with stage IV disease at diagnosis, 11 patients developed distant recurrence during follow up. For these 48 patients, recurrent model was established by two step Cox proportional hazard regression: in first step, 35 candidate recurrent genes were selected from 20173 genes with significant level less than 0.0005. Then, we randomly choose 4 genes from the 35 candidate genes to construct recurrent model to avoid overfitting. TN related signaling pathways were discovered using Ingenuity Pathway Analysis(IPA) and GSEA(Gene Set Enrichment Analysis).
Results: Using non-supervised analysis, we found the eastern and western breast cancers have their own TN cancer clustering phenomenon, obviously in a different cluster.
This represented the eastern and western breast cancer have fundamental differences. The model including PKRAG3, MORC2, GRB7, FAM43A showed the best recurrence prediction power in 52360 combination models(R Square 0.71). This model was cross-validated by Vector machine(SVM) with leave one out setting. The overall accuracy was 87.5%. The sensitivity and specificity were 72.7% and 91.9%. This model was failed to predict recurrence in Luminal or Her-2 Molecular type. With IPA, we found 9 TN related pathway. The top two were cAMP-mediated and Ephrin Receptor signaling. 10 pathways were found from GSEA. Nicotinate, Olfactory transduction and Axon guidance were on the top of the list. Further functional study is on going.
Discussion: This is the first study to compare the gene expression between eastern and western breast cancer on the same gene expression platform. The gene expression profile is fundamentally different between eastern and western TN breast cancers. This phenomenon infers different biological behavior and drug sensitivity may exist among different ethnic groups. We established recurrent prediction model unique for Taiwanese TN breast cancer by four genes with high accuracy. We can develop commercial recurrent kit after further clinical validation.
Figure available in online version.
Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P6-04-03.
Collapse
Affiliation(s)
- WH Kuo
- School of Medicine, National Taiwan University, Taipei, Taiwan; College of Public Health, National Taiwan University, Taipei, Taiwan; National Taiwan University, Taipei, Taiwan
| | - HL Chen
- School of Medicine, National Taiwan University, Taipei, Taiwan; College of Public Health, National Taiwan University, Taipei, Taiwan; National Taiwan University, Taipei, Taiwan
| | - CK Hsiao
- School of Medicine, National Taiwan University, Taipei, Taiwan; College of Public Health, National Taiwan University, Taipei, Taiwan; National Taiwan University, Taipei, Taiwan
| | - EY Chuang
- School of Medicine, National Taiwan University, Taipei, Taiwan; College of Public Health, National Taiwan University, Taipei, Taiwan; National Taiwan University, Taipei, Taiwan
| | - KJ. Chang
- School of Medicine, National Taiwan University, Taipei, Taiwan; College of Public Health, National Taiwan University, Taipei, Taiwan; National Taiwan University, Taipei, Taiwan
| |
Collapse
|
10
|
Rapacz J, Hasler-Rapacz J, Kuo WH, Li D. Immunogenetic polymorphism of lipoproteins in swine. 1. Four additional serum beta-lipoprotein allotypes (Lpp2, Lpp4, Lpp5 and Lpp15) in the Lpp system. Anim Blood Groups Biochem Genet 2009; 7:157-77. [PMID: 188357 DOI: 10.1111/j.1365-2052.1976.tb01391.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Four additional swine serum lipoprotein allotypes are described. Specific anti-allotype reagents were obtained from alloimmune precipitating sera produced in lipoprotein-defined-type recipients immunized with normal sera and subsequently with lipoprotein fractions. Identification studies indicate that the four serologically defined low-density lipoprotein (LDL) variants, designated Lpp2, Lpp4, Lpp5 and Lpp15, are members of a previously described Lpp system. The individual specificities, Lpp2, Lpp4 and Lpp5, are determined by three co-dominant autosomal genes, Lpp2, Lpp4 and Lpp5, respectively, whereas the common specificity, Lpp15, is controlled by a complex of genetic information of the Lpp2 and Lpp4 genes, and by the two previously described alleles, Lpp1 and Lpp3; Lpp15 occurs on the same molecule with respective individual specificity. The Lpp5 and Lpp15 antigens behave as a pair of alternative allotypic specificities. The double immunodiffusion test in agar was employed to demonstrate independent phenotypic expression of each allelic gene in the Lpp heterozygous animals, for the analysis of the immune sera, and for lipoprotein testing of 3305 sera. Marked differences in gene frequencies were found between the swine breeds tested. As a result of characteristic frequencies, only nine of 15 possible Lpp genotypes were found in the breeding herds tested; the remaining six genotypes were obtained from testcross matings.
Collapse
|
11
|
Lien HC, Hsiao YH, Lin YS, Yao YT, Juan HF, Kuo WH, Hung MC, Chang KJ, Hsieh FJ. Molecular signatures of metaplastic carcinoma of the breast by large-scale transcriptional profiling: identification of genes potentially related to epithelial-mesenchymal transition. Oncogene 2007; 26:7859-71. [PMID: 17603561 DOI: 10.1038/sj.onc.1210593] [Citation(s) in RCA: 155] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metaplastic carcinoma of the breast (MCB) is a poorly understood subtype of breast cancer. It is generally characterized by the coexistence of ductal carcinomatous and transdifferentiated sarcomatous components, but the underlying molecular alterations, possibly related to epithelial-mesenchymal transition (EMT), remain elusive. We performed transcriptional profiling using half-a-genome oligonucleotide microarrays to elucidate genetic profiles of MCBs and their differences to those of ductal carcinoma of breasts (DCBs) using discarded specimens of four MCBs and 34 DCBs. Unsupervised clustering disclosed distinctive expression profiles between MCBs and DCBs. Supervised analysis identified gene signatures discriminating MCBs from DCBs and between MCB subclasses. Notably, many of the discriminator genes were associated with downregulation of epithelial phenotypes and with synthesis, remodeling and adhesion of extracellular matrix, with some of them have known or inferred roles related to EMT. Importantly, several of the discriminator genes were upregulated in a mutant Snail-transfected MCF7 cell known to exhibit features of EMT, thereby indicating a crucial role for EMT in the pathogenesis of MCBs. Finally, the identification of SPARC and vimentin as poor prognostic factors reinforced the role of EMT in cancer progression. These data advance our understanding of MCB and offer clues to the molecular alterations underlying EMT.
Collapse
Affiliation(s)
- H C Lien
- Department of Pathology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Abstract
Early studies of the inhibitor of growth 1 ( ING1) gene, the founding member of the ING tumor suppressor family, demonstrated that this gene plays an important role in apoptosis and cellular senescence. Four other related genes have since been identified and found to be involved in various biological activities, including cell cycle arrest, regulation of gene transcription, DNA repair and apoptosis. The biochemical functions of ING proteins as histone acetyltransferases and histone deacetylase co-factors ties this new tumor suppressor family to the regulation of transcription, cell cycle check-points, DNA repair and apoptosis. This review is aimed at summarizing the known biological functions of the ING tumor suppressors and the signalling pathways that they involve.
Collapse
Affiliation(s)
- E I Campos
- Department of Medicine, Division of Dermatology, University of British Columbia, V6H 3Z6, Vancouver, British Columbia, Canada
| | | | | | | |
Collapse
|
13
|
|
14
|
Abstract
BACKGROUND Utilizing a prospectively designed community sample, we set out to estimate the rate of newly-incident suicidal ideation and attempts (non-fatal suicide behaviour) in a community sample, to evaluate antecedent sociodemographic characteristics and psychiatric disorders, and to assess use of mental health services in relation to non-fatal suicide behaviour. METHOD Prospectively-gathered data was utilized from 3481 continuing participants in the 13-year follow-up of the Baltimore sample of the NIMH Epidemiologic Catchment Area survey interviewed in 1981, 1982 and 1993/6. RESULTS The incidence of suicide attempts was estimated at 148.8 per 100,000 person-years and ideation at 419.9 per 100,000 person-years. Persons in the youngest age group, in the lowest socioeconomic status, and previously married persons were at increased risk for non-fatal suicide behaviour during the follow-up interval. Persons who reported suicidal ideation at baseline were more likely to report having attempted suicide at follow-up (RR = 6.09, 95% CI 2.58-14.36). Psychiatric disorders, especially depression and substance abuse, were associated with new-onset of non-fatal suicidal behaviour. While persons who reported newly-incident suicidal behaviour were more likely to report use of mental health services, few said that suicidal ideation or attempts were the reason for the visits. CONCLUSIONS Suicidal ideation is a common and important antecedent to suicide attempts and deserves more attention in community and general medical settings.
Collapse
Affiliation(s)
- W H Kuo
- Department of Mental Hygiene, School of Hygiene and Public Health, Johns Hopkins University, Baltimore, MD, USA
| | | | | |
Collapse
|
15
|
Kuo WH, Chou FP, Lu SC, Chu SC, Hsieh YS. Significant differences in serum activities of matrix metalloproteinase-2 and -9 between HCV- and HBV-infected patients and carriers. Clin Chim Acta 2000; 294:157-68. [PMID: 10727681 DOI: 10.1016/s0009-8981(00)00182-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
To examine the possible involvement of MMP-9 and -2 in the development of liver diseases caused by HCV or HBV infection, serum activities of both enzymes were studied by zymograph. Eight groups of subjects (60 for each) were examined in the study: healthy control, patients with hepatoma, liver cirrhosis, chronic hepatitis B or chronic hepatitis C, and carriers positive for HBsAg, both HBsAg and HBeAg, or anti-HCV. The results showed significant changes in the MMP-9 and -2 activities in the carriers. The presence of HBeAg was accompanied by a highest activity of MMP-2 and an inversely correlated (r=-0.578, P=<0.001), lowest activity of MMP-9 among all groups. For those with active liver diseases, MMPs activities were fluctuated at each stage of pathological symptoms. Chronic hepatitis B and C patients had significant different serum MMP-2 and -9 activities. These findings imply an influence on the balance of MMPs system by the existence of virus that might influence the following progression of liver disease, and a distinction between the pathological mechanisms of HCV and HBV. Since the serum MMPs activities were significantly varied between each stage of liver disease, an individual profile of these parameters might serve as an easy accessing serum marker to monitor the progression of liver disease.
Collapse
Affiliation(s)
- W H Kuo
- Division of Gastroenterology, Department of Internal Medicine, Armed-Force Taichung General Hospital, Taichung, Taiwan
| | | | | | | | | |
Collapse
|
16
|
Pasricha PJ, Hill S, Wadwa KS, Gislason GT, Okolo PI, Magee CA, Canto MI, Kuo WH, Baust JG, Kalloo AN. Endoscopic cryotherapy: experimental results and first clinical use. Gastrointest Endosc 1999; 49:627-31. [PMID: 10228263 DOI: 10.1016/s0016-5107(99)70393-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
BACKGROUND Cryotherapy or the application of extreme cold has many potential applications in gastroenterology including tissue destruction and hemostasis but until now its development has been prevented by the lack of a delivery device suitable for use through the endoscope. We report here our experience with prototype devices using both liquid nitrogen driven by a cryosurgical system and cryogenic refrigerants (nitrous oxide and carbon dioxide) at or near ambient temperature. METHODS Cryotherapy was applied to the distal esophageal mucosa of dogs via a flexible catheter passed through an upper endoscope. In other dogs, cryotherapy was used for hemostasis in a bleeding ulcer model. The procedure was also used for palliation in a 58-year-old man with unresectable adenocarcinoma of the stomach with pyloric channel obstruction. RESULTS Freezing of the superficial mucosa was nearly instantaneous. All dogs survived the procedure and appeared to thrive. Histologic evaluation revealed significant necrosis of the superficial epithelial layer accompanied by a fibrinocellular infiltrate on the surface. These markers of acute injury subside by the fourth to sixth day and are replaced by regenerating epithelium, a process that is virtually complete by day 10. In the hemostasis experiments, bleeding ceased immediately after cryospraying of the lesions but resumed on thawing in most cases. Application of cryotherapy in the patient resulted in reduction of the pyloric mass with no immediately apparent adverse effects. CONCLUSIONS These data, although preliminary, demonstrate the feasibility of endoscopic cryotherapy using a simple hand-held device. This device has broad potential for use in gastroenterology including ablation of superficial epithelium, debulking of large tumors and hemostasis.
Collapse
Affiliation(s)
- P J Pasricha
- Division of Gastroenterology and Hepatology, University of Texas Medical Branch, Galveston, Texas 77555-0764, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Abstract
Gastroparesis is a common debilitating complication in many diabetic patients. While several drugs are available for gastroparesis, many patients are not adequately treated. Many patients do not respond to available drugs or appear to develop tachyphylaxis after an initial response. New agents are needed. Erythromycin is a macrolide antibiotic that accelerates gastric emptying through interaction with motilin receptors. Many antibiotics, like erythromycin itself, have significant gastrointestinal side effects. We investigated the ability of cephalosporin antibiotics to alter gastric emptying in mice by employing phenol red spectrophotometry to monitor gastric emptying. Our results indicate that several cephalosporin antibiotics, particularly cefazolin, accelerate gastric emptying. In some cases these drugs appear more efficacious than either erythromycin or metoclopramide. At very high doses, many drugs, including erythromycin, appear to delay gastric emptying. We hypothesize that the gastrointestinal side effects of nausea and vomiting may result from delayed gastric emptying occurring at high doses while lower doses are prokinetic in the stomach.
Collapse
Affiliation(s)
- W H Kuo
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | | | | |
Collapse
|
18
|
Kuo WH, Kalloo AN. Reflux strictures of the esophagus. Gastrointest Endosc Clin N Am 1998; 8:273-81. [PMID: 9583006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Gastroesophageal reflux disease (GERD) is the most common cause of esophageal strictures, accounting for approximately 70% of all cases. Reflux strictures of the esophagus are serious complications of GERD and are associated with a high relapse rate. Goals of long-term management include the relief of dysphagia, prevention of stricture recurrence, and avoidance of complications with safe, cost-effective therapy. Despite recent advances in knowledge about GERD, reflux stricture still remains a relatively common and challenging clinical problem.
Collapse
Affiliation(s)
- W H Kuo
- Division of Gastroenterology, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | | |
Collapse
|
19
|
Kuo WH, Lee WJ, Chen CN, Yuan RH, Yu SC. Laparoscopic subtotal gastrectomy with lymphadenectomy in a patient with early gastric cancer. J Formos Med Assoc 1998; 97:127-30. [PMID: 9509849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Laparoscopic surgery is rapidly gaining in popularity among general surgeons. It is not widely used to treat abdominal malignancies because of technical difficulties and the fear of peritoneal dissemination. We describe the use of laparoscopic surgery to treat early gastric cancer. A 66-year-old man was diagnosed with early gastric adenocarcinoma by endoscopic ultrasonography and biopsy. Subtotal gastrectomy along with removal of the perigastric (D1) and selective extraperigastric lymph nodes over the celiac trunk was accomplished laparoscopically, through five punctures and a minilaparotomy. The patient's convalescence was uneventful. Bowel sounds were heard on postoperative day 1. On postoperative day 3, he passed flatus. The patient was started on a clear liquid diet on postoperative day 5. There was neither leakage nor obstruction after oral intake. He was discharged on postoperative day 11. No local recurrence or distant metastasis was found during 16 months' follow-up. This is the first report of successful laparoscopic resection of early gastric cancer with lymph node dissection in Taiwan.
Collapse
Affiliation(s)
- W H Kuo
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | | | | | | | | |
Collapse
|
20
|
Kuo WH, Pasricha PJ, Kalloo AN. The role of sphincter of Oddi manometry in the diagnosis and therapy of pancreatic disease. Gastrointest Endosc Clin N Am 1998; 8:79-85. [PMID: 9405752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Endoscopic manometry of the sphincter of Oddi (SO) is now an accepted technique in the diagnosis and therapy of biliary disease. Its role in the evaluation of pancreatic sphincter function for pancreatic diseases, however, is evolving. There are now preliminary data to suggest that pancreatic SO manometry may identify a subgroup of patients with pancreatic sphincter dysfunction that may benefit from endoscopic therapy. Further prospective clinical trials are sorely needed to evaluate the response of endoscopic therapy based on pancreatic SO basal pressure or pancreatic ductal pressure.
Collapse
Affiliation(s)
- W H Kuo
- Division of Gastroenterology, The Johns Hopkins Hospital, Baltimore, Maryland 21287, USA
| | | | | |
Collapse
|
21
|
Rapacz J, Hasler-Rapacz J, Kuo WH. Immunogenetic polymorphism of lipoproteins in swine: genetic, immunological and physiochemical characterization of the two allotypes Lpr1 and Lpr2. Genetics 1986; 113:985-1007. [PMID: 3091450 PMCID: PMC1202922 DOI: 10.1093/genetics/113.4.985] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Results of immunogenetic, immunochemical and physicochemical investigations on two serum allotypes of swine are reported. The allotypes, designated Lpr1 and Lpr2, have been identified by specific alloprecipitins in agar gel. Genetic studies indicate that the allotypes are specified by two codominant autosomal allelic genes, Lpr1 and Lpr2. All pigs 3 months of age or older were classified as belonging to one of three phenotypes, Lpr1, Lpr2 or Lpr1,2, each corresponding to one of three genotypes Lpr1/1, Lpr2/2 or Lpr1/2, respectively. The Lpr1 gene was absent or was found at low frequency in the breeds tested. The allotypes were found to occur in two physicochemical forms; in association with chylomicrons and very low density lipoproteins (VLDL) and, primarily, as a Lpr multimer free of the major lipoproteins showing very high density (VHD), d greater than 1.21 g/ml, and MW +/- 190,000. Gel-electrophoretic mobility for VHD-Lpr is different for each of the three Lpr genotypes residing in gamma-fast and beta-slow regions, but is identical for VLD-Lpr in which Lpr was found complexed with apo-B, migrating as VLDL in the alpha-2 slow (pre-beta) region. Serum levels of Lpr varied during the lifetime and between individuals and, especially, between sera of homozygous pigs being higher in Lpr1/1 than Lpr2/2. A linear relationship for Lpr1 and an atypical, inverse relationship for Lpr2 have been observed between the gene dosage, heterozygous vs. homozygous, and the Lpr serum level.
Collapse
|
22
|
Abstract
The dearth of population-based studies and epidemiological investigations on the mental health problems of Asian-Americans, especially since the change in the immigration laws in 1965, has led to contradictory speculations about the prevalence rates of mental illness and the general mental health status among Asian-Americans, as opposed to other segments of the population. We administered the Center for Epidemiologic Studies Depression (CES-D) scale to 499 samples drawn from a Northwestern coastal city in order to make an initial assessment of the amount of depression experienced by Asian-Americans. The investigation compared the Asian-Americans' CES-D scores with those of whites and other minority groups, examined the scale's patterns of factor loading by ethnicity, and discovered that, even with statistical controls, there exists a distinction among the individual groups of Chinese, Filipinos, Japanese, and Koreans with respect to their score averages of depressive symptoms.
Collapse
|
23
|
Lee DM, Valente AJ, Kuo WH, Maeda H. Properties of apolipoprotein B in urea and in aqueous buffers. The use of glutathione and nitrogen in its solubilization. Biochim Biophys Acta 1981; 666:133-46. [PMID: 6794632 DOI: 10.1016/0005-2760(81)90099-0] [Citation(s) in RCA: 94] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|
24
|
Abstract
A sample of Chinese-Americans in the District of Columbia was drawn to examine the relationship between the locus of control, the personality factor, and two indices of symptoms of psychological distress. The findings indicated that the externals scored higher on symptomatology than did the internals. A multivariate analysis further compared the predictive utility of locus of control with other determinants of psychiatric symptoms, i.e., sex, marital status, SES, kinship and friendship tie, and amount of life change. The evidence showed that locus of control is an important determinant of Chinese-Americans' symptomatology. It accounted for a greater proportion of the variance in the two indices of psychological distress than did the other independent variables.
Collapse
|