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Transcriptomic analysis reveals that NIBAN1 overexpression is associated with BRAF^(V600E)mutation and increases the aggressiveness of thyroid cancer

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Genes & Diseases 2024年第4期11卷 16-19页

作者： Paula Diana Thaise Nayane Ribeiro Carneiro Janete Maria Cerutti Reginaldo Massanobu Kuroshu Gianna Maria Griz Carvalheira Division of genetics Department of Morphology and GeneticsEscola Paulista de MedicinaUniversidade Federal de Sao PauloSao PauloRua Botucatu740Edificio Leitaoda Cunha1AndarSao PauloSP04023900Brazil genetic bases of thyroid tumors laboratory Division of GeneticsDepartment of Morphology and GeneticsEscola Paulista de MedicinaUniversidade Federal de Sao PauloPedro de Toledo 66911AndarSao PauloSP 04039-032Brazil Institute of Science and Technology Universidade Federal de Sao PauloAv Cesare Mansueto Giulio Lattes1201Eugenio deMelloSaoJose dos CamposSP12247-014Brazil

NIBAN1 overexpression has been reported in a widerange of thyroid carcinoma subtypes,and in other cancers,while it is not expressed in thyroid benign lesions and normal thy-roid.1-3 However,the mechanism associated with its expression and prognostic value remains *** this study,six independent cohorts were enrolled,in which NIBAN1 expression was evaluated.A total of 583patients with thyroid tumors,326 patients with skin cancers,293 patients with colorectal carcinoma,and 189 patients with lung carcinoma were analyzed.

关键词： BRAF lesions BAN

cDNA clone and expression analysis of a-Tropomyosin during Japanese flounder （Parafichthys ofivaceus） metamorphosis

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Zoological Research 2014年第4期35卷 307-312页

作者： Hong-Mei ZHANG Yan-Fang SU Zhi-Yi SHI Yuan-Shuai FU Key laboratory of Freshwater Aquatic genetic Resources Shanghai Ocean UniversityMinistry of Agriculture

Tropomyosin （TM） plays a critical role in skeletal and cardiac muscle development and function. To assess the fimctional significance of a-TM in Japanese flounder （Paralichthys olivaceus） development and metamorphosis, cDNA from Japanese flounder was cloned and a-TM mRNA measured during development and metamorphosis. The full-length cDNA is 1 191 bp, including a 5＇- untranslated region of 114 bp, a Y-UTR of 222 bp, and an open reading frame of 855 bp encoding a polypeptide of 284 amino acids. Real-time quantitative PCR revealed that a-TM mRNA is initially expressed in unfertilized ovum, indicating the a-TM gene is maternal. Relatively low mRNA levels were observed in different embryonic stages. A higher level of a-TM mRNA was detected 3 days post hatching （dph）, while the highest level was measured at 29 dph （metamorphic climax） after which it declined towards the end of metamorphosis. The expression of a-TM mRNA was up-regulated in thyroid hormone-treated larvae at 36 dph, but there was no marked difference at other stages when compared to control animals. After thiourea treatment, the expression of a-TM mRNA declined slightly. These data provide basic information that can be utilized in further studies into the role of a-TM in P olivaceus development and metamorphosis.

关键词： Paralichthys olivaceus Cloning Expression a-Tropomyosin thyroid hormone

Shaping polyploid wheat for success:Origins,domestication,and the genetic improvement of agronomic traits

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Journal of Integrative Plant Biology 2022年第2期64卷 536-563页

作者： Jie Liu Yingyin Yao Mingming Xin Huiru Peng Zhongfu Ni Qixin Sun State Key laboratory for Agrobiotechnology Key Laboratory of Crop Heterosis and Utilizationthe Ministry of EducationKey Laboratory of Crop Genetic ImprovementNational Plant Gene Research CentreChina Agricultural UniversityBeijing100193 China

Bread wheat(Triticum aestivum L.,AABBDD,2 n=6 x=42),which accounts for most of the cultivated wheat crop worldwide,is a typical allohexaploid with a genome derived from three diploid wild *** wheat arose and evolved via two sequential allopolyploidization events and was further polished through multiple steps of ***,cultivated allohexaploid bread wheat has numerous advantageous traits,including adaptive plasticity,favorable yield traits,and extended end-use quality,which have enabled its cultivation well beyond the ranges of its tetraploid and diploid progenitors to become a global staple food *** the past decade,rapid advances in wheat genomic research have considerably accelerated our understanding of the bases for the shaping of complex agronomic traits in this polyploid ***,we summarize recent advances in characterizing major genetic factors underlying the origin,evolution,and improvement of polyploid *** end with a brief discussion of the future prospects for the design of gene cloning strategies and modern wheat breeding.

关键词： adaptation bread wheat domestication end-use quality photoperiod response polyploid semi-dwarfing breeding vernalization

Rice MtN3/Saliva/SWEET Family Genes and Their Homologs in Cellular Organisms

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Molecular Plant 2013年第3期6卷 665-674页

作者： Meng Yuan Shiping Wang National Key laboratory of Crop genetic Improvement National Center of Plant Gene Research (Wuhan) Huazhong Agricultural University Wuhan 430070 China

The MtN3/saliva/SWEET-type genes, existing either alone or in a family group, are found in diverse organisms, from monocellular protozoa to higher eukaryotes, indicating their importance in cellular organisms. These genes encode polytopic membrane proteins that feature an MtN3/saliva domain, also known as a PQ loop repeat, The rice MtN3/saliva/SWEET gene family consists of 21 members and is among the largest families in sequenced organisms. Accumulating data suggest that these genes are involved in multiple physiological processes, including reproductive development, senescence, environmental adaptation, and host-pathogen interaction, in different species. In rice, some members of the family, including Xa13/Os8N3/OsSWEET11, which is essential for reproductive development, are used by the pathogenic bacterium Xanthomonas oryzae pv. oryzae to invade its host. Emerging data have also revealed that at least some MtN3/saliva/SWEET-type proteins may regulate different physiological processes by facilitating ion transport via interaction with ion transporters or as sugar transporters. The accumulating knowledge about MtN3/saliva/SWEET- type genes will help to elucidate the molecular bases of their function in different organisms.

关键词： MtN3/saliva PQ loop repeat membrane protein SWEET transporter.

A Positive Correlation between Elevated Altitude and Frequency of Mutant Alleles at the EPAS1 and HBB Loci in Chinese Indigenous Dogs

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Journal of genetics and Genomics 2015年第4期42卷 173-177页

作者： Ruoxi Fan Fei Liu Hong Wu Shifang Wu Chunling Zhu Yan Li Guodong Wang Yaping Zhang laboratory for Conservation and Utilization of Bio-resources Yunnan University State Key laboratory of genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic AnimalsKunming Institute of ZoologyChinese Academy of Sciences

Hypoxia represents one of the most extreme environmental conditions for both human beings and animals living at high al- titudes （Zhao et al., 2009）. Over the past few years, great attention has been focused on the genetic bases of adaption to high-altitude environments （Bigham et al., 2010; Simonson et al., 2010）. The domestic dog （Canisfamiliaris） is the first animal that developed an intimate relationship with human beings. Dogs migrated with human beings and have adapted to variety of ecological niches （Savolainen et al., 2002）. Our previous research revealed parallel evolution and convergent evolution in the adaptation of dogs and humans to the high-altitude environment of the Tibetan plateau （Wang et al., 2013, 2014）, suggesting that exploring the adaption of domestic dogs to high-altitude hypoxia is an interesting and important question.

关键词： HBB PAS A Positive Correlation between Elevated Altitude and Frequency of Mutant Alleles at the EPAS1 and HBB Loci in Chinese Indigenous Dogs

Molecular Characterization and Expression Analysis of S1 self-incompatibility Locus-linked Pollen 3.15 Gene in Citrus reticulata

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Journal of Integrative Plant Biology 2013年第5期55卷 443-452页

作者： Hong Xia Miao Zi Xing Ye Yong Hua Qin Gui Bing Hu College of Horticulture South China Agricultural University State Key laboratory for Conservation and Utilization of Subtropical Agro-bioresources South China Agricultural University Key laboratory of Biology and genetic Improvement of Horticultural Crops-South China Ministry of Agriculture

Gametophytic self-incompatibility （GSI） is controlled by a highly polymorphic locus called the S-locus, which is an important factor that can result in seedless fruit in Citrus. The S 1 self-incompatibility locus-linked pollen 3.15 gene （S1-3.15） belongs to a type of S locus gene. The role of S1-3.15 in the SI reaction of Citrus has not yet been reported. In this study, full-length sequences of cDNA and DNA encoding the S1-3.15 gene, referred to as CrS1-3.15 , were isolated from ‘Wuzishatangju’ （Self-incompatibility, SI） and ‘Shatangju’ （Self-compatibility, SC） . The predicted amino acid sequences of CrS1-3.15 between ‘Wuzishatangju’ and ‘Shatangju’ differ by only three amino acids. Compared to ‘Wuzishatangju’, three bases were substituted in the genomic DNA of CrS1-3.15 from ‘Shatangju’. Southern blot results showed that one copy of CrS1-3.15 existed in the genomic DNA of both ‘Wuzishatangju’ and ‘Shatangju’. The expression level of the CrS1-3.15 gene in the ovaries of ‘Shatangju’ was approximately 60-fold higher than that in the ovaries of ‘Wuzishatangju’. When ‘Wuzishatangju’ was cross-pollinated, the expression of CrS1-3.15 was upregulated in the ovaries at 3d, and the highest expression levels were detected in the ovaries at 6d after cross-pollination of ‘Wuzishatangju’ × ‘Shatangju’. To obtain the CrS1-3.15 protein, the full-length cDNA of CrS1-3.15 genes from ‘Wuzishatangju’ and ‘Shatangju’ was successfully expressed in Pichia pastoris. Pollen germination frequency of ‘Wuzishatangju’ was inhibited significantly with increasing CrS1-3.15 protein concentrations from SI ‘Wuzishatangju’.

关键词： Citrus reticulata expression analysis pollen germination S1 self-incompatibility locus-linked pollen 3.15 gene self-compatibility self-incompatibility.

Dissection of heterotic loci for grain yield using interconnected chromosome segment substitution lines in rice

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The Crop Journal 2022年第2期10卷 323-331页

作者： Chaopu Zhang Yongjian Sun Dianwen Wang Wenqiang Sun Yuye Yu Zhongli Hu Sibin Yu National Key laboratory of Crop genetic Improvement College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan 430070HubeiChina State Key laboratory of Hybrid Rice College of Life ScienceWuhan UniversityWuhan 430072HubeiChina

Heterosis contributes greatly to crop production, but the genetic basis of heterosis is not fully *** identify heterotic loci(HLs) for grain yield, 12 yield traits were evaluated in four rice(Oryza sativa L.)mapping populations: one parental population of chromosome segment substitution lines derived from a cross between the japonica cultivar Nipponbare and indica cultivar 9311 and three connected test populations in either a homozygous 9311 genetic background or a heterozygous background. A total of 390 HLs were detected for the measured traits in two environments. The genetic bases of heterosis differed between the backcross and testcross populations. At least 10 HLs were confirmed in F1 hybrids between9311 and near-isogenic lines, each of which carried a heterotic locus of interest in the same 9311 background. All 10 showed overdominant or dominant effects on grain yield and yield components. Among them, three were verified as being associated with yield heterosis and colocalized in the same regions as those containing previously reported heterosis-associated genes. Five HLs were identified to be promising candidate loci that could be used to achieve more than 15% yield heterosis in several commercial rice hybrids. These findings suggest the potential of indica or japonica introgression for increasing yield in hybrid rice breeding programs.

关键词： Rice Heterotic loci Grain yield Overdominance Commercial hybrids

PMN-MDSCs modulated by CCL20 from cancer cells promoted breast cancer cell stemness through CXCL2-CXCR2 pathway

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Signal Transduction and Targeted Therapy 2023年第4期8卷 1828-1841页

作者： Rui Zhang Mengxue Dong Juchuanli Tu Fengkai Li Qiaodan Deng Jiahui Xu Xueyan He Jiajun Ding Jie Xia Dandan Sheng Zhaoxia Chang Wei Ma Haonan Dong Yi Zhang Lixing Zhang Lu Zhang Suling Liu Fudan University Shanghai Cancer Center&Institutes of Biomedical Sciences State Key Laboratory of Genetic EngineeringCancer InstitutesKey Laboratory of Breast Cancer in ShanghaiThe Shanghai Key Laboratory of Medical EpigeneticsShanghai Key Laboratory of Radiation OncologyThe International Co-laboratory of Medical Epigenetics and MetabolismMinistry of Science and TechnologyShanghai Medical CollegeFudan UniversityShanghai 200032China Breast Surgery Obstetrics and Gynecology Hospital of Fudan UniversityShanghaiChina Department of Breast and thyroid Surgery Southwest Hospitalthe First Affiliated Hospital of the Army Military Medical UniversityChongqing 400038China Jiangsu Key Lab of Cancer Biomarkers Prevention and TreatmentCollaborative Innovation Center for Cancer MedicineNanjing Medical UniversityNanjing 211166China

Our previous studies have showed that C-C motif chemokine ligand 20(CCL20)advanced tumor progression and enhanced the chemoresistance of cancer cells by positively regulating breast cancer stem cell(BCSC)***,it is unclear whether CCL20 affects breast cancer progression by remodeling the tumor microenvironment(TME).Here,we observed that polymorphonuclear myeloid-derived suppressor cells(PMN-MDSCs)were remarkably enriched in TME of CCL20-overexpressing cancer cell orthotopic allograft ***,CCL20 activated the differentiation of granulocyte-monocyte progenitors(GMPs)via its receptor C-C motif chemokine receptor 6(CCR6)leading to the PMN-MDSC ***-MDSCs from CCL20-overexpressing cell orthotopic allograft tumors(CCL20-modulated PMN-MDSCs)secreted amounts of C-X-C motif chemokine ligand 2(CXCL2)and increased ALDH+BCSCs via activating CXCR2/NOTCH1/HEY1 signaling ***,C-X-C motif chemokine receptor 2(CXCR2)antagonist SB225002 enhanced the docetaxel(DTX)effects on tumor growth by decreasing BCSCs in CCL20high-expressing *** findings elucidated how CCL20 modulated the TME to promote cancer development,indicating a new therapeutic strategy by interfering with the interaction between PMN-MDSCs and BCSCs in breast cancer,especially in CCL20high-expressing breast cancer.

关键词： CCL20 CXCR2 breast

Genome assembly of the maize inbred line A188 provides a new reference genome for functional genomics

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The Crop Journal 2022年第1期10卷 47-55页

作者： Fei Ge Jingtao Qu Peng Liu Lang Pan Chaoying Zou Guangsheng Yuan Cong Yang Guangtang Pan Jianwei Huang Langlang Ma Yaou Shen Key laboratory of Biology and genetic Improvement of Maize in Southwest Region Maize Research InstituteSichuan Agricultural UniversityChengdu 611130SichuanChina Berry Genomics Corporation Beijing 100015China

The current assembled maize genomes cannot represent the broad genetic diversity of maize *** more genome sequences is critical for constructing a pan-genome and elucidating the linkage between genotype and phenotype in *** we describe the genome sequence and annotation of A188,a maize inbred line with high phenotypic variation relative to other lines,acquired by single-molecule sequencing and optical genome *** assembled a 2210-Mb genome with a scaffold N50 size of 11.61 million bases(Mb),compared to 9.73 Mb for B73 and 10.2 Mb for *** on the B73_Ref Gen_V4 genome,295 scaffolds(2084.35 Mb,94.30%of the final genome assembly)were anchored and oriented on ten *** analysis revealed that~30%of the predicted A188 genes showed large structural divergence from B73,Mo17,and W22 genomes,which causes high protein divergence and may lead to phenotypic variation among the four inbred *** a line with high embryonic callus(EC)induction capacity,A188 provides a convenient tool for elucidating the molecular mechanism underlying the formation of EC in *** our new A188 genome with previously reported QTL and RNA sequencing data revealed eight genes with large structural variation and two differentially expressed genes playing potential roles in maize EC induction.

关键词： Maize Embryonic callus A188 Genome assembly Single-molecule sequencing