ABSTRACT
Neoadjuvant chemotherapy is a common treatment for patients with gastric cancer. Although its benefits have been demonstrated, neoadjuvant chemotherapy is underutilized in gastric cancer management, because of the lack of biomarkers for patient selection and a limited understanding of resistance mechanisms. Here, we performed whole-genome, whole-exome, and RNA sequencing on 84 clinical samples (including matched pre- and posttreatment tumors) from 35 patients whose responses to neoadjuvant chemotherapy were rigorously defined. We observed increased microsatellite instability and mutation burden in nonresponse tumors. Through comparisons of response versus nonresponse tumors and pre- versus posttreatment samples, we found that C10orf71 mutations were associated with treatment resistance, which was supported by drug response data and potentially through inhibition of cell cycle, and that MYC amplification correlated with treatment sensitivity, whereas MDM2 amplification showed the opposite pattern. Neoadjuvant chemotherapy also reshapes tumor-immune signaling and microenvironment. Our study provides a critical basis for developing precision neoadjuvant regimens.
Subject(s)
Biomarkers, Tumor/genetics , Carrier Proteins/genetics , Neoadjuvant Therapy , Proto-Oncogene Proteins c-mdm2/genetics , Proto-Oncogene Proteins c-myc/genetics , Stomach Neoplasms , Female , Humans , Intercellular Signaling Peptides and Proteins , Male , Middle Aged , RNA-Seq , Stomach Neoplasms/genetics , Stomach Neoplasms/pathology , Stomach Neoplasms/therapy , Whole Genome SequencingABSTRACT
The developmental plasticity of leaf size and shape is important for leaf function and plant survival. However, the mechanisms by which plants form diverse leaves in response to environmental conditions are not well understood. Here, we identified TIE1-ASSOCIATED RING-TYPE E3 LIGASE1 (TEAR1) and found that it regulates leaf development by promoting the degradation of TCP INTERACTOR-CONTAINING EAR MOTIF PROTEIN1 (TIE1), an important repressor of CINCINNATA (CIN)-like TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors, which are key for leaf development. TEAR1 contains a typical C3H2C3-type RING domain and has E3 ligase activity. We show that TEAR1 interacts with the TCP repressor TIE1, which is ubiquitinated in vivo and degraded by the 26S proteasome system. We demonstrate that TEAR1 is colocalized with TIE1 in nuclei and negatively regulates TIE1 protein levels. Overexpression of TEAR1 rescued leaf defects caused by TIE1 overexpression, whereas disruption of TEAR1 resulted in leaf phenotypes resembling those caused by TIE1 overexpression or TCP dysfunction. Deficiency in TEAR partially rescued the leaf defects of TCP4 overexpression line and enhanced the wavy leaf phenotypes of jaw-5D We propose that TEAR1 positively regulates CIN-like TCP activity to promote leaf development by mediating the degradation of the TCP repressor TIE1.
Subject(s)
Arabidopsis Proteins/physiology , Arabidopsis/growth & development , Repressor Proteins/genetics , Ubiquitin-Protein Ligases/physiology , Arabidopsis/genetics , Arabidopsis/metabolism , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Cloning, Molecular , Gene Expression Regulation, Plant , Meristem/metabolism , Models, Genetic , Plant Leaves/genetics , Plant Leaves/growth & development , Plant Leaves/metabolism , Repressor Proteins/metabolism , Ubiquitin-Protein Ligases/genetics , Ubiquitin-Protein Ligases/metabolismABSTRACT
Plant shoot branching is pivotal for developmental plasticity and crop yield. The formation of branch meristems is regulated by several key transcription factors including REGULATOR OF AXILLARY MERISTEMS1 (RAX1), RAX2, and RAX3. However, the regulatory network of shoot branching is still largely unknown. Here, we report the identification of EXCESSIVE BRANCHES1 (EXB1), which affects axillary meristem (AM) initiation and bud activity. Overexpression of EXB1 in the gain-of-function mutant exb1-D leads to severe bushy and dwarf phenotypes, which result from excessive AM initiation and elevated bud activities. EXB1 encodes the WRKY transcription factor WRKY71, which has demonstrated transactivation activities. Disruption of WRKY71/EXB1 by chimeric repressor silencing technology leads to fewer branches, indicating that EXB1 plays important roles in the control of shoot branching. We demonstrate that EXB1 controls AM initiation by positively regulating the transcription of RAX1, RAX2, and RAX3. Disruption of the RAX genes partially rescues the branching phenotype caused by EXB1 overexpression. We further show that EXB1 also regulates auxin homeostasis in control of shoot branching. Our data demonstrate that EXB1 plays pivotal roles in shoot branching by regulating both transcription of RAX genes and auxin pathways.
Subject(s)
Arabidopsis Proteins/metabolism , Arabidopsis/genetics , Arabidopsis/metabolism , Gene Expression Regulation, Plant , Genes, Plant , Plant Shoots/growth & development , Transcription Factors/metabolism , Arabidopsis Proteins/genetics , Cell Nucleus/metabolism , Gene Silencing , Homeostasis , Indoleacetic Acids/metabolism , Meristem/metabolism , Models, Biological , Mutation/genetics , Phenotype , Plant Leaves/metabolism , Plant Shoots/genetics , Plant Shoots/ultrastructure , Repressor Proteins/metabolism , Transcription Factors/genetics , Transcriptional Activation/geneticsABSTRACT
Ovules are essential for plant reproduction and develop into seeds after fertilization. Sporocyteless/nozzle (SPL/NZZ) has been known for more than 15 years as an essential factor for ovule development in Arabidopsis, but the biochemical nature of SPL function has remained unsolved. Here, we demonstrate that SPL functions as an adaptor-like transcriptional repressor. We show that SPL recruits topless/topless-related (TPL/TPR) co-repressors to inhibit the Cincinnata (CIN)-like Teosinte branched1/cycloidea/PCF (TCP) transcription factors. We reveal that SPL uses its EAR motif at the C-terminal end to recruit TPL/TPRs and its N-terminal part to bind and inhibit the TCPs. We demonstrate that either disruption of TPL/TPRs or overexpression of TCPs partially phenocopies the defects of megasporogenesis in spl. Moreover, disruption of TCPs causes phenotypes that resemble spl-D gain-of-function mutants. These results define the action mechanism for SPL, which along with TPL/TPRs controls ovule development by repressing the activities of key transcription factors. Our findings suggest that a similar gene repression strategy is employed by both plants and fungi to control sporogenesis.
Subject(s)
Arabidopsis Proteins/metabolism , Arabidopsis/growth & development , Gene Expression Regulation, Plant , Nuclear Proteins/metabolism , Ovule/growth & development , Repressor Proteins/metabolism , Amino Acid Sequence , Arabidopsis/genetics , Arabidopsis/metabolism , Arabidopsis Proteins/chemistry , Arabidopsis Proteins/genetics , Molecular Sequence Data , Nuclear Pore Complex Proteins/genetics , Nuclear Pore Complex Proteins/metabolism , Nuclear Proteins/chemistry , Nuclear Proteins/genetics , Ovule/genetics , Ovule/metabolism , Protein Interaction Maps , Repressor Proteins/chemistry , Repressor Proteins/geneticsABSTRACT
Leaf size and shape are mainly determined by coordinated cell division and differentiation in lamina. The CINCINNATA (CIN)-like TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors are key regulators of leaf development. However, the mechanisms that control TCP activities during leaf development are largely unknown. We identified the TCP Interactor containing EAR motif protein1 (TIE1), a novel transcriptional repressor, as a major modulator of TCP activities during leaf development. Overexpression of TIE1 leads to hyponastic and serrated leaves, whereas disruption of TIE1 causes epinastic leaves. TIE1 is expressed in young leaves and encodes a transcriptional repressor containing a C-terminal EAR motif, which mediates interactions with the TOPLESS (TPL)/TOPLESS-RELATED (TPR) corepressors. In addition, TIE1 physically interacts with CIN-like TCPs. We propose that TIE1 regulates leaf size and morphology by inhibiting the activities of TCPs through recruiting the TPL/TPR corepressors to form a tertiary complex at early stages of leaf development.
Subject(s)
Arabidopsis Proteins/metabolism , Co-Repressor Proteins/metabolism , Plant Leaves/growth & development , Repressor Proteins/metabolism , Transcription Factors/metabolism , Amino Acid Motifs , Amino Acid Sequence , Arabidopsis/genetics , Arabidopsis/growth & development , Arabidopsis/metabolism , Arabidopsis Proteins/genetics , Co-Repressor Proteins/genetics , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Gene Expression Regulation, Plant , Molecular Sequence Data , Mutation , Nuclear Pore Complex Proteins , Plant Leaves/cytology , Plant Leaves/genetics , Plant Proteins/genetics , Plant Proteins/metabolism , Plants, Genetically Modified , Protein Interaction Mapping/methods , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Repressor Proteins/genetics , Transcription Factors/geneticsABSTRACT
Map-based cloning has been widely used to identify genes responsible for mutant phenotypes in Arabidopsis, especially those mutants generated by EMS or fast neutron mutagenesis. The success of map-based cloning relies on the availability of molecular markers that distinguish the polymorphisms between two Arabidopsis ecotypes. So far, most molecular markers in Arabidopsis have been generated by individual laboratories or the Arabidopsis Information Resource (TAIR). However, the TAIR markers, which are distributed unevenly on the five Arabidopsis chromosomes, only cover approximately 25% of the Arabidopsis BACs. Designing and testing molecular markers is still a time-consuming endeavor. Here we report the construction of a high-resolution BAC-based Arabidopsis mapping platform (AMP), using Col-0 and Ler as model ecotypes. The AMP comprises 1346 markers (1073 INDEL and 273 CAPS/dCAPS markers), of which 971 were newly designed and experimentally confirmed, 179 were from published papers and 196 were TAIR markers. These AMP markers cover 1186 BACs, 1121 of which are in non-centromere regions, representing approximately 75% of the Arabidopsis BACs in non-centromere regions. All the marker information is included on the AMP website (http://amp.genomics.org.cn/) for easy access and download, and sets of standard markers for initial chromosomal localization of a particular gene are recommended. The feasibility of using the AMP to map mutated genes is also discussed.
