Crystal structure of the SPRY domain-containing protein 7 reveals unique structural features

Genomic and transcriptome insight into the structure and immunity role of TRIM proteins in Chinese soft-shelled turtles (Pelodiscus sinensis) after Aeromonas hydrophila infection

BACKGROUND

TRIM proteins, recognized as a class of E3 ubiquitin ligases, are increasingly acknowledged for their antipathogen immune functions in mammals and fish. In the Chinese soft-shelled turtle (Pelodiscus sinensis), a secondary aquatic reptile that occupies a unique evolutionary position, the TRIM gene has rarely been reported.

METHODS AND RESULTS

In the present study, 48 PsTRIM proteins were identified from the genome of Pelodiscus sinensis via Hidden Markov Model (HMM) searches and Signal Transduction ATPases with Numerous Domains (SMART) analysis. These PsTRIMs were found across 43 distinct scaffolds, and phylogenetic analyses classified them into three principal clades. The PsTRIMs feature a conserved assembly of either RING-B-box-coiled-coil (RBCC) or B-box-coiled-coil (BBC) domains at the N-terminus, in addition to eight unique domains at the C-terminus, including the B30.2 domain, 19 of which were identified. Expression profiling revealed ubiquitous expression of the 48 PsTRIMs across various P. sinensis tissues. Notably, seven PsTRIMs exhibited significant differential expression in liver transcriptomes following infection with Aeromonas hydrophila. Weighted gene coexpression network analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis implicated PsTRIM14 and PsTRIM28 as key players in host defense against bacterial invasion. Real-time quantitative PCR results indicated that PsTRIM1, PsTRIM2, PsTRIM14, and PsTRIM28 experienced marked upregulation in P. sinensis livers at 12 h post-infection with A. hydrophila.

CONCLUSIONS

Our study is the first to comprehensively identify and analyze the functions of TRIM genes in P. sinensis, unveiling their considerable diversity and potential roles in modulating immune responses.

Functional Proteomics Characterization of the Role of SPRYD7 in Colorectal Cancer Progression and Metastasis

SPRY domain-containing protein 7 (SPRYD7) is a barely known protein identified via spatial proteomics as being upregulated in highly metastatic-to-liver KM12SM colorectal cancer (CRC) cells in comparison to its isogenic poorly metastatic KM12C CRC cells. Here, we aimed to analyze SPRYD7's role in CRC via functional proteomics. Through immunohistochemistry, the overexpression of SPRYD7 was observed to be associated with the poor survival of CRC patients and with an aggressive and metastatic phenotype. Stable SPRYD7 overexpression was performed in KM12C and SW480 poorly metastatic CRC cells and in their isogenic highly metastatic-to-liver-KM12SM-and-to-lymph-nodes SW620 CRC cells, respectively. Upon upregulation of SPRYD7, in vitro and in vivo functional assays confirmed a key role of SPRYD7 in the invasion and migration of CRC cells and in liver homing and tumor growth. Additionally, transient siRNA SPRYD7 silencing allowed us to confirm in vitro functional results. Furthermore, SPRYD7 was observed as an inductor of angiogenesis. In addition, the dysregulated SPRYD7-associated proteome and SPRYD7 interactors were elucidated via 10-plex TMT quantitative proteins, immunoproteomics, and bioinformatics. After WB validation, the biological pathways associated with the stable overexpression of SPRYD7 were visualized. In conclusion, it was demonstrated here that SPRYD7 is a novel protein associated with CRC progression and metastasis. Thus, SPRYD7 and its interactors might be of relevance in identifying novel therapeutic targets for advanced CRC.

Identification of SPRYD4 as a tumour suppressor predicts prognosis and correlates with immune infiltration in cholangiocarcinoma

Cholangiocarcinoma (CCA) is an aggressive solid tumour with a 5-year survival rate ranging from 7% to 20%. It is, therefore, urgent to identify novel biomarkers and therapeutic targets to improve the outcomes of patients with CCA. SPRY-domain containing protein 4 (SPRYD4) contains SPRY domains that modulate protein-protein interaction in various biological processes; however, its role in cancer development is insufficiently explored. This study is the first to identify that SPRYD4 is downregulated in CCA tissues using multiple public datasets and a CCA cohort. Furthermore, the low expression of SPRYD4 was significantly associated with unfavourable clinicopathological characteristics and poor prognosis in patients with CCA, indicating that SPRYD4 could be a prognosis indicator of CCA. In vitro experiments revealed that SPRYD4 overexpression inhibited CCA cells proliferation and migration, whereas the proliferative and migratory capacity of CCA cells was enhanced after SPRYD4 deletion. Moreover, flow cytometry showed that SPRYD4 overexpression triggered the S/G2 cell phase arrest and promoted apoptosis in CCA cells. Furthermore, the tumour-inhibitory effect of SPRYD4 was validated in vivo using xenograft mouse models. SPRYD4 also showed a close association with tumour-infiltrating lymphocytes and important immune checkpoints including PD1, PD-L1 and CTLA4 in CCA. In conclusion, this study elucidated the role of SPRYD4 during CCA development and highlighted SPRYD4 as a novel biomarker and tumour suppressor in CCA.