Association of NCAP family genes with prognosis and immune infiltration of human sarcoma.

OBJECTIVE: This study was conducted to explore the correlation of NCAP family genes with expression, prognosis, and immune infiltration in human sarcoma. RESULTS: Compared with normal human tissues, six NCAP family genes were highly expressed in sarcoma tissues, and high expression of the six genes were significantly associated with the poor prognosis of sarcoma patients. The expression of NCAPs in sarcoma was significantly related to the low infiltration level of macrophages and CD4+ T cells. GO and KEGG enrichment analysis showed that NCAPs and their interacting genes were mainly enriched in organelle fission for biological processes (BP), spindle for cellular component (CC), tubulin binding for molecular function (MF), and 'Cell cycle' pathway. METHODS: We explored the expression of NCAP family members by ONCOMINE, and GEPIA databases. Additionally, the prognostic value of NCAP family genes in sarcoma was detected by Kaplan-Meier Plotter and GEPIA databases. Moreover, we explored the relationship between NCAP family gene expression level and immune infiltration using the TIMER database. Finally, we performed GO and KEGG analysis for NCAPs-related genes by DAVID database. CONCLUSION: The six members of NCAP gene family can be used as biomarkers to predict the prognosis of sarcoma. They were also correlated with the low immune infiltration in sarcoma.

Transcriptome Sequencing Analysis of lncRNA and mRNA Expression Profiles in Bone Nonunion.

Background: Bone nonunion is a serious complication of fracture. This study explored the differentially expressed lncRNAs (DELs) and mRNAs (DEGs) and identified potential lncRNA-mRNA interactions in bone nonunion. Methods: We extracted total RNA from three bone nonunion and three bone union patient tissue samples. RNA sequencing was performed to detect DELs and DEGs between bone nonunion and union tissue samples. The lncRNAs and genes with absolute log2-fold change (log2FC) > 1 and adjusted p value < 0.05 were further chosen for gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. lncRNA and targeted mRNA interaction networks were constructed. Results: We observed 179 DELs and 415 DEGs between the bone nonunion and union tissue samples. GO analysis indicated that DELs and DEGs were mainly enriched in the chondroitin sulfate proteoglycan biosynthetic process. DELs and DEGs were enriched in "ECM-receptor interaction" and "Staphylococcus aureus infection" KEGG pathways. Several potential lncRNA-mRNA interactions were also predicted. Conclusions: This study identified bone nonunion-associated lncRNAs and mRNAs using deep sequencing that may be useful as potential biomarkers for bone nonunion.

Validation of an MRI Technique for the 6-DOF Knee Kinematics Measurement.

Background: For total knee arthroplasty (TKA), the optimal rotational position of the femoral component is felt to be critically important. The current knee joint kinematics measurement technology is unable to identify the exact rotation axis of the knee joint, the main reasons being low measurement accuracy and insufficient three-dimensional data (2D-3D image matching technology). In order to improve the effect of TKA surgery, we proposed a knee joint kinematics measurement method, based on the MRI technology, and verified its measurement accuracy. We then employed this method to identify the personalized optimal rotation axis of the knee joint for TKA patients. Purposes: The purpose of the study was 1) to propose a method for measuring knee joint kinematics and verify its accuracy and 2) to propose a method for determining the optimal rotation axis of knee joint for TKA surgery, based on accurate kinematic measurement results. Materials and Methods: The experiment was divided into two parts: in vitro and in vivo. The purpose of the in vitro experiment was to verify the measurement accuracy of our method. We fixed two aquarium stones (approximately 10 cm * 10 cm * 10 cm in size, close to the size of the distal femur and proximal tibia) firmly on the fixed and moving arms of the goniometer/vernier caliper with glue and immersed the aquarium stones in the water to capture MRI images. The MRI images were then processed with MATLAB software, and the relative motion of the two aquarium stones was measured. The measurement accuracy of our method was verified via the scale reading of the moving arm on the goniometer/vernier caliper. In vivo, 36 healthy elderly participants (22 females, 14 males) were recruited from the local community; our method was then employed to measure the relative motion of the tibia and femur and to observe the rollback and screw home motion of the medial/lateral condyle of the femur, which was identified as specific kinematic features of the knee joint. Results: In vitro, all measurements were accurate to <1 mm and <1°. In vivo, all knee measurements showed rollback motion (the rollback distance of the medial femoral condyle was 18.1 ± 3.7 mm and that of the lateral condyle was 31.1 ± 7.3 mm) and screw home motion. Conclusion: In the application scenario of knee joint kinematics measurement, our method has an accuracy of <1° of rotation angle and <1 mm of translation for all reference points, and it can be employed to identify the most stable axis of the knee joint. Significance: Using our method to accumulate data on the knee rotation axis of more subjects to establish an average rotation axis of a given population may help in knee prosthesis design and reduce the patient dissatisfaction rate. Individually measuring the patient's rotation axis before TKA surgery and adjusting the prosthesis installation in TKA may further reduce the patient dissatisfaction rate, and automatic computer measurement may be realized in the future, but it is still time-consuming for now.

Combined analysis of expression, prognosis and immune infiltration of GINS family genes in human sarcoma.

OBJECTIVE: This study was undertaken to explore the expression and prognostic value of GINS family in human sarcoma, as well as the association between the expression levels of the GINS family and sarcoma immune infiltration. RESULTS: We discovered that the mRNA expression levels of GINS1, GINS2, GINS3, and GINS4 were all higher in the majority of tumor tissues than in normal samples, of course, including sarcoma. Through the CCLE, all the four members expression were observed in high levels in sarcoma cell lines. In Gene Expression Profiling Analysis (GEPIA) and Kaplan-Meier Plotter, our results indicated that the poor overall survival (OS), disease-free survival (DFS) and relapse free survival (RFS) were tightly associated with the increased expression of GINS genes. In TIMER database, we found that highly expressed GINS was significantly correlated with the low infiltration level of CD4+ T cell and macrophage. CONCLUSIONS: The four GINS family members were all the prognostic biomarkers for the prognosis of human sarcoma and can reduce the level of immune cell infiltration in the sarcoma microenvironment. METHODS: In terms of the expression levels of mRNA for GINS family members, a particular contrast in various cancers, especially human sarcoma, was conducted through ONCOMINE and GEPIA and CCLE databases. Kaplan-Meier Plotter was used to identify the prognostic value of GINS family in sarcoma. The relationship between the expression level of GINS and the infiltration of immune cells was analyzed in TIMER database.

Comprehensive analysis of expression and prognosis for LMNB family genes in human sarcoma.

ABSTRACT: Previous studies indicated that lamin proteins were thought to be related to gene expression, chromatin structure, and unclear stability. There are 2 types of vertebrate lamins, including A and B. The 2 B type proteins are encoded by lamin B1 (LMNB1) and lamin B2 (LMNB2). The LMNBs factor has been found to be associated with the development of multiple tumors, but its association with sarcoma has been barely mentioned.The transcription levels of LMNBs were analyzed via Oncomine database. Gene Expression Profiling Interactive Analysis (GEPIA) dataset was adopted to analyze the differential expression of LMNBs in sarcoma. Cancer Cell Line Encyclopedia dataset was used to explore the expression of LMNBs in sarcoma cell line. We analyzed the prognostic value of LMNBs in GEPIA and Kaplan-Meier Plotter. Oncomine and GEPIA datasets were also used to detect the relationship between LMNBs and their co-expressed genes. We used the Database for Annotation, Visualization and Integrated Discovery to conduct the Gene Ontology analysis of LMNBs and their co-expressed genes. Kyoto Encyclopedia of Genes and Genomes was also used to analyze the pathway of LMNBs.LMNB1 and LMNB2 were reported to be hyperexpressed in sarcoma. The expression of LMNBs was elevated in various sarcoma cell lines. According to the results, we observed that LMNBs were connected to the poor overall survival, recurrence-free survival, and disease-free survival of sarcoma patients.This study indicated that hyperexpression of LMNBs was significantly related to worse outcome of sarcoma, LMNB1 and LMNB2 were expected to become potential biomarkers for human.

Expression and prognosis analyses of BUB1, BUB1B and BUB3 in human sarcoma.

Budding Uninhibited By Benzimidazoles are a group of genes encoding proteins that play central roles in spindle checkpoint during mitosis. Improper mitosis may lead to aneuploidy which is found in many types of tumors. As a key mediator in mitosis, the dysregulated expression of BUBs has been proven to be highly associated with various malignancies, such as leukemia, gastric cancer, breast cancer, and liver cancer. However, bioinformatic analysis has not been applied to explore the role of the BUBs in sarcomas. Herein, we investigate the transcriptional and survival data of BUBs in patients with sarcomas using Oncomine, Gene Expression Profiling Interactive Analysis, Cancer Cell Line Encyclopedia, Kaplan-Meier Plotter, LinkedOmics, and the Database for Annotation, Visualization and Integrated Discovery. We found that the expression levels of BUB1, BUB1B and BUB3 were higher in sarcoma samples and cell lines than in normal controls. Survival analysis revealed that the higher expression levels of BUB1, BUB1B and BUB3 were associated with lower overall and disease-free survival in patients with sarcomas. This study implies that BUB1, BUB1B and BUB3 are potential treatment targets for patients with sarcomas and are new biomarkers for the prognosis of sarcomas.