Down-regulation of HLA-A mRNA in peripheral blood mononuclear cell of colorectal cancer

A new marker constructed from immune-related lncRNA pairs can be used to predict clinical treatment effects and prognosis: in-depth exploration of underlying mechanisms in HNSCC

BACKGROUND

Long non-coding RNA (lncRNA) plays a vital role in tumor proliferation, migration, and treatment. Since it is challenging to standardize the gene expression levels detected by different platforms, the signatures composed of many immune-related single lncRNAs are still inaccurate. Utilizing a gene pair formed of two immune-related lncRNAs and strategically assigning values can effectively meet the demand for a higher-accuracy dual biomarker combination.

METHODS

Co-expression and differential expression analyses were performed on immune genes and lncRNAs data from The Cancer Genome Atlas and the ImmPort database to obtain differentially expressed immune-related lncRNAs for pairwise pairing. The prognostic-related differentially expressed immune-related lncRNAs (PR-DE-irlncRNAs) pairs were then identified by univariate Cox regression and used for lasso regression to construct a prognostic model. Various methods were used to validate the predictive prognostic performance of the model. Additionally, we explored the potential guiding value of the model in immunotherapy and chemotherapy and constructed a nomogram suitable for efficient prognosis prediction. Mechanistic exploration of anti-tumor immunity and mutational perspectives are also included. We also analyzed the correlation between the model and immune checkpoint inhibitors (ICIs)-related, N6-methyadenosine (m6A)-related, and multidrug resistance genes.

RESULTS

We used a total of 20 pairs of PR-DE-irlncRNAs to create a prognosis model. Quantitative real-time polymerase chain reaction experiments further verified the abnormal expression of 11 lncRNAs in HNSCC cells. Various methods have confirmed the excellent performance of the model in predicting patient prognosis. We reasoned that lncRNAs/TP53 mutation might play a positive/negative anti-tumor role through the immune system by multi-perspective analyses. Finally, it was found that the prognostic model was closely related to immunotherapy and chemotherapy as well as the expression of ICIs/m6A/multidrug resistance-related genes.

CONCLUSION

The prognostic model performs excellently in predicting the prognosis of patients and provides the potential value of practical guidance for treatment.

5' and 3' untranslated regions contribute to the differential expression of specific HLA-A alleles

In hematopoietic stem cell transplantation (HSCT), when no HLA full-matched donor is available, alternative donors could include one HLA-mismatched donor. Recently, the low expressed HLA-C alleles have been identified as permissive mismatches for the best donor choice. Concerning HLA-A, the degree of variability of expression is poorly understood. Here, we evaluated HLA-A expression in healthy individuals carrying HLA-A*02 allele in different genotypes using flow cytometry and allele-specific quantitative RT-PCR. While an interindividual variability of HLA-A*02 cell surface expression, not due to the allele associated, was observed, no difference of the mRNA expression level was shown, suggesting the involvement of the posttranscriptional regulation. The results of qRT-PCR analyses exhibit a differential expression of HLA-A alleles with HLA-A*02 as the strongest expressed allele independently of the second allele. The associated non-HLA-A*02 alleles were differentially expressed, particularly the HLA-A*31 and HLA-A*33 alleles (strong expression) and the HLA-A*29 (low expression). The presence of specific polymorphisms in the 5' and 3' untranslated regions of the HLA-A*31 and HLA-A*33 alleles could contribute to this high level of expression. As previously described for HLA-C, low-expressed HLA-A alleles, such as HLA-A*29, could be considered as a permissive mismatch, although this needs to be confirmed by clinical studies.

NS5ATP9 mRNA levels in peripheral blood mononuclear cells predict prognosis in patients with gastric cancer

The prognosis for gastric cancer is poor; therefore, there is urgent need for the development of novel, especially noninvasive surrogate biomarkers. NS5ATP9 is significantly overexpressed in gastric cancer tissues, and altered NS5ATP9 expression in human gastric cancer is associated with tumor recurrence. This study aimed to determine whether a correlation exists between NS5ATP9 mRNA levels in peripheral blood mononuclear cells (PBMCs) and gastric cancer prognosis in patients. NS5ATP9 mRNA levels were assessed by real-time RT-PCR in PBMC samples obtained from 207 gastric cancer patients, 47 patients with benign gastric lesions, and 78 healthy individuals. In addition, NS5ATP9 protein expression was evaluated by Western blot in PBMC samples from 30 gastric cancer patients and 30 healthy individuals, chosen randomly. Finally, clinicopathological data and survival of all gastric cancer patients were collected and analyzed. NS5ATP9 in PBMCs from gastric cancer patients was significantly upregulated both at mRNA and protein levels. Interestingly, NS5ATP9 mRNA overexpression in PBMCs was significantly associated with poor disease-free survival and overall survival of cancer patients, but not with tumor recurrence. Multivariate analysis showed NS5ATP9 mRNA levels and tumor lymph node metastasis were independent correlation with 3-year survival rate. Importantly, the diagnostic sensitivity and specificity (70.6 and 79.5 %, respectively) were higher for NS5ATP9 mRNA in PBMCs compared with the serum tumor markers CEA (45.0 and 84.6 %, respectively) and CA19-9 (61.5 and 69.2 %, respectively). These findings suggested that NS5ATP9 mRNA levels in PBMCs can be used for prognosis in gastric cancer patients.

Characterization of gene rearrangements resulted from genomic structural aberrations in human esophageal squamous cell carcinoma KYSE150 cells

Chromosomal rearrangements and involved genes have been reported to play important roles in the development and progression of human malignancies. But the gene rearrangements in esophageal squamous cell carcinoma (ESCC) remain to be identified. In the present study, array-based comparative genomic hybridization (array-CGH) was performed on the ESCC cell line KYSE150. Eight disrupted genes were detected according to the obviously distinct unbalanced breakpoints. The splitting of these genes was validated by dual-color fluorescence in-situ hybridization (FISH). By using rapid amplification of cDNA ends (RACE), genome walking and sequencing analysis, we further identified gene disruptions and rearrangements. A fusion transcript DTL-1q42.2 was derived from an intrachromosomal rearrangement of chromosome 1. Highly amplified segments of DTL and PTPRD were self-rearranged. The sequences on either side of the junctions possess micro-homology with each other. FISH results indicated that the split DTL and PTPRD were also involved in comprising parts of the derivative chromosomes resulted from t(1q;9p;12p) and t(9;1;9). Further, we found that regions harboring DTL (1q32.3) and PTPRD (9p23) were also splitting in ESCC tumors. The data supplement significant information on the existing genetic background of KYSE150, which may be used as a model for studying these gene rearrangements.