Pan-Cancer Analysis of FURIN as a Potential Prognostic and Immunological Biomarker

Plasma cell signatures predict prognosis and treatment efficacy for lung adenocarcinoma

PURPOSE

This study aims to identify key genes regulating tumor infiltrating plasma cells (PC) and provide new insights for innovative immunotherapy.

METHODS

Key genes related to PC were identified using machine learning in lung adenocarcinoma (LUAD) patients. A prognostic model called PC scores was developed using TCGA data and validated with GEO cohorts. We assessed the molecular background, immune features, and drug sensitivity of the high PC scores group. Real-time PCR was utilized to assess the expression of hub genes in both localized LUAD patients and LUAD cell lines.

RESULTS

We constructed PC scores based on seventeen PC-related hub genes (ELOVL6, MFI2, FURIN, DOK1, ERO1LB, CLEC7A, ZNF431, KIAA1324, NUCB2, TXNDC11, ICAM3, CR2, CLIC6, CARNS1, P2RY13, KLF15, and SLC24A4). Higher age, TNM stage, and PC scores independently predicted shorter overall survival. The AUC value of PC scores for one year, three years, and five years of overall survival were 0.713, 0.716, and 0.690, separately. The nomogram model that integrated age, stage, and PC scores showed significantly higher predictive value than stage alone (P < 0.01). High PC scores group exhibited an immune suppressing microenvironment with lower B, CD8 + T, CD4 + T, and dendritic cell infiltration. Docetaxel, gefitinib, and erlotinib had lower IC50 in high PC groups (P < 0.001). After validation through the local cohort and in vitro experiments, we ultimately confirmed three key potential targets: MFI2, KLF15, and CLEC7A.

CONCLUSION

We proposed a prediction mode which can effectively identify high-risk LUAD patients and found three novel genes closely correlated with PC tumor infiltration.

Impact of weight loss on cancer-related proteins in serum: results from a cluster randomised controlled trial of individuals with type 2 diabetes

BACKGROUND

Type 2 diabetes is associated with higher risk of several cancer types. However, the biological intermediates driving this relationship are not fully understood. As novel interventions for treating and managing type 2 diabetes become increasingly available, whether they also disrupt the pathways leading to increased cancer risk is currently unknown. We investigated the effect of a type 2 diabetes intervention, in the form of intentional weight loss, on circulating proteins associated with cancer risk to gain insight into potential mechanisms linking type 2 diabetes and adiposity with cancer development.

METHODS

Fasting serum samples from participants with diabetes enrolled in the Diabetes Remission Clinical Trial (DiRECT) receiving the Counterweight-Plus weight-loss programme (intervention, N = 117, mean weight-loss 10 kg, 46% diabetes remission) or best-practice care by guidelines (control, N = 143, mean weight-loss 1 kg, 4% diabetes remission) were subject to proteomic analysis using the Olink Oncology-II platform (48% of participants were female; 52% male). To identify proteins which may be altered by the weight-loss intervention, the difference in protein levels between groups at baseline and 1 year was examined using linear regression. Mendelian randomization (MR) was performed to extend these results to evaluate cancer risk and elucidate possible biological mechanisms linking type 2 diabetes and cancer development. MR analyses were conducted using independent datasets, including large cancer meta-analyses, UK Biobank, and FinnGen, to estimate potential causal relationships between proteins modified during intentional weight loss and the risk of colorectal, breast, endometrial, gallbladder, liver, and pancreatic cancers.

FINDINGS

Nine proteins were modified by the intervention: glycoprotein Nmb; furin; Wnt inhibitory factor 1; toll-like receptor 3; pancreatic prohormone; erb-b2 receptor tyrosine kinase 2; hepatocyte growth factor; endothelial cell specific molecule 1 and Ret proto-oncogene (Holm corrected P-value <0.05). Mendelian randomization analyses indicated a causal relationship between predicted circulating furin and glycoprotein Nmb on breast cancer risk (odds ratio (OR) = 0.81, 95% confidence interval (CI) = 0.67-0.99, P-value = 0.03; and OR = 0.88, 95% CI = 0.78-0.99, P-value = 0.04 respectively), though these results were not supported in sensitivity analyses examining violations of MR assumptions.

INTERPRETATION

Intentional weight loss among individuals with recently diagnosed diabetes may modify levels of cancer-related proteins in serum. Further evaluation of the proteins identified in this analysis could reveal molecular pathways that mediate the effect of adiposity and type 2 diabetes on cancer risk.

FUNDING

The main sources of funding for this work were Diabetes UK, Cancer Research UK, World Cancer Research Fund, and Wellcome.

Significance of Furin Expression in Thyroid Neoplastic Transformation

Angiotensin-Converting Enzyme 2 (ACE2), Transmembrane Serine Protease 2 (TMPRSS2), and Furin were known to be key players in the SARS-CoV-2 infection, and the thyroid gland was revealed to be one of the relevant targets of the virus. Regardless of the viral infection, the expression of these molecules in the thyroid gland and their putative role in the neoplastic transformation of the thyrocytes has not been thoroughly explored. In this work, we aimed to characterize the mRNA and protein expression pattern of ACE2, TMPRSS2, and Furin in a series of patients with thyroid lesions. Our main results revealed a significantly decreased expression of ACE2 mRNA in the thyroid neoplasms in comparison to normal adjacent tissue. Furin mRNA was significantly increased in thyroid neoplasms when compared to normal adjacent tissue. In addition, a higher Furin mRNA level in thyroid carcinomas was associated with the presence of lymph node metastasis. Furin mRNA expression revealed a high discriminatory power between adjacent tissue and neoplasms. Protein expression of these molecules did not correlate with mRNA expression. Our study shows the mRNA downregulation of ACE2 and overexpression of Furin in thyroid neoplasms. Further studies are required to clarify if Furin expression can be a potential diagnostic indicator in thyroid neoplasia.

Therapeutic potential of the Proprotein Convertase Subtilisin/Kexin family in vascular disease

Proprotein convertase subtilisin/kexins (PCSKs) constitute a family of nine related proteases: PCSK1-7, MBTPS1, and PCSK9. Apart from PCSK9, little is known about PCSKs in cardiovascular disease. Here, we aimed to investigate the expression landscape and druggability potential of the entire PCSK family for CVD. We applied an integrative approach, combining genetic, transcriptomic and proteomic data from three vascular biobanks comprising carotid atherosclerosis, thoracic and abdominal aneurysms, with patient clinical parameters and immunohistochemistry of vascular biopsies. Apart from PCSK4, all PCSK family members lie in genetic regions containing variants associated with human cardiovascular traits. Transcriptomic analyses revealed that FURIN, PCSK5, MBTPS1 were downregulated, while PCSK6/7 were upregulated in plaques vs. control arteries. In abdominal aneurysms, FURIN, PCSK5, PCSK7, MBTPS1 were downregulated, while PCSK6 was enriched in diseased media. In thoracic aneurysms, only FURIN was significantly upregulated. Network analyses of the upstream and downstream pathways related to PCSKs were performed on the omics data from vascular biopsies, revealing mechanistic relationships between this protein family and disease. Cell type correlation analyses and immunohistochemistry showed that PCSK transcripts and protein levels parallel each other, except for PCSK9 where transcript was not detected, while protein was abundant in vascular biopsies. Correlations to clinical parameters revealed a positive association between FURIN plaque levels and serum LDL, while PCSK6 was negatively associated with Hb. PCSK5/6/7 were all positively associated with adverse cardiovascular events. Our results show that PCSK6 is abundant in plaques and abdominal aneurysms, while FURIN upregulation is characteristic for thoracic aneurysms. PCSK9 protein, but not the transcript, was present in vascular lesions, suggesting its accumulation from circulation. Integrating our results lead to the development of a novel ‘molecular’ 5D framework. Here, we conducted the first integrative study of the proprotein convertase family in this context. Our results using this translational pipeline, revealed primarily PCSK6, followed by PCSK5, PCSK7 and FURIN, as proprotein convertases with the highest novel therapeutic potential.

Pancancer Analysis of Revealed TDO2 as a Biomarker of Prognosis and Immunotherapy

Background

Tryptophan 2,3-dioxygenase (TDO) encoded by TDO2, a rate-limiting enzyme in the kynurenine pathway, catabolizes tryptophan to kynurenine, evades immune surveillance, and promotes tumor growth. Although accumulating evidence suggests a crucial role of TDO2 during tumor formation and development, systematic evaluation of TDO2 across human cancers has rarely been reported.

Methods

To shed more light on the role of TDO2 in human cancer, we explored the expression profiles of TDO2 and identified its prognostic value in pancancer analysis through TCGA, CCLE, and GTEx databases. We further utilized TCGA data to evaluate the association between TDO2 and tumor immunological features, such as mismatch repair (MMR), tumor immune infiltration, immune checkpoint-related genes, tumor mutational burden (TMB), microsatellite instability (MSI), and DNA methyltransferase (DNMT).

Results

TDO2 exhibited different expression levels in various cancer cell lines. Frequently, TDO2 was detected to be highly expressed in the majority of cancers. In addition, high TDO2 expression was correlated with an unfavorable prognosis for patients in KIRP, LGG, TGCT, and UVM. Moreover, high TDO2 expression level positively correlated with higher immune infiltration, especially dendritic cells. Additionally, there is a close relationship between TDO2 and immune checkpoint-related gene markers, such as LAIR1, CD276, NRP1, CD80, and CD86. Finally, correlation analysis has demonstrated a high-correlation between TDO2 and TMB, MSI, MMR, and DNMT of multiple cancer types.

Conclusion

Therefore, our results suggest that TDO2 can function as a potential prognostic biomarker due to its role in tumor immunity regulation.

Comprehensive Landscape of RRM2 with Immune Infiltration in Pan-Cancer

Simple Summary

RRM2 is a crucial subunit of ribonucleotide reductase. In this article, we provided a comprehensive analysis of RRM2 with immune infiltration in pan-cancer. We focused on the hotspots of ferroptosis-related gene RRM2 and immunotherapy. Via bioinformatics analysis, multiple indicators suggested that RRM2 high expression may enhance immunotherapy sensitivity. For the first time, we systematically analyzed the role of RRM2 in pan-cancer. We provided the prospect of RRM2 and immunotherapy for pan-cancer. Additionally, we proved the expression pattern, clinical value, prognostic value and potential pathways of RRM2 with different platforms. In particular, we confirmed RRM2 expression and function in bladder cancer in our clinical samples and cell lines. Collectively, we found that RRM2 is a novel prognostic biomarker, and these findings may aid in an improved understanding of the role of RRM2 and its clinical application in human cancers.

Abstract

As a crucial subunit of ribonucleotide reductase, RRM2 plays a significant part in DNA synthesis. This study aimed to elucidate the comprehensive landscape of RRM2 in human cancers. With different bioinformatics platforms, we investigated the expression pattern, prognostic significance, mutational landscapes, gene interaction network, signaling pathways and immune infiltration of RRM2 in tumors. We found that RRM2 expression was predominantly up-expressed in tumor tissues in most tumors. Concurrently, RRM2 expression was significantly associated with worse prognosis and tumor stage across TCGA cancers. Moreover, RRM2 high levels were critically associated with the infiltration of natural killer T cells and immune scores. RRM2 was positively related to immune checkpoints, tumor mutation burden, microsatellite instability, neoantigen, and cytotoxic T lymphocyte in several cancers, predicting effective response to immunotherapy. Meanwhile, a strong co-expression of RRM2 with immune-related genes was observed. Additionally, multiple Cox regression analysis showed that RRM2 was an independent prognostic factor in bladder cancer (BLCA). Eventually, we verified that RRM2 was overexpressed in BLCA clinical samples and cell lines. Blocking RRM2 could suppress BLCA cells’ growth and proliferation while enhancing sensitivity to cisplatin. This study provided a new perspective for understanding RRM2 in cancers and new strategies for tumor immunotherapy.

Zinc finger C3H1-type containing serves as a novel prognostic biomarker in human pan-cancer

BACKGROUND

Zinc finger C3H1 domain-containing protein (ZFC3H1) is differentially expressed between primary tumor and the normal in most cancers. Additionally, a recent study has suggested that ZFC3H1 could serve as a novel marker for the prognosis of prostate adenocarcinoma (PRAD). However, the relationship between ZFC3H1 expression and the prognostic values in most tumors remains unclear. Our study is mainly for exploring the prognosis of ZFC3H1 in pan-cancer and for further discovering a potential therapeutics target.

METHODS

Based on the clinical big data, we performed a pan-cancer analysis of ZFC3H1, including gene expression, survival prognosis, genetic alteration, protein phosphorylation, immune infiltration and enrichment analysis. In addition, Real-Time PCR and Western Blot were used to further confirm the role of ZFC3H1 in the colorectal cancer.

RESULTS

We found that ZFC3H1 expression was connected with the prognosis of multiple malignant tumors. Furthermore, we also observed that ZFC3H1 was highly expressed in colorectal cancer through Real-Time PCR and Western Blot. The primary tumors presented higher phosphorylation level of the S655 site in lung adenocarcinoma, colon adenocarcinoma and uterine corpus endometrial carcinoma. ZFC3H1 expression was positively correlated with the immune infiltration of Cancer-associated fibroblasts (CAFs) in some tumors, such as liver hepatocellular carcinoma. And RNA surveillance pathways may be closely associated with the occurrence of tumors.

CONCLUSIONS

Our study first reveals that ZFC3H1 could serve as a novel prognostic biomarker of pan-cancer, especially colorectal cancer.

A Novel Prognostic Signature for Survival Prediction and Immune Implication Based on SARS-CoV-2–Related Genes in Kidney Renal Clear Cell Carcinoma

Kidney renal clear cell carcinoma (KIRC) is a common aggressive malignancy of the urinary system. COVID-19, a highly infectious and severe disease caused by SARS-CoV-2, has become a significant challenge for global public health. Cancer patients have been reported to be more vulnerable to SARS-CoV-2 infection and have a higher risk for serious complications than the general population. However, the correlation between KIRC and COVID-19 remains incompletely elucidated. In this study, we comprehensively investigated the expression and prognostic significance of 333 SARS-CoV-2 infection–related genes in KIRC using the TCGA dataset and identified 31 SARS-CoV-2–related differently expressed genes between KIRC and normal renal tissues. Based on these genes, we constructed and validated a 5-gene prognostic signature (including ACADM, CENPF, KDELC1, PLOD2, and TRMT1) to distinguish low- and high-risk KIRC patients of poor survival in TCGA and E-MTAB-1980 cohorts. Gene set enrichment analysis (GSEA) showed that some inflammatory/immune-related pathways were significantly enriched in the high-risk group. The ESTIMATE analysis indicated that patients in the high-risk group had higher stromal and immune cell scores, therefore lower tumor purity. Moreover, they presented higher proportions of macrophages M0, regulatory T cells (Tregs), and T follicular helper cells and higher expression of immune checkpoints CTLA-4, LAG-3, TIGIT, and PDCD1 than low-risk patients. Besides, we also developed a nomogram to expand clinical applicability, which exhibits excellent predictive accuracy for survival. In conclusion, we identified a novel prognostic signature and nomogram based on SARS-CoV-2–related genes as reliable prognostic predictors for KIRC patients and provided potential therapeutic targets for KIRC and COVID-19.

Immune Infiltration of MMP14 in Pan Cancer and Its Prognostic Effect on Tumors

Background

Matrix metalloproteinase 14 (MMP14) is a member of the MMP family, which interacts with tissue inhibitors of metalloproteinase (TIMPs), and is involved in normal physiological functions such as cell migration, invasion, metastasis, angiogenesis, and proliferation, as well as tumor genesis and progression. However, there has been a lack of relevant reports on the effect of MMP14 across cancers. This study aims to explore the correlation between MMP14 and pan-cancer prognosis, immune infiltration, and the effects of pan-cancer gene mismatch repair (MMR), microsatellite instability (MSI), tumor mutational burden (TMB), DNA methylation, and immune checkpoint genes.

Methods

In this study, we used bioinformatics to analyze data from multiple databases, including The Cancer Genome Atlas (TCGA), ONCOMINE, and Kaplan–Meier plotter. We investigated the relationship between the expression of MMP14 in tumors and tumor prognosis, the relationship between MMP14 expression and tumor cell immune infiltration, and the relationship between MMR gene MMR, MSI, TMB, DNA methylation, and immune checkpoint genes.

Results

MMP14 expression is highly associated with the prognosis of a variety of cancers and tumor immune invasion and has important effects on pan oncologic MMR, MSI, TMB, DNA methylation, and immune checkpoint genes.

Conclusion

MMP14 is highly correlated with tumor prognosis and immune invasion and affects the occurrence and progression of many tumors. All of these results fully indicate that MMP14 may be a biomarker for the prognosis, diagnosis, and treatment of many tumors and provide new ideas and direction for subsequent tumor immune research and treatment strategies.

Aggresome-Autophagy Associated Gene HDAC6 Is a Potential Biomarker in Pan-Cancer, Especially in Colon Adenocarcinoma

Background

Histone deacetylase 6 (HDAC6) regulates cytoplasmic signaling networks through the deacetylation of various cytoplasmic substrates. Recent studies have identified the role of HDAC6 in tumor development and immune metabolism, but its specific function remains unclear.

Methods

The current study determined the role of HDAC6 in tumor metabolism and tumor immunity through a multi-database pan-cancer analysis. The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), and Cancer Cell Line Encyclopedia (CCLE) datasets were used to determine the expression levels, prognosis, tumor progression, immune checkpoints, and immune metabolism of HDAC6 in 33 tumors. Pathways, immune checkpoints, immune neoantigens, immune microenvironment, tumor mutational burden (TMB), microsatellite instability (MSI), DNA mismatch repair (MMR), and the value of methyltransferases. The R package was used for quantitative analysis and panoramic description.

Results

In the present study, we determined that HDAC6 is differentially expressed in pan carcinomas, and by survival, we found that HDAC6 was generally associated with the prognosis of pancreatic adenocarcinoma, Thymoma, and uveal melanoma, where low expression of HDAC6 had a significantly worse prognosis. Secondly, through this experiment, we confirmed that HDAC6 expression level was associated with tumor immune infiltration and tumor microenvironment, especially in PAAD. Finally, HDAC6 was associated with immune neoantigen and immune checkpoint gene expression profiles in all cancers in addition to TMB and MSI in pan-cancers.

Conclusion

HDAC6 is differentially expressed in pan-cancers and plays an essential role in tumor metabolism and immunity. HDAC6 holds promise as a tumor potential prognostic marker, especially in colon cancer.