A Three-Gene Expression Signature Identifies a Cluster of Patients with Short Survival in Chronic Lymphocytic Leukemia

Upregulated PPP1R14B is connected to cancer progression and immune infiltration in kidney renal clear cell carcinoma

BACKGROUND

Protein phosphatase 1 regulatory subunit 14B (PPP1R14B) is an oncogenic gene found in a variety of tumors, but its role in the prognosis and development of kidney renal clear cell carcinoma (KIRC) remains unknown. Our study aimed to determine whether PPP1R14B could be a prognostic biomarker for KIRC and its role in the development of KIRC.

METHODS

In this work, we used The Cancer Genome Atlas (TCGA) database to explore the expression of PPP1R14B in tumor tissues, its relationship with the prognosis of tumor patients, and its role in tumor occurrence and development. We validated our findings using the International Cancer Genome Consortium (ICGC) cohort, our clinical samples, and in vitro experiments.

RESULTS

PPP1R14B was upregulated in KIRC compared to adjacent normal tissue. Moreover, multivariate analysis revealed that upregulated PPP1R14B expression was an independent risk factor for KIRC progression. High-PPP1R14B groups had shorter overall survival (OS) and disease-free survival (DFS) in TCGA and ICGC cohorts. We used Cell Counting Kit-8 (CCK8) and scratch wound healing assay to explore the proliferation and migration of KIRC cells following PPP1R14B knockdown. Our results indicated that PPP1R14B knockdown significantly reduced the proliferation and migration of KIRC cells in vitro. We also explored the possible cellular mechanisms of PPP1R14B through the Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene ontology (GO) analysis, and TISIDB analysis. The function enrich analysis revealed that PPP1R14B-related genes were mainly enriched in purine metabolism and the macromolecule catabolic process. PPP1R14B expression was associated with tumor-infiltrating immune cells (TIICs) in the TCGA cohort, and the results of single-cell RNA-seq (scRNA) further demonstrated that PPP1R14B expression was associated with the enhanced infiltration of CD8 + T lymphocytes.

CONCLUSION

PPP1R14B may serve as a prognostic biomarker in KIRC, affect purine metabolism, activate immune infiltration, and promote KIRC cell migration.

Genes selection using deep learning and explainable artificial intelligence for chronic lymphocytic leukemia predicting the need and time to therapy

Analyzing gene expression profiles (GEP) through artificial intelligence provides meaningful insight into cancer disease. This study introduces DeepSHAP Autoencoder Filter for Genes Selection (DSAF-GS), a novel deep learning and explainable artificial intelligence-based approach for feature selection in genomics-scale data. DSAF-GS exploits the autoencoder's reconstruction capabilities without changing the original feature space, enhancing the interpretation of the results. Explainable artificial intelligence is then used to select the informative genes for chronic lymphocytic leukemia prognosis of 217 cases from a GEP database comprising roughly 20,000 genes. The model for prognosis prediction achieved an accuracy of 86.4%, a sensitivity of 85.0%, and a specificity of 87.5%. According to the proposed approach, predictions were strongly influenced by CEACAM19 and PIGP, moderately influenced by MKL1 and GNE, and poorly influenced by other genes. The 10 most influential genes were selected for further analysis. Among them, FADD, FIBP, FIBP, GNE, IGF1R, MKL1, PIGP, and SLC39A6 were identified in the Reactome pathway database as involved in signal transduction, transcription, protein metabolism, immune system, cell cycle, and apoptosis. Moreover, according to the network model of the 3D protein-protein interaction (PPI) explored using the NetworkAnalyst tool, FADD, FIBP, IGF1R, QTRT1, GNE, SLC39A6, and MKL1 appear coupled into a complex network. Finally, all 10 selected genes showed a predictive power on time to first treatment (TTFT) in univariate analyses on a basic prognostic model including IGHV mutational status, del(11q) and del(17p), NOTCH1 mutations, β2-microglobulin, Rai stage, and B-lymphocytosis known to predict TTFT in CLL. However, only IGF1R [hazard ratio (HR) 1.41, 95% CI 1.08-1.84, P=0.013), COL28A1 (HR 0.32, 95% CI 0.10-0.97, P=0.045), and QTRT1 (HR 7.73, 95% CI 2.48-24.04, P<0.001) genes were significantly associated with TTFT in multivariable analyses when combined with the prognostic factors of the basic model, ultimately increasing the Harrell's c-index and the explained variation to 78.6% (versus 76.5% of the basic prognostic model) and 52.6% (versus 42.2% of the basic prognostic model), respectively. Also, the goodness of model fit was enhanced (χ2 = 20.1, P=0.002), indicating its improved performance above the basic prognostic model. In conclusion, DSAF-GS identified a group of significant genes for CLL prognosis, suggesting future directions for bio-molecular research.

Protein Phosphatase 1 Subunit PPP1R14B Stabilizes STMN1 to Promote Progression and Paclitaxel Resistance in Triple-Negative Breast Cancer

Triple-negative breast cancer (TNBC) represents the most lethal subtype of breast cancer due to its aggressive clinical features and the lack of effective therapeutic targets. To identify novel approaches for targeting TNBC, we examined the role of protein phosphatases in TNBC progression and chemoresistance. Protein phosphatase 1 regulatory subunit 14B (PPP1R14B), a poorly defined member of the protein phosphatase 1 regulatory subunits, was aberrantly upregulated in TNBC tissues and predicted poor prognosis. PPP1R14B was degraded mainly through the ubiquitin-proteasome pathway. RPS27A recruited deubiquitinase USP9X to deubiquitinate and stabilize PPP1R14B, resulting in overexpression of PPP1R14B in TNBC tissues. Gain- and loss-of-function assays demonstrated that PPP1R14B promoted TNBC cell proliferation, colony formation, migration, invasion, and resistance to paclitaxel in vitro. PPP1R14B also induced xenograft tumor growth, lung metastasis, and paclitaxel resistance in vivo. Mechanistic investigations revealed that PPP1R14B maintained phosphorylation and stability of oncoprotein stathmin 1 (STMN1), a microtubule-destabilizing phosphoprotein critically involved in cancer progression and paclitaxel resistance, which was dependent on PP1 catalytic subunits α and γ. Importantly, the tumor-suppressive effects of PPP1R14B deficiency could be partially rescued by ectopic expression of wild-type but not phosphorylation-deficient STMN1. Moreover, PPP1R14B decreased STMN1-mediated α-tubulin acetylation, microtubule stability, and promoted cell-cycle progression, leading to resistance of TNBC cells to paclitaxel. Collectively, these findings uncover a functional and mechanistic role of PPP1R14B in TNBC progression and paclitaxel resistance, indicating PPP1R14B is a potential therapeutic target for TNBC.

SIGNIFICANCE

PPP1R14B upregulation induced by RPS27A/USP9X in TNBC increases STMN1 activity, leading to cancer progression and paclitaxel resistance.

Comprehensive analysis of protein phosphatase 1 regulatory inhibitor subunit 14B, a molecule related to tumorigenesis, poor prognosis, and immune cell infiltration in lung adenocarcinoma

OBJECTIVE

To explore the relationship between Protein Phosphatase 1 Regulatory Inhibitor Subunit 14B (PPP1R14B) and the occurrence of lung adenocarcinoma (LUAD).

METHOD

PPP1R14B expression was investigated using various databases, and its molecular functions and pathways were evaluated using Gene Set Variation Analysis (GSVA) and Gene Set Enrichment Analysis (GSEA). Then, the correlation between tumor mutations and PPP1R14B expression was analyzed. Furthermore, the regulation network and expression pathway axes of PPP1R14B were constructed. The correlation analysis between PPP1R14B and immune cell infiltration was performed using deconvolution algorithm analysis and the Tumor Immune Dysfunction and Exclusion (TIDE) algorithm. Finally, quantitative real-time polymerase chain reaction (qRT-PCR) and immunohistochemical (IHC) staining of the clinical samples were used for expression validation.

RESULTS

PPP1R14B showed high expression in tumor tissue. PPP1R14B was associated with T and N stages and poor prognosis and was linked to the cell cycle, DNA repair, and low immune response. High PPP1R14B expression was associated with high tumor mutation rates. The upstream and downstream genes of PPP1R14B were identified, along with the construction of a protein-protein interaction network (PPI network) and the expression pathway axes of PPP1R14B. PPP1R14B expression was associated with poor immune cell infiltration and a negative correlation between PPP1R14B and mast cell and eosinophil infiltration.

CONCLUSION

This study reveals high PPP1R14B expression in LUAD, its contribution to poor prognosis, molecular function, biological pathways, and impact on immune cell infiltration, and provides great insight into the role of PPP1R14B in LUAD tumorigenesis.

In vitro assessment of roles of PPP1R14B in cervical and endometrial cancer

Cervical and endometrial cancers are common gynecologic cancers. Protein phosphatase 1 regulatory subunit 14B (PPP1R14B) is aberrantly expressed in several tumors, while its functions in cervical and endometrial cancers remain largely uncertain. The differentially expression of PPP1R14B in cervical and endometrial cancers was predicted by GEPIA2 and Human Protein Atlas databases. The diagnostic value was analyzed by AUC curve. The association between PPP1R14B expression and overall survival was predicted using Kaplan-Meier Plotter database. The function of PPP1R14B was investigated according to in vitro assessment. PPP1R14B and phosphorylation level of Akt were analyzed through western blotting. Cell proliferation was investigated by CCK-8 and EdU staining assays. Cell apoptosis was evaluated via TUNEL staining and caspase-3 activity assays. PPP1R14B level was upregulated in cervical and endometrial cancers, and it was associated with diagnosis and worse prognosis. PPP1R14B silencing constrained cell proliferation and promoted cell death in cervical and endometrial cancers cells. PPP1R14B knockdown suppressed activation of the Akt pathway. Re-activation of the Akt signaling reversed the anti-proliferative and cell death-promoting roles of PP1R14B knockdown in cervical and endometrial cancers cells. In conclusion, PPP1R14B knockdown represses cell proliferation and facilitates cell death by inhibiting the activation of the Akt signaling in cervical and endometrial cancers.

PPP1R14B Is a Prognostic and Immunological Biomarker in Pan-Cancer

Recent studies have shown that PPP1R14B was highly expressed in tumor tissues and patients with high expression of PPP1R14B had poor survival rates. However, the function and mechanisms of PPP1R14B in tumor progression remain ill defined. There was also lack of pan-cancer evidence for the relationship between PPP1R14B and various tumor types based on abundant clinical data. We used the TCGA project and GEO databases to perform pan-cancer analysis of PPP1R14B, including expression differences, correlations between expression levels and survival, genetic alteration, immune infiltration, and relevant cellular pathways, to investigate the functions and potential mechanisms of PPP1R14B in the pathogenesis or clinical prognosis of different cancers. Herein, we found that PPP1R14B was involved in the prognosis of pan-cancer and closely related to immune infiltration. Increased PPP1R14B expression correlated with poor prognosis and increased immune infiltration levels in myeloid-derived suppressor cells (MDSCs). Our studies suggest that PPP1R14B can be used as a prognostic biomarker for pan-cancer. Our findings may provide an antitumor strategy targeting PPP1R14B, including manipulation of tumor cell growth or the tumor microenvironment, especially myeloid-derived suppressor cell infiltration.

Peripherally Inserted Central Catheter lines for Intensive Care Unit and onco-hematologic patients: A systematic review and meta-analysis

BACKGROUND

It is unclear whether Peripherally Inserted Central Catheter (PICC) lines are associated with lower complication rates as compared to conventional Central Venous Catheters (CVCs), especially in high risk patients.

OBJECTIVE

To compare Central Line Associated Bloodstream Infection (CLABSI) and catheter-related thrombosis rates in Intensive Care Unit (ICU) and onco-hematologic patients with PICC lines and CVCs.

METHODS

We systematically reviewed the PubMed, Cochrane and Google Scholar databases to identify relevant studies. Study quality was evaluated using appropriate assessment tools and the pooled odds ratio (OR) and confidence interval (CI) were calculated. Sensitivity analyses were performed based on meta-analysis method, type of study and prophylaxis implementation.

RESULTS

Thirteen studies were included in our meta-analysis. PICC lines were associated with a significantly higher rate of thrombosis in ICU [OR (95%CI): 2.58(1.80,3.70); P_z<0.00001] and onco-hematologic [OR (95%CI): 2.91(2.11,4.02); P_z<0.00001] patients. CLABSI rates with PICC lines were not significantly different in ICU patients [OR (95%CI): 1.65(0.91,2.99); P_z= 0.1], but significantly lower CLABSI rates were observed in onco-hematologic patients [OR (95%CI): 0.38(0.16,0.91); P_z=0.03]. Sensitivity analyses verified the robustness of our results.

CONCLUSIONS

PICC lines are associated with higher rates of thrombotic events. However, they might be suitable for onco-hematologic patients due to lower CLABSI rates.