ARL14 as a Prognostic Biomarker in Non-Small Cell Lung Cancer

Determination of the Immunomodulatory Role of OTOP2 in Colon Adenocarcinoma

Background: Otopetrin 2 (OTOP2) is a conserved ion channel protein that regulates cell signaling, growth, and development. Although the role of OTOP2 in tumor suppression has been reported in several studies of colon adenocarcinoma (COAD), characterized its immunomodulatory effects on tumors. Methods: We conducted a thorough analysis of OTOP2 expression and its association with clinicopathological characteristics, immune-related pathways, and immune-related molecules in individuals with COAD using data from The Cancer Genome Atlas (TCGA) and confirmed the findings with tissue microarrays (TMAs). We conducted in vitro assays to demonstrate the tumor suppressive effect of OTOP2 in COAD cells. Results: OTOP2 expression was abnormal in multiple types of tumors and was significantly downregulated in patients with COAD (P<0.001). Moreover, the presence of OTOP2 was linked to enhanced survival in individuals diagnosed with COAD. In vitro experiments showed that OTOP2 suppressed cell proliferation, migration, invasion, and adhesion. Gene set enrichment analysis of the TCGA database indicated that OTOP2 was positively correlated with antigen presentation pathways and T cell responses. The immunophenoscore (IPS) indicated a positive correlation between OTOP2 expression and MHC molecule expression (P<0.001) as well as between OTOP2 expression and the number of effector cells (P<0.01). Immunohistochemical analysis of the TMAs revealed strong associations between OTOP2 expression and MHC-I, TAP1, and TAP2 expression, and between OTOP2 expression and CD8+ T cell infiltration in COAD patients. Conclusion: In summary, our research emphasizes the role of OTOP2 as a tumor suppressor, suggesting its use as a prognostic indicator and predictor of response to immunotherapy in COAD patients.

Assessing the benefits and safety profile of incorporating poly ADP-ribose polymerase (PARP) inhibitors in the treatment of advanced lung cancer: a thorough systematic review and meta-analysis

Background

Poly (ADP-Ribose) Polymerase (PARP) inhibitors represent a novel class of drugs that hinder DNA repair mechanisms in tumor cells, leading to cell death. This systematic review aims to evaluate the effectiveness, safety, and potential adverse effects of PARP inhibitors (PARPi) in the management of patients with advanced lung cancer.

Materials and Methods

We conducted a comprehensive search for relevant studies in PubMed, Embase, Cochrane, and ClinicalTrials.gov. We extracted primary and secondary outcome measures, including progression-free survival (PFS), overall survival (OS), and adverse events (AEs), from the identified literature for subsequent meta-analysis and systematic review.

Results

This study encompassed twelve randomized controlled trials, involving 3,132 patients with advanced lung cancer. In comparison to non-PARPi treatments, the administration of PARPi significantly extended OS (hazard ratio (HR) = 0.90, 95% CI = 0.83-0.97, p = 0.006). However, the difference in PFS did not reach statistical significance.

Conclusion

In summary, therapies incorporating PARPi provide a degree of benefit by extending OS in patients with advanced lung cancer. Nonetheless, further trials are necessary to furnish additional evidence regarding the efficacy and safety of PARPi in the treatment of lung cancer.

Systematic Review Registration: https://www.crd.york.ac.uk/PROSPERO/, identifier number: CRD42023424673.

Mapping the global interactome of the ARF family reveals spatial organization in cellular signaling pathways

The ADP-ribosylation factors (ARFs) and ARF-like (ARL) GTPases serve as essential molecular switches governing a wide array of cellular processes. In this study, we used proximity-dependent biotin identification (BioID) to comprehensively map the interactome of 28 out of 29 ARF and ARL proteins in two cellular models. Through this approach, we identified ∼3000 high-confidence proximal interactors, enabling us to assign subcellular localizations to the family members. Notably, we uncovered previously undefined localizations for ARL4D and ARL10. Clustering analyses further exposed the distinctiveness of the interactors identified with these two GTPases. We also reveal that the expression of the understudied member ARL14 is confined to the stomach and intestines. We identified phospholipase D1 (PLD1) and the ESCPE-1 complex, more precisely, SNX1, as proximity interactors. Functional assays demonstrated that ARL14 can activate PLD1 in cellulo and is involved in cargo trafficking via the ESCPE-1 complex. Overall, the BioID data generated in this study provide a valuable resource for dissecting the complexities of ARF and ARL spatial organization and signaling.

Mapping the global interactome of the ARF family reveals spatial organization in cellular signaling pathways

The ADP-ribosylation factors (ARFs) and ARF-like (ARLs) GTPases serve as essential molecular switches governing a wide array of cellular processes. In this study, we utilized proximity-dependent biotin identification (BioID) to comprehensively map the interactome of 28 out of 29 ARF and ARL proteins in two cellular models. Through this approach, we identified ~3000 high-confidence proximal interactors, enabling us to assign subcellular localizations to the family members. Notably, we uncovered previously undefined localizations for ARL4D and ARL10. Clustering analyses further exposed the distinctiveness of the interactors identified with these two GTPases. We also reveal that the expression of the understudied member ARL14 is confined to the stomach and intestines. We identified phospholipase D1 (PLD1) and the ESCPE-1 complex, more precisely SNX1, as proximity interactors. Functional assays demonstrated that ARL14 can activate PLD1 in cellulo and is involved in cargo trafficking via the ESCPE-1 complex. Overall, the BioID data generated in this study provide a valuable resource for dissecting the complexities of ARF and ARL spatial organization and signaling.

Arginine methylation and respiratory disease

Arginine methylation, a vital post-translational modification, plays a pivotal role in numerous cellular functions such as signal transduction, DNA damage response and repair, regulation of gene transcription, mRNA splicing, and protein interactions. Central to this modification is the role of protein arginine methyltransferases (PRMTs), which have been increasingly recognized for their involvement in the pathogenesis of various respiratory diseases. This review begins with an exploration of the biochemical underpinnings of arginine methylation, shedding light on the intricate molecular regulatory mechanisms governed by PRMTs. It then delves into the impact of arginine methylation and the dysregulation of arginine methyltransferases in diverse pulmonary disorders. Concluding with a focus on the therapeutic potential and recent advancements in PRMT inhibitors, this article aims to offer novel perspectives and therapeutic avenues for the management and treatment of respiratory diseases.

A novel telomere-related genes model for predicting prognosis and treatment responsiveness in diffuse large B-cell lymphoma

Diffuse large B cell lymphoma (DLBCL) is a highly heterogeneous disease with diverse clinical and molecular features. Telomere maintenance is widely present in tumors, but there is a lack of relevant reports on the role of telomere-related genes (TRGs) in DLBCL. In this study, we used consensus clustering based on TRGs expression to identify two molecular clusters with distinct prognoses and immune cell infiltration. We developed a TRGs scoring model using univariate Cox regression and LASSO regression in the GSE10846 training cohort. DLBCL patients in the high-risk group had a worse prognosis than those in the low-risk group, as revealed by Kaplan-Meier curves. The scoring model was validated in the GSE10846 testing cohort and GSE87371 cohort, respectively. The high-risk group was characterized by elevated infiltration of activated DCs, CD56 dim natural killer cells, myeloid-derived suppressor cells, monocytes, and plasmacytoid DCs, along with reduced infiltration of activated CD4 T cells, Type 2 T helper cells, γδ T cells, NK cells, and neutrophils. Overexpression of immune checkpoints, such as PDCD1, CD274, and LAG3, was observed in the high-risk group. Furthermore, high-risk DLBCL patients exhibited increased sensitivity to bortezomib, rapamycin, AZD6244, and BMS.536924, while low-risk DLBCL patients showed sensitivity to cisplatin and ABT.263. Using RT-qPCR, we found that three protective model genes, namely TCEAL7, EPHA4, and ELOVL4, were down-regulated in DLBCL tissues compared with control tissues. In conclusion, our novel TRGs-based model has great predictive value for the prognosis of DLBCL patients and provides a promising direction for treatment optimization.

High Expression of PSRC1 Predicts Poor Prognosis in Lung Adenocarcinoma

Background: The incidence of lung cancer is increasing annually, but the mechanism of its occurrence and development requires further study. This study aimed to investigate the biological function and prognostic value of proline- and serine-rich coiled-coil 1 (PSRC1) in lung cancer. Methods: We used data from The Cancer Genome Atlas (TCGA) to analyze the association between clinical features and PSRC1 expression in non-small cell carcinoma. The relationship between PSRC1 expression and prognosis in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) was analyzed using Kaplan-Meier curves. The function of PSRC1 was identified using enrichment analysis, and the relationship between PSRC1 expression and immune cell infiltration was studied. In addition, the expression of PSRC1 in 150 patients with non-small cell carcinoma was detected using immunohistochemistry, and its clinical significance was analyzed. Results: It was found that the expression level of PSRC1 was higher in LUAD and LUSC tumor tissues than in normal tissues, and the results were confirmed by immunohistochemistry in 150 patients. TCGA data showed that high PSRC1 expression in LUAD was associated with poorer overall survival (p = 0.003) and progression-free interval (p = 0.012). Multivariable analysis showed that PSRC1 was an independent risk factor for LUAD. Functional enrichment analysis showed that PSRC1 is related to tumor development. Conclusion: High PSRC1 expression is significantly associated with LUAD survival and may be a promising prognostic biomarker.

Development and Verification of a novel cuproptosis- and immune-associated based prognostic genetic signature for pancreatic ductal adenocarcinoma

OBJECTIVE

Pancreatic ductal adenocarcinoma (PDAC) is a malignancy with a dismal prognosis. Cuproptosis, a novel mechanism mediated by protein lipoylation, results in acute proteotoxic stress and ultimately cell death. However, the clinical impacts of cuproptosis-associated genes and their relationship with immune status in PDAC have not been documented. In this study, we aimed at constructing a cuproptosis- and immune-associated prognostic signature to stratify and predict the prognosis for PDAC patients.

METHODS

The gene expression profiles of 176 PDAC patients from The Cancer Genome Atlas and 167 normal pancreas tissues from the Genotype-Tissue Expression Project were analyzed for differentially expressed genes (DEGs) between PDAC and normal tissues. Pearson correlation analyses were performed to screen out cuproptosis- and immune-associated DEGs. The risk signature of DEGs was constructed using the least absolute shrinkage and selection operator (LASSO) Cox regression analysis, which was validated in the Gene Expression Omnibus (GEO) cohort (n = 114). The immune characteristics in the two risk groups were evaluated using single-sample gene set enrichment analysis and ESTIMATE algorithms.

RESULTS

A total of 91 cuproptosis- and immune-associated DEGs were screened out, and eight prognostic-related genes were identified using LASSO Cox regression. The prognostic-related genes were then used to construct a risk scoring model, which stratified patients into low- and high-risk groups and were further verified in the external GEO database. The patients in the high-risk group had significantly shorter overall survival than those in the low-risk group. A nomogram based on the risk signature was then constructed. Immune infiltration evaluation suggested that immune status was more activated in the low-risk group. The mutation spectrum also differed between high- and low-risk groups.

CONCLUSIONS

Our cuproptosis- and immune-associated genetic risk signature could be a prognostic biomarker for PDAC. Cuproptosis might be a promising therapeutic target for PDAC.

Serum cytokine levels and other associated factors as possible immunotherapeutic targets and prognostic indicators for lung cancer

Lung cancer is one of the most prevalent cancer types and the leading cause of cancer-related deaths worldwide. Non-small cell lung cancer (NSCLC) accounts for 80-85% of all cancer incidences. Lung cancer therapy and prognosis largely depend on the disease's degree at the diagnosis time. Cytokines are soluble polypeptides that contribute to cell-to-cell communication, acting paracrine or autocrine on neighboring or distant cells. Cytokines are essential for developing neoplastic growth, but they are also known to operate as biological inducers following cancer therapy. Early indications are that inflammatory cytokines such as IL-6 and IL-8 play a predictive role in lung cancer. Nevertheless, the biological significance of cytokine levels in lung cancer has not yet been investigated. This review aimed to assess the existing literature on serum cytokine levels and additional factors as potential immunotherapeutic targets and lung cancer prognostic indicators. Changes in serum cytokine levels have been identified as immunological biomarkers for lung cancer and predict the effectiveness of targeted immunotherapy.

Pyroptosis-based risk score predicts prognosis and drug sensitivity in lung adenocarcinoma

Pyroptosis is a recently identified form of programmed cell death; however, its role in lung adenocarcinoma (LUAD) remains unclear. Therefore, we set out to explore the prognostic potential of pyroptosis-related genes in LUAD. The pyroptosis-related risk score (PRRS) was developed by least absolute shrinkage and selection operator Cox regression and multivariate Cox regression. We found that PRRS was an independent prognostic factor for LUAD. LUAD patients in the high-PRRS group showed a significantly shorter overall survival (OS) and enriched in cell proliferation-related pathways. Then pathway enrichment analyses, mutation profile, tumor microenvironment, and drug sensitivity analysis were further studied in PRRS stratified LUAD patients. Tumor purity (TP) analyses revealed that L-PRRS LUAD patients had a lower TP, and patients in L-TP + L-PRRS subgroup had the most prolonged OS. Mutation analyses suggested that the L-PRRS LUAD patients had a lower tumor mutation burden (TMB), and patients in H-TMB + L-PRRS subgroup had the most prolonged OS. Drug sensitivity analyses showed that PRRS was significantly negatively correlated with the sensitivity of cisplatin, besarotene, etc., while it was significantly positively correlated with the sensitivity of kin001-135. Eventually, a nomogram was constructed based on PRRS and clinical characters of LUAD. Overall, the pyroptosis-related signature is helpful for prognostic prediction and in guiding treatment for LUAD patients.

High Expression of DEPDC1B Predicts Poor Prognosis in Lung Adenocarcinoma

Introduction

Lung adenocarcinoma (LUAD) is the most common type of lung cancer. DEP domain-containing 1 B (DEPDC1B) is involved in the development of several cancers; however, its role in LUAD is unknown. Therefore, we aimed to determine the biological function and prognostic value of DEPDC1B in LUAD.

Material and Methods

We analyzed the correlation between DEPDC1B expression and the clinical features of LUAD and lung squamous cell carcinoma (LUSC). Survival was evaluated by generating Kaplan-Meier curves, which were used to analyze the relationship between DEPDC1B expression and prognosis in LUAD and LUSC. DEPDC1B expression in tumor and normal tissues from patients with LUAD and LUSC was determined using immunohistochemistry, and its clinical significance was analyzed. Finally, the correlation between the expression and biological function of DEPDC1B in LUAD was examined.

Results

Our findings revealed that DEPDC1B expression was higher in tumor tissues than that in normal tissues from patients with LUAD and LUSC (P < 0.001). These results were confirmed in clinical samples from patients using immunohistochemistry. Analysis of a dataset from The Cancer Genome Atlas (TCGA) showed that high DEPDC1B expression was associated with poor prognosis only in patients with LUAD (P < 0.001). Similarly, high DEPDC1B expression was related to shorter overall survival (OS) and progression-free interval (PFI) in patients with LUAD. These associations were not observed in LUSC. Functional enrichment analysis suggested that DEPDC1B promoted tumor development in LUAD by regulating the cell cycle.

Conclusion

High DEPDC1B expression predicts poor prognosis in patients with LUAD. Thus, DEPDC1B has potential as a therapeutic target for LUAD.

A Systematic Review of Companion Diagnostic Tests by Immunohistochemistry for the Screening of Alectinib-Treated Patients in ALK-Positive Non-Small Cell Lung Cancer

Companion diagnostic tests and targeted therapy changed the management of non-small cell lung cancer by diagnosing genetic modifications and enabling individualized treatment. The purpose of this systematic review is to assess the clinical applicability of companion diagnostic tests (IHC method) by comparing the effects of alectinib and crizotinib in patients with ALK-positive NSCLC. We searched for literature up to March 2022 in PubMed, Web of Science, Cochrane, and Google Scholar. The inclusion criteria were randomized controlled trials comparing the effectiveness of alectinib and crizotinib using an IHC-based companion diagnostic test. The primary outcome was progression-free survival (PFS). The secondary outcomes were objective response rate (ORR), duration of response (DOR), and overall survival (OS). PFS was longer in alectinib (68.4 [61.0, 75.9]) than crizotinib (48.7 [40.4, 56.9]). This indicated that alectinib had a superior efficacy to that of crizotinib (HR range 0.15–0.47). In all secondary outcomes, alectinib was better than crizotinib. Particularly for the ORR, the odds ratio (OR) confirmed that alectinib had a lower risk rate (OR: 2.21, [1.46–3.36], p = 0.0002, I² = 39%). Therefore, the companion diagnostic test (immunohistochemistry) is an effective test to determine whether to administer alectinib to ALK-positive NSCLC patients.