DDA1, a novel oncogene, promotes lung cancer progression through regulation of cell cycle

Roles of lncRNAs in NF-κB-Mediated Macrophage Inflammation and Their Implications in the Pathogenesis of Human Diseases

Over the past century, molecular biology's focus has transitioned from proteins to DNA, and now to RNA. Once considered merely a genetic information carrier, RNA is now recognized as both a vital element in early cellular life and a regulator in complex organisms. Long noncoding RNAs (lncRNAs), which are over 200 bases long but do not code for proteins, play roles in gene expression regulation and signal transduction by inducing epigenetic changes or interacting with various proteins and RNAs. These interactions exhibit a range of functions in various cell types, including macrophages. Notably, some macrophage lncRNAs influence the activation of NF-κB, a crucial transcription factor governing immune and inflammatory responses. Macrophage NF-κB is instrumental in the progression of various pathological conditions including sepsis, atherosclerosis, cancer, autoimmune disorders, and hypersensitivity. It orchestrates gene expression related to immune responses, inflammation, cell survival, and proliferation. Consequently, its malfunction is a key contributor to the onset and development of these diseases. This review aims to summarize the function of lncRNAs in regulating NF-κB activity in macrophage activation and inflammation, with a particular emphasis on their relevance to human diseases and their potential as therapeutic targets. The insights gained from studies on macrophage lncRNAs, as discussed in this review, could provide valuable knowledge for the development of treatments for various pathological conditions involving macrophages.

Macrophage lncRNAs in cancer development: Long-awaited therapeutic targets

In the tumor microenvironment, the interplay among macrophages, cancer cells, and endothelial cells is multifaceted. Tumor-associated macrophages (TAMs), which often exhibit an M2 phenotype, contribute to tumor growth and angiogenesis, while cancer cells and endothelial cells reciprocally influence macrophage behavior. This complex interrelationship highlights the importance of targeting these interactions for the development of novel cancer therapies aimed at disrupting tumor progression and angiogenesis. Accumulating evidence underscores the indispensable involvement of lncRNAs in shaping macrophage functionality and contributing to the development of cancer. Animal studies have further validated the therapeutic potential of manipulating macrophage lncRNA activity to ameliorate disease severity and reduce morbidity rates. This review provides a survey of our current understanding of macrophage-associated lncRNAs, with a specific emphasis on their molecular targets and their regulatory impact on cancer progression. These lncRNAs predominantly govern macrophage polarization, favoring the dominance of M2 macrophages or TAMs. Exosomes or extracellular vesicles mediate lncRNA transfer between macrophages and cancer cells, affecting cellular functions of each other. Moreover, this review presents therapeutic strategies targeting cancer-associated lncRNAs. The insights and findings presented in this review pertaining to macrophage lncRNAs can offer valuable information for the development of treatments against cancer.

Integrative exploration of the mutual gene signatures and immune microenvironment between benign prostate hyperplasia and castration-resistant prostate cancer

BACKGROUND

Benign prostate hyperplasia (BPH) and prostate cancer (CaP) are among the most frequently occurring prostatic diseases. When CaP progressed to castration-resistant CaP (CRPC), the prognosis is poor. Although CaP/CRPC and BPH frequently coexist in prostate, the inter-relational mechanism between them is largely unknown.

METHODS

Single-cell RNA sequencing, bulk-RNA sequencing, and microarray data of BPH, CaP in the Gene Expression Omnibus database were obtained and comprehensively analyzed. Weighted Gene Co-Expression Network Analysis (WGCNA) and lasso regression analysis were performed to explore the potential biomarkers.

RESULTS

With WGCNA, five modules in BPH, two in CaP, and three in CRPC were identified as significant modules. Pathway enrichment analysis found that the epigenetics and chromosomal-related signaling were dominantly clustered in the CaP group but not in BPH and CRPC. Lasso regression analysis was used to analyze further the mutual genes between the BPH module and the CRPC module. As a result, DDA1, ERG28, OGFOD1, and OXA1L were significantly correlated with the transcriptomic features in both BPH and CRPC. More importantly, the role of the four gene signatures was validated in two independent anti-PD-1 immunotherapy cohort.

CONCLUSION

This study revealed the shared gene signatures and immune microenvironment between BPH and CRPC. The identified hub genes, including DDA1, ERG28, OGFOD1, and OXA1L, might be potential therapeutic targets for facilitating immunotherapy in prostate cancer.

H4S47 O-GlcNAcylation regulates the activation of mammalian replication origins

The transmission and maintenance of genetic information in eukaryotic cells relies on the faithful duplication of the entire genome. In each round of division, excessive replication origins are licensed, with only a fraction activated to give rise to bi-directional replication forks in the context of chromatin. However, it remains elusive how eukaryotic replication origins are selectively activated. Here we demonstrate that O-GlcNAc transferase (OGT) enhances replication initiation by catalyzing H4S47 O-GlcNAcylation. Mutation of H4S47 impairs DBF4-dependent protein kinase (DDK) recruitment on chromatin, causing reduced phosphorylation of the replicative helicase mini-chromosome maintenance (MCM) complex and compromised DNA unwinding. Our short nascent-strand sequencing results further confirm the importance of H4S47 O-GlcNAcylation in origin activation. We propose that H4S47 O-GlcNAcylation directs origin activation through facilitating MCM phosphorylation, and this may shed light on the control of replication efficiency by chromatin environment.

A clinically compatible drug-screening platform based on organotypic cultures identifies vulnerabilities to prevent and treat brain metastasis

We report a medium-throughput drug-screening platform (METPlatform) based on organotypic cultures that allows to evaluate inhibitors against metastases growing in situ. By applying this approach to the unmet clinical need of brain metastasis, we identified several vulnerabilities. Among them, a blood-brain barrier permeable HSP90 inhibitor showed high potency against mouse and human brain metastases at clinically relevant stages of the disease, including a novel model of local relapse after neurosurgery. Furthermore, in situ proteomic analysis applied to metastases treated with the chaperone inhibitor uncovered a novel molecular program in brain metastasis, which includes biomarkers of poor prognosis and actionable mechanisms of resistance. Our work validates METPlatform as a potent resource for metastasis research integrating drug-screening and unbiased omic approaches that is compatible with human samples. Thus, this clinically relevant strategy is aimed to personalize the management of metastatic disease in the brain and elsewhere.

Development and validation of a prognostic nomogram for patients with lung adenocarcinoma based on a novel 6-DNA repair-related gene signature

DNA repair-related genes (DRGs) have attracted much attention in the field of oncology. However, the prognostic role of DRGs and their biological function in lung adenocarcinoma (LUAD) remains rudimentary and inconclusive. In this study, 716 LUAD cases from two different cohorts were collected. Samples from The Cancer Genome Atlas (TCGA) were used as the training set, and data from Gene Expression Omnibus (GEO) datasets were used for validation. Using multivariate Cox analysis and LASSO regression, we constructed a DRG signature and used it, together with clinical indices, to develop a nomogram to predict 1-, 3-, and 5-year survival rates. We identified a six-DRG signature to estimate the survival of LUAD patients, which distinguished high-risk from low-risk patients with LUAD in both the training and validation cohorts. We also observed elevated levels of infiltrating CD4 memory activated T cells, resting NK cells, M0 and M1 macrophages, and activated mast cells in the high-risk group. Finally, a nomogram incorporating the signature and clinical parameters was superior to the American Joint Committee on Cancer (AJCC) staging system in predicting the survival of LUAD patients. The DRG prognostic signature and integrated nomogram could be a useful tool to predict prognosis in patients with LUAD.

Identification of key genes associated with progression and prognosis for lung squamous cell carcinoma

Background

Lung squamous cell carcinoma (LUSC) is a major subtype of lung cancer with limited therapeutic options and poor clinical prognosis.

Methods

Three datasets (GSE19188, GSE33532 and GSE33479) were obtained from the gene expression omnibus (GEO) database. Differentially expressed genes (DEGs) between LUSC and normal tissues were identified by GEO2R, and functional analysis was employed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) online tool. Protein-protein interaction (PPI) and hub genes were identified via the Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape software. Hub genes were further validated in The Cancer Genome Atlas (TCGA) database. Subsequently, survival analysis was performed using the Kapla-Meier curve and Cox progression analysis. Based on univariate and multivariate Cox progression analysis, a gene signature was established to predict overall survival. Receiver operating characteristic curve was used to evaluate the prognostic value of the model.

Results

A total of 116 up-regulated genes and 84 down-regulated genes were identified. These DEGs were mainly enriched in the two pathways: cell cycle and p53 signaling way. According to the degree of protein nodes in the PPI network, 10 hub genes were identified. The mRNA expression levels of the 10 hub genes in LUSC were also significantly up-regulated in the TCGA database. Furthermore, a novel seven-gene signature (FLRT3, PPP2R2C, MMP3, MMP12, CAPN8, FILIP1 and SPP1) from the DEGs was constructed and acted as a significant and independent prognostic signature for LUSC.

Conclusions

The 10 hub genes might be tightly correlated with LUSC progression. The seven-gene signature might be an independent biomarker with a significant predictive value in LUSC overall survival.

SEZ6L2 knockdown impairs tumour growth by promoting caspase-dependent apoptosis in colorectal cancer

Seizure‐related 6 homolog (mouse)‐like 2 (SEZ6L2) was shown to be involved in transcription of a type 1 transmembrane protein for regulating cell fate. Until now, the expression and function of SEZ6L2 in various cancers, including colorectal cancer (CRC), were unclear. In the present study, we determined the expression of SEZ6L2 in a tissue microarray from patients with CRC and then, analysed the correlation between SEZ6L2 expression and the prognosis of the patients. Furthermore, the potential function of SEZ6L2 in CRC was determined using cell counting kit, colony formation assay and xenograft model in vitro and in vivo. Flow cytometry, Western blotting, immunohistochemical staining and a blocking experiment were employed to investigate the underlying mechanism of SEZ6L2 regulating CRC growth. Our results indicated that SEZ6L2 was significantly up‐regulated in tumour tissues of patients with CRC compared with adjacent normal tissues. Up‐regulation of SEZ6L2 was correlated with a poor prognosis in patients with CRC. In vitro experiments suggested that the knockdown of SEZ6L2 inhibits CRC cell growth and colony formation, but it has no significant impact on the invasion. The antitumour effects of shSEZ6L2 were also confirmed by a xenograft model. Investigations of the mechanisms indicated that the knockdown of SEZ6L2 impairs the growth of the CRC cells by inducing caspase‐dependent apoptosis, which was mediated by mitochondria‐related proteins. Furthermore, SEZ6L2 expression was inversely correlated with the expression of cytochrome C in malignant tissues in patients with CRC. Collectively, the present study indicates that SEZ6L2 is a potential prognosis biomarker and therapy target for CRC.

lncRNA-ATB promotes stemness maintenance in colorectal cancer by regulating transcriptional activity of the β-catenin pathway

Long non-coding RNA activated by transforming growth factor-β (ATB) was recently reported to be involved in a wide range of physiological and pathological processes. However, the role of ATB in colorectal cancer (CRC) stemness remains unclear. In the present study, the functional role of ATB in maintaining stemness of CRC was determined using colony formation and sphere formation assays, and xenograft models. Reverse transcription-quantitative PCR, western blotting and immunohistochemistry were performed to investigate the mechanisms underlying the effects of ATB. Knockdown of ATB impaired colony formation and sphere formation in CRC cells, accompanied by an inhibition of colon tumor growth. Further results suggested that ATB regulated the transcriptional activity of the β-catenin pathway by inhibiting β-catenin expression. In addition, the results confirmed the role of β-catenin in ATB-mediated regulation of stemness in CRC. Collectively, the results indicated that ATB is a promising therapeutic target for CRC.

Inhibition of Sirt6 suppresses tumor growth by inducing G1/S phase arrest in renal cancer cells

Sirt6 is a vital member of the Sirtuin family that plays a key role in cellular apoptosis, aging, DNA damage repair, telomere homeostasis and integrity, energy metabolism, glucose homeostasis, and gene regulation. In recent studies, Sirt6 is down-regulated in several cancers and predicted to be a tumor suppressor, but as a tumor oncogene in other cancers. In this study, we explored the specific role of Sirt6 in human renal cell carcinoma (RCC). We found that Sirt6 was up-expressed in renal tumor tissues and cells. Sirt6 silence in RCC led to G1/S phase arrest, a rise in apoptosis and a decrease in cell viability, as well as an enhancement of chemotherapeutic sensitivity. In conclusion, these findings suggest that Sirt6 acted as an oncogene in human RCC and it could be a potential target for RCC treatment.

Arabidopsis CRL4 Complexes: Surveying Chromatin States and Gene Expression

CULLIN4 (CUL4) RING ligase (CRL4) complexes contain a CUL4 scaffold protein, associated to RBX1 and to DDB1 proteins and have traditionally been associated to protein degradation events. Through DDB1, these complexes can associate with numerous DCAF proteins, which directly interact with specific targets promoting their ubiquitination and subsequent degradation by the proteasome. A characteristic feature of the majority of DCAF proteins that associate with DDB1 is the presence of the DWD motif. DWD-containing proteins sum up to 85 in the plant model species Arabidopsis. In the last decade, numerous Arabidopsis DWD proteins have been studied and their molecular functions uncovered. Independently of whether their association with CRL4 has been confirmed or not, DWD proteins are often found as components of additional multimeric protein complexes that play key roles in essential nuclear events. For most of them, the significance of their complex partnership is still unexplored. Here, we summarize recent findings involving both confirmed and putative CRL4-associated DCAF proteins in regulating nuclei architecture remodelling, DNA damage repair, histone post-translational modification, mRNA processing and export, and ribosome biogenesis, that definitely have an impact in gene expression and de novo protein synthesis. We hypothesized that, by maintaining accurate levels of regulatory proteins through targeted degradation and transcriptional control, CRL4 complexes help to surveil nuclear processes essential for plant development and survival.

MicroRNA-29c restores cisplatin sensitivity in liver cancer through direct inhibition of sirtuin 1 expression

Liver cancer is one of the most prevalent human tumors in the world. Despite recent advances regarding the understanding of the molecular basis of liver cancer and the introduction of novel chemotherapeutic approaches, liver cancer remains associated with a poor prognosis. Sirtuin 1 (SIRT1) was identified to be abnormally upregulated in liver cancer. Dysregulation of microRNAs (miRs/miRNAs) is associated with a variety of types of cancer, and miRNAs may also serve a role in tumorigenesis and progression. The present study demonstrated that following the selection of the cisplatin chemoresistant HepG2 cell line, miR-29c is downregulated using reverse transcription-quantitative polymerase chain reaction. Furthermore, overexpression of miR-29c in cisplatin-resistant cancer cells was demonstrated to inhibit tumor cell proliferation and to promote apoptosis in vitro and in vivo, as well as restoring cisplatin chemosensitivity by using a cell counting assay, colony formation assay, Annexin V-fluorescein isothocyanate/propidium iodide apoptosis analysis, terminal deoxynucleotidyl transferase dUTP nick end labeling and xenograft tumors in nude mice. Mechanistically, according to bioinformatics analysis and a luciferase assay, miR-29c may directly target SIRT1 mRNA and repress SIRT1 expression, which is positively associated with the chemoresistance of liver cancer and may ultimately provide a novel therapeutic method.

Necrostatin-1 attenuates lipopolysaccharide-induced acute lung injury in mice

AIM OF THE STUDY

Receptor-interacting protein (RIP) kinase family members are involved in several biological processes. However, their role in acute lung injury (ALI) is still unclear. In the present study, we aim to determine the expression and function of RIP kinase family in ALI.

MATERIALS AND METHODS

In the present study, ALI was induced in BALB/c male mice by intravenously injecting lipopolysaccharide (LPS). The expression levels of the RIP kinase family in ALI mice were determined using western blotting and immunohistochemical staining. The specific RIP-1 inhibitor, necrostatin-1, was used to treat LPS-induced ALI mice, followed by survival time recording, as well as histopathological and immunohistochemical staining of lung tissues, western blotting, myeloperoxidase (MPO) assay and enzyme-linked immunosorbent assay (ELISA) of related cytokines and downstream target expression.

RESULTS

We found that RIP-1 expression was upregulated in the lung of ALI mice and inhibition of RIP-1 by necrostatin-1 significantly prolonged the survival time of mice, which was accompanied by less serve lung injury. Furthermore, lower expression of pro-inflammatory cytokines (interleukin [IL]-6, tumor necrosis factor [TNF]-α, IL-8, cyclooxygenase [COX]-2, monocyte chemoattractant protein [MCP]-1, and IL-1β), MPO and nuclear factor (NF)-κB activation were found in bronchoalveolar lavage fluid (BALF) and lung tissues of necrostatin-1-treated ALI mice. Necrostatin-1 also attenuated LPS-induced pro-inflammatory cytokine expression and NF-κB activation in RAW 264.7 cells.

CONCLUSIONS

In summary, necrostatin-1 protected against LPS-induced ALI in mice by inhibiting inflammation and pulmonary NF-κB activation. Thus, necrostatin-1 could be a novel therapeutic strategy for ALI.

TIPE1 function as a prognosis predictor and negative regulator of lung cancer

TIPE1 (tumor necrosis factor-α-induced protein 8-like 1 or TNFAIP8L1) belongs to the TIPE (TNFAIP8) family, which act as a regulator of cell death. However, the expression and biologic functions of TIPE1 in lung cancer are largely unknown. Here, we investigated the roles of TIPE1 in lung cancer. Evaluated by qRT-PCR and immunohistochemical staining, lower TIPE1 mRNA and protein expression was found in the lung tumor tissue, compared with adjacent non-tumor tissues, which positively correlated with tumor patient survival. Overexpression of TIPE1 by lentivirus system in TIPE1-downregulated lung cancer cells significantly diminished cell growth and colony formation, companied with proliferation inhibition, apoptosis induction and invasion inhibition. It was identified to be due to TIPE1-regulated Cyclin D1, Cyclin B1, caspase 8, Caspase3, MM2 and MMP9 expression. Consistently, using a homograft tumor model in Balb/c mice, we discovered that TIPE1 prevented the growth and tumor weight of murine lung cancer homografts. Our findings revealed the anti-tumor role of TIPE1 in lung cancer cells and TIPE1 might be a novel prognostic indicator for lung cancer patients.

Identification of proteasome subunit alpha type-1 as a novel biomarker in HBV-associated hepatocellular carcinoma tissue interstitial fluid by proteomic analysis

Differentially expressed proteins between HCC TIF and normal interstitial fluid of adjacent nontumor tissues were identified through comparative proteomics approach. Then, two-dimensional gel electrophoresis (2-DE), matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), In-Cell Western technique, and reverse transcription-polymerase chain reaction (RT-PCR) were used to verify differentially expressed proteins. As a result, through 2-DE, 69 spots were roughly recognized as differentially expressed protein spots, while 44 proteins were identified as differentially expressed spots through MALDI-TOF-MS. Of the identified differential protein spots, 31 were significant according to the bioinformatics analysis results. Proteasome subunit alpha type-1 (PSMA1) expression was down-regulated in HCC TIF. Thus, PSMA1 is considered as a potential biomarker for HBV-associated hepatocellular carcinoma.