PDLIM5 inhibits STUB1-mediated degradation of SMAD3 and promotes the migration and invasion of lung cancer cells

Targeting p97-Npl4 interaction inhibits tumor Treg cell development to enhance tumor immunity

Targeting tumor-infiltrating regulatory T (TI-Treg) cells is a potential strategy for cancer therapy. The ATPase p97 in complex with cofactors (such as Npl4) has been investigated as an antitumor drug target; however, it is unclear whether p97 has a function in immune cells or immunotherapy. Here we show that thonzonium bromide is an inhibitor of the interaction of p97 and Npl4 and that this p97-Npl4 complex has a critical function in TI-Treg cells. Thonzonium bromide boosts antitumor immunity without affecting peripheral Treg cell homeostasis. The p97-Npl4 complex bridges Stat3 with E3 ligases PDLIM2 and PDLIM5, thereby promoting Stat3 degradation and enabling TI-Treg cell development. Collectively, this work shows an important role for the p97-Npl4 complex in controlling Treg-TH17 cell balance in tumors and identifies possible targets for immunotherapy.

Novel SERCA2 inhibitor Diphyllin displays anti-tumor effect in non-small cell lung cancer by promoting endoplasmic reticulum stress and mitochondrial dysfunction

Abnormal calcium signaling is associated with non-small cell lung cancer (NSCLC) malignant progression, poor survival and chemotherapy resistance. Targeting endoplasmic reticulum (ER) Ca2+ channels or pumps to block calcium uptake in the ER induces ER stress and concomitantly promotes mitochondrial calcium uptake, leading to mitochondrial dysfunction and ultimately inducing cell death. Here, we identified Diphyllin was a potential specific inhibitor of endoplasmic reticulum (ER) calcium-importing protein sarco/endoplasmic-reticulum Ca2+ ATPase 2 (SERCA2). In vitro and in vivo studies showed that Diphyllin increased NSCLC cell apoptosis, along with inhibition of cell proliferation and migration. Mechanistically, Diphyllin promoted ER stress by directly inhibiting SERCA2 activity and decreasing ER Ca2+ levels. At the same time, the accumulated Ca2+ in cytoplasm flowed into mitochondria to increase reactive oxygen species (ROS) and decrease mitochondrial membrane potential (MMP), leading to cytochrome C (Cyto C) release and mitochondrial dysfunction. In addition, we found that Diphyllin combined with cisplatin could have a synergistic anti-tumor effect in vitro and in vivo. Taken together, our results suggested that Diphyllin, as a potential novel inhibitor of SERCA2, exerts anti-tumor effects by blocking ER Ca2+ uptake and thereby promoting ER stress and mitochondrial dysfunction.

Advances of E3 ligases in lung cancer

Lung cancer is a leading cause of cancer-related death, and the most common type of lung cancer is non-small cell lung cancer, which accounts for approximately 85 % of lung cancer diagnoses. Recent studies have revealed that ubiquitination acts as a crucial part of the development and progression of lung cancer. The E1-E2-E3 three-enzyme cascade has a core function in ubiquitination, so targeted adjustments of E3 ligases could be used in lung cancer treatment. Hence, we elucidate research advances in lung cancer-related E3 ligases by briefly describing the structure and categorization of E3 ligases. Here, we provide a detailed review of the mechanisms by which lung cancer-related E3 ligases modify substrate proteins and regulate signaling pathways to facilitate or suppress cancer progression. We hope to show a new perspective on targeted precision therapy for lung cancer.

A Novel Effect of Id2 in Microglia TNFα Regulation

Microglia are the most important immune cells in the central nervous system (CNS), which can defend against external pathogens and stimuli. Dysregulation of microglia releases excessive proinflammatory cytokines and leads to neuroinflammation, which is fundamental to the pathophysiology of multiple neurological diseases. However, the molecular mechanisms underlying the regulation of proinflammatory cytokines in microglia are still not well-understood. Here, we identified that inhibitor of DNA binding protein 2 (Id2) was a negative regulator of tumor necrosis factor-α (TNFα) in cultured microglia. Knockdown of Id2 significantly increased the expression of TNFα in microglia, while overexpression of Id2 inhibited TNFα expression. Furthermore, by interacting with the p65 subunit of nuclear factor kappa-B (NF-κB), Id2 suppressed the transcription activation of NF-κB and inhibited TNFα expression. Interestingly, in lipopolysaccharides (LPS)-treated microglia, Id2 increased and underwent a cytoplasmic relocation. Immunoprecipitation and immunostaining results showed that by binding to the LIM domain of Id2, a scaffold protein PDZ and LIM 5 (PDLIM5) involved in the Id2 cytoplasmic relocation, which inactivated Id2 and resulted in higher TNFα expression in LPS-treated microglia. Collectively, our data delineate a novel effect of Id2 on TNFα regulation in microglia, which may shed a light on the proinflammatory cytokines regulating in microglia associated neuroimmune disorders.

Linc00673-V3 positively regulates autophagy by promoting Smad3-mediated LC3B transcription in NSCLC

Since its first discovery, long noncoding RNA Linc00673 has been linked to carcinogenesis and metastasis of various human cancers. Linc00673 had five transcriptional isoforms and their biological functions remained to be explored. Here we have reported that Linc00673-V3, one of the isoforms of Linc00673, promoted non-small cell lung cancer chemoresistance, and increased Linc00673-V3 expression level was associated with enhanced autophagy. Mechanistically, we discerned the existence of a stem-loop configuration engendered by the 1-100-nt and 2200-2275-nt fragments within Linc00673-V3. This structure inherently interacted with Smad3, thereby impeding its ubiquitination and subsequent degradation orchestrated by E3 ligase STUB1. The accumulation of Smad3 contributed to autophagy via up-regulation of LC3B transcription and ultimately conferred chemoresistance in NSCLC. Our results revealed a novel transcriptional regulation network between Linc00673-V3, Smad3, and LC3B, which provided an important insight into the interplay between autophagy regulation and non-canonical function of Smad3. Furthermore, the results from in vivo experiments suggested Linc00673-V3 targeted antisense oligonucleotide as a promising therapeutic strategy to overcome chemotherapy resistance in NSCLC.

Expression of PDLIM5 Spliceosomes and Regulatory Functions on Myogenesis in Pigs

Meat yield, determined by muscle growth and development, is an important economic trait for the swine industry and a focus of research in animal genetics and breeding. PDZ and LIM domain 5 (PDLIM5) are cytoskeleton-related proteins that play key roles in various tissues and cells. These proteins have multiple isoforms, primarily categorized as short (PDLIM5-short) and long (PDLIM5-long) types, distinguished by the absence and presence of an LIM domain, respectively. However, the expression patterns of swine PDLIM5 isoforms and their regulation during porcine skeletal muscle development remain largely unexplored. We observed that PDLIM5-long was expressed at very low levels in pig muscles and that PDLIM5-short and total PDLIM5 were highly expressed in the muscles of slow-growing pigs, suggesting that PDLIM5-short, the dominant transcript in pigs, is associated with a slow rate of muscle growth. PDLIM5-short suppressed myoblast proliferation and myogenic differentiation in vitro. We also identified two single nucleotide polymorphisms (-258 A > T and -191 T > G) in the 5' flanking region of PDLIM5, which influenced the activity of the promoter and were associated with muscle growth rate in pigs. In summary, we demonstrated that PDLIM5-short negatively regulates myoblast proliferation and differentiation, providing a theoretical basis for improving pig breeding programs.

Identification of ATAD3A as a key regulator in non-small cell lung cancer by promoting STAT3-induced cell proliferation and tumor angiogenesis

Malignant proliferation and abundant angiogenesis are major causes of lung adenocarcinoma (LUAD) with high morbidity and mortality. Therefore, the exploration of the key regulatory mechanisms of malignant proliferation and angiogenesis in LUAD provides an opportunity for the development of targeted precision therapy. In this study, we found that the high expression of ATPase family AAA domain-containing protein 3A (ATAD3A) in LUAD was positively associated with the poor survival of patients, while its high expression was positively associated with the angiogenesis of LUAD. Further knockdown of ATAD3A in LUAD significantly inhibited cell proliferation and suppressed expression of vascular endothelial growth factor A, FGF-2, ANG-1, and TGF-β. The opposite effect was observed with ATAD3A overexpression. Furthermore, ATAD3A knockdown significantly inhibited tumor growth and angiogenesis in an in vivo subcutaneous xenograft tumor model. Mechanistic studies suggest that ATAD3A may promote signal transducer and activator of transcription 3 activation, a key signal regulating lung cancer cell proliferation and transcriptional secretion of proangiogenic factors. Therefore, targeted inhibition of ATAD3A may be an effective strategy for LUAD therapy, and ATAD3A may be a potential biomarker for predicting malignant progression.

POH1 induces Smad3 deubiquitination and promotes lung cancer metastasis

Smad3 is the key mediator of TGF-β1-triggered signal transduction and the related biological responses, promoting cell invasion and metastasis in various cancers, including lung cancer. However, the deubiquitinase stabilizing Smad3 remains unknown. In this study, we present a paradigm in which POH1 is identified as a novel deubiquitinase of Smad3 that plays a tumor-promoting role in lung adenocarcinoma (LUAD) by regulating Smad3 stability. POH1 markedly increased Smad3 protein levels and prolonged its half-life. POH1 directly interacted and colocalized with Smad3, leading to the removal of poly-deubiquitination of Smad3. Functionally, POH1 facilitated cell proliferation, migration, and invasion by stabilizing Smad3. Importantly, POH1 also promoted liver metastasis of lung cancer cells. The protein levels of both POH1 and Smad3 were raised in the tumor tissues of patients with LUAD, which predicts poor prognosis. Collectively, we demonstrate that POH1 acts as an oncoprotein by enhancing TGF-β1/Smad3 signaling and TGF-β1-mediated metastasis of lung cancer.

E3 ubiquitin ligases in lung cancer: Emerging insights and therapeutic opportunities

Aim In this review, we have attempted to provide the readers with an updated account of the role of a family of proteins known as E3 ligases in different aspects of lung cancer progression, along with insights into the deregulation of expression of these proteins during lung cancer. A detailed account of the therapeutic strategies involving E3 ligases that have been developed or currently under development has also been provided in this review. MATERIALS AND METHODS: The review article employs extensive literature search, along with differential gene expression analysis of lung cancer associated E3 ligases using the DESeq2 package in R, and the Gene Expression Profiling Interactive Analysis (GEPIA) database (http://gepia.cancer-pku.cn/). Protein expression analysis of CPTAC lung cancer samples was carried out using the UALCAN webtool (https://ualcan.path.uab.edu/index.html). Assessment of patient overall survival (OS) in response to high and low expression of selected E3 ligases was performed using the online Kaplan-Meier plotter (https://kmplot.com/analysis/index.php?p=background). KEY FINDINGS: SIGNIFICANCE: The review provides an in-depth understanding of the role of E3 ligases in lung cancer progression and an up-to-date account of the different therapeutic strategies targeting oncogenic E3 ligases for improved lung cancer management.

miRNA-660-3p inhibits malignancy in glioblastoma via negative regulation of APOC1-TGFβ2 signaling pathway

Glioblastoma as the most common and aggressive central nervous system tumor in adults. Its prognosis and therapeutic outcome are poor due to the limited understanding of its molecular mechanism. Apolipoprotein C-1 (APOC1) as a member of the apolipoprotein family that acts as a tumor promoter in various cancers. MicroRNA (miRNA) can silence gene expression and suppress tumor progression. However, the role of APOC1 and its upstream miRNA has not been explored in glioblastoma. Two glioblastoma cell lines (U87 and U251) were used to explore the role of APOC1 and its upstream miRNA-660-3p in glioblastoma tumorigenesis in vitro. Cells with APOC1/miRNA-660-3p overexpression or knockdown were assessed for their proliferation, migration, and invasion in vitro, and tumorigenesis in vivo. Gene and protein expression was assessed by qRT-PCR and western blot, respectively. Cell proliferation was assessed by the MTT assay and the EdU and Ki67 staining. Cell migration and invasion were assessed by the transwell assay. Tumorigenesis in vivo was assessed in U87 cells with a xenograft mouse model. APOC1 was overexpressed in glioblastoma compared with normal peritumoral tissue and was inversely related to patient prognosis. APOC1 overexpression promotes cell proliferation, migration, and invasion in vitro. APOC1 inhibition reduced tumor growth in vivo. miRNA-660-3p inhibits tumorigenesis by directly targeting APOC1. Mechanistically, APOC1 drives the malignancy of glioblastoma by activating the TGFβ2 signaling pathway. miRNA-660-3p suppresses tumorigenesis by targeting APOC1. Therefore, miRNA-660-3p/APOC1 axis can serve as potential intervention targets in managing glioblastoma progression.

Differential co-expression network analysis elucidated genes associated with sensitivity to farnesyltransferase inhibitor and prognosis of acute myeloid leukemia

Acute myeloid leukemia (AML) is a heterogeneous disease and the most common form of acute leukemia with a poor prognosis. Due to its complexity, the disease requires the identification of biomarkers for reliable prognosis. To identify potential disease genes that regulate patient prognosis, we used differential co-expression network analysis and transcriptomics data from relapsed, refractory, and previously untreated AML patients based on their response to treatment in the present study. In addition, we combined functional genomics and transcriptomics data to identify novel and therapeutically potential systems biomarkers for patients who do or do not respond to treatment. As a result, we constructed co-expression networks for response and non-response cases and identified a highly interconnected group of genes consisting of SECISBP2L, MAN1A2, PRPF31, VASP, and SNAPC1 in the response network and a group consisting of PHTF2, SLC11A2, PDLIM5, OTUB1, and KLRD1 in the non-response network, both of which showed high prognostic performance with hazard ratios of 4.12 and 3.66, respectively. Remarkably, ETS1, GATA2, AR, YBX1, and FOXP3 were found to be important transcription factors in both networks. The prognostic indicators reported here could be considered as a resource for identifying tumorigenesis and chemoresistance to farnesyltransferase inhibitor. They could help identify important research directions for the development of new prognostic and therapeutic techniques for AML.

LINC02253 promote the malignant phenotype of Colon adenocarcinoma cells by up-regulating WWP1-mediated SMAD3 ubiquitination

OBJECTIVES

Colon adenocarcinoma (COAD) represents a type of common malignant tumor originating in the digestive tract. Long non-coding RNAs (lncRNAs) have been identified to engage in regulating the initiation and development of COAD. LncRNA LINC02253 has been reported abnormal expressed in COAD, but the underlying mechanism has not been discussed so far. This study aimed to determine the role and the molecular biology mechanism of LINC02253 in COAD progression and unearthed its specific molecular mechanism.

MATERIALS AND RESULTS

RT-qPCR and Western blot assays were conducted to detect gene expression. Function assays were performed to evaluate the effect of gene expression on COAD cell phenotype. Mechanism analyses were done to verify the association among genes after bioinformatics analysis. The obtained data revealed that LINC02253 demonstrated a high expression in COAD tissues and cells. This gene served as an oncogene, permitting to stimulate proliferation and suppress apoptosis of COAD cells. Mechanically, it was found that LINC02253 recruited FUS to stabilize WWP1 mRNA and WWP1 could mediate SMAD3 ubiquitination, thereby promoting the malignant phenotype formation of COAD cells.

CONCLUSIONS

LINC02253 was uncovered to exert an oncogenic role, enhancing the proliferation of COAD cells and repressing the cell apoptosis by recruiting FUS and encouraging WWP1-mediated SMAD3 ubiquitination.

PDZ and LIM Domain-Encoding Genes: Their Role in Cancer Development

PDZ-LIM family proteins (PDLIMs) are a kind of scaffolding proteins that contain PDZ and LIM interaction domains. As protein-protein interacting molecules, PDZ and LIM domains function as scaffolds to bind to a variety of proteins. The PDLIMs are composed of evolutionarily conserved proteins found throughout different species. They can participate in cell signal transduction by mediating the interaction of signal molecules. They are involved in many important physiological processes, such as cell differentiation, proliferation, migration, and the maintenance of cellular structural integrity. Studies have shown that dysregulation of the PDLIMs leads to tumor formation and development. In this paper, we review and integrate the current knowledge on PDLIMs. The structure and function of the PDZ and LIM structural domains and the role of the PDLIMs in tumor development are described.

STUB1/CHIP: New insights in cancer and immunity

The STUB1 gene (STIP1 homology and U-box-containing protein 1), located at 16q13.3, encodes the CHIP (carboxyl terminus of Hsc70-interacting protein), an essential E3 ligase involved in protein quality control. CHIP comprises three domains: an N-terminal tetratricopeptide repeat (TPR) domain, a middle coiled-coil domain, and a C-terminal U-box domain. It functions as a co-chaperone for heat shock protein (HSP) via the TPR domain and as an E3 ligase, ubiquitinating substrates through its U-box domain. Numerous studies suggest that STUB1 plays a crucial role in various physiological process, such as aging, autophagy, and bone remodeling. Moreover, emerging evidence has shown that STUB1 can degrade oncoproteins to exert tumor-suppressive functions, and it has recently emerged as a novel player in tumor immunity. This review provides a comprehensive overview of STUB1's role in cancer, including its clinical significance, impact on tumor progression, dual roles, tumor stem cell-like properties, angiogenesis, drug resistance, and DNA repair. In addition, we explore STUB1's functions in immune cell differentiation and maturation, inflammation, autoimmunity, antiviral immune response, and tumor immunity. Collectively, STUB1 represents a promising and valuable therapeutic target in cancer and immunology.

SMAD Proteins in TGF-β Signalling Pathway in Cancer: Regulatory Mechanisms and Clinical Applications

Suppressor of mother against decapentaplegic (SMAD) family proteins are central to one of the most versatile cytokine signalling pathways in metazoan biology, the transforming growth factor-β (TGF-β) pathway. The TGF-β pathway is widely known for its dual role in cancer progression as both an inhibitor of tumour cell growth and an inducer of tumour metastasis. This is mainly mediated through SMAD proteins and their cofactors or regulators. SMAD proteins act as transcription factors, regulating the transcription of a wide range of genes, and their rich post-translational modifications are influenced by a variety of regulators and cofactors. The complex role, mechanisms, and important functions of SMAD proteins in tumours are the hot topics in current oncology research. In this paper, we summarize the recent progress on the effects and mechanisms of SMAD proteins on tumour development, diagnosis, treatment and prognosis, and provide clues for subsequent research on SMAD proteins in tumours.

STUB1-mediated ubiquitination regulates the stability of GLUD1 in lung adenocarcinoma

The dysregulation of glutamine metabolism provides survival advantages for tumors by supplementing tricarboxylic acid cycle. Glutamate dehydrogenase 1 (GLUD1) is one of the key enzymes in glutamine catabolism. Here, we found that enhanced protein stability was the key factor for the upregulation of GLUD1 in lung adenocarcinoma. We discovered that GLUD1 showed a high protein expression in lung adenocarcinoma cells or tissues. We elucidated that STIP1 homology and U-box-containing protein 1 (STUB1) was the key E3 ligase responsible for ubiquitin-mediated proteasomal degradation of GLUD1. We further showed that lysine 503 (K503) was the main ubiquitination site of GLUD1, inhibiting the ubiquitination at this site promoted the proliferation and tumor growth of lung adenocarcinoma cells. Taken together, this study clarifies the molecular mechanism of GLUD1 in maintaining protein homeostasis in lung adenocarcinoma, which provides a theoretical basis for the development of anti-cancer drugs targeting GLUD1.

Ultrasound-mediated mesoporous silica nanoparticles loaded with PDLIM5 siRNA inhibit gefitinib resistance in NSCLC cells by attenuating EMT

Epidermal growth factor receptor tyrosine kinase inhibitor (EGFR TKIs) was one of the main drugs in the treatment of non-small cell lung cancer (NSCLC). Previous studies had demonstrated that PDZ and LIM Domain 5 (PDLIM5) played an important role in EGFR TKIs resistance. However, there was no feasible method to eliminate EGFR TKIs resistance by suppressing this gene. Here, we formulated a novel mesoporous silica-loaded PDLIM5 siRNA (Small interfering RNA) nanoplatforms. The results have shown that PDLIM5 siRNA could be effectively bound to the nanoplatforms and had good biocompatibility. Further exploration suggested that the nano-platform combined with ultrasonic irradiation could be very effective for siRNA delivery and ultrasound imaging. Moreover, Epithelial-mesenchymal transformation (EMT) changes occurred in PC-9 Gefitinib resistance (PC-9/GR) cells during the development of drug resistance. When PDLIM5 siRNA entered PC-9/GR cells, the sensitivity of drug-resistant cells to gefitinib could be restored through the transforming growth factor-β (TGF-β)/EMT pathway. Therefore, PDLIM5 may be an important reason for the resistance of NSCLC cells to gefitinib, and this nanoplatform may become a novel treatment for EGFR TKIs resistance in NSCLC patients.

cRGD-targeted gold-based nanoparticles overcome EGFR-TKI resistance of NSCLC via low-temperature photothermal therapy combined with sonodynamic therapy

Epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI) is a first-line targeted drug for the treatment of advanced non-small cell lung cancer (NSCLC) in clinical practice, but EGFR-TKI-acquired resistance limits its therapeutic effect. To address this challenge, a novel multifunctional gold-based targeted nanoparticle-based drug delivery system is fabricated. The gold-based nanoparticle is loaded with the EGFR-TKI (gefitinib) and IR780, and the surface-modified gold nanoshell layer has a photothermal effect for thermally triggered drug release. Finally, the unique binding of cyclic arginine-glycine-aspartic acid (cRGD) to the α_vβ₃ receptor ensured that the nanoparticle (cRGD-GIPG) targeted transport into drug-resistant NSCLC cells was functional. Due to the sonodynamic properties of IR780, ultrasound (US) irradiation promoted reactive oxygen species (ROS) generation, while low-temperature photothermal therapy (PTT) not only promoted the release of drug, but also further enhanced the cytotoxic effects of ROS. In turn, it blocked the activation of TGF-β/PDLIM5/SMAD resistance pathway and induced apoptosis of drug-resistant cells through mitochondrial apoptosis, enabling the treatment of EGFR-TKI-resistant NSCLC. The low-temperature PTT combined with sonodynamic therapy (SDT) by cRGD-GIPG thus shows potent anticancer activity against EGFR-TKI-resistant NSCLC cells in vitro and in vivo. The present work provides a valuable strategy for highly targeted and EGFR-TKI-resistant reversal therapy in NSCLC.

Comprehensive Analyses and Immunophenotyping of LIM Domain Family Genes in Patients with Non-Small-Cell Lung Cancer

The LIM domain family genes play a crucial role in various tumors, including non-small-cell lung cancer (NSCLC). Immunotherapy is one of the most significant treatments for NSCLC, and its effectiveness largely depends on the tumor microenvironment (TME). Currently, the potential roles of LIM domain family genes in the TME of NSCLC remain elusive. We comprehensively evaluated the expression and mutation patterns of 47 LIM domain family genes in 1089 NSCLC samples. Using unsupervised clustering analysis, we classified patients with NSCLC into two distinct gene clusters, i.e., the LIM-high group and the LIM-low group. We further investigated the prognosis, TME cell infiltration characteristics, and immunotherapy in the two groups. The LIM-high and LIM-low groups had different biological processes and prognoses. Moreover, there were significant differences in TME characteristics between the LIM-high and LIM-low groups. Specifically, enhanced survival, immune cell activation, and high tumor purity were demonstrated in patients of the LIM-low group, implying an immune-inflamed phenotype. Moreover, the LIM-low group had higher immune cell proportion scores than the LIM-high group and was more responsive to immunotherapy than the LIM-low group. Additionally, we screened out LIM and senescent cell antigen-like domain 1 (LIMS1) as a hub gene of the LIM domain family via five different algorithms of plug-in cytoHubba and the weighted gene co-expression network analysis. Subsequently, proliferation, migration, and invasion assays demonstrated that LIMS1 acts as a pro-tumor gene that promotes the invasion and progression of NSCLC cell lines. This is the first study to reveal a novel LIM domain family gene-related molecular pattern associated with the TME phenotype, which would increase our understanding of the heterogeneity and plasticity of the TME in NSCLC. LIMS1 may serve as a potential therapeutic target for NSCLC.

Long noncoding RNA 02027 inhibits proliferation, migration and invasion of hepatocellular carcinoma via miR-625-3p/PDLIM5 pathway

BACKGROUND

Long non-coding RNAs have been established to promote or inhibit the oncogenic and tumorigenic potential of various cancers, acting as competing endogenous RNAs (ceRNAs) for specific microRNAs. The primary objective of the study was to investigate the underlying mechanism by which the LINC02027/miR-625-3p/PDLIM5 axis affects proliferation, migration and invasion in hepatocellular carcinoma (HCC).

METHODS

The differentially expressed gene was selected based on gene sequencing and bioinformation database analysis of HCC and adjacent non-tumor tissues. The expression of LINC02027 in HCC tissues and cells and its regulatory effect on the development of HCC were detected by colony formation, cell counting kit-8 assays, wound healing assays, Transwell assays and subcutaneous tumorigenesis assays in nude mice. According to the results of database prediction, quantitative real-time polymerase chain reaction and dual-luciferase reporter assay, the downstream microRNA and target gene were searched. Finally, HCC cells were transfected with lentivirus and used for cell function assays in vitro and in vivo.

RESULTS

Downregulation of LINC02027 was detected in HCC tissues and cell lines and was associated with poor prognosis. The overexpression of LINC02027 suppressed the proliferation, migration and invasion of HCC cells. Mechanistically, LINC02027 inhibited epithelial-to-mesenchymal transition. As a ceRNA, LINC02027 inhibited the malignant ability of HCC by competitively binding to miR-625-3p to regulate the expression of PDLIM5.

CONCLUSIONS

The LINC02027/miR-625-3p/PDLIM5 axis inhibits the development of HCC.

VEZF1, destabilized by STUB1, affects cellular growth and metastasis of hepatocellular carcinoma by transcriptionally regulating PAQR4

Hepatocellular carcinoma (HCC) is an aggressive solid malignancy, and recurrence and metastasis are major incentives contributing to its poor outcome. Vascular endothelial zinc finger 1 (VEZF1) has been recognized as an oncoprotein in certain types of cancer, but the expression pattern and regulatory mechanism in HCC remains unclear. This study focused on the functional effect and regulatory basis of VEZF1 in HCC. Microarray analysis identified the differentially expressed VEZF1 in HCC, and we validated its raised expression in HCC clinical samples. Artificial modulation of VEZF1 (knockdown and overexpression) was conducted to explore its role in HCC progression both in vitro and in vivo. It was shown that silencing of VEZF1 suppressed, whereas its overexpression promoted HCC cellular proliferation and metastasis abilities. Mechanistically, VEZF1 transcriptionally activated progestin and adipoQ receptor 4 (PAQR4) to accelerate HCC progression. Furthermore, VEZF1 is confirmed as a substrate of stress-inducible phosphoprotein 1 homology and U-box containing protein 1 (STUB1), and its stability is impacted by STUB1-mediated ubiquitination degradation. Conjointly, our work suggested that VEZF1, destabilized by STUB1, participates in HCC progression by regulating PAQR4. The STUB1/VEZF1/PAQR4 mechanism might provide novel insights on guiding early diagnosis and therapy in HCC patients.

To Ub or not to Ub: a regulatory question in TGF-β signaling

The transforming growth factor β (TGF-β) superfamily controls a wide spectrum of biological processes in metazoans, including cell proliferation, apoptosis, differentiation, cell-fate determination, and embryonic development. Deregulation of TGF-β-Smad signaling contributes to developmental anomalies and a variety of disorders and diseases such as tumorigenesis, fibrotic disorders, and immune diseases. In cancer, TGF-β has dual effects through its antiproliferative and prometastatic actions. At the cellular level, TGF-β functions mainly through the canonical Smad-dependent pathway in a cell type-specific and context-dependent manner. Accumulating evidence has demonstrated that ubiquitination plays a vital role in regulating TGF-β-Smad signaling. We summarize current progress on ubiquitination (Ub) and the ubiquitin ligases that regulate TGF-β-Smad signaling.

The unexpected versatility of ALP/Enigma family proteins

One of the most intriguing features of multicellular animals is their ability to move. On a cellular level, this is accomplished by the rearrangement and reorganization of the cytoskeleton, a dynamic network of filamentous proteins which provides stability and structure in a stationary context, but also facilitates directed movement by contracting. The ALP/Enigma family proteins are a diverse group of docking proteins found in numerous cellular milieus and facilitate these processes among others. In vertebrates, they are characterized by having a PDZ domain in combination with one or three LIM domains. The family is comprised of CLP-36 (PDLIM1), Mystique (PDLIM2), ALP (PDLIM3), RIL (PDLIM4), ENH (PDLIM5), ZASP (PDLIM6), and Enigma (PDLIM7). In this review, we will outline the evolution and function of their protein domains which confers their versatility. Additionally, we highlight their role in different cellular environments, focusing specifically on recent advances in muscle research using Drosophila as a model organism. Finally, we show the relevance of this protein family to human myopathies and the development of muscle-related diseases.

Large-scale sequencing identifies multiple genes and rare variants associated with Crohn's disease susceptibility

Genome-wide association studies (GWASs) have identified hundreds of loci associated with Crohn's disease (CD). However, as with all complex diseases, robust identification of the genes dysregulated by noncoding variants typically driving GWAS discoveries has been challenging. Here, to complement GWASs and better define actionable biological targets, we analyzed sequence data from more than 30,000 patients with CD and 80,000 population controls. We directly implicate ten genes in general onset CD for the first time to our knowledge via association to coding variation, four of which lie within established CD GWAS loci. In nine instances, a single coding variant is significantly associated, and in the tenth, ATG4C, we see additionally a significantly increased burden of very rare coding variants in CD cases. In addition to reiterating the central role of innate and adaptive immune cells as well as autophagy in CD pathogenesis, these newly associated genes highlight the emerging role of mesenchymal cells in the development and maintenance of intestinal inflammation.

Correlation between Genomic Variants and Worldwide Epidemiology of Prostate Cancer

Prostate cancer (PCa) incidence and mortality vary across territories and populations. This can be explained by the genetic factor of this disease. This article aims to correlate the epidemiological data, worldwide incidence, and mortality of PCa with single-nucleotide polymorphisms (SNPs) associated with the susceptibility and severity of this neoplasm in different populations. Eighty-four genetic variants associated with prostate cancer susceptibility were selected from the literature through genome association studies (GWAS). Allele frequencies were obtained from the 1000 Genomes Project, and epidemiological data were obtained from Surveillance, Epidemiology, and End Results (SEER). The PCa incidence, mortality rates, and allele frequencies of variants were evaluated by Pearson’s correlation. Our study demonstrated that 12 SNPs (rs2961144, rs1048169, rs7000448, rs4430796, rs2066827, rs12500426, rs6983267, rs11649743, rs2075110, rs114798100, rs855723, and rs2075109) were correlated with epidemiological data in different ethnic groups. Ten SNPs (rs2961144, rs1048169, rs7000448, rs4430796, rs2066827, rs12500426, rs11649743, rs2075110, rs114798100, and rs2075109) were positively correlated with the mortality rate. Seven SNPs (rs1048169, rs2961144, rs7000448, rs4430796, rs2066827, rs12500426, and rs114798100) were positively correlated with incidence. Positive correlations of incidence and mortality rates were more frequent in the African population. The genetic variants investigated here are likely to predispose to PCa and could play a role in its progression and aggressiveness. This genetic study demonstrated here is promising for implementing personalized strategies to screen for prostate cancer in diverse populations.

High Expression of PDLIM2 Predicts a Poor Prognosis in Prostate Cancer and Is Correlated with Epithelial-Mesenchymal Transition and Immune Cell Infiltration

Purpose

To elucidate the clinical and prognostic role of PDZ and LIM domain protein (PDLIM) genes and the association to epithelial-mesenchymal transition (EMT) and immune cell infiltration in patients with prostate cancer (PRAD).

Methods

The data of RNA-seq, DNA methylation, and clinical features of PRAD patients were collected from The Cancer Genome Atlas (TCGA) database to define the prognostic value of PDLIM gene expression and the association with EMT and immune cell infiltration. A tissue microarray including 134 radical prostatectomy specimens was served as validation by immunohistochemistry (IHC) staining analysis.

Results

The mRNA levels of PDLIM1/2/3/4/6/7 were significantly downregulated, while PDLIM5 was upregulated in PRAD (P < 0.05). High expression of PDLIM2 mRNA suggests poor progression free interval in PRAD patients. DNA methylation of PDLIM2 was correlated with its mRNA expression level, and that the cg22973076 methylation site in PDLIM2 was associated with shorter PFI (P < 0.05) in PRAD. Single-sample gene-set enrichment and gene functional enrichment results showed that PDLIM2 was correlated with EMT and immune processes. Spearman's test showed a significant correlation with six reported EMT signatures and several EMT signature-related genes. Tumor microenvironment analysis revealed that the PDLIM2 mRNA expression was positively correlated with the immune score, stromal score, and various tumor infiltrating immune cells. Additionally, the results showed that patients in the high-PDLIM2 mRNA expression group may be more sensitive to immune checkpoint blockade therapy. Finally, IHC analysis further implicated the protein level of PDLIM2 was upregulated in PRAD and acts as a novel potential biomarker in predicting tumor progression.

Conclusion

Our study suggests that PDLIM family genes might be significantly correlated with oncogenesis and the progression of PRAD. PDLIM2 correlated with EMT and immune cell infiltration by acting as an oncogene in PRAD, which may serve as a potential prognostic biomarker for PRAD patients.

GAB1 is upregulated to promote anaplastic thyroid cancer cell migration through AKT-MDR1

Anaplastic thyroid carcinoma (ATC) represents an undifferentiated, aggressive and highly metastatic form of thyroid cancer with high mortality. GAB1, through direct interaction with the kinase PI3K and phosphatase SHP2, is tightly involved in the activation of oncogenic signals; however, the role of GAB1 in ATC remains unclear. GAB1 was significantly increased in ATC, accompanied with AKT activation. Cell proliferation, migration and invasion were impaired or enhanced by GAB1 knockdown in ATC cells or overexpression in PTC cells. Moreover, GAB1 knockdown in ATC cells inhibited and overexpression in PTC cells promoted the growth of thyroid cancer in nude mice. GAB1 mutation disrupting the interaction between GAB1 and PI3K failed to restore cell migration and invasion in GAB1-knockdown ATC cells. RNA sequencing data showed GAB1-knockdown partially reprogramed gene expression in ATC cells back to that in normal thyroid cells. MDR1 was transcriptionally regulated by GAB1, which was mediated by AKT. MDR1 was upregulated in ATC cells and MDR1 knockdown in ATC cells decreased migration and invasion. In addition, MDR1 overexpression restored cell migration and invasion and lung metastasis of GAB1-knockdown ATC cells. Collectively, GAB1 is upregulated in ATC to promote AKT activation and cellular migration and invasion through regulating MDR1 expression.

RAB26 contributes to the progression of non-small cell lung cancer after being transcriptionally activated by SMAD3

Non-small cell lung cancer (NSCLC) accounts for 85% of all cases of lung cancer, which constitutes the leading cause of cancer mortality. RAB26, a member of Rab GTPase superfamily, has been suggested to play a role in the tumorigenesis of NSCLC. The present work aimed to explore whether and how RAB26 contributed to the progression of NSCLC. NSCLC cell line A549 was transfection with short hairpin RNA (shRNA) or overexpression (Ov) vector to knockdown RAB26 or overexpress SMAD3, respectively. Then the malignant processes of A549 cells including proliferation, migration, invasion and apoptosis were evaluated by CCK-8, colony formation, wound-healing, transwell and TUNEL assays, respectively. Expression of proteins involved in these processes was measured by western blot. A549 xenograft mice model was established to confirm the effect of RAB26 silence on NSCLC progression in vivo. The relationship between RAB26 and SMAD3 was analyzed by bioinformatics and then verified by dual-luciferase reporter and chromatin immunoprecipitation (ChIP) assays. We found that silence of RAB26 inhibited the proliferation, migration and invasion but promoted apoptosis of A549 cells. In vivo studies revealed that the tumor growth of A549 xenograft was markedly suppressed upon RAB26 silence. Moreover, it was confirmed that SMAD3 bound to the promoter of RAB26 and enhance its expression. Finally, we observed that overexpression of SMAD3 significantly blocked the inhibitory effect of RAB26 silence on NSCLC progression. Collectively, RAB26 may contribute to the progression of NSCLC after being transcriptionally activated by SMAD3.

Chaperone-mediated Autophagy Regulates Cell Growth by Targeting SMAD3 in Glioma

Previous studies suggest that the reduction of SMAD3 (mothers against decapentaplegic homolog 3) has a great impact on tumor development, but its exact pathological function remains unclear. In this study, we found that the protein level of SMAD3 was greatly reduced in human-grade IV glioblastoma tissues, in which LAMP2A (lysosome-associated membrane protein type 2A) was significantly up-regulated. LAMP2A is a key rate-limiting protein of chaperone-mediated autophagy (CMA), a lysosome pathway of protein degradation that is activated in glioma. We carefully analyzed the amino-acid sequence of SMAD3 and found that it contained a pentapeptide motif biochemically related to KFERQ, which has been proposed to be a targeting sequence for CMA. In vitro, we confirmed that SMAD3 was degraded in either serum-free or KFERQ motif deleted condition, which was regulated by LAMP2A and interacted with HSC70 (heat shock cognate 71 kDa protein). Using isolated lysosomes, amino-acid residues 75 and 128 of SMAD3 were found to be of importance for this process, which affected the CMA pathway in which SMAD3 was involved. Similarly, down-regulating SMAD3 or up-regulating LAMP2A in cultured glioma cells enhanced their proliferation and invasion. Taken together, these results suggest that excessive activation of CMA regulates glioma cell growth by promoting the degradation of SMAD3. Therefore, targeting the SMAD3-LAMP2A-mediated CMA-lysosome pathway may be a promising approach in anti-cancer therapy.

TKI resistant-based prognostic immune related gene signature in LUAD, in which FSCN1 contributes to tumor progression

Drug resistance reflects the evolution of tumors, which is the main cause of recurrence and death. Currently, EGFR-TKI treatment is the first-line therapy for lung adenocarcinoma (LUAD) patients. Although EGFR-TKI achieved good effects at the beginning, most of the LUAD patients eventually acquired resistance. Therefore, it's urgently need to develop a strong criterion for identifying these patients who may benefit from additional therapy. In this study, we established a three TKI resistant-related gene signature (DDIT4, OAS3, FSCN1), and determined that's an accuracy, independent and specific prognostic model for LUAD patients. Patients categorized as high-risk by this signature showed more sensitive to chemotherapy, and exhibited higher expression of common immune checkpoints such as PD-L1/B3H7/PD-L2/IDO1. Moreover, these patients were characterized by increased infiltration of M0 macrophage and activated memory CD4⁺ T cells. The expression and prognostic values of DDIT4, FSCN1 and OAS3 were further confirmed in clinical data. In addition, experimental data showed that FSCN1 promoted LUAD development via PI3K/AKT signaling. In conclusion, this signature is highly predictive of prognostic in LUAD patients, and may serve as a powerful prediction tool for LUAD patients to further choose chemo- and immunotherapies.

Molecular Pathogenesis of Pulmonary Fibrosis, with Focus on Pathways Related to TGF-β and the Ubiquitin-Proteasome Pathway

Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal interstitial lung disease. During the past decade, novel pathogenic mechanisms of IPF have been elucidated that have shifted the concept of IPF from an inflammatory-driven to an epithelial-driven disease. Dysregulated repair responses induced by recurrent epithelial cell damage and excessive extracellular matrix accumulation result in pulmonary fibrosis. Although there is currently no curative therapy for IPF, two medications, pirfenidone and nintedanib, have been introduced based on understanding the pathogenesis of the disease. In this review, we discuss advances in understanding IPF pathogenesis, highlighting epithelial-mesenchymal transition (EMT), the ubiquitin-proteasome system, and endothelial cells. TGF-β is a central regulator involved in EMT and pulmonary fibrosis. HECT-, RING finger-, and U-box-type E3 ubiquitin ligases regulate TGF-β-Smad pathway-mediated EMT via the ubiquitin-proteasome pathway. p27 degradation mediated by the SCF-type E3 ligase, Skp2, contributes to the progression of pulmonary fibrosis by promotion of either mesenchymal fibroblast proliferation, EMT, or both. In addition to fibroblasts as key effector cells in myofibroblast differentiation and extracellular matrix deposition, endothelial cells also play a role in the processes of IPF. Endothelial cells can transform into myofibroblasts; therefore, endothelial-mesenchymal transition can be another source of myofibroblasts.

APOBEC1 complementation factor facilitates cell migration by promoting nucleus translocation of SMAD3 in renal cell carcinoma cells

Metastasis is inevitable in about 30% of patients with primary renal cell carcinoma after nephrectomy treatment. APOBEC1 complementation factor (A1CF), an RNA binding protein, participates in tumor progressions such as growth, apoptosis, differentiation, and invasion. Here, we explored biological functions of A1CF and provided a new insight into renal cell carcinoma metastasis. Wound healing assay was conducted to detect migration in A1CF overexpression and knockdown stable cell lines. Quantitative PCR and western blot assays were utilized to test transcriptional and translation levels of A1CF and SMAD3 in A1CF overexpression and knockdown renal carcinoma cells. Nuclear and cytoplasmic protein separation assays were conducted to evaluate the subcellular distribution of A1CF and SMAD3. Immunoprecipitation assay was conducted to detect the interaction between A1CF and SMAD3. Our study demonstrated A1CF overexpression facilitated cell migration in renal carcinoma cells. A1CF deficiency downregulated expression of SMAD3, Snail1, and N-cadherin. In addition, A1CF promoted nucleus translocation of SMAD3 and interacted with SMAD3. SMAD3 knockdown attenuated cell migration induced by A1CF overexpression. Our study suggested A1CF facilitated cell migration by promoting nucleus translocation of SMAD3 in renal cell carcinoma cells.

Identification of Hub Genes and Construction of a Transcriptional Regulatory Network Associated With Tumor Recurrence in Colorectal Cancer by Weighted Gene Co-expression Network Analysis

Tumor recurrence is one of the most important risk factors that can negatively affect the survival rate of colorectal cancer (CRC) patients. However, the key regulators dictating this process and their exact mechanisms are understudied. This study aimed to construct a gene co-expression network to predict the hub genes affecting CRC recurrence and to inspect the regulatory network of hub genes and transcription factors (TFs). A total of 177 cases from the GSE17536 dataset were analyzed via weighted gene co-expression network analysis to explore the modules related to CRC recurrence. Functional annotation of the key module genes was assessed through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses. The protein and protein interaction network was then built to screen hub genes. Samples from the Cancer Genome Atlas (TCGA) were further used to validate the hub genes. Construction of a TFs-miRNAs–hub genes network was also conducted using StarBase and Cytoscape approaches. After identification and validation, a total of five genes (TIMP1, SPARCL1, MYL9, TPM2, and CNN1) were selected as hub genes. A regulatory network of TFs-miRNAs-targets with 29 TFs, 58 miRNAs, and five hub genes was instituted, including model GATA6-MIR106A-CNN1, SP4-MIR424-TPM2, SP4-MIR326-MYL9, ETS1-MIR22-TIMP1, and ETS1-MIR22-SPARCL1. In conclusion, the identification of these hub genes and the prediction of the Regulatory relationship of TFs-miRNAs-hub genes may provide a novel insight for understanding the underlying mechanism for CRC recurrence.

PADs in cancer: Current and future

Protein arginine deiminases (PADs), is a group of calcium-dependent enzymes, which play crucial roles in citrullination, and can catalyze arginine residues into citrulline. This chemical reaction induces citrullinated proteins formation with altered structure and function, leading to numerous pathological diseases, including inflammation and autoimmune diseases. To date, multiple studies have provided solid evidence that PADs are implicated in cancer progression. Nevertheless, the findings on PADs functions in tumors are too complex to understand due to its involvements in variable signaling pathways. The increasing interest in PADs has heightened the need for a comprehensive description for its role in cancer. The present study aims to identify the gaps in present knowledge, including its structures, biological substrates and tissue distribution. Since several irreversible inhibitors for PADs with good potency and selectivity have been explored, the mechanisms on the dysregulation in tumors remain poorly understood. The present study discusses the relationship between PADs and tumor apoptosis, EMT formation and metastasis as well as the implication of neutrophil extracellular traps (NETs) in tumorigenesis. In addition, the potential uses of citrullinated antigens for immunotherapy were proposed.