CCR9 Promotes Migration and Invasion of Lung Adenocarcinoma Cancer Stem Cells

A Niche-Based Perspective to Stem and Cancer Stem Cells of the Lung

Lungs carry the principle function for the conduction and exchange of air through the primary, secondary, tertiary bronchi, bronchioles, and alveoli, resulting in the exchange of oxygen to carbon dioxide within the human tissues. Lung stem and progenitor cells enable differentiation of parenchymal and stromal elements and provide homeostasis and regeneration in the microenvironment against pulmonary diseases. Tumor-initiating cancer cells (TICs) refer to a subpopulation named as cancer stem cells (CSCs) of lung cancer exhibiting high self-renewal and proliferation capacity by Notch, Hippo, Hedgehog, and Wnt signaling pathways that leads to tumor development or recurrence. Lung cancer stem cells (LCSCs) are characterized by distinct genotypic or phenotypic alterations compared to healthy lung stem cells (LSCs) that provide a potential target to treat lung cancer. Therefore, understanding the cascades responsible for the transformation of healthy to CSCs is essential to develop new targeted therapy approaches. In this chapter, we precisely highlight the latest researches on LSCs and CSCs, key signaling mechanisms within the perspective of novel targeted therapy strategies.

Comprehensive bioinformatics analysis of co-mutation of FLG2 and TP53 reveals prognostic effect and influences on the immune infiltration in ovarian serous cystadenocarcinoma

Background

Ovarian cancer remains one of the most lethal gynecological malignancies, characterized by late-stage diagnosis and high rates of recurrence. The present study aims to explore the prognostic and immunological implications of FLG2 and TP53, the two genes exhibiting a high mutation frequency across various cancer types, in the context of ovarian serous cystadenocarcinoma (OV).

Methods

The study systematically analyzed and discussed the potential implications of co-mutation of FLG2 and TP53 on prognosis and immune response using a cohort of 585 ovarian cancer samples. The differentially expressed genes (DEGs) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed on 300 ovarian cancer samples with RNA sequencing (RNA-seq) data.

Results

The co-mutation of FLG2 and TP53 was identified in the 585 ovarian cancer cohort, and the group with co-mutation exhibited improved outcomes in terms of overall survival (OS), progression-free survival (PFS), and disease-specific survival (DSS). Additionally, the co-mutation (FLG2 +/TP53 +) group demonstrated higher scores in tumor mutation burden (TMB) comparing to that of the other three groups. The score of microsatellite instability (MSI) in the co-mutant group was only higher than that of the co-wild-type (FLG2 -/TP53 -). A total of 327 DEGs were identified in both the co-mutation and non-co-mutation (NCM) groups using limma analysis in the subgroup of 300 patients with RNA-seq data. Subsequent KEGG analysis revealed that these DEGs were implicated in various biological processes, including thermogenesis, Parkinson's disease (PD), and oxidative phosphorylation signaling pathways. Additionally, the co-mutation group exhibited elevated levels of various immune cells. Furthermore, a nomogram with high predictive accuracy was developed by integrating co-mutation status with clinical characteristics.

Conclusions

In the context of OV, the concurrent mutation of FLG2 and TP53 not only induces immune activation, but also helps identify a subset of patients with a more favorable prognosis.

Identification of immune characteristics of two lung adenocarcinoma subtypes based on immune- and pyroptosis-related genes to improve immunotherapy

BACKGROUND

Lung adenocarcinoma (LUAD) is the most prevalent histological subtype of lung cancer. Pyroptosis is a programmatic cell death linked to inflammation.

METHODS

The data information of 541 LUAD samples and 59 normal samples were obtained from TCGA database. The analysis of differentially expressed genes (DEGs) was carried out on LUAD patients. The intersection of integrated PRGs and IRGs with DEGs yielded IPRGs. We utilized univariate Cox regression to determine IPRGs linked to overall survival (OS). Based on their expression levels, unsupervised clustering of LUAD was conducted. Patients were divided into two clusters. Analyses of immunity and drugs were performed in two clusters.

RESULTS

One hundred and thirty-two IPRGs were linked with OS. Cluster 1 had a longer OS. Two thousand two hundred and fifty-six DEGs were detected in various subtypes. The results of immune analysis showed that most of the immune cells in cluster 2, which had a worse prognosis, had a low degree of infiltration. High Th2 cell infiltration may be related to poor prognosis in LUAD patients. Higher tumor immune dysfunction and exclusion (TIDE) and immunophenotypic scores in Cluster 1 indicated that these patients may have a better response to immunotherapy. There were significant differences in human leukocyte antigen (HLA), immune checkpoints, immunophenoscore (IPS), and TIDE scores in the two subtypes. The mutation frequencies of the top 10 genes in cluster 2 were higher than those in cluster 1. Different subtypes also had distinct sensitivities to different drugs.

CONCLUSION

IPRGs can be utilized for LUAD subtyping. Different subtypes have varied immune landscapes and immunotherapy responses.

Pleiotropic role of CCR9/CCL25 signaling in adriamycin-induced cardiomyopathy

INTRODUCTION

Adriamycin (ADR)-induced cardiomyopathy is a common problem in many cancer survivors. Recently, specific chemokine receptors have garnered interest as therapeutic targets in cardiovascular diseases.

OBJECTIVES

This study aim to report the role of C-C chemokine receptor 9 (CCR9)/C-C chemokine ligand 25 (CCL25) and its therapeutic potential in ADR-induced cardiomyopathy.

METHODS

Functional gene knockout and overexpression mouse models were utilized to investigate the role of CCR9 against ADR-induced cardiomyopathy. Transcriptome sequencing was also performed to identify the downstream molecular mechanisms of CCR9.

RESULTS

This study revealed that CCR9 and CCL25 levels were increased in mice and HL-1 cells injured by ADR, consistent with the results of patients with heart failure. Both in vivo and in vitro, CCR9 overexpression overtly aggravated cardiac dysfunction, accompanied by decreased AMPK activity and increased mitochondrial dysfunction, fibrosis, oxidative stress, and apoptosis. However, the cardiac harmful effects of ADR were reserved by CCR9 knockdown, as well as CCR9 overexpression aggravated cardiotoxicity were reserved by AMPK agonist GSK621. By constructing different domain-missing CCR9 mutants, we suspected that the △4 region of CCR9 is important for AMPK activity. Furthermore, transcriptome sequencing  further illustrated the mechanism of CCR9 overexpression aggravated ADR-induced cardiotoxicity, which was associated with CYP1A1. Finally, lithospermic acid (LA) was screened and alleviated ADR-induced cardiotoxicity through regulation of CCR9/CCL25-AMPK signaling, bolstering CCR9-targeted potential clinical application.

CONCLUSION

These findings present a promising target and drug for treating chemotherapy-induced cardiotoxicity.

Molecular targets, therapeutic agents and multitasking nanoparticles to deal with cancer stem cells: A narrative review

There is increasing evidence that malignant tumors are initiated and maintained by a sub-population of tumor cells that have similar biological properties to normal adult stem cells. This very small population of Cancer Stem Cells (CSC) comprises tumor initiating cells responsible for cancer recurrence, drug resistance and metastasis. Conventional treatments such as chemotherapy, radiotherapy and surgery, in addition to being potentially toxic and non-specific, may paradoxically increase the population, spread and survival of CSCs. Next-generation sequencing and omics technologies are increasing our understanding of the pathways and factors involved in the development of CSCs, and can help to discover new therapeutic targets against CSCs. In addition, recent advances in nanomedicine have provided hope for the development of optimal specific therapies to eradicate CSCs. Moreover, the use of artificial intelligence and nano-informatics can elucidate new drug targets, and help to design drugs and nanoparticles (NPs) to deal with CSCs. In this review, we first summarize the properties of CSCs and describe the signaling pathways and molecular characteristics responsible for the emergence and survival of CSCs. Also, the location of CSCs within the tumor and the effect of host factors on the creation and maintenance of CSCs are discussed. Newly discovered molecular targets involved in cancer stemness and some novel therapeutic compounds to combat CSCs are highlighted. The optimum properties of anti-CSC NPs, including blood circulation and stability, tumor accumulation and penetration, cellular internalization, drug release, endosomal escape, and aptamers designed for specific targeting of CSCs are covered. Finally, some recent smart NPs designed for therapeutic and theranostic purposes to overcome CSCs are discussed.

Determination of the Binding Epitope of an Anti-Mouse CCR9 Monoclonal Antibody (C9Mab-24) Using the 1× Alanine and 2× Alanine-Substitution Method

C-C chemokine receptor 9 (CCR9) is a receptor for C-C-chemokine ligand 25 (CCL25). CCR9 is crucial in the chemotaxis of immune cells and inflammatory responses. Moreover, CCR9 is highly expressed in tumors, including several solid tumors and T-cell acute lymphoblastic leukemia. Several preclinical studies have shown that anti-CCR9 monoclonal antibodies (mAbs) exert antitumor activity. Therefore, CCR9 is an attractive target for tumor therapy. In this study, we conducted the epitope mapping of an anti-mouse CCR9 (mCCR9) mAb, C₉Mab-24 (rat IgG_2a, kappa), using the 1× alanine (1× Ala)- and 2× alanine (2× Ala)-substitution methods via enzyme-linked immunosorbent assay. We first performed the 1× Ala-substitution method using one alanine-substituted peptides of the mCCR9 N-terminus (amino acids 1-19). C₉Mab-24 did not recognize two peptides (F14A and F17A), indicating that Phe14 and Phe17 are critical for C₉Mab-24-binding to mCCR9. Furthermore, we conducted the 2× Ala-substitution method using two consecutive alanine-substituted peptides of the mCCR9 N-terminus, and showed that C₉Mab-24 did not react with four peptides (M13A-F14A, F14A-D15A, D16A-F17A, and F17A-S18A), indicating that _13-MFDDFS_-18 is involved in C₉Mab-24-binding to mCCR9. Overall, combining, the 1× Ala- or 2× Ala-scanning methods could be useful for understanding for target-antibody interaction.

Subtype Classification, Immune Infiltration, and Prognosis Analysis of Lung Adenocarcinoma Based on Pyroptosis-Related Genes

The effect of pyroptosis-related genes (PRGs) on the tumor microenvironment (TME) in lung adenocarcinoma (LUAD) remains unclear. Thus, this study is aimed at evaluating the prognostic value of PRGs in patients with LUAD and to elucidate their role in the TME and their effect on immunotherapy. Transcriptomic and clinical data were obtained from the Cancer Genome Atlas and the Gene Expression Omnibus databases (GSE3141, GSE31210). Patients with LUAD were classified using consistent clustering, and the differences in the TME for each type were determined using the ESTIMATE and CIBERSORT algorithms. PRGs were screened using univariate regression analysis, and a prognostic risk model was constructed using LASSO regression analysis. The tumor mutational burden and the tumor immune dysfunction and exclusion algorithms were used to predict therapeutic sensitivity in LUAD patients. Then, we evaluated the potential therapeutic interventions using the GDSC database. LUAD patients in cluster 2 had significantly shorter overall survival and progression-free survival rates, lower immune scores, and higher infiltration of T follicular helper cells than those in cluster 1. We used five PRGs to classify patients with LUAD into different risks groups and found that the high-risk group is sensitive to immunotherapy; however, its immune-related pathways were inhibited, which may be related to tumor metabolic reprogramming. Lastly, we identified several potential therapeutic drugs for application in low-risk patients who were less sensitive to immunotherapy. Overall, our findings showed that PRGs can be used to predict prognosis and may aid in the development of personalized therapeutic strategies in LUAD patients.

Peripheral Blood Mononuclear Cells Predict Therapeutic Efficacy of Immunotherapy in NSCLC

Simple Summary

Biomarkers to guide clinical decisions and efficacy are limited in advanced non-small cell lung cancer’s anti-PD-1 immune checkpoint inhibitors. We prospectively explored baseline peripheral blood mononuclear cells in order to asses’ immunotherapy predictors in this setting. We included 39 patients diagnosed with non-small cell lung cancer treated with immunotherapy in the study group and 40 patients with advanced malignancies treated with non-immunotherapy treatment, as control group. We detected that high baseline levels of circulating T cell subpopulations related to tissue lymphocyte recruitment are associated with poorer outcomes of immunotherapy-treated advanced non-small cell lung cancer patients, and these differences were specific to immunotherapy-treated patients.

Abstract

In lung cancer immunotherapy, biomarkers to guide clinical decisions are limited. We now explore whether the detailed immunophenotyping of circulating peripheral blood mononuclear cells (PBMCs) can predict the efficacy of anti-PD-1 immunotherapy in patients with advanced non-small-cell lung cancer (NSCLC). We determined 107 PBMCs subpopulations in a prospective cohort of NSCLC patients before starting single-agent anti-PD-1 immunotherapy (study group), analyzed by flow cytometry. As a control group, we studied patients with advanced malignancies before initiating non-immunotherapy treatment. The frequency of PBMCs was correlated with treatment outcome. Patients were categorized as having either high or low expression for each biomarker, defined as those above the 55th or below the 45th percentile of the overall marker expression within the cohort. In the study group, three subpopulations were associated with significant differences in outcome: high pretreatment levels of circulating CD4+CCR9+, CD4+CCR10+, or CD8+CXCR4+ T cells correlated with poorer overall survival (15.7 vs. 35.9 months, HR 0.16, p = 0.003; 22.0 vs. NR months, HR 0.10, p = 0.003, and 22.0 vs. NR months, HR 0.29, p = 0.02). These differences were specific to immunotherapy-treated patients. High baseline levels of circulating T cell subpopulations related to tissue lymphocyte recruitment are associated with poorer outcomes of immunotherapy-treated advanced NSCLC patients.

A Transcriptome Analysis of mRNAs and Long Non-Coding RNAs in Patients with Parkinson's Disease

Parkinson's disease (PD) is the second most common neurodegenerative disorder. The number of cases of PD is expected to double by 2030, representing a heavy burden on the healthcare system. Clinical symptoms include the progressive loss of dopaminergic neurons in the substantia nigra of the midbrain, which leads to striatal dopamine deficiency and, subsequently, causes motor dysfunction. Certainly, the study of the transcriptome of the various RNAs plays a crucial role in the study of this neurodegenerative disease. In fact, the aim of this study was to evaluate the transcriptome in a cohort of subjects with PD compared with a control cohort. In particular we focused on mRNAs and long non-coding RNAs (lncRNA), using the Illumina NextSeq 550 DX System. Differential expression analysis revealed 716 transcripts with padj ≤ 0.05; among these, 630 were mRNA (coding protein), lncRNA, and MT_tRNA. Ingenuity pathway analysis (IPA, Qiagen) was used to perform the functional and pathway analysis. The highest statistically significant pathways were: IL-15 signaling, B cell receptor signaling, systemic lupus erythematosus in B cell signaling pathway, communication between innate and adaptive immune cells, and melatonin degradation II. Our findings further reinforce the important roles of mitochondria and lncRNA in PD and, in parallel, further support the concept of inverse comorbidity between PD and some cancers.

A Transcriptome Analysis of mRNAs and Long Non-Coding RNAs in Patients with Parkinson's Disease

Parkinson's disease (PD) is the second most common neurodegenerative disorder. The number of cases of PD is expected to double by 2030, representing a heavy burden on the healthcare system. Clinical symptoms include the progressive loss of dopaminergic neurons in the substantia nigra of the midbrain, which leads to striatal dopamine deficiency and, subsequently, causes motor dysfunction. Certainly, the study of the transcriptome of the various RNAs plays a crucial role in the study of this neurodegenerative disease. In fact, the aim of this study was to evaluate the transcriptome in a cohort of subjects with PD compared with a control cohort. In particular we focused on mRNAs and long non-coding RNAs (lncRNA), using the Illumina NextSeq 550 DX System. Differential expression analysis revealed 716 transcripts with padj ≤ 0.05; among these, 630 were mRNA (coding protein), lncRNA, and MT_tRNA. Ingenuity pathway analysis (IPA, Qiagen) was used to perform the functional and pathway analysis. The highest statistically significant pathways were: IL-15 signaling, B cell receptor signaling, systemic lupus erythematosus in B cell signaling pathway, communication between innate and adaptive immune cells, and melatonin degradation II. Our findings further reinforce the important roles of mitochondria and lncRNA in PD and, in parallel, further support the concept of inverse comorbidity between PD and some cancers.

TIPE polarity proteins are required for mucosal deployment of T lymphocytes and mucosal defense against bacterial infection

Mucosal surfaces are continuously exposed to, and challenged by, numerous commensal and pathogenic organisms. To guard against infections, a majority of the thymus-derived T lymphocytes are deployed at the mucosa. Although chemokines are known to be involved in the mucosal lymphocyte deployment, it is not clear whether lymphocytes enter the mucosa through directed migration or enhanced random migration. Here we report that TIPE (tumor necrosis factor-α-induced protein 8 (TNFAIP8)-like) proteins mediate directed migration of T lymphocytes into lung mucosa, and they are crucial for mucosal immune defense against Streptococcus pneumoniae infection. Knockout of both Tnfaip8 and Tipe2, which encode polarity proteins that control the directionality of lymphocyte migration, significantly reduced the numbers of T lymphocytes in the lung of mice. Compared with wild-type mice, Tnfaip8^−/−Tipe2^−/− mice also developed more severe infection with more pathogens entering blood circulation upon nasal Streptococcus pneumoniae challenge. Single-cell RNA-sequencing analysis revealed that TIPE proteins selectively affected mucosal homing of a unique subpopulation of T cells, called “T cells-2”, which expressed high levels of Ccr9, Tcf7, and Rag1/2 genes. TNFAIP8 and TIPE2 appeared to have overlapping functions since deficiency in both yielded the strongest phenotype. These data demonstrate that TIPE family of proteins are crucial for lung mucosal immunity. Strategies targeting TIPE proteins may help develop mucosal vaccines or treat inflammatory diseases of the lung.

CCR9 initiates epithelial-mesenchymal transition by activating Wnt/β-catenin pathways to promote osteosarcoma metastasis

Background

Osteosarcoma (OS) patients with lung metastasis have poor prognoses, and effective therapeutic strategies for delaying or inhibiting the spread of lung metastasis from the primary OS site are lacking. Hence, it is critical to elucidate the underlying mechanisms of OS metastasis and to identify additional new effective treatment strategies for patients.

Methods

Differential expression and functional analyses were performed to identify key genes and relevant signaling pathways associated with OS lung metastasis. The expression of CCR9 in OS cell lines and tissues was measured by RT-qPCR, western blotting and immunohistochemistry. Cell migration and invasion were assessed by wound healing and Transwell Matrigel invasion assays, respectively. The regulatory relationship between CCR9 and the Wnt/β-catenin signaling pathway was further evaluated by rescue experiments.

Results

The expression of CCR9 was elevated in OS cell lines and patients with lung metastasis. CCR9 promoted MG63 and HOS cell migration and invasion by activating the Wnt/β-catenin signaling pathway. Furthermore, knockdown of CCR9 repressed epithelial–mesenchymal transition (EMT) by downregulating mesenchymal markers (N-cadherin and Vimentin) and EMT-associated transcription factors (twist and snail) and upregulating an epithelial marker (E-cadherin).

Conclusions

Our findings suggest that CCR9 promotes EMT by activating Wnt/β-catenin pathways to promote OS metastasis. CCR9 may be a promising therapeutic target to inhibit lung metastasis and serve as a novel prognostic marker for OS.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12935-021-02320-0.

Identification and Construction of a Long Noncoding RNA Prognostic Risk Model for Stomach Adenocarcinoma Patients

Background

Long noncoding RNA-based prognostic biomarkers have demonstrated great potential in the diagnosis and prognosis of cancer patients. However, systematic assessment of a multiple lncRNA-composed prognostic risk model is lacking in stomach adenocarcinoma (STAD). This study is aimed at constructing a lncRNA-based prognostic risk model for STAD patients.

Methods

RNA sequencing data and clinical information of STAD patients were retrieved from The Cancer Genome Atlas (TCGA) database. Differentially expressed lncRNAs (DElncRNAs) were identified using the R software. Univariate and multivariate Cox regression analyses were performed to construct a prognostic risk model. The survival analysis, C-index, and receiver operating characteristic (ROC) curve were employed to assess the sensitivity and specificity of the model. The results were verified using the GEPIA online tool and our clinical samples. Pearson correlation coefficient analysis, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment were performed to indicate the potential biological functions of the selected lncRNA.

Results

A total of 1917 DElncRNAs were identified from 343 cases of STAD tissues and 30 cases of noncancerous tissues. According to univariate and multivariable Cox regression analyses, four DElncRNAs (AC129507.1, LINC02407, AL022316.1, and AP000695.2) were selected to establish a prognostic risk model. There was a significant difference in the overall survival between high-risk patients and low-risk patients based on this risk model. The C-index of the model was 0.652. The area under the curve (AUC) for the ROC curve was 0.769. GEPIA results confirmed the expression and prognostic significance of AP000695.2 in STAD. Our clinical data confirmed that upregulated expression of AP000695.2 was correlated with the T stage, distant metastasis, and TNM stage in STAD. GO and KEGG analyses demonstrated that AP000695.2 was closely related to the tumorigenesis process.

Conclusions

In this study, we constructed a lncRNA-based prognostic risk model for STAD patients. Our study will provide novel insight into the diagnosis and prognosis of STAD patients.

NSE, positively regulated by LINC00657-miR-93-5p axis, promotes small cell lung cancer (SCLC) invasion and epithelial-mesenchymal transition (EMT) process

Background: Neuron specific enolase (NSE) is a specific biomarker for SCLC. However, the biological roles and aberrant expression of NSE in SCLC have not been well illustrated. Methods: The expression of NSE, miR-93-5p and LINC00657 in SCLC tissues and cell lines were detected using real time quantitative PCR (qRT-PCR) or immunohistochemistry. CCK8 assay was performed to detect cell proliferation. Cell migration and invasion capabilities were investigated by transwell assay. Epithelial-mesenchymal transition (EMT) process was verified by detecting epithelial marker E-cadherin and mesenchymal marker N-cadherin. The direct interactions between miR-93-5p and NSE or LINC00657 were predicted by bioinformatics tools and verified using dual luciferase reporter assay. Results: Upregulated expression of NSE in SCLC tumor tissues were positively associated with advanced tumor stage, distant metastasis and poor overall survival. Overexpression of NSE promoted cell proliferation, migration, invasion and EMT in SCLC cells, while silence of NSE inhibited these effects. Mechanically, NSE expression was positively correlated with LINC00657, and negatively correlated with miR-93-5p. Moreover, NSE was positively regulated by LINC00657 through sponging of miR-93-5p. LINC00657 and miR-93-5p promoted SCLC cell migration, invasion and EMT by NSE-mediated manner. Conclusion: Overall, our study revealed a novel role of NSE in SCLC. NSE was positively regulated by LINC00657 through competitively interacting with miR-93-5p, which may be potential targets for SCLC patients.