The relationship between autophagy and the immune system and its applications for tumor immunotherapy

Senescence and cancer - role and therapeutic opportunities

Cellular senescence is a state of stable, terminal cell cycle arrest associated with various macromolecular changes and a hypersecretory, pro-inflammatory phenotype. Entry of cells into senescence can act as a barrier to tumorigenesis and, thus, could in principle constitute a desired outcome for any anticancer therapy. Paradoxically, studies published in the past decade have demonstrated that, in certain conditions and contexts, malignant and non-malignant cells with lastingly persistent senescence can acquire pro-tumorigenic properties. In this Review, we first discuss the major mechanisms involved in the antitumorigenic functions of senescent cells and then consider the cell-intrinsic and cell-extrinsic factors that participate in their switch towards a tumour-promoting role, providing an overview of major translational and emerging clinical findings. Finally, we comprehensively describe various senolytic and senomorphic therapies and their potential to benefit patients with cancer.

The entry of cells into senescence can act as a barrier to tumorigenesis; however, in certain contexts senescent malignant and non-malignant cells can acquire pro-tumorigenic properties. The authors of this Review discuss the cell-intrinsic and cell-extrinsic mechanisms involved in both the antitumorigenic and tumour-promoting roles of senescent cells, and describe the potential of various senolytic and senomorphic therapeutic approaches in oncology.

Cellular senescence is a natural barrier to tumorigenesis; senescent cells are widely detected in premalignant lesions from patients with cancer.

Cellular senescence is induced by anticancer therapy and can contribute to some treatment-related adverse events (TRAEs).

Senescent cells exert both protumorigenic and antitumorigenic effects via cell-autonomous and paracrine mechanisms.

Pharmacological modulation of senescence-associated phenotypes has the potential to improve therapy efficacy and reduce the incidence of TRAEs.

Involvement of the Autophagy Protein Atg1 in Development and Virulence in Botryosphaeria dothidea

Botryosphaeria canker and fruit rot caused by the fungus Botryosphaeria dothidea is one of the most destructive diseases of apple worldwide. Autophagy is an evolutionarily conserved self-degradation process that is important for maintaining homeostasis to ensure cellular functionality. To date, the role of autophagy in B. dothidea is not well elucidated. In this study, we identified and characterized the autophagy-related protein Atg1 in B. dothidea. The BdAtg1 deletion mutant ΔBdAtg1 showed autophagy blockade and phenotypic defects in mycelial growth, conidiation, ascosporulation and virulence. In addition, ΔBdAtg1 exhibited an increased number of nuclei in the mycelial compartment. Comparative transcriptome analysis revealed that inactivation of BdAtg1 significantly influenced multiple metabolic pathways. Taken together, our results indicate that BdAtg1 plays an important role in vegetative differentiation and the pathogenicity of B. dothidea. The results of this study will provide a reference for the development of new target-based fungicides.

Natural phytochemicals that affect autophagy in the treatment of oral diseases and infections: A review

Autophagy is a critical factor in eukaryotic evolution. Cells provide nutrition and energy during autophagy by destroying non-essential components, thereby allowing intracellular material conversion and managing temporary survival stress. Autophagy is linked to a variety of oral disorders, including the type and extent of oral malignancies. Furthermore, autophagy is important in lymphocyte formation, innate immunity, and the regulation of acquired immune responses. It is also required for immunological responses in the oral cavity. Knowledge of autophagy has aided in the identification and treatment of common oral disorders, most notably cancers. The involvement of autophagy in the oral immune system may offer a new understanding of the immune mechanism and provide a novel approach to eliminating harmful bacteria in the body. This review focuses on autophagy creation, innate and acquired immunological responses to autophagy, and the status of autophagy in microbial infection research. Recent developments in the regulatory mechanisms of autophagy and therapeutic applications in oral illnesses, particularly oral cancers, are also discussed. Finally, the relationship between various natural substances that may be used as medications and autophagy is investigated.

The trilogy of P21 activated kinase, autophagy and immune evasion in pancreatic ductal adenocarcinoma

Pancreatic Ductal Adenocarcinoma (PDA) is one of the most lethal types of cancer with a dismal prognosis. KRAS mutation is a commonly identified oncogene in PDA tumorigenesis and P21-activated kinases (PAKs) are its downstream mediator. While PAK1 is more well-studied, PAK4 also attracted increasing interest. In PDA, PAK inhibition not only reduces cancer cell viability but also sensitises it to chemotherapy. While PDA remains resistant to existing immunotherapies, PAK inhibition has been shown to increase cancer immunogenicity of melanoma, glioblastoma and PDA. Furthermore, autophagy plays an important role in PDA immune evasion, and accumulating evidence has pointed to a connection between PAK and cancer cell autophagy. In this literature review, we aim to summarize currently available studies that have assessed the potential connection between PAK, autophagy and immune evasion in PDA biology to guide future research.

Genetic variants in autophagy-related gene ATG2B predict the prognosis of colorectal cancer patients receiving chemotherapy

Autophagy-related genes have a vital effect on colorectal cancer (CRC) by affecting genomic stability and regulating immune responses. However, the associations between genetic variants in autophagy-related genes and CRC outcomes for chemotherapy therapy remain unclear. The Cox regression model was used to evaluate the associations between single-nucleotide polymorphisms (SNPs) in autophagy-related genes and overall survival (OS) and progression-free survival (PFS) of CRC patients. The results were corrected by the false discovery rate (FDR) correction. We used the logistic regression model to investigate the associations of SNPs with the disease control rate (DCR) of patients. Gene expression analysis was explored based on an in-house dataset and other databases. The associations between gene expression and infiltrating immune cells were evaluated using the Tumor Immune Estimation Resource (TIMER) database. We observed that ATG2B rs17094017 A > T was significantly associated with increased OS (HR = 0.65, 95% CI = 0.50-0.86, P = 2.54×10^-3), PFS (HR = 0.76, 95% CI = 0.62-0.93, P = 7.34×10^-3), and DCR (OR = 0.60, 95% CI = 0.37-0.96, P = 3.31×10^-2) of CRC patients after chemotherapy. The expression of ATG2B was down-expressed in CRC tissues than in adjacent normal tissues. Moreover, ATG2B expression influenced the infiltration of CD8+ T cells, CD4+ T cells, B cells, and T cell receptor signaling pathways, which may inhibit the occurrence of CRC by affecting the immune system. This study suggests that genetic variants in the autophagy-related gene ATG2B play a critical role in predicting the prognosis of CRC prognosis undergoing chemotherapy.

Autophagy-Associated Immunogenic Modulation and Its Applications in Cancer Therapy

Autophagy, a lysosome-mediated cellular degradation pathway, recycles intracellular components to maintain metabolic balance and survival. Autophagy plays an important role in tumor immunotherapy as a “double-edged sword” that can both promote and inhibit tumor progression. Autophagy acts on innate and adaptive immunity and interacts with immune cells to modulate tumor immunotherapy. The discovery of autophagy inducers and autophagy inhibitors also provides new insights for clinical anti-tumor therapy. However, there are also difficulties in the application of autophagy-related regulators, such as low bioavailability and the lack of efficient selectivity. This review focuses on autophagy-related immunogenic regulation and its application in cancer therapy.

Association of ATG16L1 rs2241880 and TP53 rs1042522 with characteristics and course of diffuse large B-cell lymphoma

BACKGROUND

Diffuse large B-cell lymphoma (DLBCL) represents the most frequent lymphoma in adults. Prognosis for DLBCL patients may be evaluated through the most prominent clinical/laboratory parameters or pattern of gene expression. In order to improve prognostic/prediction scores or provide new therapeutic targets, novel genetic markers are needed. This study evaluates the association of ATG16L1 rs2241880 and TP53 rs1042522 with clinical characteristics and course of DLBCL.

METHODS

The study included 108 DLCBL patients treated with R-CHOP. Of these, 44 patients were subjected to stem cell transplantation and 55 to radiotherapy. Genotyping was performed by TaqMan genotyping assays.

RESULTS

Amongst analyzed characteristics and prognostic scores, genotypes were associated with clinical stage (TP53 CG+CC vs GG p = 0.06), extranodal disease (ATG16L1 AG vs AA p = 0.07; AG vs GG p = 0.04), lymphocyte-to-monocyte ratio (LMR) (ATG16L1 AA vs AG+GG, p = 0.052; AA vs GG, p = 0.054) and neutrophils-to-lymphocytes ratio (NLR) (ATG16L1 AA vs AG+GG, p = 0.033; AA vs GG, p = 0.003). Analyzed genotypes didn't impact response to therapy, relapse and therapy-related complications. Considering outcome, patients with ATG16L1 AA had higher survival rate than GG carriers (p = 0.04). In all patients, duration of overall survival (OS) and relapse free survival (RFS) was not affected by analyzed genotypes. When subjected to radiotherapy, patients with ATG16L1 A allele (p = 0.05) or AA genotype (p = 0.03) had superior OS.

CONCLUSION

Our results demonstrated the association of TP53 rs1042522 with clinical stage and ATG16L1 rs2241880 with extranodal disease, LMR and NLR. The impact of ATG16L1 genotypes on OS in patients subjected to radiotherapy, indicates significance of individual single nucleotide polymorphisms (SNPs) in particular subgroups of DLBCL.

Autophagy-Related Gene Signature Highlights Metabolic and Immunogenic Status of Malignant Cells in Non-Small Cell Lung Cancer Adenocarcinoma

Simple Summary

The role of autophagy in lung cancers is still controversial, mainly because the visualization of autophagy levels in patients remains challenging. One interesting approach consists of studying autophagy at the transcriptomic level. In this line, many transcriptomics analyses performed on autophagy genes focused on the discovery of new biomarkers to predict the efficiency of antitumor therapies. However, the majority of these studies were based on global transcriptomic analysis of the whole tumor microenvironment, and few investigations have been performed on malignant cells themselves. The goal of this study was not to determine another new predictive signature based on autophagy-related genes. Instead, we investigated the expression of autophagy genes to understand the involvement of this process in lung cancer homeostasis. Specifically, we discovered a new autophagy signature that correlates with the metabolic and immunogenic status of malignant cells, supporting the relationship between autophagy and tumor growth in lung cancer patients.

Abstract

Autophagy is a self-degradative mechanism involved in many biological processes, including cell death, survival, proliferation or migration. In tumors, autophagy plays an important role in tumorigenesis as well as cancer progression and resistance to therapies. Usually, a high level of autophagy in malignant cells has been associated with tumor progression and poor prognostic for patients. However, the investigation of autophagy levels in patients remains difficult, especially because quantification of autophagy proteins is challenging in the tumor microenvironment. In this study, we analyzed the expression of autophagy genes in non-small cell lung (NSCLC) cancer patients using public datasets and revealed an autophagy gene signature for proliferative and immune-checkpoint-expressed malignant cells in lung adenocarcinoma (LUAD). Analysis of autophagy-related gene expression profiles in tumor and adjacent tissues revealed differential signatures, namely signature A (23 genes) and signature B (12 genes). Signature B correlated with a bad prognosis and poor overall and disease-specific survival. Univariate and multivariate analyses revealed that this signature was an independent factor for prognosis. Moreover, patients with high expression of signature B exhibited more genes related to proliferation and fewer genes related to immune cells or immune response. The analysis of datasets from sorted fresh tumor cells or single cells revealed that signature B is predominantly represented in malignant cells, with poor expression in pan-immune population or in fibroblast or endothelial cells. Interestingly, autophagy was increased in malignant cells exhibiting high levels of signature B, which correlated with an elevated expression of genes involved in cell proliferation and immune checkpoint signaling. Taken together, our analysis reveals a novel autophagy-based signature to define the metabolic and immunogenic status of malignant cells in LUAD.

The Route of the Malignant Plasma Cell in Its Survival Niche: Exploring “Multiple Myelomas”

Growing evidence points to multiple myeloma (MM) and its stromal microenvironment using several mechanisms to subvert effective immune and anti-tumor responses. Recent advances have uncovered the tumor-stromal cell influence in regulating the immune-microenvironment and have envisioned targeting these suppressive pathways to improve therapeutic outcomes. Nevertheless, some subgroups of patients include those with particularly unfavorable prognoses. Biological stratification can be used to categorize patient-, disease- or therapy-related factors, or alternatively, these biological determinants can be included in a dynamic model that customizes a given treatment to a specific patient. Genetic heterogeneity and current knowledge enforce a systematic and comprehensive bench-to-bedside approach. Given the increasing role of cancer stem cells (CSCs) in better characterizing the pathogenesis of solid and hematological malignancies, disease relapse, and drug resistance, identifying and describing CSCs is of paramount importance in the management of MM. Even though the function of CSCs is well-known in other cancer types, their role in MM remains elusive. With this review, we aim to provide an update on MM homing and resilience in the bone marrow micro milieu. These data are particularly interesting for clinicians facing unmet medical needs while designing novel treatment approaches for MM.

An Autophagy-Related Gene Signature can Better Predict Prognosis and Resistance in Diffuse Large B-Cell Lymphoma

Background: Diffuse large B-cell lymphoma (DLBCL) is a highly heterogeneous disease, and about 30%–40% of patients will develop relapsed/refractory DLBCL. In this study, we aimed to develop a gene signature to predict survival outcomes of DLBCL patients based on the autophagy-related genes (ARGs).

Methods: We sequentially used the univariate, least absolute shrinkage and selector operation (LASSO), and multivariate Cox regression analyses to build a gene signature. The Kaplan–Meier curve and the area under the receiver operating characteristic curve (AUC) were performed to estimate the prognostic capability of the gene signature. GSEA analysis, ESTIMATE and ssGSEA algorithms, and one-class logistic regression were performed to analyze differences in pathways, immune response, and tumor stemness between the high- and low-risk groups.

Results: Both in the training cohort and validation cohorts, high-risk patients had inferior overall survival compared with low-risk patients. The nomogram consisted of the autophagy-related gene signature, and clinical factors had better discrimination of survival outcomes, and it also had a favorable consistency between the predicted and actual survival. GSEA analysis found that patients in the high-risk group were associated with the activation of doxorubicin resistance, NF-κB, cell cycle, and DNA replication pathways. The results of ESTIMATE, ssGSEA, and mRNAsi showed that the high-risk group exhibited lower immune cell infiltration and immune activation responses and had higher similarity to cancer stem cells.

Conclusion: We proposed a novel and reliable autophagy-related gene signature that was capable of predicting the survival and resistance of patients with DLBCL and could guide individualized treatment in future.

Aberrant SPOP-CHAF1A ubiquitination axis triggers tumor autophagy that endows a therapeutical vulnerability in diffuse large B cell lymphoma

Purpose

Aberrant epigenetic changes, like DNA methylation, histone modifications, or ubiquitination, could trigger metabolic disorders in human cancer cells. This study planed to uncover the biological roles of epigenetic SPOP/CHAF1A axis in modulating tumor autophagy during Diffuse large B-cell lymphoma (DLBCL) tumorigenesis.

Materials and methods

The Immunohistochemistry (IHC) was performed to assess the CHAF1A expressions. The expression data of CHAF1A was derived from The Cancer Genome Atlas (TCGA), GSE32918 and GSE83632 datasets. Bioinformatic assays contain differential analysis, functional enrichment analysis and Kaplan–Meier survival curve analysis. The colony generation assay, Transwell assay and CCK-8 assays were conducted for the in vitro assays. The in vivo ubiquitination assays were used to assess regulations of SPOP on CHAF1A. The Chromatin immunoprecipitation (ChIP) assays were used to uncover epigenetic regulations of CHAF1A on TFEB. The relevant DLBCL cells were subcutaneously injected to SCID beige mice to establish the xenograft models.

Results

Bioinformatic results revealed that CHAF1A expressed highly in DLBCL that were validated in patients samples. Patients with high CHAF1A suffered from inferior prognosis with shorter survival months relative to those with low CHAF1A. High CHAF1A enhanced DLBCL aggressiveness, including cell proliferation, migration and in vivo growth. Mechanistically, E3 ubiquitin ligase SPOP binds to and induces the degradative ubiquitination of CHAF1A via recognizing a consensus SPOP-binding motif in CHAF1A. SPOP is down-regulated in DLBCL and habours two DLBCL-associated mutations. Deficient SPOP leads to accumulated CHAF1A proteins that promote malignant features of DLBCL. Subsequently, ChIP-qPCR assay revealed that CHAF1A directly binds to TFEB promoters to activate the expressions. High CHAF1A could enhance the transcriptional activity of TFEB and downstream genes. The SPOP/CHAF1A axis modulates TFEB-dependent transactivation to regulate the lysosomal biogenesis and autophagy. The in vivo models suggested that TFEB inhibition is effective to suppress growth of SPOP-deficient DLBCLs.

Conclusions

CHAF1A is aberrantly elevated in SPOP-deficient DLBCL. The in‐depth mechanism understanding of SPOP/CHAF1A/TFEB axis endows novel targets for DLBCL treatment.

Autophagy, ferroptosis, pyroptosis, and necroptosis in tumor immunotherapy

In recent years, immunotherapy represented by immune checkpoint inhibitors (ICIs) has led to unprecedented breakthroughs in cancer treatment. However, the fact that many tumors respond poorly or even not to ICIs, partly caused by the absence of tumor-infiltrating lymphocytes (TILs), significantly limits the application of ICIs. Converting these immune “cold” tumors into “hot” tumors that may respond to ICIs is an unsolved question in cancer immunotherapy. Since it is a general characteristic of cancers to resist apoptosis, induction of non-apoptotic regulated cell death (RCD) is emerging as a new cancer treatment strategy. Recently, several studies have revealed the interaction between non-apoptotic RCD and antitumor immunity. Specifically, autophagy, ferroptosis, pyroptosis, and necroptosis exhibit synergistic antitumor immune responses while possibly exerting inhibitory effects on antitumor immune responses. Thus, targeted therapies (inducers or inhibitors) against autophagy, ferroptosis, pyroptosis, and necroptosis in combination with immunotherapy may exert potent antitumor activity, even in tumors resistant to ICIs. This review summarizes the multilevel relationship between antitumor immunity and non-apoptotic RCD, including autophagy, ferroptosis, pyroptosis, and necroptosis, and the potential targeting application of non-apoptotic RCD to improve the efficacy of immunotherapy in malignancy.

Macrophages evoke autophagy of hepatic stellate cells to promote liver fibrosis in NAFLD mice via the PGE2/EP4 pathway

The pathogenesis of liver fibrosis in nonalcoholic fatty liver disease (NAFLD) remains unclear and the effective treatments have not been explored yet. The activation of hepatic stellate cells (HSCs) is considered as the most critical factor in the progression of liver fibrosis and cirrhosis. Autophagy has recently been identified as a new mechanism to regulate HSC activation. Here, we found that liver macrophages were polarized toward type 2 (M2) during the progression of nonalcoholic steatohepatitis (NASH) and liver fibrosis in both patients and NAFLD mice. Using the methionine-choline-deficient (MCD) diet NAFLD murine model and the in vitro cell culture system, we identified that the M2 macrophages promoted HSC autophagy by secreting prostaglandin E2 (PGE2) and binding its receptor EP4 on the surface of HSCs, which consequently enhanced HSC activation, extracellular matrix deposition, and liver fibrosis. Mechanistically, PGE2/EP4 signals enhanced HSC autophagy through the Erk pathway. A specific PGE2/EP4 antagonist E7046 significantly inhibited M2 macrophage-mediated HSC autophagy and improved liver fibrosis and histopathology in NAFLD mice. Our study provides novel mechanistic insights into the regulation of HSC activation and liver fibrosis. Our findings suggest that the PGE2/EP4 pathway is a promising therapeutic target to prevent NASH progression into cirrhosis.

Crosstalk Between Autophagy and Innate Immunity: A Pivotal Role in Hepatic Fibrosis

Liver fibrosis is a repair process of chronic liver injuries induced by toxic substances, pathogens, and inflammation, which exhibits a feature such as deposition of the extracellular matrix. The initiation and progression of liver fibrosis heavily relies on excessive activation of hepatic stellate cells (HSCs). The activated HSCs express different kinds of chemokine receptors to further promote matrix remodulation. The long-term progression of liver fibrosis will contribute to dysfunction of the liver and ultimately cause hepatocellular carcinoma. The liver also has abundant innate immune cells, including DCs, NK cells, NKT cells, neutrophils, and Kupffer cells, which conduct complicated functions to activation and expansion of HSCs and liver fibrosis. Autophagy is one specific type of cell death, by which the aberrantly expressed protein and damaged organelles are transferred to lysosomes for further degradation, playing a crucial role in cellular homeostasis. Autophagy is also important to innate immune cells in various aspects. The previous studies have shown that dysfunction of autophagy in hepatic immune cells can result in the initiation and progression of inflammation in the liver, directly or indirectly causing activation of HSCs, which ultimately accelerate liver fibrosis. Given the crosstalk between innate immune cells, autophagy, and fibrosis progression is complicated, and the therapeutic options for liver fibrosis are quite limited, the exploration is essential. Herein, we review the previous studies about the influence of autophagy and innate immunity on liver fibrosis and the molecular mechanism to provide novel insight into the prevention and treatment of liver fibrosis.

Effects of autophagy modulators tamoxifen and chloroquine on the expression profiles of long non-coding RNAs in MIAMI cells exposed to IFNγ

Mesenchymal stromal cells (MSCs) can be utilized clinically for treatment of conditions that result from excessive inflammation. In a pro-inflammatory environment, MSCs adopt an anti-inflammatory phenotype resulting in immunomodulation. A sub-type of MSCs referred to as “marrow-isolated adult multilineage inducible” (MIAMI) cells, which were isolated from bone marrow, were utilized to show that the addition of autophagy modulators, tamoxifen (TX) or chloroquine (CQ), can alter how MIAMI cells respond to IFNγ exposure in vitro resulting in an increased immunoregulatory capacity of the MIAMI cells. Molecularly, it was also shown that TX and CQ each alter both the levels of immunomodulatory genes and microRNAs which target such genes. However, the role of other non-coding RNAs (ncRNAs) such as long non-coding RNAs (lncRNAs) in regulating the response of MSCs to inflammation has been poorly studied. Here, we utilized transcriptomics and data mining to analyze the putative roles of various differentially regulated lncRNAs in MIAMI cells exposed to IFNγ with (or without) TX or CQ. The aim of this study was to investigate how the addition of TX and CQ alters lncRNA levels and evaluate how such changes could alter previously observed TX- and CQ-driven changes to the immunomodulatory properties of MIAMI cells. Data analysis revealed 693 long intergenic non-coding RNAS (lincRNAs), 480 pseudogenes, and 642 antisense RNAs that were differentially regulated with IFNγ, IFNγ+TX and IFNγ+CQ treatments. Further analysis of these RNA species based on the existing literature data revealed 6 antisense RNAs, 2 pseudogenes, and 5 lincRNAs that have the potential to modulate MIAMI cell’s response to IFNγ treatment. Functional analysis of these genomic species based on current literature linking inflammatory response and ncRNAs indicated their potential for regulation of several key pro- and anti-inflammatory responses, including NFκB signaling, cytokine secretion and auto-immune responses. Overall, this work found potential involvement of multiple pro-and anti-inflammatory pathways and molecules in modulating MIAMI cells’ response to inflammation.

Combination Therapy of Ledipasvir and Itraconazole in the Treatment of COVID-19 Patients Coinfected with Black Fungus: An In Silico Statement

The manuscript mainly aimed at providing clues on improving the innate immunity of coronavirus patients and safeguarding them from both new mutant strains and black fungus infections. Coronavirus is readily mutating from one variant to another. Among the several variants, we selected SARS-CoV-2 B.1.1.7 in this study. Upon infection of any virus, ideally, the phagocytic cells of the host engulf and destroy the virus by a mechanism called phagocytosis. However, compromised immunity impairs phagocytosis, and thus, restoring the immune system is crucial for a speedy recovery of infected patients. The autophagy and activation of Toll-like receptor-4 are the only ways to restore innate immunity. Recently, immunocompromised COVID-19 patients have been suffering from the coinfection of black fungus. Rhizomucor, a black fungus species, causes more than 75% of cases of mucormycosis. Here, we present the results of molecular docking studies of sixty approved antiviral drugs targeting receptors associated with the SARS-CoV-2 B 1.1.7 variant (PDB id: 7NEH), activating the innate immune system (PDB id: 5YEC and 5IJC). We also studied the twenty approved antifungal drugs with Rhizomucor miehei lipase propeptide (PDB id: 6QPR) to identify the possible combination therapy for patients coinfected with coronavirus and black fungus. The ledipasvir showed excellent docking interactions with the 7NEH, 5YEC, and 5IJC, indicating that it is a perfect candidate for the treatment of COVID-19 patients. Itraconazole showed significant interaction with 6QPR of Rhizomucor miehei, suggesting that itraconazole can treat black fungus infections. In conclusion, the combination therapy of ledipasvir and itraconazole can be a better alternative for treating COVID-19 patients coinfected with black fungus.

Identification of autophagy-related biomarker and analysis of immune infiltrates in oral carcinoma

Background

Autophagy plays a vital role in the progression of the tumor. We aimed to investigate the expression, prognostic value, and immune infiltration of autophagy‐related genes in oral carcinoma via bioinformatics analysis.

Methods

The microarray datasets (GSE146483 and GSE23558) of oral carcinoma were downloaded from Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between normal and diseased groups were identified by the Limma package. The screened autophagy‐related gene was further validated by the human protein atlas (HPA) database, TCGA database, and GSE78060 dataset.

Results

A total of 18 upregulated (top 10: EGFR, TNF, FADD, AURKA, E2F1, CHEK1, BRCA1, BIRC5, EIF2AK2, and CSF2) and 31 downregulated (top 10: MAP1LC3A, PARK2, AGT, IGF1, TP53INP1, CXCL12, IKBKB, SESN1, ULK2, and RRAGD) autophagy‐related (DEGs) were identified, and FADD was found to be related to the prognosis of oral cancer patients. Gene set enrichment analysis indicated that FADD‐associated genes were significantly enriched in immune‐related pathways. Moreover, correlation analysis revealed that FADD expression was associated with immune infiltrates. Upregulation of FADD is associated with poor survival and immune infiltrates in oral cancer.

Conclusion

We speculated that FADD is involved in the immune regulation of oral cancer, as well as autophagy.

A Novel Four Genes of Prognostic Signature for Uveal Melanoma

Autophagy and immunity play critical roles in various cancers, but the prognostic impact of autophagy and immunity for uveal melanoma (UM) remains lacking. Therefore, the RNA sequencing of data in the TCGA-UVM dataset was downloaded from UCSC Xena database. The prognostic autophagy- and immunity-related genes (AIRGs) were selected via univariate Cox regression. Next, we applied LASSO method to construct four genes of signature in the TCGA-UVM and verified in another two GEO datasets (GSE84976 and GSE22138). This signature intimately associated with overall survival (OS) time and metastasis-free survival (MFS) time of UM, which could be considered as a prognostic indicator. Besides, by applying risk assessment, the patients of UM can be divided into two subgroups (high/low risk) with different survival time, distinct clinical outcomes, and immune microenvironments. Gene set enrichment analysis (GSEA) manifested that cancer hallmark epithelial-mesenchymal transition and KRAS pathways were positively activated in the high-risk group. Moreover, the high-risk group could be more sensitive to chemotherapies than the low-risk group. Thus, our finding suggested that the four genes of signature closely linked with UM risk and survival can afford more accurate survival prediction and potential therapeutic targets for clinical application.

Non-apoptotic cell death-based cancer therapy: Molecular mechanism, pharmacological modulators, and nanomedicine

As an emerging cancer therapeutic target, non-apoptotic cell death such as ferroptosis, necroptosis and pyroptosis, etc., has revealed significant potential in cancer treatment for bypassing apoptosis to enhance the undermined therapeutic efficacy triggered by apoptosis resistance. A variety of anticancer drugs, synthesized compounds and natural products have been proven recently to induce non-apoptotic cell death and exhibit excellent anti-tumor effects. Moreover, the convergence of nanotechnology with functional materials and biomedicine science has provided tremendous opportunities to construct non-apoptotic cell death-based nanomedicine for innovative cancer therapy. Nanocarriers are not only employed in targeted delivery of non-apoptotic inducers, but also used as therapeutic components to induce non-apoptotic cell death to achieve efficient tumor treatment. This review first introduces the main characteristics, the mechanism and various pharmacological modulators of different non-apoptotic cell death forms, including ferroptosis, necroptosis, pyroptosis, autophagy, paraptosis, lysosomal-dependent cell death, and oncosis. Second, we comprehensively review the latest progresses of nanomedicine that induces various forms of non-apoptotic cell death and focus on the nanomedicine targeting different pathways and components. Furthermore, the combination therapies of non-apoptotic cell death with photothermal therapy, photodynamic therapy, immunotherapy and other modalities are summarized. Finally, the challenges and future perspectives in this regard are also discussed.

Novel Insights into Autophagy and Prostate Cancer: A Comprehensive Review

Autophagy is a complex process involved in several cell activities, including tissue growth, differentiation, metabolic modulation, and cancer development. In prostate cancer, autophagy has a pivotal role in the regulation of apoptosis and disease progression. Several molecular pathways are involved, including PI3K/AKT/mTOR. However, depending on the cellular context, autophagy may play either a detrimental or a protective role in prostate cancer. For this purpose, current evidence has investigated how autophagy interacts within these complex interactions. In this article, we discuss novel findings about autophagic machinery in order to better understand the therapeutic response and the chemotherapy resistance of prostate cancer. Autophagic-modulation drugs have been employed in clinical trials to regulate autophagy, aiming to improve the response to chemotherapy or to anti-cancer treatments. Furthermore, the genetic signature of autophagy has been found to have a potential means to stratify prostate cancer aggressiveness. Unfortunately, stronger evidence is needed to better understand this field, and the application of these findings in clinical practice still remains poorly feasible.

Understanding autophagy role in cancer stem cell development

Cancer stem cells (CSCs) are a small subpopulation of immature cells located in the tumor mass. These cells are responsible for tumor development, proliferation, resistance and spreading. CSCs are characterized by three unique features: the ability to self-renew, differentiation and tumor formation. CSCs are similar to stem cells, but they differ in the malignant phenotype. CSCs become immortal and survive harsh environmental conditions such as hypoxia, starvation and oxidative stress. However, this harsh tumor microenvironment induces the activation of autophagy, which further increases the CSCs stemness profile, and all these features further increase tumorigenicity and metastasis capacity. Autophagy is induced by the extracellular and cellular microenvironment. Hypoxia is one of the most common factors that highly increases the activity of autophagy in CSCs. Therefore, hypoxia-induced autophagy and CSCs proliferation should be elucidated in order to find a novel cure to defeat cancer cells (CSCs and non-CSCs). The remaining challenges to close the gap between the laboratory bench and the development of therapies, to use autophagy against CSCs in patients, could be addressed by adopting a 3D platform to better-mimic the natural environment in which these cells reside. Ultimately allowing to obtain the blueprints for bioprocess scaling up and to develop the production pipeline for safe and cost-effective autophagy-based novel biologics.

BCL2A1 and CCL18 Are Predictive Biomarkers of Cisplatin Chemotherapy and Immunotherapy in Colon Cancer Patients

Background: Cisplatin enhances the antitumor T cell response, and the combination of PD-L1 blockade produces a synergistic therapeutic effect. However, the clinical correlation between cisplatin and immunotherapy in colon cancer (CC) is unknown.

Methods: Using the “pRRophetic” package, we calculated the IC50 of cisplatin. The correlation between cisplatin IC50, cisplatin resistance–related genes (CCL18 and BCL2A1), and immunotherapy were preliminarily verified in TCGA and further validated in independent cohorts (GSE39582 and GSE17538), cisplatin-resistant CC cell line DLD1, and our own clinical specimens. Classification performance was evaluated using the AUC value of the ROC curve. Scores of immune signatures, autophagy, ferroptosis, and stemness were quantified using the ssGSEA algorithm.

Results: Based on respective medians of three CC cohorts, patients were divided into high- and low-IC50 groups. Compared with the high IC50 group, the low-IC50 group had significantly higher tumor microenvironment (TME) scores and lower tumor purity. Most co-signaling molecules were upregulated in low IC50 group. CC patients with good immunotherapy efficacy (MSI, dMMR, and more TMB) were more attributable to the low-IC50 group. Among seven shared differentially expressed cisplatin resistance–related genes, CCL18 and BCL2A1 had the best predictive efficacy of the above immunotherapy biomarkers. For wet experimental verification, compared with cisplatin-resistant DLD1, similar to PD-L1, CCL18 and BCL2A1 were significantly upregulated in wild-type DLD1. In our own CC tissues, the mRNA expression of CCL18, BCL2A1, and PD-L1 in dMMR were significantly increased. The high group of CCL18 or BCL2A1 had a higher proportion of MSI, dMMR, and more TMB. IC50, CCL18, BCL2A1, and PD-L1 were closely related to scores of immune-related pathways, immune signatures, autophagy, ferroptosis, and stemness. The microRNA shared by BCL2A1 and PD-L1, hsa-miR-137, were significantly associated with CCL18, BCL2A1, and PD-L1, and downregulated in low-IC50 group. The activity of the TOLL-like receptor signaling pathway affected the sensitivity of CC patients to cisplatin and immunotherapy. For subtype analysis, immune C2, immune C6, HM-indel, HM-SNV, C18, and C20 were equally sensitive to cisplatin chemotherapy and immunotherapy.

Conclusions: CC patients sensitive to cisplatin chemotherapy were also sensitive to immunotherapy. CCL18 and BCL2A1 were novel biomarkers for cisplatin and immunotherapy.

Autophagy mediates ER stress and inflammation in Helicobacter pylori-related gastric cancer

Autophagy is a cellular degradation mechanism, which is triggered by the bacterium Helicobacter pylori. A single nucleotide polymorphism (SNP) in the autophagy gene ATG16L1 (rs2241880, G-allele) has been shown to dysregulate autophagy and increase intestinal endoplasmic reticulum (ER) stress. Here, we investigate the role of this SNP in H.pylori-mediated gastric carcinogenesis and its molecular pathways. ATG16L1 rs2241880 was genotyped in subjects from different ethnic cohorts (Dutch and Australian) presenting with gastric (pre)malignant lesions of various severity. Expression of GRP78 (a marker for ER stress) was assessed in gastric tissues. The effect of ATG16L1 rs2241880 on H.pylori-mediated ER stress and pro-inflammatory cytokine induction was investigated in organoids and CRISPR/Cas9 modified cell lines. Development of gastric cancer was associated with the ATG16L1 rs2241880 G-allele. Intestinal metaplastic cells in gastric tissue of patients showed increased levels of ER-stress. In vitro models showed that H.pylori increases autophagy while reducing ER stress, which appeared partly mediated by the ATG16L1 rs2241880 genotype. H.pylori-induced IL-8 production was increased while TNF-α production was decreased, in cells homozygous for the G-allele. The ATG16L1 rs2241880 G-allele is associated with progression of gastric premalignant lesions and cancer. Modulation of H.pylori-induced ER stress pathways and pro-inflammatory mediators by ATG16L1 rs2441880 may underlie this increased risk.

Nano-ultrasonic Contrast Agent for Chemoimmunotherapy of Breast Cancer by Immune Metabolism Reprogramming and Tumor Autophagy

The functional status of innate immune cells is a considerable determinant of effective antitumor immune response. However, the triple-negative breast cancer tumor microenvironment with high lactic acid metabolism and high antioxidant levels limits immune cell survival, differentiation, and function. Here, we determine that the tumor microenvironment-responsive nano-ultrasonic contrast agent Pt(IV)/CQ/PFH NPs-^DPPA-1 boosts the ratio of mature dendritic cells (mDCs) and proinflammatory macrophages by reprogramming the metabolism of immature DCs (iDCs) and tumor-associated macrophages (TAMs). Specifically, platinum(IV) in cancer cells or iDCs was reduced to cisplatin, which can increase the intracellular content of ROS and therefore enhance the ratio of mDCs and apoptotic tumor cells. Meanwhile, chloroquine (CQ) released from nanoparticles (NPs) minimizes protective autophagy caused by cisplatin in tumor cells and reprograms the metabolism of TAMs to enhance the proportion of proinflammatory macrophages, achieving a superior synergistic effect of chemoimmunotherapy combined with Pt(IV) and anti-PD-L1 peptide (^DPPA-1). Furthermore, perfluorohexane (PFH) in NPs realizes monitoring treatment corresponding to ultrasound. Collectively, the nano-ultrasonic contrast agent supports a candidate for monitoring treatment and augmenting antitumor chemoimmunotherapy by suppressing tumor cell autophagy and reprogramming immunocyte metabolism.

The Role of Autophagy in Childhood Central Nervous System Tumors

OPINION STATEMENT

Autophagy is a physiological process that occurs in normal tissues. Under external environmental pressure or internal environmental changes, cells can digest part of their contents through autophagy in order to reduce metabolic pressure or remove damaged organelles. In cancer, autophagy plays a paradoxical role, acting as a tumor suppressor-by removing damaged organelles and inhibiting inflammation or by promoting genome stability and the tumor-adaptive responses-as a pro-survival mechanism to protect cells from stress. In this article, we review the autophagy-dependent mechanisms driving childhood central nervous system tumor cell death, malignancy invasion, chemosensitivity, and radiosensitivity. Autophagy inhibitors and inducers have been developed, and encouraging results have been achieved in autophagy modulation, suggesting that these might be potential therapeutic agents for the treatment of pediatric central nervous system (CNS) tumors.

The Yin and Yang dualistic features of autophagy in thermal burn wound healing

Burn healing should be regarded as a dynamic process consisting of two main, interrelated phases: (a) the inflammatory phase when neutrophils and monocytes infiltrate the injury site, through localized vasodilation and fluid extravasation, and (b) the proliferative-remodeling phase, which represents a key event in wound healing. In the skin, both canonical autophagy (induced by starvation, oxidative stress, and environmental aggressions) and non-canonical or selective autophagy have evolved to play a discrete, but, essential, “housekeeping” role, for homeostasis, immune tolerance, and survival. Experimental data supporting the pro-survival roles of autophagy, highlighting its Yang, luminous and positive feature of this complex but insufficient explored molecular pathway, have been reported. Autophagic cell death describes an “excessive” degradation of important cellular components that are necessary for normal cell function. This deadly molecular mechanism brings to light the darker, concealed, Yin feature of autophagy. Autophagy seems to perform dual, conflicting roles in the angiogenesis context, revealing once again, its Yin–Yang features. Autophagy with its Yin–Yang features remains the shadow player, able to decide quietly whether the cell survives or dies.

The dual role of neutrophils in cancer

For the past decade, the role and importance of neutrophils in cancer is being increasingly appreciated. Research has focused on the ability of cancer-related neutrophils to either support tumor growth or interfere with it, showing diverse mechanisms through which the effects of neutrophils take place. In contrast to the historic view of neutrophils as terminally differentiated cells, mounting evidence has demonstrated that neutrophils are a plastic and diverse population of cells. These dynamic and plastic abilities allow them to perform varied and sometimes opposite functions simultaneously. In this review, we summarize and detail clinical and experimental evidence for, and underlying mechanisms of, the dual impact of neutrophils' functions, both supporting and inhibiting cancer development. We first discuss the effects of various basic functions of neutrophils, namely direct cytotoxicity, secretion of reactive oxygen species (ROS), nitric oxide (NO) and proteases, NETosis, autophagy and modulation of other immune cells, on tumor growth and metastatic progression. We then describe the clinical evidence for pro- vs anti-tumor functions of neutrophils in human cancer. We believe and show that the "net" impact of neutrophils in cancer is the sum of a complex balance between contradicting effects which occur simultaneously.

The impact of dawn to sunset fasting on immune system and its clinical significance in Covid-19 pandemic

Dawn to sunset fasting, a type of intermittent fasting commonly practiced in the month of Ramadan, requires fasting from dawn to sunset without food or liquid intake. Dawn and dusk are two transition time zones of the day that play a critical role in the human circadian rhythm. Practicing dawn to sunset fasting requires the alignment of mealtimes and wake-sleep times with the human biological dawn and dusk. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) impairs immune cell responses at multiple levels and leads to severe Coronavirus Disease 2019 (COVID-19). It generates high levels of pro-inflammatory cytokines and chemokines, also known as a cytokine storm, leads to mitochondrial dysfunction and generation of excessive amounts of mitochondrial reactive oxygen species, downregulates autophagy to escape detection for unchecked replication, and alters gut microbiome composition. Severe cases of COVID-19 have been associated with several comorbidities that impair immune responses (e.g., obesity, diabetes, malignancy) and blood laboratory abnormalities (e.g., elevated procalcitonin, C-reactive protein, interleukin-6 (IL-6), leukocytosis, lymphopenia). Several studies of dawn to sunset fasting showed anti-inflammatory effect by suppressing several pro-inflammatory cytokines, reducing oxidative stress, inducing a proteome response associated with increased autophagy, remodeling the gut microbiome, and improving the components of metabolic syndrome (e.g., obesity, blood glucose levels, blood pressure, lipids). In conclusion, dawn to sunset fasting has the potential to optimize the immune system function against SARS-CoV-2 during the COVID-19 pandemic as it suppresses chronic inflammation and oxidative stress, improves metabolic profile, and remodels the gut microbiome. This review presents scientific literature related to the effects of dawn to sunset fasting on the immune system. Studies are needed to assess and confirm the potential benefits of dawn to sunset fasting against SARS-CoV-2.

TGF-β Signaling and Resistance to Cancer Therapy

The transforming growth factor β (TGF-β) pathway, which is well studied for its ability to inhibit cell proliferation in early stages of tumorigenesis while promoting epithelial-mesenchymal transition and invasion in advanced cancer, is considered to act as a double-edged sword in cancer. Multiple inhibitors have been developed to target TGF-β signaling, but results from clinical trials were inconsistent, suggesting that the functions of TGF-β in human cancers are not yet fully explored. Multiple drug resistance is a major challenge in cancer therapy; emerging evidence indicates that TGF-β signaling may be a key factor in cancer resistance to chemotherapy, targeted therapy and immunotherapy. Finally, combining anti-TGF-β therapy with other cancer therapy is an attractive venue to be explored for the treatment of therapy-resistant cancer.

Four Autophagy-Related Long Noncoding RNAs Provide Coexpression and ceRNA Mechanisms in Retinoblastoma through Bioinformatics and Experimental Evidence

Retinoblastoma (RB) is the most common type of intraocular malignant tumor that lowers the quality of life among children worldwide. Long noncoding RNAs (lncRNAs) are reported to play a dual role in tumorigenesis and development of RB. Autophagy is also reported to be involved in RB occurrence. Although several studies of autophagy-related lncRNAs in RB have been explored before, there are still unknown potential mechanisms in RB. In the present study, we mined dataset GSE110811 from the Gene Expression Omnibus database and downloaded autophagy-related genes from the Human Autophagy Database for further bioinformatic analysis. By implementing the differential expression analysis and Pearson correlation analysis on the lncRNA expression matrix and autophagy-related genes expression matrix, we identified four autophagy-related lncRNAs (namely, N4BP2L2-IT2, SH3BP5-AS1, CDKN2B-AS1, and LINC-PINT) associated with RB. We then performed differential expression analysis on microRNA (miRNA) from dataset GSE39105 for further analyses of lncRNA-miRNA-mRNA regulatory mechanisms. With the miRNA-lncRNA module on the StarBase 3.0 website, we predicted the differentially expressed miRNAs that could target the autophagy-related lncRNAs and constructed a potential lncRNA-miRNA-mRNA regulatory network. Furthermore, the functional annotations of these target genes in regulatory networks were presented using the Cytoscape and the Metascape annotation tool. Finally, the expression pattern of the four autophagy-related lncRNAs was evaluated via qRT-PCR. In conclusion, our findings suggest that the four autophagy-related lncRNAs could be critical molecules associated with the development of RB and affect the occurrence and development of RB through the lncRNA-miRNA-mRNA regulatory network. Genes (GRP13B, IFT88, EPHA3, GABARAPL1, and EIF4EBP1) may serve as potential novel therapeutic targets and biomarkers in RB.

Identification of a Five Autophagy Subtype-Related Gene Expression Pattern for Improving the Prognosis of Lung Adenocarcinoma

Background: Autophagy plays an important role in lung adenocarcinoma (LUAD). In this study, we aimed to explore the autophagy-related gene (ARG) expression pattern and to identify promising autophagy-related biomarkers to improve the prognosis of LUAD.

Methods: The gene expression profiles and clinical information of LUAD patients were downloaded from the Cancer Genome Atlas (TCGA), and validation cohort information was extracted from the Gene Expression Omnibus database. The Human Autophagy Database (HADb) was used to extract ARGs. Gene expression data were analyzed using the limma package and visualized using the ggplot2 package as well as the pheatmap package in R software. Functional enrichment analysis was also performed for the differentially expressed ARGs (DEARGs). Then, consensus clustering revealed autophagy-related tumor subtypes, and differentially expressed genes (DEGs) were screened according to the subtypes. Next, the univariate Cox and multivariate Cox regression analyses were used to identify independent prognostic ARGs. After overlapping DEGs and the independent prognostic ARGs, the predictive risk model was established and validated. Correlation analyses between ARGs and clinicopathological variables were also explored. Finally, the TIMER and TISIDB databases were used to further explore the correlation analysis between immune cell infiltration levels and the risk score as well as clinicopathological variables in the predictive risk model.

Results: A total of 222 genes from the HADb were identified as ARGs, and 28 of the 222 genes were pooled as DEARGs. The most significant GO term was autophagy (p = 3.05E-07), and KEGG analysis results indicated that 28 DEARGs were significantly enriched in the ErbB signaling pathway (p < 0.001). Then, consensus clustering analysis divided the LUAD into two clusters, and a total of 168 DEGs were identified according to cluster subtypes. Then univariate and multivariate Cox regression analyses were used to identify 12 genes that could serve as independent prognostic indicators. After overlapping 168 DEGs and 12 genes, 10 genes (ATG4A, BAK1, CAPNS1, CCR2, CTSD, EIF2AK3, ITGB1, MBTPS2, SPHK1, ST13) were selected for the further exploration of the prognostic pattern. Survival analysis results indicated that this risk model identified the prognosis (p = 4.379E-10). Combined with the correlation analysis results between ARGs and clinicopathological variables, five ARGs were screened as prognostic genes. Among them, SPHK1 expression levels were positively correlated with CD4⁺ T cells and dendritic cell infiltration levels.

Conclusions: In this study, we constructed a predictive risk model and identified a five autophagy subtype-related gene expression pattern to improve the prognosis of LUAD. Understanding the subtypes of LUAD is helpful to accurately characterize the LUAD and develop personalized treatment.

Signatures of 4 autophagy-related genes as diagnostic markers of MDD and their correlation with immune infiltration

BACKGROUND

Major depressive disorder (MDD) is a debilitating mental illness and one of the primary causes of suicide. This study attempted to develop and validate a multigene joint signature for diagnosing MDD based on autophagy-related genes (ARGs) and to explore their biological role in MDD.

METHODS

We downloaded data from the Gene Expression Omnibus (GEO) database and retrieved ARGs from the Human Autophagy Database. The limma package in R software was used to identify differentially expressed genes (DEGs). We used CIBERSORT to analyze differences in the immune microenvironment between MDD patients and controls. Finally, we examined the correlation between diagnostic markers and infiltrating immune cells to better understand the molecular immune mechanism.

RESULTS

In this study, we identified 20 differentially expressed ARGs in MDD compared to controls. A signature of 4 autophagy-related genes (GPR18, PDK4, NRG1 and EPHB2) was obtained. ROC analysis showed that our model has good diagnostic performance (AUC=0.779, 95% CI=0.709-0.848). Bioinformatics analysis validated that GPR18 may represent a new candidate gene for MDD. Correlation analysis revealed that GPR18 was positively correlated with regulatory T cells (Treg), CD8+ T cells, naive B cells, and memory B cells and negatively correlated with M0 macrophages and neutrophils in MDD.

LIMITATIONS

This was a second mining of previously published data sets. Independent studies are warranted to validate and improve the clinical utility of the identified signature.

CONCLUSIONS

We identified a novel four-ARG gene signature that has good diagnostic performance and identified an association between ARG genes and the immune microenvironment in MDD.

Tumor metastasis: Mechanistic insights and therapeutic interventions

Cancer metastasis is responsible for the vast majority of cancer-related deaths worldwide. In contrast to numerous discoveries that reveal the detailed mechanisms leading to the formation of the primary tumor, the biological underpinnings of the metastatic disease remain poorly understood. Cancer metastasis is a complex process in which cancer cells escape from the primary tumor, settle, and grow at other parts of the body. Epithelial-mesenchymal transition and anoikis resistance of tumor cells are the main forces to promote metastasis, and multiple components in the tumor microenvironment and their complicated crosstalk with cancer cells are closely involved in distant metastasis. In addition to the three cornerstones of tumor treatment, surgery, chemotherapy, and radiotherapy, novel treatment approaches including targeted therapy and immunotherapy have been established in patients with metastatic cancer. Although the cancer survival rate has been greatly improved over the years, it is still far from satisfactory. In this review, we provided an overview of the metastasis process, summarized the cellular and molecular mechanisms involved in the dissemination and distant metastasis of cancer cells, and reviewed the important advances in interventions for cancer metastasis.

ATIC inhibits autophagy in hepatocellular cancer through the AKT/FOXO3 pathway and serves as a prognostic signature for modeling patient survival

Background: Autophagy regulates many cell functions related to cancer, ranging from cell proliferation and angiogenesis to metabolism. Due to the close relationship between autophagy and tumors, we investigated the predictive value of autophagy-related genes.

Methods: Data from patients with hepatocellular carcinoma were obtained from The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) databases. A regression analysis of differentially expressed genes was performed. Based on a prognostic model, patients were divided into a high-risk or low-risk group. Kaplan-Meier survival analyses of patients were conducted. The immune landscapes, as determined using single-sample gene set enrichment analysis (ssGSEA), exhibited different patterns in the two groups. The prognostic model was verified using the ICGC database and clinical data from patients collected at Zhongnan Hospital. Based on the results of multivariate Cox regression analysis, 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/inosine monophosphate (IMP) cyclohydrolase (ATIC) had the largest hazard ratio, and thus we studied the effect of ATIC on autophagy and tumor progression by performing in vitro and in vivo experiments.

Results: Fifty-eight autophagy-related genes were differentially expressed (false discovery rate (FDR)<0.05, log₂ fold change (logFC)>1); 23 genes were related to the prognosis of patients. A prognostic model based on 12 genes (ATG10, ATIC, BIRC5, CAPN10, FKBP1A, GAPDH, HDAC1, PRKCD, RHEB, SPNS1, SQSTM1 and TMEM74) was constructed. A significant difference in survival rate was observed between the high-risk group and low-risk group distinguished by the model (P<0.001). The model had good predictive power (area under the curve (AUC)>0.7). Risk-related genes were related to the terms type II IFN response, MHC class I (P<0.001) and HLA (P<0.05). ATIC was confirmed to inhibit autophagy and promote the proliferation, invasion and metastasis of liver cancer cells through the AKT/Forkhead box subgroup O3 (FOXO3) signaling pathway in vitro and in vivo.

Conclusions: The prediction model effectively predicts the survival time of patients with liver cancer. The risk score reflects the immune cell features and immune status of patients. ATIC inhibits autophagy and promotes the progression of liver cancer through the AKT/FOXO3 signaling pathway.

Hepatitis B virus X Protein Promotes Liver Cancer Progression through Autophagy Induction in Response to TLR4 Stimulation

Hepatitis B virus X (HBx) protein has been reported as a key protein regulating the pathogenesis of HBV-induced hepatocellular carcinoma (HCC). Recent evidence has shown that HBx is implicated in the activation of autophagy in hepatic cells. Nevertheless, the precise molecular and cellular mechanism by which HBx induces autophagy is still controversial. Herein, we investigated the molecular and cellular mechanism by which HBx is involved in the TRAF6-BECN1-Bcl-2 signaling for the regulation of autophagy in response to TLR4 stimulation, therefore influencing the HCC progression. HBx interacts with BECN1 (Beclin 1) and inhibits the association of the BECN1-Bcl-2 complex, which is known to prevent the assembly of the pre-autophagosomal structure. Furthermore, HBx enhances the interaction between VPS34 and TRAF6-BECN1 complex, increases the ubiquitination of BECN1, and subsequently enhances autophagy induction in response to LPS stimulation. To verify the functional role of HBx in liver cancer progression, we utilized different HCC cell lines, HepG2, SK-Hep-1, and SNU-761. HBx-expressing HepG2 cells exhibited enhanced cell migration, invasion, and cell mobility in response to LPS stimulation compared to those of control HepG2 cells. These results were consistently observed in HBx-expressed SK-Hep-1 and HBx-expressed SNU-761 cells. Taken together, our findings suggest that HBx positively regulates the induction of autophagy through the inhibition of the BECN1-Bcl-2 complex and enhancement of the TRAF6-BECN1-VPS34 complex, leading to enhance liver cancer migration and invasion.

Understanding the genomic architecture of clinical mastitis in Bos indicus

This study elucidated potential genetic variants and QTLs associated with clinical mastitis incidence traits in Bos indicus breed, Sahiwal. Estimated breeding values for the traits (calculated using Bayesian inference) were used as pseudo-phenotypes for association with genome-wide SNPs and further QTL regions underlying the traits were identified. In all, 25 SNPs were found to be associated with the traits at the genome-wide suggestive threshold (p ≤ 5 × 10^-4) and these SNPs were used to define QTL boundaries based on the linkage disequilibrium structure. A total of 16 QTLs were associated with the trait EBVs including seven each for clinical mastitis incidence (CMI) in first and second lactations and two for CMI in third lactation. Nine out of sixteen QTLs overlapped with the already reported QTLs for mastitis traits, whereas seven were adjudged as novel ones. Important candidates for clinical mastitis in the identified QTL regions included DNAJB9, ELMO1, ARHGAP26, NR3C1, CACNB2, RAB4A, GRB2, NUP85, SUMO2, RBPJ, and RAB33B genes. These findings shed light on the genetic architecture of the disease in Bos indicus, and present potential regions for fine mapping and downstream analysis in future.

Non-coding RNA-mediated autophagy in cancer: A protumor or antitumor factor?

Autophagy, usually referred to as macroautophagy, is a cytoprotective behavior that helps cells, especially cancer cells, escape crises. However, the role of autophagy in cancer remains controversial. The induction of autophagy is favorable for tumor growth, as it can degrade damaged cell components accumulated during nutrient deficiency, chemotherapy, or other stresses in a timely manner. Whereas the antitumor effect of autophagy might be closely related to its crosstalk with metabolism, immunomodulation, and other pathways. Recent studies have verified that lncRNAs and circRNAs modulate autophagy in carcinogenesis, cancer cells proliferation, apoptosis, metastasis, and chemoresistance via multiple mechanisms. A comprehensive understanding of the regulatory relationships between ncRNAs and autophagy in cancer might resolve chemoresistance and also offer intervention strategies for cancer therapy. This review systematically displays the regulatory effects of lncRNAs and circRNAs on autophagy in the contexts of cancer initiation, progression, and resistance to chemo- or radiotherapy and provides a novel insight into cancer therapy.

New Look of EBV LMP1 Signaling Landscape

Simple Summary

Epstein-Barr Virus (EBV) infection is associated with various lymphomas and carcinomas as well as other diseases in humans. The transmembrane protein LMP1 plays versatile roles in EBV life cycle and pathogenesis, by perturbing, reprograming, and regulating a large range of host cellular mechanisms and functions, which have been increasingly disclosed but not fully understood so far. We summarize recent research progress on LMP1 signaling, including the novel components LIMD1, p62, and LUBAC in LMP1 signalosome and LMP1 novel functions, such as its induction of p62-mediated selective autophagy, regulation of metabolism, induction of extracellular vehicles, and activation of NRF2-mediated antioxidative defense. A comprehensive understanding of LMP1 signal transduction and functions may allow us to leverage these LMP1-regulated cellular mechanisms for clinical purposes.

Abstract

The Epstein–Barr Virus (EBV) principal oncoprotein Latent Membrane Protein 1 (LMP1) is a member of the Tumor Necrosis Factor Receptor (TNFR) superfamily with constitutive activity. LMP1 shares many features with Pathogen Recognition Receptors (PRRs), including the use of TRAFs, adaptors, and kinase cascades, for signal transduction leading to the activation of NFκB, AP1, and Akt, as well as a subset of IRFs and likely the master antioxidative transcription factor NRF2, which we have gradually added to the list. In recent years, we have discovered the Linear UBiquitin Assembly Complex (LUBAC), the adaptor protein LIMD1, and the ubiquitin sensor and signaling hub p62, as novel components of LMP1 signalosome. Functionally, LMP1 is a pleiotropic factor that reprograms, balances, and perturbs a large spectrum of cellular mechanisms, including the ubiquitin machinery, metabolism, epigenetics, DNA damage response, extracellular vehicles, immune defenses, and telomere elongation, to promote oncogenic transformation, cell proliferation and survival, anchorage-independent cell growth, angiogenesis, and metastasis and invasion, as well as the development of the tumor microenvironment. We have recently shown that LMP1 induces p62-mediated selective autophagy in EBV latency, at least by contributing to the induction of p62 expression, and Reactive Oxygen Species (ROS) production. We have also been collecting evidence supporting the hypothesis that LMP1 activates the Keap1-NRF2 pathway, which serves as the key antioxidative defense mechanism. Last but not least, our preliminary data shows that LMP1 is associated with the deregulation of cGAS-STING DNA sensing pathway in EBV latency. A comprehensive understanding of the LMP1 signaling landscape is essential for identifying potential targets for the development of novel strategies towards targeted therapeutic applications.

Crosstalk between autophagy inhibitors and endosome-related secretory pathways: a challenge for autophagy-based treatment of solid cancers

Autophagy is best known for its role in organelle and protein turnover, cell quality control, and metabolism. The autophagic machinery has, however, also adapted to enable protein trafficking and unconventional secretory pathways so that organelles (such as autophagosomes and multivesicular bodies) delivering cargo to lysosomes for degradation can change their mission from fusion with lysosomes to fusion with the plasma membrane, followed by secretion of the cargo from the cell. Some factors with key signalling functions do not enter the conventional secretory pathway but can be secreted in an autophagy-mediated manner.Positive clinical results of some autophagy inhibitors are encouraging. Nevertheless, it is becoming clear that autophagy inhibition, even within the same cancer type, can affect cancer progression differently. Even next-generation inhibitors of autophagy can have significant non-specific effects, such as impacts on endosome-related secretory pathways and secretion of extracellular vesicles (EVs). Many studies suggest that cancer cells release higher amounts of EVs compared to non-malignant cells, which makes the effect of autophagy inhibitors on EVs secretion highly important and attractive for anticancer therapy. In this review article, we discuss how different inhibitors of autophagy may influence the secretion of EVs and summarize the non-specific effects of autophagy inhibitors with a focus on endosome-related secretory pathways. Modulation of autophagy significantly impacts not only the quantity of EVs but also their content, which can have a deep impact on the resulting pro-tumourigenic or anticancer effect of autophagy inhibitors used in the antineoplastic treatment of solid cancers.

Autophagy in Tumor Immunity and Viral-Based Immunotherapeutic Approaches in Cancer

Autophagy is a fundamental catabolic process essential for the maintenance of cellular and tissue homeostasis, as well as directly contributing to the control of invading pathogens. Unsurprisingly, this process becomes critical in supporting cellular dysregulation that occurs in cancer, particularly the tumor microenvironments and their immune cell infiltration, ultimately playing a role in responses to cancer therapies. Therefore, understanding "cancer autophagy" could help turn this cellular waste-management service into a powerful ally for specific therapeutics. For instance, numerous regulatory mechanisms of the autophagic machinery can contribute to the anti-tumor properties of oncolytic viruses (OVs), which comprise a diverse class of replication-competent viruses with potential as cancer immunotherapeutics. In that context, autophagy can either: promote OV anti-tumor effects by enhancing infectivity and replication, mediating oncolysis, and inducing autophagic and immunogenic cell death; or reduce OV cytotoxicity by providing survival cues to tumor cells. These properties make the catabolic process of autophagy an attractive target for therapeutic combinations looking to enhance the efficacy of OVs. In this article, we review the complicated role of autophagy in cancer initiation and development, its effect on modulating OVs and immunity, and we discuss recent progress and opportunities/challenges in targeting autophagy to enhance oncolytic viral immunotherapy.

Establishment and validation of five autophagy-related signatures for predicting survival and immune microenvironment in glioma

BACKGROUND

Gliomas, especially Glioblastoma multiforme, are the most frequent type of primary tumors in central nervous system. Increasing researches have revealed the relationship between autophagy and tumor, while the molecular mechanism of autophagy in glioma is still rarely reported.

OBJECTIVE

Our research aims to conform the autophagy-related genes (ARGs) implicated in the development and progression of glioma and improve our understanding of autophagy in glioma.

METHODS

20 candidate ARGs were screened through the protein-protein interaction network. We also downloaded the publicly accessible glioma data for 665 individuals from TCGA and 970 individuals from CGGA with RNA sequences and clinicopathological information. Subsequently, univariate and multivariate Cox regression analysis identified 5 key ARGs among the 20 candidate genes as key prognostic genes for survival, GSEA and immune response analysis.

RESULTS

ATG5, BCL2L1, CASP3, CASP8, GAPDH were identified as key ARGs in our research. Further studies showed that the high-risk population was linked to a dismal prognosis and suggested an immune-inhibitory microenvironment. GSEA results demonstrated that high risk population was closely related to DNA repair, hypoxia pathways, implicated in immunosuppression and carcinogenesis. Through CMap, we finally identified 14 candidate drugs for the ARG high risk population.

CONCLUSIONS

This study established and verified an ARG risk model, which can serve as an independent predictor for prognosis, reflect on the strength of the immune response and predict the potential drugs in glioma. Our findings offer new understandings of ARG molecular mechanism and promising therapeutic targets for glioma treatment.

A Transcriptome Insight During Early Fish Larval Development Followed by Starvation in Seriola rivoliana

We investigated a time-course larval transcriptional analysis (RNA-seq) in the longfin yellowtail Seriola rivoliana, from hatching to day four at 22 °C, without providing zooplankton as food. Larval starvation is a critical physiological stage that must be prevented to ensure survival. However, the transcriptional mechanisms to endure starvation have not been investigated in marine fish. Differential gene expression showed newly day-specific transcriptome events during larval development. On day 1 (yolk sac absorption), the predominant upregulated developmental processes were larval growth, muscle and vision development, cytoskeletal structure, protein synthesis, protein and fat digestion-absorption, and hormone biosynthesis, whereas the cell cycle was suppressed. On day 2 (yolk sac exhaustion), a new stage of energy regeneration (ATP) was supplied by the oil drop reserve, whereas protein digestion-absorption and growth were suppressed. On day 3 (mouth opening and starvation), stress signals and nutrition deprivation upregulated the p53 signal and triggered autophagy and the AMP-activated protein kinase (AMPK) pathways as an alternative catabolic pathway to enduring starvation, and the circadian rhythm was established. On day 4 (starving and weakened larvae condition), autophagy supported subsequent protein synthesis, activated the immune system, and promoted estrogen signaling and skeleton renovation. However, larvae suppressed muscle development, vision and carbohydrate, and fat digestion-absorption and became lethargic, evidencing limited physiological support by autophagy to maintain survival without exogenous nutrition in this species.

Identification of Autophagy Related circRNA-miRNA-mRNA-Subtypes Network With Radiotherapy Responses and Tumor Immune Microenvironment in Non-small Cell Lung Cancer

Lung cancer (LC) is one of the most frequently diagnosed cancers and the leading cause of cancer death worldwide, and most LCs are non-small cell lung cancer (NSCLC). Radiotherapy is one of the most effective treatments for patients with lung cancer, either alone or in combination with other treatment methods. However, radiotherapy responses vary considerably among NSCLC patients. The efficacy of radiotherapy is influenced by several factors, among which autophagy is of importance. Autophagy is induced by radiotherapy and also influences cell responses to radiation. We explored the clinical significance of autophagy-related genes (ARGs) and gene sets (ARGSs) and the underlying mechanism in NSCLC patients treated with radiotherapy. First, differentially expressed ARGs (SNCA, SESN3, DAPL1, and ELAPOR1) and miRNAs (miR-205-5p, miR-26a-1-3p, miR-6510-3p, miR-194-3p, miR-215-5p, and miR-375-3p) were identified between radiotherapy-resistant and radiotherapy-sensitive groups. An autophagy-related radiosensitivity risk signature (ARRS) by nine ARmRNAs/miRNAs and an autophagy-related overall survival risk signature (AROS) by three ARmRNAs were then constructed with estimated AUCs of 0.8854 (95% CI: 0.8131–0.9576) and 0.7901 (95% CI: 0.7168–0.8685), respectively. The correlations between ARGSs or prognostic signatures and clinicopathological factors, short-term radiotherapy responses (radiotherapy sensitivity), long-term radiotherapy responses (overall survival), and immune characteristics were analyzed. Both ARGSs and prognostic signatures were related to immune checkpoint inhibitors (ICIs), infiltration of tumor-infiltrating immune cells (TIICs), and the activity of the cancer immune cycle. Finally, after target prediction and correlation analysis, circRNA (hsa_circ_0019709, hsa_circ_0081983, hsa_circ_0112354, hsa_circ_0040569, hsa_circ_0135500, and hsa_circ_0098966)-regulated miRNA/ARmRNA axes (miR-194-3p/SESN3, miR-205-5p/ELAPOR1, and miR-26a-1-3p/SNCA) were considered potential modulatory mechanisms by influencing the regulation of autophagy, macroautophagy, and chaperone-mediated autophagy.

VPS38/UVRAG and ATG14, the variant regulatory subunits of the ATG6/Beclin1-PI3K complexes, are crucial for the biogenesis of the yolk organelles and are transcriptionally regulated in the oocytes of the vector Rhodnius prolixus

In insects the reserve proteins are stored in the oocytes into endocytic-originated vesicles named yolk organelles. VPS38/UVRAG and ATG14 are the variant regulatory subunits of two class-III ATG6/Beclin1 PI3K complexes that regulate the recruitment of the endocytic (complex II) and autophagic (complex I) machineries. In a previous work from our group, we found that the silencing of ATG6/Beclin1 resulted in the formation of yolk-deficient oocytes due to defects in the endocytosis of the yolk proteins. Because ATG6/Beclin1 is present in the two above-described PI3K complexes, we could not identify the contributions of each complex to the yolk defective phenotypes. To address this, here we investigated the role of the variant subunits VPS38/UVRAG (complex II, endocytosis) and ATG14 (complex I, autophagy) in the biogenesis of the yolk organelles in the insect vector of Chagas Disease Rhodnius prolixus. Interestingly, the silencing of both genes phenocopied the silencing of ATG6/Beclin1, generating 1) accumulation of yolk proteins in the hemolymph; 2) white, smaller, and yolk-deficient oocytes; 3) abnormal yolk organelles in the oocyte cortex; and 4) unviable F1 embryos. However, we found that the similar phenotypes were the result of a specific cross-silencing effect among the PI3K subunits where the silencing of VPS38/UVRAG and ATG6/Beclin1 resulted in the specific silencing of each other, whereas the silencing of ATG14 triggered the silencing of all three PI3K components. Because the silencing of VPS38/UVRAG and ATG6/Beclin1 reproduced the yolk-deficiency phenotypes without the cross silencing of ATG14, we concluded that the VPS38/UVRAG PI3K complex II was the major contributor to the previously observed phenotypes in silenced insects. Altogether, we found that class-III ATG6/Beclin1 PI3K complex II (VPS38/UVRAG) is essential for the yolk endocytosis and that the subunits of both complexes are under an unknown transcriptional regulatory system.

Roles of the Immune/Methylation/Autophagy Landscape on Single-Cell Genotypes and Stroke Risk in Breast Cancer Microenvironment

This study sought to perform integrative analysis of the immune/methylation/autophagy landscape on breast cancer prognosis and single-cell genotypes. Breast Cancer Recurrence Risk Score (BCRRS) and Breast Cancer Prognostic Risk Score (BCPRS) were determined based on 6 prognostic IMAAGs obtained from the TCGA-BRCA cohort. BCRRS and BCPRS, respectively, were used to construct a risk prediction model of overall survival and progression-free survival. Predictive capacity of the model was evaluated using clinical data. Analysis showed that BCRRS is associated with a high risk of stroke. In addition, PPI and drug-ceRNA networks based on differences in BCPRS were constructed. Single cells were genotyped through integrated scRNA-seq of the TNBC samples based on clustering results of BCPRS-related genes. The findings of this study show the potential regulatory effects of IMAAGs on breast cancer tumor microenvironment. High AUCs of 0.856 and 0.842 were obtained for the OS and PFS prognostic models, respectively. scRNA-seq analysis showed high expression levels of adipocytes and adipose tissue macrophages (ATMs) in high BCPRS clusters. Moreover, analysis of ligand-receptor interactions and potential regulatory mechanisms were performed. The LINC00276&MALAT1/miR-206/FZD4-Wnt7b pathway was also identified which may be useful in future research on targets against breast cancer metastasis and recurrence. Neural network-based deep learning models using BCPRS-related genes showed that these genes can be used to map the tumor microenvironment. In summary, analysis of IMAAGs, BCPRS, and BCRRS provides information on the breast cancer microenvironment at both the macro- and microlevels and provides a basis for development of personalized treatment therapy.

Whole exome and transcriptome sequencing reveal clonal evolution and exhibit immune-related features in metastatic colorectal tumors

Liver is the most common site where metastatic lesions of colorectal cancer (CRC) arise. Although researches have shown mutations in driver genes, copy number variations (CNV) and alterations in relevant signaling pathways promoted the tumor evolution and immune escape during colorectal liver metastasis (CLM), the underlying mechanism remains largely elusive. Tumor and matched metastatic tissues were collected from 16 patients diagnosed with colorectal cancer and subjected to whole-exome sequencing (WES) and RNA sequencing (RNA-seq) for studying colorectal cancer clonal evolution and immune escape during CLM. Shared somatic mutations between primary and metastatic tissues with a commonly observed subclonal-clonal (S-C) changing pattern indicated a common clonal origin between two lesions. The recurrent mutations with S-C changing pattern included those in KRAS, SYNE1, CACNA1H, PCLO, FBXL2, and DNAH11. The main CNV events underwent clonal-clonal evolution (20q amplification (amp), 17p deletion (del), 18q del and 8p del), subclonal-clonal evolution (8q amp, 13q amp, 8p del) and metastasis-specific evolution (8q amp) during the process of CLM. In addition, we revealed a potential mechanism of tumor cell immune escape by analyzing human leukocytes antigens (HLA) related clonal neoantigens and immune cell components in CLM. Our study proposed a novel liver metastasis-related evolutionary process in colorectal cancer and emphasized the theory of neo-immune escape in colorectal liver metastasis.

Autophagy Modulators in Cancer: Focus on Cancer Treatment

Uncontrolled autophagy has been associated with the development and progression of various cancers that are resistant to cancer therapy. Therefore, many efforts to modulate uncontrolled autophagy as a cancer treatment have been attempted, from basic science to clinical trials. However, it remains difficult to equally apply autophagy modulators to cancer therapy because autophagy is a double-edged sword in cancer: it can be tumor-suppressive or tumor-protective. Therefore, the precise mechanisms of autophagy modulators and their varied responsiveness to each cancer type should be addressed in detail. This study will describe the precise mechanisms of developing various autophagy modulators, their current therapeutic applications and future perspectives.