Low neighbor of Brca1 gene expression predicts poor clinical outcome and resistance of sunitinib in clear cell renal cell carcinoma

Construction of a Prognostic Nomogram Based on Autophagy-Related Genes for Children With Neuroblastoma

Neuroblastoma (NB) is the most common solid malignancy in children. MYCN gene amplification is the most relevant genetic alteration in patients with NB and is associated with poor prognosis. Autophagy plays specific roles in the occurrence, development, and progression of NB. Here, we aimed to identify and assess the prognostic effects of autophagy-related genes (ARGs) in patients with NB and MYCN gene amplification. Differentially expressed ARGs were identified in patients with NB with and without MYCN gene amplification, and the ARG expression patterns and related clinical data from the Therapeutically Applicable Research to Generate Effective Treatments database were used as the training cohort. Least absolute shrinkage and selection operator analyses were used to identify prognostic ARGs associated with event-free survival (EFS), and a prognostic risk score model was developed. Model performance was assessed using the Kaplan–Meier method and receiver operating characteristic (ROC) curves. The prognostic ARG mode l was verified using the validation cohort dataset, GSE49710. Finally, a nomogram was constructed by combining the ARGbased risk score with clinicopathological factors. Three ARGs (GABARAPL1, NBR1, and PINK1) were selected to build a prognostic risk score model. The EFS in the low-risk group was significantly better than that in the high-risk group in both the training and validation cohorts. A nomogram incorporating the prognostic risk score, age, and International Neuroblastoma Staging System stage showed a favorable predictive ability for EFS rates according to the area under the ROC curve at 3 years (AUC = 0.787) and 5 years (AUC = 0.787). The nomogram demonstrated good discrimination and calibration. Our risk score model for the 3 ARGs can be used as an independent prognostic factor in patients with NB and MYCN gene amplification. The model can accurately predict the 3- and 5-year survival rates.

Stratification of diabetic kidney diseases via data-independent acquisition proteomics-based analysis of human kidney tissue specimens

AIM

The aims of this study were to analyze the proteomic differences in renal tissues from patients with diabetes mellitus (DM) and diabetic kidney disease (DKD) and to select sensitive biomarkers for early identification of DKD progression.

METHODS

Pressure cycling technology-pulse data-independent acquisition mass spectrometry was employed to investigate protein alterations in 36 formalin-fixed paraffin-embedded specimens. Then, bioinformatics analysis was performed to identify important signaling pathways and key molecules. Finally, the target proteins were validated in 60 blood and 30 urine samples.

RESULTS

A total of 52 up- and 311 down-regulated differential proteins were identified as differing among the advanced DKD samples, early DKD samples, and DM controls (adjusted p<0.05). These differentially expressed proteins were mainly involved in ion transport, apoptosis regulation, and the inflammatory response. UniProt database analysis showed that these proteins were mostly enriched in signaling pathways related to metabolism, apoptosis, and inflammation. NBR1 was significantly up-regulated in both early and advanced DKD, with fold changes (FCs) of 175 and 184, respectively (both p<0.01). In addition, VPS37A and ATG4B were significantly down-regulated with DKD progression, with FCs of 0.140 and 0.088, respectively, in advanced DKD and 0.533 and 0.192, respectively, in early DKD compared with the DM control group (both p<0.01). Bioinformatics analysis showed that NBR1, VPS37A, and ATG4B are closely related to autophagy. We also found that serum levels of the three proteins and urine levels of NBR1 decreased with disease progression. Moreover, there was a significant difference in serum VPS37A and ATG4B levels between patients with early and advanced DKD (both p<0.05). The immunohistochemistry assaay exhibited that the three proteins were expressed in renal tubular cells, and NBR1 was also expressed in the cystic wall of renal glomeruli.

CONCLUSION

The increase in NBR1 expression and the decrease in ATG4B and VPS37 expression in renal tissue are closely related to inhibition of the autophagy pathway, which may contribute to DKD development or progression. These three proteins may serve as sensitive serum biomarkers for early identification of DKD progression.

Suppression of optineurin impairs the progression of hepatocellular carcinoma through regulating mitophagy

Autophagy removes damaged organelles to inhibit malignant transformation during tumor initiation. Once a cancer matures, it uses the autophagic pathway as an energy source. Optineurin (OPTN) is an autophagy adaptor protein that recruits microtubule‐associated protein 1 light chain 3, an autophagosome marker, to the autophagosome. Despite studies of the relation between cancer progression and autophagy adaptor proteins, there are no reports to our knowledge of a correlation between hepatocellular carcinoma (HCC) and OPTN. We aimed here to investigate the effects of OPTN expression on HCC progression through autophagy. Immunohistochemistry was used to measure the OPTN expression in the tissues of 141 Japanese patients with HCC. The effects of OPTN expression on HCC progression and mitophagy were assessed using an OPTN knockout (KO) cell line in vitro. We used this KO cell line to establish and exploit a mouse model of HCC to determine the effects of OPTN expression on tumor progression. Immunohistochemical analysis showed that patients with elevated expression of OPTN experienced shorter overall survival (OS) and recurrence‐free survival (RFS). OPTN KO cells proliferated relatively slower versus wild‐type (WT) cells in vitro. Western blot analysis showed that mitophagy was suppressed in OPTN KO cells, and ATP synthesis and beta‐oxidation were reduced. The mouse model of HCC showed that OPTN KO cells formed smaller tumors versus WT cells less 10 weeks after implantation. Overall, the present findings suggest that OPTN is a key mediator of mitophagy that contributes to HCC progression through mitochondrial energy production.

Pro-Tumoral Functions of Autophagy Receptors in the Modulation of Cancer Progression

Cancer progression involves a variety of pro-tumorigenic biological processes including cell proliferation, migration, invasion, and survival. A cellular pathway implicated in these pro-tumorigenic processes is autophagy, a catabolic route used for recycling of cytoplasmic components to generate macromolecular building blocks and energy, under stress conditions, to remove damaged cellular constituents to adapt to changing nutrient conditions and to maintain cellular homeostasis. During autophagy, cells form a double-membrane sequestering a compartment termed the phagophore, which matures into an autophagosome. Following fusion with the lysosome, the cargo is degraded inside the autolysosomes and the resulting macromolecules released back into the cytosol for reuse. Cancer cells use this recycling system during cancer progression, however the key autophagy players involved in this disease is unclear. Accumulative evidences show that autophagy receptors, crucial players for selective autophagy, are overexpressed during cancer progression, yet the mechanisms whereby pro-tumorigenic biological processes are modulated by these receptors remains unknown. In this review, we summarized the most important findings related with the pro-tumorigenic role of autophagy receptors p62/SQSTM1, NBR1, NDP52, and OPTN in cancer progression. In addition, we showed the most relevant cargos degraded by these receptors that have been shown to function as critical regulators of pro-tumorigenic processes. Finally, we discussed the role of autophagy receptors in the context of the cellular pathways implicated in this disease, such as growth factors signaling, oxidative stress response and apoptosis. In summary, we highlight that autophagy receptors should be considered important players of cancer progression, which could offer a niche for the development of novel diagnosis and cancer treatment strategies.

Mining therapeutic and prognostic significance of STATs in renal cell carcinoma with bioinformatics analysis

Renal cell carcinoma is one of the most common malignancies with high morbidity and mortality. STAT proteins play a significant role in cell biological behavior and immune response associated with cancer progression. In our study, the datasets analyzed for the expression and potential functions can be found in several bioinformatics analysis tools. We found that STAT1/2/4/6 were upregulated in RCC while STAT3/5B were downregulated. The expression of STAT2/4/5B were significantly associated with the pathological stage of RCC patients. RCC patients with high expression of STAT2/4 and low/medium expression of STAT5B had a poor overall survival. The function of STATs and the neighboring genes mainly enriched in JAK-STAT signaling pathway and NOD-like receptor signaling pathway. Several transcription factor, kinase, and miRNA targets were identified. Close correlations were obtained between immune cell infiltration and STATs in RCC. Our results have provided novel insights for the selection of immunotherapeutic targets and prognostic biomarkers.

Role of AMPK/mTOR-independent autophagy in clear cell renal cell carcinoma

We examined the status and role of autophagy, a process of lysosomal recycling of cellular material, in clear cell renal cell carcinoma (ccRCC). Paired samples of tumor and adjacent non-malignant tissue were collected from 20 patients with ccRCC after radical nephrectomy. The mRNA levels of apoptosis (BAD, BAX, BCL2, BCLXL, BIM) and autophagy (ATG4, BECN1, GABARAP, p62, UVRAG) regulators were measured by RT-qPCR. The protein levels of autophagosome-associated LC3-II, autophagy receptor p62, apoptotic marker PARP, as well as phosphorylation of autophagy initiator Unc 51-like kinase 1 (ULK1), its activator AMP-activated protein kinase (AMPK) and 4EBP1, the substrate of ULK1 inhibitor mechanistic target of rapamycin (mTOR), were analyzed by immunoblotting. The mRNA levels of pro-apoptotic BAX, anti-apoptotic BCLXL and pro-autophagic ATG4, p62 and UVRAG were higher in ccRCC tumors. Autophagy induction was confirmed by an increase in phospho-ULK1 and degradation of the autophagic target p62, while apoptotic PARP cleavage was unaltered. AMPK phosphorylation was reduced and 4EBP1 phosphorylation was increased in ccRCC tissue. The expression of apoptosis regulators did not correlate with clinicopathological features of ccRCC. Conversely, high mRNA levels of ATG4, GABARAP and p62 were associated with lower tumor stage, as well as with smaller tumor size and better disease-specific 5-year survival (ATG4 and p62). Accordingly, low p62 protein levels, corresponding to increased autophagic flux, were associated with lower tumor stage, reduced metastasis and improved 5-year survival. These data demonstrate that transcriptional induction of autophagy in ccRCC is accompanied by AMPK/mTOR-independent increase in ULK1 activation and autophagic flux, which might slow tumor progression and metastasis independently of apoptosis.

Regulation of ATP-binding cassette subfamily B member 1 by Snail contributes to chemoresistance in colorectal cancer

Although accumulating evidence has indicated the intimate association between epithelial‐mesenchymal transition (EMT) and acquired resistance to chemotherapy for colorectal cancer (CRC), the underlying mechanisms remain elusive. Herein, we reported that Snail, a crucial EMT controller, was upregulated in CRC tissues. Colorectal cancer cells overexpressing Snail were found to be more resistant to 5‐fluorouracil (5‐Fu). Mechanistic studies reveal that Snail could increase the expression of ATP‐binding cassette subfamily B member 1 (ABCB1) rather than the other 23 chemoresistance‐related genes. Additionally, knockdown of ABCB1 significantly attenuated Snail‐induced 5‐Fu resistance in CRC cells. Oxaliplatin increased Snail and ABCB1 expression in CRC cells. Snail and ABCB1 were upregulated in 5‐Fu‐resistant HCT‐8 (HCT‐8/5‐Fu) cells and inhibition of Snail decreased ABCB1 in HCT‐8/5‐Fu cells. These results confirm the vital role played by ABCB1 in Snail‐induced chemoresistance. Further investigation into the relevant molecular mechanism revealed Snail‐mediated ABCB1 upregulation was independent of β‐catenin, STAT3, PXR, CAR and Foxo3a, which are commonly involved in modulating ABCB1 transcription. Instead, Snail upregulated ABCB1 transcription by directly binding to its promoter. Clinical analysis confirms that increased Snail expression correlated significantly with tumor size (P = .018), lymph node metastasis (P = .033), distant metastasis (P = .025), clinical stage grade (P = .024), and poor prognosis (P = .045) of CRC patients. Moreover, coexpression of Snail and ABCB1 was observed in CRC patients. Our study revealed that direct regulation of ABCB1 by Snail was critical for conferring chemoresistance in CRC cells. These findings unraveled the mechanisms underlying the association between EMT and chemoresistance, and provided potential targets for CRC clinical treatment.

Expression Profile of Genes Associated with the Proteins Degradation Pathways in Colorectal adenocarcinoma

Background:

Changes in expression of genes associated with proteins or organelles degradation system in the cell may be a cause or signal to carcinogenesis. Thus, the aim of this study was to assess the profile of gene expression linked to the degradation systems of proteins or organelles in histo-pathologically confirmed colorectal adenocarcinoma in relation to normal colon tissue.

Methods:

Using oligonucleotide microarrays and GeneSpring 13.0, and PANTHER 13.1 software’s we characterized 1095 mRNAs linked to the degradation system of proteins and organelles in sections of colorectal cancer from patients at various clinical stages of disease. Subsequent analyses with restrictive assumptions narrowed down the number of genes differentiating cancer, assuming a P-value of less than 0.05.

Results:

We found that most of the significant genes were silenced in the development of colorectal cancer. The FOXO1 had the lowest fold change value in the first clinical stage (CSI) comparing to the control. The HSPA8 was up-regulated in the two early clinical stages (CSI and CSII), and UBB only in the CSI. Only little-known PTPN22 showed increasing expression at all stages.

Conclusion:

In summary, the examined colorectal adenocarcinoma samples were characterized by almost complete silencing of the significant genes associated with the degradation of proteins and mitochondria in transcriptomic level. The FOXO1, HSPA8 and UBB genes may become potential diagnostic and/or therapeutic targets in the early stage of this cancer.