Integrative analysis of single-cell and bulk RNA sequencing unveils a machine learning-based pan-cancer major histocompatibility complex-related signature for predicting immunotherapy efficacy.

Major histocompatibility complex (MHC) could serve as a potential biomarker for tumor immunotherapy, however, it is not yet known whether MHC could distinguish potential beneficiaries. Single-cell RNA sequencing datasets derived from patients with immunotherapy were collected to elucidate the association between MHC and immunotherapy response. A novel MHCsig was developed and validated using large-scale pan-cancer data, including The Cancer Genome Atlas and immunotherapy cohorts. The therapeutic value of MHCsig was further explored using 17 CRISPR/Cas9 datasets. MHC-related genes were associated with drug resistance and MHCsig was significantly and positively associated with immunotherapy response and total mutational burden. Remarkably, MHCsig significantly enriched 6% top-ranked genes, which were potential therapeutic targets. Moreover, we generated Hub-MHCsig, which was associated with survival and disease-special survival of pan-cancer, especially low-grade glioma. This result was also confirmed in cell lines and in our own clinical cohort. Later low-grade glioma-related Hub-MHCsig was established and the regulatory network was constructed. We provided conclusive clinical evidence regarding the association between MHCsig and immunotherapy response. We developed MHCsig, which could effectively predict the benefits of immunotherapy for multiple tumors. Further exploration of MHCsig revealed some potential therapeutic targets and regulatory networks.

Identification of potential LncRNAs as papillary thyroid carcinoma biomarkers based on integrated bioinformatics analysis using TCGA and RNA sequencing data.

The roles and mechanisms of long non-coding RNAs (lncRNAs) in papillary thyroid cancer (PTC) remain elusive. We obtained RNA sequencing (RNA-seq) data of surgical PTC specimens from patients with thyroid cancer (THCA; n = 20) and identified differentially expressed genes (DEGs) between cancer and cancer-adjacent tissue samples. We identified 2309 DEGs (1372 significantly upregulated and 937 significantly downregulated). We performed Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, gene set enrichment, and protein-protein interaction network analyses and screened for hub lncRNAs. Using the same methods, we analyzed the RNA-seq data from THCA dataset in The Cancer Genome Atlas (TCGA) database to identify differentially expressed lncRNAs. We identified 15 key differentially expressed lncRNAs and pathways that were closely related to PTC. Subsequently, by intersecting the differentially expressed lncRNAs with hub lncRNAs, we identified LINC02407 as the key lncRNA. Assessment of the associated clinical characteristics and prognostic correlations revealed a close correlation between LINC02407 expression and N stage of patients. Furthermore, receiver operating characteristic curve analysis showed that LINC02407 could better distinguish between cancerous and cancer-adjacent tissues in THCA patients. In conclusion, our findings suggest that LINC02407 is a potential biomarker for PTC diagnosis and the prediction of lymph node metastasis.

Detection of BRAF V600E in Fine-Needle Aspiration Samples of Thyroid Nodules by Droplet Digital PCR.

Background: BRAF exon 15 p.V600E (BRAF V600E) mutation has been established as an important molecular marker for papillary thyroid carcinoma diagnosis by ultrasound-guided fine-needle aspiration biopsy (FNAB). Sanger sequencing is the gold standard for detecting BRAF V600E mutations but fails to identify low-frequency mutations. However, droplet digital PCR (ddPCR) is a popular new method for detecting low-frequency mutations. Here, we compare the efficiency of droplet digital PCR (ddPCR) and Sanger sequencing for detection of the BRAF V600E mutation in thyroid fine-needle aspiration (FNA) samples. Methods: Thyroid fine-needle aspiration samples from 278 patients with 310 thyroid nodules were collected. Sanger sequencing and ddPCR were conducted to detect the BRAF V600E mutation. Results: The BRAF V600E mutation was found in 94 nodules (30.32%) by ddPCR and 40 nodules (12.90%) by Sanger sequencing in 310 FNA samples. A total of 119 nodules were confirmed PTC by postsurgical pathology. Among which the BRAF mutation was found in 80 (67.23%) nodules by ddPCR and 31 (26.05%) by Sanger sequencing. All nodules carrying the mutation detected by Sanger sequencing (SS+) were verified by ddPCR (ddPCR+). Also, all nodules with no mutation detected by ddPCR were interpreted as wild-type by Sanger sequencing (SS-). In addition. Almost all SS+/ddPCR + nodules (95.00%; 38/40) and SS-/ddPCR + nodules (100.00%; 54/54) displayed a BRAF mutation rate of >5% and <15%, respectively, indicating easy misdetection by Sanger sequencing when the mutation rate is between 5 and 15%. Conclusion: ddPCR has higher sensitivity than Sanger sequencing and we propose ddPCR as a supplement to Sanger sequencing in molecular testing of BRAF using FNAB samples.

Long non­coding RNA MEG3 suppresses epithelial­to­mesenchymal transition by inhibiting the PSAT1­dependent GSK­3ß/Snail signaling pathway in esophageal squamous cell carcinoma.

Esophageal squamous cell carcinoma (ESCC) is the main subtype of esophageal cancer in China, and the prognosis of patients remains poor mainly due to the occurrence of lymph node and distant metastasis. The long non­coding RNA (lncRNA) maternally expressed gene 3 (MEG3) has been shown to have tumor­suppressive properties and to play an important role in epithelial­to­mesenchymal transition (EMT) in some solid tumors. However, whether MEG3 is involved in EMT in ESCC remains unclear. In the present study, the MEG3 expression level and its association with tumorigenesis were determined in 43 tumor tissues of patients with ESCC and in ESCC cells using reverse transcription­quantitative PCR analysis. Gene microarray analysis was performed to detect differentially expressed genes (DEGs). Based on the functional annotation results, the effects of ectopic expression of MEG3 on cell growth, migration, invasion and EMT were assessed. MEG3 expression level was found to be markedly lower in tumor tissues and cells. Statistical analysis revealed that MEG3 expression was significantly negatively associated with lymph node metastasis and TNM stage in ESCC. Fluorescence in situ hybridization assay demonstrated that MEG3 was expressed mainly in the nucleus. Ectopic expression of MEG3 inhibited cell proliferation, migration, invasion and cell cycle progression in EC109 cells. Gene microarray results demonstrated that 177 genes were differentially expressed ≥2.0 fold in MEG3­overexpressing cells, including 23 upregulated and 154 downregulated genes. Functional annotation revealed that the DEGs were mainly involved in amino acid biosynthetic process, mitogen­activated protein kinase signaling, and serine and glycine metabolism. Further experiments indicated that the ectopic expression of MEG3 significantly suppressed cell proliferation, migration, invasion and EMT by downregulating phosphoserine aminotransferase 1 (PSAT1). In pathological tissues, PSAT1 and MEG3 were significantly negatively correlated, and high expression of PSAT1 predicted poor survival. Taken together, these results suggest that MEG3 may be a useful prognostic biomarker and may suppress EMT by inhibiting the PSAT1­dependent glycogen synthase kinase­3ß/Snail signaling pathway in ESCC.

Inhibition of autophagy enhances adenosine­induced apoptosis in human hepatoblastoma HepG2 cells.

In cancer research, autophagy acts as a double­edged sword: it increases cell viability or induces cell apoptosis depending upon the cell context and functional status. Recent studies have shown that adenosine (Ado) has cytotoxic effects in many tumors. However, the role of autophagy in Ado­induced apoptosis is still poorly understood. In the present study, Ado­induced apoptotic death and autophagy in hepatoblastoma HepG2 cells was investigated and the relationship between autophagy and apoptosis was identified. In the present study, it was demonstrated that Ado inhibited HepG2 cell growth in a time­ and concentration­dependent manner and activated endoplasmic reticulum (ER) stress, as indicated by G0/G1 cell cycle arrest, the increased mRNA and protein levels of GRP78/BiP, PERK, ATF4, CHOP, cleaved caspase­3, cytochrome c and the loss of mitochon-drial membrane potential (ΔΨm). Ado also induced autophagic flux, revealed by the increased expression of the autophagy marker microtubule­associated protein 1 light chain 3­II (LC3­II), Beclin­1, autophagosomes, and the degradation of p62, as revealed by western blot analysis and macrophage­derived chemokine (MDC) staining. Blocking autophagy using LY294002 notably entrenched Ado­induced growth inhibition and cell apoptosis, as demonstrated with the increased expression of cytochrome c and p62, and the decreased expression of LC3­II. Conversely, the autophagy inducer rapamycin alleviated Ado­induced apoptosis and markedly increased the ΔΨm. Moreover, knockdown of AMPK with si­AMPK partially abolished Ado­induced ULK1 activation and mTOR inhibition, and thus reinforced CHOP expression and Ado­induced apoptosis. These results indicated that Ado­induced ER stress resulted in apoptosis and autophagy concurrently. The AMPK/mTOR/ULK1 signaling pathway played a protective role in the apoptotic procession. Inhibition of autophagy may effectively enhance the anticancer effect of Ado in human hepatoblastoma HepG2 cells.

Involvement of endoplasmic reticulum stress and p53 in lncRNA MEG3-induced human hepatoma HepG2 cell apoptosis.

Long non-coding RNAs (lncRNAs) play important roles in diverse biological processes. Although downregulation of lncRNA maternally expressed gene 3 (MEG3) has been identified in several types of cancers, little is known concerning its biological role and regulatory mechanism in hepatoma. Our previous studies demonstrated that MEG3 induces apoptosis in a p53-dependent manner. The aim of the present study was to determine whether endoplasmic reticulum (ER) stress is involved in MEG3­induced apoptosis. Recombinant lentiviral vectors containing MEG3 (Lv­MEG3) were constructed and transfected into HepG2 cells. A 3­(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, RT­PCR, flow cytometry, western blot analysis, immunofluorescence and immunohistochemistry were applied. Transfected HepG2 cells were also transplanted into nude mice, and the tumor growth curves were determined. The results showed that the recombinant lentivirus of MEG3 was transfected successfully into the HepG2 cells and the expression level of MEG3 was significantly increased. Ectopic expression of MEG3 inhibited HepG2 cell proliferation in vitro and in vivo, and also induced apoptosis. Ectopic expression of MEG3 increased ER stress­related proteins 78­kDa glucose­regulated protein (GRP78), inositol­requiring enzyme 1 (IRE1), RNA­dependent protein kinase­like ER kinase (PERK), activating transcription factor 6 (ATF6), C/EBP homologous protein (CHOP), caspase­3, as well as p53 and NF­κB expression accompanied by NF­κB translocation from the cytoplasm to the nucleus. Furthermore, inhibition of NF­κB with Bay11­7082 decreased p53 expression in the MEG3­transfected cells. These results indicate that MEG3 inhibits cell proliferation and induces apoptosis, partially via the activation of the ER stress and p53 pathway, in which NF­κB signaling is required for p53 activation in ER stress.

Enhanced antitumor effects of adenoviral-mediated siRNA against GRP78 gene on adenosine-induced apoptosis in human hepatoma HepG2 cells.

Our previous studies show that adenosine-induced apoptosis is involved in endoplasmic reticulum stress in HepG2 cells. In this study, we have investigated whether knockdown of GRP78 by short hairpin RNA (shRNA) increases the cytotoxic effects of adenosine in HepG2 cells. The adenovirus vector-delivered shRNA targeting GRP78 (Ad-shGRP78) was constructed and transfected into HepG2 cells. RT-PCR assay was used to determine RNA interference efficiency. Effects of knockdown of GRP78 on adenosine-induced cell viabilities, cell-cycle distribution and apoptosis, as well as relative protein expressions were determined by flow cytometry and/or Western blot analysis. The intracellular Ca2+ concentration was detected by laser scanning confocal microscope. Mitochondrial membrane potential (ΔΨm) was measured by a fluorospectrophotometer. The results revealed that GRP78 mRNA was significantly downregulated by Ad-shGRP78 transfection. Knockdown of GRP78 enhanced HepG2 cell sensitivity to adenosine by modulating G0/G1 arrest and stimulating Bax, Bak, m-calpain, caspase-4 and CHOP protein levels. Knockdown of GRP78 worsened cytosolic Ca2+ overload and ΔΨm loss. Knockdown of caspase-4 by shRNA decreased caspase-3 mRNA expression and cell apoptosis. These findings indicate that GRP 78 plays a protective role in ER stress-induced apoptosis and show that the combination of chemotherapy drug and RNA interference adenoviruses provides a new treatment strategy against malignant tumors.

Apoptosis induced by adenosine involves endoplasmic reticulum stress in EC109 cells.

Apoptosis plays a critical role in the development and homeostasis of multicellular organisms, and endoplasmic reticulum stress (ERS) is one of the intrinsic apoptosis pathways. Previous studies have shown that adenosine induces apoptosis in several cancer cell lines. However, the molecular mechanism remains poorly understood. In this study, we explored whether adenosine triggers apoptosis of EC109 esophageal carcinoma (EC) cells by ERS. The MTT assay was used to determine cell proliferation; cell cycle detection (FCM) and terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL) assay were performed to determine cell apoptosis. The subcellular distribution and expression of the ERS-related proteins GRP78, cleaved caspase-3, cleaved caspase-4, CHOP and NF-κB p65 were detected by western blot techniques. NF-κB activation was measured by electrophoretic mobility shift assay (EMSA). The MTT assay demonstrated that adenosine inhibited EC109 cell proliferation in a dose- and time-dependent manner. FCM and TUNEL assay verified that adenosine caused an apoptotic peak in cell cycle arrest and a higher percentage of apoptotic cells. Western blot analysis confirmed that the expression of GRP78, cleaved caspase-4, CHOP, NF-κB p65 and cleaved caspase-3 were upregulated in a dose-dependent manner after adenosine treatment. EMSA revealed that adenosine activated NF-κB p65. This is the first demonstration that adenosine inhibits cell proliferation, increases GRP78 and NF-κB p65 expression and induces apoptosis by CHOP and caspase-4 pathways. The ERS pathway is involved in adenosine-induced apoptosis in EC109 cells.

Involvement of endoplasmic reticulum stress in adenosine-induced human hepatoma HepG2 cell apoptosis.

Endoplasmic reticulum stress (ERS)-mediated cell apoptosis has been implicated in the development of multiple diseases such as cancer, neurodegenerative diseases and ischemic reperfusion damage. Previous studies have demonstrated the adenosine-induced apoptosis in several tumor cell lines. However, the role of ERS in adenosine-induced human hepatoma HepG2 cell apoptosis remains unclear. The present study was designed to determine whether ERS is involved in adenosine-induced HepG2 cell apoptosis. The MTT assay was used to determine proliferation, and DAPI staining of cell nuclei was performed to determine cell apoptosis. The translocation of CHOP and caspase-3 was observed by immunofluorescence analysis, and the protein expression of CHOP, caspase-4 and caspase-3 was detected by Western blotting. The MTT assay demonstrated that adenosine inhibited HepG2 cell proliferation in a dose-dependent manner. DAPI staining of cell nuclei and cell cycle analysis verified cell apoptosis. The immunofluorescence assay demonstrated that adenosine induced the translocation of CHOP and of caspase-3 from the cytoplasm to the nucleus. Western blotting confirmed that CHOP, caspase-4 and caspase-3 were up-regulated in HepG2 cells after treatment with adenosine. However, JNK protein expression was not altered. These results show that ERS is involved in the adenosine-induced HepG2 cell apoptosis.

Involvement of NF-kappaB activation in the apoptosis induced by extracellular adenosine in human hepatocellular carcinoma HepG2 cells.

Adenosine can exhibit cytotoxic activity in vivo and in vitro, though its mechanisms are still uncertain. In this study, we investigated the adenosine-mediated apoptotic signaling pathway and the role of NF-kappaB in human hepatocellular carcinoma HepG2 cells. HepG2 cells were treated with different concentrations of adenosine for 12-48 h, and the effect of adenosine on cell proliferation was evaluated by MTT assay. The cytotoxicity of adenosine alone or in combination with an NF-kappaB inhibitor, pyrrolidine dithiocarbamate (PDTC), was also evaluated by MTT assay and the mode of cell death was detected by Hoechst 33342 staining. Cell cycle progress was performed by flow cytometry with PI staining. The protein expressions of Bcl-2, p53, NF-kappaB subunit p65, and caspase-3 were assayed by Western blot. Caspase-3 activity was measured by spectrophotomteric assay. The results showed that adenosine significantly reduced the viability of HepG2 cells in a dose- and time-dependent manner, with IC 50 (24 and 48 h) of 2.52 and 1.89 mmol x L(-1), respectively. The apoptotic index (percentage of sub-G1 phase) of HepG2 cells in adenosine treatment alone for 12 and 24 h or in combination with PDTC were 8.30%, 22.32% and 20.18%, 30.89%, respectively. All of them were higher than that in the control group (0.81%, p < 0.01). The characteristic changes of cell apoptosis (chromatin condensation and sub-G1 peak) were observed under fluorescent microscopy and flow cytometry. We also found that the apoptotic process triggered by adenosine was involved in G0-G1 cell-cycle arrest, enhanced the activity of caspase-3, upregulated p53 and NF-kappaB p65 expression, and downregulated Bcl-2 expression. Inhibition of NF-kappaB by PDTC decreased NF-kappaB p65 expression, enhanced cell apoptosis ratio, and increased caspase-3 activity. NF-kappaB may play an anti-apoptosis role in adenosine-induced HepG2 cytotoxicity.

Molecular mechanisms of adenosine-induced apoptosis in human HepG2 cells.

AIM: To investigate effects of adenosine on cell proliferation and apoptosis in human HepG2 cells. METHODS: HepG2 cells were incubated in the presence of adenosine (0.1-5 mmol/L) for 12-48 h, and the effect of adenosine on cell proliferation was evaluated by using 3-(4,5-dimethyl-2-yl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay. Hoechst 33342 fluorescent staining, dUTP-fluorescein isothiocyanate (FITC) fluorescence and flow cytometric analysis techniques were used to observe cell apoptosis. The effects of adenosine receptor (A1, A2a, A3 and nonspecific receptor) antagonists (8-cpt, DMPX, MRS1191, and theophylline) and an adenosine transporter protein inhibitor (dipyridamole) on adenosine-induced cell apoptosis were observed. Mitochondrial membrane potential was analyzed using DePsipher fluorescent staining, and caspase activity was detected using a Fluorometric assay kit and a fluorescence microplate reader. RESULTS: Adenosine significantly reduced cell viability in a dose- and time-dependent manner. The cytotoxicity of adenosine was related to the induction of cell apoptosis. Four adenosine receptor antagonists had no effect on cell apoptosis. However, dipyridamole significantly reduced the percentage of adenosine-induced apoptotic cells from 27.3% to 7.1% (P<0.05). At 48 h after treatment, 3 mmol/L adenosine increased caspase-3 activity 3.5-fold; dipyridamole markedly decreased caspase-3 activity 1.6-fold, and decreased apoptotic cell numbers. When HepG2 cells were treated with 3 mmol/L adenosine, mitochondrial membrane potential and the activity of caspase-8 or -9 remained unchanged. CONCLUSION: Our results suggest that adenosine-induced apoptosis in HepG2 cells is related to intracellular events rather than cell surface receptors, and that a caspase-3 cascade activation is required, which is not mediated via a mitochondrial pathway.

Preoperative TN staging of esophageal cancer: comparison of miniprobe ultrasonography, spiral CT and MRI.

AIM: To evaluate the value of miniprobe sonography (MPS), spiral CT and MR imaging (MRI) in the tumor and regional lymph node staging of esophageal cancer. METHODS: Eight-six patients (56 men and 30 women; age range of 39-73 years, mean 62 years) with esophageal carcinoma were staged preoperatively with imaging modalities. Of them, 81 (94 %) had squamous cell carcinoma, 4(5 %) adenocarcinoma, and 1(1 %) adenoacanthoma. Eleven patients (12 %) had malignancy of the upper one third, 41 (48 %) of the mid-esophagus and 34 (40 %) of the distal one third. Forty-one were examined by spiral CT in whom 13 were co-examined by MPS, and forty-five by MRI in whom 18 were also co-examined by MPS. These imaging results were compared with the findings of the histopathologic examination for resected specimens. RESULTS: In staging the depth of tumor growth, MPS was significantly more accurate (84 %) than spiral CT and MRI (68 % and 60 %, respectively, P<0.05). The specificity and sensitivity were 82 % and 85 % for MPS; 60 % and 69 % for spiral CT; and 40 % and 63 % for MRI, respectively. In staging regional lymph nodes, spiral CT was more accurate (78 %) than MPS and MRI (71 % and 64 %, respectively), but the difference was not statistically significant. The specificity and sensitivity were 79 % and 77 % for spiral CT; 75 % and 68 % for MPS; and 68 % and 62 % for MRI, respectively. CONCLUSION: MPS is superior to spiral CT or MRI for T staging, especially in early esophageal cancer. However, the three modalities have the similar accuracy in N staging. Spiral CT or MRI is helpful for the detection of far-distance metastasis in esophageal cancer.