Enhancing Specific Fluorescence In Situ Hybridization with Quantum Dots for Single-Molecule RNA Imaging in Formalin-Fixed Paraffin-Embedded Tumor Tissues

Single-molecule fluorescence in situ hybridization (smFISH) represents a promising approach for the quantitative analysis of nucleic acid biomarkers in clinical tissue samples. However, low signal intensity and high background noise are complications that arise from diagnostic pathology when performed with smFISH-based RNA imaging in formalin-fixed paraffin-embedded (FFPE) tissue specimens. Moreover, the associated complex procedures can produce uncertain results and poor image quality. Herein, by combining the high specificity of split DNA probes with the high signal readout of ZnCdSe/ZnS quantum dot (QD) labeling, we introduce QD split-FISH, a high-brightness smFISH technology, to quantify the expression of mRNA in both cell lines and clinical FFPE tissue samples of breast cancer and lung squamous carcinoma. Owing to its high signal-to-noise ratio, QD split-FISH is a fast, inexpensive, and sensitive method for quantifying mRNA expression in FFPE tumor tissues, making it suitable for biomarker imaging and diagnostic pathology.

Potential of radiomics analysis and machine learning for predicting brain metastasis in newly diagnosed lung cancer patients

AIM

To explore the potential of utilising radiomics analysis and machine-learning models that incorporate intratumoural and peritumoural regions of interest (ROIs) for predicting brain metastasis (BM) in newly diagnosed lung cancer patients.

MATERIALS AND METHODS

The study comprised 183 lung cancer patients (training cohort: n=146; validation cohort: n=37) whose radiomics features were extracted from plain computed tomography (CT) images of the primary lesion. Four machine-learning algorithms (logistic regression [LR], support vector machine [SVM], k-nearest neighbour algorithm [KNN], and random forest [RF]) were employed to develop predictive models. Model diagnostic performance was assessed through receiver operating characteristic (ROC) analysis, and clinical utility was evaluated using decision curve analysis (DCA). Finally, the radiomics model's generalisation ability was further validated in the prediction of metachronous brain metastasis (MBM).

RESULTS

After feature screening, 22 radiomics features were identified as highly predictive, of which nine were derived from the peritumour region. All four machine-learning models demonstrated predictive capability, with SVM showing superior efficiency and robustness. The area under the ROC curve (AUC) of SVM was 0.918 in the training cohort and 0.901 in the validation cohort. DCA indicated the highest net benefit. Furthermore, the time-dependent ROC curve exhibited predictive efficacy for MBM occurrence across 1-, 2-, and 3-year follow-up periods, with all AUC values exceeding 0.7.

CONCLUSION

The optimal SVM model integrating intratumoural and peritumoural radiomics features was confirmed and defined as an imaging biomarker for predicting BM in newly diagnosed lung cancer patients, underscoring its potential to significantly impact clinical diagnosis and treatment.

Serum Protein Fishing for Machine Learning-Boosted Diagnostic Classification of Small Nodules of Lung

Diagnosis of benign and malignant small nodules of the lung remains an unmet clinical problem which is leading to serious false positive diagnosis and overtreatment. Here, we developed a serum protein fishing-based spectral library (ProteoFish) for data independent acquisition analysis and a machine learning-boosted protein panel for diagnosis of early Non-Small Cell Lung Cancer (NSCLC) and classification of benign and malignant small nodules. We established an extensive NSCLC protein bank consisting of 297 clinical subjects. After testing 5 feature extraction algorithms and six machine learning models, the Lasso algorithm for a 15-key protein panel selection and Random Forest was chosen for diagnostic classification. Our random forest classifier achieved 91.38% accuracy in benign and malignant small nodule diagnosis, which is superior to the existing clinical assays. By integrating with machine learning, the 15-key protein panel may provide insights to multiplexed protein biomarker fishing from serum for facile cancer screening and tackling the current clinical challenge in prospective diagnostic classification of small nodules of the lung.

Palbociclib sensitizes ER-positive breast cancer cells to fulvestrant by promoting the ubiquitin-mediated degradation of ER-α via SNHG17/Hippo-YAP axis

PURPOSE

Endocrine therapy is the anti-tumor therapy for human breast cancer but endocrine resistance was a major burden. It has been reported that Palbociclib and fulvestrant can be used in combination for the treatment of patients who are experiencing endocrine resistance. However, the underlying mechanism is unclear. In this study, we aimed to investigate the mechanism by which Palbocicilib affected ER-positive breast cancer, combined with fulvestrant.

METHODS

We first detected the effect of palbociclib on cell survival, growth and cycle distribution separately by MTT, colony formation and flow cytometry. Then SNHG17 was screened as palbociclib-targeted LncRNA by LncRNA-seq, and the SNHG17-targeted mRNAs were selected by mRNA-seq for further determination. Subsequently, the underlying mechanism by which palbociclib promoted the cytotoxicity of fulvestrant was confirmed by qRT-PCR, western blot, and immunoprecipitation. Eventually, the xenograft model and immunohistochemistry experiments were used to validate the sensitization effect of palbociclib on fulvestrant and its mechanism in vivo.

RESULTS

Palbociclib significantly enhanced the cytotoxicity of fulvestrant in fulvestrant-resistant breast cancer cell lines. Interestingly, this might be related to the lncRNA SNHG17 and the Hippo signaling pathway. And our subsequent western blotting experiments confirmed that overexpressing SNHG17 induced the down-regulation of LATS1 and up-regulated YAP expression. Furthermore, we found that the increased sensitivity of breast cancer cells was closely associated with the LATS1-mediated degradation of ER-α. The following animal experiments also indicated that overexpressing SNHG17 obviously impaired the anti-cancer effect of co-treatment of palbociclib and fulvestrant accompanied by decreased LATS1 and increased ER-α levels.

CONCLUSION

Palbociclib might sensitize the cytotoxicity of fulvestrant in ER-positive breast cancer cells by down-regulating SNHG17 expression, and then resulted in the LATS1-inactivated oncogene YAP and LATS1-mediated degradation of ER-α.

[Research Progress of Granulocytic Myeloid-derived Suppressor Cells in Non-small Cell Lung Cancer]

Granulocytic myeloid-derived suppressor cells (G-MDSCs) are one of the main subgroups of MDSCs, which are widely enriched in most cancers. It can inhibit the killing function of T-lymphocyte through the expression of arginase-1 (Arg-1) and reactive oxygen species (ROS), reshape the tumor immune microenvironment, and promote the occurrence and development of tumors. In recent years, more and more studies have found that G-MDSCs are significantly correlated with the prognosis and immunotherapy efficacy of patients with non-small cell lung cancer, and the use of drugs specifically targeting the recruitment, differentiation and function of G-MDSCs can effectively inhibit tumor progression. This article reviews the immunosuppressive effect of G-MDSCs in non-small cell lung cancer and the progress of related pathway targeting drugs.
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Pathomic Features Reveal Immune and Molecular Evolution From Lung Preneoplasia to Invasive Adenocarcinoma

Recent statistics on lung cancer, including the steady decline of advanced diseases and the dramatically increasing detection of early-stage diseases and indeterminate pulmonary nodules, mark the significance of a comprehensive understanding of early lung carcinogenesis. Lung adenocarcinoma (ADC) is the most common histologic subtype of lung cancer, and atypical adenomatous hyperplasia is the only recognized preneoplasia to ADC, which may progress to adenocarcinoma in situ (AIS) and minimally invasive adenocarcinoma (MIA) and eventually to invasive ADC. Although molecular evolution during early lung carcinogenesis has been explored in recent years, the progress has been significantly hindered, largely due to insufficient materials from ADC precursors. Here, we employed state-of-the-art deep learning and artificial intelligence techniques to robustly segment and recognize cells on routinely used hematoxylin and eosin histopathology images and extracted 9 biology-relevant pathomic features to decode lung preneoplasia evolution. We analyzed 3 distinct cohorts (Japan, China, and United States) covering 98 patients, 162 slides, and 669 regions of interest, including 143 normal, 129 atypical adenomatous hyperplasia, 94 AIS, 98 MIA, and 205 ADC. Extracted pathomic features revealed progressive increase of atypical epithelial cells and progressive decrease of lymphocytic cells from normal to AAH, AIS, MIA, and ADC, consistent with the results from tissue-consuming and expensive molecular/immune profiling. Furthermore, pathomics analysis manifested progressively increasing cellular intratumor heterogeneity along with the evolution from normal lung to invasive ADC. These findings demonstrated the feasibility and substantial potential of pathomics in studying lung cancer carcinogenesis directly from the low-cost routine hematoxylin and eosin staining.

Immune-active tumor-adjacent tissues are associated with favorable prognosis in stage I lung squamous cell carcinoma

The immunogenomic features of tumor-adjacent lungs (TALs) in stage I lung squamous cell carcinoma (LUSC) are not clear. Multiomics analyses of tumor tissues and paired TALs from 59 stage I LUSC patients were performed. Compared to tumors, TALs exhibited a better-preserved immune contexture indicated by upregulation of immune pathways, increased immune infiltration, and higher expression of immune effector molecules. Notably, TALs had no mutations in PTEN and KEAP1, a lower incidence of human leukocyte antigen (HLA) loss and higher expression of HLA class I genes, major histocompatibility complex (MHC) I chaperones, and interferon (IFN)-γ-associated genes. Digital spatial profiling validated the generally higher immune infiltration in TALs and revealed a higher level of immune heterogeneity in LUSC tumors. Importantly, patients with higher immune infiltration in TALs had significantly longer survival, while high immune heterogeneity was associated with inferior patient survival. Our work can be considered in the selection of patients for adjuvant therapy, especially immunotherapy.

NOD1 mediates interleukin-18 processing in epithelial cells responding to Helicobacter pylori infection in mice

The interleukin-1 family members, IL-1β and IL-18, are processed into their biologically active forms by multi-protein complexes, known as inflammasomes. Although the inflammasome pathways that mediate IL-1β processing in myeloid cells have been defined, those involved in IL-18 processing, particularly in non-myeloid cells, are still not well understood. Here we report that the host defence molecule NOD1 regulates IL-18 processing in mouse epithelial cells in response to the mucosal pathogen, Helicobacter pylori. Specifically, NOD1 in epithelial cells mediates IL-18 processing and maturation via interactions with caspase-1, instead of the canonical inflammasome pathway involving RIPK2, NF-κB, NLRP3 and ASC. NOD1 activation and IL-18 then help maintain epithelial homoeostasis to mediate protection against pre-neoplastic changes induced by gastric H. pylori infection in vivo. Our findings thus demonstrate a function for NOD1 in epithelial cell production of bioactive IL-18 and protection against H. pylori-induced pathology.

PDZ-binding kinase aggravates pancreatic neuroendocrine neoplasm progression by activating the AKT/mTOR pathway

The therapeutic effects of existing drug regimens against pancreatic neuroendocrine neoplasms (pNENs) remain limited, and identifying ideal therapeutic targets is warranted. PDZ binding kinase (PBK) may play an oncogenic role in most solid tumors. However, its function in pNEN remains unclear. In this study, pNEN samples and International Cancer Genome Consortium data were used to determine the clinical significance of PBK. Cell counting and CCK8 assays were used to assess cell proliferation. Flow cytometry was used to assess drug-induced apoptosis and cell cycle arrest. An in vivo PBK-targeting experiment was performed in mice bearing pNENs. Western blotting, quantitative PCR, and immunohistochemistry were performed to assess the molecular mechanisms. PBK was significantly upregulated in pNEN tissues compared with paracancerous tissues. Additionally, PBK was a poor prognostic factor for pNEN patients. PBK was found to promote the proliferation of pNEN cells by activating the AKT/mTOR pathway. Furthermore, PBK inhibition combined with everolimus treatment had enhanced antitumour effects on pNEN via inhibiting AKT/mTOR pathway and inducing G0/G1 phase cell cycle arrest. This study highlights that PBK plays an oncogenic role in and is a promising therapeutic target for pNEN.

Ubiquitin-specific peptidase 22 in cancer

Recently, many studies have shown that deubiquitination modification of proteins is of great significance in major physiological processes such as cell proliferation, apoptosis, and differentiation. The ubiquitin-specific peptidase (USP) family is one of the most numerous and structurally diverse of the deubiquitinates known to date. USP22, an important member of the USP family, has been found to be closely associated with tumor cell cycle regulation, stemness maintenance, invasion and metastasis, chemoresistance, and immune regulation. We focus on recent advances regarding USP22's function in cancer and discuss the prospect of USP22 in this review.

Immune evolution from preneoplasia to invasive lung adenocarcinomas and underlying molecular features

The mechanism by which anti-cancer immunity shapes early carcinogenesis of lung adenocarcinoma (ADC) is unknown. In this study, we characterize the immune contexture of invasive lung ADC and its precursors by transcriptomic immune profiling, T cell receptor (TCR) sequencing and multiplex immunofluorescence (mIF). Our results demonstrate that anti-tumor immunity evolved as a continuum from lung preneoplasia, to preinvasive ADC, minimally-invasive ADC and frankly invasive lung ADC with a gradually less effective and more intensively regulated immune response including down-regulation of immune-activation pathways, up-regulation of immunosuppressive pathways, lower infiltration of cytotoxic T cells (CTLs) and anti-tumor helper T cells (Th), higher infiltration of regulatory T cells (Tregs), decreased T cell clonality, and lower frequencies of top T cell clones in later-stages. Driver mutations, chromosomal copy number aberrations (CNAs) and aberrant DNA methylation may collectively impinge host immune responses and facilitate immune evasion, promoting the outgrowth of fit subclones in preneoplasia into dominant clones in invasive ADC.

Evolution of DNA methylome from precancerous lesions to invasive lung adenocarcinomas

The evolution of DNA methylome and methylation intra-tumor heterogeneity (ITH) during early carcinogenesis of lung adenocarcinoma has not been systematically studied. We perform reduced representation bisulfite sequencing of invasive lung adenocarcinoma and its precursors, atypical adenomatous hyperplasia, adenocarcinoma in situ and minimally invasive adenocarcinoma. We observe gradual increase of methylation aberrations and significantly higher level of methylation ITH in later-stage lesions. The phylogenetic patterns inferred from methylation aberrations resemble those based on somatic mutations suggesting parallel methylation and genetic evolution. De-convolution reveal higher ratio of T regulatory cells (Tregs) versus CD8 + T cells in later-stage diseases, implying progressive immunosuppression with neoplastic progression. Furthermore, increased global hypomethylation is associated with higher mutation burden, copy number variation burden and AI burden as well as higher Treg/CD8 ratio, highlighting the potential impact of methylation on chromosomal instability, mutagenesis and tumor immune microenvironment during early carcinogenesis of lung adenocarcinomas.

[Pathological diagnosis of lung cancer based on deep transfer learning]

Objective: To establish an artificial intelligence (AI)-assisted diagnostic system for lung cancer via deep transfer learning. Methods: The researchers collected 519 lung pathologic slides from 2016 to 2019, covering various lung tissues, including normal tissues, adenocarcinoma, squamous cell carcinoma and small cell carcinoma, from the Beijing Chest Hospital, the Capital Medical University. The slides were digitized by scanner, and 316 slides were used as training set and 203 as the internal test set. The researchers labeled all the training slides by pathologists and establish a semantic segmentation model based on DeepLab v3 with ResNet-50 to detect lung cancers at the pixel level. To perform transfer learning, the researchers utilized the gastric cancer detection model to initialize the deep neural network parameters. The lung cancer detection convolutional neural network was further trained by fine-tuning of the labeled data. The deep learning model was tested by 203 slides in the internal test set and 1 081 slides obtained from TCIA database, named as the external test set. Results: The model trained with transfer learning showed substantial accuracy advantage against the one trained from scratch for the internal test set [area under curve (AUC) 0.988 vs. 0.971, Kappa 0.852 vs. 0.832]. For the external test set, the transferred model achieved an AUC of 0.968 and Kappa of 0.828, indicating superior generalization ability. By studying the predictions made by the model, the researchers obtained deeper understandings of the deep learning model. Conclusions: The lung cancer histopathological diagnostic system achieves higher accuracy and superior generalization ability. With the development of histopathological AI, the transfer learning can effectively train diagnosis models and shorten the learning period, and improve the model performance.

Genetic polymorphisms and cardiovascular outcomes in Chinese patients undergoing PCI and treated with clopidogrel and aspirin

Background

Genetic polymorphisms of key proteins involved in clopidogrel absorption, metabolism, and action may contribute to variability in platelet inhibition in patients undergoing percutaneous coronary intervention (PCI), but their impacts on cardiovascular outcomes remain unclear.

Purpose

To examine the associations between genetic polymorphisms and cardiovascular outcomes in Chinese patients undergoing PCI and treated with clopidogrel and aspirin.

Methods

This prospective cohort study consecutively enrolled 2,453 post-PCI patients treated with clopidogrel and aspirin. Adenosine diphosphate-induced platelet aggregation was measured by light transmission aggregometry. A total of 40 single nucleotide polymorphisms (SNPs) of 18 genes selected according to published studies were investigated using an improved multiplex ligation detection reaction technique. The primary outcome was major adverse cardiovascular event (MACE), the composite of cardiovascular death, non-fatal myocardial infarction (MI), and ischemic stroke within one year after PCI.

Results

We restricted the analyses to the first 1,452 patients who had finished one-year follow-up and complete data on genotyping and platelet aggregation. 44 (3.03%) patients suffered MACE. Among the 40 SNPs, only the A-allele carriers of CYP2C19*2 had a significant higher risk of MACE (adjusted HR 2.05; 95% CI, 1.01–4.19; p=0.048) and platelet aggregation than non-A-carriers after adjusting age, sex, MI presentation, and left ventricular ejection fraction. CYP2C19*3, CYP2B6 rs3745274, and PEAR1 rs12041331 variants were also significantly associated with platelet aggregation (all p<0.05) but not with MACE at 1 year.

Conclusion

About 54.2% of Chinese patients with PCI were A-allele carriers of CYP2C19*2, who face a two-fold higher risk of MACE than non-A-allele carriers in Chinese patients after PCI. It would help identify low clopidogrel responders and optimize antiplatelet therapy before drug administration.

Figure 1

Funding Acknowledgement

Type of funding source: Public grant(s) – National budget only. Main funding source(s): National Natural Science Funding of China

Non-disruptive mutation in TP53 DNA-binding domain is a beneficial factor of esophageal squamous cell carcinoma

Background

TP53 is frequently altered in esophageal squamous cell carcinoma (ESCC). However, the landscape of TP53 mutation and its effects on patients remain controversial.

Methods

Somatic mutations of TP53 in 161 patients with resectable ESCC were identified by next-generation sequencing (NGS) and verified by immunohistochemistry (IHC). Patients were stratified into seven TP53 mutations, and depending on the extent of the effect on the encoded protein, it was divided into "disruptive" and "non-disruptive" types. The association of TP53 mutation with clinicopathological properties and disease outcome was investigated.

Results

TP53 mutations were discovered in 85.7% patients, of which 68.9% carried mutations in the DNA-binding domain (DBD). A total of 47.8% and 37.9% patients had disruptive and non-disruptive TP53 mutations, respectively. Most patients carried only one TP53 mutation, but 15.5% had double mutations. TP53 mutations were dominant in exons 5 to 8. Missense mutation was the most frequent (97/163, 59.5%), and the top five frequently occurring variations included R273X, Y220X, H193, H179X, and R175H. Multivariable analysis revealed non-disruptive mutation in TP53 DBD as the independent prognostic predictor for progression-free survival (PFS) and overall survival (OS). The expression of p53 positively correlated with non-disruptive mutation in DBD. Patients with high p53 protein expression showed better outcomes.

Conclusions

Non-disruptive mutation in TP53 DBD serves as an independent beneficial prognostic factor of prolonged survival in resectable ESCC.

Identification of predictors of drug sensitivity using patient-derived models of esophageal squamous cell carcinoma

Previous studies from the Cancer Cell Line Encyclopedia (CCLE) project have adopted commercial pan-cancer cell line models to identify drug sensitivity biomarkers. However, drug sensitivity biomarkers in esophageal squamous cell carcinoma (ESCC) have not been widely explored. Here, eight patient-derived cell lines (PDCs) are successfully established from 123 patients with ESCC. The mutation profiling of PDCs can partially recapture the tumor tissue actionable mutations from 161 patients with ESCC. Based on these mutations and relative pathways in eight PDCs, 46 targeted drugs are selected for screening. Interestingly, some drug and biomarker relationships are established that were not discovered in the CCLE project. For example, CDKN2A or CDKN2B loss is significantly associated with the sensitivity of CDK4/6 inhibitors. Furthermore, both PDC xenografts and patient-derived xenografts confirm CDKN2A/2B loss as a biomarker predictive of CDK4/6 inhibitor sensitivity. Collectively, patient-derived models could predict targeted drug sensitivity associated with actionable mutations in ESCC.

Predicting the drug response of patients with cancer is crucial for implementing targeted therapy. Here, Su et al. make patient-derived cell lines and perform targeted sequencing and RNA-seq to identify CDKN2A/2B loss as a predictor of response to CDK4/6 inhibitors in esophageal squamous cell carcinoma.

A Nomogram to Predict the Pathologic Complete Response of Neoadjuvant Chemotherapy in Triple-Negative Breast Cancer Based on Simple Laboratory Indicators

BACKGROUND

Triple-negative breast cancer (TNBC) patients who achieve a pathologic complete response (pCR) after neoadjuvant chemotherapy (NAC) have better prognoses.

OBJECTIVE

This study aimed to develop an intuitive nomogram based on simple laboratory indexes to predict the pCR of standard NAC in TNBC patients.

METHODS

A total of 80 TNBC patients who received eight cycles of thrice-weekly standard NAC (anthracycline and cyclophosphamide followed by taxane) and subsequently underwent surgery in Zhejiang Cancer Hospital were retrospectively enrolled, and data on their pretreatment clinical features and multiple simple laboratory indexes were collected. The optimal cut-off values of the laboratory indexes were determined by the Youden index using receiver operating characteristic (ROC) curve analyses. Forward stepwise logistic regression (likelihood ratio) analysis was applied to identify predictive factors for a pCR of NAC. A nomogram was then developed according to the logistic model, and internally validated using the bootstrap resampling method.

RESULTS

pCR was achieved in 39 (48.8%) patients after NAC. Multivariate analysis identified four independent indicators: clinical tumor stage, lymphocyte to monocyte ratio, fibrinogen level, and D-dimer level. The nomogram established based on these factors showed its discriminatory ability, with an area under the curve (AUC) of 0.803 (95% confidence interval 0.706-0.899) and a bias-corrected AUC of 0.771. The calibration curve and Hosmer-Lemeshow test showed that the predictive ability of the nomogram was a good fit to actual observation.

CONCLUSIONS

The nomogram proposed in the present study exhibited a sufficient discriminatory ability for predicting pCR of NAC in TNBC patients.

Multi-region exome sequencing reveals genomic evolution from preneoplasia to lung adenocarcinoma

There has been a dramatic increase in the detection of lung nodules, many of which are preneoplasia atypical adenomatous hyperplasia (AAH), adenocarcinoma in situ (AIS), minimally invasive adenocarcinoma (MIA) or invasive adenocarcinoma (ADC). The molecular landscape and the evolutionary trajectory of lung preneoplasia have not been well defined. Here, we perform multi-region exome sequencing of 116 resected lung nodules including AAH (n = 22), AIS (n = 27), MIA (n = 54) and synchronous ADC (n = 13). Comparing AAH to AIS, MIA and ADC, we observe progressive genomic evolution at the single nucleotide level and demarcated evolution at the chromosomal level supporting the early lung carcinogenesis model from AAH to AIS, MIA and ADC. Subclonal analyses reveal a higher proportion of clonal mutations in AIS/MIA/ADC than AAH suggesting neoplastic transformation of lung preneoplasia is predominantly associated with a selective sweep of unfit subclones. Analysis of multifocal pulmonary nodules from the same patients reveal evidence of convergent evolution.

There has been a drastic increase in detection of lung nodules, many of which are precancers, preinvasive, minimally invasive or sometimes invasive lung cancers. Here, Hu et al. perform multi-region exome sequencing to discern the evolutional trajectory from precancers to invasive lung cancers.

Abstract 4896: A novel approach identifies the potential biomarkers of targeted drug sensitivity in esophageal squamous cell carcinoma

Purpose: Esophageal squamous cell carcinoma (ESCC) has a high mortality with no effective targeted therapies. Previous studies from Cancer Cell Line Encyclopedia (CCLE) project adopted a commercial human pan-cancer cell line model incorporating genomic landscape to systematically identify drug sensitivity biomarkers. However, the biomarker of drug sensitivity in ESCC is still lack of widely exploring. Here, we established a novel approach combined patient-derived models, targeted deep sequencing and a drug sensitivity evaluation system to investigate potential biomarkers of targeted drug sensitivity in ESCC.

Materials and Methods: Deep sequencing of 365 tumor drug-related genes was performed in tumor tissues and matched blood from an ESCC cohort (n = 161). In order to explore the potential biomarkers of drug sensitivity, we systematically established patient-derived cell lines (PDCs) from an independent cohort including 123 operable ESCC patients. Targeted deep sequencing, RNA sequencing and high-through drug sensitivity were integrated to identify the potential biomarkers of targeted drug sensitivity in ESCC PDCs. Molecular characterization methods and animal models were used to validate the potential biomarker in vitro and in vivo. In addition, patient-derived xenograft (PDX) was further confirmed the results.

Results: The mutational profile of tumor drug-related genes indicated a mean of 9 non-silent somatic mutations (mutation allele frequency >= 0.05) per patient and a high recurrence rate of copy number variation (CNV) were discovered. To explore potential biomarkers of targeted drug sensitivity, we established eight PDCs derived from 123 ESCC patients were successfully established and used for molecular characterization and drug screening. Drug sensitivity evaluation and pharmacogenomics analyses of the eight PDCs revealed prevalent CDKN2A or CDKN2B loss as potentially sensitive biomarkers of the CDK4/6 inhibitors palbociclib and ribociclib, which was neither found in the previous study from CCLE models nor in the present study using commercial ESCC cell lines. Importantly, patient-derived models integrated with DNA and RNA sequencing validated this result in vitro. Moreover, ESCC patient-derived cell line xenografts (PDCX) models with CDKN2A/2B loss are more sensitive to the CDK4/6 inhibitor palbociclib than that in PDCX models with wild-type CDKN2A/2B. Furthermore, mouse model with PDX further confirmed CDKN2A/2B loss as a biomarker of the CDK4/6 inhibitor sensitivity.

Conclusions: These results suggested that patient-derived models combined with deep sequencing and a drug sensitivity evaluation system, incorporating in vitro and in vivo validation platform, could be used as a novel and effective approach for exploring biomarkers of drug sensitivity in ESCC.

Citation Format: Dan Su, Dadong Zhang, Jiaoyue Jin, Lisha Ying, Miao Han, Kaiyan Chen, Bin Li, Junzhou Wu, Zhenghua Xie, Fanrong Zhang, Yihui Lin, Guoping Cheng, Jinchao Wang, Minran Huang, Jing-Yu Li, Jianjun Zhang, Fugen Li, Lei Xiong, Andrew Futreal, Weimin Mao. A novel approach identifies the potential biomarkers of targeted drug sensitivity in esophageal squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4896.

GAP43, a novel metastasis promoter in non-small cell lung cancer

BACKGROUND

Brain metastasis is an extremely serious sequela with a dismal prognosis in non-small cell lung cancer (NSCLC). The present study aimed to identify novel biomarkers and potential therapeutic targets for brain metastases of NSCLC.

METHODS

We performed high-throughput Luminex assays to profile the transcriptional levels of 36 genes in 70 operable NSCLC patients, among whom 37 developed brain metastases as the first relapse within 3 years after surgery. The Cox proportional hazards regression model was used to evaluate the association between genes and brain metastases. Wound healing assay and transwell assay was carried out to estimate the function of target gene in vitro. And left ventricular injection on nude mice was used to evaluate the effect of target gene in vivo.

RESULTS

Growth-associated protein 43 (GAP43) was found to be related to brain metastasis. Multivariate Cox regression analysis showed that NSCLC patients with elevated GAP43 had a 3.29-fold increase in the risk for brain metastasis compared with those with low levels (95% confidence interval: 1.55-7.00; P = 0.002). Kaplan-Meier survival curves revealed that GAP43 was also associated with overall survival. Analysis of a cohort of 1926 NSCLC patients showed similar results: patients with high levels of GAP43 had worse progression-free and overall survival rates. Furthermore, in vitro experiments showed that GAP43 facilitated cell migration. Animal studies demonstrated that GAP43-silenced NSCLC cells were less likely to metastasize to the brain and bone than control cells. Immunofluorescence and F-actin/G-actin in vivo assays indicated that GAP43 knockdown triggered depolymerization of the F-actin cytoskeleton. Rho GTPase activation assays showed that Rac1 was deactivated after GAP43 was silenced.

CONCLUSIONS

Our findings suggest that GAP43 is an independent predictor of NSCLC brain metastasis and that it may facilitate metastasis by regulating the Rac1/F-actin pathway.

Abstract 1083: GAP43, a novel potential metastases promoter in non-small cell lung cancer

Metastasis is a serious sequela with dismal prognosis in non-small cell lung cancer (NSCLC). To identify novel biomarkers for predicting NSCLC metastasis, we performed high-throughput Luminex assays to profile the transcriptional level of 36 genes in 37 operable NSCLC patients who had distant metastases within 3 years after surgery and 33 paired patients without relapse after operation. Among the 36 genes, growth associated protein 43 (GAP43), an axonal membrane protein, was identified related to distant metastases. Multivariate cox regression analysis showed that NSCLC patients with elevated GAP43 had a 3.71-fold increase in risk for metastasis than those with low levels (95% confidence interval 1.69-8.14, P = 0.001). Analysis of a patient cohort of 1,926 NSCLC revealed that patients with high levels of GAP43 had worse progression-free and overall survival. In vitro experiments showed that GAP43 knockdown suppressed NSCLC cell migration and invasion, while GAP43 overexpression facilitated their migration and invasion. Immunofluorescence assay indicated that the linear polymer microfilament F-actin became cracked after GAP43 knockdown. Furthermore, animal studies using left ventrical injection demonstrated that GAP43 silenced NSCLC cells were less likely to metastasize to brain and bone than the controls. Together, our findings suggest that GAP43 may be an independent predictor for NSLCL metastasis, and it may facilitate distant metastasis through targeting F-actin.

Citation Format: Fanrong Zhang, Jiaoyue Jin, Junzhou Wu, Kaiyan Chen, Minran Huang, Herbert Yu, Lisha Ying, Dan Su. GAP43, a novel potential metastases promoter in non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1083.

Abstract 4686: T cell repertoire evolution from the normal lung to invasive lung adenocarcinoma

Background: Our knowledge in early lung carcinogenesis is rudimentary. Atypical adenomatous hyperplasia (AAH) is the only preneoplasia type that has been recognized by histopathology and It has been postulated that AAH can progress to adenocarcinoma in situ (AIS), to minimally invasive adenocarcinoma (MIA), and finally to invasive adenocarcinoma (ADC). However, the definition of these lesions remains controversial due to limited supporting molecular evidence. Carcinogenesis results from accumulation of multiple genetic and epigenetic events, with selection for events conferring phenotypic advantage. Immune surveillance, particularly anti-tumor response from T cells is an important host protection process to inhibit carcinogenesis. However, the T cell repertoire landscape and its evolution during lung carcinogenesis have not been well defined. Methods: We performed T cell receptor (TCR) sequencing on multiple spatially separated regions (2-6 regions per lesion) from 23 AAH, 26 AIS, 54 MIA and 14 ADC lesions and paired histologically normal lung tissues from 52 patients clinically presenting with indeterminate pulmonary nodules. Forty-one patients had multifocal diseases and 23 patients carried more than one type of pathology. Results: Compared to pre-/micro-invasive neoplastic lesions (AAH, AIS, MIA) or invasive ADC, normal lung tissues demonstrated significantly less T cell infiltration (p<0.0001) but a significantly higher clonality (p<0.0001). Furthermore, T cell diversity increased and as did evenness in pre-/micro-invasive neoplastic lesions (AAH, AIS, MIA) (p<0.0001) and invasive ADC (p<0.005) accompanied with higher frequency of the top T cell clones observed in the normal lung (p<0.05). Interestingly, homology with normal lung T cell repertoire decreased in invasive ADC compared to pre-/micro-invasive neoplastic lesions (p<0.05). Distinct T cell repertoire overlap was also observed between pre-/micro-invasive neoplastic lesions and invasive ADC (p<0.01). Conclusions: Our preliminary analyses demonstrate the distinct T cell repertoire between the normal lung and pre-/micro-invasive neoplastic lesions and invasive ADC, and that immunosuppression of T cells may have occurred prior to the development of pre-neoplastic states and T cell repertoire becomes progressively suppressed with disease evolution. The distinct overlap of pre-/micro-invasive neoplastic lesions and invasive ADC suggests that with disease evolution, the immune microenvironment of invasive ADC increases in complexity. Integration of the molecular landscape with T cell and immune profiling across different stage lesions is underway.

Citation Format: Runzhe Chen, Junya Fujimoto, Alexandre Reuben, Lisha Ying, Xin Hu, Chi-Wan Chow, Jaime Rodriguez Canales, Wenyong Sun, Jinlin Hu, Edwin R. Parra Cuentas, Carmen Behrens, Chang-Jiun Wu, Latasha Little, Curtis Gumbs, Diana Wiesnoski, Guangchun Han, Won-Chul Lee, Paul Scheet, Humam Kadara, Mara Antonoff, Ara A. Vaporciyan, Stephen Swisher, Jianhua Zhang, John Heymach, Waun Ki Hong, Ignacio Wistuba, Andrew Futreal, Dan Su, Jianjun Zhang. T cell repertoire evolution from the normal lung to invasive lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4686.

Abstract 4408: Development and validation of a serum miRNA biomarker panel for the detection of early stage lung cancer

Lung cancer is the most prevalent cancer and leading cause of cancer death worldwide. Low-dose spiral computed tomography (LDCT) scan is being recommended as a screening test for smokers in the U.S. However, the poor specificity (73% specificity at 94% sensitivity) of LDCT has raised significant concern for its high chance of false positive (96% of LDCT positives are benign nodules). This study aims to develop a blood (serum) miRNA based molecular diagnostic test for the detection of early stage lung cancer. In the discovery phase, more than 400 miRNAs were profiled with MiRXES's qPCR based high throughput assay platform through a highly defined Chinese male smoker case-control cohort (n=424) where the cases were collected from Zhejiang Cancer Hospital and the controls were collected from the LDCT screening program in Zhejiang province, China. 29 miRNA biomarkers with p-value (FDR) < 0.01 and more than one z-score (standardized score) difference were identified and validated in another Chinese case-control cohort (n=432) collected from similar sources and a Caucasian case-control cohort (n=218) collected from EU and US. 18 out of the 29 miRNA biomarkers were validated in both cohorts (p-value < 0.01 and z-score >0.4). With multiple time of two-fold cross-validation, 5 miRNAs were found to be minimally required to form the biomarker panel for the accurate prediction of early stage lung cancer and the panel gives 0.984 (95% CI 0.973-0.991) AUC for the discovery cohort, 0.936 (95% CI 0.912-0.957) AUC for the Chinese validation cohort and 0.970 (95% CI 0.939-0.986) AUC for the Caucasian validation cohort. The 5-miRNA biomarker panel were then further validated in three additional Asian cohorts: a Chinese cohort collected from the similar sources (0.973, 95% CI 0.950-0.986, AUC), a Chinese cohort collected from independent sources (0.916, 95% CI 0.852-0.949, AUC) and a Singaporean cohort (Chinese, Malay and Indian population) (0.911, 95% CI 0.822-0.963, AUC).

Citation Format: Lisha Ying, Ruiyang Zou, Lingbin Du, Lei Shi, Nan Zhang, Jiaoyue Jin, Junzhou Wu, Fanrong Zhang, Kaiyan Chen, Herbert Yu, Weimin Mao, Dan Su. Development and validation of a serum miRNA biomarker panel for the detection of early stage lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4408.

Abstract 5377: Tracking genomic and epigenomic evolution from preneoplastic lesions to lung adenocarcinoma by multiregion sequencing

Background: Carcinogenesis may result from accumulation of genomic and epigenomic aberrations. It has been postulated that atypical adenomatous hyperplasia (AAH) represents lung preneoplastic lesion that may progress to adenocarcinoma in situ (AIS), minimally invasive adenocarcinoma (MIA) and further to frankly invasive adenocarcinoma (ADC). Yet the pathologic definition and management of these lesions remain controversial due to lack of sufficient molecular evidences. This aim of this study is to delineate the temporal molecular carcinogenetic events and evolutionary process during the evolution from preneoplastic lesions to early-stage adenocarcinoma.

Methods: We have collected 116 resected pre- and early neoplastic lung lesions including AAH (N=22), AIS (N=27), MIA (N=54) and ADC (N=13) from 53 patients, including 39 patients presenting with multifocal disease and 23 patients carrying more than two different types of lesions. Two to five spatially separated regions were subjected to whole-exome sequencing and reduced representation bisulfite sequencing.

Results: Mutation burden progressively increases from AAH (average SNVs 0.57/Mb) to AIS (2.04/MB), to MIA (2.98/MB) and ADC (5.4/MB), p <2.2e-16 with evidence of positive selection of non-silent mutations (60.2% in AAH, 69.7% in AIS, 74.4% in MIA, 84.4% in ADC, p = 0.009). APOBEC signature also progressively increases with APOBEC enrichment scores of 0.94 in AAH, 0.99 in AIS, 1.04 in MIA and 1.28 in ADC (p = 0.011). In addition, genomic heterogeneity becomes more complex with neoplastic evolution with tumor allelic frequency-derived median Shannon index of 1.24 in AAH, 1.52 in AIS, 1.64 in MIA and 1.79 in ADC (p = 0.0004). On the other hand, the proportion of trunk mutations (detected in all regions within the same lesion) progressively increased (35.6% in AAH, 73.6% in AIS, 73.1% in MIA, 70.8% in ADC and p = 1.758e-07). Phylogenetic analysis revealed varying evolutional processes in different pre- and early neoplastic lung lesions with progressive increase in perturbance of genes involved MAPK pathway. Certain key driver mutations were found to be early molecular events occurring at the stage of AAH (e.g., KRAS), while others tend to occur at a later stage (e.g., EGFR). Copy number alterations and genomic doubling were observed in AIS, MIA and ADC, but not in AAH. In addition, DNA methylation profiling revealed that epigenome aberrations fuel preinvasive progression from AIS to MIA and ADC, with parallel phylogenic evolution pattern of the genome.

Conclusions: We provide molecular evidence supporting the pathologic model of early lung carcinogenesis from AAH, to AIS, MIA and ADC. With disease evolution, both genomic and epigenomic landscape of lung neoplastic lesions has become progressively more complex along with sequential acquisition of molecular events with concomitant selective sweep of subclone in preneoplasias.

Citation Format: Xin Hu, Junya Fujimoto, Lisha Ying, Runzhe Chen, Marcos Roberto Estecio, Chi-Wan Chow, Jaime Rodriguez Canales, Xingzhi Song, Xizeng Mao, Paul Scheet, Humam Kadara, Edwin R. Parra Cuentas Cuentas, Carmen Behrens, Chang-Jiun Wu, J. Jack Lee, Mara Antonoff, Ara A Vaporciyan, Stephen Swisher, Jianhua zhang, John Heymach, Waun Ki Hong, Ignacio I. Wistuba, Wenyong Sun, Jinlin Hu, P. Andrew Futreal, Dan Su, Jianjun Zhang. Tracking genomic and epigenomic evolution from preneoplastic lesions to lung adenocarcinoma by multiregion sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5377.

Prognostic Significance of Pre-Operative Monocyte-to-Lymphocyte Ratio in Lung Cancer Patients Undergoing Radical Surgery

Background

Inflammatory response is known to play a vital role in carcinogenesis and cancer progression. The prognostic relevance of monocyte-to-lymphocyte ratio (MLR), as a biomarker of inflammatory response has been demonstrated in patients with hematologic cancers.

Objectives

In this study, we assessed the prognostic relevance of MLR in patients with resectable lung carcinoma.

Methods

Clinical records of 705 lung cancer patients who underwent radical resection at our hospital between October 2006 and January 2011 were retrospectively reviewed. The optimal cutoff value of MLR as a prognostic indicator was determined on receiver operating characteristic curve analysis.

Results

On multivariate analysis using Cox proportional hazards regression model, MLR was an independent predictor of both overall survival (hazard ratio [HR] 1.494, 95% confidence interval [CI] 1.158-1.927, P = .002) and disease-free survival (HR 1.547, 95% CI 1.172-2.043, P = .002).

Conclusions

Preoperative MLR may be a simple, reliable prognostic marker for risk stratification and be used to guide treatment decision-making in lung cancer patients.

Complement component 7 (C7), a potential tumor suppressor, is correlated with tumor progression and prognosis

Our previous study found copy number variation of chromosome fragment 5p13.1-13.3 might involve in the progression of ovarian cancer. In the current study, the alteration was validated and complement component 7 (C7), located on 5p13.1, was identified. To further explore the clinical value of C7 in tumors, 156 malignant, 22 borderline, 33 benign and 24 normal ovarian tissues, as well as 173 non-small cell lung cancer (NSCLC) tissues along with corresponding adjacent and normal tissues from the tissue bank of Zhejiang Cancer Hospital were collected. The expression of C7 was analyzed using reverse transcriptase quantitative polymerase chain reaction. As a result, the C7 expression displayed a gradual downward trend in normal, benign, borderline and malignant ovarian tissues, and the decreased expression of C7 was correlative to poor differentiation in patients with ovarian cancer. Interestingly, a similar change of expression of C7 was found in normal, adjacent and malignant tissues in patients with NSCLC, and low expression of C7 was associated with worse grade and advanced clinical stage. Both results from this cohort and the public database indicated that NSCLC patients with low expression of C7 had a worse outcome. Furthermore, multivariate cox regression analysis showed NSCLC patients with low C7 had a 3.09 or 5.65-fold higher risk for relapse or death than those with high C7 respectively, suggesting C7 was an independent prognostic predictor for prognoses of patients with NSCLC. Additionally, overexpression of C7 inhibited colony formation of NSCLC cells, which hints C7 might be a potential tumor suppressor.

A decrease in serum 1,5-anhydroglucitol levels is associated with the presence of a first-degree family history of diabetes in a Chinese population with normal glucose tolerance

AIM

This study aimed to investigate alterations in HbA_1c , glycated albumin (GA) and 1,5-anhydroglucitol (1,5-AG) in Chinese first-degree relatives of individuals with diabetes (FDR) in pursuit of an index for early screening of glucose metabolism disturbance.

METHODS

A total of 467 participants (age range: 20-78 years) with normal weight and normal glucose tolerance, as determined by a 75-g oral glucose tolerance test, were enrolled. HbA_1c was measured using high-performance liquid chromatography. Serum GA and 1,5-AG levels were determined by enzymatic methods. Serum insulin levels were measured using an electrochemiluminescence immunoassay.

RESULTS

The study population included 208 FDR and 259 non-FDR. Serum 1,5-AG levels were lower in FDR than that in non-FDR (20.4 ± 7.5 vs 23.8 ± 8.3 μg/ml, P < 0.001), but HbA_1c and GA levels did not differ between them (P = 0.835 and 0.469, respectively). Logistic regression analysis revealed an independent relationship between a first-degree family history of diabetes and reduced serum 1,5-AG levels (odds ratio = 0.944, P < 0.001). Multiple regression analysis showed that a first-degree family history of diabetes (β = -3.041, P < 0.001) and insulinogenic index (β = 0.081, P = 0.001) were independently associated with serum 1,5-AG levels.

CONCLUSION

In a Chinese population with normal glucose tolerance, serum 1,5-AG levels were lower among FDR, and serum 1,5-AG levels were independently associated with FDR status. For FDR, serum 1,5-AG levels were more sensitive than HbA_1c or GA levels to early-phase abnormality in glucose metabolism.

Vitamin A maintains the airway epithelium in a murine model of asthma by suppressing glucocorticoid-induced leucine zipper

BACKGROUND

The effects of glucocorticoids (GCs) on the repair of the airway epithelium in asthma are controversial, and we previously reported that the GC dexamethasone (Dex) inhibits the repair of human airway epithelial cells and that this process is mediated by glucocorticoid-induced leucine zipper (GILZ) through MAPK-ERK signaling in vitro. Vitamin A (VA) is involved in the regulation of the MAPK-ERK pathway but has not been widely supplied during asthma treatment. It is unclear whether VA attenuates the negative regulation of GILZ on the MAPK-ERK pathway and maintains airway epithelium integrity during asthma treatment.

METHODS

Female BALB/c mice were sensitized and challenged with ovalbumin (OVA) and subsequently treated with Dex, VA or intranasal inhalation of adenovirus sh-GILZ vectors. Indexes of airway epithelium integrity, including pathological alterations, pulmonary EGFR expression and airway hyperresponsiveness (AHR), were then measured. The expression of GILZ and key components of activated MAPK-ERK signals (p-Raf-1, p-MEK, and p-Erk1/2) were also detected.

RESULTS

Dex failed to relieve OVA-induced asthma airway epithelium injury, as assessed through H&E staining, EGFR expression and AHR. Moreover, in the OVA-challenged mice treated with Dex, GLIZ expression was increased, whereas the ratios of p-Raf-1/Raf-1, p-MEK/MEK and p-Erk1/2/Erk1/2 were significantly decreased. Further study indicated that GILZ expression was decreased and that the ratios of p-Raf-1/Raf-1, p-MEK/MEK and p-Erk1/2/Erk1/2 were up-regulated in the GILZ-silenced OVA-challenged mice and VA-fed OVA-challenged mice, independent of Dex treatment. The airway epithelium integrity of the OVA-challenged mice was maintained by treatment with both VA and Dex.

CONCLUSIONS

Vitamin A maintained the Dex-treated asthma airway epithelium via the down-regulation of GILZ expression and the activation MAPK-ERK signaling, and these effects might contribute to improving the effects of GC therapeutics on asthma.

Tumor-Infiltrating CD4+ Lymphocytes Predict a Favorable Survival in Patients with Operable Esophageal Squamous Cell Carcinoma

Background

The immune status within the tumor microenvironment has not been well determined in esophageal squamous cell carcinoma (ESCC). The aim of this study was to investigate the distributions of tumor-infiltrating T lymphocytes (TILs), and analyze their associations with clinical characteristics and prognosis; as well as investigate the expression of programmed death-ligand 1 (PD-L1) which has been identified as a favorable indicator of prognosis in our previous study on ESCC.

Material/Methods

Five hundred and thirty-six patients who underwent radical surgery for ESCC between January 2008 and April 2012 in Department of Thoracic Surgery at Zhejiang Cancer Hospital were included in the study. Immunohistochemistry was used to investigate the infiltration of various TILs (CD3+, CD4+, CD8+ T lymphocytes) in ESCC tissues. Chi-square test and Cox proportional hazards regression were used to explore the correlations between TILs abundance and clinicopathological variables and survival.

Results

The infiltration of intraepithelial CD4+ (iCD4+) lymphocytes was markedly higher than it in the stromal region (44.2% for intraepithelial versus 28.9% for stromal, p<0.001). Moreover, increased iCD4+ lymphocytes were significantly associated with longer overall survival (OS, p=0.001) in univariate analysis and were identified as an independent predictor for improved OS in multivariate analysis (hazard ratio [HR]=0.67, 95% confidence interval [CI]: 0.51–0.88, p=0.040). Neither the infiltration of CD3+ nor CD8+ lymphocytes showed the prognostic value in ESCC (p>0.05). Unexpectedly, combined with our previous study results, the TILs infiltration in ESCC showed an inverse association with the expression of PD-L1 (p=0.027).

Conclusions

Our results suggested that iCD4+ lymphocytes infiltration could be a favorable indicator for prognosis in ESCC.

High performance of targeted next generation sequencing on variance detection in clinical tumor specimens in comparison with current conventional methods

Background

Next generation sequencing (NGS) is being increasingly applied for assisting cancer molecular diagnosis. However, it is still needed to validate NGS accuracy on detection of DNA alternations based on a large number of clinical samples, especially for DNA rearrangements and copy number variations (CNVs). This study is to set up basic parameters of targeted NGS for clinical diagnosis and to understand advantage of targeted NGS in comparison with the conventional methods of molecular diagnosis.

Methods

Genomic DNA from 1000 Genomes Project and DNA from cancer cell lines have been used to establish the basic parameters for targeted NGS. The following confirmation was conducted by clinical samples. The multiple variants tested by amplification-refractory mutation system (ARMS), fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC) were evaluated by targeted NGS to determine the sensitivity. Furthermore, the multiple variants detected by targeted NGS were confirmed by current conventional methods to elucidate the specificity.

Results

At sequencing depth of 500×, the maximal sensitivities on detecting single nucletic variances (SNVs) and small insertions/deletions (Indels) can reach 99% and 98.7% respectively, and in 20% of cancer cells, CNV detection can reach to the maximal level. The following confirmation of the sensitivity and specificity was conducted by a large cohort of clinical samples. For SNV and indel detection in clinical samples, targeted NGS can identify all hotspot mutations with 100% sensitivity and specificity. On ALK fusion detection, about 86% IHC-identified cases could be identified by targeted NGS and all ALK fusion detected by targeted NGS were confirmed by IHC. For HER2-amplification, 14 HER2-amplification cases identified by target NGS were all confirmed by FISH and about 93.3% of Her-2 IHC (3+) cases were identified by targeted NGS. Finally, the targeted NGS platform developed here has accurately detected EGFR hotspot mutations in 215 NSCLC patients.

Conclusions

DNA from cancer cell lines is better than standard DNA as a reference to establish basic parameters for targeted NGS. Comparison of the conventional methods using a large cohort of patient samples confirmed the high preformance of targeted NGS on detecting DNA alterations.

Electronic supplementary material

The online version of this article (10.1186/s13046-017-0591-4) contains supplementary material, which is available to authorized users.

Regenerating Family Member 4 (Reg4) Enhances 5-Fluorouracil Resistance of Gastric Cancer Through Activating MAPK/Erk/Bim Signaling Pathway

BACKGROUND Reg4, a member of the Reg multigene family, is highly upregulated in many gastrointestinal cancers including gastric cancer (GC). The enhanced expression of Reg4 is associated with the resistance of GC to 5-fluorouracil (5-FU), while the underlying mechanism is not clear. The aim of the present study was to explore the resistant mechanism underlying 5-FU resistance. MATERIAL AND METHODS Reg4 expression was assessed by Western blot analysis for SGC-7901, BGC-823, AGS, MKN28, and MKN45. Synthetic short single strand RNA oligonucleotides and Flag-Reg4 plasmid were used to investigate the biological function of Reg4 in vitro. The cell viability assay was performed by MTT. Flow cytometry was carried out to measure the apoptosis caused by 5-FU. Reverse-transcriptase quantitative polymerase chain reaction (RT-qPCR) was used to examine the expression of 5-FU metabolism related enzymes. The effect of Reg4 on intracellular signaling was evaluated by Western blot. RESULTS Western blot analysis of 5 GC cells showed that Reg4 was low or null in SGC-7901 and BGC-823, while high in AGS, MKN28, and MKN45. Over-expression of flag-Reg4 in SGC-7901 led to an increase in cell viability and lower apoptosis with 5-FU treatment. In contrast, siRNA knockdown of Reg4 enhanced 5-FU induced apoptosis. However, over-expression or knockdown of Reg4 had no significant influence on the expression of 5-FU metabolic enzymes. Further investigation revealed that Reg4 could activate Erk1/2-Bim-caspase3 cascade. CONCLUSIONS Reg4 inhibited apoptosis through regulating MAPK/Erk/Bim signaling pathway and thereby enhanced the resistance of GC to 5-FU.

Overcoming Linsitinib intrinsic resistance through inhibition of nuclear factor-κB signaling in esophageal squamous cell carcinoma

The aim of this study is to evaluate the efficacy of insulin-like growth factor 1 receptor (IGF-1R) inhibitor Linsitinib, in esophageal squamous cell carcinoma (ESCC), and to characterize special biomarker to screen Linsitinib-sensitive patients as well as explore the molecular-resistant mechanism to Linsitinib in ESCC. Our study evaluated the sensitivity of insulin-like growth factor 1 receptor (IGF-1R) inhibitor, Linsitinib in ESCC cells with MTT assay. After Linsitinib treatment, the expressions of downstream signaling molecules and apoptosis pathways were measured by western blot. And the antitumor effect of Linsitinib and JSH-23, an inhibitor of nuclear factor-κB transcriptional activity, was analyzed both as single agent and in combination in ESCC. Apoptosis, cell viability, and clonogenic survival analysis were also investigated. The sensitivity of Linsitinib was relatively variable in patient-derived primary ESCC cells as well as in human commercial cell lines. And the downstream AKT/mTOR and ERK signaling pathways were inhibited by Linsitinib, while phosphorylation level of NF-κB p65 was obviously activated to reduce apoptosis effect in Linsitinib-resistant cell lines. Most importantly, blockage of NF-κB activity by JSH-23 could sensitize resistant cells to Linsitinib treatment. Results from this study demonstrated that the intrinsic resistance to Linsitinib was predominantly mediated by NF-κB activation in ESCC. Moreover, combination of Linsitinib and JSH-23 as therapy provides a novel strategy to overcome resistance to Linsitinib in ESCC.

[Recombinant human tumor necrosis factor receptor type Ⅱ-IgG Fc fusion protein for treatment of occupational medicamentosa-like dermatitis induced by trichloroethylene]

Objective: To investigate the efficacy and safety of the recombinant human tumor necrosis factor receptor Ⅱ-IgG Fc fusion protein (rhTNFR: Fc, etanercept) for the treatment of occupational medicamentosa-like dermatitis induced by trichloroethylene (OMLDT) . Methods: In September 2011 to February 2016, 12 patients with OMLDT were treated with etanercept 25 mg, subcutaneous injection, twice per week, doubling of first dose. The course of treatment was 6 weeks. The drug eruption area and severity index (DASI) score, the proportion of patients achieving a 50%, 75% and 90% reduction in DASI (DASI50, DASI75, DASI90) and the serum level of TNF-α were used to assess the efficacy at different times. Adverse reactions were also recorded and evaluated. The results were statistically analyzed by nonparametric Friedman test and repetitive measurement ANOVA using the software SPSS19.0. Results: After 4 weeks treatment, the DASI score decreased form 56.33±7.02 to 0.50±0.91 (P<0.01) . The DASI50, DASI75 and DASI90 were all increased to 12 (100%) . The serum level of TNF-α decreased form (43.74±41.62) pg/ml to (3.03±0.47) pg/ml (P<0.01) . Statistically significant difference was observed from the above indexes. There were no adverse reactions in clinical application. Conclusion: Recombinant human tumor necrosis factor receptor Ⅱ-IgG Fc fusion protein may be a safe and effective drug in the treatment of OMLDT.

The C-reactive protein/albumin ratio predicts long-term outcomes of patients with operable non-small cell lung cancer

PURPOSE

To investigate the association between C-reactive protein/albumin ratio (CAR), an inflammation-based prognostic score, and clinicopathological factors, as well as its association with long-term outcomes in patients with operable non-small cell lung cancer (NSCLC).

METHODS

A total of 617 operable NSCLC patients were retrospectively evaluated and the data of preoperative serum CRP and serum albumin was collected. The correlation between the CAR and clinicopathological factors was analyzed using the chi-square test. A Cox proportional hazards regression model was performed to evaluate the association between the CAR and outcome.

RESULTS

The CAR was significantly related to sex, smoking status, BMI, histology type and clinical stage (p ≤ 0.05). The patients with characteristic of male, smoker, BMI under 18.5, squamous cell carcinoma or clinical stage III had a high level of CAR. Additionally, elevated CAR indicated a worse outcome, and the patients with higher CAR had 2.02-fold risk for disease progression (95% CI 1.48-2.74, p < 0.001) and 2.61-fold risk for death (95 % CI 2.02-3.37, p < 0.001). Multivariate analyses showed the similar results after adjusted by clinicopathological factors and another four inflammation-based prognostic scores.

CONCLUSIONS

The CAR is a potential independent predictor for disease progression and death in patients with operable NSCLC.

Study on expression of CDH4 in lung cancer

Background

The human CDH4 gene, which encodes the R-cadherin protein, has an important role in cell migration and cell adhesion, sorting, tissue morphogenesis, and tumor genesis. This study analyzed the relationship of CDH4 mRNA expression with lung cancer.

Methods

Real time PCR was applied to detect CDH4 mRNA transcription in 142 paired cases of lung cancer and noncancerous regions.

Results

No correlation was identified between CDH4 mRNA expression and gender, age, lymphnode metastasis, TNM stage, family history, smoking state, drinking state (P > 0.05), but grade and histotype (P < 0.05). The relative CDH4 mRNA value was remarkably decreased in lung cancer tissues compared with noncancerous tissues (P = 0.001).

Conclusions

We found that CDH4 mRNA expression was associated with grade and histotype. What is more, the relative CDH4 mRNA value was decreased in the lung cancer tissues. Our results suggested that CDH4 might be a putative tumor suppressor gene (TSG) in lung cancer.

Expression of LRIG1 in pituitary tumor and its clinical significance

OBJECTIVE

To analyze the expression of leucine-rich and immunoglobulin-like domain gene1 (LRIG1) in pituitary tumor and its clinical significance.

PATIENTS AND METHODS

Patients were divided into two groups: hypophysoma group (n = 80) and normal group (normal brain tissue, n = 30). The immune tissue chemical streptavidin avidin-peroxidase was applied to detect the expression of LRIG1 of both groups and to analyze its relationship with the patients' prognosis.

RESULTS

The positive expression rate of LRIG1 in normal brain tissues was significantly higher than that in pituitary adenomas (100% vs. 53.8%) (p < 0.05). The positive expression rate of LRIG1 in pituitary tumors was not significantly related to age and gender, the difference was not statistically significant (p > 0.05). The positive expression rate of LRIGl in non-invasive pituitary adenomas was higher than that in invasive pituitary tumors (68.4% vs. 21.7%), the difference was statistically significant (p < 0.05). Cox multivariate survival analysis showed that LRIG1 can be used as an independent factor for prognosis evaluation. Meier survival analysis showed that the LRIG1 and pituitary tumor types were significantly associated with the prognosis of patients (p < 0.05).

CONCLUSIONS

LRIG1 was involved in the occurrence and development of pituitary tumor, the expression of LRIG1 can be used as an indicator for prognosis evaluation, and low expression indicated a poor prognosis.

A Nomogram to Predict Brain Metastases of Resected Non-Small Cell Lung Cancer Patients

PURPOSE

Brain metastasis is a major cause leading to the failure of treatment management for non-small cell lung cancer (NSCLC) patients. The goal of this study was to establish an effective nomogram for prediction of brain metastases of resected NSCLC patients.

METHODS

We retrospectively investigated 637 operable NSCLC patients who received treatment at Zhejiang Cancer Hospital, China. A Cox proportional hazards regression model was performed to identify significant risk factors, and a nomogram was developed for predicting 3- and 5-year brain metastases rates.

RESULTS

Multivariate analysis identified four independent risk factors: neuron-specific enolase, histological type, number of metastatic lymph nodes, and tumor grade, and a nomogram was developed based on these factors. The effectiveness of the nomogram was validated using an internal bootstrap resampling approach, showing that the nomogram exhibited a sufficient level of discrimination according to the C-index (0.74, 95 % confidence interval 0.67-0.82).

CONCLUSIONS

The nomogram developed in this study demonstrated its discrimination capability for predicting 3- and 5-year occurrence of brain metastases, and can be used to identify high-risk patients.

Combined Effects of Suberoylanilide Hydroxamic Acid and Cisplatin on Radiation Sensitivity and Cancer Cell Invasion in Non-Small Cell Lung Cancer

Lung cancer is a leading cause of cancer-related mortality worldwide, and concurrent chemoradiotherapy has been explored as a therapeutic option. However, the chemotherapeutic agents cannot be administered for most patients at full doses safely with radical doses of thoracic radiation, and further optimizations of the chemotherapy regimen to be given with radiation are needed. In this study, we examined the effects of suberoylanilide hydroxamic acid (SAHA) and cisplatin on DNA damage repairs, and determined the combination effects of SAHA and cisplatin on human non-small cell lung cancer (NSCLC) cells in response to treatment of ionizing radiation (IR), and on tumor growth of lung cancer H460 xenografts receiving radiotherapy. We also investigated the potential differentiation effect of SAHA and its consequences on cancer cell invasion. Our results showed that SAHA and cisplatin compromise distinct DNA damage repair pathways, and treatment with SAHA enhanced synergistic radiosensitization effects of cisplatin in established NSCLC cell lines in a p53-independent manner, and decreased the DNA damage repair capability in cisplatin-treated primary NSCLC tumor tissues in response to IR. SAHA combined with cisplatin also significantly increased inhibitory effect of radiotherapy on tumor growth in the mouse xenograft model. In addition, SAHA can induce differentiation in stem cell-like cancer cell population, reduce tumorigenicity, and decrease invasiveness of human lung cancer cells. In conclusion, our data suggest a potential clinical impact for SAHA as a radiosensitizer and as a part of a chemoradiotherapy regimen for NSCLC. Mol Cancer Ther; 15(5); 842-53. ©2016 AACR.

Development of a cellular biosensor system for genotoxicity detection based on Trp53 promoter

OBJECTIVE

To develop a mouse cell biosensor system for the high-throughput genotoxicity detection of chemicals, such as environmental pollutants.

METHOD

We developed a novel reporter vector pGL4-GFP, wherein the firefly luciferase reporter gene in the pGL4.82 vector was replaced by the green fluorescent protein (GFP) gene from the pAcGFP1-N1 vector. To construct the reporter pGL4-p53-GFP (p53 promoter linked to GFP), a fragment containing the p53 gene promoter was generated by amplifying a region from -481 to +180 of mouse genomic DNA isolated from mouse tail tissue. We developed a mouse cell biosensor system for the high-throughput genotoxicity detection of new drugs by stably integrating the reporter plasmid of pGL4-p53-GFP into the mouse embryonic fibroblast cells. Various genotoxic agents were used to treat this biosensor system. The resulting fluorescence was directly observed under a fluorescence microscope, and the GFP protein level was measured through Western blot analysis.

RESULT

The biosensor system was treated with genotoxic agents, such as doxorubicin, cyclophosphamide, and benzo(a)pyrene. The GFP protein expression was significantly increased in cells exposed to genotoxic agents but negatively responded to the non-genotoxic agent dimethyl sulfoxide, thereby proving the specificity and sensitivity of the biosensor system.

CONCLUSION

This novel in vitro biosensor system can be especially useful in genotoxicity detection.

Upregulation of circulating cytokeratin 20, urokinase plasminogen activator and C-reactive protein is associated with poor prognosis in gastric cancer

Gastric cancer is one of the most common types of cancer, with a high mortality rate. The aim of this study was to investigate the role of several key molecules, including cytokeratin (CK) 19 and CK20, urokinase plasminogen activator (uPA), C-reactive protein (CRP) and matrix metalloproteinase (MMP)-9, which are involved in cancer invasion and metastasis, in order to determine whether they may be considered as novel prognostic factors for gastric cancer. Peripheral blood was collected from 165 patients with gastric adenocarcinoma who underwent curative surgical resection at Zhejiang Cancer Hospital (Hangzhou, China) between 2010 and 2011. The mRNA levels of CK19, CK20, uPA and MMP-9 were detected by reverse transcription-quantitative polymerase chain reaction. The protein expression of CRP was measured by immunoturbidimetry. The Students t-test was used in the univariate analyses and the Kaplan-Meier method was used to analyze the survival curves. The relative mRNA expression of CK19 and MMP-9 was not found to be significantly associated with gender, age or cancer stage, whereas that of CK20 and uPA was associated with gastric cancer stage: The low-expression group was associated with early-stage and the high-expression group with more advanced-stage disease (P<0.05). The CRP protein level was associated with gender and cancer stage: The low-expression group was predominantly associated with male gender and early-stage disease, whereas the high-expression group was associated with female gender and advanced-stage disease (P<0.05). The expression of CK19, CK20, uPA and CRP, but not MMP-9, was negatively associated with overall survival (OS): The OS rate in the high-expression groups was significantly lower compared with that in the low-expression groups (P<0.05). In conclusion, the upregulation of CK20, uPA and CRP was found to be a negative prognostic factor for gastric cancer.

Down Expression of FBP1 Is a Negative Prognostic Factor for Non-Small-Cell Lung Cancer

Downregulation of fructose-1,6-bisphosphatse-1 (FBP1) was observed in several cancers but its role in the lung cancer still remains unknown. We examined the cancer tissues from 140 patients with nonsmall cell lung cancer patients and found that the relative gene expression of FBP1 was significantly lower in lung cancer tissues as compared to incisal marginal tissues and normal tissues. The patients with higher level of FBP1 RNA expression have significantly longer disease free survival and overall survival as compared to the lower expression groups. There was a negative correlation with the level of FBP1 and recurrence of the lung cancer.

Randomised clinical trial evaluating best-corrected visual acuity and central macular thickness after 532-nm subthreshold laser grid photocoagulation treatment in diabetic macular oedema

Purpose

To compare best-corrected visual acuity (BCVA) and central macular thickness (CMT) after 532-nm subthreshold laser grid photocoagulation and threshold laser grid photocoagulation for the treatment of diabetic macular oedema (DME).

Patients and methods

Twenty-three patients (46 eyes) with binocular DME were enroled in this study. The two eyes of each patient were divided into a subthreshold photocoagulation group and a threshold photocoagulation group. The eyes of the subthreshold group underwent 532-nm patter scan laser system (PASCAL) 50% end point subthreshold laser grid photocoagulation therapy, whereas the threshold photocoagulation group underwent short-pulse grid photocoagulation with a 532-nm PASCAL system. BCVA and CMT were assessed in all patients before treatment, 7 days after treatment, and 1, 3, and 6 months after treatment.

Results

After grid photocoagulation, the mean BCVA improved in both the subthreshold group, and the threshold group, and the two groups did not differ statistically significantly from each other. Similarly, the macular oedema diminished in both groups after treatment, and the two groups did not differ statistically significantly from each other with regard to CMT.

Conclusion

Both 532-nm subthreshold laser grid photocoagulation and threshold laser grid photocoagulation can improve the visual acuity and reduce CMT in DME patients.