bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cancer-IgG upregulation of radioresistance in non-small cell lung cancer patients and cell lines.
Authors: Zhu Guangying , Yang Xiongtao , Guohui Wang , You Jing 
Published: May 2020

e21013 Background: Immunoglobulin G (IgG) is produced by B lymphocytes which is an important effector molecule of human immunity. However,our collaborators in China Peking University have found that malignant tumor cells can also express IgG (cancer-IgG). This study was designed to investigate the relationship between cancer-IgG and radiosensitivity and to explore its possible mechanisms in NSCLC. Methods: First, the expression of IGHG1 (immunoglobulin heavy constant gamma 1, IGHG1) and cancer-IgG in NSCLC and their relationship with clinicopathological features and prognosis were analyzed by TCGA(The Cancer Genome Atlas, TCGA), GEO(Gene Expression Omnibus, GEO) databases and immunohistochemistry. Secondly, after silencing the expression of cancer-IgG, cell scratch test, transwell, clone formation and apoptosis experiments were performed to observe the changes of EMT and radiation sensitivity of tumor cells after irradiation. Finally, the key proteins of PI3K/Akt signaling pathway and EMT-related proteins were detected by western blot and real-time PCR. Results: 1. The expression levels of IGHG1 and cancer-IgG in NSCLC were significantly higher than those in normal lung tissues, and high expression of IGHG1 and cancer-IgG were factors of poor prognosis. And cancer-IgG was closely related to clinical stage (P = 0.042), T stage (P = 0.044) and metastasis (P = 0.007). 2. Cell scratches and transwell experiments showed that the cell migration and invasion ability of si-control+IR group were significantly enhanced, but in si-Cancer-IgG+IR group were significantly lower than si-control+IR group. 3. Cloning formation experiments showed that the number of cell clones formed in the si-cancer-IgG group was significantly less than that in the control group under 2-6 Gy irradiation. Apoptosis results showed that the apoptosis rates of si-control group, si-Cancer-IgG group, si-control+IR group and si-Cancer-IgG group were 6.36±1.69%, 21.33±1.21%, 23.31±0.96% and 52.69±2.33% respectively. The apoptotic cells in the Si-cancer-IgG group were significantly more than the si-control group. (P < 0.01). 4. Western blot results showed that p-AKT, p-GSK3β, bcl2 and Vimentin were significantly decreased in si-Cancer-IgG+IR group compared with si-control+IR, and the expression levels of BAD and E-cadherin were increased. Conclusions: Cancer-IgG may mediate radiation-induced EMT and radiotherapy resistance through the PI3K/AKT pathway.
Immunoscore classifier:A gene based prognostic tool in early non-small cell lung cancer.
Authors: Guo Meiying , Sun Xindong , Yu Jinming , Wang Linlin 
Published: May 2020

e21030 Background: The clinical benefits of immunotherapy in patients with stage I non-small cell lung cancer (NSCLC) is still controversial. Immune status plays critical role in the development and progression of NSCLC, and is associated with the patient survival outcomes. The analysis of immune features is thus valuable for the determination of immunotherapy. However, one single immune feature cannot reflect the complex immune status, and its prognostic value is extremely limited. In this study, we aimed to construct an immunoscore classifier based on multiple immuno-genes to predict the prognosis of patients with early NSCLC. Methods: A total of 522 patients with stage I NSCLC were included in this study. All patients' follow-up records and gene expression data were completely preserved. A least absolute shrinkage and selection operator (LASSO) algorithm was used to screen immune-related genes, and a COX proportional hazard regression model was used to construct the immunoscore classifier based on multiple immune-genes. Besides, the net reclassification improvement (NRI) calculation and concordance index (C-index) were applied to quantify the improvement of usefulness added by the immunoscore classifier compared to TNM staging system. Results: The immunoscore classifier including CCL5, CD8A, CXCL9, HLA-DQA1, LAG3, STAT1, and CD276 was significantly correlated with OS (HR: 2.785 CI: 1.809-4.289 P < 0.001) in patients with stage I NSCLC. With the optimal cut-off value of 4.32, all patients can be divided into a low-risk immune group and a high-risk immune group. The 10-year survival rates of the two groups were 36.8% and 12.3%, respectively. Besides, the immunoscore classifier was superior to the traditional TNM staging system in terms of distinguishing ability (C-index improvement by 0.075) and net reclassification ability (NRI improvement by 11.29%), indicating that the immunoscore classifier plays an important role in improving prognostic value. Conclusions: Multiple immune-genes based immunoscore classifiers can effectively predict the prognosis of patients with stage I NSCLC, and is significantly superior to the traditional TNM staging system in terms of prediction effectiveness and accuracy. As a new assessment tool, the immunoscore classifier may be helpful for determining the immune status of patients with stage I NSCLC and screening patients suitable for subsequent immunotherapy.
Characterizing the molecular and immunological features of lung micropapillary adenocarcinoma.
Authors: Zhang Shirong , Xu Yang , Zhao Pan , Bao Hua , Wang Xiyong , Liu Rui , Xu Rujun , Xiang Jingjing , Jiang Hong , Yan Junrong , Wu Xue , Shao Yang , Liang Jiafeng , Wu Qiong , Zhang Zhihao , Lu Shun , Ma Shenglin 
Published: May 2020

e21036 Background: Micropapillary adenocarcinoma (MPC) is one of the most aggressive histologic subtypes of lung adenocarcinoma (ADC). Although the incidence of MPC predominant ADC is low, nearly half of ADCs contain a minor proportion of MPC, which could contribute to poor prognosis in these patients. Comprehensive analysis of genetic and immunological features of ADC with different MPC contents would help better understand cancer biology of this ADC subtype and direct future treatments. Methods: We performed panel next-generation sequencing (NGS) of 425 cancer-related genes for a discovery cohort of 43 ADC patients whose tumors were microdissected to separate MPC and non-MPC regions and a reference cohort of 113 ADC patients with unknown ADC histologic subtypes. MPC-enriched mutations were identified by comparing tumors with different original MPC contents within these cohorts, which was then confirmed using a validation cohort of 183 ADC patients. Staining of immunological markers was also conducted for MPC samples from the discovery cohort to investigate their tumor microenvironment. Results: We found that ADC tumors with higher MPC contents/similarities tended to harbor more tumor mutation burdens (TMBs) and chromosome instability (CIN). In addition, genetic alterations in transcription termination factor 1 ( TTF1), brain-specific angiogenesis inhibitor 3 ( BAI3), mammalian target of rapamycin ( MTOR), cyclin-dependent kinase inhibitor 2A ( CDKN2A), and CDKN2A were found to be enriched in MPC using the discovery and reference cohorts, which could then be cross-validated using the validation cohort. Tumors with higher MPC content were associated with elevated infiltration of CD4+, CD8+ and FOXP3+ T cells, especially at the peritumor regions. Higher percentage of PD-L1+ tumor cells were also found to be correlated with higher MPC content, suggesting of more immunosuppression in MPC predominant tumors than low MPC tumors. Conclusions: We identified multiple novel MPC-enriched genetic changes that could help understand the nature of MPC. MPC predominant tumors tended to have higher levels of TMBs, T cell infiltration, and immunosuppression than low MPC tumors, making it a potential candidate for immunotherapy, especially the combination therapy of anti-PD-1/PD-L1 drugs and anti-CTLA-4 drugs, which could inhibit PD-1/PD-L1 pathway and FOXP3+ Treg cells simultaneously.
Liquid chromatography coupled to multiple reaction monitoring (LC-MRM) for quantification of PD-L1 and PD1-signaling proteins in non-small cell lung carcinoma (NSCLC).
Authors: Lacasse Vincent , Zahedi Rene , Richard Vincent , Wang Hangjun , Mitsa Georgia , Poetz Olivier , Redpath Margaret , Papadakis Andreas , Elchebly Mounib , Cohen Victor , Agulnik Jason Scott , Batist Gerald , Borchers Christopher , Spatz Alan 
Published: May 2020

e21040 Background: Improving the predictive biomarkers arena of checkpoint inhibitors (CPIs) beyond PD-L1 immunohistochemistry (IHC) is one of the most important unmet need in NSCLC. Up to 50% of patients that show positive PD-L1 expression by IHC do not respond to anti-PD-L1 treatments, and patients with low/undetectable PD-L1 have significantly improved survival with CPI. Moreover, PD-L1 IHC is heterogeneous, can be affected by tissue fixation time and post-translational modifications like glycosylation. Also, multiple studies indicated that PD-L1 expression alone does not reliably reflect the immune status of the tumor, thus requiring the measurement of other members of the PD1 signalling pathway. Methods: To address these issues, we developed a multiplexed targeted mass spectrometry-based (MS) assay for the quantitation of protein members of the PD-1/PD-L1 axis in formalin fixed paraffin-embedded (FFPE) tissue.The effect of fixation time on protein recovery was determined using differentially fixed H1915 cells. Liquid chromatography (LC) coupled to MRM was used to develop a targeted assay for PD-L1, PD-1, PD-L2, NT5E, LCK and ZAP70. Results: After 30 minutes fixation 33.6 µg of protein were extracted per mg of FFPE H1915 cells, while protein recovery after 7 days was 55.8 µg/mg, with greater variability (18% and 28% CV, p-value = ns). The optimized LC-MRM method allows the quantitation of PD-L1 and PD-1 down to 23 amol on-column. We evaluated the utility of our MRM assays using the H1915 FFPE cells (PD-L1 3+ by IHC) and determined an endogenous concentration of PD-L1 and NT5E as being 33.2±0.1 amol/µg of total protein and 4.8±0.5 fmol/µg respectively. Noteworthy, a known glycosylation site of PD-L1 was quantified at 10.9±0.3 amol/µg of total protein (30% of total). As increases sensitivity was required, anti-peptide antibodies were generated against the 15 best peptides. We then evaluated this LC-MRM method using MDA-MB-436 cells with lower levels of PD-L1 protein assessed by IHC. Determination of endogenous PD-L1 concentration (3.0 amol/µg of total protein) was achieved using anti-peptide immuno-enrichment followed by MRM. Conclusions: We developed a fixation time independent extraction technique for FFPE and optimized a highly sensitive LC-MRM method that allows the absolute quantification of our targets. This proteomic workflow allows absolute quantification of the PD-1/PD-L1 axis from FFPE tissue using immuno-enrichment and a multiplexed LC-MRM method.
Changes of plasma GARP-LTGFβ1 complex during chemoradiotherapy may predict survival in non-small cell lung cancer (NSCLC).
Authors: Yu Yishan , Li Anqi , Wang Weili , Fu Pingfu , Jolly Shruti , Lawrence Theodore Steven , Machtay Mitchell , Li Zihai , Kong Feng-Ming Spring 
Published: May 2020

e21042 Background: Glycoprotein-A repetitions predominant protein (GARP), a cell surface docking and activating receptor for latent transforming growth factor β1 (LTGFβ1), has been implicated in promoting oncogenesis. We report recently that GARP-LTGFβ can be clipped by thrombin but its clinical significance remains unclear. Herein, we hypothesized that 1) the baseline plasma GARP-LTGFβ1 complex is associated with clinical stage of cancers; 2) the baseline and/or changes of plasma GARP-LTGFβ1 complex during chemo-radiotherapy is associated with overall survival (OS) in patients with NSCLC. Methods: This is a correlative study for patients with stage I-III NSCLC receiving chemo-radiotherapy. Levels of GARP-LTGFβ1 complex in platelet-poor plasma were determined by a modified ELISA at pre-RT, 2,4 weeks during-RT and post-RT. Values were calculated based on the following formula: (ODtest-ODnegative control)/ODpostive control-ODnegative control). The primary endpoint was OS, analyzed using the Kaplan-Meier method and Cox proportional hazard model. Platelet-poor plasma samples from healthy subjects were used as normal controls. Results: A total of 155 patients were included: 41 stage I-II, 111 stage III. There were 115 male, 50 female with a median age of 66 years. Compared to 13 normal controls (0.638, 95% CI:0.477-0.799), NSCLC patients had a significantly higher plasma GARP-LTGFβ1 (0.965, 95%CI: 0.881-1.048, p = 0.014). The same trend was observed for stage, higher level in more advanced stage (1.037, 95%CI: 0.930-1.145) vs for stage I-II (0.854, 95%CI: 0.720-0.988) (p = 0.0375). Univariate analysis demonstrated that age, gender, clinical stage, smoking history, histology, KPS, and radiation dose were significantly associated with OS. Post/pre RT GARP-LTGFβ1 complex (high vs. low HR = 0.384, p = 0.043) instead of pre-RT (p = 0.538), during RT (p = 0.739 for 2 weeks, p = 0.570 for 4 weeks) or post-RT (p = 0.507) plasma GARP-LTGFβ1 complex during the course of radiation therapy correlated significantly with OS under univariate analysis. On multivariate Cox regression models after adjusting for above significant clinical factors, the changes of plasma GARP-LTGFβ1 level had significance in correlating with OS (HR = 0.359, p = 0.0087). Conclusions: Baseline plasma GARP-LTGFβ1 were significantly associated with presence of cancer and advanced stages in NSCLC patients. Changes of GARP-LTGFβ1 level in plasma could be useful to predict outcomes and reflect the changes of immune status after chemoradiation.
Association between homologous recombination deficiency and tumor mutational burden in lung cancer.
Authors: Jiang Yong , Dang Shiying , Yang Li , Han Yin , Zhang Yongshen , Mu Tianhao , Chen Shifu , Kong Feng-Ming 
Published: May 2020

e21043 Background: Homologous recombination (HR) is an important repair method for DNA double-strand damage. HR is involved with complex signaling pathways and multiple steps, including BRCA1/2. Homologous Recombination Deficiency (HRD) can be caused by the loss of function of BRCA1/2 proteins due to gene mutation. Tumor mutational burden (TMB) was indicated to involved with HRD, which is critical to the guidance of immunotherapy. Methods: Patients available with tumor specimen genomic testing for lung cancer were enrolled in this study. The sequencing library was captured using a 605-gene panel. Homologous recombination (HR)-related gene list included 102 genes. Genomic alterations of HR-related genes were assessed by next-generation sequencing assay, including nonsense, nonstop, frameshift, splice site, damaging missense mutations in somatic variants and pathogenic germline variants. Then, TMB was calculated by dividing the total number of mutations counted by the size of the coding region. Results: A total of 741 patients was enrolled and 182 of them (25.6%) had at least one genomic alteration of the HR genes. The top mutant HR genes included ATM (4.1%), DNMT3A (2.8%), ATR (1.8%), CHEK2 (1.5%), BRCA2 (1.5%), ABL1 (1.4%), FANCA (1.2%), RIF1 (1.1%), FANCI (1.1%), RAD50 (0.9%), BRCA1 (0.9%), and MRE11A (0.9%). The most common mutational type was missense mutation (69.2%), followed by frameshift (15.6%), and nonsense mutation (15.2%). The median age was 62 in the HRD group (age < 45:5.4%, 45-65:59.6%, > 65:34.9%) compared to 60 in the rest of the patients (age < 45:11.3%, 45-65:61.3%, > 65:27.4%). There were overall 57.5% males and 42.5% females in terms of gender. HRD group had a significantly higher rate than Non-HRD group in males (72.1% vs 52.8%, p < 0.01). The occurrence of HRD mutations was significantly correlated with a high level of TMB (p < 0.01). The median TMB of HRD group (7.9 muts/Mb, 95%CI:7.1-9.2 muts/Mb) was significantly higher than that of Non-HRD group (3.8 muts/Mb, 95%CI:3.3-4.2 muts/Mb). In addition, the upper quantile value (7.5 muts/Mb) was used to identify patients with high TMB. HRD group had a significantly higher rate of TMB-high patients than Non-HRD group (51.1% vs 17.0%, p < 0.01). Conclusions: Our study demonstrated genomic alterations of the HR genes in about one fourth’s lung cancer. Besides, there was a significant positive correlation between HRD mutations and TMB level. The significance of HRD genomic mutation on predicting the efficacy of immunotherapy deserves further study.
Development and validation of a CT-based radiomic model combined with margin-related radiomic features to distinguish precancerous lesions from early-stage lung adenocarcinoma.
Authors: Huang Luyu , Zhou Haiyu , Yao Herui , Yu Yunfang , Zhu Hongyuan , Zheng Shaopeng , Lin Weihuan , Xie Daipeng , Zeng Fanjun , Liao Guoqing , Lin Zenan , Li Fasheng , Zhang Peirong , Xu Bin , Wu Shaowei , Yao Lintong , Li Wanshan 
Published: May 2020

e21044 Background: The purpose of this study was to investigate whether the combined radiomic model based on tumor-associated and margin-related (5mm) radiomic features can effectively improve prediction performance of distinguishing precancerous lesions from early stage lung adenocarcinoma. Methods: 264 patients underwent preoperative chest CT in Guangdong Provincial People’s hospital from March 1, 2015 to December 31,2019 were sorted by three cohorts. All lesions were pathologically confirmed as precancerous lesions or Stage I lung adenocarcinoma and a total of 861 analyzable radiomic features were extracted from two segmented lesions including pulmonary lesions and margins, using PyRadiomics by two senior radiologists. In training cohort, 145 patients (70%) are selected randomly from the single-nodular patients (N = 207). As for the validation cohorts, the models were validated using the resting 62 patients from single-nodular cohort and multi-nodular cohort (n = 57) respectively. Least Absolute Shrinkage and Selector Operation and Support Vector Machine-Recursive Feature Elimination were used for feature selection. ROC analysis and AUC were used to evaluate the performance of three models which were developed by multiple logistic regression on distinguishing the precancerous lesions from early stage lung adenocarcinoma. Results: Selected features from pulmonary lesions and pericarcinous tissue were developed into two independent radiomic models and a combined model. Margin-related radiomic model performs well in three validation cohorts. The AUC Brock of single-nodular cohort in training cohort was 0.912 (95% CI: 0.876-0.948), while in single-nodular validation cohort was 0.93 (95% CI: 0.862-0.966). Multi-nodular validation cohort in this model shows an AUC of 0.891 (95% CI = 0.824–0.943). Comparing combined model and tumor-associated radiomic model, it is found that the AUC of combined model was improved from 0.865 (95% CI: 0.767-0.963) to 0.94 (95% CI: 0.767-0.963) for single-nodular validation cohort. Respectively, this combined model also performs well in multi-nodular validation cohort. Conclusions: This study demonstrated the potential of margin-related radiomic features based on preoperative CT scans to distinguish precancerous lesions from early stage lung adenocarcinoma. The constructed radiomic model provided an easy-to-use, preoperative tool for surgeons to develop accurate therapeutic strategies for multi-nodular patients.
Epigenetic imprinted gene biomarkers significantly improve the accuracy of presurgical bronchoscopy diagnosis of lung cancer.
Authors: Zhou Jian , Cheng Tong , Li Xing , Pineda John P. , Lu Shaohua , Yu Hongyu , Ding Ming , Wang Xiaonan , Si Han , Shi Panying , Zhou Ning , Bai Chunxue 
Published: May 2020

e21055 Background: The ability to diagnose earlier stages of carcinogenesis using less invasive presurgical tissue samples is especially desirable, but is often inconclusive because of insufficient morphological evidences of cancer. Many of the epigenetic biomarkers are involved in lung cancer, but are challenging to clinically evaluate. In this study, Quantitative Chromogenic Imprinting Gene In-Situ Hybridization (QCIGISH) was applied to directly visualize and quantitatively assess the biallelic and multiallelic alterations of imprinted gene expressions in order to characterize lung cancer carcinogenesis and progression. We updated an imprinted gene panel and developed an accurate lung cancer diagnostic grading model from minimally invasive biopsies using the QCIGISH method. Methods: 225 surgical (151 lung cancer, 74 benign lung lesion) and 95 pre-surgical samples (77 lung cancer, 18 benign lung lesion) were collected from 320 patients under clinical trial NCT03882684 involving five medical centers between 2015 and 2019. The QCIGISH method was applied to detect the allelic expression status of the GNAS, GRB10, SNRPN and HM13 imprinted gene panel. A diagnostic grading model for lung cancer progression was trained using 225 retrospectively collected surgical tissue set with known diagnosis, refined using 25 presurgical samples, and blindly validated using 70 presurgical samples. Results: The diagnostic grading model collectively achieved high sensitivity (98.7%) which is significantly higher than standard presurgical bronchoscopy diagnostic methods including transbronchial brushing (58-74%), transbronchial biopsy (61-75%), alveolar lavage (35-64%) and the combination of the aforementioned three methods (64-80%). Thus, epigenetic imprinted gene biomarkers significantly improve bronchoscopy diagnostic accuracy by 18.7% (98.7% vs 80%), while demonstrating even higher specificity (100% vs 94-96%). Conclusions: Epigenetic imprinted gene biomarkers are shown to be highly accurate in effectively differentiating benign lesions and malignant lung cancer cases. In addition, the improved accuracy demonstrated by QCIGISH over standard presurgical bronchoscopy diagnostic procedures makes it a viable and revolutionary epigenetics-based cancer detection method for practical clinical applications especially for small samples and less advanced grades of lung cancer.
Multiple immune features based signature for predicting recurrence and survival of inoperable la-NSCLC patients.
Authors: Guo Meiying , Li Wanlong , Fan Bingjie , Zou Bing , Sun Xindong , Yu Jinming , Wang Linlin 
Published: May 2020

e21066 Background: The immune status of tumor microenvironment is extremely complex. One single immune feature cannot reflect the integral immune status and its prognostic value was limited. We postulated that the immune signature based on multiple immuno-features could markedly improve the prediction of post-chemoradiotherapeutic survival in inoperable locally advanced non-small-cell lung cancer (LA-NSCLC) patients. Methods: In this study, 100 patients who were diagnosed as inoperable LA-NSCLC between January 2005 and January 2016 were analyzed. A 5-immune feature-based signature was then constructed using the nested repeat 10-fold cross validation with LASSO Cox regression model. Nomograms were then established for predicting prognosis. Results: Immune signature combining 5 immuno-features were significantly associated with OS and PFS (P = 0.002 and P = 0.014, respectively) in patients with inoperable LA-NSCLC, and at a cutoff of -0.198 stratified patients into two groups with 5-year OS rates of 39.8% and 8.8%, and 2-year PFS rates of 22.2% and 5.5% for the high- and low-immune signature groups, respectively. Using immune signature, we proposed immune signature nomograms, which were better than the traditional TNM staging system in terms of discriminating ability (OS: 0.692 vs. 0.588; PFS: 0.672 vs. 0.586, respectively) or net weight classification (OS: 32.96%; PFS: 9.22%), suggesting that immune signature plays a complementary role in the prognosis prediction of patients with inoperable LA-NSCLC. Conclusions: Multiple immune features based immune signature could effectively predict recurrence and survival of inoperable LA-NSCLC patients, and complemented the prognostic value of the TNM staging system.