bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive immune cell analysis from lung cancer patients with PD-1 inhibitor neoadjuvant immunotherapy using single cell sequencing.
Authors: Hui Zhenzhen , Zhang Jiali , Xiao Shanshan , Pu Yue , Lin Rui , Wang Tao , You Jian , Ren Xiubao 
Published: May 2020

e21001 Background: Single-cell RNA sequencing (scRNA-seq) is a powerful tool to investigate the tumor microenvironment including infiltration of different types of immune cells. However, there is limited study utilizing scRNA-seq technology to investigate patient response to immunotherapy using a comprehensive set of samples. In this study, we used scRNA-seq approach to study tumor infiltrating immune cells in lung cancer patients receiving PD-1 inhibitor neoadjuvant immunotherapy. Methods: CD45 cells were collected from the tumor tissues, the adjacent normal tissues, peripheral blood, lymph nodes, and normal lung tissues for three lung cancer patients receiving PD-1 inhibitor neoadjuvant immunotherapy and four treatment naive lung cancer patients, followed by single cell library construction using 10x Genomics technology and sequenced on Illumina HiSeq X-Ten platform. CellRanger was used to generate expression matrices, and Seurat was used to identify cell subpopulations. Results: From a total of 62,970 single cells, we identified 23 clusters that belonged to different types of immune cells including myeloid cells, T cells, NK cells, mast cells, and B cells. Compared with the adjacent normal tissues, the tumor tissues had lower proportion of NK cells and higher percentage of B cells in all but one patient, and higher percentage of Treg cells for all the seven patients. We observed that patients treated with neoadjuvant immunotherapy had higher proportion of tumor-infiltrating T cells and lower percentage of myeloid cells compared with the treatment naive patients. Patients in the two groups showed differential gene expression in categories including leukocyte cell-cell adhesion, and cell-cycle arrest. Furthermore, the three patients undergoing immunotherapy had different response; the gene expression pattern for the patients differed in functional groups including regulation of inflammatory response, leukocyte migration, and regulation of immune effector process. These results support the potential application for scRNA-Seq in monitoring patient response to neoadjuvant immunotherapy. Conclusions: scRNA-Seq technology can detect the composition of tumor-infiltrating immune cells after neoadjuvant immunotherapy, which provides new tool for predicting the efficacy of treatment. We will next focus on the gene expression of tumor-infiltrating Treg cells and its effect on the therapeutic response.
Contribution of DNA damage repair gene mutations and concomitant TP53 variations to the efficacy of platinum-based chemotherapy as initial therapeutic option in Chinese NSCLC patients.
Authors: Ma Ke , Peng Jun , Zhang Huachuan , He Jintao , Xiao Bo , Zhu Jiang , Zhu Changbin , Rong Hao 
Published: May 2020

e21002 Background: Though targeted, immune-, even combinational therapies have been applied widely, platinum-based chemotherapy still plays irreplaceable role as initial management for patient with either resected or advanced NSCLC without actionable target. Platinum is sought to increase DNA damage burden inducing cell death, especially in cells with intrinsic DNA damage repair (DDR) dysfunction. This study aims to explore impact of DDR genes as well as co-occurrence of TP53 mutations on prognosis of NSCLC patients. Methods: 110 NSCLC patients were consecutively recruited from 2016-2018. 508 cancer related genes were sequenced by BGI-seq 500. COX regression was used to evaluate risk of disease progression as well as cancer-related death among patients with various DDR/TP53 status. Results: 61 NSCLC patients with stage II-IV (median age of onset: 55 years) were recruited who received platinum-based therapy as adjuvant or 1st line systemic therapy. Till 15th.Oct.2019, median follow-up time was 24 months. 21 patients (34.4% of 61) carried DDR mutations. TP53 mutations were detected in 36 patients (59% of 61). 11 patients (18% of 61) displayed TP53/DDR co-mutations. COX regression analysis indicated NSCLC patients with DDR mutation would have lower risk of disease progression (HR:0.37, P = 0.19) as well as superior overall survival time (HR:0.35, P = 0.035). Patients with DDR co-mutations had no superior survival benefit. Patients with HRR mutations presented similar result. Patients with TP53 mutations had similar risk as ones with other mutations. While those with DDR concomitant mutations showed significantly improved clinical benefit (HR for PFS:0.28, P = 0.05; HR for OS:0.22, P = 0.023). Conclusions: DNA damage repair genes in Chinese NSCLC patients may play vital roles in predicting efficacy of platinum-based chemotherapy even in the context of TP53 co-mutation. Further, combination of BRCA2 and PALB2 may be better associated with patients’ prognosis. Large cohort should be set up to validate this finding in near future. [Table: see text]
The mutation frequency of HPD related genes in different lung cancer stages.
Authors: Wan Yanhui , Fang Fuyuan , Wu Guodong , Zhang Xing , Song Chao , Tian Minqi , Tang Jiyu 
Published: May 2020

e21006 Background: Clinical detections of hyper-progressive disease (HPD) gene mutations in advanced lung cancer should be considered to avoid the inappropriate immunotherapy, and recently neoadjuvnat and adjuvant immunotherapy also proved to be efficacy in early stage of lung cancer. Nevertheless, it still remains poorly understanding of the distribution of HPD related mutations in early stage lung cancer. Methods: In this study, according to information of patient specimens from public database TCGA, Ⅰ and Ⅱ stages were defined as early stage, Ⅲ and Ⅳ stages were defined as advanced stage. The mutations in HPD related genes were evaluated including CNVs of CCND1, FGF19, FGF3, FGF4, MDM2 and MDM4, and SNVs of DNMT3A. Chi-square test was performed to analyze the differences of HPD related gene mutation frequency in early and advanced stages. Results: Based on the statistics of clinical data from TCGA, we found 399 early stage cases and 110 advanced stage cases in patients with lung adenocarcinoma (LUAD), 402 early stage cases and 91 advanced stage cases in patients with lung squamous cell carcinoma (LUSC). In early stage, we found 76, 76, 76, 75, 89, 201 cases of CNVs of CCND1, FGF19, FGF3, FGF4, MDM2 and MDM4, 10 cases of SNVs of DNMT3A, respectively. In advanced stage, we counted 32, 32, 32, 29, 21, 37 cases of CNVs of CCND1, FGF19, FGF3, FGF4, MDM2 and MDM4, 4 cases of SNVs of DNMT3A, respectively. No significant differences of mutation frequency HPD related gene between early and advanced stages were found via χ2 test. CNVs frequencies of CCND1, FGF19, FGF3, FGF4 and MDM4 in LUAD were significantly lower than them in LUSC. No significant differences of CNVs frequency of MDM2 and SNVs frequency of DNMT3A beween patients with LUAD and patients with LUSC were found. Conclusions: Our analysis indicated that immunotherapy for patients with early stage lung cancer also needed to test these mutations. LUSC patients required paying more attentions on HPD related mutations of which frequencies were significantly higher than LUAD patients. As a retrospective study with a relatively small population, the conclusions of this study needed to be verified with a larger sample.
Management of bronchopulmonary carcinoid: NCDB database analysis.
Authors: Zhu Mojun , Fuentes Harry E , Westin Gustavo Figueiredo Marcondes , Sonbol Mohamad Bassam , Leventakos Konstantinos , Wigle Dennis A. , Jaroszewski Dawn E. , Molina Julian R. , Halfdanarson Thorvardur Ragnar 
Published: May 2020

e21007 Background: There is a lack of data to guide the management of resectable bronchopulmonary carcinoid tumors (BCTs). Methods: The NCDB database was retrospectively reviewed to analyze the roles of surgery, chemotherapy and radiation. Patients with a diagnosis of clinically staged T1-2/N0-1 typical carcinoid (TC) and atypical carcinoid (AC) between 2004-2012 were included. Kaplan-Meier methods and multivariable analysis were performed. Results: A total of 2148 patients (TC 1874 & AC 274; T1/1648 & T2/500) were identified. The median age was 59 (range 18-89). There was a female (69.7%) and right lung (56.9%) predominance. Fifty-three patients received pneumonectomy, 68 chemotherapy, and 84 radiation therapy. The impact of age, histology (TC vs. AC), medical comorbidities (Charlson/Deyo score 0 vs. ≥1) and type of surgery [sublobar resection (SR) vs. lobectomy vs. lobectomy with mediastinal lymph node dissection (L/MLND)] were subsequently examined. AC, older age, and comorbidities were associated with shorter overall survival (OS) by both univariate and multivariable analysis. Patients who underwent lobectomy had longer OS (119 months) than those with SR (109 months) or L/MLND (115 months). However, this association was not significant by multivariable analysis with age incorporated as either a categorical ( < 60 vs. ≥60) or a continuous variable (Table). In the subgroup analysis of patients with T1, T2, TC and AC respectively, type of surgical resection was not significantly associated with OS by multivariable analysis. Conclusions: Patients with resectable BCTs have excellent OS. Atypical histology, older age, and comorbidities predicted inferior OS. There were insufficient data to support the use of perioperative chemotherapy or radiation therapy. Lobectomy was associated with prolonged OS by univariate analysis but this was not significant in the multivariable model, suggesting that SR is a reasonable approach for patients who cannot tolerate lobectomy. MLND did not seem to provide additional survival benefits. [Table: see text]
Stereotactic body radiation therapy (SBRT) in a developing country: Patterns of failure and response rates.
Authors: Przybysz Daniel 
Published: May 2020

e21010 Background: Surgery remains the treatment of choice for early stage lung cancer. For patients without clinical conditions or those who refuse to this procedure, Stereotactic Body Radiation Therapy (SBRT) is the treatment of choice. It is important to understand the patterns of treatment response and toxicities within this practice. Therefore, we aim to analyze and review our data on lung SBRT for Non-Small Cell Lung Cancer (NSCLC) treated in our institution. Purpose: To describe response and toxicity patterns for NSCLC treatment with SBRT in a single third world country private institution. Methods: We retrospectively collected and analyzed data from patients treated at a single private institution in Rio de Janeiro between January 2017 and May 2019. Inclusion criteria were histopathological diagnosis of NSCLC, 18 years old or older, SBRT treatment, who were closely followed-up according to international guidelines. All data was analyzed and reviewed by the radiation oncologist and medical oncologist responsible, as well as kept in a reliable way for future comparisons. Results: 121 patients were analyzed. 77 were excluded. Only patients diagnosed with NSCLC from 2017 to 2019 who received SBRT as primary treatment. The average age was 74 (56-94). The highest prevalence among patients were females 68% (n = 30). 26 patients were smokers (59%), 4 non-smokers (9%) and 14 patients were not recorded in the medical records. Molecular assessment for non-smokers will not be described in this study. Adenocarcinoma was the most common subtype (77%, n = 35), 15% were squamous cell carcinoma subtype (n = 7), 4.4% poorly differentiated (n = 2). The patients were distributed between early stage lung cancer and metastatic disease - foreseeing oligometastatic disease being continuously treated as potentially curable. 11 patients are not classified in the medical record. Twelve patients had metastasis: central nervous system (33%), lung (41%), bone (8.3%) and patients with more than two metastases 16.6% (bone and CNS, bone and lung). Eleven patients had adjuvant chemotherapy (QT) 25%. Ten of the patients (22%) had toxicities, all with different doses and SBRT fractions. Among them, cough was the most prevalent (40%); nausea / vomiting and rash accounted for 30%; pneumonitis accounted for 17%; and mucositis in 10% of patients. Of the 44 patients, 7 died. Conclusions: The study data corroborates the worldwide published literature. SBRT in treating early stage lung cancer is a safe and effective treatment modality, with acceptable low-grade toxicities and high response rates.
Peripheral blood leukocytes-related early diagnosis for lung cancer.
Authors: Mei Qi , Li Jian , Cheng Weiting , Mansmann Ulrich Robert , Hu Guangyuan , Yuan Xianglin 
Published: May 2020

e21020 Background: Early diagnosis of lung cancer is critically important to reduce disease severity and improve overall survival. For patients with suspicious lung lesions, a definitive diagnosis of malignant cancer currently requires surgical biopsy. Newer, minimally invasive biopsy procedures often fail to provide adequate specimens for accurate tumor subtyping or staging which is necessary to inform appropriate use of molecular targeted therapies and immune checkpoint inhibitors. Thus newer approaches to diagnosis and staging in early lung cancer are needed. Methods: In order to address this need, peripheral blood samples from 99 individuals with clinically evident pulmonary nodules (benign and malignant), as well as ten healthy persons, were obtained. Average RNA sequencing (RNAseq) data from these samples were integrated into an artificial intelligence (AI) model in order to perform a pathway flux analysis at the system level. The AI model utilized the biological knowledge derived from the literature and publicly available databases and possessed four layers with following relationship: (1) gene→ (2) RNA→ (3) protein/complex/compound → (4) pathway. The last layer (pathway) was connected back to the first layer (gene) via diverse feedback mechanisms. Based on these results, an immune index system, IM-Index, was defined and tested for early lung cancer diagnosis and staging. Results: The leukocyte-based IM-Index correctly identified the malignancy status of lung cancer patients with high accuracy (specificity 93.5%, sensitivity 70.5%), and was able to differentiate between the three accepted phases of the cancer immunoediting concept (i.e., elimination, equilibrium, escape) (odds ratio: 1.17 [95% CI: 1.1-1.25, p< 0.001). Further, the IM-Index clearly differentiated between adenocarcinoma and squamous cell carcinoma (OR: 1.2 [95% CI 1.14-1.35, p = 0.019]). In addition, tumor- and host-specific signaling pathways and metabolic profiles were identified that fully distinguished between tumor and host immunity (p < 0.05). Conclusions: Taken together, these findings suggest that our rapid, non-invasive peripheral blood leukocyte-based AI approach may be useful for early definitive cancer diagnosis and staging.
Correlation of gene expression profile to identify tumors with extreme sensitivity to the alkylating agent LP184.
Authors: Kathad Umesh , Kulkarni Aditya , Bhatia Kishor , Barnhart Kerry , Sharma Panna 
Published: May 2020

e21021 Background: Lantern Pharma is advancing LP184, a next generation alkylating acylfulvene class prodrug. LP184 damages DNA that is subject to preferential repair by Transcription-Coupled Nucleotide Excision Repair. LP184 efficacy in 35 cell lines from solid tumor origin with known transcriptomic profiles identifies gene expression patterns that strongly correlate with response in cell lines. This gene expression profile allows the interrogation of clinical transcriptomics datasets to identify tumors that would potentially be highly responsive to LP184. Methods: LP184 cytotoxicity in cell lines was tested in a concentration range from 14 nM to 10 uM. Cell viability readout using CellTiter Fluor reagent was measured 72h post drug addition, and IC50 value was generated using GraphPad Prism. Bioinformatic analyses were run using the Morpheus tool from the Broad Institute. CCLE microarray expression data were used for gene signature findings and TCGA patient data were used for gene signature validation. Results: LP184 showed broad anti-tumor cytotoxicity in solid tumor cell lines including liver, NSCLC, prostate, ovarian, kidney and thyroid cancers (median IC50: 358.9 nM). Across this spectrum, LP184 sensitivity was found to be most highly correlated with high transcript levels of PTGR1, and with low transcript levels of KDM4A. Analysis of top 10 sensitive cell lines showed that NSCLC cell lines had the highest representation (5 of 10). Differential sensitivity and gene expression pattern analyses on NSCLC cell lines correlated with high relative expression of PTGR1, CASP6, NAMPT, SMARCD3 and GLRX genes along with low relative expression of KMD4A, HPGD, PTPRF and KRT14 genes in the highly sensitive cell lines. The oxidoreductase activity of PTGR1 is likely involved in bioactivation of LP184 and CASP6 mediates drug-induced apoptosis. HPGD acts upstream of PTGR1 in the prostaglandin metabolism pathway in turn modulating the turnover of endogenous PTGR1 substrate. Assessing relative expression of these genes in selected clinical NSCLC data indicates that around 37% of such tumors would potentially respond with high sensitivity to LP184. Conclusions: Overall, LP184 is a novel alkylating agent with nanomolar potency in solid tumor cell lines, especially NSCLC, and can serve as a molecularly guided therapy option in multiple tumors. The correlated genes KDM4A/ HPGD that impart high sensitivity at low expression levels, suggest potential synergistic combinations of their respective inhibitors in development PKF118-310/ ML147 with LP184.
The impact of estrogen receptor status on EGFR/TP53/CTNNB1 axis in the evolution of non-small cell lung cancer.
Authors: Tani Yoko , Koh Yasuhiro , Tamiya Akihiro , Isa Shun-ichi , Kubo Akihito , Ando Masahiko , Saka Hideo , Izumi Motohiro , Ogawa Koichi , Matsumoto Yoshiya , Sawa Kenji , Yoshimoto Naoki , Suzumura Tomohiro , Watanabe Tetsuya , Kaneda Hiroyasu , Mitsuoka Shigeki , Asai Kazuhisa , Kawaguchi Tomoya 
Published: May 2020

e21035 Background: The role of estrogen receptor status in the carcinogenesis of lung cancer remains elusive. A census of clonal and sub-clonal mutations has been defined through the analyses of evolutionary histories of cancers. We previously reported a prospective multicenter molecular epidemiology study (JME study; Kawaguchi T, J Clin Oncol 2016), which included the expression levels of estrogen receptors β (ER) using immunohistochemistry(IHC) and the mutational profile using next generation sequencing as well as solid smoking information and reproductive/ hormonal risk factors from the detailed questionnaire. Methods: Utilizing the data of the JME study, the impact of ER in lung cancer development was explored. All the patients underwent surgery. In 441 ever- and 435 never-smokers, ER were observed in 46.4% and 53.5%, respectively. The cancer-associated 72 gene mutations and 5 gene amplifications examined in this study included EGFR, SMAD4, APC, FBXW7, BRAF, STK11, PIK3CA, TP53, PTEN, KRAS, CTNNB1, NFE2L2, NF1, and MET. ALK fusion was detected by IHC. Patients were enrolled between July 2012 and December 2013, with follow up until November 30th, 2017.Cox proportional hazards models were used to assess the ER expression on relapse free survival (RFS) and overall survival (OS). A logistic regression model was applied to assess the impact of ER (positive vs. negative) on gene alterations, using sex, smoking history, age and stage as independent variables. Results: ER expression was significantly higher in never smokers (vs. ever smokers; p = 0.022) and earlier stage (stage I vs. II-IV; p = 0.002). Patients with ER positive tumors had a longer RFS than those with negative tumors (RFS rate at 4 years: 33.7 vs. 26.5%; p = 0.021), however, there was no significant difference in OS between the two groups (p = 0.108). In the impact of ER status on the gene alterations, mutations in EGFR (p = 0.003), TP53 (p = 0.007) and CTNNB1 (p = 0.027) were significantly associated with ER expression. Multivariate analysis showed that EGFR mutations (OR = 1.394, 95%CI: 1.029-1.890, p = 0.032) and CTNNB1 mutations (OR = 0.272, 95%CI: 0.087-0.853, p = 0.026) were significantly associated with ER expression, while there was a trend for significance with TP53 mutations (OR = 0.737, 95%CI: 0.537-1.011, p = 0.059). Conclusions: ER positive status triggered the clonal EGFR mutations and suppressed the sub-clonal mutations of TP53 and CTNNB1. It is suggested that ER plays a critical role in the alterations of EGFR/TP53/ CTNNB1 axis in lung cancer evolution.
Deciphering molecular characters of multiple lung lesion using comprehensive genomic profiling and its association of histology.
Authors: Zhu Changbin , Qiu Yuan , Deng Qiuhua , Yang Haihong , Chen Hanzhang , Liu Liping , Xiao Dakai , Shao Di , Li Weiwei , Jiang Wenxi , Lin Yongping , He Jianxing 
Published: May 2020

e21051 Background: Differentiating multiple pulmonary lesions as multiple primary lung cancer (MLC) or intra-pulmonary metastasis (IPM) is critical for clinics. Radiological or histological (dis)concordance may be informative, while, genetic information may aid tracing lineage information on multiple lung lesions. This study aims to apply comprehensive genomic profiling deciphering intrinsic genetics of multiple lung lesions. Methods: 32 patients, 69 FFPE samples were applied to perform high-through put sequencing. 636 cancer-related genes were captured and sequenced by MGI-seq 2000. Raw data was processed via in-house developed pipeline. Unsupervised clustering was applied to cluster samples based on genetic characters after variant calling and annotation. Patients were categorized into “Genomic related” and “Genomic unrelated” groups. Another cohort consisting of 402 patients with mono-lesion was used as control cohort. Results: No difference of age of onset was found between 32 patients and 403 patients with mono lesion (60.5 versus 60 years). Male had relatively lower incidence of multiple lung lesions (RR:0.46,95%CI: 0.20-0.93, P = 0.04). Eight patients were classified as “Genomic related” by presenting same mutation in driver or tumor suppressor genes. Six of eight patients were characterized to carry EGFR L858R, in addition, two patients presented co-mutation of RB1(c.1814+1G > T, p.E48Kfs*18) and TP53 mutations (p.H193R, p.R249S). Another two patients carried EGFR 19 Deletion. Two lesions from one patient with predefined diagnosis of intra-pulmonary metastasis showed biallelic loss of function mutations in same loci of NF1 gene (p.S2311*/ p.Q1360*) together with same KRAS mutation (p.G13C). Radiologically, no same lobe as well as left-right preference were revealed between “Genomic related” and “Genomic unrelated” groups. Histologically, there was no enrichment of patients with same histology subtype in “genomic related” group, verse visa. While, patients in “genomic related” group had higher ages at initial diagnosis (median age 69.5 vs 56.5 years, P = 0.04). Conclusions: Comprehensive genomic profiling should be applied to clinics distinguishing the nature of multiple lung lesion irrespective of radiological and histological diagnosis. [Table: see text]