bluuebunny/crossref_metadata_2025_split huggingface dataset:
Revealing distinct immune landscape in EGFR mutant and EGFR wild type lung adenocarcinoma by using single-cell RNA sequencing.
Authors: Yin Tianwen , Liu Chao , Lei Tianyu , Wang Peiliang , Bai Menglin , Yu Jinming , Teng Feifei 
Published: June 2023

e21008 Background: Non-small cell lung cancer (NSCLC) with EGFR mutations displays heterogeneity in the extent of intratumoral immunocytes infiltration compared to those with EGFR wild types, which may explain their variable responsiveness to PD-1 blockade. Here, we performed single-cell RNA sequencing (scRNA-seq) to unveil the immunescape and heterogeneity of lung adenocarcinoma (LUAD) between EGFR mutant (EGFR-mut) patients and wild type (EGFR-wt) patients. Methods: Eleven EGFR-mut and 7 EGFR-wt NSCLC tumor samples were analyzed. Immune cells (CD45+) were enriched through fluorescence-activated cell sorting (FACS) and subjected to single-cell RNA sequencing (scRNA-seq) using the 10X Genomics platform. Sequencing reads were normalized and analyzed using the R/Seurat package. Cellular components of each sample were determined based on known marker genes. Wilcox test was used to compare promotion by subtype composition and immune cell infiltrates. Results: Different immune cell compositions were observed between EGFR-mut and EGFR-wt LUAD tumor samples. We found EGFR-wt tumors are marked by an enrichment of CCL15+ tumor-associated macrophages(TAMs), which display pro-inflammatory properties and high expressions of TNF-a-signaling genes. In contrast, EGFR-mut tumors exhibit enrichment of SPARCL1+TAMs, which are involved in epithelial-mesenchymal transition (EMT) and angiogenesis. EGFR-wt tumors exhibited enrichment of CD8-Teff-MX1 and Gamma delta T cells, both of which displayed higher cytotoxic and naive features. Moreover, the high expression of Gamma delta T corresponds with a better clinical prognosis. In contrast, CD8-Teff-XCL1 and NKT-FGFBP2 were found enriched in EGFR-mut tumors, both of which contributed to higher exhaustion and decreased cytotoxic function. Additionally, NK-IL32 was found enriched in EGFR-mut tumors, showing a downregulated T cell receptor signaling and stronger exhausted features. The high expression of this subcluster correlated with poor outcomes in LUAD patients harboring EGFR mutation. Conclusions: Our study provided a deeper understanding of the immune landscape of EGFR-mut and EGFR-wt LUAD and gained better insights into the immunological mechanisms involved in the response to ICIs. The results of our study could be instructive for the development of future immunotherapy strategies for NSCLC patients harboring EGFR mutations.
Single cell RNA sequencing to reveal immune microenvironment in primary and brain metastatic lesion of non-small cell lung cancer.
Authors: Teng Feifei , Bai Menglin , Liu Chao , Li Xiaohui , Meng Xiangji , Wang Peiliang , Yu Jinming 
Published: June 2023

e21009 Background: Despite immune checkpoint inhibitors (ICIs) have been proven effective in patients with advanced NSCLC, suboptimal therapeutic responses are seen in brain metastatic lesions. The heterogeneous cellular components in the tumor immune microenvironment (TIME) pose a challenge in understanding the low immune response. A comprehensive understanding of the heterogeneous TIME in primary and brain metastatic NSCLC is currently lacking, but crucial for improving ICI therapeutic responses in NSCLC patients with brain metastasis. Therefore, we use single cell RNA sequencing (scRNA-seq) to reveal distinct immune microenvironment in primary and brain metastatic lesion of NSCLC. Methods: Eight primary and nine brain metastatic NSCLC tumor samples were obtained through surgical resection. Immune cells (CD45+) were enriched through fluorescence-activated cell sorting (FACS) and subjected to scRNA-seq using the 10X Genomics platform. Sequencing reads were normalized and analyzed using R/Seurat package. Cellular components of each sample were determined based on known marker genes. Results: In our study, we observed a significant difference in the immune cell composition between primary and brain metastatic tumor samples. We found brain metastatic tumors are marked by an enrichment of TIMP1+ monocytes and PLTP+ tumor-associated macrophages (TAMs), both of which display heightened anti-inflammatory properties. In contrast, primary tumors exhibit an enrichment of FCN1+ monocytes and MARCO+ TAMs. Further analysis has revealed that the enrichment of TIMP1+ monocytes and PLTP+ TAMs is associated with a worse prognosis in patients receiving immunotherapy. Additionally, our examination of the transcriptome profile of CD8+ T cells showed an upregulation of inhibitory and exhausted signatures in brain metastatic tumor samples. Conclusions: Our study provided a comprehensive understanding of the TIME of primary and brain metastatic NSCLC and to gain deeper insights into the immunological mechanisms involved in the response to ICIs. The results of our study could prove valuable for the development of future immunotherapy strategies for NSCLC patients with brain metastasis.
Does the landscape of comprehensive genomic profiling in patients with advanced stage lung cancer in India differ from data from the western countries.
Authors: Bahl Ankur , Raizada Niti , Dhar Aparna , Agarwal Amit , Bajaj Rajat , Rohatgi Nitesh 
Published: June 2023

e21011 Background: Lung cancer is one of the leading causes of cancer related deaths worldwide and India. The understanding of the molecular basis of lung cancer has led to increased number of FDA approved targeted therapies and therefore survival. Data on the molecular landscape of lung cancers has a preponderance of western and east Asia. India while may harbour one third of world new lung cancer case, the understanding of comprehensive molecular landscape of lung cancer in India is poor. Methods: We have retrospectively compared comprehensive genomic profiling of lung cancer patients across three centres over a period of two years using foundation one cdx. We aim to compare this to available data from rest of the world and present the differences and commonalities. We believe this will help understand both differences in presentations and pattern of disease as well as question if treatment algorithms should be same or different. At least on this occasion we will limit our study to foundation one CDx patients only so that comparison with western data is not confounded by differences in technology. Results: We have Highlighted 44 such patients and will be comparing their data to the available data on foundation on CDX from available literature. 27 (61.3%) patients had one of the most common targetable mutations including EGFR ALK ROS MET BRAF ERBB2 and NTRK. Surprisingly 9(20.4%) had mutations in the homologus repair pathway. 3 patients also had MSI High. We will present comparison of this Indian data to that's available across the world. Conclusions: Precision Oncology and molecular biology is cornerstone of cancer care especially in Lung Cancer. We want to deepen the understanding of the comparison of Indian cohort and believe its different with arguably more targetable abnormalities detected than in the west and similar to the eastern population of the world.
Comparison of mutation detection rate between cell pellet DNA and cell-free DNA from cerebrospinal fluid in patients with advanced lung cancer.
Authors: Hu Shukun , Wang Xue , Peisu Suo , Li Yingmei , Chen Shifu , Zhang Yi 
Published: June 2023

e21014 Background: Liquid biopsy of cerebrospinal fluid (CSF) has been approved to be a promising strategy for molecular pathology testing in patients with lung cancer. Numerous studies showed that CSF-derived DNA can recapitulate the molecular characteristics of metastatic lung cancer. However, differences in mutation detection rate and the overall mutational profile between cell pellet DNA and supernatant cell-free DNA (cfDNA) from CSF in patients with lung cancer have rarely been reported. Methods: Matched CSF cell pellet and supernatant sample sets were selected from 51 lung cancer patients in our sequencing center. CSF was centrifuged (1000g, 10 min) to separate the cell pellet and supernatant components. Cellular DNA and cfDNA were extracted and underwent library preparation procedures for next-generation sequencing respectively. Cut adapter, mapping, fusion calling and cnv calling were performed for sequencing data analysis. Results: At the sample level, gene mutation could be detected in both CSF cell pellet and cfDNA, and the positive detection rate of gene mutation was consistent. The positive percent agreement (PPA) of CSF cfDNA sequencing compared with CSF cell pellet DNA was 93%. At the genetic variation level, 223 gene mutation sites were detected, and the positive rate of gene mutation in the CSF cfDNA (32.51%) was significantly higher than that in the CSF cell pellet (10.74%, p＜0.01). Additionally，the variation rate of less than 1% was defined as the low-frequency mutation range. Results showed that variant allele frequency (VAF) in CSF cfDNA were remarkably higher than those in the CSF cell pellet in both low-and high-frequency mutation ranges ( p＜0.01, p＜0.01). Conclusions: Both cell pellet DNA and cfDNA isolated from CSF can be used for molecular subtyping of lung cancer. Given that CSF is inevitably contaminated with blood cells in clinical procedures, the dynamic range of tumor cells in CSF could be quite large. CSF cfDNA better recapitulate the mutational status and is recommended to consider first for liquid biopsy in advanced lung cancer with brain metastases or suspicious brain metastases. Key words: Next-generation sequencing; CSF; cell pellet DNA; cfDNA; advanced lung cancer.
RNA sequencing to characterize pathways in EGFR-mutated non-small cell lung cancer.
Authors: Yun Nicole , Naqib Ankur D , Borgia Jeffrey Allen , Batus Marta , Fidler Mary Jo J. 
Published: June 2023

e21019 Background: The purpose of our study is to explore patterns in gene expression for patients with EGFR-mutated non-small cell lung cancer (NSCLC). Methods: 287 patients with EGFR-mutated lung cancer were identified using the Tempus Lens database. Raw RNA sequence expression data was requested from TEMPUS XT RNA analysis. Sequences were processed through the EdgeR analysis in the R programming environment. Differential abundance analysis was done to further filter out genes and Benjamini-Hochberg correction selected genes with a corrected p-value of < 0.05 for further pathway analysis. Pathway analysis was performed using GSEA (Gene Set Enrichment Analysis). Enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and GSEA Molecular Signatures Database (MsigDB) was performed for overexpressed and under-expressed genes in patients. Results: Pathway analysis run against the KEGG reference database and GSEA MSigDB helped to illustrate genes shared in activated and suppressed pathways in our patient cohort. For example, using the KEGG reference database, enriched pathways meeting p value significance threshold of < 0.005 included the nicotine addiction, olfactory transduction, and cortisol synthesis and secretion pathways, amongst others. Suppressed pathways using the KEGG reference database meeting p value significance threshold of < 0.005 included fat digestion and absorption, vitamin digestion and absorption, PPAR signaling pathway, and drug metabolism by cytochrome P450 and other enzymes. Using the GSEA MSigDB, enriched pathways included G protein-coupled receptor activity, sensory perception, synaptic signaling and trans-synaptic signaling, meanwhile suppressed pathways included cytolysis by host of symbiont cells, negative regulation of very-low-density lipoprotein particle remodeling, and oxidoreductase activity. Conclusions: Patterns in gene and pathway expression were observed in our cohort of patients with EGFR-mutated NSCLC. Analyzing RNA sequencing pathways showed differential up and down regulation of multiple pathways. For example, suppression of the fat and vitamin digestion and absorption pathways may shed light on processes involved in cancer cachexia and metabolism. Though further work needs to be done, RNA sequencing results for patients with EGFR-mutated lung cancer may lead to information on cancer development and additional therapeutic targets.
Effect of bevacizumab plus double dose icotinib on advanced non-small cell lung cancer with EGFR L858R mutation.
Authors: Jiang Zhansheng , Li Yong , Yan Zhuchen , Lan Lan , Zhang Xinwei , Ren Baozhu , Wang Fei , Zhang Wencheng , Pan Zhanyu 
Published: June 2023

e21020 Background: Double-dose icotinib has been proven effective and well tolerated for advanced NSCLC patients with the Epidermal Growth Factor Receptor (EGFR) L858R mutation. For the same patients, the excellent efficacy of bevacizumab combined with erlotinib has been proven in previous studies. In this study, we would investigate the efficacy of the combined therapy bevacizumab and double-dose icotinib for advanced NSCLC patients with EGFR L858R mutation. Methods: 35 patients diagnosed from September 2, 2021 to September 28, 2022 were enrolled in this study and 5 patients were excluded for analysis due to missing efficacy evaluation data. All patients were treated with intravenous bevacizumab (15mg / kg) combined with oral double-dose icotinib (250mg, tid). The primary endpoint was progression-free survival (PFS), and the secondary endpoints were safety, efficacy, and overall survival (OS). Results: Among the 35 patients, 12 were male and 23 were female. The median age at diagnosis was 66. Eight patients were diagnosed with brain metastases. All of the patients have EGFR L858R mutation, and 14 patients were with other coexisting mutations. To the data of December 31, 2022, the median follow-up time was 10 months (range: 3 to 18 months). For 30 patients with complete efficacy evaluation data, 20 patients achieved partial responses (PR), 9 patients had stable disease (SD), and 1 patient developed progress disease (PD). The objective response rate (ORR) was 66.7%, the disease control rate (DCR) was 96.7%, and the median PFS was 14.8 months. For adverse reaction evaluation, the grade 3 adverse events were albuminuria (n = 1) and hepatotoxicity (n = 1). Other adverse events were grade 1-2, mainly oral mucositis, rash, diarrhea and hypertension. Conclusions: The combination of bevacizumab with double-dose icotinib is an effective and relatively safe treatment for advanced NSCLC patients with EGFR L858R mutation. Further exploration will provide more evidence for this type of treatment. Clinical trial information: NCT05263947 .
A series of nine newly developed techniques in CT-guided percutaneous lung biopsyPreliminary results from a prospective study.
Authors: Zhang Hanxi , Wang Xiaolu , Lv Xin , Zhou Xia , Liu Baorui , Wang Lifeng , Li Rutian 
Published: June 2023

e21023 Background: CT-guided percutaneous lung biopsy is important for the diagnosis of lung cancer especially in the area of precision medicine. In ASCO 2015, we reported that "Liquid withdraw" technique (to inject small amount of liquid while withdraw of the needle) can prominently reduce incidence of pneumothorax when combined with co-axial technigue in 38 cases. In ASCO 2017, we retrospectively studied 90 patients undergoing CT-guided percutaneous lung biopsy to investigate the role of this technigue in reducing complications and promoting biopsy effectiveness. Based on the above studies, we conducted a prospective study to further evaluate the role of this technique in conjunction with the other eight techniques (Position compensation, Cushion for position adjustment, Skin expansion in advance, Secondary location outside the pleura, Needle core instantaneous replacement, Mutual fix, Simultaneous bleeding arrest, and Cortical displacement) in the precision diagnosis and treatment of lung cancer. Methods: From January 16th, 2018 to October 11th, 2021, a total of 150 CT-guided percutaneous transthoracic biopsy procedures performed in 146 patients were prospectively evaluated. The pathologies and complications secondary to biopsy procedure were analyzed. Pneumothorax and bleeding was graded as mild/very mild, moderate, and severe. All patients were divided into two groups: the lesion depth was < 30mm from the pleura and ≥30mm from pleura. Different complications between the two groups were analyzed using Pearson’s Chi-squared test for categorical values. Results: 148 cases was diagnosed out of 150 biopsies (98.67%), of which 118 cases were malignant (108 cases can be identified which type and source (91.53%), in which 68 cases were adenocarcinoma), 30 cases were benign. Pneumothorax occurred in 27 (18%) cases, among which, 12% were very mild pneumothorax and 6% were mild to moderate pneumothorax. 44 cases (29.33%) happened bleeding, among which, 21.33% could be classified as very mild, while 8% could be classified as mild to moderate. No infection, tumor implantation or aeroembolism observed. There were no statistically significant differences in the incidence of pneumothorax and bleeding at different distances from the pleura( < 30mm vs ≥30mm, P＞0.05). Conclusions: This series of new techniques in CT-guided percutaneous lung biopsy significantly reduced the incidence of pneumothorax and bleeding and were preliminarily proved that can facilitate acquiring more tumor tissue for molecular testing and re-biopsy of lung cancer. Clinical trial information: ChiCTR1800017958 .
Sex- and co-mutation-dependent prognosis of patients with SMARCA4-mutated malignancies.
Authors: Pan Minggui , Jiang Chen , Achacoso Ninah , Solorzano-Pinto Aleyda V , Tse Pamela , Suga Jennifer Marie , Thomas Sachdev P. , Habel Laurel A. 
Published: June 2023

e21031 Background: Whether sex and co-mutations impact prognosis of patients with SMARCA4-mutated (mutSMARCA4) malignancies is not clear. Methods: This cohort included patients from Northern California Kaiser Permanente with next-generation sequencing (NGS) performed from August 2020 to October 2022. We used Cox regression modeling to examine the association between sex and overall survival (OS), adjusting for demographics, performance status, Charlson comorbidity index, receipt of treatment, tumor mutation burden (TMB), and TP53, KRAS, CDKN2A and STK11 co-mutations. Results: Out of 9221 cases with NGS performed, 125 cases (1.3%) had a mut SMARCA4. The most common malignancies with a mutSMARCA4 were non-small cell lung cancer (NSCLC, 35.2%), esophageal and stomach adenocarcinoma (12.8%), and cancer of unknown primary (11.2%). The most common co-mutations were p53 (mutp53, 59.2%), KRAS (mutKRAS, 28.8%), CDKN2A (mutCDKN2A, 31.2%) and STK11 (12.8%) mutations. Male patients had substantially worse OS than female patients both among the entire cohort (HR = 1.76, [95% CI .94-3.30]) with a median OS of 3.0 versus 43.3 months ( P < .001), and among NSCLC cohort (HR = 9.72, [95% CI 2.19-43.19]) with a median OS of 2.75 months versus un-estimable ( P = .02). Among the entire cohort, mutp53 versus wtp53 (HR = 2.16, [95% CI 1.06-4.41]) and mutSTJ11 versus wtSTK11 (HR = 3.09, [95% CI 1.10-8.68]) were associated with worse OS. Among NSCLC cohort, mutp53 versus wtp53 (HR = .20, [.03-1.31]) and mutKRAS versus wtKRAS (HR = .13, [.01-1.03]) were associated with better OS, while mutCDKN2A versus wtCDKN2A (HR = 4.38, [1.13-16.9]) and mutSTK11 versus wtSTK11 (HR = 18.1, [95% CI 1.30-251]) were associated with worse OS. Conclusions: Male patients had substantially worse prognosis than female patients, while MutTP53, mutKRAS, mutCDKN2A and mutSTK11 were differentially associated with prognosis among the entire cohort and among NSCLC cohort. Our results, if confirmed, could suggest potentially unidentified mechanisms that underly this sex and co-mutation-dependent prognostic disparity among patients whose tumor bears a mutSMARCA4.
Cerebrospinal fluid circulating tumor DNA for the detection and characterization of leptomeningeal metastasis in non-small cell lung cancer.
Authors: Miao Qian , Zheng Xinlong , Zheng Xiaobin , Jiang Kan , Lin Gen , Zhang Longfeng 
Published: June 2023

e21039 Background: Cerebrospinal fluid (CSF) has revealed the unique genetic characteristics of leptomeningeal metastasis (LM) from non-small cell lung cancer (NSCLC). However, the research in this area is still very limited. Methods: Patients with LM from NSCLC were retrospectively analyzed. Circulating tumor DNA (ctDNA) of CSFand pairedextracranial tissue or plasma were tested by ARMS or next-generation sequencing(NGS).Clinical outcomes were compared with Kaplan-Meier log-rank test and Coxproportional hazards methodologies. Results: We reviewed charts of 80 patients with LM treated atFujian Cancer Hospital. A total of 57 CSF and of which 30 contemporaneouslypaired extracranial samples tested by NGS were analyzed. Most interestingly, CSF ctDNA revealed EGFR mutations in 4 patients previously diagnosed as wild-type by extracranial specimens, and survival was extended by targeted therapy. In the gene map of paired samples, CSF showed more abundant cell-cycle regulatory genes and complex independent evolutionary. CDKN2A/2B CNVs-del was enriched threefold in CSF (~26.3%) with LM compared to extracranial specimens (~8.9%)in lung adenocarcinoma without LM. The median overall survival (OS) was 14.1 months [95% confidence interval (CI): 10.7–17.5 months]. Univariate analyses and multivariate Cox analyses demonstrated that patients with CDKN2A/CDKN2Bco-mutation had poor prognosis. Conclusions: CSF-based ctDNA testing contributes to the phenotypic detection and unique characterization of resistance mechanisms of LM in NSCLC. CDKN2A/2B mutation maybe a poor prognostic factor in LM patients.