Publications by authors named "Tongji Xie"

Background: Existing biomarkers and models for predicting response to programmed cell death protein 1 monoclonal antibody in advanced squamous-cell non-small cell lung cancer (sqNSCLC) did not have enough accuracy. We used data from the ORIENT-3 study to construct artificial neural network (ANN) systems to predict the response to sintilimab for sqNSCLC.

Methods: Four ANN systems based on bulk RNA data to predict disease control (DC), immune DC (iDC), objective response (OR) and immune OR (iOR) were constructed and tested for patients with sqNSCLC treated with sintilimab.

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Background: Microvascular invasion (MVI) is a critical prognostic factor in intrahepatic cholangiocarcinoma (ICC), strongly associated with postoperative recurrence. However, the phenotypic features and spatial organization of MVI remain inadequately understood.

Methods: We performed a spatial transcriptomic analysis on 29,632 spots from six ICC samples, manually delineating MVI clusters using the cloupe software.

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Intra-tumor immune infiltration plays a pivotal role in the interaction with tumor cells in hepatocellular carcinoma (HCC). However, its phenotype and related spatial structure remained elusive. To address these limitations, we conducted a comprehensive study combining spatial data (38,191 spots from eight samples) and single-cell data (56,022 cells from 20 samples).

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Intra-tumor immune infiltration is a crucial element interacting with tumor cells in intrahepatic cholangiocarcinoma (ICC). However, its phenotype and related spatial structure remained elusive. To address these limitations, we undertook a comprehensive study combining spatial data (29,632 spots from six samples) and single-cell data (21,158 cells from 35 samples).

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Spread through air spaces (STAS) is a recognized aggressive pattern in lung cancer, serving as a crucial risk factor for postoperative recurrence. However, its phenotype and related spatial structure have remained elusive. To address these limitations, we conducted a comprehensive study based on spatial data, analyzing over 30,000 spots from 14 non-STAS samples and one STAS sample.

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Patients with relapsed/refractory (r/r) diffuse large B-cell lymphoma (DLBCL) show varied responses to PD-1 monoclonal antibody (mAb) containing regimens. The mechanisms and predictive biomarkers for the efficacy of this regimen are unclear. This study retrospectively collected r/r DLBCL patients who received PD-1 mAb and rituximab regimens as salvage therapy.

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Small-cell lung cancer (SCLC) transformation accounts for 3-14% of resistance in EGFR-TKI relapsed lung adenocarcinomas (LUADs), with unknown molecular mechanisms and optimal treatment strategies. We performed transcriptomic analyses (including bulk and spatial transcriptomics) and multiplex immunofluorescence on pre-treated samples from LUADs without transformation after EGFR-TKI treatment (LUAD-NT), primary SCLCs (SCLC-P) and LUADs with transformation after EGFR-TKI treatment (before transformation: LUAD-BT; after transformation: SCLC-AT). Our study found that LUAD-BT exhibited potential transcriptomic characteristics for transformation compared with LUAD-NT.

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Article Synopsis
  • Intra-tumour immune infiltration significantly impacts the effectiveness of immunotherapy in non-small cell lung cancer (NSCLC), with two key patterns identified: immune exclusion (linked with myeloid cells) and immune activation (linked with plasma cells).
  • The study found that immune exclusion is associated with poor patient survival due to increased epithelial–mesenchymal transition and reduced immune activity, particularly marked by the presence of CD14+APOE+ cells and MMP7+ tumour cells.
  • Additionally, patients in an immunotherapy trial showing worse responses had higher levels of CD14+APOE+ and MMP7+ cells, revealing a critical link between these cell types and immune resistance mechanisms in NSCLC.
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Introduction: Identifying new biomarkers for predicting immune checkpoint inhibitors (ICIs) response in non-small cell lung cancer (NSCLC) is crucial. We aimed to assess the variant allele frequency (VAF)-related profile as a novel biomarker for NSCLC personalized therapy.

Methods: We utilized genomic data of 915 NSCLC patients via cBioPortal and a local cohort of 23 patients for model construction and mutational analysis.

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Background: Diffuse large B-cell lymphoma (DLBCL) is a heterogeneous malignancy characterized by varied responses to treatment and prognoses. Understanding the metabolic characteristics driving DLBCL progression is crucial for developing personalized therapies.

Methods: This study utilized multiple omics technologies including single-cell transcriptomics (n = 5), bulk transcriptomics (n = 966), spatial transcriptomics (n = 10), immunohistochemistry (n = 34), multiple immunofluorescence (n = 20) and to elucidate the metabolic features of highly malignant DLBCL cells and tumor-associated macrophages (TAMs), along with their associated tumor microenvironment.

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In hepatocellular carcinoma (HCC), classical cancer stem cells (CSC) markers were shared by normal stem cells, targeting which may hinder hepatic regeneration and cause liver failure. Additionally, the spatial structure of CSC still remained elusive. To address these limitations, we undertook a comprehensive study combining single-cell data (56,022 cells from 20 samples) and spatial data (38,191 spots from eight samples) to obtain CSC signature and uncover its spatial structure.

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Article Synopsis
  • Chemoimmunotherapy is a common treatment for advanced non-small cell lung cancer (aNSCLC), but drug resistance limits its effectiveness, creating a need for reliable biomarkers to predict patient responses.
  • Researchers conducted a three-phase study to identify and validate specific autoantibodies (AAbs) from 528 plasma samples of aNSCLC patients before and after treatment, using various microarray techniques and statistical analyses.
  • They discovered two AAbs (MAX and DHX29) as pre-treatment biomarkers and two others (MAX and TAPBP) as predictive markers during treatment, with all showing significant correlations to patient outcomes like response rates and progression-free survival.
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Background: R-CHOP (rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone) is a standard first-line treatment for diffuse large B-cell lymphoma (DLBCL). However, 20%-40% of patients survive less than 5 years. Novel prognostic biomarkers remain in demand.

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Senescent tumor cells (STCs) can induce immunosuppression, promoting tumor progression and therapy resistance. However, the specific characteristics of immunosuppressive STC have not been thoroughly investigated. This study aimed to characterize and elucidate the immunosuppressive phenotype of STC in lung adenocarcinoma by employing single-cell and bulk transcriptomics, as well as serum proteomics profiling.

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Background: TP53 mutation heterogeneity should be considered when using TP53 as a predictive biomarker for anti-programmed death (ligand) 1 (PD-(L)1) monotherapy in lung adenocarcinoma (LUAD). However, whether TP53 variant allele frequency (VAF) should also be considered remains unknown.

Methods: Patients with LUAD from both published research and the local cohort were included to discover and validate the relationship between TP53 VAF and the efficacy of PD-(L)1 inhibitors.

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Article Synopsis
  • Researchers identified a gene signature related to antigen-presenting, T, and NK cells (ATNKGS) that can help predict the risk and treatment outcomes for lung adenocarcinoma (LUAD) patients.
  • They developed a risk model based on 16 genes, determining that high-risk patients had significantly worse overall survival compared to low-risk patients, validated across multiple datasets.
  • Additionally, the gene CTSL was linked to immune responses and poor prognosis in LUAD, but its high expression correlated with favorable responses to immune checkpoint inhibitors in therapy.
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Background: The brain is a common metastatic site in patients with non-small cell lung cancer (NSCLC), resulting in a relatively poor prognosis. Systemic therapy with epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitors (TKIs) is recommended as the first-line treatment for EGFR -mutated, advanced NSCLC patients. However, intracranial activity varies in different drugs.

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Background: Pulmonary large cell neuroendocrine carcinoma (LCNEC) and small cell lung cancer (SCLC) are two types of high-grade neuroendocrine carcinomas of the lung with poor prognosis. LCNEC has not been thoroughly studied due to its rarity, data are also lacking regarding the survival comparison and prognosis analysis of patients with locally advanced or metastatic LCNEC and SCLC.

Methods: Data of patients with LCNEC, SCLC, and other NSCLC who were diagnosed from 1975 to 2019 were extracted from the Surveillance, Epidemiology and End Results (SEER) database to estimate incidence.

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An emerging view regarding cancer-associated fibroblast (CAF) is that it plays a critical role in tumorigenesis and immunosuppression in the tumor microenvironment (TME), but the clinical significance and biological functions of CAFs in non-small cell lung cancer (NSCLC) are still poorly explored. Here, we aimed to identify the CAF-related signature for NSCLC through integrative analyses of bulk and single-cell genomics, transcriptomics, and proteomics profiling. Using CAF marker genes identified in weighted gene co-expression network analysis (WGCNA), we constructed and validated a CAF-based risk model that stratifies patients into two prognostic groups from four independent NSCLC cohorts.

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Introduction: Dysregulated ARID1A expression is frequently detected in lung adenocarcinoma (LUAD) and mediates significant changes in cancer behaviors and a poor prognosis. ARID1A deficiency in LUAD enhances proliferation and metastasis, which could be induced by activation of the Akt signaling pathway. However, no further exploration of the mechanisms has been performed.

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To find biomarkers for immunity and immunotherapy in lung adenocarcinoma (LUAD) through multiomics analysis. The multiomics data of patients with LUAD were downloaded from the TCGA and GEO databases. CIBERSORT, quanTIseq, ESTIMATEScore, k-means clustering, gene set enrichment analysis, gene set variation analysis, immunophenoscore and logistic regression were used in this study.

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Unlabelled: Brain metastases (BM) is one of the main reasons for lung cancer-related deaths but lack prediction methods. Many patients with BMs do not benefit from immunotherapy. A comprehensive genomic analysis of matched primary tumors (PT) and their BM lesions may provide new insight into the evolutionary and immune characteristics.

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Esophageal basaloid squamous cell carcinoma (bSCC) is a subtype of squamous cell carcinoma (SCC) with a different behavior and poor prognosis. Exploring bSCC's molecular characteristics and treatment strategies are of great clinical significance. We performed multi-omics analysis of paired bSCC and common SCC (cSCC) using whole exome sequencing and a NanoString nCounter gene expression panel.

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Background: It is still an unmet clinical need to identify potent biomarkers for immunotherapy on patients with lung squamous cell carcinoma (LUSC).

Methods: In this study, we explored the differentially expressed genes (DEGs) that were simultaneously correlated with four pathways (i.e.

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Introduction: EGFR mutations in non-small cell lung cancer (NSCLC) are associated with a poor response to immune checkpoint inhibitors (ICIs), and only 20% of NSCLC patients harboring EGFR mutations benefit from immunotherapy. Novel biomarkers or therapeutics are needed to predict NSCLC prognosis and enhance the efficacy of ICIs in NSCLC patients harboring EGFR mutations, especially lung adenocarcinoma (LUAD) patients, who account for approximately 40-50% of all NSCLC cases.

Methods: An ARID1A-knockdown (ARID1A-KD) EGFR-mutant LUAD cell line was constructed using lentivirus.

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