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  • American Association for Cancer Research (AACR)  (7)
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  • American Association for Cancer Research (AACR)  (7)
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  • 1
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 82, No. 12_Supplement ( 2022-06-15), p. 5916-5916
    Abstract: Background: Patient-specific flexible gene panels designed based on whole-exome sequencing (WES) of resected tumor tissues is a promising strategy for ctDNA-based detection of molecular residual disease (MRD) in early-stage NSCLC. Flexible gene panels could potentially overcome the limitations of fixed panels by incorporating more unique genomic regions that might be absent in fixed panels; however, no study has reported a head-to-head comparison of these two approaches in postoperative disease monitoring. In this study, we investigated the clinical utility of a novel Patient-specific pROgnostic and Potential tHErapeutic marker Tracking (PROPHET) tumor-informed ctDNA assay. Using the same set of longitudinal blood samples, we further compared the performance of PROPHET assay with tumor-informed (TI) and tumor-naïve (TN) fixed panels for predicting MRD and prognosis in surgical NSCLC patients. Methods: Fifty-three patients with stage I-III resected NSCLC from the MEDAL study (NCT03634826) with adequate samples and median follow-up of 647 days were analyzed. Matched surgical tumor tissue and blood samples collected at various time points, including before surgery (baseline), 3-days (B) and 1-month (C) postoperative time points before any adjuvant therapy and subsequent follow-up time points (F) were analyzed. PROPHET assay involved four major steps: identify somatic mutations using WES, customized design of a patient-specific panel consisting of 50 single nucleotide variants, ultra-deep unique molecular-identifier-based next-generation sequencing (UMI-NGS) of serial blood samples using the patient-specific panel, and MRD risk prediction. Fixed panel assay of serial blood samples was performed using UMI-NGS with 168 gene panel spanning 273 kb of human genome. Results: At 1-month post-surgery, PROPHET assay accurately predicted MRD-positive cases among relapsed patients (50%, 13/26), whereas all disease-free patients were MRD-negative (100%, 21/21). Three-year prognostication with PROPHET assay at B+C yielded higher sensitivity (59% vs 26% vs 22%), negative predictive value (66% vs 51% vs 50%), and hazard ratio (7.15, 95%CI [3.2-15.9] vs 4.48 [1.9-10.9] vs 5.58 [2.1-14.7]) as compared with TI and TN fixed panel assays. Disease monitoring using PROPHET assay at B/C/F accurately predicted the MRD risk in 70% (21/30) of relapsed patients at a median lead time of 318 days (range: 20-751), whereas TI assay predicted 43% (13/30) at 282 days (range 20-716) and TN assay predicted 37% (11/30) at 282 days (range: 20-634). Conclusion: Patient-specific tumor-informed ctDNA-based postoperative monitoring enables risk stratification at early postoperative settings better than fixed panel, which paves an alternative strategy in the individualized management of surgical NSCLC patients. Citation Format: Kezhong Chen, Haifeng Shen, Shuailai Wu, Pengfei Zhu, Chenyang Wang, Analyn Lizaso, Guannan Kang, Yang Wang, Juan Lv, Shuai Fang, Wenjun Wu, Fujun Qiu, Yuan Sun, Qiang Lu, Heng Zhao, Shannon Chuai, Fan Yang, Zhihong Zhang. Tumor-informed patient-specific panel outperforms tumor-naïve and tumor-informed fixed panel for circulating tumor DNA (ctDNA)-based postoperative monitoring of non-small cell lung cancer (NSCLC) [abstract]. In: Proceedings of the Amer ican Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5916.
    Type of Medium: Online Resource
    ISSN: 1538-7445
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2022
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  • 2
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 82, No. 12_Supplement ( 2022-06-15), p. 5917-5917
    Abstract: Background: Identifying molecular residual disease (MRD) with tailored tumor-informed ctDNA based next-generation sequencing (NGS) assays after curative surgery could facilitate the individualized management of resected CRC patients. Here, we investigated the clinical utility of tumor-informed ctDNA mutation analysis using a novel Patient-specific pROgnostic and Potential tHErapeutic marker Tracking (PROPHET) approach for accessing MRD in resected CRC patients. Using the same set of baseline and post-operative blood samples, we compared the performance of PROPHET assay with tumor-naïve fixed panel for detecting MRD and predicting recurrence in resected CRC patients. Methods: The prospective study recruited 42 patients diagnosed with stage I-III CRC from May 2019 to Jun 2020 at the First Affiliated Hospital of Soochow University. Tumor tissue samples were collected at surgery. Blood samples collected before surgery (baseline), 8-day post-operative time point before any adjuvant therapy were analyzed. The detection and quantification of ctDNA for MRD assessment was investigated using PROPHET, a personalized, tumor-informed ctDNA assay designed to track up to 50 top-ranked patient-specific somatic variants based on whole-exome sequencing (WES) of the tumor tissue and matched white blood cells (WBCs). Tumor- naïve fixed assay was performed using targeted NGS panel, containing 41 gastrointestinal cancer-related genes. Results: Baseline ctDNA status was detected in 95.23% (40/42) of the patients with PROPHET assay, and 69.05% (29/42) of the patients with fixed panel. Of 42 patients included in the analysis, 1, 25, and 16 patients had pathological stages I, II, and III CRC with baseline ctDNA detected in 100% (1/1), 92% (23/25), 100% (16/16) patients with PROPHET assay, and 100% (1/1), 64% (16/25), 75% (12/16) patients with fixed panel. Post-operative ctDNA-positive status with PROPHET assay was associated with 3-year DFS, compared with ctDNA-negative group (hazard ratio [HR], 16.57, 95% confidence interval [CI] :3.01-91.36, p=0.014). 15% (6/40) patients were identified to be MRD- positive and 83.33% (5/6) patients eventually relapsed at 3-years follow-up. Although fixed panel also showed high performance in predicting relapse HR, 4.48, 95% CI:1.9-10.9; p & lt; 0.001, 27.5% (11/40) patients were identified to be MRD-positive and only 45.45% (5/11) patients eventually relapsed. 3-year prognostication with PROPHET assay at 8-day post-operation yielded higher positive predictive value (83.33% vs 45.45%), negative predictive value (91.18% vs 89.66%), and specificity (96.88% vs 81.25%) as compared with tumor-naïve fixed panel. Conclusion: Patient-specific PROPHET assay based on unique somatic mutation profiles detects patients with high-risk of recurrence, which achieved higher specificity than tumor-naïve fixed panel. Citation Format: Jian Zhou, Jian Yang, Zixiang Zhang, Ye Li, Bin Yi, Yuchen Tang, Dechun Li, Xiaozhe Li, Di Peng, XI Li, Yang Wang, Haiyan Li, Bing Li, Chenyang Wang, Pengfei Zhu, Longfei Chen, Shuailai Wu, Shuai Fang, Chenxi Li, Fujun Qiu, Shannon Chuai, Zhihong Zhang. Patient-specific tumor-informed circulating tumor DNA (ctDNA) analysis for postoperative monitoring of patients with stages I-III colorectal cancer (CRC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5917.
    Type of Medium: Online Resource
    ISSN: 1538-7445
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2022
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  • 3
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 83, No. 7_Supplement ( 2023-04-04), p. 97-97
    Abstract: Introduction: Intratumor heterogeneity (ITH) describes the distinct tumor cell populations and microenvironments within the same tumor, which may profoundly impact cancer evolution and clinical outcomes. Non-small cell lung cancer (NSCLC) is not only a genetically diverse disease but also has high transcriptomic heterogeneity (RNA-ITH). The RNA-ITH limits the reproducibility of expression-based prognostic models, which is poorly understood. Methods: To address the issue, we investigated the effect of RNA-ITH on prognosis at both gene and signature levels using multiregional RNA-seq data from 45 NSCLC patients (145 regions) in the TRACERx study. We also performed multiregional RNA-seq of 25 NSCLC tumors (64 regions) for independent validation. Results: At the gene level, we found that the maximal expression of hazardous genes (Hazard Ration (HR) & gt; 1) and the minimal expression of protective (HR & lt; 1) genes across different regions within a tumor are more prognostic than their average expression. As for prognostic signatures, we first designed five different functions to transform the multiregional expression of signature genes into patient-level values. To calculate individual risk scores, we applied them to assist two existing prognostic gene signatures, ORACLE (Outcome Risk Associated Clonal Lung Expression) and WTGS (whole-transcriptomic gene signature). As a result, the best performance was achieved using the combination of maximal hazardous signature expressions and minimal protective signature expressions. We next developed a new signature called PACEG (Prognosis-Associated Clonally Expressed Genes) and proposed a multiregional assay for higher prognostic accuracy in NSCLC. We demonstrated significant improvement in PACEG performance by leveraging RNA-ITH captured by multiregional expression of signature genes. Finally, we utilized the same strategy to study the impact of tumor immune microenvironment ITH on patient prognosis. Consistently, the minimal/maximal infiltration of protective/hazardous immune cells across tumor regions was the best measurement associated with prognosis in NSCLC. These results were independently validated by our local datasets. Conclusions: The prognosis of NSCLC patients is often driven by the most aggressive tumor subclones. Our study proposed a novel strategy to incorporate RNA-ITH with expression-based prognostic models. Multiple distinct tumor regions should be considered to overcome the ITH issue for better prognostic evaluation, e.g., using the minimal/maximal expression of protective/hazardous signature genes across all regions to calculate the risk score in individuals. We also developed the PACEG panel composed of 26 genes that could be potentially applied in clinical specimens to identify high-risk NSCLC patients who may benefit from intensified adjuvant therapy. Citation Format: Chenyang Li, Thinh T. Nguyen, Jian-Rong Li, Xingzhi Song, Ignacio I. Wistuba, Andy Futureal, Jianhua Zhang, Shawna M. Hubert, Jia Wu, Jianjun Zhang, Chao Cheng. Multiregional profiling revealed intra-tumor transcriptomic heterogeneity associated with the prognosis in non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 97.
    Type of Medium: Online Resource
    ISSN: 1538-7445
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2023
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  • 4
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2019
    In:  Cancer Research Vol. 79, No. 13_Supplement ( 2019-07-01), p. 140-140
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 79, No. 13_Supplement ( 2019-07-01), p. 140-140
    Abstract: The tumor microenvironment is composed of numerous cell types, including tumor, immune and stromal cells. Cancer cells interact with the tumor microenvironment to suppress anticancer immunity. In this study, we molecularly dissected the tumor microenvironment of breast cancer by single-cell RNA-seq. The breast tumor microenvironment was profiled by analyzing the single-cell transcriptomes of 52,163 cells from the tumor tissues of 15 breast cancer patients. The tumor cells and immune cells from individual patients were analyzed simultaneously at the single-cell level. Among more than 40,000 tumor cells, we identified distinct cell clusters with different molecular subtypes and gene signatures in the same tumor, which revealed intra-tumor heterogeneity in breast cancer. We comprehensively profiled the functional state of T cells, macrophages, B cells, CAFs in breast cancer tumor microenvironment, which highlight the immune cell and CAF diversity in the breast cancer TME. Moreover, we analyzed intercellular communication in the breast cancer TME using a dataset of human ligand receptor pairs, which showed distinct cell interaction models across tumors. The evolution of the tumor microenvironment during clinical treatment was dissected by comparing tumor microenvironment of breast cancer pre- and post-chemotherapy. This study investigated the diversity of the cell types in the tumor microenvironment and provided information on the mechanisms of escape from clearance by immune cells in breast cancer, which could be a beneficial resource for immunotherapy development. Citation Format: Jianhua Yin, Hanlin Zhou, Chen Yan, Ruqian lv, Ting Wang, Chenyang He, Chen Huang, Yong Hou, Shida Zhu, Ling Wang, Michael Dean, Kui Wu, Hong Hu, Guibo Li. Comprehensive analysis of immune evasion in breast cancer by single-cell RNA-seq [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 140.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
    RVK:
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2019
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  • 5
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 83, No. 7_Supplement ( 2023-04-04), p. 1039-1039
    Abstract: Background: Through parallel testing and comparison of personalized and fixed panel minimal residual disease (MRD) assays, to establish the best technique and application strategy of dynamic MRD detection for prognosis prediction and disease assessment among non-small cell lung cancer (NSCLC) patients. Method: We analyzed 760 plasma samples from prospectively enrolled 181 patients with NSCLC recruited to the MEDAL study (NCT03634826), with disease stage I (63%), II (19%) and III (18%). 80% were adenocarcinomas. Plasma samples were collected at baseline (n=157), landmark 3-day and 1-month (n=334), and longitudinal points (n=248) were analyzed. Additional plasma was collected after relapse for 14 patients (n=21). Median follow-up was 1092 days, and 48 patients progressed. We employed a novel personalized tumor-informed technology named PROPHET using deep sequencing of 50 patient-specific variants. The PROPHET was developed to detect MRD with a limit of detection (LoD) of 0.004% and sample-level specificity of greater than 99% in the analytical validation. Detection and quantification of MRD through tumor-informed (TI) and tumor-agnostic (TA) fixed panel assays in the same samples were conducted for a head-to-head comparison. Results: ctDNA was detected by PROPHET prior to treatment in 45% of samples (83%, 75% and 23% for disease stage III, II and I), and showed a higher positive rate than the TI and TA assays (22% and 19%). PROPHET identified 30 more ctDNA positive patients with a median ctDNA fraction of 0.01% at baseline. From the landmark single test, the sensitivity was 45%; integrating longitudinal time points increased the sensitivity to 85%. Landmark PROPHET status was the only risk factor other than clinical features to predict the clinical relapse (p & lt;0.001, multivariate Cox model). MRD positive patients defined by non-canonical variants (n=8) had similar disease-free survival (DFS) as MRD positive patients defined by canonical variants (n=9). Landmark PROPHET-based MRD status combined with clinical TNM stage outperformed TNM stage for prediction of prognosis (p & lt;0.001). Longitudinal MRD achieved negative predictive value (NPV) of 99% with an interval of 150 days, and demonstrated 299 days of longer lead-time than other state-of-the-art fixed-panel assays. Among 16 patients with equivocal radiological diagnosis, all the MRD positive patients relapsed (n=6). Among relapsed patients received next-line treatments, 7 ctDNA negative patients survived or died other disease, 67% (2/3) ctDNA positive patients died from cancer. Sensitivity for bone and brain metastasis was 100% (11/11) and 50% (2/4), respectively. Conclusion: The sensitive tumor-informed personalized MRD approach could provide advantages in prognosis prediction at landmark and disease assessment during surveillance for NSCLC patients. Citation Format: Kezhong Chen, Chenyang Wang, Haifeng Shen, Xi Li, Yichen Jin, Shuailai Wu, Fujun Qiu, Qiang Lu, Di Peng, Shuai Fang, Bing Li, Juan Lv, Jinlei Song, Yang Wang, Shannon Chuai, Zhihong Zhang. Individualized tumor-informed circulating tumor DNA (ctDNA) analysis for postoperative monitoring of non-small cell lung cancer (NSCLC) - the MEDAL study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1039.
    Type of Medium: Online Resource
    ISSN: 1538-7445
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2023
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  • 6
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 83, No. 7_Supplement ( 2023-04-04), p. 6513-6513
    Abstract: Introduction: An improved understanding of early lung carcinogenesis may facilitate development of novel diagnostic, screening, and prevention strategies to decrease lung cancer mortality. We have previously led a series of studies on the molecular and immune landscape of lung adenocarcinoma (LUAD) precursors. However, resected human specimens only provide molecular snapshots. Here, we sought to establish and characterize human-relevant murine lung precancer models to depict molecular evolution during early lung carcinogenesis and to provide novel insights for lung cancer interception. Methods: We have established 3 genetically engineered mouse models (GEMMs) (K: KrasLSL-G12D/+, KP: KrasLSL-G12D/+/Trp53R172H/+, KL: KrasLSL-G12D/+/Lkb1fl/fl) and 2 carcinogen-induced models (CITMs) (UWT: Urethane in wild type mice, URG: Urethane in Rag2−/− mice). Lung tissues were serially collected at multiple time points after induction and subjected to whole exome sequencing (WES), single cell RNA sequencing (scRNA-seq), spatial transcriptomics (Visium), and imaging mass cytometry (IMC). Results: Pathological review of specimens from 252 mice revealed normal lung, precancers and LUAD at different timepoints mirroring the evolution of human LUAD. Overall, the tumor burden was significantly higher in GEMMs than CITMs (p & lt;0.05). Tumor mutation burden progressively increased with progression from precancers to LUADs across all models. scRNA-seq demonstrated a progressive decrease of CD4+ T cell, CD8+ T cell, NK cell, and B cell infiltration in all models except the B/T cell-deficient WRG model; and a progressive increase of neutrophils (in KL model) and macrophages (in K, KP, UWT and URG models) along with progression of precancers. These findings were confirmed by spatial Visium and IMC profiling. Infiltration of T cells, B cells and NK cells inside tumors was not different between GEMMs (K, KP, KL) and CITMs (UWT). However, UWT showed significantly higher density of immune cells at the peritumor regions (P & lt;0.05). Compared to the immune-competent UWT model, the B/T-cell deficient URG model showed similar progression and tumor burden at early phases, but rapid progression and larger tumor burden in the later phases. URG had no mature B/T cells but significantly higher NK cell infiltration than UWT (p & lt;0.05). Conclusion: We have established 5 murine carcinogen-dependent and -independent precancer models, morphologically resembling human LUAD and its precursors. Although progressive immunosuppression along with progression of lung precancers is universal across all models, the evolution patterns and the molecular/immune features underlying immunosuppression vary in different models, particularly between CITMs and GEMMs. These models may be valuable assets for studying early lung carcinogenesis and lung cancer interception. Citation Format: Bo Zhu, Jian-Rong Li, Hong Chen, Pingjun Chen, Junya Fujimoto, Yanhua Tian, Muhammad Aminu, Chenyang Li, Lingzhi Hong, Alexandre Reuben, Edwin Roger Parra Cuentas, Ou Shi, Monique Nilsson, Alissa Poteete, Shawna Hubert, Khaja Khan, Wei Lu, Daniel Kraushaar, Xingzhi Song, Jianhua Zhang, Don Gibbons, Luisa Solis Soto, Ignacio Wistuba, Jia Wu, John Heymach, Chao Cheng, Jianjun Zhang. Single cell and spatial profiling reveal molecular and immune evolution from precancers to invasive lung adenocarcinomas in genetic and carcinogen-induced mouse models. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6513.
    Type of Medium: Online Resource
    ISSN: 1538-7445
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2023
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  • 7
    In: Cancer Immunology Research, American Association for Cancer Research (AACR), Vol. 5, No. 2 ( 2017-02-01), p. 148-156
    Abstract: T lymphocytes infiltrate the microenvironment of breast cancer tumors and play a pivotal role in tumor immune surveillance. Relationships between the T-cell receptors (TCR) borne by T cells within tumors, in the surrounding tissues, and in draining lymph nodes are largely unexplored in human breast cancer. Consequently, information about the relative extent of possible T-cell exchange between these tissues is also lacking. Here, we have analyzed the TCR repertoire of T cells using multiplex PCR and high-throughput sequencing of the TCRβ chain in the tissues of tumor, adjacent nontumor, and axillary lymph nodes of breast cancer patients. T-cell repertoire diversity in tumors was lower than in lymph nodes, but higher than in nontumor tissue, with a preferential use of variable and joining genes. These data are consistent with the hypothesis that most of the T cells in tumors derive from the lymph node, followed by their expansion in tumor tissue. Positive nodes appeared to enhance T-cell infiltration into tumors and T-cell clonal expansion in lymph nodes. Additionally, the similarity in TCR repertoire between tumor and nontumor tissue was significantly higher in luminal-like, rather than basal-like, breast cancer. Our study elucidated the high heterogeneity of the TCR repertoire and provides potential for future improvements in immune-related diagnosis, therapy, and prognosis for breast cancer patients. Cancer Immunol Res; 5(2); 148–56. ©2016 AACR.
    Type of Medium: Online Resource
    ISSN: 2326-6066 , 2326-6074
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2017
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