4.7 Article

Generating immunogenomic data-guided virtual patients using a QSP model to predict response of advanced NSCLC to PD-L1 inhibition

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Oncology

Cancer statistics, 2022

Rebecca L. Siegel et al.

Summary: Each year, the American Cancer Society compiles data on cancer occurrence and outcomes in the United States. The latest data shows that breast and prostate cancer progress has stagnated, while lung cancer has shown improvements in survival rates. Lung cancer incidence for advanced disease has declined while localized-stage rates have increased, resulting in higher survival rates. Mortality patterns align with incidence trends, with lung cancer deaths declining rapidly, breast cancer deaths slowing, and prostate cancer deaths stabilizing.

CA-A CANCER JOURNAL FOR CLINICIANS (2022)

Review Pharmacology & Pharmacy

Recent applications of quantitative systems pharmacology and machine learning models across diseases

Sara Sadat Aghamiri et al.

Summary: Quantitative systems pharmacology (QSP) is a quantitative and mechanistic platform that describes the interactions between drugs, biological networks, and disease conditions to predict optimal therapeutic responses. Recent studies have shown a growing diversity in the applications of QSP models in various therapeutic areas, methodologies, and software platforms, which can facilitate the discovery and reusability of these models. The meta-analysis highlights the increasing focus on Immuno-Oncology within QSP efforts, as well as the benefits of integrative approaches and Machine Learning methods in drug discovery and model development.

JOURNAL OF PHARMACOKINETICS AND PHARMACODYNAMICS (2022)

Article Biochemical Research Methods

Classical mathematical models for prediction of response to chemotherapy and immunotherapy

Narmin Ghaffari Laleh et al.

Summary: This study fitted differential equation models to tumor volume measurements of patients undergoing chemotherapy or cancer immunotherapy. The Gompertz model provided the best fit to the data and the general Bertalanffy and Gompertz models performed best in predicting treatment outcome. The study provides a benchmark for classical textbook models and state-of-the-art models of human tumor growth.

PLOS COMPUTATIONAL BIOLOGY (2022)

Editorial Material Pharmacology & Pharmacy

Model-informed target identification and validation through combining quantitative systems pharmacology with network-based analysis

Vijayalakshmi Chelliah et al.

Summary: The combination of QSP and NBA enhances the efficiency and effectiveness of in silico target identification and validation.

CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY (2022)

Article Multidisciplinary Sciences

An immune gene signature to predict prognosis and immunotherapeutic response in lung adenocarcinoma

Hongquan Chen et al.

Summary: This study constructed a stable immune gene signature for lung adenocarcinoma patients, which can be used to predict prognosis and the benefits of immune checkpoint inhibitors (ICIs) treatment. The research found that the low-risk group of the immune gene signature had a higher survival rate and lower gene mutation rate, which were associated with a better prognosis. In contrast, the high-risk group had higher immune cell infiltration but was associated with a poorer prognosis.

SCIENTIFIC REPORTS (2022)

Article Immunology

Multi-Scale Spatial Analysis of the Tumor Microenvironment Reveals Features of Cabozantinib and Nivolumab Efficacy in Hepatocellular Carcinoma

Haoyang Mi et al.

Summary: This study used fluorescent cell mapping technology to analyze the tumor microenvironment in patients with HCC, and found that the expression patterns of PD-L1 and Granzyme B were different in different regions. The close contact between CD8(+) T cells and Arg1(hi) macrophages was a prominent feature in non-responders. In addition, cell community analysis found that the communication between macrophage-enriched cell communities and lymphocyte-enriched cell communities with tumor cell communities was stronger in non-responders.

FRONTIERS IN IMMUNOLOGY (2022)

Article Oncology

Long-term outcomes of operable stage III NSCLC in the pre-immunotherapy era: results from a pooled analysis of the SAKK 16/96, SAKK 16/00, SAKK 16/01, and SAKK 16/08 trials

D. Koenig et al.

Summary: In operable stage III non-small-cell lung cancer, neoadjuvant chemotherapy with cisplatin and docetaxel +/- neoadjuvant sequential radiotherapy has shown favorable long-term outcomes. Complete resection and pathological complete remission are important predictors of prognosis.

ESMO OPEN (2022)

Article Biochemical Research Methods

DeepMHCII: a novel binding core-aware deep interaction model for accurate MHC-II peptide binding affinity prediction

Ronghui You et al.

Summary: This study proposes a deep learning model, DeepMHCII, based on peptide binding cores and introduces a binding interaction convolution layer to better model the biological interactions between peptides and MHC II molecules. Extensive experiments demonstrate that DeepMHCII outperforms existing methods in terms of performance and can effectively predict binding cores.

BIOINFORMATICS (2022)

Article Biochemical Research Methods

Simulations of tumor growth and response to immunotherapy by coupling a spatial agentbased model with a whole-patient quantitative systems pharmacology model

Alvaro Ruiz-Martinez et al.

Summary: This study extends the spatial QSP model to analyze tumor growth dynamics and immune therapy response, which functions as a coarse-grained model at the whole-tumor scale and an agent-based model at the regions of interest scale. The model characterizes tumor growth, identifies T cell hotspots, and performs qualitative and quantitative descriptions of cell density at the invasive front of the tumor.

PLOS COMPUTATIONAL BIOLOGY (2022)

Review Oncology

Addressing CPI resistance in NSCLC: targeting TAM receptors to modulate the tumor microenvironment and future prospects

Solange Peters et al.

Summary: Lung cancer, especially non-small-cell lung cancer (NSCLC), is a major cause of cancer death. The immunosuppressive tumor microenvironment (TME) plays a crucial role in developing resistance to immune checkpoint inhibitors (CPIs) for NSCLC. Targeting TAM receptors and immune checkpoints simultaneously may overcome CPI resistance and improve survival rates for lung cancer patients.

JOURNAL FOR IMMUNOTHERAPY OF CANCER (2022)

Article Multidisciplinary Sciences

Dynamics of tumor-associated macrophages in a quantitative systems pharmacology model of immunotherapy in triple-negative breast cancer

Hanwen Wang et al.

Summary: Quantitative systems pharmacology (QSP) modeling is an emerging computational approach that combines drug kinetics/dynamics and disease progression. It has shown importance in drug development, particularly in complex cases such as TNBC. Incorporating the dynamics of tumor-associated macrophages (TAMs) into the QSP model can help understand their impact on cancer treatment. Despite its complexity, the modularized QSP platform is reproducible and applicable for clinical trial simulation.

ISCIENCE (2022)

Article Oncology

Quantitative Spatial Profiling of Immune Populations in Pancreatic Ductal Adenocarcinoma Reveals Tumor Microenvironment Heterogeneity and Prognostic Biomarkers

Haoyang Mi et al.

Summary: Quantitative image analysis of PDAC specimens reveals intertumoral and intratumoral heterogeneity of immune populations and identifies spatial immune architectures that are significantly associated with disease prognosis.

CANCER RESEARCH (2022)

Article Oncology

Virtual clinical trials of anti-PD-1 and anti-CTLA-4 immunotherapy in advanced hepatocellular carcinoma using a quantitative systems pharmacology model

Richard J. Sove et al.

Summary: This study uses quantitative systems pharmacology (QSP) framework to conduct a virtual clinical trial for nivolumab and ipilimumab in HCC patients. The model incorporates detailed biological mechanisms of immune cell-cancer cell interactions and generates virtual patients for the trial. The predictions of the model are consistent with clinically observed outcomes, demonstrating the potential of QSP models in patient selection and trial design.

JOURNAL FOR IMMUNOTHERAPY OF CANCER (2022)

Review Engineering, Biomedical

Hybrid computational modeling methods for systems biology

Daniel A. Cruz et al.

Summary: This review surveys hybrid modeling methodologies that blend two or more mathematical forms to describe time-dependent processes in a multivariate system. These models can bridge different scales and forms, providing new opportunities for studying biological systems.

PROGRESS IN BIOMEDICAL ENGINEERING (2022)

Review Pharmacology & Pharmacy

Quantitative Systems Pharmacology Approaches for Immuno-Oncology: Adding Virtual Patients to the Development Paradigm

Vijayalakshmi Chelliah et al.

Summary: Drug development in oncology often uses molecular biology tools to reprogram cellular responses for therapeutic benefits. In immuno-oncology, the goal is to mobilize the patient's immune system against cancer. While successful with antibodies targeting specific receptors, the trend has shifted towards combination therapies, which presents challenges in efficiency and sustainability.

CLINICAL PHARMACOLOGY & THERAPEUTICS (2021)

Article

Immunotherapy for Advanced Non–Small Cell Lung Cancer: A Decade of Progress

Misty Dawn Shields et al.

American Society of Clinical Oncology educational book / ASCO. American Society of Clinical Oncology. Meeting (2021)

Review Oncology

Regulation of PD-L1 expression in the tumor microenvironment

Ming Yi et al.

Summary: PD-L1 expression is regulated by various factors, impacting the treatment effect and patient selection. Understanding the mechanisms of PD-L1 regulation helps enhance the efficacy of immunotherapy.

JOURNAL OF HEMATOLOGY & ONCOLOGY (2021)

Article Oncology

Tumor mutation score is more powerful than tumor mutation burden in predicting response to immunotherapy in non-small cell lung cancer

Yuan Li et al.

Summary: TMS18, a novel tumor mutation score, was found to be more accurate and efficient in predicting response to immunotherapy in NSCLC compared to TMB. Combined with PD-L1, TMS18 showed improved accuracy and efficiency in predicting response to ICIs, suggesting its potential as a promising biomarker in larger cohorts.

CANCER IMMUNOLOGY IMMUNOTHERAPY (2021)

Article Oncology

Quantitative systems pharmacology model predictions for efficacy of atezolizumab and nab-paclitaxel in triple-negative breast cancer

Hanwen Wang et al.

Summary: This study introduces a modular quantitative systems pharmacology (QSP) platform for predicting immunotherapy efficacy and identifying predictive biomarkers. Virtual clinical trials were conducted using a virtual patient cohort generated by the model, with retrospective analysis and model validation based on clinical trial data.

JOURNAL FOR IMMUNOTHERAPY OF CANCER (2021)

Article Oncology

Update of Incidence, Prevalence, Survival, and Initial Treatment in Patients With Non-Small Cell Lung Cancer in the US

Apar Kishor Ganti et al.

Summary: In this study, the latest US data show a decreasing overall incidence of non-small cell lung cancer (NSCLC) from 2010 to 2017, while the incidence of early stage I disease has risen. NSCLC prevalence has increased, and the estimated 5-year survival rate was found to be 26.4%; a significant proportion of patients aged 65 years or older with stage IV disease were not treated.

JAMA ONCOLOGY (2021)

Article Pharmacology & Pharmacy

Quantitative systems pharmacology: Landscape analysis of regulatory submissions to the US Food and Drug Administration

Jane P. F. Bai et al.

Summary: QSP is increasingly utilized to model and simulate drug effectiveness and safety across various disease areas in the drug development process.

CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY (2021)

Article Multidisciplinary Sciences

Immuno-profiling and cellular spatial analysis using five immune oncology multiplex immunofluorescence panels for paraffin tumor tissue

Edwin Roger Parra et al.

Summary: The study optimized five mIF panels for immuno-profiling tumor tissues, identifying correlations between B7-H4 and OX40 expression with malignant cells and revealing an immunosuppressive microenvironment.

SCIENTIFIC REPORTS (2021)

Review Oncology

Multiplexed Immunohistochemistry and Digital Pathology as the Foundation for Next-Generation Pathology in Melanoma: Methodological Comparison and Future Clinical Applications

Yannick Van Herck et al.

Summary: In recent years, there has been a significant revolution in the field of melanoma treatment, transitioning from traditional chemotherapy to personalized molecular and immunological therapies, necessitating a deep understanding of the immune microenvironment and cellular composition for improving treatment efficacy. The introduction of single-cell profiling methods offers the potential to study the specific cellular structures and interactions within tumor tissues.

FRONTIERS IN ONCOLOGY (2021)

Review Biochemistry & Molecular Biology

Peripheral Blood-Based Biomarkers for Immune Checkpoint Inhibitors

Ho Jung An et al.

Summary: Recent advances in high-throughput multiplexed analytical technologies have identified various peripheral blood-based immune biomarkers that can be crucial for selecting cancer patients suitable for ICIs treatment. The identification of these biomarkers helps overcome the limitations of previously used tissue-based biomarkers and offers non-invasive and repeatable methods for detection from blood samples.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Article Oncology

Course of postoperative relapse in non-small cell lung cancer is strongly associated with post-progression survival

Hisao Imai et al.

Summary: The post-progression survival (PPS) is significantly more strongly associated with overall survival (OS) than relapse-free survival (RFS) in patients with postoperative recurrence of NSCLC. This suggests that treatment following postoperative recurrence plays a crucial role in patient survival outcomes and should be further investigated in large prospective studies.

THORACIC CANCER (2021)

Review Oncology

Oncogenic driver mutations in non-small cell lung cancer: Past, present and future

Mathieu Chevallier et al.

Summary: Lung cancer, particularly non-small cell lung cancer, is the leading cause of cancer related-death globally, with alterations in oncogenic drivers playing a key role in cancer development. There are over fifteen targeted agents approved for treatment of non-small cell lung cancer, emphasizing the importance of understanding the biology and resistance mechanisms associated with each driver mutation for developing optimal treatment strategies.

WORLD JOURNAL OF CLINICAL ONCOLOGY (2021)

Letter Pharmacology & Pharmacy

Modeling is data driven: Use it for successful virtual patient generation

Theodore R. Rieger et al.

CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY (2021)

Article Pharmacology & Pharmacy

A Quantitative Systems Pharmacology Model of T Cell Engager Applied to Solid Tumor

Huilin Ma et al.

AAPS JOURNAL (2020)

Review Immunology

Predicting Cross-Reactivity and Antigen Specificity of T Cell Receptors

Chloe H. Lee et al.

FRONTIERS IN IMMUNOLOGY (2020)

Review Multidisciplinary Sciences

Revisiting the PD-1 pathway

Nikolaos Patsoukis et al.

SCIENCE ADVANCES (2020)

Proceedings Paper Automation & Control Systems

Virtual Patient Generation using Physiological Models through a Compressed Latent Parameterization

Ali Tivay et al.

2020 AMERICAN CONTROL CONFERENCE (ACC) (2020)

Article Pharmacology & Pharmacy

QSP-IO: A Quantitative Systems Pharmacology Toolbox for Mechanistic Multiscale Modeling for Immuno-Oncology Applications

Richard J. Sove et al.

CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY (2020)

Article Pharmacology & Pharmacy

A Computational Model of Neoadjuvant PD-1 Inhibition in Non-Small Cell Lung Cancer

Mohammad Jafarnejad et al.

AAPS JOURNAL (2019)

Article Respiratory System

Radiographic pulmonary vessel volume, lung function and airways disease in the Framingham Heart Study

Andrew J. Synn et al.

EUROPEAN RESPIRATORY JOURNAL (2019)

Review Oncology

Stochastic Evolution of Pancreatic Cancer Metastases During Logistic Clonal Expansion

Kimiyo N. Yamamoto et al.

JCO CLINICAL CANCER INFORMATICS (2019)

Article Pharmacology & Pharmacy

Population Pharmacokinetics of Durvalumab in Cancer Patients and Association With Longitudinal Biomarkers of Disease Status

Paul G. Baverel et al.

CLINICAL PHARMACOLOGY & THERAPEUTICS (2018)

Article Immunology

The Immune Landscape of Cancer

Vesteinn Thorsson et al.

IMMUNITY (2018)

Article Multidisciplinary Sciences

Local mutational diversity drives intratumoral immune heterogeneity in non-small cell lung cancer

Qingzhu Jia et al.

NATURE COMMUNICATIONS (2018)

Letter Medicine, General & Internal

Tumor Mutational Burden and Response Rate to PD-1 Inhibition

Mark Yarchoan et al.

NEW ENGLAND JOURNAL OF MEDICINE (2017)

Article Mathematics, Interdisciplinary Applications

Parameter Selection and Verification Techniques Based on Global Sens Analysis Illustrated for an HIV Model

Mami T. Wentworth et al.

SIAM-ASA JOURNAL ON UNCERTAINTY QUANTIFICATION (2016)

Article Pharmacology & Pharmacy

Efficient Generation and Selection of Virtual Populations in Quantitative Systems Pharmacology Models

R. J. Allen et al.

CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY (2016)

Editorial Material Pharmacology & Pharmacy

Editorial: The emerging discipline of quantitative systems pharmacology

Tarek A. Leil et al.

FRONTIERS IN PHARMACOLOGY (2015)

Article Multidisciplinary Sciences

Comprehensive molecular profiling of lung adenocarcinoma

Eric A. Collisson et al.

NATURE (2014)

Review Immunology

Oncology Meets Immunology: The Cancer-Immunity Cycle

Daniel S. Chen et al.

IMMUNITY (2013)

Article Biochemistry & Molecular Biology

Structure and Interactions of the Human Programmed Cell Death 1 Receptor

Xiaoxiao Cheng et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2013)

Article Pharmacology & Pharmacy

Predicting the Effects of Anti-angiogenic Agents Targeting Specific VEGF Isoforms

Stacey D. Finley et al.

AAPS JOURNAL (2012)

Article Multidisciplinary Sciences

Comprehensive genomic characterization of squamous cell lung cancers

Peter S. Hammerman et al.

NATURE (2012)

Article Oncology

New response evaluation criteria in solid tumours: Revised RECIST guideline (version 1.1)

E. A. Eisenhauer et al.

EUROPEAN JOURNAL OF CANCER (2009)