Transcriptome and Single-Cell Sequencing Analyses to Classify Immune Subtypes, Uncover Novel Biomarkers, and Assess Immunotherapeutic Responses in Cancer

Transcriptome and Single-Cell Sequencing Analyses to Classify Immune Subtypes, Uncover Novel Biomarkers, and Assess Immunotherapeutic Responses in Cancer
Author: Hongda Liu
Publisher: Frontiers Media SA
Total Pages: 242
Release: 2024-07-24
Genre: Medical
ISBN: 2832552064

According to the most recent projections of the International Agency for Research on Cancer (IARC), there would be around 19.3 million new cases of cancer and 10 million cancer-related deaths globally in 2022. Cancer research has never halted. In particular, research into the cancer immunological microenvironment is gaining popularity.

Novel biomarkers in tumor immunity and immunotherapy

Novel biomarkers in tumor immunity and immunotherapy
Author: Takaji Matsutani
Publisher: Frontiers Media SA
Total Pages: 343
Release: 2024-07-26
Genre: Science
ISBN: 283254794X

Immune checkpoint inhibitors (ICIs) such as anti-PD-1 and anti-PD-L1 antibodies are highly effective against many types of cancer, yet durable responses are limited to a subset of patients highlighting the need for the development of effective biomarkers to predict prognosis and efficacy. Currently, PD-L1 expression in tumors, microsatellite instability (MSI) or mismatch repair deficiency (dMMR), and tumor mutation burden (TMB) are known as biomarkers for cancer immunotherapy but are not sufficient. Combination therapy with immune checkpoint inhibitors and chemotherapy or radiation therapy, as well as diverse therapies targeting intra-tumoral regulatory T cells have been described, but there are currently no unifying biomarkers that are applicable to clinically, a simple, fast, non-invasive method that can yield biomarkers of disease with a minimal adverse effect on patients is desirable. Recent findings suggest that the balancing of effector T cells and regulatory cells in the tumor microenvironment is associated with cancer progression and prognosis. Cells and molecules involved in the control of cancer are complex, and a better understanding of the tumor immune environment will lead to the development of truly effective biomarkers. This topic will focus on novel biomarkers that predict efficacy, prognosis, or the development of adverse events in various cancer immunotherapies, and extensive basic research leading to the development of biomarkers. Manuscripts consisting solely of bioinformatics or computational analysis of public genomic or transcriptomic databases which are not accompanied by robust and relevant validation (clinical cohort or biological validation in vitro or in vivo) are out of scope for this topic. We expect a wide range of research, not only in serology, genetics, and immunocytochemistry but also in bacterial flora. Research on the development of novel assays and bioinformatics methods is also welcome: • Non-invasive biomarkers for cancer immunotherapy. • Bulk RNA-seq, scRNA-seq, or Rep-seq methods. • Correlation of tumor immune cells with gut microbiota in tumor immunotherapy. • Impact of Teff and Treg balance in the tumor microenvironment on tumor prognosis. • Inflammatory and immune signatures associated with drug response versus resistance in cancer.

Single-Cell Transcriptome Analysis in Tumor Tissues

Single-Cell Transcriptome Analysis in Tumor Tissues
Author: Sadahiro Iwabuchi
Publisher:
Total Pages: 0
Release: 2020
Genre: Science
ISBN:

The tumor microenvironment is comprised of cancer cells and their surroundings, including various normal cells and non-cellular components, and each tumor tissue has a distinctive microenvironment. Cancer progression is affected by different microenvironmental states, such as the heterogeneity of infiltrating immune cells. Therefore, it is necessary to understand the complex cell-to-cell interactions associated with tumor developmental stages in different tissues. Recent revolution of single-cell RNA sequencing technology can uncover the tumor microenvironment diversity. We have developed a novel strategy of single-cell transcriptome analysis: next generation 1-cell sequencing (Nx1-seq) technology, and it allows for profiling of thousands of single cells from tumor tissue. Our microwell with cell bar-code beads device can detect genes with high sensitivity, and it is easily transported anywhere without any other dedicated devices. Further, the developmental cost is relatively cheaper than other single-cell RNA sequencing methods. In this study, we introduce representative application of the single-cell RNA sequencing technique in gynecological cancers, and we show the result of Nx1-seq application in human endometrioid adenocarcinoma tissue.

Novel Biomarkers for Predicting Response to Cancer Immunotherapy

Novel Biomarkers for Predicting Response to Cancer Immunotherapy
Author: Jinghua Pan
Publisher: Frontiers Media SA
Total Pages: 493
Release: 2023-07-11
Genre: Medical
ISBN: 2832525490

Immunotherapy has revolutionized the treatment of malignancies. Targeting of immune checkpoints cytotoxic T-lymphocyte-associated protein 4, programmed cell death protein 1 (PD-1) and its ligand (PD-L1) has led to improving survival in a subset of patients. Despite their remarkable success, clinical benefit remains limited to only a subset of patients. A significant limitation behind these current treatment modalities is an irregularity in clinical response, which is especially pronounced among checkpoint inhibition. Currently, relevant predictors of cancer immunotherapy response include microsatellite instability-high/deficient mismatch repair (MSI-H/dMMR), expression of PD-L1, tumor mutation burden (TMB), immune genomic characteristics, and tumor infiltrating lymphocytes (TILs). However, none of them have sufficient evidence to be a stratification factor. Moreover, as the combined strategies for effective cancer immunotherapy had been developed in multiple tumors, such as Immunotherapy combined with chemotherapy, radiotherapy, targeted therapy and anti-angiogenesis therapy. Therefore, the development of novel biomarkers endowed with high sensitivity, specificity and accuracy able to identify which patients may truly benefit from the treatment with cancer immunotherapy would allow to refine the therapeutic selection and to better tailor the treatment strategy.

Single Cell Sequencing and Systems Immunology

Single Cell Sequencing and Systems Immunology
Author: Xiangdong Wang
Publisher: Springer
Total Pages: 184
Release: 2015-03-27
Genre: Medical
ISBN: 9401797536

The volume focuses on the genomics, proteomics, metabolomics, and bioinformatics of a single cell, especially lymphocytes and on understanding the molecular mechanisms of systems immunology. Based on the author’s personal experience, it provides revealing insights into the potential applications, significance, workflow, comparison, future perspectives and challenges of single-cell sequencing for identifying and developing disease-specific biomarkers in order to understand the biological function, activation and dysfunction of single cells and lymphocytes and to explore their functional roles and responses to therapies. It also provides detailed information on individual subgroups of lymphocytes, including cell characters, function, surface markers, receptor function, intracellular signals and pathways, production of inflammatory mediators, nuclear receptors and factors, omics, sequencing, disease-specific biomarkers, bioinformatics, networks and dynamic networks, their role in disease and future prospects. Dr. Xiangdong Wang is a Professor of Medicine, Director of Shanghai Institute of Clinical Bioinformatics, Director of Fudan University Center for Clinical Bioinformatics, Director of the Biomedical Research Center of Zhongshan Hospital, Deputy Director of Shanghai Respiratory Research Institute, Shanghai, China.

Tertiary Lymphoid Structures

Tertiary Lymphoid Structures
Author: Marie-Caroline Dieu-Nosjean
Publisher: Humana Press
Total Pages: 289
Release: 2018-09-05
Genre: Medical
ISBN: 9781493987085

This volume explores the various methods used to study tertiary lymphoid structures (TLS) in pathological situations. Pre-clinical models are also discussed in detail to show how TLS structure, development, and maintenance can be targeted and studied in vivo. The chapters in this book cover topics such as humans and mice; strategies to quantify TLS in order to use it in stained tissue sections; classifying a gene signature form fixed and paraffin-embedded tissues; and development of murine inflammatory models to help look at TLS in the context of infection or malignancy. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and thorough, Tertiary Lymphoid Structures: Methods and Protocols is a valuable resource that increases the reader’s knowledge on immune functions and how they will pave the way to future therapeutic applications.

Deep Learning for Cancer Diagnosis

Deep Learning for Cancer Diagnosis
Author: Utku Kose
Publisher: Springer Nature
Total Pages: 311
Release: 2020-09-12
Genre: Technology & Engineering
ISBN: 9811563217

This book explores various applications of deep learning to the diagnosis of cancer,while also outlining the future face of deep learning-assisted cancer diagnostics. As is commonly known, artificial intelligence has paved the way for countless new solutions in the field of medicine. In this context, deep learning is a recent and remarkable sub-field, which can effectively cope with huge amounts of data and deliver more accurate results. As a vital research area, medical diagnosis is among those in which deep learning-oriented solutions are often employed. Accordingly, the objective of this book is to highlight recent advanced applications of deep learning for diagnosing different types of cancer. The target audience includes scientists, experts, MSc and PhD students, postdocs, and anyone interested in the subjects discussed. The book can be used as a reference work to support courses on artificial intelligence, medical and biomedicaleducation.

Identification of Biomarkers for Cancer Immunotherapy: From Bench to Bedside, volume I

Identification of Biomarkers for Cancer Immunotherapy: From Bench to Bedside, volume I
Author: Chang Gu
Publisher: Frontiers Media SA
Total Pages: 191
Release: 2023-10-20
Genre: Science
ISBN: 2832529275

During the past few decades, immunotherapy has become an established pillar of cancer treatment improving the survival of numerous patients with diverse solid and hematologic tumors. The leading causes behind the success are the discovery of immune checkpoint inhibitors (ICIs) and the development of chimeric antigen receptor (CAR) T/M/NK cells. As for ICIs, malignancies take advantage of the inhibitory programmed cell death protein 1/programmed cell death protein ligand 1 (PD-1/PD-L1) or cytotoxic T-lymphocyte-associated protein (CTLA-4) pathways to evade the immune system, and disruption of the axis by immune checkpoint inhibitors can achieve durable disease remissions, which has been proved by basic researches and (pre-) clinical studies among lung cancer, melanoma, renal cell cancer, head, and neck squamous cell carcinoma, urothelial cancer, and Hodgkin’s disease. However, the 5-year survival rate of patients treated with ICIs varies with each individual and also relies on tumor specific pathological or molecular subtypes. Besides, the efficacy of ICIs is still limited in terms of drug resistance and fewer potential responders. Thus, there is a big challenge to identify and develop more novel reliable ICIs, as well as sensibilize existing ICIs for patients with drug resistance or even for non-responders.

The Mouse Nervous System

The Mouse Nervous System
Author: Charles Watson
Publisher: Academic Press
Total Pages: 815
Release: 2011-11-28
Genre: Medical
ISBN: 0123694973

The Mouse Nervous System provides a comprehensive account of the central nervous system of the mouse. The book is aimed at molecular biologists who need a book that introduces them to the anatomy of the mouse brain and spinal cord, but also takes them into the relevant details of development and organization of the area they have chosen to study. The Mouse Nervous System offers a wealth of new information for experienced anatomists who work on mice. The book serves as a valuable resource for researchers and graduate students in neuroscience. Systematic consideration of the anatomy and connections of all regions of the brain and spinal cord by the authors of the most cited rodent brain atlases A major section (12 chapters) on functional systems related to motor control, sensation, and behavioral and emotional states A detailed analysis of gene expression during development of the forebrain by Luis Puelles, the leading researcher in this area Full coverage of the role of gene expression during development and the new field of genetic neuroanatomy using site-specific recombinases Examples of the use of mouse models in the study of neurological illness