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Cells
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Novel Microenvironment-Based Immune Changes Revealed by RNA Sequencing in Cancer...
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Novel Microenvironment-Based Immune Changes Revealed by RNA Sequencing in Cancer or Metabolic Diseases

A special issue of Cells (ISSN 2073-4409). This special issue belongs to the section "Cellular Immunology".

Deadline for manuscript submissions: closed (31 March 2024) | Viewed by 10141

Special Issue Editors

Prof. Dr. Yasuhito Ishigaki

E-Mail Website
Guest Editor
Medical Research Institute, Kanazawa Medical University, Kahoku 920-0293, Japan
Interests: adipose-derived stem cells; mRNA decay; noncoding RNA; RNA bindings; transcriptome analysis
Special Issues, Collections and Topics in MDPI journals
Dr. Lili Qu

E-Mail Website
Guest Editor
Health Center, University of Connecticut, Farmington, CT, USA
Interests: bioinformatics; immune; microenvironment; RNA sequencing
Dr. Baihai Jiao

E-Mail
Guest Editor
Nephrology, School of Medicine, University of Connecticut Health Center, Farmington, CT 06030-1405, USA
Interests: immunology; inflammation; fibrosis; molecular mechanisms; epigenetic regulation
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,      

Microenvironment-based immune changes always happen in all types of diseases, such as cancer or metabolic diseases. These changes include not only subtypes of the immune cells but also their cellular or molecular functions. With the development of cutting-edge technologies such as RNA sequencing, CITE-seq, or ATAC-seq, tracking immune changes following the development of diseases becomes reliable, which is beneficial for the development of efficient treatments, such as immunotherapy in cancer. We invite all scientists working in the immunology field to participate in this Special Issue. Original research articles, reviews, or shorter perspective articles on all aspects related to immune changes in the microenvironment revealed by RNA sequencing are welcome, including topics such as immune cell constituent changes or molecular and cellular functional changes.

Prof. Dr. Yasuhito Ishigaki
Dr. Lili Qu
Dr. Baihai Jiao
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Cells is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

  • immune changes
  • RNA sequencing
  • microenvironment
  • CITE-seq
  • ATAC-seq
  • molecular changes
  • function changes
  • metabolic diseases
  • cancer

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Published Papers (3 papers)

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Research

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15 pages, 3095 KiB  
Article
Distinct Infiltration of T Cell Populations in Bladder Cancer Molecular Subtypes
by Viktor Sincic, Ken F. Arlenhold, Sarah Richtmann, Henrik Lilljebjörn, Pontus Eriksson, Gottfrid Sjödahl, Mats Wokander, Karin Hägerbrand, Peter Ellmark, Thoas Fioretos, Carl A. K. Borrebaeck, Fredrik Liedberg and Kristina Lundberg
Cells 2024, 13(11), 926; https://doi.org/10.3390/cells13110926 - 28 May 2024
Cited by 1 | Viewed by 1868
Abstract
Bladder cancer is a heterogenous disease, and molecular subtyping is a promising method to capture this variability. Currently, the immune compartment in relation to subtypes is poorly characterized. Here, we analyzed the immune compartment in bladder tumors and normal bladder urothelium with a [...] Read more.
Bladder cancer is a heterogenous disease, and molecular subtyping is a promising method to capture this variability. Currently, the immune compartment in relation to subtypes is poorly characterized. Here, we analyzed the immune compartment in bladder tumors and normal bladder urothelium with a focus on T cell subpopulations using flow cytometry and RNA sequencing. The results were investigated in relation to tumor invasiveness (NMIBC/MIBC) and molecular subtypes according to the Lund Taxonomy system. Whereas the NMIBC/MIBC differed in the overall immune infiltration only, the molecular subtypes differed both in terms of immune infiltration and immune compartment compositions. The Basal/Squamous (Ba/Sq) and genomically unstable (GU) tumors displayed increased immune infiltration compared to urothelial-like (Uro) tumors. Additionally, the GU tumors had a higher proportion of regulatory T cells within the immune compartment compared to Uro tumors. Furthermore, sequencing showed higher levels of exhaustion in CD8+ T cells from GU tumors compared to both Uro tumors and the control. Although no such difference was detected at the transcriptomic level in Uro tumors compared to the controls, CD8+ T cells in Uro tumors showed higher expression of several exhaustion markers at the protein level. Taken together, our findings indicate that depending on the molecular subtype, different immunotherapeutic interventions might be warranted. Full article
(This article belongs to the Special Issue Novel Microenvironment-Based Immune Changes Revealed by RNA Sequencing in Cancer or Metabolic Diseases)
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14 pages, 3832 KiB  
Article
Early Pharmacodynamic Changes Measured Using RNA Sequencing of Peripheral Blood from Patients in a Phase I Study with Mitazalimab, a Potent CD40 Agonistic Monoclonal Antibody
by Hampus Andersson, Aastha Sobti, David Gomez Jimenez, Yago Pico de Coaña, Sumeet Vijay Ambarkhane, Karin Hägerbrand, Karin Enell Smith, Malin Lindstedt and Peter Ellmark
Cells 2023, 12(19), 2365; https://doi.org/10.3390/cells12192365 - 27 Sep 2023
Cited by 4 | Viewed by 2517
Abstract
CD40-targeting therapies can enhance the dendritic cell priming of tumor-specific T cells and repolarize intratumoral macrophages to alleviate the tumoral immunosuppressive environment and remodel the extracellular matrix. Mitazalimab is a potent agonistic CD40 monoclonal IgG1 antibody currently under clinical development. This study used [...] Read more.
CD40-targeting therapies can enhance the dendritic cell priming of tumor-specific T cells and repolarize intratumoral macrophages to alleviate the tumoral immunosuppressive environment and remodel the extracellular matrix. Mitazalimab is a potent agonistic CD40 monoclonal IgG1 antibody currently under clinical development. This study used RNA sequencing of blood samples from a subset of patients from a Phase I trial with mitazalimab (NCT02829099) to assess peripheral pharmacodynamic activity. We found that mitazalimab induced transient peripheral transcriptomic alterations (at 600 µg/kg and 900 µg/kg dose administered intravenously), which mainly were attributed to immune activation. In particular, the transcriptomic alterations showed a reduction in effector cells (e.g., CD8+ T cells and natural killer cells) and B cells peripherally with the remaining cells (e.g., dendritic cells, monocytes, B cells, and natural killer cells) showing transcription profiles consistent with activation. Lastly, distinct patient subgroups based on the pattern of transcriptomic alterations could be identified. In summary, the data presented herein reinforce the anticipated mode of action of mitazalimab and support its ongoing clinical development. Full article
(This article belongs to the Special Issue Novel Microenvironment-Based Immune Changes Revealed by RNA Sequencing in Cancer or Metabolic Diseases)
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Review

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17 pages, 697 KiB  
Review
The Interplay between Immune and Metabolic Pathways in Kidney Disease
by Lili Qu and Baihai Jiao
Cells 2023, 12(12), 1584; https://doi.org/10.3390/cells12121584 - 8 Jun 2023
Cited by 30 | Viewed by 5173
Abstract
Kidney disease is a significant health problem worldwide, affecting an estimated 10% of the global population. Kidney disease encompasses a diverse group of disorders that vary in their underlying pathophysiology, clinical presentation, and outcomes. These disorders include acute kidney injury (AKI), chronic kidney [...] Read more.
Kidney disease is a significant health problem worldwide, affecting an estimated 10% of the global population. Kidney disease encompasses a diverse group of disorders that vary in their underlying pathophysiology, clinical presentation, and outcomes. These disorders include acute kidney injury (AKI), chronic kidney disease (CKD), glomerulonephritis, nephrotic syndrome, polycystic kidney disease, diabetic kidney disease, and many others. Despite their distinct etiologies, these disorders share a common feature of immune system dysregulation and metabolic disturbances. The immune system and metabolic pathways are intimately connected and interact to modulate the pathogenesis of kidney diseases. The dysregulation of immune responses in kidney diseases includes a complex interplay between various immune cell types, including resident and infiltrating immune cells, cytokines, chemokines, and complement factors. These immune factors can trigger and perpetuate kidney inflammation, causing renal tissue injury and progressive fibrosis. In addition, metabolic pathways play critical roles in the pathogenesis of kidney diseases, including glucose and lipid metabolism, oxidative stress, mitochondrial dysfunction, and altered nutrient sensing. Dysregulation of these metabolic pathways contributes to the progression of kidney disease by inducing renal tubular injury, apoptosis, and fibrosis. Recent studies have provided insights into the intricate interplay between immune and metabolic pathways in kidney diseases, revealing novel therapeutic targets for the prevention and treatment of kidney diseases. Potential therapeutic strategies include modulating immune responses through targeting key immune factors or inhibiting pro-inflammatory signaling pathways, improving mitochondrial function, and targeting nutrient-sensing pathways, such as mTOR, AMPK, and SIRT1. This review highlights the importance of the interplay between immune and metabolic pathways in kidney diseases and the potential therapeutic implications of targeting these pathways. Full article
(This article belongs to the Special Issue Novel Microenvironment-Based Immune Changes Revealed by RNA Sequencing in Cancer or Metabolic Diseases)
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