1
|
Long SA, Linsley PS. Integrating Omics into Functional Biomarkers of Type 1 Diabetes. Cold Spring Harb Perspect Med 2024; 14:a041602. [PMID: 38772709 DOI: 10.1101/cshperspect.a041602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Biomarkers are critical to the staging and diagnosis of type 1 diabetes (T1D). Functional biomarkers offer insights into T1D immunopathogenesis and are often revealed using "omics" approaches that integrate multiple measures to identify involved pathways and functions. Application of the omics biomarker discovery may enable personalized medicine approaches to circumvent the more recently appreciated heterogeneity of T1D progression and treatment. Use of omics to define functional biomarkers is still in its early years, yet findings to date emphasize the role of cytokine signaling and adaptive immunity in biomarkers of progression and response to therapy. Here, we share examples of the use of omics to define functional biomarkers focusing on two signatures, T-cell exhaustion and T-cell help, which have been associated with outcomes in both the natural history and treatment contexts.
Collapse
Affiliation(s)
- S Alice Long
- Center for Translational Immunology, Benaroya Research Institute, Seattle, Washington 98101, USA
| | - Peter S Linsley
- Center for Systems Immunology, Benaroya Research Institute, Seattle, Washington 98101, USA
| |
Collapse
|
2
|
Carriero F, Rubino V, Leone S, Montanaro R, Brancaleone V, Ruggiero G, Terrazzano G. Regulatory T R3-56 Cells in the Complex Panorama of Immune Activation and Regulation. Cells 2023; 12:2841. [PMID: 38132162 PMCID: PMC10742044 DOI: 10.3390/cells12242841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023] Open
Abstract
The interplay between immune activation and immune regulation is a fundamental aspect of the functional harmony of the immune system. This delicate balance is essential to triggering correct and effective immune responses against pathogens while preventing excessive inflammation and the immunopathogenic mechanisms of autoimmunity. The knowledge of all the mechanisms involved in immune regulation is not yet definitive, and, probably, the overall picture is much broader than what has been described in the scientific literature so far. Given the plasticity of the immune system and the diversity of organisms, it is highly probable that numerous other cells and molecules are still to be ascribed to the immune regulation process. Here, we report a general overview of how immune activation and regulation interact, based on the involvement of molecules and cells specifically dedicated to these processes. In addition, we discuss the role of TR3-56 lymphocytes as a new cellular candidate in the immune regulation landscape.
Collapse
Affiliation(s)
- Flavia Carriero
- Department of Sciences, University of Basilicata, 85100 Potenza, Italy; (F.C.); (R.M.); (V.B.)
| | - Valentina Rubino
- Department of Translational Medicine, University of Naples Federico II, 80131 Naples, Italy; (V.R.); (G.R.)
| | - Stefania Leone
- Hematopoietic Stem Cell Transplantation Unit, Azienda Ospedaliera A. Cardarelli, 80131 Naples, Italy;
| | - Rosangela Montanaro
- Department of Sciences, University of Basilicata, 85100 Potenza, Italy; (F.C.); (R.M.); (V.B.)
| | - Vincenzo Brancaleone
- Department of Sciences, University of Basilicata, 85100 Potenza, Italy; (F.C.); (R.M.); (V.B.)
| | - Giuseppina Ruggiero
- Department of Translational Medicine, University of Naples Federico II, 80131 Naples, Italy; (V.R.); (G.R.)
| | - Giuseppe Terrazzano
- Department of Sciences, University of Basilicata, 85100 Potenza, Italy; (F.C.); (R.M.); (V.B.)
| |
Collapse
|
3
|
Celada SI, Lim CX, Carisey AF, Ochsner SA, Arce Deza CF, Rexie P, Poli De Frias F, Cardenas-Castillo R, Polverino F, Hengstschläger M, Tsoyi K, McKenna NJ, Kheradmand F, Weichhart T, Rosas IO, Van Kaer L, Celada LJ. SHP2 promotes sarcoidosis severity by inhibiting SKP2-targeted ubiquitination of TBET in CD8 + T cells. Sci Transl Med 2023; 15:eade2581. [PMID: 37703351 PMCID: PMC11126869 DOI: 10.1126/scitranslmed.ade2581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 08/24/2023] [Indexed: 09/15/2023]
Abstract
Sarcoidosis is an interstitial lung disease (ILD) characterized by interferon-γ (IFN-γ) and T-box expressed in T cells (TBET) dysregulation. Although one-third of patients progress from granulomatous inflammation to severe lung damage, the molecular mechanisms underlying this process remain unclear. Here, we found that pharmacological inhibition of phosphorylated SH2-containing protein tyrosine phosphatase-2 (pSHP2), a facilitator of aberrant IFN-γ abundance, decreased large granuloma formation and macrophage infiltration in the lungs of mice with sarcoidosis-like disease. Positive treatment outcomes were dependent on the effective enhancement of TBET ubiquitination within CD8+ T cells. Mechanistically, we identified a posttranslational modification pathway in which the E3 F-box protein S-phase kinase-associated protein 2 (SKP2) targets TBET for ubiquitination in T cells under normal conditions. However, this pathway was disrupted by aberrant pSHP2 signaling in CD8+ T cells from patients with progressive pulmonary sarcoidosis and end-stage disease. Ex vivo inhibition of pSHP2 in CD8+ T cells from patients with end-stage sarcoidosis enhanced TBET ubiquitination and suppressed IFN-γ and collagen synthesis. Therefore, these studies provided new mechanistic insights into the SHP2-dependent posttranslational regulation of TBET and identified SHP2 inhibition as a potential therapeutic intervention against severe sarcoidosis. Furthermore, these studies also suggest that the small-molecule SHP2 inhibitor SHP099 might be used as a therapeutic measure against human diseases linked to TBET or ubiquitination.
Collapse
Affiliation(s)
- Sherly I. Celada
- Department of Biological Sciences, Tennessee State University, Nashville, TN 37209, USA
| | - Clarice X. Lim
- Center of Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
| | - Alexandre F. Carisey
- William T. Shearer Center for Human Immunobiology, Texas Children’s Hospital, Houston, TX 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Cell and Molecular Biology, St. Jude Children’s Hospital, Memphis, TN 38105, USA
| | - Scott A. Ochsner
- Department of Molecular and Cellular Biology, Houston, TX 77030, USA
| | - Carlos F. Arce Deza
- Department of Medicine, Section of Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Praveen Rexie
- Center of Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
| | - Fernando Poli De Frias
- Department of Medicine, Section of Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Mout Sinai Medical Center, Miami Beach, FL 33140, USA
| | - Rafael Cardenas-Castillo
- Department of Medicine, Section of Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Francesca Polverino
- Department of Medicine, Section of Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Markus Hengstschläger
- Center of Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
| | - Konstantin Tsoyi
- Department of Medicine, Section of Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Neil J. McKenna
- Department of Molecular and Cellular Biology, Houston, TX 77030, USA
| | - Farrah Kheradmand
- Department of Medicine, Section of Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Translational Research on Inflammatory Diseases, Michael E. DeBakey, Houston, TX 77030, USA
| | - Thomas Weichhart
- Center of Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
| | - Ivan O. Rosas
- Department of Medicine, Section of Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Luc Van Kaer
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232 USA
| | - Lindsay J. Celada
- Department of Medicine, Section of Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232 USA
| |
Collapse
|
4
|
Ochsner SA, Pedroza M, Pillich RT, Krishnan V, Konicek BW, Dow ER, Park SY, Agarwal SK, McKenna NJ. IL17A Blockade with Ixekizumab Suppresses MuvB Signaling in Clinical Psoriasis. J Invest Dermatol 2023; 143:1689-1699. [PMID: 36967086 DOI: 10.1016/j.jid.2023.03.1658] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 04/07/2023]
Abstract
Unbiased informatics approaches have the potential to generate insights into uncharacterized signaling pathways in human disease. In this study, we generated longitudinal transcriptomic profiles of plaque psoriasis lesions from patients enrolled in a clinical trial of the anti-IL17A antibody ixekizumab (IXE). This dataset was then computed against a curated matrix of over 700 million data points derived from published psoriasis and signaling node perturbation transcriptomic and chromatin immunoprecipitation-sequencing datasets. We observed substantive enrichment within both psoriasis-induced and IXE-repressed gene sets of transcriptional targets of members of the MuvB complex, a master regulator of the mitotic cell cycle. These gene sets were similarly enriched for pathways involved in the regulation of the G2/M transition of the cell cycle. Moreover, transcriptional targets for MuvB nodes were strongly enriched within IXE-repressed genes whose expression levels correlated strongly with the extent and severity of the psoriatic disease. In models of human keratinocyte proliferation, genes encoding MuvB nodes were transcriptionally repressed by IXE, and depletion of MuvB nodes reduced cell proliferation. Finally, we made the expression and regulatory networks that supported this study available as a freely accessible, cloud-based hypothesis generation platform. Our study positions inhibition of MuvB signaling as an important determinant of the therapeutic impact of IXE in psoriasis.
Collapse
Affiliation(s)
- Scott A Ochsner
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA; Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Mesias Pedroza
- Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Rudolf T Pillich
- Department of Medicine, University of California San Diego, California, USA
| | | | | | - Ernst R Dow
- Eli Lilly and Company, Indianapolis, Indiana, USA
| | | | - Sandeep K Agarwal
- Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Neil J McKenna
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA.
| |
Collapse
|