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Martelloni G, Turchi A, Fallerini C, Degl’Innocenti A, Baldassarri M, Olmi S, Furini S, Renieri A. Host genetics and COVID-19 severity: increasing the accuracy of latest severity scores by Boolean quantum features. Front Genet 2024; 15:1362469. [PMID: 38841724 PMCID: PMC11150643 DOI: 10.3389/fgene.2024.1362469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 04/09/2024] [Indexed: 06/07/2024] Open
Abstract
The impact of common and rare variants in COVID-19 host genetics has been widely studied. In particular, in Fallerini et al. (Human genetics, 2022, 141, 147-173), common and rare variants were used to define an interpretable machine learning model for predicting COVID-19 severity. First, variants were converted into sets of Boolean features, depending on the absence or the presence of variants in each gene. An ensemble of LASSO logistic regression models was used to identify the most informative Boolean features with respect to the genetic bases of severity. After that, the Boolean features, selected by these logistic models, were combined into an Integrated PolyGenic Score (IPGS), which offers a very simple description of the contribution of host genetics in COVID-19 severity.. IPGS leads to an accuracy of 55%-60% on different cohorts, and, after a logistic regression with both IPGS and age as inputs, it leads to an accuracy of 75%. The goal of this paper is to improve the previous results, using not only the most informative Boolean features with respect to the genetic bases of severity but also the information on host organs involved in the disease. In this study, we generalize the IPGS adding a statistical weight for each organ, through the transformation of Boolean features into "Boolean quantum features," inspired by quantum mechanics. The organ coefficients were set via the application of the genetic algorithm PyGAD, and, after that, we defined two new integrated polygenic scores (IPGS p h 1 and IPGS p h 2 ). By applying a logistic regression with both IPGS, (IPGS p h 2 (or indifferently IPGS p h 1 ) and age as inputs, we reached an accuracy of 84%-86%, thus improving the results previously shown in Fallerini et al. (Human genetics, 2022, 141, 147-173) by a factor of 10%.
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Affiliation(s)
| | - Alessio Turchi
- INAF Osservatorio Astrofisico di Arcetri, Florence, Italy
| | - Chiara Fallerini
- Medical Genetics, University of Siena, Siena, Italy
- Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
| | - Andrea Degl’Innocenti
- Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
| | - Margherita Baldassarri
- Medical Genetics, University of Siena, Siena, Italy
- Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
| | - Simona Olmi
- CNR-Consiglio Nazionale delle Ricerche—Istituto dei Sistemi Complessi, Sesto Fiorentino, Italy
| | - Simone Furini
- Department of Electrical, Electronic and Information Engineering “Guglielmo Marconi”, University of Bologna, Cesena, Italy
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy
- Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
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Khalid K, Padda J, Wijeratne Fernando R, Mehta KA, Almanie AH, Al Hennawi H, Padda S, Cooper AC, Jean-Charles G. Stem Cell Therapy and Its Significance in HIV Infection. Cureus 2021; 13:e17507. [PMID: 34595076 PMCID: PMC8468364 DOI: 10.7759/cureus.17507] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2021] [Indexed: 12/02/2022] Open
Abstract
Human immunodeficiency virus (HIV) infection is a major global public health issue. Despite this, the only treatment available in mainstay is antiretroviral therapy. This treatment is not curative, it needs to be used lifelong, and there are many issues with compliance and side effects. In recent years, stem cell therapy has shown promising results in HIV management, and it can have a major impact on the future of HIV treatment and prevention. The idea behind anti-HIV hematopoietic stem/progenitor cell (HSPC)-directed gene therapy is to genetically engineer patient-derived (autologous) HSPC to acquire an inherent resistance to HIV infection. Multiple stem-cell-based gene therapy strategies have been suggested that may infer HIV resistance including anti-HIV gene reagents and gene combinatorial strategies giving rise to anti-HIV gene-modified HSPCs. Such stem cells can hamper HIV progression in the body by interrupting key stages of HIV proliferation: viral entry, viral integration, HIV gene expression, etc.Hematopoietic stem cells (HSCs) may also protect leukocytes from being infected. Additionally, genetically engineered HSCs have the ability to continuously produce protected immune cells by prolonged self-renewal that can attack the HIV virus. Therefore, a successful treatment strategy has the potential to control the infection at a steady state and eradicate HIV from patients. This will allow for a potential future benefit with stem cell therapy in HIV treatment.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Gutteridge Jean-Charles
- Internal Medicine, JC Medical Center, Orlando, USA.,Internal Medicine, AdventHealth & Orlando Health Hospital, Orlando, USA
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Pernet O, Yadav SS, An DS. Stem cell-based therapies for HIV/AIDS. Adv Drug Deliv Rev 2016; 103:187-201. [PMID: 27151309 PMCID: PMC4935568 DOI: 10.1016/j.addr.2016.04.027] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 04/21/2016] [Accepted: 04/25/2016] [Indexed: 12/26/2022]
Abstract
One of the current focuses in HIV/AIDS research is to develop a novel therapeutic strategy that can provide a life-long remission of HIV/AIDS without daily drug treatment and, ultimately, a cure for HIV/AIDS. Hematopoietic stem cell-based anti-HIV gene therapy aims to reconstitute the patient immune system by transplantation of genetically engineered hematopoietic stem cells with anti-HIV genes. Hematopoietic stem cells can self-renew, proliferate and differentiate into mature immune cells. In theory, anti-HIV gene-modified hematopoietic stem cells can continuously provide HIV-resistant immune cells throughout the life of a patient. Therefore, hematopoietic stem cell-based anti-HIV gene therapy has a great potential to provide a life-long remission of HIV/AIDS by a single treatment. Here, we provide a comprehensive review of the recent progress of developing anti-HIV genes, genetic modification of hematopoietic stem progenitor cells, engraftment and reconstitution of anti-HIV gene-modified immune cells, HIV inhibition in in vitro and in vivo animal models, and in human clinical trials.
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Affiliation(s)
- Olivier Pernet
- School of Nursing, University of California Los Angeles, 188 BSRB, 615 Charles E. Young Dr. South, Los Angeles, CA 90095, USA; UCLA AIDS Institute, 188 BSRB, 615 Charles E. Young Dr. South, Los Angeles, CA 90095, USA.
| | - Swati Seth Yadav
- School of Nursing, University of California Los Angeles, 188 BSRB, 615 Charles E. Young Dr. South, Los Angeles, CA 90095, USA; UCLA AIDS Institute, 188 BSRB, 615 Charles E. Young Dr. South, Los Angeles, CA 90095, USA.
| | - Dong Sung An
- School of Nursing, University of California Los Angeles, 188 BSRB, 615 Charles E. Young Dr. South, Los Angeles, CA 90095, USA; UCLA AIDS Institute, 188 BSRB, 615 Charles E. Young Dr. South, Los Angeles, CA 90095, USA; Hematology-Oncology, The Department of Medicine, David Geffen School of Medicine at UCLA, 188 BSRB, 615 Charles E. Young Dr. South, Los Angeles, CA 90095, USA.
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