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Kim MJ, Kulkarni V, Goode MA, Hernandez J, Graham S, Sivesind TE, Manchadi ML. Utilizing systems genetics to enhance understanding into molecular targets of skin cancer. Exp Dermatol 2024; 33:e15043. [PMID: 38459629 PMCID: PMC11018140 DOI: 10.1111/exd.15043] [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: 12/31/2023] [Revised: 02/12/2024] [Accepted: 02/16/2024] [Indexed: 03/10/2024]
Abstract
Despite progress made with immune checkpoint inhibitors and targeted therapies, skin cancer remains a significant public health concern in the United States. The intricacies of the disease, encompassing genetics, immune responses, and external factors, call for a comprehensive approach. Techniques in systems genetics, including transcriptional correlation analysis, functional pathway enrichment analysis, and protein-protein interaction network analysis, prove valuable in deciphering intricate molecular mechanisms and identifying potential diagnostic and therapeutic targets for skin cancer. Recent studies demonstrate the efficacy of these techniques in uncovering molecular processes and pinpointing diagnostic markers for various skin cancer types, highlighting the potential of systems genetics in advancing innovative therapies. While certain limitations exist, such as generalizability and contextualization of external factors, the ongoing progress in AI technologies provides hope in overcoming these challenges. By providing protocols and a practical example involving Braf, we aim to inspire early-career experimental dermatologists to adopt these tools and seamlessly integrate these techniques into their skin cancer research, positioning them at the forefront of innovative approaches in combating this devastating disease.
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Affiliation(s)
- Minjae J Kim
- University of Tennessee Health Science Center School of Medicine, Memphis, Tennessee, USA
| | | | - Micah A Goode
- University of Tennessee Health Science Center School of Medicine, Memphis, Tennessee, USA
| | - Jacob Hernandez
- University of Tennessee Health Science Center School of Medicine, Memphis, Tennessee, USA
| | - Sean Graham
- University of Tennessee Health Science Center School of Medicine, Memphis, Tennessee, USA
| | - Torunn E Sivesind
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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Kim MJ, Martin CA, Kim J, Jablonski MM. Computational methods in glaucoma research: Current status and future outlook. Mol Aspects Med 2023; 94:101222. [PMID: 37925783 PMCID: PMC10842846 DOI: 10.1016/j.mam.2023.101222] [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: 08/01/2023] [Revised: 10/06/2023] [Accepted: 10/19/2023] [Indexed: 11/07/2023]
Abstract
Advancements in computational techniques have transformed glaucoma research, providing a deeper understanding of genetics, disease mechanisms, and potential therapeutic targets. Systems genetics integrates genomic and clinical data, aiding in identifying drug targets, comprehending disease mechanisms, and personalizing treatment strategies for glaucoma. Molecular dynamics simulations offer valuable molecular-level insights into glaucoma-related biomolecule behavior and drug interactions, guiding experimental studies and drug discovery efforts. Artificial intelligence (AI) technologies hold promise in revolutionizing glaucoma research, enhancing disease diagnosis, target identification, and drug candidate selection. The generalized protocols for systems genetics, MD simulations, and AI model development are included as a guide for glaucoma researchers. These computational methods, however, are not separate and work harmoniously together to discover novel ways to combat glaucoma. Ongoing research and progresses in genomics technologies, MD simulations, and AI methodologies project computational methods to become an integral part of glaucoma research in the future.
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Affiliation(s)
- Minjae J Kim
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
| | - Cole A Martin
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
| | - Jinhwa Kim
- Graduate School of Artificial Intelligence, Graduate School of Metaverse, Department of Management Information Systems, Sogang University, 1 Shinsoo-Dong, Mapo-Gu, Seoul, South Korea.
| | - Monica M Jablonski
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
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Mukherjee S, Patra R, Behzadi P, Masotti A, Paolini A, Sarshar M. Toll-like receptor-guided therapeutic intervention of human cancers: molecular and immunological perspectives. Front Immunol 2023; 14:1244345. [PMID: 37822929 PMCID: PMC10562563 DOI: 10.3389/fimmu.2023.1244345] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/07/2023] [Indexed: 10/13/2023] Open
Abstract
Toll-like receptors (TLRs) serve as the body's first line of defense, recognizing both pathogen-expressed molecules and host-derived molecules released from damaged or dying cells. The wide distribution of different cell types, ranging from epithelial to immune cells, highlights the crucial roles of TLRs in linking innate and adaptive immunity. Upon stimulation, TLRs binding mediates the expression of several adapter proteins and downstream kinases, that lead to the induction of several other signaling molecules such as key pro-inflammatory mediators. Indeed, extraordinary progress in immunobiological research has suggested that TLRs could represent promising targets for the therapeutic intervention of inflammation-associated diseases, autoimmune diseases, microbial infections as well as human cancers. So far, for the prevention and possible treatment of inflammatory diseases, various TLR antagonists/inhibitors have shown to be efficacious at several stages from pre-clinical evaluation to clinical trials. Therefore, the fascinating role of TLRs in modulating the human immune responses at innate as well as adaptive levels directed the scientists to opt for these immune sensor proteins as suitable targets for developing chemotherapeutics and immunotherapeutics against cancer. Hitherto, several TLR-targeting small molecules (e.g., Pam3CSK4, Poly (I:C), Poly (A:U)), chemical compounds, phytocompounds (e.g., Curcumin), peptides, and antibodies have been found to confer protection against several types of cancers. However, administration of inappropriate doses of such TLR-modulating therapeutics or a wrong infusion administration is reported to induce detrimental outcomes. This review summarizes the current findings on the molecular and structural biology of TLRs and gives an overview of the potency and promises of TLR-directed therapeutic strategies against cancers by discussing the findings from established and pipeline discoveries.
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Affiliation(s)
- Suprabhat Mukherjee
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol, West Bengal, India
| | - Ritwik Patra
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol, West Bengal, India
| | - Payam Behzadi
- Department of Microbiology, Shahr-e-Qods Branch, Islamic Azad University, Tehran, Iran
| | - Andrea Masotti
- Research Laboratories, Bambino Gesù Children’s Hospital-IRCCS, Rome, Italy
| | - Alessandro Paolini
- Research Laboratories, Bambino Gesù Children’s Hospital-IRCCS, Rome, Italy
| | - Meysam Sarshar
- Research Laboratories, Bambino Gesù Children’s Hospital-IRCCS, Rome, Italy
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Yin C, Yan B. Machine learning in basic scientific research on oral diseases. DIGITAL MEDICINE 2023; 9. [DOI: 10.1097/dm-2023-00001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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Alotaibi F. Exosomal microRNAs in cancer: Potential biomarkers and immunotherapeutic targets for immune checkpoint molecules. Front Genet 2023; 14:1052731. [PMID: 36873941 PMCID: PMC9982116 DOI: 10.3389/fgene.2023.1052731] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 02/07/2023] [Indexed: 02/19/2023] Open
Abstract
Exosomes are small extracellular vesicles with a lipid bilayer structure secreted from different cell types which can be found in various body fluids including blood, pleural fluid, saliva and urine. They carry different biomolecules including proteins, metabolites, and amino acids such as microRNAs which are small non-coding RNAs that regulate gene expression and promote cell-to-cell communication. One main function of the exosomal miRNAs (exomiRs) is their role in cancer pathogenesis. Alternation in exomiRs expression could indicate disease progression and can regulate cancer growth and facilitate drug response/resistance. It can also influence the tumour microenvironment by controlling important signaling that regulating immune checkpoint molecules leading to activation of T cell anti-tumour immunity. Therefore, they can be used as potential novel cancer biomarkers and innovative immunotherapeutic agents. This review highlights the use of exomiRs as potential reliable biomarkers for cancer diagnosis, treatment response and metastasis. Finally, discuses their potential as immunotherapeutic agents to regulate immune checkpoint molecules and promote T cell anti-tumour immunity.
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Affiliation(s)
- Faizah Alotaibi
- College of Science and Health Professions, King Saud bin Abdulaziz University for Health Sciences and King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
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Sarshar M, Scribano D, Palamara AT, Ambrosi C, Masotti A. The Acinetobacter baumannii model can explain the role of small non-coding RNAs as potential mediators of host-pathogen interactions. Front Mol Biosci 2022; 9:1088783. [PMID: 36619166 PMCID: PMC9810633 DOI: 10.3389/fmolb.2022.1088783] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Bacterial small RNAs (sRNAs) research has accelerated over the past decade, boosted by advances in RNA-seq technologies and methodologies for capturing both protein-RNA and RNA-RNA interactions. The emerging picture is that these regulatory sRNAs play important roles in controlling complex physiological processes and are required to survive the antimicrobial challenge. In recent years, the RNA content of OMVs/EVs has also gained increasing attention, particularly in the context of infection. Secreted RNAs from several bacterial pathogens have been characterized but the exact mechanisms promoting pathogenicity remain elusive. In this review, we briefly discuss how secreted sRNAs interact with targets in infected cells, thus representing a novel perspective of host cell manipulation during bacterial infection. During the last decade, Acinetobacter baumannii became clinically relevant emerging pathogens responsible for nosocomial and community-acquired infections. Therefore, we also summarize recent findings of regulation by sRNAs in A. baumannii and discuss how this emerging bacterium utilizes many of these sRNAs to adapt to its niche and become successful human pathogen.
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Affiliation(s)
- Meysam Sarshar
- Research Laboratories, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy,*Correspondence: Meysam Sarshar, ; Andrea Masotti,
| | - Daniela Scribano
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Anna Teresa Palamara
- Laboratory Affiliated to Institute Pasteur Italia-Cenci Bolognetti Foundation, Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy,Department of Infectious Diseases, National Institute of Health, Rome, Italy
| | - Cecilia Ambrosi
- Department of Human Sciences and Promotion of the Quality of Life, San Raffaele Roma Open University, Rome, Italy,IRCCS San Raffaele Roma, Rome, Italy
| | - Andrea Masotti
- Research Laboratories, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy,*Correspondence: Meysam Sarshar, ; Andrea Masotti,
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Urinary Levels of miR-491-5p and miR-592 as Potential Diagnostic Biomarkers in Female Aging Patients with OAB: A Pilot Study. Metabolites 2022; 12:metabo12090820. [PMID: 36144224 PMCID: PMC9501158 DOI: 10.3390/metabo12090820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/17/2022] [Accepted: 08/19/2022] [Indexed: 11/17/2022] Open
Abstract
Women with overactive bladder syndrome (OAB) have a lower urinary ratio of nerve growth factor (NGF) to its precursor (proNGF) compared to healthy controls. MicroRNAs related to NGF and proNGF metabolism and to their receptors may be present in urine and may possess diagnostic value. Urine and blood samples from 20 control and 20 OAB women (50–80 years) were obtained, together with validated questionnaires and other clinical parameters. The relative expression of urinary microRNAs was measured with RT-qPCR. MiR-491-5p, which negatively controls the translation of the matrix metalloproteinase-9 (MMP-9), the main enzyme degrading NGF, was significantly decreased in OAB. Similarly, miR-592, which represses p75NTR receptor synthesis, was down-regulated in OAB. Age, renal function and insulin resistance did not affect these results. ROC curves confirmed the high sensitivity of miR-491-5p and miR-592 for diagnosis. On the other hand, miRNAs involved in the expression of proNGF, of survival receptor TrkA and of markers of nerve integrity were similar between groups. The detection of miR-491-5p and miR-592 in urine could be a useful and non-invasive tool for the diagnosis of OAB syndrome in aging women.
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