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Sharma M, Jha IP, Chawla S, Pandey N, Chandra O, Mishra S, Kumar V. Associating pathways with diseases using single-cell expression profiles and making inferences about potential drugs. Brief Bioinform 2022; 23:6623725. [PMID: 35772850 DOI: 10.1093/bib/bbac241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/22/2022] [Accepted: 05/23/2022] [Indexed: 11/14/2022] Open
Abstract
Finding direct dependencies between genetic pathways and diseases has been the target of multiple studies as it has many applications. However, due to cellular heterogeneity and limitations of the number of samples for bulk expression profiles, such studies have faced hurdles in the past. Here, we propose a method to perform single-cell expression-based inference of association between pathway, disease and cell-type (sci-PDC), which can help to understand their cause and effect and guide precision therapy. Our approach highlighted reliable relationships between a few diseases and pathways. Using the example of diabetes, we have demonstrated how sci-PDC helps in tracking variation of association between pathways and diseases with changes in age and species. The variation in pathways-disease associations in mice and humans revealed critical facts about the suitability of the mouse model for a few pathways in the context of diabetes. The coherence between results from our method and previous reports, including information about the drug target pathways, highlights its reliability for multidimensional utility.
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Affiliation(s)
- Madhu Sharma
- Department of computational biology, Indraprastha Institute of Information Technology, Okhla Ph-III, New Delhi
| | - Indra Prakash Jha
- Department of computational biology, Indraprastha Institute of Information Technology, Okhla Ph-III, New Delhi
| | - Smriti Chawla
- Department of computational biology, Indraprastha Institute of Information Technology, Okhla Ph-III, New Delhi
| | - Neetesh Pandey
- Department of computational biology, Indraprastha Institute of Information Technology, Okhla Ph-III, New Delhi
| | - Omkar Chandra
- Department of computational biology, Indraprastha Institute of Information Technology, Okhla Ph-III, New Delhi
| | - Shreya Mishra
- Department of computational biology, Indraprastha Institute of Information Technology, Okhla Ph-III, New Delhi
| | - Vibhor Kumar
- Department of computational biology, Indraprastha Institute of Information Technology, Okhla Ph-III, New Delhi
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Goldberg EK, Lal A, Fung EB. Nutrition in Thalassemia: A Systematic Review of Deficiency, Relations to Morbidity, and Supplementation Recommendations. J Pediatr Hematol Oncol 2022; 44:1-11. [PMID: 34486568 PMCID: PMC8732300 DOI: 10.1097/mph.0000000000002291] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 06/24/2021] [Indexed: 01/03/2023]
Abstract
BACKGROUND Reports of nutritional deficiencies in patients with thalassemia (Thal) are common. Despite its importance, however, nutritionally focused research in Thal has been limited by inadequate sample size, inconsistent methodology, a lack of control comparisons, and few interventional trials. Due to these limitations, clinicians lack evidence-based nutrition recommendations to support clinical decision-making. This systematic review summarizes observed relationships between nutrition and morbidity in Thal published in the last 3 decades. METHODS PubMed, Web of Science, and Embase were screened for articles pertaining to nutrition in Thal using comprehensive search terms. Studies performed in humans, written in English, and published between 1990 and 2020 were included. Over 2100 manuscripts were identified, from which 97 were included. RESULTS Patients with Thal were most often deficient in vitamins A, C, D, selenium, and zinc. Prevalence of nutritional deficiency was positively correlated with age and iron overload. Evidence to support the role of vitamin D and zinc for bone health was observed; zinc was also found to improve glucose metabolism. CONCLUSIONS Due to the risk for multinutrient deficiency, nutritional status should be assessed annually in patients with Thal with prompt nutrient replacement when deficiency is detected. Routine supplementation with vitamin D and zinc is recommended.
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Affiliation(s)
| | - Ashutosh Lal
- Division of Hematology, UCSF Benioff Children's Hospital Oakland, Oakland, CA
| | - Ellen B Fung
- Children's Hospital Oakland Research Institute (CHORI)
- Division of Hematology, UCSF Benioff Children's Hospital Oakland, Oakland, CA
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Al-Hakeim HK, Najm AH, Moustafa SR, Maes M. Construction of an exposure-pathway-phenotype in children with depression due to transfusion-dependent thalassemia: Results of (un)supervised machine learning. J Affect Disord 2021; 282:644-655. [PMID: 33445087 DOI: 10.1016/j.jad.2020.12.089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 11/05/2020] [Accepted: 12/22/2020] [Indexed: 01/19/2023]
Abstract
BACKGROUND Transfusion dependent thalassemia (TDT) patients are treated with continued blood transfusions and show a higher prevalence of depression. TDT with consequent iron overload and inflammation is associated with increased severity of depressive symptoms in TDT children. AIM OF THE STUDY To construct a pathway-phenotype which combines iron overload and neuro-immune biomarkers with depressive symptom subdomains in TDT children. METHODS We measured iron status parameters (iron, ferritin, transferrin saturation percentage) and inflammatory (interleukin-1β and tumour necrosis factor-α) biomarkers in TDT (n=111) and healthy (n=53) children and analyzed the results using machine learning. RESULTS Cluster analysis separated TDT children with depression from those without depression and revealed two depressive subgroups one with low self-esteem and another with increased social-irritability scores. Exploratory factor analysis validated four depressive symptom dimensions as reliable constructs, namely key depressive, physiosomatic, lowered self-esteem and social-irritability dimensions. Partial Least Squares showed that 73.0% of the variance in a latent vector extracted from those four clinical subdomains, immune-inflammatory and iron overload biomarkers was explained by exposure variables including the number of blood transfusions and hospitalizations and use of deferoxamine. The exposure data, iron and immune biomarkers, and symptom subdomains are reflective manifestations of a single latent trait, which shows internal consistency reliability and predictive relevance. CONCLUSIONS The nomological network combining exposure, pathways and behavioral phenome manifestations provides an index of overall severity and disease risk and, therefore, constitutes a new drug target, indicating that iron overload and immune activation should be targeted to treat depression due to TDT.
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Affiliation(s)
| | | | - Shatha Rouf Moustafa
- Clinical Analysis Department, College of Pharmacy, Hawler Medical University, Havalan City, Erbil, Iraq.
| | - Michael Maes
- Department of Psychiatry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Department of Psychiatry, Medical University of Plovdiv, Plovdiv, Bulgaria; IMPACT Strategic Research Centre, Deakin University, PO Box 281, Geelong, VIC, 3220, Australia.
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Al-Hakeim HK, Al-Mayali HH, Moustafa SR, Maes M. Cytokine dependent hematopoietic cell linker (CLNK) is highly elevated in blood transfusion dependent beta-thalassemia major patients. Transfus Clin Biol 2021; 28:194-198. [PMID: 33453373 DOI: 10.1016/j.tracli.2021.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/23/2020] [Accepted: 01/05/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND Transfusion-dependent β-thalassemia (TDT) is a severe form of thalassemia caused by mutations in the β-globin gene, resulting in partial or complete deficiency of β-globin chains. This deficiency results in oxidative stress, dyserythropoiesis, and chronic anemia. Cytokine-dependent hematopoietic cell linker (CLNK) belongs to adaptor proteins that have the capacity to interact with multiple signalling proteins and function in the organisation of the molecular components required for signal transduction. OBJECTIVES This is the first study which measured serum CLNK in TDT patients and examines the correlation between CLNK and iron overload biomarkers. PATIENTS AND METHODS Sixty children with TDT and 30 normal children (aged 3-12 years old) participated in the present study. The patients were on blood transfusion as a part of their treatment regimen. Serum C-reactive protein was negative in all samples. RESULTS The results showed significantly higher (P<0.001) serum CLNK levels in TDT patients as compared with controls. The TDT diagnosis explained 19.4% of the variance in CLNK levels. The increased levels of CLNK were significantly associated with indicants of iron overload, namely increased ferritin levels. CONCLUSIONS Increased CLNK levels in TDT may be explained by reciprocal effects between immune signalling and immature erythrocytes, which release soluble receptors and signalling molecules, including CLNK, in the blood.
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Affiliation(s)
- H K Al-Hakeim
- Department of Chemistry, College of Science, University of Kufa, Najaf, Iraq.
| | - H H Al-Mayali
- Department of Chemistry, College of Science, University of Kufa, Najaf, Iraq.
| | - S R Moustafa
- Clinical analysis department, College of Pharmacy, Hawler Medical University, Havalan City, Erbil, Iraq.
| | - M Maes
- Department of psychiatry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Department of psychiatry, Medical University Plovdiv, Plovdiv, Bulgaria; IMPACT research centre, Deakin University, Geelong, Australia.
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Smesam HNK, Albuthabhak HAQ, Arjmand S, Al-Hakeim HK, R Siadat SO. Evaluation of Erythroferrone, Hepcidin, and Iron Overload Status in Iraqi Transfusion-Dependent β-Thalassemia Major Patients. Hemoglobin 2020; 44:272-277. [PMID: 32718192 DOI: 10.1080/03630269.2020.1794888] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Patients with β-thalassemia major (β-TM) show ineffective erythropoiesis and iron overload, which is the leading cause of mortality and organ injury. The present study aimed to investigate the relationships between two iron regulatory hormones, hepcidin and erythroferrone (ERFE) levels, and iron status parameters in Iraqi patients with β-TM. Iron status parameters and hormones were measured in 60 patients and compared with 30 healthy controls. The results indicated significant changes in different iron status parameters, while ferritin with the ∼11-fold increase showed the most change. Significant reduction in hepcidin and an increase in ERFE levels were detected in patients when compared to the control group, while no direct correlation was identified with the other measured iron status parameters. The receiver operating characteristic (ROC) analysis showed that the z-score of the composite of ERFE + ferritin has a full diagnostic ability for β-TM. In conclusion, our findings indicated the correlation between different iron status parameters and ferritin as the leading predictor of iron overload and two main iron regulatory hormones.
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Affiliation(s)
- Hasan N K Smesam
- Department of Chemistry, College of Science, University of Kufa, Kufa, Iraq
| | | | - Sareh Arjmand
- Protein Research Center, Shahid Beheshti University, G.C., Tehran, Iran
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Al-Dujaili AH, Al-Hakeim HK, Twayej AJ, Maes M. Total and ionized calcium and magnesium are significantly lowered in drug-naïve depressed patients: effects of antidepressants and associations with immune activation. Metab Brain Dis 2019; 34:1493-1503. [PMID: 31292851 DOI: 10.1007/s11011-019-00458-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/03/2019] [Indexed: 02/06/2023]
Abstract
Major depressive disorder (MDD) is associated with alterations in calcium (Ca) and magnesium (Mg), as well as circulating pro- and anti-inflammatory cytokines. Anti-inflammatory drugs are commonly used as adjuvant treatments for MDD. However, no studies examined the effects of a combinatorial treatment with sertraline and ketoprofen, an anti-inflammatory drug, on Ca and Mg levels in MDD. The present study examined a) differences in both cations between drug-naïve MDD patients and controls, and b) the effects of sertraline and ketoprofen on Ca and Mg (both total and ionized). In the same patients, we also examined the associations between both cations and IL-1β, IL-4, IL-6, IL-18, IFN-γ, TGF-β1, zinc, and indoleamine 2,3-dioxygenase (IDO). Clinical improvement was assessed using the Beck Depression Inventory-II (BDI-II) at baseline and after follow up for 2 months. Serum Ca and Mg (total and ionized) were significantly lower in MDD patients as compared with controls, while treatment significantly increased calcium but decreased magnesium levels. There were significant and inverse correlations between the BDI-II scores from baseline to endpoint and Ca (both total and ionized), but not Mg, levels. The effects of calcium on the BDI-II score remained significant after considering the effects of zinc, IDO and an immune activation z unit-weighted composite score based on the sum of all cytokines. There was a significant and inverse association between this immune activation index and calcium levels from baseline to endpoint. In conclusion, lowered levels of both cations play a role in the pathophysiology of major depression. Antidepressant-induced increases in Ca are associated with clinical efficacy and attenuation of the immune response. The suppressant effect of antidepressants on Mg levels is probably a side effect of those drugs. New antidepressant treatments should be developed that increase the levels both Ca and Mg. Graphical abstract.
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Affiliation(s)
| | | | - Ahmed Jasim Twayej
- Pathological Analysis Department, College of Health and Medical, Al-Kafeel University, Najaf, Iraq
| | - Michael Maes
- Department of Psychiatry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
- Department of Psychiatry, Medical University of Plovdiv, Plovdiv, Bulgaria.
- School of Medicine, IMPACT Strategic Research Centre, Deakin University, PO Box 281, Geelong, VIC, 3220, Australia.
- IMPACT Strategic Research Center, Barwon Health, Deakin University, Geelong, VIC, Australia.
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