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Keshavarz A, Navidinia AA, Kuhestani Dehaghi BH, Amiri V, Mohammadi MH, Allahbakhshian Farsani M. Identification of Prognostic Genes in Acute Myeloid Leukemia Microenvironment: A Bioinformatic and Experimental Analysis. Mol Biotechnol 2024:10.1007/s12033-024-01128-3. [PMID: 38714601 DOI: 10.1007/s12033-024-01128-3] [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: 08/30/2023] [Accepted: 02/27/2024] [Indexed: 05/10/2024]
Abstract
Acute myeloid leukemia (AML) is a lethal hematologic malignancy with a variable prognosis that is highly dependent on the bone marrow microenvironment. Consequently, a better understanding of the AML microenvironment is crucial for early diagnosis, risk stratification, and personalized therapy. In recent years, the role of bioinformatics as a powerful tool in clarifying the complexities of cancer has become more prominent. Gene expression profile and clinical data of 173 AML patients were downloaded from the TCGA database, and the xCell algorithm was applied to calculate the microenvironment score (MS). Then, the correlation of MS with FAB classification, and CALGB cytogenetic risk category was investigated. Differentially expressed genes (DEGs) were identified, and the correlation analysis of DEGs with patient survival was done using univariate cox. The prognostic value of candidate prognostic DEGs was confirmed based on the GEO database. In the last step, real-time PCR was used to compare the expression of the top three prognostic genes between patients and the control group. During TCGA data analysis, 716 DEGs were identified, and survival analysis results showed that 152 DEGs had survival-related changes. In addition, the prognostic value of 31 candidate prognostic genes was confirmed by GEO data analysis. Finally, the expression analysis of FLVCR2, SMO, and CREB5 genes, the most related genes to patients' survival, was significantly different between patients and control groups. In summary, we identified key microenvironment-related genes that influence the survival of AML patients and may serve as prognostic and therapeutic targets.
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Affiliation(s)
- Ali Keshavarz
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box: 15468-15514, Tehran, Iran
| | - Amir Abbas Navidinia
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box: 15468-15514, Tehran, Iran
| | - Bentol Hoda Kuhestani Dehaghi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box: 15468-15514, Tehran, Iran
| | - Vahid Amiri
- Department of Laboratory Sciences, School of Paramedicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Mohammad Hossein Mohammadi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box: 15468-15514, Tehran, Iran
- HSCT Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Allahbakhshian Farsani
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box: 15468-15514, Tehran, Iran.
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Abdulrazaq ZA, Al-Ouqaili MT, Talib NM. The impact of circulating 25-hydroxyvitamin D and vitamin D receptor variation on leukemia-lymphoma outcome: Molecular and cytogenetic study. Saudi J Biol Sci 2024; 31:103882. [PMID: 38125732 PMCID: PMC10730835 DOI: 10.1016/j.sjbs.2023.103882] [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: 10/12/2023] [Revised: 11/11/2023] [Accepted: 11/24/2023] [Indexed: 12/23/2023] Open
Abstract
Vitamin D (VD) potentially has a crucial function in the development of cancerous cells. This study aims to detect the role of vitamin D concentration and its receptor polymorphisms as possible prognostic biomarkers in patients with leukemia/lymphoma and further will attempt to detect the presence of the Philadelphia chromosome abnormality in chronic myeloid leukemia (CML). Seventy-five patients, in addition to 50 healthy individuals were included. Three single nucleotide polymorphisms of the vitamin D receptor (FokI, Tru91, and ApaI) were identified via Polymerase Chain Reaction- Fragment Length Polymorphism (PCR-RFLP). Sanger sequencing and karyotyping for all patients has been undertaken. Out of 75 patients, 69 (92.0%) were vitamin D deficient. The homozygous genotype TT of FokI is the most commonly found in non-Hodgkin's lymphoma, while the heterozygous CT is observed markedly in CML, chronic lymphoid leukemia, and Hodgkin's lymphoma. The AC and CC genotypes of ApaI are more frequent in patients with CML, while the AC genotype is the most common in HL. In Tru9I, the GG genotype has a wider distribution in individuals diagnosed with leukemia. The PCR-RFLP and Sanger sequencing techniques together confirmed significant genotype respectively. The Philadelphia chromosome, t (9;22) was found in five (17%) cases with CML. There is a marked relationship between FokI, ApaI, and Tru91 polymorphisms and the chance of developing leukemia. In lymphoma, a significant connection between the polymorphisms of FokI and ApaI is frequently detected. Cytogenetic and molecular testing are essential for detection of CML and monitoring therapy response.
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Fibi-Smetana S, Inglis C, Schuster D, Eberle N, Granados-Soler JL, Liu W, Krohn S, Junghanss C, Nolte I, Taher L, Murua Escobar H. The TiHoCL panel for canine lymphoma: a feasibility study integrating functional genomics and network biology approaches for comparative oncology targeted NGS panel design. Front Vet Sci 2023; 10:1301536. [PMID: 38144469 PMCID: PMC10748409 DOI: 10.3389/fvets.2023.1301536] [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: 09/25/2023] [Accepted: 11/20/2023] [Indexed: 12/26/2023] Open
Abstract
Targeted next-generation sequencing (NGS) enables the identification of genomic variants in cancer patients with high sensitivity at relatively low costs, and has thus opened the era to personalized human oncology. Veterinary medicine tends to adopt new technologies at a slower pace compared to human medicine due to lower funding, nonetheless it embraces technological advancements over time. Hence, it is reasonable to assume that targeted NGS will be incorporated into routine veterinary practice in the foreseeable future. Many animal diseases have well-researched human counterparts and hence, insights gained from the latter might, in principle, be harnessed to elucidate the former. Here, we present the TiHoCL targeted NGS panel as a proof of concept, exemplifying how functional genomics and network approaches can be effectively used to leverage the wealth of information available for human diseases in the development of targeted sequencing panels for veterinary medicine. Specifically, the TiHoCL targeted NGS panel is a molecular tool for characterizing and stratifying canine lymphoma (CL) patients designed based on human non-Hodgkin lymphoma (NHL) research outputs. While various single nucleotide polymorphisms (SNPs) have been associated with high risk of developing NHL, poor prognosis and resistance to treatment in NHL patients, little is known about the genetics of CL. Thus, the ~100 SNPs featured in the TiHoCL targeted NGS panel were selected using functional genomics and network approaches following a literature and database search that shielded ~500 SNPs associated with, in nearly all cases, human hematologic malignancies. The TiHoCL targeted NGS panel underwent technical validation and preliminary functional assessment by sequencing DNA samples isolated from blood of 29 lymphoma dogs using an Ion Torrent™ PGM System achieving good sequencing run metrics. Our design framework holds new possibilities for the design of similar molecular tools applied to other diseases for which limited knowledge is available and will improve drug target discovery and patient care.
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Affiliation(s)
- Silvia Fibi-Smetana
- Institute of Biomedical Informatics, Graz University of Technology, Graz, Austria
| | - Camila Inglis
- Small Animal Clinic, University of Veterinary Medicine Hannover Foundation, Hannover, Germany
- Clinic for Hematology, Oncology and Palliative Care, Rostock University Medical Center, University of Rostock, Rostock, Germany
| | - Daniela Schuster
- Division of Bioinformatics, Department of Biology, Friedrich-Alexander-University, Erlangen, Germany
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, University of Rostock, Rostock, Germany
| | - Nina Eberle
- Small Animal Clinic, University of Veterinary Medicine Hannover Foundation, Hannover, Germany
| | - José Luis Granados-Soler
- Small Animal Clinic, University of Veterinary Medicine Hannover Foundation, Hannover, Germany
- UQVETS Small Animal Hospital, School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia
| | - Wen Liu
- Clinic for Hematology, Oncology and Palliative Care, Rostock University Medical Center, University of Rostock, Rostock, Germany
| | - Saskia Krohn
- Clinic for Hematology, Oncology and Palliative Care, Rostock University Medical Center, University of Rostock, Rostock, Germany
| | - Christian Junghanss
- Clinic for Hematology, Oncology and Palliative Care, Rostock University Medical Center, University of Rostock, Rostock, Germany
| | - Ingo Nolte
- Small Animal Clinic, University of Veterinary Medicine Hannover Foundation, Hannover, Germany
| | - Leila Taher
- Institute of Biomedical Informatics, Graz University of Technology, Graz, Austria
- Clinic for Hematology, Oncology and Palliative Care, Rostock University Medical Center, University of Rostock, Rostock, Germany
- Division of Bioinformatics, Department of Biology, Friedrich-Alexander-University, Erlangen, Germany
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, University of Rostock, Rostock, Germany
| | - Hugo Murua Escobar
- Clinic for Hematology, Oncology and Palliative Care, Rostock University Medical Center, University of Rostock, Rostock, Germany
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Hino C, Pham B, Park D, Yang C, Nguyen MH, Kaur S, Reeves ME, Xu Y, Nishino K, Pu L, Kwon SM, Zhong JF, Zhang KK, Xie L, Chong EG, Chen CS, Nguyen V, Castillo DR, Cao H. Targeting the Tumor Microenvironment in Acute Myeloid Leukemia: The Future of Immunotherapy and Natural Products. Biomedicines 2022; 10:biomedicines10061410. [PMID: 35740430 PMCID: PMC9219790 DOI: 10.3390/biomedicines10061410] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/09/2022] [Accepted: 06/09/2022] [Indexed: 12/12/2022] Open
Abstract
The tumor microenvironment (TME) plays an essential role in the development, proliferation, and survival of leukemic blasts in acute myeloid leukemia (AML). Within the bone marrow and peripheral blood, various phenotypically and functionally altered cells in the TME provide critical signals to suppress the anti-tumor immune response, allowing tumor cells to evade elimination. Thus, unraveling the complex interplay between AML and its microenvironment may have important clinical implications and are essential to directing the development of novel targeted therapies. This review summarizes recent advancements in our understanding of the AML TME and its ramifications on current immunotherapeutic strategies. We further review the role of natural products in modulating the TME to enhance response to immunotherapy.
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Affiliation(s)
- Christopher Hino
- Department of Internal Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (C.H.); (B.P.); (K.N.); (L.P.); (S.M.K.)
| | - Bryan Pham
- Department of Internal Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (C.H.); (B.P.); (K.N.); (L.P.); (S.M.K.)
| | - Daniel Park
- Department of Internal Medicine, School of Medicine, University of California San Francisco–Fresno, Fresno, CA 93701, USA;
| | - Chieh Yang
- Department of Internal Medicine, School of Medicine, University of California Riverside, Riverside, CA 92521, USA;
| | - Michael H.K. Nguyen
- Department of Oncology/Hematology, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (M.H.K.N.); (S.K.); (M.E.R.); (Y.X.); (E.G.C.); (C.-S.C.)
| | - Simmer Kaur
- Department of Oncology/Hematology, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (M.H.K.N.); (S.K.); (M.E.R.); (Y.X.); (E.G.C.); (C.-S.C.)
| | - Mark E. Reeves
- Department of Oncology/Hematology, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (M.H.K.N.); (S.K.); (M.E.R.); (Y.X.); (E.G.C.); (C.-S.C.)
| | - Yi Xu
- Department of Oncology/Hematology, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (M.H.K.N.); (S.K.); (M.E.R.); (Y.X.); (E.G.C.); (C.-S.C.)
| | - Kevin Nishino
- Department of Internal Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (C.H.); (B.P.); (K.N.); (L.P.); (S.M.K.)
| | - Lu Pu
- Department of Internal Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (C.H.); (B.P.); (K.N.); (L.P.); (S.M.K.)
| | - Sue Min Kwon
- Department of Internal Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (C.H.); (B.P.); (K.N.); (L.P.); (S.M.K.)
| | - Jiang F. Zhong
- Department of Basic Sciences, Loma Linda University, Loma Linda, CA 92354, USA;
| | - Ke K. Zhang
- Department of Nutrition, Texas A&M University, College Station, TX 77030, USA; (K.K.Z.); (L.X.)
- Center for Epigenetics & Disease Prevention, Institute of Biosciences & Technology, College of Medicine, Texas A&M University, Houston, TX 77030, USA
| | - Linglin Xie
- Department of Nutrition, Texas A&M University, College Station, TX 77030, USA; (K.K.Z.); (L.X.)
- Center for Epigenetics & Disease Prevention, Institute of Biosciences & Technology, College of Medicine, Texas A&M University, Houston, TX 77030, USA
| | - Esther G. Chong
- Department of Oncology/Hematology, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (M.H.K.N.); (S.K.); (M.E.R.); (Y.X.); (E.G.C.); (C.-S.C.)
| | - Chien-Shing Chen
- Department of Oncology/Hematology, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (M.H.K.N.); (S.K.); (M.E.R.); (Y.X.); (E.G.C.); (C.-S.C.)
| | - Vinh Nguyen
- Department of Biology, University of California Riverside, Riverside, CA 92521, USA;
| | - Dan Ran Castillo
- Department of Oncology/Hematology, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (M.H.K.N.); (S.K.); (M.E.R.); (Y.X.); (E.G.C.); (C.-S.C.)
- Correspondence: (D.R.C.); (H.C.)
| | - Huynh Cao
- Department of Oncology/Hematology, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (M.H.K.N.); (S.K.); (M.E.R.); (Y.X.); (E.G.C.); (C.-S.C.)
- Correspondence: (D.R.C.); (H.C.)
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Reisi N, Mirzaei A, Moafi A, Raeissi P, Naghdhassani M. Vitamin D abnormalities of children with recurrence of malignancy and comparison with newly diagnosed patients. CASPIAN JOURNAL OF INTERNAL MEDICINE 2022; 13:735-740. [PMID: 36420327 PMCID: PMC9659826 DOI: 10.22088/cjim.13.4.735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 09/13/2021] [Accepted: 09/22/2021] [Indexed: 06/16/2023]
Abstract
BACKGROUND Vitamin D (Vit-D) is a necessary ingredient for human growth and its deficiency may increase the risk of cancer and its recurrence. The main purpose of this research was to assess the levels of Vit-D in children with recurrence of malignancy and compare it with new cases of malignancy and the control group. METHODS The status of 25(OH) Vit-D was determined utilizing the HPLC method in 47 patients with recurrence of malignancy (group A), 50 children with new malignancy (group B) and 49 normal healthy siblings of the two groups as a control (group C). RESULTS Vit-D was low (<30 ng/ml) in the 92% of patients with recurrence of malignancy, which was a significant difference compared to groups B (60%) and C (45%). Vit-D insufficiency (10-30 ng/dl) in group A was also higher than the other two groups. The mean levels of Vit-D in patients with recurrence were significantly lower than the new cases and controls. Low Vit-D (<30 ng/ml) in group A in both male and female, and also in all ages (<6 and ≥ 6 years) was higher than groups B and C. Also, low Vit-D in terms of the type of malignancy in group A was higher than group B only in leukemic patients while this was not different for non-leukemic patients in these two groups. CONCLUSION Results of this study showed an increased prevalence of low Vit-D in children with recurrence of malignancies. Therefore, it may increase the risk of recurrence of malignancies in children.
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Affiliation(s)
- Nahid Reisi
- Department of Pediatric Hematology and Oncology, Faculty of Medicine, Child Growth and Development Research Center and Isfahan Immunodeficiency Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Azar Mirzaei
- Department of Pediatrics, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Alireza Moafi
- Department of Pediatric Hematology and Oncology, Faculty of Medicine, Child Growth and Development Research Center and Isfahan Immunodeficiency Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Pouran Raeissi
- Department of Health Service Management, School of Health Management and Medical Information Science, Iran University of Medical Sciences, Tehran, Iran
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Impact of Epigenetics on Complications of Fanconi Anemia: The Role of Vitamin D-Modulated Immunity. Nutrients 2020; 12:nu12051355. [PMID: 32397406 PMCID: PMC7285109 DOI: 10.3390/nu12051355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/02/2020] [Accepted: 05/06/2020] [Indexed: 12/14/2022] Open
Abstract
Fanconi anemia (FA) is a rare disorder with the clinical characteristics of (i) specific malformations at birth, (ii) progressive bone marrow failure already during early childhood and (iii) dramatically increased risk of developing cancer in early age, such as acute myeloid leukemia and squamous cell carcinoma. Patients with FA show DNA fragility due to a defect in the DNA repair machinery based on predominately recessive mutations in 23 genes. Interestingly, patients originating from the same family and sharing an identical mutation, frequently show significant differences in their clinical presentation. This implies that epigenetics plays an important role in the manifestation of the disease. The biologically active form of vitamin D, 1α,25-dihydroxyvitamin D3 controls cellular growth, differentiation and apoptosis via the modulation of the immune system. The nuclear hormone activates the transcription factor vitamin D receptor that affects, via fine-tuning of the epigenome, the transcription of >1000 human genes. In this review, we discuss that changes in the epigenome, in particular in immune cells, may be central for the clinical manifestation of FA. These epigenetic changes can be modulated by vitamin D suggesting that the individual FA patient’s vitamin D status and responsiveness are of critical importance for disease progression.
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