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Li X, Li X, Yang B, Sun S, Wang S, Yu F, Wang T. Enhancing breast cancer outcomes with machine learning-driven glutamine metabolic reprogramming signature. Front Immunol 2024; 15:1369289. [PMID: 38756785 PMCID: PMC11097668 DOI: 10.3389/fimmu.2024.1369289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/22/2024] [Indexed: 05/18/2024] Open
Abstract
Background This study aims to identify precise biomarkers for breast cancer to improve patient outcomes, addressing the limitations of traditional staging in predicting treatment responses. Methods Our analysis encompassed data from over 7,000 breast cancer patients across 14 datasets, which included in-house clinical data and single-cell data from 8 patients (totaling 43,766 cells). We utilized an integrative approach, applying 10 machine learning algorithms in 54 unique combinations to analyze 100 existing breast cancer signatures. Immunohistochemistry assays were performed for empirical validation. The study also investigated potential immunotherapies and chemotherapies. Results Our research identified five consistent glutamine metabolic reprogramming (GMR)-related genes from multi-center cohorts, forming the foundation of a novel GMR-model. This model demonstrated superior accuracy in predicting recurrence and mortality risks compared to existing clinical and molecular features. Patients classified as high-risk by the model exhibited poorer outcomes. IHC validation in 30 patients reinforced these findings, suggesting the model's broad applicability. Intriguingly, the model indicates a differential therapeutic response: low-risk patients may benefit more from immunotherapy, whereas high-risk patients showed sensitivity to specific chemotherapies like BI-2536 and ispinesib. Conclusions The GMR-model marks a significant leap forward in breast cancer prognosis and the personalization of treatment strategies, offering vital insights for the effective management of diverse breast cancer patient populations.
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Affiliation(s)
- Xukui Li
- Research Laboratory Center, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
- NHC Key Laboratory of Pulmonary Immune-related Diseases, Guizhou Provincial People’s Hospital, Guizhou University, Guiyang, Guizhou, China
| | - Xue Li
- Research Laboratory Center, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
- NHC Key Laboratory of Pulmonary Immune-related Diseases, Guizhou Provincial People’s Hospital, Guizhou University, Guiyang, Guizhou, China
| | - Bin Yang
- Research Laboratory Center, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
- NHC Key Laboratory of Pulmonary Immune-related Diseases, Guizhou Provincial People’s Hospital, Guizhou University, Guiyang, Guizhou, China
| | - Songyang Sun
- Research Laboratory Center, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
- NHC Key Laboratory of Pulmonary Immune-related Diseases, Guizhou Provincial People’s Hospital, Guizhou University, Guiyang, Guizhou, China
| | - Shu Wang
- Department of Breast Surgery, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
| | - Fuxun Yu
- Research Laboratory Center, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
- NHC Key Laboratory of Pulmonary Immune-related Diseases, Guizhou Provincial People’s Hospital, Guizhou University, Guiyang, Guizhou, China
| | - Tao Wang
- Research Laboratory Center, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
- NHC Key Laboratory of Pulmonary Immune-related Diseases, Guizhou Provincial People’s Hospital, Guizhou University, Guiyang, Guizhou, China
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Asif M, Hussain A, Wali A, Ahmed N, Ali I, Iqbal Z, Amir M, Shafiq M, Rasool M. Molecular, Cytogenetic, and Hematological Analysis of Chronic Myeloid Leukemia Patients and Discovery of Two Novel Translocations. Anal Cell Pathol (Amst) 2021; 2021:4909012. [PMID: 34422550 PMCID: PMC8378985 DOI: 10.1155/2021/4909012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/12/2021] [Accepted: 07/26/2021] [Indexed: 11/18/2022] Open
Abstract
Chronic myeloid leukemia (CML) is a disease of hematopoietic stem cells and is caused by the balanced translocations among the long arms of chromosomes 9 and 22, which are called the Philadelphia (Ph) chromosome. In this study, 131 CML patients were enrolled. Complete blood cell count was performed at the time of diagnosis for all the patients. Cytogenetic (karyotyping) examination using bone marrow samples was conducted on 76 CML patients for the confirmation of Ph-positive (9;22)(q34;q11) standard translocation, complex variant translocation, and additional chromosome abnormalities. FISH was performed on 38 patients for diagnostic purposes and on 39 patients for monitoring purposes. Twenty-two samples of CML patients were evaluated by reverse transcriptase PCR and real-time PCR for the patients who failed to respond against imatinib mesylate. In this study, 72 (54.96%) were males and 59 (45.03%) were females with a median age of 38.5 years. CBC values in the diagnosis process showed that 75 patients had high values of WBC being >100 × 103/μl, while 71 (58.01) patients exhibited reduced values of hemoglobin, i.e., <10.00 mg/dl, and high values of PLTs > 100 were observed in 40 (30.53%) patients. Cytogenetic results show that standard translocation was developed in 63 (82.89%), development of complex variant translocations in 4 (5.32%), additional chromosomal abnormalities (ACAs) in 3 (3.94%), and ACAs together with complex variant translocations in 1 (1.31%) patient. At the time of diagnosis, 61 (92.95%) patients were in the chronic phase, 4 (5.63%) were in the accelerated phase, and only 1 (1.40%) was in the blast crisis. Out of twenty-two patients, only 6 CML patients who were shifted from imatinib mesylate to nilotinib showed BCR-ABL-positive amplification. However, only 7 out of twenty-one patients exhibit BCR-ABL gene values ≥ 1 after three months of follow-up when analyzed by the quantitative real-time PCR. In conclusion, we found a novel five-way translocation 46XX,t(1;2;2;17;9;22)(p36.3,q21;q11.2,q21,q34,q11.2) and a novel four-way complex variant translocation 48XY,+8(8;17)(9;22),+der(22)(q11.2;q23)(q34;q11.2) in the accelerated phase.
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MESH Headings
- Adolescent
- Adult
- Antineoplastic Agents/therapeutic use
- Biomarkers, Tumor/genetics
- Drug Substitution
- Female
- Humans
- Imatinib Mesylate/therapeutic use
- In Situ Hybridization, Fluorescence
- Karyotyping
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/blood
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Male
- Middle Aged
- Philadelphia Chromosome
- Protein Kinase Inhibitors/therapeutic use
- Pyrimidines/therapeutic use
- Translocation, Genetic
- Treatment Outcome
- Young Adult
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Affiliation(s)
- Muhammad Asif
- Department of Biotechnology, BUITEMS, Quetta, Pakistan
- Office of Research Innovation and Commercialization, BUITEMS, Quetta, Pakistan
| | - Abrar Hussain
- Department of Biotechnology, BUITEMS, Quetta, Pakistan
| | - Abdul Wali
- Department of Biotechnology, BUITEMS, Quetta, Pakistan
| | - Nazeer Ahmed
- Department of Biotechnology, BUITEMS, Quetta, Pakistan
| | - Irfan Ali
- Centre of Agricultural Biochemistry and Biotechnology, Agriculture University of Faisalabad, Pakistan
| | - Zafar Iqbal
- Clinical Laboratory Sciences Program, College of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences/KAIMRC/SSBMT, National Guard Health Affairs, King Abdulaziz Medical City, Al-Ahsa, Saudi Arabia
| | - Muhammad Amir
- Department of Biotechnology, BUITEMS, Quetta, Pakistan
| | - Muhammad Shafiq
- Department of Biotechnology, University of Sialkot, Pakistan
| | - Mahmood Rasool
- Center of Excellence in Genomic Medicine Research, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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