1
|
Li X, Huang Z, Zhu L, Lai W, Li Y, Chen H, Liu D, Huang J, Zhou D, Li Y, Weng W, Xu H, Xu L, Luo Z, Fang J. The potential role of RNA sequencing in diagnosing unexplained insensitivity to conventional chemotherapy in pediatric patients with B-cell acute lymphoblastic leukemia. BMC Med Genomics 2024; 17:149. [PMID: 38811988 PMCID: PMC11137891 DOI: 10.1186/s12920-024-01892-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 04/25/2024] [Indexed: 05/31/2024] Open
Abstract
Pediatric B-cell acute lymphoblastic leukemia (B-ALL) is a highly heterogeneous disease. According to large-scale RNA sequencing (RNA-seq) data, B-ALL patients can be divided into more than 10 subgroups. However, many genomic defects associated with resistance mechanisms have not yet been identified. As an individual clinical tool for molecular diagnostic risk classification, RNA-seq and gene expression pattern-based therapy could be potential upcoming strategies. In this study, we retrospectively analyzed the RNA-seq gene expression profiles of 45 children whose molecular diagnostic classifications were inconsistent with the response to chemotherapy. The relationship between the transcriptome and chemotherapy response was analyzed. Fusion gene identification was conducted for the included patients who did not have known high-risk associated fusion genes or gene mutations. The most frequently detected fusion gene pair in the high-risk group was the DHRSX duplication, which is a novel finding. Fusions involving ABL1, LMNB2, NFATC1, PAX5, and TTYH3 at onset were more frequently detected in the high-risk group, while fusions involving LFNG, TTYH3, and NFATC1 were frequently detected in the relapse group. According to the pathways involved, the underlying drug resistance mechanism is related to DNA methylation, autophagy, and protein metabolism. Overall, the implementation of an RNA-seq diagnostic system will identify activated markers associated with chemotherapy response, and guide future treatment adjustments.
Collapse
Affiliation(s)
- Xinyu Li
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, China
| | - Zaoli Huang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, 510080, Guangzhou, China
| | - Liwen Zhu
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Weixin Lai
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Yunyao Li
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Han Chen
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Diandian Liu
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Junjiu Huang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Dunhua Zhou
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Yang Li
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Wenjun Weng
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Honggui Xu
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Luhong Xu
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China.
| | - Zhenhua Luo
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, 510080, Guangzhou, China.
| | - Jianpei Fang
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China.
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, China.
| |
Collapse
|
2
|
Gupta DG, Varma N, Sharma P, Truica MI, Abdulkadir SA, Singh P, Singh Sachdeva MU, Naseem S, Siddiqui MR, Bose P, Binota J, Malhotra P, Khadwal A, Trehan A, Varma S. Hematological, clinical, immunophenotypic characterization, and treatment outcomes of prognostically significant genetic subtypes of B-lineage acute lymphoblastic leukemia: A report of 1021 patients from India. Cancer 2023; 129:3390-3404. [PMID: 37498973 DOI: 10.1002/cncr.34957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 07/29/2023]
Abstract
BACKGROUND The published literature on hematological, clinical, flowcytometric-immunophenotyping, and minimal residual disease outcomes of the prognostically important genetic subtypes of acute lymphoblastic leukemia (ALL) is scarce from low-income countries. For newer classifications such as BCR::ABL1-like ALLs, the scarcity of patient-level data is even more pronounced. METHODS The authors performed comprehensive detection of recurrent gene fusions and BCR::ABL1-like ALL cases followed by immunophenotypic profiling and obtained clinical outcome parameters for a large cohort (n = 1021) of patients from India. This cohort included a significant number of patients with BCR::ABL1-like ALL subtype and other genetic subtypes of ALL. RESULTS Patients with BCR::ABL1-positive and BCR::ABL1-like ALL were significantly older, had male preponderance, and expressed a higher white blood cell count than BCR::ABL1-negative cases (p < .05). Logistic regression modeling of B-lineage-ALL (B-ALL) subtypes revealed that cluster of differentiation (CD)36 is a strong statistically significant predictive marker of BCR::ABL1-like ALL (p < .05). Furthermore, patients with BCR::ABL1-like ALLs show a significantly higher frequency of CD36 expression compared to BCR::ABL1-negative ALLs (p < .05). In terms of clinical symptoms, lymphadenopathy is a strong statistically significant predictive marker in BCR::ABL1-like ALLs compared to BCR::ABL1-negative ALL cases (p < .05). In terms of treatment outcomes, minimal residual disease (MRD) positivity in BCR::ABL1-positive ALL cases were statistically significant (p < .05), and BCR::ABL1-like ALL cases had high MRD-positivity as compared to BCR::ABL1-negative ALL cases but did not show statistical significance. CONCLUSIONS The findings evince the use of novel therapies and personalized treatment regimens to improve the overall survival of the newer incorporated entities in B-ALLs. This is the first report characterizing the hematological, clinical, flowcytometric-immunophenotyping, and minimal residual disease outcomes of the prognostically significant subtypes of ALLs in patients from India. PLAIN LANGUAGE SUMMARY Characterizing the hematological, clinical, flowcytometric-immunophenotyping, and minimal residual disease outcomes of the prognostically significant subtypes (n = 1021) of acute lymphoblastic leukemia (ALLs) in patients from India. We have made two independent logistic regression models of cluster of differentiation (CD) markers and clinical symptoms to differentiate prognostically significant subtypes of ALLs. Logistic regression analysis of CD markers revealed CD36 as a strong predictor in BCR::ABL1-like ALL cases compared to BCR::ABL1-negative ALL cases. Logistic regression analysis of clinical symptoms revealed lymphadenopathy significantly predicts BCR::ABL1-like ALLs (p < .05). In terms of treatment outcomes, BCR::ABL1-positive ALL had statistically significant minimal residual disease (MRD) (p < .05), and BCR::ABL1-like ALL cases had high MRD-positivity but did not show statistical significance as compared to BCR::ABL1-negative ALLs.
Collapse
Affiliation(s)
- Dikshat Gopal Gupta
- Department of Urology and Pathology, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Neelam Varma
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Praveen Sharma
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Mihai I Truica
- Department of Urology and Pathology, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Sarki A Abdulkadir
- Department of Urology and Pathology, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Parmod Singh
- Department of Anatomy, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Man Updesh Singh Sachdeva
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Shano Naseem
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Mohammad Rizwan Siddiqui
- Department of Pediatrics, Northwestern University Feinberg School of Medicine and Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Parveen Bose
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Jogeshwar Binota
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Pankaj Malhotra
- Department of Clinical Hematology and Medical Oncology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Alka Khadwal
- Department of Internal Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Amita Trehan
- Pediatric Hematology Oncology Unit, Department of Pediatrics, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Subhash Varma
- Department of Internal Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| |
Collapse
|
3
|
Franca R, Stocco G, Kiren V, Tessitore A, Fagioli F, Quarello P, Bertorello N, Rizzari C, Colombini A, Bettini LR, Locatelli F, Vinti L, Girardi K, Silvestri D, Valsecchi MG, Decorti G, Rabusin M. Impact of Mercaptopurine Metabolites on Disease Outcome in the AIEOP-BFM ALL 2009 Protocol for Acute Lymphoblastic Leukemia. Clin Pharmacol Ther 2023; 114:1082-1092. [PMID: 37550838 DOI: 10.1002/cpt.3022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 08/01/2023] [Indexed: 08/09/2023]
Abstract
In the maintenance phase of Associazione Italiana di Ematologia e Oncologia Pediatrica (AIEOP)- Berlin-Frankfurt-Muenster (BFM) acute lymphoblastic leukemia (ALL) 2009 protocol, mercaptopurine (MP) is given at the planned dose of 50 mg/m2 /day; however, dose adjustments are routinely performed to target patients' white blood cells to the optimal range of 2,000-3,000 cells/μL. Pediatric patients with ALL (n = 290, age: median (1st-3rd quartile): 4.8 (3.0-8.1) years; boys: 56.9%) were enrolled mainly in 4 medium-large Italian pediatric hospitals; 14.1% of patients relapsed after a median (1st-3rd quartile) follow-up time of 4.43 (3.82-5.46) years from maintenance beginning. MP metabolites (thionucleotide (TGN) and methyl-derivatives (MMPN)) were measured in the erythrocytes of 387 blood samples of 200 patients by high performance liquid chromatography with ultraviolet detection. Single-nucleotide polymorphisms (SNPs; (rs1800462, rs1800460, and rs1142345 in TPMT gene, rs116855232 in NUDT15, rs1127354, rs7270101, rs6051702 in ITPA, and rs2413739 in PACSIN2) were characterized by Taqman SNP genotyping assays. Cox proportional hazard models did not show an impact of TGN levels and variability on relapse. In contrast, after multivariate analysis, relapse hazard ratio (HR) increased in children with ALL of the intermediate risk arm compared with those in standard risk arm (3.44, 95% confidence interval (CI), 1.31-9.05, P = 0.012), and in carriers of the PACSIN2 rs2413739 T allele compared with those with the CC genotype (heterozygotes CT: HR, 2.32, 95% CI, 0.90-5.97, P = 0.081; and homozygous TT: HR, 4.14, 95% CI, 1.54-11.11, P = 0.005). Future studies are needed to confirm the lack of impact of TGN levels and variability on relapse in the AIEOP-BFM ALL trials, and to clarify the mechanism of PACSIN2 rs2413739 on outcome.
Collapse
Affiliation(s)
- Raffaella Franca
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Gabriele Stocco
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Trieste, Italy
| | - Valentina Kiren
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Trieste, Italy
| | - Antimo Tessitore
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Franca Fagioli
- Paediatric Onco-Haematology Department, Regina Margherita Children's Hospital, Turin, Italy
- Department of Public Health and Pediatrics, University of Turin, Turin, Italy
| | - Paola Quarello
- Paediatric Onco-Haematology Department, Regina Margherita Children's Hospital, Turin, Italy
- Department of Public Health and Pediatrics, University of Turin, Turin, Italy
| | - Nicoletta Bertorello
- Paediatric Onco-Haematology Department, Regina Margherita Children's Hospital, Turin, Italy
| | - Carmelo Rizzari
- University of Milano-Bicocca, Milan, Italy
- Pediatric Hematology Oncology Unit, MBBM Foundation, ASST Monza, Monza, Italy
| | - Antonella Colombini
- Pediatric Hematology Oncology Unit, MBBM Foundation, ASST Monza, Monza, Italy
| | - Laura Rachele Bettini
- University of Milano-Bicocca, Milan, Italy
- Pediatric Hematology Oncology Unit, MBBM Foundation, ASST Monza, Monza, Italy
| | - Franco Locatelli
- Pediatric Hematology and Oncology, IRCCS Ospedale Pediatrico Bambin Gesù, Rome, Italy
| | - Luciana Vinti
- Pediatric Hematology and Oncology, IRCCS Ospedale Pediatrico Bambin Gesù, Rome, Italy
| | - Katia Girardi
- Pediatric Hematology and Oncology, IRCCS Ospedale Pediatrico Bambin Gesù, Rome, Italy
| | - Daniela Silvestri
- Pediatric Hematology Oncology Unit, MBBM Foundation, ASST Monza, Monza, Italy
| | - Maria Grazia Valsecchi
- Bicocca Centre of Bioinformatics, Biostatistics and Bioimaging, School of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Giuliana Decorti
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Trieste, Italy
| | - Marco Rabusin
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Trieste, Italy
| |
Collapse
|
4
|
Boni C, Bonifacio M, Vezzalini M, Scaffidi L, Tomasello L, Parker LL, Boscarino D, Paladin D, Krampera M, Sorio C. Successful Preservation of Native BCR::ABL1 in Chronic Myeloid Leukemia Primary Leukocytes Reveals a Reduced Kinase Activity. Front Oncol 2022; 12:904510. [PMID: 35756686 PMCID: PMC9216732 DOI: 10.3389/fonc.2022.904510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 04/19/2022] [Indexed: 11/25/2022] Open
Abstract
Chronic myeloid leukemia (CML) is a myeloproliferative disease caused by the acquisition of t(9;22) generating the fusion tyrosine kinase BCR::ABL1. However, despite the crucial role of this protein in the dysregulation of numerous signal transduction pathways, a direct measure of BCR::ABL1 kinase activity in chronic phase (CP) CML was never accomplished due to intense degradative activity present in mature leukocytes. Therefore, we developed a procedure suitable to preserve BCR::ABL1 protein under non-denaturing, neutral pH conditions in primary, chronic phase (CP)-CML samples. As a result, specific kinase activity was detected utilizing a biotinylated peptide substrate highly selective for c-ABL1. Furthermore, through this approach, BCR::ABL1 kinase activity was barely detectable in CP-CML compared to Ph+ acute lymphoblastic leukemia primary samples, where kinase activity is comparable to those measured in Ph+ cell lines. These in vitro findings provide the first direct measure of BCR::ABL1 kinase activity in primary CP-CML and reveal the presence of a still uncharacterized inhibitory mechanism that maintains BCR::ABL1 in a low activity state in CP-CML despite its overexpression.
Collapse
Affiliation(s)
- Christian Boni
- Department of Medicine, General Pathology Section, University of Verona, Verona, Italy
| | | | - Marzia Vezzalini
- Department of Medicine, General Pathology Section, University of Verona, Verona, Italy
| | - Luigi Scaffidi
- Department of Medicine, Hematology Section, University of Verona, Verona, Italy
| | - Luisa Tomasello
- Department of Medicine, General Pathology Section, University of Verona, Verona, Italy
| | - Laurie L Parker
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, University of Minnesota, Minneapolis, United States
| | | | | | - Mauro Krampera
- Department of Medicine, Hematology Section, University of Verona, Verona, Italy
| | - Claudio Sorio
- Department of Medicine, General Pathology Section, University of Verona, Verona, Italy
| |
Collapse
|
5
|
Solomon O, Sapir H, Mervinetsky E, Chen Y, Friedler A, Yitzchaik S. Kinase Sensing Based on Protein Interactions at the Catalytic Site. Chemistry 2022; 28:e202104227. [DOI: 10.1002/chem.202104227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Indexed: 12/12/2022]
Affiliation(s)
- Ohad Solomon
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology The Hebrew University of Jerusalem Safra Campus, Givat Ram Jerusalem 91904 Israel
| | - Hannah Sapir
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology The Hebrew University of Jerusalem Safra Campus, Givat Ram Jerusalem 91904 Israel
| | - Evgeniy Mervinetsky
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology The Hebrew University of Jerusalem Safra Campus, Givat Ram Jerusalem 91904 Israel
| | - Yu‐Ju Chen
- Institute of Chemistry Academia Sinica No. 128, Section2, Academia Road Taipei 115 Taiwan
| | - Assaf Friedler
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology The Hebrew University of Jerusalem Safra Campus, Givat Ram Jerusalem 91904 Israel
| | - Shlomo Yitzchaik
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology The Hebrew University of Jerusalem Safra Campus, Givat Ram Jerusalem 91904 Israel
| |
Collapse
|