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Luedersen J, Stadt UZ, Richter J, Oschlies I, Klapper W, Rosenwald A, Kalinova M, Simonitsch-Klupp I, Siebert R, Zimmermann M, Qi M, Nakel J, Scheinemann K, Knörr F, Attarbaschi A, Kabickova E, Woessmann W, Damm-Welk C. Variant ALK-fusion positive anaplastic large cell lymphoma (ALCL): A population-based paediatric study of the NHL-BFM study group. Br J Haematol 2024; 204:1894-1898. [PMID: 38279625 DOI: 10.1111/bjh.19308] [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: 11/02/2023] [Revised: 12/08/2023] [Accepted: 01/10/2024] [Indexed: 01/28/2024]
Abstract
Frequency, distribution and prognostic meaning of ALK-partner genes other than NPM1 in ALK-positive anaplastic large-cell lymphoma (ALCL) are unknown. Forty-nine of 316 ALCL diagnosed in the NHL-BFM study group showed no nuclear ALK expression suggestive of a variant ALK-partner; 41 were analysed by genomic capture high-throughput sequencing or specific RT-PCRs. NPM1::ALK was detected in 13 cases. Among the 28 patients with a non-NPM1::ALK-fusion partner, ATIC (n = 8; 29%) and TPM3 (n = 9; 32%) were the most common. Five of eight patients with ATIC::ALK-positive ALCL relapsed, none of nine with TPM3::ALK. Variant ALK-partners are rare and potentially associated with different prognoses.
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Affiliation(s)
- Jette Luedersen
- Paediatric Haematology and Oncology and NHL-BFM Study Centre, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Udo Zur Stadt
- Paediatric Haematology and Oncology and CoALL Study Centre, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Julia Richter
- Department of Pathology, Haematopathology Section and Lymph Node Registry, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Ilske Oschlies
- Department of Pathology, Haematopathology Section and Lymph Node Registry, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Wolfram Klapper
- Department of Pathology, Haematopathology Section and Lymph Node Registry, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Andreas Rosenwald
- Department of Pathology, University of Wuerzburg, Wuerzburg, Germany
| | - Marketa Kalinova
- Department of Pathology and Molecular Medicine, 2nd Faculty of Medicine, Charles University Prague and University Hospital in Motol, Prague, Czech Republic
- Department of Pathology, 3rd Faculty of Medicine, Charles University Prague and University Hospital Kralovske Vinohrady, Prague, Czech Republic
| | | | - Reiner Siebert
- Institute of Human Genetics, Ulm University & Ulm University Medical Centre, Ulm, Germany
| | - Martin Zimmermann
- Department of Paediatric Haematology and Oncology, Hannover Medical School, and NHL-BFM Study Centre, Hannover, Germany
| | - Minyue Qi
- Bioinformatics Core, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | | | - Katrin Scheinemann
- Division of Paediatric Haematology/Oncology, Children's Hospital of Eastern Switzerland, St. Gallen, Switzerland
- Faculty of Health Science and Medicine, University of Lucerne, Lucerne, Switzerland
- Department of Paediatrics, McMaster Children's Hospital and McMaster University, Hamilton, Ontario, Canada
| | - Fabian Knörr
- Paediatric Haematology and Oncology and NHL-BFM Study Centre, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
- Mildred Scheel Cancer Career Centre HaTriCS4, University Medical Centre Hamburg- Eppendorf, Hamburg, Germany
| | - Andishe Attarbaschi
- Department of Paediatric Haematology and Oncology, St. Anna Children's Hospital, Medical University of Vienna, Vienna, Austria
- St. Anna Children's Cancer Research Institute, Vienna, Austria
| | - Edita Kabickova
- Department of Pediatric Hematology and Oncology, Charles University Prague and University Hospital Motol, Prague, Czech Republic
| | - Wilhelm Woessmann
- Paediatric Haematology and Oncology and NHL-BFM Study Centre, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Christine Damm-Welk
- Paediatric Haematology and Oncology and NHL-BFM Study Centre, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
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Shang C, Lai J, Haque M, Chen W, Wang P, Lai R. Nuclear NPM-ALK Protects Myc from Proteasomal Degradation and Contributes to Its High Expression in Cancer Stem-Like Cells in ALK-Positive Anaplastic Large Cell Lymphoma. Int J Mol Sci 2023; 24:14337. [PMID: 37762644 PMCID: PMC10531997 DOI: 10.3390/ijms241814337] [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: 08/17/2023] [Revised: 09/13/2023] [Accepted: 09/16/2023] [Indexed: 09/29/2023] Open
Abstract
In ALK-positive anaplastic large cell lymphoma (ALK+ALCL), a small subset of cancer stem-like (or RR) cells characterized by high Myc expression have been identified. We hypothesize that NPM-ALK contributes to their high Myc expression. While transfection of NPM-ALK into HEK293 cells effectively increased Myc by inhibiting its proteosomal degradation (PD-Myc), this effect was dramatically attenuated when the full-length NPM1 (FL-NPM1) was downregulated using shRNA, highlighting the importance of the NPM-ALK:FL-ALK heterodimers in this context. Consistent with this concept, immunoprecipitation experiments showed that the heterodimers are abundant only in RR cells, in which the half-life of Myc is substantially longer than the bulk cells. Fbw7γ, a key player in PD-Myc, is sequestered by the heterodimers in RR cells, and this finding correlates with a Myc phosphorylation pattern indicative of ineffective PD-Myc. Using confocal microscopy and immunofluorescence staining, we found that the fusion signal between ALK and FL-NPM1, characteristic of the heterodimers, correlates with the Myc level in ALK+ALCL cells from cell lines and patient samples. To conclude, our findings have revealed a novel oncogenic function of NPM-ALK in the nucleus. Specifically, the NPM-ALK:FL-NPM1 heterodimers increase cancer stemness by blocking PD-Myc and promoting Myc accumulation in the cancer stem-like cell subset.
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Affiliation(s)
- Chuquan Shang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2R3, Canada; (C.S.); (M.H.); (W.C.)
| | - Justine Lai
- Department of Medicine, Division of Hematology, University of Alberta, Edmonton, AB T6G 2R3, Canada; (J.L.); (P.W.)
| | - Moinul Haque
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2R3, Canada; (C.S.); (M.H.); (W.C.)
- Department of Pathology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Will Chen
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2R3, Canada; (C.S.); (M.H.); (W.C.)
| | - Peng Wang
- Department of Medicine, Division of Hematology, University of Alberta, Edmonton, AB T6G 2R3, Canada; (J.L.); (P.W.)
- Department of Oncology, Cross Cancer Institute, Edmonton, AB T6G 1Z2, Canada
| | - Raymond Lai
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2R3, Canada; (C.S.); (M.H.); (W.C.)
- Department of Oncology, Cross Cancer Institute, Edmonton, AB T6G 1Z2, Canada
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Zhang X, Zhen D, Li X, Yi F, Zhang Z, Yang W, Li X, Sheng Y, Liu X, Jin T, He Y. NOTCH2, ATIC, MRI1, SLC6A13, ATP13A2 Genetic Variations are Associated with Ventricular Septal Defect in the Chinese Tibetan Population Through Whole-Exome Sequencing. Pharmgenomics Pers Med 2023; 16:389-400. [PMID: 37138656 PMCID: PMC10150769 DOI: 10.2147/pgpm.s404438] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/31/2023] [Indexed: 05/05/2023] Open
Abstract
Background Ventricular septal defect (VSD) is the most common congenital cardiac abnormality in children and the second most common in adults. This study aimed to explore the potentially causative genes in VSD patients in the Chinese Tibetan population, and to provide a theoretical basis for the genetic mechanism of VSD. Methods Peripheral venous blood was collected from 20 VSD subjects, and whole-genome DNA was extracted. High-throughput sequencing was performed on qualified DNA samples using whole-exome sequencing (WES) technology. After filtering, detecting, and annotating qualified data, single nucleotide variations (SNVs) and insertion-deletion (InDel) markers were analyzed, and data processing software such as GATK, SIFT, Polyphen, and MutationTaster were used for comparative evaluation and prediction of pathogenic deleterious variants associated with VSD. Results A total of 4793 variant loci, including 4168 SNVs, 557 InDels and 68 unknown loci and 2566 variant genes were obtained from 20 VSD subjects through bioinformatics analysis. According to the screening of the prediction software and database, the occurrence of VSD was predicted to be associated with five inherited pathogenic gene mutations, all of which were missense mutations, including NOTCH2 (c.1396C >A:p.Gln466Lys), ATIC (c.235C >T:p.Arg79Cys), MRI1 (c.629G >A:p.Arg210Gln), SLC6A13 (c.1138G >A:p.Gly380Arg), ATP13A2 (c.1363C >T:p.Arg455Trp). Conclusion This study demonstrated that NOTCH2, ATIC, MRI1, SLC6A13, ATP13A2 gene variants were potentially associated with VSD in Chinese Tibetan population.
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Affiliation(s)
- Xiaohui Zhang
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang, People’s Republic of China
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, People’s Republic of China
- Department of Ultrasound, the Affiliated Hospital of Xizang Minzu University, Xianyang, People’s Republic of China
| | - Da Zhen
- Department of Medical, Tibet Autonomous Region Maternity and Children’s Hospital, Lhasa, People’s Republic of China
| | - Xuemei Li
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang, People’s Republic of China
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, People’s Republic of China
- School of Medicine, Xizang Minzu University, Xianyang, People’s Republic of China
| | - Faling Yi
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang, People’s Republic of China
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, People’s Republic of China
- School of Medicine, Xizang Minzu University, Xianyang, People’s Republic of China
| | - Zhanhao Zhang
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang, People’s Republic of China
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, People’s Republic of China
- School of Medicine, Xizang Minzu University, Xianyang, People’s Republic of China
| | - Wei Yang
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang, People’s Republic of China
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, People’s Republic of China
- Department of Emergency, the Affiliated Hospital of Xizang Minzu University, Xianyang, People’s Republic of China
| | - Xuguang Li
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang, People’s Republic of China
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, People’s Republic of China
- School of Medicine, Xizang Minzu University, Xianyang, People’s Republic of China
| | - Yemeng Sheng
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang, People’s Republic of China
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, People’s Republic of China
- School of Medicine, Xizang Minzu University, Xianyang, People’s Republic of China
| | - Xiaoli Liu
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang, People’s Republic of China
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, People’s Republic of China
- School of Medicine, Xizang Minzu University, Xianyang, People’s Republic of China
| | - Tianbo Jin
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang, People’s Republic of China
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, People’s Republic of China
- School of Medicine, Xizang Minzu University, Xianyang, People’s Republic of China
- Correspondence: Tianbo Jin; Yongjun He, Xizang Minzu University, #6 East Wenhui Road, Xianyang, Shaanxi, 712082, People’s Republic of China, Email ;
| | - Yongjun He
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang, People’s Republic of China
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, People’s Republic of China
- School of Medicine, Xizang Minzu University, Xianyang, People’s Republic of China
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Wang Y, He J, Xu M, Xue Q, Zhu C, Liu J, Zhang Y, Shi W. Holistic View of ALK TKI Resistance in ALK-Positive Anaplastic Large Cell Lymphoma. Front Oncol 2022; 12:815654. [PMID: 35211406 PMCID: PMC8862178 DOI: 10.3389/fonc.2022.815654] [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: 11/15/2021] [Accepted: 01/04/2022] [Indexed: 11/23/2022] Open
Abstract
Anaplastic lymphoma kinase (ALK) is a receptor tyrosine kinase expressed at early stages of normal development and in various cancers including ALK-positive anaplastic large cell lymphoma (ALK+ ALCL), in which it is the main therapeutic target. ALK tyrosine kinase inhibitors (ALK TKIs) have greatly improved the prognosis of ALK+ALCL patients, but the emergence of drug resistance is inevitable and limits the applicability of these drugs. Although various mechanisms of resistance have been elucidated, the problem persists and there have been relatively few relevant clinical studies. This review describes research progress on ALK+ ALCL including the application and development of new therapies, especially in relation to drug resistance. We also propose potential treatment strategies based on current knowledge to inform the design of future clinical trials.
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Affiliation(s)
- Yuan Wang
- Department of Oncology, Affiliated Hospital of Nantong University, Nantong, China.,Nantong University School of Medicine, Nantong, China
| | - Jing He
- Department of Oncology, Affiliated Hospital of Nantong University, Nantong, China.,Nantong University School of Medicine, Nantong, China
| | - Manyu Xu
- Department of Clinical Biobank, Affiliated Hospital of Nantong University, Nantong, China
| | - Qingfeng Xue
- Department of Oncology, Affiliated Hospital of Nantong University, Nantong, China
| | - Cindy Zhu
- Department of Psychology, University of California, Los Angeles (UCLA), Los Angeles, CA, United States
| | - Juan Liu
- Department of Oncology, Affiliated Hospital of Nantong University, Nantong, China.,Nantong University School of Medicine, Nantong, China
| | - Yaping Zhang
- Department of Hematology, Affiliated Hospital of Nantong University, Nantong, China
| | - Wenyu Shi
- Department of Oncology, Affiliated Hospital of Nantong University, Nantong, China.,Department of Hematology, Affiliated Hospital of Nantong University, Nantong, China
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Impact of Variants in the ATIC and ARID5B Genes on Therapeutic Failure with Imatinib in Patients with Chronic Myeloid Leukemia. Genes (Basel) 2022; 13:genes13020330. [PMID: 35205374 PMCID: PMC8872593 DOI: 10.3390/genes13020330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/24/2021] [Accepted: 01/04/2022] [Indexed: 02/04/2023] Open
Abstract
Chronic myeloid leukemia (CML) is a myeloproliferative neoplasm derived from the balanced reciprocal translocation of chromosomes 9 and 22 t (9q34 and 22q11), which leads to the formation of the Philadelphia chromosome and fusion of the BCR-ABL genes. The first-line treatment for CML is imatinib, a tyrosine kinase inhibitor that acts on the BCR-ABL protein. However, even though it is a target-specific drug, about 25% of patients do not respond to this treatment. The resistance mechanisms involved in this process have been investigated and studies have shown that germinal alterations can influence this mechanism. The aim of this work was to investigate 32 polymorphisms in 24 genes of carcinogenic pathway to verify the influence of these genetic variants on the response to treatment with imatinib. Our results demonstrated that individuals with the recessive GG genotype for the rs2372536 variant in the ATIC gene are approximately three times more likely to experience treatment failure with imatinib (p = 0.045, HR = 2.726, 95% CI = 0.9986–7.441), as well as individuals with the TT genotype for the rs10821936 variant in the ARID5B gene, who also have a higher risk for treatment failure with imatinib over time (p = 0.02, HR = 0.4053, IC 95% = 0.1802–0.911). In conclusion, we show that variants in the ATIC and ARIDB5 gene, never screened in previous studies, could potentially influence the therapeutic response to imatinib in patients treated for CML.
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Du M, Liang Y, Liu Z, Li X, Liang M, Zhou B, Gao Y. Identification of Key Genes Related to CD8+ T-Cell Infiltration as Prognostic Biomarkers for Lung Adenocarcinoma. Front Oncol 2021; 11:693353. [PMID: 34650911 PMCID: PMC8505972 DOI: 10.3389/fonc.2021.693353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 09/06/2021] [Indexed: 01/11/2023] Open
Abstract
Background CD8+ T cells are one of the central effector cells in the immune microenvironment. CD8+ T cells play a vital role in the development and progression of lung adenocarcinoma (LUAD). This study aimed to explore the key genes related to CD8+ T-cell infiltration in LUAD and to develop a novel prognosis model based on these genes. Methods With the use of the LUAD dataset from The Cancer Genome Atlas (TCGA), the differentially expressed genes (DEGs) were analyzed, and a co-expression network was constructed by weighted gene co-expression network analysis (WGCNA). Combined with the CIBERSORT algorithm, the gene module in WGCNA, which was the most significantly correlated with CD8+ T cells, was selected for the subsequent analyses. Key genes were then identified by co-expression network analysis, protein–protein interactions network analysis, and least absolute shrinkage and selection operator (Lasso)-penalized Cox regression analysis. A risk assessment model was built based on these key genes and then validated by the dataset from the Gene Expression Omnibus (GEO) database and multiple fluorescence in situ hybridization experiments of a tissue microarray. Results Five key genes (MZT2A, ALG3, ATIC, GPI, and GAPDH) related to prognosis and CD8+ T-cell infiltration were identified, and a risk assessment model was established based on them. We found that the risk score could well predict the prognosis of LUAD, and the risk score was negatively related to CD8+ T-cell infiltration and correlated with the advanced tumor stage. The results of the GEO database and tissue microarray were consistent with those of TCGA. Furthermore, the risk score was higher significantly in tumor tissues than in adjacent lung tissues and was correlated with the advanced tumor stage. Conclusions This study may provide a novel risk assessment model for prognosis prediction and a new perspective to explore the mechanism of tumor immune microenvironment related to CD8+ T-cell infiltration in LUAD.
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Affiliation(s)
- Minjun Du
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yicheng Liang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zixu Liu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xingkai Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mei Liang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Boxuan Zhou
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yushun Gao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Sarkar P, Thirumurugan K. In silico explanation for the causalities of deleterious RNF213 SNPs in Moyamoya disease and insulin resistance. Comput Biol Chem 2021; 92:107488. [PMID: 33930741 DOI: 10.1016/j.compbiolchem.2021.107488] [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: 07/14/2020] [Revised: 12/08/2020] [Accepted: 04/20/2021] [Indexed: 11/30/2022]
Abstract
Moyamoya disease (MMD), a cerebrovascular disorder caused by the RNF213 gene, is a cerebrovascular, neurological disorder leading to ischemic strokes. Our previous work suggested that RNF213 might be involved in the pro-inflammatory TNFα-mediated insulin-resistance pathway in adipocytes. Insulin resistance can lead to cerebrovascular diseases and ischemic strokes. Though p. R4810 K has been reported as the founder mutation for Asian population with this disease, there are several mutations continuously reported in clinical diagnosis. We are interested to know whether these mutations can modulate insulin resistance. Also, we are intended to understand the causalities of RNF213 and its associated mutations in MMD. For this, we have adopted a computational approach to characterize RNF213 and its naturally occurring SNPs. Clinically reported SNPs and the predicted SNPs were analyzed for their pathogenicity and effect on the biological function of the protein. To increase accuracy, this was performed through three different analysis software (PROVEAN, SIFT, and SNAP2). The mutations that were found to be deleterious in all the three platforms were further analyzed for their effect on the thermal stability of the protein through I-mutant and iStable. It was found that R4810 K and other mutations decreased the thermodynamic stability of the protein. Loss of function of RNF213 was suggested in some reports. Contrary to this, some studies reported a gain of function state due to the R4810K mutation. To understand this we have measured the ligand-binding ability of this mutated protein through COFACTOR and COACH. An increase in ligand binding is always related to the functional stability of a protein. We have observed that the R4810K mutation might increase the iron-binding efficiency of the amino acid residues. This increase in binding was further validated by analyzing the binding efficiencies by docking. Since RNF213 was previously reported as a target for Protein Tyrosine Phosphatase 1B (PTP1B), we have also analyzed whether PTP1B-binding positions are susceptible to mutations. We have re-analyzed our earlier report on the differential expression pattern of RNF213 in cancer and obese samples. We have provided a detailed analysis of the most deleterious SNPs related to RNF213. Also, we provide a prediction for the loss of function and gain of function attributes of RNF213 and its predicted causalities in MMD and insulin resistance.
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Affiliation(s)
- Priyanka Sarkar
- 206, Structural Biology Lab, Centre for Biomedical Research, School of Biosciences & Technology, Vellore Institute of Technology, Vellore, India
| | - Kavitha Thirumurugan
- 206, Structural Biology Lab, Centre for Biomedical Research, School of Biosciences & Technology, Vellore Institute of Technology, Vellore, India.
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Kuravi S, Cheng J, Fangman G, Polireddy K, McCormick S, Lin TL, Singh AK, Abhyankar S, Ganguly S, Welch DR, Jensen RA, McGuirk JP, Balusu R. Preclinical Evaluation of Gilteritinib on NPM1-ALK-Driven Anaplastic Large Cell Lymphoma Cells. Mol Cancer Res 2021; 19:913-920. [PMID: 33514657 DOI: 10.1158/1541-7786.mcr-20-0738] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 12/14/2020] [Accepted: 01/22/2021] [Indexed: 11/16/2022]
Abstract
Anaplastic large cell lymphoma (ALCL) is an aggressive type of non-Hodgkin lymphoma. More than three-fourths of anaplastic lymphoma kinase (ALK)-positive ALCL cases express the nucleophosmin 1 (NPM1)-ALK fusion gene as a result of t(2;5) chromosomal translocation. The homodimerization of NPM1-ALK fusion protein mediates constitutive activation of the chimeric tyrosine kinase activity and downstream signaling pathways responsible for lymphoma cell proliferation and survival. Gilteritinib is a tyrosine kinase inhibitor recently approved by the FDA for the treatment of FMS-like tyrosine kinase mutation-positive acute myeloid leukemia. In this study, we demonstrate for the first time gilteritinib-mediated growth inhibitory effects on NPM1-ALK-driven ALCL cells. We utilized a total of five ALCL model cell lines, including both human and murine. Gilteritinib treatment inhibits NPM1-ALK fusion kinase phosphorylation and downstream signaling, resulting in induced apoptosis. Gilteritinib-mediated apoptosis was associated with caspase 3/9, PARP cleavage, the increased expression of proapoptotic protein BAD, and decreased expression of antiapoptotic proteins, survivin and MCL-1. We also found downregulation of fusion kinase activity resulted in decreased c-Myc protein levels. Furthermore, cell-cycle analysis indicated gilteritinib induced G0-G1-phase cell-cycle arrest and reduced CD30 expression. In summary, our preclinical studies explored the novel therapeutic potential of gilteritinib in the treatment of ALCL cells expressing NPM1-ALK and potentially in other ALK or ALK fusion-driven hematologic or solid malignancies. IMPLICATIONS: Our preclinical results explore the use of gilteritinib for the treatment of NPM1-ALK-driven ALCL cells and pave a path for developing future clinical trials. VISUAL OVERVIEW: http://mcr.aacrjournals.org/content/molcanres/19/5/913/F1.large.jpg.
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Affiliation(s)
- Sudhakiranmayi Kuravi
- Division of Hematologic Malignancies and Cellular Therapeutics, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas
| | - Janice Cheng
- Division of Hematologic Malignancies and Cellular Therapeutics, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas
| | | | - Kishore Polireddy
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, Kansas
| | - Sophia McCormick
- Biospecimen Repository Core Facility, University of Kansas Medical Center, Kansas City, Kansas
| | - Tara L Lin
- Division of Hematologic Malignancies and Cellular Therapeutics, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas
- The University of Kansas Cancer Center, Kansas City, Kansas
| | - Anurag K Singh
- Division of Hematologic Malignancies and Cellular Therapeutics, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas
- The University of Kansas Cancer Center, Kansas City, Kansas
| | - Sunil Abhyankar
- Division of Hematologic Malignancies and Cellular Therapeutics, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas
- The University of Kansas Cancer Center, Kansas City, Kansas
| | - Siddhartha Ganguly
- Division of Hematologic Malignancies and Cellular Therapeutics, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas
- The University of Kansas Cancer Center, Kansas City, Kansas
| | - Danny R Welch
- The University of Kansas Cancer Center, Kansas City, Kansas
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas
| | - Roy A Jensen
- The University of Kansas Cancer Center, Kansas City, Kansas
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas
| | - Joseph P McGuirk
- Division of Hematologic Malignancies and Cellular Therapeutics, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas
- The University of Kansas Cancer Center, Kansas City, Kansas
| | - Ramesh Balusu
- Division of Hematologic Malignancies and Cellular Therapeutics, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas.
- The University of Kansas Cancer Center, Kansas City, Kansas
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9
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Su WJ, Lu PZ, Wu Y, Kalpana K, Yang CK, Lu GD. Identification of Key Genes in Purine Metabolism as Prognostic Biomarker for Hepatocellular Carcinoma. Front Oncol 2021; 10:583053. [PMID: 33520699 PMCID: PMC7841304 DOI: 10.3389/fonc.2020.583053] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 11/30/2020] [Indexed: 12/13/2022] Open
Abstract
Background Deregulated purine metabolism is critical for fast-growing tumor cells by providing nucleotide building blocks and cofactors. Importantly, purine antimetabolites belong to the earliest developed anticancer drugs and are still prescribed in clinics today. However, these antimetabolites can inhibit non-tumor cells and cause undesired side effects. As liver has the highest concentration of purines, it makes liver cancer a good model to study important nodes of dysregulated purine metabolism for better patient selection and precisive cancer treatment. Methods By using a training dataset from TCGA, we investigated the differentially expressed genes (DEG) of purine metabolism pathway (hsa00230) in hepatocellular carcinoma (HCC) and determined their clinical correlations to patient survival. A prognosis model was established by Lasso-penalized Cox regression analysis, and then validated through multiple examinations including Cox regression analysis, stratified analysis, and nomogram using another ICGC test dataset. We next treated HCC cells using chemical drugs of the key enzymes in vitro to determine targetable candidates in HCC. Results The DEG analysis found 43 up-regulated and 2 down-regulated genes in the purine metabolism pathway. Among them, 10 were markedly associated with HCC patient survival. A prognostic correlation model including five genes (PPAT, DCK, ATIC, IMPDH1, RRM2) was established and then validated using the ICGC test dataset. Multivariate Cox regression analysis found that both prognostic risk model (HR = 4.703 or 3.977) and TNM stage (HR = 2.303 or 2.957) independently predicted HCC patient survival in the two datasets respectively. The up-regulations of the five genes were further validated by comparing between 10 pairs of HCC tissues and neighboring non-tumor tissues. In vitro cellular experiments further confirmed that inhibition of IMPDH1 significantly repressed HCC cell proliferation. Conclusion In summary, this study suggests that purine metabolism is deregulated in HCC. The prognostic gene correlation model based on the five purine metabolic genes may be useful in predicting HCC prognosis and patient selection. Moreover, the deregulated genes are targetable by specific inhibitors.
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Affiliation(s)
- Wen-Jing Su
- Department of Toxicology, School of Public Health, Guangxi Medical University, Nanning, China
| | - Pei-Zhi Lu
- Department of Toxicology, School of Public Health, Guangxi Medical University, Nanning, China
| | - Yong Wu
- Department of Toxicology, School of Public Health, Guangxi Medical University, Nanning, China
| | - Kumari Kalpana
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Cheng-Kun Yang
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Guo-Dong Lu
- Department of Toxicology, School of Public Health, Guangxi Medical University, Nanning, China.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Key Laboratory of High-incidence-Tumor Prevention & Treatment (Guangxi Medical University), Ministry of Education of China, Nanning, China
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10
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Hodkinson BP, Schaffer M, Brody JD, Jurczak W, Carpio C, Ben-Yehuda D, Avivi I, Forslund A, Özcan M, Alvarez J, Ceulemans R, Fourneau N, Younes A, Balasubramanian S. Biomarkers of response to ibrutinib plus nivolumab in relapsed diffuse large B-cell lymphoma, follicular lymphoma, or Richter's transformation. Transl Oncol 2020; 14:100977. [PMID: 33395752 PMCID: PMC7723809 DOI: 10.1016/j.tranon.2020.100977] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/11/2020] [Accepted: 11/25/2020] [Indexed: 12/30/2022] Open
Abstract
Biomarkers of response to ibrutinib + nivolumab were analyzed in diffuse large B-cell lymphoma (DLBCL), follicular lymphoma and Richter transformation. DLBCL patients with elevated PD-L1 by immunohistochemistry tended to have better response and survival. Whole exome sequencing identified gene mutations in alternate B-cell receptor pathways linked to response in DLBCL. Enriched pathways by gene expression profiling were related to immune activation in responders and proliferation/replication in nonresponders. This preliminary work may help to generate hypotheses on genetically defined subsets of patients most likely to benefit from ibrutinib + nivolumab.
We analyzed potential biomarkers of response to ibrutinib plus nivolumab in biopsies from patients with diffuse large B-cell lymphoma (DLBCL), follicular lymphoma (FL), and Richter's transformation (RT) from the LYM1002 phase I/IIa study, using programmed death ligand 1 (PD-L1) immunohistochemistry, whole exome sequencing (WES), and gene expression profiling (GEP). In DLBCL, PD-L1 elevation was more frequent in responders versus nonresponders (5/8 [62.5%] vs. 3/16 [18.8%]; p = 0.065; complete response 37.5% vs. 0%; p = 0.028). Overall response rates for patients with WES and GEP data, respectively, were: DLBCL (38.5% and 29.6%); FL (46.2% and 43.5%); RT (76.5% and 81.3%). In DLBCL, WES analyses demonstrated that mutations in RNF213 (40.0% vs. 6.2%; p = 0.055), KLHL14 (30.0% vs. 0%; p = 0.046), and LRP1B (30.0% vs. 6.2%; p = 0.264) were more frequent in responders. No responders had mutations in EBF1, ADAMTS20, AKAP9, TP53, MYD88, or TNFRSF14, while the frequency of these mutations in nonresponders ranged from 12.5% to 18.8%. In FL and RT, genes with different mutation frequencies in responders versus nonresponders were: BCL2 (75.0% vs. 28.6%; p = 0.047) and ROS1 (0% vs. 50.0%; p = 0.044), respectively. Per GEP, the most upregulated genes in responders were LEF1 and BTLA (overall), and CRTAM (germinal center B-cell–like DLBCL). Enriched pathways were related to immune activation in responders and resistance-associated proliferation/replication in nonresponders. This preliminary work may help to generate hypotheses regarding genetically defined subsets of DLBCL, FL, and RT patients most likely to benefit from ibrutinib plus nivolumab.
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Affiliation(s)
- Brendan P Hodkinson
- Oncology Translational Research, Janssen Research & Development, Spring House, PA 19477, United States
| | - Michael Schaffer
- Oncology Translational Research, Janssen Research & Development, Spring House, PA 19477, United States
| | - Joshua D Brody
- Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Wojciech Jurczak
- Department of Clinical Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, Krakow, 31-115, Poland
| | - Cecilia Carpio
- Department of Hematology, University Hospital Vall d'Hebron, Department of Medicine. Universitat Autònoma de Barcelona (UAB), Vall d'Hebron Institut of Oncology (VHIO), Barcelona, Spain
| | - Dina Ben-Yehuda
- Department of Hematology, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Irit Avivi
- Department of Hematology and Bone Marrow Transplantation, Tel Aviv Sourasky Medical Center and Sackler Faculty of Medicine, Tel Aviv 6997801, Israel
| | - Ann Forslund
- Oncology Biomarkers, Bristol-Myers Squibb, Lawrenceville, NJ 08543, United States
| | - Muhit Özcan
- Department of Hematology, Ankara University School of Medicine, Ankara 06100, Turkey
| | - John Alvarez
- Oncology Translational Research, Janssen Research & Development, Spring House, PA 19477, United States
| | - Rob Ceulemans
- Translational Medicine, Janssen Research & Development, Beerse 2340, Belgium
| | - Nele Fourneau
- Translational Medicine, Janssen Research & Development, Beerse 2340, Belgium
| | - Anas Younes
- Lymphoma Department, Memorial Sloan Kettering Cancer Center, New York, NY 10065, United States
| | - Sriram Balasubramanian
- Oncology Translational Research, Janssen Research & Development, Spring House, PA 19477, United States.
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11
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Clinical, Histologic, and Molecular Characteristics of Anaplastic Lymphoma Kinase-positive Primary Cutaneous Anaplastic Large Cell Lymphoma. Am J Surg Pathol 2020; 44:776-781. [PMID: 32412717 DOI: 10.1097/pas.0000000000001449] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Unlike systemic anaplastic large cell lymphoma, the vast majority of primary cutaneous anaplastic large cell lymphomas (C-ALCL) do not carry translocations involving the ALK gene and do not express ALK. Expression of ALK protein therefore strongly suggests secondary cutaneous involvement of a systemic anaplastic large cell lymphoma. Recent studies described a small subgroup of ALK-positive C-ALCL, but information on frequency, prognosis, and translocation partners is virtually lacking. A total of 6/309 (2%) C-ALCL patients included in the Dutch registry for cutaneous lymphomas between 1993 and 2019 showed immunohistochemical ALK expression. Clinical and histopathologic characteristics, immunophenotype and disease course were evaluated. Underlying ALK translocations were analyzed with anchored multiplex polymerase chain reaction-based targeted next-generation sequencing. Median age at diagnosis was 39 years (range: 16 to 53 y). All patients presented with a solitary lesion. Treatment with radiotherapy (n=5) or anthracycline-based chemotherapy (n=1) resulted in complete responses in all 6 patients. Three patients developed a relapse, of whom 2 extracutaneous. After a median follow-up of 41 months, 5 patients were alive without disease and 1 patient died of lymphoma. Immunohistochemically, 3 cases (50%) showed combined nuclear and cytoplasmic ALK expression with underlying NPM1-ALK fusions, while 3 cases (50%) showed solely cytoplasmic ALK expression with variant ALK fusion partners (TRAF1, ATIC, TPM3). ALK-positive C-ALCL is extremely uncommon, has a comparable favorable prognosis to ALK-negative C-ALCL, and should be treated in the same way with radiotherapy as first-line treatment.
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12
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CRISPR genome editing of murine hematopoietic stem cells to create Npm1-Alk causes ALK + lymphoma after transplantation. Blood Adv 2020; 3:1788-1794. [PMID: 31189527 DOI: 10.1182/bloodadvances.2018025247] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 05/06/2019] [Indexed: 12/22/2022] Open
Abstract
Key Points
CRISPR/Cas9 genomic editing of wild-type hematopoietic stem cells generates Npm1-Alk, leading to ALK+ large-cell lymphomas in recipients. CD30+ postthymic T-cell lymphomas are polyclonal but transplantable to secondary recipients with long latency.
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13
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RNF213 suppresses carcinogenesis in glioblastoma by affecting MAPK/JNK signaling pathway. Clin Transl Oncol 2020; 22:1506-1516. [PMID: 31953610 DOI: 10.1007/s12094-020-02286-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 01/01/2020] [Indexed: 02/06/2023]
Abstract
PURPOSE Glioblastoma is the most common malignant brain tumor in central nervous system. Due to absence of the mechanism underlying glioblastoma, the clinical outcome is poor. RNF213 is a ring finger protein and mutation in RNF213 gene is detected in cancers. But the role of RNF213 in glioblastoma is unknown. METHODS RNF213 expression was detected by qPCR, western blotting, IHC technology. RNF213 was overexpressed in plasmid pcDNA3.1. Assays including CCK-8, plate colony formation, wound healing, transwell and FITC/PI dye were used to detect cell behaviors. RESULTS RNF213 was shown to express much lower in tumor tissues and in tumor cell lines compared to control. The patients with higher RNF213 expression displayed longer survival time. When RNF213 was overexpressed in U87MG cells, cell proliferation and colony formation were inhibited significantly. The ability of cell migration and invasion was also suppressed. FAC analysis demonstrated that cell apoptosis was increased after RNF213 overexpression. But cell cycle distribution was not affected by RNF213. Then the expression level of MEKK1, JNK, c-Jun, and cdc42 was decreased after RNF213 overexpression, but increased reversely when RNF213 was knocked down by RNAi technology. CONCLUSIONS RNF213 suppresses carcinogenesis and affects MAPK/JNK signaling pathway in glioblastoma. This study suggests that RNF213 might be a promising target for therapy of glioblastoma.
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14
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Marchi E, O'Connor OA. The rapidly changing landscape in mature T-cell lymphoma (MTCL) biology and management. CA Cancer J Clin 2020; 70:47-70. [PMID: 31815293 DOI: 10.3322/caac.21589] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 10/01/2019] [Accepted: 10/15/2019] [Indexed: 02/06/2023] Open
Abstract
Historical advances in the care of patients with non-Hodgkin lymphoma (NHL) have been restricted largely to patients with B-cell lymphoma. The peripheral T-cell lymphomas (PTCLs), which are rare and heterogeneous in nature, have yet to experience the same degree of improvement in outcome over the past 20 to 30 years. It is estimated that there are approximately 80,000 and 14,000 cases, respectively, of NHL and Hodgkin lymphoma per year in the United States. As a subgroup of NHL, the PTCLs account for 6% to 10% of all cases of NHL, making them exceedingly rare. In addition, the World Health Organization 2017 classification describes 29 distinct subtypes of PTCL. This intrinsic diversity, coupled with its rarity, has stymied progress in the disease. In addition, most subtypes carry an inferior prognosis compared with their B-cell counterparts, an outcome largely attributed to the fact that most treatment paradigms for patients with PTCL have been derived from B-cell neoplasms, a radically different disease. In fact, the first drug ever approved for patients with PTCL was approved only a decade ago. The plethora of recent drug approvals in PTCL, coupled with a deeper understanding of the molecular pathogenesis of the disease, has stimulated the field to pursue new avenues of research that are now largely predicated on the development of novel, targeted small molecules, which include a host of epigenetic modifiers and biologics. There is an expectation these advances may begin to favorably challenge the chemotherapy paradigms that have been used in the T-cell malignancies.
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Affiliation(s)
- Enrica Marchi
- Department of Medicine, Center for Lymphoid Malignancies, Columbia University Medical Center, College of Physicians and Surgeons, New York, New York
| | - Owen A O'Connor
- Department of Medicine, Center for Lymphoid Malignancies, Columbia University Medical Center, College of Physicians and Surgeons, New York, New York
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15
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Kong X, Pan P, Sun H, Xia H, Wang X, Li Y, Hou T. Drug Discovery Targeting Anaplastic Lymphoma Kinase (ALK). J Med Chem 2019; 62:10927-10954. [PMID: 31419130 DOI: 10.1021/acs.jmedchem.9b00446] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
As a receptor tyrosine kinase of insulin receptor (IR) subfamily, anaplastic lymphoma kinase (ALK) has been validated to play important roles in various cancers, especially anaplastic large cell lymphoma (ALCL), nonsmall cell lung cancer (NSCLC), and neuroblastomas. Currently, five small-molecule inhibitors of ALK, including Crizotinib, Ceritinib, Alectinib, Brigatinib, and Lorlatinib, have been approved by the U.S. Food and Drug Administration (FDA) against ALK-positive NSCLCs. Novel type-I1/2 and type-II ALK inhibitors with improved kinase selectivity and enhanced capability to combat drug resistance have also been reported. Moreover, the "proteolysis targeting chimera" (PROTAC) technique has been successfully applied in developing ALK degraders, which opened a new avenue for targeted ALK therapies. This review provides an overview of the physiological and biological functions of ALK, the discovery and development of drugs targeting ALK by focusing on their chemotypes, activity, selectivity, and resistance as well as potential therapeutic strategies to overcome drug resistance.
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Affiliation(s)
- Xiaotian Kong
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences , Zhejiang University , Hangzhou , Zhejiang 310058 , China.,Institute of Functional Nano and Soft Materials (FUNSOM) , Soochow University , Suzhou , Jiangsu 215123 , China
| | - Peichen Pan
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences , Zhejiang University , Hangzhou , Zhejiang 310058 , China
| | - Huiyong Sun
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences , Zhejiang University , Hangzhou , Zhejiang 310058 , China
| | - Hongguang Xia
- Department of Biochemistry & Research Center of Clinical Pharmacy of the First Affiliated Hospital , Zhejiang University , Hangzhou 310058 , China
| | - Xuwen Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences , Zhejiang University , Hangzhou , Zhejiang 310058 , China
| | - Youyong Li
- Institute of Functional Nano and Soft Materials (FUNSOM) , Soochow University , Suzhou , Jiangsu 215123 , China
| | - Tingjun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences , Zhejiang University , Hangzhou , Zhejiang 310058 , China
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16
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Satou A, Bennani NN, Feldman AL. Update on the classification of T-cell lymphomas, Hodgkin lymphomas, and histiocytic/dendritic cell neoplasms. Expert Rev Hematol 2019; 12:833-843. [PMID: 31365276 DOI: 10.1080/17474086.2019.1647777] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Introduction: The classification of lymphomas is based on the postulated normal counterparts of lymphoid neoplasms and currently constitutes over 100 definite or provisional entities. As this number of entities implies, lymphomas show marked pathological, genetic, and clinical heterogeneity. Recent molecular findings have significantly advanced our understanding of lymphomas. Areas covered: The World Health Organization (WHO) classification of lymphoid neoplasms was updated in 2017. The present review summarizes the new findings that have been gained in the areas of mature T-cell neoplasms, Hodgkin lymphomas, and histiocytic/dendritic cell neoplasms since the publication of the 2017 WHO classification. Expert opinion: Although formal revisions to the WHO classification are published only periodically, our understanding of the pathologic, genetic, and clinical features of lymphoid neoplasms is constantly evolving, particularly in the age of -omics technologies and targeted therapeutics. Even in the relatively short time since the publication of the 2017 WHO classification, many significant findings have been identified in the entities covered in this review.
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Affiliation(s)
- Akira Satou
- Department of Laboratory Medicine and Pathology, Mayo Clinic , Rochester , MN , USA.,Department of Surgical Pathology, Aichi Medical University Hospital , Nagakute , Aichi , Japan
| | - N Nora Bennani
- Division of Hematology, Mayo Clinic , Rochester , MN , USA
| | - Andrew L Feldman
- Department of Laboratory Medicine and Pathology, Mayo Clinic , Rochester , MN , USA
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17
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Translatome analysis reveals altered serine and glycine metabolism in T-cell acute lymphoblastic leukemia cells. Nat Commun 2019; 10:2542. [PMID: 31186416 PMCID: PMC6559966 DOI: 10.1038/s41467-019-10508-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/10/2019] [Indexed: 12/26/2022] Open
Abstract
Somatic ribosomal protein mutations have recently been described in cancer, yet their impact on cellular transcription and translation remains poorly understood. Here, we integrate mRNA sequencing, ribosome footprinting, polysomal RNA sequencing and mass spectrometry datasets from a mouse lymphoid cell model to characterize the T-cell acute lymphoblastic leukemia (T-ALL) associated ribosomal RPL10 R98S mutation. Surprisingly, RPL10 R98S induces changes in protein levels primarily through transcriptional rather than translation efficiency changes. Phosphoserine phosphatase (PSPH), encoding a key serine biosynthesis enzyme, was the only gene with elevated transcription and translation leading to protein overexpression. PSPH upregulation is a general phenomenon in T-ALL patient samples, associated with elevated serine and glycine levels in xenograft mice. Reduction of PSPH expression suppresses proliferation of T-ALL cell lines and their capacity to expand in mice. We identify ribosomal mutation driven induction of serine biosynthesis and provide evidence supporting dependence of T-ALL cells on PSPH. The ribosomal protein RPL10 is frequently mutated in T-cell acute lymphoblastic leukemia (T-ALL). Here, the authors show that it promotes proliferation of T-ALL cells by upregulating the serine biosynthesis enzyme phosphoserine phosphatase which in turn modulates serine and glycine metabolism.
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18
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Graetz D, Crews KR, Azzato EM, Singh RK, Raimondi S, Mason J, Valentine M, Mullighan CG, Holland A, Inaba H, Leventaki V. Leukemic presentation of ALK-positive anaplastic large cell lymphoma with a novel partner, poly(A) binding protein cytoplasmic 1 (PABPC1), responding to single-agent crizotinib. Haematologica 2019; 104:e218-e221. [PMID: 30819904 DOI: 10.3324/haematol.2018.215103] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Dylan Graetz
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Kristine R Crews
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Elizabeth M Azzato
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
| | - Ravi K Singh
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
| | - Susana Raimondi
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
| | - John Mason
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
| | - Marcus Valentine
- Department of Cytogenetics, St. Jude Children's Research Hospital, Memphis, TN
| | | | - Ashley Holland
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Hiroto Inaba
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Vasiliki Leventaki
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN .,Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, USA
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19
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ALK Gene Fusions in Epithelioid Fibrous Histiocytoma: A Study of 14 Cases, With New Histopathological Findings. Am J Dermatopathol 2019; 40:805-814. [PMID: 29329131 DOI: 10.1097/dad.0000000000001085] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Previous studies showed that ALK is often positive in epithelioid fibrous histiocytoma (EFH). Two cases of EFH with ALK gene fusions have been recorded. Our objective was to study a series of EFH to present histopathological variations of EFH, identify novel ALK gene fusions, and determine whether there is a correlation between histopathological features and particular gene. We investigated 14 cases of EFH, all ALK immunopositive. The cases were assessed histopathologically as well as for ALK and TFE-3 rearrangements using FISH and ALK gene fusions using next-generation sequencing. The analysis of the sequencing results was performed using the Archer Analysis software (v5; ArcherDX Inc). The study group consisted of 8 female and 6 male patients, ranging in age from 18 to 79 years (mean 42 years; median 37.5 years). All presented with a solitary lesion. Microscopically, most lesions were polypoid and composed of epithelioid cells with ample cytoplasm. In addition, a variable number of bi-, tri-, or multinucleated, spindled, multilobated, cells with eccentric nuclei, cells with nuclear pseudoinclusions, mucinous, and grooved cells were admixed. In 5 cases, the predominant epithelioid cell component consisted of rather small cells, whereas spindled cells dominated in 3 cases. Of these, 2 lesions were composed rather of pale eosinophilic to clear cells, occasioning a resemblance to PEComa or leiomyoma. Immunohistochemically, all cases expressed ALK and 11 were positive for TFE-3. The break apart test for ALK was positive in 11 cases, whereas specimens from the remaining 3 cases were not analyzable. ALK genes fusions were found in all but 3 cases and included SQSTM1-ALK (3), VCL-ALK (3), TMP3-ALK (2), PRKAR2A-ALK (1), MLPH-ALK (1), and EML4-ALK (1). No correlation between histological features and type of ALK fusion was found. TFE-3 break apart test was negative. It is concluded that ALK-immunopositive EFH shows ALK gene fusions that involve various protein-coding genes, implicated in a variety of biological processes. Rare variants of EFH rather consist of spindled "non-epithelioid" cells.
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Davis LE, Nusser KD, Przybyl J, Pittsenbarger J, Hofmann NE, Varma S, Vennam S, Debiec-Rychter M, van de Rijn M, Davare MA. Discovery and Characterization of Recurrent, Targetable ALK Fusions in Leiomyosarcoma. Mol Cancer Res 2018; 17:676-685. [DOI: 10.1158/1541-7786.mcr-18-1075] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 10/28/2018] [Accepted: 11/27/2018] [Indexed: 11/16/2022]
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21
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Pratap S, Scordino TS. Molecular and cellular genetics of non-Hodgkin lymphoma: Diagnostic and prognostic implications. Exp Mol Pathol 2018; 106:44-51. [PMID: 30465756 DOI: 10.1016/j.yexmp.2018.11.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 11/02/2018] [Accepted: 11/19/2018] [Indexed: 02/08/2023]
Abstract
Non-Hodgkin lymphoma (NHL) is a diverse collection of malignant neoplasms with lymphoid-cell origin which includes all the malignant lymphomas that are not classified as Hodgkin lymphoma. NHL is one of the most common types of cancer diagnosed in men and women in the developed world. In the United States of America, the past few decades have seen a significant rise in the incidence of NHL and it accounts for about 4% of all cancers now. The overall survival of NHL has improved drastically over the past ten years. This can be attributed to better understanding of pathogenesis, refined classification, enhanced supportive care, and data from collaborative clinical trials. The prognosis of a newly diagnosed NHL patient depends, among other factors, on the specific subtype of lymphoma, stage of the disease, and age of the patient. Advances in the fields of molecular biology and innovations in cytogenetic techniques have led to the discovery of several oncogenic pathways involved in lymphomagenesis, which in turn has amplified the diagnostic and therapeutic approaches available for NHL. Our comprehension of the genetic features that determine the character of NHL, and ultimately guide the therapy, has undergone significant shift and it is essential that scientists as well as clinicians stay in tune with this rapidly evolving knowledge. In this review we have summarized the current concepts about cellular and molecular genetics of the common subtypes of NHL and their clinical implications.
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Affiliation(s)
- Suraj Pratap
- University of Oklahoma Health Sciences Center (OUHSC), Jimmy Everest Section of Pediatric Hematology & Oncology, 1200 Children's Ave, Suite 14500, Oklahoma City, OK 73104, USA.
| | - Teresa S Scordino
- University of Oklahoma Health Sciences Center (OUHSC), Department of Pathology, 940 Stanton L. Young Blvd, BMSB 451, Oklahoma City, OK 73104, USA.
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22
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Babin L, Piganeau M, Renouf B, Lamribet K, Thirant C, Deriano L, Mercher T, Giovannangeli C, Brunet EC. Chromosomal Translocation Formation Is Sufficient to Produce Fusion Circular RNAs Specific to Patient Tumor Cells. iScience 2018; 5:19-29. [PMID: 30240643 PMCID: PMC6123901 DOI: 10.1016/j.isci.2018.06.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 05/05/2018] [Accepted: 06/14/2018] [Indexed: 12/14/2022] Open
Abstract
Circular RNAs constitute a unique class of RNAs whose precise functions remain to be elucidated. In particular, cancer-associated chromosomal translocations can give rise to fusion circular RNAs that play a role in leukemia progression. However, how and when fusion circular RNAs are formed and whether they are being selected in cancer cells remains unknown. Here, we used CRISPR/Cas9 to generate physiological translocation models of NPM1-ALK fusion gene. We showed that, in addition to generating fusion proteins and activating specific oncogenic pathways, chromosomal translocation induced by CRISPR/Cas9 led to the formation of de novo fusion circular RNAs. Specifically, we could recover different classes of circular RNAs composed of different circularization junctions, mainly back-spliced species. In addition, we identified fusion circular RNAs identical to those found in related patient tumor cells providing evidence that fusion circular RNAs arise early after chromosomal formation and are not just a consequence of the oncogenesis process. CRISPR/Cas9 model of ALCL translocation leads to oncogene pathway activation CRISPR/Cas9 translocations generate de novo fusion circular RNAs Shared fusion circular RNAs are found in CRISPR/Cas9 models and ALCL tumor cells
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Affiliation(s)
- Loelia Babin
- Laboratory "Genome Dynamics in the Immune System", Equipe Labellisée Ligue Contre le Cancer, INSERM UMR1163; Université Paris Descartes Sorbonne Paris Cité, Institut Imagine, Paris 75015, France; Museum National d'Histoire Naturelle, INSERM U1154, CNRS UMR7196, Sorbonne Université, Paris 75005, France
| | - Marion Piganeau
- Museum National d'Histoire Naturelle, INSERM U1154, CNRS UMR7196, Sorbonne Université, Paris 75005, France
| | - Benjamin Renouf
- Museum National d'Histoire Naturelle, INSERM U1154, CNRS UMR7196, Sorbonne Université, Paris 75005, France
| | - Khadija Lamribet
- Museum National d'Histoire Naturelle, INSERM U1154, CNRS UMR7196, Sorbonne Université, Paris 75005, France
| | - Cecile Thirant
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Institute, Université Paris Diderot, Université Paris-Sud, Villejuif 94800, Francet
| | - Ludovic Deriano
- Genome Integrity, Immunity and Cancer Unit, Department of Immunology, Department of Genomes and Genetics, Institut Pasteur, Paris 75015, France
| | - Thomas Mercher
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Institute, Université Paris Diderot, Université Paris-Sud, Villejuif 94800, Francet
| | - Carine Giovannangeli
- Museum National d'Histoire Naturelle, INSERM U1154, CNRS UMR7196, Sorbonne Université, Paris 75005, France
| | - Erika C Brunet
- Laboratory "Genome Dynamics in the Immune System", Equipe Labellisée Ligue Contre le Cancer, INSERM UMR1163; Université Paris Descartes Sorbonne Paris Cité, Institut Imagine, Paris 75015, France; Museum National d'Histoire Naturelle, INSERM U1154, CNRS UMR7196, Sorbonne Université, Paris 75005, France.
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Tong Y, Zhao Z, Liu B, Bao A, Zheng H, Gu J, McGrath M, Xia Y, Tan B, Song C, Li Y. 5'/ 3' imbalance strategy to detect ALK fusion genes in circulating tumor RNA from patients with non-small cell lung cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2018; 37:68. [PMID: 29587818 PMCID: PMC5870746 DOI: 10.1186/s13046-018-0735-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 03/15/2018] [Indexed: 02/07/2023]
Abstract
Background Detecting an ALK fusion gene in patients with non-small cell lung cancer (NSCLC) could provide evidence to guide individualized therapy. Methods The 5′/3′ imbalance strategy for quantitative reverse transcription-PCR (RT-qPCR) was developed to detect ALK fusion genes in circulating tumor RNA (ctRNA) of NSCLC patients. Results This method was validated in patients with the ALK fusion gene confirmed by next generation sequencing (NGS). The amount of the ALK fusion gene detected by the new method ranged from 33.2 to 987.4, (mean 315.2), in the patients confirmed to have the ALK fusion gene (+). This is much higher than the amount of fusion gene detected in the patients who are negative for the ALK fusion gene (−). The amount detected in the ALK fusion gene (−) samples ranged from 0.36 to 13.04, (mean 4.58). In 188 NSCLC patients, the specificity and sensitivity of the method was compared to that of the FISH method. About 10.64% of the patients showed higher ALK fusion gene expression, and were classified as ALK fusion gene (+). This is identical to the percentage of patients detected by the FISH method to be ALK fusion gene (+). The cutoff value for diagnosis of ALK fusion (+) is 32.9 as determined by this method. Conclusions A new RT-PCR method using a 5′/3′ imbalance strategy was developed, with high specificity and sensitivity, for detection of the ALK fusion gene in ctRNA of NSCLC patients. This method can rapidly detect ALK fusion genes in patients, which will be helpful for guiding targeted therapy, particularly the individualized usage of TKIs in these patients.
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Affiliation(s)
- Yongqing Tong
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, 99 Ziyang Road of Wuchang District, Wuhan, 430060, People's Republic of China
| | - Zhijun Zhao
- Laboratory Medicine Center of General Hospital of Ningxia Medical University, Yinchuan, 750004, People's Republic of China
| | - Bei Liu
- Department of Pathology Affiliated Tianyou Hospital of Wuhan University of Science and Technology, Wuhan, 430064, People's Republic of China
| | - Anyu Bao
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, 99 Ziyang Road of Wuchang District, Wuhan, 430060, People's Republic of China
| | - Hongyun Zheng
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, 99 Ziyang Road of Wuchang District, Wuhan, 430060, People's Republic of China
| | - Jian Gu
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, 99 Ziyang Road of Wuchang District, Wuhan, 430060, People's Republic of China
| | - Mary McGrath
- Pennsylvania State University College of Medicine and Hershey Medical center, Penn State Hershey Children's Hospital, PO Box 850, 500 University Drive, Hershey, PA, 17033, USA
| | - Ying Xia
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230022, People's Republic of China
| | - Bihua Tan
- Pennsylvania State University College of Medicine and Hershey Medical center, Penn State Hershey Children's Hospital, PO Box 850, 500 University Drive, Hershey, PA, 17033, USA
| | - Chunhua Song
- Pennsylvania State University College of Medicine and Hershey Medical center, Penn State Hershey Children's Hospital, PO Box 850, 500 University Drive, Hershey, PA, 17033, USA.
| | - Yan Li
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, 99 Ziyang Road of Wuchang District, Wuhan, 430060, People's Republic of China.
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van Krieken JH. New developments in the pathology of malignant lymphoma: a review of the literature published from May to August 2017. J Hematop 2017; 10:65-73. [PMID: 29057015 PMCID: PMC5630645 DOI: 10.1007/s12308-017-0303-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- J H van Krieken
- Department of Pathology, Radboud University Medical Centre, P.O. Box 9101, 6500, HB Nijmegen, The Netherlands
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25
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Takita J. The role of anaplastic lymphoma kinase in pediatric cancers. Cancer Sci 2017; 108:1913-1920. [PMID: 28756644 PMCID: PMC5623752 DOI: 10.1111/cas.13333] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/20/2017] [Accepted: 07/24/2017] [Indexed: 01/08/2023] Open
Abstract
The anaplastic lymphoma kinase (ALK) gene was initially identified as a fusion partner of the nucleophosmin gene in anaplastic large-cell lymphoma with t(2;5)(p23;q35) translocation, and then described with different genetic abnormalities in a number of tumors. Although ALK is known to be involved in the pathogenesis of neuroblastoma through activating mutations or gene amplification, its role in the pathogenesis of other pediatric cancers is still elusive. In addition to neuroblastoma, the high-grade amplification of ALK has been described in a subset of rhabdomyosarcoma cases. Normal ALK protein expression is restricted to the nervous systems of adult mammals, but the aberrant expression of ALK has been observed in a variety of pediatric cancers, including glioma and Ewing sarcoma. The discovery of oncogenic activation of ALK in neuroblastoma suggests that this cancer could be potentially treated with an ALK inhibitor, as could other cancers, such as non-small-cell lung cancer and anaplastic large-cell lymphoma. However, cellular responses to mutant ALK are complex when compared to rearranged ALK, and treatment remains a challenge. This review focuses on the biology of ALK in pediatric cancers and possible therapeutic strategies for ALK-associated tumors.
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Affiliation(s)
- Junko Takita
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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