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Birgersson M, Chi M, Miller C, Brzozowski JS, Brown J, Schofield L, Taylor OG, Pearsall EA, Hewitt J, Gedye C, Lincz LF, Skelding KA. A Novel Role for Brain and Acute Leukemia Cytoplasmic (BAALC) in Human Breast Cancer Metastasis. Front Oncol 2021; 11:656120. [PMID: 33968759 PMCID: PMC8101327 DOI: 10.3389/fonc.2021.656120] [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: 01/20/2021] [Accepted: 03/29/2021] [Indexed: 11/29/2022] Open
Abstract
Brain and Acute Leukemia, Cytoplasmic (BAALC) is a protein that controls leukemia cell proliferation, differentiation, and survival and is overexpressed in several cancer types. The gene is located in the chromosomal region 8q22.3, an area commonly amplified in breast cancer and associated with poor prognosis. However, the expression and potential role of BAALC in breast cancer has not widely been examined. This study investigates BAALC expression in human breast cancers with the aim of determining if it plays a role in the pathogenesis of the disease. BAALC protein expression was examined by immunohistochemistry in breast cancer, and matched lymph node and normal breast tissue samples. The effect of gene expression on overall survival (OS), disease-free and distant metastasis free survival (DMFS) was assessed in silico using the Kaplan-Meier Plotter (n=3,935), the TCGA invasive breast carcinoma (n=960) and GOBO (n=821) data sets. Functional effects of BAALC expression on breast cancer proliferation, migration and invasion were determined in vitro. We demonstrate herein that BAALC expression is progressively increased in primary and breast cancer metastases when compared to normal breast tissue. Increased BAALC mRNA is associated with a reduction in DMFS and disease-free survival, but not OS, in breast cancer patients, even when corrected for tumor grade. We show that overexpression of BAALC in MCF-7 breast cancer cells increases the proliferation, anchorage-independent growth, invasion, and migration capacity of these cells. Conversely, siRNA knockdown of BAALC expression in Hs578T breast cancer cells decreases proliferation, invasion and migration. We identify that this BAALC associated migration and invasion is mediated by focal adhesion kinase (FAK)-dependent signaling and is accompanied by an increase in matrix metalloproteinase (MMP)-9 but not MMP-2 activity in vitro. Our data demonstrate a novel function for BAALC in the control of breast cancer metastasis, offering a potential target for the generation of anti-cancer drugs to prevent breast cancer metastasis.
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Affiliation(s)
- Madeleine Birgersson
- Cancer Cell Biology Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, NSW, Australia.,School of Biomedical Sciences and Pharmacy, Karolinska Intitutet, Solna, Sweden
| | - Mengna Chi
- Cancer Cell Biology Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, NSW, Australia.,Hunter Cancer Research Alliance and Cancer Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Chrissy Miller
- Cancer Cell Biology Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, NSW, Australia.,Hunter Cancer Research Alliance and Cancer Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Joshua S Brzozowski
- Cancer Cell Biology Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, NSW, Australia.,Hunter Cancer Research Alliance and Cancer Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Jeffrey Brown
- Cancer Cell Biology Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, NSW, Australia.,Hunter Cancer Research Alliance and Cancer Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Lachlan Schofield
- Cancer Cell Biology Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, NSW, Australia.,Hunter Cancer Research Alliance and Cancer Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Olivia G Taylor
- Cancer Cell Biology Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, NSW, Australia.,Hunter Cancer Research Alliance and Cancer Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Elizabeth A Pearsall
- Cancer Cell Biology Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, NSW, Australia.,Hunter Cancer Research Alliance and Cancer Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Jasmine Hewitt
- Cancer Cell Biology Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, NSW, Australia.,Hunter Cancer Research Alliance and Cancer Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Craig Gedye
- Cancer Cell Biology Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, NSW, Australia.,Hunter Cancer Research Alliance and Cancer Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia.,Department of Medical Oncology, Calvary Mater Newcastle Hospital, Waratah, NSW, Australia
| | - Lisa F Lincz
- Cancer Cell Biology Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, NSW, Australia.,Hunter Cancer Research Alliance and Cancer Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia.,Hunter Hematology Research Group, Calvary Mater Newcastle Hospital, Waratah, NSW, Australia
| | - Kathryn A Skelding
- Cancer Cell Biology Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, NSW, Australia.,Hunter Cancer Research Alliance and Cancer Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
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Mitrovic M, Kostic T, Virijevic M, Karan‐Djurasevic T, Suvajdzic Vukovic N, Pavlovic S, Tosic N. The influence of Wilms' tumor 1 gene expression level on prognosis and risk stratification of acute promyelocytic leukemia patients. Int J Lab Hematol 2019; 42:82-87. [DOI: 10.1111/ijlh.13144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 11/05/2019] [Accepted: 11/25/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Mirjana Mitrovic
- Clinic of Hematology Clinical Center of Serbia Belgrade Serbia
- School of Medicine University of Belgrade Belgrade Serbia
| | - Tatjana Kostic
- Institute for Molecular Genetics and Genetic Engineering University of Belgrade Belgrade Serbia
| | - Marijana Virijevic
- Clinic of Hematology Clinical Center of Serbia Belgrade Serbia
- School of Medicine University of Belgrade Belgrade Serbia
| | | | - Nada Suvajdzic Vukovic
- Clinic of Hematology Clinical Center of Serbia Belgrade Serbia
- School of Medicine University of Belgrade Belgrade Serbia
| | - Sonja Pavlovic
- Institute for Molecular Genetics and Genetic Engineering University of Belgrade Belgrade Serbia
| | - Natasa Tosic
- Institute for Molecular Genetics and Genetic Engineering University of Belgrade Belgrade Serbia
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3
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Combining gene mutation with gene expression analysis improves outcome prediction in acute promyelocytic leukemia. Blood 2019; 134:951-959. [PMID: 31292112 DOI: 10.1182/blood.2019000239] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 05/23/2019] [Indexed: 12/15/2022] Open
Abstract
By combining the analysis of mutations with aberrant expression of genes previously related to poorer prognosis in both acute promyelocytic leukemia (APL) and acute myeloid leukemia, we arrived at an integrative score in APL (ISAPL) and demonstrated its relationship with clinical outcomes of patients treated with all-trans retinoic acid (ATRA) in combination with anthracycline-based chemotherapy. Based on fms-like tyrosine kinase-3-internal tandem duplication mutational status; the ΔNp73/TAp73 expression ratio; and ID1, BAALC, ERG, and KMT2E gene expression levels, we modeled ISAPL in 159 patients (median ISAPL score, 3; range, 0-10). ISAPL modeling identified 2 distinct groups of patients, with significant differences in early mortality (P < .001), remission (P = .004), overall survival (P < .001), cumulative incidence of relapse (P = .028), disease-free survival (P = .03), and event-free survival (P < .001). These data were internally validated by using a bootstrap resampling procedure. At least for patients treated with ATRA and anthracycline-based chemotherapy, ISAPL modeling may identify those who need to be treated differently to maximize their chances for a cure.
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Lucena-Araujo AR, Pereira-Martins DA, Koury LC, Franca-Neto PL, Coelho-Silva JL, de Deus Wagatsuma VM, Melo RAM, Bittencourt R, Pagnano K, Pasquini R, Chiattone CS, Fagundes EM, Chauffaille MDL, Schrier SL, Tallman MS, Ribeiro RC, Grimwade D, Ganser A, Löwenberg B, Lo-Coco F, Sanz MA, Berliner N, Rego EM. Clinical impact of BAALC expression in high-risk acute promyelocytic leukemia. Blood Adv 2017; 1:1807-1814. [PMID: 29296827 PMCID: PMC5728094 DOI: 10.1182/bloodadvances.2017005926] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 07/13/2017] [Indexed: 01/08/2023] Open
Abstract
Although overexpression of the brain and acute leukemia, cytoplasmic (BAALC) gene is associated with primary resistant disease and shorter relapse-free, disease-free, and overall survival in different subsets of acute myeloid leukemia (AML), little is known about its clinical impact in acute promyelocytic leukemia (APL). Using real-time reverse transcriptase polymerase chain reaction, we showed that BAALC expression is significantly lower in APL compared with other subsets of AML (P < .001). We also demonstrated that BAALC overexpression was associated with shorter disease-free survival (DFS) (hazard ratio [HR], 4.43; 95% confidence interval [CI], 1.29-15.2; P = .018) in 221 consecutive patients (median age, 35 years; range, 18-82 years) with newly diagnosed APL homogeneously treated with all-trans retinoic acid and anthracycline-based chemotherapy. Cox proportional hazard modeling showed that BAALC overexpression was independently associated with shorter DFS in the total cohort (HR, 5.26; 95% CI, 1.52-18.2; P = .009) and in patients with high-risk disease (ie, those with initial leukocyte counts >10 × 109/L) (HR, 5.3; 95% CI, 1.14-24.5; P = .033). We conclude that BAALC expression could be useful for refining risk stratification in APL, although this needs to be confirmed in independent cohorts.
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Affiliation(s)
- Antonio R Lucena-Araujo
- Department of Genetics, Federal University of Pernambuco, Recife, Brazil
- Department of Internal Medicine, Medical School of Ribeirao Preto and
- Center for Cell Based Therapy, University of São Paulo, Ribeirao Preto, Brazil
| | - Diego A Pereira-Martins
- Department of Genetics, Federal University of Pernambuco, Recife, Brazil
- Department of Internal Medicine, Medical School of Ribeirao Preto and
- Center for Cell Based Therapy, University of São Paulo, Ribeirao Preto, Brazil
| | - Luisa C Koury
- Center for Cell Based Therapy, University of São Paulo, Ribeirao Preto, Brazil
| | | | - Juan L Coelho-Silva
- Department of Genetics, Federal University of Pernambuco, Recife, Brazil
- Department of Internal Medicine, Medical School of Ribeirao Preto and
- Center for Cell Based Therapy, University of São Paulo, Ribeirao Preto, Brazil
| | - Virginia M de Deus Wagatsuma
- Department of Internal Medicine, Medical School of Ribeirao Preto and
- Center for Cell Based Therapy, University of São Paulo, Ribeirao Preto, Brazil
| | - Raul A M Melo
- Department of Internal Medicine, Federal University of Pernambuco, Recife, Brazil
| | - Rosane Bittencourt
- Hematology Division, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Katia Pagnano
- Hematology and Hemotherapy Center, University of Campinas, Campinas, Brazil
| | - Ricardo Pasquini
- Hematology Division, Federal University of Paraná, Curitiba, Brazil
| | | | - Evandro M Fagundes
- Hematology Division, Department of Internal Medicine, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | | | - Martin S Tallman
- Leukemia Service, Memorial Sloan Kettering Cancer Center/Weill Cornell Medical College, New York, NY
| | - Raul C Ribeiro
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - David Grimwade
- Department of Medical and Molecular Genetics, School of Medicine, King's College London, London, United Kingdom
| | - Arnold Ganser
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Bob Löwenberg
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Francesco Lo-Coco
- Department of Biopathology, University Tor Vergata, Rome, Italy
- Santa Lucia Foundation, Rome, Italy
| | - Miguel A Sanz
- Department of Hematology, Valencia University Medical School, Valencia, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Instituto Carlos III, Madrid, Spain; and
| | - Nancy Berliner
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Eduardo M Rego
- Department of Internal Medicine, Medical School of Ribeirao Preto and
- Center for Cell Based Therapy, University of São Paulo, Ribeirao Preto, Brazil
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Hecht A, Doll S, Altmann H, Nowak D, Lengfelder E, Röllig C, Ehninger G, Spiekermann K, Hiddemann W, Weiß C, Hofmann WK, Nolte F, Platzbecker U. Validation of a Molecular Risk Score for Prognosis of Patients With Acute Promyelocytic Leukemia Treated With All-trans Retinoic Acid and Chemotherapy-containing Regimens. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2017; 17:889-896.e5. [PMID: 28923666 DOI: 10.1016/j.clml.2017.08.095] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 08/04/2017] [Accepted: 08/07/2017] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Although treatment of acute promyelocytic leukemia (APL) has evolved dramatically during the past decades, especially with the introduction of all-trans retinoic acid, risk stratification remains an important issue. To date, relapse risk can be predicted by leukocyte and platelet counts only. In the present report, we present a validation study on 3 candidate genes and a newly developed molecular risk score for APL in 2 independent patient cohorts. PATIENTS AND METHODS An integrative risk score combining the expression levels of BAALC, ERG, and WT1 was calculated for 79 de novo APL patients from the original cohort and 76 de novo APL patients from a validation cohort. Gene expression analysis was executed the same for both cohorts, and the results regarding the effect on patient outcomes were compared. RESULTS The expression levels of BAALC, ERG, and WT1 were similar in both cohorts compared with the healthy controls. The relapse and survival rates were not different between the low- and high-risk patients according to the Sanz score. However, application of the molecular risk score on the validation cohort distinctly discriminated patients according to their risk of relapse and death just as in the original APL cohort, although single gene analyses could not reproduce the negative prognostic impact. CONCLUSION The analysis clearly validated the prognostic effect of the integrative risk score on the outcome in APL patients. The value was further empowered because the single gene analyses did not show similar results. Whether the integrative risk score retains its prognostic power in the chemotherapy-free setting should be investigated further.
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Affiliation(s)
- Anna Hecht
- Department of Hematology and Oncology, University Hospital Mannheim, Medical Faculty, University of Heidelberg, Mannheim, Germany.
| | - Seraphina Doll
- Department of Hematology and Oncology, University Hospital Mannheim, Medical Faculty, University of Heidelberg, Mannheim, Germany
| | - Heidi Altmann
- Department of Medicine I, University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - Daniel Nowak
- Department of Hematology and Oncology, University Hospital Mannheim, Medical Faculty, University of Heidelberg, Mannheim, Germany
| | - Eva Lengfelder
- Department of Hematology and Oncology, University Hospital Mannheim, Medical Faculty, University of Heidelberg, Mannheim, Germany
| | - Christoph Röllig
- Department of Medicine I, University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - Gerhard Ehninger
- Department of Medicine I, University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | | | - Wolfgang Hiddemann
- Department of Hematology/Oncology, University of Munich, Munich, Germany
| | - Christel Weiß
- Department for Medical Statistics and Biomathematics, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Wolf-Karsten Hofmann
- Department of Hematology and Oncology, University Hospital Mannheim, Medical Faculty, University of Heidelberg, Mannheim, Germany
| | - Florian Nolte
- Department of Hematology and Oncology, University Hospital Mannheim, Medical Faculty, University of Heidelberg, Mannheim, Germany
| | - Uwe Platzbecker
- Department of Medicine I, University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany
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Hecht A, Nowak D, Nowak V, Hanfstein B, Büchner T, Spiekermann K, Weiß C, Hofmann WK, Lengfelder E, Nolte F. A molecular risk score integrating BAALC, ERG and WT1 expression levels for risk stratification in acute promyelocytic leukemia. Leuk Res 2015; 39:S0145-2126(15)30363-5. [PMID: 26344466 DOI: 10.1016/j.leukres.2015.08.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 08/15/2015] [Indexed: 11/23/2022]
Abstract
To date risk stratification in acute promyelocytic leukemia (APL) is based on highly dynamic leukocyte and platelet counts only. To identify a more robust risk stratification model, a molecular risk score was developed based on expression levels of the genes BAALC, ERG and WT1. Hereby, the main focus was on prediction of relapse. The integrative risk score divided patients into two groups with highly significant differences in outcome. It discriminated a high risk group with a high incidence of relapse successfully from a low risk group with no APL-related events after achievement of first remission. Especially the concurrent presence of molecular risk factors showed to be a negative prognostic factor in APL. The molecular risk score might be a promising approach to guide monitoring of APL patients and therapeutic decisions in the future.
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Affiliation(s)
- Anna Hecht
- Department of Hematology and Oncology, University Hospital Mannheim, University of Heidelberg, Germany.
| | - Daniel Nowak
- Department of Hematology and Oncology, University Hospital Mannheim, University of Heidelberg, Germany
| | - Verena Nowak
- Department of Hematology and Oncology, University Hospital Mannheim, University of Heidelberg, Germany
| | - Benjamin Hanfstein
- Department of Hematology and Oncology, University Hospital Mannheim, University of Heidelberg, Germany
| | - Thomas Büchner
- Department of Hematology/Oncology, University of Münster, Münster, Germany
| | | | - Christel Weiß
- Department for Medical Statistics and Biomathematics, Medical Faculty Mannheim, University of Heidelberg, Germany
| | - Wolf-Karsten Hofmann
- Department of Hematology and Oncology, University Hospital Mannheim, University of Heidelberg, Germany
| | - Eva Lengfelder
- Department of Hematology and Oncology, University Hospital Mannheim, University of Heidelberg, Germany
| | - Florian Nolte
- Department of Hematology and Oncology, University Hospital Mannheim, University of Heidelberg, Germany
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Hecht A, Nolte F, Nowak D, Nowak V, Reinwald M, Hanfstein B, Faldum A, Büchner T, Spiekermann K, Sauerland C, Weiss C, Hofmann WK, Lengfelder E. Prognostic importance of expression of the Wilms’ tumor 1 gene in newly diagnosed acute promyelocytic leukemia. Leuk Lymphoma 2015; 56:2289-95. [DOI: 10.3109/10428194.2014.990011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Overexpression of BAALC: clinical significance in Chinese de novo acute myeloid leukemia. Med Oncol 2014; 32:386. [PMID: 25428390 DOI: 10.1007/s12032-014-0386-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Accepted: 11/18/2014] [Indexed: 10/24/2022]
Abstract
To investigate the expression of brain and acute leukemia, cytoplasmic (BAALC) and analyze its clinical significance in Chinese de novo acute myeloid leukemia (AML). Real-time quantitative PCR (RQ-PCR) was carried out to detect BAALC transcript level in 121 de novo AML patients and 41 normal controls. BAALC transcript level in AML patients was significantly up-regulated compared with normal controls (P < 0.001). Patients with high BAALC expression had significantly older age than those with low BAALC expression (P = 0.021). The percentage of blasts in bone marrow of the BAALC high-expressed patients was significantly higher than that in the low-expressed patients (P < 0.001). The incidence of BAALC overexpression was significantly higher in M0/M1 (8/9, 89 %) and M2 subtypes (33/48, 68 %) than in M3 subtype (6/27, 22 %) (P < 0.001). The frequency of IDH1/2 wild type in CN-AML patients with high BAALC expression was significantly higher than those with low BAALC expression (P = 0.031). BAALC high-expressed patients had a significantly lower complete remission than low-expressed patients in both entire AML cohort and CN-AML (P = 0.013 and 0.029, respectively). Furthermore, both whole AML cohort and CN-AML patients with high BAALC expression showed a shorter overall survival than those with low BAALC expression (P = 0.002 and 0.008, respectively). Multivariate analysis confirmed high BAALC expression as an independent adverse prognostic factor in both AML and CN-AML patients. Our study indicates that overexpression of BAALC serves as an independent prognostic biomarker in both whole AML cohort and CN-AML patients.
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Liu Y, Ying W, Ren Z, Gu W, Zhang Y, Yan G, Yang P, Liu Y, Yin X, Chang C, Jiang J, Fan F, Zhang C, Xu P, Wang Q, Wen B, Lin L, Wang T, Du C, Zhong J, Wang T, He QY, Qian X, Lou X, Zhang G, Zhong F. Chromosome-8-coded proteome of Chinese Chromosome Proteome Data set (CCPD) 2.0 with partial immunohistochemical verifications. J Proteome Res 2013; 13:126-36. [PMID: 24328083 DOI: 10.1021/pr400902u] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We upgraded the preliminary CCPD 1.0 to CCPD 2.0 using the latest deep-profiling proteome (CCPD 2013) of three hepatocellular carcinoma (HCC) cell lines, namely, Hep3B, MHCC97H, and HCCLM3 (ProteomeXchange identifiers: PXD000529, PXD000533, and PXD000535). CCPD 2.0 totally covered 63.6% (438/689) of Chr. 8-coded proteins and 62.6% (439/701) of Chr. 8-coded protein-coding genes. Interestingly, we found that the missing proteins exhibited a tendency to form a cluster region in chromosomes, such as two β-defensins clusters in Chr. 8, caused perhaps by their inflammation-related features. For the 41 Chr. 8-coded proteins being weakly or barely identified previously, we have performed an immunohistochemical (IHC) verification in 30 pairs of carcinoma/para-carcinoma HCC and 20 noncancerous liver tissues and confirmed their expressional evidence and occurrence proportions in tissue samples. We also verified 13 Chr. 8-coded HCC tumorigenesis-associated depleting or deficient proteins reported in CCPD 1.0 using IHC and screened 16 positive and 24 negative HCC metastatic potential-correlated proteins from large-scale label-free proteome quantitation data of CCPD 2013. Our results suggest that the selection of proper samples and the methodology to look for targeted missing proteins should be carefully considered in further verifications for the remaining Chr. 8-coded proteins.
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Affiliation(s)
- Yang Liu
- Institutes of Biomedical Sciences, Fudan University , Mingdao Bldg. 815, 138 Yixueyuan Road, Shanghai 200032, China
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