1
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Carey-Smith SL, Simad MH, Panchal K, Aya-Bonilla C, Smolders H, Lin S, Armitage JD, Nguyen VT, Bentley K, Ford J, Singh S, Oommen J, Laurent AP, Mercher T, Crispino JD, Montgomery AP, Kassiou M, Besson T, Deau E, Meijer L, Cheung LC, Kotecha RS, Malinge S. Efficacy of DYRK1A inhibitors in novel models of Down syndrome acute lymphoblastic leukemia. Haematologica 2024. [PMID: 38426275 DOI: 10.3324/haematol.2023.284271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Indexed: 03/02/2024] Open
Abstract
Not available.
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Affiliation(s)
- Shannon L Carey-Smith
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia; Curtin Medical School, Curtin University, Perth, WA
| | - Maryam H Simad
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA
| | - Kunjal Panchal
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia; Curtin Medical School, Curtin University, Perth, WA
| | | | - Hannah Smolders
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA
| | - Sang Lin
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA
| | | | - Vivien T Nguyen
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA
| | - Kathryn Bentley
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA
| | - Jette Ford
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA
| | - Sajla Singh
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA
| | - Joyce Oommen
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA
| | | | | | - John D Crispino
- Department of Hematology, St Jude Children's Hospital, Memphis, TN
| | | | | | - Thierry Besson
- University Rouen Normandie, INSA Rouen Normandie, CNRS, COBRA UMR 6014, 76000
| | | | | | - Laurence C Cheung
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia; Curtin Medical School, Curtin University, Perth, WA, Australia; Curtin Health Innovation Research Institute, Curtin University, Perth, WA
| | - Rishi S Kotecha
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia; Curtin Medical School, Curtin University, Perth, WA, Australia; Department of Clinical Haematology, Oncology, Blood and Marrow Transplantation, Perth Children's Hospital, Perth, WA, Australia; University of Western Australia, Perth, WA
| | - Sébastien Malinge
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia; Curtin Medical School, Curtin University, Perth, WA, Australia; University of Western Australia, Perth, WA.
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2
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Hughes AM, Kuek V, Oommen J, Chua GA, van Loenhout M, Malinge S, Kotecha RS, Cheung LC. Characterization of mesenchymal stem cells in pre-B acute lymphoblastic leukemia. Front Cell Dev Biol 2023; 11:1005494. [PMID: 36743421 PMCID: PMC9897315 DOI: 10.3389/fcell.2023.1005494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 01/10/2023] [Indexed: 01/21/2023] Open
Abstract
Components of the bone marrow microenvironment (BMM) have been shown to mediate the way in which leukemia develops, progresses and responds to treatment. Increasing evidence shows that leukemic cells hijack the BMM, altering its functioning and establishing leukemia-supportive interactions with stromal and immune cells. While previous work has highlighted functional defects in the mesenchymal stem cell (MSC) population from the BMM of acute leukemias, thorough characterization and molecular profiling of MSCs in pre-B cell acute lymphoblastic leukemia (B-ALL), the most common cancer in children, has not been conducted. Here, we investigated the cellular and transcriptome profiles of MSCs isolated from the BMM of an immunocompetent BCR-ABL1+ model of B-ALL. Leukemia-associated MSCs exhibited reduced self-renewal capacity in vitro and significant changes in numerous molecular signatures, including upregulation of inflammatory signaling pathways. Additionally, we found downregulation of genes involved in extracellular matrix organization and osteoblastogenesis in leukemia-associated MSCs. This study provides cellular and molecular insights into the role of MSCs during B-ALL progression.
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Affiliation(s)
- Anastasia M. Hughes
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia,Curtin Medical School, Curtin University, Perth, WA, Australia
| | - Vincent Kuek
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia,Curtin Medical School, Curtin University, Perth, WA, Australia,School of Medicine, University of Western Australia, Perth, WA, Australia
| | - Joyce Oommen
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Grace-Alyssa Chua
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Maria van Loenhout
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Sebastien Malinge
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia,School of Medicine, University of Western Australia, Perth, WA, Australia
| | - Rishi S. Kotecha
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia,Curtin Medical School, Curtin University, Perth, WA, Australia,School of Medicine, University of Western Australia, Perth, WA, Australia,Department of Clinical Haematology, Oncology, Blood and Marrow Transplantation, Perth Children’s Hospital, Perth, WA, Australia
| | - Laurence C. Cheung
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia,Curtin Medical School, Curtin University, Perth, WA, Australia,Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia,*Correspondence: Laurence C. Cheung, ,
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3
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Cheung LC, Aya-Bonilla C, Cruickshank MN, Chiu SK, Kuek V, Anderson D, Chua GA, Singh S, Oommen J, Ferrari E, Hughes AM, Ford J, Kunold E, Hesselman MC, Post F, Faulk KE, Breese EH, Guest EM, Brown PA, Loh ML, Lock RB, Kees UR, Jafari R, Malinge S, Kotecha RS. Preclinical efficacy of azacitidine and venetoclax for infant KMT2A-rearranged acute lymphoblastic leukemia reveals a new therapeutic strategy. Leukemia 2023; 37:61-71. [PMID: 36380143 PMCID: PMC9883157 DOI: 10.1038/s41375-022-01746-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 10/20/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022]
Abstract
Infants with KMT2A-rearranged B-cell acute lymphoblastic leukemia (ALL) have a dismal prognosis. Survival outcomes have remained static in recent decades despite treatment intensification and novel therapies are urgently required. KMT2A-rearranged infant ALL cells are characterized by an abundance of promoter hypermethylation and exhibit high BCL-2 expression, highlighting potential for therapeutic targeting. Here, we show that hypomethylating agents exhibit in vitro additivity when combined with most conventional chemotherapeutic agents. However, in a subset of samples an antagonistic effect was seen between several agents. This was most evident when hypomethylating agents were combined with methotrexate, with upregulation of ATP-binding cassette transporters identified as a potential mechanism. Single agent treatment with azacitidine and decitabine significantly prolonged in vivo survival in KMT2A-rearranged infant ALL xenografts. Treatment of KMT2A-rearranged infant ALL cell lines with azacitidine and decitabine led to differential genome-wide DNA methylation, changes in gene expression and thermal proteome profiling revealed the target protein-binding landscape of these agents. The selective BCL-2 inhibitor, venetoclax, exhibited in vitro additivity in combination with hypomethylating or conventional chemotherapeutic agents. The addition of venetoclax to azacitidine resulted in a significant in vivo survival advantage indicating the therapeutic potential of this combination to improve outcome for infants with KMT2A-rearranged ALL.
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Affiliation(s)
- Laurence C Cheung
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
- Curtin Medical School, Curtin University, Perth, WA, Australia
- Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Carlos Aya-Bonilla
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
- The University of Western Australia, Perth, WA, Australia
| | | | - Sung K Chiu
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Vincent Kuek
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
- Curtin Medical School, Curtin University, Perth, WA, Australia
- The University of Western Australia, Perth, WA, Australia
| | - Denise Anderson
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Grace-Alyssa Chua
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Sajla Singh
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Joyce Oommen
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Emanuela Ferrari
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Anastasia M Hughes
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Jette Ford
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Elena Kunold
- Department of Oncology-Pathology, Clinical Proteomics Mass Spectrometry, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Maria C Hesselman
- Department of Oncology-Pathology, Clinical Proteomics Mass Spectrometry, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Frederik Post
- Department of Oncology-Pathology, Clinical Proteomics Mass Spectrometry, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Kelly E Faulk
- University of Colorado Anschutz Medical Campus, Children's Hospital Colorado, Aurora, CO, USA
| | - Erin H Breese
- Cancer and Blood Diseases Institute, Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Erin M Guest
- Division of Hematology, Oncology, Blood and Marrow Transplantation, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Patrick A Brown
- Division of Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, John Hopkins University, Baltimore, MD, USA
| | - Mignon L Loh
- Division of Pediatric Hematology, Oncology, Bone Marrow Transplant and Cellular Therapy, Seattle Children's Hospital, Seattle, WA, USA
| | - Richard B Lock
- Children's Cancer Institute, Lowy Cancer Research Centre/School of Women's and Children's Health/UNSW Centre for Childhood Cancer Research, UNSW Sydney, Kensington, NSW, Australia
| | - Ursula R Kees
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
- The University of Western Australia, Perth, WA, Australia
| | - Rozbeh Jafari
- Department of Oncology-Pathology, Clinical Proteomics Mass Spectrometry, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Sébastien Malinge
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
- The University of Western Australia, Perth, WA, Australia
| | - Rishi S Kotecha
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia.
- Curtin Medical School, Curtin University, Perth, WA, Australia.
- The University of Western Australia, Perth, WA, Australia.
- Department of Clinical Haematology, Oncology, Blood and Marrow Transplantation, Perth Children's Hospital, Perth, WA, Australia.
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4
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Stirnweiss A, Dholaria H, Oommen J, Hardy K, Jevon G, Beesley AH, Kotecha RS. Case Report: Long-Term Survival of a Pediatric Patient With an Intra-Abdominal Undifferentiated Carcinoma of Unknown Primary. Front Oncol 2021; 11:590913. [PMID: 34041014 PMCID: PMC8141844 DOI: 10.3389/fonc.2021.590913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 04/08/2021] [Indexed: 11/23/2022] Open
Abstract
An 8-year and 10-month-old boy presented following 2 weeks of abdominal pain, vomiting, constipation, and rectal pain. A diffuse lower-abdominal mass was felt upon palpation, with radiological findings confirming the presence of a large, multilobulated intraperitoneal mass with mesenteric lymphadenopathy and hepatic metastatic disease. A biopsy of the mass revealed anatomical pathological findings consistent with a diagnosis of intra-abdominal undifferentiated carcinoma of unknown primary (CUP). The patient was treated with six cycles of carboplatin and gemcitabine prior to surgery. Following incomplete resection of the tumor, four further cycles were administered resulting in resolution of the pelvic mass, but progression in the right and left lobes of the liver. Therapy was accordingly adjusted, with administration of six cycles of ifosfamide and doxorubicin followed by 1 year of metronomic vinorelbine and cyclophosphamide maintenance therapy. The patient remains in remission 7 years from completion of therapy. Whole exome sequencing revealed missense mutations in the DNA-repair and chromatin-remodeling genes FANCM and SMARCD2, and a tumor-derived cell line revealed a complex karyotype suggesting chromosomal instability. CUP is an extremely rare diagnosis in the pediatric population, previously reported during adolescence. This report provides detailed characterization of CUP in a young child and in the absence of defined therapeutic guidelines for pediatric CUP, the successful treatment strategy described should be considered for similar cases.
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Affiliation(s)
- Anja Stirnweiss
- Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Hetal Dholaria
- Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia.,Department of Clinical Haematology, Oncology, Blood and Marrow Transplantation, Perth Children's Hospital, Perth, WA, Australia
| | - Joyce Oommen
- Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | | | - Gareth Jevon
- Department of Anatomical Pathology, Perth Children's Hospital, Perth, WA, Australia
| | - Alex H Beesley
- Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Rishi S Kotecha
- Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia.,Department of Clinical Haematology, Oncology, Blood and Marrow Transplantation, Perth Children's Hospital, Perth, WA, Australia.,Curtin Medical School, Curtin University, Perth, WA, Australia
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5
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Cheung LC, de Kraa R, Oommen J, Chua GA, Singh S, Hughes AM, Ferrari E, Ford J, Chiu SK, Stam RW, Kees UR, Malinge S, Kotecha RS. Preclinical Evaluation of Carfilzomib for Infant KMT2A-Rearranged Acute Lymphoblastic Leukemia. Front Oncol 2021; 11:631594. [PMID: 33937032 PMCID: PMC8082024 DOI: 10.3389/fonc.2021.631594] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 02/25/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Infants with KMT2A-rearranged B-cell precursor acute lymphoblastic leukemia (ALL) have poor outcomes. There is an urgent need to identify novel agents to improve survival. Proteasome inhibition has emerged as a promising therapeutic strategy for several hematological malignancies. The aim of this study was to determine the preclinical efficacy of the selective proteasome inhibitor carfilzomib, for infants with KMT2A-rearranged ALL. METHODS Eight infant ALL cell lines were extensively characterized for immunophenotypic and cytogenetic features. In vitro cytotoxicity to carfilzomib was assessed using a modified Alamar Blue assay with cells in logarithmic growth. The Bliss Independence model was applied to determine synergy between carfilzomib and the nine conventional chemotherapeutic agents used to treat infants with ALL. Established xenograft models were used to identify the maximal tolerated dose of carfilzomib and determine in vivo efficacy. RESULTS Carfilzomib demonstrated low IC50 concentrations within the nanomolar range (6.0-15.8 nm) across the panel of cell lines. Combination drug testing indicated in vitro synergy between carfilzomib and several conventional chemotherapeutic agents including vincristine, daunorubicin, dexamethasone, L-asparaginase, and 4-hydroperoxycyclophosphamide. In vivo assessment did not lead to a survival advantage for either carfilzomib monotherapy, when used to treat both low or high disease burden, or for carfilzomib in combination with multi-agent induction chemotherapy comprising of vincristine, dexamethasone, and L-asparaginase. CONCLUSIONS Our study highlights that in vitro efficacy does not necessarily translate to benefit in vivo and emphasizes the importance of in vivo validation prior to suggesting an agent for clinical use. Whilst proteasome inhibitors have an important role to play in several hematological malignancies, our findings guard against prioritization of carfilzomib for treatment of KMT2A-rearranged infant ALL in the clinical setting.
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Affiliation(s)
- Laurence C. Cheung
- Division of Children’s Leukaemia and Cancer Research, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
- Curtin Medical School, Curtin University, Perth, WA, Australia
| | | | - Joyce Oommen
- Division of Children’s Leukaemia and Cancer Research, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Grace-Alyssa Chua
- Division of Children’s Leukaemia and Cancer Research, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Sajla Singh
- Division of Children’s Leukaemia and Cancer Research, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Anastasia M. Hughes
- Division of Children’s Leukaemia and Cancer Research, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Emanuela Ferrari
- Division of Children’s Leukaemia and Cancer Research, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Jette Ford
- Division of Children’s Leukaemia and Cancer Research, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Sung K. Chiu
- Division of Children’s Leukaemia and Cancer Research, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Ronald W. Stam
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Ursula R. Kees
- Division of Children’s Leukaemia and Cancer Research, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Sébastien Malinge
- Division of Children’s Leukaemia and Cancer Research, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Rishi S. Kotecha
- Division of Children’s Leukaemia and Cancer Research, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
- Curtin Medical School, Curtin University, Perth, WA, Australia
- Department of Clinical Haematology, Oncology, Blood and Marrow Transplantation, Perth Children’s Hospital, Perth, WA, Australia
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6
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Cheung LC, Cruickshank MN, Hughes AM, Singh S, Chua GA, Ford J, Ferrari E, Oommen J, Malinge S, Lock RB, Kees UR, Kotecha RS. Romidepsin enhances the efficacy of cytarabine in vivo, revealing histone deacetylase inhibition as a promising therapeutic strategy for KMT2A-rearranged infant acute lymphoblastic leukemia. Haematologica 2019; 104:e300-e303. [PMID: 30679330 DOI: 10.3324/haematol.2018.192906] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Laurence C Cheung
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth.,School of Pharmacy and Biomedical Sciences, Curtin University, Perth
| | - Mark N Cruickshank
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth
| | - Anastasia M Hughes
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth
| | - Sajla Singh
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth
| | - Grace-Alyssa Chua
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth
| | - Jette Ford
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth
| | - Emanuela Ferrari
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth
| | - Joyce Oommen
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth
| | - Sébastien Malinge
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth
| | - Richard B Lock
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney
| | - Ursula R Kees
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth
| | - Rishi S Kotecha
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth .,School of Pharmacy and Biomedical Sciences, Curtin University, Perth.,Department of Haematology and Oncology, Perth Children's Hospital, Perth.,Division of Paediatrics, School of Medicine, University of Western Australia, Perth, Australia
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7
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Singh B, Fakiola M, Sudarshan M, Oommen J, Singh SS, Sundar S, Blackwell JM. HLA-DR Class II expression on myeloid and lymphoid cells in relation to HLA-DRB1 as a genetic risk factor for visceral leishmaniasis. Immunology 2018; 156:174-186. [PMID: 30403401 DOI: 10.1111/imm.13018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/22/2018] [Accepted: 10/29/2018] [Indexed: 11/27/2022] Open
Abstract
Genetic variation at HLA-DRB1 is a risk factor for visceral leishmaniasis (VL) caused by Leishmania donovani. The single nucleotide polymorphism rs9271252 upstream of the DRB1 gene provides a perfect tag for protective versus risk HLA-DRB1 four-digit alleles. In addition to the traditional role of the membrane-distal region of HLA class II molecules in antigen presentation and CD4 T-cell activation, the membrane-proximal region mediates 'non-traditional' multi-functional activation, differentiation, or death signals, including in DR-expressing T cells. To understand how HLA-DR contributes to disease pathogenesis, we examined expression at the protein level in circulating myeloid (CD14+ , CD16+ ) and lymphoid (CD4+ , CD8+ , CD19+ ) cells of VL patients (pre- and post-treatment) compared with endemic healthy controls (EHC). Although DR expression is reduced in circulating myeloid cells in active disease relative to EHC and post-treatment groups, expression is enhanced on CD4+ DR+ and CD8+ DR+ T cells consistent with T-cell activation. Cells of all myeloid and lymphoid populations from active cases were refractory to stimulation of DR expression with interferon-γ (IFN-γ). In contrast, all populations except CD19+ B cells from healthy blood bank controls showed enhanced DR expression following IFN-γ stimulation. The rs9271252 genotype did not impact significantly on IFN-γ-activated DR expression in myeloid, B or CD8+ T cells, but CD4+ T cells from healthy individuals homozygous for the risk allele were particularly refractory to activated DR expression. Further analysis of DR expression on subsets of CD4+ T cells regulating VL disease could uncover additional ways in which pleiotropy at HLA DRB1 contributes to disease pathogenesis.
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Affiliation(s)
- Bhawana Singh
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, UP, India
| | - Michaela Fakiola
- Department of Pathology, The University of Cambridge, Cambridge, UK
| | - Medhavi Sudarshan
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, UP, India
| | - Joyce Oommen
- Telethon Kids Institute, The University of Western Australia, West Perth, WA, Australia
| | - Siddharth Sankar Singh
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, UP, India
| | - Shyam Sundar
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, UP, India
| | - Jenefer M Blackwell
- Department of Pathology, The University of Cambridge, Cambridge, UK.,Telethon Kids Institute, The University of Western Australia, West Perth, WA, Australia
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8
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Cheung LC, Tickner J, Hughes AM, Skut P, Howlett M, Foley B, Oommen J, Wells JE, He B, Singh S, Chua GA, Ford J, Mullighan CG, Kotecha RS, Kees UR. New therapeutic opportunities from dissecting the pre-B leukemia bone marrow microenvironment. Leukemia 2018; 32:2326-2338. [PMID: 29740160 PMCID: PMC6224400 DOI: 10.1038/s41375-018-0144-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 04/03/2018] [Accepted: 04/13/2018] [Indexed: 12/23/2022]
Abstract
The microenvironments of leukemia and cancer are critical for multiple stages of malignancies, and they are an attractive therapeutic target. While skeletal abnormalities are commonly seen in children with acute lymphoblastic leukemia (ALL) prior to initiating osteotoxic therapy, little is known about the alterations to the bone marrow microenvironment during leukemogenesis. Therefore, in this study, we focused on the development of precursor-B cell ALL (pre-B ALL) in an immunocompetent BCR-ABL1+ model. Here we show that hematopoiesis was perturbed, B lymphopoiesis was impaired, collagen production was reduced, and the number of osteoblastic cells was decreased in the bone marrow microenvironment. As previously found in children with ALL, the leukemia-bearing mice exhibited severe bone loss during leukemogenesis. Leukemia cells produced high levels of receptor activator of nuclear factor κB ligand (RANKL), sufficient to cause osteoclast-mediated bone resorption. In vivo administration of zoledronic acid rescued leukemia-induced bone loss, reduced disease burden and prolonged survival in leukemia-bearing mice. Taken together, we provide evidence that targeting leukemia-induced bone loss is a therapeutic strategy for pre-B ALL.
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Affiliation(s)
- Laurence C Cheung
- Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia.
- School of Pharmacy and Biomedical Sciences, Curtin University, Perth, WA, Australia.
| | - Jennifer Tickner
- School of Pathology and Laboratory Medicine, University of Western Australia, Perth, WA, Australia
| | - Anastasia M Hughes
- Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Patrycja Skut
- Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Meegan Howlett
- Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Bree Foley
- Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Joyce Oommen
- Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Julia E Wells
- Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Bo He
- Harry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, Perth, WA, Australia
| | - Sajla Singh
- Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Grace-Alyssa Chua
- Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Jette Ford
- Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Rishi S Kotecha
- Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
- Department of Haematology and Oncology, Princess Margaret Hospital for Children, Perth, WA, Australia
- School of Medicine, University of Western Australia, Perth, WA, Australia
| | - Ursula R Kees
- Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
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Singh T, Fakiola M, Oommen J, Singh AP, Singh AK, Smith N, Chakravarty J, Sundar S, Blackwell JM. Epitope-Binding Characteristics for Risk versus Protective DRB1 Alleles for Visceral Leishmaniasis. J Immunol 2018; 200:2727-2737. [PMID: 29507109 DOI: 10.4049/jimmunol.1701764] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 02/08/2018] [Indexed: 11/19/2022]
Abstract
HLA-DRB1 is the major genetic risk factor for visceral leishmaniasis (VL). We used SNP2HLA to impute HLA-DRB1 alleles and SNPTEST to carry out association analyses in 889 human cases and 977 controls from India. NetMHCIIpan 2.1 was used to map epitopes and binding affinities across 49 Leishmania vaccine candidates, as well as across peptide epitopes captured from dendritic cells treated with crude Leishmania Ag and identified using mass spectrometry and alignment to amino acid sequences of a reference Leishmania genome. Cytokines were measured in peptide-stimulated whole blood from 26 cured VL cases and eight endemic healthy controls. HLA-DRB1*1501 and DRB1*1404/DRB1*1301 were the most significant protective and risk alleles, respectively, with specific residues at aa positions 11 and 13 unique to protective alleles. We observed greater peptide promiscuity in sequence motifs for 9-mer core epitopes predicted to bind to risk (*1404/*1301) compared with protective (*1501) DRB1 alleles. There was a higher frequency of basic amino acids in DRB1*1404/*1301-specific epitopes compared with hydrophobic and polar amino acids in DRB1*1501-specific epitopes at anchor residues pocket 4 and pocket 6, which interact with residues at DRB1 positions 11 and 13. Cured VL patients made variable, but robust, IFN-γ, TNF, and IL-10 responses to 20-mer peptides based on captured epitopes, with peptides based on DRB1*1501-captured epitopes resulting in a higher proportion (odds ratio 2.23, 95% confidence interval 1.17-4.25, p = 0.017) of patients with IFN-γ/IL-10 ratios > 2-fold compared with peptides based on DRB1*1301-captured epitopes. Our data provide insight into the molecular mechanisms underpinning the association of HLA-DRB1 alleles with risk versus protection in VL in humans.
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Affiliation(s)
- Toolika Singh
- Institute of Medical Sciences, Banaras Hindu University, Varanasi OS 221 005, India
| | - Michaela Fakiola
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Joyce Oommen
- Telethon Kids Institute, The University of Western Australia, Subiaco, Western Australia 6008, Australia; and
| | - Akhil Pratap Singh
- Institute of Medical Sciences, Banaras Hindu University, Varanasi OS 221 005, India
| | - Abhishek K Singh
- Institute of Medical Sciences, Banaras Hindu University, Varanasi OS 221 005, India
| | - Noel Smith
- Lonza Biologics PLC, Great Abington, Cambridge CB21 6GS, United Kingdom
| | - Jaya Chakravarty
- Institute of Medical Sciences, Banaras Hindu University, Varanasi OS 221 005, India
| | - Shyam Sundar
- Institute of Medical Sciences, Banaras Hindu University, Varanasi OS 221 005, India
| | - Jenefer M Blackwell
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom; .,Telethon Kids Institute, The University of Western Australia, Subiaco, Western Australia 6008, Australia; and
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Stirnweiss A, Oommen J, Kotecha RS, Kees UR, Beesley AH. Molecular-genetic profiling and high-throughput in vitro drug screening in NUT midline carcinoma-an aggressive and fatal disease. Oncotarget 2017; 8:112313-112329. [PMID: 29348827 PMCID: PMC5762512 DOI: 10.18632/oncotarget.22862] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 11/26/2017] [Indexed: 12/11/2022] Open
Abstract
NUT midline carcinoma (NMC) is a rare and aggressive cancer, with survival typically less than seven months, that can arise in people of any age. Genetically, NMC is defined by the chromosomal fusion of NUTM1 with a chromatin-binding partner, typically the bromodomain-containing protein BRD4. However, little is known about other genetic aberrations in this disease. In this study, we used a unique panel of cell lines to describe the molecular-genetic features of NMC. Next-generation sequencing identified a recurring high-impact mutation in the DNA-helicase gene RECQL5 in 75% of lines studied, and biological signals from mutation-signature and network analyses consistent with a general failure in DNA-repair. A high-throughput drug screen confirmed that microtubule inhibitors, topoisomerase inhibitors and anthracyclines are highly cytotoxic in the majority of NMC lines, and that cell lines expressing the BRD4-NUTM1 (exon11:exon2) variant are an order of magnitude more responsive to bromodomain inhibitors (iBETs) on average than those with other BRD4-NUTM1 translocation variants. We also identified a highly significant correlation between iBET and aurora kinase inhibitor efficacy in this study. Integration of exome sequencing, transcriptome, and drug sensitivity profiles suggested that aberrant activity of the nuclear receptor co-activator NCOA3 may correlate with poor response to iBETs. In conclusion, our data emphasize the heterogeneity of NMC and highlights genetic aberrations that could be explored to improve therapeutic strategies. The novel finding of a recurring RECQL5 mutation, together with recent reports of chromoplexy in this disease, suggests that DNA-repair pathways are likely to play a central role in NMC tumorigenesis.
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Affiliation(s)
- Anja Stirnweiss
- Leukaemia and Cancer Genetics Program, Telethon Kids Institute, The University of Western Australia, Perth, Australia.,Drug Discovery Group, Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | - Joyce Oommen
- Leukaemia and Cancer Genetics Program, Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | - Rishi S Kotecha
- Leukaemia and Cancer Genetics Program, Telethon Kids Institute, The University of Western Australia, Perth, Australia.,Department of Haematology and Oncology, Princess Margaret Hospital for Children, Perth, Australia.,School of Paediatrics and Child Health, University of Western Australia, Perth, Australia
| | - Ursula R Kees
- Leukaemia and Cancer Genetics Program, Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | - Alex H Beesley
- Leukaemia and Cancer Genetics Program, Telethon Kids Institute, The University of Western Australia, Perth, Australia
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Ljubisavljevic M, Maxood K, Bjekic J, Oommen J, Nagelkerke N. Long-Term Effects of Repeated Prefrontal Cortex Transcranial Direct Current Stimulation (tDCS) on Food Craving in Normal and Overweight Young Adults. Brain Stimul 2016; 9:826-833. [PMID: 27498606 DOI: 10.1016/j.brs.2016.07.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 06/28/2016] [Accepted: 07/09/2016] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The dorsolateral prefrontal cortex (DLPFC) plays an important role in the regulation of food intake. Several previous studies demonstrated that a single session of transcranial direct current stimulation (tDCS) of the DLPFC reduces food craving and caloric intake. OBJECTIVES We hypothesized that repeated tDCS of the right DLPFC cortex may exert long-term changes in food craving in young, healthy adults and that these changes may differ between normal and overweight subjects. METHODS Thirty healthy individuals who reported frequent food cravings without a prior history of eating disorders were initially recruited. Subjects were randomized into an ACTIVE group who received 5 days of real tDCS (20 minutes, anode right-cathode left montage, 2 mA with current density kept at 0.06 mA/cm2, 1 min ramp-up/ramp-down), and a SHAM group, who received one day of real tDCS, on the first day (same parameters), followed by 4 days of sham tDCS. Food craving intensity was examined by Food Craving Questionnaires State and Trait and Food Craving Inventory before, during, (5-days) and one month (30-days) after tDCS. RESULTS Single session of tDCS significantly reduced the intensity of current food craving (FCQ-S). Five days of active tDCS significantly reduced habitual experiences of food craving (FCQ-T), when compared to baseline pre-stimulation levels. Furthermore, both current (FCQ-S) and habitual craving (FCQ-T) were significantly reduced 30 days after active tDCS, while sham tDCS, i.e. a single tDCS session did not have significant effects. Also, active tDCS significantly decreased craving for fast food and sweets, and to a lesser degree for fat, while it did not have significant effects on craving for carbohydrates (FCI). There were no significant differences between individual FCQ-T subscales (craving dimensions) after 5 or 30 days of either sham or active tDCS. Changes in craving were not significantly associated with the initial weight, or with weight changes 30 days after the stimulation in the subjects. CONCLUSIONS The results confirm earlier findings that single session of tDCS has immediate effects in reducing food craving. They also show that repeated tDCS over the right DLPFC may increase the duration of its effects, which may be present 30 days after the stimulation. These results support further investigation of the use of tDCS in obesity.
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Affiliation(s)
- M Ljubisavljevic
- Department of Physiology, College of Medicine and Health Sciences, UAE University, PO Box 17666, Al Ain, United Arab Emirates.
| | - K Maxood
- Department of Physiology, College of Medicine and Health Sciences, UAE University, PO Box 17666, Al Ain, United Arab Emirates
| | - J Bjekic
- Department of Neurophysiology, Institute for Medical Research, University of Belgrade, PO Box 124, Belgrade, Serbia
| | - J Oommen
- Department of Physiology, College of Medicine and Health Sciences, UAE University, PO Box 17666, Al Ain, United Arab Emirates
| | - N Nagelkerke
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, Queen Elizabeth Central Hospital, Malawi; Institute of Public Health, College of Medicine and Health Sciences, PO Box 17666, UAE University, Al Ain, United Arab Emirates
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12
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Stirnweiss A, McCarthy K, Oommen J, Crook ML, Hardy K, Kees UR, Wilton SD, Anazodo A, Beesley AH. A novel BRD4-NUT fusion in an undifferentiated sinonasal tumor highlights alternative splicing as a contributing oncogenic factor in NUT midline carcinoma. Oncogenesis 2015; 4:e174. [PMID: 26551281 PMCID: PMC4670959 DOI: 10.1038/oncsis.2015.33] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 09/22/2015] [Indexed: 12/22/2022] Open
Abstract
NUT midline carcinoma (NMC) is a fatal cancer that arises in various tissues along the upper midline of the body. The defining molecular feature of NMC is a chromosomal translocation that joins (in the majority of cases) the nuclear testis gene NUT (NUTM1) to the bromodomain protein family member 4 (BRD4) and thereby creating a fusion oncogene that disrupts cellular differentiation and drives the disease. In this study, we report the case of an adolescent NMC patient presenting with severe facial pain, proptosis and visual impairment due to a mass arising from the ethmoid sinus that invaded the right orbit and frontal lobe. Treatment involved radical resection, including exenteration of the affected eye with the view to consolidate treatment with radiation therapy; however, the patient experienced rapid tumor progression and passed away 79 days post resection. Molecular analysis of the tumor tissue identified a novel in-frame BRD4-NUT transcript, with BRD4 exon 15 fused to the last 124 nucleotides of NUT exon 2 (BRD4-NUT ex15:ex2Δnt1–585). The partial deletion of NUT exon 2 was attributed to a mid-exonic genomic breakpoint and the subsequent activation of a cryptic splice site further downstream within the exon. Inhibition of the canonical 3′ acceptor splice site of NUT intron 1 in cell lines expressing the most common NMC fusion transcripts (PER-403, BRD4-NUT ex11:ex2; PER-624, BRD4-NUT ex15:ex2) induced alternative splicing from the same cryptic splice site as identified in the patient. Detection of low levels of an in-frame BRD4-NUT ex11:ex2Δnt1–585 transcript in PER-403 confirmed endogenous splicing from this alternative exon 2 splice site. Although further studies are necessary to assess the clinical relevance of the increasing number of variant fusions described in NMC, the findings presented in this case identify alternative splicing as a mechanism that contributes to this pathogenic complexity.
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Affiliation(s)
- A Stirnweiss
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Institute, The University of Western Australia, West Perth, WA, Australia
| | - K McCarthy
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
| | - J Oommen
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Institute, The University of Western Australia, West Perth, WA, Australia
| | - M L Crook
- Department of Pathology, Princess Margaret Hospital for Children, Perth, WA, Australia
| | - K Hardy
- Cyto Labs Pty Ltd, Perth, WA, Australia
| | - U R Kees
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Institute, The University of Western Australia, West Perth, WA, Australia
| | - S D Wilton
- Molecular Therapy Laboratory, Western Australian Neuroscience Research Institute, Centre for Comparative Genomics, Murdoch University, Perth, WA, Australia
| | - A Anazodo
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia.,Prince of Wales Hospital, Randwick, NSW, Australia
| | - A H Beesley
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Institute, The University of Western Australia, West Perth, WA, Australia
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13
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Singh T, Fakiola M, Oommen J, Chakravarty J, Sundar S, Blackwell J. HLA class II association with visceral leishmaniasis: The road to identifying vaccine candidates. Int J Infect Dis 2014. [DOI: 10.1016/j.ijid.2014.03.1319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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14
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Schmid-Tannwald C, Dahi F, Jiang Y, Ivancevic MK, Rist C, Sethi I, Oommen J, Oto A. DW-MRI of liver lesions: can a single ADC-value represent the entire lesion? Clin Radiol 2014; 69:492-8. [PMID: 24625693 DOI: 10.1016/j.crad.2013.12.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 12/06/2013] [Accepted: 12/12/2013] [Indexed: 01/07/2023]
Abstract
AIM To evaluate whether focal liver lesions (FLLs) exhibit a homogeneous appearance on apparent diffusion coefficient (ADC) maps and whether there is inter-section variation in the calculated ADC values of FLLs (inter-section range). MATERIALS AND METHODS Eighty-eight patients with 128 FLLs (70 benign, 58 malignant) who underwent abdominal magnetic resonance imaging (MRI) including diffusion-weighted (DW)-MRI were included. Two observers evaluated variation of signal intensity of each FLL within each ADC map image (intra-section) and among different ADC map images through the lesion (inter-section). ADC values of each FLL and neighbouring liver parenchyma were measured on all sections. The inter-section range of FLLs was compared with the neighbouring liver parenchyma. RESULTS Intra-section inhomogeneity was noted in 39.8% (97/244 sections) and 38.9% (95/244) of benign lesions, and 61% (114/187 sections) and 61.5% (115/187) of malignant lesions, by observer 1 and observer 2, respectively. Inter-section inhomogeneity was noted in 25.7% (18/70) and 27.1% (19/70) of benign lesions, and 51.7% (30/58) and 50% (29/58) of malignant lesions, by observer 1 and observer 2, respectively. The inter-section range for both benign (0.28 × 10(-3) mm(2)/s) and malignant (0.25 × 10(-3) mm(2)/s) FLLs were significantly greater than that of liver parenchyma surrounding benign (0.16 × 10(-3) mm(2)/s, p < 0.001) and malignant (0.14 × 10(-3) mm(2)/s, p = 0.01) FLLs. CONCLUSION Due to intra-/inter-section variations in ADC values of benign and malignant FLLs, a single ADC value may not reliably represent the entire lesion.
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Affiliation(s)
- C Schmid-Tannwald
- Department of Radiology, The University of Chicago, Chicago, IL, USA; Ludwig-Maximilians-University Hospital Munich, Institute for Clinical Radiology, Munich, Germany.
| | - F Dahi
- Department of Radiology, The University of Chicago, Chicago, IL, USA
| | - Y Jiang
- Department of Radiology, The University of Chicago, Chicago, IL, USA
| | - M K Ivancevic
- Department of Radiology, The University of Chicago, Chicago, IL, USA; Philips Healthcare, MR Clinical Science, Cleveland, OH, USA
| | - C Rist
- Ludwig-Maximilians-University Hospital Munich, Institute for Clinical Radiology, Munich, Germany
| | - I Sethi
- Department of Radiology, The University of Chicago, Chicago, IL, USA
| | - J Oommen
- Department of Radiology, The University of Chicago, Chicago, IL, USA
| | - A Oto
- Department of Radiology, The University of Chicago, Chicago, IL, USA
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15
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Cukic M, Oommen J, Mutavdzic D, Jorgovanovic N, Ljubisavljevic M. The effect of single-pulse transcranial magnetic stimulation and peripheral nerve stimulation on complexity of EMG signal: fractal analysis. Exp Brain Res 2013; 228:97-104. [PMID: 23652725 DOI: 10.1007/s00221-013-3541-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 04/23/2013] [Indexed: 11/26/2022]
Abstract
The aim of this study was to examine whether single-pulse transcranial magnetic stimulation (spTMS) affects the pattern of corticospinal activity once voluntary drive has been restored after spTMS-induced EMG silence. We used fractal dimension (FD) to explore the 'complexity' of the electromyography (EMG) signal, and median frequency of the spectra (MDF) to examine changes in EMG spectral characteristics. FD and MDF of the raw EMG epochs immediately before were compared with those obtained from epochs after the EMG silence. Changes in FD and MDF after spTMS were examined with three levels of muscle contraction corresponding to weak (20-40%), moderate (40-60%) and strong (60-80% of maximal voluntary contraction) and three intensities of stimulation set at 10, 20 and 30% above the resting motor threshold. FD was calculated using the Higuchi fractal dimension algorithm. Finally, to discern the origin of FD changes between the CNS and muscle, we compared the effects of spTMS with the effects of peripheral nerve stimulation (PNS) on FD and MDF. The results show that spTMS induced significant decrease in both FD and MDF of EMG signal after stimulation. PNS did not have any significant effects on FD nor MDF. Changes in TMS intensity did not have any significant effect on FD or MDF after stimulation nor had the strength of muscle contraction. However, increase in contraction strength decreased FD before stimulation but only between weak and moderate contraction. The results suggest that the effects of spTMS on corticospinal activity, underlying voluntary motor output, outlast the TMS stimulus. It appears that the complexity of the EMG signal is reduced after spTMS, suggesting that TMS alters the dynamics of the ongoing corticospinal activity most likely temporarily synchronizing the neural network activity. Further studies are needed to confirm whether observed changes after TMS occur at the cortical level.
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Affiliation(s)
- M Cukic
- Biomedical Center, Torlak Institute, Belgrade, Serbia
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16
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Ljubisavljevic M, El-Agnaf O, Ismail F, Oommen J, Hayate J, Filipovic S. 3.313 CHANGES IN BEHAVIORAL RESPONSE TO PAIN IN ROTENONE MODEL OF PARKINSON'S DISEASE IN AGED RATS. Parkinsonism Relat Disord 2012. [DOI: 10.1016/s1353-8020(11)70947-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Mehrotra S, Fakiola M, Oommen J, Jamieson SE, Mishra A, Sudarshan M, Tiwary P, Rani DS, Thangaraj K, Rai M, Sundar S, Blackwell JM. Genetic and functional evaluation of the role of CXCR1 and CXCR2 in susceptibility to visceral leishmaniasis in north-east India. BMC Med Genet 2011; 12:162. [PMID: 22171941 PMCID: PMC3260103 DOI: 10.1186/1471-2350-12-162] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 12/15/2011] [Indexed: 11/10/2022]
Abstract
Background IL8RA and IL8RB, encoded by CXCR1 and CXCR2, are receptors for interleukin (IL)-8 and other CXC chemokines involved in chemotaxis and activation of polymorphonuclear neutrophils (PMN). Variants at CXCR1 and CXCR2 have been associated with susceptibility to cutaneous and mucocutaneous leishmaniasis in Brazil. Here we investigate the role of CXCR1/CXCR2 in visceral leishmaniasis (VL) in India. Methods Three single nucleotide polymorphisms (SNPs) (rs4674259, rs2234671, rs3138060) that tag linkage disequilibrium blocks across CXCR1/CXCR2 were genotyped in primary family-based (313 cases; 176 nuclear families; 836 individuals) and replication (941 cases; 992 controls) samples. Family- and population-based analyses were performed to look for association between CXCR1/CXCR2 variants and VL. Quantitative RT/PCR was used to compare CXCR1/CXCR2 expression in mRNA from paired splenic aspirates taken before and after treatment from 19 VL patients. Results Family-based analysis using FBAT showed association between VL and SNPs CXCR1_rs2234671 (Z-score = 2.935, P = 0.003) and CXCR1_rs3138060 (Z-score = 2.22, P = 0.026), but not with CXCR2_rs4674259. Logistic regression analysis of the case-control data under an additive model of inheritance showed association between VL and SNPs CXCR2_rs4674259 (OR = 1.15, 95%CI = 1.01-1.31, P = 0.027) and CXCR1_rs3138060 (OR = 1.25, 95%CI = 1.02-1.53, P = 0.028), but not with CXCR1_rs2234671. The 3-locus haplotype T_G_C across these SNPs was shown to be the risk haplotype in both family- (TRANSMIT; P = 0.014) and population- (OR = 1.16, P = 0.028) samples (combined P = 0.002). CXCR2, but not CXCR1, expression was down regulated in pre-treatment compared to post-treatment splenic aspirates (P = 0.021). Conclusions This well-powered primary and replication genetic study, together with functional analysis of gene expression, implicate CXCR2 in determining outcome of VL in India.
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Affiliation(s)
- Sanjana Mehrotra
- Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
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Mehrotra S, Oommen J, Mishra A, Sudharshan M, Tiwary P, Jamieson SE, Fakiola M, Rani DS, Thangaraj K, Rai M, Sundar S, Blackwell JM. No evidence for association between SLC11A1 and visceral leishmaniasis in India. BMC Med Genet 2011; 12:71. [PMID: 21599885 PMCID: PMC3128845 DOI: 10.1186/1471-2350-12-71] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Accepted: 05/20/2011] [Indexed: 01/09/2023]
Abstract
Background SLC11A1 has pleiotropic effects on macrophage function and remains a strong candidate for infectious disease susceptibility. 5' and/or 3' polymorphisms have been associated with tuberculosis, leprosy, and visceral leishmaniasis (VL). Most studies undertaken to date were under-powered, and none has been replicated within a population. Association with tuberculosis has replicated variably across populations. Here we investigate SLC11A1 and VL in India. Methods Nine polymorphisms (rs34448891, rs7573065, rs2276631, rs3731865, rs17221959, rs2279015, rs17235409, rs17235416, rs17229009) that tag linkage disequilibrium blocks across SLC11A1 were genotyped in primary family-based (313 cases; 176 families) and replication (941 cases; 992 controls) samples. Family- and population-based analyses were performed to look for association between SLC11A1 variants and VL. Quantitative RT/PCR was used to compare SLC11A1 expression in mRNA from paired splenic aspirates taken before and after treatment from 24 VL patients carrying different genotypes at the functional promoter GTn polymorphism (rs34448891). Results No associations were observed between VL and polymorphisms at SLC11A1 that were either robust to correction for multiple testing or replicated across primary and replication samples. No differences in expression of SLC11A1 were observed when comparing pre- and post-treatment samples, or between individuals carrying different genotypes at the GTn repeat. Conclusions This is the first well-powered study of SLC11A1 as a candidate for VL, which we conclude does not have a major role in regulating VL susceptibility in India.
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Affiliation(s)
- Sanjana Mehrotra
- Institute of Medical Sciences, Banaras Hindu University, Varanasi, OS 221 005, India
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Rye MS, Wiertsema SP, Scaman ESH, Oommen J, Sun W, Francis RW, Ang W, Pennell CE, Burgner D, Richmond P, Vijayasekaran S, Coates HL, Brown SD, Blackwell JM, Jamieson SE. FBXO11, a regulator of the TGFβ pathway, is associated with severe otitis media in Western Australian children. Genes Immun 2011; 12:352-9. [PMID: 21293382 DOI: 10.1038/gene.2011.2] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Otitis media (OM) is a common childhood disease characterised by middle ear inflammation following infection. Susceptibility to recurrent acute OM (rAOM) and chronic OM with effusion (COME) is highly heritable. Two murine mutants, Junbo and Jeff, spontaneously develop severe OM with similar phenotypes to human disease. Fine-mapping of these mutants identified two genes (Evi1 and Fbxo11) that interact with the transforming growth factor β (TGFβ) signalling pathway. We investigated these genes, as well as four Sma- and Mad-related (SMAD) genes of the TGFβ pathway, as candidate rAOM/COME susceptibility genes in two predominantly Caucasian populations. Single-nucleotide polymorphisms (SNPs) within FBXO11 (family-based association testing Z-Score=2.61; P(best)=0.009) were associated with severe OM in family-based analysis of 434 families (561 affected individuals) from the Western Australian Family Study of OM. The FBXO11 association was replicated by directed analysis of Illumina 660W-Quad Beadchip data available for 253 cases and 866 controls (OR=1.55 (95% CI 1.28-1.89); P(best)=6.9 × 10(-6)) available within the Western Australian Pregnancy Cohort (Raine) Study. Combined primary and replication results show P(combined)=2.98 × 10(-6). Neither cohort showed an association with EVI1 variants. Family-based associations at SMAD2 (P=0.038) and SMAD4 (P=0.048) were not replicated. Together, these data provide strong evidence for FBXO11 as a susceptibility gene for severe OM.
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Affiliation(s)
- M S Rye
- Telethon Institute for Child Health Research, Centre for Child Health Research, The University of Western Australia, Subiaco, Western Australia, Australia
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Smit E, Pretorius E, Anderson R, Oommen J, Potjo M. Differentiation of human monocytes in vitro following exposure to Canova in the absence of cytokines. Ultrastruct Pathol 2008; 32:147-52. [PMID: 18696400 DOI: 10.1080/01913120802062729] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Canova is an immunomodulatory, homeopathic preparation that has been shown to activate macrophages in vitro and in vivo, with resultant enhanced spreading of the cells and formation of microvillus extensions from the cell body. Since monocytes are the precursor cells of macrophages and dendritic cells, the objective of the current study was to investigate the effects of Canova on the differentiation of human blood monocytes in vitro. Monocytes were isolated, grown in culture, and exposed to 10 and 20% Canova without the addition of cytokines. After 48 h, monocytes were prepared for analysis by scanning electron microscopy, while cells kept in culture for 7 days and exposed to Canova on days 1, 3, and 4 were analyzed by flow cytometry for alterations in the levels of expression of CD1a, CD11c, CD14, CD80, CD83, CD86, and HLA-DR. SEM revealed that monocytes exposed to 10% Canova had a morphological appearance similar to that of macrophages. Various cytoplasmic projections were observed with pseudopodia formation. Flow cytometric analysis after exposure of monocytes to 10 and 20% Canova indicated high cell viability and upregulation of CD80, compatible with differentiation into either macrophages or dendritic cells. Exposure to Canova per se causes activation of monocytes with resultant differentiation into large macrophage-like cells of indeterminate phenotype that have increased expression of CD80. Like cytokines, Canova induces differentiation of monocytes, an activity that may underpin the immunomodulatory activity of this product.
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Affiliation(s)
- Eureke Smit
- Department of Anatomy, School of Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
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Fickl H, Theron AJ, Grimmer H, Oommen J, Ramafi GJ, Steel HC, Visser SS, Anderson R. Vanadium promotes hydroxyl radical formation by activated human neutrophils. Free Radic Biol Med 2006; 40:146-55. [PMID: 16337888 DOI: 10.1016/j.freeradbiomed.2005.09.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2005] [Revised: 09/13/2005] [Accepted: 09/18/2005] [Indexed: 10/25/2022]
Abstract
This study was undertaken to investigate the effects of vanadium in the +2, +3, +4, and +5 valence states on superoxide generation, myeloperoxidase (MPO) activity, and hydroxyl radical formation by activated human neutrophils in vitro, using lucigenin-enhanced chemiluminescence (LECL), autoiodination, and electron spin resonance with 5,5-dimethyl-l-pyrroline N-oxide as the spin trap, respectively. At concentrations of up to 25 microM, vanadium, in the four different valence states used, did not affect the LECL responses of neutrophils activated with either the chemoattractant, N-formyl-l-methionyl-l-leucyl-l-phenylalanine (1 microM), or the phorbol ester, phorbol 12-myristate 12-acetate (25 ng/ml). However, exposure to vanadium in the +2, +3, and +4, but not the +5, valence states was accompanied by significant augmentation of hydroxyl radical formation by activated neutrophils and attenuation of MPO-mediated iodination. With respect to hydroxyl radical formation, similar effects were observed using cell-free systems containing either hydrogen peroxide (100 microM) or xanthine/xanthine oxidase together with vanadium (+2, +3, +4), while the activity of purified MPO was inhibited by the metal in these valence states. These results demonstrate that vanadium in the +2, +3, and +4 valence states interacts prooxidatively with human neutrophils, competing effectively with MPO for hydrogen peroxide to promote formation of the highly toxic hydroxyl radical.
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Affiliation(s)
- Heidi Fickl
- Medical Research Council Unit for Inflammation and Immunity, Department of Immunology, Tshwane Academic Division of the National Health Laboratory Service and Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa
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Oommen J, Steel HC, Theron AJ, Anderson R. Investigation into the relationship between calyculin A-mediated potentiation of NADPH oxidase activity and inhibition of store-operated uptake of calcium by human neutrophils. Biochem Pharmacol 2004; 68:1721-8. [PMID: 15450937 DOI: 10.1016/j.bcp.2004.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2004] [Accepted: 07/13/2004] [Indexed: 11/18/2022]
Abstract
The primary objective of the current study was to investigate possible relationships between calyculin A (CA)-mediated potentiation of nicotinamide adenine dinucleotide phosphate (NADPH) oxidase activity and inhibition of store-operated uptake of Ca2+ by chemoattractant-activated human neutrophils. Treatment of neutrophils with 100 nM CA, but not at lower concentrations (12.5-50 nM), prior to the addition of the N-formylated chemotactic tripeptide, N-formyl-L-methionyl-L-leucyl-L-phenylalanine (FMLP) (1 microM), both potentiated and prolonged the activity of NADPH oxidase which was accompanied by exaggerated membrane depolarisation, delayed and attenuated membrane repolarisation, and inhibition of store-operated Ca2+ influx. Inclusion of diphenylene iodonium chloride (DPI, 10 microM), an inhibitor of NADPH oxidase, antagonised the effects of CA on NADPH oxidase activity and the membrane repolarisation responses of FMLP-activated neutrophils, but failed to restore store-operated influx of Ca2+. Similarly, CA also inhibited store-operated influx of Ca2+ into FMLP-activated neutrophils from a patient with chronic granulomatous disease, a primary immunodeficiency disorder characterised by the absence of a functional NADPH oxidase. CA also inhibited the store-operated influx of Ca2+ into control neutrophils treated with 1 microM thapsigargin, a selective inhibitor of the endomembrane Ca2+-ATPase, which does not activate NADPH oxidase. Taken together, these observations demonstrate that augmentation of NADPH oxidase activity is not primarily involved in CA-mediated inhibition of the store-operated influx of Ca2+ into activated human neutrophils.
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Affiliation(s)
- Joyce Oommen
- Medical Research Council Unit for Inflammation and Immunity, Department of Immunology, School of Medicine, Faculty of Health Sciences, University of Pretoria, South Africa
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Aras N, Altinel I, Oommen J. A Kohonen-like decomposition method for the euclidean traveling salesman problem - KNIES_DECOMPOSE. ACTA ACUST UNITED AC 2003; 14:869-90. [DOI: 10.1109/tnn.2003.811562] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Oommen J, Altinel IK, Aras N. Discrete vector quantization for arbitrary distance function estimation. IEEE Trans Syst Man Cybern B Cybern 1998; 28:496-510. [PMID: 18255969 DOI: 10.1109/3477.704289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
There are currently many vastly different areas of research involving adaptive learning. Among them are the two areas that concern neural networks and learning automata. This paper develops a method by which the general philosophies of vector quantization (VQ) and discretized automata learning can be incorporated for the computation of arbitrary distance functions. The latter is a problem which has important applications in logistics and location analysis. The input to our problem is the set of coordinates of a large number of nodes whose internode arbitrary "distances" have to be estimated. To render the problem interesting, nontrivial, and realistic, we assume that the explicit form of this distance function is both unknown and uncomputable. Unlike traditional operations research methods, which use optimized parametric functional estimators, we have utilized discretized VQ principles to first adaptively polarize the nodes into subregions. Subsequently, the parameters characterizing the subregions are learned by using a variety of methods (including, for academic purposes, a VQ strategy in the meta-domain). After an initial training phase, a system which achieves distance estimation attempts to yield an estimate of any node-pair distance without actually deriving an explicit form for the unknown function. The algorithms have been rigorously tested for the actual road-travel distances involving cities in Turkey and the results obtained are conclusive. Indeed, these present results are the best currently available from any single or hybrid strategy.
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Affiliation(s)
- J Oommen
- Sch. of Comput. Sci., Carleton Univ., Ottawa, Ont
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