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Rezapour M, Wesolowski R, Gurcan MN. Identifying Key Genes Involved in Axillary Lymph Node Metastasis in Breast Cancer Using Advanced RNA-Seq Analysis: A Methodological Approach with GLMQL and MAS. Int J Mol Sci 2024; 25:7306. [PMID: 39000413 PMCID: PMC11242629 DOI: 10.3390/ijms25137306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/23/2024] [Accepted: 07/01/2024] [Indexed: 07/16/2024] Open
Abstract
Our study aims to address the methodological challenges frequently encountered in RNA-Seq data analysis within cancer studies. Specifically, it enhances the identification of key genes involved in axillary lymph node metastasis (ALNM) in breast cancer. We employ Generalized Linear Models with Quasi-Likelihood (GLMQLs) to manage the inherently discrete and overdispersed nature of RNA-Seq data, marking a significant improvement over conventional methods such as the t-test, which assumes a normal distribution and equal variances across samples. We utilize the Trimmed Mean of M-values (TMMs) method for normalization to address library-specific compositional differences effectively. Our study focuses on a distinct cohort of 104 untreated patients from the TCGA Breast Invasive Carcinoma (BRCA) dataset to maintain an untainted genetic profile, thereby providing more accurate insights into the genetic underpinnings of lymph node metastasis. This strategic selection paves the way for developing early intervention strategies and targeted therapies. Our analysis is exclusively dedicated to protein-coding genes, enriched by the Magnitude Altitude Scoring (MAS) system, which rigorously identifies key genes that could serve as predictors in developing an ALNM predictive model. Our novel approach has pinpointed several genes significantly linked to ALNM in breast cancer, offering vital insights into the molecular dynamics of cancer development and metastasis. These genes, including ERBB2, CCNA1, FOXC2, LEFTY2, VTN, ACKR3, and PTGS2, are involved in key processes like apoptosis, epithelial-mesenchymal transition, angiogenesis, response to hypoxia, and KRAS signaling pathways, which are crucial for tumor virulence and the spread of metastases. Moreover, the approach has also emphasized the importance of the small proline-rich protein family (SPRR), including SPRR2B, SPRR2E, and SPRR2D, recognized for their significant involvement in cancer-related pathways and their potential as therapeutic targets. Important transcripts such as H3C10, H1-2, PADI4, and others have been highlighted as critical in modulating the chromatin structure and gene expression, fundamental for the progression and spread of cancer.
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Affiliation(s)
- Mostafa Rezapour
- Center for Artificial Intelligence Research, Wake Forest University School of Medicine, Winston-Salem, NC 27101, USA
| | - Robert Wesolowski
- Division of Medical Oncology, James Cancer Hospital and the Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Metin Nafi Gurcan
- Center for Artificial Intelligence Research, Wake Forest University School of Medicine, Winston-Salem, NC 27101, USA
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Tod NP, Vogelauer M, Cheng C, Karimian A, Schmollinger S, Camacho D, Kurdistani SK. The role of histone H3 leucine 126 in fine-tuning the copper reductase activity of nucleosomes. J Biol Chem 2024; 300:107314. [PMID: 38657861 PMCID: PMC11134540 DOI: 10.1016/j.jbc.2024.107314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 04/08/2024] [Accepted: 04/17/2024] [Indexed: 04/26/2024] Open
Abstract
The copper reductase activity of histone H3 suggests undiscovered characteristics within the protein. Here, we investigated the function of leucine 126 (H3L126), which occupies an axial position relative to the copper binding. Typically found as methionine or leucine in copper-binding proteins, the axial ligand influences the reduction potential of the bound ion, modulating its tendency to accept or yield electrons. We found that mutation of H3L126 to methionine (H3L126M) enhanced the enzymatic activity of native yeast nucleosomes in vitro and increased intracellular levels of Cu1+, leading to improved copper-dependent activities including mitochondrial respiration and growth in oxidative media with low copper. Conversely, H3L126 to histidine (H3L126H) mutation decreased nucleosome's enzymatic activity and adversely affected copper-dependent activities in vivo. Our findings demonstrate that H3L126 fine-tunes the copper reductase activity of nucleosomes and highlights the utility of nucleosome enzymatic activity as a novel paradigm to uncover previously unnoticed features of histones.
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Affiliation(s)
- Nataliya P Tod
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Maria Vogelauer
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Chen Cheng
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Ansar Karimian
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Stefan Schmollinger
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Dimitrios Camacho
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Siavash K Kurdistani
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA.
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Leszczynska KB, Freitas-Huhtamäki A, Jayaprakash C, Dzwigonska M, Vitorino FNL, Horth C, Wojnicki K, Gielniewski B, Szadkowska P, Kaza B, Nazarian J, Ciolkowski MK, Trubicka J, Grajkowska W, Garcia BA, Majewski J, Kaminska B, Mieczkowski J. H2A.Z histone variants facilitate HDACi-dependent removal of H3.3K27M mutant protein in pediatric high-grade glioma cells. Cell Rep 2024; 43:113707. [PMID: 38306270 PMCID: PMC11026119 DOI: 10.1016/j.celrep.2024.113707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 10/22/2023] [Accepted: 01/11/2024] [Indexed: 02/04/2024] Open
Abstract
Diffuse intrinsic pontine gliomas (DIPGs) are deadly pediatric brain tumors, non-resectable due to brainstem localization and diffusive growth. Over 80% of DIPGs harbor a mutation in histone 3 (H3.3 or H3.1) resulting in a lysine-to-methionine substitution (H3K27M). Patients with DIPG have a dismal prognosis with no effective therapy. We show that histone deacetylase (HDAC) inhibitors lead to a significant reduction in the H3.3K27M protein (up to 80%) in multiple glioma cell lines. We discover that the SB939-mediated H3.3K27M loss is partially blocked by a lysosomal inhibitor, chloroquine. The H3.3K27M loss is facilitated by co-occurrence of H2A.Z, as evidenced by the knockdown of H2A.Z isoforms. Chromatin immunoprecipitation sequencing (ChIP-seq) analysis confirms the occupancy of H3.3K27M and H2A.Z at the same SB939-inducible genes. We discover a mechanism showing that HDAC inhibition in DIPG leads to pharmacological modulation of the oncogenic H3.3K27M protein levels. These findings show the possibility of directly targeting the H3.3K27M oncohistone.
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Affiliation(s)
- Katarzyna B Leszczynska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland.
| | | | - Chinchu Jayaprakash
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Monika Dzwigonska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Francisca N L Vitorino
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Cynthia Horth
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Kamil Wojnicki
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Bartlomiej Gielniewski
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Paulina Szadkowska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Beata Kaza
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Javad Nazarian
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA; Department of Pediatrics, University Children's Hospital Zürich, Zürich, Switzerland
| | | | | | | | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Bozena Kaminska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Jakub Mieczkowski
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland; 3P-Medicine Laboratory, Medical University of Gdansk, Gdansk, Poland.
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Zhang X, Fawwal DV, Spangle JM, Corbett AH, Jones CY. Exploring the Molecular Underpinnings of Cancer-Causing Oncohistone Mutants Using Yeast as a Model. J Fungi (Basel) 2023; 9:1187. [PMID: 38132788 PMCID: PMC10744705 DOI: 10.3390/jof9121187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/27/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023] Open
Abstract
Understanding the molecular basis of cancer initiation and progression is critical in developing effective treatment strategies. Recently, mutations in genes encoding histone proteins that drive oncogenesis have been identified, converting these essential proteins into "oncohistones". Understanding how oncohistone mutants, which are commonly single missense mutations, subvert the normal function of histones to drive oncogenesis requires defining the functional consequences of such changes. Histones genes are present in multiple copies in the human genome with 15 genes encoding histone H3 isoforms, the histone for which the majority of oncohistone variants have been analyzed thus far. With so many wildtype histone proteins being expressed simultaneously within the oncohistone, it can be difficult to decipher the precise mechanistic consequences of the mutant protein. In contrast to humans, budding and fission yeast contain only two or three histone H3 genes, respectively. Furthermore, yeast histones share ~90% sequence identity with human H3 protein. Its genetic simplicity and evolutionary conservation make yeast an excellent model for characterizing oncohistones. The power of genetic approaches can also be exploited in yeast models to define cellular signaling pathways that could serve as actionable therapeutic targets. In this review, we focus on the value of yeast models to serve as a discovery tool that can provide mechanistic insights and inform subsequent translational studies in humans.
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Affiliation(s)
- Xinran Zhang
- Department of Biology, Emory University, Atlanta, GA 30322, USA; (X.Z.); (D.V.F.); (A.H.C.)
| | - Dorelle V. Fawwal
- Department of Biology, Emory University, Atlanta, GA 30322, USA; (X.Z.); (D.V.F.); (A.H.C.)
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA;
- Biochemistry, Cell & Developmental Biology Graduate Program, Emory University, Atlanta, GA 30322, USA
| | - Jennifer M. Spangle
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA;
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Anita H. Corbett
- Department of Biology, Emory University, Atlanta, GA 30322, USA; (X.Z.); (D.V.F.); (A.H.C.)
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Celina Y. Jones
- Department of Biology, Emory University, Atlanta, GA 30322, USA; (X.Z.); (D.V.F.); (A.H.C.)
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
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5
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Grebstad Tune B, Sareen H, Powter B, Kahana-Edwin S, Cooper A, Koh ES, Lee CS, Po JW, McCowage G, Dexter M, Cain L, O'Neill G, Prior V, Karpelowsky J, Tsoli M, Baumbusch LO, Ziegler D, Roberts TL, DeSouza P, Becker TM, Ma Y. From Pediatric to Adult Brain Cancer: Exploring Histone H3 Mutations in Australian Brain Cancer Patients. Biomedicines 2023; 11:2907. [PMID: 38001908 PMCID: PMC10669073 DOI: 10.3390/biomedicines11112907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/14/2023] [Accepted: 10/19/2023] [Indexed: 11/26/2023] Open
Abstract
Genetic histone variants have been implicated in cancer development and progression. Mutations affecting the histone 3 (H3) family, H3.1 (encoded by HIST1H3B and HIST1H3C) and H3.3 (encoded by H3F3A), are mainly associated with pediatric brain cancers. While considered poor prognostic brain cancer biomarkers in children, more recent studies have reported H3 alterations in adult brain cancer as well. Here, we established reliable droplet digital PCR based assays to detect three histone mutations (H3.3-K27M, H3.3-G34R, and H3.1-K27M) primarily linked to childhood brain cancer. We demonstrate the utility of our assays for sensitively detecting these mutations in cell-free DNA released from cultured diffuse intrinsic pontine glioma (DIPG) cells and in the cerebral spinal fluid of a pediatric patient with DIPG. We further screened tumor tissue DNA from 89 adult patients with glioma and 1 with diffuse hemispheric glioma from Southwestern Sydney, Australia, an ethnically diverse region, for these three mutations. No histone mutations were detected in adult glioma tissue, while H3.3-G34R presence was confirmed in the diffuse hemispheric glioma patient.
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Affiliation(s)
- Benedicte Grebstad Tune
- Department of Pediatric Research, Division of Paediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, 0372 Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW 2170, Australia
| | - Heena Sareen
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW 2170, Australia
- South Western Sydney Clinical School, University of New South Wales, Goulburn St, Liverpool, NSW 2170, Australia
| | - Branka Powter
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW 2170, Australia
| | - Smadar Kahana-Edwin
- Children's Cancer Research Unit, Kids Research, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Adam Cooper
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW 2170, Australia
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
| | - Eng-Siew Koh
- South Western Sydney Clinical School, University of New South Wales, Goulburn St, Liverpool, NSW 2170, Australia
- Department of Radiation Oncology, Liverpool Hospital, Liverpool, NSW 2170, Australia
| | - Cheok S Lee
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
- Department of Radiation Oncology, Liverpool Hospital, Liverpool, NSW 2170, Australia
| | - Joseph W Po
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW 2170, Australia
| | - Geoff McCowage
- Cancer Centre for Children, The Children Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Mark Dexter
- Neurosurgery, The Children Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Lucy Cain
- Cancer Centre for Children, The Children Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Geraldine O'Neill
- Children's Cancer Research Unit, Kids Research, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
- The University of Sydney Children's Hospital Westmead Clinical School, Faculty of Medicine & Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Victoria Prior
- Children's Cancer Research Unit, Kids Research, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
- The University of Sydney Children's Hospital Westmead Clinical School, Faculty of Medicine & Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Jonathan Karpelowsky
- Children's Cancer Research Unit, Kids Research, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
- Paediatric Oncology and Thoracic Surgery, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
- Division of Child and Adolescent Health, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Maria Tsoli
- Children's Cancer Institute, Randwick, NSW 2031, Australia
| | - Lars O Baumbusch
- Department of Pediatric Research, Division of Paediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, 0372 Oslo, Norway
- Faculty of Health, Welfare and Organization, Østfold University College, 1757 Halden, Norway
| | - David Ziegler
- Children's Cancer Institute, Randwick, NSW 2031, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW 2052, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Tara L Roberts
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW 2170, Australia
- South Western Sydney Clinical School, University of New South Wales, Goulburn St, Liverpool, NSW 2170, Australia
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
| | - Paul DeSouza
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW 2170, Australia
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
| | - Therese M Becker
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW 2170, Australia
- South Western Sydney Clinical School, University of New South Wales, Goulburn St, Liverpool, NSW 2170, Australia
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
| | - Yafeng Ma
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW 2170, Australia
- South Western Sydney Clinical School, University of New South Wales, Goulburn St, Liverpool, NSW 2170, Australia
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
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