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Raboni S, Montalbano S, Stransky S, Garcia BA, Buschini A, Bettati S, Sidoli S, Mozzarelli A. A Key Silencing Histone Mark on Chromatin Is Lost When Colorectal Adenocarcinoma Cells Are Depleted of Methionine by Methionine γ-Lyase. Front Mol Biosci 2021; 8:735303. [PMID: 34660696 PMCID: PMC8517235 DOI: 10.3389/fmolb.2021.735303] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/02/2021] [Indexed: 12/12/2022] Open
Abstract
Methionine is an essential amino acid used, beyond protein synthesis, for polyamine formation and DNA/RNA/protein methylation. Cancer cells require particularly high methionine supply for their homeostasis. A successful approach for decreasing methionine concentration is based on the systemic delivery of methionine γ-lyase (MGL), with in vitro and in vivo studies demonstrating its efficacy in cancer therapy. However, the mechanisms explaining how cancer cells suffer from the absence of methionine more significantly than non-malignant cells are still unclear. We analyzed the outcome of the human colorectal adenocarcinoma cancer cell line HT29 to the exposure of MGL for up to 72 h by monitoring cell viability, proteome expression, histone post-translational modifications, and presence of spurious transcription. The rationale of this study was to verify whether reduced methionine supply would affect chromatin decondensation by changing the levels of histone methylation and therefore increasing genomic instability. MGL treatment showed a time-dependent cytotoxic effect on HT29 cancer cells, with an IC50 of 30 µg/ml, while Hs27 normal cells were less affected, with an IC50 of >460 µg/ml. Although the levels of total histone methylation were not altered, a loss of the silencing histone mark H3K9me2 was observed, as well as a decrease in H4K20me3. Since H3K9me2/3 decorate repetitive DNA elements, we proved by qRT-PCR that MGL treatment leads to an increased expression of major satellite units. Our data indicate that selected histone methylation marks may play major roles in the mechanism of methionine starvation in cancer cells, proving that MGL treatment directly impacts chromatin homeostasis.
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Affiliation(s)
- Samanta Raboni
- Interdepartmental Center SITEIA.PARMA, University of Parma, Parma, Italy.,Institute of Biophysics, National Research Center, Pisa, Italy
| | - Serena Montalbano
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Stephanie Stransky
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Annamaria Buschini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.,Interdepartmental Centre for Molecular and Translational Oncology COMT, University of Parma, Parma, Italy
| | - Stefano Bettati
- Interdepartmental Center SITEIA.PARMA, University of Parma, Parma, Italy.,Institute of Biophysics, National Research Center, Pisa, Italy.,Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Andrea Mozzarelli
- Institute of Biophysics, National Research Center, Pisa, Italy.,Department of Food and Drug, University of Parma, Parma, Italy
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Sun Y, Stransky S, Aguilan J, Koul S, Garforth SJ, Brenowitz M, Sidoli S. High throughput and low bias DNA methylation and hydroxymethylation analysis by direct injection mass spectrometry. Anal Chim Acta 2021; 1180:338880. [PMID: 34538324 DOI: 10.1016/j.aca.2021.338880] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 12/17/2022]
Abstract
We present a direct injection mass spectrometry (DI-MS) platform that accurately, precisely, and quickly quantitates global levels of DNA cytidine methylation (5 mC) and hydroxymethylation (5hmC). Our platform combines an Advion TriVersa NanoMate coupled online to a Thermo Scientific Orbitrap Fusion Lumos. Following digestion to nucleosides, the DNA samples are analyzed at the rate of <1 min per injection with comparable detection limits of 0.63 ng/μL and 0.31 ng/μL, respectively. In contrast, the detection limits for 5 mC and 5hmC in state-of-art nano liquid chromatography (LC) coupled to online mass spectrometry (nLC-MS) are notably different (0.04 ng/μL and 2.5 ng/μL, respectively). The high sensitivity of DI-MS is achieved by optimizing sample buffer composition, the source fragmentation energy, and the radio frequency of the instrument ion funnel. DI-MS accurately reports the relative abundance of 5 mC and 5hmC over a range of 1%-7% (R2 > 0.98) and 0.13%-1.75% (R2 > 0.99), respectively. Accurate measurement of C, 5 mC and 5hmC is achieved by optimizing in-source fragmentation to obtain a population of up to 93% of just the nucleoside base. This protocol minimizes base dimer formation and partial base-deoxyribose dissociation in gas phase and greatly improves modified base quantitation. We also demonstrate that DI-MS overcomes biases in differential chromatographic retention and issues of sample degradation in the autosampler due to its high throughput. Finally, we present an application of our workflow to quantify DNA modifications on a batch of 81 samples in about 1.5 h.
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Affiliation(s)
- Yan Sun
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Stephanie Stransky
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Jennifer Aguilan
- Laboratory for Macromolecular Analysis and Proteomics Facility, Albert Einstein College of Medicine, New York, NY, USA; Department of Pathology, Albert Einstein College of Medicine, New York, NY, USA
| | - Sanjay Koul
- Department of Biological Sciences, CUNY Queensborough Community College, New York, NY, USA
| | - Scott J Garforth
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Michael Brenowitz
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA; Department of Molecular Pharmacology, Albert Einstein College of Medicine, New York, NY, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA.
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