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Chu SS, Nguyen HA, Zhang J, Tabassum S, Cao H. Towards Multiplexed and Multimodal Biosensor Platforms in Real-Time Monitoring of Metabolic Disorders. SENSORS (BASEL, SWITZERLAND) 2022; 22:5200. [PMID: 35890880 PMCID: PMC9323394 DOI: 10.3390/s22145200] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Metabolic syndrome (MS) is a cluster of conditions that increases the probability of heart disease, stroke, and diabetes, and is very common worldwide. While the exact cause of MS has yet to be understood, there is evidence indicating the relationship between MS and the dysregulation of the immune system. The resultant biomarkers that are expressed in the process are gaining relevance in the early detection of related MS. However, sensing only a single analyte has its limitations because one analyte can be involved with various conditions. Thus, for MS, which generally results from the co-existence of multiple complications, a multi-analyte sensing platform is necessary for precise diagnosis. In this review, we summarize various types of biomarkers related to MS and the non-invasively accessible biofluids that are available for sensing. Then two types of widely used sensing platform, the electrochemical and optical, are discussed in terms of multimodal biosensing, figure-of-merit (FOM), sensitivity, and specificity for early diagnosis of MS. This provides a thorough insight into the current status of the available platforms and how the electrochemical and optical modalities can complement each other for a more reliable sensing platform for MS.
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Affiliation(s)
- Sung Sik Chu
- Department of Biomedical Engineering, Henry Samueli School of Engineering, University of California Irvine, Irvine, CA 92697, USA; (S.S.C.); (J.Z.)
| | - Hung Anh Nguyen
- Department of Electrical Engineering and Computer Science, Henry Samueli School of Engineering, University of California Irvine, Irvine, CA 92697, USA;
| | - Jimmy Zhang
- Department of Biomedical Engineering, Henry Samueli School of Engineering, University of California Irvine, Irvine, CA 92697, USA; (S.S.C.); (J.Z.)
| | - Shawana Tabassum
- Department of Electrical Engineering, College of Engineering, The University of Texas at Tyler, Tyler, TX 75799, USA
| | - Hung Cao
- Department of Biomedical Engineering, Henry Samueli School of Engineering, University of California Irvine, Irvine, CA 92697, USA; (S.S.C.); (J.Z.)
- Department of Electrical Engineering and Computer Science, Henry Samueli School of Engineering, University of California Irvine, Irvine, CA 92697, USA;
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2
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Adhikari S, Guha D, Mohan C, Mukherjee S, Tyler JK, Das C. Reprogramming Carbohydrate Metabolism in Cancer and Its Role in Regulating the Tumor Microenvironment. Subcell Biochem 2022; 100:3-65. [PMID: 36301490 PMCID: PMC10760510 DOI: 10.1007/978-3-031-07634-3_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Altered metabolism has become an emerging feature of cancer cells impacting their proliferation and metastatic potential in myriad ways. Proliferating heterogeneous tumor cells are surrounded by other resident or infiltrating cells, along with extracellular matrix proteins, and other secretory factors constituting the tumor microenvironment. The diverse cell types of the tumor microenvironment exhibit different molecular signatures that are regulated at their genetic and epigenetic levels. The cancer cells elicit intricate crosstalks with these supporting cells, exchanging essential metabolites which support their anabolic processes and can promote their survival, proliferation, EMT, angiogenesis, metastasis and even therapeutic resistance. In this context, carbohydrate metabolism ensures constant energy supply being a central axis from which other metabolic and biosynthetic pathways including amino acid and lipid metabolism and pentose phosphate pathway are diverged. In contrast to normal cells, increased glycolytic flux is a distinguishing feature of the highly proliferative cancer cells, which supports them to adapt to a hypoxic environment and also protects them from oxidative stress. Such rewired metabolic properties are often a result of epigenetic alterations in the cancer cells, which are mediated by several factors including, DNA, histone and non-histone protein modifications and non-coding RNAs. Conversely, epigenetic landscapes of the cancer cells are also dictated by their diverse metabolomes. Altogether, this metabolic and epigenetic interplay has immense potential for the development of efficient anti-cancer therapeutic strategies. In this book chapter we emphasize upon the significance of reprogrammed carbohydrate metabolism in regulating the tumor microenvironment and cancer progression, with an aim to explore the different metabolic and epigenetic targets for better cancer treatment.
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Affiliation(s)
- Swagata Adhikari
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
- Homi Bhaba National Institute, Mumbai, India
| | - Deblina Guha
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Chitra Mohan
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Shravanti Mukherjee
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Jessica K Tyler
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India.
- Homi Bhaba National Institute, Mumbai, India.
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3
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Shteinfer-Kuzmine A, Verma A, Arif T, Aizenberg O, Paul A, Shoshan-Barmaz V. Mitochondria and nucleus cross-talk: Signaling in metabolism, apoptosis, and differentiation, and function in cancer. IUBMB Life 2021; 73:492-510. [PMID: 33179373 DOI: 10.1002/iub.2407] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/15/2020] [Accepted: 10/21/2020] [Indexed: 12/12/2022]
Abstract
The cross-talk between the mitochondrion and the nucleus regulates cellular functions, including differentiation and adaptation to stress. Mitochondria supply metabolites for epigenetic modifications and other nuclear-associated activities and certain mitochondrial proteins were found in the nucleus. The voltage-dependent anion channel 1 (VDAC1), localized at the outer mitochondrial membrane (OMM) is a central protein in controlling energy production, cell growth, Ca2+ homeostasis, and apoptosis. To alter the cross-talk between the mitochondria and the nucleus, we used specific siRNA to silence the expression of VDAC1 in glioblastoma (GBM) U87-MG and U118-MG cell-derived tumors, and then monitored the nuclear localization of mitochondrial proteins and the methylation and acetylation of histones. Depletion of VDAC1 from tumor cells reduced metabolism, leading to inhibition of tumor growth, and several tumor-associated processes and signaling pathways linked to cancer development. In addition, we demonstrate that certain mitochondrial pro-apoptotic proteins such as caspases 3, 8, and 9, and p53 were unexpectedly overexpressed in tumors, suggesting that they possess additional non-apoptotic functions. VDAC1 depletion and metabolic reprograming altered their expression levels and subcellular localization, specifically their translocation to the nucleus. In addition, VDAC1 depletion also leads to epigenetic modifications of histone acetylation and methylation, suggesting that the interchange between metabolism and cancer signaling pathways involves mitochondria-nucleus cross-talk. The mechanisms regulating mitochondrial protein trafficking into and out of the nucleus and the role these proteins play in the nucleus remain to be elucidated.
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Affiliation(s)
- Anna Shteinfer-Kuzmine
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Beersheba, Israel
| | - Ankit Verma
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Beersheba, Israel
| | - Tasleem Arif
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Beersheba, Israel
- Department of Cell, Developmental, & Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Or Aizenberg
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Beersheba, Israel
| | - Avijit Paul
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Beersheba, Israel
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Varda Shoshan-Barmaz
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Beersheba, Israel
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4
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Shoshan-Barmatz V, Shteinfer-Kuzmine A, Verma A. VDAC1 at the Intersection of Cell Metabolism, Apoptosis, and Diseases. Biomolecules 2020; 10:E1485. [PMID: 33114780 PMCID: PMC7693975 DOI: 10.3390/biom10111485] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/02/2020] [Accepted: 10/22/2020] [Indexed: 02/07/2023] Open
Abstract
The voltage-dependent anion channel 1 (VDAC1) protein, is an important regulator of mitochondrial function, and serves as a mitochondrial gatekeeper, with responsibility for cellular fate. In addition to control over energy sources and metabolism, the protein also regulates epigenomic elements and apoptosis via mediating the release of apoptotic proteins from the mitochondria. Apoptotic and pathological conditions, as well as certain viruses, induce cell death by inducing VDAC1 overexpression leading to oligomerization, and the formation of a large channel within the VDAC1 homo-oligomer. This then permits the release of pro-apoptotic proteins from the mitochondria and subsequent apoptosis. Mitochondrial DNA can also be released through this channel, which triggers type-Ι interferon responses. VDAC1 also participates in endoplasmic reticulum (ER)-mitochondria cross-talk, and in the regulation of autophagy, and inflammation. Its location in the outer mitochondrial membrane, makes VDAC1 ideally placed to interact with over 100 proteins, and to orchestrate the interaction of mitochondrial and cellular activities through a number of signaling pathways. Here, we provide insights into the multiple functions of VDAC1 and describe its involvement in several diseases, which demonstrate the potential of this protein as a druggable target in a wide variety of pathologies, including cancer.
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Affiliation(s)
- Varda Shoshan-Barmatz
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; (A.S.-K.); (A.V.)
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5
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Liu XR, Zhang RY, Gong H, Rugo HS, Chen LB, Fu Y, Che JW, Tie J, Shao B, Wan FL, Kong WY, Song GH, Jiang HF, Xu GB, Li HP. Methylome Variation Predicts Exemestane Resistance in Advanced ER + Breast Cancer. Technol Cancer Res Treat 2020; 19:1533033819896331. [PMID: 32129154 PMCID: PMC7057408 DOI: 10.1177/1533033819896331] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Background: More than 30% of estrogen receptor-positive breast cancers are resistant to primary
hormone therapy, and about 40% that initially respond to hormone therapy eventually
acquire resistance. Although the mechanisms of hormone therapy resistance remain
unclear, aberrant DNA methylation has been implicated in oncogenesis and drug
resistance. Purpose: We investigated the relationship between methylome variations in circulating tumor DNA
and exemestane resistance, to track hormone therapy efficacy. Methods: We prospectively recruited 16 patients who were receiving first-line therapy in our
center. All patients received exemestane-based hormone therapy after enrollment. We
collected blood samples at baseline, first follow-up (after 2 therapeutic cycles) and at
detection of disease progression. Disease that progressed within 6 months under
exemestane treatment was considered exemestane resistance but was considered relatively
exemestane-sensitive otherwise. We obtained circulating tumor DNA-derived methylomes
using the whole-genome bisulfide sequencing method. Methylation calling was done by
BISMARK software; differentially methylated regions for exemestane resistance were
calculated afterward. Results: Median follow-up for the 16 patients was 19.0 months. We found 7 exemestane
resistance-related differentially methylated regions, located in different chromosomes,
with both significantly different methylation density and methylation ratio. Baseline
methylation density and methylation ratio of chromosome 6 [32400000-32599999] were both
high in exemestane resistance. High baseline methylation ratios of chromosome 3
[67800000-67999999] (P = .013), chromosome 3 [140200000-140399999]
(P = .037), and chromosome 12 [101200000-101399999]
(P = .026) could also predict exemestane resistance. During
exemestane treatment, synchronized changes in methylation density and methylation ratio
in chromosome 6 [32400000-32599999] could accurately stratify patients in terms of
progression-free survival (P = .000033). Cutoff values of methylation
density and methylation ratio for chromosome 6 [149600000-149799999] were 0.066 and
0.076, respectively. Conclusion: Methylation change in chromosome 6 [149600000-149799999] is an ideal predictor of
exemestane resistance with great clinical potential.
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Affiliation(s)
- Xiao-Ran Liu
- Department of Breast Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China.,The authors contributed eually to the article
| | - Ru-Yan Zhang
- Department of Breast Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China.,The authors contributed eually to the article
| | - Hao Gong
- M3 Genomics, Inc, Guangzhou, Guangdong, China.,The authors contributed eually to the article
| | - Hope S Rugo
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, CA, USA
| | | | - Yuan Fu
- M3 Genomics, Inc, Guangzhou, Guangdong, China
| | - Jian-Wei Che
- M3 Genomics, Inc, Guangzhou, Guangdong, China.,Life Healthcare Group Ltd, Beijing, China
| | - Jian Tie
- Department of Breast Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Bin Shao
- Department of Breast Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Feng-Ling Wan
- Department of Breast Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Wei-Yao Kong
- Department of Breast Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Guo-Hong Song
- Department of Breast Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Han-Fang Jiang
- Department of Breast Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Guo-Bing Xu
- Department of Breast Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Hui-Ping Li
- Department of Breast Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
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6
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Alakwaa FM, Savelieff MG. Bioinformatics Analysis of Metabolomics Data Unveils Association of Metabolic Signatures with Methylation in Breast Cancer. J Proteome Res 2020; 19:2879-2889. [PMID: 31886666 DOI: 10.1021/acs.jproteome.9b00755] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Breast cancer (BC) contributes the highest global cancer mortality in women. BC tumors are highly heterogeneous, so subtyping by cell-surface markers is inadequate. Omics-driven tumor stratification is urgently needed to better understand BC and tailor therapies for personalized medicine. We used unsupervised k-means and partition around medoids (pam) to cluster metabolomics data from two data sets. The first comprised 271 BC tumors (data set 1) that were estrogen receptor (ER) positive (ER+, n = 204) or negative (ER-, n = 67) with 162 identified and validated metabolites. The second data set contained 67 BC samples (data set 2; ER+, n = 33; ER-, n = 34) and 352 known metabolites. Significance Analysis of Microarrays (SAM) was used to identify the most significant metabolites among these clusters, which were then reassigned into new clusters using prediction analysis of microarrays (PAM). Generally, metabolome-defined BC subtypes identified from either data set 1 or data set 2 were different from the well-known receptor- or transcriptome-defined subtypes. Metabolomics-directed clustering of data set 2 identified distinctive BC tumors characterized by metabolome profiles that associated with DNA methylation (p-value = 0.000 048, χ2 test). Pathway analysis of cluster metabolites revealed that nitrogen metabolism and aminoacyl-tRNA biosynthesis were highly related to BC subtyping. The pipeline may be run from GitHub: https://github.com/FADHLyemen/Metabolomics_signature. Our proposed bioinformatics pipeline analyzed metabolomics data from BC tumors, revealing clusters characterized by unique metabolic signatures that may potentially stratify BC patients and tailor precision treatment.
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Affiliation(s)
- Fadhl M Alakwaa
- Department of Neurology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Masha G Savelieff
- Department of Neurology, University of Michigan, Ann Arbor, Michigan 48109, United States
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7
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Amsalem Z, Arif T, Shteinfer-Kuzmine A, Chalifa-Caspi V, Shoshan-Barmatz V. The Mitochondrial Protein VDAC1 at the Crossroads of Cancer Cell Metabolism: The Epigenetic Link. Cancers (Basel) 2020; 12:cancers12041031. [PMID: 32331482 PMCID: PMC7226296 DOI: 10.3390/cancers12041031] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/14/2020] [Accepted: 04/17/2020] [Indexed: 12/29/2022] Open
Abstract
Carcinogenesis is a complicated process that involves the deregulation of epigenetics, resulting in cellular transformational events, such as proliferation, differentiation, and metastasis. Most chromatin-modifying enzymes utilize metabolites as co-factors or substrates and thus are directly dependent on such metabolites as acetyl-coenzyme A, S-adenosylmethionine, and NAD+. Here, we show that using specific siRNA to deplete a tumor of VDAC1 not only led to reprograming of the cancer cell metabolism but also altered several epigenetic-related enzymes and factors. VDAC1, in the outer mitochondrial membrane, controls metabolic cross-talk between the mitochondria and the rest of the cell, thus regulating the metabolic and energetic functions of mitochondria, and has been implicated in apoptotic-relevant events. We previously demonstrated that silencing VDAC1 expression in glioblastoma (GBM) U-87MG cell-derived tumors, resulted in reprogramed metabolism leading to inhibited tumor growth, angiogenesis, epithelial-mesenchymal transition and invasiveness, and elimination of cancer stem cells, while promoting the differentiation of residual tumor cells into neuronal-like cells. These VDAC1 depletion-mediated effects involved alterations in transcription factors regulating signaling pathways associated with cancer hallmarks. As the epigenome is sensitive to cellular metabolism, this study was designed to assess whether depleting VDAC1 affects the metabolism-epigenetics axis. Using DNA microarrays, q-PCR, and specific antibodies, we analyzed the effects of si-VDAC1 treatment of U-87MG-derived tumors on histone modifications and epigenetic-related enzyme expression levels, as well as the methylation and acetylation state, to uncover any alterations in epigenetic properties. Our results demonstrate that metabolic rewiring of GBM via VDAC1 depletion affects epigenetic modifications, and strongly support the presence of an interplay between metabolism and epigenetics.
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Affiliation(s)
- Zohar Amsalem
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; (Z.A.); (T.A.); (A.S.-K.)
| | - Tasleem Arif
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; (Z.A.); (T.A.); (A.S.-K.)
| | - Anna Shteinfer-Kuzmine
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; (Z.A.); (T.A.); (A.S.-K.)
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel;
| | - Vered Chalifa-Caspi
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel;
| | - Varda Shoshan-Barmatz
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; (Z.A.); (T.A.); (A.S.-K.)
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel;
- Correspondence: ; Fax: +972-8-647-2992
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8
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Rewiring of Cancer Cell Metabolism by Mitochondrial VDAC1 Depletion Results in Time-Dependent Tumor Reprogramming: Glioblastoma as a Proof of Concept. Cells 2019; 8:cells8111330. [PMID: 31661894 PMCID: PMC6912264 DOI: 10.3390/cells8111330] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/18/2019] [Accepted: 10/23/2019] [Indexed: 12/16/2022] Open
Abstract
Reprograming of the metabolism of cancer cells is an event recognized as a hallmark of the disease. The mitochondrial gatekeeper, voltage-dependent anion channel 1 (VDAC1), mediates transport of metabolites and ions in and out of mitochondria, and is involved in mitochondria-mediated apoptosis. Here, we compared the effects of reducing hVDAC1 expression in a glioblastoma xenograft using human-specific si-RNA (si-hVDAC1) for a short (19 days) and a long term (40 days). Tumors underwent reprograming, reflected in rewired metabolism, eradication of cancer stem cells (CSCs) and differentiation. Short- and long-term treatments of the tumors with si-hVDAC1 similarly reduced the expression of metabolism-related enzymes, and translocator protein (TSPO) and CSCs markers. In contrast, differentiation into cells expressing astrocyte or neuronal markers was noted only after a long period during which the tumor cells were hVDAC1-depleted. This suggests that tumor cell differentiation is a prolonged process that precedes metabolic reprograming and the “disappearance” of CSCs. Tumor proteomics analysis revealing global changes in the expression levels of proteins associated with signaling, synthesis and degradation of proteins, DNA structure and replication and epigenetic changes, all of which were highly altered after a long period of si-hVDAC1 tumor treatment. The depletion of hVDAC1 greatly reduced the levels of the multifunctional translocator protein TSPO, which is overexpressed in both the mitochondria and the nucleus of the tumor. The results thus show that VDAC1 depletion-mediated cancer cell metabolic reprograming involves a chain of events occurring in a sequential manner leading to a reversal of the unique properties of the tumor, indicative of the interplay between metabolism and oncogenic signaling networks.
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9
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Metabolic Dysregulations and Epigenetics: A Bidirectional Interplay that Drives Tumor Progression. Cells 2019; 8:cells8080798. [PMID: 31366176 PMCID: PMC6721562 DOI: 10.3390/cells8080798] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 07/24/2019] [Accepted: 07/29/2019] [Indexed: 02/07/2023] Open
Abstract
Cancer has been considered, for a long time, a genetic disease where mutations in key regulatory genes drive tumor initiation, growth, metastasis, and drug resistance. Instead, the advent of high-throughput technologies has revolutionized cancer research, allowing to investigate molecular alterations at multiple levels, including genome, epigenome, transcriptome, proteome, and metabolome and showing the multifaceted aspects of this disease. The multi-omics approaches revealed an intricate molecular landscape where different cellular functions are interconnected and cooperatively contribute to shaping the malignant phenotype. Recent evidence has brought to light how metabolism and epigenetics are highly intertwined, and their aberrant crosstalk can contribute to tumorigenesis. The oncogene-driven metabolic plasticity of tumor cells supports the energetic and anabolic demands of proliferative tumor programs and secondary can alter the epigenetic landscape via modulating the production and/or the activity of epigenetic metabolites. Conversely, epigenetic mechanisms can regulate the expression of metabolic genes, thereby altering the metabolome, eliciting adaptive responses to rapidly changing environmental conditions, and sustaining malignant cell survival and progression in hostile niches. Thus, cancer cells take advantage of the epigenetics-metabolism crosstalk to acquire aggressive traits, promote cell proliferation, metastasis, and pluripotency, and shape tumor microenvironment. Understanding this bidirectional relationship is crucial to identify potential novel molecular targets for the implementation of robust anti-cancer therapeutic strategies.
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10
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D'Aniello C, Cermola F, Palamidessi A, Wanderlingh LG, Gagliardi M, Migliaccio A, Varrone F, Casalino L, Matarazzo MR, De Cesare D, Scita G, Patriarca EJ, Minchiotti G. Collagen Prolyl Hydroxylation-Dependent Metabolic Perturbation Governs Epigenetic Remodeling and Mesenchymal Transition in Pluripotent and Cancer Cells. Cancer Res 2019; 79:3235-3250. [PMID: 31061065 DOI: 10.1158/0008-5472.can-18-2070] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 01/03/2019] [Accepted: 04/16/2019] [Indexed: 11/16/2022]
Abstract
Collagen prolyl hydroxylation (CPH), which is catalyzed by prolyl 4-hydroxylase (P4H), is the most prevalent posttranslational modification in humans and requires vitamin C (VitC). Here, we demonstrate that CPH acts as an epigenetic modulator of cell plasticity. Increased CPH induced global DNA/histone methylation in pluripotent stem and tumor cells and promoted cell state transition (CST). Interfering with CPH by either genetic ablation of P4H subunit alpha-2 (P4HA2) or pharmacologic treatment reverted epigenetic changes and antagonized CST. Mechanistically, we suggest that CPH modifies the epigenetic landscape by reducing VitC for DNA and histone demethylases. Repurposed drugs targeting CPH-mediated metabolic perturbation, such as the antiasthmatic budesonide, blocked metastatic dissemination of breast cancer cells in vivo by preventing mesenchymal transition. Our study provides mechanistic insights into how metabolic cues and epigenetic factors integrate to control CST and paves the way for the development of novel antimetastatic strategies. SIGNIFICANCE: A phenotype-based high-throughput screening reveals unforeseen metabolic control of cell plasticity and identifies budesonide as a drug candidate for metastatic cancer.Graphical Abstract: http://cancerres.aacrjournals.org/content/canres/79/13/3235/F1.large.jpg.
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Affiliation(s)
- Cristina D'Aniello
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics, 'A. Buzzati-Traverso', CNR, Naples, Italy.,Institute of Genetics and Biophysics, 'A. Buzzati-Traverso', CNR, Naples, Italy
| | - Federica Cermola
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics, 'A. Buzzati-Traverso', CNR, Naples, Italy.,Institute of Genetics and Biophysics, 'A. Buzzati-Traverso', CNR, Naples, Italy
| | | | | | - Miriam Gagliardi
- Institute of Genetics and Biophysics, 'A. Buzzati-Traverso', CNR, Naples, Italy
| | - Agnese Migliaccio
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics, 'A. Buzzati-Traverso', CNR, Naples, Italy
| | | | - Laura Casalino
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics, 'A. Buzzati-Traverso', CNR, Naples, Italy.,Institute of Genetics and Biophysics, 'A. Buzzati-Traverso', CNR, Naples, Italy
| | - Maria R Matarazzo
- Institute of Genetics and Biophysics, 'A. Buzzati-Traverso', CNR, Naples, Italy
| | - Dario De Cesare
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics, 'A. Buzzati-Traverso', CNR, Naples, Italy.,Institute of Genetics and Biophysics, 'A. Buzzati-Traverso', CNR, Naples, Italy
| | - Giorgio Scita
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Eduardo J Patriarca
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics, 'A. Buzzati-Traverso', CNR, Naples, Italy. .,Institute of Genetics and Biophysics, 'A. Buzzati-Traverso', CNR, Naples, Italy
| | - Gabriella Minchiotti
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics, 'A. Buzzati-Traverso', CNR, Naples, Italy. .,Institute of Genetics and Biophysics, 'A. Buzzati-Traverso', CNR, Naples, Italy
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Arif T, Krelin Y, Nakdimon I, Benharroch D, Paul A, Dadon-Klein D, Shoshan-Barmatz V. VDAC1 is a molecular target in glioblastoma, with its depletion leading to reprogrammed metabolism and reversed oncogenic properties. Neuro Oncol 2018; 19:951-964. [PMID: 28339833 DOI: 10.1093/neuonc/now297] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background Glioblastoma (GBM), an aggressive brain tumor with frequent relapses and a high mortality, still awaits an effective treatment. Like many cancers, GBM cells acquire oncogenic properties, including metabolic reprogramming, vital for growth. As such, tumor metabolism is an emerging avenue for cancer therapy. One relevant target is the voltage-dependent anion channel 1 (VDAC1), a mitochondrial protein controlling cell energy and metabolic homeostasis. Methods We used VDAC1-specific short interfering (si)RNA (si-VDAC1) to treat GBM cell lines and subcutaneous or intracranial-orthotopic GBM xenograft mouse models. Tumors were monitored using MRI, immunohistochemistry, immunoblotting, immunofluorescence, quantitative real-time PCR, transcription factor expression, and DNA microarray analyses. Results Silencing VDAC1 expression using si-VDAC1 in 9 glioblastoma-related cell lines, including patient-derived cells, led to marked decreases in VDAC1 levels and cell growth. Using si-VDAC1 in subcutaneous or intracranial-orthotopic GBM models inhibited tumor growth and reversed oncogenic properties, such as reprogrammed metabolism, stemness, angiogenesis, epithelial-mesenchymal transition, and invasiveness. In cells in culture, si-VDAC1 inhibits cancer neurosphere formation and, in tumors, targeted cancer stem cells, leading to their differentiation into neuronal-like cells. These VDAC1 depletion-mediated effects involved alterations in transcription factors regulating signaling pathways associated with cancer hallmarks. Conclusion VDAC1 offers a target for GBM treatment, allowing for attacks on the interplay between metabolism and oncogenic signaling networks, leading to tumor cell differentiation into neuron- and astrocyte-like cells. Simultaneously attacking all of these processes, VDAC1 depletion overcame GBM heterogeneity and can replace several anticancer drugs that separately target angiogenesis, proliferation, or metabolism.
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Affiliation(s)
- Tasleem Arif
- Department of Life Sciences, and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev,Beer-Sheva, Israel; Department of Pathology, Soroka University Medical Centre, and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yakov Krelin
- Department of Life Sciences, and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev,Beer-Sheva, Israel; Department of Pathology, Soroka University Medical Centre, and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Itay Nakdimon
- Department of Life Sciences, and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev,Beer-Sheva, Israel; Department of Pathology, Soroka University Medical Centre, and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Daniel Benharroch
- Department of Life Sciences, and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev,Beer-Sheva, Israel; Department of Pathology, Soroka University Medical Centre, and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Avijit Paul
- Department of Life Sciences, and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev,Beer-Sheva, Israel; Department of Pathology, Soroka University Medical Centre, and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Daniela Dadon-Klein
- Department of Life Sciences, and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev,Beer-Sheva, Israel; Department of Pathology, Soroka University Medical Centre, and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Varda Shoshan-Barmatz
- Department of Life Sciences, and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev,Beer-Sheva, Israel; Department of Pathology, Soroka University Medical Centre, and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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Shteinfer-Kuzmine A, Arif T, Krelin Y, Tripathi SS, Paul A, Shoshan-Barmatz V. Mitochondrial VDAC1-based peptides: Attacking oncogenic properties in glioblastoma. Oncotarget 2018; 8:31329-31346. [PMID: 28412744 PMCID: PMC5458211 DOI: 10.18632/oncotarget.15455] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 11/21/2016] [Indexed: 01/06/2023] Open
Abstract
Glioblastoma multiforme (GBM), a primary brain malignancy characterized by high morbidity, invasiveness, proliferation, relapse and mortality, is resistant to chemo- and radiotherapies and lacks effective treatment. GBM tumors undergo metabolic reprograming and develop anti-apoptotic defenses. We targeted GBM with a peptide derived from the mitochondrial protein voltage-dependent anion channel 1 (VDAC1), a key component of cell energy, metabolism and apoptosis regulation. VDAC1-based cell-penetrating peptides perturbed cell energy and metabolic homeostasis and induced apoptosis in several GBM and GBM-derived stem cell lines. We found that the peptides simultaneously attacked several oncogenic properties of human U-87MG cells introduced into sub-cutaneous xenograft mouse model, inhibiting tumor growth, invasion, and cellular metabolism, stemness and inducing apoptosis. Peptide-treated tumors showed decreased expression of all tested metabolism-related enzymes and transporters, and elevated levels of apoptotic proteins, such as p53, cytochrome c and caspases. Retro-Tf-D-LP4, containing the human transferrin receptor (TfR)-recognition sequence, crossed the blood-brain barrier (BBB) via the TfR that is highly expressed in the BBB to strongly inhibit tumor growth in an intracranial xenograft mouse model. In summary, the VDAC1-based peptides tested here offer a potentially affordable and innovative new conceptual therapeutic paradigm that might overcome GBM stemness and invasiveness and reduce relapse rates.
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Affiliation(s)
- Anna Shteinfer-Kuzmine
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Tasleem Arif
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Yakov Krelin
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Shambhoo Sharan Tripathi
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Avijit Paul
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Varda Shoshan-Barmatz
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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Abstract
Glucose and Glutamine are two essential ingredients for cell growth. However, it remains open for investigation whether there is a general mechanism that coordinates the consumption of glucose and glutamine in cancer cells. Glutamine is mainly metabolized through the glutaminolysis pathway and our previous report indicated that CtBP increases GDH activity and promotes glutaminolysis through repressing the expression of SIRT4, a well-known mitochondrion-located factor that inhibits glutaminolysis pathway. CtBP is known to be a sensor of intracellular metabolic status; we thus hypothesized that a consensus CtBP-SIRT4-GDH axis may mediate the crosstalk between glycolysis and glutaminolysis. Herein, supporting this hypothesis, we observed the coordinated consumption of glucose and glutamine across different cell lines. This coordination was found to be related to CtBP repression activity on SIRT4 expression under high level of glucose but not low glucose level. Low level of glucose supply was found to decrease GDH activity via blocking CtBP dimerization. Mechanically, low glucose also abolished CtBP binding to SIRT4 promoter and the repression of SIRT4 expression. Consistently, the CtBP dimerization inhibitor MTOB mimicked low glucose effects on SIRT4 expression, and GDH activity suggest that CtBP requires high glucose supply to act as a suppressor of SIRT4 gene. In conclusion, we propose that a general molecular pathway composed by CtBP-SIRT4-GDH coordinating the metabolism of glucose and glutamine in cancer cells.
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Wang Y, Hao DP, Li JJ, Wang L, Di LJ. Genome-wide methylome and chromatin interactome identify abnormal enhancer to be risk factor of breast cancer. Oncotarget 2017; 8:44705-44719. [PMID: 28621677 PMCID: PMC5546512 DOI: 10.18632/oncotarget.18348] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 05/15/2017] [Indexed: 11/25/2022] Open
Abstract
Enhancer is critical cis regulatory elements in gene expression. To understand whether and how the aberrant enhancer activation may contribute to cancer risk, the differentially methylated enhancers (eDMRs) in normal and malignant breast tissues were identified and analyzed. By incorporating genome-wide chromatin interaction, integrated analysis of eDMRs and target gene expression identified 1,272 enhancer-promoter pairs. Surprisingly, two functionally distinct groups of genes were identified in these pairs, one showing better correlation to enhancer methylation (eRGs) and the other showing better correlation to promoter methylation (pRGs), and the former group is functionally enriched with cancer related genes. Moreover, enhancer methylation based clustering of breast cancer samples is capable of discriminating basal breast cancer from other subtypes. By correlating enhancer methylation status to patient survival, 345 enhancers show the impact on the disease outcome and the majority of their target genes are important regulators of cell survival pathways including known cancer related genes. Together, these results suggest reactivation of enhancers in cancer cells has the add-on effect and contributes to cancer risk in combination.
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Affiliation(s)
- Yuan Wang
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, China
| | - Da-Peng Hao
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, China
| | - Jing-Jing Li
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, China
| | - Li Wang
- Metabolomics Core, Faculty of Health Sciences, University of Macau, Macau, China
| | - Li-Jun Di
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, China
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