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Furth N, Cohen N, Spitzer A, Salame TM, Dassa B, Mehlman T, Brandis A, Moussaieff A, Friedmann-Morvinski D, Castro MG, Fortin J, Suvà ML, Tirosh I, Erez A, Ron G, Shema E. Oncogenic IDH1 mut drives robust loss of histone acetylation and increases chromatin heterogeneity. Proc Natl Acad Sci U S A 2025; 122:e2403862122. [PMID: 39793065 PMCID: PMC11725805 DOI: 10.1073/pnas.2403862122] [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: 02/23/2024] [Accepted: 11/15/2024] [Indexed: 01/12/2025] Open
Abstract
Malignant gliomas are heterogeneous tumors, mostly incurable, arising in the central nervous system (CNS) driven by genetic, epigenetic, and metabolic aberrations. Mutations in isocitrate dehydrogenase (IDH1/2mut) enzymes are predominantly found in low-grade gliomas and secondary high-grade gliomas, with IDH1 mutations being more prevalent. Mutant-IDH1/2 confers a gain-of-function activity that favors the conversion of a-ketoglutarate (α-KG) to the oncometabolite 2-hydroxyglutarate (2-HG), resulting in an aberrant hypermethylation phenotype. Yet, the complete depiction of the epigenetic alterations in IDHmut cells has not been thoroughly explored. Here, we applied an unbiased approach, leveraging epigenetic-focused cytometry by time-of-flight (CyTOF) analysis, to systematically profile the effect of mutant-IDH1 expression on a broad panel of histone modifications at single-cell resolution. This analysis revealed extensive remodeling of chromatin patterns by mutant-IDH1, with the most prominent being deregulation of histone acetylation marks. The loss of histone acetylation occurs rapidly following mutant-IDH1 induction and affects acetylation patterns over enhancers and intergenic regions. Notably, the changes in acetylation are not predominantly driven by 2-HG, can be rescued by pharmacological inhibition of mutant-IDH1, and reversed by acetate supplementations. Furthermore, cells expressing mutant-IDH1 show higher epigenetic and transcriptional heterogeneity and upregulation of oncogenes such as KRAS and MYC, highlighting its tumorigenic potential. Our study underscores the tight interaction between chromatin and metabolism dysregulation in glioma and highlights epigenetic and oncogenic pathways affected by mutant-IDH1-driven metabolic rewiring.
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Affiliation(s)
- Noa Furth
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Niv Cohen
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Avishay Spitzer
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot7610001, Israel
- Oncology Institute, Tel Aviv Sourasky Medical Center, Tel Aviv6423906, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv6997801, Israel
| | - Tomer-Meir Salame
- Mass Cytometry Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Bareket Dassa
- Bioinformatics Unit, Department of Life Sciences Core Facilities, Faculty of Biochemistry, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Tevie Mehlman
- Targeted Metabolomics Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Alexander Brandis
- Targeted Metabolomics Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Arieh Moussaieff
- The Institute for Drug Research, Faculty of Medicine, Hebrew University, Jerusalem9112102, Israel
| | - Dinorah Friedmann-Morvinski
- Sagol School of Neurobiology, Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv6997801, Israel
| | - Maria G. Castro
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI48109
| | - Jerome Fortin
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, QCH3A 2B4, Canada
| | - Mario L. Suvà
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA02114
- Broad Institute of Harvard and MIT, Cambridge, MA02142
| | - Itay Tirosh
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Ayelet Erez
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Guy Ron
- Racah Institute of Physics, Hebrew University, Jerusalem9190401, Israel
| | - Efrat Shema
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot7610001, Israel
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2
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Gaiaschi L, Bottone MG, De Luca F. Towards Effective Treatment of Glioblastoma: The Role of Combination Therapies and the Potential of Phytotherapy and Micotherapy. Curr Issues Mol Biol 2024; 46:14324-14350. [PMID: 39727987 DOI: 10.3390/cimb46120859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2024] [Revised: 12/12/2024] [Accepted: 12/16/2024] [Indexed: 12/28/2024] Open
Abstract
Glioblastoma multiforme (GBM) is one of the most aggressive and difficult-to-treat brain tumors, with a poor prognosis due to its high resistance to conventional therapies. Current treatment options, including surgical resection, radiotherapy, and chemotherapy, have limited effectiveness in improving long-term survival. Despite the emergence of new therapies, monotherapy approaches have not shown significant improvements, highlighting the need for innovative therapeutic strategies. Combination therapies appear to be the most promising solution, as they target multiple molecular pathways involved in GBM progression. One area of growing interest is the incorporation of phytotherapy and micotherapy as complementary treatments, which offer potential benefits due to their anti-tumor, anti-inflammatory, and immunomodulatory properties. This review examines the current challenges in GBM treatment, discusses the potential of combination therapies, and highlights the promising role of phytotherapy and micotherapy as integrative therapeutic options for GBM management.
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Affiliation(s)
- Ludovica Gaiaschi
- Laboratory of Cell Biology and Neurobiology, Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Maria Grazia Bottone
- Laboratory of Cell Biology and Neurobiology, Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Fabrizio De Luca
- Laboratory of Cell Biology and Neurobiology, Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
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3
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Lanskikh D, Kuziakova O, Baklanov I, Penkova A, Doroshenko V, Buriak I, Zhmenia V, Kumeiko V. Cell-Based Glioma Models for Anticancer Drug Screening: From Conventional Adherent Cell Cultures to Tumor-Specific Three-Dimensional Constructs. Cells 2024; 13:2085. [PMID: 39768176 PMCID: PMC11674823 DOI: 10.3390/cells13242085] [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: 11/10/2024] [Revised: 12/08/2024] [Accepted: 12/14/2024] [Indexed: 01/11/2025] Open
Abstract
Gliomas are a group of primary brain tumors characterized by their aggressive nature and resistance to treatment. Infiltration of surrounding normal tissues limits surgical approaches, wide inter- and intratumor heterogeneity hinders the development of universal therapeutics, and the presence of the blood-brain barrier reduces the efficiency of their delivery. As a result, patients diagnosed with gliomas often face a poor prognosis and low survival rates. The spectrum of anti-glioma drugs used in clinical practice is quite narrow. Alkylating agents are often used as first-line therapy, but their effectiveness varies depending on the molecular subtypes of gliomas. This highlights the need for new, more effective therapeutic approaches. Standard drug-screening methods involve the use of two-dimensional cell cultures. However, these models cannot fully replicate the conditions present in real tumors, making it difficult to extrapolate the results to humans. We describe the advantages and disadvantages of existing glioma cell-based models designed to improve the situation and build future prospects to make drug discovery comprehensive and more effective for each patient according to personalized therapy paradigms.
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Affiliation(s)
| | | | | | | | | | | | | | - Vadim Kumeiko
- School of Medicine and Life Sciences, Far Eastern Federal University, 690922 Vladivostok, Russia; (D.L.); (O.K.); (I.B.); (A.P.); (V.D.); (I.B.); (V.Z.)
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4
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Choate KA, Pratt EPS, Jennings MJ, Winn RJ, Mann PB. IDH Mutations in Glioma: Molecular, Cellular, Diagnostic, and Clinical Implications. BIOLOGY 2024; 13:885. [PMID: 39596840 PMCID: PMC11592129 DOI: 10.3390/biology13110885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Revised: 10/21/2024] [Accepted: 10/28/2024] [Indexed: 11/29/2024]
Abstract
In 2021, the World Health Organization classified isocitrate dehydrogenase (IDH) mutant gliomas as a distinct subgroup of tumors with genetic changes sufficient to enable a complete diagnosis. Patients with an IDH mutant glioma have improved survival which has been further enhanced by the advent of targeted therapies. IDH enzymes contribute to cellular metabolism, and mutations to specific catalytic residues result in the neomorphic production of D-2-hydroxyglutarate (D-2-HG). The accumulation of D-2-HG results in epigenetic alterations, oncogenesis and impacts the tumor microenvironment via immunological modulations. Here, we summarize the molecular, cellular, and clinical implications of IDH mutations in gliomas as well as current diagnostic techniques.
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Affiliation(s)
- Kristian A. Choate
- Upper Michigan Brain Tumor Center, Northern Michigan University, Marquette, MI 49855, USA; (K.A.C.); (E.P.S.P.); (M.J.J.); (R.J.W.)
| | - Evan P. S. Pratt
- Upper Michigan Brain Tumor Center, Northern Michigan University, Marquette, MI 49855, USA; (K.A.C.); (E.P.S.P.); (M.J.J.); (R.J.W.)
- Department of Chemistry, Northern Michigan University, Marquette, MI 49855, USA
| | - Matthew J. Jennings
- Upper Michigan Brain Tumor Center, Northern Michigan University, Marquette, MI 49855, USA; (K.A.C.); (E.P.S.P.); (M.J.J.); (R.J.W.)
- School of Clinical Sciences, Northern Michigan University, Marquette, MI 49855, USA
| | - Robert J. Winn
- Upper Michigan Brain Tumor Center, Northern Michigan University, Marquette, MI 49855, USA; (K.A.C.); (E.P.S.P.); (M.J.J.); (R.J.W.)
- Department of Biology, Northern Michigan University, Marquette, MI 49855, USA
| | - Paul B. Mann
- Upper Michigan Brain Tumor Center, Northern Michigan University, Marquette, MI 49855, USA; (K.A.C.); (E.P.S.P.); (M.J.J.); (R.J.W.)
- School of Clinical Sciences, Northern Michigan University, Marquette, MI 49855, USA
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5
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Elahi LS, Condro MC, Kawaguchi R, Qin Y, Alvarado AG, Gruender B, Qi H, Li T, Lai A, Castro MG, Lowenstein PR, Garrett MC, Kornblum HI. Valproic acid targets IDH1 mutants through alteration of lipid metabolism. NPJ METABOLIC HEALTH AND DISEASE 2024; 2:20. [PMID: 39149696 PMCID: PMC11321993 DOI: 10.1038/s44324-024-00021-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 07/01/2024] [Indexed: 08/17/2024]
Abstract
Histone deacetylases (HDACs) have a wide range of targets and can rewire both the chromatin and lipidome of cancer cells. In this study, we show that valproic acid (VPA), a brain penetrant anti-seizure medication and histone deacetylase inhibitor, inhibits the growth of IDH1 mutant tumors in vivo and in vitro, with at least some selectivity over IDH1 wild-type tumors. Surprisingly, genes upregulated by VPA showed no enhanced chromatin accessibility at the promoter, but there was a correlation between VPA-downregulated genes and diminished promoter chromatin accessibility. VPA inhibited the transcription of lipogenic genes and these lipogenic genes showed significant decreases in promoter chromatin accessibility only in the IDH1 MT glioma cell lines tested. VPA inhibited the mTOR pathway and a key lipogenic gene, fatty acid synthase (FASN). Both VPA and a selective FASN inhibitor TVB-2640 rewired the lipidome and promoted apoptosis in an IDH1 MT but not in an IDH1 WT glioma cell line. We further find that HDACs are involved in the regulation of lipogenic genes and HDAC6 is particularly important for the regulation of FASN in IDH1 MT glioma. Finally, we show that FASN knockdown alone and VPA in combination with FASN knockdown significantly improved the survival of mice in an IDH1 MT primary orthotopic xenograft model in vivo. We conclude that targeting fatty acid metabolism through HDAC inhibition and/or FASN inhibition may be a novel therapeutic opportunity in IDH1 mutant gliomas.
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Affiliation(s)
- Lubayna S. Elahi
- Department of Psychiatry and Behavioral Sciences and the UCLA Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine, UCLA, Los Angeles, CA USA
| | - Michael C. Condro
- Department of Psychiatry and Behavioral Sciences and the UCLA Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine, UCLA, Los Angeles, CA USA
| | - Riki Kawaguchi
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA USA
| | - Yue Qin
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA USA
| | - Alvaro G. Alvarado
- Department of Psychiatry and Behavioral Sciences and the UCLA Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine, UCLA, Los Angeles, CA USA
| | - Brandon Gruender
- Department of Psychiatry and Behavioral Sciences and the UCLA Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine, UCLA, Los Angeles, CA USA
| | - Haocheng Qi
- Department of Psychiatry and Behavioral Sciences and the UCLA Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine, UCLA, Los Angeles, CA USA
| | - Tie Li
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA USA
| | - Albert Lai
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA USA
| | - Maria G. Castro
- Department of Neurosurgery, Department of Cell and Developmental Biology, and Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI USA
| | - Pedro R. Lowenstein
- Department of Neurosurgery, Department of Cell and Developmental Biology, and Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI USA
| | | | - Harley I. Kornblum
- Department of Psychiatry and Behavioral Sciences and the UCLA Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine, UCLA, Los Angeles, CA USA
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA USA
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6
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Wang L, Lin Y, Hou G, Yang M, Peng Y, Jiang Y, He C, She M, Chen Q, Li M, Zhang Y, Zhang Y, Wang Y, He W, Wang X, Tang H, Luo Y. A histone deacetylase, FaSRT1-2, plays multiple roles in regulating fruit ripening, plant growth and stresses resistance of cultivated strawberry. PLANT, CELL & ENVIRONMENT 2024; 47:2258-2273. [PMID: 38482979 DOI: 10.1111/pce.14885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/29/2024] [Accepted: 03/03/2024] [Indexed: 04/30/2024]
Abstract
Sirtuins (SRTs) are a group of nicotinamide adenine dinucleotide (NAD+)-dependent deacetylase that target both histone and nonhistone proteins. The biological function of SRT in horticultural plants has been rarely studied. In this study, FaSRT1-2 was identified as a key member of the 8 FaSRTs encoded in cultivated strawberry genome. Transient overexpression of FaSRT1-2 in strawberry fruit accelerated ripening, increased the content of anthocyanins and sugars, enhanced ripening-related gene expression. Moreover, stable transformation of FaSRT1-2 in strawberry plants resulted in enhanced vegetative growth, increased sensitivity to heat stress and increased susceptibility to Botrytis cinerea infection. Interestingly, knocking out the homologous gene in woodland strawberry had the opposite effects. Additionally, we found the content of stress-related hormone abscisic acid (ABA) was decreased, while the growth-related gibberellin (GA) concentration was increased in FaSRT1-2 overexpression lines. Gene expression analysis revealed induction of heat shock proteins, transcription factors, stress-related and antioxidant genes in the FaSRT1-2-overexpressed plants while knocked-out of the gene had the opposite impact. In conclusion, our findings demonstrated that FaSRT1-2 could positively promote strawberry plant vegetative growth and fruit ripening by affecting ABA and GA pathways. However, it negatively regulates the resistance to heat stress and B. cinerea infection by influencing the related gene expression.
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Affiliation(s)
- Liangxin Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yuanxiu Lin
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Guoyan Hou
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Min Yang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yuting Peng
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yuyan Jiang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Caixia He
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Musha She
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mengyao Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yong Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yunting Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yan Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Wen He
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaorong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
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7
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Uba AI, Hryb M, Singh M, Bui-Linh C, Tran A, Atienza J, Misbah S, Mou X, Wu C. Discovery of novel inhibitors of histone deacetylase 6: Structure-based virtual screening, molecular dynamics simulation, enzyme inhibition and cell viability assays. Life Sci 2024; 338:122395. [PMID: 38181853 DOI: 10.1016/j.lfs.2023.122395] [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: 10/16/2023] [Revised: 12/23/2023] [Accepted: 12/26/2023] [Indexed: 01/07/2024]
Abstract
Histone deacetylase 6 (HDAC6) contributes to cancer metastasis in several cancers, including triple-negative breast cancer (TNBC)-the most lethal form that lacks effective therapy. Although several efforts have been invested to develop selective HDAC6 inhibitors, none have been approved by the FDA. Toward this goal, existing computational studies used smaller compound libraries and shorter MD simulations. Here, we conducted a structure-based virtual screening of ZINC "Druglike" library containing 17,900,742 compounds using a Glide virtual screening protocol comprising various filters with increasing accuracy. The top 20 hits were subjected to molecular dynamics simulation, MM-GBSA binding energy calculations, and further ADMET prediction. Furthermore, enzyme inhibition assay and cell viability assay were performed on six available compounds from the identified hits. C4 (ZINC000077541942) with a good profile of predicted drug properties was found to inhibit HDAC6 (IC50: 4.7 ± 11.6 μM) with comparative affinity to that of the known HDAC6 selective inhibitor Tubacin (TA) in our experiments. C4 also demonstrated cytotoxic effects against triple-negative breast cancer (TNBC) cell line MDA-MB-231 with EC50 of 40.6 ± 12.7 μM comparable to that of TA (2-20 μM). Therefore, this compound, with pharmacophore features comprising a non-hydroxamic acid zinc-binding group, heteroaromatic linker, and cap group, is proposed as a novel HDAC6 inhibitor.
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Affiliation(s)
- Abdullahi Ibrahim Uba
- Complex Systems Division, Beijing Computational Science Research Center, Beijing 100193, China
| | - Mariya Hryb
- College of Science and Mathematics, Rowan University, Glassboro, NJ 08028, USA
| | - Mursalin Singh
- College of Science and Mathematics, Rowan University, Glassboro, NJ 08028, USA
| | - Candice Bui-Linh
- College of Science and Mathematics, Rowan University, Glassboro, NJ 08028, USA
| | - Annie Tran
- College of Science and Mathematics, Rowan University, Glassboro, NJ 08028, USA
| | - Jiancarlo Atienza
- College of Science and Mathematics, Rowan University, Glassboro, NJ 08028, USA
| | - Sarah Misbah
- College of Science and Mathematics, Rowan University, Glassboro, NJ 08028, USA
| | - Xiaoyang Mou
- College of Science and Mathematics, Rowan University, Glassboro, NJ 08028, USA.
| | - Chun Wu
- College of Science and Mathematics, Rowan University, Glassboro, NJ 08028, USA.
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