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Crouch SA, Krause J, Dandekar T, Breitenbach T. DataXflow: Synergizing data-driven modeling with best parameter fit and optimal control - An efficient data analysis for cancer research. Comput Struct Biotechnol J 2024; 23:1755-1772. [PMID: 38707537 PMCID: PMC11068525 DOI: 10.1016/j.csbj.2024.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 05/07/2024] Open
Abstract
Building data-driven models is an effective strategy for information extraction from empirical data. Adapting model parameters specifically to data with a best fitting approach encodes the relevant information into a mathematical model. Subsequently, an optimal control framework extracts the most efficient targets to steer the model into desired changes via external stimuli. The DataXflow software framework integrates three software pipelines, D2D for model fitting, a framework solving optimal control problems including external stimuli and JimenaE providing graphical user interfaces to employ the other frameworks lowering the barriers for the need of programming skills, and simultaneously automating reoccurring modeling tasks. Such tasks include equation generation from a graph and script generation allowing also to approach systems with many agents, like complex gene regulatory networks. A desired state of the model is defined, and therapeutic interventions are modeled as external stimuli. The optimal control framework purposefully exploits the model-encoded information by providing those external stimuli that effect the desired changes most efficiently. The implementation of DataXflow is available under https://github.com/MarvelousHopefull/DataXflow. We showcase its application by detecting specific drug targets for a therapy of lung cancer from measurement data to lower proliferation and increase apoptosis. By an iterative modeling process refining the topology of the model, the regulatory network of the tumor is generated from the data. An application of the optimal control framework in our example reveals the inhibition of AURKA and the activation of CDH1 as the most efficient drug target combination. DataXflow paves the way to an agile interplay between data generation and its analysis potentially accelerating cancer research by an efficient drug target identification, even in complex networks.
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Affiliation(s)
| | | | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland 97074, Würzburg, Germany
| | - Tim Breitenbach
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland 97074, Würzburg, Germany
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2
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Saranya KR, Vimina ER, Pinto FR. TransNeT-CGP: A cluster-based comorbid gene prioritization by integrating transcriptomics and network-topological features. Comput Biol Chem 2024; 110:108038. [PMID: 38461796 DOI: 10.1016/j.compbiolchem.2024.108038] [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: 10/06/2023] [Revised: 01/11/2024] [Accepted: 02/25/2024] [Indexed: 03/12/2024]
Abstract
The local disruptions caused by the genes of one disease can influence the pathways associated with the other diseases resulting in comorbidity. For gene therapies, it is necessary to prioritize the key genes that regulate common biological mechanisms to tackle the issues caused by overlapping diseases. This work proposes a clustering-based computational approach for prioritising the comorbid genes within the overlapping disease modules by analyzing Protein-Protein Interaction networks. For this, a sub-network with gene interactions of the disease pair was extracted from the interactome. The edge weights are assigned by combining the pairwise gene expression correlation and betweenness centrality scores. Further, a weighted graph clustering algorithm is applied and dominant nodes of high-density clusters are ranked based on clustering coefficients and neighborhood connectivity. Case studies based on neurodegenerative diseases such as Amyotrophic Lateral Sclerosis- Spinal Muscular Atrophy (ALS-SMA) pair and cancers such as Ovarian Carcinoma-Invasive Ductal Breast Carcinoma (OC-IDBC) pair were conducted to examine the efficacy of the proposed method. To identify the mechanistic role of top-ranked genes, we used Functional and Pathway enrichment analysis, connectivity analysis with leave-one-out (LOO) method, analysis of associated disease-related protein complexes, and prioritization tools such as TOPPGENE and Heml2.0. From pathway analysis, it was observed that the top 10 genes obtained using the proposed method were associated with 10 pathways in ALS-SMA comorbidity and 15 in the case of OC-IDBC, while that in similar methods like SAPDSB and S2B were 4, 6 respectively for ALS-SMA and 9, 10 respectively for OC-IDBC. In both case studies, 70 % of the disease-specific benchmark protein complexes were linked to top-ranked genes of the proposed method while that of SAPDSB and S2B were 55 % and 60 % respectively. Additionally, it was found that the removal of the top 10 genes disconnect the network into 14 distinct components in the case of ALS-SMA and 9 in the case of OC-IDBC. The experimental results shows that the proposed method can be effectively used for identifying key genes in comorbidity and can offer insights about the intricate molecular relationship driving comorbid diseases.
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Affiliation(s)
- K R Saranya
- Department of Computer Science & IT, School of Computing, Amrita Vishwa Vidyapeetham, Kochi Campus, India.
| | - E R Vimina
- Department of Computer Science & IT, School of Computing, Amrita Vishwa Vidyapeetham, Kochi Campus, India.
| | - F R Pinto
- Chemistry and Biochemistry Department, Faculty of Sciences, University of Lisbon, Portugal.
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Strachowska M, Robaszkiewicz A. Characteristics of anticancer activity of CBP/p300 inhibitors - Features of their classes, intracellular targets and future perspectives of their application in cancer treatment. Pharmacol Ther 2024; 257:108636. [PMID: 38521246 DOI: 10.1016/j.pharmthera.2024.108636] [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: 11/02/2023] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 03/25/2024]
Abstract
Due to the contribution of highly homologous acetyltransferases CBP and p300 to transcription elevation of oncogenes and other cancer promoting factors, these enzymes emerge as possible epigenetic targets of anticancer therapy. Extensive efforts in search for small molecule inhibitors led to development of compounds targeting histone acetyltransferase catalytic domain or chromatin-interacting bromodomain of CBP/p300, as well as dual BET and CBP/p300 inhibitors. The promising anticancer efficacy in in vitro and mice models led CCS1477 and NEO2734 to clinical trials. However, none of the described inhibitors is perfectly specific to CBP/p300 since they share similarity of a key functional domains with other enzymes, which are critically associated with cancer progression and their antagonists demonstrate remarkable clinical efficacy in cancer therapy. Therefore, we revise the possible and clinically relevant off-targets of CBP/p300 inhibitors that can be blocked simultaneously with CBP/p300 thereby improving the anticancer potential of CBP/p300 inhibitors and pharmacokinetic predicting data such as absorption, distribution, metabolism, excretion (ADME) and toxicity.
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Affiliation(s)
- Magdalena Strachowska
- University of Lodz, Faculty of Biology and Environmental Protection, Department of General Biophysics, Pomorska 141/143, 90-236 Lodz, Poland; University of Lodz, Bio-Med-Chem Doctoral School of the University of Lodz and Lodz Institutes of the Polish Academy of Sciences, Banacha 12 /16, 90-237 Lodz, Poland.
| | - Agnieszka Robaszkiewicz
- University of Lodz, Faculty of Biology and Environmental Protection, Department of General Biophysics, Pomorska 141/143, 90-236 Lodz, Poland; Johns Hopkins University School of Medicine, Institute of Fundamental and Basic Research, 600 5(th) Street South, Saint Petersburg FL33701, United States of America.
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4
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Wu W, Jiang Y, Xing D, Zhai Y, Sun H, He X, Luo K, Xu P, Pan F, Dong G, Ren G, Zhao Z. The epigenetic regulators EP300/CREBBP represent promising therapeutic targets in MLL-rearranged acute myeloid leukemia. Cell Death Discov 2024; 10:206. [PMID: 38693103 PMCID: PMC11063202 DOI: 10.1038/s41420-024-01940-5] [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: 01/10/2024] [Revised: 03/27/2024] [Accepted: 04/02/2024] [Indexed: 05/03/2024] Open
Abstract
Acute myeloid leukemia (AML) with mixed-lineage leukemia (MLL) gene rearrangements (MLL-r) is an aggressive subtype of blood cancer with dismal prognosis, underscoring the urgent need for novel therapeutic strategies. E1A-binding protein (EP300) and CREB-binding protein (CREBBP) function as essential transcriptional coactivators and acetyltransferases, governing leukemogenesis through diverse mechanisms. Targeting EP300/CREBBP holds great promise for treating leukemia with some certain cytogenetic abnormalities. Here, we demonstrated that EP300 and CREBBP are core epigenetic regulators in the pathogenesis of MLL-r AML through assaying the transposase-accessible chromatin with high-throughput sequencing (ATAC-seq). Knocking-out EP300/CREBBP and inhibitor (A-485) treatment depressed the MLL-r cells proliferation, while the MLL wild-type cells remained uninfluenced. We found that the CDK4/RB/E2F axis was downregulated specifically in MLL-r AML cell after A-485 treatment by RNA-seq, western blot and cut-tag analyses. EP300/CREBBP inhibitor selectively exerted potent anti-leukemia activity through blocking the MLL-r-BET complex binding to H3K27Ac modification on critical genes loci, distinct from global histone acetylation. Collectively, our study identified EP300/CREBBP as a critical epigenetic driver of MLL-r leukemia and validated their therapeutic potential through targeting inhibition, offering a promising avenue for improving clinical outcomes in this aggressive leukemia.
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Affiliation(s)
- Wenqi Wu
- Department of Senior ward, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Yanan Jiang
- Department of Medical Oncology, Tianjin First Central Hospital, School of Medicine. Nankai University, Tianjin, 300192, China
| | - Donghui Xing
- Department of Senior ward, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Yixin Zhai
- Department of Senior ward, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Huimeng Sun
- Department of Senior ward, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Xiang He
- Department of Senior ward, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Kaiping Luo
- Department of Senior ward, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Pengpeng Xu
- Department of Oncology, Characteristic Medical Center of Chinese People's Armed Police Force, Tianjin, 300162, China
| | - Feng Pan
- Department of Molecular Medicine, the University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229-3904, USA
| | - Guolei Dong
- Department of Breast Oncology, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China.
| | - Guibing Ren
- Department of Oncology, Characteristic Medical Center of Chinese People's Armed Police Force, Tianjin, 300162, China.
| | - Zhigang Zhao
- Department of Medical Oncology, Tianjin First Central Hospital, School of Medicine. Nankai University, Tianjin, 300192, China.
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Williams D, Hargrove-Wiley E, Bindeman W, Valent D, Miranda AX, Beckstead J, Fingleton B. Type II Interleukin-4 Receptor Activation in Basal Breast Cancer Cells Promotes Tumor Progression via Metabolic and Epigenetic Modulation. Int J Mol Sci 2024; 25:4647. [PMID: 38731867 PMCID: PMC11083536 DOI: 10.3390/ijms25094647] [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: 03/14/2024] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 05/13/2024] Open
Abstract
Interleukin-4 (IL4) is a Th2 cytokine that can signal through two different receptors, one of which-the type II receptor-is overexpressed by various cancer cells. Previously, we have shown that type II IL4 receptor signaling increases proliferation and metastasis in mouse models of breast cancer, as well as increasing glucose and glutamine metabolism. Here, we expand on those findings to determine mechanistically how IL4 signaling links glucose metabolism and histone acetylation to drive proliferation in the context of triple-negative breast cancer (TNBC). We used a combination of cellular, biochemical, and genomics approaches to interrogate TNBC cell lines, which represent a cancer type where high expression of the type II IL4 receptor is linked to reduced survival. Our results indicate that type II IL4 receptor activation leads to increased glucose uptake, Akt and ACLY activation, and histone acetylation in TNBC cell lines. Inhibition of glucose uptake through the deletion of Glut1 ablates IL4-induced proliferation. Additionally, pharmacological inhibition of histone acetyltransferase P300 attenuates IL4-mediated gene expression and proliferation in vitro. Our work elucidates a role for type II IL4 receptor signaling in promoting TNBC progression, and highlights type II IL4 signaling, as well as histone acetylation, as possible targets for therapy.
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Affiliation(s)
- Demond Williams
- Program in Cancer Biology, Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; (D.W.); (E.H.-W.); (W.B.); (D.V.); (A.X.M.)
| | - Ebony Hargrove-Wiley
- Program in Cancer Biology, Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; (D.W.); (E.H.-W.); (W.B.); (D.V.); (A.X.M.)
| | - Wendy Bindeman
- Program in Cancer Biology, Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; (D.W.); (E.H.-W.); (W.B.); (D.V.); (A.X.M.)
| | - Daniel Valent
- Program in Cancer Biology, Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; (D.W.); (E.H.-W.); (W.B.); (D.V.); (A.X.M.)
| | - Adam X. Miranda
- Program in Cancer Biology, Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; (D.W.); (E.H.-W.); (W.B.); (D.V.); (A.X.M.)
| | - Jacob Beckstead
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA;
| | - Barbara Fingleton
- Program in Cancer Biology, Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; (D.W.); (E.H.-W.); (W.B.); (D.V.); (A.X.M.)
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6
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Pastena P, Perera H, Martinino A, Kartsonis W, Giovinazzo F. Unraveling Biomarker Signatures in Triple-Negative Breast Cancer: A Systematic Review for Targeted Approaches. Int J Mol Sci 2024; 25:2559. [PMID: 38473804 DOI: 10.3390/ijms25052559] [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: 01/21/2024] [Revised: 02/16/2024] [Accepted: 02/18/2024] [Indexed: 03/14/2024] Open
Abstract
Triple-negative breast cancer (TNBC) is one of the most aggressive subtypes of breast cancer, marked by poor outcomes and dismal prognosis. Due to the absence of targetable receptors, chemotherapy still represents the main therapeutic option. Therefore, current research is now focusing on understanding the specific molecular pathways implicated in TNBC, in order to identify novel biomarker signatures and develop targeted therapies able to improve its clinical management. With the aim of identifying novel molecular features characterizing TNBC, elucidating the mechanisms by which these molecular biomarkers are implicated in the tumor development and progression, and assessing the impact on cancerous cells following their inhibition or modulation, we conducted a literature search from the earliest works to December 2023 on PubMed, Scopus, and Web Of Science. A total of 146 studies were selected. The results obtained demonstrated that TNBC is characterized by a heterogeneous molecular profile. Several biomarkers have proven not only to be characteristic of TNBC but also to serve as potential effective therapeutic targets, holding the promise of a new era of personalized treatments able to improve its prognosis. The pre-clinical findings that have emerged from our systematic review set the stage for further investigation in forthcoming clinical trials.
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Affiliation(s)
- Paola Pastena
- Department of Medicine, Stony Brook University, Stony Brook, Brookhaven, NY 11794, USA
| | - Hiran Perera
- Renaissance School of Medicine at Stony Brook University, Stony Brook, Brookhaven, NY 11794, USA
| | | | - William Kartsonis
- Renaissance School of Medicine at Stony Brook University, Stony Brook, Brookhaven, NY 11794, USA
| | - Francesco Giovinazzo
- Department of Surgery, Saint Camillus Hospital, 31100 Treviso, Italy
- Department of Surgery, UniCamillus-Saint Camillus International University of Health Sciences, 00131 Rome, Italy
- Department of Surgery, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
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7
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Jiang H, Li G. Transcription factors direct epigenetic reprogramming at specific loci in human cancers. Front Genet 2023; 14:1234515. [PMID: 37876590 PMCID: PMC10591108 DOI: 10.3389/fgene.2023.1234515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 09/21/2023] [Indexed: 10/26/2023] Open
Abstract
The characterization of epigenetic changes during cancer development and progression led to notable insights regarding the roles of cancer-specific epigenetic reprogramming. Recent studies showed that transcription factors (TFs) are capable to regulate epigenetic reprogramming at specific loci in different cancer types through their DNA-binding activities. However, the causal association of dynamic histone modification change mediated by TFs is still not well elucidated. Here we evaluated the impacts of 636 transcription factor binding activities on histone modification in 24 cancer types. We performed Instrumental Variables analysis by using genetic lesions of TFs as our instrumental proxies, which previously discovered to be associated with histone mark activities. As a result, we showed a total of 6 EpiTFs as strong directors of epigenetic reprogramming of histone modification in cancers, which alters the molecular and clinical phenotypes of cancer. Together our findings highlight a causal mechanism driven by the TFs and genome-wide histone modification, which is relevant to multiple status of oncogenesis.
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Affiliation(s)
| | - Guoxin Li
- Department of General Surgery, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, China
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8
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Ma N, Zhao S, Yang W, Wang Y. B-cell-specific Moloney murine leukemia virus integration site 1 knockdown impairs adriamycin resistance of gastric cancer cells. Arab J Gastroenterol 2023; 24:168-174. [PMID: 36878814 DOI: 10.1016/j.ajg.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 01/13/2023] [Accepted: 02/23/2023] [Indexed: 03/07/2023]
Abstract
BACKGROUND AND STUDY AIMS The B-cell-specific Moloney murine leukemia virus integration site 1 (BMI-1) is associated with the progression of gastric cancer (GC). However, its role in drug resistance of gastric cancer stem cell (GCSC) remains unclear. This study aimed to explore the biological function of BMI-1 in GC cells and its role in drug resistance of GCSCs. PATIENTS AND METHODS We assessed BMI-1 expression in the GEPIA database and in our collected samples from patients with GC. We silenced BMI-1 using siRNA to study the cell proliferation and migration of GC cells. We also used Hoechst 33342 staining to verify the effect of adriamycin (ADR) on side population (SP) cells, and measured the effects of BMI-1 on the expression of N-cadherin, E-cadherin, and drug-resistance-related proteins (multidrug resistance mutation 1 and lung resistance-related protein). Finally, we analyzed BMI-1-related proteins uing the STRING and GEPIA databases. RESULTS BMI-1 mRNA was upregulated in GC tissues and cell lines, especially in MKN-45 and HGC-27 cells. Silencing BMI-1 reduced the proliferation and migration of GC cells. Knocking down BMI-1 significantly decreased epithelial-mesenchymal transition progression, expression levels of drug-resistant proteins, and the number of SP cells in ADR-treated GC cells. Bioinformatics analysis showed that EZH2, CBX8, CBX4, and SUZ12 were positively correlated with BMI-1 in GC tissues. CONCLUSION Our study demonstrates that BMI-1 affects the cellular activity, proliferation, migration, and invasion of GC cells. Silencing the BMI-1 gene significantly reduces the number of SP cells and the expression of drug-resistant proteins in ADR-treated GC cells. We speculate that inhibition of BMI-1 increases the drug resistance of GC cells by affecting GCSCs, and that EZH2, CBX8, CBX4, and SUZ12 may participate in BMI-1-induced enhancement of GCSC-like phenotype and viability.
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Affiliation(s)
- Ning Ma
- Department of General Surgery Ⅱ, the First People's Hospital of Yunnan Province, the Affiliated Hospital of Kunming University of Science and Technology, Kunming 650032, Yunnan Province, China.
| | - Sihui Zhao
- Department of General Surgery Ⅱ, the First People's Hospital of Yunnan Province, the Affiliated Hospital of Kunming University of Science and Technology, Kunming 650032, Yunnan Province, China
| | - Wei Yang
- Department of General Surgery Ⅱ, the First People's Hospital of Yunnan Province, the Affiliated Hospital of Kunming University of Science and Technology, Kunming 650032, Yunnan Province, China
| | - Yongfang Wang
- Department of General Surgery Ⅱ, the First People's Hospital of Yunnan Province, the Affiliated Hospital of Kunming University of Science and Technology, Kunming 650032, Yunnan Province, China
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9
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Iosef C, Knauer MJ, Nicholson M, Van Nynatten LR, Cepinskas G, Draghici S, Han VKM, Fraser DD. Plasma proteome of Long-COVID patients indicates HIF-mediated vasculo-proliferative disease with impact on brain and heart function. J Transl Med 2023; 21:377. [PMID: 37301958 PMCID: PMC10257382 DOI: 10.1186/s12967-023-04149-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/25/2023] [Indexed: 06/12/2023] Open
Abstract
AIMS Long-COVID occurs after SARS-CoV-2 infection and results in diverse, prolonged symptoms. The present study aimed to unveil potential mechanisms, and to inform prognosis and treatment. METHODS Plasma proteome from Long-COVID outpatients was analyzed in comparison to matched acutely ill COVID-19 (mild and severe) inpatients and healthy control subjects. The expression of 3072 protein biomarkers was determined with proximity extension assays and then deconvoluted with multiple bioinformatics tools into both cell types and signaling mechanisms, as well as organ specificity. RESULTS Compared to age- and sex-matched acutely ill COVID-19 inpatients and healthy control subjects, Long-COVID outpatients showed natural killer cell redistribution with a dominant resting phenotype, as opposed to active, and neutrophils that formed extracellular traps. This potential resetting of cell phenotypes was reflected in prospective vascular events mediated by both angiopoietin-1 (ANGPT1) and vascular-endothelial growth factor-A (VEGFA). Several markers (ANGPT1, VEGFA, CCR7, CD56, citrullinated histone 3, elastase) were validated by serological methods in additional patient cohorts. Signaling of transforming growth factor-β1 with probable connections to elevated EP/p300 suggested vascular inflammation and tumor necrosis factor-α driven pathways. In addition, a vascular proliferative state associated with hypoxia inducible factor 1 pathway suggested progression from acute COVID-19 to Long-COVID. The vasculo-proliferative process predicted in Long-COVID might contribute to changes in the organ-specific proteome reflective of neurologic and cardiometabolic dysfunction. CONCLUSIONS Taken together, our findings point to a vasculo-proliferative process in Long-COVID that is likely initiated either prior hypoxia (localized or systemic) and/or stimulatory factors (i.e., cytokines, chemokines, growth factors, angiotensin, etc). Analyses of the plasma proteome, used as a surrogate for cellular signaling, unveiled potential organ-specific prognostic biomarkers and therapeutic targets.
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Affiliation(s)
- Cristiana Iosef
- Children's Health Research Institute, Victoria Research Laboratories, 800 Commissioners Road East, London, ON, N6C 2V5, Canada.
| | - Michael J Knauer
- Department of Pathology and Laboratory Medicine, London, ON, N6A 5C1, Canada
| | - Michael Nicholson
- Department of Medicine, Western University, London, ON, N6A 5C1, Canada
| | | | - Gediminas Cepinskas
- Lawson Health Research Institute, London, ON, N6C 2R5, Canada
- Department of Medical Biophysics, Western University, London, ON, N6A 5C1, Canada
| | - Sorin Draghici
- Department of Computer Science College of Engineering, Wayne State University, Ann Arbor, MI, 48202, USA
- Advaita Bioinformatics, Ann Arbor, 48105-2552, USA
- National Science Foundation, Alexandria, VA, 22314, USA
| | - Victor K M Han
- Children's Health Research Institute, Victoria Research Laboratories, 800 Commissioners Road East, London, ON, N6C 2V5, Canada
- Department of Pediatrics, Western University, London, ON, N6A 5C1, Canada
| | - Douglas D Fraser
- Children's Health Research Institute, Victoria Research Laboratories, 800 Commissioners Road East, London, ON, N6C 2V5, Canada.
- Lawson Health Research Institute, London, ON, N6C 2R5, Canada.
- Department of Pediatrics, Western University, London, ON, N6A 5C1, Canada.
- Department of Physiology & Pharmacology, Western University, London, ON, N6A 5C1, Canada.
- Department of Clinical Neurological Sciences, Western University, London, ON, N6A 5C1, Canada.
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10
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Naghizadeh MM, Bakhshandeh B, Noorbakhsh F, Yaghmaie M, Masoudi-Nejad A. Rewiring of miRNA-mRNA bipartite co-expression network as a novel way to understand the prostate cancer related players. Syst Biol Reprod Med 2023:1-12. [PMID: 37018429 DOI: 10.1080/19396368.2023.2187268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
The differential expression and direct targeting of mRNA by miRNA are two main logics of the traditional approach to constructing the miRNA-mRNA network. This approach, could be led to the loss of considerable information and some challenges of direct targeting. To avoid these problems, we analyzed the rewiring network and constructed two miRNA-mRNA expression bipartite networks for both normal and primary prostate cancer tissue obtained from PRAD-TCGA. We then calculated beta-coefficient of the regression-model when miR was dependent and mRNA independent for each miR and mRNA and separately in both networks. We defined the rewired edges as a significant change in the regression coefficient between normal and cancer states. The rewired nodes through multinomial distribution were defined and network from rewired edges and nodes was analyzed and enriched. Of the 306 rewired edges, 112(37%) were new, 123(40%) were lost, 44(14%) were strengthened, and 27(9%) weakened connections were discovered. The highest centrality of 106 rewired mRNAs belonged to PGM5, BOD1L1, C1S, SEPG, TMEFF2, and CSNK2A1. The highest centrality of 68 rewired miRs belonged to miR-181d, miR-4677, miR-4662a, miR-9.3, and miR-1301. SMAD and beta-catenin binding were enriched as molecular functions. The regulation was a frequently repeated concept in the biological process. Our rewiring analysis highlighted the impact of β-catenin and SMAD signaling as also some transcript factors like TGFB1I1 in prostate cancer progression. Altogether, we developed a miRNA-mRNA co-expression bipartite network to identify the hidden aspects of the prostate cancer mechanism, which traditional analysis -like differential expression- was not detect it.
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Affiliation(s)
- Mohammad Mehdi Naghizadeh
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Behnaz Bakhshandeh
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Farshid Noorbakhsh
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Marjan Yaghmaie
- Hematology, Oncology and Stem Cell Transplantation Research Center, Institute for Oncology, Hematology and Cell Therapy, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Masoudi-Nejad
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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11
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Li CH, Fang CY, Chan MH, Lu PJ, Ger LP, Chu JS, Chang YC, Chen CL, Hsiao M. The activation of EP300 by F11R leads to EMT and acts as a prognostic factor in triple-negative breast cancers. J Pathol Clin Res 2023; 9:165-181. [PMID: 36782375 PMCID: PMC10073929 DOI: 10.1002/cjp2.313] [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: 08/19/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 02/15/2023]
Abstract
Cancer progression is influenced by junctional adhesion molecule (JAM) family members. The relationship between JAM family members and different types of cancer was examined using The Cancer Genome Atlas dataset. mRNA levels of the F11R (F11 receptor) in tumours were inversely correlated to the expression of JAM-2 and JAM-3. This relationship was unique to breast cancer (BCa) and was associated with poor prognosis (p = 0.024, hazard ratio = 1.44 [1.05-1.99]). A 50-gene molecular signature (prediction analysis of microarray 50) was used to subtype BCa. F11R mRNA expression significantly increased in human epidermal growth factor receptor 2 (HER2)-enriched (p = 0.0035) and basal-like BCa tumours (p = 0.0005). We evaluated F11R protein levels in two different compositions of BCa subtype patient tissue array cohorts to determine the relationship between BCa subtype and prognosis. Immunohistochemistry staining revealed that a high F11R protein level was associated with poor overall survival (p < 0.001; Taipei Medical University [TMU] cohort, p < 0.001; Kaohsiung Veterans General Hospital [KVGH] cohort) or disease-free survival (p < 0.001 [TMU cohort], p = 0.034 [KVGH cohort]) in patients with BCa. Comparison of F11R levels in different subtypes revealed the association of poor prognosis with high levels of F11R among luminal (p < 0.001 [TMU cohort], p = 0.027 [KVGH cohort]), HER2 positive (p = 0.018 [TMU cohort], p = 0.037 [KVGH cohort]), and triple-negative (p = 0.013 [TMU cohort], p = 0.037 [KVGH cohort]) BCa. F11R-based RNA microarray analysis and Ingenuity Pathway Analysis were successful in profiling the detailed gene ontology of triple-negative BCa cells regulated by F11R. The EP300 transcription factor was highly correlated with F11R in BCa (R = 0.51, p < 0.001). By analysing these F11R-affected molecules with the L1000CDs datasets, we were able to predict some repurposing drugs for potential application in F11R-positive BCa treatment.
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Affiliation(s)
- Chien-Hsiu Li
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Chih-Yeu Fang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
| | | | - Pei-Jung Lu
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Clinical Medicine Research Center, College of Medicine, National Cheng Kung University Hospital, National Cheng Kung University, Tainan, Taiwan
| | - Luo-Ping Ger
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Jan-Show Chu
- Department of Pathology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Department of Pathology, Taipei Medical University Hospital, Taipei, Taiwan
| | - Yu-Chan Chang
- Department of Biomedical Imaging and Radiological Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chi-Long Chen
- Department of Pathology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Department of Pathology, Taipei Medical University Hospital, Taipei, Taiwan
| | - Michael Hsiao
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.,Department and Graduate Institute of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, Taipei, Taiwan
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12
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Selim MS, Kassem AB, El-Bassiouny NA, Salahuddin A, Abu El-Ela RY, Hamza MS. Polymorphic renal transporters and cisplatin's toxicity in urinary bladder cancer patients: current perspectives and future directions. Med Oncol 2023; 40:80. [PMID: 36650399 PMCID: PMC9845168 DOI: 10.1007/s12032-022-01928-0] [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: 10/28/2022] [Accepted: 12/10/2022] [Indexed: 01/19/2023]
Abstract
Urinary bladder cancer (UBC) holds a potentially profound social burden and affects over 573,278 new cases annually. The disease's primary risk factors include occupational tobacco smoke exposure and inherited genetic susceptibility. Over the past 30 years, a number of treatment modalities have emerged, including cisplatin, a platinum molecule that has demonstrated effectiveness against UBC. Nevertheless, it has severe dose-limiting side effects, such as nephrotoxicity, among others. Since intracellular accumulation of platinum anticancer drugs is necessary for cytotoxicity, decreased uptake or enhanced efflux are the root causes of platinum resistance and response failure. Evidence suggests that genetic variations in any transporter involved in the entry or efflux of platinum drugs alter their kinetics and, to a significant extent, determine patients' responses to them. This review aims to consolidate and describe the major transporters and their polymorphic variants in relation to cisplatin-induced toxicities and resistance in UBC patients. We concluded that the efflux transporters ABCB1, ABCC2, SLC25A21, ATP7A, and the uptake transporter OCT2, as well as the organic anion uptake transporters OAT1 and OAT2, are linked to cisplatin accumulation, toxicity, and resistance in urinary bladder cancer patients. While suppressing the CTR1 gene's expression reduced cisplatin-induced nephrotoxicity and ototoxicity, inhibiting the expression of the MATE1 and MATE2-K genes has been shown to increase cisplatin's nephrotoxicity and resistance. The roles of ABCC5, ABCA8, ABCC10, ABCB10, ABCG1, ATP7B, ABCG2, and mitochondrial SLC25A10 in platinum-receiving urinary bladder cancer patients should be the subject of further investigation.
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Affiliation(s)
- Mohamed S Selim
- Clinical Pharmacy Practice Department, Faculty of Pharmacy, The British University in Egypt, Cairo, Egypt.
| | - Amira B Kassem
- Clinical Pharmacy & Pharmacy Practice Department, Faculty of Pharmacy, Damanhour University, Damanhour, Egypt
| | - Noha A El-Bassiouny
- Clinical Pharmacy & Pharmacy Practice Department, Faculty of Pharmacy, Damanhour University, Damanhour, Egypt
| | - Ahmad Salahuddin
- Biochemistry Department, Faculty of Pharmacy, Damanhour University, Damanhour, Egypt
- Biochemistry Department, Scientific Research Center, Al-Ayen University, Thi-Qar, Iraq
| | - Raghda Y Abu El-Ela
- Medical Oncology Department, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Marwa Samir Hamza
- Clinical Pharmacy Practice Department, Faculty of Pharmacy, The British University in Egypt, Cairo, Egypt
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13
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Czerwinska P, Mackiewicz AA. Bromodomain (BrD) Family Members as Regulators of Cancer Stemness-A Comprehensive Review. Int J Mol Sci 2023; 24:995. [PMID: 36674511 PMCID: PMC9861003 DOI: 10.3390/ijms24020995] [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: 11/29/2022] [Revised: 12/30/2022] [Accepted: 12/31/2022] [Indexed: 01/06/2023] Open
Abstract
Epigenetic mechanisms involving DNA methylation and chromatin modifications have emerged as critical facilitators of cancer heterogeneity, substantially affecting cancer development and progression, modulating cell phenotypes, and enhancing or inhibiting cancer cell malignant properties. Not surprisingly, considering the importance of epigenetic regulators in normal stem cell maintenance, many chromatin-related proteins are essential to maintaining the cancer stem cell (CSC)-like state. With increased tumor-initiating capacities and self-renewal potential, CSCs promote tumor growth, provide therapy resistance, spread tumors, and facilitate tumor relapse after treatment. In this review, we characterized the epigenetic mechanisms that regulate the acquisition and maintenance of cancer stemness concerning selected epigenetic factors belonging to the Bromodomain (BrD) family of proteins. An increasing number of BrD proteins reinforce cancer stemness, supporting the maintenance of the cancer stem cell population in vitro and in vivo via the utilization of distinct mechanisms. As bromodomain possesses high druggable potential, specific BrD proteins might become novel therapeutic targets in cancers exhibiting de-differentiated tumor characteristics.
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Affiliation(s)
- Patrycja Czerwinska
- Department of Cancer Immunology, Poznan University of Medical Sciences, 61-866 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 61-866 Poznan, Poland
| | - Andrzej Adam Mackiewicz
- Department of Cancer Immunology, Poznan University of Medical Sciences, 61-866 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 61-866 Poznan, Poland
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14
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Mezentsev Y, Ershov P, Yablokov E, Kaluzhskiy L, Kupriyanov K, Gnedenko O, Ivanov A. Protein Interactome Profiling of Stable Molecular Complexes in Biomaterial Lysate. Int J Mol Sci 2022; 23:ijms232415697. [PMID: 36555337 PMCID: PMC9779103 DOI: 10.3390/ijms232415697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/05/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Most proteins function as part of various complexes, forming via stable and dynamic protein-protein interactions (PPIs). The profiling of PPIs expands the fundamental knowledge about the structures, functions, and regulation patterns of protein complexes and intracellular molecular machineries. Protein interactomics aims at solving three main tasks: (1) identification of protein partners and parts of complex intracellular structures; (2) analysis of PPIs parameters (affinity, molecular-recognition specificity, kinetic rate constants, and thermodynamic-parameters determination); (3) the study of the functional role of novel PPIs. The purpose of this work is to update the current state and prospects of multi-omics approaches to profiling of proteins involved in the formation of stable complexes. Methodological paradigm includes a development of protein-extraction and -separation techniques from tissues or cellular lysates and subsequent identification of proteins using mass-spectrometry analysis. In addition, some aspects of authors' experimental platforms, based on high-performance size-exclusion chromatography, procedures of molecular fishing, and protein identification, as well as the possibilities of interactomic taxonomy of each protein, are discussed.
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15
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Wei Y, Yu N, Wang Z, Hao Y, Wang Z, Yang Z, Liu J, Wang J. Analysis of the multi-physiological and functional mechanism of wheat alkylresorcinols based on reverse molecular docking and network pharmacology. Food Funct 2022; 13:9091-9107. [PMID: 35943408 DOI: 10.1039/d2fo01438f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Alkylresorcinols (ARs) are phenolic lipids present in the bran part of whole grain wheat and rye, which possess antioxidant, anti-inflammatory, anti-cancer and anti-tumor properties. The physiological activities of ARs have been proven to be diverse; however, the specific molecular mechanisms are still unclear. In this study, reverse virtual screening and network pharmacology were used to explore the potential molecular mechanisms of the physiological function of ARs and their endogenous metabolites. The Metascape database was used for GO enrichment and KEGG pathway analysis. Furthermore, molecular docking was used to investigate the interactions between active compounds and potential targets. The results showed that the bioavailability of most ARs and their endogenous metabolites was 0.55 and 0.56, while the bioavailability of certain endogenous metabolites was only 0.11. Multiplex analysis was used to screen 73 important targets and 4 core targets (namely, HSP90AA1, EP300, HSP90AB1 and ERBB2) out of the 163 initial targets. The important targets involved in the key KEGG pathway were pathways in cancer (hsa05200), lipid and atherosclerosis (hsa05417), Th17 cell differentiation (hsa04659), chemical carcinogenesis-receptor activation (hsa05207), and prostate cancer (hsa05215). The compounds involved in the core targets were AR-C21, AR-C19, AR-C17, 3,5-DHPHTA-S, 3,5-DHPHTA-G, 3,5-DHPPTA, 3,5-DHPPTA-S, 3,5-DHPPTA-G, 3,5-DHPPTA-Gly and 3,5-DHPPA-G. The interaction force between them was mainly related to hydrogen bonds and van der Waals. Overall, the physiological activities of ARs are not only related to their multiple targets, but may also be related to the synergistic effect of their endogenous metabolites.
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Affiliation(s)
- Yulong Wei
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University (BTBU), Beijing 100048, China.
| | - Ning Yu
- Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Ziyuan Wang
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University (BTBU), Beijing 100048, China.
| | - Yiming Hao
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University (BTBU), Beijing 100048, China.
| | - Zongwei Wang
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University (BTBU), Beijing 100048, China.
| | - Zihui Yang
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University (BTBU), Beijing 100048, China.
| | - Jie Liu
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University (BTBU), Beijing 100048, China.
| | - Jing Wang
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University (BTBU), Beijing 100048, China.
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16
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Sarvari P, Sarvari P, Ramírez-Díaz I, Mahjoubi F, Rubio K. Advances of Epigenetic Biomarkers and Epigenome Editing for Early Diagnosis in Breast Cancer. Int J Mol Sci 2022; 23:ijms23179521. [PMID: 36076918 PMCID: PMC9455804 DOI: 10.3390/ijms23179521] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 12/02/2022] Open
Abstract
Epigenetic modifications are known to regulate cell phenotype during cancer progression, including breast cancer. Unlike genetic alterations, changes in the epigenome are reversible, thus potentially reversed by epi-drugs. Breast cancer, the most common cause of cancer death worldwide in women, encompasses multiple histopathological and molecular subtypes. Several lines of evidence demonstrated distortion of the epigenetic landscape in breast cancer. Interestingly, mammary cells isolated from breast cancer patients and cultured ex vivo maintained the tumorigenic phenotype and exhibited aberrant epigenetic modifications. Recent studies indicated that the therapeutic efficiency for breast cancer regimens has increased over time, resulting in reduced mortality. Future medical treatment for breast cancer patients, however, will likely depend upon a better understanding of epigenetic modifications. The present review aims to outline different epigenetic mechanisms including DNA methylation, histone modifications, and ncRNAs with their impact on breast cancer, as well as to discuss studies highlighting the central role of epigenetic mechanisms in breast cancer pathogenesis. We propose new research areas that may facilitate locus-specific epigenome editing as breast cancer therapeutics.
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Affiliation(s)
- Pourya Sarvari
- Department of Clinical Genetics, National Institute of Genetic Engineering and Biotechnology, Tehran P.O. Box 14965/161, Iran
| | - Pouya Sarvari
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico
| | - Ivonne Ramírez-Díaz
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico
- Facultad de Biotecnología, Campus Puebla, Universidad Popular Autónoma del Estado de Puebla (UPAEP), Puebla 72410, Mexico
| | - Frouzandeh Mahjoubi
- Department of Clinical Genetics, National Institute of Genetic Engineering and Biotechnology, Tehran P.O. Box 14965/161, Iran
| | - Karla Rubio
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
- Correspondence:
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17
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TWIST1-EP300 Expedites Gastric Cancer Cell Resistance to Apatinib by Activating the Expression of COL1A2. Anal Cell Pathol (Amst) 2022; 2022:5374262. [PMID: 35242497 PMCID: PMC8888114 DOI: 10.1155/2022/5374262] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/27/2022] [Indexed: 11/18/2022] Open
Abstract
The association between collagen type I alpha (COL1A) and chemoresistance has been verified in cancers. However, the specific role of COL1A2 in gastric cancer (GC) cell resistance to apatinib, a highly selective small-molecule inhibitor of vascular endothelial growth factor receptor 2, has not been investigated before. The purpose of this study was to explore the potential factors associated with COL1A2 regulation on GC cell apatinib resistance in vitro. With the aid of the Oncomine database and integrated bioinformatics methods, we identified COL1A2 overexpression in GC and its prognostic value. Mechanistically, the COL1A2 promoter has a distinct H3K27ac modification site and that E1A binding protein p300 (EP300) and twist family bHLH transcription factor 1 (TWIST1) can bind to the COL1A2 promoter, which in turn transcriptionally activated COL1A2 expression. In addition, overexpression of COL1A2 significantly promoted resistance to apatinib in GC cells, but knockdown of EP300 or TWIST1 remarkably inhibited COL1A2 expression and promoted sensitivity of GC cells to apatinib. Our findings demonstrated that the combination of EP300 and TWIST1 has a synergistically regulatory effect on COL1A2 expression, thus contributing to apatinib resistance in GC cells.
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18
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Activation of ABCC Genes by Cisplatin Depends on the CoREST Occurrence at Their Promoters in A549 and MDA-MB-231 Cell Lines. Cancers (Basel) 2022; 14:cancers14040894. [PMID: 35205642 PMCID: PMC8870433 DOI: 10.3390/cancers14040894] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/03/2022] [Accepted: 02/09/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Cisplatin resistance is a common issue that affects patients with a variety of cancers who are treated with this drug. In this research, we present a novel epigenetic mechanism that controls the expression of ABC-family transporters, which are involved in multidrug resistance. We report that the CoREST complex may be a key factor that determines the transcription of ABC transporters in non-small cell lung and triple-negative breast cancer cells (A549 and MDA-MB-231, respectively) treated with cisplatin. By occupying gene promoters, this multi-subunit repressor prevents both an EP300-dependent increase in ABCC transcription induced by the alkylating drug and gene overexpression in cisplatin-resistant phenotypes. Moreover, the CoREST-free promoter of ABCC10 responds to cisplatin with EP300-mediated gene activation, which is only possible in p53-proficient cells. Abstract Although cisplatin-based therapies are common among anticancer approaches, they are often associated with the development of cancer drug resistance. This phenomenon is, among others, caused by the overexpression of ATP-binding cassette, membrane-anchored transporters (ABC proteins), which utilize ATP to remove, e.g., chemotherapeutics from intracellular compartments. To test the possible molecular basis of increased expression of ABCC subfamily members in a cisplatin therapy mimicking model, we generated two cisplatin-resistant cell lines derived from non-small cell lung cancer cells (A549) and triple-negative breast cancer cells (MDA-MB-231). Analysis of data for A549 cells deposited in UCSC Genome Browser provided evidence on the negative interdependence between the occurrence of the CoREST complex at the gene promoters and the overexpression of ABCC genes in cisplatin-resistant lung cancer cells. Pharmacological inhibition of CoREST enzymatic subunits—LSD1 and HDACs—restored gene responsiveness to cisplatin. Overexpression of CoREST-free ABCC10 in cisplatin-resistant phenotypes was caused by the activity of EP300 that was enriched at the ABCC10 promoter in drug-treated cells. Cisplatin-induced and EP300-dependent transcriptional activation of ABCC10 was only possible in the presence of p53. In summary, the CoREST complex prevents the overexpression of some multidrug resistance proteins from the ABCC subfamily in cancer cells exposed to cisplatin. p53-mediated activation of some ABCC genes by EP300 occurs once their promoters are devoid of the CoREST complex.
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Hu X, Ono M, Chimge NO, Chosa K, Nguyen C, Melendez E, Lou CH, Lim P, Termini J, Lai KKY, Fueger PT, Teo JL, Higuchi Y, Kahn M. Differential Kat3 Usage Orchestrates the Integration of Cellular Metabolism with Differentiation. Cancers (Basel) 2021; 13:cancers13235884. [PMID: 34884992 PMCID: PMC8656857 DOI: 10.3390/cancers13235884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/12/2021] [Accepted: 11/19/2021] [Indexed: 11/29/2022] Open
Abstract
Simple Summary The coupling of metabolism with cellular status is critically important and highly evolutionarily conserved. However, how cells coordinate metabolism with transcription as they change their status is not clear. Utilizing multiomic and functional studies, we now demonstrate the dichotomous roles of the Kat3 coactivators CBP and p300 and, in particular, their extreme N-termini, in coordinating cellular metabolism with cell differentiation. Using multiple in vitro and in vivo systems, our study sheds new light on metabolic regulation in homeostasis and disease, including cancer. Abstract The integration of cellular status with metabolism is critically important and the coupling of energy production and cellular function is highly evolutionarily conserved. This has been demonstrated in stem cell biology, organismal, cellular and tissue differentiation and in immune cell biology. However, a molecular mechanism delineating how cells coordinate and couple metabolism with transcription as they navigate quiescence, growth, proliferation, differentiation and migration remains in its infancy. The extreme N-termini of the Kat3 coactivator family members, CBP and p300, by far the least homologous regions with only 66% identity, interact with members of the nuclear receptor family, interferon activated Stat1 and transcriptionally competent β-catenin, a critical component of the Wnt signaling pathway. We now wish to report based on multiomic and functional investigations, utilizing p300 knockdown, N-terminal p300 edited and p300 S89A edited cell lines and p300 S89A knockin mice, that the N-termini of the Kat3 coactivators provide a highly evolutionarily conserved hub to integrate multiple signaling cascades to coordinate cellular metabolism with the regulation of cellular status and function.
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Affiliation(s)
- Xiaohui Hu
- Department of Pathology, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China;
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (N.-O.C.); (K.C.); (C.N.); (E.M.); (P.L.); (J.T.); (K.K.Y.L.); (J.-L.T.); (Y.H.)
| | - Masaya Ono
- Department of Clinical Proteomics, National Cancer Center Research Institute, Tokyo 104-0045, Japan;
| | - Nyam-Osor Chimge
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (N.-O.C.); (K.C.); (C.N.); (E.M.); (P.L.); (J.T.); (K.K.Y.L.); (J.-L.T.); (Y.H.)
| | - Keisuke Chosa
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (N.-O.C.); (K.C.); (C.N.); (E.M.); (P.L.); (J.T.); (K.K.Y.L.); (J.-L.T.); (Y.H.)
| | - Cu Nguyen
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (N.-O.C.); (K.C.); (C.N.); (E.M.); (P.L.); (J.T.); (K.K.Y.L.); (J.-L.T.); (Y.H.)
| | - Elizabeth Melendez
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (N.-O.C.); (K.C.); (C.N.); (E.M.); (P.L.); (J.T.); (K.K.Y.L.); (J.-L.T.); (Y.H.)
| | - Chih-Hong Lou
- Gene Editing and Viral Vector Core, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA;
- City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA;
| | - Punnajit Lim
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (N.-O.C.); (K.C.); (C.N.); (E.M.); (P.L.); (J.T.); (K.K.Y.L.); (J.-L.T.); (Y.H.)
| | - John Termini
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (N.-O.C.); (K.C.); (C.N.); (E.M.); (P.L.); (J.T.); (K.K.Y.L.); (J.-L.T.); (Y.H.)
- City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA;
| | - Keane K. Y. Lai
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (N.-O.C.); (K.C.); (C.N.); (E.M.); (P.L.); (J.T.); (K.K.Y.L.); (J.-L.T.); (Y.H.)
- City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA;
| | - Patrick T. Fueger
- City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA;
- Department of Molecular and Cellular Endocrinology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Jia-Ling Teo
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (N.-O.C.); (K.C.); (C.N.); (E.M.); (P.L.); (J.T.); (K.K.Y.L.); (J.-L.T.); (Y.H.)
| | - Yusuke Higuchi
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (N.-O.C.); (K.C.); (C.N.); (E.M.); (P.L.); (J.T.); (K.K.Y.L.); (J.-L.T.); (Y.H.)
| | - Michael Kahn
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; (N.-O.C.); (K.C.); (C.N.); (E.M.); (P.L.); (J.T.); (K.K.Y.L.); (J.-L.T.); (Y.H.)
- City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA;
- Correspondence:
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Qiao EQ, Yang HJ, Yu XF, Gong LJ, Zhang XP, Chen DB. Curcuma zedoaria petroleum ether extract reverses the resistance of triple-negative breast cancer to docetaxel via pregnane X receptor. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1389. [PMID: 34733941 PMCID: PMC8506551 DOI: 10.21037/atm-21-4199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/02/2021] [Indexed: 11/21/2022]
Abstract
Background Triple-negative breast cancer (TNBC) is characterized by its aggressiveness and poor prognosis. Docetaxel is the common chemotherapeutic drug used in the treatment of TNBC. However, resistance to docetaxel has limited the effectiveness of TNBC treatment. Petroleum ether extracts of Curcuma zedoaria (PECZ) can inhibit the proliferation of MDA-MB-231 cells. However, the effect of PECZ on docetaxel resistance is not clear. Methods A docetaxel-resistant MDA-MB-231 (MDA-MB-231/docetaxel) cell line was established, and Cell Counting Kit-8 (CCK-8), quantitative real-time PCR (qRT-PCR), and western blotting assays were used to evaluate the effect of docetaxel resistance in MDA-MB-231 cells. Next, CCK-8 was also performed to detect the effect of docetaxel or the combination treatment of docetaxel and PECZ on the proliferation of MDA-MB-231/docetaxel cells. Thereafter, MDA-MB-231/docetaxel cells were subcutaneously injected into nude mice to induce a TNBC xenograft model, and the mice were divided into a model group, docetaxel group, PECZ group, and combination of docetaxel and PECZ group. Subsequently, hematoxylin and eosin (HE) staining, immunohistochemical, qRT-PCR, and western blotting were used to estimate the effect of pre-treatment with PECZ on docetaxel tolerance reversal. Results PECZ significantly inhibited the expression of pregnane X receptor (PXR), multidrug resistance 1 (MDR1), breast cancer resistance protein (BCRP), and cytochrome P-450 (CYP3A4) in MDA-MB-231/docetaxel cells. Only higher concentrations of docetaxel could inhibit the viability of MDA-MB-231/docetaxel cells. When pre-treated with PECZ, lower concentrations of docetaxel could significantly inhibit cell viability. Meanwhile, combination treatment also reduced the tumor volume, ameliorated the pathological change of tumor tissues, and down-regulated the expressions of PXR, MDR1, BCRP, and CYP3A4 (according to HE staining, immunohistochemical, qRT-PCR and western blotting results in vivo). Conclusions Our research showed that PECZ reversed docetaxel resistance in TNBC by PXR both in vitro and in vivo, which provides the basis for further investigations into the potential therapeutic impact of docetaxel resistance in TNBC.
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Affiliation(s)
- En-Qi Qiao
- Department of Breast Tumor Surgery, Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
| | - Hong-Jian Yang
- Department of Breast Tumor Surgery, Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
| | - Xing-Fei Yu
- Department of Breast Tumor Surgery, Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
| | - Li-Jie Gong
- Department of Breast Tumor Surgery, Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
| | - Xi-Ping Zhang
- Department of Breast Tumor Surgery, Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
| | - Dao-Bao Chen
- Department of Breast Tumor Surgery, Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
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21
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Yu P, Zhu L, Cui K, Du Y, Zhang C, Ma W, Guo J. B4GALNT2 Gene Promotes Proliferation, and Invasiveness and Migration Abilities of Model Triple Negative Breast Cancer (TNBC) Cells by Interacting With HLA-B Protein. Front Oncol 2021; 11:722828. [PMID: 34589428 PMCID: PMC8473878 DOI: 10.3389/fonc.2021.722828] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/16/2021] [Indexed: 12/26/2022] Open
Abstract
B4GALNT2 gene encodes the enzyme β1,4-N-acetylgalactosaminyltransferase 2 that biosynthesizes the histo-blood group antigen Sda, which is expressed on the surface of erythrocytes and in body secretions. Analysis of The Cancer Genome Atlas (TCGA) database revealed that this gene was highly expressed in breast cancer tissues in comparison with adjacent healthy ones. In-vitro lentivirus-assisted B4GALNT2 gene knockdown experiments in model triple negative breast cancer (TNBC) cell lines (HCC1937 and MDA-MB-231) showed inhibition in cell proliferation, decrease in cell viability, promotion of cell apoptosis and inhibitions in cell migration and invasiveness abilities in comparison with empty lentivirus transfectant controls. Also, in cell cycle tests, the number of cells in the G1 phase increased, in the S phase decreased and did not change in the G2/M phase (indicative of the presence of a block in the G1 phase). In-vivo tumor formation experiments in mice revealed that knockdown of the B4GALNT2 gene in MDA-MB-231 cells inhibited their proliferation. Using co-immunoprecipitation (Co-IP) mass spectroscopy-assisted analysis, it was found that HLA-B protein [a product of the human leukocyte antigen (HLA) class I gene] interacts with B4GALNT2 protein. In-vitro overexpression of HLA-B in B4GALNT2-knocked down MDA-MB-231 cell lines significantly recovered the cell proliferation, viability and migration ability of B4GALNT2 gene. These indicate that HLA-B is one of the interaction proteins in the downstream pathway of the B4GALNT2 gene.
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Affiliation(s)
- Pu Yu
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lili Zhu
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Kang Cui
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yabing Du
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chaojie Zhang
- Nephrology Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wang Ma
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jia Guo
- Nephrology Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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22
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Gangapuram M, Mazzio EA, Redda KK, Soliman KFA. Transcriptome Profile Analysis of Triple-Negative Breast Cancer Cells in Response to a Novel Cytostatic Tetrahydroisoquinoline Compared to Paclitaxel. Int J Mol Sci 2021; 22:ijms22147694. [PMID: 34299315 PMCID: PMC8306781 DOI: 10.3390/ijms22147694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/09/2021] [Accepted: 07/16/2021] [Indexed: 12/13/2022] Open
Abstract
The absence of chemotherapeutic target hormone receptors in breast cancer is descriptive of the commonly known triple-negative breast cancer (TNBC) subtype. TNBC remains one of the most aggressive invasive breast cancers, with the highest mortality rates in African American women. Therefore, new drug therapies are continually being explored. Microtubule-targeting agents such as paclitaxel (Taxol) interfere with microtubules dynamics, induce mitotic arrest, and remain a first-in-class adjunct drug to treat TNBC. Recently, we synthesized a series of small molecules of substituted tetrahydroisoquinolines (THIQs). The lead compound of this series, with the most potent cytostatic effect, was identified as 4-Ethyl-N-(7-hydroxy-3,4-dihydroisoquinolin-2(1H)-yl) benzamide (GM-4-53). In our previous work, GM-4-53 was similar to paclitaxel in its capacity to completely abrogate cell cycle in MDA-MB-231 TNBC cells, with the former not impairing tubulin depolymerization. Given that GM-4-53 is a cytostatic agent, and little is known about its mechanism of action, here, we elucidate differences and similarities to paclitaxel by evaluating whole-transcriptome microarray data in MDA-MB-231 cells. The data obtained show that both drugs were cytostatic at non-toxic concentrations and caused deformed morphological cytoskeletal enlargement in 2D cultures. In 3D cultures, the data show greater core penetration, observed by GM-4-53, than paclitaxel. In concentrations where the drugs entirely blocked the cell cycle, the transcriptome profile of the 48,226 genes analyzed (selection criteria: (p-value, FDR p-value < 0.05, fold change −2< and >2)), paclitaxel evoked 153 differentially expressed genes (DEGs), GM-4-53 evoked 243 DEGs, and, of these changes, 52/153 paclitaxel DEGs were also observed by GM-4-53, constituting a 34% overlap. The 52 DEGS analysis by String database indicates that these changes involve transcripts that influence microtubule spindle formation, chromosome segregation, mitosis/cell cycle, and transforming growth factor-β (TGF-β) signaling. Of interest, both drugs effectively downregulated “inhibitor of DNA binding, dominant negative helix-loop-helix” (ID) transcripts; ID1, ID3 and ID4, and amphiregulin (AREG) and epiregulin (EREG) transcripts, which play a formidable role in cell division. Given the efficient solubility of GM-4-53, its low molecular weight (MW; 296), and capacity to penetrate a small solid tumor mass and effectively block the cell cycle, this drug may have future therapeutic value in treating TNBC or other cancers. Future studies will be required to evaluate this drug in preclinical models.
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23
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Multiregional Sequencing of IDH-WT Glioblastoma Reveals High Genetic Heterogeneity and a Dynamic Evolutionary History. Cancers (Basel) 2021; 13:cancers13092044. [PMID: 33922652 PMCID: PMC8122908 DOI: 10.3390/cancers13092044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/07/2021] [Accepted: 04/20/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Glioblastoma is the most common and aggressive primary brain malignancy in adults. In addition to extensive inter-patient heterogeneity, glioblastoma shows intra-tumor extensive cellular and molecular heterogeneity, both spatially and temporally. This heterogeneity is one of the main reasons for the poor prognosis and overall survival. Moreover, it raises the important question of whether the molecular characterization of a single biopsy sample, as performed in standard diagnostics, actually represents the entire lesion. In this study, we sequenced the whole exome of nine spatially different cancer regions of three primary glioblastomas. We characterized their mutational profiles and copy number alterations, with implications for our understanding of tumor biology in relation to clonal architecture and evolutionary dynamics, as well as therapeutically relevant alterations. Abstract Glioblastoma is one of the most common and lethal primary neoplasms of the brain. Patient survival has not improved significantly over the past three decades and the patient median survival is just over one year. Tumor heterogeneity is thought to be a major determinant of therapeutic failure and a major reason for poor overall survival. This work aims to comprehensively define intra- and inter-tumor heterogeneity by mapping the genomic and mutational landscape of multiple areas of three primary IDH wild-type (IDH-WT) glioblastomas. Using whole exome sequencing, we explored how copy number variation, chromosomal and single loci amplifications/deletions, and mutational burden are spatially distributed across nine different tumor regions. The results show that all tumors exhibit a different signature despite the same diagnosis. Above all, a high inter-tumor heterogeneity emerges. The evolutionary dynamics of all identified mutations within each region underline the questionable value of a single biopsy and thus the therapeutic approach for the patient. Multiregional collection and subsequent sequencing are essential to try to address the clinical challenge of precision medicine. Especially in glioblastoma, this approach could provide powerful support to pathologists and oncologists in evaluating the diagnosis and defining the best treatment option.
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24
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Cava C, Sabetian S, Castiglioni I. Patient-Specific Network for Personalized Breast Cancer Therapy with Multi-Omics Data. ENTROPY 2021; 23:e23020225. [PMID: 33670375 PMCID: PMC7918754 DOI: 10.3390/e23020225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/04/2021] [Accepted: 02/09/2021] [Indexed: 01/06/2023]
Abstract
The development of new computational approaches that are able to design the correct personalized drugs is the crucial therapeutic issue in cancer research. However, tumor heterogeneity is the main obstacle to developing patient-specific single drugs or combinations of drugs that already exist in clinics. In this study, we developed a computational approach that integrates copy number alteration, gene expression, and a protein interaction network of 73 basal breast cancer samples. 2509 prognostic genes harboring a copy number alteration were identified using survival analysis, and a protein–protein interaction network considering the direct interactions was created. Each patient was described by a specific combination of seven altered hub proteins that fully characterize the 73 basal breast cancer patients. We suggested the optimal combination therapy for each patient considering drug–protein interactions. Our approach is able to confirm well-known cancer related genes and suggest novel potential drug target genes. In conclusion, we presented a new computational approach in breast cancer to deal with the intra-tumor heterogeneity towards personalized cancer therapy.
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Affiliation(s)
- Claudia Cava
- Institute of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), Via F.Cervi 93, Segrate, 20090 Milan, Italy
- Correspondence:
| | - Soudabeh Sabetian
- Infertility Research Center, Shiraz University of Medical Sciences, Shiraz, Iran;
| | - Isabella Castiglioni
- Department of Physics “Giuseppe Occhialini”, University of Milan-Bicocca Piazza dell’Ateneo Nuovo, 20126 Milan, Italy;
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