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Modification of BRCA1-associated breast cancer risk by HMMR overexpression. Nat Commun 2022; 13:1895. [PMID: 35393420 PMCID: PMC8989921 DOI: 10.1038/s41467-022-29335-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 03/09/2022] [Indexed: 12/12/2022] Open
Abstract
Breast cancer risk for carriers of BRCA1 pathological variants is modified by genetic factors. Genetic variation in HMMR may contribute to this effect. However, the impact of risk modifiers on cancer biology remains undetermined and the biological basis of increased risk is poorly understood. Here, we depict an interplay of molecular, cellular, and tissue microenvironment alterations that increase BRCA1-associated breast cancer risk. Analysis of genome-wide association results suggests that diverse biological processes, including links to BRCA1-HMMR profiles, influence risk. HMMR overexpression in mouse mammary epithelium increases Brca1-mutant tumorigenesis by modulating the cancer cell phenotype and tumor microenvironment. Elevated HMMR activates AURKA and reduces ARPC2 localization in the mitotic cell cortex, which is correlated with micronucleation and activation of cGAS-STING and non-canonical NF-κB signaling. The initial tumorigenic events are genomic instability, epithelial-to-mesenchymal transition, and tissue infiltration of tumor-associated macrophages. The findings reveal a biological foundation for increased risk of BRCA1-associated breast cancer.
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Dalal H, Dahlgren M, Gladchuk S, Brueffer C, Gruvberger-Saal SK, Saal LH. Clinical associations of ESR2 (estrogen receptor beta) expression across thousands of primary breast tumors. Sci Rep 2022; 12:4696. [PMID: 35304506 PMCID: PMC8933558 DOI: 10.1038/s41598-022-08210-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/03/2022] [Indexed: 12/31/2022] Open
Abstract
Estrogen receptor alpha (ERα, encoded by ESR1) is a well-characterized transcription factor expressed in more than 75% of breast tumors and is the key biomarker to direct endocrine therapies. On the other hand, much less is known about estrogen receptor beta (ERβ, encoded by ESR2) and its importance in cancer. Previous studies had some disagreement, however most reports suggested a more favorable prognosis for patients with high ESR2 expression. To add further clarity to ESR2 in breast cancer, we interrogated a large population-based cohort of primary breast tumors (n = 3207) from the SCAN-B study. RNA-seq shows ESR2 is expressed at low levels overall with a slight inverse correlation to ESR1 expression (Spearman R = −0.18, p = 2.2e−16), and highest ESR2 expression in the basal- and normal-like PAM50 subtypes. ESR2-high tumors had favorable overall survival (p = 0.006), particularly in subgroups receiving endocrine therapy (p = 0.03) and in triple-negative breast cancer (p = 0.01). These results were generally robust in multivariable analyses accounting for patient age, tumor size, node status, and grade. Gene modules consistent with immune response were associated to ESR2-high tumors. Taken together, our results indicate that ESR2 is generally expressed at low levels in breast cancer but associated with improved overall survival and may be related to immune response modulation.
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Affiliation(s)
- Hina Dalal
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Lund University, Medicon Village 404-B2, 22381, Lund, Sweden.,Lund University Cancer Center, Medicon Village, Lund, Sweden
| | - Malin Dahlgren
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Lund University, Medicon Village 404-B2, 22381, Lund, Sweden.,Lund University Cancer Center, Medicon Village, Lund, Sweden
| | - Sergii Gladchuk
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Lund University, Medicon Village 404-B2, 22381, Lund, Sweden.,Lund University Cancer Center, Medicon Village, Lund, Sweden
| | - Christian Brueffer
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Lund University, Medicon Village 404-B2, 22381, Lund, Sweden.,Lund University Cancer Center, Medicon Village, Lund, Sweden
| | - Sofia K Gruvberger-Saal
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Lund University, Medicon Village 404-B2, 22381, Lund, Sweden.,Section for Molecular Diagnostics, Skåne University Hospital, Lund, Sweden
| | - Lao H Saal
- Division of Oncology, Department of Clinical Sciences Lund, Lund University Cancer Center, Lund University, Medicon Village 404-B2, 22381, Lund, Sweden. .,Lund University Cancer Center, Medicon Village, Lund, Sweden.
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Fan Y, Xie G, Wang Z, Wang Y, Wang Y, Zheng H, Zhong X. PTEN promoter methylation predicts 10-year prognosis in hormone receptor-positive early breast cancer patients who received adjuvant tamoxifen endocrine therapy. Breast Cancer Res Treat 2022; 192:33-42. [PMID: 34978016 PMCID: PMC8841328 DOI: 10.1007/s10549-021-06463-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/17/2021] [Indexed: 02/07/2023]
Abstract
Purpose There remain a lack of biomarkers for endocrine therapy resistance in patients with breast cancer (BC), which is proving to be a great challenge. In vitro experiments have shown that downregulation of PTEN expression leads to resistance to tamoxifen (TAM) in BC cells. We aimed to investigate the predictive role of tumor PTEN promoter methylation and PTEN expression in long-term survival after TAM adjuvant therapy in patients with early-stage BC. Methods From 2001 to 2013, 105 patients with stage I–III BC who were treated with standardized adjuvant TAM for 5 years or until relapse in West China Hospital (WCH) were enrolled in this study. PTEN expression and DNA methylation of three specified sequences from the PTEN promoter in primary tumors were measured using immunohistochemistry and pyrosequencing. A cohort of 159 hormone receptor-positive patients receiving TAM treatment from The Cancer Genome Atlas (TCGA) database was used for verification. Results Median follow-up time for the WCH cohort was 141.7 months. The low, moderate, and high PTEN expression groups had differing 10-year disease-free survival (DFS) (42.3%, 55%, 81%, respectively, P = 0.027) and overall survival (OS) rates (65%, 84.2%, 90.5%, respectively, P = 0.027). Higher methylation levels of the second sequence (− 819 to − 787 bp), rather than the first (− 1143 to − 1107 bp) or third sequence (− 663 to − 593 bp), independently increased the risk of disease recurrence (hazard ratio = 2.60) and death (hazard ratio = 3.79) in the WCH cohort, according to multivariate Cox regression analysis. Importantly, out of the five CpG islands located within this sequence, only high methylation of the − 796 CpG island predicted shorter DFS and OS. In TCGA validation cohort, there was also a trend of higher methylation of the − 796 CpG island correlating with shorter disease-free intervals, with borderline significance (P = 0.057). Conclusion Low PTEN expression and high methylation of its promoter (sequence − 819 to − 787 bp) in tissue predict poor DFS and OS in hormone receptor-positive early BC patients who received adjuvant TAM. Supplementary Information The online version contains supplementary material available at 10.1007/s10549-021-06463-6.
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Affiliation(s)
- Yu Fan
- Laboratory of Molecular Diagnosis of Cancer, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Guiqin Xie
- Laboratory of Molecular Diagnosis of Cancer, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Zhu Wang
- Laboratory of Molecular Diagnosis of Cancer, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Yu Wang
- Laboratory of Molecular Diagnosis of Cancer, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Yanping Wang
- Laboratory of Molecular Diagnosis of Cancer, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Hong Zheng
- Laboratory of Molecular Diagnosis of Cancer, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China.,Department of Head, Neck and Mammary Gland Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Xiaorong Zhong
- Laboratory of Molecular Diagnosis of Cancer, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China. .,Department of Head, Neck and Mammary Gland Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China.
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Li B, Pei G, Yao J, Ding Q, Jia P, Zhao Z. Cell-type deconvolution analysis identifies cancer-associated myofibroblast component as a poor prognostic factor in multiple cancer types. Oncogene 2021; 40:4686-4694. [PMID: 34140640 DOI: 10.1038/s41388-021-01870-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 05/10/2021] [Accepted: 05/26/2021] [Indexed: 01/04/2023]
Abstract
Cancer-associated fibroblasts (CAFs) constitute a prominent component of the tumor microenvironment and play critical roles in cancer progression and drug resistance. Although recent studies indicate CAFs may consist of several CAF subtypes, the breadth of CAF heterogeneity and functional roles of CAF subtypes in cancer progression remain unclear. In this study, we implemented a cell-type deconvolutional approach to comprehensively characterize cell-type alternations across 18 cancer types from The Cancer Genome Atlas (TCGA). Pan-cancer survival analysis using deconvoluted CAF subtypes revealed myofibroblastic CAF (myCAF) composition as a poor prognostic factor in nine cancer types. Patients with higher myCAF compositions tend to have worse response to six antineoplastic drugs predicted by a lncRNA-based Elastic Net prediction model (LENP). In addition, integrative mutational analysis identified 14 and 413 genes associated with the differentiation degree of myCAF and inflammatory CAF (iCAF), respectively, with significant enrichment of genes involved in fibroblast and extracellular matrix (ECM)-related pathways. In summary, our findings systematically illustrated the complex roles of CAF subtypes in patient prognosis and drug response, and identified putative driver genes in CAF-subtype differentiation. These results provided novel therapeutic perspectives for targeting CAF subtypes in tumor microenvironment and arranging treatment scheme based on the CAF compositions in different cancer types.
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Affiliation(s)
- Bingrui Li
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Guangsheng Pei
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Jun Yao
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Qingqing Ding
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA. .,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA. .,MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, TX, 77030, USA.
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Antisense oligonucleotides targeting lncRNA AC104041.1 induces antitumor activity through Wnt2B/β-catenin pathway in head and neck squamous cell carcinomas. Cell Death Dis 2020; 11:672. [PMID: 32826863 PMCID: PMC7443144 DOI: 10.1038/s41419-020-02820-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/16/2020] [Accepted: 07/16/2020] [Indexed: 12/14/2022]
Abstract
Long non-coding RNAs (lncRNAs) contribute to the initiation and progression of various tumors, including head and neck squamous carcinoma (HNSCC), which is a common malignancy with high morbidity and low survival rate. However, the mechanism of lncRNAs in HNSCC tumorigenesis remains largely unexplored. In this work, we identified a novel lncRNA AC104041.1 which is highly upregulated and correlated with poor survival in HNSCC patients. Moreover, AC104041.1 overexpression significantly promoted tumor growth and metastasis of HNSCC in vitro and in vivo. Mechanistically, AC104041.1 mainly located in the cytoplasm and could function as ceRNA (competing endogenous RNA) for miR-6817-3p, thereby stabilized Wnt2B, and consequently inducing β-catenin nuclear translocation and activation. Moreover, we demonstrate that salinomycin, which as a highly effective antibiotic in the elimination of cancer stem cells through the Wnt/β-catenin signaling, could enhance the inhibition of tumor growth by antisense oligonucleotides (ASO) targeting AC104041.1 in HNSCC cells and PDXs (patient-derived xenograft) model. Thus, our data provide preclinical evidence to support a novel strategy of ASOs targeting AC104041.1 in combination with salinomycin and may as a beneficial treatment approach for HNSCC.
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Milanez-Almeida P, Martins AJ, Germain RN, Tsang JS. Cancer prognosis with shallow tumor RNA sequencing. Nat Med 2020; 26:188-192. [PMID: 32042193 DOI: 10.1038/s41591-019-0729-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 12/06/2019] [Indexed: 12/13/2022]
Abstract
Disrupted molecular pathways are often robustly associated with disease outcome in cancer1-3. Although biologically informative transcriptional pathways can be revealed by RNA sequencing (RNA-seq) at up to hundreds of folds reduction in conventionally used coverage4-6, it remains unknown how low-depth sequencing datasets perform in the challenging context of developing transcriptional signatures to predict clinical outcomes. Here we assessed the possibility of cancer prognosis with shallow tumor RNA-seq, which would potentially enable cost-effective assessment of much larger numbers of samples for deeper biological and predictive insights. By statistically modeling the relative risk of an adverse outcome for thousands of subjects in The Cancer Genome Atlas7-13, we present evidence that subsampled tumor RNA-seq data with a few hundred thousand reads per sample provide sufficient information for outcome prediction in several types of cancer. Analysis of predictive models revealed robust contributions from pathways known to be associated with outcomes. Our findings indicate that predictive models of outcomes in cancer may be developed with dramatically increases in sample numbers at low cost, thus potentially enabling the development of more realistic predictive models that incorporate diverse variables and their interactions. This strategy could also be used, for example, in longitudinal analysis of multiple regions of a tumor alongside treatment for quantitative modeling and prediction of outcome in personalized oncology.
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Affiliation(s)
- Pedro Milanez-Almeida
- Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. .,Trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD, USA.
| | - Andrew J Martins
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ronald N Germain
- Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John S Tsang
- Trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD, USA.,Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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A qualitative transcriptional signature for determining the grade of colorectal adenocarcinoma. Cancer Gene Ther 2019; 27:680-690. [PMID: 31595030 DOI: 10.1038/s41417-019-0139-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 08/18/2019] [Accepted: 08/25/2019] [Indexed: 01/10/2023]
Abstract
Histological grading (HG) is an important prognostic factor of colorectal adenocarcinoma (CRAC): the high-grade CRAC patients have poorer prognosis after tumor resection. Especially, the high-grade stage II CRAC patients are recommended to receive adjuvant chemotherapy. Due to the subjective nature of HG assessment, it is difficult to achieve consistency among pathologists, which brings patients uncertain grading outcomes and inappropriate treatments. We developed a qualitative transcriptional signature based on the within-sample relative expression orderings (REOs) of gene pairs to discriminate high-grade and low-grade CRAC. Using the stage II-III CRAC samples, we detected gene pairs with stable REOs in the high-grade samples and reversal stable REOs in the low-grade samples, and retained the gene pairs whose specific REO patterns were significantly associated with the disease-free survival of patients by univariate Cox regression model. Then, we used a forward-backward searching procedure to extract gene pairs with the highest concordance index as the final grading signature. Finally, 9 gene pairs (9-GPS) were developed to divide CRAC patients into high-grade and low-grade groups. With the signature, there were more differential expression characteristics between reclassified high-grade and low-grade groups. Significant difference of prognosis between the classified two group patients could be seen in four independent datasets. Additionally, genomic analyses showed that the classified high-grade groups were characterized by hypermutation while classified low-grade groups were characterized by frequent copy number alternations. In conclusion, the 9-GPS can provide an objective and robust grading assessment for CRAC patients, which could assist clinical treatment decision.
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Zimmer C, Wähnert U. Nonintercalating DNA-binding ligands: specificity of the interaction and their use as tools in biophysical, biochemical and biological investigations of the genetic material. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1986; 47:31-112. [PMID: 2422697 DOI: 10.1016/0079-6107(86)90005-2] [Citation(s) in RCA: 642] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Saucier JM. Physicochemical studies on the interaction of irehdiamine A with bihelical DNA. Biochemistry 1977; 16:5879-89. [PMID: 588563 DOI: 10.1021/bi00645a036] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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10
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Sunaga K, Koide SS, Tatum AH. Interaction of 21-dehydrocorticosteroids with peptides. BIOCHIMICA ET BIOPHYSICA ACTA 1971; 232:347-51. [PMID: 5553681 DOI: 10.1016/0005-2787(71)90587-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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11
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Hahn FE, Krey AK. Interactions of Alkaloids with DNA. PROCEEDINGS OF THE RESEARCH SYMPOSIUM ON COMPLEXES OF BIOLOGICALLY ACTIVE SUBSTANCES WITH NUCLEIC ACIDS AND THEIR MODES OF ACTION 1971. [DOI: 10.1007/978-3-642-65141-0_13] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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12
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13
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Silver S, Wendt L, Bhattacharyya P, Beauchamp RS. EFFECTS OF POLYAMINES ON MEMBRANE PERMEABILITY. Ann N Y Acad Sci 1970. [DOI: 10.1111/j.1749-6632.1970.tb39392.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Silver S, Levine E. Action of steroidal diamines on active transport and permeability properties of Escherichia coli. J Bacteriol 1968; 96:338-45. [PMID: 4877122 PMCID: PMC252303 DOI: 10.1128/jb.96.2.338-345.1968] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The steroidal diamine irehdiamine A (IDA) is a potent inhibitor of bacteriophage growth and macromolecular synthesis in Escherichia coli. By using radioactive (42)K and (14)C-thiomethylgalactoside (TMG), rapid effects of IDA and related steroids, both on the influx of potassium and TMG via their respective transport systems and on the efflux (leakage) of radioactivity from the treated cells, have been measured. IDA affects both the influx and efflux of (42)K at concentrations of steroid as low as 2 x 10(-5)m. Because of the increased leakage, it is not possible to tell whether there is a direct effect reducing the rate of active transport of potassium. The primary diamine, IDA, and its bis-secondary, bis-tertiary, and bis-quaternary diamine analogues are decreasingly effective in altering cell permeability properties in the order 1 degrees > 2 degrees > 3 degrees > 4 degrees . The effects of IDA on potassium transport are mirrored by similar effects on the transport of TMG. Therefore, the action of IDA is on the cell membrane and not directly on one or another transport system. The effects of IDA on cell permeability can reasonably explain the inhibitory actions of the drugs on bacteriophage growth and cellular metabolism.
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Silver S, Levine E. Reversible alterations in membrane permeability of Escherichia coli induced by a steroidal diamine, irehdiamine A. Biochem Biophys Res Commun 1968; 31:743-8. [PMID: 4874968 DOI: 10.1016/0006-291x(68)90624-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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