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Hong R, Cao B, Chen D, Wu W, Luo T, Lv D, Zhang W, Wang S, Shao K. Multi-omics portrait of ductal carcinoma in situ in young women. Breast Cancer Res Treat 2024; 206:105-118. [PMID: 38704773 DOI: 10.1007/s10549-024-07254-5] [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: 10/19/2023] [Accepted: 01/08/2024] [Indexed: 05/07/2024]
Abstract
BACKGROUND Young patients with breast ductal carcinoma in situ (DCIS) often face a poorer prognosis. The genomic intricacies in young-onset DCIS, however, remain underexplored. METHODS To address this gap, we undertook a comprehensive study encompassing exome, transcriptome, and vmethylome analyses. Our investigation included 20 DCIS samples (including 15 young-onset DCIS) and paired samples of normal breast tissue and blood. RESULTS Through RNA sequencing, we identified two distinct DCIS subgroups: "immune hot" and "immune cold". The "immune hot" subgroup was characterized by increased infiltration of lymphocytes and macrophages, elevated expression of PDCD1 and CTLA4, and reduced GATA3 expression. This group also exhibited active immunerelated transcriptional regulators. Mutational analysis revealed alterations in TP53 (38%), GATA3 (25%), and TTN (19%), with two cases showing mutations in APC, ERBB2, and SMARCC1. Common genomic alterations, irrespective of immune status, included gains in copy numbers at 1q, 8q, 17q, and 20q, and losses at 11q, 17p, and 22q. Signature analysis highlighted the predominance of signatures 2 and 1, with "immune cold" samples showing a significant presence of signature 8. Our methylome study on 13 DCIS samples identified 328 hyperdifferentially methylated regions (DMRs) and 521 hypo-DMRs, with "immune cold" cases generally showing lower levels of methylation. CONCLUSION In summary, the molecular characteristics of young-onset DCIS share similarities with invasive breast cancer (IBC), potentially indicating a poor prognosis. Understanding these characteristics, especially the immune microenvironment of DCIS, could be pivotal in identifying new therapeutic targets and preventive strategies for breast cancer.
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Affiliation(s)
- Ruoxi Hong
- State Key Laboratory of Oncology in South China, Department of Medical Oncology, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P.R. China
| | - Boyang Cao
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, BGI Research, Hangzhou, 310030, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI-Research, Shenzhen, 518083, China
| | - Dongshao Chen
- State Key Laboratory of Oncology in South China, Department of Medical Oncology, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P.R. China
| | - Wei Wu
- State Key Laboratory of Oncology in South China, Department of Medical Oncology, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P.R. China
| | - Tian Luo
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, BGI Research, Hangzhou, 310030, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI-Research, Shenzhen, 518083, China
| | - Dian Lv
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, BGI Research, Hangzhou, 310030, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI-Research, Shenzhen, 518083, China
| | - Weimin Zhang
- Institute of Intelligent Medical Research (IIMR), BGI Genomics, Shenzhen, 518083, China.
| | - Shusen Wang
- State Key Laboratory of Oncology in South China, Department of Medical Oncology, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P.R. China.
| | - Kang Shao
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, BGI Research, Hangzhou, 310030, China.
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI-Research, Shenzhen, 518083, China.
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Beaven E, Kumar R, Bhatt HN, Esquivel SV, Nurunnabi M. Myofibroblast specific targeting approaches to improve fibrosis treatment. Chem Commun (Camb) 2022; 58:13556-13571. [PMID: 36445310 PMCID: PMC9946855 DOI: 10.1039/d2cc04825f] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Fibrosis has been shown to develop in individuals with underlying health conditions, especially chronic inflammatory diseases. Fibrosis is often diagnosed in various organs, including the liver, lungs, kidneys, heart, and skin, and has been described as excessive accumulation of extracellular matrix that can affect specific organs in the body or systemically throughout the body. Fibrosis as a chronic condition can result in organ failure and result in death of the individual. Understanding and identification of specific biomarkers associated with fibrosis has emerging potential in the development of diagnosis and targeting treatment modalities. Therefore, in this review, we will discuss multiple signaling pathways such as TGF-β, collagen, angiotensin, and cadherin and outline the chemical nature of the different signaling pathways involved in fibrogenesis as well as the mechanisms. Although it has been well established that TGF-β is the main catalyst initiating and driving multiple pathways for fibrosis, targeting TGF-β can be challenging as this molecule regulates essential functions throughout the body that help to keep the body in homeostasis. We also discuss collagen, angiotensin, and cadherins and their role in fibrosis. We comprehensively discuss the various delivery systems used to target collagen, angiotensin, and cadherins to manage fibrosis. Nevertheless, understanding the steps by which this molecule drives fibrosis development can aid in the development of specific targets of its cascading mechanism. Throughout the review, we will demonstrate the mechanism of fibrosis targeting to improve targeting delivery and therapy.
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Affiliation(s)
- Elfa Beaven
- Department of Pharmaceutical Sciences, School of Pharmacy, The University of Texas El Paso, El Paso, TX 79902, USA.
- Department of Biomedical Engineering, The University of Texas El Paso, El Paso, TX 79968, USA
| | - Raj Kumar
- Department of Pharmaceutical Sciences, School of Pharmacy, The University of Texas El Paso, El Paso, TX 79902, USA.
- Department of Biomedical Engineering, The University of Texas El Paso, El Paso, TX 79968, USA
| | - Himanshu N Bhatt
- Department of Pharmaceutical Sciences, School of Pharmacy, The University of Texas El Paso, El Paso, TX 79902, USA.
- Department of Biomedical Engineering, The University of Texas El Paso, El Paso, TX 79968, USA
| | - Stephanie V Esquivel
- Department of Pharmaceutical Sciences, School of Pharmacy, The University of Texas El Paso, El Paso, TX 79902, USA.
- Aerospace Center (cSETR), The University of Texas El Paso, El Paso, TX 79968, USA
| | - Md Nurunnabi
- Department of Pharmaceutical Sciences, School of Pharmacy, The University of Texas El Paso, El Paso, TX 79902, USA.
- Department of Biomedical Engineering, The University of Texas El Paso, El Paso, TX 79968, USA
- Aerospace Center (cSETR), The University of Texas El Paso, El Paso, TX 79968, USA
- Border Biomedical Research Center, The University of Texas El Paso, El Paso, TX 79968, USA
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Zhang D, Pan J, Zhou H, Cao Y. Evidence from ileum and liver transcriptomes of resistance to high-salt and water-deprivation conditions in camel. ZOOLOGICAL LETTERS 2020; 6:8. [PMID: 32518679 PMCID: PMC7275387 DOI: 10.1186/s40851-020-00159-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 05/21/2020] [Indexed: 06/11/2023]
Abstract
Camels have evolved various resistance characteristics adaptive to their desert habitats. In the present study, we used high-throughput sequencing to investigate stress-induced alternative splicing events as well as different genes involved in resistance to water deprivation and salt absorption in the ileum and liver in Camelus bactrianus. Through association analyses of mRNA, miRNA and lncRNA, we sought to explicate how camels respond to high salt and water scarcity conditions. There were two modes by which genes driven by alternative splicing were enriched to molecular functions, invoking of which was potentially fixed by organ and stress types. With qRT-PCR detection, the differentially expressed MUC6, AQP5, LOC105076960, PKP4, CDH11, TENM1, SDS, LOC105061856, PLIN2 and UPP2 were screened as functionally important genes, along with miR-29b, miR-484, miR-362-5p, miR-96, miR-195, miR-128 and miR-148a. These genes contributed to cellular stress resistance, for instance by reducing water loss, inhibiting excessive import of sodium, improving protective barriers and sodium ion homeostasis, and maintaining uridine content. The underlying competing endogenous RNAs referred to LNC001664, let-7e and LOC105076960 mRNA in ileum, and LNC001438, LNC003417, LNC001770, miR-199c and TENM1 mRNA in liver. Besides competent interpretation to resistance, there may be inspirations for curing human diseases triggered by high-salt intake.
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Affiliation(s)
- Dong Zhang
- College of Life Sciences, Inner Mongolia Agricultural University, No. 306 Zhaowuda Road, Hohhot, 010018 P.R. China
| | - Jing Pan
- College of Life Sciences, Inner Mongolia Agricultural University, No. 306 Zhaowuda Road, Hohhot, 010018 P.R. China
| | - Huanmin Zhou
- College of Life Sciences, Inner Mongolia Agricultural University, No. 306 Zhaowuda Road, Hohhot, 010018 P.R. China
| | - Yu Cao
- College of Life Sciences, Inner Mongolia Agricultural University, No. 306 Zhaowuda Road, Hohhot, 010018 P.R. China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, No. 10 Poyanghu Road, Tianjin, 301617 P.R. China
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Singaraju GS, Sagar A, Kumar A, Samuel JS, Hazra JP, Sannigrahi MK, Yennamalli RM, Ashish , Rakshit S. Structural basis of the strong cell-cell junction formed by cadherin-23. FEBS J 2019; 287:2328-2347. [PMID: 31729176 PMCID: PMC7317872 DOI: 10.1111/febs.15141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 08/13/2019] [Accepted: 11/13/2019] [Indexed: 12/03/2022]
Abstract
Cadherin-23, a giant atypical cadherin, forms homophilic interactions at the cell-cell junction of epithelial cells and heterophilic interactions with protocadherin-15 at the tip-links of neuroepithelial cells. While the molecular structure of the heterodimer is solved, the homodimer structure is yet to be resolved. The homodimers play an essential role in cell-cell adhesion as the downregulation of cadherin-23 in cancers loosen the intercellular junction resulting in faster-migration of cancer cells and a significant drop in patient survival. In vitro studies have measured a stronger aggregation-propensity of cadherin-23 compared to typical E-cadherin. Here, we deciphered the unique trans-homodimer structure of cadherin-23 in solution, and show that it consists of two electrostatic-based interfaces extended up to two terminal domains. The interface is robust, with a low off-rate of ~8x10-4 s-1 that supports its strong aggregation-propensity. We identified a point-mutation, E78K, that disrupts this binding. Interestingly, a mutation at the interface was reported in skin cancer. Overall, the structural basis of the strong cadherin-23 adhesion may have far-reaching applications in the fields of mechanobiology and cancer.
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Affiliation(s)
- Gayathri S. Singaraju
- Department of Chemical SciencesIndian Institute of Science Education and Research MohaliPunjabIndia
| | - Amin Sagar
- Department of Chemical SciencesIndian Institute of Science Education and Research MohaliPunjabIndia
| | - Anuj Kumar
- Department of Physical SciencesIndian Institute of Science Education and Research MohaliPunjabIndia
| | - Jesse S. Samuel
- Department of Chemical SciencesIndian Institute of Science Education and Research MohaliPunjabIndia
| | - Jagadish P. Hazra
- Department of Chemical SciencesIndian Institute of Science Education and Research MohaliPunjabIndia
| | - Malay K. Sannigrahi
- Department of Chemical SciencesIndian Institute of Science Education and Research MohaliPunjabIndia
| | - Ragothaman M. Yennamalli
- Department of Biotechnology and BioinformaticsJaypee University of Information TechnologyWaknaghatIndia
| | - Ashish
- Institute of Microbial Technology (CSIR)ChandigarhIndia
| | - Sabyasachi Rakshit
- Department of Chemical SciencesIndian Institute of Science Education and Research MohaliPunjabIndia
- Centre for Protein Science Design and EngineeringIndian Institute of Science Education and Research MohaliPunjabIndia
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Yu W, Yang L, Li T, Zhang Y. Cadherin Signaling in Cancer: Its Functions and Role as a Therapeutic Target. Front Oncol 2019; 9:989. [PMID: 31637214 PMCID: PMC6788064 DOI: 10.3389/fonc.2019.00989] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 09/16/2019] [Indexed: 12/12/2022] Open
Abstract
Cadherin family includes lists of transmembrane glycoproteins which mediate calcium-dependent cell-cell adhesion. Cadherin-mediated adhesion regulates cell growth and differentiation throughout life. Through the establishment of the cadherin-catenin complex, cadherins provide normal cell-cell adhesion and maintain homeostatic tissue architecture. In the process of cell recognition and adhesion, cadherins act as vital participators. As results, the disruption of cadherin signaling has significant implications on tumor formation and progression. Altered cadherin expression plays a vital role in tumorigenesis, tumor progression, angiogenesis, and tumor immune response. Based on ongoing research into the role of cadherin signaling in malignant tumors, cadherins are now being considered as potential targets for cancer therapies. This review will demonstrate the mechanisms of cadherin involvement in tumor progression, and consider the clinical significance of cadherins as therapeutic targets.
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Affiliation(s)
- Weina Yu
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory for Tumor Immunology and Biotherapy, Zhengzhou, China
| | - Li Yang
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory for Tumor Immunology and Biotherapy, Zhengzhou, China
| | - Ting Li
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory for Tumor Immunology and Biotherapy, Zhengzhou, China
| | - Yi Zhang
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory for Tumor Immunology and Biotherapy, Zhengzhou, China.,School of Life Sciences, Zhengzhou University, Zhengzhou, China
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