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Ali R, Laskar SA, Khan NJ, Wahab S, Khalid M. Non-coding RNA's prevalence as biomarkers for prognostic, diagnostic, and clinical utility in breast cancer. Funct Integr Genomics 2023; 23:195. [PMID: 37270446 DOI: 10.1007/s10142-023-01123-y] [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: 02/27/2023] [Revised: 05/19/2023] [Accepted: 05/25/2023] [Indexed: 06/05/2023]
Abstract
Noncoding RNAs (ncRNAs), which make up a significant portion of the mammalian transcriptome and plays crucial regulatory roles in expression of genes and other biological processes, have recently been found. The most extensively researched of the sncRNAs, microRNAs (miRNAs), have been characterized in terms of their synthesis, roles, and significance in the tumor development. Its crucial function in the stem cell regulation, another class of sncRNAs known as aspirRNAs, has attracted attention in cancer research. The investigations have shown that long non-coding RNAs have a crucial role in controlling developmental stages, such as mammary gland development. Additionally, it has been discovered that lncRNA dysregulation precedes the development of several malignancies, including breast cancer. The functions of sncRNAs (including miRNAs and piRNAs) and lncRNAs in the onset and development of the breast cancer are described in this study. Additionally, future perspectives of various ncRNA-based diagnostic, prognostic, and therapeutic approaches also discussed.
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Affiliation(s)
- Rafat Ali
- Department of Biosciences, Jamia Millia Islamia University, New Delhi, India
| | - Sorforaj A Laskar
- Department of Biosciences, Jamia Millia Islamia University, New Delhi, India
| | - Nida Jamil Khan
- Department of Biosciences, Jamia Millia Islamia University, New Delhi, India.
| | - Shadma Wahab
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha, 62529, Saudi Arabia
| | - Mohammad Khalid
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, P.O. Box 173, Al-Kharj, 11942, Saudi Arabia
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Walsh LA, Alvarez MJ, Sabio EY, Reyngold M, Makarov V, Mukherjee S, Lee KW, Desrichard A, Turcan Ş, Dalin MG, Rajasekhar VK, Chen S, Vahdat LT, Califano A, Chan TA. An Integrated Systems Biology Approach Identifies TRIM25 as a Key Determinant of Breast Cancer Metastasis. Cell Rep 2018; 20:1623-1640. [PMID: 28813674 DOI: 10.1016/j.celrep.2017.07.052] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 06/19/2017] [Accepted: 07/19/2017] [Indexed: 12/27/2022] Open
Abstract
At the root of most fatal malignancies are aberrantly activated transcriptional networks that drive metastatic dissemination. Although individual metastasis-associated genes have been described, the complex regulatory networks presiding over the initiation and maintenance of metastatic tumors are still poorly understood. There is untapped value in identifying therapeutic targets that broadly govern coordinated transcriptional modules dictating metastatic progression. Here, we reverse engineered and interrogated a breast cancer-specific transcriptional interaction network (interactome) to define transcriptional control structures causally responsible for regulating genetic programs underlying breast cancer metastasis in individual patients. Our analyses confirmed established pro-metastatic transcription factors, and they uncovered TRIM25 as a key regulator of metastasis-related transcriptional programs. Further, in vivo analyses established TRIM25 as a potent regulator of metastatic disease and poor survival outcome. Our findings suggest that identifying and targeting keystone proteins, like TRIM25, can effectively collapse transcriptional hierarchies necessary for metastasis formation, thus representing an innovative cancer intervention strategy.
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Affiliation(s)
- Logan A Walsh
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mariano J Alvarez
- Department of Systems Biology, Columbia University, New York, NY, USA; DarwinHealth, Inc., New York, NY, USA
| | - Erich Y Sabio
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marsha Reyngold
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Vladimir Makarov
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Ken-Wing Lee
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexis Desrichard
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Şevin Turcan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martin G Dalin
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Shuibing Chen
- Department of Surgery, Weill Cornell Medical College, New York, NY, USA
| | - Linda T Vahdat
- Department of Medicine, Weill Cornell Medical Center, New York, NY, USA
| | - Andrea Califano
- Department of Systems Biology, Columbia University, New York, NY, USA.
| | - Timothy A Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Brain Tumor Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Cellular and Developmental Biology, Weill Cornell Medical College, New York, NY, USA; Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Araujo TG, Marangoni K, Rocha RM, Maia YCP, Araujo GR, Alcântar TM, Alves PT, Calábria L, Neves AF, Soares FA, Goulart LR. Dynamic dialog between cytokeratin 18 and annexin A1 in breast cancer: a transcriptional disequilibrium. Acta Histochem 2014; 116:1178-84. [PMID: 25028131 DOI: 10.1016/j.acthis.2014.06.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 06/19/2014] [Accepted: 06/23/2014] [Indexed: 11/30/2022]
Abstract
Cytokeratins (CKs) constitute the cytoskeletal network and are regulated by post-translational modifications, acting not only as a mechanical support, but also in cell signaling and regulatory processes. Signaling is mediated by CK-associated proteins, such as Annexin A1 (ANXA1), a ligand of the CK18/CK8 complex. ANXA1 has a pivotal role in cellular and immunological responses, and together with CK18 have been implicated in several processes related to malignant transformation in breast cancer (BC). Our aim was to demonstrate how their interaction might be linked to BC development. We investigated transcript levels, protein expression and distribution for both targets in breast tissues of 92 patients (42 BCs and 50 benign diseases) using qPCR and immunohistochemistry, respectively. ANXA1 and CK18 mRNAs were inversely correlated, and their ratio in each TNM stage significantly differentiated BC from benign diseases (OR=5.62). These differences did not mirror tissue protein levels, but a significant dichotomous protein distribution in tumor tissues was observed, differing from the expected co-localization observed during cell homeostasis. The disequilibrium of transcriptional levels between ANXA1/CK18 and alterations in their tissue distribution are present either in initial events or tumor progression, which suggest a critical event in BC. The broken dialog between ANXA1 and CK18 in normal breast tissues may play a critical role in BC development, and together may be used as combined targets for BC diagnostics.
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Affiliation(s)
- Thaise G Araujo
- Laboratory of Nanobiotechnology, Institute of Genetics and Biochemistry, Federal University of Uberlandia, Uberlandia, MG, Brazil.
| | - Karina Marangoni
- Laboratory of Nanobiotechnology, Institute of Genetics and Biochemistry, Federal University of Uberlandia, Uberlandia, MG, Brazil
| | | | - Yara C P Maia
- School of Medicine, Federal University of Uberlandia, Uberlandia, MG, Brazil
| | - Galber R Araujo
- Laboratory of Nanobiotechnology, Institute of Genetics and Biochemistry, Federal University of Uberlandia, Uberlandia, MG, Brazil
| | - Tânia M Alcântar
- Department of Pathology, Clinical Hospital of Uberlandia, Federal University of Uberlandia, Uberlandia, MG, Brazil
| | - Patrícia T Alves
- Laboratory of Nanobiotechnology, Institute of Genetics and Biochemistry, Federal University of Uberlandia, Uberlandia, MG, Brazil
| | - Luanda Calábria
- Obstetrics Division, Internal Medicine, University Hospital, Federal University of Uberlandia, Uberlandia, MG, Brazil
| | - Adriana F Neves
- Laboratory of Genetics and Biotechnology, Federal University of Goias, Catalao, GO, Brazil
| | | | - Luiz R Goulart
- Laboratory of Nanobiotechnology, Institute of Genetics and Biochemistry, Federal University of Uberlandia, Uberlandia, MG, Brazil; Department of Medical Microbiology and Immunology, University of California Davis, Davis, CA, USA
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Gene expression correlation for cancer diagnosis: a pilot study. BIOMED RESEARCH INTERNATIONAL 2014; 2014:253804. [PMID: 24818135 PMCID: PMC4000964 DOI: 10.1155/2014/253804] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 03/11/2014] [Indexed: 01/18/2023]
Abstract
Poor prognosis for late-stage, high-grade, and recurrent cancers has been motivating cancer researchers to search for more efficient biomarkers to identify the onset of cancer. Recent advances in constructing and dynamically analyzing biomolecular networks for different types of cancer have provided a promising novel strategy to detect tumorigenesis and metastasis. The observation of different biomolecular networks associated with normal and cancerous states led us to hypothesize that correlations for gene expressions could serve as valid indicators of early cancer development. In this pilot study, we tested our hypothesis by examining whether the mRNA expressions of three randomly selected cancer-related genes PIK3C3, PIM3, and PTEN were correlated during cancer progression and the correlation coefficients could be used for cancer diagnosis. Strong correlations (0.68 ≤ r ≤ 1.0) were observed between PIK3C3 and PIM3 in breast cancer, between PIK3C3 and PTEN in breast and ovary cancers, and between PIM3 and PTEN in breast, kidney, liver, and thyroid cancers during disease progression, implicating that the correlations for cancer network gene expressions could serve as a supplement to current clinical biomarkers, such as cancer antigens, for early cancer diagnosis.
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Abstract
PURPOSE OF REVIEW Animals born with a deficiency in the cell surface receptor for growth hormone (GH) have a significantly reduced risk of developing cancer. Conversely, increased expression levels of GH and the GH receptor (GHR) are detectable in a variety of different human cancers. Here we discuss recent literature contributing to our understanding of the field. RECENT FINDINGS In addition to animal evidence, studies of individuals with Laron syndrome suggest that congenital GHR deficiency may also protect humans against cancer. GH expression in certain malignancies is correlated with clinicohistopathological parameters and may contribute the therapeutic resistance. Other recent studies have identified novel aspects of the GH signal transduction pathway, including receptor crosstalk and the involvement of microRNA in endocrine regulation of GH. SUMMARY Substantial evidence suggests the GH/insulin-like growth factor-1 axis initiates and promotes progression of cancer. However, important questions remain unanswered regarding the therapeutic utility of GH or GHR antagonism in cancer. Further clinical studies regarding the clinical association of GH expression with human malignancies and translational studies investigating GHR antagonism in animal models of human cancer are critical.
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Affiliation(s)
- Jo K Perry
- Liggins Institute, University of Auckland, Auckland, New Zealand.
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Abstract
A substantial body of evidence supports a role for the growth hormone (GH)-IGF-1 axis in cancer incidence and progression. This includes epidemiological evidence relating elevated plasma IGF-1 to cancer incidence as well as a lack of cancers in GH/IGF-1 deficiency. Rodent models lacking GH or its receptor are strikingly resistant to the induction of a wide range of cancers, and treatment with the GH antagonist pegvisomant slows tumor progression. While GH receptor expression is elevated in many cancers, autocrine GH is present in several types, and overexpression of autocrine GH can induce cell transformation. While the mechanism of autocrine action is not clear, it does involve both STAT5 and STAT3 activation, and probably nuclear translocation of the GH receptor. Development of a more potent GH receptor antagonist or secretion inhibitor is warranted for cancer therapy.
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Affiliation(s)
- Yash Chhabra
- a The University of Queensland, Institute for Molecular Bioscience, Brisbane, Qld 4072, Australia
| | - Michael J Waters
- a The University of Queensland, Institute for Molecular Bioscience, Brisbane, Qld 4072, Australia
- b
| | - Andrew J Brooks
- a The University of Queensland, Institute for Molecular Bioscience, Brisbane, Qld 4072, Australia
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Appels R, Barrerro R, Keeble G, Bellgard M. Advances in genome studies: The PAG 2010 conference. Funct Integr Genomics 2010; 10:1-9. [PMID: 20182762 DOI: 10.1007/s10142-010-0164-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
An overview is provided of the advances in plant, animal and human genome studies by summarizing the contents of seven plenary lectures presented at the Plant and Animal Genome (PAG) meeting in January 2010. The area of biology covered was wide and reflected the nature of this fast moving science.
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Affiliation(s)
- R Appels
- Centre for Comparative genomics, Murdoch University, Perth, WA 6510, USA.
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