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Chari T, Gorin G, Pachter L. Biophysically interpretable inference of cell types from multimodal sequencing data. NATURE COMPUTATIONAL SCIENCE 2024; 4:677-689. [PMID: 39317762 DOI: 10.1038/s43588-024-00689-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 08/08/2024] [Indexed: 09/26/2024]
Abstract
Multimodal, single-cell genomics technologies enable simultaneous measurement of multiple facets of DNA and RNA processing in the cell. This creates opportunities for transcriptome-wide, mechanistic studies of cellular processing in heterogeneous cell populations, such as regulation of cell fate by transcriptional stochasticity or tumor proliferation through aberrant splicing dynamics. However, current methods for determining cell types or 'clusters' in multimodal data often rely on ad hoc approaches to balance or integrate measurements, and assumptions ignoring inherent properties of the data. To enable interpretable and consistent cell cluster determination, we present meK-means (mechanistic K-means) which integrates modalities through a unifying model of transcription to learn underlying, shared biophysical states. With meK-means we can cluster cells with nascent and mature mRNA measurements, utilizing the causal, physical relationships between these modalities. This identifies shared transcription dynamics across cells, which induce the observed molecule counts, and provides an alternative definition for 'clusters' through the governing parameters of cellular processes.
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Affiliation(s)
- Tara Chari
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | - Lior Pachter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA.
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2
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Di Fiore R, Drago-Ferrante R, Suleiman S, Calleja N, Calleja-Agius J. The role of microRNA-9 in ovarian and cervical cancers: An updated overview. EUROPEAN JOURNAL OF SURGICAL ONCOLOGY 2024:108546. [PMID: 39030109 DOI: 10.1016/j.ejso.2024.108546] [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: 04/02/2024] [Accepted: 07/11/2024] [Indexed: 07/21/2024]
Abstract
Ovarian and cervical cancers are the two most frequent kind of gynaecological cancers (GCs). In spite of advances in prevention, screening and treatment, cervical cancer still leads to an increased morbidity and mortality worldwide. Ovarian cancer is often detected at a late stage, which significantly reduces the effectiveness of available treatments. Therefore, novel methods are desperately needed to improve the clinical care of GC patients. MicroRNAs, also known as short noncoding RNAs (miRNAs/miRs), are a diverse group of RNAs with a length of 22 nucleotides. These typically cause translational repression and mRNA degradation by interacting with target mRNAs' 3' untranslated region (3'-UTR), together with other regions and gene promoters. Under certain conditions, they are also able to activate translation or regulate transcription. It has been demonstrated that miRNAs are crucial to several biological processes leading to tumorigenesis, including GCs. Recent research has shown that miR-9 affects carcinogenesis. In this review, we will provide an overview of current research on the potential utility of miR-9 in the diagnosis, prognosis, and therapy of ovarian and cervical malignancies.
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Affiliation(s)
- Riccardo Di Fiore
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, MSD, 2080, Msida, Malta; Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA.
| | - Rosa Drago-Ferrante
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, MSD, 2080, Msida, Malta; BioDNA Laboratories, Malta Life Sciences Park, SGN, 3000, San Gwann, Malta.
| | - Sherif Suleiman
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, MSD, 2080, Msida, Malta.
| | - Neville Calleja
- Department of Public Health, Faculty of Medicine and Surgery, University of Malta, MSD, 2080, Msida, Malta.
| | - Jean Calleja-Agius
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, MSD, 2080, Msida, Malta.
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3
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Di Fiore R, Drago-Ferrante R, Suleiman S, Veronese N, Pegreffi F, Calleja-Agius J. Sarcopenia in gynaecological cancers. EUROPEAN JOURNAL OF SURGICAL ONCOLOGY 2024:108403. [PMID: 38760237 DOI: 10.1016/j.ejso.2024.108403] [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: 01/08/2024] [Revised: 04/26/2024] [Accepted: 05/07/2024] [Indexed: 05/19/2024]
Abstract
Gynaecological cancers (GCs) comprise a group of cancers that originate in the female reproductive organs. Each GC is unique, with different signs and symptoms, risk factors and therapeutic strategies. Worldwide, the majority of GCs are still associated with high mortality rates, especially ovarian, due to difficulty in early detection. Despite numerous studies on the underlying pathophysiology, research in the field of GCs poses unique scientific and technological challenges. These challenges require a concerted multi- and inter-disciplinary effort by the clinical, scientific and research communities to accelerate the advancement of prognostic, diagnostic, and therapeutic approaches. Sarcopenia is a multifactorial disease which leads to the systemic loss of skeletal muscle mass and function. It can be caused by malignancies, as well as due to malnutrition, physical inactivity, ageing and neuromuscular, inflammatory, and/or endocrine diseases. Anorexia and systemic inflammation can shift the metabolic balance of patients with cancer cachexia towards catabolism of skeletal muscle, and hence sarcopenia. Therefore, sarcopenia is considered as an indicator of poor general health status, as well as the possible indicator of advanced cancer. There is a growing body of evidence showing the prognostic significance of sarcopenia in various cancers, including GCs. This review will outline the clinical importance of sarcopenia in patients with GCs.
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Affiliation(s)
- Riccardo Di Fiore
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, MSD 2080, Msida, Malta; Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, 19122, USA.
| | - Rosa Drago-Ferrante
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, MSD 2080, Msida, Malta; BioDNA Laboratories, Malta Life Sciences Park, SGN 3000, San Gwann, Malta.
| | - Sherif Suleiman
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, MSD 2080, Msida, Malta.
| | - Nicola Veronese
- Department of Internal Medicine, Geriatrics Section, University of Palermo, 90128, Palermo, Italy.
| | - Francesco Pegreffi
- Department of Medicine and Surgery, Kore University of Enna, 94100, Enna, Italy.
| | - Jean Calleja-Agius
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, MSD 2080, Msida, Malta.
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4
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Kadian LK, Verma D, Lohani N, Yadav R, Ranga S, Gulshan G, Pal S, Kumari K, Chauhan SS. Long non-coding RNAs in cancer: multifaceted roles and potential targets for immunotherapy. Mol Cell Biochem 2024:10.1007/s11010-024-04933-1. [PMID: 38413478 DOI: 10.1007/s11010-024-04933-1] [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: 06/06/2023] [Accepted: 01/05/2024] [Indexed: 02/29/2024]
Abstract
Cancer remains a major global health concern with high mortality rates mainly due to late diagnosis and poor prognosis. Long non-coding RNAs (lncRNAs) are emerging as key regulators of gene expression in human cancer, functioning through various mechanisms including as competing endogenous RNAs (ceRNAs) and indirectly regulating miRNA expression. LncRNAs have been found to have both oncogenic and tumor-suppressive roles in cancer, with the former promoting cancer cell proliferation, migration, invasion, and poor prognosis. Recent research has shown that lncRNAs are expressed in various immune cells and are involved in cancer cell immune escape and the modulation of the tumor microenvironment, thus highlighting their potential as targets for cancer immunotherapy. Targeting lncRNAs in cancer or immune cells could enhance the anti-tumor immune response and improve cancer immunotherapy outcomes. However, further research is required to fully understand the functional roles of lncRNAs in cancer and the immune system and their potential as targets for cancer immunotherapy. This review offers a comprehensive examination of the multifaceted roles of lncRNAs in human cancers, with a focus on their potential as targets for cancer immunotherapy. By exploring the intricate mechanisms underlying lncRNA-mediated regulation of cancer cell proliferation, invasion, and immune evasion, we provide insights into the diverse therapeutic applications of these molecules.
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Affiliation(s)
- Lokesh K Kadian
- Dept of Biochemistry, All India Institute of Medical Sciences, New Delhi, 110029, India
- Dept of Dermatology, Indiana University School of Medicine, Indianapolis, 46202, USA
| | - Deepika Verma
- Dept of Biochemistry, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Neelam Lohani
- Dept of Biochemistry, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Ritu Yadav
- Dept of Genetics, MD University, Rohtak, 124001, India
| | - Shalu Ranga
- Dept of Genetics, MD University, Rohtak, 124001, India
| | - Gulshan Gulshan
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, Maharashtra, India
| | - Sanghapriya Pal
- Dept of Biochemistry, Maulana Azad Medical College and Associated Hospital, New Delhi, 110002, India
| | - Kiran Kumari
- Dept of Forensic Science, Lovely Professional University, Jalandhar, Punjab, 144411, India
| | - Shyam S Chauhan
- Dept of Biochemistry, All India Institute of Medical Sciences, New Delhi, 110029, India.
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5
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Mazarei M, Shahabi Rabori V, Ghasemi N, Salehi M, Rayatpisheh N, Jahangiri N, Saberiyan M. LncRNA MALAT1 signaling pathway and clinical applications in overcome on cancers metastasis. Clin Exp Med 2023; 23:4457-4472. [PMID: 37695391 DOI: 10.1007/s10238-023-01179-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 08/27/2023] [Indexed: 09/12/2023]
Abstract
In spite of its high mortality rate and difficulty in finding a cure, scientific advancements have contributed to a reduction in cancer-related fatalities. Aberrant gene expression during carcinogenesis emphasizes the importance of targeting the signaling networks that control gene expression in cancer treatment. Long noncoding RNAs (lncRNAs), which are transcribed RNA molecules that play a role in gene expression regulation, are a recent innovative therapeutic approach for diagnosing and treating malignancies. MALAT1, a well-known lncRNA, functions in gene expression, RNA processing, and epigenetic control. High expression levels of MALAT1 are associated with several human disorders, including metastasis, invasion, autophagy, and proliferation of cancer cells. MALAT1 affects various signaling pathways and microRNAs (miRNAs), and this study aims to outline its functional roles in cancer metastasis and its interactions with cellular signaling pathways. Moreover, MALAT1 and its interactions with signaling pathways can be promising target for cancer treatment.
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Affiliation(s)
- Madineh Mazarei
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | | | - Nazila Ghasemi
- Department of Biology, Jahrom Branch, Islamic Azad University, Jahrom, Iran
| | - Mehrnaz Salehi
- School of Medicine, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Najmeh Rayatpisheh
- School of Medicine, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Negin Jahangiri
- Department of Biology, Faculty of Basic Sciences and Engineering, Gonbad Kavous University, Gonbad-e Kavus, Iran
| | - Mohammadreza Saberiyan
- Department of Medical Genetics, Faculty of Medicine, School of Medical Sciences, Hormozgan University of Medical Sciences, Bandar Abbas, Iran.
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Nasrolahi A, Khojasteh Pour F, Mousavi Salehi A, Kempisty B, Hajizadeh M, Feghhi M, Azizidoost S, Farzaneh M. Potential roles of lncRNA MALAT1-miRNA interactions in ocular diseases. J Cell Commun Signal 2023:10.1007/s12079-023-00787-2. [PMID: 37870615 DOI: 10.1007/s12079-023-00787-2] [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: 04/18/2023] [Accepted: 10/09/2023] [Indexed: 10/24/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are non-protein coding transcripts that are longer than 200 nucleotides in length. LncRNAs are implicated in gene expression at the transcriptional, translational, and epigenetic levels, and thereby impact different cellular processes including cell proliferation, migration, apoptosis, angiogenesis, and immune response. In recent years, numerous studies have demonstrated the significant contribution of lncRNAs to the pathogenesis and progression of various diseases, such as stroke, heart disease, and cancer. Further investigations have shown that lncRNAs have altered expression patterns in ocular tissues and cell lines during pathological conditions. The pathogenesis of various ocular diseases, including glaucoma, cataract, corneal diseases, proliferative vitreoretinopathy, diabetic retinopathy, and retinoblastoma, is influenced by the involvement of specific lncRNAs which play a critical role in the development and progression of these diseases. Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is a well-researched lncRNA in the context of ocular diseases, which has been shown to exert its biological effects through several signaling pathways and downstream targets. The present review provides a comprehensive summary of the molecular mechanisms underlying the biological functions and roles of MALAT1 in ocular diseases.
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Affiliation(s)
- Ava Nasrolahi
- Infectious Ophthalmologic Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Fatemeh Khojasteh Pour
- Department of Obstetrics and Gynecology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Abdolah Mousavi Salehi
- Department of Immunology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Bartosz Kempisty
- Department of Human Morphology and Embryology, Division of Anatomy, Wroclaw Medical University, Wrocław, Poland
- Institute of Veterinary Medicine, Department of Veterinary Surgery, Nicolaus Copernicus University, Torun, Poland
- North Carolina State University College of Agriculture and Life Sciences, Raleigh, NC, 27695, USA
| | - Maryam Hajizadeh
- Infectious Ophthalmologic Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Department of Ophthalmology, Imam Khomeini Hospital, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mostafa Feghhi
- Infectious Ophthalmologic Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Department of Ophthalmology, Imam Khomeini Hospital, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Shirin Azizidoost
- Atherosclerosis Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Maryam Farzaneh
- Fertility, Infertility and Perinatology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
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Iordanishvili S, Metreveli T, Lipartia E, Gachechiladze K, Khuntsaria I, Qobulashvili T, Jorbenadze M, Revazishvili T, Kldiashvili E, Kaufmann AM. The HPV-TP53-MALAT1 Axis: Unravelling interactions in cervical cancer development. PLoS One 2023; 18:e0291725. [PMID: 37812599 PMCID: PMC10561830 DOI: 10.1371/journal.pone.0291725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 09/05/2023] [Indexed: 10/11/2023] Open
Abstract
INTRODUCTION Cervical cancer, primarily driven by Human Papillomavirus (HPV) infection, stands as a substantial global health challenge. The TP53 gene's, Arg72Pro polymorphism has emerged as a noteworthy player in cervical cancer development, particularly among individuals harboring high-risk (HR) HPV types. Additionally, long non-coding RNAs (lncRNAs), exemplified by metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), exert critical roles in cancer biology. This study delves into unravelling the intricate connections linking HPV infection, TP53 Arg72Pro polymorphism, and MALAT1 expression in the context of cervical cancer. MATERIALS AND METHODS Within a cohort of cervical cancer patients, we discerned HPV infection statuses, executed genotyping for the TP53 Arg72Pro polymorphism, and quantified MALAT1 expression through quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Statistical analyses meticulously probed relationships intertwining HPV infection, TP53 polymorphism, and MALAT1 expression. FINDINGS Our investigation revealed a striking prevalence of the TP53 Arg72Pro polymorphism among HPV-positive subjects, accompanied by a robust and statistically significant correlation linking MALAT1 overexpression (p<0.01) and HR-HPV positivity (p<0.03). Importantly, a subset of MALAT1 overexpression cases unveiled a concomitant TP53 Pro72Pro polymorphism. In contrast, HPV-negative invasive cervical carcinoma samples exhibited no discernible shifts in MALAT1 expression. CONCLUSION The contours of our findings sketch a compelling landscape wherein HR-HPV infection, TP53 polymorphism, and MALAT1 expression intertwine significantly in cervical cancer. The voyage ahead entails delving deeper into molecular underpinnings to decipher MALAT1's nuanced role and its dance with TP53 within HPV-associated cervical carcinogenesis. This expedition promises insights that may engender targeted therapeutic interventions and bespoke prognostic markers, tailored to the realm of HR-HPV-related cervical cancer.
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Affiliation(s)
| | | | - Elene Lipartia
- Petre Shotadze Tbilisi Medical Academy, Tbilisi, Georgia
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8
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Hu J, Huang K, Bao F, Zhong S, Fan Q, Li W. Low-dose lipopolysaccharide inhibits spinal cord injury-induced neuronal apoptosis by regulating autophagy through the lncRNA MALAT1/Nrf2 axis. PeerJ 2023; 11:e15919. [PMID: 37663283 PMCID: PMC10470450 DOI: 10.7717/peerj.15919] [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: 05/05/2023] [Accepted: 07/27/2023] [Indexed: 09/05/2023] Open
Abstract
Background Spinal cord injury (SCI) is a neurological disease associated with a high disability rate. Low-dose lipopolysaccharide (LPS) has been reported to activate cross-immune tolerance and alleviate the effects of various traumatic stimuli. The present study aimed to explore the effect of LPS on SCI and the potential molecular mechanism. Methods Male Sprague-Dawley (SD) rats were used to established an in vivo SCI model and were intraperitoneally injected with lentivirus particles encoding a MALAT1 small interfering RNA (siRNA) on day 10 prior to SCI and with 0.2 mg/kg LPS 72 h prior to SCI. Basso, Beattie, and Bresnahan (BBB) scoring; HE staining; and TUNEL assay were used to assess neurological function and pathophysiological changes. Western blot and immunohistochemistry (IHC) were used to detect cell autophagy and Nrf2 nuclear translocation. PC12 cells were exposed to oxygen-glucose deprivation/reoxygenation (OGD/R) to establish an in vitro SCI model. In vitro SCI model cells were pretreated with LPS and transfected with siMALAT1 or MALAT1 overexpression plasmid aimed at knocking down MALAT1 or overexpressing MALAT1. The cell counting kit-8 (CCK-8) assay was used to measure the toxicity of LPS towards PC12 cells. Flow cytometry and immunofluorescence analysis were performed to investigate cell apoptosis and Nrf2 nuclear translocation. Results SCI rats preconditioned with low-dose LPS had higher BBB scores, reduced SCI injury, increased MALAT1 expression and activated autophagy and Nrf2 nuclear translocation in the in vivo SCI model. In the in vitro SCI model, low-dose LPS treatment suppressed the apoptotic ratio of PC12 cells, increased MALAT1 expression, activated autophagy, and promoted Nrf2 nuclear translocation. Silencing MALAT1 exacerbated OGD/R injury in vitro and weakened the protective effect of low-dose LPS. Overexpression of MALAT1 inhibits OGD/R-induced apoptosis by inducing autophagy and promoting Nrf2 nuclear translocation. This was also been confirmed in animal experiments, silencing MALAT1 blocked the promotion of Nrf2 by low-dose LPS and the alleviated of SCI apoptosis. Conclusions Low-dose LPS exhibited a protective role on SCI by activating autophagy and suppressing nerve cell apoptosis via the lncRNA MALAT1/Nrf2 axis.
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Affiliation(s)
- Jianhua Hu
- Orthopedic Surgery, The First People’s Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
- Faculty of Medical Science, Kunming University of Science and Technology, Kunming, China
| | - Kun Huang
- Orthopedic Surgery, The First People’s Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Feilong Bao
- Faculty of Medical Science, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Digital Orthopaedics, Kunming, China
| | - Shixiao Zhong
- Faculty of Medical Science, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Digital Orthopaedics, Kunming, China
| | - Qianbo Fan
- Faculty of Medical Science, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Digital Orthopaedics, Kunming, China
| | - Weichao Li
- Orthopedic Surgery, The First People’s Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
- Faculty of Medical Science, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Digital Orthopaedics, Kunming, China
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Hou J, Zhang G, Wang X, Wang Y, Wang K. Functions and mechanisms of lncRNA MALAT1 in cancer chemotherapy resistance. Biomark Res 2023; 11:23. [PMID: 36829256 PMCID: PMC9960193 DOI: 10.1186/s40364-023-00467-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/17/2023] [Indexed: 02/26/2023] Open
Abstract
Chemotherapy is one of the most important treatments for cancer therapy. However, chemotherapy resistance is a big challenge in cancer treatment. Due to chemotherapy resistance, drugs become less effective or no longer effective at all. In recent years, long non-coding RNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) has been found to be associated with the development of chemotherapy resistance, suggesting that MALAT1 may be an important target to overcome chemotherapy resistance. In this review, we introduced the main mechanisms of chemotherapy resistance associated with MALAT1, which may provide new approaches for cancer treatment.
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Affiliation(s)
- Junhui Hou
- grid.412467.20000 0004 1806 3501Department of Urology, Shengjing Hospital of China Medical University, #36 Sanhao Street, Heping District, Shenyang, 110004 Liaoning China
| | - Gong Zhang
- grid.412467.20000 0004 1806 3501Department of Urology, Shengjing Hospital of China Medical University, #36 Sanhao Street, Heping District, Shenyang, 110004 Liaoning China
| | - Xia Wang
- grid.412467.20000 0004 1806 3501Department of Urology, Shengjing Hospital of China Medical University, #36 Sanhao Street, Heping District, Shenyang, 110004 Liaoning China
| | - Yuan Wang
- Department of General Surgery, Shengjing Hospital of China Medical University, #36 Sanhao Street, Heping District, Shenyang, 110004, Liaoning, China.
| | - Kefeng Wang
- Department of Urology, Shengjing Hospital of China Medical University, #36 Sanhao Street, Heping District, Shenyang, 110004, Liaoning, China.
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10
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Hao L, Wu W, Xu Y, Chen Y, Meng C, Yun J, Wang X. LncRNA-MALAT1: A Key Participant in the Occurrence and Development of Cancer. Molecules 2023; 28:molecules28052126. [PMID: 36903369 PMCID: PMC10004581 DOI: 10.3390/molecules28052126] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/18/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
LncRNAs are a group of non-coding RNA transcripts with lengths of over 200 nucleotides and can interact with DNA, RNA, and proteins to regulate gene expression of malignant tumors in human tissues. LncRNAs participate in vital processes, such as chromosomal nuclear transport in the cancerous site of human tissue, activation, and the regulation of proto-oncogenes, the differentiation of immune cells, and the regulation of the cellular immune system. The lncRNA metastasis-associated lung cancer transcript 1 (MALAT1) is reportedly involved in the occurrence and development of many cancers and serves as a biomarker and therapeutic target. These findings highlight its promising role in cancer treatment. In this article, we comprehensively summarized the structure and functions of lncRNA, notably the discoveries of lncRNA-MALAT1 in different cancers, the action mechanisms, and the ongoing research on new drug development. We believe our review would serve as a basis for further research on the pathological mechanism of lncRNA-MALAT1 in cancer and provide evidence and novel insights into its application in clinical diagnoses and treatments.
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Affiliation(s)
- Longhui Hao
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Wenzheng Wu
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Yankun Xu
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Yufan Chen
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Chengzhen Meng
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Jingyi Yun
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Xiaoyu Wang
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
- Correspondence:
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11
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Shi C, Ren S, Zhao X, Li Q. lncRNA MALAT1 regulates the resistance of breast cancer cells to paclitaxel via the miR-497-5p/ SHOC2 axis. Pharmacogenomics 2022; 23:973-985. [PMID: 36420706 DOI: 10.2217/pgs-2022-0077] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Aim: To explore the roles of lncRNA MALAT1 and SHOC2 in breast cancer, and the potential connections to chemotherapy resistance in breast cancer. Materials & methods: Paclitaxel-resistant breast cancer cells were induced by gradually increasing intermittent doses. Bioinformatic analyses were performed to predict the regulated miRNAs of MALAT1. Results: High expressions of MALAT1 and SHOC2 contribute to paclitaxel resistance in breast cancer cells. MALAT1 sponges miR-497-5p enhance SHOC2 expression in paclitaxel-resistant breast cancer cells and contribute to paclitaxel resistance in breast cancer cells. Conclusion: Patients with high expression of MALAT1 and SHOC2 have a poorer response to paclitaxel. Upregulation of miR-497-5p could improve the treatment response to paclitaxel in patients with breast cancer by inhibiting MALAT1 and SHOC2.
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Affiliation(s)
- Chang Shi
- The Fourth Department of General Surgery, the Second Hospital of Hebei Medical University
| | - Shuangjie Ren
- Department of Traditional Chinese Medicine Surgery, the Second Hospital of Hebei Medical University
| | - Xiaodong Zhao
- The Fourth Department of General Surgery, the Second Hospital of Hebei Medical University
| | - Qinghuai Li
- The Sixth Department of General Surgery, the Second Hospital of Hebei Medical University, Shijiazhuang City, Hebei Province, 050000, China
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Flnc: Machine Learning Improves the Identification of Novel Long Noncoding RNAs from Stand-Alone RNA-Seq Data. Noncoding RNA 2022; 8:ncrna8050070. [DOI: 10.3390/ncrna8050070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/01/2022] [Accepted: 10/06/2022] [Indexed: 11/16/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) play critical regulatory roles in human development and disease. Although there are over 100,000 samples with available RNA sequencing (RNA-seq) data, many lncRNAs have yet to be annotated. The conventional approach to identifying novel lncRNAs from RNA-seq data is to find transcripts without coding potential but this approach has a false discovery rate of 30–75%. Other existing methods either identify only multi-exon lncRNAs, missing single-exon lncRNAs, or require transcriptional initiation profiling data (such as H3K4me3 ChIP-seq data), which is unavailable for many samples with RNA-seq data. Because of these limitations, current methods cannot accurately identify novel lncRNAs from existing RNA-seq data. To address this problem, we have developed software, Flnc, to accurately identify both novel and annotated full-length lncRNAs, including single-exon lncRNAs, directly from RNA-seq data without requiring transcriptional initiation profiles. Flnc integrates machine learning models built by incorporating four types of features: transcript length, promoter signature, multiple exons, and genomic location. Flnc achieves state-of-the-art prediction power with an AUROC score over 0.92. Flnc significantly improves the prediction accuracy from less than 50% using the conventional approach to over 85%. Flnc is available via GitHub platform.
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Nuñez-Olvera SI, Puente-Rivera J, Ramos-Payán R, Pérez-Plasencia C, Salinas-Vera YM, Aguilar-Arnal L, López-Camarillo C. Three-Dimensional Genome Organization in Breast and Gynecological Cancers: How Chromatin Folding Influences Tumorigenic Transcriptional Programs. Cells 2021; 11:75. [PMID: 35011637 PMCID: PMC8750285 DOI: 10.3390/cells11010075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/15/2021] [Accepted: 12/24/2021] [Indexed: 12/19/2022] Open
Abstract
A growing body of research on the transcriptome and cancer genome has demonstrated that many gynecological tumor-specific gene mutations are located in cis-regulatory elements. Through chromosomal looping, cis-regulatory elements interact which each other to control gene expression by bringing distant regulatory elements, such as enhancers and insulators, into close proximity with promoters. It is well known that chromatin connections may be disrupted in cancer cells, promoting transcriptional dysregulation and the expression of abnormal tumor suppressor genes and oncogenes. In this review, we examine the roles of alterations in 3D chromatin interactions. This includes changes in CTCF protein function, cancer-risk single nucleotide polymorphisms, viral integration, and hormonal response as part of the mechanisms that lead to the acquisition of enhancers or super-enhancers. The translocation of existing enhancers, as well as enhancer loss or acquisition of insulator elements that interact with gene promoters, is also revised. Remarkably, similar processes that modify 3D chromatin contacts in gene promoters may also influence the expression of non-coding RNAs, such as long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), which have emerged as key regulators of gene expression in a variety of cancers, including gynecological malignancies.
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Affiliation(s)
- Stephanie I. Nuñez-Olvera
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Jonathan Puente-Rivera
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City 03100, Mexico;
| | - Rosalio Ramos-Payán
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacan City 80030, Mexico;
| | | | - Yarely M. Salinas-Vera
- Departamento de Bioquímica, Centro de Investigación y Estudios Avanzados, Mexico City 07360, Mexico;
| | - Lorena Aguilar-Arnal
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City 03100, Mexico;
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