1
|
Li Y, Huang J, Li LF, Guo P, Wang Y, Cushman SA, Shang FD. Roles and regulatory patterns of protein isoforms in plant adaptation and development. THE NEW PHYTOLOGIST 2024. [PMID: 39645578 DOI: 10.1111/nph.20327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Accepted: 11/20/2024] [Indexed: 12/09/2024]
Abstract
Protein isoforms (PIs) play pivotal roles in regulating plant growth and development that confer adaptability to diverse environmental conditions. PIs are widely present in plants and generated through alternative splicing (AS), alternative polyadenylation (APA), alternative initiation (AI), and ribosomal frameshifting (RF) events. The widespread presence of PIs not only significantly increases the complexity of genomic information but also greatly enriches regulatory networks and enhances their flexibility. PIs may also play important roles in phenotypic diversity, ecological niche differentiation, and speciation, thereby increasing the dimensions of research in molecular ecology. However, PIs pose new challenges for the quantitative analysis, annotation, and identification of genetic regulatory mechanisms. Thus, focus on PIs make genomic and epigenomic studies both more powerful and more challenging. This review summarizes the origins, functions, regulatory patterns of isoforms, and the challenges they present for future research in molecular ecology and molecular biology.
Collapse
Affiliation(s)
- Yong Li
- College of Life Science and Technology, Inner Mongolia Normal University, Hohhot, 010020, China
- Key Laboratory of Biodiversity Conservation and Sustainable Utilization in Mongolian Plateau for College and University of Inner Mongolia Autonomous Region, Hohhot, 010022, China
| | - Jinling Huang
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Science, Henan University, Kaifeng, 475004, China
| | - Lin-Feng Li
- College of Life Science and Technology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Peng Guo
- College of Life Science, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yihan Wang
- College of Life Science, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, 450002, China
| | - Samuel A Cushman
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX5QL, UK
| | - Fu-De Shang
- College of Life Science, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, 450002, China
| |
Collapse
|
2
|
Lu H, Yu X, Li W, Zhang Y, Sun S. Prognosis and metabolism with a Golgi apparatus-related genes-based formula in breast cancer. Medicine (Baltimore) 2024; 103:e39177. [PMID: 39151519 PMCID: PMC11332736 DOI: 10.1097/md.0000000000039177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 03/20/2024] [Accepted: 07/15/2024] [Indexed: 08/19/2024] Open
Abstract
The Golgi apparatus (GA), an organelle that processes, sorts, and transports proteins synthesized by the endoplasmic reticulum, is also involved in many cellular processes associated with cancer, such as angiogenesis, the innate immune response, and tumor invasion and migration. We aimed to construct a breast cancer (BC) prognosis prediction model based on GA-related genetic information to evaluate the prognosis of patients with BC more accurately than existing models and to stratify patients for clinical therapy. In this study, The Cancer Genome Atlas-breast invasive carcinoma was used as the training cohort, and the Molecular Taxonomy of Breast Cancer International Consortium cohort was used as the validation cohort. Using bioinformatics methods, we constructed a GA-related gene risk score (GRS). The GRS was used to divide BC patients into a high-GRS group and a low-GRS group, and functional analysis, survival analysis, mutation analysis, immune landscape analysis, and metabolic analysis were performed to compare the 2 groups. Finally, a nomogram was constructed for clinical application. The genes in the GRS model were mainly related to the glucose metabolism pathway, and the main mutations in the 2 groups of patients were mutations in TP53 and CHD1. The mutation rate in the high-GRS group was greater than that in the low-GRS group. The high GRS group had higher tumor immune activity glycolysis; the pentose phosphate pathway tended to be the dominant metabolic pathways in this group, while fatty acid oxidation and glutamine catabolism tended to be dominant in the low-GRS group. GA-related genes were used to construct a prediction model for BC patients and had high accuracy in predicting prognosis. The mutations associated with the GRS are mainly TP53 and CDH1. Interestingly, the GRS is correlated with glucose metabolism in terms of gene expression and functional enrichment. In summary, the role of GRS-related genes in glucose metabolism is worthy of further study.
Collapse
Affiliation(s)
- Hang Lu
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, China
- Department of Cardiovascular Surgery, Xijing Hospital, Xi’an, China
| | - Xin Yu
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Wenge Li
- Department of Oncology, Shanghai Artemed Hospital, Shanghai, China
| | - Yimin Zhang
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Shengrong Sun
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| |
Collapse
|
3
|
Favero A, Segatto I, Capuano A, Mattevi MC, Rampioni Vinciguerra GL, Musco L, D'Andrea S, Dall'Acqua A, Gava C, Perin T, Massarut S, Marchini C, Baldassarre G, Spessotto P, Belletti B. Loss of the extracellular matrix glycoprotein EMILIN1 accelerates Δ16HER2-driven breast cancer initiation in mice. NPJ Breast Cancer 2024; 10:5. [PMID: 38184660 PMCID: PMC10771445 DOI: 10.1038/s41523-023-00608-0] [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: 07/10/2023] [Accepted: 12/02/2023] [Indexed: 01/08/2024] Open
Abstract
The extracellular matrix (ECM) is an important component of the tumor microenvironment and undergoes extensive remodeling during both initiation and progression of breast cancer (BC). EMILIN1 is an ECM glycoprotein, whose function has been linked to cancer and metastasis. However, EMILIN1 role during mammary gland and BC development has never been investigated. In silico and molecular analyses of human samples from normal mammary gland and BC showed that EMILIN1 expression was lower in tumors than in healthy mammary tissue and it predicted poor prognosis, particularly in HER2-positive BC. HER2+ BC accounts for 15-20% of all invasive BC and is characterized by high aggressiveness and poor prognosis. The Δ16HER2 isoform, a splice variant with very high oncogenic potential, is frequently expressed in HER2+ BC and correlates with metastatic disease. To elucidate the role of EMILIN1 in BC, we analyzed the phenotype of MMTV-Δ16HER2 transgenic mice, developing spontaneous multifocal mammary adenocarcinomas, crossed with EMILIN1 knock-out (KO) animals. We observed that Δ16HER2/EMILIN1 KO female mice exhibited an accelerated normal mammary gland development and a significantly anticipated appearance of palpable tumors (13.32 vs 15.28 weeks). This accelerated tumor initiation was corroborated by an increased number of tumor foci observed in mammary glands from Δ16HER2/EMILIN1 KO mice compared to the wild-type counterpart. Altogether our results underscore the centrality of ECM in the process of BC initiation and point to a role for EMILIN1 during normal mammary gland development and in protecting from HER2-driven breast tumorigenesis.
Collapse
Affiliation(s)
- Andrea Favero
- Unit of Molecular Oncology, Centro di Riferimento Oncologico (CRO) di Aviano, IRCCS, National Cancer Institute, 33081, Aviano, Italy
| | - Ilenia Segatto
- Unit of Molecular Oncology, Centro di Riferimento Oncologico (CRO) di Aviano, IRCCS, National Cancer Institute, 33081, Aviano, Italy
| | - Alessandra Capuano
- Unit of Molecular Oncology, Centro di Riferimento Oncologico (CRO) di Aviano, IRCCS, National Cancer Institute, 33081, Aviano, Italy
| | - Maria Chiara Mattevi
- Unit of Molecular Oncology, Centro di Riferimento Oncologico (CRO) di Aviano, IRCCS, National Cancer Institute, 33081, Aviano, Italy
| | - Gian Luca Rampioni Vinciguerra
- Unit of Molecular Oncology, Centro di Riferimento Oncologico (CRO) di Aviano, IRCCS, National Cancer Institute, 33081, Aviano, Italy
- Faculty of Medicine and Psychology, Department of Clinical and Molecular Medicine, University of Rome "Sapienza", Santo Andrea Hospital, 00189, Rome, Italy
| | - Lorena Musco
- Unit of Molecular Oncology, Centro di Riferimento Oncologico (CRO) di Aviano, IRCCS, National Cancer Institute, 33081, Aviano, Italy
| | - Sara D'Andrea
- Unit of Molecular Oncology, Centro di Riferimento Oncologico (CRO) di Aviano, IRCCS, National Cancer Institute, 33081, Aviano, Italy
| | - Alessandra Dall'Acqua
- Unit of Molecular Oncology, Centro di Riferimento Oncologico (CRO) di Aviano, IRCCS, National Cancer Institute, 33081, Aviano, Italy
| | - Chiara Gava
- Unit of Molecular Oncology, Centro di Riferimento Oncologico (CRO) di Aviano, IRCCS, National Cancer Institute, 33081, Aviano, Italy
- Medical Department, University of Udine, Udine, Italy
| | - Tiziana Perin
- Unit of Pathology, Centro di Riferimento Oncologico (CRO) di Aviano, IRCCS, National Cancer Institute, 33081, Aviano, Italy
| | - Samuele Massarut
- Unit of Breast Surgery, Centro di Riferimento Oncologico (CRO) di Aviano, IRCCS, National Cancer Institute, 33081, Aviano, Italy
| | - Cristina Marchini
- School of Biosciences and Veterinary Medicine, Biology Division, University of Camerino, via Gentile III da Varano, 62032, Camerino, Italy
| | - Gustavo Baldassarre
- Unit of Molecular Oncology, Centro di Riferimento Oncologico (CRO) di Aviano, IRCCS, National Cancer Institute, 33081, Aviano, Italy
| | - Paola Spessotto
- Unit of Molecular Oncology, Centro di Riferimento Oncologico (CRO) di Aviano, IRCCS, National Cancer Institute, 33081, Aviano, Italy
| | - Barbara Belletti
- Unit of Molecular Oncology, Centro di Riferimento Oncologico (CRO) di Aviano, IRCCS, National Cancer Institute, 33081, Aviano, Italy.
| |
Collapse
|
4
|
Kar A, Jain D, Kumar S, Rajput K, Pal S, Rana K, Kar R, Jha SK, Medatwal N, Yavvari PS, Pandey N, Mehta D, Sharma H, Bhattacharya D, Pradhan MK, Sharma RD, Srivastava A, Agrawal U, Mukhopadhyay A, Sengupta S, Patil VS, Bajaj A, Dasgupta U. A localized hydrogel-mediated chemotherapy causes immunogenic cell death via activation of ceramide-mediated unfolded protein response. SCIENCE ADVANCES 2023; 9:eadf2746. [PMID: 37390205 PMCID: PMC10313169 DOI: 10.1126/sciadv.adf2746] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 05/25/2023] [Indexed: 07/02/2023]
Abstract
Treatment of triple-negative breast cancer (TNBC) is challenging because of its "COLD" tumor immunosuppressive microenvironment (TIME). Here, we present a hydrogel-mediated localized delivery of a combination of docetaxel (DTX) and carboplatin (CPT) (called DTX-CPT-Gel therapy) that ensured enhanced anticancer effect and tumor regression on multiple murine syngeneic and xenograft tumor models. DTX-CPT-Gel therapy modulated the TIME by an increase of antitumorigenic M1 macrophages, attenuation of myeloid-derived suppressor cells, and increase of granzyme B+CD8+ T cells. DTX-CPT-Gel therapy elevated ceramide levels in tumor tissues that activated the protein kinase R (PKR)-like endoplasmic reticulum kinase (PERK)-mediated unfolded protein response (UPR). This UPR-mediated activation of apoptotic cell death led to release of damage-associated molecular patterns, thereby activating the immunogenic cell death that could even clear the metastatic tumors. This study provides a promising hydrogel-mediated platform for DTX-CPT therapy that induces tumor regression and effective immune modulation and, therefore, can be explored further for treatment of TNBC.
Collapse
Affiliation(s)
- Animesh Kar
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3 Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | - Dolly Jain
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3 Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | - Sandeep Kumar
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3 Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | - Kajal Rajput
- Amity Institute of Integrative Sciences and Health, Amity University Haryana, Panchgaon, Manesar, Gurgaon, 122413, Haryana, India
| | - Sanjay Pal
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3 Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | - Kajal Rana
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3 Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | - Raunak Kar
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Somesh K. Jha
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3 Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | - Nihal Medatwal
- Amity Institute of Integrative Sciences and Health, Amity University Haryana, Panchgaon, Manesar, Gurgaon, 122413, Haryana, India
| | - Prabhu Srinivas Yavvari
- Department of Chemistry, Indian Institute of Science Education and Research, Bhopal, 462066, Madhya Pradesh, India
| | - Nishant Pandey
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3 Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | - Devashish Mehta
- Amity Institute of Integrative Sciences and Health, Amity University Haryana, Panchgaon, Manesar, Gurgaon, 122413, Haryana, India
| | - Harsh Sharma
- Amity Institute of Integrative Sciences and Health, Amity University Haryana, Panchgaon, Manesar, Gurgaon, 122413, Haryana, India
| | - Debanjan Bhattacharya
- National Institute of Pathology, Safdarjung Hospital Campus, Ansari Nagar West, New Delhi, 110029, India
| | - Manas K. Pradhan
- Department of Chemistry, Indian Institute of Science Education and Research, Bhopal, 462066, Madhya Pradesh, India
| | - Ravi Datta Sharma
- Amity Institute of Integrative Sciences and Health, Amity University Haryana, Panchgaon, Manesar, Gurgaon, 122413, Haryana, India
| | - Aasheesh Srivastava
- Department of Chemistry, Indian Institute of Science Education and Research, Bhopal, 462066, Madhya Pradesh, India
| | - Usha Agrawal
- National Institute of Pathology, Safdarjung Hospital Campus, Ansari Nagar West, New Delhi, 110029, India
| | - Arnab Mukhopadhyay
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Sagar Sengupta
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
- National Institute of Biomedical Genomics, Kalyani, 741251, West Bengal, India
| | - Veena S. Patil
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Avinash Bajaj
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3 Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | - Ujjaini Dasgupta
- Amity Institute of Integrative Sciences and Health, Amity University Haryana, Panchgaon, Manesar, Gurgaon, 122413, Haryana, India
| |
Collapse
|