1
|
Jiang R, Li P, Meng E, Cheng X, Wu X, Wu H. Hsa_Circ_0008035 drives immune evasion of gastric cancer via promoting EXT1-mediated nuclear translocation of PKM2. Transl Oncol 2024; 48:102004. [PMID: 39053344 DOI: 10.1016/j.tranon.2024.102004] [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: 03/30/2024] [Revised: 05/15/2024] [Accepted: 05/17/2024] [Indexed: 07/27/2024] Open
Abstract
Circular RNAs (circRNAs) have been reported to be associated with the malignant phenotypes of cancer. However, the role and underlying mechanism of hsa_Circ_0008035 in colorectal cancer (CRC) remains unclear. In this study, we elucidated the pivotal role of hsa_circ_0008035 in gastric cancer progression and immune evasion. Elevated hsa_circ_0008035 levels in gastric cancer patient serum correlated positively with disease advancement, including tumor stages and lymph node metastasis. Functional analyses revealed a negative association between hsa_circ_0008035 and CD8+ T cell number and function. Mechanistically, hsa_circ_0008035 encoded the novel protein EXT1-219aa, suppressing EXT1 phosphorylation and expression. Additionally, hsa_circ_0008035 regulated pyruvate metabolism by influencing the nucleus localization of PKM2. The identified EXT1/PKM2 axis further underscored the intricate regulatory mechanisms orchestrated by hsa_circ_0008035 in gastric cancer, offering potential diagnostic and therapeutic implications in the ongoing pursuit of targeted therapies for gastric cancer patients.
Collapse
Affiliation(s)
- Rongqi Jiang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, Jiangsu Province, PR China
| | - Ping Li
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, Jiangsu Province, PR China
| | - Enqing Meng
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, Jiangsu Province, PR China
| | - Xu Cheng
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, Jiangsu Province, PR China
| | - Xinyi Wu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, Jiangsu Province, PR China
| | - Hao Wu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, Jiangsu Province, PR China.
| |
Collapse
|
2
|
Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2021-2022. MASS SPECTROMETRY REVIEWS 2024. [PMID: 38925550 DOI: 10.1002/mas.21873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/05/2024] [Accepted: 02/12/2024] [Indexed: 06/28/2024]
Abstract
The use of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry for the analysis of carbohydrates and glycoconjugates is a well-established technique and this review is the 12th update of the original article published in 1999 and brings coverage of the literature to the end of 2022. As with previous review, this review also includes a few papers that describe methods appropriate to analysis by MALDI, such as sample preparation, even though the ionization method is not MALDI. The review follows the same format as previous reviews. It is divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of computer software for structural identification. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other general areas such as medicine, industrial processes, natural products and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. MALDI is still an ideal technique for carbohydrate analysis, particularly in its ability to produce single ions from each analyte and advancements in the technique and range of applications show little sign of diminishing.
Collapse
|
3
|
Dubois M, Boulghobra D, Rochebloine G, Pallot F, Yehya M, Bornard I, Gayrard S, Coste F, Walther G, Meyer G, Gaillard JC, Armengaud J, Alpha-Bazin B, Reboul C. Hyperglycemia triggers RyR2-dependent alterations of mitochondrial calcium homeostasis in response to cardiac ischemia-reperfusion: Key role of DRP1 activation. Redox Biol 2024; 70:103044. [PMID: 38266577 PMCID: PMC10835010 DOI: 10.1016/j.redox.2024.103044] [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: 11/21/2023] [Revised: 01/04/2024] [Accepted: 01/14/2024] [Indexed: 01/26/2024] Open
Abstract
Hyperglycemia increases the heart sensitivity to ischemia-reperfusion (IR), but the underlying cellular mechanisms remain unclear. Mitochondrial dynamics (the processes that govern mitochondrial morphology and their interactions with other organelles, such as the reticulum), has emerged as a key factor in the heart vulnerability to IR. However, it is unknown whether mitochondrial dynamics contributes to hyperglycemia deleterious effect during IR. We hypothesized that (i) the higher heart vulnerability to IR in hyperglycemic conditions could be explained by hyperglycemia effect on the complex interplay between mitochondrial dynamics, Ca2+ homeostasis, and reactive oxygen species (ROS) production; and (ii) the activation of DRP1, a key regulator of mitochondrial dynamics, could play a central role. Using transmission electron microscopy and proteomic analysis, we showed that the interactions between sarcoplasmic reticulum and mitochondria and mitochondrial fission were increased during IR in isolated rat hearts perfused with a hyperglycemic buffer compared with hearts perfused with a normoglycemic buffer. In isolated mitochondria and cardiomyocytes, hyperglycemia increased mitochondrial ROS production and Ca2+ uptake. This was associated with higher RyR2 instability. These results could contribute to explain the early mPTP activation in mitochondria from isolated hearts perfused with a hyperglycemic buffer and in hearts from streptozotocin-treated rats (to increase the blood glucose). DRP1 inhibition by Mdivi-1 during the hyperglycemic phase and before IR induction, normalized Ca2+ homeostasis, ROS production, mPTP activation, and reduced the heart sensitivity to IR in streptozotocin-treated rats. In conclusion, hyperglycemia-dependent DRP1 activation results in higher reticulum-mitochondria calcium exchange that contribute to the higher heart vulnerability to IR.
Collapse
Affiliation(s)
- Mathilde Dubois
- LAPEC UPR-4278, Avignon Université, F-84000, Avignon, France
| | | | | | - Florian Pallot
- LAPEC UPR-4278, Avignon Université, F-84000, Avignon, France
| | - Marc Yehya
- LAPEC UPR-4278, Avignon Université, F-84000, Avignon, France
| | - Isabelle Bornard
- UR407 INRAE Pathologie Végétale, INRAE, 84140, Montfavet, France
| | | | - Florence Coste
- LAPEC UPR-4278, Avignon Université, F-84000, Avignon, France
| | | | - Gregory Meyer
- LAPEC UPR-4278, Avignon Université, F-84000, Avignon, France
| | - Jean-Charles Gaillard
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200, Bagnols-sur-Cèze, France
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200, Bagnols-sur-Cèze, France
| | - Béatrice Alpha-Bazin
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200, Bagnols-sur-Cèze, France
| | - Cyril Reboul
- LAPEC UPR-4278, Avignon Université, F-84000, Avignon, France.
| |
Collapse
|
4
|
Ahmadzada T, Vijayan A, Vafaee F, Azimi A, Reid G, Clarke S, Kao S, Grau GE, Hosseini-Beheshti E. Small and Large Extracellular Vesicles Derived from Pleural Mesothelioma Cell Lines Offer Biomarker Potential. Cancers (Basel) 2023; 15:cancers15082364. [PMID: 37190292 DOI: 10.3390/cancers15082364] [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: 02/02/2023] [Revised: 03/21/2023] [Accepted: 03/27/2023] [Indexed: 05/17/2023] Open
Abstract
Pleural mesothelioma, previously known as malignant pleural mesothelioma, is an aggressive and fatal cancer of the pleura, with one of the poorest survival rates. Pleural mesothelioma is in urgent clinical need for biomarkers to aid early diagnosis, improve prognostication, and stratify patients for treatment. Extracellular vesicles (EVs) have great potential as biomarkers; however, there are limited studies to date on their role in pleural mesothelioma. We conducted a comprehensive proteomic analysis on different EV populations derived from five pleural mesothelioma cell lines and an immortalized control cell line. We characterized three subtypes of EVs (10 K, 18 K, and 100 K), and identified a total of 4054 unique proteins. Major differences were found in the cargo between the three EV subtypes. We show that 10 K EVs were enriched in mitochondrial components and metabolic processes, while 18 K and 100 K EVs were enriched in endoplasmic reticulum stress. We found 46 new cancer-associated proteins for pleural mesothelioma, and the presence of mesothelin and PD-L1/PD-L2 enriched in 100 K and 10 K EV, respectively. We demonstrate that different EV populations derived from pleural mesothelioma cells have unique cancer-specific proteomes and carry oncogenic cargo, which could offer a novel means to extract biomarkers of interest for pleural mesothelioma from liquid biopsies.
Collapse
Affiliation(s)
- Tamkin Ahmadzada
- School of Medical Sciences, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Abhishek Vijayan
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia
| | - Fatemeh Vafaee
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia
- UNSW Data Science Hub, University of New South Wales, Sydney, NSW 2052, Australia
| | - Ali Azimi
- Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia
- Department of Dermatology, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Glen Reid
- Department of Pathology, University of Otago, Dunedin 9016, New Zealand
| | - Stephen Clarke
- School of Medical Sciences, The University of Sydney, Camperdown, NSW 2006, Australia
- Department of Medical Oncology, Royal North Shore Hospital, Sydney, NSW 2065, Australia
| | - Steven Kao
- School of Medical Sciences, The University of Sydney, Camperdown, NSW 2006, Australia
- Department of Medical Oncology, Chris O'Brien Lifehouse, Sydney, NSW 2050, Australia
- Asbestos Diseases Research Institute, Sydney, NSW 2139, Australia
| | - Georges E Grau
- School of Medical Sciences, The University of Sydney, Camperdown, NSW 2006, Australia
- The Sydney Nano Institute, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Elham Hosseini-Beheshti
- School of Medical Sciences, The University of Sydney, Camperdown, NSW 2006, Australia
- The Sydney Nano Institute, The University of Sydney, Camperdown, NSW 2006, Australia
| |
Collapse
|
5
|
Han P, Yu Y, Zhang L, Ruan Z. Citrus peel ameliorates mucus barrier damage in HFD-fed mice. J Nutr Biochem 2023; 112:109206. [PMID: 36370925 DOI: 10.1016/j.jnutbio.2022.109206] [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: 02/24/2022] [Revised: 09/17/2022] [Accepted: 11/03/2022] [Indexed: 11/10/2022]
Abstract
Citrus peel is rich in bioactive components, especially polyphenols, which are considered to have great potential in the prevention of intestinal diseases. The intestinal mucus barrier is the first defense against the invasion of foreign substances. In this study, we aimed to explore the possibility and mechanism of citrus peel in alleviating the mucus barrier damage in high-fat-diet (HFD) mice. We found that citrus peel powder (CPP) supplementation effectively reduced body weight, fat weight, intestinal permeability, hyperlipidemia, and systemic inflammation in HFD-fed mice. In particular, CPP increased the number of goblet cells, the protein expression of Mucin-2 (Muc2), and the thickness of the mucus layer, thereby strengthening the colonic mucus barrier function. Moreover, CPP supplementation also reduced the expression of endoplasmic reticulum stress (ERS) proteins (GRP78 and CHOP) and increased the expression of T-synthase (O-glycosylation rate-limiting enzyme) and its chaperone protein (Cosmc) in the colon of HFD-fed mice, which suggested that CPP could improve the abnormal protein folding and O-glycosylation of Muc2 during processing and modification. In summary, our study indicates that CPP plays an effective role in relieving mucus barrier damage by improving the production and properties of Muc2, providing new perspectives on the development of CPP as a dietary supplement for strengthening the intestinal barrier.
Collapse
Affiliation(s)
- Peiheng Han
- State Key Laboratory of Food Science and Technology, Institute of Nutrition and School of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, P R China
| | - Yujuan Yu
- State Key Laboratory of Food Science and Technology, Institute of Nutrition and School of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, P R China
| | - Li Zhang
- State Key Laboratory of Food Science and Technology, Institute of Nutrition and School of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, P R China.
| | - Zheng Ruan
- State Key Laboratory of Food Science and Technology, Institute of Nutrition and School of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, P R China
| |
Collapse
|
6
|
Guadagno NA, Progida C. Probing the ER-Focal Adhesion Link During Cell Migration. Methods Mol Biol 2023; 2608:39-50. [PMID: 36653700 DOI: 10.1007/978-1-0716-2887-4_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Focal adhesions (FAs) are contact points of the cell with the extracellular matrix (ECM) and play a major role in several cellular functions including migration, proliferation, differentiation, and growth. During cell migration, FAs are continuously assembled and disassembled. It is well established that FA dynamics are regulated by the cytoskeleton, motor proteins, small GTPases, and specific kinases and phosphatases. However, more recently, the establishment of contacts between FAs and the endoplasmic reticulum (ER) has been shown to be another factor implicated in the regulation of FA dynamics. The transport of ER tubules along microtubules to contact FAs is indeed crucial to support FA growth. Alteration of such ER-FA contacts affects FA growth, dynamics, and thus cell migration. Here, we present a protocol for live-cell imaging and analysis of ER-FA contact points during cell migration. Our analysis pipeline includes two examples showing physiological conditions and disruption of ER-FA contacts upon nocodazole treatment. The described method can be adapted to different cell lines.
Collapse
Affiliation(s)
| | - Cinzia Progida
- Department of Biosciences, University of Oslo, Oslo, Norway.
| |
Collapse
|
7
|
Impact of Hypermannosylation on the Structure and Functionality of the ER and the Golgi Complex. Biomedicines 2023; 11:biomedicines11010146. [PMID: 36672654 PMCID: PMC9856158 DOI: 10.3390/biomedicines11010146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/20/2022] [Accepted: 12/29/2022] [Indexed: 01/10/2023] Open
Abstract
Proteins of the secretory pathway undergo glycosylation in the endoplasmic reticulum (ER) and the Golgi apparatus. Altered protein glycosylation can manifest in serious, sometimes fatal malfunctions. We recently showed that mutations in GDP-mannose pyrophosphorylase A (GMPPA) can cause a syndrome characterized by alacrima, achalasia, mental retardation, and myopathic alterations (AAMR syndrome). GMPPA acts as a feedback inhibitor of GDP-mannose pyrophosphorylase B (GMPPB), which provides GDP-mannose as a substrate for protein glycosylation. Loss of GMPPA thus enhances the incorporation of mannose into glycochains of various proteins, including α-dystroglycan (α-DG), a protein that links the extracellular matrix with the cytoskeleton. Here, we further characterized the consequences of loss of GMPPA for the secretory pathway. This includes a fragmentation of the Golgi apparatus, which comes along with a regulation of the abundance of several ER- and Golgi-resident proteins. We further show that the activity of the Golgi-associated endoprotease furin is reduced. Moreover, the fraction of α-DG, which is retained in the ER, is increased. Notably, WT cells cultured at a high mannose concentration display similar changes with increased retention of α-DG, altered structure of the Golgi apparatus, and a decrease in furin activity. In summary, our data underline the importance of a balanced mannose homeostasis for the secretory pathway.
Collapse
|
8
|
Zhang Y, Zhang M, Xie Z, Ding Y, Huang J, Yao J, Lv Y, Zuo J. Research Progress and Direction of Novel Organelle-Migrasomes. Cancers (Basel) 2022; 15:cancers15010134. [PMID: 36612129 PMCID: PMC9817827 DOI: 10.3390/cancers15010134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/17/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
Migrasomes are organelles that are similar in structure to pomegranates, up to 3 μm in diameter, and contain small vesicles with a diameter of 50-100 nm. These membranous organelles grow at the intersections or tips of retracting fibers at the back of migrating cells. The process by which cells release migrasomes and their contents outside the cell is called migracytosis. The signal molecules are packaged in the migrasomes and released to the designated location by migrasomes to activate the surrounding cells. Finally, the migrasomes complete the entire process of information transmission. In this sense, migrasomes integrate time, space, and specific chemical information, which are essential for regulating physiological processes such as embryonic development and tumor invasion and migration. In this review, the current research progress of migrasomes, including the discovery of migrasomes and migracytosis, the structure of migrasomes, and the distribution and functions of migrasomes is discussed. The migratory marker protein TSPAN4 is highly expressed in various cancers and is associated with cancer invasion and migration. Therefore, there is still much research space for the pathogenesis of migratory bodies and cancer. This review also makes bold predictions and prospects for the research directions of the combination of migrasomes and clinical applications.
Collapse
Affiliation(s)
- Yu Zhang
- The Laboratory of Translational Medicine, Hengyang Medical School, University of South China, 28 Changsheng Road, Hengyang 421001, China
| | - Minghui Zhang
- The Laboratory of Translational Medicine, Hengyang Medical School, University of South China, 28 Changsheng Road, Hengyang 421001, China
| | - Zhuoyi Xie
- The Laboratory of Translational Medicine, Hengyang Medical School, University of South China, 28 Changsheng Road, Hengyang 421001, China
| | - Yubo Ding
- Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang 421002, China
| | - Jialu Huang
- The Laboratory of Translational Medicine, Hengyang Medical School, University of South China, 28 Changsheng Road, Hengyang 421001, China
| | - Jingwei Yao
- Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang 421002, China
| | - Yufan Lv
- Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang 421002, China
| | - Jianhong Zuo
- The Laboratory of Translational Medicine, Hengyang Medical School, University of South China, 28 Changsheng Road, Hengyang 421001, China
- Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang 421002, China
- Clinical Laboratory, The Third Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421900, China
- Correspondence:
| |
Collapse
|
9
|
Physiology and Pathophysiology of Heparan Sulfate in Animal Models: Its Biosynthesis and Degradation. Int J Mol Sci 2022; 23:ijms23041963. [PMID: 35216081 PMCID: PMC8876164 DOI: 10.3390/ijms23041963] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/05/2022] [Accepted: 02/08/2022] [Indexed: 12/17/2022] Open
Abstract
Heparan sulfate (HS) is a type of glycosaminoglycan that plays a key role in a variety of biological functions in neurology, skeletal development, immunology, and tumor metastasis. Biosynthesis of HS is initiated by a link of xylose to Ser residue of HS proteoglycans, followed by the formation of a linker tetrasaccharide. Then, an extension reaction of HS disaccharide occurs through polymerization of many repetitive units consisting of iduronic acid and N-acetylglucosamine. Subsequently, several modification reactions take place to complete the maturation of HS. The sulfation positions of N-, 2-O-, 6-O-, and 3-O- are all mediated by specific enzymes that may have multiple isozymes. C5-epimerization is facilitated by the epimerase enzyme that converts glucuronic acid to iduronic acid. Once these enzymatic reactions have been completed, the desulfation reaction further modifies HS. Apart from HS biosynthesis, the degradation of HS is largely mediated by the lysosome, an intracellular organelle with acidic pH. Mucopolysaccharidosis is a genetic disorder characterized by an accumulation of glycosaminoglycans in the body associated with neuronal, skeletal, and visceral disorders. Genetically modified animal models have significantly contributed to the understanding of the in vivo role of these enzymes. Their role and potential link to diseases are also discussed.
Collapse
|
10
|
Garcia-Pardo ME, Simpson JC, O'Sullivan NC. A novel automated image analysis pipeline for quantifying morphological changes to the endoplasmic reticulum in cultured human cells. BMC Bioinformatics 2021; 22:427. [PMID: 34496765 PMCID: PMC8425006 DOI: 10.1186/s12859-021-04334-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/24/2021] [Indexed: 11/10/2022] Open
Abstract
Background In mammalian cells the endoplasmic reticulum (ER) comprises a highly complex reticular morphology that is spread throughout the cytoplasm. This organelle is of particular interest to biologists, as its dysfunction is associated with numerous diseases, which often manifest themselves as changes to the structure and organisation of the reticular network. Due to its complex morphology, image analysis methods to quantitatively describe this organelle, and importantly any changes to it, are lacking. Results In this work we detail a methodological approach that utilises automated high-content screening microscopy to capture images of cells fluorescently-labelled for various ER markers, followed by their quantitative analysis. We propose that two key metrics, namely the area of dense ER and the area of polygonal regions in between the reticular elements, together provide a basis for measuring the quantities of rough and smooth ER, respectively. We demonstrate that a number of different pharmacological perturbations to the ER can be quantitatively measured and compared in our automated image analysis pipeline. Furthermore, we show that this method can be implemented in both commercial and open-access image analysis software with comparable results. Conclusions We propose that this method has the potential to be applied in the context of large-scale genetic and chemical perturbations to assess the organisation of the ER in adherent cell cultures. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04334-x.
Collapse
Affiliation(s)
- M Elena Garcia-Pardo
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Jeremy C Simpson
- Cell Screening Laboratory, UCD School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
| | - Niamh C O'Sullivan
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin 4, Ireland.
| |
Collapse
|