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Zhao K, Ebrahimie E, Mohammadi-Dehcheshmeh M, Lewsey MG, Zheng L, Hoogenraad NJ. Transcriptomic signature of cancer cachexia by integration of machine learning, literature mining and meta-analysis. Comput Biol Med 2024; 172:108233. [PMID: 38452471 DOI: 10.1016/j.compbiomed.2024.108233] [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: 09/10/2023] [Revised: 01/23/2024] [Accepted: 02/25/2024] [Indexed: 03/09/2024]
Abstract
BACKGROUND Cancer cachexia is a severe metabolic syndrome marked by skeletal muscle atrophy. A successful clinical intervention for cancer cachexia is currently lacking. The study of cachexia mechanisms is largely based on preclinical animal models and the availability of high-throughput transcriptomic datasets of cachectic mouse muscles is increasing through the extensive use of next generation sequencing technologies. METHODS Cachectic mouse muscle transcriptomic datasets of ten different studies were combined and mined by seven attribute weighting models, which analysed both categorical variables and numerical variables. The transcriptomic signature of cancer cachexia was identified by attribute weighting algorithms and was used to evaluate the performance of eleven pattern discovery models. The signature was employed to find the best combination of drugs (drug repurposing) for developing cancer cachexia treatment strategies, as well as to evaluate currently used cachexia drugs by literature mining. RESULTS Attribute weighting algorithms ranked 26 genes as the transcriptomic signature of muscle from mice with cancer cachexia. Deep Learning and Random Forest models performed better in differentiating cancer cachexia cases based on muscle transcriptomic data. Literature mining revealed that a combination of melatonin and infliximab has negative interactions with 2 key genes (Rorc and Fbxo32) upregulated in the transcriptomic signature of cancer cachexia in muscle. CONCLUSIONS The integration of machine learning, meta-analysis and literature mining was found to be an efficient approach to identifying a robust transcriptomic signature for cancer cachexia, with implications for improving clinical diagnosis and management of this condition.
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Affiliation(s)
- Kening Zhao
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China; La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
| | - Esmaeil Ebrahimie
- Genomics Research Platform, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC, 3086, Australia; School of Animal and Veterinary Science, The University of Adelaide, Adelaide, SA 5371, Australia; School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Manijeh Mohammadi-Dehcheshmeh
- Genomics Research Platform, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC, 3086, Australia; School of Animal and Veterinary Science, The University of Adelaide, Adelaide, SA 5371, Australia.
| | - Mathew G Lewsey
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia; La Trobe Institute for Sustainable Agriculture and Food, Department of Plant, Animal and Soil Sciences, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia; Australian Research Council Centre of Excellence in Plants for Space, AgriBio Building, La Trobe University, Bundoora, VIC, 3086, Australia.
| | - Lei Zheng
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Nick J Hoogenraad
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia; Tumour Targeting Laboratory, Olivia Newton-John Cancer Research Institute, School of Cancer Medicine, La Trobe University, Melbourne, VIC, 3084, Australia.
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2
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Govic A, Nasser H, Levay EA, Zelko M, Ebrahimie E, Mohammadi Dehcheshmeh M, Kent S, Penman J, Hazi A. Long-Term Calorie Restriction Alters Anxiety-like Behaviour and the Brain and Adrenal Gland Transcriptomes of the Ageing Male Rat. Nutrients 2022; 14:nu14214670. [PMID: 36364936 PMCID: PMC9654051 DOI: 10.3390/nu14214670] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/28/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Further examination of the molecular regulators of long-term calorie restriction (CR), reported to have an anxiolytic effect, may highlight novel therapeutic targets for anxiety disorders. Here, adult male Hooded Wistar rats were exposed to a 25% CR whilst anxiety-like behaviour was assessed at 6-, 12-, and 18-months of age via the elevated plus maze, open field, and acoustic startle tests. Next-generation sequencing was then used to measure transcriptome-wide gene expression in the hypothalamus, amygdala, pituitary, and adrenal glands. Results showed an anxiolytic behavioural profile across early, middle, and late adulthood by CR, with the strongest effects noted at 6-months. Transcriptomic analysis by seven attribute weighting algorithms, including Info Gain Ratio, Rule, Chi Squared, Gini Index, Uncertainty, Relief, and Info Gain, led to the development of a signature of long-term CR, independent of region. Complement C1q A chain (C1qa), an extracellular protein, expression was significantly decreased by CR in most regions examined. Furthermore, text mining highlighted the positive involvement of C1qa in anxiety, depression, neurodegeneration, stress, and ageing, collectively identifying a suitable biomarker candidate for CR. Overall, the current study identified anxiety-related phenotypic changes and a novel transcriptome signature of long-term CR, indicating potential therapeutic targets for anxiety, depression, and neurodegeneration.
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Affiliation(s)
- Antonina Govic
- School of Psychology and Public Health, La Trobe University, Melbourne, VIC 3010, Australia
- Epigenes Australia Pty Ltd., Melbourne, VIC 3010, Australia
- Correspondence: or ; Tel.: +61-3-9780-9996
| | - Helen Nasser
- School of Psychology and Public Health, La Trobe University, Melbourne, VIC 3010, Australia
- Epigenes Australia Pty Ltd., Melbourne, VIC 3010, Australia
| | - Elizabeth A. Levay
- School of Psychology and Public Health, La Trobe University, Melbourne, VIC 3010, Australia
- Epigenes Australia Pty Ltd., Melbourne, VIC 3010, Australia
| | - Matt Zelko
- School of Psychology and Public Health, La Trobe University, Melbourne, VIC 3010, Australia
- Epigenes Australia Pty Ltd., Melbourne, VIC 3010, Australia
| | - Esmaeil Ebrahimie
- Genomics Research Platform, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC 3000, Australia
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, SA 5371, Australia
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Manijeh Mohammadi Dehcheshmeh
- Genomics Research Platform, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC 3000, Australia
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, SA 5371, Australia
| | - Stephen Kent
- School of Psychology and Public Health, La Trobe University, Melbourne, VIC 3010, Australia
| | - Jim Penman
- Epigenes Australia Pty Ltd., Melbourne, VIC 3010, Australia
| | - Agnes Hazi
- School of Psychology and Public Health, La Trobe University, Melbourne, VIC 3010, Australia
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Ogawa E, Nomura H, Nakamuta M, Furusyo N, Kajiwara E, Dohmen K, Kawano A, Ooho A, Azuma K, Takahashi K, Satoh T, Koyanagi T, Ichiki Y, Kuniyoshi M, Yanagita K, Amagase H, Morita C, Sugimoto R, Kato M, Shimoda S, Hayashi J. Incidence of Hepatocellular Carcinoma after Treatment with Sofosbuvir-Based or Sofosbuvir-Free Regimens in Patients with Chronic Hepatitis C. Cancers (Basel) 2020; 12:cancers12092602. [PMID: 32933027 PMCID: PMC7563479 DOI: 10.3390/cancers12092602] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/03/2020] [Accepted: 09/09/2020] [Indexed: 01/17/2023] Open
Abstract
Simple Summary The development of hepatocellular carcinoma (HCC) has not been well-controlled, even after the elimination of hepatitis C virus (HCV), especially for those with cirrhosis or of high-age. Fibrosis-related biomarkers have been recognized as useful predictors for the development of HCC; however, there are few analyses of the HCC incidence for the various regimens with direct-acting antivirals (DAA). We found that DAA treatment with sofosbuvir, an oral nucleotide analogue inhibitor of HCV NS5B polymerase, was not associated with the development of de novo HCC within five years by propensity score matched analysis. Moreover, the distribution of the early stage of HCC (the Barcelona Clinic Liver Cancer stage 0/A) was similar for all treatment regimens, irrespective of the use of sofosbuvir. Abstract Advanced fibrosis/cirrhosis and related biomarkers have been recognized as useful predictors of the development of hepatocellular carcinoma (HCC) by patients with chronic hepatitis C (CHC) following hepatitis C virus (HCV) cure by direct-acting antivirals (DAAs). However, it remains unclear if DAAs themselves have an influence on or facilitate the development of HCC. This multicenter cohort study included CHC patients without a history of HCC who achieved HCV elimination by DAAs. Cohorts of 835 patients treated with a sofosbuvir (SOF)-based regimen and 835 treated with a SOF-free regimen were matched 1:1 by propensity scoring with nine variables to evaluate differences in HCC incidence. The median observation period was 3.5 years. Sixty-nine cases of HCC were found during 5483.9 person-years (PY) over the entire follow-up period. The annual incidence was similar for both groups (SOF-based 1.25 and SOF-free 1.27 per 100 PY, respectively: adjusted hazard ratio (HR) 1.26, 95% confidence interval (CI) 0.75–2.12, p = 0.39). However, the annual incidence within the first two years was higher for patients treated with SOF than for those without, but did not reach significance (1.50 and 0.97 per 100 PY incidence rates, respectively: adjusted HR 2.05, 95% CI 0.98–4.25, p = 0.06). In summary, DAA treatment with SOF was not associated with an increase in the development of de novo HCC.
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Affiliation(s)
- Eiichi Ogawa
- Department of General Internal Medicine, Kyushu University Hospital, Fukuoka 8128582, Japan;
- Correspondence:
| | - Hideyuki Nomura
- The Center for Liver Disease, Shin-Kokura Hospital, Kitakyushu 8038505, Japan;
- Department of Internal Medicine, Haradoi Hospital, Fukuoka 8138588, Japan
| | - Makoto Nakamuta
- Department of Gastroenterology, National Hospital Organization Kyushu Medical Center, Fukuoka 8108563, Japan;
| | - Norihiro Furusyo
- Department of General Internal Medicine, Kyushu University Hospital, Fukuoka 8128582, Japan;
- General Internal Medicine, Taihaku Avenue Clinic, Fukuoka 8120039, Japan
| | | | - Kazufumi Dohmen
- Department of Internal Medicine, Chihaya Hospital, Fukuoka 8138501, Japan;
| | - Akira Kawano
- Department of Medicine, Kitakyushu Municipal Medical Center, Kitakyushu 8028561, Japan;
| | - Aritsune Ooho
- Department of Hepatology, Steel Memorial Yawata Hospital, Kitakyushu 8058508, Japan;
| | - Koichi Azuma
- Department of Medicine, Kyushu Central Hospital, Fukuoka 8158588, Japan;
| | | | - Takeaki Satoh
- Center for Liver Disease, National Hospital Organization Kokura Medical Center, Kitakyushu 8028533, Japan;
| | - Toshimasa Koyanagi
- Department of Medicine, Fukuoka City Hospital, Higashi-ku, Fukuoka 8120046, Japan;
| | - Yasunori Ichiki
- Department of Internal Medicine, JCHO Kyushu Hospital, Kitakyushu 8068501, Japan;
| | - Masami Kuniyoshi
- Department of Gastroenterology, Kyushu Rosai Hospital, Kitakyushu 8000296, Japan;
| | - Kimihiko Yanagita
- Department of Internal Medicine, Saiseikai Karatsu Hospital, Karatsu 8470852, Japan;
| | | | - Chie Morita
- Department of Internal Medicine, Kyushu Railway Memorial Hospital, Kitakyushu 8000031, Japan;
| | - Rie Sugimoto
- Department of Gastroenterology, Kyushu Cancer Center, Fukuoka 8111395, Japan;
| | - Masaki Kato
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 8128582, Japan;
| | - Shinji Shimoda
- Department of Medicine and Biosystemic Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 8128582, Japan;
| | - Jun Hayashi
- Kyushu General Internal Medicine Center, Haradoi Hospital, Fukuoka 8138588, Japan;
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Alanazi IO, AlYahya SA, Ebrahimie E, Mohammadi-Dehcheshmeh M. Computational systems biology analysis of biomarkers in lung cancer; unravelling genomic regions which frequently encode biomarkers, enriched pathways, and new candidates. Gene 2018; 659:29-36. [DOI: 10.1016/j.gene.2018.03.038] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 02/07/2018] [Accepted: 03/15/2018] [Indexed: 12/15/2022]
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5
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Fisher SA, Tam RY, Fokina A, Mahmoodi MM, Distefano MD, Shoichet MS. Photo-immobilized EGF chemical gradients differentially impact breast cancer cell invasion and drug response in defined 3D hydrogels. Biomaterials 2018; 178:751-766. [PMID: 29452913 DOI: 10.1016/j.biomaterials.2018.01.032] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/15/2017] [Accepted: 01/20/2018] [Indexed: 01/08/2023]
Abstract
Breast cancer cell invasion is influenced by growth factor concentration gradients in the tumor microenvironment. However, studying the influence of growth factor gradients on breast cancer cell invasion is challenging due to both the complexities of in vivo models and the difficulties in recapitulating the tumor microenvironment with defined gradients using in vitro models. A defined hyaluronic acid (HA)-based hydrogel crosslinked with matrix metalloproteinase (MMP) cleavable peptides and modified with multiphoton labile nitrodibenzofuran (NDBF) was synthesized to photochemically immobilize epidermal growth factor (EGF) gradients. We demonstrate that EGF gradients can differentially influence breast cancer cell invasion and drug response in cell lines with different EGF receptor (EGFR) expression levels. Photopatterned EGF gradients increase the invasion of moderate EGFR expressing MDA-MB-231 cells, reduce invasion of high EGFR expressing MDA-MB-468 cells, and have no effect on invasion of low EGFR-expressing MCF-7 cells. We evaluate MDA-MB-231 and MDA-MB-468 cell response to the clinically tested EGFR inhibitor, cetuximab. Interestingly, the cellular response to cetuximab is completely different on the EGF gradient hydrogels: cetuximab decreases MDA-MB-231 cell invasion but increases MDA-MB-468 cell invasion and cell number, thus demonstrating the importance of including cell-microenvironment interactions when evaluating drug targets.
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Affiliation(s)
- Stephanie A Fisher
- The Donnelly Centre for Cellular and Biomolecular Research, Department of Chemical Engineering and Applied Chemistry, Institute of Biomaterials and Biomedical Engineering, University of Toronto, 160 College Street, Toronto Ontario, M5S 3E1, Canada
| | - Roger Y Tam
- The Donnelly Centre for Cellular and Biomolecular Research, Department of Chemical Engineering and Applied Chemistry, Institute of Biomaterials and Biomedical Engineering, University of Toronto, 160 College Street, Toronto Ontario, M5S 3E1, Canada
| | - Ana Fokina
- The Donnelly Centre for Cellular and Biomolecular Research, Department of Chemical Engineering and Applied Chemistry, Institute of Biomaterials and Biomedical Engineering, University of Toronto, 160 College Street, Toronto Ontario, M5S 3E1, Canada
| | - M Mohsen Mahmoodi
- Department of Chemistry, University of Minnesota, Minneapolis MN, 55455, USA
| | - Mark D Distefano
- Department of Chemistry, University of Minnesota, Minneapolis MN, 55455, USA
| | - Molly S Shoichet
- The Donnelly Centre for Cellular and Biomolecular Research, Department of Chemical Engineering and Applied Chemistry, Institute of Biomaterials and Biomedical Engineering, University of Toronto, 160 College Street, Toronto Ontario, M5S 3E1, Canada.
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6
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Zhang Y, Luo Q, Zheng W, Wang Z, Lin Y, Zhang E, Lü S, Xiang J, Zhao Y, Wang F. Luminescent cyclometallated platinum(ii) complexes: highly promising EGFR/DNA probes and dual-targeting anticancer agents. Inorg Chem Front 2018. [DOI: 10.1039/c7qi00346c] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cyclometallated platinum complexes bearing 4-anilinoquinazolines exhibit high potential as luminescent probes for EGFR/DNA in living cells and dual-targeting anticancer agents.
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7
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Qian H, Tao Y, Jiang L, Wang Y, Lan T, Wu M, Pang J, Appiah-Kubi K, Chen Y, Wu Y. PKG II effectively reversed EGF-induced protein expression alterations in human gastric cancer cell lines. Cell Biol Int 2017; 42:435-442. [PMID: 29150923 DOI: 10.1002/cbin.10912] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 11/16/2017] [Indexed: 01/02/2023]
Abstract
Epidermal growth factor receptor (EGFR) plays an important role in gastric cancer (GC) progression. Our previous data demonstrated that type II cGMP-dependent protein kinase (PKG II) could block the EGF-EGFR axis as well as down-stream signaling pathways, for example, MAPK, PI3 K, and PLC in GC cells. However, the exact mechanisms of PKG II against cancer remain unclear. Therefore, the present work was to address the above question. Human GC cell line AGS was infected with adenoviral construct encoding cDNA of PKG II (Ad-PKG II) to up-regulate PKG II and then treated with 8-pCPT-cGMP. Two-dimensional electrophoresis (2-DE) was used to analyze the changes of protein expression in the cells. The results showed that 17 proteins had more than twofold changes in EGF-treated group compared with control. However, Ad-PKG II could effectively reversed the changes. Furthermore, far upstream element-binding protein 1 (FUBP1) and MarvelD3 were chosen and PKG II activation reversed EGF/EGFR-induced up-regulation of FUBP1 and downregulation of MarvelD3, respectively. MarvelD3 silence effectively abolished the inhibitory effect of PKG II on EGF-triggered migration. These data indicated that the inhibitory effect of PKG II partially was associated with MarvelD3.
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Affiliation(s)
- Hai Qian
- Medical School, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, P. R. China
| | - Yan Tao
- Medical School, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, P. R. China
| | - Lu Jiang
- Medical School, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, P. R. China
| | - Ying Wang
- Medical School, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, P. R. China
| | - Ting Lan
- Medical School, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, P. R. China
| | - Min Wu
- Medical School, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, P. R. China
| | - Ji Pang
- Medical School, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, P. R. China
| | - Kwaku Appiah-Kubi
- Department of Applied Biology, University for Development Studies, Navrongo, Ghana
| | - Yongchang Chen
- Medical School, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, P. R. China
| | - Yan Wu
- Medical School, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, P. R. China
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Ebrahimie E, Moussavi Nik SH, Newman M, Van Der Hoek M, Lardelli M. The Zebrafish Equivalent of Alzheimer's Disease-Associated PRESENILIN Isoform PS2V Regulates Inflammatory and Other Responses to Hypoxic Stress. J Alzheimers Dis 2017; 52:581-608. [PMID: 27031468 DOI: 10.3233/jad-150678] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Dominant mutations in the PRESENILIN genes PSEN1 and PSEN2 cause familial Alzheimer's disease (fAD) that usually shows onset before 65 years of age. In contrast, genetic variation at the PSEN1 and PSEN2 loci does not appear to contribute to risk for the sporadic, late onset form of the disease (sAD), leading to doubts that these genes play a role in the majority of AD cases. However, a truncated isoform of PSEN2, PS2V, is upregulated in sAD brains and is induced by hypoxia and high cholesterol intake. PS2V can increase γ-secretase activity and suppress the unfolded protein response (UPR), but detailed analysis of its function has been hindered by lack of a suitable, genetically manipulable animal model since mice and rats lack this PRESENILIN isoform. We recently showed that zebrafish possess an isoform, PS1IV, that is cognate to human PS2V. Using an antisense morpholino oligonucleotide, we can block specifically the induction of PS1IV that normally occurs under hypoxia. Here, we exploit this ability to identify gene regulatory networks that are modulated by PS1IV. When PS1IV is absent under hypoxia-like conditions, we observe changes in expression of genes controlling inflammation (particularly sAD-associated IL1B and CCR5), vascular development, the UPR, protein synthesis, calcium homeostasis, catecholamine biosynthesis, TOR signaling, and cell proliferation. Our results imply an important role for PS2V in sAD as a component of a pathological mechanism that includes hypoxia/oxidative stress and support investigation of the role of PS2V in other diseases, including schizophrenia, when these are implicated in the pathology.
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Affiliation(s)
- Esmaeil Ebrahimie
- Department of Genetics and Evolution, School of Biological Sciences, University of Adelaide, Adelaide, Australia.,School of Information Technology and Mathematical Sciences, Division of Information Technology, Engineering and the Environment, University of South Australia, Adelaide, Australia.,School of Biological Sciences, Faculty of Science and Engineering, Flinders University, Adelaide, Australia
| | - Seyyed Hani Moussavi Nik
- Department of Genetics and Evolution, School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Morgan Newman
- Department of Genetics and Evolution, School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Mark Van Der Hoek
- Centre for Cancer Biology, SA Pathology, Frome Road, Adelaide, Australia
| | - Michael Lardelli
- Department of Genetics and Evolution, School of Biological Sciences, University of Adelaide, Adelaide, Australia
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Zhang HB, Cheng SX, Tu Y, Zhang S, Hou SK, Yang Z. Protective effect of mild-induced hypothermia against moderate traumatic brain injury in rats involved in necroptotic and apoptotic pathways. Brain Inj 2017; 31:406-415. [PMID: 28140659 DOI: 10.1080/02699052.2016.1225984] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
AIM To investigate the protective effect of hypothermia (HT) on brain injury in moderate traumatic brain injury (TBI) rat models and the potential mechanisms, especially the involvement of RIPK1 in apoptosis and necroptosis. METHODS Adult Sprague-Dawley rats were randomized to four groups: sham+normothermia (sham+NT), sham+hypothermia (sham+HT), moderate TBI+normothermia (TBI+NT) and moderate TBI+hypothermia (TBI+HT). The sham+HT and TBI+HT groups were submitted to 32°C for 6 hours. The regional cerebral blood flow (rCBF) was assessed 24 hours after TBI; 24 and 48 hours after TBI, the modified neurological severity score (mNSS) was assessed. Immediately after behavioural tests, rats were sacrificed to harvest the brain tissues. RESULTS mNSS scores were lower in the TBI+HT group compared with the TBI+NT group (p < 0.01) and cerebral blood flow was better (p < 0.01). H&E staining of the cortex and ipsilateral hippocampus showed pyknotic and irregularly shaped neurons in TBI+NT rats, which were less frequent in TBI+HT rats. The TBI+NT and TBI+HT groups showed higher TNF-α, TRAIL, FasL, FADD, caspase-3, caspase-8, PARP-1, RIPK-1 and RIPK-3 levels than the sham+NT group (all p < 0.05), but the levels of these proteins were all lower in the TBI+HT group compared with the TBI+NT group (all p < 0.01). CONCLUSION HT treatment significantly reduced RIPK-1 upregulation, which may inhibit necroptosis and apoptosis pathways after moderate TBI.
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Affiliation(s)
- Hai-Bo Zhang
- a Tianjin Key Laboratory of Neurotrauma Repair, Institute of Traumatic Brain Injury and Neuroscience of Chinese People's Armed Police Forces (PAP) , Neurosurgical and Neurological Hospital of PAP , Tianjin , PR China
| | - Shi-Xiang Cheng
- a Tianjin Key Laboratory of Neurotrauma Repair, Institute of Traumatic Brain Injury and Neuroscience of Chinese People's Armed Police Forces (PAP) , Neurosurgical and Neurological Hospital of PAP , Tianjin , PR China
| | - Yue Tu
- a Tianjin Key Laboratory of Neurotrauma Repair, Institute of Traumatic Brain Injury and Neuroscience of Chinese People's Armed Police Forces (PAP) , Neurosurgical and Neurological Hospital of PAP , Tianjin , PR China
| | - Sai Zhang
- a Tianjin Key Laboratory of Neurotrauma Repair, Institute of Traumatic Brain Injury and Neuroscience of Chinese People's Armed Police Forces (PAP) , Neurosurgical and Neurological Hospital of PAP , Tianjin , PR China
| | - Shi-Ke Hou
- a Tianjin Key Laboratory of Neurotrauma Repair, Institute of Traumatic Brain Injury and Neuroscience of Chinese People's Armed Police Forces (PAP) , Neurosurgical and Neurological Hospital of PAP , Tianjin , PR China
| | - Zhen Yang
- a Tianjin Key Laboratory of Neurotrauma Repair, Institute of Traumatic Brain Injury and Neuroscience of Chinese People's Armed Police Forces (PAP) , Neurosurgical and Neurological Hospital of PAP , Tianjin , PR China
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10
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Koch H, Wilhelm M, Ruprecht B, Beck S, Frejno M, Klaeger S, Kuster B. Phosphoproteome Profiling Reveals Molecular Mechanisms of Growth-Factor-Mediated Kinase Inhibitor Resistance in EGFR-Overexpressing Cancer Cells. J Proteome Res 2016; 15:4490-4504. [PMID: 27794612 DOI: 10.1021/acs.jproteome.6b00621] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Although substantial progress has been made regarding the use of molecularly targeted cancer therapies, resistance almost invariably develops and presents a major clinical challenge. The tumor microenvironment can rescue cancer cells from kinase inhibitors by growth-factor-mediated induction of pro-survival pathways. Here we show that epidermal growth factor receptor (EGFR) inhibition by Gefitinib is counteracted by growth factors, notably FGF2, and we assessed the global molecular consequences of this resistance at the proteome and phosphoproteome level in A431 cells. Tandem mass tag peptide labeling and quantitative mass spectrometry allowed the identification and quantification of 22 000 phosphopeptides and 8800 proteins in biological triplicates without missing values. The data show that FGF2 protects the cells from the antiproliferative effect of Gefitinib and largely prevents reprogramming of the proteome and phosphoproteome. Simultaneous EGFR/FGFR or EGFR/GSG2 (Haspin) inhibition overcomes this resistance, and the phosphoproteomic experiments further prioritized the RAS/MEK/ERK as well as the PI3K/mTOR axis for combination treatment. Consequently, the MEK inhibitor Trametinib prevented FGF2-mediated survival of EGFR inhibitor-resistant cells when used in combination with Gefitinib. Surprisingly, the PI3K/mTOR inhibitor Omipalisib reversed resistance mediated by all four growth factors tested, making it an interesting candidate for mitigating the effects of the tumor microenvironment.
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Affiliation(s)
- Heiner Koch
- Chair for Proteomics and Bioanalytics, Technical University of Munich , 85354 Freising, Germany.,German Cancer Consortium (DKTK) , 69120 Heidelberg, Germany.,German Cancer Research Center (DKFZ) , 69120 Heidelberg, Germany
| | - Mathias Wilhelm
- Chair for Proteomics and Bioanalytics, Technical University of Munich , 85354 Freising, Germany
| | - Benjamin Ruprecht
- Chair for Proteomics and Bioanalytics, Technical University of Munich , 85354 Freising, Germany.,Center for Integrated Protein Science Munich (CIPSM) , 81377 Munich, Germany
| | - Scarlet Beck
- Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry , 82152 Martinsried, Germany
| | - Martin Frejno
- Chair for Proteomics and Bioanalytics, Technical University of Munich , 85354 Freising, Germany.,Department of Oncology, University of Oxford , OX3 7DQ Oxford, United Kingdom
| | - Susan Klaeger
- Chair for Proteomics and Bioanalytics, Technical University of Munich , 85354 Freising, Germany.,German Cancer Consortium (DKTK) , 69120 Heidelberg, Germany.,German Cancer Research Center (DKFZ) , 69120 Heidelberg, Germany
| | - Bernhard Kuster
- Chair for Proteomics and Bioanalytics, Technical University of Munich , 85354 Freising, Germany.,German Cancer Consortium (DKTK) , 69120 Heidelberg, Germany.,German Cancer Research Center (DKFZ) , 69120 Heidelberg, Germany.,Center for Integrated Protein Science Munich (CIPSM) , 81377 Munich, Germany.,Bavarian Biomolecular Mass Spectrometry Center, Technische Universität München , 85354 Freising, Germany
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11
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Liu S, Cadaneanu RM, Zhang B, Huo L, Lai K, Li X, Galet C, Grogan TR, Elashoff D, Freedland SJ, Rettig M, Aronson WJ, Knudsen BS, Lewis MS, Garraway IP. Keratin 13 Is Enriched in Prostate Tubule-Initiating Cells and May Identify Primary Prostate Tumors that Metastasize to the Bone. PLoS One 2016; 11:e0163232. [PMID: 27711225 PMCID: PMC5053503 DOI: 10.1371/journal.pone.0163232] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/06/2016] [Indexed: 01/14/2023] Open
Abstract
Background Benign human prostate tubule-initiating cells (TIC) and aggressive prostate cancer display common traits, including tolerance of low androgen levels, resistance to apoptosis, and microenvironment interactions that drive epithelial budding and outgrowth. TIC can be distinguished from epithelial and stromal cells that comprise prostate tissue via cell sorting based upon Epcam, CD44, and CD49f antigenic profiles. Fetal prostate epithelial cells (FC) possess a similar antigenic profile to adult TIC and are capable of inducing tubule formation. To identify the TIC niche in human prostate tissue, differential keratin (KRT) expression was evaluated. Results Gene expression data generated from Affymetrix Gene Chip human U133 Plus 2.0 array of sorted adult and fetal epithelial cells revealed KRT13 to be significantly enriched in FC and TIC compared to basal cells (BC) and luminal cells (LC) (p<0.001). Enriched KRT13 expression was confirmed by RT-PCR and cytospin immunostaining. Immunohistochemical analysis of KRT13 expression revealed rare KRT13+ epithelia throughout prostatic ducts/acini in adult tissue specimens and differentiated tubules in 24-week recombinant grafts, In contrast, abundant KRT13 expression was observed in developing ducts/acini in fetal prostate and cord-like structures composing 8-week recombinant grafts. Immunostaining of a prostate tissue microarray revealed KRT13+ tumor foci in approximately 9% of cases, and this subset displayed significantly shorter time to recurrence (p = 0.031), metastases (p = 0.032), and decreased overall survival (p = 0.004). Diagnostic prostate needle biopsies (PNBX) from untreated patients with concurrent bone metastases (clinical stage M1) displayed KRT13+ tumor foci, as did bone metastatic foci. Conclusions The expression profile of KRT13 in benign fetal and adult prostate tissue and in recombinant grafts, as well as the frequency of KRT13 expression in primary and metastatic prostate cancer indicates that it may be a marker of a stem/progenitor-like cell state that is co-opted in aggressive tumor cells. KRT13 is enriched in benign stem-like cells that display androgen-resistance, apoptosis-resistance, and branching morphogenesis properties. Collectively our data demonstrate that KRT13 expression is associated with poor prognosis at multiple stages of disease progression and may represent an important biomarker of adverse outcome in patients with prostate cancer.
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Affiliation(s)
- Sandy Liu
- Department of Hematology-Oncology, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Radu M. Cadaneanu
- Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Baohui Zhang
- Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Lihong Huo
- Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Kevin Lai
- Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Xinmin Li
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Colette Galet
- Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Tristan R. Grogan
- Department of Medicine Statistics Core, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - David Elashoff
- Department of Medicine Statistics Core, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Stephen J. Freedland
- Urologic Section, Department of Surgery, Durham VA Medical Center, Durham, North Carolina, United States of America
| | - Matthew Rettig
- Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, California, United States of America
| | - William J. Aronson
- Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, California, United States of America
- Urology Section, Department of Surgery, Greater Los Angeles Veterans Affairs Healthcare System, Los Angeles, California, United States of America
| | - Beatrice S. Knudsen
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Michael S. Lewis
- Department of Pathology, Greater Los Angeles Veterans Affairs Health System, Los Angeles, California, United States of America
| | - Isla P. Garraway
- Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, California, United States of America
- Urology Section, Department of Surgery, Greater Los Angeles Veterans Affairs Healthcare System, Los Angeles, California, United States of America
- * E-mail:
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12
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Isolation, Characterization, Cryopreservation of Human Amniotic Stem Cells and Differentiation to Osteogenic and Adipogenic Cells. PLoS One 2016; 11:e0158281. [PMID: 27434028 PMCID: PMC4951121 DOI: 10.1371/journal.pone.0158281] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Accepted: 06/13/2016] [Indexed: 01/27/2023] Open
Abstract
Human stem cells and progenitor cells can be used to treat cancer and replace dysfunctional cells within a tissue or organ. The objective of this study was to identify the appropriate cells type in regenerative medicine and targeted therapy. As an alternative to embryonic and bone marrow stem cells, we examined human amniotic fluid stem cells (hAFSCs), one of the potential source of multipotent stem cells isolated from both cell pellet (using single-stage method), and supernatant of human amniotic fluid. Source of isolation and unique property of the cells emphasize that these cells are one of the promising new tools in therapeutic field. Double sources for isolation and availability of the left over samples in diagnostic laboratory at the same time have less legal and ethical concerns compared with embryonic stem cell studies. Cells were isolated, cultured for 18th passage for 6 months and characterized using qPCR and flow cytometry. Cells showed good proliferative ability in culture condition. The cells successfully differentiated into the adipogenic and osteogenic lineages. Based on these findings, amniotic fluid can be considered as an appropriate and convenient source of human amniotic fluid stem cells. These cells provide potential tools for therapeutic applications in the field of regenerative medicine. To get a better understanding of crosstalk between Oct4/NANOG with osteogenesis and adipogenesis, we used network analysis based on Common Targets algorithm and Common Regulators algorithm as well as subnetwork discovery based on gene set enrichment. Network analysis highlighted the possible role of MIR 302A and MIR let-7g. We demonstrated the high expression of MIR 302A and low expression of MIR let7g in hAFSCs by qPCR.
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13
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Alanazi IO, Ebrahimie E. Computational Systems Biology Approach Predicts Regulators and Targets of microRNAs and Their Genomic Hotspots in Apoptosis Process. Mol Biotechnol 2016; 58:460-79. [DOI: 10.1007/s12033-016-9938-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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14
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Treda C, Popeda M, Ksiazkiewicz M, Grzela DP, Walczak MP, Banaszczyk M, Peciak J, Stoczynska-Fidelus E, Rieske P. EGFR Activation Leads to Cell Death Independent of PI3K/AKT/mTOR in an AD293 Cell Line. PLoS One 2016; 11:e0155230. [PMID: 27153109 PMCID: PMC4859505 DOI: 10.1371/journal.pone.0155230] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 04/26/2016] [Indexed: 12/14/2022] Open
Abstract
The Epidermal Growth Factor Receptor (EGFR) and its mutations contribute in various ways to tumorigenesis and biology of human cancers. They are associated with tumor proliferation, progression, drug resistance and the process of apoptosis. There are also reports that overexpression and activation of wild-type EGFR may lead to cell apoptosis. To study this phenomenon, we overexpressed in an AD293 cell line two most frequently observed forms of the EGFR receptor: wild-type and the constitutively active mutant–EGFR variant III (EGFRvIII). Then, we compared the effect of EGF stimulation on cell viability and downstream EGFR signaling. AD293 cells overexpressing wild-type EGFR, despite a significant proliferation increase in serum supplemented medium, underwent apoptosis after EGF stimulation in serum free conditions. EGFRvIII expressing cells, however, were unaffected by either serum starvation or EGF treatment. The effect of EGF was completely neutralized by tyrosine kinase inhibitors (TKIs), indicating the specificity of this observation. Moreover, apoptosis was not prevented by inhibiting EGFR downstream proteins (PI3K, AKT and mTOR). Here we showed another EGFR function, dependent on environmental factors, which could be employed in therapy and drug design. We also proposed a new tool for EGFR inhibitor analysis.
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Affiliation(s)
- Cezary Treda
- Department of Research and Development, Celther Polska Ltd., Lodz, Poland
- * E-mail:
| | - Marta Popeda
- Department of Research and Development, Celther Polska Ltd., Lodz, Poland
| | | | - Dawid P. Grzela
- Department of Research and Development, Celther Polska Ltd., Lodz, Poland
| | - Maciej P. Walczak
- Department of Research and Development, Celther Polska Ltd., Lodz, Poland
| | - Mateusz Banaszczyk
- Department of Research and Development, Celther Polska Ltd., Lodz, Poland
- Department of Tumor Biology, Medical University of Lodz, Lodz, Poland
| | - Joanna Peciak
- Department of Research and Development, Celther Polska Ltd., Lodz, Poland
- Department of Tumor Biology, Medical University of Lodz, Lodz, Poland
| | - Ewelina Stoczynska-Fidelus
- Department of Research and Development, Celther Polska Ltd., Lodz, Poland
- Department of Tumor Biology, Medical University of Lodz, Lodz, Poland
| | - Piotr Rieske
- Department of Research and Development, Celther Polska Ltd., Lodz, Poland
- Department of Tumor Biology, Medical University of Lodz, Lodz, Poland
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15
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Mehrfarjam Z, Esmaeili F, Shabani L, Ebrahimie E. Induction of pancreatic β cell gene expression in mesenchymal stem cells. Cell Biol Int 2016; 40:486-500. [DOI: 10.1002/cbin.10567] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 11/23/2015] [Indexed: 12/13/2022]
Affiliation(s)
- Zahra Mehrfarjam
- Razi Herbal Medicines Research Center; Lorestan University of Medical Sciences; P.O. Box 681499468 Khorramabad Iran
| | - Fariba Esmaeili
- Faculty of Basic Sciences; Department of Biology; University of Isfahan; P.O. Box 8174673441 Isfahan Iran
- Research Institute of Biotechnology; Shahrekord University; P.O. Box 115 Shahrekord Iran
| | - Leila Shabani
- Research Institute of Biotechnology; Shahrekord University; P.O. Box 115 Shahrekord Iran
| | - Esmaeil Ebrahimie
- Institute of Biotechnology; Shiraz University; Shiraz Iran
- Division of Information Technology, Engineering & Environment; School of Information Technology and Mathematical Sciences; University of South Australia; Adelaide Australia
- Department of Genetics and Evolution; The University of Adelaide; Adelaide Australia
- Faculty of Science and Engineering; School of Biological Sciences; Flinders University; Adelaide Australia
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16
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Lindblad O, Chougule RA, Moharram SA, Kabir NN, Sun J, Kazi JU, Rönnstrand L. The role of HOXB2 and HOXB3 in acute myeloid leukemia. Biochem Biophys Res Commun 2015; 467:742-7. [PMID: 26482852 DOI: 10.1016/j.bbrc.2015.10.071] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 10/13/2015] [Indexed: 01/08/2023]
Abstract
Acute myeloid leukemia (AML) is a heterogeneous aggressive disease and the most common form of adult leukemia. Mutations in the type III receptor tyrosine kinase FLT3 are found in more than 30% of AML patients. Drugs against FLT3 have been developed for the treatment of AML, but they lack specificity, show poor response and lead to the development of a resistant phenotype upon treatment. Therefore, a deeper understanding of FLT3 signaling will facilitate identification of additional pharmacological targets in FLT3-driven AML. In this report, we identify HOXB2 and HOXB3 as novel regulators of oncogenic FLT3-ITD-driven AML. We show that HOXB2 and HOXB3 expression is upregulated in a group of AML patients carrying FLT3-ITD. Overexpression of HOXB2 or HOXB3 in mouse pro-B cells resulted in decreased FLT3-ITD-dependent cell proliferation as well as colony formation and increased apoptosis. Expression of HOXB2 or HOXB3 resulted in a significant decrease in FLT3-ITD-induced AKT, ERK, p38 and STAT5 phosphorylation. Our data suggest that HOXB2 and HOXB3 act as tumor suppressors in FLT3-ITD driven AML.
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Affiliation(s)
- Oscar Lindblad
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden; Lund Stem Cell Center, Department of Laboratory Medicine, Lund University, Lund, Sweden; Department of Hematology and Vascular Disorders, Skåne University Hospital, Lund, Sweden
| | - Rohit A Chougule
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden; Lund Stem Cell Center, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Sausan A Moharram
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden; Lund Stem Cell Center, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Nuzhat N Kabir
- Laboratory of Computational Biochemistry, KN Biomedical Research Institute, Barisal, Bangladesh
| | - Jianmin Sun
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden; Lund Stem Cell Center, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Julhash U Kazi
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden; Lund Stem Cell Center, Department of Laboratory Medicine, Lund University, Lund, Sweden; Laboratory of Computational Biochemistry, KN Biomedical Research Institute, Barisal, Bangladesh
| | - Lars Rönnstrand
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden; Lund Stem Cell Center, Department of Laboratory Medicine, Lund University, Lund, Sweden.
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17
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Atefi E, Joshi R, Mann JA, Tavana H. Interfacial Tension Effect on Cell Partition in Aqueous Two-Phase Systems. ACS APPLIED MATERIALS & INTERFACES 2015; 7:21305-21314. [PMID: 26356592 DOI: 10.1021/acsami.5b05757] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Aqueous two-phase systems (ATPS) provide a mild environment for the partition and separation of cells. We report a combined experimental and theoretical study on the effect of interfacial tension of polymeric ATPS on the partitioning of cells between two phases and their interface. Two-phase systems are generated using polyethylene glycol and dextran of specific properties as phase-forming polymers and culture media as the solvent component. Ultralow interfacial tensions of the solutions are precisely measured using an axisymmetric drop shape analysis method. Partition experiments show that two-phase systems with an interfacial tension of 30 μJ/m(2) result in distribution of majority of cells to the bottom dextran phase. An increase in the interfacial tension results in a distribution of cells toward the interface. An independent cancer cell spheroid formation assay confirms these observations: a drop of the dextran phase containing cancer cells is dispensed into the immersion polyethylene glycol phase to form a cell-containing drop. Only at very small interfacial tensions do cells remain within the drop to aggregate into a spheroid. We perform a thermodynamic modeling of cell partition to determine variations of free energy associated with displacement of cells in ATPS with respect to the ultralow interfacial tensions. This modeling corroborates with the experimental results and demonstrates that at the smallest interfacial tension of 30 μJ/m(2), the free energy is a minimum with cells in the bottom phase. Increasing the interfacial tension shifts the minimum energy and partition of cells toward the interfacial region of the two aqueous phases. Examining differences in the partition behavior and minimum free energy modeling of A431.H9 cancer cells and mouse embryonic stem cells shows that the surface properties of cells further modulate partition in ATPS. This combined approach provides a fundamental understanding of interfacial tension role on cell partition in ATPS and a framework for future studies.
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Affiliation(s)
- Ehsan Atefi
- Department of Biomedical Engineering, The University of Akron , Akron, Ohio 44325, United States
| | - Ramila Joshi
- Department of Biomedical Engineering, The University of Akron , Akron, Ohio 44325, United States
| | - Jay Adin Mann
- Department of Chemical and Biomolecular Engineering, Case Western Reserve University , Cleveland, Ohio 44106, United States
| | - Hossein Tavana
- Department of Biomedical Engineering, The University of Akron , Akron, Ohio 44325, United States
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18
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Alanazi I, Hoffmann P, Adelson DL. MicroRNAs are part of the regulatory network that controls EGF induced apoptosis, including elements of the JAK/STAT pathway, in A431 cells. PLoS One 2015; 10:e0120337. [PMID: 25781916 PMCID: PMC4364457 DOI: 10.1371/journal.pone.0120337] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Accepted: 02/05/2015] [Indexed: 12/20/2022] Open
Abstract
MiRNAs are known to regulate gene expression and in the context of cancer have been shown to regulate metastasis, cell proliferation and cell death. In this report we describe potential miRNA regulatory roles with respect to induction of cell death by pharmacologic dose of Epidermal Growth Factor (EGF). Our previous work suggested that multiple pathways are involved in the induction of apoptosis, including interferon induced genes, cytokines, cytoskeleton and cell adhesion and TP53 regulated genes. Using miRNA time course expression profiling of EGF treated A431 cells and coupling this to our previous gene expression and proteomic data, we have been able to implicate a number of additional miRNAs in the regulation of apoptosis. Specifically we have linked miR-134, miR-145, miR-146b-5p, miR-432 and miR-494 to the regulation of both apoptotic and anti-apoptotic genes expressed as a function of EGF treatment. Whilst additional miRNAs were differentially expressed, these had the largest number of apoptotic and anti-apoptotic targets. We found 5 miRNAs previously implicated in the regulation of apoptosis and our results indicate that an additional 20 miRNAs are likely to be involved based on their correlated expression with targets. Certain targets were linked to multiple miRNAs, including PEG10, BTG1, ID1, IL32 and NCF2. Some miRNAs that target the interferon pathway were found to be down regulated, consistent with a novel layer of regulation of interferon pathway components downstream of JAK/STAT. We have significantly expanded the repertoire of miRNAs that may regulate apoptosis in cancer cells as a result of this work.
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Affiliation(s)
- Ibrahim Alanazi
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Peter Hoffmann
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - David L. Adelson
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Zhendong Australia—China Centre for Molecular Chinese Medicine, The University of Adelaide, Adelaide, South Australia, Australia
- * E-mail:
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19
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Overexpression of Serpinb1 in Chinese hamster ovary cells increases recombinant IgG productivity. J Biotechnol 2015; 193:91-9. [DOI: 10.1016/j.jbiotec.2014.10.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 09/25/2014] [Accepted: 10/31/2014] [Indexed: 11/23/2022]
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20
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Ebrahimi Khaksefidi R, Mirlohi S, Khalaji F, Fakhari Z, Shiran B, Fallahi H, Rafiei F, Budak H, Ebrahimie E. Differential expression of seven conserved microRNAs in response to abiotic stress and their regulatory network in Helianthus annuus. FRONTIERS IN PLANT SCIENCE 2015; 6:741. [PMID: 26442054 PMCID: PMC4585256 DOI: 10.3389/fpls.2015.00741] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 08/31/2015] [Indexed: 05/03/2023]
Abstract
Biotic and abiotic stresses affect plant development and production through alternation of the gene expression pattern. Gene expression itself is under the control of different regulators such as miRNAs and transcription factors (TFs). MiRNAs are known to play important roles in regulation of stress responses via interacting with their target mRNAs. Here, for the first time, seven conserved miRNAs, associated with drought, heat, salt and cadmium stresses were characterized in sunflower. The expression profiles of miRNAs and their targets were comparatively analyzed between leaves and roots of plants grown under the mentioned stress conditions. Gene ontology analysis of target genes revealed that they are involved in several important pathways such as auxin and ethylene signaling, RNA mediated silencing and DNA methylation processes. Gene regulatory network highlighted the existence of cross-talks between these stress-responsive miRNAs and the other stress responsive genes in sunflower. Based on network analysis, we suggest that some of these miRNAs in sunflower such as miR172 and miR403 may play critical roles in epigenetic responses to stress. It seems that depending on the stress type, theses miRNAs target several pathways and cellular processes to help sunflower to cope with drought, heat, salt and cadmium stress conditions in a tissue-associated manner.
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Affiliation(s)
| | - Shirin Mirlohi
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord UniversityShahrekord, Iran
| | - Fahimeh Khalaji
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord UniversityShahrekord, Iran
| | - Zahra Fakhari
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord UniversityShahrekord, Iran
| | - Behrouz Shiran
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord UniversityShahrekord, Iran
- Department of Agricultural Biotechnology, Institute of Biotechnology, Shahrekord UniversityShahrekord, Iran
- *Correspondence: Behrouz Shiran, Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, PO Box 115, Shahrekord 8818634141, Iran ;
| | - Hossein Fallahi
- Department of Biology, School of Sciences, Razi UniversityKermanshah, Iran
| | - Fariba Rafiei
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord UniversityShahrekord, Iran
| | - Hikmet Budak
- Biological Sciences and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci UniversityIstanbul, Turkey
| | - Esmaeil Ebrahimie
- Faculty of Agriculture, Institute of Biotechnology, Shiraz UniversityShiraz, Iran
- Department of Genetics and Evolution, School of Biological Sciences, University of AdelaideAdelaide, SA, Australia
- School of Biological Sciences, Faculty of Science and Engineering, Flinders UniversityAdelaide, Australia
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21
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Franco C, Hess S. Recent proteomic advances in developmental, regeneration, and cancer governing signaling pathways. Proteomics 2014; 15:1014-25. [PMID: 25316175 DOI: 10.1002/pmic.201400368] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/16/2014] [Accepted: 10/09/2014] [Indexed: 12/12/2022]
Abstract
Embryonic development, adult tissue repair, and cancer share a number of common regulating pathways. The basic processes that govern the events that induce mesenchymal properties in epithelial cells-a process known as epithelial-mesenchymal transition-are central for embryonic development, and can be resumed in adults either during wound healing or tissue regeneration. A misregulation of these pathways is involved in pathological situations, such as tissue fibrosis and cancer. Proteomic approaches have emerged as promising tools to better understand the signaling pathways that govern these complex biological processes. This review focuses on the recent proteomic-based contributions to better understand the modulation of transforming growth factor-beta (TGF-β), wingless-type MMTV integration site family (Wnt), Notch and Receptor tyrosine kinase (RTK) signaling pathways. New advances include the description of new protein interactions, the formation of new protein complexes or the description on how some PTMs are regulating these pathways. Understanding protein interactions and the tempo-spatial modulation of these pathways might lead us to interesting research quests in cancer, embryonic development or even on improving adult tissue regeneration capabilities.
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Affiliation(s)
- Catarina Franco
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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22
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Alisoltani A, Fallahi H, Ebrahimi M, Ebrahimi M, Ebrahimie E. Prediction of potential cancer-risk regions based on transcriptome data: towards a comprehensive view. PLoS One 2014; 9:e96320. [PMID: 24796549 PMCID: PMC4010480 DOI: 10.1371/journal.pone.0096320] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 04/07/2014] [Indexed: 12/20/2022] Open
Abstract
A novel integrative pipeline is presented for discovery of potential cancer-susceptibility regions (PCSRs) by calculating the number of altered genes at each chromosomal region, using expression microarray datasets of different human cancers (HCs). Our novel approach comprises primarily predicting PCSRs followed by identification of key genes in these regions to obtain potential regions harboring new cancer-associated variants. In addition to finding new cancer causal variants, another advantage in prediction of such risk regions is simultaneous study of different types of genomic variants in line with focusing on specific chromosomal regions. Using this pipeline we extracted numbers of regions with highly altered expression levels in cancer condition. Regulatory networks were also constructed for different types of cancers following the identification of altered mRNA and microRNAs. Interestingly, results showed that GAPDH, LIFR, ZEB2, mir-21, mir-30a, mir-141 and mir-200c, all located at PCSRs, are common altered factors in constructed networks. We found a number of clusters of altered mRNAs and miRNAs on predicted PCSRs (e.g.12p13.31) and their common regulators including KLF4 and SOX10. Large scale prediction of risk regions based on transcriptome data can open a window in comprehensive study of cancer risk factors and the other human diseases.
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Affiliation(s)
- Arghavan Alisoltani
- Department of Plant Breeding and Biotechnology, University of Shahrekord, Shahrekord, Iran
| | - Hossein Fallahi
- Department of Biology, School of Sciences, Razi University, Kermanshah, Iran
| | - Mahdi Ebrahimi
- Department of Informatics, Saarland University, Saarbrucken, Germany
| | - Mansour Ebrahimi
- Bioinformatics Research Group and Department of Biology, University of Qom, Qom, Iran
| | - Esmaeil Ebrahimie
- School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, Australia
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Huang P, Xu X, Wang L, Zhu B, Wang X, Xia J. The role of EGF-EGFR signalling pathway in hepatocellular carcinoma inflammatory microenvironment. J Cell Mol Med 2013; 18:218-30. [PMID: 24268047 PMCID: PMC3930409 DOI: 10.1111/jcmm.12153] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Accepted: 09/04/2013] [Indexed: 12/14/2022] Open
Abstract
Epidermal growth factor (EGF) and their receptor (EGFR) play an important role in the development of cancer proliferation, and metastasis, although the mechanism remains unclear. The present study aimed at investigating the role of EGF-EGFR signalling pathway in the development of human hepatocellular carcinoma (HCC) inflammatory environment. Gene profiles of inflammatory cytokines from HCC were measured. Cell bio-behaviours of HCC with low or high metastasis were detected by the live cell monitoring system. Cell proliferation was measured by CCK8. The protein level of CXCL5 and CXCL8 was measured by ELISA. The phosphorylation of PI3K, ERK, MAPK was measured by western blot. EGF significantly induced cell proliferation in HepG2 cells, but not in HCCLM3 cells. EGF prompted the cell movement in both HepG2 and HCCLM3 and regulated the production of CXCL5 and CXCL8 from HCC, which were inhibited by EGFR inhibitor, Erk inhibitor (U0126), or PI3K inhibitors (BEZ-235 and SHBM1009). HCC proliferation, metastasis and production of inflammatory cytokines were regulated via EGF-EGFR signal pathways. CXCL5 could interact with CXCL8, possibly by CXCR2 or the cross-talk between CXCR2 and EGFR. EGF-EGFR signaling pathway can be the potential target of therapies for HCC.
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Affiliation(s)
- Peixin Huang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
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