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Pang WG, Ye M, Chen JR, Zhang L, Wang Z. Data mining-based identification of epigenetic signatures with discrimination potential of lung adenocarcinoma and squamous cell carcinoma. Mol Biol Rep 2024; 51:255. [PMID: 38302782 DOI: 10.1007/s11033-024-09216-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/05/2024] [Indexed: 02/03/2024]
Abstract
BACKGROUND Mounting evidence suggests that lung adenocarcinoma (LAC) and lung squamous cell carcinoma (LSC) have different biological behaviors and therapeutic regimens in clinical practice. However, limited improvements in molecular differential diagnosis of the two entities have been achieved in recent decades. We aimed to find novel markers that could define non-small cell lung cancer (NSCLC) subtypes. METHODS We first explored publically available databases to search for DNA methylation signatures that enable a precise discrimination of LAC and LSC. Next-generation sequencing (NGS) was then used to analyze the methylation status and sites of candidate genes in LAC/LSC tissue samples, and a quantitative methylation-sensitive PCR (qMS-PCR) assay was conducted to test the performance of the selected maker in tissue samples and bronchoalveolar lavage fluid (BALF) specimens. RESULTS We screened 19 top-ranked methylation loci that are differentially methylated between LAC and LSC. Among these hits, 6 methylation sites are enriched within the PREX1 gene promoter, thus becoming our focus. NGS analysis confirmed markedly higher PREX1 methylation levels in LAC than in LSC and revealed the right sites for detection of PREX1 methylation. Furthermore, PREX1 methylation analysis in lung cancer tissue samples defined 9 of 11 pathologically proven LACs, as well as 12 of 14 LSCs. In addition, ~ 80% LAC BALF samples showed methylated PREX1 compared to substantially lower test positivity (0-9%) of it in LSC and other lung conditions (P < 0.01). CONCLUSION Our pilot study identified a unique epigenetic signature that could effectively distinguish LAC from LSC in various lung samples. It may enhance our in-depth understanding of the biology of lung cancer and pave the way for better accurate diagnosis and treatment stratification in the future.
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Affiliation(s)
- Wen-Guang Pang
- Department of Thoracic Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, 510630, China
- Department of Thoracic Surgery, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Min Ye
- Department of Thoracic Surgery, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Jia-Rong Chen
- Department of Oncology, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Liang Zhang
- Translational Medicine Center, Maternal and Child Health Research Institute, Guangdong Women and Children Hospital, 521 Xingnan Road, Guangzhou, 511400, China.
| | - Zheng Wang
- Department of Thoracic Surgery, The 2nd Clinical Medical College of Jinan University, 1017 Dongmen North Road, Luohu District, Shenzhen, 518020, China.
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Fayez AG, Esmaiel NN, Ashaat EA, Refeat MM, Lotfy RS, Raouf HA, El Ruby MO. New drug-like small molecule antagonizes phosphatidylinositol (3,4,5)-trisphosphate (PIP3) in patients with conotruncal heart defects. J Taibah Univ Med Sci 2023; 18:1244-1253. [PMID: 37250809 PMCID: PMC10213100 DOI: 10.1016/j.jtumed.2023.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 02/02/2023] [Accepted: 04/20/2023] [Indexed: 05/31/2023] Open
Abstract
Objectives Conotruncal heart defects (CTDs) are highly heritable, and approximately one-third of all congenital heart defects are due to CTDs. Through post-analysis of GWAS data relevant to CTDs, a new putative signal transduction pathway, called Vars2-Pic3ca-Akt, associated with CTD has been hypothesized. Here, we aimed to validate the Vars2-Pic3ca-Akt pathway experimentally by measuring Vars2 and PIP3 in patients with CTDs and controls, and to construct a PIP3 inhibitor, as one of harmful-relevant CTD pathogenesis, through an Akt-based drug design strategy. Methods rs2517582 genotype and relative Vars2 expression in 207 individuals were determined by DNA sequencing and qPCR respectively, and free plasma PIP3 in 190 individuals was quantified through ELISA. An Akt-pharmacophore feature model was used to discover PIP3 antagonists with multiple computational and drug-like estimation tools. Results CTD pathogenesis due to Vars2-Pic3ca-Akt overstimulation was confirmed by elevated Vars2 and PIP3 in patients with CTDs. We identified a new small molecule, 322PESB, that antagonizes PIP3 binding. This molecule was prioritized via virtual screening of 21 hypothetical small molecules and it showed minimal RMSD change, high binding affinity andlower dissociation constant than PIP3-Akt complex by 1.99 Kcal/Mol, thus resulting in an equilibrium shift toward 322PESB-Akt complex formation. Moreover, 322PESB exhibited acceptable pharmacokinetics and drug likeness features according to ADME and Lipinski's rule of five classifiers. This compound is the first potential drug-like molecule reported for patients with CTDs with elevated PIP3. Conclusion PIP3 is a useful diagnostic biomarker for patients with CTDs. The Akt-pharmacophore feature model is a feasible approach for discovery of PIP3 signalling antagonists. Further 322PESB development and testing are recommended.
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Affiliation(s)
- Alaaeldin G. Fayez
- Molecular Genetics and Enzymology Department, Human Genetics and Genome Research Institute, National Research Centre, Giza, Egypt
| | - Nora N. Esmaiel
- Molecular Genetics and Enzymology Department, Human Genetics and Genome Research Institute, National Research Centre, Giza, Egypt
| | - Engy A. Ashaat
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Giza, Egypt
| | - Miral M. Refeat
- Medical Molecular Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Giza, Egypt
| | - Randa S. Lotfy
- Molecular Genetics and Enzymology Department, Human Genetics and Genome Research Institute, National Research Centre, Giza, Egypt
| | - Haiam Abdel Raouf
- Immunogenetics Department, Human Genetics and Genome Research Institute, National Research Centre, Giza, Egypt
| | - Mona O. El Ruby
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Giza, Egypt
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Floerchinger A, Murphy KJ, Latham SL, Warren SC, McCulloch AT, Lee YK, Stoehr J, Mélénec P, Guaman CS, Metcalf XL, Lee V, Zaratzian A, Da Silva A, Tayao M, Rolo S, Phimmachanh M, Sultani G, McDonald L, Mason SM, Ferrari N, Ooms LM, Johnsson AKE, Spence HJ, Olson MF, Machesky LM, Sansom OJ, Morton JP, Mitchell CA, Samuel MS, Croucher DR, Welch HCE, Blyth K, Caldon CE, Herrmann D, Anderson KI, Timpson P, Nobis M. Optimizing metastatic-cascade-dependent Rac1 targeting in breast cancer: Guidance using optical window intravital FRET imaging. Cell Rep 2021; 36:109689. [PMID: 34525350 DOI: 10.1016/j.celrep.2021.109689] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 07/06/2021] [Accepted: 08/18/2021] [Indexed: 01/18/2023] Open
Abstract
Assessing drug response within live native tissue provides increased fidelity with regards to optimizing efficacy while minimizing off-target effects. Here, using longitudinal intravital imaging of a Rac1-Förster resonance energy transfer (FRET) biosensor mouse coupled with in vivo photoswitching to track intratumoral movement, we help guide treatment scheduling in a live breast cancer setting to impair metastatic progression. We uncover altered Rac1 activity at the center versus invasive border of tumors and demonstrate enhanced Rac1 activity of cells in close proximity to live tumor vasculature using optical window imaging. We further reveal that Rac1 inhibition can enhance tumor cell vulnerability to fluid-flow-induced shear stress and therefore improves overall anti-metastatic response to therapy during transit to secondary sites such as the lung. Collectively, this study demonstrates the utility of single-cell intravital imaging in vivo to demonstrate that Rac1 inhibition can reduce tumor progression and metastases in an autochthonous setting to improve overall survival.
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Affiliation(s)
- Alessia Floerchinger
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Kendelle J Murphy
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Sharissa L Latham
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Sean C Warren
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Andrew T McCulloch
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Young-Kyung Lee
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Janett Stoehr
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Pauline Mélénec
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Cris S Guaman
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Xanthe L Metcalf
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Victoria Lee
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Anaiis Zaratzian
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Andrew Da Silva
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Michael Tayao
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Sonia Rolo
- Cancer Research UK Beatson Institute, Switchback Road, Bearsden, Glasgow G611BD, UK
| | - Monica Phimmachanh
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Ghazal Sultani
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Laura McDonald
- Cancer Research UK Beatson Institute, Switchback Road, Bearsden, Glasgow G611BD, UK
| | - Susan M Mason
- Cancer Research UK Beatson Institute, Switchback Road, Bearsden, Glasgow G611BD, UK
| | - Nicola Ferrari
- Cancer Research UK Beatson Institute, Switchback Road, Bearsden, Glasgow G611BD, UK; Institute of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow G111QH, UK
| | - Lisa M Ooms
- Cancer Program, Monash Biomedicine Discovery Institute, and Department of Biochemistry and Molecular Biology, Monash University, VIC 3800, Australia
| | | | - Heather J Spence
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Michael F Olson
- Department of Chemistry and Biology, Ryerson University, Toronto ON, M5B 2K3, Canada
| | - Laura M Machesky
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Owen J Sansom
- Cancer Research UK Beatson Institute, Switchback Road, Bearsden, Glasgow G611BD, UK; Institute of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow G111QH, UK
| | - Jennifer P Morton
- Cancer Research UK Beatson Institute, Switchback Road, Bearsden, Glasgow G611BD, UK; Institute of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow G111QH, UK
| | - Christina A Mitchell
- Cancer Program, Monash Biomedicine Discovery Institute, and Department of Biochemistry and Molecular Biology, Monash University, VIC 3800, Australia
| | - Michael S Samuel
- Centre for Cancer Biology, SA Pathology and University of South Australia; and the School of Medicine, University of Adelaide, Adelaide, SA 5000, Australia
| | - David R Croucher
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Heidi C E Welch
- Signalling Programme, Babraham Institute, Cambridge CB223AT, UK
| | - Karen Blyth
- Cancer Research UK Beatson Institute, Switchback Road, Bearsden, Glasgow G611BD, UK; Institute of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow G111QH, UK
| | - C Elizabeth Caldon
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - David Herrmann
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Kurt I Anderson
- Cancer Research UK Beatson Institute, Switchback Road, Bearsden, Glasgow G611BD, UK; Francis Crick Institute, London NW11AT, UK
| | - Paul Timpson
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia.
| | - Max Nobis
- The Garvan Institute of Medical Research, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia.
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