1
|
Rosano D, Sofyali E, Dhiman H, Ghirardi C, Ivanoiu D, Heide T, Vingiani A, Bertolotti A, Pruneri G, Canale E, Dewhurst HF, Saha D, Slaven N, Barozzi I, Li T, Zemlyanskiy G, Phillips H, James C, Győrffy B, Lynn C, Cresswell GD, Rehman F, Noberini R, Bonaldi T, Sottoriva A, Magnani L. Long-term Multimodal Recording Reveals Epigenetic Adaptation Routes in Dormant Breast Cancer Cells. Cancer Discov 2024; 14:866-889. [PMID: 38527495 PMCID: PMC11061610 DOI: 10.1158/2159-8290.cd-23-1161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/10/2024] [Accepted: 02/20/2024] [Indexed: 03/27/2024]
Abstract
Patients with estrogen receptor-positive breast cancer receive adjuvant endocrine therapies (ET) that delay relapse by targeting clinically undetectable micrometastatic deposits. Yet, up to 50% of patients relapse even decades after surgery through unknown mechanisms likely involving dormancy. To investigate genetic and transcriptional changes underlying tumor awakening, we analyzed late relapse patients and longitudinally profiled a rare cohort treated with long-term neoadjuvant ETs until progression. Next, we developed an in vitro evolutionary study to record the adaptive strategies of individual lineages in unperturbed parallel experiments. Our data demonstrate that ETs induce nongenetic cell state transitions into dormancy in a stochastic subset of cells via epigenetic reprogramming. Single lineages with divergent phenotypes awaken unpredictably in the absence of recurrent genetic alterations. Targeting the dormant epigenome shows promising activity against adapting cancer cells. Overall, this study uncovers the contribution of epigenetic adaptation to the evolution of resistance to ETs. SIGNIFICANCE This study advances the understanding of therapy-induced dormancy with potential clinical implications for breast cancer. Estrogen receptor-positive breast cancer cells adapt to endocrine treatment by entering a dormant state characterized by strong heterochromatinization with no recurrent genetic changes. Targeting the epigenetic rewiring impairs the adaptation of cancer cells to ETs. See related commentary by Llinas-Bertran et al., p. 704. This article is featured in Selected Articles from This Issue, p. 695.
Collapse
Affiliation(s)
- Dalia Rosano
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- The Breast Cancer Now Toby Robins Research Center, The Institute of Cancer Research, London, United Kingdom
| | - Emre Sofyali
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Heena Dhiman
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- The Breast Cancer Now Toby Robins Research Center, The Institute of Cancer Research, London, United Kingdom
| | - Chiara Ghirardi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Diana Ivanoiu
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Timon Heide
- Human Technopole, Milan, Italy
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | | | | | - Giancarlo Pruneri
- Istituto Nazionale Tumori, Milan, Italy
- Department of Oncology and Haematology-Oncology, University of Milano, Milano, Italy
| | - Eleonora Canale
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Hannah F. Dewhurst
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Debjani Saha
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Neil Slaven
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley
| | - Iros Barozzi
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Centre for Cancer Research, Medical University of Vienna, Austria
| | - Tong Li
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Grigory Zemlyanskiy
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Henry Phillips
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Chela James
- Human Technopole, Milan, Italy
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
- RCNS Cancer Biomarker Research Group, Budapest, Hungary
- Department of Biophysics, Medical School, University of Pecs, Pecs, Hungary
| | - Claire Lynn
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | - George D. Cresswell
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | - Farah Rehman
- Charing Cross Hospital, Imperial College NHS Trust, London, United Kingdom
| | - Roberta Noberini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Haematology-Oncology, University of Milano, Milano, Italy
| | - Andrea Sottoriva
- Human Technopole, Milan, Italy
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- The Breast Cancer Now Toby Robins Research Center, The Institute of Cancer Research, London, United Kingdom
| |
Collapse
|
2
|
Ungvari Z, Ungvari A, Bianchini G, Győrffy B. Prognostic significance of a signature based on senescence-related genes in colorectal cancer. GeroScience 2024:10.1007/s11357-024-01164-6. [PMID: 38658505 DOI: 10.1007/s11357-024-01164-6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 04/15/2024] [Indexed: 04/26/2024] Open
Abstract
Colorectal cancer, recognized as a quintessential age-related disease, underscores the intricate interplay between aging mechanisms and disease pathogenesis. Cellular senescence, a DNA damage-induced cellular stress response, is characterized by cell cycle arrest, the expression of an inflammatory senescence-associated secretory phenotype, and alterations in extracellular matrix metabolism. It is widely recognized as a fundamental and evolutionarily conserved mechanism of aging. Guided by geroscience principles, which assert that the pathogenesis of age-related diseases involves cellular mechanisms of aging, this study delves into the role of senescence-related genes in colon cancer progression. Leveraging a gene set reflective of senescence-associated pathways, we employed uni- and multivariate Cox proportional hazards survival analysis combined with the determination of the false discovery rate to analyze correlations between gene expression and survival. The integrated database of 1130 colon cancer specimens with available relapse-free survival time and relapse event data from ten independent cohorts provided a robust platform for survival analyses. We identified senescence-related genes associated with differential expression levels linked to shorter survival. Our findings unveil a prognostic signature utilizing cellular senescence-related genes (hazard ratio: 2.73, 95% CI 2.12-3.52, p = 6.4E - 16), offering valuable insights into survival prediction in colon cancer. Multivariate analysis underscored the independence of the senescence-related signature from available epidemiological and pathological variables. This study highlights the potential of senescence-related genes as prognostic biomarkers. Overall, our results underscore the pivotal role of cellular senescence, a fundamental mechanism of aging, in colon cancer progression.
Collapse
Affiliation(s)
- Zoltan Ungvari
- Vascular Cognitive Impairment, Neurodegeneration and Healthy Brain Aging Program, Department of Neurosurgery, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Stephenson Cancer Center, University of Oklahoma, Oklahoma City, OK, USA
- Oklahoma Center for Geroscience and Healthy Brain Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Health Promotion Sciences, College of Public Health, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- International Training Program in Geroscience, Doctoral College/Department of Public Health, Semmelweis University, Budapest, Hungary
| | - Anna Ungvari
- Department of Public Health, Semmelweis University, Semmelweis University, Budapest, Hungary.
| | | | - Balázs Győrffy
- Dept. of Bioinformatics, Semmelweis University, 1094, Budapest, Hungary
- Dept. of Biophysics, Medical School, University of Pecs, 7624, Pecs, Hungary
- Cancer Biomarker Research Group, Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, 1117, Budapest, Hungary
| |
Collapse
|
3
|
Parreno V, Loubiere V, Schuettengruber B, Fritsch L, Rawal CC, Erokhin M, Győrffy B, Normanno D, Di Stefano M, Moreaux J, Butova NL, Chiolo I, Chetverina D, Martinez AM, Cavalli G. Transient loss of Polycomb components induces an epigenetic cancer fate. Nature 2024:10.1038/s41586-024-07328-w. [PMID: 38658752 DOI: 10.1038/s41586-024-07328-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/15/2024] [Indexed: 04/26/2024]
Abstract
Although cancer initiation and progression are generally associated with the accumulation of somatic mutations1,2, substantial epigenomic alterations underlie many aspects of tumorigenesis and cancer susceptibility3-6, suggesting that genetic mechanisms might not be the only drivers of malignant transformation7. However, whether purely non-genetic mechanisms are sufficient to initiate tumorigenesis irrespective of mutations has been unknown. Here, we show that a transient perturbation of transcriptional silencing mediated by Polycomb group proteins is sufficient to induce an irreversible switch to a cancer cell fate in Drosophila. This is linked to the irreversible derepression of genes that can drive tumorigenesis, including members of the JAK-STAT signalling pathway and zfh1, the fly homologue of the ZEB1 oncogene, whose aberrant activation is required for Polycomb perturbation-induced tumorigenesis. These data show that a reversible depletion of Polycomb proteins can induce cancer in the absence of driver mutations, suggesting that tumours can emerge through epigenetic dysregulation leading to inheritance of altered cell fates.
Collapse
Affiliation(s)
- V Parreno
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - V Loubiere
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - B Schuettengruber
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - L Fritsch
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - C C Rawal
- University of Southern California, Los Angeles, CA, USA
| | - M Erokhin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - B Győrffy
- Semmelweis University Department of Bioinformatics, Budapest, Hungary
- Department of Biophysics, Medical School, University of Pécs, Pécs, Hungary
| | - D Normanno
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - M Di Stefano
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - J Moreaux
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
- Department of Biological Hematology, CHU Montpellier, Montpellier, France
- UFR Medicine, University of Montpellier, Montpellier, France
| | - N L Butova
- University of Southern California, Los Angeles, CA, USA
| | - I Chiolo
- University of Southern California, Los Angeles, CA, USA
| | - D Chetverina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - A-M Martinez
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France.
| | - G Cavalli
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France.
| |
Collapse
|
4
|
Li J, Hilimire TA, Yueying L, Wang L, Liang J, Győrffy B, Sikirzhytski V, Ji H, Zhang L, Cheng C, Ding X, Kerr KR, Dowling CE, Chumanevich AA, Mack ZT, Schools GP, Lim CU, Ellis L, Zi X, Porter DC, Broude EV, McInnes C, Wilding G, Lilly MB, Roninson IB, Chen M. Mediator kinase inhibition reverses castration resistance of advanced prostate cancer. J Clin Invest 2024:e176709. [PMID: 38546787 DOI: 10.1172/jci176709] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024] Open
Abstract
Mediator kinases CDK19 and CDK8, pleiotropic regulators of transcriptional reprogramming, are differentially regulated by androgen signaling but both kinases are upregulated in castration-resistant prostate cancer (CRPC). Genetic or pharmacological inhibition of CDK8 and CDK19 reverses the castration-resistant phenotype and restores the sensitivity of CRPC xenografts to androgen deprivation in vivo. Prolonged CDK8/19 inhibitor treatment combined with castration not only suppresses the growth of CRPC xenografts but also induces tumor regression and cures. Transcriptomic analysis revealed that Mediator kinase inhibition amplifies and modulates the effects of castration on gene expression, disrupting CRPC adaptation to androgen deprivation. Mediator kinase inactivation in tumor cells also affects stromal gene expression, indicating that Mediator kinase activity in CRPC molds the tumor microenvironment. The combination of castration and Mediator kinase inhibition downregulates the MYC pathway, and Mediator kinase inhibition suppresses a MYC-driven CRPC tumor model even without castration. CDK8/19 inhibitors show efficacy in patient-derived xenograft models of CRPC, and a gene signature of Mediator kinase activity correlates with tumor progression and overall survival in clinical samples of metastatic CRPC. These results indicate that Mediator kinases mediate androgen-independent in vivo growth of CRPC, supporting the development of CDK8/19 inhibitors for the treatment of this presently incurable disease.
Collapse
Affiliation(s)
- Jing Li
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, United States of America
| | - Thomas A Hilimire
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, United States of America
| | - Liu Yueying
- Division of Hematology-Oncology, Medical University of South Carolina, Charlseton, United States of America
| | - Lili Wang
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, United States of America
| | - Jiaxin Liang
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, United States of America
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
| | - Vitali Sikirzhytski
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, United States of America
| | - Hao Ji
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, United States of America
| | - Li Zhang
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, United States of America
| | - Chen Cheng
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, United States of America
| | - Xiaokai Ding
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, United States of America
| | - Kendall R Kerr
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, United States of America
| | - Charles E Dowling
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, United States of America
| | - Alexander A Chumanevich
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, United States of America
| | - Zachary T Mack
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, United States of America
| | - Gary P Schools
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, United States of America
| | - Chang-Uk Lim
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, United States of America
| | - Leigh Ellis
- Murtha Cancer Center Research Program, Department of Surgery, Center for Prostate Disease Research, Bethesda, United States of America
| | - Xiaolin Zi
- Chao Cancer Center, University of California, Irvine, irvine, United States of America
| | - Donald C Porter
- Senex Biotechnology, Inc., Columbia, United States of America
| | - Eugenia V Broude
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, United States of America
| | - Campbell McInnes
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, United States of America
| | - George Wilding
- Senex Biotechnology, Inc., Columbia, United States of America
| | - Michael B Lilly
- Division of Hematology-Oncology, Medical University of South Carolina, Charlseton, United States of America
| | - Igor B Roninson
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, United States of America
| | - Mengqian Chen
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, United States of America
| |
Collapse
|
5
|
Menyhárt O, Győrffy B. Dietary approaches for exploiting metabolic vulnerabilities in cancer. Biochim Biophys Acta Rev Cancer 2024; 1879:189062. [PMID: 38158024 DOI: 10.1016/j.bbcan.2023.189062] [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: 06/20/2023] [Revised: 12/20/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
Renewed interest in tumor metabolism sparked an enthusiasm for dietary interventions to prevent and treat cancer. Changes in diet impact circulating nutrient levels in the plasma and the tumor microenvironment, and preclinical studies suggest that dietary approaches, including caloric and nutrient restrictions, can modulate tumor initiation, progression, and metastasis. Cancers are heterogeneous in their metabolic dependencies and preferred energy sources and can be addicted to glucose, fructose, amino acids, or lipids for survival and growth. This dependence is influenced by tumor type, anatomical location, tissue of origin, aberrant signaling, and the microenvironment. This review summarizes nutrient dependencies and the related signaling pathway activations that provide targets for nutritional interventions. We examine popular dietary approaches used as adjuvants to anticancer therapies, encompassing caloric restrictions, including time-restricted feeding, intermittent fasting, fasting-mimicking diets (FMDs), and nutrient restrictions, notably the ketogenic diet. Despite promising results, much of the knowledge on dietary restrictions comes from in vitro and animal studies, which may not accurately reflect real-life situations. Further research is needed to determine the optimal duration, timing, safety, and efficacy of dietary restrictions for different cancers and treatments. In addition, well-designed human trials are necessary to establish the link between specific metabolic vulnerabilities and targeted dietary interventions. However, low patient compliance in clinical trials remains a significant challenge.
Collapse
Affiliation(s)
- Otília Menyhárt
- Semmelweis University, Department of Bioinformatics, Tűzoltó u. 7-9, H-1094 Budapest, Hungary; Research Centre for Natural Sciences, Cancer Biomarker Research Group, Institute of Enzymology, Magyar tudósok krt. 2, H-1117 Budapest, Hungary; National Laboratory for Drug Research and Development, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
| | - Balázs Győrffy
- Semmelweis University, Department of Bioinformatics, Tűzoltó u. 7-9, H-1094 Budapest, Hungary; Research Centre for Natural Sciences, Cancer Biomarker Research Group, Institute of Enzymology, Magyar tudósok krt. 2, H-1117 Budapest, Hungary; National Laboratory for Drug Research and Development, Magyar tudósok krt. 2, H-1117 Budapest, Hungary.
| |
Collapse
|
6
|
Győrffy B. Transcriptome-level discovery of survival-associated biomarkers and therapy targets in non-small-cell lung cancer. Br J Pharmacol 2024; 181:362-374. [PMID: 37783508 DOI: 10.1111/bph.16257] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 06/12/2023] [Revised: 08/06/2023] [Accepted: 09/23/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND AND PURPOSE Survival rate of patients with lung cancer has increased by over 60% in the recent two decades. With longer survival, the identification of genes associated with survival has emerged as an issue of utmost importance to uncover the most promising biomarkers and therapeutic targets. EXPERIMENTAL APPROACH An integrated database was set up by combining multiple independent datasets with clinical data and transcriptome-level gene expression measurements. Univariate and multivariate survival analyses were performed to identify genes with higher expression levels linked to shorter survival. The strongest genes were filtered to include only those with known druggability. KEY RESULTS The entire database includes 2852 tumour specimens from 17 independent cohorts. Of these, 2227 have overall survival data and 1256 samples have progression-free survival time. The most significant genes associated with survival were MIF, UBC and B2M in lung adenocarcinoma and ANXA2, CSNK2A2 and KRT18 in squamous cell carcinoma. We also aimed to reveal the best druggable targets in non-smokers lung cancer. The three most promising hits in this cohort were MDK, THY1 and PADI2. The established lung cancer cohort was added to the Kaplan-Meier plotter (https://www.kmplot.com) enabling the validation of future gene expression-based biomarkers in both the present and yet unexamined subgroups of patients. CONCLUSIONS AND IMPLICATIONS In this study, we established a comprehensive database of transcriptome-level data for lung cancer. The database can be utilized to identify and rank the most promising biomarkers and therapeutic targets for different subtypes of lung cancer.
Collapse
Affiliation(s)
- Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
| |
Collapse
|
7
|
Menyhárt O, Fekete JT, Győrffy B. Resistance to Combined Anthracycline-Taxane Chemotherapy Is Associated with Altered Metabolism and Inflammation in Breast Carcinomas. Int J Mol Sci 2024; 25:1063. [PMID: 38256136 PMCID: PMC10816584 DOI: 10.3390/ijms25021063] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/08/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
Approximately 30% of early-stage breast cancer (BC) patients experience recurrence after systemic chemotherapy; thus, understanding therapy resistance is crucial in developing more successful treatments. Here, we investigated the mechanisms underlying resistance to combined anthracycline-taxane treatment by comparing gene expression patterns with subsequent therapeutic responses. We established a cohort of 634 anthracycline-taxane-treated patients with pathological complete response (PCR) and a separate cohort of 187 patients with relapse-free survival (RFS) data, each having transcriptome-level expression data of 10,017 unique genes. Patients were categorized as responders and non-responders based on their PCR and RFS status, and the expression for each gene was compared between the two groups using a Mann-Whitney U-test. Statistical significance was set at p < 0.05, with fold change (FC) > 1.44. Altogether, 224 overexpressed genes were identified in the tumor samples derived from the patients without PCR; among these, the gene sets associated with xenobiotic metabolism (e.g., CYP3A4, CYP2A6) exhibited significant enrichment. The genes ORAI3 and BCAM differentiated non-responders from responders with the highest AUC values (AUC > 0.75, p < 0.0001). We identified 51 upregulated genes in the tumor samples derived from the patients with relapse within 60 months, participating primarily in inflammation and innate immune responses (e.g., LYN, LY96, ANXA1). Furthermore, the amino acid transporter SLC7A5, distinguishing non-responders from responders, had significantly higher expression in tumors and metastases than in normal tissues (Kruskal-Wallis p = 8.2 × 10-20). The identified biomarkers underscore the significance of tumor metabolism and microenvironment in treatment resistance and can serve as a foundation for preclinical validation studies.
Collapse
Affiliation(s)
- Otília Menyhárt
- Oncology Biomarker Research Group, Institute of Molecular Life Sciences, Hungarian Research Network, Magyar Tudósok Körútja 2, 1117 Budapest, Hungary; (O.M.); (J.T.F.)
- National Laboratory for Drug Research and Development, Magyar Tudósok Körútja 2, 1117 Budapest, Hungary
- Department of Bioinformatics, Semmelweis University, 1094 Budapest, Hungary
| | - János Tibor Fekete
- Oncology Biomarker Research Group, Institute of Molecular Life Sciences, Hungarian Research Network, Magyar Tudósok Körútja 2, 1117 Budapest, Hungary; (O.M.); (J.T.F.)
- National Laboratory for Drug Research and Development, Magyar Tudósok Körútja 2, 1117 Budapest, Hungary
- Department of Bioinformatics, Semmelweis University, 1094 Budapest, Hungary
| | - Balázs Győrffy
- Oncology Biomarker Research Group, Institute of Molecular Life Sciences, Hungarian Research Network, Magyar Tudósok Körútja 2, 1117 Budapest, Hungary; (O.M.); (J.T.F.)
- National Laboratory for Drug Research and Development, Magyar Tudósok Körútja 2, 1117 Budapest, Hungary
- Department of Bioinformatics, Semmelweis University, 1094 Budapest, Hungary
| |
Collapse
|
8
|
Zhou W, Zhao Z, Lin A, Yang JZ, Xu J, Wilder-Romans K, Yang A, Li J, Solanki S, Speth JM, Walker N, Scott AJ, Wang L, Wen B, Andren A, Zhang L, Kothari AU, Yao Y, Peterson ER, Korimerla N, Werner CK, Ullrich A, Liang J, Jacobson J, Palavalasa S, O’Brien AM, Elaimy AL, Ferris SP, Zhao SG, Sarkaria JN, Győrffy B, Zhang S, Al-Holou WN, Umemura Y, Morgan MA, Lawrence TS, Lyssiotis CA, Peters-Golden M, Shah YM, Wahl DR. GTP Signaling Links Metabolism, DNA Repair, and Responses to Genotoxic Stress. Cancer Discov 2024; 14:158-175. [PMID: 37902550 PMCID: PMC10872631 DOI: 10.1158/2159-8290.cd-23-0437] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 09/07/2023] [Accepted: 10/19/2023] [Indexed: 10/31/2023]
Abstract
How cell metabolism regulates DNA repair is incompletely understood. Here, we define a GTP-mediated signaling cascade that links metabolism to DNA repair and has significant therapeutic implications. GTP, but not other nucleotides, regulates the activity of Rac1, a guanine nucleotide-binding protein, which promotes the dephosphorylation of serine 323 on Abl-interactor 1 (Abi-1) by protein phosphatase 5 (PP5). Dephosphorylated Abi-1, a protein previously not known to activate DNA repair, promotes nonhomologous end joining. In patients and mouse models of glioblastoma, Rac1 and dephosphorylated Abi-1 mediate DNA repair and resistance to standard-of-care genotoxic treatments. The GTP-Rac1-PP5-Abi-1 signaling axis is not limited to brain cancer, as GTP supplementation promotes DNA repair and Abi-1-S323 dephosphorylation in nonmalignant cells and protects mouse tissues from genotoxic insult. This unexpected ability of GTP to regulate DNA repair independently of deoxynucleotide pools has important implications for normal physiology and cancer treatment. SIGNIFICANCE A newly described GTP-dependent signaling axis is an unexpected link between nucleotide metabolism and DNA repair. Disrupting this pathway can overcome cancer resistance to genotoxic therapy while augmenting it can mitigate genotoxic injury of normal tissues. This article is featured in Selected Articles from This Issue, p. 5.
Collapse
Affiliation(s)
- Weihua Zhou
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Zitong Zhao
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
- Department of Oncology, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shan Xi, PR China
| | - Angelica Lin
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - John Z Yang
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Jie Xu
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Kari Wilder-Romans
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Annabel Yang
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Jing Li
- Cell Signaling Technology, Inc., Danvers, MA, USA
| | - Sumeet Solanki
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer M Speth
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Natalie Walker
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Andrew J Scott
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Lu Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA
| | - Bo Wen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA
| | - Anthony Andren
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Li Zhang
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Ayesha U Kothari
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Yangyang Yao
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
- Department of Oncology, the First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, PR China
| | - Erik R Peterson
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Navyateja Korimerla
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Christian K Werner
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Alexander Ullrich
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Jessica Liang
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Janna Jacobson
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Sravya Palavalasa
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Alexandra M O’Brien
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Ameer L Elaimy
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Sean P Ferris
- Department of Pathology, Division of Neuropathology, University of Michigan, Ann Arbor, MI, USA
| | - Shuang G Zhao
- Department of Human Oncology, University of Wisconsin Madison, WI, USA
| | | | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary; and TTK Cancer Biomarker Research Group, Institute of Enzymology, Budapest, Hungary
| | - Shuqun Zhang
- Department of Oncology, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shan Xi, PR China
| | - Wajd N Al-Holou
- Department of Neurosurgery, University of Michigan, Ann Arbor, MI, United States
| | - Yoshie Umemura
- Department of Neurology, University of Michigan, Ann Arbor, MI, United States
| | - Meredith A Morgan
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Theodore S Lawrence
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Costas A Lyssiotis
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular and Integrative Physiology and Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Marc Peters-Golden
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Yatrik M Shah
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Daniel R Wahl
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
- Lead contact
| |
Collapse
|
9
|
Schittenhelm MM, Kaiser M, Győrffy B, Kampa-Schittenhelm KM. Evaluation of apoptosis stimulating protein of TP53-1 (ASPP1/PPP1R13B) to predict therapy resistance and overall survival in acute myeloid leukemia (AML). Cell Death Dis 2024; 15:25. [PMID: 38195541 PMCID: PMC10776670 DOI: 10.1038/s41419-023-06372-0] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 11/26/2023] [Accepted: 12/05/2023] [Indexed: 01/11/2024]
Abstract
ASPP1 (PPP1R13B) belongs to a family of p53-binding proteins and enhances apoptosis by stimulation of p53-transactivation of selected proapoptotic target genes. It is preferentially expressed in hematopoietic stem cells (HSC) and together with p53 preserves the genomic integrity of the HSC pool. Consequently, dysfunction of ASPP1 has been associated with malignant transformation and development of acute lymphoblastic leukemias and lymphomas - whereas methylation of the promoter region is linked to reduced transcription and ultimately attenuated expression of ASPP1. The role of ASPP1 in AML is not known. We now show that impaired regulation of PPP1R13B contributes to the biology of leukemogenesis and primary therapy resistance in AML. PPP1R13B mRNA expression patterns thereby define a distinct prognostic profile - which is not reflected by the European leukemia net (ELN) risk score. These findings have direct therapeutic implications and we provide a strategy to restore ASPP1 protein levels using hypomethylating agents to sensitize cells towards proapoptotic drugs. Prospective clinical trials are warranted to investigate the role of ASPP1 (PPP1R13B) as a biomarker for risk stratification and as a potential therapeutic target to restore susceptibility to chemotherapy.
Collapse
Affiliation(s)
- Marcus M Schittenhelm
- Medical research center (MFZ) and Clinic of Medical Oncology and Hematology, Cantonal Hospital St. Gallen (KSSG), St. Gallen, Switzerland
| | - Max Kaiser
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen (UKT), Tübingen, Germany
| | - Balázs Győrffy
- Semmelweis University Dept. of Bioinformatics and Dept. of Pediatrics, Budapest, H-1094, Hungary
- TTK Cancer Biomarker Research Group, Institute of Enzymology, Budapest, H-1117, Hungary
| | - Kerstin M Kampa-Schittenhelm
- Medical research center (MFZ) and Clinic of Medical Oncology and Hematology, Cantonal Hospital St. Gallen (KSSG), St. Gallen, Switzerland.
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen (UKT), Tübingen, Germany.
| |
Collapse
|
10
|
Prekovic S, Chalkiadakis T, Roest M, Roden D, Lutz C, Schuurman K, Opdam M, Hoekman L, Abbott N, Tesselaar T, Wajahat M, Dwyer AR, Mayayo‐Peralta I, Gomez G, Altelaar M, Beijersbergen R, Győrffy B, Young L, Linn S, Jonkers J, Tilley W, Hickey T, Vareslija D, Swarbrick A, Zwart W. Luminal breast cancer identity is determined by loss of glucocorticoid receptor activity. EMBO Mol Med 2023; 15:e17737. [PMID: 37902007 PMCID: PMC10701603 DOI: 10.15252/emmm.202317737] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 09/27/2023] [Accepted: 10/04/2023] [Indexed: 10/31/2023] Open
Abstract
Glucocorticoid receptor (GR) is a transcription factor that plays a crucial role in cancer biology. In this study, we utilized an in silico-designed GR activity signature to demonstrate that GR relates to the proliferative capacity of numerous primary cancer types. In breast cancer, the GR activity status determines luminal subtype identity and has implications for patient outcomes. We reveal that GR engages with estrogen receptor (ER), leading to redistribution of ER on the chromatin. Notably, GR activation leads to upregulation of the ZBTB16 gene, encoding for a transcriptional repressor, which controls growth in ER-positive breast cancer and associates with prognosis in luminal A patients. In relation to ZBTB16's repressive nature, GR activation leads to epigenetic remodeling and loss of histone acetylation at sites proximal to cancer-driving genes. Based on these findings, epigenetic inhibitors reduce viability of ER-positive breast cancer cells that display absence of GR activity. Our findings provide insights into how GR controls ER-positive breast cancer growth and may have implications for patients' prognostication and provide novel therapeutic candidates for breast cancer treatment.
Collapse
Affiliation(s)
- Stefan Prekovic
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Center for Molecular MedicineUMC UtrechtUtrechtThe Netherlands
| | | | - Merel Roest
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Daniel Roden
- Cancer Ecosystems ProgramGarvan Institute of Medical ResearchDarlinghurstNSWAustralia
- School of Clinical Medicine, Faculty of Medicine and HealthUNSW SydneySydneyNSWAustralia
| | - Catrin Lutz
- Division of Molecular Pathology, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Karianne Schuurman
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Mark Opdam
- Division of Molecular Pathology, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Liesbeth Hoekman
- Mass Spectrometry/Proteomics FacilityThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Nina Abbott
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Tanja Tesselaar
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Maliha Wajahat
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical SchoolUniversity of AdelaideAdelaideSAAustralia
| | - Amy R Dwyer
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical SchoolUniversity of AdelaideAdelaideSAAustralia
| | - Isabel Mayayo‐Peralta
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Gabriela Gomez
- School of Pharmacy and Biomolecular SciencesThe Royal College of Surgeons University of Medicine and Health SciencesDublinIreland
| | - Maarten Altelaar
- Mass Spectrometry/Proteomics FacilityThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical SciencesUtrecht UniversityUtrechtThe Netherlands
| | - Roderick Beijersbergen
- Division of Molecular Carcinogenesis and Robotics and Screening CentreNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Balázs Győrffy
- TTK Cancer Biomarker Research GroupInstitute of EnzymologyBudapestHungary
- Department of Bioinformatics and 2nd Department of PediatricsSemmelweis UniversityBudapestHungary
| | - Leonie Young
- Endocrine Oncology Research Group, Department of SurgeryThe Royal College of Surgeons University of Medicine and Health SciencesDublinIreland
- Beaumont RCSI Cancer CentreBeaumont HospitalDublinIreland
| | - Sabine Linn
- Division of Molecular Pathology, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Jos Jonkers
- Division of Molecular Pathology, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Wayne Tilley
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical SchoolUniversity of AdelaideAdelaideSAAustralia
- Freemasons Centre for Male Health and WellbeingUniversity of AdelaideAdelaideSAAustralia
| | - Theresa Hickey
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical SchoolUniversity of AdelaideAdelaideSAAustralia
| | - Damir Vareslija
- School of Pharmacy and Biomolecular SciencesThe Royal College of Surgeons University of Medicine and Health SciencesDublinIreland
- Beaumont RCSI Cancer CentreBeaumont HospitalDublinIreland
| | - Alexander Swarbrick
- Cancer Ecosystems ProgramGarvan Institute of Medical ResearchDarlinghurstNSWAustralia
- School of Clinical Medicine, Faculty of Medicine and HealthUNSW SydneySydneyNSWAustralia
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical EngineeringEindhoven University of TechnologyEindhovenThe Netherlands
| |
Collapse
|
11
|
DeAngelo SL, Győrffy B, Koutmos M, Shah YM. Selenoproteins and tRNA-Sec: regulators of cancer redox homeostasis. Trends Cancer 2023; 9:1006-1018. [PMID: 37716885 PMCID: PMC10843386 DOI: 10.1016/j.trecan.2023.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 06/06/2023] [Revised: 08/01/2023] [Accepted: 08/08/2023] [Indexed: 09/18/2023]
Abstract
In the past two decades significant progress has been made in uncovering the biological function of selenium. Selenium, an essential trace element, is required for the biogenesis of selenocysteine which is then incorporated into selenoproteins. These selenoproteins have emerged as central regulators of cellular antioxidant capacity and maintenance of redox homeostasis. This review provides a comprehensive examination of the multifaceted functions of selenoproteins with a particular emphasis on their contributions to cellular antioxidant capacity. Additionally, we highlight the promising potential of targeting selenoproteins and the biogenesis of selenocysteine as avenues for therapeutic intervention in cancer. By understanding the intricate relationship between selenium, selenoproteins, and reactive oxygen species (ROS), insights can be gained to develop therapies that exploit the inherent vulnerabilities of cancer cells.
Collapse
Affiliation(s)
- Stephen L DeAngelo
- Department of Cancer Biology, University of Michigan, Ann Arbor, MI, USA
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
| | - Markos Koutmos
- Department of Cancer Biology, University of Michigan, Ann Arbor, MI, USA; Department of Chemistry, University of Michigan, Ann Arbor, MI, USA; Program in Biophysics, University of Michigan, Ann Arbor, MI, USA
| | - Yatrik M Shah
- Department of Cancer Biology, University of Michigan, Ann Arbor, MI, USA; Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.
| |
Collapse
|
12
|
Bosi C, Bartha Á, Galbardi B, Notini G, Naldini MM, Licata L, Viale G, Mariani M, Pistilli B, Ali HR, André F, Piras M, Callari M, Barreca M, Locatelli A, Viganò L, Criscitiello C, Pusztai L, Curigliano G, Győrffy B, Dugo M, Bianchini G. Pan-cancer analysis of antibody-drug conjugate targets and putative predictors of treatment response. Eur J Cancer 2023; 195:113379. [PMID: 37913680 DOI: 10.1016/j.ejca.2023.113379] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 10/09/2023] [Indexed: 11/03/2023]
Abstract
BACKGROUND Antibody-drug conjugates (ADCs) are a rapidly expanding class of compounds in oncology. Our goal was to assess the expression of ADC targets and potential downstream determining factors of activity across pan-cancer and normal tissues. MATERIALS AND METHODS ADCs in clinical trials (n = 121) were identified through ClinicalTrials.gov, corresponding to 54 targets. Genes potentially implicated in treatment response were identified in the literature. Gene expression from The Cancer Genome Atlas (9000+ cancers of 31 cancer types), the Genotype-Tissue Expression database (n = 19,000 samples from 31 normal tissue types), and the TNMplot.com (n = 12,494 unmatched primary and metastatic samples) were used in this analysis. To compare relative expression across and within tumour types we used pooled normal tissues as reference. RESULTS For most ADC targets, mRNA levels correlated with protein expression. Pan-cancer target expression distributions identified appealing cancer types for each ADC development. Co-expression of multiple targets was common and suggested opportunities for ADC combinations. Expression levels of genes potentially implicated in ADC response downstream of the target might provide additional information (e.g. TOP1 was highly expressed in many tumour types, including breast and lung cancers). Metastatic compared to primary tissues overexpressed some ADCs targets. Single sample "targetgram" plots were generated to visualise the expression of potentially competing ADC targets and resistance/sensitivity markers highlighting high inter-patient heterogeneity. Off-cancer target expression only partially explains adverse events, while expression of determinants of payload activity explained more of the observed toxicities. CONCLUSION Our findings draw attention to new therapeutic opportunities for ADCs that can be tested in the clinic and our web platform (https://tnmplot.com) can assist in prioritising upcoming ADC targets for clinical development.
Collapse
Affiliation(s)
- Carlo Bosi
- Università Vita-Salute San Raffaele, Milan, Italy; Department of Medical Oncology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Áron Bartha
- Department of Bioinformatics, Semmelweis University, Tűzoltó Utca 7-9, 1094 Budapest, Hungary; Research Centre for Natural Sciences, Oncology Biomarker Research Group, Institute of Molecular Life Sciences, Eötvös Loránd Research Network, Magyar Tudósok Körútja 2, 1117 Budapest, Hungary
| | - Barbara Galbardi
- Department of Medical Oncology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Giulia Notini
- Università Vita-Salute San Raffaele, Milan, Italy; Department of Medical Oncology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Matteo M Naldini
- Università Vita-Salute San Raffaele, Milan, Italy; Department of Medical Oncology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Luca Licata
- Department of Medical Oncology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Giulia Viale
- Department of Medical Oncology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Marco Mariani
- Università Vita-Salute San Raffaele, Milan, Italy; Department of Medical Oncology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Barbara Pistilli
- Department of Medical Oncology, Gustave Roussy Cancer Center, Villejuif, France
| | - H Raza Ali
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK; Department of Histopathology, Addenbrookes Hospital, Cambridge, UK
| | - Fabrice André
- Department of Medical Oncology, Gustave Roussy Cancer Center, Villejuif, France
| | - Marta Piras
- Department of Medical Oncology, IRCCS Ospedale San Raffaele, Milan, Italy
| | | | | | - Alberta Locatelli
- Department of Medical Oncology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Lucia Viganò
- Department of Medical Oncology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Carmen Criscitiello
- Division of Early Drug Development, European Institute of Oncology, IRCCS, Milano, Italy; Department of Oncology and Hemato-Oncology, University of Milano, Milano, Italy
| | - Lajos Pusztai
- Department of Internal Medicine, Section of Medical Oncology, Yale School of Medicine, New Haven, CT, USA
| | - Giuseppe Curigliano
- Division of Early Drug Development, European Institute of Oncology, IRCCS, Milano, Italy; Department of Oncology and Hemato-Oncology, University of Milano, Milano, Italy
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Tűzoltó Utca 7-9, 1094 Budapest, Hungary; Research Centre for Natural Sciences, Oncology Biomarker Research Group, Institute of Molecular Life Sciences, Eötvös Loránd Research Network, Magyar Tudósok Körútja 2, 1117 Budapest, Hungary
| | - Matteo Dugo
- Department of Medical Oncology, IRCCS Ospedale San Raffaele, Milan, Italy.
| | - Giampaolo Bianchini
- Università Vita-Salute San Raffaele, Milan, Italy; Department of Medical Oncology, IRCCS Ospedale San Raffaele, Milan, Italy.
| |
Collapse
|
13
|
Szepesi Kovács D, Kontra B, Chiovini B, Müller D, Tóth EZ, Ábrányi-Balogh P, Wittner L, Várady G, Turczel G, Farkas Ö, Owen MC, Katona G, Győrffy B, Keserű GM, Mucsi Z, Rózsa BJ, Kovács E. Effective synthesis, development and application of a highly fluorescent cyanine dye for antibody conjugation and microscopy imaging. Org Biomol Chem 2023; 21:8829-8836. [PMID: 37917021 DOI: 10.1039/d3ob01471a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
An asymmetric cyanine-type fluorescent dye was designed and synthesized via a versatile, multi-step process, aiming to conjugate with an Her2+ receptor specific antibody by an azide-alkyne click reaction. The aromaticity and the excitation and relaxation energetics of the fluorophore were characterized by computational methods. The synthesized dye exhibited excellent fluorescence properties for confocal microscopy, offering efficient applicability in in vitro imaging due to its merits such as a high molar absorption coefficient (36 816 M-1 cm-1), excellent brightness, optimal wavelength (627 nm), larger Stokes shift (26 nm) and appropriate photostability compared to cyanines. The conjugated cyanine-trastuzumab was constructed via an effective, metal-free, strain-promoted azide-alkyne click reaction leading to a regulated number of dyes being conjugated. This novel cyanine-labelled antibody was successfully applied for in vitro confocal imaging and flow cytometry of Her2+ tumor cells.
Collapse
Affiliation(s)
- Dénes Szepesi Kovács
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, H-1111 Budapest, Hungary
- National Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Bence Kontra
- Brain Vision Center, H-1094 Budapest, Hungary
- Femtonics Ltd., H-1094 Budapest, Hungary
- Semmelweis University Doctoral School, H-1085 Budapest, Hungary
| | - Balázs Chiovini
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, H-1444 Budapest, Hungary
| | - Dalma Müller
- Semmelweis University Doctoral School, H-1085 Budapest, Hungary
- Oncology Biomarker Research Group, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary
- Department of Bioinformatics, Semmelweis University, H-1094, Budapest, Hungary
| | - Estilla Zsófia Tóth
- National Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
- Semmelweis University Doctoral School, H-1085 Budapest, Hungary
- Integrative Neuroscience Research Group, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary
| | - Péter Ábrányi-Balogh
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, H-1111 Budapest, Hungary
- National Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Lucia Wittner
- National Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
- Integrative Neuroscience Research Group, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary
| | - György Várady
- Molecular Cell Biology Research Group, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary
| | - Gábor Turczel
- NMR Research Laboratory, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary
| | - Ödön Farkas
- Department of Organic Chemistry, Eötvös Loránd University, H-1117 Budapest, Hungary
| | - Michael C Owen
- Institute of Chemistry, University of Miskolc, Miskolc H-3515, Hungary
- Higher Education and Industrial Cooperation Centre, University of Miskolc, Miskolc H-3515, Hungary
| | - Gergely Katona
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, H-1444 Budapest, Hungary
| | - Balázs Győrffy
- National Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
- Oncology Biomarker Research Group, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary
- Department of Bioinformatics, Semmelweis University, H-1094, Budapest, Hungary
| | - György Miklós Keserű
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, H-1111 Budapest, Hungary
- National Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Zoltán Mucsi
- Brain Vision Center, H-1094 Budapest, Hungary
- Femtonics Ltd., H-1094 Budapest, Hungary
- Institute of Chemistry, University of Miskolc, Miskolc H-3515, Hungary
| | - Balázs J Rózsa
- Brain Vision Center, H-1094 Budapest, Hungary
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, H-1444 Budapest, Hungary
- Laboratory of 3D Functional Network and Dendritic Imaging, HUN-REN Institute of Experimental Medicine, H-1083 Budapest, Hungary
| | - Ervin Kovács
- Femtonics Ltd., H-1094 Budapest, Hungary
- Polymer Chemistry and Physics Research Group, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary.
| |
Collapse
|
14
|
Roche ME, Ko YH, Domingo-Vidal M, Lin Z, Whitaker-Menezes D, Birbe RC, Tuluc M, Győrffy B, Caro J, Philp NJ, Bartrons R, Martinez-Outschoorn U. TP53 Induced Glycolysis and Apoptosis Regulator and Monocarboxylate Transporter 4 drive metabolic reprogramming with c-MYC and NFkB activation in breast cancer. Int J Cancer 2023; 153:1671-1683. [PMID: 37497753 DOI: 10.1002/ijc.34660] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/22/2023] [Accepted: 06/29/2023] [Indexed: 07/28/2023]
Abstract
Breast cancer is composed of metabolically coupled cellular compartments with upregulation of TP53 Induced Glycolysis and Apoptosis Regulator (TIGAR) in carcinoma cells and loss of caveolin 1 (CAV1) with upregulation of monocarboxylate transporter 4 (MCT4) in fibroblasts. The mechanisms that drive metabolic coupling are poorly characterized. The effects of TIGAR on fibroblast CAV1 and MCT4 expression and breast cancer aggressiveness was studied using coculture and conditioned media systems and in-vivo. Also, the role of cytokines in promoting tumor metabolic coupling via MCT4 on cancer aggressiveness was studied. TIGAR downregulation in breast carcinoma cells reduces tumor growth. TIGAR overexpression in carcinoma cells drives MCT4 expression and NFkB activation in fibroblasts. IL6 and TGFB drive TIGAR upregulation in carcinoma cells, reduce CAV1 and increase MCT4 expression in fibroblasts. Tumor growth is abrogated in the presence of MCT4 knockout fibroblasts and environment. We discovered coregulation of c-MYC and TIGAR in carcinoma cells driven by lactate. Metabolic coupling primes the tumor microenvironment allowing for production, uptake and utilization of lactate. In sum, aggressive breast cancer is dependent on metabolic coupling.
Collapse
Affiliation(s)
- Megan E Roche
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Ying-Hui Ko
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Marina Domingo-Vidal
- Immunology, Microenvironment & Metastasis Program, Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Zhao Lin
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Diana Whitaker-Menezes
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Ruth C Birbe
- Department of Pathology, Cooper University Hospital, Camden, New Jersey, USA
| | - Madalina Tuluc
- Department of Pathology, Anatomy and Cell Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Balázs Győrffy
- MTA TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Budapest, Hungary
- Semmelweis University 2nd Department of Pediatrics, Budapest, Hungary
| | - Jaime Caro
- Department of Medicine, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Nancy J Philp
- Department of Pathology, Anatomy and Cell Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Ramon Bartrons
- Department of Physiological Sciences, University of Barcelona, Barcelona, Spain
| | - Ubaldo Martinez-Outschoorn
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| |
Collapse
|
15
|
Giordano C, Accattatis FM, Gelsomino L, Del Console P, Győrffy B, Giuliano M, Veneziani BM, Arpino G, De Angelis C, De Placido P, Pietroluongo E, Zinno F, Bonofiglio D, Andò S, Barone I, Catalano S. miRNAs in the Box: Potential Diagnostic Role for Extracellular Vesicle-Packaged miRNA-27a and miRNA-128 in Breast Cancer. Int J Mol Sci 2023; 24:15695. [PMID: 37958677 PMCID: PMC10649351 DOI: 10.3390/ijms242115695] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
Circulating extracellular vesicle (EV)-derived microRNAs (miRNAs) are now considered the next generation of cancer "theranostic" tools, with strong clinical relevance. Although their potential in breast cancer diagnosis has been widely reported, further studies are still required to address this challenging issue. The present study examined the expression profiles of EV-packaged miRNAs to identify novel miRNA signatures in breast cancer and verified their diagnostic accuracy. Circulating EVs were isolated from healthy controls and breast cancer patients and characterized following the MISEV 2018 guidelines. RNA-sequencing and real-time PCR showed that miRNA-27a and miRNA-128 were significantly down-regulated in patient-derived EVs compared to controls in screening and validation cohorts. Bioinformatics analyses of miRNA-target genes indicated several enriched biological processes/pathways related to breast cancer. Receiver operating characteristic (ROC) curves highlighted the ability of these EV-miRNAs to distinguish breast cancer patients from non-cancer controls. According to other reports, the levels of EV-miRNA-27a and EV-miRNA-128 are not associated with their circulating ones. Finally, evidence from the studies included in our systematic review underscores how the expression of these miRNAs in biofluids is still underinvestigated. Our findings unraveled the role of serum EV-derived miRNA-27a and miRNA-128 in breast cancer, encouraging further investigation of these two miRNAs within EVs towards improved breast cancer detection.
Collapse
Affiliation(s)
- Cinzia Giordano
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Via P. Bucci, Arcavacata di Rende (CS), 87036 Cosenza, Italy; (F.M.A.); (L.G.); (P.D.C.); (D.B.); (S.A.); (I.B.)
- Centro Sanitario, University of Calabria, Via P. Bucci, Arcavacata di Rende (CS), 87036 Cosenza, Italy
- Clinical Laboratory Unit, A.O. “Annunziata”, 87100 Cosenza, Italy
| | - Felice Maria Accattatis
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Via P. Bucci, Arcavacata di Rende (CS), 87036 Cosenza, Italy; (F.M.A.); (L.G.); (P.D.C.); (D.B.); (S.A.); (I.B.)
- Centro Sanitario, University of Calabria, Via P. Bucci, Arcavacata di Rende (CS), 87036 Cosenza, Italy
| | - Luca Gelsomino
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Via P. Bucci, Arcavacata di Rende (CS), 87036 Cosenza, Italy; (F.M.A.); (L.G.); (P.D.C.); (D.B.); (S.A.); (I.B.)
- Centro Sanitario, University of Calabria, Via P. Bucci, Arcavacata di Rende (CS), 87036 Cosenza, Italy
| | - Piercarlo Del Console
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Via P. Bucci, Arcavacata di Rende (CS), 87036 Cosenza, Italy; (F.M.A.); (L.G.); (P.D.C.); (D.B.); (S.A.); (I.B.)
- Centro Sanitario, University of Calabria, Via P. Bucci, Arcavacata di Rende (CS), 87036 Cosenza, Italy
| | - Balázs Győrffy
- Departments of Bioinformatics and Pediatrics, Semmelweis University, 1094 Budapest, Hungary;
- TTK Cancer Biomarker Research Group, 1117 Budapest, Hungary
| | - Mario Giuliano
- Department of Clinical Medicine and Surgery, University of Naples Federico II, 80133 Naples, Italy; (M.G.); (G.A.); (C.D.A.); (P.D.P.); (E.P.)
| | - Bianca Maria Veneziani
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80133 Naples, Italy;
| | - Grazia Arpino
- Department of Clinical Medicine and Surgery, University of Naples Federico II, 80133 Naples, Italy; (M.G.); (G.A.); (C.D.A.); (P.D.P.); (E.P.)
| | - Carmine De Angelis
- Department of Clinical Medicine and Surgery, University of Naples Federico II, 80133 Naples, Italy; (M.G.); (G.A.); (C.D.A.); (P.D.P.); (E.P.)
| | - Pietro De Placido
- Department of Clinical Medicine and Surgery, University of Naples Federico II, 80133 Naples, Italy; (M.G.); (G.A.); (C.D.A.); (P.D.P.); (E.P.)
| | - Erica Pietroluongo
- Department of Clinical Medicine and Surgery, University of Naples Federico II, 80133 Naples, Italy; (M.G.); (G.A.); (C.D.A.); (P.D.P.); (E.P.)
| | - Francesco Zinno
- Immunohaematology and Transfusion Medicine, A.O. “Annunziata”, 87100 Cosenza, Italy;
| | - Daniela Bonofiglio
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Via P. Bucci, Arcavacata di Rende (CS), 87036 Cosenza, Italy; (F.M.A.); (L.G.); (P.D.C.); (D.B.); (S.A.); (I.B.)
- Centro Sanitario, University of Calabria, Via P. Bucci, Arcavacata di Rende (CS), 87036 Cosenza, Italy
| | - Sebastiano Andò
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Via P. Bucci, Arcavacata di Rende (CS), 87036 Cosenza, Italy; (F.M.A.); (L.G.); (P.D.C.); (D.B.); (S.A.); (I.B.)
- Centro Sanitario, University of Calabria, Via P. Bucci, Arcavacata di Rende (CS), 87036 Cosenza, Italy
| | - Ines Barone
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Via P. Bucci, Arcavacata di Rende (CS), 87036 Cosenza, Italy; (F.M.A.); (L.G.); (P.D.C.); (D.B.); (S.A.); (I.B.)
- Centro Sanitario, University of Calabria, Via P. Bucci, Arcavacata di Rende (CS), 87036 Cosenza, Italy
| | - Stefania Catalano
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Via P. Bucci, Arcavacata di Rende (CS), 87036 Cosenza, Italy; (F.M.A.); (L.G.); (P.D.C.); (D.B.); (S.A.); (I.B.)
- Centro Sanitario, University of Calabria, Via P. Bucci, Arcavacata di Rende (CS), 87036 Cosenza, Italy
- Clinical Laboratory Unit, A.O. “Annunziata”, 87100 Cosenza, Italy
| |
Collapse
|
16
|
Sánchez-Tilló E, Pedrosa L, Vila I, Chen Y, Győrffy B, Sánchez-Moral L, Siles L, Lozano JJ, Esteve-Codina A, Darling DS, Cuatrecasas M, Castells A, Maurel J, Postigo A. The EMT factor ZEB1 paradoxically inhibits EMT in BRAF-mutant carcinomas. JCI Insight 2023; 8:e164629. [PMID: 37870961 PMCID: PMC10619495 DOI: 10.1172/jci.insight.164629] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 08/18/2022] [Accepted: 09/05/2023] [Indexed: 10/25/2023] Open
Abstract
Despite being in the same pathway, mutations of KRAS and BRAF in colorectal carcinomas (CRCs) determine distinct progression courses. ZEB1 induces an epithelial-to-mesenchymal transition (EMT) and is associated with worse progression in most carcinomas. Using samples from patients with CRC, mouse models of KrasG12D and BrafV600E CRC, and a Zeb1-deficient mouse, we show that ZEB1 had opposite functions in KRAS- and BRAF-mutant CRCs. In KrasG12D CRCs, ZEB1 was correlated with a worse prognosis and a higher number of larger and undifferentiated (mesenchymal or EMT-like) tumors. Surprisingly, in BrafV600E CRC, ZEB1 was associated with better prognosis; fewer, smaller, and more differentiated (reduced EMT) primary tumors; and fewer metastases. ZEB1 was positively correlated in KRAS-mutant CRC cells and negatively in BRAF-mutant CRC cells with gene signatures for EMT, cell proliferation and survival, and ERK signaling. On a mechanistic level, ZEB1 knockdown in KRAS-mutant CRC cells increased apoptosis and reduced clonogenicity and anchorage-independent growth; the reverse occurred in BRAFV600E CRC cells. ZEB1 is associated with better prognosis and reduced EMT signature in patients harboring BRAF CRCs. These data suggest that ZEB1 can function as a tumor suppressor in BRAF-mutant CRCs, highlighting the importance of considering the KRAS/BRAF mutational background of CRCs in therapeutic strategies targeting ZEB1/EMT.
Collapse
Affiliation(s)
- Ester Sánchez-Tilló
- Group of Gene Regulation in Stem Cells, Cell Plasticity, Differentiation, and Cancer, Department of Oncology and Hematology, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Group of Gastrointestinal and Pancreatic Oncology, Department of Liver, Digestive System and Metabolism, IDIBAPS, Barcelona, Spain
- Biomedical Research Network in Gastrointestinal and Liver Diseases (CIBEREHD), Carlos III National Health Institute (ISCIII), Barcelona, Spain
| | - Leire Pedrosa
- Group of Translational Genomics and Targeted Therapeutics in Solid Tumors, IDIBAPS, and Department of Medical Oncology, Hospital Clinic, Barcelona, Spain
| | - Ingrid Vila
- Group of Gene Regulation in Stem Cells, Cell Plasticity, Differentiation, and Cancer, Department of Oncology and Hematology, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Yongxu Chen
- Group of Gene Regulation in Stem Cells, Cell Plasticity, Differentiation, and Cancer, Department of Oncology and Hematology, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Balázs Győrffy
- Cancer Biomarker Research Group, Research Centre for Natural Sciences (TKK), and Department of Bioinformatics and 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Lidia Sánchez-Moral
- Group of Gene Regulation in Stem Cells, Cell Plasticity, Differentiation, and Cancer, Department of Oncology and Hematology, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Laura Siles
- Group of Gene Regulation in Stem Cells, Cell Plasticity, Differentiation, and Cancer, Department of Oncology and Hematology, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Juan J. Lozano
- Bioinformatics Platform, CIBEREHD, ISCIII, Barcelona, Spain
| | - Anna Esteve-Codina
- National Centre for Genomic Analysis (CNAG) Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Department of Medicine and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Douglas S. Darling
- Department of Oral Immunology, and Center for Genetics and Molecular Medicine, University of Louisville, Louisville, Kentucky, USA
| | - Miriam Cuatrecasas
- Biomedical Research Network in Gastrointestinal and Liver Diseases (CIBEREHD), Carlos III National Health Institute (ISCIII), Barcelona, Spain
- Group of Molecular Pathology of Inflammatory Conditions and Solid Tumours, Department of Oncology and Hematology, IDIBAPS, Barcelona, Spain
- Department of Pathology, Hospital Clínic and University of Barcelona School of Medicine, Barcelona, Spain
| | - Antoni Castells
- Group of Gastrointestinal and Pancreatic Oncology, Department of Liver, Digestive System and Metabolism, IDIBAPS, Barcelona, Spain
- Biomedical Research Network in Gastrointestinal and Liver Diseases (CIBEREHD), Carlos III National Health Institute (ISCIII), Barcelona, Spain
- Department of Gastroenterology, Hospital Clinic and University of Barcelona School of Medicine, Barcelona, Spain
| | - Joan Maurel
- Biomedical Research Network in Gastrointestinal and Liver Diseases (CIBEREHD), Carlos III National Health Institute (ISCIII), Barcelona, Spain
- Group of Translational Genomics and Targeted Therapeutics in Solid Tumors, IDIBAPS, and Department of Medical Oncology, Hospital Clinic, Barcelona, Spain
| | - Antonio Postigo
- Group of Gene Regulation in Stem Cells, Cell Plasticity, Differentiation, and Cancer, Department of Oncology and Hematology, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Biomedical Research Network in Gastrointestinal and Liver Diseases (CIBEREHD), Carlos III National Health Institute (ISCIII), Barcelona, Spain
- Molecular Targets Program, Department of Medicine, J.G. Brown Cancer Center, Louisville, Kentucky, USA
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| |
Collapse
|
17
|
Wang Z, Zhang N, Zhang M, Jiang Y, Ng AS, Bridges E, Zhang W, Zeng X, Luo Q, Liang J, Győrffy B, Hublitz P, Liang Z, Fischer R, Kerr D, Harris AL, Cai S. GTP Cyclohydrolase Drives Breast Cancer Development and Promotes EMT in an Enzyme-Independent Manner. Cancer Res 2023; 83:3400-3413. [PMID: 37463466 DOI: 10.1158/0008-5472.can-22-3471] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 04/27/2023] [Accepted: 07/14/2023] [Indexed: 07/20/2023]
Abstract
GTP cyclohydrolase (GCH1) is the rate-limiting enzyme for tetrahydrobiopterin (BH4) biosynthesis. The catalysis of BH4 biosynthesis is tightly regulated for physiological neurotransmission, inflammation, and vascular tone. Paradoxically, BH4 has emerged as an oncometabolite regulating tumor growth, but the effects on tumor development remain controversial. Here, we found that GCH1 potentiated the growth of triple-negative breast cancer (TNBC) and HER2+ breast cancer and transformed nontumor breast epithelial cells. Independent of BH4 production, GCH1 protein induced epithelial-to-mesenchymal transition by binding to vimentin (Vim), which was mediated by HSP90. Conversely, GCH1 ablation impaired tumor growth, suppressed Vim in TNBC, and inhibited EGFR/ERK signaling while activating the p53 pathway in estrogen receptor-positive tumor cells. GCH1 deficiency increases tumor cell sensitivity to HSP90 inhibition and endocrine treatments. In addition, high GCH1 correlated with poor breast cancer survival. Together, this study reveals an enzyme-independent oncogenic role of GCH1, presenting it as a potential target for therapeutic development. SIGNIFICANCE GTP cyclohydrolase functions as an oncogene in breast cancer and binds vimentin to induce epithelial-to-mesenchymal transition independently of its enzyme activity, which confers targetable vulnerabilities for developing breast cancer treatment strategies.
Collapse
Affiliation(s)
- Zijing Wang
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- Sichuan University-Oxford University Huaxi Joint Centre for Gastrointestinal Cancer, West China Hospital, Sichuan University, Chengdu, China
| | - Nan Zhang
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- Sichuan University-Oxford University Huaxi Joint Centre for Gastrointestinal Cancer, West China Hospital, Sichuan University, Chengdu, China
| | - Miao Zhang
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- School of Acupuncture and Moxibustion, Fujian University of Traditional Chinese Medicine, China
| | - Yao Jiang
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Aik Seng Ng
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Esther Bridges
- Molecular Oncology Laboratories, University Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Wei Zhang
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Xin Zeng
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Qi Luo
- Xiamen Cancer Hospital, Xiamen First Hospital, Xiamen University, Fujian, China
| | - Jiabien Liang
- Xiamen Cancer Hospital, Xiamen First Hospital, Xiamen University, Fujian, China
| | - Balázs Győrffy
- TTK Cancer Biomarker Research Group, Institute of Enzymology, and Semmelweis University Department Bioinformatics and Department of Paediatrics, Budapest, Hungary
| | - Philip Hublitz
- Genome Engineering Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Zhu Liang
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, United Kingdom
| | - Roman Fischer
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, United Kingdom
| | - David Kerr
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Adrian L Harris
- Molecular Oncology Laboratories, University Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Shijie Cai
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| |
Collapse
|
18
|
Menyhárt O, Fekete TJ, Győrffy B. [Increased activity of inflammation-related signaling pathways in anthracycline- paclitaxel resistant breast carcinomas]. Magy Onkol 2023; 67:203-212. [PMID: 37768118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023]
Abstract
A frequently recommended systemic therapy for breast cancer involves a combination of anthracyclines and taxanes, however, approximately 30% of patients experience recurrence. We aimed to investigate the mechanisms of resistance to anthracycline-paclitaxel based treatment by analyzing gene expression patterns in tumor samples collected during surgery and subsequent therapeutic responses. A database of 187 patients with information about relapse-free survival (RFS) allowed the analysis of 10,017 genes. Patients were divided into responders and nonresponders based on whether relapse occurred within sixty months. The expression of each gene was compared between the two groups using the Mann-Whitney U-test, with a statistical significance set at p <0.05 and fold change (FC) ≥1.44. We identified 51 up-regulated genes among nonresponders, primarily associated with inflammatory processes and the innate immune response. The high expression of SLC7A5, encoding an amino acid transporter, was linked to worse overall survival (p = 2.3E-10), with elevated expression in tumors (p = 2.94E-20), and further increase in metastases (p = 1.33E-10). Our results emphasize the significance of tumor microenvironment and metabolism in therapy resistance. These findings may allow better patient classification and identification of relevant treatment targets.
Collapse
Affiliation(s)
- Otília Menyhárt
- Bioinformatikai Tanszék, Semmelweis Egyetem, Budapest, Hungary.
| | | | - Balázs Győrffy
- Bioinformatikai Tanszék, Semmelweis Egyetem, Budapest, Hungary.
| |
Collapse
|
19
|
Wang XQ, Danenberg E, Huang CS, Egle D, Callari M, Bermejo B, Dugo M, Zamagni C, Thill M, Anton A, Zambelli S, Russo S, Ciruelos EM, Greil R, Győrffy B, Semiglazov V, Colleoni M, Kelly CM, Mariani G, Del Mastro L, Biasi O, Seitz RS, Valagussa P, Viale G, Gianni L, Bianchini G, Ali HR. Spatial predictors of immunotherapy response in triple-negative breast cancer. Nature 2023; 621:868-876. [PMID: 37674077 PMCID: PMC10533410 DOI: 10.1038/s41586-023-06498-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [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: 06/28/2022] [Accepted: 07/28/2023] [Indexed: 09/08/2023]
Abstract
Immune checkpoint blockade (ICB) benefits some patients with triple-negative breast cancer, but what distinguishes responders from non-responders is unclear1. Because ICB targets cell-cell interactions2, we investigated the impact of multicellular spatial organization on response, and explored how ICB remodels the tumour microenvironment. We show that cell phenotype, activation state and spatial location are intimately linked, influence ICB effect and differ in sensitive versus resistant tumours early on-treatment. We used imaging mass cytometry3 to profile the in situ expression of 43 proteins in tumours from patients in a randomized trial of neoadjuvant ICB, sampled at three timepoints (baseline, n = 243; early on-treatment, n = 207; post-treatment, n = 210). Multivariate modelling showed that the fractions of proliferating CD8+TCF1+T cells and MHCII+ cancer cells were dominant predictors of response, followed by cancer-immune interactions with B cells and granzyme B+ T cells. On-treatment, responsive tumours contained abundant granzyme B+ T cells, whereas resistant tumours were characterized by CD15+ cancer cells. Response was best predicted by combining tissue features before and on-treatment, pointing to a role for early biopsies in guiding adaptive therapy. Our findings show that multicellular spatial organization is a major determinant of ICB effect and suggest that its systematic enumeration in situ could help realize precision immuno-oncology.
Collapse
Affiliation(s)
- Xiao Qian Wang
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Esther Danenberg
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Chiun-Sheng Huang
- National Taiwan University Hospital, College of Medicine, National Taiwan University and Taiwan Breast Cancer Consortium, Taipei, Taiwan
| | - Daniel Egle
- Department of Gynecology, Brust Gesundheit Zentrum Tirol, Medical University Innsbruck, Innsbruck, Austria
| | | | - Begoña Bermejo
- Medical Oncology, Hospital Clínico Universitario de Valencia, Biomedical Research Institute INCLIVA, Valencia, Spain
- Medicine Department, Universidad de Valencia, Valencia, Spain
- Oncology Biomedical Research National Network (CIBERONC-ISCIII), Madrid, Spain
| | | | - Claudio Zamagni
- IRCCS Azienda Ospedaliero-universitaria di Bologna, Bologna, Italy
| | - Marc Thill
- Department of Gynecology and Gynecological Oncology, Agaplesion Markus Krankenhaus, Frankfurt am Main, Germany
| | - Anton Anton
- Hospital Universitario Miguel Servet, Zaragoza, Spain
| | | | - Stefania Russo
- Department of Oncology, Azienda Sanitaria Universitaria Friuli Centrale, Udine, Italy
| | | | - Richard Greil
- 3rd Medical Department, Paracelsus Medical University Salzburg, Salzburg, Austria
- Salzburg Cancer Research Institute-CCCIT, Salzburg, Austria
- Cancer Cluster Salzburg, Salzburg, Austria
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
- Cancer Biomarker Research Group, Research Centre for Natural Sciences, Institute of Enzymology, Budapest, Hungary
| | | | | | - Catherine M Kelly
- Mater Private Hospital, Dublin and Cancer Trials Ireland Breast Group, Dublin, Ireland
| | | | - Lucia Del Mastro
- IRCCS Ospedale Policlinico San Martino, UO Clinica di Oncologia Medica, Genoa, Italy
- Dipartimento di Medicina Interna e Specialità Mediche (Di.M.I.), Università di Genova, Genoa, Italy
| | - Olivia Biasi
- IEO, Istituto Europeo di Oncologia, IRCCS, Milan, Italy
| | | | | | - Giuseppe Viale
- IEO, Istituto Europeo di Oncologia, IRCCS, Milan, Italy
- University of Milan, Milan, Italy
| | | | | | - H Raza Ali
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK.
- Department of Histopathology, Addenbrookes Hospital, Cambridge, UK.
| |
Collapse
|
20
|
Kovács SA, Fekete JT, Győrffy B. Predictive biomarkers of immunotherapy response with pharmacological applications in solid tumors. Acta Pharmacol Sin 2023; 44:1879-1889. [PMID: 37055532 PMCID: PMC10462766 DOI: 10.1038/s41401-023-01079-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [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: 11/06/2022] [Accepted: 03/14/2023] [Indexed: 04/15/2023] Open
Abstract
Immune-checkpoint inhibitors show promising effects in the treatment of multiple tumor types. Biomarkers are biological indicators used to select patients for a systemic anticancer treatment, but there are only a few clinically useful biomarkers such as PD-L1 expression and tumor mutational burden, which can be used to predict immunotherapy response. In this study, we established a database consisting of both gene expression and clinical data to identify biomarkers of response to anti-PD-1, anti-PD-L1, and anti-CTLA-4 immunotherapies. A GEO screening was executed to identify datasets with simultaneously available clinical response and transcriptomic data regardless of cancer type. The screening was restricted to the studies involving administration of anti-PD-1 (nivolumab, pembrolizumab), anti-PD-L1 (atezolizumab, durvalumab) or anti-CTLA-4 (ipilimumab) agents. Receiver operating characteristic (ROC) analysis and Mann-Whitney test were executed across all genes to identify features related to therapy response. The database consisted of 1434 tumor tissue samples from 19 datasets with esophageal, gastric, head and neck, lung, and urothelial cancers, plus melanoma. The strongest druggable gene candidates linked to anti-PD-1 resistance were SPIN1 (AUC = 0.682, P = 9.1E-12), SRC (AUC = 0.667, P = 5.9E-10), SETD7 (AUC = 0.663, P = 1.0E-09), FGFR3 (AUC = 0.657, P = 3.7E-09), YAP1 (AUC = 0.655, P = 6.0E-09), TEAD3 (AUC = 0.649, P = 4.1E-08) and BCL2 (AUC = 0.634, P = 9.7E-08). In the anti-CTLA-4 treatment cohort, BLCAP (AUC = 0.735, P = 2.1E-06) was the most promising gene candidate. No therapeutically relevant target was found to be predictive in the anti-PD-L1 cohort. In the anti-PD-1 group, we were able to confirm the significant correlation with survival for the mismatch-repair genes MLH1 and MSH6. A web platform for further analysis and validation of new biomarker candidates was set up and available at https://www.rocplot.com/immune . In summary, a database and a web platform were established to investigate biomarkers of immunotherapy response in a large cohort of solid tumor samples. Our results could help to identify new patient cohorts eligible for immunotherapy.
Collapse
Affiliation(s)
- Szonja Anna Kovács
- Department of Bioinformatics, Semmelweis University, Tűzoltó utca 7-9, 1094, Budapest, Hungary
- Doctoral School of Pathological Sciences, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
- National Laboratory for Drug Research and Development, Magyar tudósok körútja 2 1117, Budapest, Hungary
| | - János Tibor Fekete
- National Laboratory for Drug Research and Development, Magyar tudósok körútja 2 1117, Budapest, Hungary
- Research Centre for Natural Sciences, Oncology Biomarker Research Group, Institute of Enzymology, Eötvös Loránd Research Network, Magyar Tudósok körútja 2, 1117, Budapest, Hungary
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Tűzoltó utca 7-9, 1094, Budapest, Hungary.
- Department of Pediatrics, Semmelweis University, Tűzoltó utca 7-9, 1094, Budapest, Hungary.
| |
Collapse
|
21
|
Szluka P, Csajbók E, Győrffy B. Relationship between bibliometric indicators and university ranking positions. Sci Rep 2023; 13:14193. [PMID: 37648684 PMCID: PMC10468493 DOI: 10.1038/s41598-023-35306-1] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 05/16/2023] [Indexed: 09/01/2023] Open
Abstract
A growing interest for demonstrating prestige and status of higher education institutions has spurred the establishment of several international ranking systems. A major percentage of these rankings include parameters related to scientific productivity. Here, we examined the differences between diverse rankings as well as correlation with bibliometric parameters and disciplines for the top universities. We investigated the top 300 universities from four international rankings, the Times Higher Education World University Ranking (THE), the QS World University Rankings (QS) the ShanghaiRanking-Academic Ranking of World Universities (ARWU) and the U.S.News Best Global Universities Ranking (USNews). The assessed parameters include ranking positions, size related and bibliometrics-related indicators of each selected ranking. The weight of scientometric parameters ranges between 20% (QS) and 75% (USNews). The most important parameters defining ranking positions include citations, international reputation, and the number of researchers, but the correlation strength varies among ranking systems. The absolute number of publications and citations are particularly important in ARWU and USNews rankings, and scientific category normalized (field weighted) citation impact is central in THE and USNews rankings. Our results confirm that universities having outstanding results in rankings using size-independent indicators (QS and THE) compared to others have significantly lower number of students. High impact research can improve position in ARWU and USNews ranking lists. Regarding to different disciplines, the main results show that outstanding universities in THE ranking have higher publication activity in social sciences and universities which perform better in USNews and QS ranking have more publications in science, technology, and medicine fields and lower score in social sciences. In brief, here we present a comprehensive analysis of the correlation between scientometric parameters and university ranking positions, as well as the performance of outstanding universities and their correlation with different disciplines, to help decision makers select parameters for strengthening and to attract the interest of prospective students and their parents via a better understanding of the functions of different ranks.
Collapse
Affiliation(s)
- Péter Szluka
- Central Library, Semmelweis University, 1088, Budapest, Hungary
| | - Edit Csajbók
- Central Library, Semmelweis University, 1088, Budapest, Hungary
- Research Center for Natural Sciences, Institute of Enzymology, Magyar Tudósok Körútja 2, 1117, Budapest, Hungary
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Tűzoltó Utca 7-9, 1094, Budapest, Hungary.
- 2nd Department of Pediatrics, Semmelweis University, 1094, Budapest, Hungary.
| |
Collapse
|
22
|
Fu X, Pereira R, Liu CC, De Angelis C, Shea MJ, Nanda S, Qin L, Mitchell T, Cataldo ML, Veeraraghavan J, Sethunath V, Giuliano M, Gutierrez C, Győrffy B, Trivedi MV, Cohen O, Wagle N, Nardone A, Jeselsohn R, Rimawi MF, Osborne CK, Schiff R. High FOXA1 levels induce ER transcriptional reprogramming, a pro-metastatic secretome, and metastasis in endocrine-resistant breast cancer. Cell Rep 2023; 42:112821. [PMID: 37467106 DOI: 10.1016/j.celrep.2023.112821] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 11/03/2022] [Accepted: 07/03/2023] [Indexed: 07/21/2023] Open
Abstract
Aberrant activation of the forkhead protein FOXA1 is observed in advanced hormone-related cancers. However, the key mediators of high FOXA1 signaling remain elusive. We demonstrate that ectopic high FOXA1 (H-FOXA1) expression promotes estrogen receptor-positive (ER+) breast cancer (BC) metastasis in a xenograft mouse model. Mechanistically, H-FOXA1 reprograms ER-chromatin binding to elicit a core gene signature (CGS) enriched in ER+ endocrine-resistant (EndoR) cells. We identify Secretome14, a CGS subset encoding ER-dependent cancer secretory proteins, as a strong predictor for poor outcomes of ER+ BC. It is elevated in ER+ metastases vs. primary tumors, irrespective of ESR1 mutations. Genomic ER binding near Secretome14 genes is also increased in mutant ER-expressing or mitogen-treated ER+ BC cells and in ER+ metastatic vs. primary tumors, suggesting a convergent pathway including high growth factor receptor signaling in activating pro-metastatic secretome genes. Our findings uncover H-FOXA1-induced ER reprogramming that drives EndoR and metastasis partly via an H-FOXA1/ER-dependent secretome.
Collapse
Affiliation(s)
- Xiaoyong Fu
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Resel Pereira
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chia-Chia Liu
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Carmine De Angelis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA; Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Martin J Shea
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarmistha Nanda
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lanfang Qin
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tamika Mitchell
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Maria L Cataldo
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA; Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Jamunarani Veeraraghavan
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Vidyalakshmi Sethunath
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mario Giuliano
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Carolina Gutierrez
- Department of Pathology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, 1085 Budapest, Hungary; RCNS Cancer Biomarker Research Group, Institute of Enzymology, Magyar Tudósok körútja 2, 1117 Budapest, Hungary
| | - Meghana V Trivedi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pharmacy Practice and Translational Research, University of Houston, Houston, TX 77204, USA; Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Houston, TX 77204, USA
| | - Ofir Cohen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02210, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University, Beer-Sheva 84105, Israel
| | - Nikhil Wagle
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02210, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Agostina Nardone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02210, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02210, USA
| | - Rinath Jeselsohn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02210, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02210, USA
| | - Mothaffar F Rimawi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - C Kent Osborne
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rachel Schiff
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA.
| |
Collapse
|
23
|
Qin Y, Ashrafizadeh M, Mongiardini V, Grimaldi B, Crea F, Rietdorf K, Győrffy B, Klionsky DJ, Ren J, Zhang W, Zhang X. Autophagy and cancer drug resistance in dialogue: Pre-clinical and clinical evidence. Cancer Lett 2023; 570:216307. [PMID: 37451426 DOI: 10.1016/j.canlet.2023.216307] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [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: 06/02/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
The emergence of drug resistance is a major challenge for oncologists. Resistance can be categorized as acquired or intrinsic; the alteration of several biological mechanisms contributes to both intrinsic and acquired resistance. Macroautophagy/autophagy is the primary process in eukaryotes for the degradation of macromolecules and organelles. This process is critical in maintaining cellular homeostasis. Given its function as either a pro-survival or a pro-death phenomenon, autophagy has a complex physio-pathological role. In some circumstances, autophagy can confer chemoresistance and promote cell survival, whereas in others it can promote chemosensitivity and contribute to cell death. The role of autophagy in the modulation of cancer drug resistance reflects its impact on apoptosis and metastasis. The regulation of autophagy in cancer is mediated by various factors including AMP-activated protein kinase (AMPK), MAPK, phosphoinositide 3-kinase (PI3K)-AKT, BECN1 and ATG proteins. Non-coding RNAs are among the main regulators of autophagy, e.g., via the modulation of chemoresistance pathways. Due to the significant contribution of autophagy in cancer drug resistance, small molecule modulators and natural compounds targeting autophagy have been introduced to alter the response of cancer cells to chemotherapy. Furthermore, nanotherapeutic approaches based on autophagy regulation have been introduced in pre-clinical cancer therapy. In this review we consider the potential for using autophagy regulators for the clinical treatment of malignancies.
Collapse
Affiliation(s)
- Yi Qin
- Department of Lab, Chifeng Cancer Hospital (The 2nd Affliated Hospital of Chifeng University), Chifeng University, Chifeng City, Inner Mongolia Autonomous Region, 024000, China.
| | - Milad Ashrafizadeh
- Department of General Surgery and Institute of Precision Diagnosis and Treatment of Digestive System Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong, 518055, China; Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
| | - Vera Mongiardini
- Molecular Medicine Research Line, Fondazione Istituto Italiano di Tecnologia (IIT), Genoa, 16163, Italy
| | - Benedetto Grimaldi
- Molecular Medicine Research Line, Fondazione Istituto Italiano di Tecnologia (IIT), Genoa, 16163, Italy
| | - Francesco Crea
- Cancer Research Group-School of Life Health and Chemical Sciences, The Open University, Milton Keynes, UK
| | - Katja Rietdorf
- Cancer Research Group-School of Life Health and Chemical Sciences, The Open University, Milton Keynes, UK
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Tüzoltó u. 7-9, 1094, Budapest, Hungary; Department of Pediatrics, Semmelweis University, Tüzoltó u. 7-9, 1094, Budapest, Hungary; Cancer Biomarker Research Group, Institute of Molecular Life Sciences, Research Centre for Natural Sciences, Magyar tudosok korutja 2, 1117, Budapest, Hungary
| | - Daniel J Klionsky
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Jun Ren
- Shanghai Institute of Cardiovascular Diseases, Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Wei Zhang
- Department of General Surgery and Institute of Precision Diagnosis and Treatment of Digestive System Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong, 518055, China
| | - Xianbin Zhang
- Department of General Surgery and Institute of Precision Diagnosis and Treatment of Digestive System Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong, 518055, China.
| |
Collapse
|
24
|
Posta M, Győrffy B. Analysis of a large cohort of pancreatic cancer transcriptomic profiles to reveal the strongest prognostic factors. Clin Transl Sci 2023; 16:1479-1491. [PMID: 37260110 PMCID: PMC10432876 DOI: 10.1111/cts.13563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 05/04/2023] [Accepted: 05/11/2023] [Indexed: 06/02/2023] Open
Abstract
Pancreatic adenocarcinoma remains a leading cause of cancer-related deaths. In order to develop appropriate therapeutic and prognostic tools, a comprehensive mapping of the tumor's molecular abnormalities is essential. Here, our aim was to integrate available transcriptomic data to uncover genes whose elevated expression is simultaneously linked to cancer pathogenesis and inferior survival. A comprehensive search was performed in GEO to identify clinical studies with transcriptome-level gene expression data of pancreatic carcinoma with overall survival data and normal pancreatic tissues. After quantile normalization, the entire database was used to identify genes with altered expression. Cox proportional hazard regression was employed to uncover genes most strongly correlated with survival with a Bonferroni corrected p < 0.01. Perturbed biological processes and molecular pathways were identified to enable the understanding of underlying processes. A total of 16 available datasets were combined. The aggregated database comprised data of 1640 samples for 20,443 genes. When comparing with normal pancreatic tissues, a total of 2612 upregulated and 1977 downregulated genes were uncovered in pancreatic carcinoma. Among these, we found 24 genes with higher expression which significantly correlated with overall survival length also. The most significant genes were ANXA8, FAM83A, KRT6A, MET, MUC16, NT5E, and SLC2A1. These genes remained significant after a multivariate analysis also including grade and stage. Here, we assembled a large-scale database of pancreatic carcinoma samples and used this cohort to identify carcinoma-specific genes linked to altered survival outcomes. As our analysis focused on genes with higher expression, these could serve as future therapy targets.
Collapse
Affiliation(s)
- Máté Posta
- Károly Rácz Doctoral School of Clinical MedicineSemmelweis UniversityBudapestHungary
- Oncology Biomarker Research Group, Institute of EnzymologyResearch Centre for Natural SciencesBudapestHungary
- Systems Biology of Reproduction Research Group, Institute of EnzymologyResearch Centre for Natural SciencesBudapestHungary
| | - Balázs Győrffy
- Department of Bioinformatics and Department of PediatricsSemmelweis UniversityBudapestHungary
| |
Collapse
|
25
|
Szepesi Kovács D, Chiovini B, Müller D, Tóth EZ, Fülöp A, Ábrányi-Balogh P, Wittner L, Várady G, Farkas Ö, Turczel G, Katona G, Győrffy B, Keserű GM, Mucsi Z, Rózsa BJ, Kovács E. Synthesis and Application of Two-Photon Active Fluorescent Rhodol Dyes for Antibody Conjugation and In Vitro Cell Imaging. ACS Omega 2023; 8:22836-22843. [PMID: 37396252 PMCID: PMC10308389 DOI: 10.1021/acsomega.3c01796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/01/2023] [Indexed: 07/04/2023]
Abstract
A novel family of julolidine-containing fluorescent rhodols equipped with a wide variety of substituents was synthesized in a versatile two-step process. The prepared compounds were fully characterized and exhibited excellent fluorescence properties for microscopy imaging. The best candidate was conjugated to the therapeutic antibody trastuzumab through a copper-free strain-promoted azide-alkyne click reaction. The rhodol-labeled antibody was successfully applied for in vitro confocal and two-photon microscopy imaging of Her2+ cells.
Collapse
Affiliation(s)
- Dénes Szepesi Kovács
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Budapest
University of Technology and Economics, H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Balázs Chiovini
- Faculty
of Information Technology and Bionics, Pázmány
Péter Catholic University, H-1444 Budapest, Hungary
| | - Dalma Müller
- Oncology
Biomarker Research Group, Research Centre
for Natural Sciences, H-1117 Budapest, Hungary
- Department
of Bioinformatics, Semmelweis University, H-1094 Budapest, Hungary
- Semmelweis
University Doctoral School, H-1085 Budapest Hungary
| | - Estilla Zsófia Tóth
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
- Semmelweis
University Doctoral School, H-1085 Budapest Hungary
- Integrative
Neuroscience Research Group, Research Centre
for Natural Sciences, H-1117 Budapest, Hungary
| | - Anna Fülöp
- Femtonics
Ltd., H-1094 Budapest, Hungary
| | - Péter Ábrányi-Balogh
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Budapest
University of Technology and Economics, H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Lucia Wittner
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
- Integrative
Neuroscience Research Group, Research Centre
for Natural Sciences, H-1117 Budapest, Hungary
| | - György Várady
- Molecular
Cell Biology Research Group, Research Centre
for Natural Sciences, H-1117 Budapest, Hungary
| | - Ödön Farkas
- Department
of Organic Chemistry, Eötvös
Loránd University, H-1117 Budapest, Hungary
| | - Gábor Turczel
- NMR
Research Laboratory, Research Centre for
Natural Sciences, H-1117 Budapest, Hungary
| | - Gergely Katona
- Faculty
of Information Technology and Bionics, Pázmány
Péter Catholic University, H-1444 Budapest, Hungary
| | - Balázs Győrffy
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
- Oncology
Biomarker Research Group, Research Centre
for Natural Sciences, H-1117 Budapest, Hungary
- Department
of Bioinformatics, Semmelweis University, H-1094 Budapest, Hungary
- Department
of Pediatrics, Semmelweis University, H-1094 Budapest, Hungary
| | - György Miklós Keserű
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Budapest
University of Technology and Economics, H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Zoltán Mucsi
- Brain Vision Center, H-1094 Budapest, Hungary
- Faculty
of Materials and Chemical Sciences, University
of Miskolc, Miskolc H-3515, Hungary
| | - Balázs J. Rózsa
- Faculty
of Information Technology and Bionics, Pázmány
Péter Catholic University, H-1444 Budapest, Hungary
- Brain Vision Center, H-1094 Budapest, Hungary
- Laboratory of 3D Functional Network and Dendritic Imaging, Institute of Experimental Medicine, H-1083 Budapest, Hungary
| | - Ervin Kovács
- Femtonics
Ltd., H-1094 Budapest, Hungary
- Polymer
Chemistry and Physics Research Group, Research
Centre for Natural Sciences, H-1117 Budapest, Hungary
| |
Collapse
|
26
|
Naimo GD, Forestiero M, Paolì A, Malivindi R, Gelsomino L, Győrffy B, Leonetti AE, Giordano F, Panza S, Conforti FL, Ruffo P, Panno ML, Mauro L, Andò S. ERα/LKB1 complex upregulates E-cadherin expression and stimulates breast cancer growth and progression upon adiponectin exposure. Int J Cancer 2023. [PMID: 37323038 DOI: 10.1002/ijc.34626] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 04/14/2023] [Accepted: 04/20/2023] [Indexed: 06/17/2023]
Abstract
Adiponectin is the major adipocytes-secreted protein involved in obesity-related breast cancer growth and progression. We proved that adiponectin promotes proliferation in ERα-positive breast cancer cells, through ERα transactivation and the recruitment of LKB1 as ERα-coactivator. Here, we showed that adiponectin-mediated ERα transactivation enhances E-cadherin expression. Thus, we investigated the molecular mechanism through which ERα/LKB1 complex may modulate the expression of E-cadherin, influencing tumor growth, progression and distant metastasis. We demonstrated that adiponectin increases E-cadherin expression in ERα-positive 2D and higher extent in 3D cultures. This occurs through a direct activation of E-cadherin gene promoter by ERα/LKB1-complex. The impact of E-cadherin on ERα-positive breast cancer cell proliferation comes from the evidence that in the presence of E-cadherin siRNA the proliferative effects of adiponectin is no longer noticeable. Since E-cadherin connects cell polarity and growth, we investigated if the adiponectin-enhanced E-cadherin expression could influence the localization of proteins cooperating in cell polarity, such as LKB1 and Cdc42. Surprisingly, immunofluorescence showed that, in adiponectin-treated MCF-7 cells, LKB1 and Cdc42 mostly colocalize in the nucleus, impairing their cytosolic cooperation in maintaining cell polarity. The orthotopic implantation of MCF-7 cells revealed an enhanced E-cadherin-mediated breast cancer growth induced by adiponectin. Moreover, tail vein injection of MCF-7 cells showed a higher metastatic burden in the lungs of mice receiving adiponectin-treated cells compared to control. From these findings it emerges that adiponectin treatment enhances E-cadherin expression, alters cell polarity and stimulates ERα-positive breast cancer cell growth in vitro and in vivo, sustaining higher distant metastatic burden.
Collapse
Affiliation(s)
| | - Martina Forestiero
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Alessandro Paolì
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Rocco Malivindi
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Luca Gelsomino
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
- Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary
| | | | - Francesca Giordano
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Salvatore Panza
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Francesca Luisa Conforti
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
- Medical Genetics Laboratory, Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Paola Ruffo
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Maria Luisa Panno
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Loredana Mauro
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Sebastiano Andò
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
- Centro Sanitario, Via P. Bucci, University of Calabria, Rende, Italy
| |
Collapse
|
27
|
Matsumoto S, Tsunashima R, Kitano S, Watanabe A, Kato C, Morita M, Sakaguchi K, Győrffy B, Naoi Y. Multi-gene assay 95- and 155-gene classifiers for prognosis prediction and chemotherapy omission in lymphnode positive luminal-type breast cancer. Cancer Treat Res Commun 2023; 36:100711. [PMID: 37245351 DOI: 10.1016/j.ctarc.2023.100711] [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: 02/08/2023] [Revised: 04/06/2023] [Accepted: 04/23/2023] [Indexed: 05/30/2023]
Abstract
BACKGROUND The prognosis of lymphnode positive breast cancer is worse than that of lymph node negative breast cancer but some cases may not require chemotherapy. We investigated the ability of the new multi-gene assays, 95GC and 155GC, to identify patients with lymphnode positive Luminal-type breast cancer whose chemotherapy can be omitted relatively safely. PATIENTS AND METHODS We extracted 1721 cases of lymphnode positive Luminal-type breast cancer from 22 public database Caucasoid cohorts and 3 Asian cohorts, and performed recurrence prognosis analysis with 95GC and 155GC. RESULTS Using 95GC, the cases were stratified as the high (n = 917) and low (n = 202) groups according to the prognosis of lymphnode positive Luminal-type endocrine only breast cancer. The 5 years DRFS in the low risk group was relatively good at 90%, and no additional effect of chemotherapy was observed, suggesting omission of chemotherapy. The recurrence prognosis was also significantly dichotomized into the high and low risks by 95GC in 21GC RS 0-25 cases. Here, we found a group with poor prognosis even in post-menopause RS 0-25 and requiring chemotherapy. Additionally, a group in which the prognosis was good in pre-menopause RS 0-25, and the omission of chemotherapy could be considered. Patients in the high-risk group at 155GC had poor prognosis after chemotherapy. 155GC also showed a group that chemotherapy alone was not sufficient. CONCLUSION In this study, we demonstrated the possibility of accurately selecting patient groups for which chemotherapy can be omitted from lymphnode positive Luminal-type breast cancer.
Collapse
Affiliation(s)
- Saya Matsumoto
- Division of Endocrine and Breast Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Ryo Tsunashima
- Department of Breast and Endocrine Surgery, Rinku General Medical Center, Osaka, Japan
| | - Sae Kitano
- Division of Endocrine and Breast Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Akira Watanabe
- Department of Breast and Endocrine Surgery, Rinku General Medical Center, Osaka, Japan
| | - Chikage Kato
- Division of Endocrine and Breast Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Midori Morita
- Division of Endocrine and Breast Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Koichi Sakaguchi
- Division of Endocrine and Breast Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Tüzoltó u. 7-9, 1094 Budapest, Hungary
| | - Yasuto Naoi
- Division of Endocrine and Breast Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan.
| |
Collapse
|
28
|
Zhou W, Zhao Z, Lin A, Yang J, Xu J, Kari WR, Yang A, Li J, Solanki S, Speth J, Walker N, Scott AJ, Kothari AU, Yao Y, Peterson ER, Korimerla N, Werner CK, Liang J, Jacobson J, Palavalasa S, Obrien AM, Elaimy AL, Ferris SP, Zhao SG, Sarkaria JN, Győrffy B, Zhang S, Al-Holou WN, Umemura Y, Morgan MA, Lawrence TS, Lyssiotis CA, Peters-Golden M, Shah YM, Wahl DR. GTP signaling links metabolism, DNA repair, and responses to genotoxic stress. bioRxiv 2023:2023.04.12.536297. [PMID: 37090571 PMCID: PMC10120670 DOI: 10.1101/2023.04.12.536297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
How cell metabolism regulates DNA repair is incompletely understood. Here, we define a GTP-mediated signaling cascade that links metabolism to DNA repair and has significant therapeutic implications. GTP, but not other nucleotides, regulates the activity of Rac1, a G protein, that promotes the dephosphorylation of serine 323 on Abl-interactor 1 (Abi-1) by protein phosphatase 5 (PP5). Dephosphorylated Abi-1, a protein previously not known to activate DNA repair, promotes non-homologous end joining. In patients and mouse models of glioblastoma, Rac1 and dephosphorylated Abi-1 mediate DNA repair and resistance to standard of care genotoxic treatments. The GTP-Rac1-PP5-Abi-1 signaling axis is not limited to brain cancer, as GTP supplementation promotes DNA repair and Abi-1-S323 dephosphorylation in non-malignant cells and protects mouse tissues from genotoxic insult. This unexpected ability of GTP to regulate DNA repair independently of deoxynucleotide pools has important implications for normal physiology and cancer treatment.
Collapse
|
29
|
Munkácsy G, Santarpia L, Győrffy B. Therapeutic Potential of Tumor Metabolic Reprogramming in Triple-Negative Breast Cancer. Int J Mol Sci 2023; 24:ijms24086945. [PMID: 37108109 PMCID: PMC10138520 DOI: 10.3390/ijms24086945] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/28/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer, with clinical features of high metastatic potential, susceptibility to relapse, and poor prognosis. TNBC lacks the expression of the estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2). It is characterized by genomic and transcriptional heterogeneity and a tumor microenvironment (TME) with the presence of high levels of stromal tumor-infiltrating lymphocytes (TILs), immunogenicity, and an important immunosuppressive landscape. Recent evidence suggests that metabolic changes in the TME play a key role in molding tumor development by impacting the stromal and immune cell fractions, TME composition, and activation. Hence, a complex inter-talk between metabolic and TME signaling in TNBC exists, highlighting the possibility of uncovering and investigating novel therapeutic targets. A better understanding of the interaction between the TME and tumor cells, and the underlying molecular mechanisms of cell-cell communication signaling, may uncover additional targets for better therapeutic strategies in TNBC treatment. In this review, we aim to discuss the mechanisms in tumor metabolic reprogramming, linking these changes to potential targetable molecular mechanisms to generate new, physical science-inspired clinical translational insights for the cure of TNBC.
Collapse
Affiliation(s)
- Gyöngyi Munkácsy
- National Laboratory for Drug Research and Development, Magyar Tudósok Körútja 2, 1117 Budapest, Hungary
- Oncology Biomarker Research Group, Research Centre for Natural Sciences, Institute of Enzymology, Magyar Tudósok Körútja 2, 1117 Budapest, Hungary
| | | | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Tűzoltó u. 5-7, 1094 Budapest, Hungary
- Department of Pediatrics, Semmelweis University, Tűzoltó u. 5-7, 1094 Budapest, Hungary
| |
Collapse
|
30
|
Olah C, Reis H, Hoffmann MJ, Mairinger F, Ting S, Hadaschik B, Krafft U, Grünwald V, Nyirady P, Varadi M, Győrffy B, Kiss A, Szekely E, Sjödahl G, Szarvas T. Predictive value of molecular subtypes and APOBEC3G for adjuvant chemotherapy in urothelial bladder cancer. Cancer Med 2023; 12:5222-5232. [PMID: 36204983 PMCID: PMC10028049 DOI: 10.1002/cam4.5324] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/08/2022] [Accepted: 09/23/2022] [Indexed: 11/07/2022] Open
Abstract
OBJECTIVE Although targeted approaches have become available in second- and third-line settings, platinum-based chemotherapy remains the standard first-line treatment for advanced muscle-invasive bladder cancer (MIBC). Therefore, the prediction of platinum resistance is of utmost clinical importance. METHODS In this study, we established a routine compatible method for the molecular classification of MIBC samples according to various classification systems and applied this method to evaluate the impact of subtypes on survival after adjuvant chemotherapy. This retrospective study included 191 patients with advanced MIBC (pT≥3 or pN+) who underwent radical cystectomy, with or without adjuvant chemotherapy. A 48-gene panel and classifier rule set were established to determine molecular subtypes according to TCGA, MDA, LundTax, and Consensus classifications. Additionally, 12 single platinum-predictive candidate genes were assessed. The results were correlated with patients' clinicopathological and follow-up data and were validated using independent data sets. RESULTS Our final evaluation of 159 patients demonstrated better survival in the luminal groups for those who received chemotherapy compared with those who did not. In contrast, no such differences were observed in basal subtypes. The use of chemotherapy was associated with better survival in patients with high APOBEC3G expression (p < 0.002). This association was confirmed using an independent data set of patients who received neoadjuvant platinum therapy. CONCLUSIONS The proposed method robustly replicates the most commonly used transcriptome-based subtype classifications from paraffin-embedded tissue samples. The luminal, but not basal, molecular subtypes had the greatest benefit from adjuvant platinum therapy. We identified and validated APOBEC3G as a novel predictive marker for platinum-treated patients.
Collapse
Affiliation(s)
- Csilla Olah
- Department of Urology, University of Duisburg-Essen, Essen, Germany
| | - Henning Reis
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Michèle J Hoffmann
- Department of Urology, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Fabian Mairinger
- Institute of Pathology, University Medicine Essen, University of Duisburg-Essen, Essen, Germany
| | - Saskia Ting
- Institute of Pathology, University Medicine Essen, University of Duisburg-Essen, Essen, Germany
| | - Boris Hadaschik
- Department of Urology, University of Duisburg-Essen, Essen, Germany
| | - Ulrich Krafft
- Department of Urology, University of Duisburg-Essen, Essen, Germany
| | - Viktor Grünwald
- Department of Medical Oncology, University of Duisburg-Essen, Essen, Germany
| | - Peter Nyirady
- Department of Urology, Semmelweis University, Budapest, Hungary
| | - Melinda Varadi
- Department of Urology, Semmelweis University, Budapest, Hungary
| | - Balázs Győrffy
- Research Centre for Natural Sciences, Cancer Biomarker Research Group, Institute of Enzymology, Budapest, Hungary
- 2nd Department of Pediatrics and Department of Bioinformatics, Semmelweis University, Budapest, Hungary
| | - Andras Kiss
- 2nd Department of Pathology, Semmelweis University, Budapest, Hungary
| | - Eszter Szekely
- 2nd Department of Pathology, Semmelweis University, Budapest, Hungary
| | - Gottfrid Sjödahl
- Department of Translational Medicine, Lund University, Lund, Sweden
| | - Tibor Szarvas
- Department of Urology, University of Duisburg-Essen, Essen, Germany
- Department of Urology, Semmelweis University, Budapest, Hungary
| |
Collapse
|
31
|
Győrffy B. Discovery and ranking of the most robust prognostic biomarkers in serous ovarian cancer. GeroScience 2023:10.1007/s11357-023-00742-4. [PMID: 36856946 PMCID: PMC10400493 DOI: 10.1007/s11357-023-00742-4] [Citation(s) in RCA: 83] [Impact Index Per Article: 83.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 01/25/2023] [Indexed: 03/02/2023] Open
Abstract
Progress in ovarian cancer treatment lags behind other tumor types. With diagnosis usually at an advanced stage, there is a high demand for reliable prognostic biomarkers capable of the selection of effective chemo- and targeted therapies. Our goal was to establish a large-scale transcriptomic database and use it to uncover and rank survival-associated genes. Ovarian cancer cohorts with transcriptome-level gene expression data and clinical follow-up were identified from public repositories. All samples were normalized and entered into an integrated database. Cox univariate survival analysis was performed for all genes and was followed by multivariate analysis for selected genes involving clinical and pathological variables. False discovery rate was computed for multiple hypothesis testing and a 1% cutoff was used to determine statistical significance. The complete integrated database comprises 1816 samples from 17 datasets. Altogether, 2468 genes were correlated to progression-free survival (PFS), and 704 genes were correlated with overall survival (OS). The most significant genes were WBP1L, ASAP3, CNNM2, and NCAPH2 for progression-free survival and CSE1L, NUAK1, ALPK2, and SHKBP1 for overall survival. Genes significant for PFS were also preferentially significant for predicting OS as well. All data including HR and p values as well as the used cutoff values for all genes for both PFS and OS are provided to enable the ranking of future biomarker candidates across all genes. Our results help to prioritize genes and to neglect those which are most likely to fail in studies aiming to establish new clinically useful biomarkers and therapeutic targets in serous ovarian cancer.
Collapse
Affiliation(s)
- Balázs Győrffy
- Dept. of Bioinformatics, Semmelweis University, Tuzolto U. 7-9, 1094, Budapest, Hungary.
| |
Collapse
|
32
|
Morafraile EC, Saiz-Ladera C, Nieto-Jiménez C, Győrffy B, Nagy A, Velasco G, Pérez-Segura P, Ocaña A. Mapping Immune Correlates and Surfaceome Genes in BRAF Mutated Colorectal Cancers. Curr Oncol 2023; 30:2569-2581. [PMID: 36975409 PMCID: PMC10047091 DOI: 10.3390/curroncol30030196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 02/05/2023] [Accepted: 02/15/2023] [Indexed: 02/24/2023] Open
Abstract
Despite the impressive results obtained with immunotherapy in several cancer types, a significant fraction of patients remains unresponsive to these treatments. In colorectal cancer (CRC), B-RafV600 mutations have been identified in 8–15% of the patients. In this work we interrogated a public dataset to explore the surfaceome of these tumors and found that several genes, such as GP2, CLDN18, AQP5, TM4SF4, NTSR1, VNN1, and CD109, were upregulated. By performing gene set enrichment analysis, we also identified a striking upregulation of genes (CD74, LAG3, HLA-DQB1, HLA-DRB5, HLA-DMA, HLA-DMB, HLA-DPB1, HLA-DRA, HLA-DOA, FCGR2B, HLA-DQA1, HLA-DRB1, and HLA-DPA1) associated with antigen processing and presentation via MHC class II. Likewise, we found a strong correlation between PD1 and PD(L)1 expression and the presence of genes encoding for proteins involved in antigen presentation such as CD74, HLA-DPA1, and LAG3. Furthermore, a similar association was observed for the presence of dendritic cells and macrophages. Finally, a low but positive relationship was observed between tumor mutational burden and neoantigen load. Our findings support the idea that a therapeutic strategy based on the targeting of PD(L)1 together with other receptors also involved in immuno-modulation, such as LAG3, could help to improve current treatments against BRAF-mutated CRC tumors.
Collapse
Affiliation(s)
- Esther Cabañas Morafraile
- Center for Biological Research Margarita Salas (CIB-CSIC), Spanish National Research Council, 28040 Madrid, Spain
- Experimental Therapeutics Unit, Medical Oncology Department, Hospital Clínico Universitario San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), 28040 Madrid, Spain
- Correspondence: (E.C.M.); (A.O.)
| | - Cristina Saiz-Ladera
- Experimental Therapeutics Unit, Medical Oncology Department, Hospital Clínico Universitario San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), 28040 Madrid, Spain
| | - Cristina Nieto-Jiménez
- Experimental Therapeutics Unit, Medical Oncology Department, Hospital Clínico Universitario San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), 28040 Madrid, Spain
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, 1094 Budapest, Hungary
- 2nd Department of Pediatrics, Semmelweis University, 1094 Budapest, Hungary
- TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, 1117 Budapest, Hungary
| | - Adam Nagy
- Department of Bioinformatics, Semmelweis University, 1094 Budapest, Hungary
- 2nd Department of Pediatrics, Semmelweis University, 1094 Budapest, Hungary
- TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, 1117 Budapest, Hungary
| | - Guillermo Velasco
- Experimental Therapeutics Unit, Medical Oncology Department, Hospital Clínico Universitario San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), 28040 Madrid, Spain
- Department of Biochemistry and Molecular Biology, Complutense University, 28040 Madrid, Spain
| | - Pedro Pérez-Segura
- Experimental Therapeutics Unit, Medical Oncology Department, Hospital Clínico Universitario San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), 28040 Madrid, Spain
| | - Alberto Ocaña
- Experimental Therapeutics Unit, Medical Oncology Department, Hospital Clínico Universitario San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), 28040 Madrid, Spain
- Centro de Investigación Biomédica en Red en Oncología (CIBERONC), 28029 Madrid, Spain
- Correspondence: (E.C.M.); (A.O.)
| |
Collapse
|
33
|
Kothalawala WJ, Győrffy B. Transcriptomic and Cellular Content Analysis of Colorectal Cancer by Combining Multiple Independent Cohorts. Clin Transl Gastroenterol 2023; 14:e00517. [PMID: 35858620 PMCID: PMC9945259 DOI: 10.14309/ctg.0000000000000517] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 06/30/2022] [Indexed: 11/17/2022] Open
Abstract
INTRODUCTION By linking cellular content and molecular subtypes of colorectal cancer (CRC), we aim to uncover novel features useful for targeted therapy. Our first goal was to evaluate gene expression alterations linked to CRC pathogenesis, and then, we aimed to evaluate the cellular composition differences between normal colon mucosa and tumor and between different colon cancer molecular subtypes. METHODS We collected microarray and RNA sequencing data of patients with CRC from the Genome Expression Omnibus and The Cancer Genome Atlas. We combined all cases and performed quantile normalization. Genes with a fold change of >2 were further investigated. We used xCell for cellular decomposition and CMScaller for molecular subtyping. For statistical analyses, the Kruskal-Wallis H test and Mann-Whitney U tests were performed with Bonferroni correction. RESULTS We established an integrated database of normal colon and CRC using transcriptomic data of 1,082 samples. By using this data set, we identified genes showing the highest differential expression in colon tumors. The top genes were linked to calcium signaling, matrix metalloproteinases, and transcription factors. When compared with normal samples, CD4+ memory T cells, CD8+ naive T cells, CD8+ T cells, Th1 cells, Th2 cells, and regulatory T cells were enriched in tumor tissues. The ImmuneScore was decreased in tumor samples compared with normal samples. The CMS1 and CMS4 molecular subtypes were the most immunogenic, with the highest ImmuneScore but also high infiltration by CD8+ T cells, Th1 cells, and Th2 cells in CMS1 and B-cell subtypes and CD8+ T cells in CMS4. DISCUSSION Our analysis uncovers features enabling advanced treatment selection and the development of novel therapies in CRC.
Collapse
Affiliation(s)
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
- 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
- TTK Cancer Biomarker Research Group, Budapest, Hungary
| |
Collapse
|
34
|
Győrffy B, Weltz B, Szabó I. Supporting grant reviewers through the scientometric ranking of applicants. PLoS One 2023; 18:e0280480. [PMID: 36662799 PMCID: PMC9858403 DOI: 10.1371/journal.pone.0280480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 01/03/2023] [Indexed: 01/21/2023] Open
Abstract
INTRODUCTION Comparing the scientific output of different researchers applying for a grant is a tedious work. In Hungary, to help reviewers to rapidly rank the scientific productivity of a researcher, a grant decision support tool was established and is available at www.scientometrics.org. In the present study, our goal was to assess the impact of this decision support tool on grant review procedures. METHODS The established, publicly available scientometric portal uses four metrics, including the H-index, the yearly citations without self-citations, the number of publications in the last five years, and the number of highly cited publications of a researcher within eleven independent scientific disciplines. Publication-age matched researchers are then ranked and the results are provided to grant reviewers. A questionnaire was completed by reviewers regarding utilization of the scientometric ranking system. The outcome of the grant selection was analyzed by comparing scientometric parameters of applying and funded applicants. We compared three grant allocation rounds before to two grant allocation rounds after the introduction of the portal. RESULTS The scientometric decision support tool was introduced in 2020 to assist grant selection in Hungary and all basic research grant applicants (n = 6,662) were screened. The average score of funded proposals compared to submitted proposals increased by 94% after the introduction of the ranking. Correlation between ranking scores and actual grant selection was strong in life and material sciences but some scientific panels had opposite correlation in social sciences and humanities. When comparing selection outcome to H-index across all applicants, both type I and type II errors decreased. All together 540 reviewers provided feedback representing all eleven scientific disciplines and 83.05% of the reviewers (especially younger reviewers) found the ranking useful. CONCLUSIONS The scientometric decision support tool can save time and increase transparency of grant review processes. The majority of reviewers found the ranking-based scientometric analysis useful when assessing the publication performance of an applicant.
Collapse
Affiliation(s)
- Balázs Győrffy
- Department of Bioinformatics and 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
- RCNS Cancer Biomarker Research Group, Institute of Enzymology, Budapest, Hungary
- National Laboratory for Drug Research and Development, Budapest, Hungary
| | - Boglarka Weltz
- Department of Bioinformatics and 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
- National Laboratory for Drug Research and Development, Budapest, Hungary
| | | |
Collapse
|
35
|
Fekete JT, Győrffy B. New Transcriptomic Biomarkers of 5-Fluorouracil Resistance. Int J Mol Sci 2023; 24:ijms24021508. [PMID: 36675023 PMCID: PMC9867124 DOI: 10.3390/ijms24021508] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
The overall response rate to fluoropyrimidine monotherapy in colorectal cancer (CRC) is limited. Transcriptomic datasets of CRC patients treated with 5-fluorouracil (5FU) could assist in the identification of clinically useful biomarkers. In this research, we aimed to analyze transcriptomic cohorts of 5FU-treated cell lines to uncover new predictive biomarker candidates and to validate the strongest hits in 5FU-treated human colorectal cancer samples with available clinical response data. We utilized an in vitro dataset of cancer cell lines treated with 5FU and used the reported area under the dose-response curve values to determine the therapeutic response to 5FU treatment. Mann-Whitney and ROC analyses were performed to identify significant genes. The strongest genes were combined into a single signature using a random forest classifier. The compound 5-fluorouracil was tested in 592 cell lines (294 nonresponders and 298 responders). The validation cohort consisted of 157 patient samples with 5FU monotherapy from three datasets. The three strongest associations with treatment outcome were observed in SHISA4 (AUC = 0.745, p-value = 5.5 × 10-25), SLC38A6 (AUC = 0.725, p-value = 3.1 × 10-21), and LAPTM4A (AUC = 0.723, p-value = 6.4 × 10-21). A random forest model utilizing the top genes reached an AUC value of 0.74 for predicting therapeutic sensitivity. The model correctly identified 83% of the nonresponder and 73% of the responder patients. The cell line cohort is available and the entire human colorectal cohort have been added to the ROCPlot analysis platform. Here, by using in vitro and in vivo data, we present a framework enabling the ranking of future biomarker candidates of 5FU resistance. A future option is to conduct an independent validation of the established predictors of resistance.
Collapse
Affiliation(s)
- János Tibor Fekete
- Research Center for Natural Sciences, Cancer Biomarker Research Group, Institute of Enzymology, Magyar Tudósok Krt. 2, H-1117 Budapest, Hungary
- National Laboratory for Drug Research and Development, Magyar Tudósok Krt. 2, H-1117 Budapest, Hungary
| | - Balázs Győrffy
- Department of Pediatrics, Semmelweis University, H-1094 Budapest, Hungary
- Department of Bioinformatics, Semmelweis University, H-1094 Budapest, Hungary
- Correspondence: ; Tel.: +36-30-514-2822
| |
Collapse
|
36
|
Bell HN, Huber AK, Singhal R, Korimerla N, Rebernick RJ, Kumar R, El-Derany MO, Sajjakulnukit P, Das NK, Kerk SA, Solanki S, James JG, Kim D, Zhang L, Chen B, Mehra R, Frankel TL, Győrffy B, Fearon ER, Pasca di Magliano M, Gonzalez FJ, Banerjee R, Wahl DR, Lyssiotis CA, Green M, Shah YM. Microenvironmental ammonia enhances T cell exhaustion in colorectal cancer. Cell Metab 2023; 35:134-149.e6. [PMID: 36528023 PMCID: PMC9841369 DOI: 10.1016/j.cmet.2022.11.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/11/2022] [Accepted: 11/23/2022] [Indexed: 12/23/2022]
Abstract
Effective therapies are lacking for patients with advanced colorectal cancer (CRC). The CRC tumor microenvironment has elevated metabolic waste products due to altered metabolism and proximity to the microbiota. The role of metabolite waste in tumor development, progression, and treatment resistance is unclear. We generated an autochthonous metastatic mouse model of CRC and used unbiased multi-omic analyses to reveal a robust accumulation of tumoral ammonia. The high ammonia levels induce T cell metabolic reprogramming, increase exhaustion, and decrease proliferation. CRC patients have increased serum ammonia, and the ammonia-related gene signature correlates with altered T cell response, adverse patient outcomes, and lack of response to immune checkpoint blockade. We demonstrate that enhancing ammonia clearance reactivates T cells, decreases tumor growth, and extends survival. Moreover, decreasing tumor-associated ammonia enhances anti-PD-L1 efficacy. These findings indicate that enhancing ammonia detoxification can reactivate T cells, highlighting a new approach to enhance the efficacy of immunotherapies.
Collapse
Affiliation(s)
- Hannah N Bell
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Amanda K Huber
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Rashi Singhal
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Navyateja Korimerla
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA; University of Michigan Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Ryan J Rebernick
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Roshan Kumar
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Marwa O El-Derany
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biochemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Peter Sajjakulnukit
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nupur K Das
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Samuel A Kerk
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sumeet Solanki
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jadyn G James
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Donghwan Kim
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Li Zhang
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Brandon Chen
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rohit Mehra
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Timothy L Frankel
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Balázs Győrffy
- Department of Bioinformatics and 2(nd) Department of Pediatrics, Semmelweis University, Budapest, Hungary; TTK Cancer Biomarker Research Group, Institute of Enzymology, Budapest, Hungary
| | - Eric R Fearon
- University of Michigan Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Marina Pasca di Magliano
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Frank J Gonzalez
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ruma Banerjee
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Daniel R Wahl
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA; University of Michigan Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Costas A Lyssiotis
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA; University of Michigan Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Michael Green
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA; University of Michigan Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA; Veteran's Affairs Ann Arbor Healthcare System, Ann Arbor, MI, USA
| | - Yatrik M Shah
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA; University of Michigan Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.
| |
Collapse
|
37
|
Győrffy B, Weltz B, Munkácsy G, Herman P, Szabó I. Evaluating individual scientific output normalized to publication age and academic field through the Scientometrics.org project. Methodology 2022. [DOI: 10.5964/meth.9463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
When evaluating the publication performance of a scientist one has to consider not only the difference in publication norms in different scientific fields, but also the length of the academic career of the investigated researcher. Here, our goal was to establish a database suitable as a reference for the ranking of scientific performance by normalizing the researchers output to those with the same academic career length and active in same scientific field. By using the complete publication and citation data of 17,072 Hungarian researchers, we established a framework enabling the quick assessment of a researcher’s scientific output by comparing four parameters (h-index, yearly independent citations received, number of publications, and number of high impact publications), to the age-matched values of all other researchers active in the same scientific discipline. The established online tool available at www.scientometrics.org could be an invaluable help for faster and more evidence-based grant review processes.
Collapse
|
38
|
Menyhárt O, Győrffy B, Szabó A. Gyermekkori genetikai rendellenességek diagnosztikája újgenerációs szekvenálással. Orv Hetil 2022; 163:2027-2040. [DOI: 10.1556/650.2022.32688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 10/31/2022] [Indexed: 12/24/2022]
Abstract
Az újgenerációs szekvenáláson (NGS) alapuló diagnosztika legnagyobb előnye, hogy
nagyszámú gén párhuzamos szekvenálása révén a genetikai rendellenességek
kiterjedt repertoárját képes egyetlen vizsgálattal lefedni. Az analízis
viszonylag kisebb költsége és az adatmennyiség kezelhetőbb mennyisége folytán a
célzott génpanelek használata, illetve a teljesexom-szekvenálás (WES) a
leginkább elérhető NGS-alapú módszer. Összefoglalónkban az NGS létjogosultságát
vizsgáljuk gyermekkori genetikai rendellenességek diagnosztikájában. Áttekintjük
az öröklött anyagcserezavarok, daganatos megbetegedések és egyéb gyermekkori
genetikai rendellenességek NGS-alapú diagnosztikájában fontos szerepet játszó
géneket. A kora gyermekkori rendellenességek NGS-alapú diagnosztikájának
rutinszerű használata előtt számos technikai és klinikai kérdés vár még
megválaszolásra. Jelenleg a legnagyobb kihívást a ritka genetikai variánsok
értelmezése és a mutációk patogenitásának igazolása jelenti. Orv Hetil. 2022;
163(51): 2027–2040.
Collapse
Affiliation(s)
- Otília Menyhárt
- Semmelweis Egyetem, Általános Orvostudományi Kar, Bioinformatika Tanszék Budapest Magyarország
- Természettudományi Kutatóközpont, Enzimológiai Intézet, Onkológiai Biomarker Kutatócsoport Budapest Magyarország
| | - Balázs Győrffy
- Semmelweis Egyetem, Általános Orvostudományi Kar, Bioinformatika Tanszék Budapest Magyarország
- Természettudományi Kutatóközpont, Enzimológiai Intézet, Onkológiai Biomarker Kutatócsoport Budapest Magyarország
- Semmelweis Egyetem, Általános Orvostudományi Kar, II. Sz. Gyermekgyógyászati Klinika Budapest, Tűzoltó u. 7–9., 1094 Magyarország
| | - András Szabó
- Semmelweis Egyetem, Általános Orvostudományi Kar, II. Sz. Gyermekgyógyászati Klinika Budapest, Tűzoltó u. 7–9., 1094 Magyarország
| |
Collapse
|
39
|
Mazzeschi M, Sgarzi M, Romaniello D, Gelfo V, Cavallo C, Ambrosi F, Morselli A, Miano C, Laprovitera N, Girone C, Ferracin M, Santi S, Rihawi K, Ardizzoni A, Fiorentino M, D’Uva G, Győrffy B, Palmer R, Lauriola M. The autocrine loop of ALK receptor and ALKAL2 ligand is an actionable target in consensus molecular subtype 1 colon cancer. J Exp Clin Cancer Res 2022; 41:113. [PMID: 35351152 PMCID: PMC8962179 DOI: 10.1186/s13046-022-02309-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 03/03/2022] [Indexed: 12/25/2022] Open
Abstract
Background In the last years, several efforts have been made to classify colorectal cancer (CRC) into well-defined molecular subgroups, representing the intrinsic inter-patient heterogeneity, known as Consensus Molecular Subtypes (CMSs). Methods In this work, we performed a meta-analysis of CRC patients stratified into four CMSs. We identified a negative correlation between a high level of anaplastic lymphoma kinase (ALK) expression and relapse-free survival, exclusively in CMS1 subtype. Stemming from this observation, we tested cell lines, patient-derived organoids and mice with potent ALK inhibitors, already approved for clinical use. Results ALK interception strongly inhibits cell proliferation already at nanomolar doses, specifically in CMS1 cell lines, while no effect was found in CMS2/3/4 groups. Furthermore, in vivo imaging identified a role for ALK in the dynamic formation of 3D tumor spheroids. Consistently, ALK appeares constitutively phosphorylated in CMS1, and it signals mainly through the AKT axis. Mechanistically, we found that CMS1 cells display several copies of ALKAL2 ligand and ALK-mRNAs, suggesting an autocrine loop mediated by ALKAL2 in the activation of ALK pathway, responsible for the invasive phenotype. Consequently, disruption of ALK axis mediates the pro-apoptotic action of CMS1 cell lines, both in 2D and 3D and enhanced cell-cell adhesion and e-cadherin organization. In agreement with all these findings, the ALK signature encompassing 65 genes statistically associated with worse relapse-free survival in CMS1 subtype. Finally, as a proof of concept, the efficacy of ALK inhibition was demonstrated in both patient-derived organoids and in tumor xenografts in vivo. Conclusions Collectively, these findings suggest that ALK targeting may represent an attractive therapy for CRC, and CMS classification may provide a useful tool to identify patients who could benefit from this treatment. These findings offer rationale and pharmacological strategies for the treatment of CMS1 CRC. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-022-02309-1.
Collapse
|
40
|
Pai P, Wang G, Teo WW, Raez-Rodriguez D, Gabrielson KL, Győrffy B, Downs BM, Aggarwal A, Sukumar S. HOXA5-Mediated Stabilization of IκBα Inhibits the NF-κB Pathway and Suppresses Malignant Transformation of Breast Epithelial Cells. Cancer Res 2022; 82:3802-3814. [PMID: 36166646 PMCID: PMC9588663 DOI: 10.1158/0008-5472.can-21-4277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 06/01/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022]
Abstract
HOXA5 is a transcription factor and tumor suppressor that promotes differentiation of breast epithelial cells and is frequently lost during malignant transformation. HOXA5 loss alone, however, does not confer tumorigenicity. To determine which molecular alterations combined with loss of HOXA5 expression can transform cells, we examined isogenic derivatives of a nonmalignant breast epithelial cell line containing knock-in or knockout mutations in key breast cancer genes. Knockdown (KD) of HOXA5 in cells harboring double knock-in (DKI) of mutated PIK3CA (E545K) and HER2 (V777L) induced epithelial-mesenchymal transition and migration and promoted invasive tumor outgrowth within mouse mammary ducts. The NF-κB pathway was significantly upregulated in DKI cells following HOXA5 KD. HOXA5 KD upregulated multiple NF-κB target genes, including IL6. IκBα protein, but not RNA, expression was reduced in HOXA5-KD cells. HOXA5 bound and stabilized IκBα, forming a nuclear HOXA5-IκBα complex. Chromatin immunoprecipitation sequencing database queries revealed that HOXA5 and IκBα are co-enriched at 528 genomic loci. In patients with breast cancer, high coexpression of HOXA5 and IκBα conferred a significantly better overall and progression-free survival. Collectively, these data suggest that HOXA5 suppresses malignancy in breast epithelial cells by blunting NF-κB action via stabilization of its inhibitor IκBα. SIGNIFICANCE Loss of HOXA5 reduces IκBα stability and increases NF-κB signaling to exacerbate breast cancer aggressiveness, providing new insights into the tumor suppressor functions of HOXA5.
Collapse
Affiliation(s)
- Priya Pai
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Guannan Wang
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Wei Wen Teo
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Diana Raez-Rodriguez
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kathleen L Gabrielson
- Department of Molecular and Comparative Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Balázs Győrffy
- Semmelweis University Department of Bioinformatics, Budapest, Hungary
| | - Bradley M Downs
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Akanksha Aggarwal
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Saraswati Sukumar
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| |
Collapse
|
41
|
Menyhart O, Weltz B, Győrffy B. Correction: MultipleTesting.com: A tool for life science researchers for multiple hypothesis testing correction. PLoS One 2022; 17:e0274662. [PMID: 36084071 PMCID: PMC9462819 DOI: 10.1371/journal.pone.0274662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
42
|
López-Cade I, García-Barberán V, Cabañas Morafraile E, Díaz-Tejeiro C, Saiz-Ladera C, Sanvicente A, Pérez Segura P, Pandiella A, Győrffy B, Ocaña A. Genomic mapping of copy number variations influencing immune response in breast cancer. Front Oncol 2022; 12:975437. [PMID: 36119512 PMCID: PMC9476651 DOI: 10.3389/fonc.2022.975437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
Identification of genomic alterations that influence the immune response within the tumor microenvironment is mandatory in order to identify druggable vulnerabilities. In this article, by interrogating public genomic datasets we describe copy number variations (CNV) present in breast cancer (BC) tumors and corresponding subtypes, associated with different immune populations. We identified regulatory T-cells associated with the Basal-like subtype, and type 2 T-helper cells with HER2 positive and the luminal subtype. Using gene set enrichment analysis (GSEA) for the Type 2 T-helper cells, the most relevant processes included the ERBB2 signaling pathway and the Fibroblast Growth Factor Receptor (FGFR) signaling pathway, and for CD8+ T-cells, cellular response to growth hormone stimulus or the JAK-STAT signaling pathway. Amplification of ERBB2, GRB2, GRB7, and FGF receptor genes strongly correlated with the presence of type 2 T helper cells. Finally, only 8 genes were highly upregulated and present in the cellular membrane: MILR1, ACE, DCSTAMP, SLAMF8, CD160, IL2RA, ICAM2, and SLAMF6. In summary, we described immune populations associated with genomic alterations with different BC subtypes. We observed a clear presence of inhibitory cells, like Tregs or Th2 when specific chromosomic regions were amplified in basal-like or HER2 and luminal groups. Our data support further evaluation of specific therapeutic strategies in specific BC subtypes, like those targeting Tregs in the basal-like subtype.
Collapse
Affiliation(s)
- Igor López-Cade
- Experimental Therapeutics Unit, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Vanesa García-Barberán
- Molecular Oncology Laboratory, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Esther Cabañas Morafraile
- Center for Biological Research, Margarita Salas Centro de Investigaciones Biologicas (CIB)-Consejo Superior de Investigaciones Cientificas (CSIC), Spanish National Research Council, Madrid, Spain
| | - Cristina Díaz-Tejeiro
- Experimental Therapeutics Unit, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Cristina Saiz-Ladera
- Experimental Therapeutics Unit, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Adrián Sanvicente
- Experimental Therapeutics Unit, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Pedro Pérez Segura
- Medical Oncology Department, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Atanasio Pandiella
- Instituto de Biología Molecular y Celular del Cáncer [IBMCC-Centro de Investigacion del Cancer (CIC)], Instituto de Investigación Biomédica de Salamanca (IBSAL), Consejo Superior de Investigaciones Científicas (CSIC) Salamanca, Salamanca, Spain
- Centro de Investigación Biomédica en Red en Oncología (CIBERONC), Madrid, Spain
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
- 2Department of Pediatrics, Semmelweis University, Budapest, Hungary
- Termeszettudomanyi Kutatokozpont (TTK) Lendület Cancer Biomarker Research Group, Institute of Enzymology, Budapest, Hungary
| | - Alberto Ocaña
- Experimental Therapeutics Unit, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
- Centro de Investigación Biomédica en Red en Oncología (CIBERONC), Madrid, Spain
- Translational Oncology Laboratory, Translational Research Unit, Albacete University Hospital, Albacete, Spain
- Centro Regional de Investigaciones Biomédicas, Castilla-La Mancha University (CRIB-UCLM), Albacete, Spain
- *Correspondence: Alberto Ocaña,
| |
Collapse
|
43
|
Ding X, Sharko AC, McDermott MSJ, Schools GP, Chumanevich A, Ji H, Li J, Zhang L, Mack ZT, Sikirzhytski V, Shtutman M, Ivers L, O’Donovan N, Crown J, Győrffy B, Chen M, Roninson IB, Broude EV. Inhibition of CDK8/19 Mediator kinase potentiates HER2-targeting drugs and bypasses resistance to these agents in vitro and in vivo. Proc Natl Acad Sci U S A 2022; 119:e2201073119. [PMID: 35914167 PMCID: PMC9371674 DOI: 10.1073/pnas.2201073119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 06/28/2022] [Indexed: 02/03/2023] Open
Abstract
Breast cancers (BrCas) that overexpress oncogenic tyrosine kinase receptor HER2 are treated with HER2-targeting antibodies (such as trastuzumab) or small-molecule kinase inhibitors (such as lapatinib). However, most patients with metastatic HER2+ BrCa have intrinsic resistance and nearly all eventually become resistant to HER2-targeting therapy. Resistance to HER2-targeting drugs frequently involves transcriptional reprogramming associated with constitutive activation of different signaling pathways. We have investigated the role of CDK8/19 Mediator kinase, a regulator of transcriptional reprogramming, in the response of HER2+ BrCa to HER2-targeting drugs. CDK8 was in the top 1% of all genes ranked by correlation with shorter relapse-free survival among treated HER2+ BrCa patients. Selective CDK8/19 inhibitors (senexin B and SNX631) showed synergistic interactions with lapatinib and trastuzumab in a panel of HER2+ BrCa cell lines, overcoming and preventing resistance to HER2-targeting drugs. The synergistic effects were mediated in part through the PI3K/AKT/mTOR pathway and reduced by PI3K inhibition. Combination of HER2- and CDK8/19-targeting agents inhibited STAT1 and STAT3 phosphorylation at S727 and up-regulated tumor suppressor BTG2. The growth of xenograft tumors formed by lapatinib-sensitive or -resistant HER2+ breast cancer cells was partially inhibited by SNX631 alone and strongly suppressed by the combination of SNX631 and lapatinib, overcoming lapatinib resistance. These effects were associated with decreased tumor cell proliferation and altered recruitment of stromal components to the xenograft tumors. These results suggest potential clinical benefit of combining HER2- and CDK8/19-targeting drugs in the treatment of metastatic HER2+ BrCa.
Collapse
Affiliation(s)
- Xiaokai Ding
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina College of Pharmacy, 715 Sumter St., Columbia, SC, 29208
| | - Amanda C. Sharko
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina College of Pharmacy, 715 Sumter St., Columbia, SC, 29208
| | - Martina S. J. McDermott
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina College of Pharmacy, 715 Sumter St., Columbia, SC, 29208
| | - Gary P. Schools
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina College of Pharmacy, 715 Sumter St., Columbia, SC, 29208
| | - Alexander Chumanevich
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina College of Pharmacy, 715 Sumter St., Columbia, SC, 29208
| | - Hao Ji
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina College of Pharmacy, 715 Sumter St., Columbia, SC, 29208
| | - Jing Li
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina College of Pharmacy, 715 Sumter St., Columbia, SC, 29208
| | - Li Zhang
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina College of Pharmacy, 715 Sumter St., Columbia, SC, 29208
| | - Zachary T. Mack
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina College of Pharmacy, 715 Sumter St., Columbia, SC, 29208
| | - Vitali Sikirzhytski
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina College of Pharmacy, 715 Sumter St., Columbia, SC, 29208
| | - Michael Shtutman
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina College of Pharmacy, 715 Sumter St., Columbia, SC, 29208
| | - Laura Ivers
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Norma O’Donovan
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
| | - John Crown
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Budapest, H-1085, Hungary
- Oncology Biomarker Research Group, Research Center for Natural Sciences, H-1117, Budapest, Hungary
| | - Mengqian Chen
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina College of Pharmacy, 715 Sumter St., Columbia, SC, 29208
- Senex Biotechnology, Inc., 715 Sumter St., Columbia, SC, 29208
| | - Igor B. Roninson
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina College of Pharmacy, 715 Sumter St., Columbia, SC, 29208
| | - Eugenia V. Broude
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina College of Pharmacy, 715 Sumter St., Columbia, SC, 29208
| |
Collapse
|
44
|
Munkácsy G, Herman P, Győrffy B. Comparison of scientometric achievements at PhD and scientific output ten years later for 4,790 academic researchers. PLoS One 2022; 17:e0271218. [PMID: 35895676 PMCID: PMC9328526 DOI: 10.1371/journal.pone.0271218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 06/25/2022] [Indexed: 12/04/2022] Open
Abstract
Introduction PhD is the highest awarded degree offered by universities in different disciplines. Owners of a PhD can teach at universities, start independent research and receive a higher salary while further building a scientific career. We examined whether the publication output before the PhD degree has a correlation with subsequent research activities. Methods We downloaded publication and citation data from the Hungarian Scientific Bibliography for Hungarian researchers who obtained PhD between the ages of 24 and 45. The researchers were grouped into eleven scientific sections. We examined the number of Q1 publications published in the previous 5 years, the H-index, the total number of citations for the last complete year, and the biological age of the researcher. Each parameter was computed for the year at which the PhD was obtained and ten years later. Pre-PhD publications (and citations for these) were excluded when assessing post-PhD track records. Spearman rank correlation and Kruskal-Wallis test were computed. Results We analyzed all together 4,790 researchers. We obtained a positive correlation between the number of Q1 publications before and after PhD (corr. coeff. = 0.21–0.54, p<0.01 in all sections), between the H-index before and after PhD (corr. coeff. = 0.32–0.56, p<0.01 in all sections), and between the citations received before and after PhD (corr. coeff. = 0.34–0.51, p<0.01 in all sections). All three metrics measured ten years after the PhD were negatively correlated with the age of the researcher at the time of obtaining the PhD (number of publications corr. coeff. = -0.09–0.22, p<0.05; H-index corr. coeff. = -0.09–0.29, p<0.08; number of citations corr. coeff. = -0.14–0.30, p<0.01). Among all disciplines, Philosophy and History and Engineering sciences show the strongest correlation between pre- and post-PhD output. When running multiple regression analysis for all three metrics as dependent variables and the number of articles, the H-index, the number of citations in the year of the PhD, the calendar year of PhD, and the gender of the researcher as independent variables, the number of articles and the H-index in the year of PhD reached the strongest positive correlations while gender had a negative correlation. Conclusions We independently evaluated pre- and post-PhD publication performance. In connection with age, the discipline-specific reference values of scientometric parameters at the time of obtaining the PhD can help to select candidates for postdoctoral grants and positions.
Collapse
Affiliation(s)
- Gyöngyi Munkácsy
- Department of Bioinformatics and 2nd Dept. of Pediatrics, Semmelweis University, Budapest, Hungary
- TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Budapest, Hungary
| | - Péter Herman
- Department of Bioinformatics and 2nd Dept. of Pediatrics, Semmelweis University, Budapest, Hungary
- TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Budapest, Hungary
| | - Balázs Győrffy
- Department of Bioinformatics and 2nd Dept. of Pediatrics, Semmelweis University, Budapest, Hungary
- TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Budapest, Hungary
| |
Collapse
|
45
|
Riecks J, Parnigoni A, Győrffy B, Kiesel L, Passi A, Vigetti D, Götte M. The hyaluronan-related genes HAS2, HYAL1-4, PH20 and HYALP1 are associated with prognosis, cell viability and spheroid formation capacity in ovarian cancer. J Cancer Res Clin Oncol 2022; 148:3399-3419. [PMID: 35767191 PMCID: PMC9587083 DOI: 10.1007/s00432-022-04127-6] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 06/08/2022] [Indexed: 11/25/2022]
Abstract
Purpose Hyaluronan modulates tumour progression, including cell adhesion, cohesion, proliferation and invasion, and the cancer stem cell phenotype. In ovarian cancer, high levels of stromal hyaluronan are associated with poor prognosis. In this work, hyaluronan synthases (HAS1-3) and hyaluronidases (HYAL1-4, PH-20, HYALP1) were examined with regard to different levels of gene expression and its influence on ovarian cancer patients’ survival. The impact of a siRNA depletion of HAS2 was investigated in vitro. Methods Using the Kaplan–Meier Plotter tool, we investigated the influence of hyaluronic synthases and hyaluronidases on the survival of a collective of 1435 ovarian cancer patients. Differences in gene expression between normal (n = 46) and cancerous (n = 744) ovarian tissue were examined using the TNMplot database. Following an evaluation of hyaluronan-related gene expression in the ATCC ovarian cancer panel, we studied SKOV3 and SW 626 ovarian cancer cells subjected to HAS2 siRNA or control siRNA treatment in terms of HAS1-3, HYAL2 and HYAL3 mRNA expression. We investigated the ability to form spheroids using the Hanging Drop method and the response to chemotherapy at different concentrations using the MTT Assay. By STRING analysis, interactions within the enzymes of the hyaluronic acid system and with binding partners were visualized. Results HAS1, HYAL1 and HYAL4 mRNA expression is significantly upregulated, whereas HAS2, HYAL2 and HYAL3 mRNA expression is significantly downregulated in ovarian cancer tissue compared to controls. HAS2 improves cell viability, the capability to form tumour spheroids and has a negative prognostic value regarding overall survival. Lower HAS2 expression and high expression of HYAL2 and HYAL3 favours the survival of ovarian cancer patients. HAS2 knockdown cells and control cells showed a moderate response to combinatorial in vitro chemotherapy with taxol and cisplatin. Conclusion In conclusion, our study shows that the hyaluronic acid system has a relevant influence on the survival of ovarian cancer patients and could therefore be considered as a possible prognostic factor.
Collapse
Affiliation(s)
- Jette Riecks
- Department of Gynecology and Obstetrics, Münster University Hospital, Albert-Schweitzer-Campus 1, 11, 48149, Münster, Germany
| | - Arianna Parnigoni
- Department of Gynecology and Obstetrics, Münster University Hospital, Albert-Schweitzer-Campus 1, 11, 48149, Münster, Germany
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
- 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
- TTK Momentum Cancer Biomarker Research Group, Budapest, Hungary
| | - Ludwig Kiesel
- Department of Gynecology and Obstetrics, Münster University Hospital, Albert-Schweitzer-Campus 1, 11, 48149, Münster, Germany
| | - Alberto Passi
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Davide Vigetti
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Martin Götte
- Department of Gynecology and Obstetrics, Münster University Hospital, Albert-Schweitzer-Campus 1, 11, 48149, Münster, Germany.
| |
Collapse
|
46
|
Tibor Fekete J, Győrffy B. A unified platform enabling biomarker ranking and validation for 1,562 drugs using transcriptomic data of 1,250 cancer cell lines. Comput Struct Biotechnol J 2022; 20:2885-2894. [PMID: 35765648 PMCID: PMC9198269 DOI: 10.1016/j.csbj.2022.06.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/01/2022] [Accepted: 06/01/2022] [Indexed: 12/21/2022] Open
Abstract
Intro In vitro cell line models provide a valuable resource to investigate compounds useful in the systemic chemotherapy of cancer. However, the due to the dispersal of the data into several different databases, the utilization of these resources is limited. Here, our aim was to establish a platform enabling the validation of chemoresistance-associated genes and the ranking of available cell line models. Methods We processed four independent databases, DepMap, GDSC1, GDSC2, and CTRP. The gene expression data was quantile normalized and HUGO gene names were assigned to have unambiguous identification of the genes. Resistance values were exported for all agents. The correlation between gene expression and therapy resistance is computed using ROC test. Results We combined four datasets with chemosensitivity data of 1562 agents and transcriptome-level gene expression of 1250 cancer cell lines. We have set up an online tool utilizing this database to correlate available cell line sensitivity data and treatment response in a uniform analysis pipeline (www.rocplot.com/cells). We employed the established pipeline to by rank genes related to resistance against afatinib and lapatinib, two inhibitors of the tyrosine-kinase domain of ERBB2. Discussion The computational tool is useful 1) to correlate gene expression with resistance, 2) to identify and rank resistant and sensitive cell lines, and 3) to rank resistance associated genes, cancer hallmarks, and gene ontology pathways. The platform will be an invaluable support to speed up cancer research by validating gene-resistance correlations and by selecting the best cell line models for new experiments.
Collapse
Affiliation(s)
- János Tibor Fekete
- Semmelweis University, Department of Bioinformatics and 2 Department of Pediatrics, Budapest H-1094, Hungary
- Research Center for Natural Sciences, Institute of Enzymology, Momentum Cancer Biomarker Research Group, Magyar tudósok körútja 2., Budapest H-1117, Hungary
| | - Balázs Győrffy
- Semmelweis University, Department of Bioinformatics and 2 Department of Pediatrics, Budapest H-1094, Hungary
- Research Center for Natural Sciences, Institute of Enzymology, Momentum Cancer Biomarker Research Group, Magyar tudósok körútja 2., Budapest H-1117, Hungary
| |
Collapse
|
47
|
Kovács SA, Győrffy B. Transcriptomic datasets of cancer patients treated with immune-checkpoint inhibitors: a systematic review. J Transl Med 2022; 20:249. [PMID: 35641998 PMCID: PMC9153191 DOI: 10.1186/s12967-022-03409-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [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: 02/18/2022] [Accepted: 04/24/2022] [Indexed: 12/12/2022] Open
Abstract
The availability of immune-checkpoint inhibitors (ICI) in the last decade has resulted in a paradigm shift in certain areas of oncology. Patients can be treated either by a monotherapy of anti-CTLA-4 (tremelimumab or ipilimumab), anti-PD-1 (nivolumab or pembrolizumab), or anti-PD-L1 (avelumab or atezolizumab or durvalumab) or as combination therapy of anti-CTLA-4 and anti-PD-1. To maximize the clinical treatment benefit of cancer immunotherapy, the prediction of the actual immune response by the identification and application of clinically useful biomarkers will be required. Whole transcriptomic datasets of patients with ICI treatment could provide the basis for large-scale discovery and ranking of such potential biomarker candidates. In this review, we summarize currently available transcriptomic data from different biological sources (whole blood, fresh-frozen tissue, FFPE) obtained by different methods (microarray, RNA-Seq, RT-qPCR). We directly include only results from clinical trials and other investigations where an ICI treatment was administered. The available datasets are grouped based on the administered treatment and we also summarize the most important results in the individual cohorts. We discuss the limitations and shortcomings of the available datasets. Finally, a subset of animal studies is reviewed to provide an overview of potential in vivo ICI investigations. Our review can provide a swift reference for researchers aiming to find the most suitable study for their investigation, thus saving a significant amount of time.
Collapse
Affiliation(s)
- Szonja Anna Kovács
- grid.11804.3c0000 0001 0942 9821Department of Bioinformatics, Semmelweis University, Tűzoltó utca 7-9, 1094 Budapest, Hungary ,grid.429187.10000 0004 0635 9129Research Centre for Natural Sciences, Oncology Biomarker Research Group, Institute of Enzymology, Eötvös Loránd Research Network, Magyar Tudósok körútja 2, 1117 Budapest, Hungary
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Tűzoltó utca 7-9, 1094, Budapest, Hungary. .,Research Centre for Natural Sciences, Oncology Biomarker Research Group, Institute of Enzymology, Eötvös Loránd Research Network, Magyar Tudósok körútja 2, 1117, Budapest, Hungary.
| |
Collapse
|
48
|
Viganò L, Locatelli A, Ulisse A, Galbardi B, Dugo M, Tosi D, Tacchetti C, Daniele T, Győrffy B, Sica L, Macchini M, Zambetti M, Zambelli S, Bianchini G, Gianni L. Modulation of the Estrogen/erbB2 Receptors Cross-talk by CDK4/6 Inhibition Triggers Sustained Senescence in Estrogen Receptor- and ErbB2-positive Breast Cancer. Clin Cancer Res 2022; 28:2167-2179. [PMID: 35254385 PMCID: PMC9595107 DOI: 10.1158/1078-0432.ccr-21-3185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 11/24/2021] [Accepted: 03/03/2022] [Indexed: 01/07/2023]
Abstract
PURPOSE The interplay between estrogen receptor (ER) and erbB tyrosine-kinase receptors (RTK) impacts growth and progression of ER-positive (ER+)/HER2-positive (HER2+) breast cancer and generates mitogenic signals converging onto the Cyclin-D1/CDK4/6 complex. We probed this cross-talk combining endocrine-therapy (fulvestrant), dual HER2-blockade (trastuzumab and pertuzumab), and CDK4/6-inhibition (palbociclib; PFHPert). EXPERIMENTAL DESIGN Cytotoxic drug effects, interactions, and pharmacodynamics were studied after 72 hours of treatment and over 6 more days of culture after drug wash-out in three ER+/HER2+, two HER2low, and two ER-negative (ER-)/HER2+ breast cancer cell lines. We assessed gene-expression dynamic and association with Ki67 downregulation in 28 patients with ER+/HER2+ breast cancer treated with neoadjuvant PFHPert in NA-PHER2 trial (NCT02530424). RESULTS In vitro, palbociclib and/or fulvestrant induced a functional activation of RTKs signalling. PFHPert had additive or synergistic antiproliferative activity, interfered with resistance mechanisms linked to the RTKs/Akt/MTORC1 axis and induced sustained senescence. Unexpected synergism was found in HER2low cells. In patients, Ki67 downregulation at week 2 and surgery were significantly associated to upregulation of senescence-related genes (P = 7.7E-4 and P = 1.8E-4, respectively). Activation of MTORC1 pathway was associated with high Ki67 at surgery (P = 0.019). CONCLUSIONS Resistance associated with the combination of drugs targeting ER and HER2 can be bypassed by cotargeting Rb, enhancing transition from quiescence to sustained senescence. MTORC1 pathway activation is a potential mechanism of escape and RTKs functional activation may be an alternative pathway for survival also in ER+/HER2low tumor. PFHPert combination is an effective chemotherapy-free regimen for ER+/HER2+ breast cancer, and the mechanistic elucidation of sensitivity/resistance patterns may provide insights for further treatment refinement.
Collapse
Affiliation(s)
- Lucia Viganò
- Department of Medical Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Alberta Locatelli
- Department of Medical Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Adele Ulisse
- Department of Medical Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Barbara Galbardi
- Department of Medical Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Matteo Dugo
- Department of Medical Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Diego Tosi
- Institut régional du Cancer de Montpellier (ICM), Montpellier, France
| | - Carlo Tacchetti
- Experimental Imaging Centre, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Tiziana Daniele
- Experimental Imaging Centre, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Balázs Győrffy
- Department of Bioinformatics, Faculty of General Medicine, Semmelweis University, Budapest, Hungary.,2nd Dept. of Pediatrics, Faculty of Medicine, Semmelweis University, Budapest, Hungary.,TTK Oncology Biomarker Research Group, Institute of Enzymology, Budapest, Hungary
| | - Lorenzo Sica
- Department of Medical Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Marina Macchini
- Department of Medical Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Milvia Zambetti
- Department of Medical Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Stefania Zambelli
- Department of Medical Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giampaolo Bianchini
- Department of Medical Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy.,Corresponding Authors: Luca Gianni, Fondazione Michelangelo, Via Agostino Bertani, 14, Milan 20121, Italy. Phone: 390-2870-8421; E-mail: ; and Giampaolo Bianchini, Department of Medical Oncology, IRCCS San Raffaele Scientific Institute, Via Olgettina, 60, Milan 20132, Italy. Phone: 3902-2643-6530; E-mail:
| | - Luca Gianni
- Fondazione Michelangelo, Milan, Italy.,Corresponding Authors: Luca Gianni, Fondazione Michelangelo, Via Agostino Bertani, 14, Milan 20121, Italy. Phone: 390-2870-8421; E-mail: ; and Giampaolo Bianchini, Department of Medical Oncology, IRCCS San Raffaele Scientific Institute, Via Olgettina, 60, Milan 20132, Italy. Phone: 3902-2643-6530; E-mail:
| |
Collapse
|
49
|
Dmello C, Sonabend A, Arrieta VA, Zhang DY, Kanojia D, Chen L, Gould A, Zhang J, Kang SJ, Winter J, Horbinski C, Amidei C, Győrffy B, Cordero A, Lee-Chang C, Castro B, Hsu P, Ahmed AU, Lesniak MS, Stupp R, Sonabend AM. Translocon-associated protein subunit SSR3 determines and predicts susceptibility to paclitaxel in breast cancer and glioblastoma. Clin Cancer Res 2022; 28:3156-3169. [PMID: 35552677 DOI: 10.1158/1078-0432.ccr-21-2563] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 12/13/2021] [Accepted: 05/09/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE Paclitaxel (PTX) is one the most potent and commonly used chemotherapies for breast and pancreatic cancer. Several ongoing clinical trials are investigating means of enhancing delivery of PTX across the blood-brain barrier for glioblastomas (GBMs). Despite the widespread use of PTX for breast cancer, and the initiative to repurpose this drug for gliomas, there are no predictive biomarkers to inform which patients will likely benefit from this therapy. EXPERIMENTAL DESIGN To identify predictive biomarkers for susceptibility to PTX, we performed a genome-wide CRISPR knock-out (KO) screen using human glioma cells. The genes whose KO was most enriched in the CRISPR screen underwent further selection based on their correlation with survival in the breast cancer patient cohorts treated with PTX and not in patients treated with other chemotherapies, a finding that was validated on a second independent patient cohort using progression-free survival. RESULTS Combination of CRISPR screen results with outcomes from taxane-treated breast cancer patients led to the discovery of endoplasmic reticulum (ER) protein SSR3 as a putative predictive biomarker for PTX. SSR3 protein levels showed positive correlation with susceptibility to PTX in breast cancer cells, glioma cells and in multiple intracranial glioma xenografts models. Knockout of SSR3 turned the cells resistant to PTX while its overexpression sensitized the cells to PTX. Mechanistically, SSR3 confers susceptibility to PTX through regulation of phosphorylation of ER stress sensor IRE1α. CONCLUSION Our hypothesis generating study showed SSR3 as a putative biomarker for susceptibility to PTX, warranting its prospective clinical validation.
Collapse
Affiliation(s)
| | - Aarón Sonabend
- Harvard T. H. Chan School of Public Health, Boston, United States
| | | | | | | | - Li Chen
- Northwestern University, Chicago, United States
| | - Andrew Gould
- Northwestern University, Chicago, Illinois, United States
| | - Jiangshan Zhang
- Harvard T. H. Chan School of Public Health, Boston, United States
| | | | - Jan Winter
- German Cancer Research Center, Heidelberg, Germany
| | - Craig Horbinski
- Northwestern University, Feinberg School of Medicine, Chicago, IL, United States
| | | | | | | | - Catalina Lee-Chang
- Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | | | - Patrick Hsu
- Innovative Genomics Institute, University of California, Berkeley, United States
| | | | - Maciej S Lesniak
- Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States
| | - Roger Stupp
- Northwestern University, Feinberg School of Medicine, Chicago, IL, United States
| | | |
Collapse
|
50
|
Regan JL, Schumacher D, Staudte S, Steffen A, Lesche R, Toedling J, Jourdan T, Haybaeck J, Golob-Schwarzl N, Mumberg D, Henderson D, Győrffy B, Regenbrecht CR, Keilholz U, Schäfer R, Lange M. Identification of a Neural Development Gene Expression Signature in Colon Cancer Stem Cells Reveals a Role for EGR2 in Tumorigenesis. iScience 2022; 25:104498. [PMID: 35720265 PMCID: PMC9204726 DOI: 10.1016/j.isci.2022.104498] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/28/2022] [Accepted: 05/26/2022] [Indexed: 11/12/2022] Open
Abstract
Recent evidence demonstrates that colon cancer stem cells (CSCs) can generate neurons that synapse with tumor innervating fibers required for tumorigenesis and disease progression. Greater understanding of the mechanisms that regulate CSC driven tumor neurogenesis may therefore lead to more effective treatments. RNA-sequencing analyses of ALDHPositive CSCs from colon cancer patient-derived organoids (PDOs) and xenografts (PDXs) showed CSCs to be enriched for neural development genes. Functional analyses of genes differentially expressed in CSCs from PDO and PDX models demonstrated the neural crest stem cell (NCSC) regulator EGR2 to be required for tumor growth and to control expression of homebox superfamily embryonic master transcriptional regulator HOX genes and the neural stem cell and master cell fate regulator SOX2. These data support CSCs as the source of tumor neurogenesis and suggest that targeting EGR2 may provide a therapeutic differentiation strategy to eliminate CSCs and block nervous system driven disease progression. Colon cancer stem cells (CSCs) are enriched for nervous system development genes Colon cancer cells express nerve cell markers EGR2 is required for CSC survival and tumor growth and regulates SOX2 and HOX genes Targeting EGR2 may block cancer neurogenesis and stop disease progression
Collapse
|