1
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Fu Y, Agrawal S, Snyder DR, Yin S, Zhong N, Grunkemeyer JA, Dietz N, Corlett R, Hansen LA, Waddah AR, Nandipati KC, Xia J. Transcriptomic changes and gene fusions during the progression from Barrett's esophagus to esophageal adenocarcinoma. Biomark Res 2024; 12:78. [PMID: 39113153 PMCID: PMC11304724 DOI: 10.1186/s40364-024-00623-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 07/19/2024] [Indexed: 08/10/2024] Open
Abstract
The incidence of esophageal adenocarcinoma (EAC) has surged by 600% in recent decades, with a dismal 5-year survival rate of just 15%. Barrett's esophagus (BE), affecting about 2% of the population, raises the risk of EAC by 40-fold. Despite this, the transcriptomic changes during the BE to EAC progression remain unclear. Our study addresses this gap through comprehensive transcriptomic profiling to identify key mRNA signatures and genomic alterations, such as gene fusions. We performed RNA-sequencing on BE and EAC tissues from 8 individuals, followed by differential gene expression, pathway and network analysis, and gene fusion prediction. We identified mRNA changes during the BE-to-EAC transition and validated our results with single-cell RNA-seq datasets. We observed upregulation of keratin family members in EAC and confirmed increased levels of keratin 14 (KRT14) using immunofluorescence. More differentiated BE marker genes are downregulated during progression to EAC, suggesting undifferentiated BE subpopulations contribute to EAC. We also identified several gene fusions absent in paired BE and normal esophagus but present in EAC. Our findings are critical for the BE-to-EAC transition and have the potential to promote early diagnosis, prevention, and improved treatment strategies for EAC.
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Affiliation(s)
- Yusi Fu
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA.
| | - Swati Agrawal
- Department of Surgery, Creighton University School of Medicine, Omaha, NE, USA
| | - Daniel R Snyder
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
| | - Shiwei Yin
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
| | - Na Zhong
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
| | - James A Grunkemeyer
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
| | - Nicholas Dietz
- Department of Surgery, Creighton University School of Medicine, Omaha, NE, USA
- Department of Pathology, Creighton University School of Medicine, Omaha, NE, USA
| | - Ryan Corlett
- Department of Surgery, Creighton University School of Medicine, Omaha, NE, USA
| | - Laura A Hansen
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
| | - Al-Refaie Waddah
- Department of Surgery, Creighton University School of Medicine, Omaha, NE, USA
| | - Kalyana C Nandipati
- Department of Surgery, Creighton University School of Medicine, Omaha, NE, USA.
| | - Jun Xia
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA.
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2
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Liu Y, Ouyang L, Jiang S, Liang L, Chen Y, Mao C, Jiang Y, Cong L. PPP2R1A silencing suppresses LUAD progression by sensitizing cells to nelfinavir-induced apoptosis and pyroptosis. Cancer Cell Int 2024; 24:145. [PMID: 38654331 DOI: 10.1186/s12935-024-03321-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 04/05/2024] [Indexed: 04/25/2024] Open
Abstract
Lung adenocarcinoma is a major public health problem with the low 5-year survival rate (15%) among cancers. Aberrant alterations of meiotic genes, which have gained increased attention recently, might contribute to elevated tumor risks. However, systematic and comprehensive studies based on the relationship between meiotic genes and LUAD recurrence and treatment response are still lacking. In this manuscript, we first confirmed that the meiosis related prognostic model (MRPM) was strongly related to LUAD progression via LASSO-Cox regression analyses. Furthermore, we identified the role of PPP2R1A in LUAD, which showed more contributions to LUAD process compared with other meiotic genes in our prognostic model. Additionally, repression of PPP2R1A enhances cellular susceptibility to nelfinavir-induced apoptosis and pyroptosis. Collectively, our findings indicated that meiosis-related genes might be therapeutic targets in LUAD and provided crucial guidelines for LUAD clinical intervention.
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Affiliation(s)
- Yating Liu
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
| | - Lianlian Ouyang
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, Changsha, 410011, China
- Research Unit of Key Technologies of Diagnosis and Treatment for Immune-Related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, 410011, China
| | - Shiyao Jiang
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, Hunan Normal University, Changsha, 410013, Hunan, People's Republic of China
- School of Medicine, Hunan Normal University, Changsha, 410013, Hunan, People's Republic of China
| | - Lu Liang
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, Hunan Normal University, Changsha, 410013, Hunan, People's Republic of China
- School of Medicine, Hunan Normal University, Changsha, 410013, Hunan, People's Republic of China
| | - Yuanbing Chen
- Department of Neurosurgery, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
| | - Chao Mao
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yiqun Jiang
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, Hunan Normal University, Changsha, 410013, Hunan, People's Republic of China.
- School of Medicine, Hunan Normal University, Changsha, 410013, Hunan, People's Republic of China.
| | - Li Cong
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, Hunan Normal University, Changsha, 410013, Hunan, People's Republic of China.
- School of Medicine, Hunan Normal University, Changsha, 410013, Hunan, People's Republic of China.
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3
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Liu W, Bruggeman JW, Lei Q, van Pelt AMM, Koster J, Hamer G. Germline specific genes increase DNA double-strand break repair and radioresistance in lung adenocarcinoma cells. Cell Death Dis 2024; 15:38. [PMID: 38216586 PMCID: PMC10786935 DOI: 10.1038/s41419-024-06433-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 12/18/2023] [Accepted: 01/04/2024] [Indexed: 01/14/2024]
Abstract
In principle, germline cells possess the capability to transmit a nearly unaltered set of genetic material to infinite future generations, whereas somatic cells are limited by strict growth constraints necessary to assure an organism's physical structure and eventual mortality. As the potential to replicate indefinitely is a key feature of cancer, we hypothesized that the activation of a "germline program" in somatic cells can contribute to oncogenesis. Our group recently described over one thousand germline specific genes that can be ectopically expressed in cancer, yet how germline specific processes contribute to the malignant properties of cancer is poorly understood. We here show that the expression of germ cell/cancer (GC) genes correlates with malignancy in lung adenocarcinoma (LUAD). We found that LUAD cells expressing more GC genes can repair DNA double strand breaks more rapidly, show higher rates of proliferation and are more resistant to ionizing radiation, compared to LUAD cells that express fewer GC genes. In particular, we identified the HORMA domain protein regulator TRIP13 to be predominantly responsible for this malignant phenotype, and that TRIP13 inhibition or expression levels affect the response to ionizing radiation and subsequent DNA repair. Our results demonstrate that GC genes are viable targets in oncology, as they induce increased radiation resistance and increased propagation in cancer cells. Because their expression is normally restricted to germline cells, we anticipate that GC gene directed therapeutic options will effectively target cancer, with limited side effects besides (temporary) infertility.
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Affiliation(s)
- Wenqing Liu
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Jan Willem Bruggeman
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Qijing Lei
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Ans M M van Pelt
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Jan Koster
- Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Geert Hamer
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.
- Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands.
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4
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Qian T, Zhou Z, Zhang Q, Liou YL, Zhou H. SEPT9, H4C6, and RASSF1A methylation in nasopharyngeal swabs: A reflection of potential minimally invasive biomarkers for early screening of nasopharyngeal cancer. Medicine (Baltimore) 2023; 102:e36583. [PMID: 38115290 PMCID: PMC10727677 DOI: 10.1097/md.0000000000036583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/21/2023] Open
Abstract
The potential value of epigenetic DNA methylation in early cancer screening has been demonstrated. Therefore, in this study, we performed QMS-PCR and quantitative reverse transcription PCR on the genes RASSF1A, H4C6, SEPT9, GSTP1, PAX1, SHOX2, and SOX2, which are common in epithelial cancers. We found hypermethylation in RASSF1A, H4C6 and SEPT9. The mRNA expressions of RASSF1A, H4C6 and SEPT9 in tumor group were significantly different from those in the inflammatory group and healthy group (P < .05). Receiver operating characteristic (ROC) analysis showed that the area under the curve (AUC) of RASSF1A, H4C6 and SEPT9 genes were 0.831, 0.856 and 0.767, respectively. The areas under the AUC curve of SEPT9 + H4C6, SEPT9 + RASSF1A and H4C6 + RASSF1A are 0.946, 0.912 and 0.851, respectively. The diagnostic ability of dual gene combination is better than that of single gene combination, among which SEPT9 and H4C6 combination has the best diagnostic effect. In conclusion, our findings suggest that H4C6, RASSF1A, and SEPT9 methylation occur more frequently in nasopharyngeal carcinoma, and their detection in nasopharyngeal swabs may be a minimally invasive tool for diagnosis of nasopharyngeal carcinoma.
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Affiliation(s)
- Tai Qian
- Department of Pharmacy, School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, China
| | - Zhiwei Zhou
- Department of Pharmacy, School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, China
| | - Qiongxia Zhang
- Department of Oncology, the First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Yu-Light Liou
- Clinical Precision Medicine Research Center, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Honghao Zhou
- Clinical Precision Medicine Research Center, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
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5
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Jacquet E, Chuffart F, Vitte AL, Nika E, Mousseau M, Khochbin S, Rousseaux S, Bourova-Flin E. Aberrant activation of five embryonic stem cell-specific genes robustly predicts a high risk of relapse in breast cancers. BMC Genomics 2023; 24:463. [PMID: 37592220 PMCID: PMC10436393 DOI: 10.1186/s12864-023-09571-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/09/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND In breast cancer, as in all cancers, genetic and epigenetic deregulations can result in out-of-context expressions of a set of normally silent tissue-specific genes. The activation of some of these genes in various cancers empowers tumours cells with new properties and drives enhanced proliferation and metastatic activity, leading to a poor survival prognosis. RESULTS In this work, we undertook an unprecedented systematic and unbiased analysis of out-of-context activations of a specific set of tissue-specific genes from testis, placenta and embryonic stem cells, not expressed in normal breast tissue as a source of novel prognostic biomarkers. To this end, we combined a strict machine learning framework of transcriptomic data analysis, and successfully created a new robust tool, validated in several independent datasets, which is able to identify patients with a high risk of relapse. This unbiased approach allowed us to identify a panel of five biomarkers, DNMT3B, EXO1, MCM10, CENPF and CENPE, that are robustly and significantly associated with disease-free survival prognosis in breast cancer. Based on these findings, we created a new Gene Expression Classifier (GEC) that stratifies patients. Additionally, thanks to the identified GEC, we were able to paint the specific molecular portraits of the particularly aggressive tumours, which show characteristics of male germ cells, with a particular metabolic gene signature, associated with an enrichment in pro-metastatic and pro-proliferation gene expression. CONCLUSIONS The GEC classifier is able to reliably identify patients with a high risk of relapse at early stages of the disease. We especially recommend to use the GEC tool for patients with the luminal-A molecular subtype of breast cancer, generally considered of a favourable disease-free survival prognosis, to detect the fraction of patients undergoing a high risk of relapse.
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Affiliation(s)
- Emmanuelle Jacquet
- Université Grenoble Alpes, INSERM U1209, CNRS UMR5309, EpiMed, Institute for Advanced Biosciences, Grenoble, France
- Université Grenoble Alpes, CHU Grenoble Alpes, Medical Oncology Unit, Cancer and Blood Diseases Department, Grenoble, France
| | - Florent Chuffart
- Université Grenoble Alpes, INSERM U1209, CNRS UMR5309, EpiMed, Institute for Advanced Biosciences, Grenoble, France
| | - Anne-Laure Vitte
- Université Grenoble Alpes, INSERM U1209, CNRS UMR5309, EpiMed, Institute for Advanced Biosciences, Grenoble, France
| | - Eleni Nika
- Université Grenoble Alpes, CHU Grenoble Alpes, Department of Pathology, Grenoble, France
| | - Mireille Mousseau
- Université Grenoble Alpes, CHU Grenoble Alpes, Medical Oncology Unit, Cancer and Blood Diseases Department, Grenoble, France
- Université Grenoble Alpes, INSERM U1039, Bioclinical Radiopharmaceuticals, Grenoble, France
| | - Saadi Khochbin
- Université Grenoble Alpes, INSERM U1209, CNRS UMR5309, EpiMed, Institute for Advanced Biosciences, Grenoble, France
| | - Sophie Rousseaux
- Université Grenoble Alpes, INSERM U1209, CNRS UMR5309, EpiMed, Institute for Advanced Biosciences, Grenoble, France
| | - Ekaterina Bourova-Flin
- Université Grenoble Alpes, INSERM U1209, CNRS UMR5309, EpiMed, Institute for Advanced Biosciences, Grenoble, France.
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6
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Bruggeman JW, Koster J, van Pelt AMM, Speijer D, Hamer G. How germline genes promote malignancy in cancer cells. Bioessays 2023; 45:e2200112. [PMID: 36300921 DOI: 10.1002/bies.202200112] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/06/2022] [Accepted: 10/14/2022] [Indexed: 02/01/2023]
Abstract
Cancers often express hundreds of genes otherwise specific to germ cells, the germline/cancer (GC) genes. Here, we present and discuss the hypothesis that activation of a "germline program" promotes cancer cell malignancy. We do so by proposing four hallmark processes of the germline: meiosis, epigenetic plasticity, migration, and metabolic plasticity. Together, these hallmarks enable replicative immortality of germ cells as well as cancer cells. Especially meiotic genes are frequently expressed in cancer, implying that genes unique to meiosis may play a role in oncogenesis. Because GC genes are not expressed in healthy somatic tissues, they form an appealing source of specific treatment targets with limited side effects besides infertility. Although it is still unclear why germ cell specific genes are so abundantly expressed in cancer, from our hypothesis it follows that the germline's reproductive program is intrinsic to cancer development.
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Affiliation(s)
- Jan Willem Bruggeman
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands.,Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
| | - Jan Koster
- Center for Experimental and Molecular Medicine, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
| | - Ans M M van Pelt
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands.,Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
| | - Dave Speijer
- Medical Biochemistry, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
| | - Geert Hamer
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands.,Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
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7
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Palacios-Blanco I, Martín-Castellanos C. Cyclins and CDKs in the regulation of meiosis-specific events. Front Cell Dev Biol 2022; 10:1069064. [PMID: 36523509 PMCID: PMC9745066 DOI: 10.3389/fcell.2022.1069064] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/14/2022] [Indexed: 07/13/2024] Open
Abstract
How eukaryotic cells control their duplication is a fascinating example of how a biological system self-organizes specific activities to temporally order cellular events. During cell cycle progression, the cellular level of CDK (Cyclin-Dependent Kinase) activity temporally orders the different cell cycle phases, ensuring that DNA replication occurs prior to segregation into two daughter cells. CDK activity requires the binding of a regulatory subunit (cyclin) to the core kinase, and both CDKs and cyclins are well conserved throughout evolution from yeast to humans. As key regulators, they coordinate cell cycle progression with metabolism, DNA damage, and cell differentiation. In meiosis, the special cell division that ensures the transmission of genetic information from one generation to the next, cyclins and CDKs have acquired novel functions to coordinate meiosis-specific events such as chromosome architecture, recombination, and synapsis. Interestingly, meiosis-specific cyclins and CDKs are common in evolution, some cyclins seem to have evolved to acquire CDK-independent functions, and even some CDKs associate with a non-cyclin partner. We will review the functions of these key regulators in meiosis where variation has specially flourished.
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