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Li X, Qu X, Wang N, Li S, Zhao X, Lin K, Shi Y. A novel M2-like tumor associated macrophages-related gene signature for predicting the prognosis and immunotherapy efficacy in gastric cancer. Discov Oncol 2024; 15:353. [PMID: 39150637 PMCID: PMC11329457 DOI: 10.1007/s12672-024-01221-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 08/05/2024] [Indexed: 08/17/2024] Open
Abstract
BACKGROUND M2-like tumor-associated macrophages (M2-like TAMs) play key roles in tumor progression and the immune response. However, the clinical significance and prognostic value of M2-like TAMs-associated regulatory genes in gastric cancer (GC) have not been clarified. METHODS Herein, we identified M2-like TAM-related genes by weighted gene coexpression network analysis of TCGA-STAD and GSE84437 cohort. Lasso-Cox regression analyses were then performed to screen for signature genes, and a novel signature was constructed to quantify the risk score for each patient. Tumor mutation burden (TMB), survival outcomes, immune cells, and immune function were analyzed in the risk groups to further reveal the immune status of GC patients. A gene-drug correlation analysis and sensitivity analysis of anticancer drugs were used to identify potential therapeutic agents. Finally, we verified the mRNA expression of signature genes in patient tissues by qRT-PCR, and analyzed the expression distribution of these genes by IHC. RESULTS A 4-gene (SERPINE1, MATN3, CD36, and CNTN1) signature was developed and validated, and the risk score was shown to be an independent prognostic factor for GC patients. Further analyses revealed that GC patients in the high-risk group had a worse prognosis than those in the low-risk group, with significant differences in TMB, clinical features, enriched pathways, TIDE score, and tumor microenvironment features. Finally, we used qRT-PCR and IHC analysis to verify mRNA and protein level expression of signature genes. CONCLUSION These findings highlight the importance of M2-like TAMs, provide a new perspective on individualized immunotherapy for GC patients.
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Affiliation(s)
- Xuezhi Li
- State key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, China
| | - Xiaodong Qu
- State key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, China
| | - Na Wang
- State key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, China
| | - Songbo Li
- State key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, China
| | - Xingyu Zhao
- State key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, China
| | - Kexin Lin
- State key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, China
| | - Yongquan Shi
- State key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, China.
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2
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Cheng K, Zhai Q, Song J, Liu B. The Co-pathogenic Target Gene CNTN1 Involved in Coronary Artery Disease and Pulmonary Arterial Hypertension Has Potential for Diagnosis of Coronary Artery Disease. Anatol J Cardiol 2024; 28:381-392. [PMID: 39087405 PMCID: PMC11317787 DOI: 10.14744/anatoljcardiol.2024.4331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 04/22/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND We aimed to find a gene for coronary artery disease (CAD) early diagnosis by detecting co-pathogenic target gene involved in CAD and pulmonary arterial hypertension (PAH).
Methods: Datasets were obtained from the Gene Expression Omnibus (GEO) database, including GSE113079, GSE113439, and GSE12288, to investigate gene expression patterns in cardiovascular diseases. Weighted Gene Co-expression Network Analysis (WGCNA) was performed to identify gene modules associated with clinical traits. Differential gene expression analysis and functional enrichment analysis were carried out. Protein-protein interaction (PPI) networks were constructed. JASPAR database and FIMO tool were utilized to predict transcription factor (TF) binding sites.
Results: Fifteen key genes were identified in CAD and PAH, with CNTN1 being prioritized for further investigation due to its high connectivity degree. Upstream regulation analysis identified potential TFs (DRGX, HOXD3, and RAX) and 7 miRNAs targeting CNTN1. The expression profile of CNTN1 was significantly upregulated in CAD samples, and ROC analysis indicated potential diagnostic value for CAD. CMap database analysis predicted potential targeted drugs for CAD.
Conclusion: CNTN1 was detected as a co-pathogenetic gene for CAD and PAH. It is highly expressed in CAD patients and has potential value for CAD diagnosis. CNTN1 is potentially regulated by 3 TFs and 7 miRNAs.
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Affiliation(s)
- Kun Cheng
- Department of Cardiovascular Surgery, Zibo Central Hospital, Shandong Province, China
| | - Qixuan Zhai
- Department of Cardiovascular Surgery, Zibo Central Hospital, Shandong Province, China
| | - Jieqiong Song
- Department of Blood Transfusion, Zibo Central Hospital, Shandong Province, China
| | - Bing Liu
- Department of Cardiovascular Surgery, Zibo Central Hospital, Shandong Province, China
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3
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Dong B, Wang M, Li K, Li Z, Liu L, Shen S. Plasma proteometabolome in lung cancer: exploring biomarkers through bidirectional Mendelian randomization and colocalization analysis. Hum Mol Genet 2024:ddae110. [PMID: 39011643 DOI: 10.1093/hmg/ddae110] [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: 04/11/2024] [Revised: 06/20/2024] [Accepted: 07/10/2024] [Indexed: 07/17/2024] Open
Abstract
Unlike other cancers with widespread screening (breast, colorectal, cervical, prostate, and skin), lung nodule biopsies for positive screenings have higher morbidity with clinical complications. Development of non-invasive diagnostic biomarkers could thereby significantly enhance lung cancer management for at-risk patients. Here, we leverage Mendelian Randomization (MR) to investigate the plasma proteome and metabolome for potential biomarkers relevant to lung cancer. Utilizing bidirectional MR and co-localization analyses, we identify novel associations, highlighting inverse relationships between plasma proteins SFTPB and KDELC2 in lung adenocarcinoma (LUAD) and positive associations of TCL1A with lung squamous cell carcinoma (LUSC) and CNTN1 with small cell lung cancer (SCLC). Additionally, our work reveals significant negative correlations between metabolites such as theobromine and paraxanthine, along with paraxanthine-related ratios, in both LUAD and LUSC. Conversely, positive correlations are found in caffeine/paraxanthine and arachidonate (20:4n6)/paraxanthine ratios with these cancer types. Through single-cell sequencing data of normal lung tissue, we further explore the role of lung tissue-specific protein SFTPB in carcinogenesis. These findings offer new insights into lung cancer etiology, potentially guiding the development of diagnostic biomarkers and therapeutic approaches.
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Affiliation(s)
- Bo Dong
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Centre for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Mengyao Wang
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Centre for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Kaixiu Li
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Centre for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zuwei Li
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Centre for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Lunxu Liu
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Centre for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Shensi Shen
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Centre for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
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4
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Chien F, Michaud ME, Bakhtiari M, Schroff C, Snuderl M, Velazquez Vega JE, MacDonald TJ, Bhasin MK. Medulloblastoma Spatial Transcriptomics Reveals Tumor Microenvironment Heterogeneity with High-Density Progenitor Cell Regions Correlating with High-Risk Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.25.600684. [PMID: 38979174 PMCID: PMC11230370 DOI: 10.1101/2024.06.25.600684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
The tumor microenvironment (TME) of medulloblastoma (MB) influences progression and therapy response, presenting a promising target for therapeutic advances. Prior single-cell analyses have characterized the cellular components of the TME but lack spatial context. To address this, we performed spatial transcriptomic sequencing on sixteen pediatric MB samples obtained at diagnosis, including two matched diagnosis-relapse pairs. Our analyses revealed inter- and intra-tumoral heterogeneity within the TME, comprised of tumor-associated astrocytes (TAAs), macrophages (TAMs), stromal components, and distinct subpopulations of MB cells at different stages of neuronal differentiation and cell cycle progression. We identified dense regions of quiescent progenitor-like MB cells enriched in patients with high-risk (HR) features and an increase in TAAs, TAMs, and dysregulated vascular endothelium following relapse. Our study presents novel insights into the spatial architecture and cellular landscape of the medulloblastoma TME, highlighting spatial patterns linked to HR features and relapse, which may serve as potential therapeutic targets.
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Affiliation(s)
- Franklin Chien
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA 30322, USA
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, GA 30322, USA
| | - Marina E. Michaud
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA 30322, USA
| | - Mojtaba Bakhtiari
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA 30322, USA
| | - Chanel Schroff
- Department of Pathology, NYU Langone Health and Grossman School of Medicine, New York, NY 10016, USA
| | - Matija Snuderl
- Department of Pathology, NYU Langone Health and Grossman School of Medicine, New York, NY 10016, USA
| | - Jose E. Velazquez Vega
- Department of Pathology and Laboratory Medicine, Children’s Healthcare of Atlanta and Emory School of Medicine, Atlanta, GA 30322, USA
| | - Tobey J. MacDonald
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA 30322, USA
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, GA 30322, USA
| | - Manoj K. Bhasin
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA 30322, USA
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, GA 30322, USA
- Department of Biomedical Engineering, Emory University, Atlanta, GA 30322, USA
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5
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Luo D, Ottesen E, Lee JH, Singh R. Transcriptome- and proteome-wide effects of a circular RNA encompassing four early exons of the spinal muscular atrophy genes. RESEARCH SQUARE 2024:rs.3.rs-3818622. [PMID: 38464174 PMCID: PMC10925445 DOI: 10.21203/rs.3.rs-3818622/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Spinal muscular atrophy (SMA) genes, SMN1 and SMN2, produce multiple circular RNAs (circRNAs), including C2A-2B-3-4 that encompasses early exons 2A, 2B, 3 and 4. Here we report the transcriptome- and proteome-wide effects of overexpression of C2A-2B-3-4 in inducible HEK293 cells. Our RNA-Seq analysis revealed altered expression of ~ 15% genes (4,172 genes) by C2A-2B-3-4. About half of the affected genes by C2A-2B-3-4 remained unaffected by L2A-2B-3-4, a linear transcript encompassing exons 2A, 2B, 3 and 4 of SMN1/SMN2. These fifindings underscore the unique role of the structural context of C2A-2B-3-4 in gene regulation. A surprisingly high number of upregulated genes by C2A-2B-3-4 were located on chromosomes 4 and 7, whereas many of the downregulated genes were located on chromosomes 10 and X. Supporting a cross-regulation of SMN1/SMN2 transcripts, C2A-2B-3-4 and L2A-2B-3-4 upregulated and downregulated SMN1/SMN2 mRNAs, respectively. Proteome analysis revealed 61 upregulated and 57 downregulated proteins by C2A-2B-3-4 with very limited overlap with those affected by L2A-2B-3-4. Independent validations confirmed the effect of C2A-2B-3-4 on expression of genes associated with chromatin remodeling, transcription, spliceosome function, ribosome biogenesis, lipid metabolism, cytoskeletal formation, cell proliferation and neuromuscular junction formation. Our findings reveal a broad role of C2A-2B-3-4, a universally expressed circRNA produced by SMN1/SMN2.
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6
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Rai V, Le H, Agrawal DK. Novel mediators regulating angiogenesis in diabetic foot ulcer healing. Can J Physiol Pharmacol 2023; 101:488-501. [PMID: 37459652 DOI: 10.1139/cjpp-2023-0193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
A non-healing diabetic foot ulcer (DFU) is a debilitating clinical problem amounting to socioeconomic and psychosocial burdens. DFUs increase morbidity due to prolonged treatment and mortality in the case of non-treatable ulcers resulting in gangrene and septicemia. The overall amputation rate of the lower extremity with DFU ranges from 3.34% to 42.83%. Wound debridement, antibiotics, applying growth factors, negative pressure wound therapy, hyperbaric oxygen therapy, topical oxygen, and skin grafts are common therapies for DFU. However, recurrence and nonhealing ulcers are still major issues. Chronicity of inflammation, hypoxic environment, poor angiogenesis, and decreased formation of the extracellular matrix (ECM) are common impediments leading to nonhealing patterns of DFUs. Angiogenesis is crucial for wound healing since proper vessel formation facilitates nutrients, oxygen, and immune cells to the ulcer tissue to help in clearing out debris and facilitate healing. However, poor angiogenesis due to decreased expression of angiogenic mediators and matrix formation results in nonhealing and ultimately amputation. Multiple proangiogenic mediators and vascular endothelial growth factor (VEGF) therapy exist to enhance angiogenesis, but the results are not satisfactory. Thus, there is a need to investigate novel pro-angiogenic mediators that can either alone or in combination enhance the angiogenesis and healing of DFUs. In this article, we critically reviewed the existing pro-angiogenic mediators followed by potentially novel factors that might play a regulatory role in promoting angiogenesis and wound healing in DFUs.
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Affiliation(s)
- Vikrant Rai
- Department of Translational Research, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Hoangvi Le
- Department of Translational Research, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Devendra K Agrawal
- Department of Translational Research, Western University of Health Sciences, Pomona, CA 91766, USA
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7
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Chataigner LMP, Gogou C, den Boer MA, Frias CP, Thies-Weesie DME, Granneman JCM, Heck AJR, Meijer DH, Janssen BJC. Structural insights into the contactin 1 - neurofascin 155 adhesion complex. Nat Commun 2022; 13:6607. [PMID: 36329006 PMCID: PMC9633819 DOI: 10.1038/s41467-022-34302-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
Cell-surface expressed contactin 1 and neurofascin 155 control wiring of the nervous system and interact across cells to form and maintain paranodal myelin-axon junctions. The molecular mechanism of contactin 1 - neurofascin 155 adhesion complex formation is unresolved. Crystallographic structures of complexed and individual contactin 1 and neurofascin 155 binding regions presented here, provide a rich picture of how competing and complementary interfaces, post-translational glycosylation, splice differences and structural plasticity enable formation of diverse adhesion sites. Structural, biophysical, and cell-clustering analysis reveal how conserved Ig1-2 interfaces form competing heterophilic contactin 1 - neurofascin 155 and homophilic neurofascin 155 complexes whereas contactin 1 forms low-affinity clusters through interfaces on Ig3-6. The structures explain how the heterophilic Ig1-Ig4 horseshoe's in the contactin 1 - neurofascin 155 complex define the 7.4 nm paranodal spacing and how the remaining six domains enable bridging of distinct intercellular distances.
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Affiliation(s)
- Lucas M. P. Chataigner
- grid.5477.10000000120346234Structural Biochemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Christos Gogou
- grid.5292.c0000 0001 2097 4740Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Maurits A. den Boer
- grid.5477.10000000120346234Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands ,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Cátia P. Frias
- grid.5292.c0000 0001 2097 4740Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Dominique M. E. Thies-Weesie
- grid.5477.10000000120346234Van’t Hoff Laboratory for Physical and Colloid Chemistry, Debye Institute of Nanomaterials Science, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Joke C. M. Granneman
- grid.5477.10000000120346234Structural Biochemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Albert J. R. Heck
- grid.5477.10000000120346234Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands ,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Dimphna H. Meijer
- grid.5292.c0000 0001 2097 4740Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Bert J. C. Janssen
- grid.5477.10000000120346234Structural Biochemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
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8
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Lu W, Wu W, Wang X, Lv Z, Han Y, Wei L, Li L, Ji G. Investigation of two ferroptosis-related molecular subtypes and biomarkers in the progression of gastric adenocarcinoma. ALL LIFE 2022. [DOI: 10.1080/26895293.2022.2066196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Weiqun Lu
- Department of Gastrointestinal Neoplasms Surgery, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Wei Wu
- Department of Medical Oncology, First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
| | - Xiaolong Wang
- Department of Gastrointestinal Surgery, Huadu District People’s Hospital, Southern Medical University, Guangzhou, People’s Republic of China
| | - Zhuo Lv
- Department of Oncology, Guangzhou Hospital of Integrated Traditional and West Medicine, Guangzhou, People’s Republic of China
| | - Yongjun Han
- General Surgery, The First Hospital of Yulin, Yulin, People’s Republic of China
| | - Lili Wei
- Department of Oncology, Guangzhou Hospital of Integrated Traditional and West Medicine, Guangzhou, People’s Republic of China
| | - Liping Li
- Department of Oncology, Dongguan People's Hospital, Dongguan, People’s Republic of China
| | - Gang Ji
- State Key Laboratory of Cancer Biology, Department of Digestive Surgery, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi’an, People’s Republic of China
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9
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Nakauma-González JA, Rijnders M, van Riet J, van der Heijden MS, Voortman J, Cuppen E, Mehra N, van Wilpe S, Oosting SF, Rijstenberg LL, Westgeest HM, Zwarthoff EC, de Wit R, van der Veldt AAM, van de Werken HJG, Lolkema MPJ, Boormans JL. Comprehensive Molecular Characterization Reveals Genomic and Transcriptomic Subtypes of Metastatic Urothelial Carcinoma. Eur Urol 2022; 81:331-336. [PMID: 35086719 DOI: 10.1016/j.eururo.2022.01.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/23/2021] [Accepted: 01/13/2022] [Indexed: 11/28/2022]
Abstract
Recent molecular characterization of primary urothelial carcinoma (UC) may guide future clinical decision-making. For metastatic UC (mUC), a comprehensive molecular characterization is still lacking. We analyzed whole-genome DNA and RNA sequencing data for fresh-frozen metastatic tumor biopsies from 116 mUC patients who were scheduled for palliative systemic treatment within the context of a clinical trial (NCT01855477 and NCT02925234). Hierarchical clustering for mutational signatures revealed two major genomic subtypes: GenS1 (67%), which was APOBEC-driven; and GenS2 (24%), which had a high fraction of de novo mutational signatures related to reactive oxygen species and is putatively clock-like. Significantly mutated genes (SMGs) did not differ between the genomic subtypes. Transcriptomic analysis revealed five mUC subtypes: luminal-a and luminal-b (40%), stroma-rich (24%), basal/squamous (23%), and a nonspecified subtype (12%). These subtypes differed regarding expression of key genes, SMGs, oncogenic pathway activity, and immune cell infiltration. We integrated the genomic and transcriptomic data to propose potential therapeutic options by transcriptomic subtype and for individual patients. This in-depth analysis of a large cohort of patients with mUC may serve as a reference for subtype-oriented and patient-specific research on the etiology of mUC and for novel drug development. PATIENT SUMMARY: We carried out an in-depth analysis of the molecular and genetic features of metastatic cancer involving the cells that line the urinary tract. We showed that this is a heterogeneous disease with different molecular subtypes and we identified possible targets for therapy for each subtype.
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Affiliation(s)
- J Alberto Nakauma-González
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands; Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands; Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Maud Rijnders
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Job van Riet
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands; Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands; Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Jens Voortman
- Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands; Hartwig Medical Foundation, Amsterdam, The Netherlands
| | - Niven Mehra
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sandra van Wilpe
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sjoukje F Oosting
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - L Lucia Rijstenberg
- Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Hans M Westgeest
- Department of Internal Medicine, Amphia Hospital, Breda, The Netherlands
| | - Ellen C Zwarthoff
- Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Ronald de Wit
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Astrid A M van der Veldt
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands; Department of Radiology & Nuclear Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Harmen J G van de Werken
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands; Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands; Department of Immunology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands.
| | - Martijn P J Lolkema
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands.
| | - Joost L Boormans
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands.
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10
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Prognostic and Therapeutic Potential of the OIP5 Network in Papillary Renal Cell Carcinoma. Cancers (Basel) 2021; 13:cancers13174483. [PMID: 34503297 PMCID: PMC8431695 DOI: 10.3390/cancers13174483] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 02/07/2023] Open
Abstract
Papillary renal cell carcinoma (pRCC) is an aggressive but minor type of RCC. The current understanding and management of pRCC remain poor. We report here OIP5 being a novel oncogenic factor and possessing robust prognostic values and therapeutic potential. OIP5 upregulation is observed in pRCC. The upregulation is associated with pRCC adverse features (T1P < T2P < CIMP, Stage1 + 2 < Stage 3 < Stage 4, and N0 < N1) and effectively stratifies the fatality risk. OIP5 promotes ACHN pRCC cell proliferation and xenograft formation; the latter is correlated with network alterations related to immune regulation, metabolism, and hypoxia. A set of differentially expressed genes (DEFs) was derived from ACHN OIP5 xenografts and primary pRCCs (n = 282) contingent to OIP5 upregulation; both DEG sets share 66 overlap genes. Overlap66 effectively predicts overall survival (p < 2 × 10-16) and relapse (p < 2 × 10-16) possibilities. High-risk tumors stratified by Overlap66 risk score possess an immune suppressive environment, evident by elevations in Treg cells and PD1 in CD8 T cells. Upregulation of PLK1 occurs in both xenografts and primary pRCC tumors with OIP5 elevations. PLK1 displays a synthetic lethality relationship with OIP5. PLK1 inhibitor BI2356 inhibits the growth of xenografts formed by ACHN OIP5 cells. Collectively, the OIP5 network can be explored for personalized therapies in management of pRCC patients.
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11
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Fusco N, Marchiò C, Ghidini M, Scatena C. Special Issue: Molecular Biomarkers in Solid Tumors. Genes (Basel) 2021; 12:genes12070984. [PMID: 34203156 PMCID: PMC8304302 DOI: 10.3390/genes12070984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 06/24/2021] [Indexed: 11/16/2022] Open
Affiliation(s)
- Nicola Fusco
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy
- Division of Pathology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy
- Correspondence: (N.F.); (C.M.); (M.G.); (C.S.)
| | - Caterina Marchiò
- Department of Medical Sciences, University of Turin, 10124 Turin, Italy
- Division of Pathology, Candiolo Cancer Institute FPO-IRCCS, 10060 Candiolo, Italy
- Correspondence: (N.F.); (C.M.); (M.G.); (C.S.)
| | - Michele Ghidini
- Division of Medical Oncology, Fondazione IRCCS Ca’ Granda—Ospedale Maggiore Policlinico, 20122 Milan, Italy
- Correspondence: (N.F.); (C.M.); (M.G.); (C.S.)
| | - Cristian Scatena
- Division of Pathology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy
- Correspondence: (N.F.); (C.M.); (M.G.); (C.S.)
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Mechanisms of Primary Membranous Nephropathy. Biomolecules 2021; 11:biom11040513. [PMID: 33808418 PMCID: PMC8065962 DOI: 10.3390/biom11040513] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/23/2021] [Accepted: 03/26/2021] [Indexed: 12/11/2022] Open
Abstract
Membranous nephropathy (MN) is an autoimmune disease of the kidney glomerulus and one of the leading causes of nephrotic syndrome. The disease exhibits heterogenous outcomes with approximately 30% of cases progressing to end-stage renal disease. The clinical management of MN has steadily advanced owing to the identification of autoantibodies to the phospholipase A2 receptor (PLA2R) in 2009 and thrombospondin domain-containing 7A (THSD7A) in 2014 on the podocyte surface. Approximately 50–80% and 3–5% of primary MN (PMN) cases are associated with either anti-PLA2R or anti-THSD7A antibodies, respectively. The presence of these autoantibodies is used for MN diagnosis; antibody levels correlate with disease severity and possess significant biomarker values in monitoring disease progression and treatment response. Importantly, both autoantibodies are causative to MN. Additionally, evidence is emerging that NELL-1 is associated with 5–10% of PMN cases that are PLA2R- and THSD7A-negative, which moves us one step closer to mapping out the full spectrum of PMN antigens. Recent developments suggest exostosin 1 (EXT1), EXT2, NELL-1, and contactin 1 (CNTN1) are associated with MN. Genetic factors and other mechanisms are in place to regulate these factors and may contribute to MN pathogenesis. This review will discuss recent developments over the past 5 years.
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Differential Expression of a Panel of Ten CNTN1-Associated Genes during Prostate Cancer Progression and the Predictive Properties of the Panel Towards Prostate Cancer Relapse. Genes (Basel) 2021; 12:genes12020257. [PMID: 33578925 PMCID: PMC7916715 DOI: 10.3390/genes12020257] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 12/18/2022] Open
Abstract
Contactin 1 (CNTN1) is a new oncogenic protein of prostate cancer (PC); its impact on PC remains incompletely understood. We observed CNTN1 upregulation in LNCaP cell-derived castration-resistant PCs (CRPC) and CNTN1-mediated enhancement of LNCaP cell proliferation. CNTN1 overexpression in LNCaP cells resulted in enrichment of the CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_3 gene set that facilitates endocrine resistance in breast cancer. The leading-edge (LE) genes (n = 10) of this enrichment consist of four genes with limited knowledge on PC and six genes novel to PC. These LE genes display differential expression during PC initiation, metastatic progression, and CRPC development, and they predict PC relapse following curative therapies at hazard ratio (HR) 2.72, 95% confidence interval (CI) 1.96–3.77, and p = 1.77 × 10−9 in The Cancer Genome Atlas (TCGA) PanCancer cohort (n = 492) and HR 2.72, 95% CI 1.84–4.01, and p = 4.99 × 10−7 in Memorial Sloan Kettering Cancer Center (MSKCC) cohort (n = 140). The LE gene panel classifies high-, moderate-, and low-risk of PC relapse in both cohorts. Additionally, the gene panel robustly predicts poor overall survival in clear cell renal cell carcinoma (ccRCC, p = 1.13 × 10−11), consistent with ccRCC and PC both being urogenital cancers. Collectively, we report multiple CNTN1-related genes relevant to PC and their biomarker values in predicting PC relapse.
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Gu Y, Lin X, Kapoor A, Li T, Major P, Tang D. Effective Prediction of Prostate Cancer Recurrence through the IQGAP1 Network. Cancers (Basel) 2021; 13:430. [PMID: 33498739 PMCID: PMC7865788 DOI: 10.3390/cancers13030430] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/11/2021] [Accepted: 01/20/2021] [Indexed: 02/07/2023] Open
Abstract
IQGAP1 expression was analyzed in: (1) primary prostate cancer, (2) xenografts produced from LNCaP, DU145, and PC3 cells, 3) tumor of PTEN-/- and TRAMP mice, and (3) castration resistant PC (CRPC) produced by LNCaP xenografts and PTEN-/- mice. IQGAP1 downregulations occurred in CRPC and advanced PCs. The downregulations were associated with rapid PC recurrence in the TCGA PanCancer (n = 492, p = 0.01) and MSKCC (n = 140, p = 4 × 10-6) cohorts. Differentially expressed genes (n = 598) relative to IQGAP1 downregulation were identified with enrichment in chemotaxis, cytokine signaling, and others along with reductions in immune responses. A novel 27-gene signature (Sig27gene) was constructed from these DEGs through random division of the TCGA cohort into a Training and Testing population. The panel was validated using an independent MSKCC cohort. Sig27gene robustly predicts PC recurrence at (hazard ratio) HR 2.72 and p < 2 × 10-16 in two independent PC cohorts. The prediction remains significant after adjusting for multiple clinical features. The novel and robust nature of Sig27gene underlie its great translational potential as a prognostic biomarker to predict PC relapse risk in patients with primary PC.
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Affiliation(s)
- Yan Gu
- Department of Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada; (Y.G.); (X.L.)
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada;
- The Research Institute of St Joe’s Hamilton, St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
| | - Xiaozeng Lin
- Department of Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada; (Y.G.); (X.L.)
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada;
- The Research Institute of St Joe’s Hamilton, St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
| | - Anil Kapoor
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada;
- The Research Institute of St Joe’s Hamilton, St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
- Department of Surgery, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Taosha Li
- Life-Tech Industry Alliance, Shenzhen 518000, China;
| | - Pierre Major
- Department of Oncology, McMaster University, Hamilton, ON L8S 4L8, Canada;
| | - Damu Tang
- Department of Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada; (Y.G.); (X.L.)
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada;
- The Research Institute of St Joe’s Hamilton, St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
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