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Li H, Chen L, Ke ZB, Chen SH, Xue XY, Zheng QS, Wei Y, Zeng K, Xu N. Angiogenesis-Related Molecular Subtypes and a Novel Prognostic Signature in Clear Cell Renal Cell Carcinoma Patients. Int J Gen Med 2021; 14:6325-6342. [PMID: 34629897 PMCID: PMC8497487 DOI: 10.2147/ijgm.s332732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 09/09/2021] [Indexed: 11/26/2022] Open
Abstract
Background This study aimed to develop and validate a novel angiogenesis-related gene (ARG) signature and molecular subtypes by bioinformatics analysis. Materials and Methods The transcriptome data and clinical data were obtained from TCGA and ICGC database. We performed consensus clustering analysis to identify angiogenesis molecular subtypes for ccRCC. Univariate and multivariate Cox regression analyses were used to develop a novel ARG-related signature as a prognostic biomarker for ccRCC. Internal and external validation were then performed in TCGA and ICGC cohort, respectively. Results We identified a total of two angiogenesis molecular subtypes of ccRCC. The overall survival (OS) of subtype 1 ccRCC was significantly decreased compared with that of subtype 2 ccRCC (P=0.001). These two molecular subtypes have significantly different tumor microenvironment and immune checkpoint inhibitor sensitivities (P<0.05). Besides, we developed a novel signature based on three ARGs (including MSX1, TIMP1 and JAG2) for subtype 1 ccRCC. The difference in OS between high- and low-risk group was statistically significant in training cohort (P=0.009), test cohort (P=0.024), the whole type 1 cohort (P<0.001), and validation cohort (P=0.041). The AUC for one-year OS prediction was 0.732, 0.710, 0.725, and 0.645 in training cohort, test cohort, the whole type 1 cohort, and validation cohort, respectively. Independent prognostic analysis showed that this signature was an independent predictor for OS of subtype 1 ccRCC (P=0.028914). The power of this prognostic signature was superior to other signatures reported in previous studies. Conclusion We developed and successfully validated a novel ARG signature for predicting prognosis of subtype 1 ccRCC, which was superior to several previous signatures.
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Affiliation(s)
- Hao Li
- Department of Anesthesiology, Anesthesiology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China.,Department of Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China
| | - Lu Chen
- Department of Anesthesiology, Anesthesiology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China.,Department of Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China
| | - Zhi-Bin Ke
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China
| | - Shao-Hao Chen
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China
| | - Xue-Yi Xue
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China
| | - Qing-Shui Zheng
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China
| | - Yong Wei
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China
| | - Kai Zeng
- Department of Anesthesiology, Anesthesiology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China.,Department of Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China
| | - Ning Xu
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China.,Fujian Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China
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Halabi S, Yang Q, Carmack A, Zhang S, Foo WC, Eisen T, Stadler WM, Jones RJ, Garcia JA, Vaishampayan UN, Picus J, Hawkins RE, Hainsworth JD, Kollmannsberger CK, Logan TF, Puzanov I, Pickering LM, Ryan CW, Protheroe A, George DJ, Armstrong AJ. Tissue based biomarkers in non-clear cell RCC: Correlative analysis from the ASPEN clinical trial. KIDNEY CANCER JOURNAL : OFFICIAL JOURNAL OF THE KIDNEY CANCER ASSOCIATION 2021; 19:64-72. [PMID: 34765076 PMCID: PMC8580377 DOI: 10.52733/kcj19n3-a1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Biomarkers are needed in patients with non-clear cell renal cell carcinomas (NC-RCC), particularly papillary renal cell carcinoma, in order to inform on initial treatment selection and identify potentially novel targets for therapy. We enrolled 108 patients in ASPEN, an international randomized open-label phase 2 trial of patients with metastatic papillary, chromophobe, or unclassified NC-RCC treated with the mTOR inhibitor everolimus (n=57) or the vascular endothelial growth factor (VEGF) receptor inhibitor sunitinib (n=51), stratified by MSKCC risk and histology. The primary endpoint was overall survival (OS) and secondary efficacy endpoints for this exploratory biomarker analysis were radiographic progression-free survival (rPFS) defined by intention-to-treat using the RECIST 1.1 criteria and radiographic response rates. Tissue biomarkers (n=78) of mTOR pathway activation (phospho-S6 and -Akt, c-kit) and VEGF pathway activation (HIF-1α, c-MET) were prospectively explored in tumor tissue by immunohistochemistry prior to treatment and associated with clinical outcomes. We found that S6 activation was more common in poor risk NC-RCC tumors and S6/Akt activation was associated with worse PFS and OS outcomes with both everolimus and sunitinib, while c-kit was commonly expressed in chromophobe tumors and associated with improved outcomes with both agents. C-MET was commonly expressed in papillary tumors and was associated with lower rates of radiographic response but did not predict PFS for either agent. In multivariable analysis, both pAkt and c-kit were statistically significant prognostic biomarkers of OS. No predictive biomarkers of treatment response were identified for clinical outcomes. Most biomarker subgroups had improved outcomes with sunitinib as compared to everolimus.
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Affiliation(s)
- Susan Halabi
- Department of Biostatistics and Bioinformatics, Duke University, Durham NC
| | - Qian Yang
- Department of Biostatistics and Bioinformatics, Duke University, Durham NC
| | - Andrea Carmack
- Department of Biostatistics and Bioinformatics, Duke University, Durham NC
| | - Shiqi Zhang
- Department of Biostatistics and Bioinformatics, Duke University, Durham NC
| | - Wen-Chi Foo
- Department of Biostatistics and Bioinformatics, Duke University, Durham NC
| | - Tim Eisen
- University of Cambridge, Cambridge, United Kingdom
| | | | - Robert J. Jones
- University of Glasgow, The Beatson West of Scotland Cancer Centre, Glasgow, United Kingdom
| | | | - Ulka N. Vaishampayan
- University of Michigan, Ann Arbor/Karmanos Cancer Institute, Wayne State University, Detroit, MI USA
| | - Joel Picus
- Washington University in St. Louis, St. Louis, MO USA
| | | | | | | | - Theodore F. Logan
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN USA
| | - Igor Puzanov
- Vanderbilt University Medical Center, Nashville, TN USA
| | | | - Christopher W. Ryan
- Oregon Health & Science University, OHSU Knight Cancer Institute, Portland, OR USA
| | - Andrew Protheroe
- University of Oxford Medical Oncology Department, Oxford, United Kingdom
| | - Daniel J. George
- Duke University and the Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, NC
| | - Andrew J. Armstrong
- Duke University and the Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, NC
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Wetzel-Strong SE, Weinsheimer S, Nelson J, Pawlikowska L, Clark D, Starr MD, Liu Y, Kim H, Faughnan ME, Nixon AB, Marchuk DA. Pilot investigation of circulating angiogenic and inflammatory biomarkers associated with vascular malformations. Orphanet J Rare Dis 2021; 16:372. [PMID: 34479577 PMCID: PMC8414780 DOI: 10.1186/s13023-021-02009-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/24/2021] [Indexed: 01/03/2023] Open
Abstract
Background Vascular malformations in the central nervous system are difficult to monitor and treat due to their inaccessible location. Angiogenic and inflammatory proteins are secreted into the bloodstream and may serve as useful biomarkers for identifying patients at risk for complications or with certain disease phenotypes.
Methods A validated multiplex protein array consisting of 26 angiogenic and inflammatory biomarkers (Angiome) was assessed in plasma isolated from healthy controls and patients with either sporadic brain arteriovenous malformation (BAVM), familial cerebral cavernous malformation (CCM), or hereditary hemorrhagic telangiectasia (HHT). These samples were obtained from archives of ongoing research studies at the University of California San Francisco and through prospective collection at the Toronto HHT Centre at St. Michael’s Hospital. Results We compared circulating biomarker levels from each patient group to healthy controls and analyzed each pairwise combination of patient groups for differences in biomarker levels. Additionally, we analyzed the HHT samples to determine the association between biomarker levels and the following HHT-specific phenotypes, BAVM, pulmonary arteriovenous malformation (PAVM), liver vascular malformation (LVM), and gastrointestinal (GI) bleeding. Compared to controls, levels of SDF1 were significantly elevated in HHT patients (Proportional Increase [PI] = 1.87, p < 0.001, q = 0.011). Levels of sENG were significantly reduced in HHT patients compared to controls (PI = 0.56, p < 0.001, q < 0.001), reflecting the prevalence of HHT1 patients in this cohort. Levels of IL6 (PI = 3.22, p < 0.001, q < 0.001) and sTGFβR3 (PI = 0.70, p = 0.001, q < 0.029) differed significantly in CCM patients compared to controls. Compared to controls, ten of the biomarkers were significantly different in sporadic BAVM patients (q-values < 0.05). Among the pairwise combinations of patient groups, a significant elevation was observed in TGFβ1 in CCM patients compared to sporadic BAVM patients (PI = 2.30, p < 0.001, q = 0.034). When examining the association of circulating biomarker levels with HHT-specific phenotypes, four markers were significantly lower in HHT patients with BAVM (q-values < 0.05), and four markers were significantly higher in patients with LVM (q-values < 0.05). Conclusions This pilot study suggests that the profile of circulating angiogenic and inflammatory biomarkers may be unique to each type of vascular malformation. Furthermore, this study indicates that circulating biomarkers may be useful for assessing phenotypic traits of vascular malformations. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-021-02009-7.
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Affiliation(s)
- Sarah E Wetzel-Strong
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, 265 CARL Bldg., Box #3175 DUMC, Durham, NC, 27710, USA
| | - Shantel Weinsheimer
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA, USA
| | - Jeffrey Nelson
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA, USA
| | - Ludmila Pawlikowska
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA, USA
| | - Dewi Clark
- Toronto HHT Centre, St. Michael's Hospital and the Li Ka Shing Knowledge Institute, Toronto, Canada
| | - Mark D Starr
- Department of Medicine, Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA
| | - Yingmiao Liu
- Department of Medicine, Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA
| | - Helen Kim
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA, USA
| | - Marie E Faughnan
- Toronto HHT Centre, St. Michael's Hospital and the Li Ka Shing Knowledge Institute, Toronto, Canada.,Division of Respirology, Department of Medicine, University of Toronto, Toronto, Canada
| | - Andrew B Nixon
- Department of Medicine, Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA
| | - Douglas A Marchuk
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, 265 CARL Bldg., Box #3175 DUMC, Durham, NC, 27710, USA.
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