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Li C, Dou P, Wang T, Lu X, Xu G, Lin X. Defining disease-related modules based on weighted miRNA synergistic network. Comput Biol Med 2023; 152:106382. [PMID: 36493730 DOI: 10.1016/j.compbiomed.2022.106382] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 11/04/2022] [Accepted: 11/28/2022] [Indexed: 11/30/2022]
Abstract
MicroRNAs (miRNAs) play an important role in the biological process. Their expression and functional changes have been observed in most cancers. Meanwhile, there exists cooperative regulation among miRNAs which is important for studying the mechanisms of complex post-transcriptional regulations. Hence, studying miRNA synergy and identifying miRNA synergistic modules can help understand the development and progression of complex diseases, such as cancers. This work studies miRNA synergy and proposes a new method for defining disease-related modules (DDRM) by combining the knowledge databases and miRNA data. DDRM measures the miRNA synergy not only by the co-regulating target subset but also by the non-common target set to construct the weighted miRNA synergistic network (WMSN). The experiments on twelve the cancer genome atlas (TCGA) datasets showed that the important modules identified by DDRM can well distinguish the cancer samples from the normal samples, and DDRM performed better than the previous method in most cases. An external dataset of prostate cancer was applied to validate the module biomarkers determined by DDRM on the prostate cancer data of TCGA. The area under the receiver operating characteristic curve (AUC) value is 0.92 and the performance is superior. Hence, combining the miRNA synergy networks from the knowledge databases and the miRNA data can determine the important functional modules related to diseases, which is of great significance to the study of disease mechanism.
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Affiliation(s)
- Chao Li
- School of Computer Science & Technology, Dalian University of Technology, 116024, Dalian, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Peng Dou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Tianxiang Wang
- School of Computer Science & Technology, Dalian University of Technology, 116024, Dalian, China
| | - Xin Lu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; Liaoning Province Key Laboratory of Metabolomics, Dalian, China
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; Liaoning Province Key Laboratory of Metabolomics, Dalian, China
| | - Xiaohui Lin
- School of Computer Science & Technology, Dalian University of Technology, 116024, Dalian, China.
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Mansoor M, Young-Speirs M, Ren B, Gotto G, Merten L, Sawhney S, Siadat F, Acosta AM, Agaimy A, Trpkov K. Extra-renal renal cell carcinoma arising in the kidney proximity but without an identifiable renal primary - an intriguing dilemma: Report of three cases and review of the literature. Histopathology 2022; 81:635-643. [PMID: 35941718 DOI: 10.1111/his.14736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/18/2022] [Accepted: 08/03/2022] [Indexed: 11/30/2022]
Abstract
We report three patients with extra-renal renal cell carcinomas (RCC) found in the renal proximity, but unattached to the kidney. None had a history of RCC or an identifiable primary renal neoplasm at the time of the diagnosis and on follow-up. The patients included two males and one female aged 57, 77 and 63 years, respectively. One carcinomas was found in the perirenal tissue adjacent to the adrenal, one involved the adrenal gland, and one was a retroperitoneal mass found within the lymph nodes. Two extra-renal RCCs represented clear cell RCCs and one was an unclassifiable RCC. No patient had evidence of metastases at presentation and disease progression during the follow-up. This report adds to the literature on this unusual clinical scenario and further supports the concept of extra-renal RCC, which is not a well-recognized clinical phenomenon. We also reviewed other similar reports documenting the absence of identifiable renal primaries in the setting of either disseminated metastatic disease or isolated distant metastases of presumed renal origin. Similarly, some carcinomas of apparent renal derivation have been also identified during a work-up of metastatic carcinomas of unknown primary. The aim of this study is to raise further awareness of this unusual and intriguing clinical scenario that currently lacks a definitive explanation and standardized therapy strategies. Establishing a correct diagnosis may allow treatment with specific targeted therapies in selected clinical cases.
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Affiliation(s)
- Mehdi Mansoor
- Cumming School of Medicine, University of Calgary and Alberta Precision Laboratories, Calgary, AB, Canada
| | - Morgan Young-Speirs
- Cumming School of Medicine, University of Calgary and Alberta Precision Laboratories, Calgary, AB, Canada
| | - Bing Ren
- Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Geoffrey Gotto
- Cumming School of Medicine, University of Calgary and Alberta Precision Laboratories, Calgary, AB, Canada
| | - Larissa Merten
- Department of Urology and Pediatric Urology, University Hospital Erlangen, Friedrich Alexander University (FAU), 91058, Erlangen, Germany
| | - Summit Sawhney
- Cumming School of Medicine, University of Calgary and Alberta Precision Laboratories, Calgary, AB, Canada
| | - Farshid Siadat
- Cumming School of Medicine, University of Calgary and Alberta Precision Laboratories, Calgary, AB, Canada
| | - Andres M Acosta
- Department of Urology and Pediatric Urology, University Hospital Erlangen, Friedrich Alexander University (FAU), 91058, Erlangen, Germany
| | - Abbas Agaimy
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kiril Trpkov
- Cumming School of Medicine, University of Calgary and Alberta Precision Laboratories, Calgary, AB, Canada
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3
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Petrinec B, Vargas BM, Harik LR, Master VA. Renal Cancer Without Primary Cancer in the Kidney: Extra-Renal TFE3 Translocation Associated Renal Cell Carcinoma. KIDNEY CANCER 2021. [DOI: 10.3233/kca-200102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
We report a case of an isolated para-aortic retroperitoneal renal cell carcinoma (RCC) in the absence of a primary cancer in the kidney. Single case reports in the literature have described extra-renal RCC in different locations with no evidence of primary renal tumor. We present the initial presentation, diagnostic imaging, surgical treatment, and pathologic evaluation. Immunohistochemistry demonstrated positivity for TFE3 and TFEB, both of which are Microphthalmia associated transcription factors (MiT) associated with translocation RCCs. We hypothesize these few cases of extra-renal RCC represent rare forms of translocation RCC.
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Affiliation(s)
- Benjamin Petrinec
- Department of Urology, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Lara R. Harik
- Department of Pathology, Emory University School of Medicine, Atlanta, GA, USA
| | - Viraj A. Master
- Department of Urology, Emory University School of Medicine, Atlanta, GA, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
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Khoda J, Sen S, Chatterjee A. Incidental detection of Zinner syndrome in a patient with nonseminomatous germ cell tumor of testis. Urol Ann 2021; 12:394-395. [PMID: 33776341 PMCID: PMC7992532 DOI: 10.4103/ua.ua_11_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 06/19/2020] [Indexed: 11/04/2022] Open
Abstract
Zinner syndrome is a rare congenital abnormality occurring in males comprising a triad of unilateral renal agenesis, ipsilateral ejaculatory duct obstruction, and seminal vesicle cyst. Most patients remain asymptomatic, and some may present with lower urinary tract symptoms or infertility. We present a case of incidentally detected Zinner syndrome in a patient with nonseminomatous germ cell tumor of testis, an association that is not reported in literature to our knowledge.
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Affiliation(s)
- Jeevitesh Khoda
- Department of Radiology, Tata Medical Center, Kolkata, West Bengal, India
| | - Saugata Sen
- Department of Radiology, Tata Medical Center, Kolkata, West Bengal, India
| | - Argha Chatterjee
- Department of Radiology, Tata Medical Center, Kolkata, West Bengal, India
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Han SI, Lim SC. Rare Case of Renal-type Clear Cell Carcinoma of the Prostate and Review of the Literature. IN VIVO (ATHENS, GREECE) 2020. [PMID: 32871810 DOI: 10.21873/invivo.12098.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
BACKGROUND/AIM Renal-type clear cell carcinoma (RTCCC) occurring as a primary tumor in an extra-renal location, especially in the prostate, is very rare. In this report, we present a rare case of RTCCC of the prostate and review the current literature on this condition. CASE REPORT The patient was a 76-year-old man who presented with urinary symptoms. Cystoscopic findings showed tumor-like lesions in the dome, neck, and anterior wall of the urinary bladder. Biopsy revealed clear cell carcinoma (CCC). Transrectal needle biopsy of the prostate revealed prostatic adenocarcinoma with CCC features. Immunohistochemically, tumor cells of the bladder and prostate were compatible with prostatic carcinoma. The whole-body radiologic workup did not reveal any renal or other organ malignancies. Transurethral resection of the prostate and bladder tumor was performed. The patient underwent regular follow-up cystoscopic examination and urine cytology. No recurrence was observed 19 months after the diagnosis. CONCLUSION This was a case of RTCCC arising in the prostate. RTCCC of the prostate is extremely rare and shows very similar histological and immunohistochemical features to those of CCC occurring in the kidney. Pathologists should be aware of such an entity whenever they see clear cells in urinary tract malignancies.
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Affiliation(s)
- Song Iy Han
- Division of Premedical Science, College of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Sung-Chul Lim
- Department of Pathology, College of Medicine, Chosun University, Gwangju, Republic of Korea
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Han SI, Lim SC. Rare Case of Renal-type Clear Cell Carcinoma of the Prostate and Review of the Literature. In Vivo 2020; 34:2751-2756. [PMID: 32871810 DOI: 10.21873/invivo.12098] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/12/2020] [Accepted: 06/12/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND/AIM Renal-type clear cell carcinoma (RTCCC) occurring as a primary tumor in an extra-renal location, especially in the prostate, is very rare. In this report, we present a rare case of RTCCC of the prostate and review the current literature on this condition. CASE REPORT The patient was a 76-year-old man who presented with urinary symptoms. Cystoscopic findings showed tumor-like lesions in the dome, neck, and anterior wall of the urinary bladder. Biopsy revealed clear cell carcinoma (CCC). Transrectal needle biopsy of the prostate revealed prostatic adenocarcinoma with CCC features. Immunohistochemically, tumor cells of the bladder and prostate were compatible with prostatic carcinoma. The whole-body radiologic workup did not reveal any renal or other organ malignancies. Transurethral resection of the prostate and bladder tumor was performed. The patient underwent regular follow-up cystoscopic examination and urine cytology. No recurrence was observed 19 months after the diagnosis. CONCLUSION This was a case of RTCCC arising in the prostate. RTCCC of the prostate is extremely rare and shows very similar histological and immunohistochemical features to those of CCC occurring in the kidney. Pathologists should be aware of such an entity whenever they see clear cells in urinary tract malignancies.
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Affiliation(s)
- Song Iy Han
- Division of Premedical Science, College of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Sung-Chul Lim
- Department of Pathology, College of Medicine, Chosun University, Gwangju, Republic of Korea
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Liao G, Zhang X, Li Z, Lan S, Huang M, Huang W. Renal-type clear cell carcinoma of prostate: A case report and review of literature. INDIAN J PATHOL MICR 2018; 61:431-433. [PMID: 30004074 DOI: 10.4103/ijpm.ijpm_396_17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
We analyzed the clinicopathological features of renal-type clear cell carcinoma (RTCCC) in the prostate and its diagnosis according to the example in our hospital and review of the literature. Clinicopathological features of RTCCC in the prostate were observed in a patient from our hospital combining with a review of the literature. Microscopically, the tumor was composed of cells with abundant and translucent cytoplasm, arranged in the form of the vesicular nest or glandular structure. Therefore, it was necessary to distinguish between metastatic clear cell renal cell carcinoma and primary RTCCC in the prostate. Immunohistochemistry (IHC) of this case showed tumor cells were positive expression for cytokeratin (CKpan), low-molecular weight cytokeratin, epithelial membrane antigen, and prostate-specific antigen (PSA), P504S, prostate-specific membrane antigen and partial positive expression for vimentin and CD10. The tumor cells displayed negative expression of high molecular weight cytokeratin, cytokeratin 7 (CK7), CK34, PAX8, and renal cell carcinoma. The morphological and immunohistochemical features of this tumor were in correspondence with RTCCC of the prostate. This tumor is a rare variant of the prostate carcinomas. To the best of our knowledge, this type of extrarenal tumor has only been reported in six previous studies. Combination of histology, IHC, imaging, and serum PSA is needed to perform a suitable diagnosis.
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Affiliation(s)
- Guangjie Liao
- Department of Pathology, Red Cross Hospital of Yulin, Yulin, China
| | - Xinke Zhang
- Department of Pathology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Zhongjian Li
- Department of Pathology, Red Cross Hospital of Yulin, Yulin, China
| | - Su Lan
- Department of Pathology, Red Cross Hospital of Yulin, Yulin, China
| | - Miaoli Huang
- Department of Pathology, Red Cross Hospital of Yulin, Yulin, China
| | - Weijian Huang
- Department of Pathology, Red Cross Hospital of Yulin, Yulin, China
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