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Classification of c...
Classification of clear cell renal cell carcinoma based on PKM alternative splicing
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- Li, Xiangyu (author)
- KTH,Systembiologi,Science for Life Laboratory, SciLifeLab
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- Turanli, B. (author)
- İstanbul Medeniyet Üniversitesi,Istanbul Medeniyet University,Istanbul Medeniyet Univ, Dept Bingn, Istanbul, Turkey.
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- Juszczak, Kajetan (author)
- KTH,Science for Life Laboratory, SciLifeLab
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- Kim, Woonghee (author)
- KTH,Systembiologi,Science for Life Laboratory, SciLifeLab
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- Arif, Muhammad (author)
- KTH,Systembiologi,Science for Life Laboratory, SciLifeLab
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- Sato, Y. (author)
- University of Tokyo, Japan,Kyoto Univ, Inst Adv Study Human Biol WPI ASHBi, Dept Pathol & Tumor Biol, Kyoto, Japan.;Univ Tokyo, Grad Sch Med, Dept Urol, Tokyo, Japan.
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- Ogawa, S. (author)
- Karolinska Institutet,Kyoto Univ, Inst Adv Study Human Biol WPI ASHBi, Dept Pathol & Tumor Biol, Kyoto, Japan.;Karolinska Inst, Ctr Hematol & Regenerat Med, Dept Med, Stockholm, Sweden.
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- Turkez, H. (author)
- Erzurum Teknik Üniversitesi,Erzurum Technical University,Erzurum Tech Univ, Dept Mol Biol & Genet, TR-25240 Erzurum, Turkey.
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- Nielsen, Jens B, 1962 (author)
- Chalmers tekniska högskola,Chalmers University of Technology,Chalmers Univ Technol, Dept Biol & Biol Engn, Gothenburg, Sweden.
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- Borén, Jan, 1963 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för medicin, avdelningen för molekylär och klinisk medicin,Institute of Medicine, Department of Molecular and Clinical Medicine,Sahlgrenska universitetssjukhuset,Sahlgrenska University Hospital,Univ Gothenburg, Sahlgrenska Univ Hosp, Dept Mol & Clin Med, Gothenburg, Sweden.
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- Uhlén, Mathias (author)
- KTH,Systembiologi,Science for Life Laboratory, SciLifeLab
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- Zhang, C. (author)
- KTH,Systembiologi,Science for Life Laboratory, SciLifeLab
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- Mardinoglu, Adil, 1982 (author)
- KTH,Systembiologi,Science for Life Laboratory, SciLifeLab
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(creator_code:org_t)
- Elsevier BV, 2020
- 2020
- English.
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In: Heliyon. - : Elsevier BV. - 2405-8440. ; 6:2
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Abstract
Subject headings
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- Clear cell renal cell carcinoma (ccRCC) accounts for 70-80% of kidney cancer diagnoses and displays high molecular and histologic heterogeneity. Hence, it is necessary to reveal the underlying molecular mechanisms involved in progression of ccRCC to better stratify the patients and design effective treatment strategies. Here, we analyzed the survival outcome of ccRCC patients as a consequence of the differential expression of four transcript isoforms of the pyruvate kinase muscle type (PKM). We first extracted a classification biomarker consisting of eight gene pairs whose within-sample relative expression orderings (REOs) could be used to robustly classify the patients into two groups with distinct molecular characteristics and survival outcomes. Next, we validated our findings in a validation cohort and an independent Japanese ccRCC cohort. We finally performed drug repositioning analysis based on transcriptomic expression profiles of drug-perturbed cancer cell lines and proposed that paracetamol, nizatidine, dimethadione and conessine can be repurposed to treat the patients in one of the subtype of ccRCC whereas chenodeoxycholic acid, fenoterol and hexylcaine can be repurposed to treat the patients in the other subtype.
Subject headings
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin -- Hematologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine -- Hematology (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin -- Urologi och njurmedicin (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine -- Urology and Nephrology (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin -- Cancer och onkologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine -- Cancer and Oncology (hsv//eng)
Keyword
- Bioinformatics
- Cancer research
- Systems biology
- PKM
- Alternative
- splicing
- Transcriptomics
- Biomarker
- Drug repositioning
- pyruvate-kinase m2
- isoform expression
- cancer metabolism
- bile-acids
- signatures
- migration
- angiogenesis
- progression
- modulation
- invasion
- Science & Technology - Other Topics
- Drug repositioning
Publication and Content Type
- ref (subject category)
- art (subject category)
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Heliyon
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- By the author/editor
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Li, Xiangyu
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Turanli, B.
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Juszczak, Kajeta ...
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Kim, Woonghee
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Arif, Muhammad
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Sato, Y.
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show more...
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Ogawa, S.
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Turkez, H.
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Nielsen, Jens B, ...
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Borén, Jan, 1963
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Uhlén, Mathias
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Zhang, C.
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Mardinoglu, Adil ...
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- About the subject
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Clinical Medicin ...
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Clinical Medicin ...
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and Hematology
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Clinical Medicin ...
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and Urology and Neph ...
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Clinical Medicin ...
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- Articles in the publication
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Heliyon
- By the university
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University of Gothenburg
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Chalmers University of Technology
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Royal Institute of Technology
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Karolinska Institutet