Article
Oncology
Sheng Tai, Dan-dan Xu, Zhixian Yu, Yu Guan, Shuiping Yin, Jun Xiao, Song Xue, Chaozhao Liang
Summary: This study describes the molecular characteristics of Renal Cell Carcinoma (RCC) and identifies a small panel of RCC-associated genes from a large panel of cancer-related genes. Analysis of clinical data from 55 RCC patients revealed frequent mutations in genes such as VHL, PBRM1, BAP1, and SETD2, and showed that non-clear cell RCC (nccRCC) is more genetically heterogeneous than clear cell RCC (ccRCC). The small panel of RCC-associated genes provides a clearer profile of genetic characteristics and may have implications for prognosis and clinical decision-making.
FRONTIERS IN ONCOLOGY
(2023)
Article
Oncology
Jiwei Huang, Wen Cai, Biao Cai, Wen Kong, Wei Zhai, Jin Zhang, Yonghui Chen, Shiqing Chen, Yuezong Bai, Yiran Huang, Wei Xue
Summary: The study investigated the molecular features of Chinese ccRCC patients, revealing differences in mutation frequencies of genes like VHL and PBRM1 compared to the TCGA database. Some patients showed positive PD-L1 expression, while a small portion carried pathogenic or likely pathogenic germline mutations.
FRONTIERS IN ONCOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Xin Huang, Di Sun, Tianzhen Wu, Xing Liu, Shixia Xu, Guang Yang
Summary: This study identified genes related to obesity and cancer control in carnivores, which may have driven the diversifying evolution of body size in the order. The evolution of an effective mechanism to resist cancer in large carnivores provides molecular evidence for Peto's paradox. Additionally, changes in rapidly evolving genes in small carnivores were found to reduce body size.
Article
Immunology
Bao Wang, Qiang Song, Yuang Wei, Xiangzheng Wu, Tian Han, Hengtao Bu, Sensheng Tang, Jian Qian, Pengfei Shao
Summary: By constructing and validating a unique risk signature and model based on cuproptosis, a great predictive value was demonstrated in distinguishing high risk/score and low risk/score patients. The cuproptosis score was found to be closely associated with the prognosis and immune features of ccRCC patients. Furthermore, cuproptosis played an indispensable role in regulating tumor microenvironment features, tumor progression, and long-term prognosis of ccRCC.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Oncology
Gennady Bratslavsky, Stephanie Gleicher, Joseph M. Jacob, Thomas H. Sanford, Oleg Shapiro, Dimitra Bourboulia, Laurie M. Gay, Julie Andrea Elvin, Jo-Anne Vergilio, James Suh, Shakti Ramkissoon, Eric Allan Severson, Jonathan Keith Killian, Alexa Betzig Schrock, Jon H. Chung, Vincent A. Miller, Mehdi Mollapour, Jeffrey S. Ross
Summary: The study found that genomic alteration patterns in collecting duct carcinoma (CDC) and renal medullary carcinoma (RMC) differ significantly from clear cell renal cell carcinoma (CCRCC). Targeted therapies for CDC and RMC appear limited, with rare opportunities to target alterations in receptor tyrosine kinase and MTOR pathways. Similarly, the low TMB and absence of MSI-High status in CDC and RMC suggest resistance to immunotherapies.
UROLOGIC ONCOLOGY-SEMINARS AND ORIGINAL INVESTIGATIONS
(2021)
Review
Cell Biology
Jiao-Yi Chen, Wai-Han Yiu, Patrick Ming-Kuen Tang, Sydney Chi-Wai Tang
Summary: Fibrotic signaling plays a crucial role in the development and progression of renal cell carcinoma. Targeting classic fibrotic signaling processes such as TGF-beta signaling and EMT shows promising antitumor effects both preclinically and clinically. A better understanding of the molecular mechanisms of fibrotic signaling in renal cell carcinoma can facilitate the development of precision therapies against solid cancers.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Urology & Nephrology
Rebecca E. Graff, Kathryn M. Wilson, Alejandro Sanchez, Steven L. Chang, David F. McDermott, Toni K. Choueiri, Eunyoung Cho, Sabina Signoretti, Edward L. Giovannucci, Mark A. Preston
Summary: Obesity is associated with an increased risk and mortality of renal cell carcinoma (RCC). Body mass index at diagnosis is not a reliable factor for predicting prognosis, as weight loss around diagnosis is correlated with worse outcomes.
Review
Oncology
Weijie Yan, Naiqiao Hou, Junhua Zheng, Wei Zhai
Summary: In recent years, there have been significant improvements in renal cell carcinoma therapy. To find effective treatments for different populations, researchers have studied predictive molecular biomarkers in response to target, immunological, and combined therapies. This review summarizes these studies and highlights the potential of predictive molecular biomarkers in metastatic RCC therapy. However, further validation is needed for most of these findings.
Article
Biochemistry & Molecular Biology
Todd A. Johnson, Shigekatsu Maekawa, Masashi Fujita, Jisong An, Young-Seok Ju, Kazuhiro Maejima, Yuki Kanazashi, Ryosuke Jikuya, Yuki Okawa, Shota Sasagawa, Ken Yagi, Yasushi Okazaki, Naoto Kuroda, Ryo Takata, Wataru Obara, Hidewaki Nakagawa
Summary: Patients with end-stage renal disease (ESRD) or receiving dialysis have a higher risk for renal cell carcinoma (RCC). This study aimed to identify the genomic features of ESRD RCC and their association with tumor histology and dialysis exposure. The study found that ESRD or dialysis may induce cellular stress leading to specific types of genomic damage.
HUMAN MOLECULAR GENETICS
(2022)
Article
Oncology
Qianlai Luo, Jonathan N. Hofmann, Ruth M. Pfeiffer, Cari M. Kitahara, Minkyo Song, Meredith S. Shiels
Summary: Since the mid-1990s, overweight/obesity appears to have significantly contributed to the rising incidence of renal cell carcinoma (RCC) in the United States, while the contribution of non-smoking has declined. Public health interventions aimed at reducing overweight and obesity could play a crucial role in curbing this trend.
INTERNATIONAL JOURNAL OF CANCER
(2023)
Article
Multidisciplinary Sciences
Yuping Zhang, Sathiya P. Narayanan, Rahul Mannan, Gregory Raskind, Xiaoming Wang, Pankaj Vats, Fengyun Su, Noshad Hosseini, Xuhong Cao, Chandan Kumar-Sinha, Stephanie J. Ellison, Thomas J. Giordano, Todd M. Morgan, Sethuramasundaram Pitchiaya, Ajjai Alva, Rohit Mehra, Marcin Cieslik, Saravana M. Dhanasekaran, Arul M. Chinnaiyan
Summary: This study used single-cell RNA sequencing to identify the cell of origin for different RCC subtypes and highlighted the crucial role of the tumor microenvironment in influencing ccRCC biology and response to therapy.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Editorial Material
Oncology
Elizabeth P. Henske, Liang Cheng, A. Ari Hakimi, Toni K. Choueiri, David A. Braun
Summary: Chromophobe renal cell carcinoma (ChRCC) is the second most common variant of non-clear cell renal cell carcinoma. ChRCC differs from clear cell RCC (ccRCC) in terms of genetics, genomics, metabolism, cell of origin, and response to targeted and immune therapies. The pathogenesis of ChRCC is not well understood, but current evidence suggests two potential mechanisms: mTORC1 hyperactivation through PTEN pathway mutations and mitochondrial dysfunction leading to oxidative stress.
Article
Oncology
Karoline Diesing, Silvia Ribback, Stefan Winter, Manuela Gellert, Antonia M. Oster, Viktoria Stuhler, Eva Glaser, Frank Adler, Christoph Hartwig, Markus Scharpf, Jens Bedke, Martin Burchardt, Matthias Schwab, Christopher H. Lillig, Nils Kroeger
Summary: Although p53 is rarely mutated in ccRCC, its overexpression is associated with poor prognosis; high p53 protein levels are poor prognostic features; functional inhibition of p53 in ccRCC is not correlated with clinical outcomes.
JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY
(2021)
Article
Oncology
Rosie K. Singleton, Alicia K. Heath, Joanna L. Clasen, Ghislaine Scelo, Mattias Johansson, Florence Le Calvez-Kelm, Elisabete Weiderpass, Fredrik Liedberg, Borje Ljungberg, Justin Harbs, Anja Olsen, Anne Tjonneland, Christina C. Dahm, Rudolf Kaaks, Renee T. Fortner, Salvatore Panico, Giovanna Tagliabue, Giovanna Masala, Rosario Tumino, Fulvio Ricceri, Inger T. Gram, Carmen Santiuste, Catalina Bonet, Miguel Rodriguez-Barranco, Mattias B. Schulze, Manuela M. Bergmann, Ruth C. Travis, Ioanna Tzoulaki, Elio Riboli, David C. Muller
Summary: The study found that the currently available RCC risk prediction models have limitations in identifying individuals at substantial risk of RCC in the general population. Further development, potentially incorporating biomarkers, is needed for more effective risk stratification of RCC.
CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION
(2021)
Review
Oncology
Francisco Zambrana, Lucia Carril-Ajuria, Alfonso Gomez de Liano, Nieves Martinez Chanza, Ray Manneh, Daniel Castellano, Guillermo de Velasco
Summary: The use of immune-checkpoint inhibitors in mRCC has led to better survival outcomes and higher rates of complete responses, but also presents challenges in defining durable responses, optimal treatment duration, and the value of complete responses. Questions remain regarding whether complete responses can be considered as a cure and if immunotherapy discontinuation should be considered after achieving a complete response.
CANCER TREATMENT REVIEWS
(2021)
Editorial Material
Genetics & Heredity
Peter W. Laird
Article
Gastroenterology & Hepatology
Shamaine Wei Ting Ho, Taotao Sheng, Manjie Xing, Wen Fong Ooi, Chang Xu, Raghav Sundar, Kie Kyon Huang, Zhimei Li, Vikrant Kumar, Kalpana Ramnarayanan, Feng Zhu, Supriya Srivastava, Zul Fazreen Bin Adam Isa, Chukwuemeka George Anene-Nzelu, Milad Razavi-Mohseni, Dustin Shigaki, Haoran Ma, Angie Lay Keng Tan, Xuewen Ong, Ming Hui Lee, Su Ting Tay, Yu Amanda Guo, Weitai Huang, Shang Li, Michael A. Beer, Roger Sik Yin Foo, Ming Teh, Anders Jacobsen Skanderup, Bin Tean Teh, Patrick Tan
Summary: This study derived and applied a consensus Mes-GC classifier to define the Mes-GC enhancer landscape, identifying the vulnerabilities of this subtype.
Article
Multidisciplinary Sciences
Kiran Krishnamachari, Dylan Lu, Alexander Swift-Scott, Anuar Yeraliyev, Kayla Lee, Weitai Huang, Sim Ngak Leng, Anders Jacobsen Skanderup
Summary: The authors develop VarNet, a weakly supervised deep learning model for somatic variant calling in cancer with robust performance across multiple cancer genomics datasets.
NATURE COMMUNICATIONS
(2022)
Article
Oncology
Whijae Roh, Yifat Geffen, Hongui Cha, Mendy Miller, Shankara Anand, Jaegil Kim, David Heiman, Justin F. Gainor, Peter W. Laird, Andrew D. Cherniack, Chan-Young Ock, Se-Hoon Lee, Gad Getz
Summary: Through consensus hierarchical clustering analysis, we identified five robust expression subtypes of lung adenocarcinoma. Integrating genomic and proteomic data, we defined biomarkers of response to targeted therapies and immunotherapies. These subtypes and biomarkers could help identify patients likely to respond to CDK4/6, MET, or PD-L1 inhibitors.
Article
Oncology
Stephanie P. L. Saw, Win Pin Ng, Siqin Zhou, Gillianne G. Y. Lai, Aaron C. Tan, Mei -Kim Ang, Wan-Teck Lim, Ravindran Kanesvaran, Quan Sing Ng, Amit Jain, Wan Ling Tan, Tanujaa Rajasekaran, Johan W. K. Chan, Yi Lin Teh, Mengyuan Pang, Jia-Chi Yeo, Angela Takano, Boon-Hean Ong, Eng-Huat Tan, Sze Huey Tan, Anders J. Skanderup, Daniel S. W. Tan
Summary: The aim of this study was to compare the prognostic value of programmed death-ligand 1 (PD-L1) score in early-stage epidermal growth factor receptor (EGFR)-mutated and EGFR-wildtype non-small cell lung cancer (NSCLC). The results showed that PD-L1 > 1% was an independent predictor of worse prognosis in EGFR-mutated NSCLC and was associated with inferior disease-free survival (DFS) regardless of EGFR status. Therefore, PD-L1 score should be evaluated as a risk stratification factor in prospective adjuvant studies among EGFR-mutated NSCLC.
EUROPEAN JOURNAL OF CANCER
(2023)
Article
Cell Biology
Yuan Liu, Neel Chudgar, Brooke Mastrogiacomo, Di He, Manendra B. Lankadasari, Samhita Bapat, Gregory D. Jones, Francisco Sanchez-Vega, Kay See Tan, Nikolaus Schultz, Semanti Mukherjee, Kenneth Offit, Yongde Bao, Matthew J. Bott, Natasha Rekhtman, Prasad S. Adusumilli, Bob T. Li, Marty W. Mayo, David R. Jones
Summary: This study reveals the role of BRMS1 gene mutation in the metastasis of lung adenocarcinoma. The BRMS1v2(A273V/A273V) mutation activates c-fos-mediated gene transcriptional regulation, promoting tumor cell invasion and metastasis. This finding offers a potential therapeutic strategy for patients with lung adenocarcinoma.
SCIENCE TRANSLATIONAL MEDICINE
(2022)
Article
Multidisciplinary Sciences
Elsie Cheruba, Ramya Viswanathan, Pui-Mun Wong, Howard John Womersley, Shuting Han, Brenda Tay, Yiting Lau, Anna Gan, Polly S. Y. Poon, Anders Skanderup, Sarah B. Ng, Aik Yong Chok, Dawn Qingqing Chong, Iain Beehuat Tan, Lih Feng Cheow
Summary: Genome-wide analysis of cell-free DNA methylation profile is a promising approach for sensitive and specific detection of many cancers. However, the high cost of whole-genome bisulfite sequencing makes it impractical for clinical translation. In this study, we developed a heat enrichment of CpG-rich regions for bisulfite sequencing (Heatrich-BS) platform, which allows for focused methylation profiling at a reduced sequencing cost suitable for frequent monitoring. Our method also enables tumor epigenetic subtyping and patient stratification. Heatrich-BS holds great potential for highly scalable screening and monitoring of cancer using liquid biopsy.
Article
Oncology
Abigail L. Miller, Naiara Perurena, Alycia Gardner, Toshinori Hinoue, Patrick Loi, Peter W. Laird, Karen Cichowski
Summary: DAB2IP is a tumor suppressor that is mutated or silenced in colorectal cancers with KRAS or BRAF mutations. Its loss promotes tumor development by activating RAS proteins and triggering inflammatory mediators and protumorigenic macrophage recruitment.
Editorial Material
Oncology
Anders Jacobsen Skanderup, Su Fen Ang, Daniel S. W. Tan
Summary: Precision oncology relies on effective molecular profiling to identify vulnerabilities for targeted therapy. Although liquid biopsies can compensate for inadequate genotyping, they are less sensitive and specific compared to tissue biopsies. The liquid biopsy toolbox is expected to expand through the development of novel assays and insights gained from longitudinal profiling.
CLINICAL CANCER RESEARCH
(2023)
Article
Gastroenterology & Hepatology
Chang Xu, Kie Kyon Huang, Jia Hao Law, Joy Shijia Chua, Taotao Sheng, Natasha M. Flores, Melissa Pool Pizzi, Atsushi Okabe, Angie Lay Keng Tan, Feng Zhu, Vikrant Kumar, Xiaoyin Lu, Ana Morales Benitez, Benedict Shi Xiang Lian, Haoran Ma, Shamaine Wei Ting Ho, Kalpana Ramnarayanan, Chukwuemeka George Anene-Nzelu, Milad Razavi-Mohseni, Siti Aishah Binte Abdul Ghani, Su Ting Tay, Xuewen Ong, Ming Hui Lee, Yu Amanda Guo, Hassan Ashktorab, Duane Smoot, Shang Li, Anders Jacobsen Skanderup, Michael A. Beer, Roger Sik Yin Foo, Joel Shi Hao Wong, Kaushal Sanghvi, Wei Peng Yong, Raghav Sundar, Atsushi Kaneda, Shyam Prabhakar, Pawel Karol Mazur, Jaffer A. Ajani, Khay Guan Yeoh, Jimmy Bok-Yan So, Patrick Tan
Summary: This study identified ARID1A as the second most frequently mutated driver gene in gastric cancer (GC). Through genomic and single-cell transcriptomic analysis, the effects of ARID1A mutation on genomic, single-cell, and epigenomic levels were revealed, and a potential therapeutic strategy for ARID1A-mutated GC was discovered.
Article
Biology
Egor Revkov, Tanmay Kulshrestha, Ken Wing-Kin Sung, Anders Jacobsen Skanderup
Summary: PUREE is a weakly supervised machine learning algorithm that accurately infers tumor purity from bulk tumor gene expression data. It can predict purity with high accuracy across different solid tumor types and is applicable to tumor samples from unseen tumor types and cohorts. In a comprehensive benchmark, PUREE outperforms existing transcriptome-based purity estimation approaches.
COMMUNICATIONS BIOLOGY
(2023)
Article
Oncology
Aaron C. Tan, Stephanie P. L. Saw, Jianbin Chen, Gillianne G. Y. Lai, Hlaing Nwe, Angela Takano, Dawn P. X. Lau, Joe P. S. Yeong, Gek San Tan, Kiat Hon Lim, Anders J. Skanderup, Johan W. K. Chan, Yi Lin Teh, Tanujaa Rajasekaran, Amit Jain, Wan Ling Tan, Quan Sing Ng, Ravindran Kanesvaran, Wan-Teck Lim, Mei-Kim Ang, Daniel S. W. Tan
Summary: This study described the molecular epidemiology and genomic features of HER2-altered NSCLC in an Asian tertiary cancer center. HER2 exon 20 insertion-mutated tumors were found to be genomically distinct from uncommon (nonexon 20 insertion) HER2 mutations, and the therapeutic implications of the genomic and clinical features of HER2-mutated NSCLC warrant further investigation.
JCO PRECISION ONCOLOGY
(2022)
Meeting Abstract
Oncology
Egor Revkov, Ken W. -K. Sung, Anders J. Skanderup
Meeting Abstract
Oncology
K. L. M. Chua, A. Tan, S. Saw, G. Lai, W. L. Tan, A. Jain, T. Rajasekaran, B. Chia, Y. Li, K. W. Fong, T. R. Siow, Q. S. Ng, A. Thiagarajan, R. Kanesvaran, W. L. Ng, S. P. Yap, E. Kalashnikova, A. Aleshin, A. J. Skanderup, W. -T. Lim, C. Yip, S. H. Tan, D. S. W. Tan, M. -K. Ang
JOURNAL OF THORACIC ONCOLOGY
(2022)
Article
Oncology
Jungyoon Choi, Andreana N. Holowatyj, Mengmeng Du, Zhishan Chen, Wanqing Wen, Nikolaus Schultz, Loren Lipworth, Xingyi Guo
Summary: This study investigated distinct somatic mutation patterns among early-onset and late-onset endometrial cancer patients. The findings revealed unique genomic landscapes in early-onset EC, suggesting potential clinical implications for targeted treatment modalities in younger patients.
JCO PRECISION ONCOLOGY
(2022)
