Article
Multidisciplinary Sciences
Belinda Kingston, Rosalind J. Cutts, Hannah Bye, Matthew Beaney, Giselle Walsh-Crestani, Sarah Hrebien, Claire Swift, Lucy S. Kilburn, Sarah Kernaghan, Laura Moretti, Katie Wilkinson, Andrew M. Wardley, Iain R. Macpherson, Richard D. Baird, Rebecca Roylance, Jorge S. Reis-Filho, Michael Hubank, Iris Faull, Kimberly C. Banks, Richard B. Lanman, Isaac Garcia-Murillas, Judith M. Bliss, Alistair Ring, Nicholas C. Turner
Summary: Genomic profiling of advanced breast cancer using plasma circulating tumour DNA sequencing revealed diverse subclonal resistance mutations, with distinct mutational processes identified in ER-positive breast cancer. This study highlights the importance of subclonal diversification in pre-treated advanced breast cancer, presenting novel therapeutic opportunities.
NATURE COMMUNICATIONS
(2021)
Editorial Material
Virology
Philippe Colson, Bernard La Scola, Mamadou Beye, Jeremy Delerce, Didier Raoult, Jacques Fantini
Summary: The emergence of the Omicron BA.2.86 variant with 39 additional mutations in the spike protein is a major event in the genetic evolution of SARS-CoV-2. This study provides insights into the phylogeny, mutation positions and frequencies, and structural model of the spike protein in BA.2.86.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Endocrinology & Metabolism
Jian Zhang, Huali Jiang, Kunpeng Du, Tao Xie, Baiyao Wang, Chengcong Chen, Russel J. Reiter, Bohong Cen, Yawei Yuan
Summary: Melatonin plays protective roles in cancer, and this study revealed the genomic alteration and clinical characteristics of melatonergic regulators in 33 cancers. Methylation-mediated downregulation of melatonergic regulator expression and the association with patient survival prediction were identified. A miRNA-mRNA interaction network involved in melatonin secretion and metabolism, as well as pathways related to inhibition of apoptosis, DNA damage response, cell cycle, and signaling activation, were also uncovered.
JOURNAL OF PINEAL RESEARCH
(2021)
Article
Multidisciplinary Sciences
Huaqiang Zhou, Yi Hu, Rongzhen Luo, Yuanyuan Zhao, Hui Pan, Liyan Ji, Ting Zhou, Lanjun Zhang, Hao Long, Jianhua Fu, Zhesheng Wen, Siyu Wang, Xin Wang, Peng Lin, Haoxian Yang, Junye Wang, Mengmeng Song, Xin Yi, Ling Yang, Xuefang Xia, Yanfang Guan, Wenfeng Fang, Yunpeng Yang, Shaodong Hong, Yan Huang, Pansong Li, Yaxiong Zhang, Ningning Zhou
Summary: Through whole-exome sequencing of 120 tumor samples from 40 early-stage small cell lung cancer (SCLC) patients, it was found that SCLC exhibits medium levels of mutational heterogeneity and tumor mutational burden. Features such as mutation distribution, ITH, and TMB may serve as prognostic biomarkers for SCLC.
NATURE COMMUNICATIONS
(2021)
Editorial Material
Multidisciplinary Sciences
Chris Amemiya
Summary: Genome sequencing and analysis of genomic interactions have revealed new insights into the evolution of the wing shapes in skates and rays, dating back over 200 million years.
Article
Biology
Elora H. Lopez-Nandam, Rebecca Albright, Erik A. Hanson, Elizabeth A. Sheets, Stephen R. Palumbi
Summary: In many animals, the germline differentiates early in embryogenesis, so only mutations that accumulate in germ cells are inherited by offspring. Stony corals, however, have been thought to produce gametes from somatic tissue. To clarify this, researchers sequenced the genomes of parent coral branches and their sperm pools and found that a significant portion of mutations were not shared between the parent and the sperm, indicating the presence of self-renewing stem cells in coral. Understanding the evolution and diversity of germlines in animals and corals can provide insights for adaptation in the face of climate change.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Medicine, General & Internal
Shaan Dudani, Guillermo de Velasco, J. Connor Wells, Chun Loo Gan, Frede Donskov, Camillo Porta, Anna Fraccon, Felice Pasini, Jae Lyun Lee, Aaron Hansen, Georg A. Bjarnason, Benoit Beuselinck, Sumanta K. Pal, Takeshi Yuasa, Nils Kroeger, Ravindran Kanesvaran, M. Neil Reaume, Christina Canil, Toni K. Choueiri, Daniel Y. C. Heng
Summary: This study found that patterns of metastasis vary between histologic subtypes of metastatic RCC and are associated with overall survival. The data highlight the clinical and biological variability between histologic subtypes and suggest that patterns of metastasis may reflect differences in underlying disease biology. Further research is encouraged to investigate differences in immune, molecular, and genetic profiles between metastatic sites and histologic subtypes.
Article
Medicine, Research & Experimental
Bing Li, Fengbin Zhang, Qikai Niu, Jun Liu, Yanan Yu, Pengqian Wang, Siqi Zhang, Huamin Zhang, Zhong Wang
Summary: A refined molecular classification scheme for gastric cancer (GC) was proposed, which utilized integrated optimal algorithms and multi-omics data to guide personalized therapies. Three subtypes linked to distinct clinical outcomes were identified based on selected important features from mRNA, microRNA, and DNA methylation data. These subtypes were validated in multiple independent cohorts and showed better clinical prediction performance compared to The Cancer Genome Atlas classification.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2023)
Article
Oncology
Paul H. Acosta, Vandana Panwar, Vipul Jarmale, Alana Christie, Jay Jasti, Vitaly Margulis, Dinesh Rakheja, John Cheville, Bradley C. Leibovich, Alexander Parker, James Brugarolas, Payal Kapur, Satwik Rajaram
Summary: Deep learning models can analyze histopathologic images to resolve intratumoral heterogeneity in clear cell renal cell carcinoma (ccRCC). These models have high sensitivity and performance in predicting the genetic heterogeneity of ccRCC genes. The predictions of these models are correlated with clinical outcomes and have diagnostic, prognostic, and biological implications.
Article
Biochemistry & Molecular Biology
Bryndis Yngvadottir, Avgi Andreou, Laia Bassaganyas, Alexey Larionov, Alex J. Cornish, Daniel Chubb, Charlie N. Saunders, Philip Smith, Huairen Zhang, Yasemin Cole, James Larkin, Lisa Browning, Samra Turajlic, Kevin Litchfield, Richard S. Houlston, Eamonn R. Maher
Summary: In unselected RCC patients, approximately 6% carry germline variants that require further follow-up analysis. Expanding the genomic panel for RCC susceptibility gene testing can improve diagnostic yield.
HUMAN MOLECULAR GENETICS
(2022)
Article
Cell Biology
Yong Liao, Zhiping Liu, Weile Ye, Zunnan Huang, Jiaojiao Wang
Summary: Monkeypox, a member of the Poxviridae family, poses a great threat to humans. This study comprehensively analyzed monkeypox-related genes (MRGs) in tumor samples from 33 types of cancer using genomic and transcriptomic approaches. The results showed that MRGs are highly correlated with immune infiltration and can predict survival in cancer patients. Genomic alterations of MRGs were associated with tumorigenesis and patient survival. Pathway analysis revealed the involvement of MRGs in various cellular processes. The study also identified potential drugs targeting MRGs.
Article
Multidisciplinary Sciences
Kaiyang Zhang, Erdogan Pekcan Erkan, Sanaz Jamalzadeh, Jun Dai, Noora Andersson, Katja Kaipio, Tarja Lamminen, Naziha Mansuri, Kaisa Huhtinen, Olli Carpen, Sakari Hietanen, Jaana Oikkonen, Johanna Hynninen, Anni Virtanen, Antti Hakkinen, Sampsa Hautaniemi, Anna Vaharautio
Summary: Chemotherapy resistance is a major contributor to cancer mortality, and a study focusing on high-grade serous ovarian cancer found that a stress-associated cell state consistently increased during chemotherapy, which was associated with poor progression-free survival.
Article
Multidisciplinary Sciences
Francis Opoku, Kweku Bedu-Addo, Nicholas Akinwale Titiloye, Elijah Atta Manu, Charity Ameh-Mensah, Babatunde Moses Duduyemi
Summary: In breast cancer, p53 overexpression is associated with high histological grade and triple negative tumors, while MDM2 overexpression is related to HER2 overexpression and high Ki-67 levels. The lack of significant correlation between p53 and MDM2 expression suggests independent genetic pathways in tumourigenesis.
Article
Urology & Nephrology
Scott Wilkinson, Huihui Ye, Fatima Karzai, Stephanie A. Harmon, Nicholas T. Terrigino, David J. VanderWeele, John R. Bright, Rayann Atway, Shana Y. Trostel, Nicole Carrabba, Nichelle C. Whitlock, Stephanie M. Walker, Rosina T. Lis, Houssein Abdul Sater, Brian J. Capaldo, Ravi A. Madan, James L. Gulley, Guinevere Chun, Maria J. Merino, Peter A. Pinto, Daniela C. Salles, Harsimar B. Kaur, Tamara L. Lotan, David J. Venzon, Peter L. Choyke, Baris Turkbey, William L. Dahut, Adam G. Sowalsky
Summary: The study aimed to identify genomic and histologic features associated with treatment resistance at baseline, finding that some prostate cancer tumors exhibit greater histologic and genomic diversity at the time of diagnosis, making them more resistant to therapy.
Article
Oncology
Christopher J. Gibson, Geoffrey Fell, Tal Sella, Adam S. Sperling, Craig Snow, Shoshana M. Rosenberg, Greg Kirkner, Ashka Patel, Deborah Dillon, Alexander G. Bick, Donna Neuberg, Ann H. Partridge, Peter G. Miller
Summary: This study aimed to investigate the presence of clonal hematopoiesis of indeterminate potential (CHIP) in young women treated for breast cancer and its impact on prognosis. The results showed that only a small number of patients had clones large enough to be diagnosed as CHIP, and there was no significant association between their prognosis and non-breast cancer-related outcomes.
CLINICAL CANCER RESEARCH
(2023)
Article
Urology & Nephrology
Sarah J. Welsh, Nicola Thompson, Anne Warren, Andrew N. Priest, Tristan Barrett, Stephan Ursprung, Ferdia A. Gallagher, Fulvio Zaccagna, Grant D. Stewart, Kate M. Fife, Athena Matakidou, Andrea J. Machin, Wendi Qian, Victoria Ingleson, Jean Mullin, Antony C. P. Riddick, James N. Armitage, Stephen Connolly, Timothy G. Q. Eisen
Summary: This study aimed to explore translational biological and imaging biomarkers for sunitinib treatment before and after debulking nephrectomy. The results showed that pre-surgical sunitinib significantly increased necrosis of tumors and reduced certain biomarkers, leading to improved overall survival and progression-free survival in patients with metastatic renal cell carcinoma.
Article
Urology & Nephrology
Hannah Harrison, Lisa Pennells, Angela Wood, Sabrina H. Rossi, Grant D. Stewart, Simon J. Griffin, Juliet A. Usher-Smith
Summary: This study validated 30 risk prediction models for kidney cancer in the UK Biobank cohort, with 10 models showing reasonable discrimination. The best models performed better in identifying high-risk individuals compared to age and sex-based screening, but had lower performance in women than in men.
Review
Urology & Nephrology
Juliet A. Usher-Smith, Lanxin Li, Lydia Roberts, Hannah Harrison, Sabrina H. Rossi, Stephen J. Sharp, Carol Coupland, Julia Hippisley-Cox, Simon J. Griffin, Tobias Klatte, Grant D. Stewart
Summary: This study systematically compared the performance of different prognostic models in predicting survival or recurrence in patients with localized renal cell cancer who underwent surgery. The study found that several models had good discriminative ability, and there was no single "best" model. When choosing a model, both the comparative performance and the availability of factors included in the model should be considered.
Review
Urology & Nephrology
Jordan G. Flitcroft, Jeroen Verheyen, Tarun Vemulkar, Emma N. Welbourne, Sabrina H. Rossi, Sarah J. Welsh, Russell P. Cowburn, Grant D. Stewart
Summary: Several urinary protein biomarkers are being validated for RCC diagnostics, but none have been approved for clinical use yet due to low sensitivity or specificity, inconsistencies in study design, or lack of external validation. Evaluation of feasibility, sample preparation, biomarker validation, and novel technologies may maximize the potential for a truly non-invasive biomarker in early RCC diagnostics.
Article
Oncology
Helen Mossop, Michael J. Grayling, Ferdia A. Gallagher, Sarah J. Welsh, Grant D. Stewart, James M. S. Wason
Summary: Efficient trial designs are crucial for prioritizing promising drugs in Phase II trials. Three trial approaches were compared in a simulation study, with the MASTER design showing extra efficiency in cases of endpoint delay or rapid recruitment. The study recommends the MASTER design as an efficient way to test multiple promising cancer treatments in non-comparative Phase II trials.
BRITISH JOURNAL OF CANCER
(2022)
Editorial Material
Urology & Nephrology
Juliet A. Usher-Smith, Grant D. Stewart
Summary: Prognostic models play a crucial role in the management of post-surgery RCC patients. Existing clinico-pathological models to predict cancer outcomes in these patients seem to have reached their performance limit. Future research should focus on identifying new prognostic markers and determining the implementation of RCC prognostic models in practice.
NATURE REVIEWS UROLOGY
(2022)
Article
Oncology
Grant D. Stewart, Sarah J. Welsh, Stephan Ursprung, Ferdia A. Gallagher, James O. Jones, Jacqui Shields, Christopher G. Smith, Thomas J. Mitchell, Anne Y. Warren, Axel Bex, Ekaterini Boleti, Jade Carruthers, Tim Eisen, Kate Fife, Abdel Hamid, Alexander Laird, Steve Leung, Jahangeer Malik, Iosif A. Mendichovszky, Faiz Mumtaz, Grenville Oades, Andrew N. Priest, Antony C. P. Riddick, Balaji Venugopal, Michelle Welsh, Kathleen Riddle, Lisa E. M. Hopcroft, Robert J. Jones
Summary: The study demonstrates that axitinib can reduce the level of VTT in patients, leading to a reduction in the extent of surgery for a significant proportion of patients. However, some patients show poor response to axitinib.
BRITISH JOURNAL OF CANCER
(2022)
Letter
Oncology
Bhavna Oza, Tim Eisen, Grant D. Stewart, Axel Bex, Patrick Royston, Angela Meade
JOURNAL OF CLINICAL ONCOLOGY
(2023)
Article
Multidisciplinary Sciences
Sabrina H. Rossi, Izzy Newsham, Sara Pita, Kevin Brennan, Gahee Park, Christopher G. Smith, Radoslaw P. Lach, Thomas Mitchell, Junfan Huang, Anne Babbage, Anne Y. Warren, John T. Leppert, Grant D. Stewart, Olivier Gevaert, Charles E. Massie, Shamith A. Samarajiwa
Summary: Current diagnostic strategies are unable to differentiate between benign and malignant small renal masses accurately, leading to unnecessary surgery in 20% of patients. The MethylBoostER machine learning model, utilizing DNA methylation data, can classify pathological subtypes of renal tumors and provide a more confident presurgical diagnosis, potentially improving treatment decision-making.
Letter
Urology & Nephrology
Tobias Klatte, Sarah J. J. Welsh, Antony C. P. Riddick, Jose A. Karam, Grant D. D. Stewart
Article
Urology & Nephrology
Hannah Harrison, Grant D. Stewart, Juliet A. Usher-Smith
Summary: The objective of this study was to explore the patient experience of follow-up care after kidney cancer surgery and develop recommendations for best practice. Two focus groups were conducted with 14 participants who had experience with kidney cancer follow-up care after surgery. Thematic analysis identified six themes describing the patient experience, including feelings of abandonment, uncertainty about the plan, anxiety about appointments, variation in care, a need for information, and a need for emotional support. Based on the results, a set of recommendations was developed to address these challenges.
Review
Oncology
Evie Papavasiliou, Valerie A. Sills, Natalia Calanzani, Hannah Harrison, Claudia Snudden, Erica di Martino, Andy Cowan, Dawnya Behiyat, Rachel Boscott, Sapphire Tan, Jennifer Bovaird, Grant D. Stewart, Fiona M. Walter, Yin Zhou
Summary: Bladder cancer is a common cancer worldwide and early diagnosis is crucial for better survival rates. Urinary biomarkers have been developed but their diagnostic performance in the general population is limited. This study systematically reviewed evidence on biomarkers suitable for use in community and primary care settings, identifying three biomarkers with similar diagnostic performance and some promising novel biomarkers. Further validation studies in the general population are needed.
Article
Biotechnology & Applied Microbiology
Francesc Muyas, Carolin M. Sauer, Jose Espejo Valle-Inclan, Ruoyan Li, Raheleh Rahbari, Thomas J. Mitchell, Sahand Hormoz, Isidro Cortes-Ciriano
Summary: SComatic is an algorithm that identifies somatic mutations from scRNA-seq and scATAC data without a matched reference sample. It distinguishes somatic mutations from other events and artefacts using filters and statistical tests. Validated against matched genome sequencing and scRNA-seq data, SComatic shows high accuracy in detecting mutations in single cells. It allows for de novo mutational signature analysis and the study of clonal heterogeneity and mutational burdens at a single-cell resolution.
NATURE BIOTECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Selma Leulmi Pichot, Tarun Vemulkar, Jeroen Verheyen, Lauren Wallis, James O. Jones, Andrew P. Stewart, Sarah J. Welsh, Grant D. Stewart, Russell P. Cowburn
Summary: This study describes a newly developed non-invasive urine-based assay for the early detection of renal cell carcinoma (RCC). The study shows that magnetic heterostructures have precise magnetic control and efficient code readout capabilities, making them suitable for screening RCC biomarkers.
NANOSCALE ADVANCES
(2023)
Review
Oncology
James O. Jones, William H. J. Ince, Sarah J. Welsh, Grant D. Stewart
Summary: ICPI treatment has shown efficacy in metastatic renal cell carcinoma, but there is limited evidence on the long-term survival benefit of ICPI therapy in localized disease in both neoadjuvant and adjuvant settings.