Article
Medicine, Research & Experimental
Junshu Li, Yanhong Ji, Na Chen, Huiling Wang, Chao Fang, Xiaonan Yin, Zhiyuan Jiang, Zhexu Dong, Dan Zhu, Jiamei Fu, Wencheng Zhou, Ruiyi Jiang, Ling He, Zhang Hantao, Gang Shi, Lin Cheng, Xiaolan Su, Lei Dai, Hongxin Deng
Summary: This study identified a specific upregulated lncRNA (SURC) in colorectal cancer (CRC), and its high expression was associated with poorer prognosis in CRC patients. Further investigation revealed that mutated adenomatous polyposis coli (APC) genes can promote the transcription of SURC by reducing the degradation of beta-catenin protein. Functional assays showed that knockdown of SURC impaired CRC cell proliferation and tumor growth. Additionally, SURC promotes CCND2 expression by inhibiting the expression of miR-185-5p in CRC cells.
Review
Oncology
Kerryn Elliott, Erik Larsson
Summary: Despite the vast size of the non-coding genome, driver mutations in this space appear to be relatively infrequent. The transition towards whole-genome analysis is enabling the discovery of potential driver mutations outside protein-coding sequences, but detecting selection signals in non-coding DNA remains challenging.
NATURE REVIEWS CANCER
(2021)
Article
Oncology
Julia Matas, Brendan Kohrn, Jeanne Fredrickson, Kelly Carter, Ming Yu, Ting Wang, Xianyong Gui, Thierry Soussi, Victor Moreno, William M. Grady, Miguel A. Peinado, Rosa Ana Risques
Summary: This study reveals that mutations in common colorectal cancer genes can be detected in the normal colon, highlighting the prevalent somatic evolution in patients with colorectal cancer. Somatic evolution contributes to clonal expansions in the normal colon, especially in individuals with early-onset colorectal cancer.
Article
Biochemical Research Methods
Lingling Li, Yulu Hu, Yunshan Xu, Sanyi Tang
Summary: Cumulative mutations in driver genes are the essential cause of cancer, including colorectal cancer. This study explores the mutation orders of the driver genes KRAS, APC, and TP53 in colorectal cancer patients and identifies the pathways that best fit the incidence rate of colorectal cancer at different ages. The findings provide guidelines for the treatment strategy of colorectal cancer.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Genetics & Heredity
Randi Istrup Juul, Morten Muhlig Nielsen, Malene Juul, Lars Feuerbach, Jakob Skou Pedersen
Summary: This study utilized large sets of whole cancer genomes to study mutation hotspots, categorize site-specific hotspots, and provide a resource of annotated hotspots genome-wide. The research found an excess of hotspots in protein-coding and gene regulatory regions, as well as identified hotspots associated with cancer genes. Additionally, some hotspots showed clear signs of positive selection.
NPJ GENOMIC MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Michael Hartung, Elisa Anastasi, Zeinab M. Mamdouh, Cristian Nogales, Harald H. H. W. Schmidt, Jan Baumbach, Olga Zolotareva, Markus List
Summary: Cancer is a heterogeneous disease and targeted therapy based on evidence-based selection of drugs is crucial. However, many cancer driver genes cannot be directly targeted, necessitating an indirect approach using functionally related targets in the gene interaction network. CADDIE is a web application that integrates databases and algorithms to guide clinical researchers in identifying drug targets and candidates.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Oncology
Samah El Ghamrasni, Rene Quevedo, James Hawley, Parisa Mazrooei, Youstina Hanna, Iulia Cirlan, Helen Zhu, Jeff P. Bruce, Leslie E. Oldfield, S. Y. Cindy Yang, Paul Guilhamon, Juri Reimand, Dave W. Cescon, Susan J. Done, Mathieu Lupien, Trevor J. Pugh
Summary: By analyzing primary breast tumors through whole-genome sequencing, we identified transcription factors and cis-regulatory elements associated with the development of breast cancer, providing insights into the driver mechanisms of breast cancer.
MOLECULAR CANCER RESEARCH
(2022)
Article
Oncology
Juan Ramon Tejedor, Alfonso Penarroya, Javier Gancedo-Verdejo, Pablo Santamarina-Ojeda, Raul F. Perez, Sara Lopez-Tamargo, Ana Diez-Borge, Juan J. Alba-Linares, Nerea Gonzalez-del-Rey, Rocio G. Urdinguio, Cristina Mangas, Annalisa Roberti, Virginia Lopez, Teresa Morales-Ruiz, Rafael R. Ariza, Teresa Roldan-Arjona, Monica Meijon, Luis Valledor, Maria Jesus Canal, Daniel Fernandez-Martinez, Maria Fernandez-Hevia, Paula Jimenez-Fonseca, Luis J. Garcia-Florez, Agustin F. Fernandez, Mario F. Fraga
Summary: This study utilized a multi-omics approach to identify gene candidates with strong correlations between DNA methylation and gene expression in human colorectal cancer (CRC) samples and colon cancer cell lines. The researchers used CRISPR-Cas9 epigenome editing tools to modulate the DNA methylation status of 56 promoters previously linked with epigenetic repression in CRC and assessed the functional consequences. Overall, the epigenetic modulation had a mild impact on gene expression reactivation and cancer cell viability, but the reactivation of RSPO2 was associated with impaired cell proliferation in p53(-/-) cancer cell lines.
CLINICAL EPIGENETICS
(2023)
Article
Biochemistry & Molecular Biology
Qianqian Song, Mingyu Li, Qian Li, Xun Lu, Kun Song, Ziliang Zhang, Jiale Wei, Liang Zhang, Jiacheng Wei, Youqiong Ye, Jinyin Zha, Qiufen Zhang, Qiang Gao, Jiang Long, Xinyi Liu, Xuefeng Lu, Jian Zhang
Summary: Driver mutations play a crucial role in cancer initiation and their identification is important for understanding tumorigenesis and drug development. Mutations at allosteric sites have been associated with protein structure and dynamics. DeepAlloDriver, a deep learning platform, achieves >93% accuracy and precision in predicting driver mutations, and it identified a missense mutation in RRAS2 as a potential allosteric driver of tumorigenesis. This research provides insights into cancer mechanisms and aids in prioritizing therapeutic targets.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Jiri Jungwirth, Marketa Urbanova, Arnoud Boot, Petr Hosek, Petra Bendova, Anna Siskova, Jiri Svec, Milan Kment, Daniela Tumova, Sandra Summerova, Zdenek Benes, Tomas Buchler, Pavel Kohout, Tomas Hucl, Radoslav Matej, Ludmila Vodickova, Tom van Wezel, Pavel Vodicka, Veronika Vymetalkova
Summary: A large proportion of colorectal carcinomas evolve from colorectal adenomas, which have a high frequency of pathogenic variants in genes such as APC, KRAS, and TP53. The mutation frequencies of APC, KRAS, and TP53 are slightly lower in adenoma samples compared to in situ carcinoma samples. KRAS mutation is associated with villous histology, and methylation of the APC promoter is significantly associated with the presence of POLE genetic variations.
SCIENTIFIC REPORTS
(2022)
Review
Medicine, General & Internal
Frank A. Sinicrope
Summary: Early-onset colorectal cancer, which accounts for 10% of cases, is increasing in incidence, particularly in high-income countries. Patients often present with advanced disease in the left colon, and one in six patients has deficient DNA mismatch repair. Screening is recommended to begin at 45 years of age.
NEW ENGLAND JOURNAL OF MEDICINE
(2022)
Article
Oncology
Andreana N. Holowatyj, Wanqing Wen, Timothy Gibbs, Hannah M. Seagle, Samantha R. Keller, Digna R. Velez Edwards, Mary K. Washington, Cathy Eng, Jose Perea, Wei Zheng, Xingyi Guo
Summary: This study investigated somatic mutation patterns in colorectal cancer patients of different races/ethnicities and sexes, finding that non-Hispanic Black and Asian/Pacific Islander patients with early-onset nonhypermutated colorectal cancer had higher tumor mutation rates compared to non-Hispanic white patients. Significant differences were observed in the mutation frequencies of several genes between racial/ethnic groups in early-onset nonhypermutated colorectal cancers. Furthermore, heterogeneity was observed in the effects of certain genes between early-onset and late-onset nonhypermutated colorectal cancer, as well as between males and females. These findings provide important insights into the genomic patterns and disparities of early-onset colorectal cancer based on race/ethnicity and sex.
Article
Biochemistry & Molecular Biology
Jiuna Zhang, Xiaoyu Jiang, Jie Yin, Shiying Dou, Xiaoli Xie, Ting Liu, Yijun Wang, Shuling Wang, Xue Zhou, Dongxuan Zhang, Huiqing Jiang
Summary: RNF141 plays an oncogenic role in colorectal cancer by upregulating KRAS activity, which promotes tumor growth, cell proliferation, migration, and apoptosis by interacting with KRAS to induce its activation and enrichment on the plasma membrane.
Article
Multidisciplinary Sciences
Qing-Lan Li, Xiang Lin, Ya-Li Yu, Lin Chen, Qi-Xin Hu, Meng Chen, Nan Cao, Chen Zhao, Chen-Yu Wang, Cheng-Wei Huang, Lian-Yun Li, Mei Ye, Min Wu
Summary: This study analyzed active enhancers in colorectal cancer patients using genomics, transcriptomics, and epigenomics, identifying variant super-enhancer loci and KLF3 as a relevant transcription factor. The research provides important epigenomic resource and functional factors for epigenetic studies in colorectal cancer, shedding light on the role of super enhancers in regulating colorectal cancer tumorigenesis. Multiple key transcription factors in colorectal cancer were predicted with motif analysis and core regulatory circuitry analysis.
NATURE COMMUNICATIONS
(2021)
Review
Gastroenterology & Hepatology
Marina Hanna, Neelendu Dey, William M. Grady
Summary: Colorectal cancer is a common cancer globally and is a leading cause of cancer-related deaths. Current screening methods for colorectal cancer have limitations and many people are not compliant with screening recommendations. Novel screening tests based on advances in molecular biology, genetics, and epigenetics, as well as sequencing technologies and computational analytic methods, have been developed to improve early detection of colorectal cancer.
CLINICAL GASTROENTEROLOGY AND HEPATOLOGY
(2023)
Article
Surgery
Johanne Gormsen, Jakob Burcharth, Ismail Gogenur, Frederik Helgstrand
Summary: Research revealed that 10% of patients undergoing RYGB surgery develop chronic abdominal pain, with 5% suffering from severe abdominal pain. Risk factors for severe self-reported pain include preoperative use of strong analgesics, unemployment, postoperative complications, and smoking.
Article
Emergency Medicine
Jakob Burcharth, Luka Abdulhady, Jakob Danker, Sarah Ekeloef, Thomas Jorgensen, Halfdan Lauridsen, Thomas Bech Lunen, Malene Lyngesen, Iben Puggaard, Ole Mathiesen, Ismail Gogenur
Summary: This study presented detailed contents and data on the implementation of an emergency abdominal perioperative protocol based on compliance. It was found that a comprehensive detailed perioperative protocol can be implemented in emergency abdominal surgery across multiple specialties with an overall good compliance of protocol items.
EUROPEAN JOURNAL OF TRAUMA AND EMERGENCY SURGERY
(2021)
Article
Pharmacology & Pharmacy
Sarah S. Poulsen, Stefan Bengtson, Andrew Williams, Nicklas R. Jacobsen, Jesper T. Troelsen, Sabina Halappanavar, Ulla Vogel
Summary: The study found differences in transcriptomic responses in the lung and liver of mice after exposure to graphene oxide (GO) and reduced graphene oxide (rGO). GO exposure induced more differentially expressed genes, affected more functions and pathways compared to rGO. The differences in responses suggest that physicochemical properties play a significant role in biological effects of graphene-based materials.
TOXICOLOGY AND APPLIED PHARMACOLOGY
(2021)
Article
Multidisciplinary Sciences
Isabella W. Paulsen, Michael Bzorek, Jesper Olsen, Birgitte Grum-Schwensen, Jesper T. Troelsen, Ole B. Pedersen
Summary: Identification of target tissue microRNAs using ISH with LNA probes is influenced by preanalytic parameters. Long fixation time results in better microRNA preservation and staining intensity, enhanced by HmiRR TRS pH 9 with or without pepsin for high sensitivity and specificity. Further studies are needed due to conflicting results with other ISH techniques that typically require shorter fixation periods.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Sylvester Larsen, Jakob Benedict Seidelin, Johanne Davidsen, Katja Dahlgaard, Claus Henrik Nielsen, Eric Paul Bennett, Ole Birger Pedersen, Mehmet Coskun, Jesper Thorvald Troelsen
Summary: The study investigated whether CDX2 regulates IL33 mRNA expression, and found that CDX2 concentration-dependently upregulates IL33 expression.
Editorial Material
Oncology
Malene Broholm, Thea Helene Degett, Sara Furbo, Anne-Marie Kanstrup Fiehn, Mustafa Bulut, Thomas Litman, Jens Ole Eriksen, Jesper T. Troelsen, Lise Mette Rahbek Gjerdrum, Ismail Gogenur
ANNALS OF SURGICAL ONCOLOGY
(2021)
Article
Oncology
Malene Broholm, Thea Helene Degett, Sara Furbo, Anne-Marie Kanstrup Fiehn, Mustafa Bulut, Thomas Litman, Jens Ole Eriksen, Jesper T. Troelsen, Lise Mette Rahbek Gjerdrum, Ismail Gogenur
Summary: The study investigated the impact of colonic stent on the tumor microenvironment and found that it may promote tumor progression in colorectal cancer, leading to a more aggressive phenotype. Future research is needed to determine the optimal timing of surgery after stent insertion in patients with obstructive colorectal cancer.
ANNALS OF SURGICAL ONCOLOGY
(2021)
Article
Infectious Diseases
Peter Kamstrup, Pradeesh Sivapalan, Josefin Eklof, Nils Hoyer, Charlotte Suppli Ulrik, Lars Pedersen, Therese S. Lapperre, Zitta Barrella Harboe, Uffe Bodtger, Rasmus Dahlin Bojesen, Kjell E. J. Hakansson, Casper Tidemandsen, Karin Armbruster, Andrea Browatzki, Howraman Meteran, Christian Niels Meyer, Kristoffer Grundtvig Skaarup, Mats Christian Hojbjerg Lassen, Jens D. Lundgren, Tor Biering-Sorensen, Jens-Ulrik Jensen
Summary: This study found that the use of hydroxychloroquine for non-COVID-19 indications did not reduce the risk of SARS-CoV-2 infection.
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2021)
Review
Oncology
Sara Furbo, Paulo Cesar Martins Urbano, Hans Henrik Raskov, Jesper Thorvald Troelsen, Anne-Marie Kanstrup Fiehn, Ismail Gogenur
Summary: Colorectal cancer is the third most common cancer globally. Tumor organoids, miniature replicas of tumors in vitro, retain the characteristics of the tumor and can be used for personalized treatment research and selection.
Article
Surgery
Rasmus D. Bojesen, Camilla Grube, Fatima Buzquurz, Rebecca E. G. Miedzianogora, Jens R. Eriksen, Ismail Gogenur
Summary: The study showed that screening for modifiable high-risk factors combined with targeted interventions before colorectal cancer surgery significantly reduced the risk of postoperative complications, especially in decreasing severe complications.
Article
Biochemical Research Methods
Stine Bull Jessen, Derya Coskun Ozkul, Yasemin Ozen, Ismail Gogenur, Jesper T. Troelsen
Summary: This study introduces a novel method for measuring cell proliferation and adhesion based on CRISPR-modified cancer cell lines secreting luciferase. The results demonstrate that the luciferase assays are reliable and have advantages over existing assays, as they are highly sensitive, easy to perform, non-invasive, and suitable for high-throughput measurements.
ANALYTICAL BIOCHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Josephine B. Olsson, Marietta B. Gugerel, Stine B. Jessen, Jannie Jorgensen, Ismail Gogenur, Camilla Hansen, Lene T. Kirkeby, Jorgen Olsen, Ole B. Pedersen, Peter M. Vestlev, Katja Dahlgaard, Jesper T. Troelsen
Summary: A risk locus at 4q32.2, between the NAF1 and FSTL5 genes, was found to be associated with an increased risk of developing colorectal cancer (CRC). The study investigated the role of this locus as a gene regulatory region and found that it acts as a repressor on NAF1 promoter activity. The SNP rs17042479(G) enhanced the repressor effect. Additionally, patients carrying the SNP rs17042479(G) showed lower NAF1 expression in tumor tissue, suggesting that reduced NAF1 expression may contribute to a more aggressive phenotype.
Article
Biochemistry & Molecular Biology
Hans Eiberg, Josephine B. Olsson, Mads Bak, Claus Heiner Bang-Berthelsen, Jesper T. Troelsen, Lars Hansen
Summary: We identified a 22.4 Mb region on chromosome 7p22.3-7p15.3 associated with ulcerative colitis (UC) in a large Danish family through whole genome linkage analyses. UC in this family was inherited as an autosomal dominant trait with variable expressivity. The whole-genome scan yielded a LOD score of Z = 3.31, and whole genome sequencing ruled out disease-causing mutations in protein coding genes. Rare heterozygote variants rs182281985:G>A and rs541426369:G>A, with low allele frequencies, were discovered near the AHR gene and the UC associated SNP rs1077773:G>A. Functional assays revealed that rs182281985:G>A influenced the AHR promoter, suggesting AHR as a candidate gene for UC susceptibility on the 7p-tel region.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Medicine, Research & Experimental
R. D. Bojesen, L. B. Jorgensen, C. Grube, S. T. Skou, C. Johansen, S. O. Dalton, I Gogenur
Summary: This study investigated the feasibility of a short course multimodal prehabilitation for high-risk, frail patients with colorectal cancer. The results showed that most patients were able to complete the intervention, but some had difficulties with intensity monitoring and nutritional support had low compliance.
PILOT AND FEASIBILITY STUDIES
(2022)
Article
Surgery
R. P. Vogelsang, R. D. Bojesen, E. R. Hoelmich, A. Orhan, F. Buzquurz, L. Cai, C. Grube, J. A. Zahid, E. Allakhverdiiev, H. H. Raskov, I Drakos, N. Derian, P. B. Ryan, P. R. Rijnbeek, I Gogenur
Summary: In this study, a prediction model was developed to accurately predict 90-day mortality risk for patients undergoing colorectal cancer surgery using pre- and intraoperative data from a nationwide cohort study. The model demonstrated excellent discriminatory power and calibration, with an AUROC of 85.3% (95% CI, 83.6 to 87.0).