Article
Oncology
Chiara Corradi, Manuel Gentiluomo, Laszlo Gajdan, Giulia Martina Cavestro, Edita Kreivenaite, Gregorio Di Franco, Cosimo Sperti, Matteo Giaccherini, Maria Chiara Petrone, Francesca Tavano, Domenica Gioffreda, Luca Morelli, Pavel Soucek, Angelo Andriulli, Jakob R. Izbicki, Niccolo Napoli, Ewa Malecka-Panas, Peter Hegyi, John P. Neoptolemos, Stefano Landi, Yogesh Vashist, Claudio Pasquali, Ye Lu, Klara Cervena, George E. Theodoropoulos, Stefania Moz, Gabriele Capurso, Oliver Strobel, Silvia Carrara, Thilo Hackert, Viktor Hlavac, Livia Archibugi, Martin Oliverius, Giuseppe Vanella, Pavel Vodicka, Paolo Giorgio Arcidiacono, Raffaele Pezzilli, Anna Caterina Milanetto, Rita T. Lawlor, Audrius Ivanauskas, Andrea Szentesi, Juozas Kupcinskas, Sabrina G. G. Testoni, Martin Lovecek, Michael Nentwich, Maria Gazouli, Claudio Luchini, Raffaella Alessia Zuppardo, Erika Darvasi, Hermann Brenner, Cristian Gheorghe, Krzysztof Jamroziak, Federico Canzian, Daniele Campa
Summary: A new PDAC risk locus was identified, with genetic variation disrupting the binding between lncRNA and miRNA possibly affecting the development of PDAC.
INTERNATIONAL JOURNAL OF CANCER
(2021)
Review
Cell Biology
Farbod Bahreini, Elham Rayzan, Nima Rezaei
Summary: Breast cancer, a multifactorial disease, may have an increased risk due to alterations in microRNA sequences. miR-SNPs are potential biomarkers for early detection of breast cancer.
JOURNAL OF CELLULAR PHYSIOLOGY
(2021)
Article
Oncology
Carmen Perez-Duran, Noelia Marquez-Pete, Jose Maria Galvez-Navas, Yasmin Cura, Susana Rojo-Tolosa, Laura Elena Pineda-Lancheros, Mcarmen Ramirez-Tortosa, Carlos Garcia-Collado, Maria del Mar Maldonado-Montoro, Jesus Maria Villar-del-Moral, Cristina Perez-Ramirez, Alberto Jimenez-Morales
Summary: Recent studies have suggested that vitamin D might influence the development and prognosis of colorectal cancer, and its activity might be influenced by single nucleotide polymorphisms in the genes involved in its metabolism. This study evaluated the influence of 13 SNPs in the vitamin D metabolic pathway on colorectal cancer survival. The results showed that variants in VDR, CYP24A1, and GC genes are associated with a lower survival rate.
Article
Oncology
Xue Wang, Zihui Zhao, Xueqing Han, Yutong Zhang, Yitong Zhang, Fenglan Li, Hui Li
Summary: This study successfully identified 42 prognostic modules for breast cancer through constructing co-expression networks and integrating gene expression profiles and clinical data. The risk values carried by genes in these modules were found to classify high-risk and low-risk groups of patients, and 16 genes were identified as potential biological markers related to breast cancer.
FRONTIERS IN ONCOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Maria Radanova, Mariya Levkova, Galya Mihaylova, Rostislav Manev, Margarita Maneva, Rossen Hadgiev, Nikolay Conev, Ivan Donev
Summary: There is a growing interest in studying single nucleotide polymorphisms (SNPs) in microRNA (miRNA) genes, as they may be associated with susceptibility, prognosis, and treatment response in colorectal cancer (CRC). These miRNA-SNPs could serve as non-invasive biomarkers for early detection of CRC. However, contradictory findings have been reported when different research groups investigated the same SNP in a gene for a specific miRNA, highlighting the need for more case-control studies involving participants from different ethnic backgrounds. According to our review, three miRNA-SNPs - miR-146a rs2910164, miR-27a rs895819, and miR-608 rs4919510 - appear to be promising prognostic, diagnostic, and predictive biomarkers for CRC.
Article
Genetics & Heredity
Cihangir Yandim, Gokhan Karakulah
Summary: This study reveals the potential links between repeat expression and survival in cancer, identifying several repeat elements and single nucleotide variations associated with patient survival. Further research in this field is warranted.
Article
Genetics & Heredity
Ziqi Jia, Yansong Huang, Jiaqi Liu, Gang Liu, Jiayi Li, Hengyi Xu, Yiwen Jiang, Song Zhang, Yidan Wang, Gang Chen, Guangdong Qiao, Yalun Li
Summary: Through a study on genetic polymorphisms, we found significant associations between breast cancer risk and SNPs rs12493607 (TGFBR2), rs4784227 (CASC16), and rs2046210 (ESR1) in the Chinese female population. Further analysis revealed associations between different subtypes of breast cancer and different SNPs. These findings provide important insights into breast cancer susceptibility and personalized treatment.
Article
Oncology
Hailei Du, Rui Mu, Lihua Liu, Hongliang Liu, Sheng Luo, Edward F. Patz, Carolyn Glass, Li Su, Mulong Du, David C. Christiani, Hecheng Li, Qingyi Wei
Summary: This study found that genetic variants in the lymphocyte activation pathway-related genes FOXP1 and RORA are associated with the survival of non-small cell lung cancer patients.
TRANSLATIONAL LUNG CANCER RESEARCH
(2022)
Review
Biochemistry & Molecular Biology
Xiaoying Li, Qijun Wu, Baosen Zhou, Yashu Liu, Jiale Lv, Qing Chang, Yuhong Zhao
Summary: This study found that only 13 SNPs were strongly correlated with lung cancer risk based on systematic reviews and meta-analyses, providing valuable insights for further genetic studies.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Medicine, General & Internal
Yaheng Li, Chuanyin Li, Shuyuan Liu, Jia Yang, Li Shi, Yufeng Yao
Summary: SNPs in miRNA genes play critical roles in the development of cervical cancer, potentially altering miRNA expression and maturation, and impacting the development of various cancers.
INTERNATIONAL JOURNAL OF MEDICAL SCIENCES
(2021)
Review
Pathology
Esmat Abdi, Saeid Latifi-Navid
Summary: Long non coding RNAs (lncRNAs) play important roles in tumor growth, invasion, metastasis, and cancer recurrence. The polymorphisms of certain lncRNAs are associated with cancer prognosis. Some lncRNA polymorphisms are specific for certain types of cancer, indicating their function in specific signaling pathways. Genotypes of lncRNA polymorphisms can be used to predict cancer prognosis. However, more large-scale trials and comprehensive health records are needed to validate the results.
PATHOLOGY RESEARCH AND PRACTICE
(2022)
Article
Genetics & Heredity
G. Vigneshwaran, Qurratulain Annie Hasan, Rahul Kumar, Avinash Eranki
Summary: This study constructed a framework to identify genes associated with triple-negative breast cancer (TNBC) and screen the single nucleotide polymorphisms (SNPs) reported in these genes. The study found the association of genes such as BRCA1, BRCA2, EGFR, PIK3CA, PTEN, and TP53 with TNBC. The framework was demonstrated to have high accuracy in identifying pathogenic alterations in breast cancer samples.
FRONTIERS IN GENETICS
(2022)
Article
Genetics & Heredity
Moumita Mukherjee, Satyajit Ghosh, Srikanta Goswami
Summary: This study explores the potential effects of SNPs on miRNA-target mRNA interactions in PDAC. Through rigorous analytical methods, common and rare variants were identified that may interfere with miRNA-mediated gene regulation in the disease. The results provide insights into the role of genetic variations in modulating miRNA function in PDAC.
Article
Cell Biology
Chen Suo, Huiyao Chen, Franciszek Binczyk, Renjia Zhao, Jiahui Fan, Xiaorong Yang, Ziyu Yuan, David Kreil, Pawel Labaj, Tiejun Zhang, Ming Lu, Li Jin, Joanna Polanska, Xingdong Chen, Weimin Ye
Summary: In patients with ESCC, a model combining sTIL, specific SNPs, and clinical characteristics showed improved prediction of survival outcomes compared to a model based on clinical characteristics alone.
Article
Pharmacology & Pharmacy
Yasmin Cura, Almudena Sanchez-Martin, Noelia Marquez-Pete, Encarnacion Gonzalez-Flores, Fernando Martinez-Martinez, Cristina Perez-Ramirez, Alberto Jimenez-Morales
Summary: This study evaluated the association of SNPs with severe toxicity and treatment suspension in colorectal cancer patients treated with Capecitabine-based therapy. SNPs CES1 rs71647871 and CDA rs1048977 were identified as potential predictive biomarkers of treatment safety.
Article
Oncology
Samuel O. Antwi, William R. Bamlet, Kari G. Rabe, Richard M. Cawthon, Isoken Umudi, Brooke R. Druliner, Hugues Sicotte, Ann L. Oberg, Aminah Jatoi, Lisa A. Boardman, Gloria M. Petersen
CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION
(2020)
Article
Oncology
Yi Qin, William Taylor, William R. Bamlet, Adharsh Ravindran, Alessia Buglioni, Xiaoming Cao, Patrick H. Foote, Seth W. Slettedahl, Douglas W. Mahoney, Paul S. Albert, Sungduk Kim, Nan Hu, Philip R. Taylor, Arash Etemadi, Masoud Sotoudeh, Reza Malekzadeh, Christian C. Abnet, Thomas C. Smyrk, David Katzka, Mark D. Topazian, Sanford M. Dawsey, David Ahlquist, John B. Kisiel, Prasad G. Iyer
CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION
(2020)
Article
Oncology
Shirsa Udgata, Naomi Takenaka, William R. Bamlet, Ann L. Oberg, Stephanie S. Yee, Erica L. Carpenter, Daniel Herman, Jungsun Kim, Gloria M. Petersen, Kenneth S. Zaret
Summary: PDAC is often diagnosed too late for effective therapy, and the classic strategy for early detection biomarker advancement involves retrospective phases of discovery and validation. However, a new study shows that THBS2 and CA19-9 fail to distinguish patients from healthy controls in the 1 to 15 years prior to a PDAC diagnosis.
CANCER PREVENTION RESEARCH
(2021)
Article
Oncology
Shounak Majumder, William R. Taylor, Patrick H. Foote, Calise K. Berger, Chung Wah Wu, Douglas W. Mahoney, William R. Bamlet, Kelli N. Burger, Neil Postier, Jaime de la Fuente, Karen A. Doering, Graham P. Lidgard, Hatim T. Allawi, Gloria M. Petersen, Suresh T. Chari, David A. Ahlquist, John B. Kisiel
Summary: This study aimed to evaluate the diagnostic performance of plasma MDMs for PDAC, and the results showed that the combination of plasma MDMs with CA19-9 detects PDAC with significantly higher accuracy compared with either biomarker individually, especially for early-stage PDAC patients.
CLINICAL CANCER RESEARCH
(2021)
Article
Oncology
Samuel O. Antwi, Kari G. Rabe, William R. Bamlet, Margaret Meyer, Shruti Chandra, Sarah E. Fagan, Chunling Hu, Fergus J. Couch, Robert R. McWilliams, Ann L. Oberg, Gloria M. Petersen
Summary: ABO blood group and germline mutation status of the index cases can influence the risk of pancreatic cancer in first-degree relatives. Mutation-positive probands and non-O blood group probands are associated with higher pancreatic cancer risk in their relatives.
CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION
(2022)
Article
Cardiac & Cardiovascular Systems
Jeanne L. Theis, Talha Niaz, Rhianna S. Sundsbak, Zachary C. Fogarty, William R. Bamlet, Donald J. Hagler, Timothy M. Olson
Summary: By performing whole-genome sequencing and filtering for rare, predicted-damaging variants, the study identified the significant role of CELSR1 gene in familial BAV and HLHS, further implicating the importance of planar cell polarity pathway perturbation in congenital heart disease.
CIRCULATION-GENOMIC AND PRECISION MEDICINE
(2022)
Article
Biochemical Research Methods
Oscar E. Ospina, Christopher M. Wilson, Alex C. Soupir, Anders Berglund, Inna Smalley, Kenneth Y. Tsai, Brooke L. Fridley
Summary: Spatially resolved transcriptomics has the potential to enhance our understanding of the tumor microenvironment and improve cancer prognosis and therapies. This article introduces spatialGE, a software that offers visualizations and quantification of tumor microenvironment heterogeneity through gene expression surfaces, spatial heterogeneity statistics, spot-level cell deconvolution, and spatially informed clustering.
Article
Health Care Sciences & Services
Joseph Ross Mitchell, Phillip Szepietowski, Rachel Howard, Phillip Reisman, Jennie D. Jones, Patricia Lewis, Brooke L. Fridley, Dana E. Rollison
Summary: This study developed a BERT-based NLP system to automatically extract detailed tumor site and histology information from oncological pathology reports. The system outperformed existing algorithms in predicting ICD-O-3 codes, which could improve cancer treatment outcomes.
JOURNAL OF MEDICAL INTERNET RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Xiang Liu, Bo Zhao, Timothy Shaw, Brooke L. Fridley, Derek R. Duckett, Aik Choon Tan, Mingxiang Teng
Summary: This study proposes a novel computational method for identifying differential SEs by considering the activities and positions of constituent enhancers. This method not only takes into account the overall activity changes, but also discovers four new classes of differential SEs with distinct enhancer structural alterations. Compared to existing methods, this approach shows improved identification of differential SEs and better discernment of cell-type-specific SE activity and functional interpretation.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Oncology
Cassandra A. Hathaway, Tianyi Wang, Mary K. Townsend, Christine Vinci, Danielle E. Jake-Schoffman, Daryoush Saeed-Vafa, Carlos Moran Segura, Jonathan V. Nguyen, Jose R. Conejo-Garcia, Brooke L. Fridley, Shelley S. Tworoger
Summary: This study found that early exposure to cigarette smoke may have a slight impact on the risk of developing ovarian cancer, as well as the systemic immunity and tumor immune response. However, no research has been conducted to evaluate the effects of cigarette smoke exposure on the ovarian tumor immune microenvironment.
CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION
(2023)
Article
Cardiac & Cardiovascular Systems
Jeanne L. Theis, Sarah-Dana H. Shatila, Zachary C. Fogarty, William R. Bamlet, Timothy M. Olson
Summary: By analyzing whole genome sequences, this study identified candidate genes for HLHS using three independent strategies. The results showed that variants in the MYO18B, MYO5A, and MYO15A genes are associated with HLHS. These findings provide further insights into HLHS pathogenesis.
CIRCULATION-GENOMIC AND PRECISION MEDICINE
(2023)
Article
Oncology
Cassandra A. Hathaway, Jose R. Conejo-Garcia, Brooke L. Fridley, Bernard Rosner, Daryoush Saeed-Vafa, Carlos Moran Segura, Jonathan V. Nguyen, Jonathan L. Hecht, Naoko Sasamoto, Kathryn L. Terry, Shelley S. Tworoger, Mary K. Townsend
Summary: This study used multiplex immunofluorescence to measure immune markers in ovarian tumors and found high correlations between markers within the tumors. However, very old samples may have reduced antigenicity. These findings are important for studying immune infiltration in ovarian tumors.
CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION
(2023)
Article
Gastroenterology & Hepatology
Laurens P. Janssens, Hiroaki Takahashi, Hiroki Nagayama, Fred Nugen, William R. Bamlet, Ann L. Oberg, Eric Fuemmeler, Ajit H. Goenka, Bradley J. Erickson, Naoki Takahashi, Shounak Majumder
Summary: This study demonstrates a strong inverse correlation between whole pancreas MR-PDFF and CT-HU, indicating that both imaging modalities can be used to assess pancreatic fat. The 2D-axial pancreas MR-PDFF is variable across slices, underscoring the need for AI-aided whole-organ measurements for objective and reproducible estimation of pancreatic fat.
Article
Pharmacology & Pharmacy
Nathan D. Seligson, Jill M. Kolesar, Benish Alam, Laura Baker, Jatinder K. Lamba, Brooke L. Fridley, Ameen A. Salahudeen, Daniel L. Hertz, J. Kevin Hicks
Summary: Precision medicine has greatly improved the clinical care for cancer patients by developing targeted therapies, identifying inherited cancer predisposition syndromes, and optimizing pharmacotherapy through pharmacogenetics. It is argued that integrating pharmacogenomics into paired germline/somatic genomic testing would be an efficient method for increasing access to pharmacogenomic testing.
Article
Oncology
Samuel O. Antwi, William R. Bamlet, Richard M. Cawthon, Kari G. Rabe, Brooke R. Druliner, Hugues Sicotte, Aminah Jatoi, Amit Mahipal, Lisa A. Boardman, Ann L. Oberg, Gloria M. Petersen
Summary: The study found that shorter treatment-naive leukocyte telomere length is associated with poorer overall survival of patients with incident pancreatic ductal adenocarcinoma (PDAC). The impact of LTL on overall mortality varies by tumor stage at diagnosis.
CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION
(2021)