Article
Multidisciplinary Sciences
Rajdeep Das, Martin Sjostrom, Raunak Shrestha, Christopher Yogodzinski, Emily A. Egusa, Lisa N. Chesner, William S. Chen, Jonathan Chou, Donna K. Dang, Jason T. Swinderman, Alex Ge, Junjie T. Hua, Shaheen Kabir, David A. Quigley, Eric J. Small, Alan Ashworth, Felix Y. Feng, Luke A. Gilbert
Summary: The study integrates clinical and functional genomics data, identifying potential driver genes KIF4A and WDR62 for metastatic prostate cancer. These genes are shown to drive aggressive prostate cancer phenotypes in multiple models, regardless of AR status, and are associated with poor patient outcomes.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Ekta Shah, Pradipta Maji
Summary: In the past few decades, research has extensively studied gene expression data and protein-protein interaction networks for their ability to depict important characteristics of disease-associated genes. This paper introduces a new gene prioritization algorithm that integrates information from both data sources to identify and prioritize cancer-causing genes. The proposed algorithm aims to maximize the importance of selected genes and their functional similarity, combining differential expression patterns and network connectivity as key features for potential biomarker discovery. Additionally, a scalable non-linear graph fusion technique, ScaNGraF, is proposed to learn disease-dependent functional similarity networks efficiently and with lower computational cost.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
Courtney D. Dill, Eric B. Dammer, Ti'ara L. Griffen, Nicholas T. Seyfried, James W. Lillard
Summary: The study aimed to identify drivers of triple-negative breast cancer survival time by analyzing transcriptomic data and network communities, resulting in predictive signatures for TNBC prognosis. By integrating various analytical approaches, a panel of key survival genes with potential clinical utility was uncovered.
Article
Chemistry, Analytical
Anna Erb, Ulrich M. Zissler, Madlen Oelsner, Adam M. Chaker, Carsten B. Schmidt-Weber, Constanze A. Jakwerth
Summary: The effects of different types of interferons on epithelial cells after viral infection were examined. It was found that type-I interferon enhances cell-cell adhesion and tight junctions, type-III interferons promote transepithelial transport, and type-II interferon stimulates proliferation and inflammatory response.
Article
Biology
Shinichi Namba, Toshihide Ueno, Shinya Kojima, Kenya Kobayashi, Katsushige Kawase, Yosuke Tanaka, Satoshi Inoue, Fumishi Kishigami, Shusuke Kawashima, Noriko Maeda, Tomoko Ogawa, Shoichi Hazama, Yosuke Togashi, Mizuo Ando, Yuichi Shiraishi, Hiroyuki Mano, Masahito Kawazu
Summary: The MuSTA pipeline enables efficient transcriptome assembly from long-read sequencing data of breast cancer samples, leading to the discovery of subtype-specific isoforms and genomic context-dependent fusion transcript structures. This method sheds light on the influence of chromosomal structural alterations on cancer transcriptomes.
COMMUNICATIONS BIOLOGY
(2021)
Review
Cell Biology
Mauro Scaravilli, Sonja Koivukoski, Leena Latonen
Summary: Androgens and their receptor play crucial roles in various diseases, particularly in prostate cancer. Genetic fusions regulated by androgens are more common in prostate cancer compared to other tumors, raising questions that require further investigation.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Yuhuan Miao, Dandan Luo, Tingting Zhao, Hongzhi Du, Zhenhua Liu, Zhongping Xu, Lanping Guo, Changjie Chen, Sainan Peng, Jin Xin Li, Lin Ma, Guogui Ning, Dahui Liu, Luqi Huang
Summary: This study reported a complex chromosome-level genome assembly of Artemisia argyi, providing scientific support for evolutionary biology, functional genomics, and breeding. The assembly revealed whole-genome duplication events, transposable element bursts, and gene expansions related to photosynthesis, DNA replication, stress response, and secondary metabolism in A. argyi.
PLANT BIOTECHNOLOGY JOURNAL
(2022)
Article
Engineering, Chemical
Seong-Beom Cho
Summary: This study analyzed muscle samples from PCOS patients to identify androgen-responsive genes (ARGs) and found that a broad range of cellular processes is affected by androgen administration. These findings provide valuable information for the identification of ARGs.
Article
Biochemistry & Molecular Biology
Guoli Ji, Shuchao Li, Lishan Ye, Jinting Guan
Summary: Multiple genetic factors contribute to the pathogenesis of ASD, with genes interacting in cell-type-specific modules. This study identified 31 cell-type-specific gene modules associated with ASD, enriched with curated ASD risk genes, offering new potential genomic targets for studying ASD pathogenesis.
Article
Biology
Dipankor Chatterjee, Md Mostafijur Rahman, Anik Kumar Saha, Mohammad Kawsar Sharif Siam, Mohammad Umer Sharif Shohan
Summary: Through transcriptomics meta-analysis, new predictive biomarkers for esophageal carcinoma were identified, offering solutions to the problems of ineffective cancer therapy, lack of efficient diagnostic tools, and costly screening. Four hub genes, including RORA, KAT2B, CDC25B, and ECT2, were discovered to play a regulatory role in carcinogenic pathways and were associated with poor prognosis.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Multidisciplinary Sciences
Hafdis T. Helgadottir, Jessada Thutkawkorapin, Kristina Lagerstedt-Robinson, Annika Lindblom
Summary: Identifying pathogenic variants in individuals with a strong family history of breast cancer remains challenging, despite advancements in sequencing technology. Through exome sequencing, known pathogenic variants in BRIP1 and PALB2 genes were identified, along with 22 high-risk variants in novel breast cancer candidate genes. Further studies are needed to validate these findings and explore the potential roles of these genes in breast cancer susceptibility.
SCIENTIFIC REPORTS
(2021)
Article
Immunology
Mingjia Xiao, Xiangjing Liang, Zhengming Yan, Jingyang Chen, Yaru Zhu, Yuan Xie, Yang Li, Xinming Li, Qingxiang Gao, Feiling Feng, Gongbo Fu, Yi Gao
Summary: This study evaluated the role of DNA methylation driven genes in pancreatic cancer and established a four-gene prognostic signature. The signature was found to be associated with tumor histologic grades and survival outcomes, as well as immune dysregulation and tumor mutation burdens. Additionally, the study identified elevated protein expression of these genes in cancerous tissues, which may serve as prognostic markers for pancreatic cancer patients.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Michelle M. Conti, Rui Li, Michelle A. Narvaez Ramos, Lihua Julie Zhu, Thomas G. Fazzio, Jennifer A. Benanti
Summary: The authors developed a high-throughput approach to quantitatively evaluate the contribution of each phosphosite within a multisite phosphorylated domain. They applied this method to study the yeast transcription factor Hcm1, revealing a complex CDK-regulatory circuit that mediates its activation.
NATURE COMMUNICATIONS
(2023)
Review
Oncology
Yaqing Zhang, Jie Sun, Yongxi Song, Peng Gao, Xin Wang, Miao Chen, Yuan Li, Zhonghua Wu
Summary: Personalized, precise treatment is life-saving for advanced digestive system cancers. With the advancement of next-generation sequencing technology, detection of fusion genes in solid tumors has become more extensive. Some fusion gene targeting therapies have been incorporated into guidelines for digestive tract tumors, and numerous fusion genes are being investigated as potential future therapeutic targets.
CRITICAL REVIEWS IN ONCOLOGY HEMATOLOGY
(2022)
Article
Oncology
Maria E. Cuevas, Chance P. Winters, Maria C. Todd
Summary: Deregulation of tight junction proteins, such as claudin-3 and claudin-4, has been found to play a significant role in the development of endometrial cancer. The overexpression of multiple genes, including OCLN, F11R, and TJP3, further supports the involvement of tight junction deregulation and downstream signaling pathways in the progression of endometrial cancer.
Article
Oncology
Andreas M. Hoff, Sigrid M. Kraggerud, Sharmini Alagaratnam, Kaja C. G. Berg, Bjarne Johannessen, Maren Holand, Gro Nilsen, Ole C. Lingjaerde, Peter W. Andrews, Ragnhild A. Lothe, Rolf Skotheim
ENDOCRINE-RELATED CANCER
(2020)
Article
Multidisciplinary Sciences
John Pluta, Louise C. Pyle, Kevin T. Nead, Rona Wilf, Mingyao Li, Nandita Mitra, Benita Weathers, Kurt D'Andrea, Kristian Almstrup, Lynn Anson-Cartwright, Javier Benitez, Christopher D. Brown, Stephen Chanock, Chu Chen, Victoria K. Cortessis, Alberto Ferlin, Carlo Foresta, Marija Gamulin, Jourik A. Gietema, Chiara Grasso, Mark H. Greene, Tom Grotmol, Robert J. Hamilton, Trine B. Haugen, Russ Hauser, Michelle A. T. Hildebrandt, Matthew E. Johnson, Robert Karlsson, Lambertus A. Kiemeney, Davor Lessel, Ragnhild A. Lothe, Jennifer T. Loud, Chey Loveday, Paloma Martin-Gimeno, Coby Meijer, Jeremie Nsengimana, David I. Quinn, Thorunn Rafnar, Shweta Ramdas, Lorenzo Richiardi, Rolf I. Skotheim, Kari Stefansson, Clare Turnbull, David J. Vaughn, Fredrik Wiklund, Xifeng Wu, Daphne Yang, Tongzhang Zheng, Andrew D. Wells, Struan F. A. Grant, Ewa Rajpert-De Meyts, Stephen M. Schwartz, D. Timothy Bishop, Katherine A. McGlynn, Peter A. Kanetsky, Katherine L. Nathanson
Summary: Testicular germ cell tumors are highly heritable, and a large genome association study identified 22 novel loci, some of which may assist screening and treatment decisions through the study of PRS, reducing the risks in survivors. These findings highlight the interconnected nature of two known pathways that promote TGCT susceptibility, and implicate an additional biological pathway.
NATURE COMMUNICATIONS
(2021)
Article
Genetics & Heredity
Anita Sveen, Bjarne Johannessen, Ina A. Eilertsen, Bard Rosok, Marie Gulla, Peter W. Eide, Jarle Bruun, Kushtrim Kryeziu, Leonardo A. Meza-Zepeda, Ola Myklebost, Bjorn A. Bjornbeth, Rolf Skotheim, Arild Nesbakken, Ragnhild A. Lothe
Summary: Only a subset of mutations in microsatellite stable colorectal cancers were expressed, and the expressed mutation dose may provide an opportunity for more fine-tuned biomarker interpretations.
Article
Oncology
Susanne G. Kidd, Kristina T. Carm, Mari Bogaard, Linn Guro Olsen, Anne Cathrine Bakken, Marthe Lovf, Ragnhild A. Lothe, Karol Axcrona, Ulrika Axcrona, Rolf I. Skotheim
Summary: In primary prostate cancer, high expression of SCHLAP1 serves as a robust prognostic biomarker for predicting biochemical recurrence and is associated with adverse clinicopathological characteristics. The heterogeneity of SCHLAP1 expression emphasizes the importance of analyzing multiple samples for determination of a patient's SCHLAP1 status.
Article
Biotechnology & Applied Microbiology
Jonas M. Stromme, Bjarne Johannessen, Susanne G. Kidd, Mari Bogaard, Kristina T. Carm, Xiaokang Zhang, Anita Sveen, Anthony Mathelier, Ragnhild A. Lothe, Ulrika Axcrona, Karol Axcrona, Rolf I. Skotheim
Summary: The study revealed extensive heterogeneity at the gene expression level in multifocal prostate cancer. Different malignant foci within the same patient showed similar levels of heterogeneity as tumors from different patients. Expression patterns linked to ETS status and extraprostatic extension were identified, and a set of 62 genes with low intrapatient heterogeneity and high interpatient heterogeneity were found, which could serve as prognostic biomarkers regardless of the sampled malignant focus.
CANCER GENE THERAPY
(2022)
Editorial Material
Urology & Nephrology
Rolf Skotheim, Ulrika Axcrona, Karol Axcrona
Summary: The research by Labanca et al strengthens the concept of an index tumor through the definition of aggressive molecular features. It suggests that molecular characterization will play a crucial role in radiogenomics development and guiding future treatment.
Article
Endocrinology & Metabolism
Anne M. A. Tryggestad, Karol Axcrona, Ulrika Axcrona, Iris Bigalke, Bjorn Brennhovd, Else M. Inderberg, Turid K. Honnashagen, Lisbeth J. Skoge, Guri Solum, Stein Saeboe-Larssen, Dag Josefsen, Richard W. Olaussen, Steinar Aamdal, Rolf I. Skotheim, Tor A. Myklebust, Dolores J. Schendel, Wolfgang Lilleby, Svein Dueland, Gunnar Kvalheim
Summary: This study aimed to reduce the risk of biochemical relapse in high-risk prostate cancer patients after robot-assisted laparoscopic prostatectomy by administering personalized dendritic cell vaccines as adjuvant therapy. The results showed promising efficacy of the vaccine in reducing biochemical relapse incidence, as well as associations between baseline immune response and vaccine response during the vaccination period. Further investigation in larger cohorts is warranted to validate these findings and explore the potential of dendritic cell vaccines in post-surgical treatment of high-risk prostate cancer.
Article
Medicine, Research & Experimental
Jacqueline Fontugne, Peter Y. Cai, Hussein Alnajar, Bhavneet Bhinder, Kyung Park, Huihui Ye, Shaham Beg, Verena Sailer, Javed Siddiqui, Mirjam Blattner-Johnson, Jaclyn A. Croyle, Zohal Noorzad, Carla Calagua, Theresa Y. MacDonald, Ulrika Axcrona, Mari Bogaard, Karol Axcrona, Douglas S. Scherr, Martin G. Sanda, Bjarne Johannessen, Arul M. Chinnaiyan, Olivier Elemento, Rolf Skotheim, Mark A. Rubin, Christopher E. Barbieri, Juan Miguel Mosquera
Summary: Prostate cancer is a multifocal disease with distinct molecular subtypes. This study reveals the presence of inter- and intrafocal molecular heterogeneity in primary prostate cancer, with approximately 60% of multifocal specimens showing discordant molecular alterations between foci. Collision tumors, characterized by discrepant molecular status within a single focus, are identified in about 10% of the specimens. These findings highlight the complexity of molecular heterogeneity in prostate cancer and have important implications for future genomic studies.
Article
Biochemistry & Molecular Biology
Camilla Wolowczyk, Ulrike Neckmann, Miriam Ragle Aure, Martina Hall, Bjarne Johannessen, Sen Zhao, Rolf Skotheim, Sonja B. Andersen, Rosalie Zwiggelaar, Tonje S. Steigedal, Ole Christian Lingjaerde, Kristine Kleivi Sahlberg, Eivind Almaas, Geir Bjorkoy
Summary: In breast cancer patients, the NRF2 gene is continuously activated in metastatic cells and tumors, with corresponding upregulation of related genes. Depletion of NRF2 increases reactive oxygen species levels and severely reduces tumor formation and lung metastasis. A set of NRF2-regulated genes is elevated in breast cancer biopsies and can significantly improve prognosis prediction.
FREE RADICAL BIOLOGY AND MEDICINE
(2022)
Article
Oncology
Susanne G. Kidd, Mari Bogaard, Kristina T. Carm, Anne Cathrine Bakken, Aase M. V. Maltau, Marthe Lovf, Ragnhild A. Lothe, Karol Axcrona, Ulrika Axcrona, Rolf I. Skotheim
Summary: This study aimed to determine the prognostic value of candidate biomarkers transcriptional regulator ERG and related ETS family genes in prostate cancer, while considering tumor heterogeneity. The results showed that ERG protein has independent prognostic value in predicting biochemical and clinical recurrence of prostate cancer, and appears to have the greatest prognostic value for patients with Grade Groups 4-5.
MOLECULAR ONCOLOGY
(2022)
Article
Oncology
Chiara Grasso, Maja Popovic, Elena Isaevska, Fulvio Lazzarato, Valentina Fiano, Daniela Zugna, John Pluta, Benita Weathers, Kurt D'Andrea, Kristian Almstrup, Lynn Anson-Cartwright, D. Timothy Bishop, Stephen J. Chanock, Chu Chen, Victoria K. Cortessis, Marlene D. Dalgaard, Siamak Daneshmand, Alberto Ferlin, Carlo Foresta, Megan N. Frone, Marija Gamulin, Jourik A. Gietema, Mark H. Greene, Tom Grotmol, Robert J. Hamilton, Trine B. Haugen, Russ Hauser, Robert Karlsson, Lambertus A. Kiemeney, Davor Lessel, Patrizia Lista, Ragnhild A. Lothe, Chey Loveday, Coby Meijer, Kevin T. Nead, Jeremie Nsengimana, Rolf I. Skotheim, Clare Turnbull, David J. Vaughn, Fredrik Wiklund, Tongzhang Zheng, Andrea Zitella, Stephen M. Schwartz, Katherine A. McGlynn, Peter A. Kanetsky, Katherine L. Nathanson, Lorenzo Richiardi
Summary: This study found that genetic variants within the MTHFR gene are associated with the risk of testicular germ cell tumors (TGCT), potentially affecting the establishment of DNA methylation patterns. This finding suggests that the pathogenesis of TGCT may be related to the status of the folate cycle, and this relation could be partly due to hereditary factors.
CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION
(2022)
Article
Oncology
Kristina T. Carm, Bjarne Johannessen, Mari Bogaard, Anne Cathrine Bakken, Aase Maltau, Andreas M. Hoff, Ulrika Axcrona, Karol Axcrona, Ragnhild A. Lothe, Rolf Skotheim
Summary: Our study highlights the spatio-temporal heterogeneity of multifocal prostate cancer and emphasizes the importance of testing a recent sample in genomics-based precision medicine for metastatic prostate cancer.
INTERNATIONAL JOURNAL OF CANCER
(2023)
Article
Cell Biology
Ricardo Celestino, Jose B. Gama, Artur F. Castro-Rodrigues, Daniel J. Barbosa, Helder Rocha, Ennio A. d'Amico, Andrea Musacchio, Ana Xavier Carvalho, Joao H. Morais-Cabral, Reto Gassmann
Summary: The MAP kinase and motor scaffold JIP3 plays a role in preventing excessive accumulation of lysosomes in axons. The interaction between JIP3 and dynein and kinesin-1 is important for organelle clearance, but the specific mechanisms are not fully understood.
JOURNAL OF CELL BIOLOGY
(2022)
Meeting Abstract
Pathology
M. Bogaard, J. M. Stromme, S. G. Kidd, B. Johannessen, A. C. Bakken, R. A. Lothe, K. Axcrona, R. I. Skotheim, U. Axcrona