Article
Biochemistry & Molecular Biology
Bob Chen, Cherie' R. Scurrah, Eliot T. McKinley, Alan J. Simmons, Marisol A. Ramirez-Solano, Xiangzhu Zhu, Nicholas O. Markham, Cody N. Heiser, Paige N. Vega, Andrea Rolong, Hyeyon Kim, Quanhu Sheng, Julia L. Drewes, Yuan Zhou, Austin N. Southard-Smith, Yanwen Xu, James Ro, Angela L. Jones, Frank Revetta, Lynne D. Berry, Hiroaki Niitsu, Mirazul Islam, Karin Pelka, Matan Hofree, Jonathan H. Chen, Siranush Sarkizova, Kimmie Ng, Marios Giannakis, Genevieve M. Boland, Andrew J. Aguirre, Ana C. Anderson, Orit Rozenblatt-Rosen, Aviv Regev, Nir Hacohen, Kenta Kawasaki, Toshiro Sato, Jeremy A. Goettel, William M. Grady, Wei Zheng, M. Kay Washington, Qiuyin Cai, Cynthia L. Sears, James R. Goldenring, Jeffrey L. Franklin, Timothy Su, Won Jae Huh, Simon Vandekar, Joseph T. Roland, Qi Liu, Robert J. Coffey, Martha J. Shrubsole, Ken S. Lau
Summary: Colorectal cancers originate from different precursor polyps, with factors related to stem cell expansion and cell differentiation playing key roles in tumor development; changes in the immune environment can also lead to mutations in tumor cells.
Article
Medicine, General & Internal
Michael Wong, Nikolaos Thanatsis, Federica Nardelli, Tejal Amin, Davor Jurkovic
Summary: This study aimed to identify patient characteristics and ultrasound morphological features of postmenopausal endometrial polyps that could predict underlying pre-malignancy or malignancy. The decision tree model based on polyp diameter, body mass index, and appearance classification on ultrasound may assist in counseling women on the benefits and risks of surgery, as well as in prioritizing women for surgery based on their risk of malignancy.
Article
Surgery
Antoine Martin, Jerome Cros, Marie-Pierre Vullierme, Safi Dokmak, Alain Sauvanet, Philippe Levy, Vinciane Rebours, Frederique Maire
Summary: This study aimed to assess the risk of pre-malignancy or malignancy in patients with dilatation of the main pancreatic duct (MPD) without visible mass or obstructive calcification on computed tomography scan (CT-scan). The results showed that 41 out of 101 patients with MPD dilatation without obvious obstructive causes had pre-malignant or malignant lesions. Symptoms before surgery, MPD dilatation without downstream stenosis, and the presence of nodules on MRI/EUS were associated with the risk of pre-malignancy or malignancy.
SURGICAL ENDOSCOPY AND OTHER INTERVENTIONAL TECHNIQUES
(2023)
Article
Cardiac & Cardiovascular Systems
Viktor Sekowski, Kathy Jackson, Kieran Halloran, Rhea Varughese, Jayan Nagendran, Justin Weinkauf, Dale Lien, Alim Hirji
Summary: In lung transplant recipients, a history of pre-transplant malignancy is associated with a more than threefold increased risk of developing post-transplant malignancy compared to recipients without a previous cancer history, with the majority of cases being unrelated to the initial malignancy. These findings underscore the importance of frequent cancer surveillance in lung transplant recipients, especially those with a history of pre-transplant malignancy.
RESPIRATORY MEDICINE
(2022)
Article
Oncology
Jenny Sprooten, Ann Vankerckhoven, Isaure Vanmeerbeek, Daniel M. Borras, Yani Berckmans, Roxanne Wouters, Raquel S. Laureano, Thais Baert, Louis Boon, Chiara Landolfo, Antonia Carla Testa, Daniela Fischerova, Caroline Van Holsbeke, Tom Bourne, Valentina Chiappa, Wouter Froyman, Dominique Schols, Patrizia Agostinis, Dirk Timmerman, Sabine Tejpar, Ignace Vergote, An Coosemans, Abhishek D. Garg
Summary: The study established a novel biomarker resource for serum screening in patients with ovarian cancer to evaluate peripheral immunodynamics, patient survival trends, malignancy risk, and preclinical chemo-immunotherapy strategies. The in silico data-driven framework predicted that analysis of myeloid NF kappa B signaling and interferon-stimulated genes' responses could capture patients' peripheral immunodynamics effectively. Multiparametric serum profiling of patients with ovarian cancer showed that the sFIS assay can decode peripheral immunology, estimate survival trends, and co-estimate malignancy risk.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2021)
Article
Cardiac & Cardiovascular Systems
Stefan Roest, Christianne Struijk, Alina A. Constantinescu, Kadir Caliskan, Elsemieke Plasmeijer, Eric Boersma, Jasper J. Brugts, Olivier C. Manintveld
Summary: Recent reports have shown that patients with heart failure (HF) and chronic kidney disease (CKD) may have an increased risk of developing malignancies, particularly after heart transplantation (HT). However, the duration of HF pre-HT was not found to be directly associated with the risk of malignancy post-HT, while CKD pre-HT was identified as an independent risk factor for malignancies after HT.
Article
Oncology
Seemadri Subhadarshini, Sarthak Sahoo, Shibjyoti Debnath, Jason A. Somarelli, Mohit Kumar Jolly
Summary: The phenotypic heterogeneity of melanoma cells and its impact on adaptation to targeted therapy and immune checkpoint inhibitors were investigated using dynamical systems modeling and transcriptomic data analysis. A regulatory network involving transcription factors was constructed to understand the mechanisms behind phenotypic heterogeneity. The model predictions were validated experimentally in melanoma cell lines, demonstrating the potential for improved treatment of metastatic melanoma.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2023)
Article
Biology
Yalda Afshar, Feyiang Ma, Austin Quach, Anhyo Jeong, Hannah L. Sunshine, Vanessa Freitas, Yasaman Jami-Alahmadi, Raphael Helaers, Xinmin Li, Matteo Pellegrini, James A. Wohlschlegel, Casey E. Romanoski, Miikka Vikkula, M. Luisa Iruela-Arispe
Summary: Environmental cues play a critical role in cell function, and this study reveals that the in vitro environment significantly affects gene expression in human endothelial cells. Long-term shear stress and heterotypic cell interactions can partially rescue the transcriptional changes caused by the in vitro environment.
Article
Medicine, General & Internal
Hui Zhao, Jundong Wang, Shuting Li, Ying Bao, Xiaoxia Zheng, Yuan Tao, Hong Wang
Summary: This study aimed to investigate the effectiveness of aflibercept and panretinal photocoagulation in the treatment of proliferative diabetic retinopathy (PDR). The results showed that aflibercept and panretinal photocoagulation improved best corrected visual acuity, central foveal thickness, and retinal vein diameter compared to pre-treatment measurements.
FRONTIERS IN MEDICINE
(2023)
Article
Transplantation
David Massicotte-Azarniouch, Randal K. Detwiler, Yichun Hu, Ronald J. Falk, Manish K. Saha, Susan L. Hogan, Vimal K. Derebail
Summary: This study found that kidney transplant patients who received pre-transplant immunosuppression (PTI) for glomerulonephritis (GN) had a higher risk of developing malignancy. Compared with kidney transplant patients without PTI, those with GN and PTI had a significantly increased risk of malignancy.
NEPHROLOGY DIALYSIS TRANSPLANTATION
(2023)
Article
Ecology
Edd Hammill, Kayla Hancey, Michael Cortez
Summary: Trophic interactions determine the structure of ecological communities by describing the rates at which consumers utilize resources. Prey traits play a role in influencing the rates at which predators consume them, and many species exhibit defensive modifications in response to predation threats. This study investigates how differences in prey traits, specifically body width, impact the rates of predation by Stenostomum predators on different clonal lines of Paramecium protists. The results demonstrate how changes in prey traits, whether evolutionary or induced, can affect the relative threat of predation, and how interference among predators and increased body width can influence predation rates.
Article
Oncology
Xinxin Zhou, Jiayuan He, Qingyuan Wang, Teng Ma
Summary: The study revealed that miR-128-3p acts as a tumor suppressor in malignant melanoma cells by inhibiting proliferation, migration, invasion, and inducing apoptosis. The oncogene neurotrophin receptor 3 (NTRK3) was found to be up-regulated in MM cells, enhancing their malignant behaviors. The interaction between miR-128-3p and NTRK3 genes modulate the malignant behavior of MM, suggesting potential new therapeutic targets.
FRONTIERS IN ONCOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Federico Dona, Cagakan Ozbalci, Andrea Paquola, Federica Ferrentino, Stephen J. Terry, Elisabeth M. Storck, Gaoge Wang, Ulrike S. Eggert
Summary: The membrane protein stomatin is found to be involved in the cytokinesis step of cell division, even though it is not a lipid biosynthetic enzyme. Depletion of stomatin leads to changes in cellular lipidomes, and exogenous phosphatidylcholines can rescue these defects.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Cardiac & Cardiovascular Systems
Stefan Roest, Muhammed T. Gurgoze, Wida S. Cherikh, Josef Stehlik, Eric H. Boersma, Felix Zijlstra, Olivier C. Manintveld
Summary: This study aimed to calculate the annual incidence of malignancies after heart transplantation, confirm the association between pre-transplant chronic kidney disease (CKD) and post-transplant malignancy risk, and determine other risk factors. The results showed that the risk of malignancy post-transplantation remains high, and pre-transplant CKD stage >= 4 was associated with an increased risk for any malignancy and solid-organ malignancy post-transplantation.
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2023)
Article
Dentistry, Oral Surgery & Medicine
Moon-Jong Kim, Hong-Seop Kho
Summary: The study focuses on the characteristics of lesions related to malignant transformation during the follow-up period of oral potentially malignant disorders (OPMD) and emphasizes the importance of monitoring changes on the lesion surface.
Article
Oncology
James Sun, Brittany J. Mathias, Weihong Sun, William J. Fulp, Jun-Min Zhou, Christine Laronga, Loretta S. Loftus, M. Catherine Lee
Summary: This study examined the impact of SLNB on treatment and outcomes in breast cancer patients aged >= 70 years who were clinically node-negative and hormone receptor-positive. The results indicated that SLN-negative patients had better overall survival and less distant recurrence, while adjuvant hormone therapy significantly improved overall survival.
ANNALS OF SURGICAL ONCOLOGY
(2021)
Article
Multidisciplinary Sciences
Elodie Hatchi, Liana Goehring, Serena Landini, Konstantina Skourti-Stathaki, Derrick K. DeConti, Fieda O. Abderazzaq, Priyankana Banerjee, Timothy M. Demers, Yaoyu E. Wang, John Quackenbush, David M. Livingston
Summary: Strong connections are found between R-loops, genome instability, and human disease. R-loops play a role in maintaining homeostasis by regulating certain physiological processes, such as the synthesis of antisense transcripts through transcription termination pause sites. A species of single-stranded, DNA-damage-associated small RNA (sdRNA) generated by a BRCA1-RNAi complex promotes DNA repair at transcriptional termination pause sites forming R-loops.
Article
Mathematical & Computational Biology
Albert T. Young, Xavier Carette, Michaela Helmel, Hanno Steen, Robert N. Husson, John Quackenbush, John Platig
Summary: The inhibition of Mtb serine/threonine protein kinases PknA and PknB leads to changes in the TF regulatory network, affecting regulatory programs involved in cell wall integrity, stress response, and energy production. This highlights the importance of incorporating signal-driven TF modifications in regulatory network approaches.
NPJ SYSTEMS BIOLOGY AND APPLICATIONS
(2021)
Article
Oncology
Camila M. Lopes-Ramos, Tatiana Belova, Tess H. Brunner, Marouen Ben Guebila, Daniel Osorio, John Quackenbush, Marieke L. Kuijjer
Summary: Analysis identified seven pathways associated with survival in glioblastoma patients, with dysregulation of PD1 signaling correlating with poor prognosis. This suggests a new approach to predict patient survival and highlights potential therapeutic interventions based on gene regulatory network analysis.
Article
Biochemistry & Molecular Biology
Marouen Ben Guebila, Camila M. Lopes-Ramos, Deborah Weighill, Abhijeet Rajendra Sonawane, Rebekka Burkholz, Behrouz Shamsaei, John Platig, Kimberly Glass, Marieke L. Kuijjer, John Quackenbush
Summary: Gene regulation networks play a crucial role in tissue identity, disease development, and therapeutic response. The GRAND database provides computationally-inferred gene regulatory network models and targeting scores for predicting drug effects on network structures and matching potential therapeutic drugs to disease states.
NUCLEIC ACIDS RESEARCH
(2022)
Meeting Abstract
Hematology
Olga Dashevsky, Ricardo De Matos Simoes, Benjamin G. Barwick, Sara Gandolfi, Ryosuke Shirasaki, Michal Sheffer, Aedin Culhane, Richard Wj Groen, Aviad Tsherniak, Francisca Vazquez, Jonathan D. Licht, Lawrence H. Boise, Constantine S. Mitsiades
Meeting Abstract
Hematology
Ricardo De Matos Simoes, Benjamin G. Barwick, Ryosuke Shirasaki, Olga Dashevsky, Sara Gandolfi, Huihui Tang, Brian Glassner, Richard W. J. Groen, Daniel Auclair, Aedin Culhane, Aviad Tsherniak, Francisca Vazquez, Jonathan D. Licht, Lawrence H. Boise, Constantine S. Mitsiades
Article
Biochemistry & Molecular Biology
Deborah Weighill, Marouen Ben Guebila, Kimberly Glass, John Quackenbush, John Platig
Summary: Understanding how individual genotypes influence gene regulation can improve our understanding of human health and development. EGRET is a method that infers genotype-specific gene regulatory networks to reveal the genetic associations driving complex phenotypes.
Article
Biochemistry & Molecular Biology
Chloe Mirzayi, Audrey Renson, Fatima Zohra, Shaimaa Elsafoury, Ludwig Geistlinger, Lora J. Kasselman, Kelly Eckenrode, Janneke van de Wijgert, Amy Loughman, Francine Z. Marques, David A. MacIntyre, Manimozhiyan Arumugam, Rimsha Azhar, Francesco Beghini, Kirk Bergstrom, Ami Bhatt, Jordan E. Bisanz, Jonathan Braun, Hector Corrada Bravo, Gregory A. Buck, Frederic Bushman, David Casero, Gerard Clarke, Maria Carmen Collado, Paul D. Cotter, John F. Cryan, Ryan T. Demmer, Suzanne Devkota, Eran Elinav, Juan S. Escobar, Jennifer Fettweis, Robert D. Finn, Anthony A. Fodor, Sofia Forslund, Andre Franke, Cesare Furlanello, Jack Gilbert, Elizabeth Grice, Benjamin Haibe-Kains, Scott Handley, Pamela Herd, Susan Holmes, Jonathan P. Jacobs, Lisa Karstens, Rob Knight, Dan Knights, Omry Koren, Douglas S. Kwon, Morgan Langille, Brianna Lindsay, Dermot McGovern, Alice C. McHardy, Shannon McWeeney, Noel T. Mueller, Luigi Nezi, Matthew Olm, Noah Palm, Edoardo Pasolli, Jeroen Raes, Matthew R. Redinbo, Malte Ruhlemann, R. Balfour Sartor, Patrick D. Schloss, Lynn Schriml, Eran Segal, Michelle Shardell, Thomas Sharpton, Ekaterina Smirnova, Harry Sokol, Justin L. Sonnenburg, Sujatha Srinivasan, Louise B. Thingholm, Peter J. Turnbaugh, Vaibhav Upadhyay, Ramona L. Walls, Paul Wilmes, Takuji Yamada, Georg Zeller, Mingyu Zhang, Ni Zhao, Liping Zhao, Wenjun Bao, Aedin Culhane, Viswanath Devanarayan, Joaquin Dopazo, Xiaohui Fan, Matthias Fischer, Wendell Jones, Rebecca Kusko, Christopher E. Mason, Tim R. Mercer, Susanna-Assunta Sansone, Andreas Scherer, Leming Shi, Shraddha Thakkar, Weida Tong, Russ Wolfinger, Christopher Hunter, Nicola Segata, Curtis Huttenhower, Jennifer B. Dowd, Heidi E. Jones, Levi Waldron
Summary: The STORMS tool is a reporting guideline for human microbiome studies, consisting of a 17-item checklist to help researchers report study results concisely and completely, facilitating manuscript preparation, peer review, and reader comprehension.
Article
Oncology
Yufei Wang, Alicia Buck, Marion Grimaud, Aedin C. Culhane, Sreekumar Kodangattil, Cecile Razimbaud, Dennis M. Bonal, Quang-De Nguyen, Zhu Zhu, Kevin Wei, Madison L. O'Donnell, Ying Huang, Sabina Signoretti, Toni K. Choueiri, Gordon J. Freeman, Quan Zhu, Wayne A. Marasco
Summary: Improving CAR-T cell therapy for solid tumors requires a better understanding of CAR design and cellular composition. A study found that CAR-T cells with a CD4/CD8 ratio of BB zeta exhibited superior efficacy in clearing clear-cell renal cell carcinoma (ccRCC) in a mouse model, demonstrating long-term tumor-free outcome.
MOLECULAR THERAPY-ONCOLYTICS
(2022)
Article
Biochemistry & Molecular Biology
Katherine H. Shutta, Deborah Weighill, Rebekka Burkholz, Marouen Ben Guebila, Dawn L. DeMeo, Helena U. Zacharias, John Quackenbush, Michael Altenbuchinger
Summary: In this study, we propose a network approach based on Gaussian Graphical Models (GGMs) called DRAGON, which allows for the joint analysis of multi-omic data. DRAGON adapts to the differences between omics layers, improving model inference and edge recovery, and can identify key molecular mechanisms.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Sheila M. Gaynor, Maud Fagny, Xihong Lin, John Platig, John Quackenbush
Summary: This study constructed twenty-nine tissue-specific eQTL networks using GTEx data and evaluated different network specifications. The researchers found that using a thresholded Benjamini-Hochberg q value weighted by the Z-statistic balanced metric reproducibility and computational efficiency. The eQTL networks were complementary to gene regulatory networks in understanding regulation, and highly connected nodes were enriched for tissue-relevant traits.
CELL REPORTS METHODS
(2022)
Article
Genetics & Heredity
Marouen Ben Guebila, Daniel C. Morgan, Kimberly Glass, Marieke L. Kuijjer, Dawn L. DeMeo, John Quackenbush
Summary: Gene regulatory network inference allows for modeling genome-scale regulatory processes. Researchers have developed a collection of tools to model various regulatory processes and improve their performance through GPU-accelerated calculations.
NAR GENOMICS AND BIOINFORMATICS
(2022)
Meeting Abstract
Oncology
Eugen Dhimolea, Ricardo De Matos Simoes, Dhvanir Kansara, Juliette Bouyssou, Jennifer Roth, Michal Sheffer, Rinath Jeselsohn, Nathanael Gray, Ulrich Steidl, Boris Bartholdy, Myles Brown, Aedin Culhane, Constantine Mitsiades
Meeting Abstract
Oncology
Michal Sheffer, Emily Lowry, Nicky Beelen, Minasri Borah, Suha Naffar-Abu Amara, Chris C. Mader, Jennifer Roth, Aviad Tsherniak, Olga Dashevsky, Sara Gandolfi, Samantha Bender, Jordan Bryan, Cong Zhu, Li Wang, Ricardo De-Matos Simoes, Channing Yu, Yiguo Hu, Olli Dufva, Marios Giannakis, Todd Golub, Rizwan Romee, Satu Mustjoki, Aedin C. Culhane, Lotte Wieten, Constantine S. Mitsiades
CANCER IMMUNOLOGY RESEARCH
(2021)