Article
Multidisciplinary Sciences
Mahashweta Basu, Kun Wang, Eytan Ruppin, Sridhar Hannenhalli
Summary: This study demonstrates that an individual's whole blood transcriptome can predict tissue-specific expression levels for around 60% of genes across various tissues, with particularly high accuracy in skeletal muscle. Predictions based on blood transcriptome are almost as effective as actual tissue expression in identifying disease states for six different complex disorders, surpassing the traditional blood transcriptome approach. The development of TEEBoT provides a valuable tool for further research in other medical conditions.
Article
Multidisciplinary Sciences
Dayle Johnston, Bernadette Earley, Matthew S. McCabe, JaeWoo Kim, Jeremy F. Taylor, Ken Lemon, Catherine Duffy, Michael McMenamy, S. Louise Cosby, Sinead M. Waters
Summary: Bovine Respiratory Syncytial Virus (BRSV) is a major viral cause of respiratory disease in young calves, inducing global gene expression changes. This study investigated the transcriptomic response in whole blood of dairy calves challenged with BRSV, revealing differential gene expression associated with viral infection pathways, potentially useful for subclinical disease diagnosis.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Yuliangzi Sun, Woo Jun Shim, Sophie Shen, Enakshi Sinniah, Duy Pham, Zezhuo Su, Dalia Mizikovsky, Melanie D. White, Joshua W. K. Ho, Quan Nguyen, Mikael Boden, Nathan J. Palpant
Summary: This article introduces a method called TRIAGE-Cluster that utilizes genome-wide epigenetic data to identify genes that delineate cell diversity in scRNA-seq data. By integrating repressive chromatin patterns with weighted density estimation, TRIAGE-Cluster determines cell type clusters in a 2D UMAP space. The article also presents TRIAGE-ParseR, a machine learning method that evaluates gene expression rank lists to define gene groups governing the identity and function of cell types.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Aliaa El-Gawady, Mohamed A. Makhlouf, BenBella S. Tawfik, Hamed Nassar
Summary: In recent years, there has been significant research on using machine learning to predict diseases based on gene expression data. However, some diseases, such as Alzheimer's disease (AD), have not received much attention due to a lack of data. This study aims to address this gap by introducing a symmetric framework for predicting AD from gene expression data, with the goal of achieving the most accurate prediction using the fewest number of genes.
Article
Gastroenterology & Hepatology
Romain Desert, Wei Chen, Xiaodong Ge, Roselyne Viel, Hui Han, Dipti Athavale, Sukanta Das, Zhuolun Song, Daniel Lantvit, Luis Cano, Alexandra Naba, Orlando Musso, Natalia Nieto
Summary: A study found that there are extracellular matrix (ECM) deposits in liver cancer tumors with high intratumor fibrosis, which contain components such as collagen and growth factors. These deposits are associated with poor patient outcomes.
Article
Multidisciplinary Sciences
Grant C. O'Connell
Summary: In this study, the influence of donor leukocyte counts on the transcriptional composition of whole blood specimens was assessed using next generation sequencing in combination with flow cytometry. Four frequently used data normalization approaches were tested, and it was found that three of these approaches masked the true biological structure of the data. The only strategy that improved the detection of true biological variance was simple scaling of read counts by sequencing depth.
SCIENTIFIC REPORTS
(2023)
Article
Oncology
Rosalie Griffin, Heidi A. Hanson, Brian J. Avery, Michael J. Madsen, Douglas W. Sborov, Nicola J. Camp
Summary: This study presents an approach called SPECTRA, which uses transcriptome data to predict clinical outcomes in multiple myeloma patients. The derived quantitative variables can provide insights into tumor differences and are associated with clinical and expression risk factors.
CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION
(2023)
Article
Biochemistry & Molecular Biology
Stephanie M. Zimmerman, Robin Fropf, Bridget R. Kulasekara, Maddy Griswold, Oliver Appelbe, Arya Bahrami, Rich Boykin, Derek L. Buhr, Kit Fuhrman, Margaret L. Hoang, Quoc Huynh, Lesley Isgur, Andrew Klock, Alecksandr Kutchma, Alexa E. Lasley, Yan Liang, Jill McKay-Fleisch, Jeffrey S. Nelson, Karen Nguyen, Erin Piazza, Aric Rininger, Daniel R. Zollinger, Michael Rhodes, Joseph M. Beechem
Summary: Emerging spatial profiling technology allows high-plex molecular profiling in biological tissues while preserving the spatial and morphological context of gene expression. By expanding the chemistry for the Digital Spatial Profiling platform, researchers have successfully quantified whole transcriptomes in human and mouse tissues, enabling applications in cancer research, molecular pathology, and developmental biology.
Article
Medicine, General & Internal
Vincent M. Tutino, Yongjun Lu, Daizo Ishii, Kerry E. Poppenberg, Hamidreza Rajabzadeh-Oghaz, Adnan H. Siddiqui, David M. Hasan
Summary: This study found expression differences in half of the IA-associated genes in the blood within the aneurysm, providing evidence for IA tissue-mediated transcriptional changes in whole blood. Additionally, some genes may be informative in assessing IA risk, as their intraluminal expression was correlated to IA size and aneurysmal wall enhancement.
Article
Biotechnology & Applied Microbiology
Jiao Wang, Yue Lan, Lewei He, Ruixiang Tang, Yuhui Li, Yuan Huang, Shan Liang, Zhan Gao, Megan Price, Bisong Yue, Miao He, Tao Guo, Zhenxin Fan
Summary: The study revealed sex-specific gene expression differences in the blood tissues of four primates, with 31 sex-specific differentially expressed genes identified in humans. Most XY gene pairs had similar expression levels between species, except for one pair (EIF1AY/EIF1AX). Humans had significant XY-biased and XX-biased X-Y gene pairs, while rhesus and Tibetan macaques did not show significant differential expression levels in their X-Y gene pairs.
Article
Biotechnology & Applied Microbiology
Grant C. O'Connell, Jing Wang, Christine Smothers
Summary: Cellular composition plays a significant role in determining gene expression patterns. This study demonstrates that the primary determinants of gene expression differences in whole blood are variations in white blood cell counts, while factors like age, sex, race, ethnicity, and disease states have minimal influence.
Article
Oncology
Lourdes Cruz-Garcia, Christophe Badie, Selvakumar Anbalagan, Jayne Moquet, Lone Gothard, Grainne O'Brien, Navita Somaiah, Elizabeth A. Ainsbury
Summary: This study identified a new panel of transcriptional changes in inflammation-associated genes in radiotherapy patients exposed to ionising radiation. The findings suggest potential use of these gene changes as biomarkers for radiation response, which varied among different cancer types and with time since exposure. Ongoing validation in a larger patient cohort is underway to further support personalized approaches in radiation medicine.
RADIATION ONCOLOGY
(2021)
Article
Biology
Shuchi Bhagi, Sudhir Chandna
Summary: Assessing alterations in the expression of radiation-responsive genes in peripheral blood cells is considered a promising approach for high-throughput radiation biodosimetry. The study found that incubating undiluted peripheral whole blood without any RNA stabilizing agent at 37°C for 24 hours resulted in the most optimal transcriptional response in the genes studied, with significant overexpression of DDB2 and FDXR.
INTERNATIONAL JOURNAL OF RADIATION BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Ashley Pacheco, Aaron Issaian, Jonathan Davis, Nathan Anderson, Travis Nemkov, Natasia Paukovich, Morkos A. Henen, Beat Vögeli, James M. Sikela, Kirk Hansen
Summary: Olduvai protein domains, which show the greatest increase in copy number in humans, are closely related to human brain evolution and cognitive diseases. These domains are processed by furin protease and are found in NBPF genes, forming Olduvai triplets. The correlation between Olduvai copy number and brain size, along with the furin data, suggests that the primary role of Olduvai in human brain expansion is through the increased dosage of autonomously functioning Olduvai triplet proteins.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Multidisciplinary Sciences
Ibrahim E. Elsemman, Angelica Rodriguez Prado, Pranas Grigaitis, Manuel Garcia Albornoz, Victoria Harman, Stephen W. Holman, Johan van Heerden, Frank J. Bruggeman, Mark M. M. Bisschops, Nikolaus Sonnenschein, Simon Hubbard, Rob Beynon, Pascale Daran-Lapujade, Jens Nielsen, Bas Teusink
Summary: The study developed a metabolic model of yeast cells to predict proteome constraints governing metabolic strategies. Under specific conditions, unicellular organisms rewire their metabolism to adapt to growth and maintenance needs.
NATURE COMMUNICATIONS
(2022)
Article
Oncology
William K. Oh, Raymond Miao, Francis Vekeman, Jennifer Sung, Wendy Y. Cheng, Marjolaine Gauthier-Loiselle, Ravinder Dhawan, Mei Sheng Duh
CLINICAL GENITOURINARY CANCER
(2018)
Article
Urology & Nephrology
Li Wang, Yixuan Gong, Abdel Saci, Peter M. Szabo, Alberto Martini, Andrea Necchi, Arlene Siefker-Radtke, Sumanta Pal, Elizabeth R. Plimack, John P. Sfakianos, Nina Bhardwaj, Amir Horowitz, Adam M. Farkas, David Mulholland, Bruce S. Fischer, William K. Oh, Padmanee Sharma, Jun Zhu, Matthew D. Galsky
Review
Urology & Nephrology
Scot A. Niglio, Rachel Jia, Jiayi Ji, Samuel Ruder, Vaibhav G. Patel, Alberto Martini, John P. Sfakianos, Kathryn E. Marqueen, Nikhil Waingankar, Reza Mehrazin, Peter Wiklund, William K. Oh, Madhu Mazumdar, Bart S. Ferket, Matthew D. Galsky
Article
Immunology
Vaibhav G. Patel, William K. Oh
Article
Oncology
Yixuan Gong, Li Wang, Haocheng Yu, Naomi Alpert, Mitchell D. Cohen, Colette Prophete, Lori Horton, Maureen Sisco, Sung-Hyun Park, Hyun-Wook Lee, Judith Zelikoff, Lung-Chi Chen, Dana Hashim, Mayte Suarez-Farinas, Michael J. Donovan, Stuart A. Aaronson, Matthew Galsky, Jun Zhu, Emanuela Taioli, William K. Oh
MOLECULAR CANCER RESEARCH
(2019)
Article
Urology & Nephrology
Silke Gillessena, Gerhardt Attard, Tomasz M. Beer, Himisha Beltran, Anders Bjartell, Alberto Bossi, Alberto Briganti, Rob G. Bristow, Kim N. Chi, Noel Clarke, Ian D. Davis, Johann de Bono, Charles G. Drake, Ignacio Duran, Ros Eeles, Eleni Efstathiou, Christopher P. Evans, Stefano Fanti, Felix Y. Feng, Karim Fizazi, Mark Frydenberg, Martin Gleave, Susan Halabi, Axel Heidenreich, Daniel Heinrich, Celestia (Tia) S. Higano, Michael S. Hofman, Maha Hussain, Nicolas James, Ravindran Kanesvaran, Philip Kantoff, Raja B. Khauli, Raya Leibowitz, Chris Logothetis, Fernando Maluf, Robin Millman, Alicia K. Morgans, Michael J. Morris, Nicolas Mottet, Hind Mrabti, Declan G. Murphy, Vedang Murthy, William K. Oh, Piet Ost, Joe M. OSullivan, Anwar R. Padhani, Chris Parker, Darren M. C. Poon, Colin C. Pritchard, Robert E. Reiter, Mack Roach, Mark Rubin, Charles J. Ryan, Fred Saad, Juan Pablo Sade, Oliver Sartor, Howard Scher, Neal Shore, Eric Small, Matthew Smith, Howard Soule, Cora N. Sternberg, Thomas Steuber, Hiroyoshi Suzuki, Christopher Sweeneyh, Matthew R. Sydes, Mary-Ellen Taplinh, Bertrand Tombal, Levent Turkeri, Inge van Oort, Almudena Zapatero, Aurelius Omlind
Editorial Material
Oncology
W. K. Oh
ANNALS OF ONCOLOGY
(2020)
Article
Oncology
Alberto Martini, John Pfail, Francesco Montorsi, Matthew D. Galsky, William K. Oh
PROSTATE CANCER AND PROSTATIC DISEASES
(2020)
Article
Oncology
M. C. Liu, G. R. Oxnard, E. A. Klein, C. Swanton, M. Seiden
ANNALS OF ONCOLOGY
(2020)
Article
Oncology
Alberto Martini, Anish B. Parikh, John P. Sfakianos, Francesco Montorsi, Matthew D. Galsky, William K. Oh, Che-Kai Tsao
Summary: Docetaxel is widely used in mCRPC, but its optimal use is unclear. This study aimed to create a predictive model for Docetaxel toxicity-related discontinuation (TRDD) using data from three clinical trials. The model identified three risk groups for TRDD, helping clinicians balance treatment toxicity and efficacy.
PROSTATE CANCER AND PROSTATIC DISEASES
(2021)
Article
Endocrinology & Metabolism
Matthew C. Riddle, William T. Cefalu, Philip H. Evans, Hertzel C. Gerstein, Michael A. Nauck, William K. Oh, Amy E. Rothberg, Carel W. le Roux, Francesco Rubino, Philip Schauer, Roy Taylor, Douglas Twenefour
Summary: Improvement of glucose levels in people with diabetes can occur spontaneously or after medical interventions. Newer forms of treatment may lead to more sustained improvement. However, the terminology and objective measures for defining this process are not established, and the long-term risks and benefits are not well understood. An international expert group proposed the term "remission" and HbA1c < 6.5% as the usual diagnostic criterion. They also suggested active observation and further research on predictors and outcomes of remission.
JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM
(2022)
Review
Medicine, General & Internal
Deepak K. Singh, Vaibhav G. Patel, William K. Oh, Julio A. Aguirre-Ghiso
Summary: Prostate cancer has a variable clinical course, with possibilities ranging from curable local disease to lethal metastatic spread. The dynamic interplay between dormant disseminated cancer cells (DCCs) and the primary tumor microenvironment (TME) as well as the secondary organ niche plays a crucial role in controlling the conversion between states of dormancy and activation.
JOURNAL OF CLINICAL MEDICINE
(2021)
Article
Oncology
Sunny Guin, Tomi Jun, Vaibhav G. Patel, Kristin L. Ayers, Matthew Deitz, Yuqin Cai, Xiang Zhou, Che-Kai Tsao, William K. Oh, Rong Chen, Bobby C. Liaw
Summary: This study utilized machine learning and natural language processing to build a clinical research database and investigate factors influencing testosterone recovery in patients with localized prostate cancer. The results demonstrated the impact of baseline testosterone levels on T-recovery and the association between ADT exposure and T-recovery.
JCO CLINICAL CANCER INFORMATICS
(2022)
Article
Oncology
Bobby C. Liaw, Che-Kai Tsao, Sonia Seng, Tomi Jun, Yixuan Gong, Matthew D. Galsky, William K. Oh
Summary: This study evaluated the feasibility and usefulness of blood-based biomarkers to identify platinum-sensitive mCRPC. Although some biomarkers were assessed, none were significantly associated with response to satraplatin.
Article
Oncology
Michael T. Schweizer, Gavin Ha, Roman Gulati, Landon Brown, Rana R. McKay, Tanya Dorff, Anna C. H. Hoge, Jonathan Reichel, Pankaj Vats, Deepak Kilari, Vaibhav Patel, William K. Oh, Arul Chinnaiyan, Colin C. Pritchard, Andrew J. Armstrong, R. Bruce Montgomery, Ajjai Alva
JCO PRECISION ONCOLOGY
(2020)