Article
Biochemistry & Molecular Biology
Yiyun Chen, Wing Yin Cheng, Hongyu Shi, Shengshuo Huang, Huarong Chen, Dabin Liu, Weiqi Xu, Jun Yu, Jiguang Wang
Summary: A molecular subtype of gastric cancer based on long non-coding RNA analysis has been proposed, with three subtypes identified, including L3 subtype associated with intestinal gastric cancer and poor survival outcomes, characterized by TP53 mutations, chromatin instability, hypomethylation, and over-expression of oncogenic long non-coding RNAs.
Article
Oncology
Sabino Russi, Luigi Marano, Simona Laurino, Giovanni Calice, Dario Scala, Graziella Marino, Alessandro Sgambato, Pellegrino Mazzone, Ludovico Carbone, Giuliana Napolitano, Franco Roviello, Geppino Falco, Pietro Zoppoli
Summary: Molecular heterogeneity is a major determinant of clinical outcomes in advanced gastric cancer. This study explored the transcriptome of two major subgroups of gastric cancer and identified different biological and molecular pathways associated with each group. The findings provide insights into the molecular mechanisms underlying carcinogenesis and disease progression, and may aid in the identification of new therapeutic targets.
Article
Microbiology
Matthew Zhao, Jonathan P. Jacobs
Summary: This study finds that colorectal cancer can be caused by either adenomatous or serrated polyps, which have different detection rates and risk of cancer progression. The study also discovers distinct fecal microbial species composition and metabolic potential associated with diet and medications in these polyp subtypes.
CELL HOST & MICROBE
(2023)
Article
Endocrinology & Metabolism
Umair Ali Khan Saddozai, Fengling Wang, Muhammad Usman Akbar, Lu Zhang, Yang An, Wan Zhu, Longxiang Xie, Yongqiang Li, Xinying Ji, Xiangqian Guo
Summary: Pheochromocytoma (PCC) is a rare neuroendocrine tumor of the adrenal gland with distinct subtypes identified through gene expression profiling. Specific genes enriched in each subtype may serve as potential therapeutic targets and provide insights into the mechanisms of tumorigenesis.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Article
Biology
Christopher E. Lietz, Erik T. Newman, Andrew D. Kelly, David H. Xiang, Ziying Zhang, Caroline A. Luscko, Santiago A. Lozano-Calderon, David H. Ebb, Kevin A. Raskin, Gregory M. Cote, Edwin Choy, G. Petur Nielsen, Benjamin Haibe-Kains, Martin J. Aryee, Dimitrios Spentzos
Summary: The study found that genomic hypomethylation in patients with primary osteosarcoma is predictive of response to standard chemotherapy. Recurrence and survival were also associated with genomic methylation patterns. These findings provide insights into potential alternative therapies for osteosarcoma patients.
COMMUNICATIONS BIOLOGY
(2022)
Letter
Oncology
Fanqin Bu, Xiangji Li, Yu Zhao, Liyi Bai, Shutian Zhang, Li Min
Summary: Cuproptosis is a newly discovered type of cell death triggered by copper accumulation. Genetic profiles of 10 cuproptosis-associated genes (CuAGs) across 21 cancer types were shown. The expression of CuAGs exhibited heterogeneity across cancer types and different correlations with MSI, TMB, immune and stromal features. Using a Non-negative Matrix Factorization method, patients of each cancer type were divided into cuproptosis-based subtypes, which showed correlation with different biological and clinical features. Four categories were summarized based on these subtypes: Genomic disturbed, Stromal remolded, Immune inhibited, and Cuproptosis inert.
BIOMARKER RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Yingying Zhu, Bi Peng, Xiaoxiao Luo, Wei Sun, Dongbo Liu, Na Li, Ping Qiu, Guoxian Long
Summary: The study utilized a Bayesian non-negative matrix factorization (BayesNMF) based consensus clustering approach to classify cases from the TCGA-HNSC cohort into subtypes. Genomic and proteomic data from HNSC cell lines were integrated to identify biomarkers for response to targeted therapies and immunotherapies. The associations between HNSC subtypes and CD8 T-cell associated effector molecules, as well as common immune checkpoint genes, were compared to evaluate the potential of HNSC subtypes for clinically predictive immune checkpoint blockade therapy.
CURRENT MEDICINAL CHEMISTRY
(2023)
Article
Oncology
Whijae Roh, Yifat Geffen, Hongui Cha, Mendy Miller, Shankara Anand, Jaegil Kim, David Heiman, Justin F. Gainor, Peter W. Laird, Andrew D. Cherniack, Chan-Young Ock, Se-Hoon Lee, Gad Getz
Summary: Through consensus hierarchical clustering analysis, we identified five robust expression subtypes of lung adenocarcinoma. Integrating genomic and proteomic data, we defined biomarkers of response to targeted therapies and immunotherapies. These subtypes and biomarkers could help identify patients likely to respond to CDK4/6, MET, or PD-L1 inhibitors.
Article
Oncology
Pushpinder Kaur, Tania B. Porras, Anthony Colombo, Alexander Ring, Janice Lu, Irene Kang, Julie E. Lang
Summary: The study found that over 30% of tumors carried potentially actionable events targetable by existing drugs, identified genes with multiple targetable alterations as candidates for combination therapy, and drivers in primary breast tumors fall into five categories. Analysis showed that copy number alterations and mutations in genes were significantly associated with gene expression, validating copy number events as a dominant oncogenic mechanism in breast cancer.
BRITISH JOURNAL OF CANCER
(2021)
Article
Oncology
Jeremiah Holt, Vonn Walter, Xiaoying Yin, David Marron, Matthew D. Wilkerson, Hyo Young Choi, Xiaobei Zhao, Heejoon Jo, David Neil Hayes, Yoon Ho Ko
Summary: This study characterizes the role of miRNAs in classifying HNSCC, identifying two validated tumor subtypes named epithelial and stromal based on associations with target gene ontology. These miRNA-based subtypes are correlated with gene expression targets and pathways related to squamous cell function and pathophysiology. The study highlights the clinical relevance of miRNA-based classification in HNSCC.
CLINICAL CANCER RESEARCH
(2021)
Article
Clinical Neurology
Blake K. Noyes, Douglas P. Munoz, Sarosh Khalid-Khan, Elisa Brietzke, Linda Booij
Summary: Subthreshold depression and major depressive disorder in adolescents share similarities in several aspects, including higher prevalence, functional impairment, comorbidity, genetic predisposition, and treatment response. However, the definition of subthreshold depression varies across studies, and adolescent-specific data are limited.
JOURNAL OF AFFECTIVE DISORDERS
(2022)
Article
Radiology, Nuclear Medicine & Medical Imaging
Xiaoyang Liu, Yang Guo, Lei Zhao, Joseph Misdraji, Tina Kapur, Thomas A. Abrams, Paul B. Shyn
Summary: This study aimed to investigate whether MRI features can serve as non-invasive markers for predicting common genetic subtypes of HCC. Through gene sequencing and MRI evaluation of HCC samples, it was found that TP53 mutation correlated with infiltrative tumor margin on MRI, while CTNNB1 mutation correlated with peritumoral enhancement on MRI.
ABDOMINAL RADIOLOGY
(2023)
Editorial Material
Clinical Neurology
Eric Smith
Summary: Perivascular spaces (PVS) are visible on brain MRI and are considered typical manifestations of cerebral small vessel disease. They have often been overlooked, but recent evidence suggests that they provide clinically relevant information for prognosis and diagnosis.
Article
Medicine, General & Internal
Ning Zhao, Zicheng Zhang, Qiang Wang, Lin Li, Zichao Wei, Hongyan Chen, Meng Zhou, Zhihua Liu, Jianzhong Su
Summary: This study characterizes DNA damage repair (DDR) subtypes in esophageal squamous cell carcinoma (ESCC) and investigates their prognostic value. Two distinct DDR subtypes, DDRactive and DDRsilent, are identified, and their independent prognostic values are observed in locoregional ESCC. Additionally, a combination immunotherapy strategy is proposed and validated for high-risk locoregional ESCC tumors.
Article
Biotechnology & Applied Microbiology
Stephanie LaHaye, James R. Fitch, Kyle J. Voytovich, Adam C. Herman, Benjamin J. Kelly, Grant E. Lammi, Jeremy A. Arbesfeld, Saranga Wijeratne, Samuel J. Franklin, Kathleen M. Schieffer, Natalie Bir, Sean D. McGrath, Anthony R. Miller, Amy Wetzel, Katherine E. Miller, Tracy A. Bedrosian, Kristen Leraas, Elizabeth A. Varga, Kristy Lee, Ajay Gupta, Bhuvana Setty, Daniel R. Boue, Jeffrey R. Leonard, Jonathan L. Finlay, Mohamed S. Abdelbaki, Diana S. Osorio, Selene C. Koo, Daniel C. Koboldt, Alex H. Wagner, Ann-Kathrin Eisfeld, Krzysztof Mrozek, Vincent Magrini, Catherine E. Cottrell, Elaine R. Mardis, Richard K. Wilson, Peter White
Summary: The EnFusion pipeline utilizes seven fusion calling algorithms to increase the accuracy of identifying clinically relevant fusions in pediatric cancer. By combining ensemble fusion-calling pipeline with a knowledge-based filtering strategy, it accurately identifies driver fusions in pediatric cancer, contributing evidence to diagnosis and guiding targeted therapies where appropriate.
Article
Statistics & Probability
Elena Tuzhilina, Leonardo Tozzi, Trevor Hastie
Summary: Canonical correlation analysis (CCA) is a technique for measuring the association between two multivariate data matrices. Regularized modification of CCA (RCCA) is widely used for high-dimensional data but may disregard data structure. This article introduces several approaches to regularizing CCA that consider the underlying data structure and demonstrates strategies for avoiding excessive computations in high dimensions.
STATISTICAL MODELLING
(2023)
Article
Clinical Neurology
Matt Lechner, Yoko Takahashi, Mario Turri-Zanoni, Marco Ferrari, Jacklyn Liu, Nicholas Counsell, Davide Mattavelli, Vittorio Rampinelli, William Vermi, Davide Lombardi, Rami Saade, Ki Wan Park, Volker H. Schartinger, Alessandro Franchi, Carla Facco, Fausto Sessa, Simonetta Battocchio, Tim R. Fenton, Francis M. Vaz, Paul O'Flynn, David Howard, Paul Stimpson, Simon Wang, S. Alam Hannan, Samit Unadkat, Jonathan Hughes, Raghav Dwivedi, Cillian T. Forde, Premjit Randhawa, Simon Gane, Jonathan Joseph, Peter J. Andrews, Manas Dave, Jason C. Fleming, David Thomson, Tianyu Zhu, Andrew Teschendorff, Gary Royle, Christopher Steele, Joaquin E. Jimenez, Jan Laco, Eric W. Wang, Carl Snyderman, Peter D. Lacy, Robbie Woods, James P. O'Neill, Anirudh Saraswathula, Raman Preet Kaur, Tianna Zhao, Murugappan Ramanathan, Gary L. Gallia, Nyall R. London, Quynh-Thu Le, Robert B. West, Zara M. Patel, Jayakar V. Nayak, Peter H. Hwang, Mario Hermsen, Jose Llorente, Fabio Facchetti, Piero Nicolai, Paolo Bossi, Paolo Castelnuovo, Amrita Jay, Dawn Carnell, Martin D. Forster, Diana M. Bell, Valerie J. Lund, Ehab Y. Hanna
Summary: This study retrospectively analyzed clinical data from 505 cases of sinonasal mucosal melanoma (SNMM). It found that further stratifying the T3 stage by sinus involvement has a high predictive value for prognosis. Adjuvant radiotherapy can improve survival rates, and immune checkpoint inhibitors show potential benefits for the treatment of recurrent, persistent, or metastatic disease.
JOURNAL OF NEUROLOGICAL SURGERY PART B-SKULL BASE
(2023)
Review
Oncology
Silvia Stacchiotti, Hans Roland Duerr, Inga-Marie Schaefer, Klaus Woertler, Rick Haas, Annalisa Trama, Augusto Caraceni, Jyoti Bajpai, Giacomo Giulio Baldi, Nicholas Bernthal, Jean-Yves Blay, Kjetil Boye, Javier-Martin Broto, Wei-Wu Tom Chen, Paolo Angelo Dei Tos, Jayesh Desai, Stephan Emhofer, Mikael Eriksson, Alessandro Gronchi, Hans Gelderblom, Jendrik Hardes, Wolfgang Hartmann, John Healey, Antoine Italiano, Robin L. Jones, Akira Kawai, Andreas Leithner, Herbert Loong, Eric Mascard, Carlo Morosi, Nadine Otten, Emanuela Palmerini, Shreyaskumar R. Patel, Peter Reichardt, Brian Rubin, Piotr Rutkowski, Claudia Sangalli, Kathrin Schuster, Beatrice M. Seddon, Morena Shkcodra, Eric L. Staals, William Tap, Matt van de Rijn, Kirsten van Langevelde, Filip M. M. Vanhoenacker, Andrew Wagner, Lisette Wiltink, Sydney Stern, Michiel Van de Sande, Sebastian Bauer
Summary: Tenosynovial giant cell tumour (TGCT) is a rare, locally aggressive tumor that arises from the joints, bursa, and tendon sheaths. There are two types of TGCT: nodular and diffuse, with the former exhibiting a slow disease course and the latter showing locally aggressive behavior. Although not life-threatening, TGCT can cause chronic pain and negatively impact function and quality of life. CSFR1 inhibitors are effective in treating TGCT but are not widely available. The lack of guidelines and uncertainty in selecting appropriate therapy lead to inconsistent adoption of new treatments and suboptimal outcomes for patients. A global consensus meeting was held in June 2022 to develop evidence-based recommendations for the optimal management of TGCT.
CANCER TREATMENT REVIEWS
(2023)
Article
Statistics & Probability
J. Kenneth Tay, Nima Aghaeepour, Trevor Hastie, Robert Tibshirani
Summary: In some supervised learning settings, practitioners may have additional information on prediction features. Our proposed method, called the feature-weighted elastic net (fwelnet), uses this information to improve prediction by adjusting penalties on feature coefficients in the elastic net penalty. In simulations, fwelnet outperforms the lasso in terms of test mean squared error and often improves true positive or false positive rates for feature selection. Comparison with other methods reveals fwelnet's superiority, and its application to early prediction of preeclampsia shows improved performance compared to the lasso.
Article
Cell Biology
Myung Chang Lee, Hongchen Cai, Christopher W. Murray, Chuan Li, Yan Ting Shue, Laura Andrejka, Andy L. He, Alessandra M. E. Hozlem, Alexandros P. Drainans, Julie H. Ko, Garry L. Coles, Christina Kong, Shirley Zhu, ChunFang Zhu, Jason Wang, Matt van de Rijn, Dmitri A. Petrov, Monte M. Winslow, Julien Sage
Summary: We developed a quantitative multiplexed approach based on lentiviral barcoding and CRISPR-Cas9-mediated genome editing to functionally study candidate regulators of tumor initiation and growth in small cell lung cancer (SCLC). Naphthalene pre-treatment enhanced lentiviral vector-mediated SCLC initiation and enabled high-throughput sequencing analysis of tumor clones. The analysis identified TSC1 in the PI3K-AKT-mTOR pathway as a robust tumor suppressor in SCLC. This approach will provide insight into drivers of SCLC and facilitate the development of precision therapies for specific SCLC genotypes.
Article
Multidisciplinary Sciences
Aaron T. Mayer, Derek R. Holman, Anav Sood, Utkarsh Tandon, Salil S. Bhate, Sunil Bodapati, Graham L. Barlow, Jeff Chang, Sarah Black, Erica C. Crenshaw, Alexander N. Koron, Sarah E. Streett, Sanjiv S. Gambhir, William J. Sandborn, Brigid S. Boland, Trevor Hastie, Robert Tibshirani, John T. Chang, Garry P. Nolan, Christian M. Schuerch, Stephan Rogalla
Summary: This study uses CODEX technology to create a tissue atlas of inflammation in UC patients and healthy individuals. The analysis reveals the association between cellular functional states and cellular neighborhoods, as well as the presence of resistant niches in UC patients with TNFi treatment. Additionally, the study explores the use of CNNs in predicting patient clinical variables and provides guidelines for reporting predictions in similar datasets.
Article
Environmental Sciences
Shinnosuke Nakayama, WenXin Dong, Richard G. G. Correro, Elizabeth R. R. Selig, Colette C. C. Wabnitz, Trevor J. J. Hastie, Jim Leape, Serena Yeung, Fiorenza Micheli
Summary: Monitoring marine vessel activities is crucial but challenging, especially with limited capacity and resources. Satellite imagery offers a promising solution to observe vessel activities not captured by publicly available tracking data. However, the lack of understanding on its complementarity with existing data hampers its broader use.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Oncology
Claire Baniel, Christopher H. Yoo, Alice Jiang, Rie von Eyben, David G. Mohler, Kristen Ganjoo, Nam Bui, Sarah S. Donaldson, Lynn Million, Matt van de Rijn, Justin Moon Oh, Susan M. Hiniker
Summary: This study retrospectively reviewed the clinical data of 30 patients with TGCT and found that postsurgical radiation therapy can effectively control disease recurrence and improve patients' quality of life.
PRACTICAL RADIATION ONCOLOGY
(2023)
Article
Oncology
Nam Q. Bui, Neda Nemat-Gorgani, Ajay Subramanian, Ileana A. Torres, Marta Lohman, Timothy J. Sears, Matt van de Rijn, Gregory W. Charville, Hans-Christoph Becker, David S. Wang, Gloria L. Hwang, Kristen N. Ganjoo, Everett J. Moding
Summary: This study evaluated the role of circulating tumor DNA (ctDNA) as a biomarker in monitoring treatment response in patients with advanced soft tissue sarcomas (STS). The results showed that ctDNA was associated with treatment response, progression-free survival, and overall survival. This suggests that ctDNA may serve as a promising biomarker in STS patients.
CLINICAL CANCER RESEARCH
(2023)
Article
Statistics & Probability
Stephen Bates, Trevor Hastie, Robert Tibshirani
Summary: Cross-validation is a widely used technique for estimating prediction error, but its behavior is not fully understood. It does not estimate the prediction error of the model trained on the data used for cross-validation, but rather the average prediction error of models trained on unseen data from the same population. The standard confidence intervals derived from cross-validation may have lower coverage than desired, due to correlations among the measured accuracies within each fold. A nested cross-validation scheme is introduced to estimate variance more accurately and improve coverage of confidence intervals.
JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION
(2023)
Article
Mathematics, Interdisciplinary Applications
Booil Jo, Trevor J. J. Hastie, Zetan Li, Eric A. A. Youngstrom, Robert L. L. Findling, Sarah McCue Horwitz
Summary: This study proposes a method for integrating latent variable (LV) modeling into supervised learning. By combining the traditions of LV modeling, psychometrics, and supervised learning, practical prediction targets can be generated and systematically validated based on clinical validators. The feasibility of this integrated approach is demonstrated using data from the LAMS Study.
MULTIVARIATE BEHAVIORAL RESEARCH
(2023)
Article
Statistics & Probability
Lukasz Kidzinski, Trevor Hastie
Summary: In clinical practice and biomedical research, it is common to collect sparse and irregularly time-series data, which can be costly and inconvenient. Traditional analysis methods, such as mixed-effect models, Gaussian processes, and functional data analysis, rely on probabilistic assumptions, require careful implementation, and tend to be slow. In this study, we propose a novel framework based on matrix completion for analyzing longitudinal data. By iteratively applying Singular Value Decomposition, our method can estimate progression curves efficiently and easily, and it can be extended to other settings. We applied this method to study the motor impairment progression in children with Cerebral Palsy, and achieved good approximations of individual progression curves and ability to identify different progression trends in subtypes of Cerebral Palsy.
JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS
(2023)
Article
Multidisciplinary Sciences
Shirley Greenbaum, Inna Averbukh, Erin Soon, Gabrielle Rizzuto, Alex Baranski, Noah F. Greenwald, Adam Kagel, Marc Bosse, Eleni G. Jaswa, Zumana Khair, Shirley Kwok, Shiri Warshawsky, Hadeesha Piyadasa, Mako Goldston, Angie Spence, Geneva Miller, Morgan Schwartz, Will Graf, David Van Valen, Virginia D. Winn, Travis Hollmann, Leeat Keren, Matt van de Rijn, Michael Angelo
Summary: A spatiotemporal atlas of the human maternal-fetal interface in the first half of pregnancy was constructed using a multiomics approach. The study revealed that gestational age significantly influenced the frequency of maternal immune and stromal cells, with tolerogenic subsets becoming enriched at later time points. Spiral artery remodeling was primarily correlated with extravillous trophoblast invasion and was defined by distinct transcriptional pathways.
Article
Medicine, General & Internal
Catherine Ley, Frederik Heath, Trevor Hastie, Zijun Gao, Myroslava Protsiv, Julie Parsonnet
Summary: This cross-sectional study determines the normal oral temperature ranges based on age, sex, height, weight, and time of day by analyzing a large number of clinical visit records. The findings have important implications for temperature assessment and disease diagnosis in clinical medicine.
JAMA INTERNAL MEDICINE
(2023)
Article
Oncology
Mushriq Al-Jazrawe, Steven Xu, Raymond Poon, Qingxia Wei, Joanna Przybyl, Sushama Varma, Matt van de Rijn, Benjamin A. Alman
Summary: The interaction between neoplastic and stromal cells in tumors is important, but distinguishing between them is challenging in mesenchymal tumors. Here, researchers identified surface markers to distinguish mutant and nonmutant cells in desmoid tumors. CD142 was found to be highly expressed by mutant cells, and its cell sorting allowed isolation of the mutant population. The study also explored the secretome of mutant and nonmutant cells, identifying factors that regulate mutant cell proliferation. This study provides a sensitive method to quantify neoplastic and stromal cells and identifies potential therapeutic targets.
CANCER RESEARCH COMMUNICATIONS
(2023)