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Sweet-Jones J, Martin AC. An antibody developability triaging pipeline exploiting protein language models. MAbs 2025; 17:2472009. [PMID: 40038849 PMCID: PMC11901365 DOI: 10.1080/19420862.2025.2472009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2024] [Revised: 02/17/2025] [Accepted: 02/20/2025] [Indexed: 03/06/2025] Open
Abstract
Therapeutic monoclonal antibodies (mAbs) are a successful class of biologic drugs that are frequently selected from phage display libraries and transgenic mice that produce fully human antibodies. However, binding affinity to the correct epitope is necessary, but not sufficient, for a mAb to have therapeutic potential. Sequence and structural features affect the developability of an antibody, which influences its ability to be produced at scale and enter trials, or can cause late-stage failures. Using data on paired human antibody sequences, we introduce a pipeline using a machine learning approach that exploits protein language models to identify antibodies which cluster with antibodies that have entered the clinic and are therefore expected to have developability features similar to clinically acceptable antibodies, and triage out those without these features. We propose this pipeline as a useful tool in candidate selection from large libraries, reducing the cost of exploration of the antibody space, and pursuing new therapeutics.
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Affiliation(s)
- James Sweet-Jones
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Andrew C.R. Martin
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
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2
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Fuellen G, Palmer D, Fruijtier C, Avelar RA. In-silico Evaluation of Aging-Related Interventions Using Omics Data and Predictive Modeling. Ageing Res Rev 2025:102777. [PMID: 40414362 DOI: 10.1016/j.arr.2025.102777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2025] [Revised: 03/12/2025] [Accepted: 05/16/2025] [Indexed: 05/27/2025]
Abstract
A major challenge in aging research is identifying interventions that can improve lifespan and health and minimize toxicity. Clinical studies cannot consider decades-long follow-up periods, and therefore, in-silico evaluations using omics-based surrogate biomarkers are emerging as key tools. However, many current approaches train predictive models on observational data, rather than on intervention data, which can lead to biased conclusions. Yet, the first classifiers for lifespan extension by compounds are now available, learned on intervention data. Here, we review evaluation methodologies and we prioritize training on intervention data whenever available, highlight the importance of safety and toxicity assessments, discuss the role of standardized benchmarks, and present a range of feature processing and predictive modeling approaches. We consider linear and non-linear methods, and automated machine learning workflows. We conclude by emphasizing the need for explainable and reproducible strategies, the integration of safety metrics, and the careful validation of predictors based on interventional benchmarks.
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Affiliation(s)
- Georg Fuellen
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Rostock, Germany; UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin, Ireland
| | - Daniel Palmer
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Rostock, Germany
| | - Claudia Fruijtier
- European Registered Toxicologist at Cats Consultants, Dietmannsried, Germany
| | - Roberto A Avelar
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Rostock, Germany
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3
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Pavel A, Grønberg MG, Clemmensen LH. The impact of dropouts in scRNAseq dense neighborhood analysis. Comput Struct Biotechnol J 2025; 27:1278-1285. [PMID: 40225837 PMCID: PMC11992407 DOI: 10.1016/j.csbj.2025.03.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2024] [Revised: 03/19/2025] [Accepted: 03/20/2025] [Indexed: 04/15/2025] Open
Abstract
Single cell RNA sequencing (scRNAseq) provides the possibility to investigate transcriptomic profiles on a single cell level. However, the data show unique challenges in comparison to bulk transcriptomic data, one being high dropout rates, which yields high sparsity data. Many classical analysis and preprocessing pipelines are based on the assumption that poor data can be counteracted by quantity and that similar cells (samples) are close to each other in space. Clustering is commonly used to detect clusters (dense local cell neighborhoods) under the assumption that similar cells are close to each other in space (where close is dependent on the (distance) metric used). The most commonly used clustering methodologies to detect dense local neighborhoods are based on graph clustering on a nearest neighbor graph. However, high dropout rates may break this assumption and make it difficult to reliably detect such dense local neighborhoods. We assess the cluster homogeneity and stability under increasing degrees of dropouts in one of the most popular clustering pipelines (dimensionality reduction + graph based clustering), as provided by scRNAseq analyses packages Seurat and Scanpy. Our study showcases that while the default pipeline performs well in terms of cluster homogeneity (i.e., cells in a cluster are of the same type), also with increasing dropout rates, the stability of clusters (i.e., cell pairs consistently being in the same cluster) decreases. This implies that sub-populations within cell types are increasingly difficult to identify under increasing dropout rates because observations are not consistently close. Our results challenge the current practice of using default clustering pipelines and the general assumption of identifiable local neighborhoods on high dropout data. Hence, these results suggest that careful consideration in interpretation and downstream analysis need to be made when relying on local neighborhoods and clusters on scRNAseq data. In addition, these results call for extensive benchmarking, to identify and provide methods robust in their local neighborhood relationships on data containing low to high dropout rates.
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Affiliation(s)
- Alisa Pavel
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Manja Gersholm Grønberg
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Line H. Clemmensen
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
- Department of Mathematical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
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4
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Wu CH, Zhou X, Chen M. Exploring and mitigating shortcomings in single-cell differential expression analysis with a new statistical paradigm. Genome Biol 2025; 26:58. [PMID: 40098192 PMCID: PMC11912664 DOI: 10.1186/s13059-025-03525-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/05/2025] [Indexed: 03/19/2025] Open
Abstract
BACKGROUND Differential expression analysis is pivotal in single-cell transcriptomics for unraveling cell-type-specific responses to stimuli. While numerous methods are available to identify differentially expressed genes in single-cell data, recent evaluations of both single-cell-specific methods and methods adapted from bulk studies have revealed significant shortcomings in performance. In this paper, we dissect the four major challenges in single-cell differential expression analysis: excessive zeros, normalization, donor effects, and cumulative biases. These "curses" underscore the limitations and conceptual pitfalls in existing workflows. RESULTS To address the limitations of current single-cell differential expression analysis methods, we propose GLIMES, a statistical framework that leverages UMI counts and zero proportions within a generalized Poisson/Binomial mixed-effects model to account for batch effects and within-sample variation. We rigorously benchmarked GLIMES against six existing differential expression methods using three case studies and simulations across different experimental scenarios, including comparisons across cell types, tissue regions, and cell states. Our results demonstrate that GLIMES is more adaptable to diverse experimental designs in single-cell studies and effectively mitigates key shortcomings of current approaches, particularly those related to normalization procedures. By preserving biologically meaningful signals, GLIMES offers improved performance in detecting differentially expressed genes. CONCLUSIONS By using absolute RNA expression rather than relative abundance, GLIMES improves sensitivity, reduces false discoveries, and enhances biological interpretability. This paradigm shift challenges existing workflows and highlights the need for careful consideration of normalization strategies, ultimately paving the way for more accurate and robust single-cell transcriptomic analyses.
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Affiliation(s)
- Chih-Hsuan Wu
- Department of Statistics, University of Chicago, Chicago, USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, USA
| | - Mengjie Chen
- Department of Human Genetics and Department of Medicine, University of Chicago, Chicago, USA.
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Wang YJ, Choo WC, Ng KY, Bi R, Wang PW. Evolution of AI enabled healthcare systems using textual data with a pretrained BERT deep learning model. Sci Rep 2025; 15:7540. [PMID: 40038367 PMCID: PMC11880528 DOI: 10.1038/s41598-025-91622-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2024] [Accepted: 02/21/2025] [Indexed: 03/06/2025] Open
Abstract
In the rapidly evolving field of healthcare, Artificial Intelligence (AI) is increasingly driving the promotion of the transformation of traditional healthcare and improving medical diagnostic decisions. The overall goal is to uncover emerging trends and potential future paths of AI in healthcare by applying text mining to collect scientific papers and patent information. This study, using advanced text mining and multiple deep learning algorithms, utilized the Web of Science for scientific papers (1587) and the Derwent innovations index for patents (1314) from 2018 to 2022 to study future trends of emerging AI in healthcare. A novel self-supervised text mining approach, leveraging bidirectional encoder representations from transformers (BERT), is introduced to explore AI trends in healthcare. The findings point out the market trends of the Internet of Things, data security and image processing. This study not only reveals current research hotspots and technological trends in AI for healthcare but also proposes an advanced research method. Moreover, by analysing patent data, this study provides an empirical basis for exploring the commercialisation of AI technology, indicating the potential transformation directions for future healthcare services. Early technology trend analysis relied heavily on expert judgment. This study is the first to introduce a deep learning self-supervised model to the field of AI in healthcare, effectively improving the accuracy and efficiency of the analysis. These findings provide valuable guidance for researchers, policymakers and industry professionals, enabling more informed decisions.
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Affiliation(s)
- Yi Jie Wang
- School of Business and Economics, Universiti Putra Malaysia, Seri Kembangan, Malaysia
| | - Wei Chong Choo
- School of Business and Economics, Universiti Putra Malaysia, Seri Kembangan, Malaysia
- Institute for Mathematical Research (INSPEM), Universiti Putra Malaysia, Seri Kembangan, Malaysia
| | - Keng Yap Ng
- Institute for Mathematical Research (INSPEM), Universiti Putra Malaysia, Seri Kembangan, Malaysia
- Department of Software Engineering and Information System, Faculty of Computer Science and Information Technology, Universiti Putra Malaysia, Seri Kembangan, Malaysia
| | - Ran Bi
- SAS Institute Inc., 100 SAS Campus Drive, Cary, USA
| | - Peng Wei Wang
- School of Physics and Electronic Information, Jiangsu Second Normal University, Nan Jing, Jiang Su, China.
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Golob J, Rao K, Berinstein JA, Singh P, Chey WD, Owyang C, Kamada N, Higgins PDR, Young V, Bishu S, Lee AA. Why Symptoms Linger in Quiescent Crohn's Disease: Investigating the Impact of Sulfidogenic Microbes and Sulfur Metabolic Pathways. Inflamm Bowel Dis 2025; 31:763-776. [PMID: 39541261 PMCID: PMC11879174 DOI: 10.1093/ibd/izae238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Indexed: 11/16/2024]
Abstract
INTRODUCTION Even in the absence of inflammation, persistent symptoms in patients with Crohn's disease (CD) are prevalent and worsen quality of life. We previously demonstrated enrichment in sulfidogenic microbes in quiescent Crohn's disease patients with (qCD + S) vs without persistent GI symptoms (qCD-S). Thus, we hypothesized that sulfur metabolic pathways would be enriched in stool while differentially abundant microbes would be associated with important sulfur metabolic pathways in qCD + S. METHODS We performed a multicenter observational study nested within SPARC IBD. Quiescent inflammation was defined by fecal calprotectin level < 150 mcg/g. Persistent symptoms were defined by CD-PRO2. Active CD (aCD) and non-IBD diarrhea-predominant irritable bowel syndrome (IBS-D) were included as controls. RESULTS Thirty-nine patients with qCD + S, 274 qCD-S, 21 aCD, and 40 IBS-D underwent paired shotgun metagenomic sequencing and untargeted metabolomic profiling. The fecal metabolome in qCD + S was significantly different relative to qCD-S and IBS-D but not aCD. Patients with qCD + S were enriched in sulfur-containing amino acid pathways, including cysteine and methionine, as well as serine, glycine, and threonine. Glutathione and nicotinate/nicotinamide pathways were also enriched in qCD + S relative to qCD-S, suggestive of mitochondrial dysfunction, a downstream target of H2S signaling. Multi-omic integration demonstrated that enriched microbes in qCD + S were associated with important sulfur metabolic pathways. Bacterial sulfur metabolic genes, including CTH, isfD, sarD, and asrC, were dysregulated in qCD + S. Finally, sulfur metabolites with and without sulfidogenic microbes showed good accuracy in predicting the presence of qCD + S. DISCUSSION Microbial-derived sulfur pathways and downstream mitochondrial function are perturbed in qCD + S, which implicate H2S signaling in the pathogenesis of this condition. Future studies will determine whether targeting H2S pathways results in improved quality of life in qCD + S.
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Affiliation(s)
- Jonathan Golob
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Krishna Rao
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Jeffrey A Berinstein
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Prashant Singh
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - William D Chey
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Chung Owyang
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Nobuhiko Kamada
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Peter D R Higgins
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Vincent Young
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Shrinivas Bishu
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Allen A Lee
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
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Xie Z, Li L, Hou W, Fan Z, Zeng L, He L, Ji Y, Zhang J, Wang F, Xing Z, Wang Y, Ye Y. Critical role of Oas1g and STAT1 pathways in neuroinflammation: insights for Alzheimer's disease therapeutics. J Transl Med 2025; 23:182. [PMID: 39953505 PMCID: PMC11829366 DOI: 10.1186/s12967-025-06112-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 01/08/2025] [Indexed: 02/17/2025] Open
Abstract
BACKGROUND Alzheimer's disease (AD) has a significant impact on an individual's health and places a heavy burden on society. Studies have emphasized the importance of microglia in the progression and development of AD. Interferon responses and Interferon-stimulated genes (ISGs) significantly function in neuroinflammatory and neurodegenerative diseases involving AD. Therefore, further exploration of the relationship among microglia, ISGs, and neuroinflammation in AD is warranted. METHODS Microglia datasets from the GEO database were retrieved, along with additional microglia RNA-seq data from laboratory mice. Weighted Correlation Network Analysis was used on the training dataset to identify gene co-expression networks. Genes from the black module were intersected with interferon-stimulated genes, and differentially expressed genes (DEGs) were identified. Machine learning algorithms were applied to DEGs, and genes selected by both methods were identified as hub genes, with ROC curves used to evaluate their diagnostic accuracy. Gene Set Enrichment Analysis was performed to reveal functional pathways closely relating to hub genes. Microglia cells were transfected with siRNAs targeting Oas1g and STAT1. Total RNA from microglia cells and mouse brain tissues was extracted, reverse-transcribed, and analyzed via qRT-PCR. Proteins were extracted from cells, quantified, separated by SDS-PAGE, transferred to PVDF membranes, and probed with antibodies. Microglia cells were fixed, permeabilized, blocked, and stained with antibodies for STAT1, then visualized and photographed. RESULTS Bioinformatics and machine learning algorithms revealed that Oas1g was identified as a hub gene, with an AUC of 0.812. Enrichment Analysis revealed that Oas1g is closely associated with interferon-related pathways. Expression of Oas1g was validated in AD mouse models, where it was significantly upregulated after microglial activation. Knockdown experiments suggested siOas1g attenuated the effect of siSTAT1, and the expressions of STAT1 and p-STAT1 were elevated. siOas1g could reverse the effect of siSTAT1, indicating that Oas1g potentially regulates the ISGs through the STAT1 pathway. CONCLUSION We demonstrated that Oas1g was identified as a hub ISG in AD and can downregulate the activation of IFN-β and STAT1, reducing the expression of ISGs in neuroinflammation. Oas1g might potentially be a beneficial candidate for both prevention and treatment of AD.
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Affiliation(s)
- Zhixin Xie
- The Second Clinical Medicine School, Guangzhou Medical University, Guangzhou, China
| | - Linxi Li
- Department of Neurosurgery, Institute of Neuroscience, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Weizhong Hou
- The Second Clinical Medicine School, Guangzhou Medical University, Guangzhou, China
| | - Zhongxi Fan
- The Third Clinical Medicine School, Guangzhou Medical University, Guangzhou, China
| | - Lifan Zeng
- The Third Clinical Medicine School, Guangzhou Medical University, Guangzhou, China
| | - Limin He
- The Sixth Clinical Medicine School, Guangzhou Medical University, Guangzhou, China
| | - Yunxiang Ji
- Department of Neurosurgery, Institute of Neuroscience, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jingbai Zhang
- Department of Neurosurgery, Institute of Neuroscience, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Fangran Wang
- Department of Neurosurgery, Institute of Neuroscience, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhou Xing
- Department of Neurosurgery, Institute of Neuroscience, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Yezhong Wang
- Department of Neurosurgery, Institute of Neuroscience, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Yongyi Ye
- Department of Neurosurgery, Institute of Neuroscience, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
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Joosse HJ, Chumsaeng-Reijers C, Huisman A, Hoefer IE, van Solinge WW, Haitjema S, van Es B. Haematology dimension reduction, a large scale application to regular care haematology data. BMC Med Inform Decis Mak 2025; 25:75. [PMID: 39939843 PMCID: PMC11823074 DOI: 10.1186/s12911-025-02899-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/28/2025] [Indexed: 02/14/2025] Open
Abstract
BACKGROUND The routine diagnostic process increasingly entails the processing of high-volume and high-dimensional data that cannot be directly visualised. This processing may provide scaling issues that limit the implementation of these types of data into research as well as integrated diagnostics in routine care. Here, we investigate whether we can use existing dimension reduction techniques to provide visualisations and analyses for a complete bloodcount (CBC) while maintaining representativeness of the original data. We considered over 3 million CBC measurements encompassing over 70 parameters of cell frequency, size and complexity from the UMC Utrecht UPOD database. We evaluated PCA as an example of a linear dimension reduction techniques and UMAP, TriMap and PaCMAP as non-linear dimension reduction techniques. We assessed their technical performance using quality metrics for dimension reduction as well as biological representation by evaluating preservation of diurnal, age and sex patterns, cluster preservation and the identification of leukemia patients. RESULTS We found that, for clinical hematology data, PCA performs systematically better than UMAP, TriMap and PaCMAP in representing the underlying data. Biological relevance was retained for periodicity in the data. However, we also observed a decrease in predictive performance of the reduced data for both age and sex, as well as an overestimation of clusters within the reduced data. Finally, we were able to identify the diverging patterns for leukemia patients after use of dimensionality reduction methods. CONCLUSIONS We conclude that for hematology data, the use of unsupervised dimension reduction techniques should be limited to data visualization applications, as implementing them in diagnostic pipelines may lead to decreased quality of integrated diagnostics in routine care.
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Affiliation(s)
- Huibert-Jan Joosse
- Central Diagnostic Laboratory, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
| | - Chontira Chumsaeng-Reijers
- Central Diagnostic Laboratory, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
| | - Albert Huisman
- Central Diagnostic Laboratory, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
| | - Imo E Hoefer
- Central Diagnostic Laboratory, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
| | - Wouter W van Solinge
- Central Diagnostic Laboratory, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
| | - Saskia Haitjema
- Central Diagnostic Laboratory, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
| | - Bram van Es
- Central Diagnostic Laboratory, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands.
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9
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Denkert C, Rachakonda S, Karn T, Weber K, Martin M, Marmé F, Untch M, Bonnefoi H, Kim SB, Seiler S, Bear HD, Witkiewicz AK, Im SA, DeMichele A, Pehl A, Van't Veer L, McCarthy N, Stiewe T, Jank P, Gelmon KA, García-Sáenz JA, Westhoff CC, Kelly CM, Reimer T, Felder B, Olivé MM, Knudsen ES, Turner N, Rojo F, Schmitt WD, Fasching PA, Teply-Szymanski J, Zhang Z, Toi M, Rugo HS, Gnant M, Makris A, Holtschmidt J, Nekljudova V, Loibl S. Dynamics of molecular heterogeneity in high-risk luminal breast cancer-From intrinsic to adaptive subtyping. Cancer Cell 2025; 43:232-247.e4. [PMID: 39933898 DOI: 10.1016/j.ccell.2025.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 01/09/2025] [Accepted: 01/09/2025] [Indexed: 02/13/2025]
Abstract
We evaluate therapy-induced molecular heterogeneity in longitudinal samples from high-risk, hormone-receptor positive/HER2-negative breast cancer patients with residual tumor after neoadjuvant chemotherapy from the Penelope-B trial (NCT01864746; EudraCT 2013-001040-62). Intrinsic subtypes are prognostic in pre-therapeutic (Tx) samples (n = 629, p < 0.0001) and post-Tx residual tumors (n = 782, p < 0.0001). After neoadjuvant chemotherapy, a shift of intrinsic subtypes is observed from pre-Tx luminal (Lum) B to post-Tx LumA, with reverse transition back to LumB in metastases. In a combined analysis of 540 paired pre-Tx and post-Tx samples, we identify five adaptive clusters (AC-1-5) based on transcriptomic changes before and after neoadjuvant chemotherapy. These AC-subtypes are prognostic beyond classical intrinsic subtyping, categorizing patients into groups with excellent prognosis (AC-1 and AC-2), poor prognosis (AC-3 and AC-4), and very poor prognosis (AC-5, enriched for basal-like subtype). Our analysis provides a basis for an extended molecular classification of breast cancer patients and improved identification of high-risk patient populations.
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Affiliation(s)
- Carsten Denkert
- Institute of Pathology, Philipps-University Marburg and University Hospital Marburg, Marburg, Germany.
| | | | - Thomas Karn
- Department of Gynecology and Obstetrics, Goethe-University, Frankfurt, Germany
| | | | - Miguel Martin
- Instituto de Investigacion Sanitaria Gregorio Marañon, CIBERONC, Universidad Complutense, Madrid, Spain; Spanish Breast Cancer Group, GEICAM, Madrid, Spain
| | - Frederik Marmé
- Medical Faculty Mannheim, Heidelberg University, University Hospital Mannheim, Mannheim, Germany
| | - Michael Untch
- Helios Kliniken Berlin-Buch, Berlin, Germany; AGO-B Study Group, Erlangen, Germany
| | - Hervé Bonnefoi
- Institut Bergonié and Université de Bordeaux UFR Collège Sciences de la Santé, INSERM U1312, Bordeaux, France
| | - Sung-Bae Kim
- Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | | | - Harry D Bear
- Division of Surgical Oncology, Massey Comprehensive Cancer Center, Virginia Commonwealth University, VCU Health, Richmond, VA, USA
| | | | - Seock-Ah Im
- Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | | | - Anika Pehl
- Institute of Pathology, Philipps-University Marburg and University Hospital Marburg, Marburg, Germany
| | | | - Nicole McCarthy
- Breast Cancer Trials Australia and New Zealand and University of Queensland, Queensland, Brisbane, Australia
| | - Thorsten Stiewe
- Genomics Core Facility, Philipps-University Marburg, Marburg, Germany
| | - Paul Jank
- Institute of Pathology, Philipps-University Marburg and University Hospital Marburg, Marburg, Germany
| | | | | | - Christina C Westhoff
- Institute of Pathology, Philipps-University Marburg and University Hospital Marburg, Marburg, Germany
| | - Catherine M Kelly
- Mater Private Hospital, Dublin and Cancer Trials Ireland Breast Group, Dublin, Ireland
| | - Toralf Reimer
- Department of Obstetrics and Gynecology, University of Rostock, Rostock, Germany
| | | | | | - Erik S Knudsen
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Nicholas Turner
- Royal Marsden Hospital and Institute of Cancer Research, London, UK
| | - Federico Rojo
- Spanish Breast Cancer Group, GEICAM, Madrid, Spain; Hospital Universitario Fundación Jiménez Díaz, Madrid, Spain
| | - Wolfgang D Schmitt
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Pathology, Berlin, Germany
| | - Peter A Fasching
- University Hospital Erlangen, Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Julia Teply-Szymanski
- Institute of Pathology, Philipps-University Marburg and University Hospital Marburg, Marburg, Germany
| | - Zhe Zhang
- Pfizer Inc., San Diego, CA, United States of America
| | - Masakazu Toi
- Breast Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan; Tokyo Metropolitan Cancer and Infectious Disease Center, Komagome Hospital, Tokyo, Japan
| | - Hope S Rugo
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA, USA
| | - Michael Gnant
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
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10
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Ramanan S, Akarca D, Henderson SK, Rouse MA, Allinson K, Patterson K, Rowe JB, Lambon Ralph MA. The graded multidimensional geometry of phenotypic variation and progression in neurodegenerative syndromes. Brain 2025; 148:448-466. [PMID: 39018014 PMCID: PMC11788217 DOI: 10.1093/brain/awae233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 05/29/2024] [Accepted: 06/17/2024] [Indexed: 07/18/2024] Open
Abstract
Clinical variants of Alzheimer's disease and frontotemporal lobar degeneration display a spectrum of cognitive-behavioural changes varying between individuals and over time. Understanding the landscape of these graded individual/group level longitudinal variations is critical for precise phenotyping; however, this remains challenging to model. Addressing this challenge, we leverage the National Alzheimer's Coordinating Center database to derive a unified geometric framework of graded longitudinal phenotypic variation in Alzheimer's disease and frontotemporal lobar degeneration. We included three time point, cognitive-behavioural and clinical data from 390 typical, atypical and intermediate Alzheimer's disease and frontotemporal lobar degeneration variants (114 typical Alzheimer's disease; 107 behavioural variant frontotemporal dementia; 42 motor variants of frontotemporal lobar degeneration; and 103 primary progressive aphasia patients). On these data, we applied advanced data-science approaches to derive low-dimensional geometric spaces capturing core features underpinning clinical progression of Alzheimer's disease and frontotemporal lobar degeneration syndromes. To do so, we first used principal component analysis to derive six axes of graded longitudinal phenotypic variation capturing patient-specific movement along and across these axes. Then, we distilled these axes into a visualizable 2D manifold of longitudinal phenotypic variation using Uniform Manifold Approximation and Projection. Both geometries together enabled the assimilation and interrelation of paradigmatic and mixed cases, capturing dynamic individual trajectories and linking syndromic variability to neuropathology and key clinical end points, such as survival. Through these low-dimensional geometries, we show that (i) specific syndromes (Alzheimer's disease and primary progressive aphasia) converge over time into a de-differentiated pooled phenotype, while others (frontotemporal dementia variants) diverge to look different from this generic phenotype; (ii) phenotypic diversification is predicted by simultaneous progression along multiple axes, varying in a graded manner between individuals and syndromes; and (iii) movement along specific principal axes predicts survival at 36 months in a syndrome-specific manner and in individual pathological groupings. The resultant mapping of dynamics underlying cognitive-behavioural evolution potentially holds paradigm-changing implications to predicting phenotypic diversification and phenotype-neurobiological mapping in Alzheimer's disease and frontotemporal lobar degeneration.
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Affiliation(s)
- Siddharth Ramanan
- Medical Research Council Cognition and Brain Sciences Unit, University of Cambridge, Cambridge CB2 7EF, UK
| | - Danyal Akarca
- Medical Research Council Cognition and Brain Sciences Unit, University of Cambridge, Cambridge CB2 7EF, UK
| | - Shalom K Henderson
- Medical Research Council Cognition and Brain Sciences Unit, University of Cambridge, Cambridge CB2 7EF, UK
- Department of Clinical Neurosciences and Cambridge University Hospitals NHS Trust, University of Cambridge, Cambridge CB2 0SZ, UK
| | - Matthew A Rouse
- Medical Research Council Cognition and Brain Sciences Unit, University of Cambridge, Cambridge CB2 7EF, UK
| | - Kieren Allinson
- Department of Clinical Neurosciences and Cambridge University Hospitals NHS Trust, University of Cambridge, Cambridge CB2 0SZ, UK
- Department of Pathology, Cambridge University Hospitals NHS Trust, Cambridge CB2 1QP, UK
| | - Karalyn Patterson
- Medical Research Council Cognition and Brain Sciences Unit, University of Cambridge, Cambridge CB2 7EF, UK
- Department of Clinical Neurosciences and Cambridge University Hospitals NHS Trust, University of Cambridge, Cambridge CB2 0SZ, UK
| | - James B Rowe
- Medical Research Council Cognition and Brain Sciences Unit, University of Cambridge, Cambridge CB2 7EF, UK
- Department of Clinical Neurosciences and Cambridge University Hospitals NHS Trust, University of Cambridge, Cambridge CB2 0SZ, UK
| | - Matthew A Lambon Ralph
- Medical Research Council Cognition and Brain Sciences Unit, University of Cambridge, Cambridge CB2 7EF, UK
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11
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Lichtarge J, Cappuccio G, Pati S, Dei-Ampeh AK, Sing S, Ma L, Liu Z, Maletic-Savatic M. MetaboLINK is a novel algorithm for unveiling cell-specific metabolic pathways in longitudinal datasets. Front Neurosci 2025; 18:1520982. [PMID: 39872998 PMCID: PMC11769959 DOI: 10.3389/fnins.2024.1520982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2024] [Accepted: 12/20/2024] [Indexed: 01/30/2025] Open
Abstract
Introduction In the rapidly advancing field of 'omics research, there is an increasing demand for sophisticated bioinformatic tools to enable efficient and consistent data analysis. As biological datasets, particularly metabolomics, become larger and more complex, innovative strategies are essential for deciphering the intricate molecular and cellular networks. Methods We introduce a pioneering analytical approach that combines Principal Component Analysis (PCA) with Graphical Lasso (GLASSO). This method is designed to reduce the dimensionality of large datasets while preserving significant variance. For the first time, we applied the PCA-GLASSO algorithm (i.e., MetaboLINK) to metabolomics data derived from Nuclear Magnetic Resonance (NMR) spectroscopy performed on neural cells at various developmental stages, from human embryonic stem cells to neurons. Results The MetaboLINK analysis of longitudinal metabolomics data has revealed distinct pathways related to amino acids, lipids, and energy metabolism, uniquely associated with specific cell progenies. These findings suggest that different metabolic pathways play a critical role at different stages of cellular development, each contributing to diverse cellular functions. Discussion Our study demonstrates the efficacy of the MetaboLINK approach in analyzing NMR-based longitudinal metabolomic datasets, highlighting key metabolic shifts during cellular transitions. We share the methodology and the code to advance general 'omics research, providing a powerful tool for dissecting large datasets in neurobiology and other fields.
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Affiliation(s)
- Jared Lichtarge
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, United States
| | - Gerarda Cappuccio
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, United States
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, United States
| | - Soumya Pati
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, United States
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, United States
| | - Alfred Kwabena Dei-Ampeh
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, United States
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, United States
| | - Senghong Sing
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, United States
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, United States
- College of Natural Sciences and Mathematics, University of Houston, Houston, TX, United States
| | - LiHua Ma
- Shared Equipment Authority, Rice University, Houston, TX, United States
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, United States
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, United States
| | - Mirjana Maletic-Savatic
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, United States
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, United States
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
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12
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Vial L, Descotes F, Lopez J, Alsugair Z, Céruse P, Philouze P, Fieux M, Wassef M, Baglin AC, Onea M, Castain C, Delvenne P, Fromont-Hankard G, Gilles H, Monnien F, Mauvais O, Lépine C, Le Gall F, Rousselet MC, Sudaka A, Uro-Coste E, Casiraghi O, Costes-Martineau V, Benzerdjeb N. Reappraisal of Oncocytic Adenocarcinoma: Unveiling Its Connection to Oncocytic Variants of Salivary Duct Carcinoma and Mucoepidermoid Carcinoma Through ImmunoHisto-Molecular Perspectives. Am J Surg Pathol 2025; 49:73-82. [PMID: 39513520 PMCID: PMC11634103 DOI: 10.1097/pas.0000000000002324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2024]
Abstract
Oncocytic adenocarcinoma (OC) of the salivary glands is a rare and controversial entity. It was recently reclassified as "salivary carcinoma NOS and emerging entities" in the 2022 WHO classification of head and neck tumors. The lack of specific molecular alterations and its potential affiliation with other salivary gland carcinomas, such as the oncocytic mucoepidermoid carcinomas (OMEC) or the oncocytic subtype of salivary duct carcinomas (OSDC) justified this reclassification. It is becoming essential to clarify the complex spectrum of potential diagnoses surrounding oncocytic tumors. The objective of this study was to explore the histologic features, as well as the immunohistochemical and molecular profiles, of cases previously diagnosed as OC or OMEC of the salivary glands. This study involved 28 cases of carcinomas with a predominantly oncocytic component. The sex distribution was equal. The median age was 59 years (range 10 to 89). Most of these cases originated from the parotid gland (25/28). The mean tumor size was 2.4 cm (range 0.5 to 6.5). Primary immuno-morphological and mutation/gene fusion profiles reclassified mainly (64.3%, 18/28). Most of them were reclassified in descending order as OSDC (8/18), OMEC (5/18), and OC (2/18). But 3 cases remained unclassified (3/18). The transcriptomic analysis found a proximity of their transcriptomic profile with the OMEC group and a distance from the OSDCs. These findings imply that OC is not distinct but represents oncocytic variants of other salivary carcinomas. It underscores the importance of thorough morphologic, immunohistochemical, and molecular examinations to accurately diagnose carcinomas with predominant oncocytic components in the salivary glands.
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Affiliation(s)
- Lucas Vial
- Department of Pathology, Institut of Pathologie Multisite, University Hospital of Lyon Sud, Hospices Civils de Lyon
| | | | - Jonathan Lopez
- Biochemistry and Molecular Biology Department
- Université Claude Bernard Lyon 1
| | - Ziyad Alsugair
- Department of Pathology, Institut of Pathologie Multisite, University Hospital of Lyon Sud, Hospices Civils de Lyon
| | - Philippe Céruse
- Université Claude Bernard Lyon 1
- Department of Oto-Rhino-Laryngology and Cervico-Facial Surgery, Hôpital La Croix Rousse, Hospices Civils de Lyon
| | - Pierre Philouze
- Université Claude Bernard Lyon 1
- Department of Oto-Rhino-Laryngology and Cervico-Facial Surgery, Hôpital La Croix Rousse, Hospices Civils de Lyon
| | - Maxime Fieux
- Department of Oto-Rhino-Laryngology and Cervico-Facial Surgery, University Hospital of Lyon Sud, Hospices Civils de Lyon, Pierre-Bénite
- Université Claude Bernard Lyon 1
| | - Michel Wassef
- Department of Pathology, Hôpital Lariboisière, AP-HP, Université Paris Diderot, Paris
| | - Anne-Catherine Baglin
- Department of Pathology, Hôpital Lariboisière, AP-HP, Université Paris Diderot, Paris
| | - Mihaela Onea
- Pathology Department, University Hospital of Strasbourg, Strasbourg
| | - Claire Castain
- Pathology Department, University Hospital of Bordeaux, Bordeaux
| | | | | | - Hugot Gilles
- Department of Pathology, University Grenoble Alpes, CHU de Grenoble-Alpes, Grenoble
| | | | - Olivier Mauvais
- Oto-Rhino-Laryngology and Cervico-Facial Surgery, University Hospital of Besançon, Besançon
| | | | | | | | - Anne Sudaka
- Department of Pathology, Centre Antoine Lacassagne, Nice
| | | | - Odile Casiraghi
- Department of Pathology, Gustave Roussy Institute, Villejuif
| | | | - Nazim Benzerdjeb
- Department of Pathology, Institut of Pathologie Multisite, University Hospital of Lyon Sud, Hospices Civils de Lyon
- EMR3738, CICLY, Université Claude Bernard Lyon 1, Lyon
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13
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Che Y, Zhao M, Gao Y, Zhang Z, Zhang X. Application of machine learning for mass spectrometry-based multi-omics in thyroid diseases. Front Mol Biosci 2024; 11:1483326. [PMID: 39741929 PMCID: PMC11685090 DOI: 10.3389/fmolb.2024.1483326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2024] [Accepted: 12/02/2024] [Indexed: 01/03/2025] Open
Abstract
Thyroid diseases, including functional and neoplastic diseases, bring a huge burden to people's health. Therefore, a timely and accurate diagnosis is necessary. Mass spectrometry (MS) based multi-omics has become an effective strategy to reveal the complex biological mechanisms of thyroid diseases. The exponential growth of biomedical data has promoted the applications of machine learning (ML) techniques to address new challenges in biology and clinical research. In this review, we presented the detailed review of applications of ML for MS-based multi-omics in thyroid disease. It is primarily divided into two sections. In the first section, MS-based multi-omics, primarily proteomics and metabolomics, and their applications in clinical diseases are briefly discussed. In the second section, several commonly used unsupervised learning and supervised algorithms, such as principal component analysis, hierarchical clustering, random forest, and support vector machines are addressed, and the integration of ML techniques with MS-based multi-omics data and its application in thyroid disease diagnosis is explored.
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Affiliation(s)
- Yanan Che
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Meng Zhao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Yan Gao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Zhibin Zhang
- Department of General Surgery, Tianjin First Central Hospital, Tianjin, China
| | - Xiangyang Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
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14
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Shao Y, Lv X, Ying S, Guo Q. Artificial Intelligence-Driven Precision Medicine: Multi-Omics and Spatial Multi-Omics Approaches in Diffuse Large B-Cell Lymphoma (DLBCL). FRONT BIOSCI-LANDMRK 2024; 29:404. [PMID: 39735973 DOI: 10.31083/j.fbl2912404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/17/2024] [Accepted: 06/25/2024] [Indexed: 12/31/2024]
Abstract
In this comprehensive review, we delve into the transformative role of artificial intelligence (AI) in refining the application of multi-omics and spatial multi-omics within the realm of diffuse large B-cell lymphoma (DLBCL) research. We scrutinized the current landscape of multi-omics and spatial multi-omics technologies, accentuating their combined potential with AI to provide unparalleled insights into the molecular intricacies and spatial heterogeneity inherent to DLBCL. Despite current progress, we acknowledge the hurdles that impede the full utilization of these technologies, such as the integration and sophisticated analysis of complex datasets, the necessity for standardized protocols, the reproducibility of findings, and the interpretation of their biological significance. We proceeded to pinpoint crucial research voids and advocated for a trajectory that incorporates the development of advanced AI-driven data integration and analytical frameworks. The evolution of these technologies is crucial for enhancing resolution and depth in multi-omics studies. We also emphasized the importance of amassing extensive, meticulously annotated multi-omics datasets and fostering translational research efforts to connect laboratory discoveries with clinical applications seamlessly. Our review concluded that the synergistic integration of multi-omics, spatial multi-omics, and AI holds immense promise for propelling precision medicine forward in DLBCL. By surmounting the present challenges and steering towards the outlined futuristic pathways, we can harness these potent investigative tools to decipher the molecular and spatial conundrums of DLBCL. This will pave the way for refined diagnostic precision, nuanced risk stratification, and individualized therapeutic regimens, ushering in a new era of patient-centric oncology care.
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Affiliation(s)
- Yanping Shao
- Department of Hematology, The Second Affiliated Hospital, Zhejiang University School of Medicine, 310009 Hangzhou, Zhejiang, China
| | - Xiuyan Lv
- Department of Hematology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, 317000 Taizhou, Zhejiang, China
| | - Shuangwei Ying
- Department of Hematology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, 317000 Taizhou, Zhejiang, China
| | - Qunyi Guo
- Department of Hematology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, 317000 Taizhou, Zhejiang, China
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15
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Kittke V, Zhao C, Lam DD, Harrer P, Krezel W, Schormair B, Oexle K, Winkelmann J. RLS-associated MEIS transcription factors control distinct processes in human neural stem cells. Sci Rep 2024; 14:28986. [PMID: 39578497 PMCID: PMC11584712 DOI: 10.1038/s41598-024-80266-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Accepted: 11/18/2024] [Indexed: 11/24/2024] Open
Abstract
MEIS1 and MEIS2 encode highly conserved homeodomain transcription factors crucial for developmental processes in a wide range of tissues, including the brain. They can execute redundant functions when co-expressed in the same cell types, but their roles during early stages of neural differentiation have not been systematically compared. By separate knockout and overexpression of MEIS1 and MEIS2 in human neural stem cells, we find they control specific sets of target genes, associated with distinct biological processes. Integration of DNA binding sites with differential transcriptomics implicates MEIS1 to co-regulate gene expression by interaction with transcription factors of the SOX and FOX families. MEIS1 harbors the strongest risk factor for restless legs syndrome (RLS). Our data suggest that MEIS1 can directly regulate the RLS-associated genes NTNG1, MDGA1 and DACH1, constituting new approaches to study the elusive pathomechanism or RLS.
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Affiliation(s)
- Volker Kittke
- Institute of Neurogenomics, Helmholtz Munich, Neuherberg, Germany.
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.
- DZPG (German Center for Mental Health), Munich, Germany.
| | - Chen Zhao
- Institute of Neurogenomics, Helmholtz Munich, Neuherberg, Germany
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Daniel D Lam
- Institute of Neurogenomics, Helmholtz Munich, Neuherberg, Germany
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Global Computational Biology & Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Philip Harrer
- Institute of Neurogenomics, Helmholtz Munich, Neuherberg, Germany
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Wojciech Krezel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
| | - Barbara Schormair
- Institute of Neurogenomics, Helmholtz Munich, Neuherberg, Germany.
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.
- DZPG (German Center for Mental Health), Munich, Germany.
| | - Konrad Oexle
- Institute of Neurogenomics, Helmholtz Munich, Neuherberg, Germany.
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.
| | - Juliane Winkelmann
- Institute of Neurogenomics, Helmholtz Munich, Neuherberg, Germany.
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.
- DZPG (German Center for Mental Health), Munich, Germany.
- Munich Cluster for Systems Neurology, SyNergy, Munich, Germany.
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16
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Lara-Ramírez EE, Rivera G, Oliva-Hernández AA, Bocanegra-Garcia V, López JA, Guo X. Unsupervised learning analysis on the proteomes of Zika virus. PeerJ Comput Sci 2024; 10:e2443. [PMID: 39650519 PMCID: PMC11623125 DOI: 10.7717/peerj-cs.2443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Accepted: 10/01/2024] [Indexed: 12/11/2024]
Abstract
Background The Zika virus (ZIKV), which is transmitted by mosquito vectors to nonhuman primates and humans, causes devastating outbreaks in the poorest tropical regions of the world. Molecular epidemiology, supported by clustering phylogenetic gold standard studies using sequence data, has provided valuable information for tracking and controlling the spread of ZIKV. Unsupervised learning (UL), a form of machine learning algorithm, can be applied on the datasets without the need of known information for training. Methods In this work, unsupervised Random Forest (URF), followed by the application of dimensional reduction algorithms such as principal component analysis (PCA), Uniform Manifold Approximation and Projection (UMAP), t-distributed stochastic neighbor embedding (t-SNE), and autoencoders were used to uncover hidden patterns from polymorphic amino acid sites extracted on the proteome ZIKV multi-alignments, without the need of an underlying evolutionary model. Results The four UL algorithms revealed specific host and geographical clustering patterns for ZIKV. Among the four dimensionality reduction (DR) algorithms, the performance was better for UMAP. The four algorithms allowed the identification of imported viruses for specific geographical clusters. The UL dimension coordinates showed a significant correlation with phylogenetic tree branch lengths and significant phylogenetic dependence in Abouheif's Cmean and Pagel's Lambda tests (p value < 0.01) that showed comparable performance with the phylogenetic method. This analytical strategy was generalizable to an external large dengue type 2 dataset. Conclusion These UL algorithms could be practical evolutionary analytical techniques to track the dispersal of viral pathogens.
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Affiliation(s)
- Edgar E. Lara-Ramírez
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa, Tamaulipas, México
| | - Gildardo Rivera
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa, Tamaulipas, México
| | - Amanda Alejandra Oliva-Hernández
- Laboratorio de Biotecnología Experimental, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa, Tamaulipas, México
| | - Virgilio Bocanegra-Garcia
- Laboratorio de Interacción Ambiente Microorganismo, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa, Tamaulipas, México
| | - Jesús Adrián López
- Laboratorio de microRNAs y Cáncer, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Zacatecas, México
| | - Xianwu Guo
- Laboratorio de Biotecnología Genómica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa, Tamaulipas, México
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17
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Jin H, Park SY, Lee JE, Park H, Jeong M, Lee H, Cho J, Lee YS. GTSE1-driven ZEB1 stabilization promotes pulmonary fibrosis through the epithelial-to-mesenchymal transition. Mol Ther 2024; 32:4138-4157. [PMID: 39342428 PMCID: PMC11573610 DOI: 10.1016/j.ymthe.2024.09.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 08/06/2024] [Accepted: 09/25/2024] [Indexed: 10/01/2024] Open
Abstract
G2 and S phase-expressed protein 1 (GTSE1) has been implicated in the development of pulmonary fibrosis (PF); however, its biological function, molecular mechanism, and potential clinical implications remain unknown. Here, we explored the genomic data of patients with idiopathic PF (IPF) and found that GTSE1 expression is elevated in their lung tissues, but rarely expressed in normal lung tissues. Thus, we explored the biological role and downstream events of GTSE1 using IPF patient tissues and PF mouse models. The comprehensive bioinformatics analyses suggested that the increase of GTSE1 in IPF is linked to the enhanced gene signature for the epithelial-to-mesenchymal transition (EMT), leading us to investigate the potential interaction between GTSE1 and EMT transcription factors. GTSE1 preferentially binds to the less stable form of zinc-finger E-box-binding homeobox 1 (ZEB1), the unphosphorylated form at Ser585, inhibiting ZEB1 degradation. Consistently, the ZEB1 protein level in IPF patient and PF mouse tissues correlates with the GTSE1 protein level and the amount of collagen accumulation, representing fibrosis severity. Collectively, our findings highlight the GTSE1-ZEB1 axis as a novel driver of the pathological EMT characteristic during PF development and progression, supporting further investigation into GTSE1-targeting approaches for PF treatment.
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Affiliation(s)
- Hee Jin
- Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - So-Yeon Park
- Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Republic of Korea; Center for Genome Engineering, Institute for Basic Science, Daejeon 34126, Republic of Korea
| | - Ji Eun Lee
- Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Hangyeol Park
- Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Michaela Jeong
- Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Hyukjin Lee
- Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Jaeho Cho
- Department of Radiation Oncology, Yonsei University Health System, Seoul 120-749, Republic of Korea
| | - Yun-Sil Lee
- Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Republic of Korea.
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Park LM, Lannigan J, Low Q, Jaimes MC, Bonilla DL. OMIP-069 version 2: Update to the 40-color full Spectrum flow cytometry panel for deep immunophenotyping of major cell subsets in human peripheral blood. Cytometry A 2024; 105:791-799. [PMID: 39268753 DOI: 10.1002/cyto.a.24898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 08/12/2024] [Accepted: 08/29/2024] [Indexed: 09/15/2024]
Affiliation(s)
- Lily M Park
- Cytek Biosciences, Inc. Scientific Commercialization, Fremont, California, USA
| | - Joanne Lannigan
- Flow Cytometry Support Services, LLC, Alexandria, Virginia, USA
| | - Quentin Low
- Cytek Biosciences, Inc. Scientific Commercialization, Fremont, California, USA
| | - Maria C Jaimes
- Cytek Biosciences, Inc. Scientific Commercialization, Fremont, California, USA
| | - Diana L Bonilla
- Cytek Biosciences, Inc. Scientific Commercialization, Fremont, California, USA
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19
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Liu D, Wei C, Guan L, Ju W, Xiang S, Lian F. Combining single-cell RNA sequencing and network pharmacology to explore the target of cangfu daotan decoction in the treatment of obese polycystic ovary syndrome from an immune perspective. Front Pharmacol 2024; 15:1451300. [PMID: 39539629 PMCID: PMC11557475 DOI: 10.3389/fphar.2024.1451300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Accepted: 09/26/2024] [Indexed: 11/16/2024] Open
Abstract
Background Polycystic ovary syndrome (PCOS) is a heterogeneous gynecological endocrine disorder linked to immunity. Cangfu Daotan Decoction (CFDT), a classic Chinese medicine prescription, is particularly effective in treating PCOS, specifically in patients with obesity; however, its specific mechanism remains unclear. Methods Part 1: Peripheral blood mononuclear cells were collected on egg retrieval day from obese and normal-weight patients with PCOS and healthy women undergoing in vitro fertilization (IVF)-embryo transfer. Next, scRNA-seq was performed to screen the key genes of bese patients with PCOS. Part 2: Active ingredients of CFDT and obesity-related PCOS targets were identified based on public databases, and the binding ability between the active ingredients and targets was analyzed. Part 3: This part was a monocentric, randomized controlled trial. The obese women with PCOS were randomized to CFDT (6 packets/day) or placebo, and the healthy women were included in the blank control group (43 cases per group). The clinical manifestations and laboratory outcomes among the three groups were compared. Results Based on the scRNA-seq data from Part 1, CYLD, ARPC3, CXCR4, RORA, JUN, FGL2, ZEB2, GNLY, FTL, SMAD3, IL7R, KIR2DL1, CTSD, BTG2, CCL5, HLA, RETN, CTSZ, and NCF2 were potential key genes associated with obese PCOS were identified. The proportions of T, B, and natural killer cells were higher in patients with PCOS compared to healthy women, with even higher proportions observed in obese patients with PCOS. Gene ontology and the Kyoto encyclopedia of genes and genomes analysis depicted that the differentially expressed genes were related to immune regulation pathways. Network pharmacology analysis identified that the key active components in CFDT were quercetin, carvacrol, β-sitosterol, cholesterol, and nobiletin, and TP53, AKT1, STAT3, JUN, SRC, etc. were the core targets. The core targets and their enrichment pathways overlapped with those in Part 1. Clinical trials in Part 3 found that CFDT reduced the dosage of gonadotropins use in patients with PCOS, increased the number of high-quality embryos, and improved the ongoing pregnancy rate. Conclusion CFDT can improve the immune microenvironment of patients to some extent, reduce their economic burden, and enhance IVF outcomes. The improvement in the immune microenvironment in obese patients with PCOS may be linked to targets such as JUN and AKT.
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Affiliation(s)
- Danqi Liu
- The First Clinical Medicine School, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON, Canada
| | - Chaofeng Wei
- The First Clinical Medicine School, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Lu Guan
- The First Clinical Medicine School, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Wenhan Ju
- The First Clinical Medicine School, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Shan Xiang
- The First Clinical Medicine School, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
- Integrative Medicine Research Centre of Reproduction and Heredity, Affiliated Hospital, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Fang Lian
- The First Clinical Medicine School, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
- Integrative Medicine Research Centre of Reproduction and Heredity, Affiliated Hospital, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
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20
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Chinni BK, Manlhiot C. Emerging Analytical Approaches for Personalized Medicine Using Machine Learning In Pediatric and Congenital Heart Disease. Can J Cardiol 2024; 40:1880-1896. [PMID: 39097187 DOI: 10.1016/j.cjca.2024.07.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/25/2024] [Accepted: 07/26/2024] [Indexed: 08/05/2024] Open
Abstract
Precision and personalized medicine, the process by which patient management is tailored to individual circumstances, are now terms that are familiar to cardiologists, despite it still being an emerging field. Although precision medicine relies most often on the underlying biology and pathophysiology of a patient's condition, personalized medicine relies on digital biomarkers generated through algorithms. Given the complexity of the underlying data, these digital biomarkers are most often generated through machine-learning algorithms. There are a number of analytic considerations regarding the creation of digital biomarkers that are discussed in this review, including data preprocessing, time dependency and gating, dimensionality reduction, and novel methods, both in the realm of supervised and unsupervised machine learning. Some of these considerations, such as sample size requirements and measurements of model performance, are particularly challenging in small and heterogeneous populations with rare outcomes such as children with congenital heart disease. Finally, we review analytic considerations for the deployment of digital biomarkers in clinical settings, including the emerging field of clinical artificial intelligence (AI) operations, computational needs for deployment, efforts to increase the explainability of AI, algorithmic drift, and the needs for distributed surveillance and federated learning. We conclude this review by discussing a recent simulation study that shows that, despite these analytic challenges and complications, the use of digital biomarkers in managing clinical care might have substantial benefits regarding individual patient outcomes.
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Affiliation(s)
- Bhargava K Chinni
- The Blalock-Taussig-Thomas Pediatric and Congenital Heart Center, Department of Pediatrics, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Cedric Manlhiot
- The Blalock-Taussig-Thomas Pediatric and Congenital Heart Center, Department of Pediatrics, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA; Research Institute, SickKids Hospital, Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada.
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21
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Golob J, Rao K, Berinstein JA, Singh P, Chey WD, Owyang C, Kamada N, Higgins PDR, Young V, Bishu S, Lee AA. Why Symptoms Linger in Quiescent Crohn's Disease: Investigating the Impact of Sulfidogenic Microbes and Sulfur Metabolic Pathways. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.09.08.24313266. [PMID: 39314983 PMCID: PMC11419226 DOI: 10.1101/2024.09.08.24313266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Introduction Even in the absence of inflammation, persistent symptoms in patients with Crohn's disease (CD) are prevalent and worsen quality of life. We previously demonstrated enrichment in sulfidogenic microbes in quiescent Crohn's disease patients with ( qCD+S ) vs. without persistent GI symptoms ( qCD-S ). Thus, we hypothesized that sulfur metabolic pathways would be enriched in stool while differentially abundant microbes would be associated with important sulfur-metabolic pathways in qCD+S. Methods We performed a multi-center observational study nested within SPARC IBD. Quiescent inflammation was defined by fecal calprotectin level <150 mcg/g. Persistent symptoms were defined by CD-PRO2. Active CD ( aCD ) and non-IBD diarrhea-predominant irritable bowel syndrome ( IBS-D ) were included as controls. Results Thirty-nine patients with qCD+S, 274 qCD-S, 21 aCD, and 40 IBS-D underwent paired shotgun metagenomic sequencing and untargeted metabolomic profiling. The fecal metabolome in qCD+S was significantly different relative to qCD-S and IBS-D but not aCD. Patients with qCD+S were enriched in sulfur-containing amino acid pathways, including cysteine and methionine, as well as serine, glycine, and threonine. Glutathione and nicotinate/nicotinamide pathways were also enriched in qCD+S relative to qCD-S, suggestive of mitochondrial dysfunction, a downstream target of H 2 S signaling. Multi-omic integration demonstrated that enriched microbes in qCD+S were associated with important sulfur-metabolic pathways. Bacterial sulfur-metabolic genes, including CTH , isfD , sarD , and asrC , were dysregulated in qCD+S. Finally, sulfur metabolites with and without sulfidogenic microbes showed good accuracy in predicting presence of qCD+S. Discussion Microbial-derived sulfur pathways and downstream mitochondrial function are perturbed in qCD+S, which implicate H 2 S signaling in the pathogenesis of this condition. Future studies will determine whether targeting H 2 S pathways results in improved quality of life in qCD+S. Key Messages What is Already Known Even in the absence of inflammation, persistent gastrointestinal symptoms are common in Crohn's disease.The microbiome is altered in quiescent Crohn's disease patients with persistent symptoms, but the functional significance of these changes is unknown. What is New Here Sulfur metabolites and sulfur metabolic pathways were enriched in stool in quiescent Crohn's disease patients with persistent symptoms.Multi-omic integration showed enriched microbes were associated with important sulfur metabolic pathways in quiescent Crohn's disease patients with persistent symptoms. How Can This Study Help Patient Care Strategies to decrease sulfidogenic microbes and associated sulfur metabolic pathways could represent a novel strategy to improve quality of life in quiescent Crohn's disease with persistent GI symptoms.
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22
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de Back TR, van Hooff SR, Sommeijer DW, Vermeulen L. Transcriptomic subtyping of gastrointestinal malignancies. Trends Cancer 2024; 10:842-856. [PMID: 39019673 DOI: 10.1016/j.trecan.2024.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 07/19/2024]
Abstract
Gastrointestinal (GI) cancers are highly heterogeneous at multiple levels. Tumor heterogeneity can be captured by molecular profiling, such as genetic, epigenetic, proteomic, and transcriptomic classification. Transcriptomic subtyping has the advantage of combining genetic and epigenetic information, cancer cell-intrinsic properties, and the tumor microenvironment (TME). Unsupervised transcriptomic subtyping systems of different GI malignancies have gained interest because they reveal shared biological features across cancers and bear prognostic and predictive value. Importantly, transcriptomic subtypes accurately reflect complex phenotypic states varying not only per tumor region, but also throughout disease progression, with consequences for clinical management. Here, we discuss methodologies of transcriptomic subtyping, proposed taxonomies for GI malignancies, and the challenges posed to clinical implementation, highlighting opportunities for future transcriptomic profiling efforts to optimize clinical impact.
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Affiliation(s)
- Tim R de Back
- Cancer Center Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands; Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Sander R van Hooff
- Cancer Center Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands; Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Dirkje W Sommeijer
- Flevohospital, Department of Internal Medicine, Hospitaalweg 1, 1315 RA, Almere, The Netherlands
| | - Louis Vermeulen
- Cancer Center Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands; Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
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23
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Verma R, Alban TJ, Parthasarathy P, Mokhtari M, Toro Castano P, Cohen ML, Lathia JD, Ahluwalia M, Tiwari P. Sexually dimorphic computational histopathological signatures prognostic of overall survival in high-grade gliomas via deep learning. SCIENCE ADVANCES 2024; 10:eadi0302. [PMID: 39178259 PMCID: PMC11343024 DOI: 10.1126/sciadv.adi0302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/16/2024] [Indexed: 08/25/2024]
Abstract
High-grade glioma (HGG) is an aggressive brain tumor. Sex is an important factor that differentially affects survival outcomes in HGG. We used an end-to-end deep learning approach on hematoxylin and eosin (H&E) scans to (i) identify sex-specific histopathological attributes of the tumor microenvironment (TME), and (ii) create sex-specific risk profiles to prognosticate overall survival. Surgically resected H&E-stained tissue slides were analyzed in a two-stage approach using ResNet18 deep learning models, first, to segment the viable tumor regions and second, to build sex-specific prognostic models for prediction of overall survival. Our mResNet-Cox model yielded C-index (0.696, 0.736, 0.731, and 0.729) for the female cohort and C-index (0.729, 0.738, 0.724, and 0.696) for the male cohort across training and three independent validation cohorts, respectively. End-to-end deep learning approaches using routine H&E-stained slides, trained separately on male and female patients with HGG, may allow for identifying sex-specific histopathological attributes of the TME associated with survival and, ultimately, build patient-centric prognostic risk assessment models.
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Affiliation(s)
- Ruchika Verma
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA
- Windreich Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tyler J. Alban
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic Foundation, Cleveland, OH, USA
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Prerana Parthasarathy
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Mojgan Mokhtari
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA
| | | | - Mark L. Cohen
- Department of Pathology, University Hospitals Case Medical Center, Cleveland, OH, USA
| | - Justin D. Lathia
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Rose Ella Burkhardt Brain Tumor and Neuro-Oncology Center, Cleveland Clinic, Cleveland, OH, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Manmeet Ahluwalia
- Miami Cancer Institute, Miami, FL, USA
- Herbert Wertheim College of Medicine, Florida International University, University Park, FL, USA
| | - Pallavi Tiwari
- Departments of Radiology and Biomedical Engineering, University of Wisconsin–Madison, Madison, WI, USA
- Carbone Cancer Center, Madison, WI, USA
- William S. Middleton Memorial Veterans Affairs Healthcare, Madison, WI, USA
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24
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Moreira-Filho JT, Ranganath D, Conway M, Schmitt C, Kleinstreuer N, Mansouri K. Democratizing cheminformatics: interpretable chemical grouping using an automated KNIME workflow. J Cheminform 2024; 16:101. [PMID: 39152469 PMCID: PMC11330086 DOI: 10.1186/s13321-024-00894-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 08/06/2024] [Indexed: 08/19/2024] Open
Abstract
With the increased availability of chemical data in public databases, innovative techniques and algorithms have emerged for the analysis, exploration, visualization, and extraction of information from these data. One such technique is chemical grouping, where chemicals with common characteristics are categorized into distinct groups based on physicochemical properties, use, biological activity, or a combination. However, existing tools for chemical grouping often require specialized programming skills or the use of commercial software packages. To address these challenges, we developed a user-friendly chemical grouping workflow implemented in KNIME, a free, open-source, low/no-code, data analytics platform. The workflow serves as an all-encompassing tool, expertly incorporating a range of processes such as molecular descriptor calculation, feature selection, dimensionality reduction, hyperparameter search, and supervised and unsupervised machine learning methods, enabling effective chemical grouping and visualization of results. Furthermore, we implemented tools for interpretation, identifying key molecular descriptors for the chemical groups, and using natural language summaries to clarify the rationale behind these groupings. The workflow was designed to run seamlessly in both the KNIME local desktop version and KNIME Server WebPortal as a web application. It incorporates interactive interfaces and guides to assist users in a step-by-step manner. We demonstrate the utility of this workflow through a case study using an eye irritation and corrosion dataset.Scientific contributionsThis work presents a novel, comprehensive chemical grouping workflow in KNIME, enhancing accessibility by integrating a user-friendly graphical interface that eliminates the need for extensive programming skills. This workflow uniquely combines several features such as automated molecular descriptor calculation, feature selection, dimensionality reduction, and machine learning algorithms (both supervised and unsupervised), with hyperparameter optimization to refine chemical grouping accuracy. Moreover, we have introduced an innovative interpretative step and natural language summaries to elucidate the underlying reasons for chemical groupings, significantly advancing the usability of the tool and interpretability of the results.
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Affiliation(s)
- José T Moreira-Filho
- National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods, Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA.
| | - Dhruv Ranganath
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Mike Conway
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Charles Schmitt
- Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Nicole Kleinstreuer
- National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods, Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Kamel Mansouri
- National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods, Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA.
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25
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Colombo F, Calesella F, Bravi B, Fortaner-Uyà L, Monopoli C, Tassi E, Carminati M, Zanardi R, Bollettini I, Poletti S, Lorenzi C, Spadini S, Brambilla P, Serretti A, Maggioni E, Fabbri C, Benedetti F, Vai B. Multimodal brain-derived subtypes of Major depressive disorder differentiate patients for anergic symptoms, immune-inflammatory markers, history of childhood trauma and treatment-resistance. Eur Neuropsychopharmacol 2024; 85:45-57. [PMID: 38936143 DOI: 10.1016/j.euroneuro.2024.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 05/20/2024] [Accepted: 05/27/2024] [Indexed: 06/29/2024]
Abstract
An estimated 30 % of Major Depressive Disorder (MDD) patients exhibit resistance to conventional antidepressant treatments. Identifying reliable biomarkers of treatment-resistant depression (TRD) represents a major goal of precision psychiatry, which is hampered by the clinical and biological heterogeneity. To uncover biologically-driven subtypes of MDD, we applied an unsupervised data-driven framework to stratify 102 MDD patients on their neuroimaging signature, including extracted measures of cortical thickness, grey matter volumes, and white matter fractional anisotropy. Our novel analytical pipeline integrated different machine learning algorithms to harmonize data, perform data dimensionality reduction, and provide a stability-based relative clustering validation. The obtained clusters were characterized for immune-inflammatory peripheral biomarkers, TRD, history of childhood trauma and depressive symptoms. Our results indicated two different clusters of patients, differentiable with 67 % of accuracy: one cluster (n = 59) was associated with a higher proportion of TRD, and higher scores of energy-related depressive symptoms, history of childhood abuse and emotional neglect; this cluster showed a widespread reduction in cortical thickness (d = 0.43-1.80) and volumes (d = 0.45-1.05), along with fractional anisotropy in the fronto-occipital fasciculus, stria terminalis, and corpus callosum (d = 0.46-0.52); the second cluster (n = 43) was associated with cognitive and affective depressive symptoms, thicker cortices and wider volumes. Multivariate analyses revealed distinct brain-inflammation relationships between the two clusters, with increase in pro-inflammatory markers being associated with decreased cortical thickness and volumes. Our stratification of MDD patients based on structural neuroimaging identified clinically-relevant subgroups of MDD with specific symptomatic and immune-inflammatory profiles, which can contribute to the development of tailored personalized interventions for MDD.
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Affiliation(s)
- Federica Colombo
- University Vita-Salute San Raffaele, Milano, Italy; Psychiatry and Clinical Psychobiology Unit, Division of Neuroscience, IRCCS San Raffaele Hospital, Milano, Italy.
| | - Federico Calesella
- Psychiatry and Clinical Psychobiology Unit, Division of Neuroscience, IRCCS San Raffaele Hospital, Milano, Italy
| | - Beatrice Bravi
- University Vita-Salute San Raffaele, Milano, Italy; Psychiatry and Clinical Psychobiology Unit, Division of Neuroscience, IRCCS San Raffaele Hospital, Milano, Italy
| | - Lidia Fortaner-Uyà
- University Vita-Salute San Raffaele, Milano, Italy; Psychiatry and Clinical Psychobiology Unit, Division of Neuroscience, IRCCS San Raffaele Hospital, Milano, Italy
| | - Camilla Monopoli
- Psychiatry and Clinical Psychobiology Unit, Division of Neuroscience, IRCCS San Raffaele Hospital, Milano, Italy
| | - Emma Tassi
- Department of Neurosciences and Mental Health, IRCCS Fondazione Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Politecnico di Milano, Department of Electronics, Information and Bioengineering, Milan, Italy
| | | | - Raffaella Zanardi
- University Vita-Salute San Raffaele, Milano, Italy; Mood Disorders Unit, Scientific Institute IRCCS San Raffaele Hospital, Milan, Italy
| | - Irene Bollettini
- Psychiatry and Clinical Psychobiology Unit, Division of Neuroscience, IRCCS San Raffaele Hospital, Milano, Italy
| | - Sara Poletti
- University Vita-Salute San Raffaele, Milano, Italy; Psychiatry and Clinical Psychobiology Unit, Division of Neuroscience, IRCCS San Raffaele Hospital, Milano, Italy
| | - Cristina Lorenzi
- Psychiatry and Clinical Psychobiology Unit, Division of Neuroscience, IRCCS San Raffaele Hospital, Milano, Italy
| | - Sara Spadini
- Psychiatry and Clinical Psychobiology Unit, Division of Neuroscience, IRCCS San Raffaele Hospital, Milano, Italy
| | - Paolo Brambilla
- Department of Neurosciences and Mental Health, IRCCS Fondazione Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Eleonora Maggioni
- Politecnico di Milano, Department of Electronics, Information and Bioengineering, Milan, Italy
| | - Chiara Fabbri
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Francesco Benedetti
- University Vita-Salute San Raffaele, Milano, Italy; Psychiatry and Clinical Psychobiology Unit, Division of Neuroscience, IRCCS San Raffaele Hospital, Milano, Italy
| | - Benedetta Vai
- University Vita-Salute San Raffaele, Milano, Italy; Psychiatry and Clinical Psychobiology Unit, Division of Neuroscience, IRCCS San Raffaele Hospital, Milano, Italy
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Bayones L, Zainos A, Alvarez M, Romo R, Franci A, Rossi-Pool R. Orthogonality of sensory and contextual categorical dynamics embedded in a continuum of responses from the second somatosensory cortex. Proc Natl Acad Sci U S A 2024; 121:e2316765121. [PMID: 38990946 PMCID: PMC11260089 DOI: 10.1073/pnas.2316765121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 06/12/2024] [Indexed: 07/13/2024] Open
Abstract
How does the brain simultaneously process signals that bring complementary information, like raw sensory signals and their transformed counterparts, without any disruptive interference? Contemporary research underscores the brain's adeptness in using decorrelated responses to reduce such interference. Both neurophysiological findings and artificial neural networks support the notion of orthogonal representation for signal differentiation and parallel processing. Yet, where, and how raw sensory signals are transformed into more abstract representations remains unclear. Using a temporal pattern discrimination task in trained monkeys, we revealed that the second somatosensory cortex (S2) efficiently segregates faithful and transformed neural responses into orthogonal subspaces. Importantly, S2 population encoding for transformed signals, but not for faithful ones, disappeared during a nondemanding version of this task, which suggests that signal transformation and their decoding from downstream areas are only active on-demand. A mechanistic computation model points to gain modulation as a possible biological mechanism for the observed context-dependent computation. Furthermore, individual neural activities that underlie the orthogonal population representations exhibited a continuum of responses, with no well-determined clusters. These findings advocate that the brain, while employing a continuum of heterogeneous neural responses, splits population signals into orthogonal subspaces in a context-dependent fashion to enhance robustness, performance, and improve coding efficiency.
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Affiliation(s)
- Lucas Bayones
- Instituto de Fisiología Celular, Departamento de Neurociencia Cognitiva, Universidad Nacional Autónoma de México, Mexico City04510, Mexico
| | - Antonio Zainos
- Instituto de Fisiología Celular, Departamento de Neurociencia Cognitiva, Universidad Nacional Autónoma de México, Mexico City04510, Mexico
| | - Manuel Alvarez
- Instituto de Fisiología Celular, Departamento de Neurociencia Cognitiva, Universidad Nacional Autónoma de México, Mexico City04510, Mexico
| | | | - Alessio Franci
- Departmento de Matemática, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City04510, Mexico
- Montefiore Institute, University of Liège, Liège4000, Belgique
- Wallon ExceLlence (WEL) Research Institute, Wavre1300, Belgique
| | - Román Rossi-Pool
- Instituto de Fisiología Celular, Departamento de Neurociencia Cognitiva, Universidad Nacional Autónoma de México, Mexico City04510, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City04510, Mexico
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27
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Smith BJ, Guest PC, Martins-de-Souza D. Maximizing Analytical Performance in Biomolecular Discovery with LC-MS: Focus on Psychiatric Disorders. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2024; 17:25-46. [PMID: 38424029 DOI: 10.1146/annurev-anchem-061522-041154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
In this review, we discuss the cutting-edge developments in mass spectrometry proteomics and metabolomics that have brought improvements for the identification of new disease-based biomarkers. A special focus is placed on psychiatric disorders, for example, schizophrenia, because they are considered to be not a single disease entity but rather a spectrum of disorders with many overlapping symptoms. This review includes descriptions of various types of commonly used mass spectrometry platforms for biomarker research, as well as complementary techniques to maximize data coverage, reduce sample heterogeneity, and work around potentially confounding factors. Finally, we summarize the different statistical methods that can be used for improving data quality to aid in reliability and interpretation of proteomics findings, as well as to enhance their translatability into clinical use and generalizability to new data sets.
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Affiliation(s)
- Bradley J Smith
- 1Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, São Paulo, Brazil;
| | - Paul C Guest
- 1Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, São Paulo, Brazil;
- 2Department of Psychiatry, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
- 3Laboratory of Translational Psychiatry, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Daniel Martins-de-Souza
- 1Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, São Paulo, Brazil;
- 4Experimental Medicine Research Cluster, University of Campinas, São Paulo, Brazil
- 5National Institute of Biomarkers in Neuropsychiatry, National Council for Scientific and Technological Development, São Paulo, Brazil
- 6D'Or Institute for Research and Education, São Paulo, Brazil
- 7INCT in Modelling Human Complex Diseases with 3D Platforms (Model3D), São Paulo, Brazil
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28
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Qing X, Lu G, Zhang X, Chen Q, Zhou X, He W, Xu L, Zhang J. Essential spectral pixels-based improvement of UMAP classifying hyperspectral imaging data to identify minor compounds in food matrix. Talanta 2024; 273:125845. [PMID: 38442566 DOI: 10.1016/j.talanta.2024.125845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/31/2024] [Accepted: 02/28/2024] [Indexed: 03/07/2024]
Abstract
Classifying big data in hyperspectral imaging (HSI) can be challenging when minor (low-concentrated) compounds are present in actual samples, as for chemical additives and adulterants in food matrix. Herein, we propose a new strategy to classify HSI data for the identification of adulterants in food material for the first time. This strategy is based on the selection of essential spectral pixels of full HSI data followed by the feature space construction using uniform manifold approximation and projection as well as the data clustering utilizing hierarchical clustering analysis on the reduced data (named ESPs-UMAP-HCA). We apply our approach to analyze two real NIR datasets and four new Raman datasets. Compared with non-ESPs UMAP-HCA and t-distributed stochastic neighbor embedding combined with ESPs and HCA (ESPs-t-SNE-HCA), the developed strategy provides well-separated clusters for major and minor compounds in food matrix. Finally, the adulterants as minor compounds are accurately identified, which is confirmed by the fact that the extracted spectra of them perfectly match with their pure spectra. In addition, their locations are found in the contribution map even though they are present in a few pixels. What's more, the proposed strategy does not need any a priori knowledge of the data structure and the class memberships and therefore reduced the studied difficulty and confirmation bias in the analysis of big HSI datasets. Overall, the proposed ESPs-UMAP-HCA method could be a potential approach for food adulteration detection.
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Affiliation(s)
- Xiangdong Qing
- Hunan Provincial Key Laboratory of Dark Tea and Jin-hua, College of Materials and Chemical Engineering, Hunan City University, Yiyang, 413000, PR China.
| | - Guiying Lu
- National Center of Dark Tea Product Quality Inspection and Testing, Yiyang Testing Institute of Product and Commodity Quality Supervision, Yiyang, 413000, PR China
| | - Xiaohua Zhang
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang, 414006, PR China
| | - Qingling Chen
- Analytical Instrumentation Center of Hunan University, Changsha, 410082, PR China
| | - Xiaohong Zhou
- Hunan Provincial Key Laboratory of Dark Tea and Jin-hua, College of Materials and Chemical Engineering, Hunan City University, Yiyang, 413000, PR China
| | - Wei He
- Hunan Provincial Key Laboratory of Dark Tea and Jin-hua, College of Materials and Chemical Engineering, Hunan City University, Yiyang, 413000, PR China
| | - Ling Xu
- Hunan Provincial Key Laboratory of Dark Tea and Jin-hua, College of Materials and Chemical Engineering, Hunan City University, Yiyang, 413000, PR China
| | - Jin Zhang
- Hunan Provincial Key Laboratory of Dark Tea and Jin-hua, College of Materials and Chemical Engineering, Hunan City University, Yiyang, 413000, PR China.
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Li L, Momma H, Chen H, Nawrin SS, Xu Y, Inada H, Nagatomi R. Dietary patterns associated with the incidence of hypertension among adult Japanese males: application of machine learning to a cohort study. Eur J Nutr 2024; 63:1293-1314. [PMID: 38403812 PMCID: PMC11139695 DOI: 10.1007/s00394-024-03342-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 01/30/2024] [Indexed: 02/27/2024]
Abstract
PURPOSE The previous studies that examined the effectiveness of unsupervised machine learning methods versus traditional methods in assessing dietary patterns and their association with incident hypertension showed contradictory results. Consequently, our aim is to explore the correlation between the incidence of hypertension and overall dietary patterns that were extracted using unsupervised machine learning techniques. METHODS Data were obtained from Japanese male participants enrolled in a prospective cohort study between August 2008 and August 2010. A final dataset of 447 male participants was used for analysis. Dimension reduction using uniform manifold approximation and projection (UMAP) and subsequent K-means clustering was used to derive dietary patterns. In addition, multivariable logistic regression was used to evaluate the association between dietary patterns and the incidence of hypertension. RESULTS We identified four dietary patterns: 'Low-protein/fiber High-sugar,' 'Dairy/vegetable-based,' 'Meat-based,' and 'Seafood and Alcohol.' Compared with 'Seafood and Alcohol' as a reference, the protective dietary patterns for hypertension were 'Dairy/vegetable-based' (OR 0.39, 95% CI 0.19-0.80, P = 0.013) and the 'Meat-based' (OR 0.37, 95% CI 0.16-0.86, P = 0.022) after adjusting for potential confounding factors, including age, body mass index, smoking, education, physical activity, dyslipidemia, and diabetes. An age-matched sensitivity analysis confirmed this finding. CONCLUSION This study finds that relative to the 'Seafood and Alcohol' pattern, the 'Dairy/vegetable-based' and 'Meat-based' dietary patterns are associated with a lower risk of hypertension among men.
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Affiliation(s)
- Longfei Li
- School of Physical Education and Health, Heze University, 2269 University Road, Mudan District, Heze, 274-015, Shandong, China
- Department of Medicine and Science in Sports and Exercise, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan
| | - Haruki Momma
- Department of Medicine and Science in Sports and Exercise, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan
| | - Haili Chen
- Department of Medicine and Science in Sports and Exercise, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan
| | - Saida Salima Nawrin
- Division of Biomedical Engineering for Health & Welfare, Tohoku University Graduate School of Biomedical Engineering, 6-6-12, Aramaki Aza Aoba Aoba-ku, Sendai, Miyagi, 980-8579, Japan
| | - Yidan Xu
- Department of Medicine and Science in Sports and Exercise, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan
| | - Hitoshi Inada
- Department of Developmental Neuroscience, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan.
- Department of Biochemistry and Cellular Biology, National Center of Neurology and Psychiatry, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo, 187-8502, Japan.
| | - Ryoichi Nagatomi
- Department of Medicine and Science in Sports and Exercise, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan.
- Division of Biomedical Engineering for Health & Welfare, Tohoku University Graduate School of Biomedical Engineering, 6-6-12, Aramaki Aza Aoba Aoba-ku, Sendai, Miyagi, 980-8579, Japan.
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Park SY, Bae H, Jeong HY, Lee JY, Kwon YK, Kim CE. Identifying Novel Subtypes of Functional Gastrointestinal Disorder by Analyzing Nonlinear Structure in Integrative Biopsychosocial Questionnaire Data. J Clin Med 2024; 13:2821. [PMID: 38792363 PMCID: PMC11122158 DOI: 10.3390/jcm13102821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 04/26/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Background/Objectives: Given the limited success in treating functional gastrointestinal disorders (FGIDs) through conventional methods, there is a pressing need for tailored treatments that account for the heterogeneity and biopsychosocial factors associated with FGIDs. Here, we considered the potential of novel subtypes of FGIDs based on biopsychosocial information. Methods: We collected data from 198 FGID patients utilizing an integrative approach that included the traditional Korean medicine diagnosis questionnaire for digestive symptoms (KM), as well as the 36-item Short Form Health Survey (SF-36), alongside the conventional Rome-criteria-based Korean Bowel Disease Questionnaire (K-BDQ). Multivariate analyses were conducted to assess whether KM or SF-36 provided additional information beyond the K-BDQ and its statistical relevance to symptom severity. Questions related to symptom severity were selected using an extremely randomized trees (ERT) regressor to develop an integrative questionnaire. For the identification of novel subtypes, Uniform Manifold Approximation and Projection and spectral clustering were used for nonlinear dimensionality reduction and clustering, respectively. The validity of the clusters was assessed using certain metrics, such as trustworthiness, silhouette coefficient, and accordance rate. An ERT classifier was employed to further validate the clustered result. Results: The multivariate analyses revealed that SF-36 and KM supplemented the psychosocial aspects lacking in K-BDQ. Through the application of nonlinear clustering using the integrative questionnaire data, four subtypes of FGID were identified: mild, severe, mind-symptom predominance, and body-symptom predominance. Conclusions: The identification of these subtypes offers a framework for personalized treatment strategies, thus potentially enhancing therapeutic outcomes by tailoring interventions to the unique biopsychosocial profiles of FGID patients.
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Affiliation(s)
- Sa-Yoon Park
- Department of Physiology, College of Korean Medicine, Gachon University, Seongnam 13120, Republic of Korea; (S.-Y.P.); (H.-Y.J.)
- Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Hyojin Bae
- Department of Physiology, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea;
| | - Ha-Yeong Jeong
- Department of Physiology, College of Korean Medicine, Gachon University, Seongnam 13120, Republic of Korea; (S.-Y.P.); (H.-Y.J.)
| | - Ju Yup Lee
- Department of Internal Medicine, Keimyung University School of Medicine, Daegu 42601, Republic of Korea;
| | - Young-Kyu Kwon
- Division of Longevity and Biofunctional Medicine, School of Korean Medicine, Pusan National University, Yangsan 50612, Republic of Korea
| | - Chang-Eop Kim
- Department of Physiology, College of Korean Medicine, Gachon University, Seongnam 13120, Republic of Korea; (S.-Y.P.); (H.-Y.J.)
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Srivastava A, Manchel A, Waters J, Ambelil M, Barnhart BK, Hoek JB, Shah AP, Vadigepalli R. Integrated transcriptomics and histopathology approach identifies a subset of rejected donor livers with potential suitability for transplantation. BMC Genomics 2024; 25:437. [PMID: 38698335 PMCID: PMC11067109 DOI: 10.1186/s12864-024-10362-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/29/2024] [Indexed: 05/05/2024] Open
Abstract
BACKGROUND Liver transplantation is an effective treatment for liver failure. There is a large unmet demand, even as not all donated livers are transplanted. The clinical selection criteria for donor livers based on histopathological evaluation and liver function tests are variable. We integrated transcriptomics and histopathology to characterize donor liver biopsies obtained at the time of organ recovery. We performed RNA sequencing as well as manual and artificial intelligence-based histopathology (10 accepted and 21 rejected for transplantation). RESULTS We identified two transcriptomically distinct rejected subsets (termed rejected-1 and rejected-2), where rejected-2 exhibited a near-complete transcriptomic overlap with the accepted livers, suggesting acceptability from a molecular standpoint. Liver metabolic functional genes were similarly upregulated, and extracellular matrix genes were similarly downregulated in the accepted and rejected-2 groups compared to rejected-1. The transcriptomic pattern of the rejected-2 subset was enriched for a gene expression signature of graft success post-transplantation. Serum AST, ALT, and total bilirubin levels showed similar overlapping patterns. Additional histopathological filtering identified cases with borderline scores and extensive molecular overlap with accepted donor livers. CONCLUSIONS Our integrated approach identified a subset of rejected donor livers that are likely suitable for transplantation, demonstrating the potential to expand the pool of transplantable livers.
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Affiliation(s)
- Ankita Srivastava
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Alexandra Manchel
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - John Waters
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Manju Ambelil
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Benjamin K Barnhart
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Jan B Hoek
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Ashesh P Shah
- Department of Surgery, Thomas Jefferson University Hospital, Jefferson University Hospitals, Philadelphia, PA, USA
| | - Rajanikanth Vadigepalli
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, PA, 19107, USA.
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Lechner K, Kia S, von Korn P, Dinges SM, Mueller S, Tjønna AE, Wisløff U, Van Craenenbroeck EM, Pieske B, Adams V, Pressler A, Landmesser U, Halle M, Kränkel N. Cardiometabolic and immune response to exercise training in patients with metabolic syndrome: retrospective analysis of two randomized clinical trials. Front Cardiovasc Med 2024; 11:1329633. [PMID: 38638882 PMCID: PMC11025358 DOI: 10.3389/fcvm.2024.1329633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 03/21/2024] [Indexed: 04/20/2024] Open
Abstract
Background Metabolic syndrome (MetS) is defined by the presence of central obesity plus ≥two metabolic/cardiovascular risk factors (RF), with inflammation being a major disease-driving mechanism. Structured endurance exercise training (ET) may positively affect these traits, as well as cardiorespiratory fitness (V̇O2peak). Aims We explore individual ET-mediated improvements of MetS-associated RF in relation to improvements in V̇O2peak and inflammatory profile. Methods MetS patients from two randomized controlled trials, ExMET (n = 24) and OptimEx (n = 34), had performed 4- or 3-months supervised ET programs according to the respective trial protocol. V̇O2peak, MetS-defining RFs (both RCTs), broad blood leukocyte profile, cytokines and plasma proteins (ExMET only) were assessed at baseline and follow-up. Intra-individual changes in RFs were analysed for both trials separately using non-parametric approaches. Associations between changes in each RF over the exercise period (n-fold of baseline values) were correlated using a non-parametrical approach (Spearman). RF clustering was explored by uniform manifold approximation and projection (UMAP) and changes in RF depending on other RF or exercise parameters were explored by recursive partitioning. Results Four months of ET reduced circulating leukocyte counts (63.5% of baseline, P = 8.0e-6), especially effector subtypes. ET response of MetS-associated RFs differed depending on patients' individual RF constellation, but was not associated with individual change in V̇O2peak. Blood pressure lowering depended on cumulative exercise duration (ExMET: ≥102 min per week; OptimEx-MetS: ≥38 min per session) and baseline triglyceride levels (ExMET: <150 mg/dl; OptimEx-MetS: <174.8 mg/dl). Neuropilin-1 plasma levels were inversely associated with fasting plasma triglycerides (R: -0.4, P = 0.004) and changes of both parameters during the ET phase were inversely correlated (R: -0.7, P = 0.0001). Conclusions ET significantly lowered effector leukocyte blood counts. The improvement of MetS-associated cardiovascular RFs depended on individual basal RF profile and exercise duration but was not associated with exercise-mediated increase in V̇O2peak. Neuropilin-1 may be linked to exercise-mediated triglyceride lowering.
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Affiliation(s)
- Katharina Lechner
- Department of Prevention and Sports Medicine, University Hospital Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- DZHK, German Centre for Cardiovascular Research, Partner Site Munich Heart Alliance, Munich, Germany
- Klinik für Herz- und Kreislauferkrankungen, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
| | - Sylvia Kia
- Deutsches Herzzentrum der Charité, Klinik für Kardiologie, Angiologie und Intensivmedizin, Berlin, Germany
- DZHK, German Centre for Cardiovascular Research, Partner Site, Berlin, Germany
| | - Pia von Korn
- Department of Prevention and Sports Medicine, University Hospital Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- DZHK, German Centre for Cardiovascular Research, Partner Site Munich Heart Alliance, Munich, Germany
| | - Sophia M. Dinges
- Department of Prevention and Sports Medicine, University Hospital Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- DZHK, German Centre for Cardiovascular Research, Partner Site Munich Heart Alliance, Munich, Germany
| | - Stephan Mueller
- Department of Prevention and Sports Medicine, University Hospital Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- DZHK, German Centre for Cardiovascular Research, Partner Site Munich Heart Alliance, Munich, Germany
| | - Arnt-Erik Tjønna
- Cardiac Exercise Research Group (CERG), Department of Circulation and Medical Imaging, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ulrik Wisløff
- Cardiac Exercise Research Group (CERG), Department of Circulation and Medical Imaging, Norwegian University of Science and Technology, Trondheim, Norway
- Centre for Research on Exercise, Physical Activity and Health, School of Human Movement and Nutrition Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Emeline M. Van Craenenbroeck
- Research Group Cardiovascular Diseases, University of Antwerp, Antwerp, Belgium
- Department of Cardiology, Antwerp University Hospital (UZA), Edegem, Belgium
| | - Burkert Pieske
- Department of Internal Medicine and Cardiology, Campus Virchow Klinikum, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Volker Adams
- Department of Cardiology and Internal Medicine, Heart Center Dresden-University Hospital, TU Dresden, Dresden, Germany
| | - Axel Pressler
- Department of Prevention and Sports Medicine, University Hospital Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- DZHK, German Centre for Cardiovascular Research, Partner Site Munich Heart Alliance, Munich, Germany
- Private Center for Sports and Exercise Cardiology, Munich, Germany
| | - Ulf Landmesser
- Deutsches Herzzentrum der Charité, Klinik für Kardiologie, Angiologie und Intensivmedizin, Berlin, Germany
- DZHK, German Centre for Cardiovascular Research, Partner Site, Berlin, Germany
- Friede Springer—Centre of Cardiovascular Prevention at Charité, Charité University Medicine Berlin, Berlin, Germany
| | - Martin Halle
- Department of Prevention and Sports Medicine, University Hospital Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- DZHK, German Centre for Cardiovascular Research, Partner Site Munich Heart Alliance, Munich, Germany
| | - Nicolle Kränkel
- Deutsches Herzzentrum der Charité, Klinik für Kardiologie, Angiologie und Intensivmedizin, Berlin, Germany
- DZHK, German Centre for Cardiovascular Research, Partner Site, Berlin, Germany
- Friede Springer—Centre of Cardiovascular Prevention at Charité, Charité University Medicine Berlin, Berlin, Germany
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Walsh JR, Sun G, Balan J, Hardcastle J, Vollenweider J, Jerde C, Rumilla K, Koellner C, Koleilat A, Hasadsri L, Kipp B, Jenkinson G, Klee E. A supervised learning method for classifying methylation disorders. BMC Bioinformatics 2024; 25:66. [PMID: 38347515 PMCID: PMC10863277 DOI: 10.1186/s12859-024-05673-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/24/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND DNA methylation is one of the most stable and well-characterized epigenetic alterations in humans. Accordingly, it has already found clinical utility as a molecular biomarker in a variety of disease contexts. Existing methods for clinical diagnosis of methylation-related disorders focus on outlier detection in a small number of CpG sites using standardized cutoffs which differentiate healthy from abnormal methylation levels. The standardized cutoff values used in these methods do not take into account methylation patterns which are known to differ between the sexes and with age. RESULTS Here we profile genome-wide DNA methylation from blood samples drawn from within a cohort composed of healthy controls of different age and sex alongside patients with Prader-Willi syndrome (PWS), Beckwith-Wiedemann syndrome, Fragile-X syndrome, Angelman syndrome, and Silver-Russell syndrome. We propose a Generalized Additive Model to perform age and sex adjusted outlier analysis of around 700,000 CpG sites throughout the human genome. Utilizing z-scores among the cohort for each site, we deployed an ensemble based machine learning pipeline and achieved a combined prediction accuracy of 0.96 (Binomial 95% Confidence Interval 0.868[Formula: see text]0.995). CONCLUSION We demonstrate a method for age and sex adjusted outlier detection of differentially methylated loci based on a large cohort of healthy individuals. We present a custom machine learning pipeline utilizing this outlier analysis to classify samples for potential methylation associated congenital disorders. These methods are able to achieve high accuracy when used with machine learning methods to classify abnormal methylation patterns.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Alaa Koleilat
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
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Wu S, Wagner G. Computational inference of eIF4F complex function and structure in human cancers. Proc Natl Acad Sci U S A 2024; 121:e2313589121. [PMID: 38266053 PMCID: PMC10835048 DOI: 10.1073/pnas.2313589121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 12/18/2023] [Indexed: 01/26/2024] Open
Abstract
The canonical eukaryotic initiation factor 4F (eIF4F) complex, composed of eIF4G1, eIF4A1, and the cap-binding protein eIF4E, plays a crucial role in cap-dependent translation initiation in eukaryotic cells. An alternative cap-independent initiation can occur, involving only eIF4G1 and eIF4A1 through internal ribosome entry sites (IRESs). This mechanism is considered complementary to cap-dependent initiation, particularly in tumors under stress conditions. However, the selection and molecular mechanism of specific translation initiation remains poorly understood in human cancers. Thus, we analyzed gene copy number variations (CNVs) in TCGA tumor samples and found frequent amplification of genes involved in translation initiation. Copy number gains in EIF4G1 and EIF3E frequently co-occur across human cancers. Additionally, EIF4G1 expression strongly correlates with genes from cancer cell survival pathways including cell cycle and lipogenesis, in tumors with EIF4G1 amplification or duplication. Furthermore, we revealed that eIF4G1 and eIF4A1 protein levels strongly co-regulate with ribosomal subunits, eIF2, and eIF3 complexes, while eIF4E co-regulates with 4E-BP1, ubiquitination, and ESCRT proteins. Utilizing Alphafold predictions, we modeled the eIF4F structure with and without eIF4E binding. For cap-dependent initiation, our modeling reveals extensive interactions between the N-terminal eIF4E-binding domain of eIF4G1 and eIF4E. Furthermore, the eIF4G1 HEAT-2 domain positions eIF4E near the eIF4A1 N-terminal domain (NTD), resulting in the collaborative enclosure of the RNA binding cavity within eIF4A1. In contrast, during cap-independent initiation, the HEAT-2 domain directly binds the eIF4A1-NTD, leading to a stronger interaction between eIF4G1 and eIF4A1, thus closing the mRNA binding cavity without the involvement of eIF4E.
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Affiliation(s)
- Su Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA02115
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA02115
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Guo Z, Zhang J, Sun J, Dong H, Huang J, Geng L, Li S, Jing X, Guo Y, Sun X. A multivariate algorithm for identifying contaminated peanut using visible and near-infrared hyperspectral imaging. Talanta 2024; 267:125187. [PMID: 37722342 DOI: 10.1016/j.talanta.2023.125187] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/29/2023] [Accepted: 09/07/2023] [Indexed: 09/20/2023]
Abstract
In this study, a novel uniform manifold approximation and projection combined-improved simultaneous optimization genetic algorithm-convolutional neural network (UMAP-ISOGA-CNN) algorithm was proposed. The improved simultaneous optimization genetic algorithm (ISOGA) combined with convolutional neural network (CNN) to optimize the architecture, hyperparameters, and optimizer of the CNN model simultaneously. Additionally, a uniform manifold approximation and projection (UMAP) method was used to visualize the feature space of all feature layers of the ISOGA-CNN model. The UMAP-ISOGA-CNN algorithm combined with visible and near-infrared hyperspectral imaging was used to identify peanut kernels contaminated with Aspergillus flavus and to distinguish their storage time, which is essential for the food industry to monitor the freshness of products. Overall, the UMAP-ISOGA-CNN algorithm provides useful insights into the feature space of the ISOGA-CNN model, contributing to a better understanding of the model's internal mechanisms. This study has practical implications for the food industry and future research on deep learning optimization.
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Affiliation(s)
- Zhen Guo
- School of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China
| | - Jing Zhang
- School of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China
| | - Jiashuai Sun
- School of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China
| | - Haowei Dong
- School of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China
| | - Jingcheng Huang
- School of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China
| | - Lingjun Geng
- School of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China
| | - Shiling Li
- School of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China
| | - Xiangzhu Jing
- School of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China
| | - Yemin Guo
- School of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China.
| | - Xia Sun
- School of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China.
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Xiang Q, Tao JS, Fu CJ, Liao LX, Liu LN, Deng J, Li XH. The integrated analysis and underlying mechanisms of FNDC5 on diabetic induced cognitive deficits. Int J Geriatr Psychiatry 2024; 39:e6047. [PMID: 38161286 DOI: 10.1002/gps.6047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 12/14/2023] [Indexed: 01/03/2024]
Abstract
OBJECTIVES Chronic hyperglycemia is considered as an important factor to promote the neurodegenerative process of brain, and the synaptic plasticity as well as heterogeneity of hippocampal cells are thought to be associated with cognitive dysfunction in the early process of neurodegeneration. To date, fibronectin type III domain-containing protein 5 (FNDC5) has been highlighted its protective role in multiple neurodegenerative diseases. However, the potential molecular and cellular mechanisms of FNDC5 on synaptic plasticity regulation in cognitive impairment (CI) induced by diabetics are still need to known. METHODS/DESIGN To investigate the heterogeneity and synaptic plasticity of hippocampus in animals with CI state induced by hyperglycemia, and explore the potential role of FNDC5 involved in this process. Firstly, the single cell sequencing was performed based on the hippocampal tissue from db diabetic mice induced CI and normal health control mice by ex vivo experiments; and then the integrated analysis and observations validation using Quantitative Real-time PCR, western blot as well as other in vitro studies. RESULTS We observed and clarified the sub-cluster of type IC spiral ganglion neurons expressed marker genes as Trmp3 and sub-cluster of astrocytes with marker gene as Atp1a2 in hippocampal cells from diabetic animals induced CI and the effect of those on neuron-glial communication. We also found that FNDC5\BDNF-Trk axis was involved in the synaptic plasticity regulation of hippocampus. In high glucose induced brain injury model in vitro, we investigated that FNDC5 significantly regulates BDNF expression and that over-expression of FNDC5 up-regulated BDNF expression (p < 0.05) and can also significantly increase the expression of synapsin-1 (p < 0.05), which is related to synaptic plasticity, In addition, the unbalanced methylation level between H3K4 and H3K9 in Fndc5 gene promoter correlated with significantly down-regulated expression of FNDC5 (p < 0.05) in the hyperglycemia state. CONCLUSION The current study revealed that the synaptic plasticity of hippocampal cells in hyperglycemia might be regulated by FNDC5\BDNF-Trk axis, playing the protective role in the process of CI induced by hyperglycemia and providing a target for the early treatment of hyperglycemia induced cognitive dysfunction in clinic.
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Affiliation(s)
- Qiong Xiang
- Institute of Medicine, Medical Research Center, Jishou University, Jishou, Hunan, China
| | - Jia-Sheng Tao
- Institute of Medicine, Medical Research Center, Jishou University, Jishou, Hunan, China
| | - Chuan-Jun Fu
- Institute of Medicine, Medical Research Center, Jishou University, Jishou, Hunan, China
| | - Li-Xiu Liao
- Institute of Pharmaceutical Sciences, Jishou University, Jishou, Hunan, China
| | - Li-Ni Liu
- Institute of Medicine, Medical Research Center, Jishou University, Jishou, Hunan, China
| | - Jing Deng
- Institute of Medicine, Medical Research Center, Jishou University, Jishou, Hunan, China
| | - Xian-Hui Li
- Institute of Pharmaceutical Sciences, Jishou University, Jishou, Hunan, China
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Filippa M, Benis D, Adam-Darque A, Grandjean D, Hüppi PS. Preterm infants show an atypical processing of the mother's voice. Brain Cogn 2023; 173:106104. [PMID: 37949001 DOI: 10.1016/j.bandc.2023.106104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023]
Abstract
To understand the consequences of prematurity on language perception, it is fundamental to determine how atypical early sensory experience affects brain development. At term equivalent age, ten preterm and ten full-term newborns underwent high-density EEG during mother or stranger speech presentation, in the forward or backward order. A general group effect terms > preterms is evident in the theta frequency band, in the left temporal area, with preterms showing significant activation for strangers' and terms for the mother's voice. A significant group contrast in the low and high theta in the right temporal regions indicates higher activations for the stranger's voice in preterms. Finally, only full terms presented a late gamma band increase for the maternal voice, indicating a more mature brain response. EEG time-frequency analysis demonstrate that preterm infants are selectively responsive to stranger voices in both temporal hemispheres, and that they lack selective brain responses to their mother's forward voice.
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Affiliation(s)
- Manuela Filippa
- Division of Development and Growth, Child and Adolescent Department, Rue Willy-Donzé 1205 Genève, University of Geneva, Geneva, Switzerland; Swiss Center for Affective Sciences, Department of Psychology and Educational Sciences, University of Geneva, Boulevard Carl-Vogt 101 Genève, Geneva, Switzerland.
| | - Damien Benis
- Division of Development and Growth, Child and Adolescent Department, Rue Willy-Donzé 1205 Genève, University of Geneva, Geneva, Switzerland; Swiss Center for Affective Sciences, Department of Psychology and Educational Sciences, University of Geneva, Boulevard Carl-Vogt 101 Genève, Geneva, Switzerland
| | - Alexandra Adam-Darque
- Laboratory of Cognitive Neurorehabilitation, Department of Clinical Neuroscience, Division of Neurorehabilitation, University Hospital of Geneva and University of Geneva, Rue Gabrielle-Perret-Gentil 4, 1211 Geneva, Switzerland
| | - Didier Grandjean
- Swiss Center for Affective Sciences, Department of Psychology and Educational Sciences, University of Geneva, Boulevard Carl-Vogt 101 Genève, Geneva, Switzerland
| | - Petra S Hüppi
- Division of Development and Growth, Child and Adolescent Department, Rue Willy-Donzé 1205 Genève, University of Geneva, Geneva, Switzerland
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Xi Z, Yang T, Huang T, Zhou J, Yang P. Identification and Preliminary Clinical Validation of Key Extracellular Proteins as the Potential Biomarkers in Hashimoto's Thyroiditis by Comprehensive Analysis. Biomedicines 2023; 11:3127. [PMID: 38137348 PMCID: PMC10740579 DOI: 10.3390/biomedicines11123127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/04/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
Hashimoto's thyroiditis (HT) is an autoimmune disruption manifested by immune cell infiltration in thyroid tissue and the production of antibodies against thyroid-specific antigens, such as the thyroid peroxidase antibody (TPOAb) and thyroglobulin antibody (TGAb). TPOAb and TGAb are commonly used in clinical tests; however, handy indicators of the diagnosis and progression of HT are still scarce. Extracellular proteins are glycosylated and are likely to enter body fluids and become readily available and detectable biomarkers. Our research aimed to discover extracellular biomarkers and potential treatment targets associated with HT through integrated bioinformatics analysis and clinical sample validations. A total of 19 extracellular protein-differentially expressed genes (EP-DEGs) were screened by the GSE138198 dataset from the Gene Expression Omnibus (GEO) database and protein annotation databases. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to analyze the function and pathway of EP-DEGs. STRING, Cytoscape, MCODE, and Cytohubba were used to construct a protein-protein interaction (PPI) network and screen key EP-DEGs. Six key EP-DEGs (CCL5, GZMK, CXCL9, CXCL10, CXCL11, and CXCL13) were further validated in the GSE29315 dataset and the diagnostic curves were evaluated, which all showed high diagnostic accuracy (AUC > 0.95) for HT. Immune profiling revealed the correlation of the six key EP-DEGs and the pivotal immune cells in HT, such as CD8+ T cells, dendritic cells, and Th2 cells. Further, we also confirmed the key EP-DEGs in clinical thyroid samples. Our study may provide bioinformatics and clinical evidence for revealing the pathogenesis of HT and improving the potential diagnosis biomarkers and therapeutic strategies for HT.
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Affiliation(s)
| | | | | | - Jun Zhou
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Peng Yang
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
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Golob J, Rao K, Berinstein JA, Chey WD, Owyang C, Kamada N, Higgins PD, Young V, Bishu S, Lee AA. The Microbiome in Quiescent Crohn's Disease With Persistent Symptoms Show Disruptions in Microbial Sulfur and Tryptophan Pathways. GASTRO HEP ADVANCES 2023; 3:167-177. [PMID: 39129952 PMCID: PMC11307550 DOI: 10.1016/j.gastha.2023.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 11/09/2023] [Indexed: 08/13/2024]
Abstract
Background and Aims Even in the absence of inflammation, persistent symptoms in Crohn's disease (CD) are prevalent and worsen quality of life. Amongst patients without inflammation (quiescent CD), we hypothesized that microbial community structure and function, including tryptophan metabolism, would differ between patients with persistent symptoms (qCD + S) and without persistent symptoms (qCD-S). Methods We performed a multicenter observational study nested within the Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease. Quiescent inflammation was defined by fecal calprotectin level <150 mcg/g. Persistent symptoms were defined by Crohn's Disease Patient-Reported Outcome-2. Active CD, diarrhea-predominant irritable bowel syndrome, and healthy controls were included as controls. Stool samples underwent whole-genome shotgun metagenomic sequencing. Results Thirty-nine patients with qCD + S, 274 qCD-S, 21 active CD, 40 diarrhea-predominant irritable bowel syndrome, and 50 healthy controls were included for analysis. Patients with qCD + S had a less-diverse microbiome. Furthermore, patients with qCD + S showed significant enrichment of bacterial species that are normal inhabitants of the oral microbiome (eg Rothia dentocariosa, Fusobacterium nucleatum) and sulfidogenic microbes (eg Prevotella copri, Bilophila spp.). Depletion of important butyrate and indole producers (eg Eubacterium rectale, Faecalibacterium prausnitzii) was also noted in qCD + S. Potential metagenome-related functional changes in cysteine and methionine metabolism, ATP transport, and redox reactions were disturbed in qCD + S, also suggestive of altered sulfur metabolism. Finally, qCD + S showed significant reductions in bacterial tnaA genes, which mediate tryptophan metabolism to indole, and significant tnaA allelic variation compared with qCD-S. Conclusion The microbiome in qCD + S showed significant differences in sulfidogenesis, butyrate producers, and typically oral microbes compared to qCD-S and active CD. These results suggest that inflammation may lead to durable microbiome alterations which may mediate persistent symptoms through testable mechanisms.
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Affiliation(s)
- Jonathan Golob
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Krishna Rao
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Jeffrey A. Berinstein
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - William D. Chey
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Chung Owyang
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Nobuhiko Kamada
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Peter D.R. Higgins
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Vincent Young
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan
| | - Shrinivas Bishu
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Allen A. Lee
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
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Sekita A, Kawasaki H, Fukushima-Nomura A, Yashiro K, Tanese K, Toshima S, Ashizaki K, Miyai T, Yazaki J, Kobayashi A, Namba S, Naito T, Wang QS, Kawakami E, Seita J, Ohara O, Sakurada K, Okada Y, Amagai M, Koseki H. Multifaceted analysis of cross-tissue transcriptomes reveals phenotype-endotype associations in atopic dermatitis. Nat Commun 2023; 14:6133. [PMID: 37783685 PMCID: PMC10545679 DOI: 10.1038/s41467-023-41857-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 09/19/2023] [Indexed: 10/04/2023] Open
Abstract
Atopic dermatitis (AD) is a skin disease that is heterogeneous both in terms of clinical manifestations and molecular profiles. It is increasingly recognized that AD is a systemic rather than a local disease and should be assessed in the context of whole-body pathophysiology. Here we show, via integrated RNA-sequencing of skin tissue and peripheral blood mononuclear cell (PBMC) samples along with clinical data from 115 AD patients and 14 matched healthy controls, that specific clinical presentations associate with matching differential molecular signatures. We establish a regression model based on transcriptome modules identified in weighted gene co-expression network analysis to extract molecular features associated with detailed clinical phenotypes of AD. The two main, qualitatively differential skin manifestations of AD, erythema and papulation are distinguished by differential immunological signatures. We further apply the regression model to a longitudinal dataset of 30 AD patients for personalized monitoring, highlighting patient heterogeneity in disease trajectories. The longitudinal features of blood tests and PBMC transcriptome modules identify three patient clusters which are aligned with clinical severity and reflect treatment history. Our approach thus serves as a framework for effective clinical investigation to gain a holistic view on the pathophysiology of complex human diseases.
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Affiliation(s)
- Aiko Sekita
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
| | - Hiroshi Kawasaki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
| | | | - Kiyoshi Yashiro
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
| | - Keiji Tanese
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
| | - Susumu Toshima
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
| | - Koichi Ashizaki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
- Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, Tokyo, Japan
| | - Tomohiro Miyai
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
| | - Junshi Yazaki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Atsuo Kobayashi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shinichi Namba
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tatsuhiko Naito
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Qingbo S Wang
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Eiryo Kawakami
- Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, Tokyo, Japan
- Artificial Intelligence Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Jun Seita
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, Tokyo, Japan
| | | | - Kazuhiro Sakurada
- Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, Tokyo, Japan
- Department of Extended Intelligence for Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Yukinori Okada
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan.
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Masayuki Amagai
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan.
| | - Haruhiko Koseki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
- Cellular and Molecular Medicine, Advanced Research Departments, Graduate School of Medicine, Chiba University, Chiba, Japan.
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Higginbotham L, Carter EK, Dammer EB, Haque RU, Johnson ECB, Duong DM, Yin L, De Jager PL, Bennett DA, Felsky D, Tio ES, Lah JJ, Levey AI, Seyfried NT. Unbiased classification of the elderly human brain proteome resolves distinct clinical and pathophysiological subtypes of cognitive impairment. Neurobiol Dis 2023; 186:106286. [PMID: 37689213 PMCID: PMC10750427 DOI: 10.1016/j.nbd.2023.106286] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/24/2023] [Accepted: 09/06/2023] [Indexed: 09/11/2023] Open
Abstract
Cognitive impairment in the elderly features complex molecular pathophysiology extending beyond the hallmark pathologies of traditional disease classification. Molecular subtyping using large-scale -omic strategies can help resolve this biological heterogeneity. Using quantitative mass spectrometry, we measured ∼8000 proteins across >600 dorsolateral prefrontal cortex tissues with clinical diagnoses of no cognitive impairment (NCI), mild cognitive impairment (MCI), and Alzheimer's disease (AD) dementia. Unbiased classification of MCI and AD cases based on individual proteomic profiles resolved three classes with expression differences across numerous cell types and biological ontologies. Two classes displayed molecular signatures atypical of AD neurodegeneration, such as elevated synaptic and decreased inflammatory markers. In one class, these atypical proteomic features were associated with clinical and pathological hallmarks of cognitive resilience. We were able to replicate these classes and their clinicopathological phenotypes across two additional tissue cohorts. These results promise to better define the molecular heterogeneity of cognitive impairment and meaningfully impact its diagnostic and therapeutic precision.
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Affiliation(s)
- Lenora Higginbotham
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA.
| | - E Kathleen Carter
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA; Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Eric B Dammer
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Rafi U Haque
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Erik C B Johnson
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Duc M Duong
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Luming Yin
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Taub Institute, Columbia University Irving Medical Center, New York Presbyterian Hospital, New York, NY, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Daniel Felsky
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada; Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Earvin S Tio
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada; Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - James J Lah
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Allan I Levey
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Nicholas T Seyfried
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA; Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA.
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Liu J, Huang T, Yao J, Zhao T, Zhang Y, Zhang R. Epitranscriptomic subtyping, visualization, and denoising by global motif visualization. Nat Commun 2023; 14:5944. [PMID: 37741827 PMCID: PMC10517956 DOI: 10.1038/s41467-023-41653-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 09/13/2023] [Indexed: 09/25/2023] Open
Abstract
Advances in sequencing technologies have empowered epitranscriptomic profiling at the single-base resolution. Putative RNA modification sites identified from a single high-throughput experiment may contain one type of modification deposited by different writers or different types of modifications, along with false positive results because of the challenge of distinguishing signals from noise. However, current tools are insufficient for subtyping, visualization, and denoising these signals. Here, we present iMVP, which is an interactive framework for epitranscriptomic analysis with a nonlinear dimension reduction technique and density-based partition. As exemplified by the analysis of mRNA m5C and ModTect variant data, we show that iMVP allows the identification of previously unknown RNA modification motifs and writers and the discovery of false positives that are undetectable by traditional methods. Using putative m6A/m6Am sites called from 8 profiling approaches, we illustrate that iMVP enables comprehensive comparison of different approaches and advances our understanding of the difference and pattern of true positives and artifacts in these methods. Finally, we demonstrate the ability of iMVP to analyze an extremely large human A-to-I editing dataset that was previously unmanageable. Our work provides a general framework for the visualization and interpretation of epitranscriptomic data.
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Affiliation(s)
- Jianheng Liu
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, P. R. China.
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA.
| | - Tao Huang
- Department of Pathology and Pathophysiology, Shantou University Medical College, Shantou, 515041, P. R. China
| | - Jing Yao
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Tianxuan Zhao
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Yusen Zhang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Rui Zhang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, P. R. China.
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Kang H, Sun H, Yang Y, Tuong ZK, Shu M, Wei Y, Zhang Y, Yu D, Tao Y. Autoimmune uveitis in Behçet's disease and Vogt-Koyanagi-Harada disease differ in tissue immune infiltration and T cell clonality. Clin Transl Immunology 2023; 12:e1461. [PMID: 37720629 PMCID: PMC10503407 DOI: 10.1002/cti2.1461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 06/16/2023] [Accepted: 08/04/2023] [Indexed: 09/19/2023] Open
Abstract
Objectives Non-infectious uveitis is often secondary to systemic autoimmune diseases, with Behçet's disease (BD) and Vogt-Koyanagi-Harada disease (VKHD) as the two most common causes. Uveitis in BD and VKHD can show similar clinical manifestations, but the underlying immunopathogenesis remains unclear. Methods To understand immune landscapes in inflammatory eye tissues, we performed single-cell RNA paired with T cell receptor (TCR) sequencing of immune cell infiltrates in aqueous humour from six patients with BD (N = 3) and VKHD (N = 3) uveitis patients. Results Although T cells strongly infiltrated in both types of autoimmune uveitis, myeloid cells only significantly presented in BD uveitis but not in VKHD uveitis. Conversely, VKHD uveitis but not BD uveitis showed an overwhelming dominance by CD4+ T cells (> 80%) within the T cell population due to expansion of CD4+ T cell clusters with effector memory (Tem) phenotypes. Correspondingly, VKHD uveitis demonstrated a selective expansion of CD4+ T cell clones which were enriched in pro-inflammatory Granzyme H+ CD4+ Tem cluster and showed TCR and Th1 pathway activation. In contrast, BD uveitis showed a preferential expansion of CD8+ T cell clones in pro-inflammatory Granzyme H+ CD8+ Tem cluster, and pathway activation for cytoskeleton remodelling, cellular adhesion and cytotoxicity. Conclusion Single-cell analyses of ocular tissues reveal distinct landscapes of immune cell infiltration and T-cell clonal expansions between VKHD and BD uveitis. Preferential involvements of pro-inflammatory CD4+ Th1 cells in VKHD and cytotoxic CD8+ T cells in BD suggest a difference in disease immunopathogenesis and can guide precision disease management.
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Affiliation(s)
- Hao Kang
- Department of Ophthalmology, Beijing Chaoyang HospitalCapital Medical UniversityBeijingChina
| | - Hongjian Sun
- Frazer Institute, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
- Shandong Artificial Intelligence InstituteQilu University of Technology (Shandong Academy of Sciences)JinanChina
| | - Yang Yang
- Frazer Institute, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
- Shandong Artificial Intelligence InstituteQilu University of Technology (Shandong Academy of Sciences)JinanChina
| | - Zewen K Tuong
- Ian Frazer Centre for Children's Immunotherapy Research, Children's Health Research Centre, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
| | - Minglei Shu
- Shandong Artificial Intelligence InstituteQilu University of Technology (Shandong Academy of Sciences)JinanChina
| | - Yunbo Wei
- School of Pharmaceutical Sciences, Laboratory of Immunology for Environment and Health, Shandong Analysis and Test CenterQilu University of Technology (Shandong Academy of Sciences)JinanChina
| | - Yu Zhang
- School of Pharmaceutical Sciences, Laboratory of Immunology for Environment and Health, Shandong Analysis and Test CenterQilu University of Technology (Shandong Academy of Sciences)JinanChina
| | - Di Yu
- Frazer Institute, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
- Ian Frazer Centre for Children's Immunotherapy Research, Children's Health Research Centre, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
| | - Yong Tao
- Department of Ophthalmology, Beijing Chaoyang HospitalCapital Medical UniversityBeijingChina
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44
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Wu S, Wagner G. Computational inference of eIF4F complex function and structure in human cancers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.10.552450. [PMID: 37609226 PMCID: PMC10441403 DOI: 10.1101/2023.08.10.552450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The canonical eukaryotic initiation factor 4F (eIF4F) complex, composed of eIF4G1, eIF4A1, and the cap-binding protein eIF4E, plays a crucial role in cap-dependent translation initiation in eukaryotic cells (1). However, cap-independent initiation can occur through internal ribosomal entry sites (IRESs), involving only eIF4G1 and eIF4A1 present, which is considered to be a complementary process to cap-dependent initiation in tumors under stress conditions (2). The selection and molecular mechanism of specific translation initiation in human cancers remains poorly understood. Thus, we analyzed gene copy number variations (CNVs) in TCGA tumor samples and found frequent amplification of genes involved in translation initiation. Copy number gains in EIF4G1 and EIF3E frequently co-occur across human cancers. Additionally, EIF4G1 expression strongly correlates with genes from cancer cell survival pathways including cell cycle and lipogenesis, in tumors with EIF4G1 amplification or duplication. Furthermore, we revealed that eIF4G1 and eIF4A1 protein levels strongly co-regulate with ribosomal subunits, eIF2, and eIF3 complexes, while eIF4E co-regulates with 4E-BP1, ubiquitination, and ESCRT proteins. Using Alphafold predictions, we modeled the eIF4F structure with and without eIF4G1-eIF4E binding. The modeling for cap-dependent initiation suggests that eIF4G1 interacts with eIF4E through its N-terminal eIF4E-binding domain, bringing eIF4E near the eIF4A1 mRNA binding cavity and closing the cavity with both eIF4G1 HEAT-2 domain and eIF4E. In the cap-independent mechanism, α-helix 5 of eIF4G1 HEAT-2 domain instead directly interacts with the eIF4A1 N-terminal domain to close the mRNA binding cavity without eIF4E involvement, resulting in a stronger interaction between eIF4G1 and eIF4A1. Significance Statement Translation initiation is primarily governed by eIF4F, employing a "cap-dependent" mechanism, but eIF4F dysregulation may lead to a "cap-independent" mechanism in stressed cancer cells. We found frequent amplification of translation initiation genes, and co-occurring copy number gains of EIF4G1 and EIF3E genes in human cancers. EIF4G1 amplification or duplication may be positively selected for its beneficial impact on the overexpression of cancer survival genes. The co-regulation of eIF4G1 and eIF4A1, distinctly from eIF4E, reveals eIF4F dysregulation favoring cap-independent initiation. Alphafold predicts changes in the eIF4F complex assembly to accommodate both initiation mechanisms. These findings have significant implications for evaluating cancer cell vulnerability to eIF4F inhibition and developing treatments that target cancer cells with dependency on the translation initiation mechanism.
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Abstract
Dimensionality reduction is standard practice for filtering noise and identifying relevant features in large-scale data analyses. In biology, single-cell genomics studies typically begin with reduction to 2 or 3 dimensions to produce "all-in-one" visuals of the data that are amenable to the human eye, and these are subsequently used for qualitative and quantitative exploratory analysis. However, there is little theoretical support for this practice, and we show that extreme dimension reduction, from hundreds or thousands of dimensions to 2, inevitably induces significant distortion of high-dimensional datasets. We therefore examine the practical implications of low-dimensional embedding of single-cell data and find that extensive distortions and inconsistent practices make such embeddings counter-productive for exploratory, biological analyses. In lieu of this, we discuss alternative approaches for conducting targeted embedding and feature exploration to enable hypothesis-driven biological discovery.
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Affiliation(s)
- Tara Chari
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Lior Pachter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, California, United States of America
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46
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Luo M, Miao YR, Ke YJ, Guo AY, Zhang Q. A comprehensive landscape of transcription profiles and data resources for human leukemia. Blood Adv 2023; 7:3435-3449. [PMID: 36595475 PMCID: PMC10362280 DOI: 10.1182/bloodadvances.2022008410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 01/04/2023] Open
Abstract
As a heterogeneous group of hematologic malignancies, leukemia has been widely studied at the transcriptome level. However, a comprehensive transcriptomic landscape and resources for different leukemia subtypes are lacking. Thus, in this study, we integrated the RNA sequencing data sets of >3000 samples from 14 leukemia subtypes and 53 related cell lines via a unified analysis pipeline. We depicted the corresponding transcriptomic landscape and developed a user-friendly data portal LeukemiaDB. LeukemiaDB was designed with 5 main modules: protein-coding gene, long noncoding RNA (lncRNA), circular RNA, alternative splicing, and fusion gene modules. In LeukemiaDB, users can search and browse the expression level, regulatory modules, and molecular information across leukemia subtypes or cell lines. In addition, a comprehensive analysis of data in LeukemiaDB demonstrates that (1) different leukemia subtypes or cell lines have similar expression distribution of the protein-coding gene and lncRNA; (2) some alternative splicing events are shared among nearly all leukemia subtypes, for example, MYL6 in A3SS, MYB in A5SS, HMBS in retained intron, GTPBP10 in mutually exclusive exons, and POLL in skipped exon; (3) some leukemia-specific protein-coding genes, for example, ABCA6, ARHGAP44, WNT3, and BLACE, and fusion genes, for example, BCR-ABL1 and KMT2A-AFF1 are involved in leukemogenesis; (4) some highly correlated regulatory modules were also identified in different leukemia subtypes, for example, the HOXA9 module in acute myeloid leukemia and the NOTCH1 module in T-cell acute lymphoblastic leukemia. In summary, the developed LeukemiaDB provides valuable insights into oncogenesis and progression of leukemia and, to the best of our knowledge, is the most comprehensive transcriptome resource of human leukemia available to the research community.
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Affiliation(s)
- Mei Luo
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, People’s Republic of China
- Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, People’s Republic of China
| | - Ya-Ru Miao
- Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Ya-Juan Ke
- Dian Diagnostics Group Co, Ltd, Hangzhou, China
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Hangzhou, China
| | - An-Yuan Guo
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
- Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Qiong Zhang
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
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47
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Coria-Rodríguez H, Ochoa S, de Anda-Jáuregui G, Hernández-Lemus E. Drug repurposing for Basal breast cancer subpopulations using modular network signatures. Comput Biol Chem 2023; 105:107902. [PMID: 37348299 DOI: 10.1016/j.compbiolchem.2023.107902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 05/30/2023] [Accepted: 06/02/2023] [Indexed: 06/24/2023]
Abstract
Breast cancer is characterized as being a heterogeneous pathology with a broad phenotype variability. Breast cancer subtypes have been developed in order to capture some of this heterogeneity. Each of these breast cancer subtypes, in turns retains varied characteristic features impacting diagnostic, prognostic and therapeutics. Basal breast tumors, in particular have been challenging in these regards. Basal breast cancer is often more aggressive, of rapid evolution and no tailor-made targeted therapies are available yet to treat it. Arguably, epigenetic variability is behind some of these intricacies. It is possible to further classify basal breast tumor in groups based on their non-coding transcriptome and methylome profiles. It is expected that these groups will have differences in survival as well as in sensitivity to certain classes of drugs. With this in mind, we implemented a computational learning approach to infer different subpopulations of basal breast cancer (from TCGA multi-omic data) based on their epigenetic signatures. Such epigenomic signatures were associated with different survival profiles; we then identified their associated gene co-expression network structure, extracted a signature based on modules within these networks, and use these signatures to find and prioritize drugs (in the LINCS dataset) that may be used to target these types of cancer. In this way we are introducing the analytical workflow for an epigenomic signature-based drug repurposing structure.
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Affiliation(s)
- Hiram Coria-Rodríguez
- Computational Genomics Division, National Institute of Genomic Medicine, Periferico Sur 4809, Mexico City, 14610, Mexico
| | - Soledad Ochoa
- Computational Genomics Division, National Institute of Genomic Medicine, Periferico Sur 4809, Mexico City, 14610, Mexico
| | - Guillermo de Anda-Jáuregui
- Computational Genomics Division, National Institute of Genomic Medicine, Periferico Sur 4809, Mexico City, 14610, Mexico; Center for Complexity Sciences, Universidad Nacional Autonoma de Mexico, Circuito Exterior, Mexico City, 04510, Mexico; Catedras Conacyt, National Council on Science and Technology, Insurgentes Sur, Mexico City, 03940, Mexico.
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Periferico Sur 4809, Mexico City, 14610, Mexico; Center for Complexity Sciences, Universidad Nacional Autonoma de Mexico, Circuito Exterior, Mexico City, 04510, Mexico.
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48
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Cai C, Yue Y, Yue B. Single-cell RNA sequencing in skeletal muscle developmental biology. Biomed Pharmacother 2023; 162:114631. [PMID: 37003036 DOI: 10.1016/j.biopha.2023.114631] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/29/2023] [Accepted: 03/29/2023] [Indexed: 04/01/2023] Open
Abstract
Skeletal muscle is the most extensive tissue in mammals, and they perform several functions; it is derived from paraxial mesodermal somites and undergoes hyperplasia and hypertrophy to form multinucleated, contractile, and functional muscle fibers. Skeletal muscle is a complex heterogeneous tissue composed of various cell types that establish communication strategies to exchange biological information; therefore, characterizing the cellular heterogeneity and transcriptional signatures of skeletal muscle is central to understanding its ontogeny's details. Studies of skeletal myogenesis have focused primarily on myogenic cells' proliferation, differentiation, migration, and fusion and ignored the intricate network of cells with specific biological functions. The rapid development of single-cell sequencing technology has recently enabled the exploration of skeletal muscle cell types and molecular events during development. This review summarizes the progress in single-cell RNA sequencing and its applications in skeletal myogenesis, which will provide insights into skeletal muscle pathophysiology.
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Affiliation(s)
- Cuicui Cai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu 610225, China; Guyuan Branch, Ningxia Academy of Agriculture and Forestry Sciences, Guyuan 7560000, China
| | - Yuan Yue
- Department of Pathobiology and Immunology, Hebei University of Chinese Medicine, Shijiazhuang 050200, China
| | - Binglin Yue
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu 610225, China.
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49
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Chandra R, Bansal C, Kang M, Blau T, Agarwal V, Singh P, Wilson LOW, Vasan S. Unsupervised machine learning framework for discriminating major variants of concern during COVID-19. PLoS One 2023; 18:e0285719. [PMID: 37200352 PMCID: PMC10194860 DOI: 10.1371/journal.pone.0285719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 04/28/2023] [Indexed: 05/20/2023] Open
Abstract
Due to the high mutation rate of the virus, the COVID-19 pandemic evolved rapidly. Certain variants of the virus, such as Delta and Omicron emerged with altered viral properties leading to severe transmission and death rates. These variants burdened the medical systems worldwide with a major impact to travel, productivity, and the world economy. Unsupervised machine learning methods have the ability to compress, characterize, and visualize unlabelled data. This paper presents a framework that utilizes unsupervised machine learning methods to discriminate and visualize the associations between major COVID-19 variants based on their genome sequences. These methods comprise a combination of selected dimensionality reduction and clustering techniques. The framework processes the RNA sequences by performing a k-mer analysis on the data and further visualises and compares the results using selected dimensionality reduction methods that include principal component analysis (PCA), t-distributed stochastic neighbour embedding (t-SNE), and uniform manifold approximation projection (UMAP). Our framework also employs agglomerative hierarchical clustering to visualize the mutational differences among major variants of concern and country-wise mutational differences for selected variants (Delta and Omicron) using dendrograms. We also provide country-wise mutational differences for selected variants via dendrograms. We find that the proposed framework can effectively distinguish between the major variants and has the potential to identify emerging variants in the future.
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Affiliation(s)
- Rohitash Chandra
- Transitional Artificial Intelligence Research Group, School of Mathematics and Statistics, UNSW Sydney, Sydney, Australia
| | - Chaarvi Bansal
- Transitional Artificial Intelligence Research Group, School of Mathematics and Statistics, UNSW Sydney, Sydney, Australia
- Department of Computer Science and Information Systems, Birla Institute of Technology and Science Pilani, Rajasthan, India
| | - Mingyue Kang
- Transitional Artificial Intelligence Research Group, School of Mathematics and Statistics, UNSW Sydney, Sydney, Australia
| | - Tom Blau
- Data 61, CSIRO, Sydney, Australia
| | - Vinti Agarwal
- Department of Computer Science and Information Systems, Birla Institute of Technology and Science Pilani, Rajasthan, India
| | - Pranjal Singh
- Department of Computer Science and Engineering, Indian Institute of Technology Guwathi, Assam, India
| | - Laurence O. W. Wilson
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation, North Ryde, Australia
| | - Seshadri Vasan
- Department of Health Sciences, University of York, York, United Kingdom
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50
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Smith RN, Rosales IA, Tomaszewski KT, Mahowald GT, Araujo-Medina M, Acheampong E, Bruce A, Rios A, Otsuka T, Tsuji T, Hotta K, Colvin R. Utility of Banff Human Organ Transplant Gene Panel in Human Kidney Transplant Biopsies. Transplantation 2023; 107:1188-1199. [PMID: 36525551 PMCID: PMC10132999 DOI: 10.1097/tp.0000000000004389] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND Microarray transcript analysis of human renal transplantation biopsies has successfully identified the many patterns of graft rejection. To evaluate an alternative, this report tests whether gene expression from the Banff Human Organ Transplant (B-HOT) probe set panel, derived from validated microarrays, can identify the relevant allograft diagnoses directly from archival human renal transplant formalin-fixed paraffin-embedded biopsies. To test this hypothesis, principal components (PCs) of gene expressions were used to identify allograft diagnoses, to classify diagnoses, and to determine whether the PC data were rich enough to identify diagnostic subtypes by clustering, which are all needed if the B-HOT panel can substitute for microarrays. METHODS RNA was isolated from routine, archival formalin-fixed paraffin-embedded tissue renal biopsy cores with both rejection and nonrejection diagnoses. The B-HOT panel expression of 770 genes was analyzed by PCs, which were then tested to determine their ability to identify diagnoses. RESULTS PCs of microarray gene sets identified the Banff categories of renal allograft diagnoses, modeled well the aggregate diagnoses, showing a similar correspondence with the pathologic diagnoses as microarrays. Clustering of the PCs identified diagnostic subtypes including non-chronic antibody-mediated rejection with high endothelial expression. PCs of cell types and pathways identified new mechanistic patterns including differential expression of B and plasma cells. CONCLUSIONS Using PCs of gene expression from the B-Hot panel confirms the utility of the B-HOT panel to identify allograft diagnoses and is similar to microarrays. The B-HOT panel will accelerate and expand transcript analysis and will be useful for longitudinal and outcome studies.
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Affiliation(s)
- Rex N Smith
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Center for Transplantation Sciences, Massachusetts General Hospital, Boston, MA
| | - Ivy A Rosales
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Center for Transplantation Sciences, Massachusetts General Hospital, Boston, MA
| | - Kristen T Tomaszewski
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Center for Transplantation Sciences, Massachusetts General Hospital, Boston, MA
| | - Grace T Mahowald
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Milagros Araujo-Medina
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Ellen Acheampong
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Amy Bruce
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Andrea Rios
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Takuya Otsuka
- Department of Surgical Pathology, Hokkaido University Hospital, Sapporo, Japan
| | - Takahiro Tsuji
- Department of Pathology, Sapporo City General Hospital, Sapporo, Japan
| | - Kiyohiko Hotta
- Department of Urology, Hokkaido University Hospital, Sapporo, Japan
| | - Robert Colvin
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Center for Transplantation Sciences, Massachusetts General Hospital, Boston, MA
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