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Panera: An innovative framework for surmounting uncertainty in microbial community modeling using pan-genera metabolic models

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ISCIENCE 2024年第7期27卷 110358页

作者： Palanikumar, Indumathi Sinha, Himanshu Raman, Karthik Indian Inst Technol IIT Madras Bhupat Jyoti Mehta Sch Biosci Dept Biotechnol Chennai 600036 India IIT Madras Ctr Integrat Biol & Syst Med IBSE Chennai 600036 India IIT Madras Robert Bosch Ctr Data Sci & Artificial Intelligen Chennai 600036 India IIT Madras Wadhwani Sch Data Sci & AI Dept Data Sci & AI Chennai 600036 Tamil Nadu India

Utilization of 16S rRNA data in constraint-based modeling to characterize microbial communities confronts a major hurdle of lack of species-level resolution, impeding the construction of community models. We introduce " Panera ,"an innovative framework designed to model communities under this uncertainty and yet perform metabolic inferences using pan-genus metabolic models (PGMMs). We demonstrated PGMMs' utility for comprehending the metabolic capabilities of a genus and in characterizing community models using amplicon data. The unique, adaptable nature of PGMMs unlocks their potential in building hybrid communities, combining genome-scale metabolic models (GSMMs) and PGMMs. Notably, these models provide predictions comparable to the standard GSMM-based community models, while achieving a nearly 46% reduction in error compared to the genus model-based communities. In essence, " Panera "presents a potent and effective approach to aid in metabolic modeling by enabling robust predictions of community metabolic potential when dealing with amplicon data, and offers insights into genus-level metabolic landscapes.

关键词： Microbiology bioinformatics computational bioinformatics Systems biology

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Analysis of age-related left ventricular collagen remodeling in living donors: Implications in arrhythmogenesis

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ISCIENCE 2022年第2期25卷 103822页

作者： Garcia-Mendivil, Laura Perez-Zabalza, Maria Mountris, Konstantinos Duwe, Sam Smisdom, Nick Perez, Marta Lujan, Lluis Wolfs, Esther Driesen, Ronald B. Maria Vallejo-Gil, Jose Carlos Fresneda-Roldan, Pedro Fananas-Mastral, Javier Vazquez-Sancho, Manuel Matamala-Adell, Marta Fernando Sorribas-Berjon, Juan Andre Bellido-Morales, Javier Javier Mancebon-Sierra, Francisco Sebastian Vaca-Nunez, Alexander Ballester-Cuenca, Carlos Olivan-Viguera, Aida Diez, Emiliano Ordovas, Laura Pueyo, Esther Univ Zaragoza Aragon Inst Engn Res Biomed Signal Interpretat & Computat Simulat Grp Zaragoza 50018 Spain IIS Aragon BSICoS Zaragoza 50018 Spain Hasselt Univ Adv Opt Microscopy Ctr Biomed Res Inst B-3500 Diepenbeek Belgium Hasselt Univ Biomed Res Inst B-3500 Diepenbeek Belgium Univ Zaragoza Dept Anat Embryol & Anim Genet Zaragoza 50013 Spain Univ Zaragoza Inst Univ Invest Mixto Agroalimentario Aragon IA2 Zaragoza 50013 Spain Univ Zaragoza Dept Anim Pathol Zaragoza 50013 Spain Univ Hosp Miguel Servet Dept Cardiovasc Surg Zaragoza 50009 Spain Biomed Res Networking Ctr Bioengn Biomat & Nanome Zaragoza 50018 Spain Consejo Nacl Invest Cient & Tecn Inst Expt Med & Biol Cuyo IMBECU RA-5500 Mendoza Argentina ARAID Fdn Zaragoza 50018 Spain

Age-related fibrosis in the left ventricle (LV) has been mainly studied in animals by assessing collagen content. Using second-harmonic generation microscopy and image processing, we evaluated amount, aggregation and spatial distribution of LV collagen in young to old pigs, and middle-age and elder living donors. All collagen features increased when comparing adult and old pigs with young ones, but not when comparing adult with old pigs or middle-age with elder individuals. Remarkably, all collagen parameters strongly correlated with lipofuscin, a biological age marker, in humans. By building patient-specific models of human ventricular tissue electrophysiology, we confirmed that amount and organization of fibrosis modulated arrhythmia vulnerability, and that distribution should be accounted for arrhythmia risk assessment. In conclusion, we characterize the age associated changes in LV collagen and its potential implications for ventricular arrhythmia development. Consistency between pig and human results substantiate the pig as a relevant model of age-related LV collagen dynamics.

关键词： Disease Pathophysiology computational bioinformatics

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Machine learning workflows identify a microRNA signature of insulin transcription in human tissues

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ISCIENCE 2021年第4期24卷 102379页

作者： Wong, Wilson K. M. Joglekar, Mugdha, V Saini, Vijit Jiang, Guozhi Dong, Charlotte X. Chaitarvornkit, Alissa Maciag, Grzegorz J. Gerace, Dario Farr, Ryan J. Satoor, Sarang N. Sahu, Subhshri Sharangdhar, Tejaswini Ahmed, Asma S. Chew, Yi Vee Liuwantara, David Heng, Benjamin Lim, Chai K. Hunter, Julie Januszewski, Andrzej S. Sorensen, Anja E. Akil, Ammira S. A. Gamble, Jennifer R. Loudovaris, Thomas Kay, Thomas W. Thomas, Helen E. O'Connell, Philip J. Guillemin, Gilles J. Martin, David Simpson, Ann M. Hawthorne, Wayne J. Dalgaard, Louise T. Ma, Ronald C. W. Hardikar, Anandwardhan A. Western Sydney Univ Sch Med Diabet & Islet Biol Grp Narellan Rd & Gilchrist Dr Campbelltown NSW 2560 Australia Univ Sydney Fac Med & Hlth Diabet & Islet Biol Grp 92-94 Parramatta Rd Camperdown NSW 2050 Australia Univ Technol Sydney Sch Life Sci 15 Broadway Ultimo NSW 2007 Australia Univ Technol Sydney Ctr Hlth Technol 15 Broadway Ultimo NSW 2007 Australia Chinese Univ Hong Kong Prince Wales Hosp Dept Med & Therapeut Hong Kong Peoples R China Chinese Univ Hong Kong Prince Wales Hosp Hong Kong Inst Diabet & Obes Hong Kong Peoples R China Chinese Univ Hong Kong Prince Wales Hosp Li Ka Shing Inst Hlth Sci Hong Kong Peoples R China Roskilde Univ Dept Sci & Environm Univ Vej 1 DK-4000 Roskilde Denmark Univ Sydney Ctr Transplant & Renal Res Westmead Inst Med Res 176 Hawkesbury Rd Westmead NSW 2145 Australia Macquarie Univ Fac Med Hlth & Human Sci Sydney NSW 2019 Australia Univ Sydney Med Sch Centenary Inst Ctr EndotheliumVasc Biol Program Locked Bag 6 Newtown NSW 2042 Australia Univ Sydney NHMRC Clin Trials Ctr 92-94 Parramatta Rd Camperdown NSW 2050 Australia Sidra Med Dept Human Genet Precis Med Program POB 26999 Doha Qatar St Vincents Inst 9 Princes St Fitzroy Vic Australia Univ Melbourne Dept Med 9 Princes St Fitzroy Vic Australia Strathfield Hosp Upper GI Surg 2-3 Everton Rd Strathfield NSW 2135 Australia

Dicer knockout mouse models demonstrated a key role for microRNAs in pancreatic beta-cell function. Studies to identify specific microRNA( s) associated with human (pro-)endocrine gene expression are needed. We profiled microRNAs and key pancreatic genes in 353 human tissue samples. Machine learning workflows identified microRNAs associated with (pro-)insulin transcripts in a discovery set of islets (n = 30) and insulin-negative tissues (n = 62). This microRNA signature was validated in remaining 261 tissues that include nine islet samples from individuals with type 2 diabetes. Top eight microRNAs (miR-183-5p, -375-3p, 216b-5p, 183-3p, -7-5p, -217-5p, -7-2-3p, and -429-3p) were confirmed to be associated with and predictive of (pro-)insulin transcript levels. Use of doxycycline-inducible microRNA-overexpressing human pancreatic duct cell lines confirmed the regulatory roles of thesemicroRNAs in (pro-)endocrine gene expression. Knockdown of these microRNAs in human islet cells reduced (pro-)insulin transcript abundance. Our data provide specific microRNAs to further study microRNA-mRNA interactions in regulating insulin transcription.

关键词： Pathophysiology computational bioinformatics Transcriptomics

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Bayesian multivariate genetic analysis improves translational insights

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ISCIENCE 2023年第10期26卷 107854页

作者： Urbut, Sarah M. Koyama, Satoshi Hornsby, Whitney Bhukar, Rohan Kheterpal, Sumeet Truong, Buu Selvaraj, Margaret S. Neale, Benjamin O'Donnell, Christopher J. Peloso, Gina M. Natarajan, Pradeep Massachusetts Gen Hosp Cardiovasc Res Ctr Boston MA 02114 USA Broad Inst Program Med & Populat Genet Cambridge MA 02142 USA Harvard Med Sch Dept Med Boston MA 02115 USA Massachusetts Gen Hosp Analyt & Translat Genet Unit Boston MA 02114 USA VA Boston Healthcare Syst Dept Vet Affairs Boston MA 02130 USA Boston Univ Sch Publ Hlth Dept Biostat Boston MA 02218 USA

While lipid traits are known essential mediators of cardiovascular disease, few approaches have taken advantage of their shared genetic effects. We apply a Bayesian multivariate size estimator, mash, to GWAS of four lipid traits in the Million Veterans Program (MVP) and provide posterior mean and local false sign rates for all effects. These estimates borrow information across traits to improve effect size accuracy. We show that controlling local false sign rates accurately and powerfully identifies replicable genetic associations and that multivariate control furthers the ability to explain complex diseases. Our application yields high concordance between independent datasets, more accurately prioritizes causal genes, and significantly improves polygenic prediction beyond state-of-the-art methods by up to 59% for lipid traits. The use of Bayesian multivariate genetic shrinkage has yet to be applied to human quantitative trait GWAS results, and we present a staged approach to prediction on a polygenic scale.

关键词： Human genetics Biocomputational method computational bioinformatics Genomic analysis Association analysis

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Radiomics and deep learning models to differentiate lung adenosquamous carcinoma: A multicenter trial

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ISCIENCE 2023年第9期26卷 107634页

作者： Chu, Xianjing Niu, Lishui Yang, Xianghui He, Shiqi Li, Aixin Chen, Liu Liang, Zhan Jing, Di Zhou, Rongrong Cent South Univ Xiangya Hosp Dept Oncol Changsha 410008 Peoples R China Changsha Cent Hosp Dept Oncol Changsha 410004 Peoples R China Univ British Columbia Dept Comp Sci 2329 West Mall Vancouver BC Canada Univ South Affiliated Hosp 1 Hengyang Med Sch Dept Radiotherapy Hengyang 421001 Peoples R China Cent South Univ Xiangya Hosp Xiangya Lung Canc Ctr Changsha 410008 Peoples R China Cent South Univ Xiangya Hosp Natl Clin Res Ctr Geriatr Disorders Changsha 410008 Peoples R China

Adenosquamous carcinoma (ASC) is frequently misdiagnosed or overlooked in clinical practice due to its dual histological components and potential transformation from either adenocarcinoma (ADC) or squamous cell carcinoma (SCC). Our study aimed to differentiate ASC from ADC and SCC by incorporating features of enhanced CTs and clinical characteristics to build radiomics and deep learning models. The classification models were trained in Xiangya Hospital and validated in two other independent hospitals. The areas under the receiver operating characteristic curves (AUC), accuracy, sensitivity, specificity, positive predictive value, and negative predictive value were used to estimate the performance. The optimal three-class classification model achieved a maximum AUC of 0.89 and accuracy of 0.81 in external validation sets, AUC of 0.99 and accuracy of 0.99 in the internal test set. These findings highlight the efficacy of our models in differentiating ASC, providing a non-invasive, timely, and accurate diagnostic approach before and during the treatment.

关键词： Health sciences Health informatics Oncology computational bioinformatics Cancer

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Gene presence/absence variation in Mytilus galloprovincialis and its implications in gene expression and adaptation

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ISCIENCE 2023年第10期26卷 107827页

作者： Saco, Amaro Rey-Campos, Magali Gallardo-Escarate, Cristian Gerdol, Marco Novoa, Beatriz Figueras, Antonio Spanish Natl Res Council Inst Marine Res Vigo Spain Univ Concepcion Ctr Aquaculture Res Concepcion Chile Univ Trieste Dept Life Sci Trieste Italy

Presence/absence variation (PAV) is a well-known phenomenon in prokaryotes that was described for the first time in bivalves in 2020 in Mytilus galloprovincialis. The objective of the present study was to further our understanding of the PAV phenomenon in mussel biology. The distribution of PAV was studied in a mussel chromosome-level genome assembly, revealing a widespread distribution but with hotspots of dispensability. Special attention was given to the effect of PAV in gene expression, since dispensable genes were found to be inherently subject to distortions due to their sparse distribution among individuals. Furthermore, the high expression and strong tissue specificity of some dispensable genes, such as myticins, strongly supported their biological relevance. The significant differences in the repertoire of dispensable genes associated with two geographically distinct populations suggest that PAV is involved in local adaptation. Overall, the PAV phenomenon would provide a key selective advantage at the population level.

关键词： Genetics bioinformatics computational bioinformatics Genomic analysis Omics

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Multi-scale spatial modeling of immune cell distributions enables survival prediction in primary central nervous system lymphoma

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ISCIENCE 2023年第8期26卷 107331页

作者： Roemer, Margaretha G. M. van de Brug, Tim Bosch, Erik Berry, Daniella Hijmering, Nathalie Stathi, Phylicia Weijers, Karin Doorduijn, Jeannette Bromberg, Jacoline van de Wiel, Mark Ylstra, Bauke de Jong, Daphne Kim, Yongsoo Vrije Univ Amsterdam Canc Ctr Amsterdam Dept Pathol Amsterdam UMC Amsterdam Netherlands Vrije Univ Amsterdam Amsterdam Publ Hlth Res Inst Dept Epidemiol & Data Sci Amsterdam UMC Amsterdam Netherlands Vrije Univ Amsterdam Dept Math Amsterdam Netherlands Univ Amsterdam Dept Pathol HOVON Pathol Facil & Biobank HOP Med Ctr Amsterdam Netherlands Univ Med Ctr Rotterdam Erasmus MC Canc Inst Dept Hematol Rotterdam Netherlands Univ Med Ctr Rotterdam Erasmus MC Canc Inst Brain Tumor Ctr Dept Neurooncol Rotterdam Netherlands

To understand the clinical significance of the tumor microenvironment (TME), it is essential to study the interactions between malignant and non-malignant cells in clinical specimens. Here, we established a computational framework for a multiplex imaging system to comprehensively characterize spatial contexts of the TME at multiple scales, including close and long-distance spatial interactions between cell type pairs. We applied this framework to a total of 1,393 multiplex imaging data newly generated from 88 primary central nervous system lymphomas with complete follow-up data and identified significant prognostic subgroups mainly shaped by the spatial context. A supervised analysis confirmed a significant contribution of spatial context in predicting patient survival. In particular, we found an opposite prognostic value of macrophage infiltration depending on its proximity to specific cell types. Altogether, we provide a comprehensive framework to analyze spatial cellular interaction that can be broadly applied to other technologies and tumor contexts.

关键词： Oncology Neuroscience Cell biology Mathematical biosciences computational bioinformatics

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Characterization of mechanisms positioning costimulatory complexes in immune synapses

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ISCIENCE 2021年第10期24卷 103100页

作者： Siokis, Anastasios Robert, Philippe A. Demetriou, Philippos Kvalvaag, Audun Valvo, Salvatore Mayya, Viveka Dustin, Michael L. Meyer-Hermann, Michael Helmholtz Ctr Infect Res Dept Syst Immunol D-38106 Braunschweig Germany Helmholtz Ctr Infect Res Braunschweig Integrated Ctr Syst Biol D-38106 Braunschweig Germany Tech Univ Carolo Wilhelmina Braunschweig Inst Biochem Biotechnol & Bioinformat D-38106 Braunschweig Germany Univ Oxford Nuffield Dept Orthopaed Rheumatol & Musculoskelet Kennedy Inst Rheumatol Oxford OX3 7FY England Oslo Univ Hosp Inst Canc Res Dept Mol Cell Biol N-0379 Oslo Norway Univ Oslo Dept Immunol N-0372 Oslo Norway

Small immunoglobulin superfamily (sIGSF) adhesion complexes form a corolla of microdomains around an integrin ring and secretory core during immunological synapse (IS) formation. The corolla recruits and retains major costimulatory/ checkpoint complexes, such as CD28, making forces that govern corolla formation of particular interest. Here, we investigated the mechanisms underlying molecular reorganization of CD2, an adhesion and costimulatory molecule of the sIGSF family during IS formation. Computer simulations showed passive distal exclusion of CD2 complexes under weak interactions with the ramified F-actin transport network. Attractive forces between CD2 and CD28 complexes relocate CD28 from the IS center to the corolla. Size-based sorting interactions with large glycocalyx components, such as CD45, or short-range CD2 self-attraction successfully explain the corolla 'petals.' This establishes a general simulation framework for complex pattern formation observed in cell-bilayer and cell-cell interfaces, and the suggestion of new therapeutic targets, where boosting or impairing characteristic pattern formation can be pivotal.

关键词： Cell biology computational bioinformatics computational molecular modelling Immunology Molecular biology

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Assessment of circulating proteins in thyroid cancer: Proteome-wide Mendelian randomization and colocalization

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ISCIENCE 2024年第6期27卷 109961页

作者： Fan, Qinghua Wen, Shifeng Zhang, Yi Feng, Xiuming Zheng, Wanting Liang, Xiaolin Lin, Yutong Zhao, Shimei Xie, Kaisheng Jiang, Hancheng Tang, Haifeng Zeng, Xiangtai Guo, You Wang, Fei Yang, Xiaobo Guangxi Med Univ Sch Publ Hlth Nanning 530000 Guangxi Peoples R China Guangxi Univ Sci & Technol Affiliated Hosp 2 Guangxi Key Lab Precise Prevent & Treatment Thyroi Liuzhou 545000 Guangxi Peoples R China Zhengzhou Univ Affiliated Hosp 1 Zhengzhou 450000 Henan Peoples R China Guangxi Univ Sci & Technol Affiliated Hosp 2 Liuzhou 545000 Guangxi Peoples R China Liuzhou Workers Hosp Liuzhou 545000 Guangxi Peoples R China Second Peoples Hosp Yulin Yulin 537000 Guangxi Peoples R China Gannan Med Univ Affiliated Hosp 1 Ganzhou 341000 Jiangxi Peoples R China

The causality between circulating proteins and thyroid cancer (TC) remains unclear. We employed five large-scale circulating proteomic genome-wide association studies (GWASs) with up to 100,000 participants and a TC meta-GWAS (n Case = 3,418, n Control = 292,703) to conduct proteome-wide Mendelian randomization (MR) and Bayesian colocalization analysis. Protein and gene expressions were validated in thyroid tissue. Through MR analysis, we identified 26 circulating proteins with a putative causal relationship with TCs, among which NANS protein passed multiple corrections ( P BH = 3.28e-5, 0.05/1,525). These proteins were involved in amino acids and organic acid synthesis pathways. Colocalization analysis further identified six proteins associated with TCs (VCAM1, LGMN, NPTX1, PLEKHA7, TNFAIP3, and BMP1). Tissue validation confirmed BMP1, LGMN, and PLEKHA7's differential expression between normal and TC tissues. We found limited evidence for linking circulating proteins and the risk of TCs. Our study highlighted the contribution of proteins, particularly those involved in amino acid metabolism, to TCs.

关键词： computational bioinformatics cancer

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Automated design of CRISPR prime editors for 56,000 human pathogenic variants

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ISCIENCE 2021年第11期24卷 103380页

作者： Morris, John A. Rahman, Jahan A. Guo, Xinyi Sanjana, Neville E. New York Genome Ctr New York NY 10013 USA NYU Dept Biol New York NY 10003 USA

Prime editors (PEs) are clustered regularly interspaced short palindromic repeats (CRISPR)-based genome engineering tools that can introduce precise base-pair edits. We developed an automated pipeline to correct (therapeutic editing) or introduce (disease modeling) human pathogenic variants from ClinVar that optimizes the design of several RNA constructs required for prime editing and avoids predicted off-targets in the human genome. However, using optimal PE design criteria, we find that only a small fraction of these pathogenic variants can be targeted. Through the use of alternative Cas9 enzymes and extended templates, we increase the number of targetable pathogenic variants from 32,000 to 56,000 variants and make these pre-designed PE constructs accessible through a web-based portal (http://***). Given the tremendous potential for therapeutic gene editing, we also assessed the possibility of developing universal PE constructs, finding that common genetic variants impact only a small minority of designed PEs.

关键词： Biotechnology computational bioinformatics

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