Proceedings. IEEE International Conference on Bioinformatics and Biomedicine最新文献

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Navigating Sex-Specific Disease Dynamics in Incident Dementia. 在老年痴呆症的性别特异性疾病动态中导航。
Proceedings. IEEE International Conference on Bioinformatics and Biomedicine Pub Date : 2023-12-01 Epub Date: 2024-01-18 DOI: 10.1109/bibm58861.2023.10385324
Muskan Garg, Xingyi Liu, Maria Vassilaki, Ronald C Petersen, Jennifer St Sauver, Sunghwan Sohn
{"title":"Navigating Sex-Specific Disease Dynamics in Incident Dementia.","authors":"Muskan Garg, Xingyi Liu, Maria Vassilaki, Ronald C Petersen, Jennifer St Sauver, Sunghwan Sohn","doi":"10.1109/bibm58861.2023.10385324","DOIUrl":"10.1109/bibm58861.2023.10385324","url":null,"abstract":"<p><p>Dementia is among the leading causes of cognitive and functional loss and disability in older adults. Past studies suggested sex differences in health conditions and progression of cognitive decline. Existing studies on the temporal trajectory of health conditions for patient characterization after dementia diagnosis are scarce and ambiguous. Thus, there's limited and unclear research on how health conditions change over time after a dementia diagnosis. To this end, we aim to analyze the shift in medical conditions and examine sex-specific changes in patterns of chronic health conditions after dementia diagnosis. We centered our analysis on a 15-year window around the point of dementia diagnosis, encompassing the 5 years leading up to the diagnosis and the 10 years following it. We introduce (i) MedMet, a network metric to quantify the contribution of each medical condition, and (ii) growth and decay function for temporal trajectory analysis of medical conditions. Our experiments demonstrate that certain health conditions are more prevalent among females than males. Thus, our findings underscore the pressing need to examine differences between men and women, which could be important for healthcare utilization after a dementia diagnosis.</p>","PeriodicalId":74563,"journal":{"name":"Proceedings. IEEE International Conference on Bioinformatics and Biomedicine","volume":"2023 ","pages":"4065-4072"},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10883293/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139974920","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Harnessing Transfer Learning for Dementia Prediction: Leveraging Sex-Different Mild Cognitive Impairment Prognosis. 利用迁移学习预测痴呆症:利用性别差异预测轻度认知障碍
Proceedings. IEEE International Conference on Bioinformatics and Biomedicine Pub Date : 2023-12-01 Epub Date: 2024-01-18 DOI: 10.1109/bibm58861.2023.10385516
Ziming Liu, Muskan Garg, Sunyang Fu, Surjodeep Sarkar, Maria Vassilaki, Ronald C Petersen, Jennifer St Sauver, Sunghwan Sohn
{"title":"Harnessing Transfer Learning for Dementia Prediction: Leveraging Sex-Different Mild Cognitive Impairment Prognosis.","authors":"Ziming Liu, Muskan Garg, Sunyang Fu, Surjodeep Sarkar, Maria Vassilaki, Ronald C Petersen, Jennifer St Sauver, Sunghwan Sohn","doi":"10.1109/bibm58861.2023.10385516","DOIUrl":"10.1109/bibm58861.2023.10385516","url":null,"abstract":"<p><p>This paper presents a machine learning-based prediction for dementia, leveraging transfer learning to reuse the knowledge learned from prediction of mild cognitive impairment, a precursor of dementia. We also examine the impacts of temporal aspects of longitudinal data and sex differences. The methodology encompasses key components such as setting the duration window, comparing different modeling strategies, conducting comprehensive evaluations, and examining the sex-specific impacts of simulated scenarios. The findings reveal that cognitive deficits in females, once detected at the mild cognitive impairment stage, tend to deteriorate over time, while males exhibit more diverse decline across various characteristics without highlighting specific ones. However, the underlying reasons for these sex differences remain unknown and warrant further investigation.</p>","PeriodicalId":74563,"journal":{"name":"Proceedings. IEEE International Conference on Bioinformatics and Biomedicine","volume":"2023 ","pages":"2097-2100"},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10883588/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139974919","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
ASD-GResTM: Deep Learning Framework for ASD classification using Gramian Angular Field. ASD-GResTM:利用格拉米安角场进行 ASD 分类的深度学习框架。
Proceedings. IEEE International Conference on Bioinformatics and Biomedicine Pub Date : 2023-12-01 Epub Date: 2024-01-18 DOI: 10.1109/bibm58861.2023.10385743
Fahad Almuqhim, Fahad Saeed
{"title":"ASD-GResTM: Deep Learning Framework for ASD classification using Gramian Angular Field.","authors":"Fahad Almuqhim, Fahad Saeed","doi":"10.1109/bibm58861.2023.10385743","DOIUrl":"10.1109/bibm58861.2023.10385743","url":null,"abstract":"<p><p>Autism Spectrum Disorder (ASD) is a heterogeneous disorder in children, and the current clinical diagnosis is accomplished using behavioral, cognitive, developmental, and language metrics. These clinical metrics can be imperfect measures as they are subject to high test-retest variability, and are influenced by assessment factors such as environment, social structure, or comorbid disorders. Advances in neuroimaging coupled with machine-learning provides an opportunity to develop methods that are more quantifiable, and reliable than existing clinical techniques. In this paper, we design and develop a deep-learning model that operates on functional magnetic resonance imaging (fMRI) data, and can classify between ASD and neurotypical brains. We introduce a novel strategy to transform time-series data extracted from fMRI signals into Gramian Angular Field (GAF) while locking in the temporal and spatial patterns in the data. Our motivation is to design and develop a novel framework that could encode the time-series, acquired from fMRI data, into images that can be used by deep-learning architectures that have been successful in computer vision. In our proposed framework called <i>ASD-GResTM</i>, we used a Convolutional Neural Network (CNN) to extract useful features from GAF images. We then used a Long Short-Term Memory (LSTM) layer to learn the activities between the regions. Finally, the output representations of the last LSTM layer are applied to a single-layer perceptron (SPL) to get the final classification. Our extensive experimentation demonstrates high accuracy across 4 centers, and outperforms state-of-the-art models on two centers with an increase in the accuracy of 17.58% and 6.7%, respectively as compared to the state of the art. Our model achieved the maximum accuracy of 81.78% with high degree of sensitivity and specificity. All training, validation, and testing was accomplished using openly available ABIDE-I benchmarking dataset.</p>","PeriodicalId":74563,"journal":{"name":"Proceedings. IEEE International Conference on Bioinformatics and Biomedicine","volume":"2023 ","pages":"2837-2843"},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11254319/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141636062","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A generalizable physiological model for detection of Delayed Cerebral Ischemia using Federated Learning. 利用联合学习检测延迟性脑缺血的通用生理模型
Proceedings. IEEE International Conference on Bioinformatics and Biomedicine Pub Date : 2023-12-01 Epub Date: 2024-01-18 DOI: 10.1109/bibm58861.2023.10385383
Ahmed Elhussein, Murad Megjhani, Daniel Nametz, Miriam Weiss, Jude Savarraj, Soon Bin Kwon, David J Roh, Sachin Agarwal, E Sander Connolly, Angela Velazquez, Jan Claassen, Huimahn A Choi, Gerrit A Schubert, Soojin Park, Gamze Gürsoy
{"title":"A generalizable physiological model for detection of Delayed Cerebral Ischemia using Federated Learning.","authors":"Ahmed Elhussein, Murad Megjhani, Daniel Nametz, Miriam Weiss, Jude Savarraj, Soon Bin Kwon, David J Roh, Sachin Agarwal, E Sander Connolly, Angela Velazquez, Jan Claassen, Huimahn A Choi, Gerrit A Schubert, Soojin Park, Gamze Gürsoy","doi":"10.1109/bibm58861.2023.10385383","DOIUrl":"10.1109/bibm58861.2023.10385383","url":null,"abstract":"<p><p>Delayed cerebral ischemia (DCI) is a complication seen in patients with subarachnoid hemorrhage stroke. It is a major predictor of poor outcomes and is detected late. Machine learning models are shown to be useful for early detection, however training such models suffers from small sample sizes due to rarity of the condition. Here we propose a Federated Learning approach to train a DCI classifier across three institutions to overcome challenges of sharing data across hospitals. We developed a framework for federated feature selection and built a federated ensemble classifier. We compared the performance of FL model to that obtained by training separate models at each site. FL significantly improved performance at only two sites. We found that this was due to feature distribution differences across sites. FL improves performance in sites with similar feature distributions, however, FL can worsen performance in sites with heterogeneous distributions. The results highlight both the benefit of FL and the need to assess dataset distribution similarity before conducting FL.</p>","PeriodicalId":74563,"journal":{"name":"Proceedings. IEEE International Conference on Bioinformatics and Biomedicine","volume":"2023 ","pages":"1886-1889"},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10883332/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139934591","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Bayesian Approach Integrating Prior Knowledge for Identifying miRNA-mRNA Interactions in Hepatocellular Carcinoma. 整合先验知识的贝叶斯方法识别肝细胞癌中miRNA-mRNA相互作用。
Proceedings. IEEE International Conference on Bioinformatics and Biomedicine Pub Date : 2023-12-01 DOI: 10.1109/bibm58861.2023.10385314
Yichen Guo, Marie Denis, Rency S Varghese, Sidharth S Jain, Mahlet G Tadesse, Habtom W Ressom
{"title":"Bayesian Approach Integrating Prior Knowledge for Identifying miRNA-mRNA Interactions in Hepatocellular Carcinoma.","authors":"Yichen Guo, Marie Denis, Rency S Varghese, Sidharth S Jain, Mahlet G Tadesse, Habtom W Ressom","doi":"10.1109/bibm58861.2023.10385314","DOIUrl":"10.1109/bibm58861.2023.10385314","url":null,"abstract":"<p><p>Oncogenesis, a complex and multifaceted process, is profoundly modulated by miRNA's regulatory role in gene expression. Over the years, a substantial body of knowledge concerning miRNA and mRNA has been accumulated, drawing from both rigorous biological experiments and intricate statistical analyses. In the realm of statistical modeling, the integration of such information as \"prior knowledge\" often amplifies the model's ability to pinpoint molecular targets of significance. This study seeks to leverage prior knowledge of miRNA-mRNA regulatory interactions to map the dynamic landscape of interactions in the specific context of hepatocellular carcinoma (HCC). To address this, we introduce an evolved iteration of a Bayesian two-step integrative method previously established in the literature. This augmented approach includes improved computing efficiency when dealing with high dimensional data and a novel mechanistic submodel, which operates autonomously, devoid of prior knowledge. Employing this method, we identified two discrete gene lists: one informed by prior knowledge and the other independently inferred. This bifurcated strategy provides a comprehensive perspective on gene interactions. Our methodological advancement allows for a nuanced analysis of gene networks, distinguishing between direct and indirect gene relationships and considering miRNA influences with two available sub-mechanistic submodels. We introduce an approach to validate our findings using a biological interaction network, emphasizing the quality and relevance of identified gene-gene relationships. Metrics like the Matthews Correlation Coefficient (MCC) and the true discovery rate (TDR) further attest to the robustness of our findings. In summation, aside from improving the existing sub-mechanistic model that requires prior knowledge, this paper presents an innovative prior knowledge-free sub-mechanistic model as an alternative. It champions the use of biological networks for validation, underscoring the significance of methodological advancements in genomics research.</p>","PeriodicalId":74563,"journal":{"name":"Proceedings. IEEE International Conference on Bioinformatics and Biomedicine","volume":"2023 ","pages":"3768-3774"},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12090934/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144112974","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Consistency of Graph Theoretical Measurements of Alzheimer's Disease Fiber Density Connectomes Across Multiple Parcellation Scales. 阿尔茨海默氏症纤维密度连接组的图形理论测量在多个分割尺度上的一致性。
Proceedings. IEEE International Conference on Bioinformatics and Biomedicine Pub Date : 2022-12-01 Epub Date: 2023-01-02 DOI: 10.1109/bibm55620.2022.9995657
Frederick Xu, Sumita Garai, Duy Duong-Tran, Andrew J Saykin, Yize Zhao, Li Shen
{"title":"Consistency of Graph Theoretical Measurements of Alzheimer's Disease Fiber Density Connectomes Across Multiple Parcellation Scales.","authors":"Frederick Xu, Sumita Garai, Duy Duong-Tran, Andrew J Saykin, Yize Zhao, Li Shen","doi":"10.1109/bibm55620.2022.9995657","DOIUrl":"10.1109/bibm55620.2022.9995657","url":null,"abstract":"<p><p>Graph theoretical measures have frequently been used to study disrupted connectivity in Alzheimer's disease human brain connectomes. However, prior studies have noted that differences in graph creation methods are confounding factors that may alter the topological observations found in these measures. In this study, we conduct a novel investigation regarding the effect of parcellation scale on graph theoretical measures computed for fiber density networks derived from diffusion tensor imaging. We computed 4 network-wide graph theoretical measures of average clustering coefficient, transitivity, characteristic path length, and global efficiency, and we tested whether these measures are able to consistently identify group differences among healthy control (HC), mild cognitive impairment (MCI), and AD groups in the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort across 5 scales of the Lausanne parcellation. We found that the segregative measure of transtivity offered the greatest consistency across scales in distinguishing between healthy and diseased groups, while the other measures were impacted by the selection of scale to varying degrees. Global efficiency was the second most consistent measure that we tested, where the measure could distinguish between HC and MCI in all 5 scales and between HC and AD in 3 out of 5 scales. Characteristic path length was highly sensitive to the variation in scale, corroborating previous findings, and could not identify group differences in many of the scales. Average clustering coefficient was also greatly impacted by scale, as it consistently failed to identify group differences in the higher resolution parcellations. From these results, we conclude that many graph theoretical measures are sensitive to the selection of parcellation scale, and further development in methodology is needed to offer a more robust characterization of AD's relationship with disrupted connectivity.</p>","PeriodicalId":74563,"journal":{"name":"Proceedings. IEEE International Conference on Bioinformatics and Biomedicine","volume":"2022 ","pages":"1323-1328"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10082965/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9301088","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Preference Matrix Guided Sparse Canonical Correlation Analysis for Genetic Study of Quantitative Traits in Alzheimer's Disease. 偏好矩阵引导稀疏典型相关分析在阿尔茨海默病数量性状遗传研究中的应用。
Proceedings. IEEE International Conference on Bioinformatics and Biomedicine Pub Date : 2022-12-01 DOI: 10.1109/bibm55620.2022.9995342
Jiahang Sha, Jingxuan Bao, Kefei Liu, Shu Yang, Zixuan Wen, Yuhan Cui, Junhao Wen, Christos Davatzikos, Jason H Moore, Andrew J Saykin, Qi Long, Li Shen
{"title":"Preference Matrix Guided Sparse Canonical Correlation Analysis for Genetic Study of Quantitative Traits in Alzheimer's Disease.","authors":"Jiahang Sha, Jingxuan Bao, Kefei Liu, Shu Yang, Zixuan Wen, Yuhan Cui, Junhao Wen, Christos Davatzikos, Jason H Moore, Andrew J Saykin, Qi Long, Li Shen","doi":"10.1109/bibm55620.2022.9995342","DOIUrl":"10.1109/bibm55620.2022.9995342","url":null,"abstract":"<p><p>Investigating the relationship between genetic variation and phenotypic traits is a key issue in quantitative genetics. Specifically for Alzheimer's disease, the association between genetic markers and quantitative traits remains vague while, once identified, will provide valuable guidance for the study and development of genetic-based treatment approaches. Currently, to analyze the association of two modalities, sparse canonical correlation analysis (SCCA) is commonly used to compute one sparse linear combination of the variable features for each modality, giving a pair of linear combination vectors in total that maximizes the cross-correlation between the analyzed modalities. One drawback of the plain SCCA model is that the existing findings and knowledge cannot be integrated into the model as priors to help extract interesting correlation as well as identify biologically meaningful genetic and phenotypic markers. To bridge this gap, we introduce preference matrix guided SCCA (PM-SCCA) that not only takes priors encoded as a preference matrix but also maintains computational simplicity. A simulation study and a real-data experiment are conducted to investigate the effectiveness of the model. Both experiments demonstrate that the proposed PM-SCCA model can capture not only genotype-phenotype correlation but also relevant features effectively.</p>","PeriodicalId":74563,"journal":{"name":"Proceedings. IEEE International Conference on Bioinformatics and Biomedicine","volume":"2022 ","pages":"541-548"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9944667/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9178366","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Identification of Social and Racial Disparities in Risk of HIV Infection in Florida using Causal AI Methods. 使用因果 AI 方法识别佛罗里达州艾滋病毒感染风险的社会和种族差异。
Proceedings. IEEE International Conference on Bioinformatics and Biomedicine Pub Date : 2022-12-01 Epub Date: 2023-01-02 DOI: 10.1109/bibm55620.2022.9995662
Mattia Prosperi, Jie Xu, Jingchuan Serena Guo, Jiang Bian, Wei-Han William Chen, Shantrel Canidate, Simone Marini, Mo Wang
{"title":"Identification of Social and Racial Disparities in Risk of HIV Infection in Florida using Causal AI Methods.","authors":"Mattia Prosperi, Jie Xu, Jingchuan Serena Guo, Jiang Bian, Wei-Han William Chen, Shantrel Canidate, Simone Marini, Mo Wang","doi":"10.1109/bibm55620.2022.9995662","DOIUrl":"10.1109/bibm55620.2022.9995662","url":null,"abstract":"<p><p>Florida -the 3<sup>rd</sup> most populous state in the USA-has the highest rates of Human Immunodeficiency Virus (HIV) infections and of unfavorable HIV outcomes, with marked social and racial disparities. In this work, we leveraged large-scale, real-world data, i.e., statewide surveillance records and publicly available data resources encoding social determinants of health (SDoH), to identify social and racial disparities contributing to individuals' risk of HIV infection. We used the Florida Department of Health's Syndromic Tracking and Reporting System (STARS) database (including 100,000+ individuals screened for HIV infection and their partners), and a novel algorithmic fairness assessment method -the Fairness-Aware Causal paThs decompoSition (FACTS)- merging causal inference and artificial intelligence. FACTS deconstructs disparities based on SDoH and individuals' characteristics, and can discover novel mechanisms of inequity, quantifying to what extent they could be reduced by interventions. We paired the deidentified demographic information (age, gender, drug use) of 44,350 individuals in STARS -with non-missing data on interview year, county of residence, and infection status- to eight SDoH, including access to healthcare facilities, % uninsured, median household income, and violent crime rate. Using an expert-reviewed causal graph, we found that the risk of HIV infection for African Americans was higher than for non- African Americans (both in terms of direct and total effect), although a null effect could not be ruled out. FACTS identified several paths leading to racial disparity in HIV risk, including multiple SDoH: education, income, violent crime, drinking, smoking, and rurality.</p>","PeriodicalId":74563,"journal":{"name":"Proceedings. IEEE International Conference on Bioinformatics and Biomedicine","volume":"2022 ","pages":"2934-2939"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9977319/pdf/nihms-1865882.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9077775","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Cell-type Deconvolution and Age Estimation Using DNA Methylation Reveals NK Cell Deficiency in the Hepatocellular Carcinoma Microenvironment. 细胞型反褶积和使用DNA甲基化的年龄估计揭示了肝癌微环境中NK细胞的缺陷。
Proceedings. IEEE International Conference on Bioinformatics and Biomedicine Pub Date : 2022-12-01 DOI: 10.1109/BIBM55620.2022.9995041
Sidharth S Jain, Megan E Barefoot, Rency S Varghese, Habtom W Ressom
{"title":"Cell-type Deconvolution and Age Estimation Using DNA Methylation Reveals NK Cell Deficiency in the Hepatocellular Carcinoma Microenvironment.","authors":"Sidharth S Jain,&nbsp;Megan E Barefoot,&nbsp;Rency S Varghese,&nbsp;Habtom W Ressom","doi":"10.1109/BIBM55620.2022.9995041","DOIUrl":"https://doi.org/10.1109/BIBM55620.2022.9995041","url":null,"abstract":"<p><p>Hepatocellular carcinoma (HCC) has been an approved indication for the administration of immunotherapy since 2017, but biomarkers that predict therapeutic response have remained limited. Understanding and characterizing the tumor immune microenvironment enables better classification of these tumors and may reveal biomarkers that predict immunotherapeutic efficacy. In this paper, we applied a cell-type deconvolution algorithm using DNA methylation array data to investigate the composition of the tumor microenvironment in HCC. Using two publicly available datasets with a total cohort size of 57 patients, each with tumor and matched normal tissue samples, we identified key differences in immune cell composition. We found that NK cell abundance was significantly decreased in HCC tumors compared to adjacent normal tissue. We also applied DNA methylation \"clocks\" which estimate phenotypic aging and compared these findings to expression-based determinations of cellular senescence. Senescence and epigenetic aging was significantly increased in HCC tumors, and the degree of age acceleration and senescence was strongly associated with decreased NK cell abundance. In summary, we found that NK cell infiltration in the tumor microenvironment is significantly diminished, and that this loss of NK abundance is strongly associated with increased senescence and age-related phenotype. These findings point to key interactions between NK cells and the senescent tumor microenvironment and offer insights into the pathogenesis of HCC as well as potential biomarkers of therapeutic efficacy.</p>","PeriodicalId":74563,"journal":{"name":"Proceedings. IEEE International Conference on Bioinformatics and Biomedicine","volume":"2022 ","pages":"444-449"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10473873/pdf/nihms-1915567.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10150390","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Mediation Analysis and Mixed-Effects Models for the Identification of Stage-specific Imaging Genetics Patterns in Alzheimer's Disease. 鉴定阿尔茨海默病阶段特异性成像遗传模式的中介分析和混合效应模型。
Proceedings. IEEE International Conference on Bioinformatics and Biomedicine Pub Date : 2022-12-01 DOI: 10.1109/bibm55620.2022.9995405
Daniele Pala, Brian Lee, Xia Ning, Dokyoon Kim, Li Shen
{"title":"Mediation Analysis and Mixed-Effects Models for the Identification of Stage-specific Imaging Genetics Patterns in Alzheimer's Disease.","authors":"Daniele Pala, Brian Lee, Xia Ning, Dokyoon Kim, Li Shen","doi":"10.1109/bibm55620.2022.9995405","DOIUrl":"10.1109/bibm55620.2022.9995405","url":null,"abstract":"<p><p>Alzheimer's disease (AD) is one of the most common and severe forms of Senile Dementia. Genome-wide association studies (GWAS) have identified dozens of AD susceptible loci. To better understand potential mechanism-of-action for AD, quantitative brain imaging features have been studied as mediators linking genetic variants to AD outcomes. In this study, Mediation analysis, Chow test and Mixed-effects Models are used to investigate the biological pathways by which genetic variants affect both brain structures/functions and disease diagnosis. We analyzed the imaging and genetics data collected from the Alzheimer's Disease Neuroimaging Initiative (ADNI) project, including a Polygenic Hazard Score (PHS) and 13 imaging quantitative traits (QTs) extracted from the AV45 PET scans quantifying the amyloid deposition in different brain regions of subjects from four separate diagnostic groups. Mediation analysis assessed the mediating effects of image QTs between PHS and diagnosis, whereas Chow test and Linear Mixed-Effects models were used to characterize intra-group differences in the associations between genetic scores and imaging QTs for different disease stages. Results show that promising stage-specific imaging QTs that mediate the genetic effect of the studied PHS on disease status have been identified, providing novel insights into the predictive power of the PHS and the mediating power of amyloid imaging QTs with respect to multiple stages over the AD progression.</p>","PeriodicalId":74563,"journal":{"name":"Proceedings. IEEE International Conference on Bioinformatics and Biomedicine","volume":"2022 ","pages":"2667-2673"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9942815/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9168979","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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