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Ling Y, Tariq MB, Tang K, Aronowski J, Fann Y, Savitz SI, Jiang X, Kim Y. An interpretable framework to identify responsive subgroups from clinical trials regarding treatment effects: Application to treatment of intracerebral hemorrhage. PLOS Digit Health 2024; 3:e0000493. [PMID: 38713647 DOI: 10.1371/journal.pdig.0000493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 03/26/2024] [Indexed: 05/09/2024]
Abstract
Randomized Clinical trials (RCT) suffer from a high failure rate which could be caused by heterogeneous responses to treatment. Despite many models being developed to estimate heterogeneous treatment effects (HTE), there remains a lack of interpretable methods to identify responsive subgroups. This work aims to develop a framework to identify subgroups based on treatment effects that prioritize model interpretability. The proposed framework leverages an ensemble uplift tree method to generate descriptive decision rules that separate samples given estimated responses to the treatment. Subsequently, we select a complementary set of these decision rules and rank them using a sparse linear model. To address the trial's limited sample size problem, we proposed a data augmentation strategy by borrowing control patients from external studies and generating synthetic data. We apply the proposed framework to a failed randomized clinical trial for investigating an intracerebral hemorrhage therapy plan. The Qini-scores show that the proposed data augmentation strategy plan can boost the model's performance and the framework achieves greater interpretability by selecting complementary descriptive rules without compromising estimation quality. Our model derives clinically meaningful subgroups. Specifically, we find those patients with Diastolic Blood Pressure≥70 mm hg and Systolic Blood Pressure<215 mm hg benefit more from intensive blood pressure reduction therapy. The proposed interpretable HTE analysis framework offers a promising potential for extracting meaningful insight from RCTs with neutral treatment effects. By identifying responsive subgroups, our framework can contribute to developing personalized treatment strategies for patients more efficiently.
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Affiliation(s)
- Yaobin Ling
- D.Bradley Mc.Williams School of Biomedical Informatics, UTHealth at Houston, Houston, Texas, United States of America
| | - Muhammad Bilal Tariq
- Department of Neurology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Kaichen Tang
- D.Bradley Mc.Williams School of Biomedical Informatics, UTHealth at Houston, Houston, Texas, United States of America
| | - Jaroslaw Aronowski
- Institute for Stroke and Cerebrovascular Disease, UTHealth at Houston, Houston, Texas, United States of America
| | - Yang Fann
- Intramural Research Program, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sean I Savitz
- Institute for Stroke and Cerebrovascular Disease, UTHealth at Houston, Houston, Texas, United States of America
| | - Xiaoqian Jiang
- D.Bradley Mc.Williams School of Biomedical Informatics, UTHealth at Houston, Houston, Texas, United States of America
| | - Yejin Kim
- D.Bradley Mc.Williams School of Biomedical Informatics, UTHealth at Houston, Houston, Texas, United States of America
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Abstract
The Biomedical Research Informatics Computing System (BRICS) was developed to support multiple disease-focused research programs. Seven service modules are integrated together to provide a collaborative and extensible web-based environment. The modules-Data Dictionary, Account Management, Query Tool, Protocol and Form Research Management System, Meta Study, Data Repository and Globally Unique Identifier -facilitate the management of research protocols, to submit, process, curate, access and store clinical, imaging, and derived genomics data within the associated data repositories. Multiple instances of BRICS are deployed to support various biomedical research communities focused on accelerating discoveries for rare diseases, Traumatic Brain Injury, Parkinson's Disease, inherited eye diseases and symptom science research. No Personally Identifiable Information is stored within the data repositories. Digital Object Identifiers are associated with the research studies. Reusability of biomedical data is enhanced by Common Data Elements (CDEs) which enable systematic collection, analysis and sharing of data. The use of CDEs with a service-oriented informatics architecture enabled the development of disease-specific repositories that support hypothesis-based biomedical research.
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Affiliation(s)
- Vivek Navale
- Office of Intramural Research, Center for Information Technology, National Institutes of Health, USA, Bethesda, Maryland, 20892, USA
| | - Michele Ji
- Office of Intramural Research, Center for Information Technology, National Institutes of Health, USA, Bethesda, Maryland, 20892, USA
| | - Olga Vovk
- General Dynamics Information Technology, Inc., Fairfax, Virginia, 22030, USA
| | | | | | - Alison Garcia
- Sapient Government Services, Arlington, Virginia, 22201, USA
| | - Yang Fann
- Intramural IT and Bioinformatics Program, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Matthew McAuliffe
- Office of Intramural Research, Center for Information Technology, National Institutes of Health, USA, Bethesda, Maryland, 20892, USA
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Unno K, Oikonomopoulos A, Fujikawa Y, Okuno Y, Narita S, Kato T, Hayashida R, Kondo K, Shibata R, Murohara T, Yang Y, Dangwal S, Sereti KI, Yiling Q, Johnson K, Jha A, Sosnovik DE, Fann Y, Liao R. Alteration in ventricular pressure stimulates cardiac repair and remodeling. J Mol Cell Cardiol 2019; 133:174-187. [PMID: 31220468 DOI: 10.1016/j.yjmcc.2019.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 06/07/2019] [Accepted: 06/11/2019] [Indexed: 12/29/2022]
Abstract
The mammalian heart undergoes complex structural and functional remodeling to compensate for stresses such as pressure overload. While studies suggest that, at best, the adult mammalian heart is capable of very limited regeneration arising from the proliferation of existing cardiomyocytes, how myocardial stress affects endogenous cardiac regeneration or repair is unknown. To define the relationship between left ventricular afterload and cardiac repair, we induced left ventricle pressure overload in adult mice by constriction of the ascending aorta (AAC). One week following AAC, we normalized ventricular afterload in a subset of animals through removal of the aortic constriction (de-AAC). Subsequent monitoring of cardiomyocyte cell cycle activity via thymidine analog labeling revealed that an acute increase in ventricular afterload induced cardiomyocyte proliferation. Intriguingly, a release in ventricular overload (de-AAC) further increases cardiomyocyte proliferation. Following both AAC and de-AAC, thymidine analog-positive cardiomyocytes exhibited characteristics of newly generated cardiomyocytes, including single diploid nuclei and reduced cell size as compared to age-matched, sham-operated adult mouse myocytes. Notably, those smaller cardiomyocytes frequently resided alongside one another, consistent with local stimulation of cellular proliferation. Collectively, our data demonstrate that adult cardiomyocyte proliferation can be locally stimulated by an acute increase or decrease of ventricular pressure, and this mode of stimulation can be harnessed to promote cardiac repair.
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Affiliation(s)
- Kazumasa Unno
- Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America; Department of Cardiology, Nagoya University Graduate School of Medicine, Nagoya, Japan.
| | - Angelos Oikonomopoulos
- Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America; Cardiovascular Research Institute, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Yusuke Fujikawa
- Department of Cardiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yusuke Okuno
- Deparment of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Singo Narita
- Department of Cardiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tomohiro Kato
- Department of Cardiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Ryo Hayashida
- Department of Cardiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuhisa Kondo
- Department of Cardiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Rei Shibata
- Department of Cardiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Toyoaki Murohara
- Department of Cardiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yanfei Yang
- Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Seema Dangwal
- Cardiovascular Research Institute, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Konstantina-Ioanna Sereti
- Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America; Department of Molecular Biology, Genentech, CA, United States of America
| | - Qiu Yiling
- Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Kory Johnson
- Bioinformatics Section, DIR, ITP, NINDS, NIH, Bethesda, MD, United States of America
| | - Alokkumar Jha
- Insight Center for Data Analytics, National University of Ireland, Galway, Ireland
| | - David E Sosnovik
- Harvard Medical School, Program in Cardiovascular Imaging, MGH-Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States of America
| | - Yang Fann
- Bioinformatics Section, DIR, ITP, NINDS, NIH, Bethesda, MD, United States of America
| | - Ronglih Liao
- Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America; Cardiovascular Research Institute, Stanford University School of Medicine, Stanford, CA, United States of America.
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Hao H, Kim DS, Klocke B, Johnson KR, Cui K, Gotoh N, Zang C, Gregorski J, Gieser L, Peng W, Fann Y, Seifert M, Zhao K, Swaroop A. Transcriptional regulation of rod photoreceptor homeostasis revealed by in vivo NRL targetome analysis. PLoS Genet 2012; 8:e1002649. [PMID: 22511886 PMCID: PMC3325202 DOI: 10.1371/journal.pgen.1002649] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 02/23/2012] [Indexed: 11/18/2022] Open
Abstract
A stringent control of homeostasis is critical for functional maintenance and survival of neurons. In the mammalian retina, the basic motif leucine zipper transcription factor NRL determines rod versus cone photoreceptor cell fate and activates the expression of many rod-specific genes. Here, we report an integrated analysis of NRL-centered gene regulatory network by coupling chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq) data from Illumina and ABI platforms with global expression profiling and in vivo knockdown studies. We identified approximately 300 direct NRL target genes. Of these, 22 NRL targets are associated with human retinal dystrophies, whereas 95 mapped to regions of as yet uncloned retinal disease loci. In silico analysis of NRL ChIP-Seq peak sequences revealed an enrichment of distinct sets of transcription factor binding sites. Specifically, we discovered that genes involved in photoreceptor function include binding sites for both NRL and homeodomain protein CRX. Evaluation of 26 ChIP-Seq regions validated their enhancer functions in reporter assays. In vivo knockdown of 16 NRL target genes resulted in death or abnormal morphology of rod photoreceptors, suggesting their importance in maintaining retinal function. We also identified histone demethylase Kdm5b as a novel secondary node in NRL transcriptional hierarchy. Exon array analysis of flow-sorted photoreceptors in which Kdm5b was knocked down by shRNA indicated its role in regulating rod-expressed genes. Our studies identify candidate genes for retinal dystrophies, define cis-regulatory module(s) for photoreceptor-expressed genes and provide a framework for decoding transcriptional regulatory networks that dictate rod homeostasis.
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Affiliation(s)
- Hong Hao
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Douglas S. Kim
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | | | - Kory R. Johnson
- Information Technology and Bioinformatics Program, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kairong Cui
- Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Norimoto Gotoh
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Chongzhi Zang
- Department of Physics, The George Washington University, Washington, D.C., United States of America
| | - Janina Gregorski
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Linn Gieser
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Weiqun Peng
- Department of Physics, The George Washington University, Washington, D.C., United States of America
| | - Yang Fann
- Information Technology and Bioinformatics Program, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | | | - Keji Zhao
- Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Anand Swaroop
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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Friedman JS, Ray JW, Waseem N, Johnson K, Brooks MJ, Hugosson T, Breuer D, Branham KE, Krauth DS, Bowne SJ, Sullivan LS, Ponjavic V, Gränse L, Khanna R, Trager EH, Gieser LM, Hughbanks-Wheaton D, Cojocaru RI, Ghiasvand NM, Chakarova CF, Abrahamson M, Göring HH, Webster AR, Birch DG, Abecasis GR, Fann Y, Bhattacharya SS, Daiger SP, Heckenlively JR, Andréasson S, Swaroop A. Mutations in a BTB-Kelch protein, KLHL7, cause autosomal-dominant retinitis pigmentosa. Am J Hum Genet 2009; 84:792-800. [PMID: 19520207 DOI: 10.1016/j.ajhg.2009.05.007] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Revised: 05/19/2009] [Accepted: 05/20/2009] [Indexed: 01/08/2023] Open
Abstract
Retinitis pigmentosa (RP) refers to a genetically heterogeneous group of progressive neurodegenerative diseases that result in dysfunction and/or death of rod and cone photoreceptors in the retina. So far, 18 genes have been identified for autosomal-dominant (ad) RP. Here, we describe an adRP locus (RP42) at chromosome 7p15 through linkage analysis in a six-generation Scandinavian family and identify a disease-causing mutation, c.449G-->A (p.S150N), in exon 6 of the KLHL7 gene. Mutation screening of KLHL7 in 502 retinopathy probands has revealed three different missense mutations in six independent families. KLHL7 is widely expressed, including expression in rod photoreceptors, and encodes a 75 kDa protein of the BTB-Kelch subfamily within the BTB superfamily. BTB-Kelch proteins have been implicated in ubiquitination through Cullin E3 ligases. Notably, all three putative disease-causing KLHL7 mutations are within a conserved BACK domain; homology modeling suggests that mutant amino acid side chains can potentially fill the cleft between two helices, thereby affecting the ubiquitination complexes. Mutations in an identical region of another BTB-Kelch protein, gigaxonin, have previously been associated with giant axonal neuropathy. Our studies suggest an additional role of the ubiquitin-proteasome protein-degradation pathway in maintaining neuronal health and in disease.
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Brody T, Yavatkar AS, Lin Y, Ross J, Kuzin A, Kundu M, Fann Y, Odenwald WF. Horizontal gene transfers link a human MRSA pathogen to contagious bovine mastitis bacteria. PLoS One 2008; 3:e3074. [PMID: 18728754 PMCID: PMC2518619 DOI: 10.1371/journal.pone.0003074] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2008] [Accepted: 08/07/2008] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Acquisition of virulence factors and antibiotic resistance by many clinically important bacteria can be traced to horizontal gene transfer (HGT) between related or evolutionarily distant microflora. Comparative genomic analysis has become an important tool for identifying HGT DNA in emerging pathogens. We have adapted the multi-genome alignment tool EvoPrinter to facilitate discovery of HGT DNA sequences within bacterial genomes and within their mobile genetic elements. PRINCIPAL FINDINGS EvoPrinter analysis of 13 different Staphylococcus aureus genomes revealed that one of the human isolates, the hospital epidemic methicillin-resistant MRSA252 strain, uniquely shares multiple putative HGT DNA sequences with different causative agents of bovine mastitis that are not found in the other human S. aureus isolates. MRSA252 shares over 14 different DNA sequence blocks with the bovine mastitis ET3 S. aureus strain RF122, and many of the HGT DNAs encode virulence factors. EvoPrinter analysis of the MRSA252 chromosome also uncovered virulence-factor encoding HGT events with the genome of Listeria monocytogenes and a Staphylococcus saprophyticus associated plasmid. Both bacteria are also causal agents of contagious bovine mastitis. CONCLUSIONS EvoPrinter analysis reveals that the human MRSA252 strain uniquely shares multiple DNA sequence blocks with different causative agents of bovine mastitis, suggesting that HGT events may be occurring between these pathogens. These findings have important implications with regard to animal husbandry practices that inadvertently enhance the contact of human and livestock bacterial pathogens.
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Affiliation(s)
- Thomas Brody
- The Neural Cell-Fate Determinants Section, National Institutes of Health (NIH), Bethesda, Maryland, USA.
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Yavatkar AS, Lin Y, Ross J, Fann Y, Brody T, Odenwald WF. Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis. BMC Genomics 2008; 9:106. [PMID: 18307801 PMCID: PMC2268679 DOI: 10.1186/1471-2164-9-106] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Accepted: 02/28/2008] [Indexed: 12/04/2022] Open
Abstract
Background Multi-genome comparative analysis has yielded important insights into the molecular details of gene regulation. We have developed EvoPrinter, a web-accessed genomics tool that provides a single uninterrupted view of conserved sequences as they appear in a species of interest. An EvoPrint reveals with near base-pair resolution those sequences that are essential for gene function. Results We describe here EvoPrinterHD, a 2nd-generation comparative genomics tool that automatically generates from a single input sequence an enhanced view of sequence conservation between evolutionarily distant species. Currently available for 5 nematode, 3 mosquito, 12 Drosophila, 20 vertebrate, 17 Staphylococcus and 20 enteric bacteria genomes, EvoPrinterHD employs a modified BLAT algorithm [enhanced-BLAT (eBLAT)], which detects up to 75% more conserved bases than identified by the BLAT alignments used in the earlier EvoPrinter program. The new program also identifies conserved sequences within rearranged DNA, highlights repetitive DNA, and detects sequencing gaps. EvoPrinterHD currently holds over 112 billion bp of indexed genomes in memory and has the flexibility of selecting a subset of genomes for analysis. An EvoDifferences profile is also generated to portray conserved sequences that are uniquely lost in any one of the orthologs. Finally, EvoPrinterHD incorporates options that allow for (1) re-initiation of the analysis using a different genome's aligning region as the reference DNA to detect species-specific changes in less-conserved regions, (2) rapid extraction and curation of conserved sequences, and (3) for bacteria, identifies unique or uniquely shared sequences present in subsets of genomes. Conclusion EvoPrinterHD is a fast, high-resolution comparative genomics tool that automatically generates an uninterrupted species-centric view of sequence conservation and enables the discovery of conserved sequences within rearranged DNA. When combined with cis-Decoder, a program that discovers sequence elements shared among tissue specific enhancers, EvoPrinterHD facilitates the analysis of conserved sequences that are essential for coordinate gene regulation.
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Affiliation(s)
- Amarendra S Yavatkar
- 1Division of Intramural Research, Information Technology Program, NINDS, NIH, Bethesda, Maryland, USA.
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Cheung H, Wang SA, Fann Y, Upender B, Chinatala S, Frazin A, Nie W, Johnson C. A web-based, meta-data drive, clinical research platform for managing multiple clinical research studies. AMIA Annu Symp Proc 2007:906. [PMID: 18694006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/14/2007] [Accepted: 10/11/2007] [Indexed: 05/26/2023]
Abstract
Clinical studies are very dynamic in nature. This poses a great challenge in building an adaptable informatics platform to support evolving clinical research needs. Center for Information Technology (CIT) at the National Institutes of Health (NIH), in collaboration with the National Institute of Neurological Disorders and Stroke (NINDS), has developed a web-based Clinical Study Information System (CSIS) to support efficient management of clinical data that would improve the quality and timeliness of conducting clinical research. CSIS allows Principal Investigators(PI) to design new electronic Case Report Forms(eCRF) using a Form Designer. A patient registry module enables the study coordinators to recruit and screen new subjects. Most importantly, an ad-hoc query engine allows investigators to stratify patient groups and export data by specifying arbitrarily complex criteria without having to learn database syntax.
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Affiliation(s)
- Huey Cheung
- Center for Information Technology, National Istitutes of Health, Bethesda, MD, USA
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