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Tripathi S, Shirnekhi HK, Gorman SD, Chandra B, Baggett DW, Park CG, Somjee R, Lang B, Hosseini SMH, Pioso BJ, Li Y, Iacobucci I, Gao Q, Edmonson MN, Rice SV, Zhou X, Bollinger J, Mitrea DM, White MR, McGrail DJ, Jarosz DF, Yi SS, Babu MM, Mullighan CG, Zhang J, Sahni N, Kriwacki RW. Defining the condensate landscape of fusion oncoproteins. Nat Commun 2023; 14:6008. [PMID: 37770423 PMCID: PMC10539325 DOI: 10.1038/s41467-023-41655-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 09/13/2023] [Indexed: 09/30/2023] Open
Abstract
Fusion oncoproteins (FOs) arise from chromosomal translocations in ~17% of cancers and are often oncogenic drivers. Although some FOs can promote oncogenesis by undergoing liquid-liquid phase separation (LLPS) to form aberrant biomolecular condensates, the generality of this phenomenon is unknown. We explored this question by testing 166 FOs in HeLa cells and found that 58% formed condensates. The condensate-forming FOs displayed physicochemical features distinct from those of condensate-negative FOs and segregated into distinct feature-based groups that aligned with their sub-cellular localization and biological function. Using Machine Learning, we developed a predictor of FO condensation behavior, and discovered that 67% of ~3000 additional FOs likely form condensates, with 35% of those predicted to function by altering gene expression. 47% of the predicted condensate-negative FOs were associated with cell signaling functions, suggesting a functional dichotomy between condensate-positive and -negative FOs. Our Datasets and reagents are rich resources to interrogate FO condensation in the future.
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Affiliation(s)
- Swarnendu Tripathi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hazheen K Shirnekhi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Scott D Gorman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Arrakis Therapeutics, 830 Winter St, Waltham, MA, 02451, USA
| | - Bappaditya Chandra
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - David W Baggett
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cheon-Gil Park
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ramiz Somjee
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Rhodes College, Memphis, TN, USA
- Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO, 63110, USA
| | - Benjamin Lang
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Center of Excellence for Data-Driven Discovery, Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Seyed Mohammad Hadi Hosseini
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Center of Excellence for Data-Driven Discovery, Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Brittany J Pioso
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yongsheng Li
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Qingsong Gao
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael N Edmonson
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stephen V Rice
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - John Bollinger
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Diana M Mitrea
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Dewpoint Therapeutics, 451 D Street, Suite 104, Boston, MA, 02210, USA
| | - Michael R White
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- IDEXX Laboratories, Inc., One IDEXX Drive, Westbrook, ME, 04092, USA
| | - Daniel J McGrail
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH, USA
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - S Stephen Yi
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, 78712, USA
- Department of Biomedical Engineering, and Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX, USA
| | - M Madan Babu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Center of Excellence for Data-Driven Discovery, Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Nidhi Sahni
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center, Memphis, TN, USA.
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Tripathi S, Mattioli P, Liguori C, Chiaravalloti A, Arnaldi D, Giancardo L. Brain Hemisphere Dissimilarity, a Self-Supervised Learning Approach for alpha-synucleinopathies prediction with FDG PET. Proc IEEE Int Symp Biomed Imaging 2023; 2023:10.1109/isbi53787.2023.10230560. [PMID: 37706192 PMCID: PMC10496490 DOI: 10.1109/isbi53787.2023.10230560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
Idiopathic Rem sleep Behavior Disorder (iRBD) is a significant biomarker for the development of alpha-synucleinopathies, such as Parkinson's disease (PD) or Dementia with Lewy bodies (DLB). Methods to identify patterns in iRBD patients can help in the prediction of the future conversion to these diseases during the long prodromal phase when symptoms are non-specific. These methods are essential for disease management and clinical trial recruitment. Brain PET scans with 18F-FDG PET radiotracers have recently shown promise, however, the scarcity of longitudinal data and PD/DLB conversion information makes the use of representation learning approaches such as deep convolutional networks not feasible if trained in a supervised manner. In this work, we propose a self-supervised learning strategy to learn features by comparing the brain hemispheres of iRBD non-convertor subjects, which allows for pre-training a convolutional network on a small data regimen. We introduce a loss function called hemisphere dissimilarity loss (HDL), which extends the Barlow Twins loss, that promotes the creation of invariant and non-redundant features for brain hemispheres of the same subject, and the opposite for hemispheres of different subjects. This loss enables the pre-training of a network without any information about the disease, which is then used to generate full brain feature vectors that are fine-tuned to two downstream tasks: follow-up conversion, and the type of conversion (PD or DLB) using baseline 18F-FDG PET. In our results, we find that the HDL outperforms the variational autoencoder with different forms of inputs.
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Affiliation(s)
- S Tripathi
- School of Biomedical Informatics, University of Texas Health Center at Houston, TX, USA
| | - P Mattioli
- Department of Neuroscience (DINOGMI), University of Genoa, Genoa, Italy
| | - C Liguori
- Department of Systems Medicine, University of Rome, Rome, Italy
- Sleep Medicine Center, Neurology Unit, University Hospital of Rome, Rome, Italy
| | - A Chiaravalloti
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
- IRCCS Neuromed, Pozzilli, Italy
| | - D Arnaldi
- Department of Neuroscience (DINOGMI), University of Genoa, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - L Giancardo
- School of Biomedical Informatics, University of Texas Health Center at Houston, TX, USA
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Pioso BJ, Michmerhuizen NL, Tripathi S, Freyaldenhoven T, Phillips AH, Mullighan CG, Kriwacki R. Uncovering the leukemogenic mechanism of non-canonical NUP98 fusion oncoproteins. Biophys J 2023; 122:486a. [PMID: 36784504 DOI: 10.1016/j.bpj.2022.11.2599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
| | | | | | | | | | | | - Richard Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
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Kinger S, Pioso BJ, Tripathi S, Phillips AH, Park CG, Maiti S, Gorman SD, Asampille G, Wahiduzzaman F, Freyaldenhoven T, Baggett DW, Shirnekhi H, Chandra B, Kriwacki R. Understanding condensate formation by fusion oncoprotein-derived intrinsically disordered regions. Biophys J 2023; 122:345a. [PMID: 36783749 DOI: 10.1016/j.bpj.2022.11.1917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Swati Kinger
- St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | | | | | | | - Snigdha Maiti
- St. Jude Children's Research Hospital, Memphis, TN, USA
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Jena R, Tripathi S, Taywade S, Yadav T, Bhargava P, Choudhary G, Sandhu A. Comparison of fdg pet-ct with conventional imaging in the staging of high-risk renal cancers and transitional cell carcinoma of bladder (COPPER-T): A prospective randomized controlled trial – trial protocol and initial short-term analysis of results. Eur Urol 2023. [DOI: 10.1016/s0302-2838(23)00572-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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Baggett DW, Medyukhina A, Tripathi S, Shirnekhi HK, Wu H, Pounds SB, Khairy K, Kriwacki R. An Image Analysis Pipeline for Quantifying the Features of Fluorescently-Labeled Biomolecular Condensates in Cells. Front Bioinform 2022; 2:897238. [PMID: 36304323 PMCID: PMC9580871 DOI: 10.3389/fbinf.2022.897238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 03/15/2022] [Accepted: 05/12/2022] [Indexed: 11/13/2022] Open
Abstract
Biomolecular condensates are cellular organelles formed through liquid-liquid phase separation (LLPS) that play critical roles in cellular functions including signaling, transcription, translation, and stress response. Importantly, condensate misregulation is associated with human diseases, including neurodegeneration and cancer among others. When condensate-forming biomolecules are fluorescently-labeled and examined with fluorescence microscopy they appear as illuminated foci, or puncta, in cells. Puncta features such as number, volume, shape, location, and concentration of biomolecular species within them are influenced by the thermodynamics of biomolecular interactions that underlie LLPS. Quantification of puncta features enables evaluation of the thermodynamic driving force for LLPS and facilitates quantitative comparisons of puncta formed under different cellular conditions or by different biomolecules. Our work on nucleoporin 98 (NUP98) fusion oncoproteins (FOs) associated with pediatric leukemia inspired us to develop an objective and reliable computational approach for such analyses. The NUP98-HOXA9 FO forms hundreds of punctate transcriptional condensates in cells, leading to hematopoietic cell transformation and leukemogenesis. To quantify the features of these puncta and derive the associated thermodynamic parameters, we developed a live-cell fluorescence microscopy image processing pipeline based on existing methodologies and open-source tools. The pipeline quantifies the numbers and volumes of puncta and fluorescence intensities of the fluorescently-labeled biomolecule(s) within them and generates reports of their features for hundreds of cells. Using a standard curve of fluorescence intensity versus protein concentration, the pipeline determines the apparent molar concentration of fluorescently-labeled biomolecules within and outside of puncta and calculates the partition coefficient (Kp) and Gibbs free energy of transfer (ΔGTr), which quantify the favorability of a labeled biomolecule partitioning into puncta. In addition, we provide a library of R functions for statistical analysis of the extracted measurements for certain experimental designs. The source code, analysis notebooks, and test data for the Punctatools pipeline are available on GitHub: https://github.com/stjude/punctatools. Here, we provide a protocol for applying our Punctatools pipeline to extract puncta features from fluorescence microscopy images of cells.
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Affiliation(s)
- David W. Baggett
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Anna Medyukhina
- Center for Bioimage Informatics, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Swarnendu Tripathi
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Hazheen K. Shirnekhi
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Huiyun Wu
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Stanley B. Pounds
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Khaled Khairy
- Center for Bioimage Informatics, St. Jude Children’s Research Hospital, Memphis, TN, United States
- *Correspondence: Khaled Khairy, ; Richard Kriwacki,
| | - Richard Kriwacki
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN, United States
- Integrated Biomedical Sciences Program, The University of Tennessee Science Center, Memphis, TN, United States
- *Correspondence: Khaled Khairy, ; Richard Kriwacki,
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Tripathi S, Murray A, Wischik C, Schelter B. Vascular risk factors affect different brain regions in people with Alzheimer’s disease. Eur Psychiatry 2022. [PMCID: PMC9566980 DOI: 10.1192/j.eurpsy.2022.851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Introduction Vascular risk factors including hypertension, diabetes and dyslipidaemia promote diverse pathological mechanisms in the brain leading to cerebral hypoperfusion and ultimately cognitive decline in people. Medial temporal, medial frontal and anterior cingulate atrophy has been closely associated with diabetes and medial temporal lobe atrophy is associated with hypertension in people with Alzheimer’s disease (AD). Objectives To assess if hypertension, diabetes and dyslipidaemia have differential effects on different brain locations using brain imaging in people with AD. Methods The current study is based on [18F] fluorodeoxyglucose- positron emission tomography (FDG-PET) data of 970 participants from two large Phase III multi-centre clinical trials of a novel tau aggregation inhibitor drug Leuco-Methylthioninium (LMTX)meeting research criteria for mild to moderate AD. Vascular risk factor data including hypertension, diabetes and dyslipidaemia were collected and quantification of FDG PET hypo-metabolism was done by calculating Standardized Uptake Value Ratio(SUVR). Results Hypertension, diabetes and dyslipidaemia were found to have differential effects on brain locations in people with AD. When people with hypertension, diabetes and dyslipidaemia were compared to those without, mean SUVR was increased significantly in both left and right parietal and occipital lobes and decreased in left and right anterior cingulate gyri in hypertensives. SUVR was significantly higher in both left and right temporal lobes in diabetics andlower in both left and right anterior cingulate gyri in people with dyslipidaemia. Conclusions Vascular risk factors including hypertension, diabetes and dyslipidaemia have differential effects on different brain regions, measured using SUVR analysis of FDG-PET. Disclosure The FDG-PET data was taken from participants of two large phase III clinical trials sponsored by TauRx Therapeutics (Singapore). TauRx Therapeutics has contributed towards my studentship during my PhD but the data related to drug used in the clinical tria
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Chandra B, Michmerhuizen NL, Shirnekhi HK, Tripathi S, Pioso BJ, Baggett DW, Mitrea DM, Iacobucci I, White MR, Chen J, Park CG, Wu H, Pounds S, Medyukhina A, Khairy K, Gao Q, Qu C, Abdelhamed S, Gorman SD, Bawa S, Maslanka C, Kinger S, Dogra P, Ferrolino MC, Di Giacomo D, Mecucci C, Klco JM, Mullighan CG, Kriwacki RW. Phase Separation Mediates NUP98 Fusion Oncoprotein Leukemic Transformation. Cancer Discov 2022; 12:1152-1169. [PMID: 34903620 PMCID: PMC8983581 DOI: 10.1158/2159-8290.cd-21-0674] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 11/08/2021] [Accepted: 12/09/2021] [Indexed: 01/07/2023]
Abstract
NUP98 fusion oncoproteins (FO) are drivers in pediatric leukemias and many transform hematopoietic cells. Most NUP98 FOs harbor an intrinsically disordered region from NUP98 that is prone to liquid-liquid phase separation (LLPS) in vitro. A predominant class of NUP98 FOs, including NUP98-HOXA9 (NHA9), retains a DNA-binding homeodomain, whereas others harbor other types of DNA- or chromatin-binding domains. NUP98 FOs have long been known to form puncta, but long-standing questions are how nuclear puncta form and how they drive leukemogenesis. Here we studied NHA9 condensates and show that homotypic interactions and different types of heterotypic interactions are required to form nuclear puncta, which are associated with aberrant transcriptional activity and transformation of hematopoietic stem and progenitor cells. We also show that three additional leukemia-associated NUP98 FOs (NUP98-PRRX1, NUP98-KDM5A, and NUP98-LNP1) form nuclear puncta and transform hematopoietic cells. These findings indicate that LLPS is critical for leukemogenesis by NUP98 FOs. SIGNIFICANCE We show that homotypic and heterotypic mechanisms of LLPS control NUP98-HOXA9 puncta formation, modulating transcriptional activity and transforming hematopoietic cells. Importantly, these mechanisms are generalizable to other NUP98 FOs that share similar domain structures. These findings address long-standing questions on how nuclear puncta form and their link to leukemogenesis. This article is highlighted in the In This Issue feature, p. 873.
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Affiliation(s)
- Bappaditya Chandra
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Hazheen K. Shirnekhi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Swarnendu Tripathi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Brittany J. Pioso
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - David W. Baggett
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Diana M. Mitrea
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Michael R. White
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jingjing Chen
- Integrated Biomedical Sciences Program, the University of Tennessee Health Science Center, Memphis, Tennessee
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Cheon-Gil Park
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Huiyun Wu
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Anna Medyukhina
- Center for Bioimage Informatics, St. Jude Children's Research Hospital Memphis, Tennessee
| | - Khaled Khairy
- Center for Bioimage Informatics, St. Jude Children's Research Hospital Memphis, Tennessee
| | - Qingsong Gao
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Chunxu Qu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Sherif Abdelhamed
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Scott D. Gorman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Simranjot Bawa
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Carolyn Maslanka
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
- Rhodes College, Memphis, Tennessee
| | - Swati Kinger
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
- Rhodes College, Memphis, Tennessee
| | - Priyanka Dogra
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Mylene C. Ferrolino
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Danika Di Giacomo
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Cristina Mecucci
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Jeffery M. Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Charles G. Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
- Corresponding Authors: Richard W. Kriwacki, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105. Phone: 901-595-3290; Fax: 901-595-3032; E-mail: ; and Charles G. Mullighan,
| | - Richard W. Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center, Memphis, Tennessee
- Corresponding Authors: Richard W. Kriwacki, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105. Phone: 901-595-3290; Fax: 901-595-3032; E-mail: ; and Charles G. Mullighan,
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Mishra P, Pandey R, Tripathi S, Dubey SK, Tripathi YB. Bronco T (Shirisadi kasaya), a polyherbal formulation prevents LPS induced septicemia in rats. Eur Rev Med Pharmacol Sci 2022; 26:1513-1523. [PMID: 35302196 DOI: 10.26355/eurrev_202203_28216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
OBJECTIVE Here, Bronco T (BT), a polyherbal formulation developed in 1984 for treating asthma, has been repurposed against septicemia-induced ALI. MATERIALS AND METHODS Lipopolysaccharides (3 mg/kg BW) were injected intraperitoneally before 24 hours of surgery to assess the cardiorespiratory parameters, blood PaO2/FiO2 and MPO, pulmonary water content and histological changes in the lungs. The pentoxifylline (PTX) (25 mg/kg BW) was used as the positive control and given one hour before LPS. BT was given 3 hours (orally at different doses of 3, 1.5 and 0.75 g/kg BW) before LPS. RESULTS The LPS treated group showed significant bradypnea, hypotension and bradycardia, through elongated peaks (RR) and (MAP) respectively and finally death after 95 minutes of LPS injection. The PTX and BT (3 g/kg BW) pretreatment significantly prevented these changes (dose-dependent in the BT group). The survival in these groups was maintained up to 190 min after LPS. The Pentoxifylline showed a better response (75%) than Bronco T (72%). In both the treatments, a significant decrease in pulmonary water content and minimal neutrophil infiltration and intact alveoli-capillary membrane was seen in the transverse section (T.S) of the lungs. CONCLUSIONS Significant improvement was noted in survival time with lesser tissue damage and improved pulmonary function was observed by pre-treating with Bronco T in LPS induced septicemia.
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Affiliation(s)
- P Mishra
- Department of Medicinal Chemistry, Physiology, Cardiology and Kriya Sharir, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India.
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Gorman SD, Shirnekhi H, Somjee R, Tripathi S, Park CG, Phillips AH, Chandra B, Asampille G, Ramani Joswala S, Sahni N, Zhang J, Mulligan CG, Babu M, Kriwacki R. Are fusion oncoproteins a source of disease-relevant, phase separation-prone protein regions? Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.1215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Chandra B, Michmerhuizen N, Shirnekhi H, Tripathi S, Pioso B, Medyukhina A, Khairy K, White MR, Mitrea DM, Iacobucci I, Klco JM, Mullighan CG, Kriwacki R. The role of phase separation by NUP98 fusion oncoproteins in leukemia. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Tripathi S, Dsouza NR, Mathison AJ, Leverence E, Urrutia R, Zimmermann MT. Enhanced interpretation of 935 hotspot and non-hotspot RAS variants using evidence-based structural bioinformatics. Comput Struct Biotechnol J 2022; 20:117-127. [PMID: 34976316 PMCID: PMC8688876 DOI: 10.1016/j.csbj.2021.12.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 12/05/2021] [Accepted: 12/05/2021] [Indexed: 12/30/2022] Open
Abstract
In the current study, we report computational scores for advancing genomic interpretation of disease-associated genomic variation in members of the RAS family of genes. For this purpose, we applied 31 sequence- and 3D structure-based computational scores, chosen by their breadth of biophysical properties. We parametrized our data by assembling a numerically homogenized experimentally-derived dataset, which when use in our calculations reveal that computational scores using 3D structure highly correlate with experimental measures (e.g., GAP-mediated hydrolysis RSpearman = 0.80 and RAF affinity Rspearman = 0.82), while sequence-based scores are discordant with this data. Performing all-against-all comparisons, we applied this parametrized modeling approach to the study of 935 RAS variants from 7 RAS genes, which led us to identify 4 groups of mutations according to distinct biochemical scores within each group. Each group was comprised of hotspot and non-hotspot KRAS variants, indicating that poorly characterized variants could functionally behave like pathogenic mutations. Combining computational scores using dimensionality reduction indicated that changes to local unfolding propensity associate with changes in enzyme activity by genomic variants. Hence, our systematic approach, combining methodologies from both clinical genomics and 3D structural bioinformatics, represents an expansion for interpreting genomic data, provides information of mechanistic value, and that is transferable to other proteins.
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Affiliation(s)
- Swarnendu Tripathi
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Nikita R Dsouza
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Angela J Mathison
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Elise Leverence
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Raul Urrutia
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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13
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Stodola TJ, Chi YI, De Assuncao TM, Leverence EN, Tripathi S, Dsouza NR, Mathison AJ, Volkman BF, Smith BC, Lomberk G, Zimmermann MT, Urrutia R. Computational modeling reveals key molecular properties and dynamic behavior of disruptor of telomeric silencing 1-like (DOT1L) and partnering complexes involved in leukemogenesis. Proteins 2021; 90:282-298. [PMID: 34414607 PMCID: PMC8671179 DOI: 10.1002/prot.26219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 08/16/2021] [Indexed: 11/18/2022]
Abstract
Disruptor of telomeric silencing 1‐like (DOT1L) is the only non‐SET domain histone lysine methyltransferase (KMT) and writer of H3K79 methylation on nucleosomes marked by H2B ubiquitination. DOT1L has elicited significant attention because of its interaction or fusion with members of the AF protein family in blood cell biology and leukemogenic transformation. Here, our goal was to extend previous structural information by performing a robust molecular dynamic study of DOT1L and its leukemogenic partners combined with mutational analysis. We show that statically and dynamically, D161, G163, E186, and F223 make frequent time‐dependent interactions with SAM, while additional residues T139, K187, and N241 interact with SAM only under dynamics. Dynamics models reveal DOT1L, SAM, and H4 moving as one and show that more than twice the number of DOT1L residues interacts with these partners, relative to the static structure. Mutational analyses indicate that six of these residues are intolerant to substitution. We describe the dynamic behavior of DOT1L interacting with AF10 and AF9. Studies on the dynamics of a heterotrimeric complex of DOT1L1‐AF10 illuminated describe coordinated motions that impact the relative position of the DOT1L HMT domain to the nucleosome. The molecular motions of the DOT1L–AF9 complex are less extensive and highly dynamic, resembling a swivel‐like mechanics. Through molecular dynamics and mutational analysis, we extend the knowledge previous provided by static measurements. These results are important to consider when describing the biochemical properties of DOT1L, under normal and in disease conditions, as well as for the development of novel therapeutic agents.
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Affiliation(s)
- Timothy J Stodola
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Young-In Chi
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Thiago M De Assuncao
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Elise N Leverence
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Swarnendu Tripathi
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Nikita R Dsouza
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Angela J Mathison
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Brian C Smith
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Gwen Lomberk
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Michael T Zimmermann
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Raul Urrutia
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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14
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Cousin MA, Creighton BA, Breau KA, Spillmann RC, Torti E, Dontu S, Tripathi S, Ajit D, Edwards RJ, Afriyie S, Bay JC, Harper KM, Beltran AA, Munoz LJ, Falcon Rodriguez L, Stankewich MC, Person RE, Si Y, Normand EA, Blevins A, May AS, Bier L, Aggarwal V, Mancini GMS, van Slegtenhorst MA, Cremer K, Becker J, Engels H, Aretz S, MacKenzie JJ, Brilstra E, van Gassen KLI, van Jaarsveld RH, Oegema R, Parsons GM, Mark P, Helbig I, McKeown SE, Stratton R, Cogne B, Isidor B, Cacheiro P, Smedley D, Firth HV, Bierhals T, Kloth K, Weiss D, Fairley C, Shieh JT, Kritzer A, Jayakar P, Kurtz-Nelson E, Bernier RA, Wang T, Eichler EE, van de Laar IMBH, McConkie-Rosell A, McDonald MT, Kemppainen J, Lanpher BC, Schultz-Rogers LE, Gunderson LB, Pichurin PN, Yoon G, Zech M, Jech R, Winkelmann J, Beltran AS, Zimmermann MT, Temple B, Moy SS, Klee EW, Tan QKG, Lorenzo DN. Pathogenic SPTBN1 variants cause an autosomal dominant neurodevelopmental syndrome. Nat Genet 2021; 53:1006-1021. [PMID: 34211179 PMCID: PMC8273149 DOI: 10.1038/s41588-021-00886-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [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: 08/27/2020] [Accepted: 05/14/2021] [Indexed: 12/22/2022]
Abstract
SPTBN1 encodes βII-spectrin, the ubiquitously expressed β-spectrin that forms micrometer-scale networks associated with plasma membranes. Mice deficient in neuronal βII-spectrin have defects in cortical organization, developmental delay and behavioral deficiencies. These phenotypes, while less severe, are observed in haploinsufficient animals, suggesting that individuals carrying heterozygous SPTBN1 variants may also show measurable compromise of neural development and function. Here we identify heterozygous SPTBN1 variants in 29 individuals with developmental, language and motor delays; mild to severe intellectual disability; autistic features; seizures; behavioral and movement abnormalities; hypotonia; and variable dysmorphic facial features. We show that these SPTBN1 variants lead to effects that affect βII-spectrin stability, disrupt binding to key molecular partners, and disturb cytoskeleton organization and dynamics. Our studies define SPTBN1 variants as the genetic basis of a neurodevelopmental syndrome, expand the set of spectrinopathies affecting the brain and underscore the critical role of βII-spectrin in the central nervous system.
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Affiliation(s)
- Margot A Cousin
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA.
| | - Blake A Creighton
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Keith A Breau
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rebecca C Spillmann
- Department of Pediatrics, Duke University Medical Center, Duke University, Durham, NC, USA
| | | | - Sruthi Dontu
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Swarnendu Tripathi
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Deepa Ajit
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Reginald J Edwards
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Simone Afriyie
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Julia C Bay
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kathryn M Harper
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alvaro A Beltran
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Human Pluripotent Stem Cell Core, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lorena J Munoz
- Human Pluripotent Stem Cell Core, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Liset Falcon Rodriguez
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | | - Yue Si
- GeneDx, Gaithersburg, MD, USA
| | | | | | - Alison S May
- Department of Neurology, Columbia University, New York, NY, USA
| | - Louise Bier
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Vimla Aggarwal
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
- Laboratory of Personalized Genomic Medicine, Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | | | - Kirsten Cremer
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Jessica Becker
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Hartmut Engels
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Stefan Aretz
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | | | - Eva Brilstra
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Koen L I van Gassen
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Paul Mark
- Spectrum Health Medical Genetics, Grand Rapids, MI, USA
| | - Ingo Helbig
- Division of Neurology, Departments of Neurology and Pediatrics, The Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Sarah E McKeown
- Division of Neurology, Departments of Neurology and Pediatrics, The Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Robert Stratton
- Genetics, Driscoll Children's Hospital, Corpus Christi, TX, USA
| | - Benjamin Cogne
- Service de Génétique Médicale, CHU Nantes, Nantes, France
- Université de Nantes, CNRS, INSERM, L'Institut du Thorax, Nantes, France
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU Nantes, Nantes, France
- Université de Nantes, CNRS, INSERM, L'Institut du Thorax, Nantes, France
| | - Pilar Cacheiro
- William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Damian Smedley
- William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Helen V Firth
- Department of Clinical Genetics, Cambridge University Hospitals, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katja Kloth
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Deike Weiss
- Neuropediatrics, Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Cecilia Fairley
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Joseph T Shieh
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Amy Kritzer
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | | | - Evangeline Kurtz-Nelson
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Raphael A Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Tianyun Wang
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Ingrid M B H van de Laar
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Allyn McConkie-Rosell
- Department of Pediatrics, Duke University Medical Center, Duke University, Durham, NC, USA
| | - Marie T McDonald
- Department of Pediatrics, Duke University Medical Center, Duke University, Durham, NC, USA
| | - Jennifer Kemppainen
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Brendan C Lanpher
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Laura E Schultz-Rogers
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Lauren B Gunderson
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Pavel N Pichurin
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Grace Yoon
- Divisions of Clinical/Metabolic Genetics and Neurology, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Michael Zech
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
- Institute of Human Genetics, Technical University of Munich, Munich, Germany
| | - Robert Jech
- Department of Neurology, Charles University, 1st Faculty of Medicine and General University Hospital in Prague, Prague, Czech Republic
| | - Juliane Winkelmann
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
- Institute of Human Genetics, Technical University of Munich, Munich, Germany
- Lehrstuhl für Neurogenetik, Technische Universität München, Munich, Germany
- Munich Cluster for Systems Neurology, SyNergy, Munich, Germany
| | - Adriana S Beltran
- Human Pluripotent Stem Cell Core, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
- Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Brenda Temple
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sheryl S Moy
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Queenie K-G Tan
- Department of Pediatrics, Duke University Medical Center, Duke University, Durham, NC, USA
| | - Damaris N Lorenzo
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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15
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Tripathi S, Dsouza NR, Urrutia R, Zimmermann MT. Structural bioinformatics enhances mechanistic interpretation of genomic variation, demonstrated through the analyses of 935 distinct RAS family mutations. Bioinformatics 2021; 37:1367-1375. [PMID: 33226070 PMCID: PMC8208742 DOI: 10.1093/bioinformatics/btaa972] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/04/2020] [Accepted: 11/11/2020] [Indexed: 12/26/2022] Open
Abstract
MOTIVATION Protein-coding genetic alterations are frequently observed in Clinical Genetics, but the high yield of variants of uncertain significance remains a limitation in decision making. RAS-family GTPases are cancer drivers, but only 54 variants, across all family members, fall within well-known hotspots. However, extensive sequencing has identified 881 non-hotspot variants for which significance remains to be investigated. RESULTS Here, we evaluate 935 missense variants from seven RAS genes, observed in cancer, RASopathies and the healthy adult population. We characterized hotspot variants, previously studied experimentally, using 63 sequence- and 3D structure-based scores, chosen by their breadth of biophysical properties. Applying scores that display best correlation with experimental measures, we report new valuable mechanistic inferences for both hot-spot and non-hotspot variants. Moreover, we demonstrate that 3D scores have little-to-no correlation with those based on DNA sequence, which are commonly used in Clinical Genetics. Thus, combined, these new knowledge bear significant relevance. AVAILABILITY AND IMPLEMENTATION All genomic and 3D scores, and markdown for generating figures, are provided in our supplemental data. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Swarnendu Tripathi
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Milwaukee, WI 53226, USA.,Precision Medicine Simulation Unit, Genomic Sciences and Precision Medicine Center, Milwaukee, WI 53226, USA
| | - Nikita R Dsouza
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Milwaukee, WI 53226, USA.,Precision Medicine Simulation Unit, Genomic Sciences and Precision Medicine Center, Milwaukee, WI 53226, USA
| | - Raul Urrutia
- Precision Medicine Simulation Unit, Genomic Sciences and Precision Medicine Center, Milwaukee, WI 53226, USA.,Department of Surgery, Genomic Sciences and Precision Medicine Center, Milwaukee, WI 53226, USA
| | - Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Milwaukee, WI 53226, USA.,Precision Medicine Simulation Unit, Genomic Sciences and Precision Medicine Center, Milwaukee, WI 53226, USA.,Clinical and Translational Sciences Institute, Genomic Sciences and Precision Medicine Center, Milwaukee, WI 53226, USA.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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16
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Chi YI, Stodola TJ, De Assuncao TM, Leverence EN, Tripathi S, Dsouza NR, Mathison AJ, Basel DG, Volkman BF, Smith BC, Lomberk G, Zimmermann MT, Urrutia R. Correction to: Molecular mechanics and dynamic simulations of well-known Kabuki syndrome-associated KDM6A variants reveal putative mechanisms of dysfunction. Orphanet J Rare Dis 2021; 16:247. [PMID: 34074320 PMCID: PMC8170813 DOI: 10.1186/s13023-021-01892-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Young-In Chi
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Timothy J Stodola
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Thiago M De Assuncao
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Elise N Leverence
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA
| | - Swarnendu Tripathi
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Nikita R Dsouza
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Angela J Mathison
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Donald G Basel
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Pediatric Genetics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Brian C Smith
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Gwen Lomberk
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA.,Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Michael T Zimmermann
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA.,Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Raul Urrutia
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA. .,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA. .,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA. .,Division of Pediatric Genetics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA.
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17
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Chi YI, Stodola TJ, De Assuncao TM, Leverence EN, Tripathi S, Dsouza NR, Mathison AJ, Basel DG, Volkman BF, Smith BC, Lomberk G, Zimmermann MT, Urrutia R. Molecular mechanics and dynamic simulations of well-known Kabuki syndrome-associated KDM6A variants reveal putative mechanisms of dysfunction. Orphanet J Rare Dis 2021; 16:66. [PMID: 33546721 PMCID: PMC7866879 DOI: 10.1186/s13023-021-01692-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/15/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Kabuki syndrome is a genetic disorder that affects several body systems and presents with variations in symptoms and severity. The syndrome is named for a common phenotype of faces resembling stage makeup used in a Japanese traditional theatrical art named kabuki. The most frequent cause of this syndrome is mutations in the H3K4 family of histone methyltransferases while a smaller percentage results from genetic alterations affecting the histone demethylase, KDM6A. Because of the rare presentation of the latter form of the disease, little is known about how missense changes in the KDM6A protein sequence impact protein function. RESULTS In this study, we use molecular mechanic and molecular dynamic simulations to enhance the annotation and mechanistic interpretation of the potential impact of eleven KDM6A missense variants found in Kabuki syndrome patients. These variants (N910S, D980V, S1025G, C1153R, C1153Y, P1195L, L1200F, Q1212R, Q1248R, R1255W, and R1351Q) are predicted to be pathogenic, likely pathogenic or of uncertain significance by sequence-based analysis. Here, we demonstrate, for the first time, that although Kabuki syndrome missense variants are found outside the functionally critical regions, they could affect overall function by significantly disrupting global and local conformation (C1153R, C1153Y, P1195L, L1200F, Q1212R, Q1248R, R1255W and R1351Q), chemical environment (C1153R, C1153Y, P1195L, L1200F, Q1212R, Q1248R, R1255W and R1351Q), and/or molecular dynamics of the catalytic domain (all variants). In addition, our approaches predict that many mutations, in particular C1153R, could allosterically disrupt the key enzymatic interactions of KDM6A. CONCLUSIONS Our study demonstrates that the KDM6A Kabuki syndrome variants may impair histone demethylase function through various mechanisms that include altered protein integrity, local environment, molecular interactions and protein dynamics. Molecular dynamics simulations of the wild type and the variants are critical to gain a better understanding of molecular dysfunction. This type of comprehensive structure- and MD-based analyses should help develop improved impact scoring systems to interpret the damaging effects of variants in this protein and other related proteins as well as provide detailed mechanistic insight that is not currently predictable from sequence alone.
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Affiliation(s)
- Young-In Chi
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Timothy J Stodola
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Thiago M De Assuncao
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Elise N Leverence
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA
| | - Swarnendu Tripathi
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Nikita R Dsouza
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Angela J Mathison
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Donald G Basel
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Pediatric Genetics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Brian C Smith
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Gwen Lomberk
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA.,Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Michael T Zimmermann
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA.,Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Raul Urrutia
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA. .,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, WI, USA. .,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA. .,Division of Pediatric Genetics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA.
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18
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Samudrala SSK, North LM, Stamm KD, Earing MG, Frommelt MA, Willes R, Tripathi S, Dsouza NR, Zimmermann MT, Mahnke DK, Liang HL, Lund M, Lin C, Geddes GC, Mitchell ME, Tomita‐Mitchell A. Novel KLHL26 variant associated with a familial case of Ebstein's anomaly and left ventricular noncompaction. Mol Genet Genomic Med 2020; 8:e1152. [PMID: 31985165 PMCID: PMC7196453 DOI: 10.1002/mgg3.1152] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 01/11/2020] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Ebstein's anomaly (EA) is a rare congenital heart disease of the tricuspid valve and right ventricle. Patients with EA often manifest with left ventricular noncompaction (LVNC), a cardiomyopathy. Despite implication of cardiac sarcomere genes in some cases, very little is understood regarding the genetic etiology of EA/LVNC. Our study describes a multigenerational family with at least 10 of 17 members affected by EA/LVNC. METHODS We performed echocardiography on all family members and conducted exome sequencing of six individuals. After identifying candidate variants using two different bioinformatic strategies, we confirmed segregation with phenotype using Sanger sequencing. We investigated structural implications of candidate variants using protein prediction models. RESULTS Exome sequencing analysis of four affected and two unaffected members identified a novel, rare, and damaging coding variant in the Kelch-like family member 26 (KLHL26) gene located on chromosome 19 at position 237 of the protein (GRCh37). This variant region was confirmed by Sanger sequencing in the remaining family members. KLHL26 (c.709C > T p.R237C) segregates only with EA/LVNC-affected individuals (FBAT p < .05). Investigating structural implications of the candidate variant using protein prediction models suggested that the KLHL26 variant disrupts electrostatic interactions when binding to part of the ubiquitin proteasome, specifically Cullin3 (CUL3), a component of E3 ubiquitin ligase. CONCLUSION In this familial case of EA/LVNC, we have identified a candidate gene variant, KLHL26 (p.R237C), which may have an important role in ubiquitin-mediated protein degradation during cardiac development.
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Affiliation(s)
- Sai Suma K. Samudrala
- Department of Cell Biology, Neurobiology and AnatomyMedical College of WisconsinMilwaukeeWIUSA
| | - Lauren M. North
- Department of Otolaryngology and Communication SciencesMedical College of WisconsinMilwaukeeWIUSA
| | - Karl D. Stamm
- Department of SurgeryDivision of Cardiothoracic SurgeryMedical College of WisconsinMilwaukeeWIUSA
| | - Michael G. Earing
- Department of PediatricsChildren’s Hospital of WisconsinMilwaukeeWIUSA
- Herma Heart InstituteChildren’s Hospital of WisconsinMilwaukeeWIUSA
| | - Michele A. Frommelt
- Department of PediatricsChildren’s Hospital of WisconsinMilwaukeeWIUSA
- Herma Heart InstituteChildren’s Hospital of WisconsinMilwaukeeWIUSA
| | - Richard Willes
- Department of PediatricsChildren’s Hospital of WisconsinMilwaukeeWIUSA
| | - Swarnendu Tripathi
- Bioinformatics Research and Developmental LabGenomic Sciences and Precision Medicine CenterMedical College of WisconsinMilwaukeeWIUSA
| | - Nikita R. Dsouza
- Bioinformatics Research and Developmental LabGenomic Sciences and Precision Medicine CenterMedical College of WisconsinMilwaukeeWIUSA
| | - Michael T. Zimmermann
- Bioinformatics Research and Developmental LabGenomic Sciences and Precision Medicine CenterMedical College of WisconsinMilwaukeeWIUSA
- Clinical and Translational Science InstituteMedical College of WisconsinMilwaukeeWIUSA
| | - Donna K. Mahnke
- Department of SurgeryDivision of Cardiothoracic SurgeryMedical College of WisconsinMilwaukeeWIUSA
| | - Huan Ling Liang
- Department of SurgeryDivision of Cardiothoracic SurgeryMedical College of WisconsinMilwaukeeWIUSA
| | - Michael Lund
- Department of Obstetrics and GynecologyMedical College of WisconsinMilwaukeeWIUSA
| | - Chien‐Wei Lin
- Division of BiostatisticsMedical College of WisconsinMilwaukeeWIUSA
| | | | - Michael E. Mitchell
- Department of SurgeryDivision of Cardiothoracic SurgeryMedical College of WisconsinMilwaukeeWIUSA
- Herma Heart InstituteChildren’s Hospital of WisconsinMilwaukeeWIUSA
| | - Aoy Tomita‐Mitchell
- Department of SurgeryDivision of Cardiothoracic SurgeryMedical College of WisconsinMilwaukeeWIUSA
- Herma Heart InstituteChildren’s Hospital of WisconsinMilwaukeeWIUSA
- Department of Biomedical EngineeringMedical College of WisconsinMilwaukeeWIUSA
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19
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Samudrala SSK, North LM, Stamm KD, Earing MG, Frommelt MA, Willes R, Tripathi S, Dsouza NR, Zimmermann MT, Mahnke DK, Liang HL, Lund M, Lin C, Geddes GC, Mitchell ME, Tomita‐Mitchell A. Cover. Mol Genet Genomic Med 2020. [DOI: 10.1002/mgg3.1271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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20
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Tripathi S, Ajit Kumar VK. Comparison of Morphologic Findings in Patients with Dextrocardia with Situs Solitus vs Situs Inversus: a Retrospective Study. Pediatr Cardiol 2019; 40:302-309. [PMID: 30334087 DOI: 10.1007/s00246-018-2007-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 10/09/2018] [Indexed: 11/27/2022]
Abstract
BACKGROUND Studies on dextrocardia have been limited by low numbers. Hence, it is very difficult to find the most common diagnosis in patients with dextrocardia, who are seeking medical attention in tertiary care center. AIMS AND OBJECTIVE To identify the most common diagnostic pattern in patients with dextrocardia with different situs. METHODS It is a retrospective study with records dating back to up to last 21 years from a major tertiary care center in south India. All the patients with diagnosis of dextrocardia (defined as right-sided baso-apical axis of heart) will be included in the study. Segmental analysis will be done as defined previously. RESULTS There were total of n = 378 patients with dextrocardia, 43.3% were females and median age was 1 year while mean age was 7 years. Situs solitus was present in 43.1%, Situs inversus in 38.1%, and Situs ambiguus in 18.8%. In patients with situs solitus and dextrocardia, the most common diagnosis was congenitally corrected TGA ± PS/PA followed by Double outlet Right ventricle ± PS/PA; whereas in patients with Situs inversus and dextrocardia, the most common diagnosis was Double outlet Right ventricle ± PS/PA followed by normal hearts and Left to right shunts. CONCLUSION In patients with dextrocardia who are seeking medical advice in a tertiary care center, they are more likely to have situs solitus followed by situs inversus. In situs solitus atrio-ventricular discordance with right ventricular outflow obstruction is the most common lesion suggesting L-looping is the most predominant mechanism. In patients with situs inversus, DORV with RVOTO is the most common lesion.
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Affiliation(s)
- S Tripathi
- Department of Cardiology, SCTIMST, Thiruvananthapuram, India.
| | - V K Ajit Kumar
- Department of Cardiology, SCTIMST, Thiruvananthapuram, India
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21
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Dua R, Kumari R, Yadav V, Ranjan M, Kumar S, Mishra M, Tripathi S. New combined assessment of chronic obstructive pulmonary disease : Utilization, pitfalls, and association with spirometry. Lung India 2019. [DOI: 10.4103/0970-2113.257721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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22
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Rosen SA, Olson TJP, Peter SD, Ilyas S, Tripathi S. Robotic-assisted subtotal colectomy for synchronous colon cancers in a patient with indeterminate colitis - a video vignette. Colorectal Dis 2018; 20:1153-1154. [PMID: 30238595 DOI: 10.1111/codi.14426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 09/10/2018] [Indexed: 02/08/2023]
Affiliation(s)
- S A Rosen
- Department of Surgery, Emory University School of Medicine, Atlanta, Georgia, USA
| | - T J P Olson
- Department of Surgery, Emory University School of Medicine, Atlanta, Georgia, USA
| | - S D Peter
- Department of Radiology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - S Ilyas
- Department of Pathology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - S Tripathi
- Department of Surgery, Emory University School of Medicine, Atlanta, Georgia, USA
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23
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Memon P, Nair T, Yadav V, Tripathi S. ISQUA18-2325Designing and Implementing Competency Based Certification Program to Improve Quality of Intra and Immediate Postpartum Care in Private Sector – Experience from India. Int J Qual Health Care 2018. [DOI: 10.1093/intqhc/mzy167.40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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24
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Tripathi S, Memon P, Kujur M, Nair T. ISQUA18-1439What it Takes to get Accreditation in Small Healthcare Organizations – Case Study from India. Int J Qual Health Care 2018. [DOI: 10.1093/intqhc/mzy167.38] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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25
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Matar HE, Tripathi S, Miller DJ. Iliac crest apophyseal insufficiency avulsion fractures. Ann R Coll Surg Engl 2018; 100:e4-e6. [PMID: 29046079 PMCID: PMC5838676 DOI: 10.1308/rcsann.2017.0175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2017] [Indexed: 11/22/2022] Open
Abstract
Iliac crest apophyseal avulsion fractures are rare injuries caused mainly through forceful contraction of attached muscles during high level sporting activities. We present the first case of a spontaneous iliac crest apophyseal avulsion insufficiency fracture in a patient with severe atopic eczema on oral steroids and review the relevant literature.
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Affiliation(s)
- H E Matar
- Department of Trauma and Orthopaedics, Leighton Hospital , Crewe
| | - S Tripathi
- Department of Trauma and Orthopaedics, Leighton Hospital , Crewe
| | - D J Miller
- Department of Trauma and Orthopaedics, Leighton Hospital , Crewe
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26
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Arora N, Tripathi S, Kumar P, Mondal P, Mishra A, Prasad A. Recent advancements and new perspectives in animal models for Neurocysticercosis immunopathogenesis. Parasite Immunol 2017; 39. [PMID: 28467600 DOI: 10.1111/pim.12439] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 04/25/2017] [Indexed: 02/06/2023]
Abstract
Neurocysticercosis (NCC), one of the most common parasitic diseases of the central nervous system, is caused by Taenia solium. This parasite involves two hosts, intermediate hosts (pig and human) and a definitive host (human) and has various stages in its complex life cycle (eggs, oncosphere, cysticerci and adult tapeworm). Hence, developing an animal model for T. solium that mimics its natural course of infection is quite challenging. We have reviewed here the animal models frequently used to study immunopathogenesis of cysticercosis and also discussed their usefulness for NCC studies. We found that researchers have used mice, rats, guinea pigs, dogs, cats and pigs as models for this disease with varying degrees of success. Mice and rats models have been utilized extensively for immunopathogenesis studies due to their relative ease of handling and abundance of commercially available reagents to study these small animal models. These models have provided some very exciting results for in-depth understanding of the disease. Of late, the experimentally/naturally infected swine model is turning out to be the best animal model as the disease progression closely resembles human infection in pigs. However, handling large experimental animals has its own challenges and limitations.
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Affiliation(s)
- N Arora
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
| | - S Tripathi
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India.,Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - P Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
| | - P Mondal
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
| | - A Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, India
| | - A Prasad
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
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27
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Maidul Haque S, De R, Tripathi S, Mukherjee C, Yadav AK, Bhattacharyya D, Jha SN, Sahoo NK. Effect of oxygen partial pressure in deposition ambient on the properties of RF magnetron sputter deposited Gd 2O 3 thin films. Appl Opt 2017; 56:6114-6125. [PMID: 29047804 DOI: 10.1364/ao.56.006114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 06/16/2017] [Indexed: 06/07/2023]
Abstract
Gadolinium oxide is an excellent optical material that offers high transmission in a wide wavelength range of 200-1600 nm and exhibits a high bulk refractive index of ∼1.80 at 550 nm. In the present study, a set of Gd2O3 thin films has been deposited on fused silica substrates by RF sputtering of a Gd2O3 target under various O2 to Ar flow ratios. The samples have been characterized by grazing incidence x-ray diffraction (GIXRD) to study the long range structural behavior, by GIXR to study density and surface roughness of the films, by atomic force microscopy measurements to study morphological properties, by Rutherford backscattering measurements for compositional studies, and by transmission spectrophotometry and spectroscopic ellipsometry techniques to study their optical properties. It has been observed that the films deposited with 10% oxygen partial pressure have low density, high surface roughness, and high void content, which results in a low value of refractive index of this film, and film quality improves as oxygen partial pressure is further increased. Extended x-ray absorption fine structure measurement with synchrotron radiation has also been employed to extract local structural information around Gd sites, which has in turn been used to explain some of the observed macroscopic properties of the films.
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28
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Zhang P, Tripathi S, Trinh H, Cheung MS. Opposing Intermolecular Tuning of Ca 2+ Affinity for Calmodulin by Neurogranin and CaMKII Peptides. Biophys J 2017; 112:1105-1119. [PMID: 28355539 PMCID: PMC5374985 DOI: 10.1016/j.bpj.2017.01.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [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: 08/03/2016] [Revised: 12/27/2016] [Accepted: 01/23/2017] [Indexed: 12/03/2022] Open
Abstract
We investigated the impact of bound calmodulin (CaM)-target compound structure on the affinity of calcium (Ca2+) by integrating coarse-grained models and all-atomistic simulations with nonequilibrium physics. We focused on binding between CaM and two specific targets, Ca2+/CaM-dependent protein kinase II (CaMKII) and neurogranin (Ng), as they both regulate CaM-dependent Ca2+ signaling pathways in neurons. It was shown experimentally that Ca2+/CaM (holoCaM) binds to the CaMKII peptide with overwhelmingly higher affinity than Ca2+-free CaM (apoCaM); the binding of CaMKII peptide to CaM in return increases the Ca2+ affinity for CaM. However, this reciprocal relation was not observed in the Ng peptide (Ng13–49), which binds to apoCaM or holoCaM with binding affinities of the same order of magnitude. Unlike the holoCaM-CaMKII peptide, whose structure can be determined by crystallography, the structural description of the apoCaM-Ng13–49 is unknown due to low binding affinity, therefore we computationally generated an ensemble of apoCaM-Ng13–49 structures by matching the changes in the chemical shifts of CaM upon Ng13–49 binding from nuclear magnetic resonance experiments. Next, we computed the changes in Ca2+ affinity for CaM with and without binding targets in atomistic models using Jarzynski’s equality. We discovered the molecular underpinnings of lowered affinity of Ca2+ for CaM in the presence of Ng13–49 by showing that the N-terminal acidic region of Ng peptide pries open the β-sheet structure between the Ca2+ binding loops particularly at C-domain of CaM, enabling Ca2+ release. In contrast, CaMKII peptide increases Ca2+ affinity for the C-domain of CaM by stabilizing the two Ca2+ binding loops. We speculate that the distinctive structural difference in the bound complexes of apoCaM-Ng13–49 and holoCaM-CaMKII delineates the importance of CaM’s progressive mechanism of target binding on its Ca2+ binding affinities.
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Affiliation(s)
- Pengzhi Zhang
- Department of Physics, University of Houston, Houston, Texas
| | | | - Hoa Trinh
- Department of Physics, University of Houston, Houston, Texas
| | - Margaret S Cheung
- Department of Physics, University of Houston, Houston, Texas; Center for Theoretical Biological Physics, Rice University, Houston, Texas.
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29
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Mehra S, Mehra D, Tripathi S. Iatrogenically ruptured pulmonary hydatid cyst presenting as haemoptysis: a case report. Intern Med J 2017. [DOI: 10.1111/imj.10_13461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- S Mehra
- Respiratory, Sleep and General Medicine, Royal Darwin Hospital; Darwin Northern Territory Australia
- Pulmonary Medicine; King George Medical University; Lucknow Uttar Pradesh India
| | - D Mehra
- Pathology; James Cook University; Townsville Queensland Australia
| | - S Tripathi
- Pulmonary Medicine; King George Medical University; Lucknow Uttar Pradesh India
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30
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Maidul Haque S, Tripathi S, Jha SN, Bhattacharyya D, Sahoo NK. EXAFS studies on Gd-doped ZrO 2 thin films deposited by RF magnetron sputtering. Appl Opt 2016; 55:7355-7364. [PMID: 27661374 DOI: 10.1364/ao.55.007355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
ZrO2 thin films with 0%, 7%, 9%, 11%, and 13% Gd doping have been prepared by RF magnetron sputtering and have been characterized by grazing incidence x-ray diffraction, spectroscopic ellipsometry, and optical transmission measurements to probe their structural and optical properties. Extended x-ray absorption fine structure (EXAFS) measurements have also been carried out on the samples at the Zr K- and Gd L3-edges. It has been observed that Gd goes to Zr sites up to 9%-11% doping concentration, and for Gd doping concentrations beyond 11%, Gd precipitates out as a separate Gd2O3 phase. The local structure information surrounding the Zr and Gd sites obtained from the analysis of the EXAFS studies have also been used to explain the macroscopic optical properties of the samples.
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31
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Trivedi S, Al-Nofal A, Kumar S, Tripathi S, Kahoud RJ, Tebben PJ. Severe non-infective systemic inflammatory response syndrome, shock, and end-organ dysfunction after zoledronic acid administration in a child. Osteoporos Int 2016; 27:2379-2382. [PMID: 26892041 DOI: 10.1007/s00198-016-3528-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 02/04/2016] [Indexed: 10/22/2022]
Abstract
INTRODUCTION Zoledronic acid is an intravenous bisphosphonate used to increase bone mineral density and reduce the risk of fractures. Its safety profile compares well with pamidronate in pediatric patients. We describe an acute, severe, life-threatening, inflammatory reaction in a child. METHODS A 7-year-old boy with complex medical problems and chronic ventilator requirements was admitted to the pediatric intensive care unit (due to ventilator needs) for zoledronic acid infusion and subsequent monitoring. His history was significant for osteoporosis secondary to immobilization with multiple fractures since 2 years of age, hypoxic-ischemic encephalopathy, quadriplegic cerebral palsy, seizure disorder, ventilator dependence, and pulmonary hypertension. He had previously been treated with four cycles of pamidronate without adverse events. He received 0.013 mg/kg of zoledronic acid infused over 30 minutes. Beginning 3 hours after completion of the infusion, he developed progressive tachycardia, fever, hypotension requiring vasopressor infusion, and increasing oxygen requirements. Laboratory studies revealed leukopenia, thrombocytopenia, elevated C-reactive protein, abnormal coagulation profile, metabolic acidosis, and negative cultures. The following day, he developed moderate acute respiratory distress syndrome and pulmonary hemorrhage requiring higher ventilatory settings, and subsequently diarrhea and abdominal distension. Initial clinical resolution was noted from the third day onward, and he was discharged on the sixth day after zoledronate administration. RESULTS Our pediatric patient demonstrated an acute, severe, life-threatening reaction to zoledronic acid requiring intensive cardiorespiratory support without an underlying pre-existing inflammatory disorder. CONCLUSION Our case highlights the importance of careful monitoring of children following zoledronic acid therapy. We recommend inpatient observation after an initial infusion of zoledronic acid in medically complex children. Children and their parents should be thoroughly counseled on the potential risks of bisphosphonate treatment, which can sometimes be severe and life threatening.
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Affiliation(s)
- S Trivedi
- Department of Pediatric and Adolescent Medicine, Division of Pediatric Critical Care, Mayo Clinic, Rochester, MN, USA
| | - A Al-Nofal
- Department of Pediatric and Adolescent Medicine, Division of Pediatric Endocrinology, Mayo Clinic, Rochester, MN, USA
| | - S Kumar
- Department of Pediatric and Adolescent Medicine, Division of Pediatric Endocrinology, Mayo Clinic, Rochester, MN, USA
| | - S Tripathi
- Department of Pediatric and Adolescent Medicine, Division of Pediatric Critical Care, Mayo Clinic, Rochester, MN, USA
| | - R J Kahoud
- Department of Pediatric and Adolescent Medicine, Division of Pediatric Critical Care, Mayo Clinic, Rochester, MN, USA
| | - P J Tebben
- Department of Pediatric and Adolescent Medicine, Division of Pediatric Endocrinology, Mayo Clinic, Rochester, MN, USA.
- Departments of Medicine and Pediatric and Adolescent Medicine, Division of Endocrinology, Mayo Clinic, 200 First ST SW, Rochester, MN, 55905, USA.
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32
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Borges TJ, O’Malley JT, Wo L, Murakami N, Smith B, Azzi J, Tripathi S, Lane JD, Bueno EM, Clark RA, Tullius SG, Chandraker A, Lian CG, Murphy GF, Strom TB, Pomahac B, Najafian N, Riella LV. Codominant Role of Interferon-γ- and Interleukin-17-Producing T Cells During Rejection in Full Facial Transplant Recipients. Am J Transplant 2016; 16:2158-71. [PMID: 26749226 PMCID: PMC4979599 DOI: 10.1111/ajt.13705] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 12/23/2015] [Accepted: 12/27/2015] [Indexed: 01/25/2023]
Abstract
Facial transplantation is a life-changing procedure for patients with severe composite facial defects. However, skin is the most immunogenic of all transplants, and better understanding of the immunological processes after facial transplantation is of paramount importance. Here, we describe six patients who underwent full facial transplantation at our institution, with a mean follow-up of 2.7 years. Seum, peripheral blood mononuclear cells, and skin biopsy specimens were collected prospectively, and a detailed characterization of their immune response (51 time points) was performed, defining 47 immune cell subsets, 24 serum cytokines, anti-HLA antibodies, and donor alloreactivity on each sample, producing 4269 data points. In a nonrejecting state, patients had a predominant T helper 2 cell phenotype in the blood. All patients developed at least one episode of acute cellular rejection, which was characterized by increases in interferon-γ/interleukin-17-producing cells in peripheral blood and in the allograft's skin. Serum monocyte chemotactic protein-1 level was significantly increased during rejection compared with prerejection time points. None of the patients developed de novo donor-specific antibodies, despite a fourfold expansion in T follicular helper cells at 1 year posttransplantation. In sum, facial transplantation is frequently complicated by a codominant interferon-γ/interleukin-17-mediated acute cellular rejection process. Despite that, medium-term outcomes are promising with no evidence of de novo donor-specific antibody development.
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Affiliation(s)
- T. J. Borges
- Schuster Transplantation Research Center, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA
| | - J. T. O’Malley
- Department of Dermatology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - L. Wo
- Division of Plastic Surgery, Department of Surgery, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA
| | - N. Murakami
- Schuster Transplantation Research Center, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA
| | - B. Smith
- Schuster Transplantation Research Center, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA
| | - J. Azzi
- Schuster Transplantation Research Center, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA
| | - S. Tripathi
- Schuster Transplantation Research Center, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA
| | - J. D. Lane
- Division of Plastic Surgery, Department of Surgery, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA
| | - E. M. Bueno
- Division of Plastic Surgery, Department of Surgery, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA
| | - R. A. Clark
- Department of Dermatology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - S. G. Tullius
- Division of Transplant Surgery, Department of Surgery, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA
| | - A. Chandraker
- Schuster Transplantation Research Center, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA
| | - C. G. Lian
- Program in Dermatopathology, Department of Pathology, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA
| | - G. F. Murphy
- Program in Dermatopathology, Department of Pathology, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA
| | - T. B. Strom
- Transplant Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - B. Pomahac
- Division of Plastic Surgery, Department of Surgery, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA
| | - N. Najafian
- Schuster Transplantation Research Center, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA,Department of Nephrology, Cleveland Clinic Florida, Weston, FL
| | - L. V. Riella
- Schuster Transplantation Research Center, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA,Corresponding author: Leonardo V. Riella,
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Menon JC, Joseph JK, Jose MP, Punde D, Mazumdar DB, Bawaskar HS, Pillay VV, Mohapatra BN, Rajendiran C, Tanwar PD, Raut S, Ragunanthatan S, Tripathi S. Management protocol of venomous snakebite in India: a consensus statement. TOXIN REV 2016. [DOI: 10.1080/15569543.2016.1185735] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Redda YT, Venkatesh G, Kalaiyarasu S, Bhatia S, Kumar DS, Nagarajan S, Pillai A, Tripathi S, Kulkarni DD, Dubey SC. Expression and purification of recombinant H5HA1 protein of H5N1 avian influenza virus in E. coli and its application in indirect ELISA. J Immunoassay Immunochem 2016; 37:346-58. [PMID: 26829111 DOI: 10.1080/15321819.2015.1135160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The PCR amplified HA1 fragment of H5N1 (H5HA1) avian influenza virus (AIV) hemagglutinin gene was cloned into pET28a (+) expression vector and expressed in Rosetta Blue (DE3) pLysS cells. The recombinant H5HA1 (rH5HA1) protein purified by passive gel elution after SDS-PAGE of the inclusion bodies reacted specifically with H5N1 serum in Western blot analysis. A subtype specific indirect enzyme linked immunosorbent assay (iELISA) using the rH5HA1 protein as the coating antigen was developed for detecting antibodies to H5 subtype of AIV. The assay had 89.04% sensitivity and 95.95% specificity when compared with haemagglutination inhibition test. The Kappa value of 0.842 indicated a perfect agreement between the tests. The iELISA developed can be used for serosurveillance of avian influenza in chickens.
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Affiliation(s)
- Y T Redda
- a ICAR - National Institute of High Security Animal Diseases , Anand Nagar, Bhopal , Madhya Pradesh , India
| | - G Venkatesh
- a ICAR - National Institute of High Security Animal Diseases , Anand Nagar, Bhopal , Madhya Pradesh , India
| | - S Kalaiyarasu
- a ICAR - National Institute of High Security Animal Diseases , Anand Nagar, Bhopal , Madhya Pradesh , India
| | - S Bhatia
- a ICAR - National Institute of High Security Animal Diseases , Anand Nagar, Bhopal , Madhya Pradesh , India
| | - D Senthil Kumar
- a ICAR - National Institute of High Security Animal Diseases , Anand Nagar, Bhopal , Madhya Pradesh , India
| | - S Nagarajan
- a ICAR - National Institute of High Security Animal Diseases , Anand Nagar, Bhopal , Madhya Pradesh , India
| | - A Pillai
- a ICAR - National Institute of High Security Animal Diseases , Anand Nagar, Bhopal , Madhya Pradesh , India
| | - S Tripathi
- a ICAR - National Institute of High Security Animal Diseases , Anand Nagar, Bhopal , Madhya Pradesh , India
| | - D D Kulkarni
- a ICAR - National Institute of High Security Animal Diseases , Anand Nagar, Bhopal , Madhya Pradesh , India
| | - S C Dubey
- a ICAR - National Institute of High Security Animal Diseases , Anand Nagar, Bhopal , Madhya Pradesh , India
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Cheung MS, Tripathi S, Waxham M, Liu Y. Lessons in Protein Design from Combined Evolution and Conformational Dynamics. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.2824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Tripathi S, Belkacemi L, Cheung MS, Bose RN. Correlation between Gene Variants, Signaling Pathways, and Efficacy of Chemotherapy Drugs against Colon Cancers. Cancer Inform 2016; 15:1-13. [PMID: 26819545 PMCID: PMC4721683 DOI: 10.4137/cin.s34506] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 11/15/2015] [Accepted: 11/15/2015] [Indexed: 12/13/2022] Open
Abstract
Efficacies, toxicities, and resistance mechanisms of chemotherapy drugs, such as oxaliplatin and 5-fluorouracil (5-FU), vary widely among various categories and subcategories of colon cancers. By understanding the differences in the drug efficacy and resistance at the level of protein–protein networks, we identified the correlation between the drug activity of oxaliplatin/5-FU and gene variations from the US National Cancer Institute-60 human cancer cell lines. The activity of either of these drugs is correlated with specific amino acid variant(s) of KRAS and other genes from the signaling pathways of colon cancer progression. We also discovered that the activity of a non-DNA-binding novel platinum drug, phosphaplatin, is comparable with oxaliplatin and 5-FU when it was tested against colon cancer cell lines. Our strategy that combines the knowledge from pharmacogenomics across cell lines with the molecular information from specific cancer cells is beneficial for predicting the outcome of a possible combination therapy for personalized treatment.
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Affiliation(s)
- Swarnendu Tripathi
- Department of Biology & Biochemistry, University of Houston, Houston, TX, USA.; Department of Physics, University of Houston, Houston, TX, USA.; Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | - Louiza Belkacemi
- Department of Biology & Biochemistry, University of Houston, Houston, TX, USA
| | - Margaret S Cheung
- Department of Physics, University of Houston, Houston, TX, USA.; Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | - Rathindra N Bose
- Department of Biology & Biochemistry, University of Houston, Houston, TX, USA
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Fatima A, Kulkarni VK, Banda NR, Agrawal AK, Singh B, Sarkar PS, Tripathi S, Shripathi T, Kashyap Y, Sinha A. Non-destructive evaluation of teeth restored with different composite resins using synchrotron based micro-imaging. J Xray Sci Technol 2016; 24:119-132. [PMID: 26890899 DOI: 10.3233/xst-160530] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
BACKGROUND Application of high resolution synchrotron micro-imaging in microdefects studies of restored dental samples. OBJECTIVE The purpose of this study was to identify and compare the defects in restorations done by two different resin systems on teeth samples using synchrotron based micro-imaging techniques namely Phase Contrast Imaging (PCI) and micro-computed tomography (MCT). With this aim acquired image quality was also compared with routinely used RVG (Radiovisiograph). METHODS Crowns of human teeth samples were fractured mechanically involving only enamel and dentin, without exposure of pulp chamber and were divided into two groups depending on the restorative composite materials used. Group A samples were restored using a submicron Hybrid composite material and Group B samples were restored using a Nano-Hybrid restorative composite material. Synchrotron based PCI and MCT was performed with the aim of visualization of tooth structure, composite resin and their interface. RESULTS The quantitative and qualitative comparison of phase contrast and absorption contrast images along with MCT on the restored teeth samples shows comparatively large number of voids in Group A samples. CONCLUSIONS Quality assessment of dental restorations using synchrotron based micro-imaging suggests Nano-Hybrid resin restorations (Group B) are better than Group A.
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Affiliation(s)
- A Fatima
- UGC- DAE Consortium for Scientific Research, University Campus, Indore (M.P.), India
| | - V K Kulkarni
- Department of Pedodontics and Preventive Dentistry, Modern Dental College, Indore (M.P.), India
| | - N R Banda
- Department of Pedodontics and Preventive Dentistry, Modern Dental College, Indore (M.P.), India
| | - A K Agrawal
- Neutron & X-ray Physics Division, Bhabha Atomic Research Center, Trombay, Mumbai, India
| | - B Singh
- Neutron & X-ray Physics Division, Bhabha Atomic Research Center, Trombay, Mumbai, India
| | - P S Sarkar
- Neutron & X-ray Physics Division, Bhabha Atomic Research Center, Trombay, Mumbai, India
| | - S Tripathi
- UGC- DAE Consortium for Scientific Research, University Campus, Indore (M.P.), India
| | - T Shripathi
- UGC- DAE Consortium for Scientific Research, University Campus, Indore (M.P.), India
| | - Y Kashyap
- Neutron & X-ray Physics Division, Bhabha Atomic Research Center, Trombay, Mumbai, India
| | - A Sinha
- Neutron & X-ray Physics Division, Bhabha Atomic Research Center, Trombay, Mumbai, India
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Tripathi S, Belkacemi L, Cheung MS, Bose RN. Abstract B1-02: Correlation between oncogenic mutations, signaling pathways, and efficacy of platinum-based drugs against colorectal cancers. Cancer Res 2015. [DOI: 10.1158/1538-7445.compsysbio-b1-02] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The purpose of this study is to correlate genetic mutations, amino-acid variants, signaling pathways with platiunum based drug activity to shed light on personalized treatment of cancer. Platinum anticancer drugs such as cisplatin, carboplatin, and oxalipaltin are widely used to treat a variety of cancers. Although DNA is the molecular target for these platinum therapies, their efficacies, toxicities, and resistance mechanisms vary widely among various categories and sub-categories of cancers. To comprehend this great variability, an integrated analysis was performed to determine the impact of somatic mutations on protein functions, signaling pathways, and drug activity (sensitivity or resistance) among the US National Cancer Institute (NCI) 60 human tumor cell lines based on Z-scores to predict a priori treatment outcome using CellMiner (http://discover.nci.nih.gov/cellminer). Specifically, somatic mutations of significantly mutated genes from the cancer genome atlas (TCGA) were analyzed along with the driver genes (oncogenes and tumor suppressor genes) from catalogue of somatic mutations in cancer (COSMIC) for total 188 genes that belong to more than 20 different signaling pathways. The functional impact of individual amino-acid variant for each gene and its correlation with the activity of carboplatin, cisplatin and oxaliplatin for each cancer cell line were explored. Particular attention was given to colon cancer for which nearly 40% of tumors are known to have mutated KRAS (Kirsten rat sarcoma viral oncogene homolog) gene. Resulting analysis revealed that colon cancer cell lines with KRAS mutations for codon 12 (G12V-mutant from SW620 cell line) and codon 13 (G13D-mutant from HCT116 and HCT15 cell lines) correlated with the sensitivity to oxaliplatin. Conversely, oxaliplatin resistant HCC2998 colon cancer cell line did not show any correlation with mutated KRAS for codon 146 (A146T-mutant). Notably, all the colon cancer cell lines were resistant to both carboplatin and cisplatin with no correlation to the KRAS mutants. Based on our integrated analysis we further predicted gene networks related to oxaliplatin activity for colon cancer. The network includes the epidermal growth factor (EGFR) signaling pathway that involves PIK3CA, PIK3CG and MTOR from the phosphoinositide 3-kinase (PI3K)/mammalian target of rapamycin (mTOR) (PIK3/mTOR) pathway, and JAK3 from Janus kinase-signal transducer and activator of transcription (JAK-STAT) pathway in addition to KRAS from Mitogen-activated protein kinases (MAPK) pathway. We conclude that instead of considering all mutations of a gene in the same way to assess their clinical significance, it may be beneficial to categorize them into different classes based on their functional impact and efficacies towards the anti-cancer drugs for personalized treatment. Similar analytical approach is being extended to non-small cell lung and ovarian cancers where platinum therapies are widely used.
S. Tripathi gratefully acknowledges the support through a training fellowship from a grant by the Cancer Prevention Research Institute of Texas (Grant No. RP140113 to R.N.Bose).
Citation Format: Swarnendu Tripathi, Louiza Belkacemi, Margaret S. Cheung, Rathindra N. Bose. Correlation between oncogenic mutations, signaling pathways, and efficacy of platinum-based drugs against colorectal cancers. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B1-02.
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Tripathi S, Belkacemi L, Cheung MS, Bose RN. Abstract A2-48: Correlation between oncogenic mutations, signaling pathways and efficacy of platinum based drugs against colorectal cancers. Cancer Res 2015. [DOI: 10.1158/1538-7445.transcagen-a2-48] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The purpose of this study is to correlate genetic mutations, amino-acid variants, signaling pathways with platiunum based drug activity to shed light on personalized treatment of cancer. Platinum anticancer drugs such as cisplatin, carboplatin, and oxalipaltin are widely used to treat a variety of cancers. Although DNA is the molecular target for these platinum therapies, their efficacies, toxicities, and resistance mechanisms vary widely among various categories and sub-categories of cancers. To comprehend this great variability, an integrated analysis was performed to determine the impact of somatic mutations on protein functions, signaling pathways, and drug activity (sensitivity or resistance) among the US National Cancer Institute (NCI) 60 human tumor cell lines based on Z-scores to predict a priori treatment outcome using CellMiner (http://discover.nci.nih.gov/cellminer). Specifically, somatic mutations of significantly mutated genes from the cancer genome atlas (TCGA) were analyzed along with the driver genes (oncogenes and tumor suppressor genes) from catalogue of somatic mutations in cancer (COSMIC) for total 188 genes that belong to more than 20 different signaling pathways. The functional impact of individual amino-acid variant for each gene and its correlation with the activity of carboplatin, cisplatin and oxaliplatin for each cancer cell line were explored. Particular attention was given to colon cancer for which nearly 40% of tumors are known to have mutated KRAS (Kirsten rat sarcoma viral oncogene homolog) gene. Resulting analysis revealed that colon cancer cell lines with KRAS mutations for codon 12 (G12V-mutant from SW620 cell line) and codon 13 (G13D-mutant from HCT116 and HCT15 cell lines) correlated with the sensitivity to oxaliplatin. Conversely, oxaliplatin resistant HCC2998 colon cancer cell line did not show any correlation with mutated KRAS for codon 146 (A146T-mutant). Notably, all the colon cancer cell lines were resistant to both carboplatin and cisplatin with no correlation to the KRAS mutants. Based on our integrated analysis we further predicted gene networks related to oxaliplatin activity for colon cancer. The network includes the epidermal growth factor (EGFR) signaling pathway that involves PIK3CA, PIK3CG and MTOR from the phosphoinositide 3-kinase (PI3K)/mammalian target of rapamycin (mTOR) (PIK3/mTOR) pathway, and JAK3 from Janus kinase-signal transducer and activator of transcription (JAK-STAT) pathway in addition to KRAS from Mitogen-activated protein kinases (MAPK) pathway. We conclude that instead of considering all mutations of a gene in the same way to assess their clinical significance, it may be beneficial to categorize them into different classes based on their functional impact and efficacies towards the anti-cancer drugs for personalized treatment. Similar analytical approach is being extended to non-small cell lung and ovarian cancers where platinum therapies are widely used.
S. Tripathi gratefully acknowledges the support through a training fellowship from a grant by the Cancer Prevention Research Institute of Texas (Grant No. RP140113 to R.N.Bose).
Citation Format: Swarnendu Tripathi, Louiza Belkacemi, Margaret S. Cheung, Rathindra N. Bose. Correlation between oncogenic mutations, signaling pathways and efficacy of platinum based drugs against colorectal cancers. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A2-48.
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Bose RN, Moghaddas S, Belkacemi L, Tripathi S, Adams NR, Majmudar P, McCall K, Dezvareh H, Nislow C. Absence of Activation of DNA Repair Genes and Excellent Efficacy of Phosphaplatins against Human Ovarian Cancers: Implications To Treat Resistant Cancers. J Med Chem 2015; 58:8387-401. [PMID: 26455832 DOI: 10.1021/acs.jmedchem.5b00732] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Phosphaplatins, platinum(II) and platinum(IV) complexes coordinated to a pyrophosphate moiety, exhibit excellent antitumor activities against a variety of cancers. To determine whether phosphaplatins trigger resistance to treatment by engaging DNA damage repair genes, a yeast genome-wide fitness assay was used. Treatment of yeast cells with pyrodach-2 (D2) or pyrodach-4 (D4) revealed no particular sensitivity to nucleotide excision repair, homologous recombination repair, or postreplication repair when compared with platin control compounds. Also, TNF receptor superfamily member 6 (FAS) protein was overexpressed in phosphaplatin-treated ovarian tumor cells, and platinum colocalized with FAS protein in lipid rafts. An overactivation of sphingomyelinase (ASMase) was noted in the treated cells, indicating participation of an extrinsic apoptotic mechanism due to increased ceramide release. Our results indicate that DNA is not the target of phosphaplatins and accordingly, that phosphaplatins might not cause resistance to treatment. Activation of ASMase and FAS along with the colocalization of platinum with FAS in lipid rafts support an extrinsic apoptotic signaling mechanism that is mediated by phosphaplatins.
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Affiliation(s)
- Rathindra N Bose
- Departments of Biology and Biochemistry, University of Houston , Houston, Texas 77204, United States
| | - Shadi Moghaddas
- Departments of Biology and Biochemistry, University of Houston , Houston, Texas 77204, United States
| | - Louiza Belkacemi
- Departments of Biology and Biochemistry, University of Houston , Houston, Texas 77204, United States
| | - Swarnendu Tripathi
- Departments of Biology and Biochemistry, University of Houston , Houston, Texas 77204, United States
| | - Nyssa R Adams
- Department of Specialty Medicine, Ohio University Heritage College of Osteopathic Medicine, Ohio University , Athens, Ohio 45701, United States
| | - Pooja Majmudar
- Department of Specialty Medicine, Ohio University Heritage College of Osteopathic Medicine, Ohio University , Athens, Ohio 45701, United States
| | - Kelly McCall
- Department of Specialty Medicine, Ohio University Heritage College of Osteopathic Medicine, Ohio University , Athens, Ohio 45701, United States
| | - Homa Dezvareh
- Departments of Biology and Biochemistry, University of Houston , Houston, Texas 77204, United States
| | - Corey Nislow
- Department of Pharmaceutical Sciences, University of British Columbia , Vancouver, British Columbia V6T 1Z3, Canada
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Tripathi S, Garcìa AE, Makhatadze GI. Alterations of Nonconserved Residues Affect Protein Stability and Folding Dynamics through Charge–Charge Interactions. J Phys Chem B 2015; 119:13103-12. [DOI: 10.1021/acs.jpcb.5b08527] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Swarnendu Tripathi
- Department
of Physics, University of Houston, Houston, Texas 77204, United States
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Tripathi S. The Comparative Study of Life Assets among Thailand Secondary and High School Students for 2009 and 2013;Finding from the Nation Positive Youth Development Survey. Int J Epidemiol 2015. [DOI: 10.1093/ije/dyv096.150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Tripathi S, Waxham MN, Cheung MS, Liu Y. Lessons in Protein Design from Combined Evolution and Conformational Dynamics. Sci Rep 2015; 5:14259. [PMID: 26388515 PMCID: PMC4585694 DOI: 10.1038/srep14259] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [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: 03/31/2015] [Accepted: 08/21/2015] [Indexed: 11/09/2022] Open
Abstract
Protein-protein interactions play important roles in the control of every cellular process. How natural selection has optimized protein design to produce molecules capable of binding to many partner proteins is a fascinating problem but not well understood. Here, we performed a combinatorial analysis of protein sequence evolution and conformational dynamics to study how calmodulin (CaM), which plays essential roles in calcium signaling pathways, has adapted to bind to a large number of partner proteins. We discovered that amino acid residues in CaM can be partitioned into unique classes according to their degree of evolutionary conservation and local stability. Holistically, categorization of CaM residues into these classes reveals enriched physico-chemical interactions required for binding to diverse targets, balanced against the need to maintain the folding and structural modularity of CaM to achieve its overall function. The sequence-structure-function relationship of CaM provides a concrete example of the general principle of protein design. We have demonstrated the synergy between the fields of molecular evolution and protein biophysics and created a generalizable framework broadly applicable to the study of protein-protein interactions.
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Affiliation(s)
- Swarnendu Tripathi
- Department of Physics, University of Houston, Houston, TX.,Center for Theoretical Biological Physics, Rice University, Houston, TX
| | - M Neal Waxham
- Department of Neurobiology and Anatomy, University of Texas, Health Science Center, Houston, TX
| | - Margaret S Cheung
- Department of Physics, University of Houston, Houston, TX.,Center for Theoretical Biological Physics, Rice University, Houston, TX
| | - Yin Liu
- Department of Neurobiology and Anatomy, University of Texas, Health Science Center, Houston, TX
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Patil Y, Khirwadkar S, Belsare S, Swamy R, Khan M, Tripathi S, Bhope K, Krishnan D, Mokaria P, Patel N, Antwala I, Galodiya K, Mehta M, Patel T. Performance of straight tungsten mono-block test mock-ups using new high heat flux test facility at IPR. Fusion Engineering and Design 2015. [DOI: 10.1016/j.fusengdes.2015.04.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Tripathi S, Nunez DJ, Katyal C, Ushay HM. Plan to Have No Unplanned: A Collaborative, Hospital-Based Quality-Improvement Project to Reduce the Rate of Unplanned Extubations in the Pediatric ICU. Respir Care 2015; 60:1105-12. [PMID: 25989811 PMCID: PMC10044263 DOI: 10.4187/respcare.03984] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Although under-reported and understudied, unplanned extubations carry a significant risk of patient harm and even death. They are an important yardstick of quality control of care of intubated patients in the ICU. A unit-based risk assessment and multidisciplinary approach is required to decrease the incidence of unplanned extubations. METHODS As part of a quality-improvement initiative of Children's Hospital at Montefiore, all planned and unplanned extubations in a multidisciplinary 20-bed pediatric ICU were evaluated over a 12-month period (January to December 2010). At the end of 6 months, an interim analysis was performed, and high-risk patient groups and patient care factors were identified. These factors were targeted in the second phase of the project. RESULTS Over this period, there were a total of 267 extubations, of which 231 (87%) were planned extubations and 36 (13%) were unplanned. A patient care policy targeting the risk factors was instituted, along with extensive nursing and other personnel education in the second phase. As a result of this intervention, the unplanned extubation rate in the pediatric ICU decreased from 3.55 to 2.59/100 intubation days. All subjects who had an unplanned extubation during nursing procedures or transport required re-intubation, whereas none of the unplanned extubations during ventilator weaning required re-intubation. CONCLUSIONS A targeted approach based on unit-specific risk factors is most effective in quality-improvement projects. A specific policy for sedation and weaning can be very helpful in managing intubated patients and preventing unintended harm.
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Tripathi S, Wang Q, Zhang P, Hoffman L, Waxham MN, Cheung MS. Conformational frustration in calmodulin-target recognition. J Mol Recognit 2015; 28:74-86. [PMID: 25622562 DOI: 10.1002/jmr.2413] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 07/30/2014] [Accepted: 07/31/2014] [Indexed: 11/10/2022]
Abstract
Calmodulin (CaM) is a primary calcium (Ca(2+) )-signaling protein that specifically recognizes and activates highly diverse target proteins. We explored the molecular basis of target recognition of CaM with peptides representing the CaM-binding domains from two Ca(2+) -CaM-dependent kinases, CaMKI and CaMKII, by employing experimentally constrained molecular simulations. Detailed binding route analysis revealed that the two CaM target peptides, although similar in length and net charge, follow distinct routes that lead to a higher binding frustration in the CaM-CaMKII complex than in the CaM-CaMKI complex. We discovered that the molecular origin of the binding frustration is caused by intermolecular contacts formed with the C-domain of CaM that need to be broken before the formation of intermolecular contacts with the N-domain of CaM. We argue that the binding frustration is important for determining the kinetics of the recognition process of proteins involving large structural fluctuations.
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Affiliation(s)
- Swarnendu Tripathi
- Department of Physics, University of Houston, Houston, TX, 77204, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX, 77005, USA
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Gleich SJ, Nemergut ME, Stans AA, Haile DT, Feigal SA, Heinrich AL, Bosley CL, Ward JW, Tripathi S. Lean Six Sigma handoff process between operating room and pediatric ICU: improvement in patient safety, efficiency and effectiveness. Crit Care 2015. [PMCID: PMC4472799 DOI: 10.1186/cc14603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Khanna R, Pandey RK, Tripathi S. Effect of intermaxillary tooth-size discrepancy on accuracy of prediction equations for mixed dentition space analysis. Eur Arch Paediatr Dent 2014; 16:211-7. [PMID: 25373496 DOI: 10.1007/s40368-014-0157-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 10/08/2014] [Indexed: 11/29/2022]
Abstract
AIM Correlation-statistical methods are widely used for prediction of size of unerupted permanent canines and premolars in mixed dentition space analysis. The present study was planned to evaluate the effect of selecting dental study casts with no intermaxillary tooth-size discrepancy on the accuracy of predicting mesiodistal widths (MDWS) of permanent canines and premolars. STUDY DESIGN Bolton ratios were calculated for all the screened study dental casts fulfilling the inclusion criteria. Subjects were divided into two groups. Group A: all subjects with no intermaxillary tooth-size discrepancy within ±2 SD (Standard deviation) of the mean values. Group B: increased percentage of subjects with intermaxillary tooth-size discrepancy beyond ±2 SD (Standard deviation) of the mean values. STATISTICS Linear regression equations were established for both maxilla and mandible in both the groups, with different tooth combinations as independent variables. Validation of best possible regression equations was done on an independent set of 40 subjects. The actual and predicted values of MDWS of permanent canines and premolars were compared by paired samples t test in both groups, for both arches. RESULTS The accuracy of equations derived from group A was higher than those derived from group B. The difference between actual and predicted values was statistically insignificant in group A and statistically significant in group B. CONCLUSION The results confirm the accuracy of simple linear regression equations derived from a sample of children with no intermaxillary tooth-size discrepancy.
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Affiliation(s)
- R Khanna
- Department of Paediatric and Preventive Dentistry, King George's Medical University, Lucknow, 226003, Uttar Pradesh, India,
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