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Article ; Online: On the error in the nucleus-centered multipolar expansion of molecular electron density and its topology: A direct-space computational study.

Michael, J Robert / Koritsanszky, Tibor

2017 Volume 146, Issue 20, Page(s) 204105

Abstract: The convergence of nucleus-centered multipolar expansion of the quantum-chemical electron density (QC-ED), gradient, and Laplacian is investigated in terms of numerical radial functions derived by projecting stockholder atoms onto real spherical ... ...

Abstract	The convergence of nucleus-centered multipolar expansion of the quantum-chemical electron density (QC-ED), gradient, and Laplacian is investigated in terms of numerical radial functions derived by projecting stockholder atoms onto real spherical harmonics at each center. The partial sums of this exact one-center expansion are compared with the corresponding Hansen-Coppens pseudoatom (HC-PA) formalism [Hansen, N. K. and Coppens, P., "Testing aspherical atom refinements on small-molecule data sets," Acta Crystallogr., Sect. A 34, 909-921 (1978)] commonly utilized in experimental electron density studies. It is found that the latter model, due to its inadequate radial part, lacks pointwise convergence and fails to reproduce the local topology of the target QC-ED even at a high-order expansion. The significance of the quantitative agreement often found between HC-PA-based (quadrupolar-level) experimental and extended-basis QC-EDs can thus be challenged.
Language	English
Publishing date	2017-05-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/1.4983633
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Article ; Online: Computational analysis of thermal-motion effects on the topological properties of the electron density.

Michael, J Robert / Koritsanszky, Tibor

Acta crystallographica. Section A, Foundations and advances

2015 Volume 71, Issue Pt 2, Page(s) 225–234

Abstract: The distributions of bond topological properties (BTPs) of the electron density upon thermal vibrations of the nuclei are computationally examined to estimate different statistical figures, especially uncertainties, of these properties. The statistical ... ...

Abstract	The distributions of bond topological properties (BTPs) of the electron density upon thermal vibrations of the nuclei are computationally examined to estimate different statistical figures, especially uncertainties, of these properties. The statistical analysis is based on a large ensemble of BTPs of the electron densities for thermally perturbed nuclear geometries of the formamide molecule. Each bond critical point (BCP) is found to follow a normal distribution whose covariance correlates with the displacement amplitudes of the nuclei involved in the bond. The BTPs are found to be markedly affected not only by normal modes of the significant bond-stretching component but also by modes that involve mainly hydrogen-atom displacements. Their probability distribution function can be decently described by Gumbel-type functions of positive (negative) skewness for the bonds formed by non-hydrogen (hydrogen) atoms.
Language	English
Publishing date	2015-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	2020844-3
ISSN	2053-2733 ; 1600-5724 ; 0108-7673
ISSN (online)	2053-2733 ; 1600-5724
ISSN	0108-7673
DOI	10.1107/S2053273315001199
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Article ; Online: Density- and wavefunction-normalized Cartesian spherical harmonics for l ≤ 20.

Michael, J Robert / Volkov, Anatoliy

Acta crystallographica. Section A, Foundations and advances

2015 Volume 71, Issue Pt 2, Page(s) 245–249

Abstract: The widely used pseudoatom formalism [Stewart (1976). Acta Cryst. A32, 565-574; Hansen & Coppens (1978). Acta Cryst. A34, 909-921] in experimental X-ray charge-density studies makes use of real spherical harmonics when describing the angular component of ...

Abstract	The widely used pseudoatom formalism [Stewart (1976). Acta Cryst. A32, 565-574; Hansen & Coppens (1978). Acta Cryst. A34, 909-921] in experimental X-ray charge-density studies makes use of real spherical harmonics when describing the angular component of aspherical deformations of the atomic electron density in molecules and crystals. The analytical form of the density-normalized Cartesian spherical harmonic functions for up to l ≤ 7 and the corresponding normalization coefficients were reported previously by Paturle & Coppens [Acta Cryst. (1988), A44, 6-7]. It was shown that the analytical form for normalization coefficients is available primarily for l ≤ 4 [Hansen & Coppens, 1978; Paturle & Coppens, 1988; Coppens (1992). International Tables for Crystallography, Vol. B, Reciprocal space, 1st ed., edited by U. Shmueli, ch. 1.2. Dordrecht: Kluwer Academic Publishers; Coppens (1997). X-ray Charge Densities and Chemical Bonding. New York: Oxford University Press]. Only in very special cases it is possible to derive an analytical representation of the normalization coefficients for 4 < l ≤ 7 (Paturle & Coppens, 1988). In most cases for l > 4 the density normalization coefficients were calculated numerically to within seven significant figures. In this study we review the literature on the density-normalized spherical harmonics, clarify the existing notations, use the Paturle-Coppens (Paturle & Coppens, 1988) method in the Wolfram Mathematica software to derive the Cartesian spherical harmonics for l ≤ 20 and determine the density normalization coefficients to 35 significant figures, and computer-generate a Fortran90 code. The article primarily targets researchers who work in the field of experimental X-ray electron density, but may be of some use to all who are interested in Cartesian spherical harmonics.
Language	English
Publishing date	2015-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	2020844-3
ISSN	2053-2733 ; 1600-5724 ; 0108-7673
ISSN (online)	2053-2733 ; 1600-5724
ISSN	0108-7673
DOI	10.1107/S2053273314024838
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Article ; Online: Compositional adaptability in NPM1-SURF6 scaffolding networks enabled by dynamic switching of phase separation mechanisms.

Ferrolino, Mylene C / Mitrea, Diana M / Michael, J Robert / Kriwacki, Richard W

Nature communications

2018 Volume 9, Issue 1, Page(s) 5064

Abstract: The nucleolus, the site for ribosome biogenesis contains hundreds of proteins and several types of RNA. The functions of many non-ribosomal nucleolar proteins are poorly understood, including Surfeit locus protein 6 (SURF6), an essential disordered ... ...

Abstract	The nucleolus, the site for ribosome biogenesis contains hundreds of proteins and several types of RNA. The functions of many non-ribosomal nucleolar proteins are poorly understood, including Surfeit locus protein 6 (SURF6), an essential disordered protein with roles in ribosome biogenesis and cell proliferation. SURF6 co-localizes with Nucleophosmin (NPM1), a highly abundant protein that mediates the liquid-like features of the granular component region of the nucleolus through phase separation. Here, we show that electrostatically-driven interactions between disordered regions of NPM1 and SURF6 drive liquid-liquid phase separation. We demonstrate that co-existing heterotypic (NPM1-SURF6) and homotypic (NPM1-NPM1) scaffolding interactions within NPM1-SURF6 liquid-phase droplets dynamically and seamlessly interconvert in response to variations in molecular crowding and protein concentrations. We propose a mechanism wherein NPM1-dependent nucleolar scaffolds are modulated by non-ribosomal proteins through active rearrangements of interaction networks that can possibly contribute to the directionality of ribosomal biogenesis within the liquid-like nucleolus.
MeSH term(s)	Cell Nucleolus/metabolism ; Fluorescence Recovery After Photobleaching ; Humans ; Nuclear Proteins/metabolism ; Organelle Biogenesis ; Protein Binding ; RNA, Ribosomal/metabolism ; Ribosomes/metabolism
Chemical Substances	Nuclear Proteins ; RNA, Ribosomal ; SURF6 protein, human ; nucleophosmin (117896-08-9)
Language	English
Publishing date	2018-11-29
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-018-07530-1
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Article ; Online: Contribution of Polygenic Risk to Hypertension Among Long-Term Survivors of Childhood Cancer.

Sapkota, Yadav / Li, Nan / Pierzynski, Jeanne / Mulrooney, Daniel A / Ness, Kirsten K / Morton, Lindsay M / Michael, J Robert / Zhang, Jinghui / Bhatia, Smita / Armstrong, Gregory T / Hudson, Melissa M / Robison, Leslie L / Yasui, Yutaka

JACC. CardioOncology

2021 Volume 3, Issue 1, Page(s) 76–84

Abstract: Background: Childhood cancer survivors experience significantly higher rates of hypertension which potentiates cardiovascular disease, but the contribution and relationship of genetic and treatment factors to hypertension risk are unknown.: Objectives! ...

Abstract	Background: Childhood cancer survivors experience significantly higher rates of hypertension which potentiates cardiovascular disease, but the contribution and relationship of genetic and treatment factors to hypertension risk are unknown. Objectives: To determine the contribution of a blood pressure polygenic risk score (PRS) from the general population and its interplay with cancer therapies to hypertension in childhood cancer survivors. Methods: Using 895 established blood pressure loci from the general population, we calculated a PRS for 3572 childhood cancer survivors of European ancestry from Childhood Cancer Survivor Study (CCSS) original cohort, 1889 from CCSS expansion cohort, and 2534 from the St. Jude Lifetime Cohort (SJLIFE). Hypertension was assessed using National Cancer Institute criteria based on self-report of a physician diagnosis in CCSS and by blood pressure measurement in SJLIFE. Results: In the combined sample of 7995 survivors, those in the top decile of the PRS had an odds ratio (OR) of 2.66 (95% CI=2.03-3.48) for hypertension compared to survivors in the bottom decile. The PRS-hypertension association was modified by being overweight/obese (per SD interaction OR=1.13; 95% CI=1.01-1.27) and exposure to hypothalamic-pituitary axis radiation (per SD interaction OR=1.18; 95% CI=1.05-1.33). Attributable fractions for hypertension to the PRS and cancer therapies were 21.0% and 15.7%, respectively, they jointly accounted for 40.2% of hypertension among survivors. Conclusions: A blood pressure PRS from the general population is significantly associated with hypertension among childhood cancer survivors and contributes to approximately one quarter of hypertension risk among survivors. These findings highlight the importance of screening for hypertension in all childhood cancer survivors, and identify higher risk subgroups.
Language	English
Publishing date	2021-03-16
Publishing country	United States
Document type	Journal Article
ISSN	2666-0873
ISSN (online)	2666-0873
DOI	10.1016/j.jaccao.2021.01.007
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Article ; Online: Polygenic Risk Score Improves Risk Stratification and Prediction of Subsequent Thyroid Cancer after Childhood Cancer.

Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology

2021 Volume 30, Issue 11, Page(s) 2096–2104

Abstract: Background: Subsequent thyroid cancer (STC) is one of the most common malignancies in childhood cancer survivors. We aimed to evaluate the polygenic contributions to STC risk and potential utility in improving risk prediction.: Methods: A polygenic ... ...

Abstract	Background: Subsequent thyroid cancer (STC) is one of the most common malignancies in childhood cancer survivors. We aimed to evaluate the polygenic contributions to STC risk and potential utility in improving risk prediction. Methods: A polygenic risk score (PRS) was calculated from 12 independent SNPs associated with thyroid cancer risk in the general population. Associations between PRS and STC risk were evaluated among survivors from St. Jude Lifetime Cohort (SJLIFE) and were replicated in survivors from Childhood Cancer Survivor Study (CCSS). A risk prediction model integrating the PRS and clinical factors, initially developed in SJLIFE, and its performance were validated in CCSS. Results: Among 2,370 SJLIFE survivors with a median follow-up of 28.8 [interquartile range (IQR) = 21.9-36.1] years, 65 (2.7%) developed STC. Among them, the standardized PRS was associated with an increased rate of STC [relative rate (RR) = 1.57; 95% confidence interval (CI) = 1.24-1.98; Conclusions: Integration of the PRS with clinical factors provided a statistically significant improvement in risk prediction of STC, although the magnitude of improvement was modest. Impact: PRS improves risk stratification and prediction of STC, suggesting its potential utility for optimizing screening strategies in survivorship care.
MeSH term(s)	Adult ; Cancer Survivors/statistics & numerical data ; Child ; Female ; Humans ; Male ; Middle Aged ; Neoplasms, Second Primary/epidemiology ; Polymorphism, Single Nucleotide ; Retrospective Studies ; Risk Assessment ; Risk Factors ; Thyroid Neoplasms/epidemiology
Language	English
Publishing date	2021-08-31
Publishing country	United States
Document type	Journal Article ; Multicenter Study ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1153420-5
ISSN	1538-7755 ; 1055-9965
ISSN (online)	1538-7755
ISSN	1055-9965
DOI	10.1158/1055-9965.EPI-21-0448
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Article ; Online: A Novel Locus on 6p21.2 for Cancer Treatment-Induced Cardiac Dysfunction Among Childhood Cancer Survivors.

Sapkota, Yadav / Ehrhardt, Matthew J / Qin, Na / Wang, Zhaoming / Liu, Qi / Qiu, Weiyu / Shelton, Kyla / Shao, Ying / Plyler, Emily / Mulder, Heather L / Easton, John / Michael, J Robert / Burridge, Paul W / Wang, Xuexia / Wilson, Carmen L / Jefferies, John L / Chow, Eric J / Oeffinger, Kevin C / Morton, Lindsay M /

Li, Chunliang / Yang, Jun J / Zhang, Jinghui / Bhatia, Smita / Mulrooney, Daniel A / Hudson, Melissa M / Robison, Leslie L / Armstrong, Gregory T / Yasui, Yutaka

Journal of the National Cancer Institute

2022 Volume 114, Issue 8, Page(s) 1109–1116

Abstract: Background: Adult survivors of childhood cancer are at increased risk of cardiac late effects.: Methods: Using whole-genome sequencing data from 1870 survivors of European ancestry in the St. Jude Lifetime Cohort (SJLIFE) study, genetic variants were ...

Abstract	Background: Adult survivors of childhood cancer are at increased risk of cardiac late effects. Methods: Using whole-genome sequencing data from 1870 survivors of European ancestry in the St. Jude Lifetime Cohort (SJLIFE) study, genetic variants were examined for association with ejection fraction (EF) and clinically assessed cancer therapy-induced cardiac dysfunction (CCD). Statistically significant findings were validated in 301 SJLIFE survivors of African ancestry and 4020 survivors of European ancestry from the Childhood Cancer Survivor Study. All statistical tests were 2-sided. Results: A variant near KCNK17 showed genome-wide significant association with EF (rs2815063-A: EF reduction = 1.6%; P = 2.1 × 10-8) in SJLIFE survivors of European ancestry, which replicated in SJLIFE survivors of African ancestry (EF reduction = 1.5%; P = .004). The rs2815063-A also showed a 1.80-fold (P = .008) risk of severe or disabling or life-threatening CCD and replicated in 4020 Childhood Cancer Survivor Study survivors of European ancestry (odds ratio = 1.40; P = .04). Notably, rs2815063-A was specifically associated among survivors exposed to doxorubicin only, with a stronger effect on EF (3.3% EF reduction) and CCD (2.97-fold). Whole blood DNA methylation data in 1651 SJLIFE survivors of European ancestry showed statistically significant correlation of rs2815063-A with dysregulation of KCNK17 enhancers (false discovery rate <5%), which replicated in 263 survivors of African ancestry. Consistently, the rs2815063-A was associated with KCNK17 downregulation based on RNA sequencing of 75 survivors. Conclusions: Leveraging the 2 largest cohorts of childhood cancer survivors in North America and survivor-specific polygenomic functional data, we identified a novel risk locus for CCD, which showed specificity with doxorubicin-induced cardiac dysfunction and highlighted dysregulation of KCNK17 as the likely molecular mechanism underlying this genetic association.
MeSH term(s)	Adult ; Cancer Survivors ; Child ; Cohort Studies ; Doxorubicin ; Heart Diseases/chemically induced ; Heart Diseases/epidemiology ; Humans ; Neoplasms/drug therapy ; Neoplasms/genetics
Chemical Substances	Doxorubicin (80168379AG)
Language	English
Publishing date	2022-06-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2992-0
ISSN	1460-2105 ; 0027-8874 ; 0198-0157
ISSN (online)	1460-2105
ISSN	0027-8874 ; 0198-0157
DOI	10.1093/jnci/djac115
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Article: CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data

Genome biology. 2020 Dec., v. 21, no. 1

2020

Abstract: To discover driver fusions beyond canonical exon-to-exon chimeric transcripts, we develop CICERO, a local assembly-based algorithm that integrates RNA-seq read support with extensive annotation for candidate ranking. CICERO outperforms commonly used ... ...

Abstract	To discover driver fusions beyond canonical exon-to-exon chimeric transcripts, we develop CICERO, a local assembly-based algorithm that integrates RNA-seq read support with extensive annotation for candidate ranking. CICERO outperforms commonly used methods, achieving a 95% detection rate for 184 independently validated driver fusions including internal tandem duplications and other non-canonical events in 170 pediatric cancer transcriptomes. Re-analysis of TCGA glioblastoma RNA-seq unveils previously unreported kinase fusions (KLHL7-BRAF) and a 13% prevalence of EGFR C-terminal truncation. Accessible via standard or cloud-based implementation, CICERO enhances driver fusion detection for research and precision oncology. The CICERO source code is available at https://github.com/stjude/Cicero .
Keywords	algorithms ; glioblastoma ; sequence analysis ; transcriptome
Language	English
Dates of publication	2020-12
Size	p. 126.
Publishing place	BioMed Central
Document type	Article
ZDB-ID	2040529-7
ISSN	1474-760X ; 1465-6906
ISSN (online)	1474-760X
ISSN	1465-6906
DOI	10.1186/s13059-020-02043-x
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Article ; Online: CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.

Genome biology

2020 Volume 21, Issue 1, Page(s) 126

Abstract	To discover driver fusions beyond canonical exon-to-exon chimeric transcripts, we develop CICERO, a local assembly-based algorithm that integrates RNA-seq read support with extensive annotation for candidate ranking. CICERO outperforms commonly used methods, achieving a 95% detection rate for 184 independently validated driver fusions including internal tandem duplications and other non-canonical events in 170 pediatric cancer transcriptomes. Re-analysis of TCGA glioblastoma RNA-seq unveils previously unreported kinase fusions (KLHL7-BRAF) and a 13% prevalence of EGFR C-terminal truncation. Accessible via standard or cloud-based implementation, CICERO enhances driver fusion detection for research and precision oncology. The CICERO source code is available at https://github.com/stjude/Cicero.
MeSH term(s)	Algorithms ; Gene Fusion ; Humans ; Molecular Sequence Annotation/methods ; Neoplasms/genetics ; Sequence Analysis, RNA ; Software
Language	English
Publishing date	2020-05-28
Publishing country	England
Document type	Evaluation Study ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-020-02043-x
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Article ; Online: St. Jude Cloud: A Pediatric Cancer Genomic Data-Sharing Ecosystem.

McLeod, Clay / Gout, Alexander M / Zhou, Xin / Thrasher, Andrew / Rahbarinia, Delaram / Brady, Samuel W / Macias, Michael / Birch, Kirby / Finkelstein, David / Sunny, Jobin / Mudunuri, Rahul / Orr, Brent A / Treadway, Madison / Davidson, Bob / Ard, Tracy K / Chiao, Arthur / Swistak, Andrew / Wiggins, Stephanie / Foy, Scott /

Wang, Jian / Sioson, Edgar / Wang, Shuoguo / Michael, J Robert / Liu, Yu / Ma, Xiaotu / Patel, Aman / Edmonson, Michael N / Wilkinson, Mark R / Frantz, Andrew M / Chang, Ti-Cheng / Tian, Liqing / Lei, Shaohua / Islam, S M Ashiqul / Meyer, Christopher / Thangaraj, Naina / Tater, Pamella / Kandali, Vijay / Ma, Singer / Nguyen, Tuan / Serang, Omar / McGuire, Irina / Robison, Nedra / Gentry, Darrell / Tang, Xing / Palmer, Lance E / Wu, Gang / Suh, Ed / Tanner, Leigh / McMurry, James / Lear, Matthew / Pappo, Alberto S / Wang, Zhaoming / Wilson, Carmen L / Cheng, Yong / Meshinchi, Soheil / Alexandrov, Ludmil B / Weiss, Mitchell J / Armstrong, Gregory T / Robison, Leslie L / Yasui, Yutaka / Nichols, Kim E / Ellison, David W / Bangur, Chaitanya / Mullighan, Charles G / Baker, Suzanne J / Dyer, Michael A / Miller, Geralyn / Newman, Scott / Rusch, Michael / Daly, Richard / Perry, Keith / Downing, James R / Zhang, Jinghui

Cancer discovery

2021 Volume 11, Issue 5, Page(s) 1082–1099

Abstract: Effective data sharing is key to accelerating research to improve diagnostic precision, treatment efficacy, and long-term survival in pediatric cancer and other childhood catastrophic diseases. We present St. Jude Cloud (https://www.stjude.cloud), a ... ...

Abstract	Effective data sharing is key to accelerating research to improve diagnostic precision, treatment efficacy, and long-term survival in pediatric cancer and other childhood catastrophic diseases. We present St. Jude Cloud (https://www.stjude.cloud), a cloud-based data-sharing ecosystem for accessing, analyzing, and visualizing genomic data from >10,000 pediatric patients with cancer and long-term survivors, and >800 pediatric sickle cell patients. Harmonized genomic data totaling 1.25 petabytes are freely available, including 12,104 whole genomes, 7,697 whole exomes, and 2,202 transcriptomes. The resource is expanding rapidly, with regular data uploads from St. Jude's prospective clinical genomics programs. Three interconnected apps within the ecosystem-Genomics Platform, Pediatric Cancer Knowledgebase, and Visualization Community-enable simultaneously performing advanced data analysis in the cloud and enhancing the Pediatric Cancer knowledgebase. We demonstrate the value of the ecosystem through use cases that classify 135 pediatric cancer subtypes by gene expression profiling and map mutational signatures across 35 pediatric cancer subtypes. SIGNIFICANCE: To advance research and treatment of pediatric cancer, we developed St. Jude Cloud, a data-sharing ecosystem for accessing >1.2 petabytes of raw genomic data from >10,000 pediatric patients and survivors, innovative analysis workflows, integrative multiomics visualizations, and a knowledgebase of published data contributed by the global pediatric cancer community.
MeSH term(s)	Anemia, Sickle Cell/genetics ; Child ; Cloud Computing ; Ecosystem ; Genomics ; Hospitals, Pediatric ; Humans ; Information Dissemination ; Neoplasms/genetics
Language	English
Publishing date	2021-01-06
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2625242-9
ISSN	2159-8290 ; 2159-8274
ISSN (online)	2159-8290
ISSN	2159-8274
DOI	10.1158/2159-8290.CD-20-1230
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