SVFX: a machine-learning framework to quantify the pathogenicity of structural variants

AbstractA rapid decline in sequencing cost has made large-scale genome sequencing studies feasible. One of the fundamental goals of these studies is to catalog all pathogenic variants. Numerous methods and tools have been developed to interpret point mutations and small insertions and deletions. However, there is a lack of approaches for identifying pathogenic genomic structural variations (SVs). That said, SVs are known to play a crucial role in many diseases by altering the sequence and three-dimensional structure of the genome. Previous studies have suggested a complex interplay of genomic and epigenomic features in the emergence and distribution of SVs. However, the exact mechanism of pathogenesis for SVs in different diseases is not straightforward to decipher. Thus, we built an agnostic machine-learning-based workflow, called SVFX, to assign a “pathogenicity score” to somatic and germline SVs in various diseases. In particular, we generated somatic and germline training models, which included genomic, epigenomic, and conservation-based features for SV call sets in diseased and healthy individuals. We then applied SVFX to SVs in six different cancer cohorts and a cardiovascular disease (CVD) cohort. Overall, SVFX achieved high accuracy in identifying pathogenic SVs. Moreover, we found that predicted pathogenic SVs in cancer cohorts were enriched among known cancer genes and many cancer-related pathways (including Wnt signaling, Ras signaling, DNA repair, and ubiquitin-mediated proteolysis). Finally, we note that SVFX is flexible and can be easily extended to identify pathogenic SVs in additional disease cohorts.

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Therapeutic Implication of Genomic Landscape of Adult Metastatic Sarcoma

JCO Precision Oncology ◽

10.1200/po.18.00325 ◽

2019 ◽

pp. 1-25 ◽

Cited By ~ 2

Author(s):

Xiaolan Feng ◽

Erin Pleasance ◽

Eric Y. Zhao ◽

Tony Ng ◽

Jasleen K. Grewal ◽

...

Keyword(s):

Copy Number ◽

Large Scale ◽

Therapeutic Potential ◽

Point Mutations ◽

Therapeutic Targets ◽

Genomic Analysis ◽

Copy Number Variations ◽

Cancer Genes ◽

Structural Variations ◽

Metastatic Sarcoma

PURPOSE This study investigated therapeutic potential of integrated genome and transcriptome profiling of metastatic sarcoma, a rare but extremely heterogeneous group of aggressive mesenchymal malignancies with few systemic therapeutic options. METHODS Forty-three adult patients with advanced or metastatic non-GI stromal tumor sarcomas of various histology subtypes who were enrolled in the Personalized OncoGenomics program at BC Cancer were included in this study. Fresh tumor tissues along with blood samples underwent whole-genome and transcriptome sequencing. RESULTS The most frequent genomic alterations in this cohort are large-scale structural variation and somatic copy number variation. Outlier RNA expression as well as somatic copy number variations, structural variations, and small mutations together suggest the presence of one or more potential therapeutic targets in the majority of patients in our cohort. Point mutations or deletions in known targetable cancer genes are rare; for example, tuberous sclerosis complex 2 provides a rationale for targeting the mammalian target of rapamycin pathway, resulting in a few patients with exceptional clinical benefit from everolimus. In addition, we observed recurrent 17p11-12 amplifications, which seem to be a sarcoma-specific event. This may suggest that this region harbors an oncogene(s) that is significant for sarcoma tumorigenesis. Furthermore, some sarcoma tumors carrying a distinct mutational signature suggestive of homologous recombination deficiency seem to demonstrate sensitivity to double-strand DNA–damaging agents. CONCLUSION Integrated large-scale genomic analysis may provide insights into potential therapeutic targets as well as novel biologic features of metastatic sarcomas that could fuel future experimental and clinical research and help design biomarker-driven basket clinical trials for novel therapeutic strategies.

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3DIV update for 2021: a comprehensive resource of 3D genome and 3D cancer genome

Nucleic Acids Research ◽

10.1093/nar/gkaa1078 ◽

2020 ◽

Vol 49 (D1) ◽

pp. D38-D46

Author(s):

Kyukwang Kim ◽

Insu Jang ◽

Mooyoung Kim ◽

Jinhyuk Choi ◽

Min-Seo Kim ◽

...

Keyword(s):

Cell Line ◽

Large Scale ◽

Three Dimensional ◽

Cancer Cell Line ◽

Cancer Genome ◽

Structural Variations ◽

3D Genome ◽

Tightly Coupled ◽

Regulatory Effects ◽

The Impact

Abstract Three-dimensional (3D) genome organization is tightly coupled with gene regulation in various biological processes and diseases. In cancer, various types of large-scale genomic rearrangements can disrupt the 3D genome, leading to oncogenic gene expression. However, unraveling the pathogenicity of the 3D cancer genome remains a challenge since closer examinations have been greatly limited due to the lack of appropriate tools specialized for disorganized higher-order chromatin structure. Here, we updated a 3D-genome Interaction Viewer and database named 3DIV by uniformly processing ∼230 billion raw Hi-C reads to expand our contents to the 3D cancer genome. The updates of 3DIV are listed as follows: (i) the collection of 401 samples including 220 cancer cell line/tumor Hi-C data, 153 normal cell line/tissue Hi-C data, and 28 promoter capture Hi-C data, (ii) the live interactive manipulation of the 3D cancer genome to simulate the impact of structural variations and (iii) the reconstruction of Hi-C contact maps by user-defined chromosome order to investigate the 3D genome of the complex genomic rearrangement. In summary, the updated 3DIV will be the most comprehensive resource to explore the gene regulatory effects of both the normal and cancer 3D genome. ‘3DIV’ is freely available at http://3div.kr.

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An Intramolecular Salt Bridge in Bacillus thuringiensis Cry4Ba Toxin Is Involved in the Stability of Helix α-3, Which Is Needed for Oligomerization and Insecticidal Activity

Applied and Environmental Microbiology ◽

10.1128/aem.01515-17 ◽

2017 ◽

Vol 83 (20) ◽

Cited By ~ 3

Author(s):

Sabino Pacheco ◽

Isabel Gómez ◽

Jorge Sánchez ◽

Blanca-Ines García-Gómez ◽

Mario Soberón ◽

...

Keyword(s):

Bacillus Thuringiensis ◽

Double Point ◽

Single Point ◽

Three Dimensional ◽

Point Mutations ◽

Salt Bridge ◽

Dimensional Structure ◽

Cry Toxins ◽

Content Type ◽

Domain I

ABSTRACT Bacillus thuringiensis three-domain Cry toxins kill insects by forming pores in the apical membrane of larval midgut cells. Oligomerization of the toxin is an important step for pore formation. Domain I helix α-3 participates in toxin oligomerization. Here we identify an intramolecular salt bridge within helix α-3 of Cry4Ba (D111-K115) that is conserved in many members of the family of three-domain Cry toxins. Single point mutations such as D111K or K115D resulted in proteins severely affected in toxicity. These mutants were also altered in oligomerization, and the mutant K115D was more sensitive to protease digestion. The double point mutant with reversed charges, D111K-K115D, recovered both oligomerization and toxicity, suggesting that this salt bridge is highly important for conservation of the structure of helix α-3 and necessary to promote the correct oligomerization of the toxin. IMPORTANCE Domain I has been shown to be involved in oligomerization through helix α-3 in different Cry toxins, and mutations affecting oligomerization also elicit changes in toxicity. The three-dimensional structure of the Cry4Ba toxin reveals an intramolecular salt bridge in helix α-3 of domain I. Mutations that disrupt this salt bridge resulted in changes in Cry4Ba oligomerization and toxicity, while a double point reciprocal mutation that restored the salt bridge resulted in recovery of toxin oligomerization and toxicity. These data highlight the role of oligomer formation as a key step in Cry4Ba toxicity.

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Biophysical and biochemical investigations of RNA catalysis in the hammerhead ribozyme

Quarterly Reviews of Biophysics ◽

10.1017/s003358350000353x ◽

1999 ◽

Vol 32 (3) ◽

pp. 241-284 ◽

Cited By ~ 29

Author(s):

William G. Scott

Keyword(s):

Metal Ions ◽

Conformational Change ◽

Large Scale ◽

Enzyme Inhibitor ◽

Hammerhead Ribozyme ◽

Three Dimensional ◽

Chemical Mechanism ◽

Dimensional Structure ◽

Three Dimensional Structure ◽

Hammerhead Rna

1. How do ribozymes work? 2412. The hammerhead RNA as a prototype ribozyme 2422.1 RNA enzymes 2422.2 Satellite self-cleaving RNAs 2422.3 Hammerhead RNAs and hammerhead ribozymes 2443. The chemical mechanism of hammerhead RNA self-cleavage 2463.1 Phosphodiester isomerization via an SN2(P) reaction 2473.2 The canonical role of divalent metal ions in the hammerhead ribozyme reaction 2513.3 The hammerhead ribozyme does not actually require metal ions for catalysis 2543.4 Hammerhead RNA enzyme kinetics 2574. Sequence requirements for hammerhead RNA self-cleavage 2604.1 The conserved core, mutagenesis and functional group modifications 2604.2 Ground-state vs. transition-state effects 2615. The three-dimensional structure of the hammerhead ribozyme 2625.1 Enzyme–inhibitor complexes 2625.2 Enzyme–substrate complex in the initial state 2645.3 Hammerhead ribozyme self-cleavage in the crystal 2645.4 The requirement for a conformational change 2655.5 Capture of conformational intermediates using crystallographic freeze-trapping 2665.6 The structure of a hammerhead ribozyme ‘early’ conformational intermediate 2675.7 The structure of a hammerhead ribozyme ‘later’ conformational intermediate 2685.8 Is the conformational change pH dependent? 2695.9 Isolating the structure of the cleavage product 2715.10 Evidence for and against additional large-scale conformation changes 2745.11 NMR spectroscopic studies of the hammerhead ribozyme 2786. Concluding remarks 2807. Acknowledgements 2818. References 2811. How do ribozymes work? 241The discovery that RNA can be an enzyme (Guerrier-Takada et al. 1983; Zaug & Cech, 1986) has created the fundamental question of how RNA enzymes work. Before this discovery, it was generally assumed that proteins were the only biopolymers that had sufficient complexity and chemical heterogeneity to catalyze biochemical reactions. Clearly, RNA can adopt sufficiently complex tertiary structures that make catalysis possible. How does the three- dimensional structure of an RNA endow it with catalytic activity? What structural and functional principles are unique to RNA enzymes (or ribozymes), and what principles are so fundamental that they are shared with protein enzymes?

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Crystal structure of a tankyrase 1–telomere repeat factor 1 complex

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x16004131 ◽

2016 ◽

Vol 72 (4) ◽

pp. 320-327 ◽

Cited By ~ 9

Author(s):

Bo Li ◽

Ruihong Qiao ◽

Zhizhi Wang ◽

Weihong Zhou ◽

Xin Li ◽

...

Keyword(s):

Crystal Structure ◽

Large Scale ◽

Sparse Matrix ◽

Critical Role ◽

Three Dimensional ◽

Mitotic Cell ◽

Ankyrin Repeat ◽

Dimensional Structure ◽

Telomere Repeat ◽

Tankyrase 1

Telomere repeat factor 1 (TRF1) is a subunit of shelterin (also known as the telosome) and plays a critical role in inhibiting telomere elongation by telomerase. Tankyrase 1 (TNKS1) is a poly(ADP-ribose) polymerase that regulates the activity of TRF1 through poly(ADP-ribosyl)ation (PARylation). PARylation of TRF1 by TNKS1 leads to the release of TRF1 from telomeres and allows telomerase to access telomeres. The interaction between TRF1 and TNKS1 is thus important for telomere stability and the mitotic cell cycle. Here, the crystal structure of a complex between the N-terminal acidic domain of TRF1 (residues 1–55) and a fragment of TNKS1 covering the second and third ankyrin-repeat clusters (ARC2-3) is presented at 2.2 Å resolution. The TNKS1–TRF1 complex crystals were optimized using an `oriented rescreening' strategy, in which the initial crystallization condition was used as a guide for a second round of large-scale sparse-matrix screening. This crystallographic and biochemical analysis provides a better understanding of the TRF1–TNKS1 interaction and the three-dimensional structure of the ankyrin-repeat domain of TNKS.

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A Novel Missense Variant in the Gene PPP2R5D Causes a Rare Neurodevelopmental Disorder with Increased Phenotype

BioMed Research International ◽

10.1155/2021/6661860 ◽

2021 ◽

Vol 2021 ◽

pp. 1-7

Author(s):

Lulu Yan ◽

Ru Shen ◽

Zongfu Cao ◽

Chunxiao Han ◽

Yuxin Zhang ◽

...

Keyword(s):

De Novo ◽

Genetic Disorder ◽

Neurodevelopmental Disorder ◽

Three Dimensional ◽

Missense Variant ◽

Pathogenic Variant ◽

Dimensional Structure ◽

Chinese Family ◽

Speech Impairment ◽

Pathogenic Variants

PPP2R5D-related neurodevelopmental disorder, which is mainly caused by de novo missense variants in the PPP2R5D gene, is a rare autosomal dominant genetic disorder with about 100 patients and a total of thirteen pathogenic variants known to exist globally so far. Here, we present a 24-month-old Chinese boy with developmental delay and other common clinical characteristics of PPP2R5D-related neurodevelopmental disorder including hypotonia, macrocephaly, intellectual disability, speech impairment, and behavioral abnormality. Trio-whole exome sequencing (WES) and Sanger sequencing were performed to identify the causal gene variant. The pathogenicity of the variant was evaluated using bioinformatics tools. We identified a novel pathogenic variant in the PPP2R5D gene (c.620G>T, p.Trp207Leu). The variant is located in the variant hotspot region of this gene and is predicted to cause PPP2R5D protein dysfunction due to an increase in local hydrophobicity and unstable three-dimensional structure. We report a novel pathogenic variant of PPP2R5D associated with PPP2R5D-related neurodevelopmental disorder from a Chinese family. Our findings expanded the phenotypic and mutational spectrum of PPP2R5D-related neurodevelopmental disorder.

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An Initiation Process of Tropical Depression-type Disturbances under the Influence of Upper-level Troughs

Journal of the Atmospheric Sciences ◽

10.1175/jas-d-20-0334.1 ◽

2021 ◽

Author(s):

Yuya Hamaguchi ◽

Yukari N. Takayabu

Keyword(s):

Large Scale ◽

Convective Available Potential Energy ◽

Three Dimensional ◽

Lower Troposphere ◽

Dimensional Structure ◽

Convective Heating ◽

Upper Troposphere ◽

Tropical Depression ◽

Upper Level ◽

Extratropical Forcing

AbstractIn this study, the statistical relationship between tropical upper-tropospheric troughs (TUTTs) and the initiation of summertime tropical-depression type disturbances (TDDs) over the western and central North Pacific is investigated. By applying a spatiotemporal filter to the 34-year record of brightness temperature and using JRA-55 reanalysis products, TDD-event initiations are detected and classified as trough-related (TR) or non-trough-related (non-TR). The conventional understanding is that TDDs originate primarily in the lower-troposphere; our results refine this view by revealing that approximately 30% of TDDs in the 10°N-20°N latitude ranges are generated under the influence of TUTTs. Lead-lag composite analysis of both TR- and non-TR-TDDs clarifies that TR-TDDs occur under relatively dry and less convergent large-scale conditions in the lower-troposphere. This result suggests that TR-TDDs can form in a relatively unfavorable low-level environment. The three-dimensional structure of the wave activity flux reveals southward and downward propagation of wave energy in the upper troposphere that converges at the mid-troposphere around the region where TR-TDDs occur, suggesting the existence of extratropical forcing. Further, the role of dynamic forcing associated with the TUTT on the TR-TDD-initiation is analyzed using the quasi-geostrophic omega equation. The result reveals that moistening in the mid-to-upper troposphere takes place in association with the sustained dynamical ascent at the southeast side of the TUTT, which precedes the occurrence of deep convective heating. Along with a higher convective available potential energy due to the destabilizing effect of TUTTs, the moistening in the mid-to-upper troposphere also helps to prepare the environment favorable to TDDs initiation.

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Hepatocyte Aggregate Culture Technique for Bioreactors in Hybrid Liver Support Systems

The International Journal of Artificial Organs ◽

10.1177/039139889301601210 ◽

1993 ◽

Vol 16 (12) ◽

pp. 843-846 ◽

Cited By ~ 29

Author(s):

J.C. Gerlach ◽

K. Klöppel ◽

C. MÜller ◽

N. Schnoy ◽

M.D. Smith ◽

...

Keyword(s):

High Performance ◽

Large Scale ◽

Support Systems ◽

Three Dimensional ◽

Culture Technique ◽

Dimensional Structure ◽

Cell Aggregates ◽

Liver Support ◽

Aggregate Culture

Utilizing a modified culture technique for hepatocytes, a high performance suspension culture is possible in which hepatocytes spontaneously form cell aggregates. The aggregates of 20-100 cells have been histologically confirmed to hold a three-dimensional structure, they show a long-term external metabolism and a survival time comparable with standard adhesion cultures. This technique has several advantages in the construction of large scale bioreactors for hybrid liver support systems.

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Structure, function and regulation of pyruvate carboxylase

Biochemical Journal ◽

10.1042/bj3400001 ◽

1999 ◽

Vol 340 (1) ◽

pp. 1-16 ◽

Cited By ~ 97

Author(s):

Sarawut JITRAPAKDEE ◽

John C. WALLACE

Keyword(s):

Pyruvate Carboxylase ◽

Limited Proteolysis ◽

Three Dimensional ◽

Point Mutations ◽

Dimensional Structure ◽

Molecular Defects ◽

X Ray Crystallography ◽

Neurotransmitter Substances ◽

Translational Mechanisms ◽

Structural Region

Pyruvate carboxylase (PC; EC 6.4.1.1), a member of the biotin-dependent enzyme family, catalyses the ATP-dependent carboxylation of pyruvate to oxaloacetate. PC has been found in a wide variety of prokaryotes and eukaryotes. In mammals, PC plays a crucial role in gluconeogenesis and lipogenesis, in the biosynthesis of neurotransmitter substances, and in glucose-induced insulin secretion by pancreatic islets. The reaction catalysed by PC and the physical properties of the enzyme have been studied extensively. Although no high-resolution three-dimensional structure has yet been determined by X-ray crystallography, structural studies of PC have been conducted by electron microscopy, by limited proteolysis, and by cloning and sequencing of genes and cDNA encoding the enzyme. Most well characterized forms of active PC consist of four identical subunits arranged in a tetrahedron-like structure. Each subunit contains three functional domains: the biotin carboxylation domain, the transcarboxylation domain and the biotin carboxyl carrier domain. Different physiological conditions, including diabetes, hyperthyroidism, genetic obesity and postnatal development, increase the level of PC expression through transcriptional and translational mechanisms, whereas insulin inhibits PC expression. Glucocorticoids, glucagon and catecholamines cause an increase in PC activity or in the rate of pyruvate carboxylation in the short term. Molecular defects of PC in humans have recently been associated with four point mutations within the structural region of the PC gene, namely Val145 → Ala, Arg451 → Cys, Ala610 → Thr and Met743 → Thr.

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Oligomeric Structure of Colicin Ia Channel in Lipid Bilayer Membranes

Journal of Biological Chemistry ◽

10.1074/jbc.m900292200 ◽

2009 ◽

Vol 284 (24) ◽

pp. 16126-16134 ◽

Cited By ~ 11

Author(s):

Sarah L. Greig ◽

Mazdak Radjainia ◽

Alok K. Mitra

Keyword(s):

Lipid Bilayer ◽

Large Scale ◽

Three Dimensional ◽

Velocity Sedimentation ◽

Dimensional Structure ◽

Lipid Bilayer Membranes ◽

Outer Membrane Receptor ◽

Bilayer Membranes ◽

Three Dimensional Structure ◽

Colicin Ia

Colicin Ia is a soluble, harpoon-shaped bacteriocin which translocates across the periplasmic space of sensitive Escherichia coli cell by parasitizing an outer membrane receptor and forms voltage-gated ion channels in the inner membrane. This process leads to cell death, which has been thought to be caused by a single colicin Ia molecule. To directly visualize the three-dimensional structure of the channel, we generated two-dimensional crystals of colicin Ia inserted in lipid-bilayer membranes and determined a ∼17 three-dimensional model by electron crystallography. Supported by velocity sedimentation, chemical cross-linking and single-particle image analysis, the three-dimensional structure is a crown-shaped oligomer enclosing a ∼35 Å-wide extrabilayer vestibule. Our study suggests that lipid insertion instigates a global conformational change in colicin Ia and that more than one molecule participates in the channel architecture with the vestibule, possibly facilitating the known large scale peptide translocation upon channel opening.

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