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Recent Publications

Genome Gerrymandering: optimal division of the genome into regions with cancer type specific differences in mutation rates.

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Genome Gerrymandering: optimal division of the genome into regions with cancer type specific differences in mutation rates.

Pac Symp Biocomput. 2020;25:274-285

Authors: Young A, Chmura J, Park Y, Morris Q, Atwal G

Abstract
The activity of mutational processes differs across the genome, and is influenced by chromatin state and spatial genome organization. At the scale of one megabase-pair (Mb), regional mutation density correlate strongly with chromatin features and mutation density at this scale can be used to accurately identify cancer type. Here, we explore the relationship between genomic region and mutation rate by developing an information theory driven, dynamic programming algorithm for dividing the genome into regions with differing relative mutation rates between cancer types. Our algorithm improves mutual information when compared to the naive approach, effectively reducing the average number of mutations required to identify cancer type. Our approach provides an efficient method for associating regional mutation density with mutation labels, and has future applications in exploring the role of somatic mutations in a number of diseases.

PMID: 31797603 [PubMed - in process]



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TrackSigFreq: subclonal reconstructions based on mutation signatures and allele frequencies.

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TrackSigFreq: subclonal reconstructions based on mutation signatures and allele frequencies.

Pac Symp Biocomput. 2020;25:238-249

Authors: Harrigan CF, Rubanova Y, Morris Q, Selega A

Abstract
Mutational signatures are patterns of mutation types, many of which are linked to known mutagenic processes. Signature activity represents the proportion of mutations a signature generates. In cancer, cells may gain advantageous phenotypes through mutation accumulation, causing rapid growth of that subpopulation within the tumour. The presence of many subclones can make cancers harder to treat and have other clinical implications. Reconstructing changes in signature activities can give insight into the evolution of cells within a tumour. Recently, we introduced a new method, TrackSig, to detect changes in signature activities across time from single bulk tumour sample. By design, TrackSig is unable to identify mutation populations with different frequencies but little to no difference in signature activity. Here we present an extension of this method, TrackSigFreq, which enables trajectory reconstruction based on both observed density of mutation frequencies and changes in mutational signature activities. TrackSigFreq preserves the advantages of TrackSig, namely optimal and rapid mutation clustering through segmentation, while extending it so that it can identify distinct mutation populations that share similar signature activities.

PMID: 31797600 [PubMed - in process]



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Identifying Transitional High Cost Users from Unstructured Patient Profiles Written by Primary Care Physicians.

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Identifying Transitional High Cost Users from Unstructured Patient Profiles Written by Primary Care Physicians.

Pac Symp Biocomput. 2020;25:127-138

Authors: Zhang H, Candido E, Wilton AS, Duchen R, Jaakkimainen L, Wodchis W, Morris Q

Abstract
Identification and subsequent intervention of patients at risk of becoming High Cost Users (HCUs) presents the opportunity to improve outcomes while also providing significant savings for the healthcare system. In this paper, the 2016 HCU status of patients was predicted using free-form text data from the 2015 cumulative patient profiles within the electronic medical records of family care practices in Ontario. These unstructured notes make substantial use of domain-specific spellings and abbreviations; we show that word embeddings derived from the same context provide more informative features than pre-trained ones based on Wikipedia, MIMIC, and Pubmed. We further demonstrate that a model using features derived from aggregated word embeddings (EmbEncode) provides a significant performance improvement over the bag-of-words representation (82.48±0.35% versus 81.85±0.36% held-out AUROC, p = 3.2 × 10-4), using far fewer input features (5,492 versus 214,750) and fewer non-zero coefficients (1,177 versus 4,284). The future HCUs of greatest interest are the transitional ones who are not already HCUs, because they provide the greatest scope for interventions. Predicting these new HCU is challenging because most HCUs recur. We show that removing recurrent HCUs from the training set improves the ability of EmbEncode to predict new HCUs, while only slightly decreasing its ability to predict recurrent ones.

PMID: 31797592 [PubMed - in process]



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Shake-it-off: a simple ultrasonic cryo-EM specimen-preparation device.

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Shake-it-off: a simple ultrasonic cryo-EM specimen-preparation device.

Acta Crystallogr D Struct Biol. 2019 Dec 01;75(Pt 12):1063-1070

Authors: Rubinstein JL, Guo H, Ripstein ZA, Haydaroglu A, Au A, Yip CM, Di Trani JM, Benlekbir S, Kwok T

Abstract
Although microscopes and image-analysis software for electron cryomicroscopy (cryo-EM) have improved dramatically in recent years, specimen-preparation methods have lagged behind. Most strategies still rely on blotting microscope grids with paper to produce a thin film of solution suitable for vitrification. This approach loses more than 99.9% of the applied sample and requires several seconds, leading to problematic air-water interface interactions for macromolecules in the resulting thin film of solution and complicating time-resolved studies. Recently developed self-wicking EM grids allow the use of small volumes of sample, with nanowires on the grid bars removing excess solution to produce a thin film within tens of milliseconds from sample application to freezing. Here, a simple cryo-EM specimen-preparation device that uses components from an ultrasonic humidifier to transfer protein solution onto a self-wicking EM grid is presented. The device is controlled by a Raspberry Pi single-board computer and all components are either widely available or can be manufactured by online services, allowing the device to be constructed in laboratories that specialize in cryo-EM rather than instrument design. The simple open-source design permits the straightforward customization of the instrument for specialized experiments.

PMID: 31793900 [PubMed - in process]



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Lineage tracing reveals the hierarchical relationship between neural stem cell populations in the mouse forebrain.

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Lineage tracing reveals the hierarchical relationship between neural stem cell populations in the mouse forebrain.

Sci Rep. 2019 Nov 27;9(1):17730

Authors: Sachewsky N, Xu W, Fuehrmann T, van der Kooy D, Morshead CM

Abstract
Since the original isolation of neural stem cells (NSCs) in the adult mammalian brain, further work has revealed a heterogeneity in the NSC pool. Our previous work characterized a distinct, Oct4 expressing, NSC population in the periventricular region, through development and into adulthood. We hypothesized that this population is upstream in lineage to the more abundant, well documented, GFAP expressing NSC. Herein, we show that Oct4 expressing NSCs give rise to neurons, astrocytes and oligodendrocytes throughout the developing brain. Further, transgenic inducible mouse models demonstrate that the rare Oct4 expressing NSCs undergo asymmetric divisions to give rise to GFAP expressing NSCs in naïve and injured brains. This lineage relationship between distinct NSC pools contributes significantly to an understanding of neural development, the NSC lineage in vivo and has implications for neural repair.

PMID: 31776378 [PubMed - in process]



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β2* nAChRs on VTA dopamine and GABA neurons separately mediate nicotine aversion and reward.

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β2* nAChRs on VTA dopamine and GABA neurons separately mediate nicotine aversion and reward.

Proc Natl Acad Sci U S A. 2019 Nov 27;:

Authors: Grieder TE, Besson M, Maal-Bared G, Pons S, Maskos U, van der Kooy D

Abstract
Evidence shows that the neurotransmitter dopamine mediates the rewarding effects of nicotine and other drugs of abuse, while nondopaminergic neural substrates mediate the negative motivational effects. β2* nicotinic acetylcholine receptors (nAChR) are necessary and sufficient for the experience of both nicotine reward and aversion in an intra-VTA (ventral tegmental area) self-administration paradigm. We selectively reexpressed β2* nAChRs in VTA dopamine or VTA γ-amino-butyric acid (GABA) neurons in β2-/- mice to double-dissociate the aversive and rewarding conditioned responses to nicotine in nondependent mice, revealing that β2* nAChRs on VTA dopamine neurons mediate nicotine's conditioned aversive effects, while β2* nAChRs on VTA GABA neurons mediate the conditioned rewarding effects in place-conditioning paradigms. These results stand in contrast to a purely dopaminergic reward theory, leading to a better understanding of the neurobiology of nicotine motivation and possibly to improved therapeutic treatments for smoking cessation.

PMID: 31776253 [PubMed - as supplied by publisher]



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Charge-Balanced Electrical Stimulation Can Modulate Neural Precursor Cell Migration in the Presence of Endogenous Electric Fields in Mouse Brains.

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Charge-Balanced Electrical Stimulation Can Modulate Neural Precursor Cell Migration in the Presence of Endogenous Electric Fields in Mouse Brains.

eNeuro. 2019 Nov 26;:

Authors: Iwasa SN, Rashidi A, Sefton E, Liu NX, Popovic MR, Morshead CM

Abstract
Electric fields can direct cell migration and are crucial during development and tissue repair. We previously reported neural precursor cells are electrosensitive cells that can undergo rapid and directed migration towards the cathode using charge-balanced electrical stimulation in vitro Here, we investigate the ability of electrical stimulation to direct neural precursor migration in mouse brains in vivo To visualize migration, fluorescent adult murine neural precursors were transplanted onto the corpus callosum of adult male mice and intracortical platinum wire electrodes were implanted medial (cathode) and lateral (anode) to the injection site. We applied a charge-balanced biphasic monopolar stimulation waveform for 3 sessions per day, for 3 or 6 days. Irrespective of stimulation, the transplanted neural precursors had a propensity to migrate laterally along the corpus callosum, and applied stimulation affected that migration. Further investigation revealed an endogenous electric field along the corpus callosum that correlated with the lateral migration, suggesting that the applied electric field would need to overcome endogenous cues. There was no difference in transplanted cell differentiation and proliferation, or inflammatory cell numbers near the electrode leads and injection site comparing stimulated and implanted non-stimulated brains. Our results support that endogenous and applied electric fields are important considerations for designing cell therapies for tissue repair in vivo. SIGNIFICANCE STATEMENT The study of electricity in biological environments outside of the well-known action potential is becoming more prominent. Applied electrical stimulation is used clinically and can modulate cell behaviour. Endogenous electric fields exist in the adult brain along the rostral migratory stream and disrupting them can reverse the migration direction of neural precursor cells. We demonstrate that an endogenous electric field exists on the corpus callosum which correlates with the preferred lateral migration of transplanted neural precursor cells. Endogenous electric fields in the brain provide migratory cues that can impact neural repair.

PMID: 31772032 [PubMed - as supplied by publisher]



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Highlights for the 60th anniversary of BBRC.

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Highlights for the 60th anniversary of BBRC.

Biochem Biophys Res Commun. 2019 Dec 17;520(4):699-700

Authors: Stagljar I

PMID: 31761084 [PubMed - in process]



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In-cell identification and measurement of RNA-protein interactions.

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In-cell identification and measurement of RNA-protein interactions.

Nat Commun. 2019 Nov 22;10(1):5317

Authors: Graindorge A, Pinheiro I, Nawrocka A, Mallory AC, Tsvetkov P, Gil N, Carolis C, Buchholz F, Ulitsky I, Heard E, Taipale M, Shkumatava A

Abstract
Regulatory RNAs exert their cellular functions through RNA-binding proteins (RBPs). Identifying RNA-protein interactions is therefore key for a molecular understanding of regulatory RNAs. To date, RNA-bound proteins have been identified primarily through RNA purification followed by mass spectrometry. Here, we develop incPRINT (in cell protein-RNA interaction), a high-throughput method to identify in-cell RNA-protein interactions revealed by quantifiable luminescence. Applying incPRINT to long noncoding RNAs (lncRNAs), we identify RBPs specifically interacting with the lncRNA Firre and three functionally distinct regions of the lncRNA Xist. incPRINT confirms previously known lncRNA-protein interactions and identifies additional interactions that had evaded detection with other approaches. Importantly, the majority of the incPRINT-defined interactions are specific to individual functional regions of the large Xist transcript. Thus, we present an RNA-centric method that enables reliable identification of RNA-region-specific RBPs and is applicable to any RNA of interest.

PMID: 31757954 [PubMed - in process]



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Anti-CRISPR AcrIIA5 Potently Inhibits All Cas9 Homologs Used for Genome Editing.

Anti-CRISPR AcrIIA5 Potently Inhibits All Cas9 Homologs Used for Genome Editing.

Cell Rep. 2019 Nov 12;29(7):1739-1746.e5

Authors: Garcia B, Lee J, Edraki A, Hidalgo-Reyes Y, Erwood S, Mir A, Trost CN, Seroussi U, Stanley SY, Cohn RD, Claycomb JM, Sontheimer EJ, Maxwell KL, Davidson AR

Abstract
CRISPR-Cas9 systems provide powerful tools for genome editing. However, optimal employment of this technology will require control of Cas9 activity so that the timing, tissue specificity, and accuracy of editing may be precisely modulated. Anti-CRISPR proteins, which are small, naturally occurring inhibitors of CRISPR-Cas systems, are well suited for this purpose. A number of anti-CRISPR proteins have been shown to potently inhibit subgroups of CRISPR-Cas9 systems, but their maximal inhibitory activity is generally restricted to specific Cas9 homologs. Since Cas9 homologs vary in important properties, differing Cas9s may be optimal for particular genome-editing applications. To facilitate the practical exploitation of multiple Cas9 homologs, here we identify one anti-CRISPR, called AcrIIA5, that potently inhibits nine diverse type II-A and type II-C Cas9 homologs, including those currently used for genome editing. We show that the activity of AcrIIA5 results in partial in vivo cleavage of a single-guide RNA (sgRNA), suggesting that its mechanism involves RNA interaction.

PMID: 31722192 [PubMed - in process]



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