Biology subjects

Cheng, K.

Publications and source records attributed to Cheng, K..

5 recordsLinked to original sources

bioRxiv2018

A systematic genome-wide mapping of the oncogenic risks associated with CRISPR-Cas9 editing

Recent studies have reported that CRISPR-Cas9 gene editing induces a p53-dependent DNA damage response in primary cells, which may select for cells with oncogenic p53 mutations11,12. It is unclear whether these CRISPR-induced changes are applicable to different cell types, and whether CRISPR gene editing may select for other oncogenic mutations. Addressing these questions, we analyzed genome-wide CRISPR and RNAi screens to systematically chart the mutation selection potential of CRISPR knockouts across the whole exome. Our analysis suggests that CRISPR gene editing can select for mutants of KRAS and VHL, at a level comparable to that reported for p53. These predictions were further validated in a genome-wide manner by analyzing independent CRISPR screens and patients tumor data. Finally, we performed a new set of pooled and arrayed CRISPR screens to evaluate the competition between CRISPR-edited isogenic p53 WT and mutant cell lines, which further validated our predictions. In summary, our study systematically charts and points to the potential selection of specific cancer driver mutations during CRISPR-Cas9 gene editing.

cancer biology↗

bioRxiv2018

Combinatorial Detection of Conserved Alteration Patterns for Identifying Cancer Subnetworks

BackgroundAdvances in large scale tumor sequencing have lead to an understanding that there are combinations of genomic and transcriptomic alterations speciflc to tumor types, shared across many patients. Unfortunately, computational identiflcation of functionally meaningful shared alteration patterns, impacting gene/protein interaction subnetworks, has proven to be challenging. FindingsWe introduce a novel combinatorial method, cd-CAP, for simultaneous detection of connected subnetworks of an interaction network where genes exhibit conserved alteration patterns across tumor samples. Our method differentiates distinct alteration types associated with each gene (rather than relying on binary information of a gene being altered or not), and simultaneously detects multiple alteration proflle conserved subnetworks. ConclusionsIn a number of The Cancer Genome Atlas (TCGA) data sets, cd-CAP identifled large biologically signiflcant subnetworks with conserved alteration patterns, shared across many tumor samples.

systems biology↗

bioRxiv2018

Breakdown of spatial coding and neural synchronization in epilepsy

Temporal lobe epilepsy causes significant cognitive deficits in both human patients and rodent models, yet the specific circuit mechanisms that alter cognitive processes remain unknown. There is dramatic and selective interneuron death and axonal reorganization within the hippocampus of both humans and animal models, but the functional consequences of these changes on information processing at the neuronal population level have not been well characterized. To examine spatial representations of epileptic and control mice, we developed a novel wire-free miniature microscope to allow for unconstrained behavior during in vivo calcium imaging of neuronal activity. We found that epileptic mice running on a linear track had severely impaired spatial processing in CA1 within a single session, as place cells were less precise and less stable, and population coding was impaired. Long-term stability of place cells was also compromised as place cells in epileptic mice were highly unstable across short time intervals and completely remapped across a week. Because of the large-scale reorganization of inhibitory circuits in epilepsy, we hypothesized that degraded spatial representations were caused by dysfunctional inhibition. To test this hypothesis, we examined the temporal dynamics of hippocampal interneurons using silicon probes to simultaneously record from CA1 and dentate gyrus during head-fixed virtual navigation. We found that epileptic mice had a profound reduction in theta coherence between the dentate gyrus and CA1 regions and altered interneuron synchronization. In particular, dentate interneurons of epileptic mice had altered phase preferences to ongoing theta oscillations, which decorrelated inhibitory population firing between CA1 and dentate gyrus. To assess the specific contribution of desynchronization on spatial coding, we built a CA1 network model to simulate hippocampal desynchronization. Critically, we found that desynchronized inputs reduced the information content and stability of CA1 neurons, consistent with the experimental data. Together, these results demonstrate that temporally precise intra-hippocampal communication is critical for forming the spatial code and that desynchronized firing of hippocampal neuronal populations contributes to poor spatial processing in epileptic mice.

neuroscience↗

bioRxiv2018

Genome-wide prediction of synthetic rescue mediators of resistance to targeted and immunotherapy

Most patients with advanced cancer eventually acquire resistance to targeted therapies, spurring extensive efforts to identify molecular events mediating therapy resistance. Many of these events involve synthetic rescue (SR) interactions, where the reduction in cancer cell viability caused by targeted gene inactivation is rescued by an adaptive alteration of another gene (the rescuer). Here we perform a genome-wide prediction of SR rescuer genes by analyzing tumor transcriptomics and survival data of 10,000 TCGA cancer patients. Predicted SR interactions are validated in new experimental screens. We show that SR interactions can successfully predict cancer patients response and emerging resistance. Inhibiting predicted rescuer genes sensitizes resistant cancer cells to therapies synergistically, providing initial leads for developing combinatorial approaches to overcome resistance proactively. Finally, we show that the SR analysis of melanoma patients successfully identifies known mediators of resistance to immunotherapy and predicts novel rescuers.

cancer biology↗

bioRxiv2017

Tracking Individual Differences in Perception by TMS-EEG Intrinsic Effective Connectivity

Non-invasive human electroencephalography (EEG) coupled with transcranial magnetic stimulation (TMS) is currently used to measure coarse stimulus-response relationships in brain physiology during behavior. However, with key modifications, the TMS-EEG technique holds even greater promise for monitoring fine-scale neural signatures of human behavior. Here, we demonstrate that a novel TMS-EEG co-registration technique can dynamically monitor individual human variation in perception based solely on EEG resting-state intrinsic effective connectivity probed by TMS-based phase resetting of ongoing activity. We used a bistable stimulus task, where the percept is perceived as either horizontal or vertical apparent motion, to record gamma band interhemispheric integration of information. Fine-grained inter-individual behavioral differences in horizontal motion bias could be measured by tracking resting-state gamma-band effective connectivity from right hMT+ to left hMT+. Thus, our method of triggering intrinsic resting-state effective connectivity in oscillatory dynamics can monitor individual differences in perception via the long-range integration of information. This technique will be useful for the manipulative dissection of individual-scale human cognition mediated by neural dynamics and may also expand neurofeedback approaches.

neuroscience↗