Biology subjects

Moore, T. W.

Publications and source records attributed to Moore, T. W..

4 recordsLinked to original sources

bioRxiv2025

Multiomic profiling of hypoxic glioblastoma stem cells reveals expansion of subpopulations with distinct epigenetic and CNV profiles

Glioblastoma is characterized by extensive intratumoral heterogeneity driven by dynamic mi-croenvironmental cues such as hypoxia. While transcriptional and epigenetic variability have been separately linked to hypoxia responses, the integrated impact of hypoxia on gene regulation and clonal architecture in glioblastoma stem cells (GSCs) remains poorly defined. We applied singlenucleus multi-omics--integrating RNA-seq and ATAC-seq--to patient-derived GSCs cultured under normoxic or hypoxic conditions. This enabled simultaneous profiling of gene expression and chromatin accessibility within the same cells. Transcription factor (TF) regulatory networks were inferred using Dictys, while RNA-chromatin dynamics were modeled with MultiVelo. Clonal structure and copy number variations (CNVs) were resolved at single-cell resolution using RIDDLER on snATAC-seq data. Hypoxia induced the emergence of four distinct GSC subpopulations with unique transcriptomic and epigenetic profiles enriched for mesenchymal, angiogenic, and proliferative signatures. Regulatory network modeling revealed novel hypoxia-associated TFs--SP2, CREM, and ETV3--that modulate downstream oncogenic pathways. Trajectory analysis uncovered hypoxia-driven reversals in RNA-chromatin coupling, revealing dysregulated future transcriptional states of key genes such as MMP16 and SVIL. CNV profiling identified 13 clonal substructures, with specific clones (e.g., 5, 6, 9) selectively enriched under hypoxia and harboring distinct chromosomal alterations. These results demonstrate coordinated remodeling of GSC gene regulation and clonal fitness in response to hypoxic stress. Our findings reveal that hypoxia drives concurrent epigenetic, transcriptomic, and clonal selection in glioblastoma stem cells. This integrated model of hypoxia-induced plasticity provides mechanistic insights into tumor adaptation and identifies novel regulators that may serve as targets for therapeutic intervention in the hypoxic niche of glioblastoma.

cancer biology↗

bioRxiv2023

Robust CNV detection using single-cell ATAC-seq

Copy number variation (CNV) is a widely studied type of structural variation seen in the genomes of cancerous and other dysfunctional cells. CNVs can have direct and indirect effects on gene dosage, and are thought to drive cancer progression and other disorders. Advancements in single-cell assays such as sc-ATAC-seq and sc-RNA-seq, along with their ubiquitous use, allows for the identification of CNVs at single cell resolution. While there are a variety of available tools for CNV detection in sc-RNA-seq, development of sc-ATAC-seq based accurate and reliable CNV callers is in the early stages, with only two available algorithms so far. We present RIDDLER, a single-cell ATAC-seq CNV detection algorithm based on outlier aware generalized linear modeling. By utilizing tools from robust statistics, we developed an extensible model that is able to identify single-cell CNVs from sc-ATAC-seq data in an unsupervised fashion, while providing probabilistic justification for results. Our statistical approach also allows us to estimate when loss of signal is likely caused by drop-out or a true genome deletion event, as well as predict reliable CNVs without the need for normative reference cells. We demonstrate the effectiveness of our algorithm on cancer cell line models where it achieves better agreement with bulk WGS derived CNVs than competing methods. We also compare our approach on 10x multimone data, where it shows better agreement and integration with RNA derived CNV estimates.

genomics↗

bioRxiv2021

Mapping the Energy Landscape of PROTAC-Mediated Protein-protein Interactions

One of the principal difficulties in computational modeling of macromolecules is the vast conformational space that arises out of large numbers of atomic degrees of freedom. This problem is a familiar issue in the area of protein-protein docking, where models of protein complexes are generated from the monomeric subunits. Although restriction of molecular flexibility is a commonly used approximation that decreases the dimensionality of the problem, the seemingly endless number of possible ways two binding partners can interact generally necessitates the use of further approximations to explore the search space. Recently, growing interest in using computational tools to build predictive models of PROTAC-mediated complexes has led to the application of state-of-the-art protein-protein docking techniques to tackle this problem. Additionally, the atomic degrees of freedom introduced by flexibility of linkers used in the construction of PROTACs further expands the configurational search space, a problem that can be tackled with conformational sampling tools. However, repurposing existing tools to carry out protein-protein docking and linker conformer generation independently results in extensive sampling of structures incompatible with PROTAC-mediated complex formation. Here we show that it is possible to restrict the search to the space of protein-protein conformations that can be bridged by a PROTAC molecule with a given linker composition by using a cyclic coordinate descent algorithm to position PROTACs into complex-bound configurations. We use this methodology to construct a picture of the energy landscape of PROTAC-mediated interactions in a model test case, and show that the global minimum lies in the space of native-like conformations.

bioinformatics↗

bioRxiv2020

Discovery of a microbially produced small molecule in a host-specific organ

The lifelong relationship between the Hawaiian bobtail squid, Euprymna scolopes, and its microbial symbiont, Vibrio fischeri, represents a simplified model system for studying microbiome establishment and maintenance. The bacteria colonize a dedicated symbiotic light organ in the squid, from which bacterial luminescence camouflages the hosts in a process termed counterillumination. The squid hosts hatch without their symbionts, which must be acquired from the ocean amid a diversity of non-beneficial bacteria, so precise molecular communication is required for initiation of the specific relationship. It is therefore likely that there may be specialized metabolites used in the light organ microenvironment to modulate these processes. To identify small molecules that may influence the establishment of this symbiosis, we used imaging mass spectrometry to analyze metabolite production in V. fischeri with altered biofilm production, which correlates directly to colonization capability in its host. Biofilm-Up and Biofilm-Down mutants were compared to a wild-type strain, and masses that were more abundantly produced by the biofilm-up mutant were detected. Using a combination of structure elucidation and synthetic chemistry, one such signal was determined to be a diketopiperazine, cyclo(O_SCPLOWDC_SCPLOW-histidyl-O_SCPLOWLC_SCPLOW-proline). This diketopiperazine modulated luminescence in V. fischeri and, using label-free imaging mass spectrometry, was directly detected in the light organ of the colonized host. This work highlights the continued need for untargeted discovery efforts in host-microbe interactions and showcases the benefits of the squid-Vibrio system for identification and characterization of small molecules that modulate microbiome behaviors. Significance StatementThe complexity of animal microbiomes presents challenges to defining signaling molecules within the microbial consortium and between the microbes and the host. By focusing on the binary symbiosis between Vibrio fischeri and Euprymna scolopes, we have combined genetic analysis with direct imaging to define and study small molecules in the intact symbiosis. We have detected and characterized a diketopiperazine produced by strong biofilm-forming V. fischeri strains that was detectable in the host symbiotic organ, and which influences bacterial luminescence. Biofilm formation and luminescence are critical for initiation and maintenance of the association, respectively, suggesting that the compound may link early and later development stages, providing further evidence that multiple small molecules are important in establishing these beneficial relationships.

microbiology↗