Marc Birtwistle

Marc Birtwistle
Clemson University | CU · Department of Chemical and Biomolecular Engineering

PhD Chemical Engineering

About

143
Publications
15,603
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
2,837
Citations

Publications

Publications (143)
Article
Full-text available
Declining success rates coupled with increased costs is leading to an inevitable breaking point in the drug development pipeline. Can we avoid it by incorporating the vast mechanistic understanding of drug action? A recent review highlights this dilemma and proposes “quantitative logic gate” modeling as a solution.1 The goal of this commentary is t...
Article
Full-text available
Background Cell-to-cell variability in protein expression can be large, and its propagation through signaling networks affects biological outcomes. Here, we apply deterministic and probabilistic models and biochemical measurements to study how network topologies and cell-to-cell protein abundance variations interact to shape signaling responses. R...
Article
Activation of ErbB receptors by epidermal growth factor (EGF) or heregulin (HRG) determines distinct cell-fate decisions, although signals propagate through shared pathways. Using mathematical modeling and experimental approaches, we unravel how HRG and EGF generate distinct, all-or-none responses of the phosphorylated transcription factor c-Fos. I...
Article
Full-text available
Extracellular signal-regulated kinase (ERK) controls fundamental cellular functions, including cell fate decisions. In PC12, cells shifting ERK activation from transient to sustained induces neuronal differentiation. As ERK associates with both regulators and effectors, we hypothesized that the mechanisms underlying the switch could be revealed by...
Article
Full-text available
Deregulation of ErbB signaling plays a key role in the progression of multiple human cancers. To help understand ErbB signaling quantitatively, in this work we combine traditional experiments with computational modeling, building a model that describes how stimulation of all four ErbB receptors with epidermal growth factor (EGF) and heregulin (HRG)...
Article
Multiangle light scattering (MALS) was used to determine the absolute molar mass of fluorescent macromolecules. It is standard protocol to install bandwidth filters before MALS detectors to suppress detection of fluorescent emissions. Fluorescence can introduce tremendous error in light scattering measurements and is a formidable challenge in accur...
Article
Full-text available
Mechanistic models of how single cells respond to different perturbations can help integrate disparate big data sets or predict response to varied drug combinations. However, the construction and simulation of such models have proved challenging. Here, we developed a python-based model creation and simulation pipeline that converts a few structured...
Article
Full-text available
Dysregulated epigenetic processes can lead to altered gene expression and give rise to malignant transformation and tumorigenesis. Epigenetic drugs aim to revert the phenotype of cancer cells to normally functioning cells, and are developed and applied to treat both hematological and solid cancers. Despite this promising therapeutic avenue, the suc...
Article
Full-text available
Drug Toxicity Signature Generation Center (DToxS) at the Icahn School of Medicine at Mount Sinai is one of the centers for the NIH Library of Integrated Network-Based Cellular Signatures (LINCS) program. Its key aim is to generate proteomic and transcriptomic signatures that can predict cardiotoxic adverse effects of kinase inhibitors approved by t...
Preprint
Western blotting is a widely-used technique for molecular-weight-resolved analysis of proteins and their post-translational modifications, but has been refractory to affordable scale-up. Here, we report the Mesowestern blot, which uses a 3D-printable gel-casting mold to enable affordable, high-throughput Western blotting with standard sample prepar...
Article
Full-text available
A library of well-characterized human induced pluripotent stem cell (hiPSC) lines from clinically healthy human subjects could serve as a useful resource of normal controls for in vitro human development, disease modeling, genotype-phenotype association studies, and drug response evaluation. We report generation and extensive characterization of a...
Article
Background: Glioblastoma (GBM) remains a largely incurable disease as current therapy fails to target the invasive nature of GBM growth in disease progression and recurrence. Here we use the FDA-approved drug and small molecule Hippo inhibitor Verteporfin to target YAP-TEAD activity, known to mediate convergent aspects of tumor invasion/metastasis...
Preprint
Full-text available
Predictive determinants of stochastic single-cell fates have been elusive, even for the well-studied mammalian cell cycle. What drives proliferation decisions of single cells at any given time? We monitored single-cell dynamics of the ERK and Akt pathways, critical cell cycle progression hubs and anti-cancer drug targets, and paired them to divisio...
Preprint
Full-text available
The phenotype of a cell and its underlying molecular state is strongly influenced by extracellular signals, including growth factors, hormones, and extracellular matrix. While these signals are normally tightly controlled, their dysregulation leads to phenotypic and molecular states associated with diverse diseases. To develop a detailed understand...
Article
Gene expression signatures (GES) connect phenotypes to differential messenger RNA (mRNA) expression of genes, providing a powerful approach to define cellular identity, function, and the effects of perturbations. The use of GES has suffered from vague assessment criteria and limited reproducibility. Because the structure of proteins defines the fun...
Preprint
Full-text available
Fluorescent antibodies are a workhorse of biomedical science, but fluorescence multiplexing has been notoriously difficult due to spectral overlap between fluorophores. We recently established proof-of-principal for fluorescence Multiplexing using Spectral Imaging and Combinatorics (MuSIC), which uses combinations of existing fluorophores to create...
Preprint
The current era of big biomedical data accumulation and availability brings data integration opportunities for leveraging its totality to make new discoveries and/or clinically predictive models. Black-box statistical and machine learning methods are powerful for such integration, but often cannot provide mechanistic reasoning, particularly on the...
Preprint
Full-text available
A library of well-characterized human induced pluripotent stem cell (hiPSC) lines from clinically healthy human subjects could serve as a powerful resource of normal controls for in vitro human development, disease modeling, genotype-phenotype association studies, and drug response evaluation. We report generation and extensive characterization of...
Article
Full-text available
Kinase inhibitors (KIs) represent an important class of anti-cancer drugs. Although cardiotoxicity is a serious adverse event associated with several KIs, the reasons remain poorly understood, and its prediction remains challenging. We obtain transcriptional profiles of human heart-derived primary cardiomyocyte like cell lines treated with a panel...
Conference Paper
The diffusely infiltrative growth and spread, complex molecular and oncogenic signaling aberrations, and inter-and intra-tumoral heterogeneity in glioblastoma (GBM) impedes gross-total resection and chemoradiation and highlight the need for improved tumor-specific brain-penetrant therapies that inhibit cell migration in addition to proliferation. I...
Preprint
Full-text available
Gene expression signatures (GES) connect phenotypes to mRNA expression patterns, providing a powerful approach to define cellular identity, function, and the effects of perturbations. However, the use of GES has suffered from vague assessment criteria and limited reproducibility. The structure of proteins defines the functional capability of genes,...
Preprint
Full-text available
The Drug Toxicity Signature Generation Center (DToxS) at the Icahn School of Medicine at Mount Sinai is one of the centers of the NIH Library of Integrated Network-Based Cellular Signatures (LINCS) program. A key aim of DToxS is to generate both proteomic and transcriptomic signatures that can predict adverse effects, especially cardiotoxicity, of...
Article
Full-text available
Reliably predicting in vivo efficacy from in vitro data would facilitate drug development, by reducing animal usage and guiding drug dosing in human clinical trials. However, such prediction remains challenging. Here, we built a quantitative pharmacokinetic/pharmacodynamic mathematical model capable of predicting in vivo efficacy in animal xenograf...
Article
Full-text available
Purpose of Review There is a contemporary push to map tissues and their disease states quantitatively at single-cell and spatial resolution, but standard assays to do so, such as immunohistochemistry, have been historically lowly multiplexed (2–4 measurements). This push has driven the development of several new multiplexed techniques for quantitat...
Article
Full-text available
Under physiological conditions, strength and persistence of memory must be regulated in order to produce behavioral flexibility. In fact, impairments in memory flexibility are associated with pathologies such as post-traumatic stress disorder or autism; however, the underlying mechanisms that enable memory flexibility are still poorly understood. H...
Article
Evidence that some high-impact biomedical results cannot be repeated has stimulated interest in practices that generate findable, accessible, interoperable, and reusable (FAIR) data. Multiple papers have identified specific examples of irreproducibility, but practical ways to make data more reproducible have not been widely studied. Here, five rese...
Article
Full-text available
Individual cells in clonal populations often respond differently to environmental changes; for binary phenotypes, such as cell death, this can be measured as a fractional response. These types of responses have been attributed to cell-intrinsic stochastic processes and variable abundances of biochemical constituents, such as proteins, but the influ...
Preprint
Full-text available
Evidence that some influential biomedical results cannot be repeated has increased interest in practices that generate data meeting findable, accessible, interoperable and reproducible (FAIR) standards. Multiple papers have identified examples of irreproducibility, but practical steps for increasing reproducibility have not been widely studied. Her...
Preprint
Under physiological conditions, strength and persistence of memory must be regulated in order to produce behavioral flexibility. In fact, impairments in memory flexibility are associated with pathologies such as post-traumatic stress disorder or autism; however the underlying mechanisms that enable memory flexibility are still poorly understood. He...
Article
Full-text available
Fluorescence-based western blots are quantitative in principal, but require determining linear range for each antibody. Here, we use microwestern array to rapidly evaluate suitable conditions for quantitative western blotting, with up to 192 antibody/dilution/replicate combinations on a single standard size gel with a seven-point, two-fold lysate d...
Preprint
Full-text available
Ultraviolet-to-infrared fluorescence is a versatile and accessible assay modality, but is notoriously hard to multiplex due to overlap of wide emission spectra. We present an approach for fluorescence multiplexing using spectral imaging and combinatorics (MuSIC). MuSIC consists of creating new independent probes from covalently-linked combinations...
Article
Epigenetic modulators are increasing in prominence as potential cancer therapies. These drugs achieve their effectiveness by inducing transcriptional changes that can inhibit cancer progression. Here, we focus on a potent and selective covalent small molecule inhibitor of LSD1 (RO7051750/ORY-1001), a lysine-specific histone demethylase enzyme. LSD1...
Preprint
Full-text available
Individual cells in clonal populations often respond differently to environmental changes; for binary phenotypes, such as cell death, this can be measured as a fractional response. These types of responses have been attributed to cell-intrinsic stochastic processes and variable abundances of biochemical constituents, such as proteins, but the influ...
Article
Full-text available
Most cancer cells harbor multiple drivers whose epistasis and interactions with expression context clouds drug and drug combination sensitivity prediction. We constructed a mechanistic computational model that is context-tailored by omics data to capture regulation of stochastic proliferation and death by pan-cancer driver pathways. Simulations and...
Data
Detailed kinetic scheme of model. This kinetic scheme depicts all of the reactions in the model. Labels correspond to the indices for each rate law in the equations and code. A “p” prior to a protein name indicates it is phosphorylated. An underscore between two proteins indicates they are in complex. An arrow pointing to a curved arrow indicates t...
Data
Gene expression parameters. Expression levels, transcription rates, translation rates, mRNA and protein half-lives, and data sources for each gene in the model. (XLSX)
Data
μ-Western blot raw images. A) Schematic outlining layout of conditions on μ-Western blot for every well. Concentrations are in units of nM. B) Raw scans of μ-Western blot membranes probed for pERK, pAKT, pEIF4E-BP1, α-Tubulin, and cyclin D (see Methods). Time points go from top-to-bottom. Treatment conditions go from left-to-right, as indicated in...
Data
Comparing experimental and simulated cell-to-cell heterogeneity. A) Left: Single cell traces of the ratio of cytoplasmic to nuclear fluorescence for ERK KTR probe (reporter of ERK kinase activity) stably expressed by MCF10A cells. Serum-starved cells were stimulated with EGF (20ng/mL) + insulin (10μg/mL). Right: Simulation results showing phosphory...
Data
Additional apoptosis integrated unit testing. A) Simulated cells are treated with low doses of TRAIL (1ng/mL and 0.1ng/mL) and plots show the cumulative sum of BIM and Bcl2 levels across the time course during which they are alive (analogous to Fig 5F). Cell trajectories are colored in terms of their time to death. Here we see no obvious relationsh...
Data
Further extrapolations and details on the inner workings of the model and how each submodel or algorithm was implemented. (PDF)
Data
Reactions and parameters for submodels. Rate equations, reaction descriptions, parameter values, and parameter sources for each submodel. (XLSX)
Data
Matlab model code. Matlab code needed to run the model, run all simulations included in this paper, and generate all figures. (ZIP)
Data
Properties of the expression submodel. A) Probability of zero (blue diamonds), one (red squares), or two (green triangles) gene switching events given different time step intervals between the stochastic and deterministic components of the model. We chose 30 seconds as a tradeoff. B) Cell-to-cell variability in the timing of the first cell division...
Data
Additional unit testing. A) Cooperativity profiles comparing the ideal case (left)—when only the receptors that bind each ligand are present on the cell surface and at appreciable levels—to those for the model tailored to expression levels for MCF10A cells (right). B) Time course plot showing dynamics of active plasma membrane-bound EGFR dimers (so...
Data
Time-averaged ERK and AKT activities in simulations. A) The average, time-integrated ppAKT levels across different types of stimuli—EGF (10nM) + insulin (10μg/mL), EGF (10nM) alone, EGF (10nM) + insulin (10μg/mL) + small AKTi dose (1nM), or EGF (10nM) + insulin (10μg/mL) + small AKTi dose (2nM). A decrease in ppAKT is observed. B) The average, time...
Article
Full-text available
Current treatments for glioblastoma multiforme (GBM)—an aggressive form of brain cancer—are minimally effective and yield a median survival of 14.6 months and a two-year survival rate of 30%. Given the severity of GBM and the limitations of its treatment, there is a need for the discovery of novel drug targets for GBM and more personalized treatmen...
Data
Frequency of ERBB4 copy number loss in HGCC cell lines. Copy number data from the HGCC cited in Xie et al. EBioMedicine, 2015 showed normal copy number for ERBB4 across 48 GBM cell lines. (TIFF)
Data
CCLE and TCGA raw copy number data. Copy number by gene for 60 glioma cell lines downloaded from the Cancer Cell Line Encyclopedia (CCLE) data portal and copy number segmented data for 526 GBM tumor samples downloaded from The Cancer Genome Atlas (TCGA) data portal. (XLSX)
Data
Copy number frequency distributions of ERBB4 and housekeeping gene TUBB in TCGA. When compared to a housekeeping gene, beta-tubulin (TUBB), centered at 2 with no loss or gain, ERBB4 exhibits notable copy number variation. Copy number loss of ERBB4 occurs in 15.4% of samples, while copy number loss of beta-tubulin occurs in only 2.4% of samples. Thr...
Preprint
Full-text available
Western blotting is often considered a semi-quantitative or even qualitative assay for assessing changes in protein or protein post-translational modification levels. Fluorescence-based measurement enables acquisition of quantitative data in principal, but requires determining the linear range of detection for each antibody—a labor-intensive task....
Article
Full-text available
Creating a cDNA library for deep mRNA sequencing (mRNAseq) is generally done by random priming, creating multiple sequencing fragments along each transcript. A 3′-end-focused library approach cannot detect differential splicing, but has potentially higher throughput at a lower cost, along with the ability to improve quantification by using transcri...
Article
The Library of Integrated Network-Based Cellular Signatures (LINCS) is an NIH Common Fund program that catalogs how human cells globally respond to chemical, genetic, and disease perturbations. Resources generated by LINCS include experimental and computational methods, visualization tools, molecular and imaging data, and signatures. By assembling...
Article
Monotherapy clinical trials with mutation-targeted kinase inhibitors, despite some success in other cancers, have yet to impact glioblastoma multiforme (GBM). Besides insufficient blood-brain-barrier penetration, combinations are key to overcoming obstacles such as intratumoral heterogeneity, adaptive resistance, and the epistatic nature of tumor g...
Article
Full-text available
Tyrosine kinase inhibitors (TKIs) are highly potent cancer therapeutics that have been linked with serious cardiotoxicity, including left ventricular dysfunction, heart failure, and QT prolongation. TKI-induced cardiotoxicity is thought to result from interference with tyrosine kinase activity in cardiomyocytes, where these signaling pathways help...
Article
Over the past decade we have seen a shift in cancer therapy from broadly cytotoxic drugs to molecular therapies targeting “driver” mutations. Although targeted therapy has seen great success for some cancers (e.g. imatinib for leukemia), it has struggled with poor efficacy in treating other cancers that can sometimes possess multiple “driver” mutat...
Article
Metastasis is the primary cause of death from most cancer types, but the relative rates of tumor cell migration through lymphatic versus blood routes remains an open question. Here we combine data from a xenograft model of metastatic breast cancer with a computational model of tumor cell growth and dissemination to help answer this question. Orthot...
Preprint
Full-text available
Current treatments for glioblastoma multiforme (GBM)—an aggressive form of brain cancer—are minimally effective and yield a median survival of 14.6 months and a two-year survival rate of 30%. Given the severity of GBM and the limitations of its treatment, there is a need for the discovery of novel drug targets for GBM and more personalized treatmen...
Preprint
Most cancer cells harbor multiple drivers whose epistasis and interactions with expression context clouds drug sensitivity prediction. We constructed a mechanistic computational model that is context-tailored by omics data to capture regulation of stochastic proliferation and death by pan-cancer driver pathways. Simulations and experiments explore...
Preprint
Full-text available
Deep mRNA sequencing (mRNAseq) is the state-of-the-art for whole transcriptome measurements. A key step is creating a library of cDNA sequencing fragments from RNA. This is generally done by random priming, creating multiple sequencing fragments along the length of each transcript. A 3’ end-focused library approach cannot detect differential splici...
Chapter
Systems pharmacology has evolved from a discipline that focuses on drug action at the organ level to a discipline that combines traditional pharmacokinetic and pharmacodynamic modeling with recent systems biology approaches. The integration of high-throughput data technologies with computational data analysis and modeling offers new opportunities t...
Chapter
Kinetic models of biochemical signaling networks are a mechanistic description of pharmacodynamics, and thus are potentially well-poised to fill gaps in the drug development pipeline by: (i) allowing putative drugs to be tested via simulations for efficacy and safety before expensive experiments and failed clinical trials; (ii) providing a framewor...