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Other Publications (25)

Articles by Sarah Franklin in JoVE

 JoVE Clinical and Translational Medicine

Quantitative Analysis of Chromatin Proteomes in Disease

1Department of Anesthesiology, David Geffen School of Medicine at UCLA, 2Department of Medicine, David Geffen School of Medicine at UCLA, 3Department of Physiology, David Geffen School of Medicine at UCLA, 4Department of Internal Medicine, Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah


JoVE 4294

Advances in mass spectrometry have allowed the high throughput analysis of protein expression and modification in a host of tissues. Combined with subcellular fractionation and disease models, quantitative mass spectrometry and bioinformatics can reveal new properties in biological systems. The method described herein analyzes chromatin-associated proteins in the setting of heart disease and is readily applicable to other in vivo models of human disease.

Other articles by Sarah Franklin on PubMed

Surrogacy on Three Continents

Dolly: a New Form of Transgenic Breedwealth

Drawing the Line at Not-fully-human: What We Already Know

Experiencing New Forms of Genetic Choice: Findings from an Ethnographic Study of Preimplantation Genetic Diagnosis

Contemporary scientific and clinical knowledges and practices continue to make available new forms of genetic information, and to create new forms of reproductive choice. For example, couples at high risk of passing on a serious genetic condition to their offspring in Britain today have the opportunity to use Preimplantation Genetic Diagnosis (PGD) to select embryos that are unaffected by serious genetic disease. This information assists these couples in making reproductive choices. This article presents an analysis of patients' experiences of making the decision to undertake PGD treatment and of making reproductive choices based on genetic information. We present qualitative interview data from an ethnographic study of PGD based in two British clinics which indicate how these new forms of genetic choice are experienced by patients. Our data suggest that PGD patients make decisions about treatment in a complex way, taking multiple variables into account, and maintaining ongoing assessments of the multiple costs of engaging with PGD. Patients are aware of broader implications of their decisions, at personal, familial, and societal levels, as well as clinical ones. Based on these findings we argue that the ethical and social aspects of PGD are often as innovative as the scientific and medical aspects of this technique, and that in this sense, science cannot be described as "racing ahead" of society.

Origin Stories Revisited: IVF As an Anthropological Project

The IVF-stem Cell Interface

'Crook' Pipettes: Embryonic Emigrations from Agriculture to Reproductive Biomedicine

While cloning, stem cells, and regenerative medicine are often imagined in a futurial idiom--as expectations, hype, hope and promises--this article approaches the remaking of genealogy in such contexts from a historical route. Through a series of somewhat disparate historical connections linking Australian sheep to the development of clinical IVF and the cloning of Dolly at the Roslin Institute in Scotland in 1996, this article explores the linkages through which agriculture, embryology, and reproductive biomedicine are thickly intertwined. Key to this examination is not only the history of experimental sheep breeding, and its somewhat unexpectedly genealogical connections to (Australian) national identity ('wool in the veins'), but also the re-emergence of a distinctive frontier ethos in the context of assisted conception, and later human embryonic stem cell derivation. I have set this scene of genealogical interconnection against the criss-crossing traffic between Britain and Australia, and the wool trade, to emphasise the importance of global, as well as local, connections in the bloodlines of animals such as Dolly. In sum, this article examines the idea of the 'biological frontier' by exploring its histories as a means to offset the assumption that this frequently encountered idiom describes a future that is, or must be, by definition, unknown and unknowable.

Obituary: Dame Dr Anne McLaren

HESCCO: Development of Good Practice Models for HES Cell Derivation

One response of the UK research community to the public sensitivity and logistical complexity of embryo donation to stem cell research has been the formation of a national network of 'human embryonic stem cell coordinators' (hESCCO). The aim of hESCCO is to contribute to the formation and implementation of national standards for hES cell derivation and banking, in particular the ethical protocols for patient information and informed consent. The hESCCO project is an innovative practical intervention within the broader attempt to establish greater transparency, consistency, efficiency and standardization of hES derivation in the UK. A major outcome of the hESCCO initiative has been the drafting and implementation of a national consent form. The lessons learned in this context may be relevant to other practitioners and regulators as a model of best practice in hES cell derivation.

Loss of Perineuronal Net in ME7 Prion Disease

Microglial activation and behavioral abnormalities occur before neuronal loss in experimental murine prion disease; the behavioral changes coincide with a reduction in synaptic plasticity. Because synaptic plasticity depends on an intact perineuronal net (PN), a specialized extracellular matrix that surrounds parvalbumin (PV)-positive GABAergic (gamma-aminobutyric acid [GABA]) inhibitory interneurons, we investigated the temporal relationships between microglial activation and loss of PN and PV-positive neurons in ME7 murine prion disease. Anesthetized C57Bl/6J mice received bilateral intracerebral microinjections of ME7-infected or normal brain homogenate into the dorsal hippocampus. Microglial activation, PrP accumulation, the number of PV-positive interneurons, and Wisteria floribunda agglutinin-positive neurons (i.e. those with an intact PN) were assessed in the ventral CA1 and subiculum at 4, 8, 12, 16, and 20 weeks postinjection. Hippocampal areas and total neuron numbers in the ventral CA1 and subiculum were also determined. Loss of PN coincided with early microglial activation and with a reduction in synaptic plasticity. No significant loss of PV-positive interneurons was observed. Our findings suggest that the substrate of the earliest synaptic and behavioral abnormalities in murine prion disease may be inflammatory microglia-mediated degradation of the PN.

Macrophage Stimulating Protein is a Neurotrophic Factor for a Sub-population of Adult Nociceptive Sensory Neurons

Macrophage stimulating protein (MSP) is a pleiotropic growth factor that signals via the RON receptor tyrosine kinase. Here we demonstrate that MSP increases the proportion of cultured adult mouse DRG neurons displaying discernable neuritic processes and promotes the elongation and branching of these processes in a dose dependent manner. RON expression in adult DRG is largely restricted to nerve growth factor (NGF)-responsive nociceptive neurons, and MSP mimics the effects of NGF by increasing the expression of several mRNAs that encode functionally important proteins that are characteristically expressed by this neuronal sub-population. MSP mRNA is expressed at high levels in the peripheral target fields of DRG somatic afferents, but is undetectable in DRG, spinal cord or freshly dissected sciatic nerve. These results suggest that MSP is a peripheral target-derived neurotrophic factor for NGF-responsive adult DRG neurons.

Post-translational Regulation of Calsarcin-1 During Pressure Overload-induced Cardiac Hypertrophy

Chronic pressure overload to the heart leads to cardiac hypertrophy and failure through processes that involve reorganization of subcellular compartments and alteration of established signaling mechanisms. To identify proteins contributing to this process, we examined changes in nuclear-associated myofilament proteins as the murine heart undergoes progressive hypertrophy following pressure overload. Calsarcin-1, a negative regulator of calcineurin signaling in the heart, was found to be enriched in cardiac nuclei and displays increased abundance following pressure overload through a mechanism that is decoupled from transcriptional regulation. Using proteomics, we identified novel processing of this protein in the setting of cardiac injury and identified four residues subject to modification by phosphorylation. These studies are the first to determine mechanisms regulating calsarcin abundance during hypertrophy and failure and reveal the first evidence of post-translational modifications of calsarcin-1 in the myocardium. Overall, the findings expand the roles of calsarcins to include nuclear tasks during cardiac growth.

Stress Signaling by Tec Tyrosine Kinase in the Ischemic Myocardium

Nonreceptor tyrosine kinases have an increasingly appreciated role in cardiac injury and protection. To investigate novel tasks for members of the Tec family of nonreceptor tyrosine kinases in cardiac phenotype, we examined the behavior of the Tec isoform in myocardial ischemic injury. Ischemia-reperfusion, but not cardiac protective agents, induced altered intracellular localization of Tec, highlighting distinct actions of this protein compared with other isoforms, such as Bmx, in the same model. Tec is abundantly expressed in cardiac myocytes and assumes a diffuse intracellular localization under basal conditions but is recruited to striated structures upon various stimuli, including ATP. To characterize Tec signaling targets in vivo, we performed an exhaustive proteomic analysis of Tec-binding partners. These experiments expand the role of the Tec family in the heart, identifying the Tec isoform as an ischemic injury-induced isoform, and map the subproteome of its interactors in isolated cells.

Why the Medical Research Council Refused Robert Edwards and Patrick Steptoe Support for Research on Human Conception in 1971

In 1971, Cambridge physiologist Robert Edwards and Oldham gynaecologist Patrick Steptoe applied to the UK Medical Research Council (MRC) for long-term support for a programme of scientific and clinical 'Studies on Human Reproduction'. The MRC, then the major British funder of medical research, declined support on ethical grounds and maintained this policy throughout the 1970s. The work continued with private money, leading to the birth of Louise Brown in 1978 and transforming research in obstetrics, gynaecology and human embryology.

Specialized Compartments of Cardiac Nuclei Exhibit Distinct Proteomic Anatomy

As host to the genome, the nucleus plays a critical role as modulator of cellular phenotype. To understand the totality of proteins that regulate this organelle, we used proteomics to characterize the components of the cardiac nucleus. Following purification, cardiac nuclei were fractionated into biologically relevant fractions including acid-soluble proteins, chromatin-bound molecules and nucleoplasmic proteins. These distinct subproteomes were characterized by liquid chromatography-tandem MS. We report a cardiac nuclear proteome of 1048 proteins--only 146 of which are shared between the distinct subcompartments of this organelle. Analysis of genomic loci encoding these molecules gives insights into local hotspots for nuclear protein regulation. High mass accuracy and complementary analytical techniques allowed the discrimination of distinct protein isoforms, including 54 total histone variants, 17 of which were distinguished by unique peptide sequences and four of which have never been detected at the protein level. These studies are the first unbiased analysis of cardiac nuclear subcompartments and provide a foundation for exploration of this organelle's proteomes during disease.

Highly Efficient Purification of Protein Complexes from Mammalian Cells Using a Novel Streptavidin-binding Peptide and Hexahistidine Tandem Tag System: Application to Bruton's Tyrosine Kinase

Tandem affinity purification (TAP) is a generic approach for the purification of protein complexes. The key advantage of TAP is the engineering of dual affinity tags that, when attached to the protein of interest, allow purification of the target protein along with its binding partners through two consecutive purification steps. The tandem tag used in the original method consists of two IgG-binding units of protein A from Staphylococcus aureus (ProtA) and the calmodulin-binding peptide (CBP), and it allows for recovery of 20-30% of the bait protein in yeast. When applied to higher eukaryotes, however, this classical TAP tag suffers from low yields. To improve protein recovery in systems other than yeast, we describe herein the development of a three-tag system comprised of CBP, streptavidin-binding peptide (SBP) and hexa-histidine. We illustrate the application of this approach for the purification of human Bruton's tyrosine kinase (Btk), which results in highly efficient binding and elution of bait protein in both purification steps (>50% recovery). Combined with mass spectrometry for protein identification, this TAP strategy facilitated the first nonbiased analysis of Btk interacting proteins. The high efficiency of the SBP-His₆ purification allows for efficient recovery of protein complexes formed with a target protein of interest from a small amount of starting material, enhancing the ability to detect low abundance and transient interactions in eukaryotic cell systems.

Metal-driven Operation of the Human Large-conductance Voltage- and Ca2+-dependent Potassium Channel (BK) Gating Ring Apparatus

Large-conductance voltage- and Ca(2+)-dependent K(+) (BK, also known as MaxiK) channels are homo-tetrameric proteins with a broad expression pattern that potently regulate cellular excitability and Ca(2+) homeostasis. Their activation results from the complex synergy between the transmembrane voltage sensors and a large (>300 kDa) C-terminal, cytoplasmic complex (the "gating ring"), which confers sensitivity to intracellular Ca(2+) and other ligands. However, the molecular and biophysical operation of the gating ring remains unclear. We have used spectroscopic and particle-scale optical approaches to probe the metal-sensing properties of the human BK gating ring under physiologically relevant conditions. This functional molecular sensor undergoes Ca(2+)- and Mg(2+)-dependent conformational changes at physiologically relevant concentrations, detected by time-resolved and steady-state fluorescence spectroscopy. The lack of detectable Ba(2+)-evoked structural changes defined the metal selectivity of the gating ring. Neutralization of a high-affinity Ca(2+)-binding site (the "calcium bowl") reduced the Ca(2+) and abolished the Mg(2+) dependence of structural rearrangements. In congruence with electrophysiological investigations, these findings provide biochemical evidence that the gating ring possesses an additional high-affinity Ca(2+)-binding site and that Mg(2+) can bind to the calcium bowl with less affinity than Ca(2+). Dynamic light scattering analysis revealed a reversible Ca(2+)-dependent decrease of the hydrodynamic radius of the gating ring, consistent with a more compact overall shape. These structural changes, resolved under physiologically relevant conditions, likely represent the molecular transitions that initiate the ligand-induced activation of the human BK channel.

Platelet-rich Plasma Protects Tenocytes from Adverse Side Effects of Dexamethasone and Ciprofloxacin

Ruptured tendons heal very slowly and complete recovery from injury is uncertain. Platelet-rich plasma (PRP), a rich source of growth factors, is currently being widely tested as a soft tissue healing agent and may accelerate tendon repair. The authors assessed the ability of PRP to prevent in vitro adverse effects of 2 drugs commonly linked to tendon rupture and tendinopathy, glucocorticoids and fluoroquinolone antibiotics.

Genomes, Proteomes, and the Central Dogma

Systems biology, with its associated technologies of proteomics, genomics, and metabolomics, is driving the evolution of our understanding of cardiovascular physiology. Rather than studying individual molecules or even single reactions, a systems approach allows integration of orthogonal data sets from distinct tiers of biological data, including gene, RNA, protein, metabolite, and other component networks. Together these networks give rise to emergent properties of cellular function, and it is their reprogramming that causes disease. We present 5 observations regarding how systems biology is guiding a revisiting of the central dogma: (1) It deemphasizes the unidirectional flow of information from genes to proteins; (2) it reveals the role of modules of molecules as opposed to individual proteins acting in isolation; (3) it enables discovery of novel emergent properties; (4) it demonstrates the importance of networks in biology; and (5) it adds new dimensionality to the study of biological systems.

Not a Flat World: the Future of Cross-border Reproductive Care

Cross-border reproductive care (CBRC) raises new issues for both medicine and social science, as well as analytical and methodological challenges. On the one hand, this phenomenon extends well-established practices, such as family formation, in new ways, for example through new technologies. Similarly, CBRC could be described as a form of globalization. Yet this sector also departs from established patterns of reproductivity, for example by combining reproductive services and substances transnationally. In this way, CBRC also changes the understanding of globalization, revealing that it is not necessarily producing a newly 'flat' world, but instead reproducing a traditionally stratified one. These aspects of CBRC must be kept in mind in the struggle to define best practice.

Investigation into the Role of Phosphatidylserine in Modifying the Susceptibility of Human Lymphocytes to Secretory Phospholipase A(2) Using Cells Deficient in the Expression of Scramblase

Normal human lymphocytes resisted the hydrolytic action of secretory phospholipase A(2) but became susceptible to the enzyme following treatment with a calcium ionophore, ionomycin. To test the hypothesis that this susceptibility requires exposure of the anionic lipid phosphatidylserine on the external face of the cell membrane, experiments were repeated with a human Burkitt's lymphoma cell line (Raji cells). In contrast to normal lymphocytes or S49 mouse lymphoma cells, most of the Raji cells (83%) did not translocate phosphatidylserine to the cell surface upon treatment with ionomycin. Those few that did display exposed phosphatidylserine were hydrolyzed immediately upon addition of phospholipase A(2). Interestingly, the remaining cells were also completely susceptible to the enzyme but were hydrolyzed at a slower rate and after a latency of about 100s. In contradistinction to the defect in phosphatidylserine translocation, Raji cells did display other physical membrane changes upon ionomycin treatment that may be relevant to hydrolysis by phospholipase A(2). These changes were detected by merocyanine 540 and trimethylammonium diphenylhexatriene fluorescence and were common among normal lymphocytes, S49 cells, and Raji cells. The levels of these latter effects corresponded well with the relative rates of hydrolysis among the three cell lines. These results suggested that while phosphatidylserine enhances the rate of cell membrane hydrolysis by secretory phospholipase A(2), it is not an absolute requirement. Other physical properties such as membrane order contribute to the level of membrane susceptibility to the enzyme independent of phosphatidylserine.

Quantitative Analysis of the Chromatin Proteome in Disease Reveals Remodeling Principles and Identifies High Mobility Group Protein B2 As a Regulator of Hypertrophic Growth

A fundamental question in biology is how genome-wide changes in gene expression are enacted in response to a finite stimulus. Recent studies have mapped changes in nucleosome localization, have determined the binding preferences for individual transcription factors, and shown that the genome adopts a non-random structure in vivo. What remains unclear is how global changes in the proteins bound to DNA alter chromatin structure and gene expression. We have addressed this question in the mouse heart, a system in which global gene expression and massive phenotypic changes occur without cardiac cell division, making the mechanisms of chromatin remodeling centrally important. To determine factors controlling genomic plasticity, we used mass spectrometry to measure chromatin-associated proteins. We have characterized the abundance of 305 chromatin-associated proteins in normal cells and measured changes in 108 proteins that accompany progression of heart disease. These studies were conducted on a high mass accuracy instrument and confirmed in multiple biological replicates, facilitating statistical analysis and allowing us to interrogate the data bioinformatically for modules of proteins involved in similar processes. Our studies reveal general principles for global shifts in chromatin accessibility: altered linker to core histone ratio; differing abundance of chromatin structural proteins; and reprogrammed histone post-translational modifications. Using siRNA-mediated loss-of-function in isolated cells, we demonstrate that the non-histone chromatin structural protein HMGB2 (but not HMGB1) suppresses pathologic cell growth in vivo and controls a gene expression program responsible for hypertrophic cell growth. Our findings reveal the basis for alterations in chromatin structure necessary for genome-wide changes in gene expression. These studies have fundamental implications for understanding how global chromatin remodeling occurs with specificity and accuracy, demonstrating that isoform-specific alterations in chromatin structural proteins can impart these features.

Features of Endogenous Cardiomyocyte Chromatin Revealed by Super-resolution STED Microscopy

Despite the extensive knowledge of the functional unit of chromatin-the nucleosome-for which structural information exists at the atomic level, little is known about the endogenous structure of eukaryotic genomes. Chromosomal capture techniques and genome-wide chromatin immunoprecipitation and next generation sequencing have provided complementary insight into global features of chromatin structure, but these methods do not directly measure structural features of the genome in situ. This lack of insight is particularly troublesome in terminally differentiated cells which must reorganize their genomes for large scale gene expression changes in the absence of cell division. For example, cardiomyocytes, which are fully committed and reside in interphase, are capable of massive gene expression changes in response to physiological stimuli, but the global changes in chromatin structure that enable such transcriptional changes are unknown. The present study addressed this problem utilizing super-resolution stimulated emission depletion (STED) microscopy to directly measure chromatin features in mammalian cells. We demonstrate that immunolabeling of histone H3 coupled with STED imaging reveals chromatin domains on a scale of 40-70 nm, several folds better than the resolution of conventional confocal microscopy. An analytical workflow is established to detect changes in chromatin structure following acute stimuli and used to investigate rearrangements in cardiomyocyte genomes following agonists that induce cellular hypertrophy. This approach is readily adaptable to investigation of other nuclear features using a similar antibody-based labeling technique and enables direct measurements of chromatin domain changes in response to physiological stimuli.

Structural Considerations for Chromatin State Models with Transcription As a Functional Readout

Lacking from the rapidly evolving field of chromatin regulation is a discrete model of chromatin states. We propose that each state in such a model should meet two conditions: a structural component and a quantifiable effect on transcription. The practical benefits to the field of a model with greater than two states (including one with six states, as described herein) would be to improve interpretation of data from disparate organ systems, to reflect temporal and developmental dynamics and to integrate the, at present, conceptually and experimentally disparate analyses of individual genetic loci (in vitro or using single gene approaches) and genome-wide features (including ChlP-seq, chromosomal capture and mRNA expression via microarrays/sequencing).

A Novel in Vitro Loading System for High Frequency Loading of Cultured Tendon Fascicles

Tendons are known to adapt to their mechanical environment, however high frequency low magnitude (HFLM) loading regimes (10-50Hz), which are effective in promoting bone anabolic effects, have not been investigated in controlled conditions in tendon. In vitro loading systems (IVLS) enable precise characterisation of the link between their controlled mechanical environment and cultured tissue biological response. We report a novel IVLS design using an applied magnetic field to produce time varying loading in cultured rat tail tendon fascicles (RTTF). The design was validated through magnetic flux, load cell and viability measurements, and we report the results of preliminary experiments testing the hypothesis that an HFLM loading regime will maintain the biochemical and mechanical properties of fresh RTTF in culture over 7 days. Tissue viability was maintained for 7 days under all loading conditions, and the average peak load applied to RTTFs using the IVLS at 20Hz was 0.125N. RTTFs cultured for 7 days with HFLM loading showed a trend for a higher tangent modulus than fresh tissue, and significantly higher modulus than unloaded RTTFs. GAG content of HFLM cultured RTTFs was not significantly changed from that of fresh RTTFs. This novel, validated IVLS will provide new knowledge of tendon mechanobiology and has already shown the potential of clinically relevant HFLM loading for influencing tendon biology.

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