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Biology subjects

White, K. A.

Publications and source records attributed to White, K. A..

18 recordsLinked to original sources

Ionizable networks mediate pH-dependent allosteryin SH2 signaling proteins

Intracellular pH dynamics regulate normal cell biology, but most molecular drivers remain unknown. We developed a computational pipeline to identify pH-sensitive proteins and their mechanisms. We applied the pipeline to SHP2, a pH-sensitive signaling protein, with unknown mechanism. We found that SHP2 phosphatase activity is pH-sensitive in vitro and in cells, and mutation of identified His116 and Glu252 abolishes pH-sensitive function. We also discovered that Src is an unrecognized pH-dependent kinase and mutation of the identified ionizable network abolishes pH-sensitive activity. Importantly, we found that Src kinase activity was pH sensitive even in the presence of EGF and with a phosphomimetic (Src-Y527E) mutant required for auto-inhibitory SH2 domain binding. Thus, the identified pH-sensitive regulation of Src kinase activity functions in concert with established mechanisms of Src regulation by phosphorylation. Constant pH molecular dynamics simulations performed on both SHP2 and Src support allosteric regulation mediated by pH-dependent binding of inhibitory SH2 domains to the respective catalytic domains. Finally, we show that evolutionarily conserved putative pH-sensing networks were identified across SH2 domain-containing signaling proteins. Taken together, our computational, biophysical, and cellular analyses reveal a role for pHi dynamics in allosterically regulating activity of modular SH2 signaling proteins to control biology. One-sentence summaryThis paper investigates the role of pH in the allosteric regulation of signaling proteins with SH2 domains, specifically focusing on SHP2 and Src

biochemistry↗

Intracellular pH dynamics respond to microenvironment stiffening and mediate vasculogenic mimicry through β-catenin

Dysregulated intracellular pH (pHi) dynamics and an altered tumor microenvironment have emerged as drivers of cancer cell phenotypes. However, the molecular integration between the physical properties of the microenvironment and dynamic intracellular signaling responses remains unclear. Here, we identify a mechanistic link between ECM stiffness and pHi dynamics in driving vasculogenic mimicry (VM), an aggressive cancer phenotype associated with poor prognosis. We performed single-cell imaging of pHi in lung and breast metastatic cell lines cultured on tunable-stiffness hydrogel systems. We used two tunable-stiffness hydrogel systems to independently model stiffness induced by increased protein secretion (Matrigel) and increased protein crosslinking (Hyaluronic acid gels). We show that increased ECM stiffness lowers single-cell pHi in both lung and breast metastatic cell lines. We also observed that stiff ECM promotes a distinct morphological phenotype called vasculogenic mimicry (VM). Importantly, we show that low pHi is a necessary mediator of VM, as raising pHi on stiff ECM reduces VM phenotypes. We also find that lowering pHi on soft ECM was sufficient to induce VM in the absence of extracellular stiffening. We characterized {beta}-catenin as a pH-dependent molecular mediator of VM, where stiffness-driven increases in {beta}-catenin abundance can be overridden by high pHi, which destabilizes {beta}-catenin to reduce VM on stiff ECM. In contrast, the transcription factor FOXC2 is activated by ECM stiffness but is insensitive to pHi, and its activity alone is insufficient to maintain VM at high pHi when {beta}-catenin is lost. We uncover a novel mechanotransduction axis in which ECM stiffness regulates intracellular pH to drive {beta}-catenin-induced VM. We also show pHi dynamics can override mechanosensitive cell responses to the extracellular microenvironment. Thus, our work positions pHi as an integrator of mechanotransduction in cancer, suggesting a new framework for therapeutically targeting pHi in cancer and perhaps in other diseases driven by ECM remodeling.

cell biology↗

Intracellular pH regulates β-catenin with low pH increasing adhesion and signaling functions

Intracellular pH (pHi) dynamics are linked to cell proliferation, migration, and differentiation. The adherens junction (AJ) and signaling protein {beta}-catenin has decreased abundance at high pHi due to increased proteasomal-mediated degradation. However, the effects of low pHi on {beta}-catenin abundance and function have not been characterized. Here, we use population-level and single-cell assays to show that low pHi stabilizes {beta}-catenin, increasing junctional, cytoplasmic, and nuclear abundance. We assayed single-cell protein degradation rates to show that {beta}-catenin half-life is longer at low pHi and shorter at high pHi compared to control. Importantly, a constitutively stabilized and pHi-insensitive {beta}-catenin mutant ({beta}-catenin-H36R), has a longer and pHi-independent half-life. We also determined that the pH-dependent stability of {beta}-catenin affects both its adhesion and signaling functions. We show that the composition of AJs changes with pHi; at low pHi, E-cadherin-containing AJs are enriched in {beta}-catenin while plakoglobin abundance is reduced. Conversely, when {beta}-catenin is lost from E-cadherin-containing AJs at high pHi, plakoglobin is increased. We also found that cell area was reduced at low pHi and increased at high pHi compared to control while cell volume was unaffected, suggesting pHi alters cell-cell adhesion. Finally, we show that low pHi increases {beta}-catenin transcriptional activity in single cells and is indistinguishable from a Wnt-on state, while high pHi reduces {beta}-catenin transcriptional activity compared to control cells. This work characterizes pHi as a true rheostat regulating {beta}-catenin abundance, stability, and function, solidifying {beta}-catenin as a molecular mediator of pHi-dependent cell processes via pH-dependent adhesion and signaling functions. SummaryIntracellular pH (pHi) regulates the degradation rate of the pH sensor {beta}-catenin, altering protein abundance, subcellular localization, and function in epithelial cells. This work shows pHi acts as a rheostat to alter both adhesion and signaling functions of {beta}-catenin.

cell biology↗

Sortilin inhibition treats multiple neurodegenerative lysosomal storage disorders.

Lysosomal storage disorders (LSDs) are a genetically and clinically diverse group of diseases characterized by lysosomal dysfunction. Batten disease is a family of severe LSDs primarily impacting the central nervous system. Here we show that AF38469, a small molecule inhibitor of sortilin, improves lysosomal and glial pathology across multiple LSD models. Live-cell imaging and comparative transcriptomics demonstrates that the transcription factor EB (TFEB), an upstream regulator of lysosomal biogenesis, is activated upon treatment with AF38469. Utilizing CLN2 and CLN3 Batten disease mouse models, we performed a short-term efficacy study and show that treatment with AF38469 prevents the accumulation of lysosomal storage material and the development of neuroinflammation, key disease associated pathologies. Tremor phenotypes, an early behavioral phenotype in the CLN2 disease model, were also completely rescued. These findings reveal sortilin inhibition as a novel and highly efficacious therapeutic modality for the treatment of multiple forms of Batten disease.

neuroscience↗

A 128-ch area-efficient neurochemical-sensing front-end for FSCV recordings of dopamine

Neurochemical recordings rely on electrochemical reactions of electroactive neurotransmitters such as dopamine, serotonin, and norepinephrine. This electrochemical technique allows for highly sensitive monitoring of neurotransmitters in the brain. Traditionally, single-channel carbon-fiber microelectrode recordings have been considered the gold standard method. However, an alternative approach involves the use of a microelectrode array, which enables high spatiotemporal resolution imaging of electroactive neurotransmitters. To enable neurochemical imaging using a microelectrode array, the development of a high-density current-sensing microchip is necessary. Here, a neurochemical microchip is introduced, featuring a 128-channel current sensing front-end capable of supporting 128 parallel neurochemical measurements. The designed amplifier array employs a highly scalable resistive feedback transimpedance amplifier design. This design allows for a large neurochemical dynamic range of {+/-}5{micro}A with a noise performance as low as 0.22nARMS. With the integration of this microchip, in vivo neurochemical imaging of dopamine can be achieved with high spatiotemporal resolution.

bioengineering↗

A novel porcine model of CLN3 Batten disease recapitulates clinical phenotypes

Mouse models of CLN3 Batten disease, a rare lysosomal storage disorder with no cure, have improved our understanding of CLN3 biology and therapeutics through their ease of use and a consistent display of cellular pathology. However, the translatability of murine models is limited by disparities in anatomy, body size, life span, and inconsistent, subtle behavior deficits that can be difficult to detect in CLN3 mutant mouse models, limiting their utility in preclinical studies. Here we present a longitudinal characterization of a novel miniswine model of CLN3 disease that recapitulates the most common human pathogenic variant, an exon 7-8 deletion (CLN3{Delta}ex7/8). Progressive pathology and neuron loss is observed in various regions of the CLN3{Delta}ex7/8 miniswine brain and retina. Additionally, mutant miniswine present with vision impairment and motor abnormalities, similar to deficits seen in human patients. Taken together, the CLN3{Delta}ex7/8 miniswine model shows consistent and progressive Batten disease pathology and behavioral impairment mirroring clinical presentation, demonstrating its value in studying the role of CLN3 and safety/efficacy of novel disease modifying therapeutics.

neuroscience↗

Intracellular pH differentially regulates transcription of metabolic and signaling pathways in normal epithelial cells

Intracellular pH (pHi) dynamics regulate normal cell function, and dysregulated pHi dynamics is an emerging hallmark of cancer (constitutively increased pHi) and neurodegeneration (constitutively decreased pHi). However, the molecular mechanisms by which pHi dynamics regulate cell biology are poorly understood. Here, we discovered that altering pHi in normal human breast epithelial cells triggers global transcriptional changes. We identified 176 genes differentially regulated by pHi, with pHi-dependent genes clustering in signaling and glycolytic pathways. Using various normal epithelial cell models, we showed pH-dependent Notch1 expression, with increased protein abundance at high pHi. This resulted in pH-dependent downstream signaling, with increased Notch1 signaling at high pHi. We also found that high pHi increased the expression of glycolytic enzymes and regulators of pyruvate fate, including lactate dehydrogenase and pyruvate dehydrogenase kinase. These transcriptional changes were sufficient to alter lactate production, with high pHi shifting these normal epithelial cells toward a glycolytic metabolism and increasing lactate production. Thus, pHi dynamics transcriptionally regulate signaling and metabolic pathways in normal epithelial cells. Our data reveal new molecular regulators of pHi-dependent biology and a role for increased pHi in driving the acquisition of cancer-associated signaling and metabolic changes in normal human epithelial cells.

biochemistry↗

A 512-ch dual-mode microchip for simultaneous measurements of electrophysiological and neurochemical activities

In the study of the brain, large and high-density microelectrode arrays have been widely used to study the behavior of neurotransmission. CMOS technology has facilitated these devices by enabling the integration of high-performance amplifiers directly on-chip. Usually, these large arrays measure only the voltage spikes resulting from action potentials traveling along firing neuronal cells. However, at synapses, communication between neurons occurs by the release of neurotransmitters, which cannot be measured on typical CMOS electrophysiology devices. Development of electrochemical amplifiers has resulted in the measurement of neurotransmitter exocytosis down to the level of a single vesicle. To effectively monitor the complete picture of neurotransmission, measurement of both action potentials and neurotransmitter activity is needed. Current efforts have not resulted in a device that is capable of the simultaneous measurement of action potential and neurotransmitter release at the same spatiotemporal resolution needed for a comprehensive study of neurotransmission. In this paper, we present a true dual-mode CMOS device that fully integrates 256-ch electrophysiology amplifiers and 256-ch electrochemical amplifiers, along with an on-chip 512 electrode microelectrode array capable of simultaneous measurement from all 512 channels. Electrochemical amplifiers achieve a noise level of 4.51 pARMS with a bandwidth of 10.3 kHz. Electrophysiology amplifiers exhibit 24.9 VRMS noise in the action potential band and a total usable bandwidth from 0.2 Hz to 10 kHz.

bioengineering↗

A CLN6-CRMP2-KLC4 complex regulates anterograde ER-derived vesicle trafficking in cortical neurites

As neurons establish extensive connections throughout the central nervous system, the transport of cargo along the microtubule network of the axon is crucial for differentiation and homeostasis. Specifically, building blocks such as membrane and cytoskeletal components, organelles, transmembrane receptors, adhesion molecules, and peptide neurotransmitters all require proper transport to the presynaptic compartment. Here, we identify a novel complex regulating vesicular endoplasmic reticulum transport in neurites, composed of CLN6: an ER-associated protein of relatively unknown function implicated in CLN6-Batten disease; CRMP2: a tubulin binding protein important in regulating neurite microtubule dynamics; and KLC4: a classic transport motor protein. We show that this "CCK" complex allows ER-derived vesicles to migrate to the distal end of the axon, aiding in proper neurite outgrowth and arborization. In the absence of CLN6, the CCK complex does not function effectively, leading to reduced vesicular transport, stunted neurite outgrowth, and deficits in CRMP2 binding to other protein partners. Treatment with a CRMP2 modulating compound, lanthionine ketimine ester, partially restores these deficits in CLN6-deficient mouse neurons, indicating that stabilization of CRMP2 interacting partners may prove beneficial in lieu of complete restoration of the CCK complex. Taken together, these findings reveal a novel mechanism of ER-derived vesicle transport in the axon and provide new insights into therapeutic targets for neurodegenerative disease.

neuroscience↗

Single-cell intracellular pH measurements reveal cell-cycle linked pH dynamics

Transient changes in intracellular pH (pHi) regulate normal cell behaviors, but roles for spatiotemporal pHi dynamics in single-cell behaviors remains unclear. Here, we mapped single-cell spatiotemporal pHi dynamics during mammalian cell cycle progression both with and without cell cycle synchronization. We found that single-cell pHi is dynamic throughout the cell cycle: pHi decreases at G1/S, increases in mid-S, decreases at late S, increases at G2/M, and rapidly decreases during mitosis. Importantly, while pHi is highly dynamic in dividing cells, non-dividing cells have attenuated pHi dynamics. Using two independent pHi manipulation methods, we found that low pHi inhibits completion of S phase while increased pHi promotes both S/G2 and G2/M transitions. Our data also suggest that low pHi cues G1 exit, with decreased pHi shortening G1 and increased pHi elongating G1. Furthermore, dynamic pHi is required for S phase timing, as high pHi elongates S phase and low pHi inhibits S/G2 transition. This work reveals spatiotemporal pHi dynamics are necessary for cell cycle progression at multiple phase transitions in single human cells.

cell biology↗

An optogenetic tool to raise intracellular pH in single cells and drive localized membrane dynamics

Intracellular pH (pHi) dynamics are critical for regulating normal cell physiology. For example, transient increases in pHi (7.2-7.6) regulate cell behaviors like cell polarization, actin cytoskeleton remodeling, and cell migration. Most studies on pH-dependent cell behaviors have been performed at the population level and use non-specific methods to manipulate pHi. The lack of tools to specifically manipulate pHi at the single-cell level has hindered investigation of the role of pHi dynamics in driving single cell behaviors. In this work, we show that Archaerhodopsin (ArchT), a light-driven outward proton pump, can be used to elicit robust and physiological pHi increases over the minutes timescale. We show that activation of ArchT is repeatable, enabling the maintenance of high pHi in single cells for approximately 45 minutes. We apply this spatiotemporal pHi manipulation tool to determine whether increased pHi is a sufficient driver of membrane ruffling in single cells. Using the ArchT tool, we show that increased pHi in single cells can drive localized membrane ruffling responses within seconds and increased membrane dynamics (both protrusion and retraction events) compared to unstimulated ArchT cells as well as control cells. Overall, this tool allows us to directly investigate the relationship between increased pHi and cell behaviors such as membrane ruffling. This tool will be transformative in facilitating experiments required to determine if increased pHi drives these cell behaviors at the single-cell level.

biochemistry↗

AAV9 gene therapy restores lifespan and treats pathological and behavioral abnormalities in a mouse model of CLN8-Batten disease

CLN8 disease is a rare form of neuronal ceroid lipofuscinosis caused by biallelic mutations in the CLN8 gene, which encodes a transmembrane endoplasmic reticulum protein involved in trafficking of lysosomal enzymes. CLN8 disease patients present with myoclonus, tonic-clonic seizures, and progressive declines in cognitive and motor function, with many cases resulting in premature death early in life. There are currently no treatments that can cure the disease or substantially slow disease progression. Using a mouse model of CLN8 disease, we tested the safety and efficacy of an intracerebroventricularly (ICV)-delivered self-complementary AAV9 (scAAV9) gene therapy vector driving expression of human CLN8. A single neonatal injection was safe and well-tolerated, resulting in robust transgene expression throughout the brain and spinal cord from 4 to 24 months, reducing histopathological and behavioral hallmarks of the disease and completely restoring lifespan from 10 months in untreated animals to beyond 24 months of age in treated animals. These results demonstrate, by far, the most successful rescue reported in an animal model of CLN8 disease, and supports gene therapy as a promising therapeutic strategy for this disorder.

neuroscience↗

An acidic residue buried in the dimer interface of isocitrate dehydrogenase 1 (IDH1) helps regulate catalysis and pH sensitivity

Isocitrate dehydrogenase 1 (IDH1) catalyzes the reversible NADP+-dependent conversion of isocitrate to -ketoglutarate (-KG) to provide critical cytosolic substrates and drive NADPH-dependent reactions like lipid biosynthesis and glutathione regeneration. In biochemical studies, the forward reaction is studied at neutral pH, while the reverse reaction is typically characterized in more acidic buffers. This led us to question whether IDH1 catalysis is pH-regulated, which would have functional implications under conditions that alter cellular pH, like apoptosis, hypoxia, cancer, and neurodegenerative diseases. Here, we show evidence of catalytic regulation of IDH1 by pH, identifying a trend of increasing kcat values for -KG production upon increasing pH in the buffers we tested. To understand the molecular determinants of IDH1 pH sensitivity, we used the pHinder algorithm to identify buried ionizable residues predicted to have shifted pKa values. Such residues can serve as pH sensors, with changes in protonation states leading to conformational changes that regulate catalysis. We identified an acidic residue buried at the IDH1 dimer interface, D273, with a predicted pKa value upshifted into the physiological range. D273 point mutations had decreased catalytic efficiency and, importantly, loss of pH-regulated catalysis. Based on these findings, we conclude that IDH1 activity is regulated, at least in part, by pH. We show this regulation is mediated by at least one buried acidic residue [~]12 [A] from the IDH1 active site. By establishing mechanisms of regulation of this well-conserved enzyme, we highlight catalytic features that may be susceptible to pH changes caused by cell stress and disease.

biochemistry↗

A Wirelessly Powered Implantable CMOS Neural Recording Sensor Array using Pulse-based Neural Amplifier

The most important organ in the human body is unquestionably the brain. Yet, despite its importance, it is one of the least well understood organs. One reason for this lack of understanding of the brain is the lack of data available to researchers from in vivo studies. Historically, collecting measurements from the brain has been difficult due to the high risk to the patient. Recently technology has been developed to allow electrical measurements to be taken from the brain directly, however most systems involve non-permanent sensors because of the requirement for transcranial wiring for power and data. Developments in the field of CMOS circuit design, wireless power transmission, and wireless data transmission have enabled the creation of implantable neural recording devices as a combination of these technologies. The implant designed in this paper is [~]15 mm in diameter and 2 mm at its thickest point on a flexible polyamide PCB. The flexible nature of the implant allows for the implant to conform to the surface of the brain. The implant requires no transcranial orifice since it is powered wirelessly and transmits data wirelessly via Bluetooth low energy. The CMOS neural amplifier chip on the implant utilizes an enhanced form of delta modulation to remove the requirement for large ADCs to be present on the die, saving space and enabling 1024 amplifiers and electrodes to be present on the chip. The implant is capable of measuring, modulating, and wirelessly transmitting a millivolt order signal to a PC for demodulation and analysis.

bioengineering↗

Parallel 1024-ch Cyclic Voltammetry on Monolithic CMOS Electrochemical Detector Array

Large-scale microelectrode arrays offers enhanced spatiotemporal resolution in electrophysiology studies.. In this paper, we discuss the design and performance of an electrochemical detector array which is capable of 1024-ch parallel cyclic voltammetry (CV) as well as other electrochemical measurements. The electrochemical detector is fabricated using a custom-designed CMOS chip which integrates both the circuity and on-chip microelectrode array, to operate and record from electrochemical measurements. For parallel 1024-ch recordings, 1024 capacitor-based integrating transimpedance amplifiers (TIA) are designed and integrated. The TIA design features the bipolar capabilities for measuring both negative and positive electrochemical currents due to reduction and oxidation of molecules. The resulted dynamic range of this TIA is -700 pA - 1968 pA. CV can be used to examine the quality of electrochemical electrodes by measuring the double-layer capacitance. Double-layer capacitance forms at the electrode-electrolyte interface and is a function of the effective area of the electrode. Thus, a contaminated electrode can have smaller effective area resulting in smaller double-layer capacitance. Using the parallel CV capability of the monolithic CMOS device, the double layer capacitance of all 1024 electrodes are simultaneously measured to examine the status of the electrodes surface in real time. The initial measurement of the electrode array showed a mean capacitance of 466 pF. After plasma treatment to remove contamination on the electrodes surface, the increased capacitance was 1.36nF nearly tripling the effective surface area. We have successfully developed of 1024-ch electrochemical detector array using the monolithic CMOS sensor. The CV functionality was validated by measuring the double-layer capacitance of the on-chip electrode array. This method can accelerate the characterization of a massive electrode array before analytical experiments to provide well-controlled electrochemical electrodes, which is crucial in conducting reliable electrochemical measurements.

bioengineering↗

A multimodal approach to identify clinically relevant parameters to monitor disease progression in a preclinical model of neuropediatric disease

While research has accelerated the development of new treatments for pediatric neurodegenerative disorders, the ability to demonstrate the long-term efficacy of these therapies has been hindered by the lack of convincing, noninvasive methods for tracking disease progression both in animal models and in human clinical trials. Here, we unveil a new translational platform for tracking disease progression in an animal model of a pediatric neurodegenerative disorder, CLN6-Batten disease. Instead of looking at a handful of parameters or a single \"needle in a haystack\", we embrace the idea that disease progression, in mice and patients alike, is a diverse phenomenon best characterized by a combination of relevant biomarkers. Thus, we employed a multi-modal quantitative approach where 144 parameters were longitudinally monitored to allow for individual variability. We use a range of noninvasive neuroimaging modalities and kinematic gait analysis, all methods that parallel those commonly used in the clinic, followed by a powerful statistical platform to identify key progressive anatomical and metabolic changes that correlate strongly with the progression of pathological and behavioral deficits. This innovative, highly sensitive platform can be used as a powerful tool for preclinical studies on neurodegenerative diseases, and provides proof-of-principle for use as a potentially translatable tool for clinicians in the future.\n\nOne Sentence SummaryPrincipal component analysis identifies a set of clinically relevant parameters able to measure progression of Batten disease in a mouse model.

pathology↗

A cortical pathway modulates sensory input into the olfactory striatum

Sensory cortices process stimuli in manners essential for perception. The piriform primary olfactory cortex (PCX) extends dense association fibers into the ventral striatums olfactory tubercle (OT), yet the function of this cortico-striatal pathway is unknown. We optically stimulated channelrhodopsin-transduced PCX glutamatergic neurons or their association fibers while recording OT neural activity in mice performing an olfactory task. Activation of PCX neurons or their association fibers within the OT controlled the firing of some OT neurons and bidirectionally modulated odor coding dependent upon the neurons intrinsic odor responsivity. Further, patch clamp recordings and retroviral tracing from D1 and D2 dopamine receptor-expressing OT medium spiny neurons revealed this input can be monosynaptic and that both cell types receive most of their input from a specific spatial zone localized within the ventro-caudal PCX. These results demonstrate that the PCX functionally accesses the direct and indirect pathways of the basal ganglia within the OT.

neuroscience↗

Prominent Features Of The Amino Acid Mutation Landscape In Cancer

Cancer can be viewed as a set of different diseases with distinctions based on tissue origin, driver mutations, and genetic signatures. Accordingly, each of these distinctions have been used to classify cancer subtypes and to reveal common features. Here, we present a different analysis of cancer based on amino acid mutation signatures. Non-negative Matrix Factorization and principal component analysis of 29 cancers revealed six amino acid mutation signatures, including four signatures that were dominated by either arginine to histidine (Arg>His) or glutamate to lysine (Glu>Lys) mutations. Sample-level analyses reveal that while some cancers are heterogeneous, others are largely dominated by one type of mutation. Using a non-overlapping set of samples from the COSMIC somatic mutation database, we validate five of six mutation signatures, including signatures with prominent arginine to histidine (Arg>His) or glutamate to lysine (Glu>Lys) mutations. This suggests that our classification of cancers based on amino acid mutation patterns may provide avenues of inquiry pertaining to specific protein mutations that may generate novel insights into cancer biology.

bioinformatics↗