Computational peptide discovery with a genetic programming approach.

The development of peptides for therapeutic targets or biomarkers for disease diagnosis is a challenging task in protein engineering. Current approaches are tedious, often time-consuming and require complex laboratory data due to the vast search spaces that need to be considered. In silico methods can accelerate research and substantially reduce costs. Evolutionary algorithms are a promising approach for exploring large search spaces and can facilitate the discovery of new peptides. This study presents the development and use of a new variant of the genetic-programming-based POET algorithm, called POET Regex , where individuals are represented by a list of regular expressions. This algorithm was trained on a small curated dataset and employed to generate new peptides improving the sensitivity of peptides in magnetic resonance imaging with chemical exchange saturation transfer (CEST). The resulting model achieves a performance gain of 20% over the initial POET models and is able to predict a candidate peptide with a 58% performance increase compared to the gold-standard peptide. By combining the power of genetic programming with the flexibility of regular expressions, new peptide targets were identified that improve the sensitivity of detection by CEST. This approach provides a promising research direction for the efficient identification of peptides with therapeutic or diagnostic potential.

Clinically Translatable Hyperpolarized 13C Bicarbonate pH Imaging Method for Use in Prostate Cancer.

Solid tumors such as prostate cancer (PCa) commonly develop an acidic microenvironment with pH 6.5-7.2, owing to heterogeneous perfusion, high metabolic activity, and rapid cell proliferation. In preclinical prostate cancer models, disease progression is associated with a decrease in tumor extracellular pH, suggesting that pH imaging may reflect an imaging biomarker to detect aggressive and high-risk disease. Therefore, we developed a hyperpolarized carbon-13 MRI method to image the tumor extracellular pH (pHe) and prepared it for clinical translation for detection and risk stratification of PCa. This method relies on the rapid breakdown of hyperpolarized (HP) 1,2-glycerol carbonate (carbonyl-13C) via base-catalyzed hydrolysis to produce HP 13CO32-, which is neutralized and converted to HP H13CO3-. After injection, HP H13CO3- equilibrates with HP 13CO2 in vivo and enables the imaging of pHe. Using insights gleaned from mechanistic studies performed in the hyperpolarized state, we solved issues of polarization loss during preparation in a clinical polarizer system. We successfully customized a reaction apparatus suitable for clinical application, developed clinical standard operating procedures, and validated the radiofrequency pulse sequence and imaging data acquisition with a wide range of animal models. The results demonstrated that we can routinely produce a highly polarized and safe HP H13CO3- contrast agent suitable for human injection. Preclinical imaging studies validated the reliability and accuracy of measuring acidification in healthy kidney and prostate tumor tissue. These methods were used to support an Investigational New Drug application to the U.S. Food and Drug Administration. This methodology is now ready to be implemented in human trials, with the ultimate goal of improving the management of PCa.

Computational Peptide Discovery with a Genetic Programming Approach.

Background: The development of peptides for therapeutic targets or biomarkers for disease diagnosis is a challenging task in protein engineering. Current approaches are tedious, often time-consuming and require complex laboratory data due to the vast search space. In silico methods can accelerate research and substantially reduce costs. Evolutionary algorithms are a promising approach for exploring large search spaces and facilitating the discovery of new peptides. Results: This study presents the development and use of a variant of the initial POET algorithm, called POETRegex, which is based on genetic programming, where individuals are represented by a list of regular expressions. The program was trained on a small curated dataset and employed to predict new peptides that can improve the problem of sensitivity in detecting peptides through magnetic resonance imaging using chemical exchange saturation transfer (CEST). The resulting model achieves a performance gain of 20% over the initial POET variant and is able to predict a candidate peptide with a 58% performance increase compared to the gold-standard peptide. Conclusions: By combining the power of genetic programming with the flexibility of regular expressions, new potential peptide targets were identified to improve the sensitivity of detection by CEST. This approach provides a promising research direction for the efficient identification of peptides with therapeutic or diagnostic potential.

Selective filtration of NMR signals arising from weakly- and strongly-coupled spin systems.

Nuclear magnetic resonance (NMR) spectroscopy is a powerful technique for analyzing chemical and biological systems. However, in complex solutions with similar molecular components, NMR signals can overlap, making it challenging to distinguish and quantify individual species. In this paper, we introduce new spectral editing sequences that exploit the differences in nuclear spin interactions (J-couplings) between weakly- and strongly-coupled two-spin systems. These sequences selectively attenuate or nullify undesired spin magnetization while they preserve the desired signals, resulting in simplified NMR spectra and potentially facilitating single-species imaging applications. We demonstrate the effectiveness of our approach using a 31P spectral filtration method on a model system of nicotinamide dinucleotide (NAD), which exists in oxidized (NAD+) and reduced (NADH) forms. The presented sequences are robust to field inhomogeneity, do not require additional sub-spectra, and retain a significant portion of the original signal.

Development of a synthetic biosensor for chemical exchange MRI utilizing in silico optimized peptides.

Chemical exchange saturation transfer (CEST) MRI has been identified as a novel alternative to classical diagnostic imaging. Over the last several decades, many studies have been conducted to determine possible CEST agents, such as endogenously expressed compounds or proteins, that can be utilized to produce contrast with minimally invasive procedures and reduced or non-existent levels of toxicity. In recent years there has been an increased interest in the generation of genetically engineered CEST contrast agents, typically based on existing proteins with CEST contrast or modified to produce CEST contrast. We have developed an in silico method for the evolution of peptide sequences to optimize CEST contrast and showed that these peptides could be combined to create de novo biosensors for CEST MRI. A single protein, superCESTide, was designed to be 198 amino acids. SuperCESTide was expressed in E. coli and purified with size exclusion chromatography. The magnetic transfer ratio asymmetry generated by superCESTide was comparable to levels seen in previous CEST reporters, such as protamine sulfate (salmon protamine) and human protamine. These data show that novel peptides with sequences optimized in silico for CEST contrast that utilize a more comprehensive range of amino acids can still produce contrast when assembled into protein units expressed in complex living environments.

A Genetic Programming Approach to Engineering MRI Reporter Genes.

Here we develop a mechanism of protein optimization using a computational approach known as "genetic programming". We developed an algorithm called Protein Optimization Engineering Tool (POET). Starting from a small library of literature values, the use of this tool allowed us to develop proteins that produce four times more MRI contrast than what was previously state-of-the-art. Interestingly, many of the peptides produced using POET were dramatically different with respect to their sequence and chemical environment than existing CEST producing peptides, and challenge prior understandings of how those peptides function. While existing algorithms for protein engineering rely on divergent evolution, POET relies on convergent evolution and consequently allows discovery of peptides with completely different sequences that perform the same function with as good or even better efficiency. Thus, this novel approach can be expanded beyond developing imaging agents and can be used widely in protein engineering.

31P spin-lattice and singlet order relaxation mechanisms in pyrophosphate studied by isotopic substitution, field shuttling NMR, and molecular dynamics simulation.

Nuclear spin relaxation mechanisms are often difficult to isolate and identify, especially in molecules with internal flexibility. Here we combine experimental work with computation in order to determine the major mechanisms responsible for 31P spin-lattice and singlet order (SO) relaxation in pyrophosphate, a physiologically relevant molecule. Using field-shuttling relaxation measurements (from 2 µT to 9.4 T) and rates calculated from molecular dynamics (MD) trajectories, we identified chemical shift anisotropy (CSA) and spin-rotation as the major mechanisms, with minor contributions from intra- and intermolecular coupling. The significant spin-rotation interaction is a consequence of the relatively rapid rotation of the -PO32- entities around the bridging P-O bonds, and is treated by a combination of MD simulations and quantum chemistry calculations. Spin-lattice relaxation was predicted well without adjustable parameters, and for SO relaxation one parameter was extracted from the comparison between experiment and computation (a correlation coefficient between the rotational motion of the groups).

31P nuclear spin singlet lifetimes in a system with switchable magnetic inequivalence: experiment and simulation.

31P NMR spectroscopy and the study of nuclear spin singlet relaxation phenomena are of interest in particular due to the importance of phosphorus-containing compounds in physiology. We report the generation and measurement of relaxation of 31P singlet order in a chemically equivalent but magnetically inequivalent case. Nuclear magnetic resonance singlet state lifetimes of 31P pairs have heretofore not been reported. Couplings between 1H and 31P nuclei lead to magnetic inequivalence and serve as a mechanism of singlet state population conversion within this molecule. We show that in this molecule singlet relaxation occurs at a rate significantly faster than spin-lattice relaxation, and that anticorrelated chemical shift anisotropy can account for this observation. Calculations of this mechanism, with the help of molecular dynamics simulations and ab initio calculations, provide excellent agreement with the experimental findings. This study could provide guidance for the study of 31P singlets within other compounds, including biomolecules.

Tumor Microenvironment Biosensors for Hyperpolarized Carbon-13 Magnetic Resonance Spectroscopy.

Hyperpolarization (HP) of a carbon-13 molecule via dynamic nuclear polarization (DNP) involves polarization at low temperature, followed by a dissolution procedure producing a solution with highly polarized spins at room temperature. This dissolution DNP method significantly increases the signal-to-noise ratio (SNR) of nuclear magnetic resonance (NMR) over 10,000-fold and facilitates the use of magnetic resonance spectroscopy (MRS) to image not only metabolism but also the extracellular microenvironment. The extracellular tumor microenvironment (TME) closely interacts with tumor cells and stimulates their growth and metastasis. Thus, the ability to detect pathological changes in the TME is pivotal for the detection and study of cancers. This review highlights the potential use of MRS to study features of the TME-elevated export of lactate, reduced interstitial pH, imbalanced redox equilibrium, and altered metal homeostasis. The promising outcomes of both in vitro and in vivo assays suggest that DNP-MRS may be a useful technique to study aspects of the TME. With continued improvements, this tool has the potential to study the TME and provide guidance for accurate patient stratification and precise personal therapy. Graphical Abstract.

Tensor image enhancement and optimal multichannel receiver combination analyses for human hyperpolarized 13 C MRSI.

PURPOSE: With the initiation of human hyperpolarized 13 C (HP-13 C) trials at multiple sites and the development of improved acquisition methods, there is an imminent need to maximally extract diagnostic information to facilitate clinical interpretation. This study aims to improve human HP-13 C MR spectroscopic imaging through means of Tensor Rank truncation-Image enhancement (TRI) and optimal receiver combination (ORC). METHODS: A data-driven processing framework for dynamic HP 13 C MR spectroscopic imaging (MRSI) was developed. Using patient data sets acquired with both multichannel arrays and single-element receivers from the brain, abdomen, and pelvis, we examined the theory and application of TRI, as well as 2 ORC techniques: whitened singular value decomposition (WSVD) and first-point phasing. Optimal conditions for TRI were derived based on bias-variance trade-off. RESULTS: TRI and ORC techniques together provided a 63-fold mean apparent signal-to-noise ratio (aSNR) gain for receiver arrays and a 31-fold gain for single-element configurations, which particularly improved quantification of the lower-SNR-[13 C]bicarbonate and [1-13 C]alanine signals that were otherwise not detectable in many cases. Substantial SNR enhancements were observed for data sets that were acquired even with suboptimal experimental conditions, including delayed (114 s) injection (8× aSNR gain solely by TRI), or from challenging anatomy or geometry, as in the case of a pediatric patient with brainstem tumor (597× using combined TRI and WSVD). Improved correlation between elevated pyruvate-to-lactate conversion, biopsy-confirmed cancer, and mp-MRI lesions demonstrated that TRI recovered quantitative diagnostic information. CONCLUSION: Overall, this combined approach was effective across imaging targets and receiver configurations and could greatly benefit ongoing and future HP 13 C MRI research through major aSNR improvements.

Hyperpolarized in vivo pH imaging reveals grade-dependent acidification in prostate cancer.

There is an unmet clinical need for new and robust imaging biomarkers to distinguish indolent from aggressive prostate cancer. Hallmarks of aggressive tumors such as a decrease in extracellular pH (pHe) can potentially be used to identify aggressive phenotypes. In this study, we employ an optimized, high signal-to-noise ratio hyperpolarized (HP) 13C pHe imaging method to discriminate between indolent and aggressive disease in a murine model of prostate cancer. Transgenic adenocarcinoma of the mouse prostate (TRAMP) mice underwent a multiparametric MR imaging exam, including HP [13C] bicarbonate MRI for pHe, with 1H apparent diffusion coefficient (ADC) mapping and HP [1-13C] pyruvate MRI to study lactate metabolism. Tumor tissue was excised for histological staining and qRT-PCR to quantify mRNA expression for relevant glycolytic enzymes and transporters. We observed good separation in pHe between low- and high-grade tumor regions, with high-grade tumors demonstrating a lower pHe. The pHe also correlated strongly with monocarboxylate transporter Mct4 gene expression across all tumors, suggesting that lactate export via MCT4 is associated with acidification in this model. Our results implicate extracellular acidification as an indicator of indolent-to-aggressive transition in prostate cancer and suggest feasibility of HP pHe imaging to detect high-grade, clinically significant disease in men as part of a multiparametric MRI examination.

Amino Acid-Derived Sensors for Specific Zn2+ Detection Using Hyperpolarized 13 C Magnetic Resonance Spectroscopy.

Alterations in Zn2+ concentration are seen in normal tissues and in disease states, and for this reason imaging of Zn2+ is an area of active investigation. Herein, enriched [1-13 C]cysteine and [1-13 C2 ]iminodiacetic acid were developed as Zn2+ -specific imaging probes using hyperpolarized 13 C magnetic resonance spectroscopy. [1-13 C]cysteine was used to accurately quantify Zn2+ in complex biological mixtures. These sensors can be employed to detect Zn2+ via imaging mechanisms including changes in 13 C chemical shift, resonance linewidth, or T1 .

Spatiotemporal pH Heterogeneity as a Promoter of Cancer Progression and Therapeutic Resistance.

Dysregulation of pH in solid tumors is a hallmark of cancer. In recent years, the role of altered pH heterogeneity in space, between benign and aggressive tissues, between individual cancer cells, and between subcellular compartments, has been steadily elucidated. Changes in temporal pH-related processes on both fast and slow time scales, including altered kinetics of bicarbonate-CO2 exchange and its effects on pH buffering and gradual, progressive changes driven by changes in metabolism, are further implicated in phenotypic changes observed in cancers. These discoveries have been driven by advances in imaging technologies. This review provides an overview of intra- and extracellular pH alterations in time and space reflected in cancer cells, as well as the available technology to study pH spatiotemporal heterogeneity.

Using bidirectional chemical exchange for improved hyperpolarized [13 C]bicarbonate pH imaging.

PURPOSE: Rapid chemical exchange can affect SNR and pH measurement accuracy for hyperpolarized pH imaging with [13 C]bicarbonate. The purpose of this work was to investigate chemical exchange effects on hyperpolarized imaging sequences to identify optimal sequence parameters for high SNR and pH accuracy. METHODS: Simulations were performed under varying rates of bicarbonate-CO2 chemical exchange to analyze exchange effects on pH quantification accuracy and SNR under different sampling schemes. Four pulse sequences, including 1 new technique, a multiple-excitation 2D EPI (multi-EPI) sequence, were compared in phantoms using hyperpolarized [13 C]bicarbonate, varying parameters such as tip angles, repetition time, order of metabolite excitation, and refocusing pulse design. In vivo hyperpolarized bicarbonate-CO2 exchange measurements were made in transgenic murine prostate tumors to select in vivo imaging parameters. RESULTS: Modeling of bicarbonate-CO2 exchange identified a multiple-excitation scheme for increasing CO2 SNR by up to a factor of 2.7. When implemented in phantom imaging experiments, these sampling schemes were confirmed to yield high pH accuracy and SNR gains. Based on measured bicarbonate-CO2 exchange in vivo, a 47% CO2 SNR gain is predicted. CONCLUSION: The novel multi-EPI pulse sequence can boost CO2 imaging signal in hyperpolarized 13 C bicarbonate imaging while introducing minimal pH bias, helping to surmount a major hurdle in hyperpolarized pH imaging.

The Role of Lactate Metabolism in Prostate Cancer Progression and Metastases Revealed by Dual-Agent Hyperpolarized 13C MRSI.

This study applied a dual-agent, 13C-pyruvate and 13C-urea, hyperpolarized 13C magnetic resonance spectroscopic imaging (MRSI) and multi-parametric (mp) ¹H magnetic resonance imaging (MRI) approach in the transgenic adenocarcinoma of mouse prostate (TRAMP) model to investigate changes in tumor perfusion and lactate metabolism during prostate cancer development, progression and metastases, and after lactate dehydrogenase-A (LDHA) knock-out. An increased Warburg effect, as measured by an elevated hyperpolarized (HP) Lactate/Pyruvate (Lac/Pyr) ratio, and associated Ldha expression and LDH activity were significantly higher in high- versus low-grade TRAMP tumors and normal prostates. The hypoxic tumor microenvironment in high-grade tumors, as measured by significantly decreased HP 13C-urea perfusion and increased PIM staining, played a key role in increasing lactate production through increased Hif1α and then Ldha expression. Increased lactate induced Mct4 expression and an acidic tumor microenvironment that provided a potential mechanism for the observed high rate of lymph node (86%) and liver (33%) metastases. The Ldha knockdown in the triple-transgenic mouse model of prostate cancer resulted in a significant reduction in HP Lac/Pyr, which preceded a reduction in tumor volume or apparent water diffusion coefficient (ADC). The Ldha gene knockdown significantly reduced primary tumor growth and reduced lymph node and visceral metastases. These data suggested a metabolic transformation from low- to high-grade prostate cancer including an increased Warburg effect, decreased perfusion, and increased metastatic potential. Moreover, these data suggested that LDH activity and lactate are required for tumor progression. The lactate metabolism changes during prostate cancer provided the motivation for applying hyperpolarized 13C MRSI to detect aggressive disease at diagnosis and predict early therapeutic response.

Late-stage deuteration of 13C-enriched substrates for T1 prolongation in hyperpolarized 13C MRI.

A robust and selective late-stage deuteration methodology was applied to 13C-enriched amino and alpha hydroxy acids to increase spin-lattice relaxation constant T1 for hyperpolarized 13C magnetic resonance imaging. For the five substrates with 13C-labeling on the C1-position ([1-13C]alanine, [1-13C]serine, [1-13C]lactate, [1-13C]glycine, and [1-13C]valine), significant increase of their T1 was observed at 3 T with deuterium labeling (+26%, 22%, +16%, +25% and +29%, respectively). Remarkably, in the case of [2-13C]alanine, [2-13C]serine and [2-13C]lactate, deuterium labeling led to a greater than four fold increase in T1. [1-13C,2-2H]alanine, produced using this method, was applied to in vitro enzyme assays with alanine aminotransferase, demonstrating a kinetic isotope effect.

Detection of Bacteria-Specific Metabolism Using Hyperpolarized [2-13C]Pyruvate.

The differentiation of bacterial infection from other causes of inflammation is difficult in clinical practice and is critical where patient outcomes rely heavily on early interventions. In addition to physical exam and laboratory markers, several imaging modalities are frequently employed, but these techniques generally target the host immune response, rather than the living microorganisms themselves. Here, we describe a method to detect bacteria-specific metabolism using hyperpolarized (HP) 13C magnetic resonance spectroscopy. This technology allows visualization of the real-time conversion of enriched 13C substrates to their metabolic products, identified by their distinct chemical shifts. We have identified the rapid metabolism of HP [2-13C]pyruvate to [1-13C]acetate as a metabolic signature of common bacterial pathogens. We demonstrate this conversion in representative Gram-negative and Gram-positive bacteria, namely, Escherichia coli and Staphylococcus aureus, and its absence in key mammalian cell types. Furthermore, this conversion was successfully modulated in three mutant strains, corresponding to deletions of relevant enzymes.

Scatter Artifact with Ga-68-PSMA-11 PET: Severity Reduced With Furosemide Diuresis and Improved Scatter Correction.

PURPOSE: To assess the utility of furosemide diuresis and the role of an improved scatter correction algorithm in reducing scatter artifact severity on Ga-68- Prostate-specific membrane antigen (PSMA)-11 positron emission tomography (PET). MATERIALS AND METHODS: A total of 139 patients underwent Ga-68-PSMA-11 PET imaging for prostate cancer: 47 non-time-of-flight (non-TOF) PET/computed tomography, 51 PET/magnetic resonance imaging (MRI) using the standard TOF scatter correction algorithm, and 41 PET/MRI using an improved TOF scatter correction algorithm. Whole-body PET acquisitions were subdivided into 3 regions: around kidneys; between kidneys and bladder; and around bladder. The images were reviewed, and scatter artifact severity was rated using a Likert-type scale. RESULTS: The worst scatter occurred when using non-TOF scatter correction without furosemide, where 42.1% of patients demonstrated severe scatter artifacts in 1 or more regions. Improved TOF scatter correction resulted in the smallest percentage of studies with severe scatter (6.5%). Scatter ratings by region were lowest using improved TOF scatter correction. Furosemide reduced mean scatter severity when using non-TOF and standard TOF. CONCLUSIONS: Both furosemide and scatter correction algorithm play a role in reducing scatter in PSMA PET. Improved TOF scatter correction resulted in the lowest scatter severity.

Application of Good's buffers to pH imaging using hyperpolarized (13)C MRI.

N-(2-Acetamido)-2-aminoethanesulfonic acid (ACES), one of Good's buffers, was applied to pH imaging using hyperpolarized (13)C magnetic resonance spectroscopy. Rapid NMR- and MRI-based pH measurements were obtained by exploiting the sensitive pH-dependence of its (13)C chemical shift within the physiologic range.