The Emerging Role of Raman Spectroscopy as an Omics Approach for Metabolic Profiling and Biomarker Detection toward Precision Medicine.

Omics technologies have rapidly evolved with the unprecedented potential to shape precision medicine. Novel omics approaches are imperative toallow rapid and accurate data collection and integration with clinical information and enable a new era of healthcare. In this comprehensive review, we highlight the utility of Raman spectroscopy (RS) as an emerging omics technology for clinically relevant applications using clinically significant samples and models. We discuss the use of RS both as a label-free approach for probing the intrinsic metabolites of biological materials, and as a labeled approach where signal from Raman reporters conjugated to nanoparticles (NPs) serve as an indirect measure for tracking protein biomarkers in vivo and for high throughout proteomics. We summarize the use of machine learning algorithms for processing RS data to allow accurate detection and evaluation of treatment response specifically focusing on cancer, cardiac, gastrointestinal, and neurodegenerative diseases. We also highlight the integration of RS with established omics approaches for holistic diagnostic information. Further, we elaborate on metal-free NPs that leverage the biological Raman-silent region overcoming the challenges of traditional metal NPs. We conclude the review with an outlook on future directions that will ultimately allow the adaptation of RS as a clinical approach and revolutionize precision medicine.

Monitoring Metabolic Changes in Response to Chemotherapies in Cancer with Raman Spectroscopy and Metabolomics.

Resistance to clinical therapies remains a major barrier in cancer management. There is a critical need for rapid and highly sensitive diagnostic tools that enable early prediction of treatment response to allow accurate clinical decisions. Here, Raman spectroscopy was employed to monitor changes in key metabolites as early predictors of response in KRAS-mutant colorectal cancer (CRC) cells, HCT116, treated with chemotherapies. We show at the single cell level that HCT116 is resistant to cetuximab (CTX), the first-line treatment in CRC, but this resistance can be overcome with pre-sensitization of cells with oxaliplatin (OX). In combination treatment of CTX + OX, sequential delivery of OX followed by CTX rather than simultaneous administration of drugs was observed to be critical for effective therapy. Our results demonstrated that metabolic changes are well aligned to cellular mechanical changes where Young's modulus decreased after effective treatment, indicating that both changes in mechanical properties and metabolism in cells are likely responsible for cancer proliferation. Raman findings were verified with mass spectrometry (MS) metabolomics, and both platforms showed changes in lipids, nucleic acids, and amino acids as predictors of resistance/response. Finally, key metabolic pathways enriched were identified when cells are resistant to CTX but downregulated with effective treatment. This study highlights that drug-induced metabolic changes both at the single cell level (Raman) and ensemble level (MS) have the potential to identify mechanisms of response to clinical cancer therapies.

Physicochemical Properties and Route of Systemic Delivery Control the In Vivo Dynamics and Breakdown of Radiolabeled Gold Nanostars.

The in vivo dynamics of nanoparticles requires a mechanistic understanding of multiple factors. Here, for the first time, the surprising breakdown of functionalized gold nanostars (F-AuNSs) conjugated with antibodies and 64 Cu radiolabels in vivo and in artificial lysosomal fluid ex vivo, is shown. The short-term biodistribution of F-AuNSs is driven by the route of systemic delivery (intravenous vs intraperitoneal) and long-term fate is controlled by the tissue type in vivo. In vitro studies including endocytosis pathways, intracellular trafficking, and opsonization, are combined with in vivo studies integrating a milieu of spectroscopy and microcopy techniques that show F-AuNSs dynamics is driven by their physicochemical properties and route of delivery. F-AuNSs break down into sub-20 nm broken nanoparticles as early as 7 days postinjection. Martini coarse-grained simulations are performed to support the in vivo findings. Simulations suggest that shape, size, and charge of the broken nanoparticles, and composition of the lipid membrane depicting various tissues govern the interaction of the nanoparticles with the membrane, and the rate of translocation across the membrane to ultimately enable tissue clearance. The fundamental study addresses critical gaps in the knowledge regarding the fate of nanoparticles in vivo that remain a bottleneck in their clinical translation.

All silicon electrode photocapacitor for integrated energy storage and conversion.

We demonstrate a simple wafer-scale process by which an individual silicon wafer can be processed into a multifunctional platform where one side is adapted to replace platinum and enable triiodide reduction in a dye-sensitized solar cell and the other side provides on-board charge storage as an electrochemical supercapacitor. This builds upon electrochemical fabrication of dual-sided porous silicon and subsequent carbon surface passivation for silicon electrochemical stability. The utilization of this silicon multifunctional platform as a combined energy storage and conversion system yields a total device efficiency of 2.1%, where the high frequency discharge capability of the integrated supercapacitor gives promise for dynamic load-leveling operations to overcome current and voltage fluctuations during solar energy harvesting.

Uncovering the intrinsic size dependence of hydriding phase transformations in nanocrystals.

A quantitative understanding of nanocrystal phase transformations would enable more efficient energy conversion and catalysis, but has been hindered by difficulties in directly monitoring well-characterized nanoscale systems in reactive environments. We present a new in situ luminescence-based probe enabling direct quantification of nanocrystal phase transformations, applied here to the hydriding transformation of palladium nanocrystals. Our approach reveals the intrinsic kinetics and thermodynamics of nanocrystal phase transformations, eliminating complications of substrate strain, ligand effects and external signal transducers. Clear size-dependent trends emerge in nanocrystals long accepted to be bulk-like in behaviour. Statistical mechanical simulations show these trends to be a consequence of nanoconfinement of a thermally driven, first-order phase transition: near the phase boundary, critical nuclei of the new phase are comparable in size to the nanocrystal itself. Transformation rates are then unavoidably governed by nanocrystal dimensions. Our results provide a general framework for understanding how nanoconfinement fundamentally impacts broad classes of thermally driven solid-state phase transformations relevant to hydrogen storage, catalysis, batteries and fuel cells.

Predicting the onset of preeclampsia by longitudinal monitoring of metabolic changes throughout pregnancy with Raman spectroscopy.

Preeclampsia is a life-threatening pregnancy disorder. Current clinical assays cannot predict the onset of preeclampsia until the late 2nd trimester, which often leads to poor maternal and neonatal outcomes. Here we show that Raman spectroscopy combined with machine learning in pregnant patient plasma enables rapid, highly sensitive maternal metabolome screening that predicts preeclampsia as early as the 1st trimester with >82% accuracy. We identified 12, 15 and 17 statistically significant metabolites in the 1st, 2nd and 3rd trimesters, respectively. Metabolic pathway analysis shows multiple pathways corresponding to amino acids, fatty acids, retinol, and sugars are enriched in the preeclamptic cohort relative to a healthy pregnancy. Leveraging Pearson's correlation analysis, we show for the first time with Raman Spectroscopy that metabolites are associated with several clinical factors, including patients' body mass index, gestational age at delivery, history of preeclampsia, and severity of preeclampsia. We also show that protein quantification alone of proinflammatory cytokines and clinically relevant angiogenic markers are inadequate in identifying at-risk patients. Our findings demonstrate that Raman spectroscopy is a powerful tool that may complement current clinical assays in early diagnosis and in the prognosis of the severity of preeclampsia to ultimately enable comprehensive prenatal care for all patients.

Inhibiting the cGAS-STING Pathway in Ulcerative Colitis with Programmable Micelles.

Ulcerative colitis is a chronic condition in which a dysregulated immune response contributes to the acute intestinal inflammation of the colon. Current clinical therapies often exhibit limited efficacy and undesirable side effects. Here, programmable nanomicelles were designed for colitis treatment and loaded with RU.521, an inhibitor of the cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) pathway. STING-inhibiting micelles (SIMs) comprise hyaluronic acid-stearic acid conjugates and include a reactive oxygen species (ROS)-responsive thioketal linker. SIMs were designed to selectively accumulate at the site of inflammation and trigger drug release in the presence of ROS. Our in vitro studies in macrophages and in vivo studies in a murine model of colitis demonstrated that SIMs leverage HA-CD44 binding to target sites of inflammation. Oral delivery of SIMs to mice in both preventive and delayed therapeutic models ameliorated colitis's severity by reducing STING expression, suppressing the secretion of proinflammatory cytokines, enabling bodyweight recovery, protecting mice from colon shortening, and restoring colonic epithelium. In vivo end points combined with metabolomics identified key metabolites with a therapeutic role in reducing intestinal and mucosal inflammation. Our findings highlight the significance of programmable delivery platforms that downregulate inflammatory pathways at the intestinal mucosa for managing inflammatory bowel diseases.

Mammary tissue-derived extracellular matrix hydrogels reveal the role of irradiation in driving a pro-tumor and immunosuppressive microenvironment.

Radiation therapy (RT) is essential for triple negative breast cancer (TNBC) treatment. However, patients with TNBC continue to experience recurrence after RT. The role of the extracellular matrix (ECM) of irradiated breast tissue in tumor recurrence is still unknown. In this study, we evaluated the structure, molecular composition, and mechanical properties of irradiated murine mammary fat pads (MFPs) and developed ECM hydrogels from decellularized tissues (dECM) to assess the effects of RT-induced ECM changes on breast cancer cell behavior. Irradiated MFPs were characterized by increased ECM deposition and fiber density compared to unirradiated controls, which may provide a platform for cell invasion and proliferation. ECM component changes in collagens I, IV, and VI, and fibronectin were observed following irradiation in both MFPs and dECM hydrogels. Encapsulated TNBC cell proliferation and invasive capacity was enhanced in irradiated dECM hydrogels. In addition, TNBC cells co-cultured with macrophages in irradiated dECM hydrogels induced M2 macrophage polarization and exhibited further increases in proliferation. Our study establishes that the ECM in radiation-damaged sites promotes TNBC invasion and proliferation as well as an immunosuppressive microenvironment. This work represents an important step toward elucidating how changes in the ECM after RT contribute to breast cancer recurrence.

Tumor-targeting cell membrane-coated nanorings for magnetic-hyperthermia-induced tumor ablation.

Magnetic hyperthermia has attracted considerable attention for efficient cancer therapy because of its noninvasive nature, deep tissue penetration, and minimal damage to healthy tissues. Herein, we have fused cancer cell membrane fragments with lipids and cloaked them on magnetic nanorings to form targeted Fe nanorings (TF) for tumor-targeted magnetic hyperthermia-induced tumor ablation. In our approach, cell membrane fragments from cancer cells were fused with lipids to form vesicles, which could efficiently encapsulate magnetic nanorings, thereby forming TF. We observed that TF have high tumor uptake via homotypic targeting, where cancer cells take up TF through membrane fusion. Under an external alternating magnetic field (AMF), TF accumulated in the tumors are heated, driving magnetic-hyperthermia-induced tumor cell death. Our in vitro studies show that self-targeting TF efficiently localized in cancer cells and induced cell death with an AMF, which was shown by a live/dead assay. Our findings demonstrate the potential of TF in tumor ablation, thereby making them promising and efficient nanosystems for tumor-targeted theranostics.

First Trimester Prediction of Preterm Birth in Patient Plasma with Machine-Learning-Guided Raman Spectroscopy and Metabolomics.

Preterm birth (PTB) is the leading cause of infant deaths globally. Current clinical measures often fail to identify women who may deliver preterm. Therefore, accurate screening tools are imperative for early prediction of PTB. Here, we show that Raman spectroscopy is a promising tool for studying biological interfaces, and we examine differences in the maternal metabolome of the first trimester plasma of PTB patients and those that delivered at term (healthy). We identified fifteen statistically significant metabolites that are predictive of the onset of PTB. Mass spectrometry metabolomics validates the Raman findings identifying key metabolic pathways that are enriched in PTB. We also show that patient clinical information alone and protein quantification of standard inflammatory cytokines both fail to identify PTB patients. We show for the first time that synergistic integration of Raman and clinical data guided with machine learning results in an unprecedented 85.1% accuracy of risk stratification of PTB in the first trimester that is currently not possible clinically. Correlations between metabolites and clinical features highlight the body mass index and maternal age as contributors of metabolic rewiring. Our findings show that Raman spectral screening may complement current prenatal care for early prediction of PTB, and our approach can be translated to other patient-specific biological interfaces.

Air-stable magnesium nanocomposites provide rapid and high-capacity hydrogen storage without using heavy-metal catalysts.

Hydrogen is a promising alternative energy carrier that can potentially facilitate the transition from fossil fuels to sources of clean energy because of its prominent advantages such as high energy density (142 MJ kg(-1); ref. 1), great variety of potential sources (for example water, biomass, organic matter), light weight, and low environmental impact (water is the sole combustion product). However, there remains a challenge to produce a material capable of simultaneously optimizing two conflicting criteria--absorbing hydrogen strongly enough to form a stable thermodynamic state, but weakly enough to release it on-demand with a small temperature rise. Many materials under development, including metal-organic frameworks, nanoporous polymers, and other carbon-based materials, physisorb only a small amount of hydrogen (typically 1-2 wt%) at room temperature. Metal hydrides were traditionally thought to be unsuitable materials because of their high bond formation enthalpies (for example MgH(2) has a ΔHf~75 kJ mol(-1)), thus requiring unacceptably high release temperatures resulting in low energy efficiency. However, recent theoretical calculations and metal-catalysed thin-film studies have shown that microstructuring of these materials can enhance the kinetics by decreasing diffusion path lengths for hydrogen and decreasing the required thickness of the poorly permeable hydride layer that forms during absorption. Here, we report the synthesis of an air-stable composite material that consists of metallic Mg nanocrystals (NCs) in a gas-barrier polymer matrix that enables both the storage of a high density of hydrogen (up to 6 wt% of Mg, 4 wt% for the composite) and rapid kinetics (loading in <30 min at 200 °C). Moreover, nanostructuring of the Mg provides rapid storage kinetics without using expensive heavy-metal catalysts.

Theranostic nanoshells: from probe design to imaging and treatment of cancer.

Recent advances in nanoscience and biomedicine have expanded our ability to design and construct multifunctional nanoparticles that combine targeting, therapeutic, and diagnostic functions within a single nanoscale complex. The theranostic capabilities of gold nanoshells, spherical nanoparticles with silica cores and gold shells, have attracted tremendous attention over the past decade as nanoshells have emerged as a promising tool for cancer therapy and bioimaging enhancement. This Account examines the design and synthesis of nanoshell-based theranostic agents, their plasmon-derived optical properties, and their corresponding applications. We discuss the design and preparation of nanoshell complexes and their ability to enhance the photoluminescence of fluorophores while maintaining their properties as MR contrast agents. In this Account, we discuss the underlying physical principles that contribute to the photothermal response of nanoshells. We then elucidate the photophysical processes that induce nanoshells to enhance the fluorescence of weak near-infrared fluorophores. Nanoshells illuminated with resonant light are either strong optical absorbers or scatterers, properties that give rise to their unique capabilities. These physical processes have been harnessed to visualize and eliminate cancer cells. We describe the application of nanoshells as a contrast agent for optical coherence tomography of breast carcinoma cells in vivo. Our recent studies examine nanoshells as a multimodal theranostic probe, using these nanoparticles for near-infrared fluorescence and magnetic resonance imaging (MRI) and for the photothermal ablation of cancer cells. Multimodal nanoshells show theranostic potential for imaging subcutaneous breast cancer tumors in animal models and the distribution of tumors in various tissues. Nanoshells also show promise as light-triggered gene therapy vectors, adding temporal control to the spatial control characteristic of nanoparticle-based gene therapy approaches. We describe the fabrication of DNA-conjugated nanoshell complexes and compare the efficiency of light-induced and thermally-induced release of DNA. Double-stranded DNA nanoshells also provide a way to deliver small molecules into cells: we describe the delivery and light-triggered release of DAPI (4',6-diamidino-2-phenylindole), a dye molecule used to stain DNA in the nuclei of cells.

Optically- and thermally-responsive programmable materials based on carbon nanotube-hydrogel polymer composites.

A simple approach is described to fabricate reversible, thermally- and optically responsive actuators utilizing composites of poly(N-isopropylacrylamide) (pNIPAM) loaded with single-walled carbon nanotubes. With nanotube loading at concentrations of 0.75 mg/mL, we demonstrate up to 5 times enhancement to the thermal response time of the nanotube-pNIPAM hydrogel actuators caused by the enhanced mass transport of water molecules. Additionally, we demonstrate the ability to obtain ultrafast near-infrared optical response in nanotube-pNIPAM hydrogels under laser excitation enabled by the strong absorption properties of nanotubes. The work opens the framework to design complex and programmable self-folding materials, such as cubes and flowers, with advanced built-in features, including tunable response time as determined by the nanotube loading.

Nanomaterials for Natural Killer Cell-Based Immunoimaging and Immunotherapies in Cancer.

Natural killer (NK) cells are an important component of the tumor immunosurveillance; activated NK cells can recognize and directly lyse tumor cells eliciting a potent antitumor immune response. Due to their intrinsic ability to unleash cytotoxicity against tumor cells, NK cell-based adoptive cell therapies have gained rapid clinical significance, and many clinical trials are ongoing. However, priming and activating NK cells, infiltration of activated NK cells in the immunosuppressive tumor microenvironment, and tracking the infiltrated NK cells in the tumors remain a critical challenge. To address these challenges, NK cells have been successfully interfaced with nanomaterials where the morphology, composition, and surface characteristics of nanoparticles (NPs) were leveraged to enable longitudinal tracking of NK cells in tumors or deliver therapeutics to prime NK cells. Distinct from other published reviews, in this tutorial review, we summarize the recent findings in the past decade where NPs were used to label NK cells for immunoimaging or deliver treatment to activate NK cells and induce long-term immunity against tumors. We discuss the NP properties that are key to surmounting the current challenges in NK cells and the different strategies employed to advance NK cells-based diagnostics and therapeutics. We conclude the review with an outlook on future directions in NP-NK cell hybrid interfaces, and overall clinical impact and patient response to such interfaces that need to be addressed to enable their clinical translation.

Light and immunostimulant mediated in situ re-education of tumor-associated macrophages using photosensitizer conjugated mannan nanoparticles for boosting immuno-photodynamic anti-metastasis therapy.

In an immunosuppressive tumor microenvironment, tumor-associated macrophages (TAMs) are the most abundant cells displaying pro-tumorigenic M2-like phenotypes, encouraging tumor growth and influencing the development of resistance against conventional therapies. TAMs are highly malleable. They can be repolarized into tumoricidal M1-like cells. In this study, we report the synthesis of novel co-operative immuno-photodynamic nanoparticles involving TAM self-targeting acrylic acid grafted mannan (a polysaccharide) conjugated with the chlorin e6 (Ce6) photosensitizer and then loaded with resiquimod (R848), a toll-like receptor (TLR7/8) agonist. The mannan conjugated Ce6 loaded with R848 (MCR) as bioconjugate nanoparticles demonstrated selective targeting of anti-inflammatory M2-like cells. Using photodynamic therapy they were repolarized to pro-inflammatory M1-like cells with combined effects of reactive oxygen species (ROS)-triggered intracellular signaling and a small-molecule immunostimulant. The MCR also demonstrated a TAM-directed adaptive immune response, inhibited tumor growth, and prevented metastasis. Our results indicate that these MCR nanoparticles can effectively target TAMs and modulate them for cancer immunotherapy.

Optically-driven collapse of a plasmonic nanogap self-monitored by optical frequency mixing.

A nanoparticle separated from a metallic surface by a few-nanometer thick polymer layer forms a nanoscale junction, or nanogap. Illuminating this structure with ultrashort optical pulses, exciting the plasmon resonance, results in a continuous, monitorable collapse of the nanogap. The four-wave mixing signal generated by this illumination of the nanogap provides a simultaneous monitoring of the collapse, increasing dramatically upon gap closure. Collapse is irreversible, occurring with simultaneous ablation of the dielectric from the junction.

Fanoshells: nanoparticles with built-in Fano resonances.

A nanoparticle consisting of a dielectric (SiO(2)) and metallic (Au) shell layer surrounding a solid Au nanoparticle core can be designed with its superradiant and subradiant plasmon modes overlapping in energy, resulting in a Fano resonance in its optical response. Synthesis of this nanoparticle around an asymmetric core yields a structure that possesses additional Fano resonances as revealed by single particle dark field microspectroscopy. A mass-and-spring coupled oscillator model provides an excellent description of the plasmon interactions and resultant optical response of this nanoparticle.

Tracking of multimodal therapeutic nanocomplexes targeting breast cancer in vivo.

Nanoparticle-based therapeutics with local delivery and external electromagnetic field modulation holds extraordinary promise for soft-tissue cancers such as breast cancer; however, knowledge of the distribution and fate of nanoparticles in vivo is crucial for clinical translation. Here we demonstrate that multiple diagnostic capabilities can be introduced in photothermal therapeutic nanocomplexes by simultaneously enhancing both near-infrared fluorescence and magnetic resonance imaging (MRI). We track nanocomplexes in vivo, examining the influence of HER2 antibody targeting on nanocomplex distribution over 72 h. This approach provides valuable, detailed information regarding the distribution and fate of complex nanoparticles designed for specific diagnostic and therapeutic functions.

Fano-like interference in self-assembled plasmonic quadrumer clusters.

Assemblies of strongly interacting metallic nanoparticles are the basis for plasmonic nanostructure engineering. We demonstrate that clusters of four identical spherical particles self-assembled into a close-packed asymmetric quadrumer support strong Fano-like interference. This feature is highly sensitive to the polarization of the incident electric field due to orientation-dependent coupling between particles in the cluster. This structure demonstrates how careful design of self-assembled colloidal systems can lead to the creation of new plasmonic modes and the enabling of interference effects in plasmonic systems.

Cancer Immunoimaging with Smart Nanoparticles.

Dynamic immunoimaging in vivo is crucial in patient-tailored immunotherapies to identify patients who will benefit from immunotherapies, monitor therapeutic efficacy post treatment, and determine alternative strategies for nonresponders. Nanoparticles have played a major role in the immunotherapy landscape. In this review, we summarize recent findings in immunoimaging where smart nanoparticles target, detect, stimulate, and deliver therapeutic dose in vivo. Nanoparticles interfaced with an immunoimaging toolbox enable the use of multiple modalities and achieve depth-resolved whole-body tracking of immunomarkers with high accuracy both before and after treatment. We highlight how functional nanoparticles track T cells, dendritic cells (DCs), tumor-associated macrophages (TAMs), and immune checkpoint receptors (ICRs), and facilitate image-guided interventions.