Plasma infrared fingerprinting with machine learning enables single-measurement multi-phenotype health screening.

Infrared spectroscopy is a powerful technique for probing the molecular profiles of complex biofluids, offering a promising avenue for high-throughput in vitro diagnostics. While several studies showcased its potential in detecting health conditions, a large-scale analysis of a naturally heterogeneous potential patient population has not been attempted. Using a population-based cohort, here we analyze 5,184 blood plasma samples from 3,169 individuals using Fourier transform infrared (FTIR) spectroscopy. Applying a multi-task classification to distinguish between dyslipidemia, hypertension, prediabetes, type 2 diabetes, and healthy states, we find that the approach can accurately single out healthy individuals and characterize chronic multimorbid states. We further identify the capacity to forecast the development of metabolic syndrome years in advance of onset. Dataset-independent testing confirms the robustness of infrared signatures against variations in sample handling, storage time, and measurement regimes. This study provides the framework that establishes infrared molecular fingerprinting as an efficient modality for populational health diagnostics.

Limits and Prospects of Molecular Fingerprinting for Phenotyping Biological Systems Revealed through In Silico Modeling.

Molecular fingerprinting via vibrational spectroscopy characterizes the chemical composition of molecularly complex media which enables the classification of phenotypes associated with biological systems. However, the interplay between factors such as biological variability, measurement noise, chemical complexity, and cohort size makes it challenging to investigate their impact on how the classification performs. Considering these factors, we developed an in silico model which generates realistic, but configurable, molecular fingerprints. Using experimental blood-based infrared spectra from two cancer-detection applications, we validated the model and subsequently adjusted model parameters to simulate diverse experimental settings, thereby yielding insights into the framework of molecular fingerprinting. Intriguingly, the model revealed substantial improvements in classifying clinically relevant phenotypes when the biological variability was reduced from a between-person to a within-person level and when the chemical complexity of the spectra was reduced. These findings quantitively demonstrate the potential benefits of personalized molecular fingerprinting and biochemical fractionation for applications in health diagnostics.

Breast-cancer detection using blood-based infrared molecular fingerprints.

BACKGROUND: Breast cancer screening is currently predominantly based on mammography, tainted with the occurrence of both false positivity and false negativity, urging for innovative strategies, as effective detection of early-stage breast cancer bears the potential to reduce mortality. Here we report the results of a prospective pilot study on breast cancer detection using blood plasma analyzed by Fourier-transform infrared (FTIR) spectroscopy - a rapid, cost-effective technique with minimal sample volume requirements and potential to aid biomedical diagnostics. FTIR has the capacity to probe health phenotypes via the investigation of the full repertoire of molecular species within a sample at once, within a single measurement in a high-throughput manner. In this study, we take advantage of cross-molecular fingerprinting to probe for breast cancer detection. METHODS: We compare two groups: 26 patients diagnosed with breast cancer to a same-sized group of age-matched healthy, asymptomatic female participants. Training with support-vector machines (SVM), we derive classification models that we test in a repeated 10-fold cross-validation over 10 times. In addition, we investigate spectral information responsible for BC identification using statistical significance testing. RESULTS: Our models to detect breast cancer achieve an average overall performance of 0.79 in terms of area under the curve (AUC) of the receiver operating characteristic (ROC). In addition, we uncover a relationship between the effect size of the measured infrared fingerprints and the tumor progression. CONCLUSION: This pilot study provides the foundation for further extending and evaluating blood-based infrared probing approach as a possible cross-molecular fingerprinting modality to tackle breast cancer detection and thus possibly contribute to the future of cancer screening.

Infrared molecular fingerprinting of blood-based liquid biopsies for the detection of cancer.

Recent omics analyses of human biofluids provide opportunities to probe selected species of biomolecules for disease diagnostics. Fourier-transform infrared (FTIR) spectroscopy investigates the full repertoire of molecular species within a sample at once. Here, we present a multi-institutional study in which we analysed infrared fingerprints of plasma and serum samples from 1639 individuals with different solid tumours and carefully matched symptomatic and non-symptomatic reference individuals. Focusing on breast, bladder, prostate, and lung cancer, we find that infrared molecular fingerprinting is capable of detecting cancer: training a support vector machine algorithm allowed us to obtain binary classification performance in the range of 0.78-0.89 (area under the receiver operating characteristic curve [AUC]), with a clear correlation between AUC and tumour load. Intriguingly, we find that the spectral signatures differ between different cancer types. This study lays the foundation for high-throughput onco-IR-phenotyping of four common cancers, providing a cost-effective, complementary analytical tool for disease recognition.

Ultra-rapid electro-optic sampling of octave-spanning mid-infrared waveforms.

We demonstrate ultra-rapid electro-optic sampling (EOS) of octave-spanning mid-infrared pulses centered at 9 µm, implemented by mechanically scanning a mirror with a sonotrode resonating at 19 kHz (forward and backward acquisition at 38 kHz). The instrument records the infrared waveform with a spectral intensity dynamic range of 1.6 × 105 for a single scan over a 1.6-ps delay range, acquired within 26 µs. The purely reflective nature of the delay scanning technique is compatible with broad optical bandwidths, short pulse durations (16 fs, centered at 1030 nm) and high average powers (Watt-level). Interferometric tracking of the sonotrode motion in combination with a predictor-corrector algorithm allows for delay-axis determination with down to single-digit attosecond precision. Ultra-rapid mid-infrared EOS will advance applications such as molecular fingerprinting of static samples as well as tracking of biological processes and chemical reactions and is likely to find new fields of application such as infrared-spectroscopic flow cytometry.

Molecular Origin of Blood-Based Infrared Spectroscopic Fingerprints*.

Infrared spectroscopy of liquid biopsies is a time- and cost-effective approach that may advance biomedical diagnostics. However, the molecular nature of disease-related changes of infrared molecular fingerprints (IMFs) remains poorly understood, impeding the method's applicability. Here we probe 148 human blood sera and reveal the origin of the variations in their IMFs. To that end, we supplemented infrared spectroscopy with biochemical fractionation and proteomic profiling, providing molecular information about serum composition. Using lung cancer as an example of a medical condition, we demonstrate that the disease-related differences in IMFs are dominated by contributions from twelve highly abundant proteins-that, if used as a pattern, may be instrumental for detecting malignancy. Tying proteomic to spectral information and machine learning advances our understanding of the infrared spectra of liquid biopsies, a framework that could be applied to probing of any disease.

Stability of person-specific blood-based infrared molecular fingerprints opens up prospects for health monitoring.

Health state transitions are reflected in characteristic changes in the molecular composition of biofluids. Detecting these changes in parallel, across a broad spectrum of molecular species, could contribute to the detection of abnormal physiologies. Fingerprinting of biofluids by infrared vibrational spectroscopy offers that capacity. Whether its potential for health monitoring can indeed be exploited critically depends on how stable infrared molecular fingerprints (IMFs) of individuals prove to be over time. Here we report a proof-of-concept study that addresses this question. Using Fourier-transform infrared spectroscopy, we have fingerprinted blood serum and plasma samples from 31 healthy, non-symptomatic individuals, who were sampled up to 13 times over a period of 7 weeks and again after 6 months. The measurements were performed directly on liquid serum and plasma samples, yielding a time- and cost-effective workflow and a high degree of reproducibility. The resulting IMFs were found to be highly stable over clinically relevant time scales. Single measurements yielded a multiplicity of person-specific spectral markers, allowing individual molecular phenotypes to be detected and followed over time. This previously unknown temporal stability of individual biochemical fingerprints forms the basis for future applications of blood-based infrared spectral fingerprinting as a multiomics-based mode of health monitoring.

Optimum Sample Thickness for Trace Analyte Detection with Field-Resolved Infrared Spectroscopy.

The strong absorption of liquid water in the infrared (IR) molecular fingerprint region constitutes a challenge for applications of vibrational spectroscopy in chemistry, biology, and medicine. While high-power IR laser sources enable the penetration of ever thicker aqueous samples, thereby mitigating the detrimental effects of strong attenuation on detection sensitivity, a basic advantage of heterodyne-measurement-based methods has-to the best of our knowledge-not been harnessed in broadband IR measurements to date. Here, employing field-resolved spectroscopy (FRS), we demonstrate in theory and experiment fundamental advantages of techniques whose signal-to-noise ratio (SNR) scales linearly with the electric field over those whose SNR scales linearly with radiation intensity, including conventional Fourier-transform infrared (FTIR) and direct absorption spectroscopy. Field-scaling brings about two major improvements. First, it squares the measurement dynamic range. Second, we show that the optimum interaction length with samples for SNR-maximized measurements is twice the value usually considered to be optimum for FTIR devices. In order to take full advantage of these properties, the measurement must not be significantly affected by technical noise, such as intensity fluctuations, which are common for high-power sources. Recently, it has been shown that subcycle, nonlinear gating of the molecular fingerprint signal renders FRS robust against intensity noise. Here, we quantitatively demonstrate this advantage of FRS for thick aqueous samples. We report sub-µg/mL detection sensitivities for transmission path lengths up to 80 µm and a limit of detection in the lower µg/mL range for transmission paths as long as 200 µm.

Field-resolved infrared spectroscopy of biological systems.

The proper functioning of living systems and physiological phenotypes depends on molecular composition. Yet simultaneous quantitative detection of a wide variety of molecules remains a challenge1-8. Here we show how broadband optical coherence opens up opportunities for fingerprinting complex molecular ensembles in their natural environment. Vibrationally excited molecules emit a coherent electric field following few-cycle infrared laser excitation9-12, and this field is specific to the sample's molecular composition. Employing electro-optic sampling10,12-15, we directly measure this global molecular fingerprint down to field strengths 107 times weaker than that of the excitation. This enables transillumination of intact living systems with thicknesses of the order of 0.1 millimetres, permitting broadband infrared spectroscopic probing of human cells and plant leaves. In a proof-of-concept analysis of human blood serum, temporal isolation of the infrared electric-field fingerprint from its excitation along with its sampling with attosecond timing precision results in detection sensitivity of submicrograms per millilitre of blood serum and a detectable dynamic range of molecular concentration exceeding 105. This technique promises improved molecular sensitivity and molecular coverage for probing complex, real-world biological and medical settings.

Broadband dispersive Ge/YbF3 mirrors for mid-infrared spectral range.

Broadband dispersive mirrors operating in the mid-infrared spectral range of 6.5-11.5 µm are developed for the first time, to the best of our knowledge. The mirrors comprise Ge and YbF3 layers, which have not been used before for manufacturing of multilayer dispersive optics. The design and production processes are described; mechanical stresses of the coatings are estimated based on experimental data; and spectral and phase properties of the produced mirrors are measured. The mirrors compensate group delay dispersion of ultrashort laser pulses accumulated by propagation through 4 mm ZnSe windows and additional residual phase modulation of an ultrashort laser pulse.

A comparison of inverted and upright laser-activated titanium nitride micropyramids for intracellular delivery.

The delivery of biomolecules into cells relies on porating the plasma membrane to allow exterior molecules to enter the cell via diffusion. Various established delivery methods, including electroporation and viral techniques, come with drawbacks such as low viability or immunotoxicity, respectively. An optics-based delivery method that uses laser pulses to excite plasmonic titanium nitride (TiN) micropyramids presents an opportunity to overcome these shortcomings. This laser excitation generates localized nano-scale heating effects and bubbles, which produce transient pores in the cell membrane for payload entry. TiN is a promising plasmonic material due to its high hardness and thermal stability. In this study, two designs of TiN micropyramid arrays are constructed and tested. These designs include inverted and upright pyramid structures, each coated with a 50-nm layer of TiN. Simulation software shows that the inverted and upright designs reach temperatures of 875 °C and 307 °C, respectively, upon laser irradiation. Collectively, experimental results show that these reusable designs achieve maximum cell poration efficiency greater than 80% and viability greater than 90% when delivering calcein dye to target cells. Overall, we demonstrate that TiN microstructures are strong candidates for future use in biomedical devices for intracellular delivery and regenerative medicine.

Laser-Activated Self-Assembled Thermoplasmonic Nanocavity Substrates for Intracellular Delivery.

Intracellular delivery is crucial for cellular engineering and the development of therapeutics. Laser-activated thermoplasmonic nanostructured surfaces are a promising platform for high-efficiency, high-viability, high-throughput intracellular delivery. Their fabrication, however, typically involves complicated nanofabrication techniques, limiting the approach's applicability. Here, colloidal self-assembly and templating are used to fabricate large arrays of thermoplasmonic nanocavities simply and cost-effectively. These laser-activated substrates are used to deliver membrane-impermeable dye into cells at an efficiency of 78% and throughput of 30 000 cells min-1 while maintaining 87% cell viability. Proof-of-concept data show delivery of large cargoes ranging from 0.6 to 2000 kDa to cells without compromising viability.

Analysis of poration-induced changes in cells from laser-activated plasmonic substrates.

Laser-exposed plasmonic substrates permeabilize the plasma membrane of cells when in close contact to deliver cell-impermeable cargo. While studies have determined the cargo delivery efficiency and viability of laser-exposed plasmonic substrates, morphological changes in a cell have not been quantified. We porated myoblast C2C12 cells on a plasmonic pyramid array using a 532-nm laser with 850-ps pulse length and time-lapse fluorescence imaging to quantify cellular changes. We obtain a poration efficiency of 80%, viability of 90%, and a pore radius of 20 nm. We quantified area changes in the plasma membrane attached to the substrate (10% decrease), nucleus (5 - 10% decrease), and cytoplasm (5 - 10% decrease) over 1 h after laser treatment. Cytoskeleton fibers show a change of 50% in the alignment, or coherency, of fibers, which stabilizes after 10 mins. We investigate structural and morphological changes due to the poration process to enable the safe development of this technique for therapeutic applications.

Active intensity noise suppression for a broadband mid-infrared laser source.

Excess relative intensity noise (RIN) constitutes one of the major limitations of most spectroscopic methods involving lasers. Here, we present an active RIN suppression scheme for a coherent mid-infrared (MIR) light source (8.4-11 µm), based on intra-pulse difference frequency generation (DFG). Three different stabilization concepts that rely on modulating the intensity of the driving near-infrared (NIR) pulse train with an acousto-optic modulator are investigated and compared. By using the wings of the NIR spectrum to generate the error signal, a RIN suppression of the MIR pulse train of up to a factor of 20 was achieved in the band between 1 Hz and 100 kHz, resulting in a total integrated RIN of 0.07%.

Intracellular Delivery Using Nanosecond-Laser Excitation of Large-Area Plasmonic Substrates.

Efficiently delivering functional cargo to millions of cells on the time scale of minutes will revolutionize gene therapy, drug discovery, and high-throughput screening. Recent studies of intracellular delivery with thermoplasmonic structured surfaces show promising results but in most cases require time- or cost-intensive fabrication or lead to unreproducible surfaces. We designed and fabricated large-area (14 × 14 mm), photolithography-based, template-stripped plasmonic substrates that are nanosecond laser-activated to form transient pores in cells for cargo entry. We optimized fabrication to produce plasmonic structures that are ultrasmooth and precisely patterned over large areas. We used flow cytometry to characterize the delivery efficiency of cargos ranging in size from 0.6 to 2000 kDa to cells (up to 95% for the smallest molecule) and viability of cells (up to 98%). This technique offers a throughput of 50000 cells/min, which can be scaled up as necessary. This technique is also cost-effective as each large-area photolithography substrate can be used to deliver cargo to millions of cells, and switching to a nanosecond laser makes the setup cheaper and easier to use. The approach we present offers additional desirable features: spatial selectivity, reproducibility, minimal residual fragments, and cost-effective fabrication. This research supports the development of safer genetic and viral disease therapies as well as research tools for fundamental biological research that rely on effectively delivering molecules to millions of living cells.

DNA-Based Self-Assembly of Fluorescent Nanodiamonds.

As a step toward deterministic and scalable assembly of ordered spin arrays we here demonstrate a bottom-up approach to position fluorescent nanodiamonds (NDs) with nanometer precision on DNA origami structures. We have realized a reliable and broadly applicable surface modification strategy that results in DNA-functionalized and perfectly dispersed NDs that were then self-assembled in predefined geometries. With optical studies we show that the fluorescence properties of the nitrogen-vacancy color centers in NDs are preserved during surface modification and DNA assembly. As this method allows the nanoscale arrangement of fluorescent NDs together with other optically active components in complex geometries, applications based on self-assembled spin lattices or plasmon-enhanced spin sensors as well as improved fluorescent labeling for bioimaging could be envisioned.

Plasmonic Tipless Pyramid Arrays for Cell Poration.

Improving the efficiency, cell survival, and throughput of methods to modify and control the genetic expression of cells is of great benefit to biology and medicine. We investigate, both computationally and experimentally, a nanostructured substrate made of tipless pyramids for plasmonic-induced transfection. By optimizing the geometrical parameters for an excitation wavelength of 800 nm, we demonstrate a 100-fold intensity enhancement of the electric near field at the cell-substrate contact area, while the low absorption typical for gold is maintained. We demonstrate that such a substrate can induce transient poration of cells by a purely optically induced process.