Metabolic Labeling of Peptidoglycan with NIR‐II Dye Enables In Vivo Imaging of Gut Microbiota

Deepening our understanding of mammalian gut microbiota has been greatly hampered by the lack of a facile, real‐time, and in vivo bacterial imaging method. To address this unmet need in microbial visualization, we herein report the development of a second near‐infrared (NIR‐II)‐based method for in vivo imaging of gut bacteria. Using d ‐propargylglycine in gavage and then click reaction with an azide‐containing NIR‐II dye, gut microbiota of a donor mouse was strongly labeled with NIR‐II fluorescence on their peptidoglycan. The bacteria could be readily visualized in recipient mouse gut with high spatial resolution and deep tissue penetration under NIR irradiation. The NIR‐II‐based metabolic labeling strategy reported herein, provides, to the best of our knowledge, the first protocol for facile in vivo visualization of gut microbiota within deep tissues, and offers an instrumental tool for deciphering the complex biology of these gut “dark matters”.     

An Activatable NIR-II Fluorescent Reporter for In Vivo Imaging of Amyloid-β Plaques

Fluorescence imaging in the second near-infrared (NIR-II) window holds great promise for in vivo visualization of amyloid-β (Aβ) pathology, which can facilitate characterization and deep understanding of Alzheimer's disease (AD); however, it has been rarely exploited. Herein, we report the development of NIR-II fluorescent reporters with a donor-π-acceptor (D-π-A) architecture for specific detection of Aβ plaques in AD-model mice. Among all the designed probes, DMP2 exhibits the highest affinity to Aβ fibrils and can specifically activate its NIR-II fluorescence after binding to Aβ fibrils via suppressed twisted intramolecular charge transfer (TICT) effect. With suitable lipophilicity for ideal blood–brain barrier (BBB) penetrability and deep-tissue penetration of NIR-II fluorescence, DMP2 possesses specific detection of Aβ plaques in in vivo AD-model mice. Thus, this study presents a potential agent for non-invasive imaging of Aβ plaques and deep deciphering of AD progression.     

Quantification of Bacterial Metabolic Activities in the Gut by d-Amino Acid-Based In Vivo Labeling

Herein, we propose a metabolic d -amino acid-based labeling and in situ hybridization-facilitated (MeDabLISH) strategy for the quantitative analysis of the indigenous metabolic status of gut bacteria. The fluorescent d -amino acid (FDAA)-based labeling intensities of bacteria were found to highly correlate with their temporal and steady-state metabolic status. Then, after taxonomic identification of bacterial genera in the in vivo FDAA-labeled mouse gut microbiota, by corresponding fluorescence in situ hybridization (FISH) probes, the metabolic activities of different gut bacterial genera are quantified by flow cytometry, using FISH signals to differentiate genera and FDAA signals to indicate their basal metabolic levels. It was found that Gram-negative genera in the mouse microbiota have stronger metabolic activities during the daytime, and Gram-positive genera have higher activities at the night. Our strategy will be instrumental in deepening our understanding of the highly complex microbiota.     

Quantification of Bacterial Metabolic Activities in the Gut by d‐Amino Acid‐Based In Vivo Labeling

Herein, we propose a metabolic d ‐amino acid‐based labeling and in situ hybridization‐facilitated (MeDabLISH) strategy for the quantitative analysis of the indigenous metabolic status of gut bacteria. The fluorescent d ‐amino acid (FDAA)‐based labeling intensities of bacteria were found to highly correlate with their temporal and steady‐state metabolic status. Then, after taxonomic identification of bacterial genera in the in vivo FDAA‐labeled mouse gut microbiota, by corresponding fluorescence in situ hybridization (FISH) probes, the metabolic activities of different gut bacterial genera are quantified by flow cytometry, using FISH signals to differentiate genera and FDAA signals to indicate their basal metabolic levels. It was found that Gram‐negative genera in the mouse microbiota have stronger metabolic activities during the daytime, and Gram‐positive genera have higher activities at the night. Our strategy will be instrumental in deepening our understanding of the highly complex microbiota.     

A Class of Activatable NIR-II Photoacoustic Dyes for High-Contrast Bioimaging

Photoacoustic (PA) imaging is emerging as one of the important non-invasive imaging techniques in biomedical research. Small molecule- second near-infrared window (NIR-II) PA dyes combined with imaging data can provide comprehensive and in-depth in vivo physiological and pathological information. However, the NIR-II PA dyes usually exhibit “always-on” properties due to the lack of a readily optically tunable group, which hinders the further applications in vivo. Herein, a novel class of dyes GX have been designed and synthesized as an activatable NIR-II PA platform, in which the absorption/emission wavelength of GX-5 extends up to 1082/1360 nm. Importantly, the GX dyes have a strong tissue penetration depth and high-resolution for the mouse vasculature structures in NIR-II PA 3D imaging and high signal-to-noise ratio in NIR-II fluorescence (FL) imaging. Furthermore, to demonstrate the applicability of GX dyes, the first NIR-II PA probe GX-5-CO activated by carbon monoxide (CO) was engineered and employed to reveal the enhancement of the CO levels in the hypertensive mice by high-contrast NIR-II PA and FL imaging. We expect that many derivatives of GX dyes will be developed to afford versatile NIR-II PA platforms for designing a wide variety activatable NIR-II PA probes as biomedical tools.     

Antibiotics-based fluorescent probes for selective labeling of Gram-negative and Gram-positive bacteria in living microbiotas

Gram-staining distinguishes bacteria into two major groups,Gram-positive and Gram-negative bacteria,and has become an essential technique in microbiology.However,Gram-staining is not compatible with living cells and thus limits its applications.Here,we report the development of a polymyxin B-based fluorescent probe that enables selective labeling of Gram-negative in the living microbiota samples.We first synthesized the polymyxin B-Cy3 conjugate and confirmed its specificity for labeling Gram-negative bacteria.In combination with a previously developed Gram-positive-specific fluorescent probe,we demonstrate two-color imaging of Gram-positive and Gram-negative bacteria in various kinds living microbiotas,including mouse gut,human oral,soil,and crude oil microbiotas,with high selectivity and coverage.Finally,a pilot use of the probes in staining bacteria on heat-fixed sputum smear was also demonstrated,showing its potentials in clinical microbiology.Our method provides a versatile tool for distinguishing Gram-positive and Gram-negative bacteria in both basic research and clinical settings.     

Doubly Strapped Zwitterionic NIR-I and NIR-II Heptamethine Cyanine Dyes for Bioconjugation and Fluorescence Imaging

Heptamethine cyanine dyes enable deep tissue fluorescence imaging in the near infrared (NIR) window. Small molecule conjugates of the benchmark dye ZW800-1 have been tested in humans. However, long-term imaging protocols using ZW800-1 conjugates are limited by their instability, primarily because the chemically labile C4′-O-aryl linker is susceptible to cleavage by biological nucleophiles. Here, we report a modular synthetic method that produces novel doubly strapped zwitterionic heptamethine cyanine dyes, including a structural analogue of ZW800-1 , with greatly enhanced dye stability. NIR-I and NIR-II versions of these doubly strapped dyes can be conjugated to proteins, including monoclonal antibodies, without causing undesired fluorophore degradation or dye stacking on the protein surface. The fluorescent antibody conjugates show excellent tumor-targeting specificity in a xenograft mouse tumor model. The enhanced stability provided by doubly strapped molecular design will enable new classes of in vivo NIR fluorescence imaging experiments with possible translation to humans.     

Theranostic Gold Nanoclusters for NIR-II Imaging and Photodynamic Therapy

Fluorescence imaging in the second near-infrared window(NIR-II, 1000-1700 nm) has demonstrated tremendous promise for biomedical applications, with its extraordinarily high resolution and deep tissue penetration. Ultrasmall gold nanoclusters(AuNCs) have shown unique features for NIR-II imaging, such as photostability and biocompatibility, as compared to organic NIR-II molecules or other inorganic NIR-II nanoparticles. Here, we report the first-in-class protein-capped ultrasmall AuNCs(BSA-AuNCs, BSA=bovine serum albumin) for simultaneous NIR-II imaging and photodynamic therapy. The BSA-AuNCs show a uniform size, high quantum yield and excellent photostability, display a high accumulation and long retention in 4T1 tumor, and are used for clear imaging of blood vessels and lymph nodes. Moreover, laser irradiation of these AuNCs can rapidly trigger ROS generation, leading to effective inhibition of tumor cell growth in vitro and in vivo. This study demonstrates the feasibility of a protein-capped ultrasmall AuNCs platform for theranostic applications by combining NIR-II imaging and photodynamic cancer therapy.     

NIR-II Chemiluminescence Molecular Sensor for In Vivo High-Contrast Inflammation Imaging

Chemiluminescence (CL) sensing without external excitation by light and autofluorescence interference has been applied to high-contrast in vitro immunoassays and in vivo inflammation and tumor microenvironment detection. However, conventional CL sensing usually operates in the range of 400–850 nm, which limits the performance of in vivo imaging due to serious light scattering effects and signal attenuation in tissue. To address this challenge, a new type of CL sensor is presented that functions in the second near-infrared window (NIR-II CLS) with a deep penetration depth (≈8 mm). Successive CL resonance energy transfer (CRET) and Förster resonance energy transfer (FRET) from the activated CL substrate to two rationally designed donor-acceptor-donor fluorophores BTD540 and BBTD700 occurs. NIR-II CLS can be selectively activated by hydrogen peroxide over other reactive oxygen species (ROSs). Moreover, NIR-II CLS is capable of detecting local inflammation in mice with a 4.5-fold higher signal-to-noise ratio (SNR) than that under the NIR-II fluorescence modality.     

A NIR Programmable In Vivo miRNA Magnifier for NIR-II Imaging of Early Stage Cancer

Aberrant expressions of biomolecules occur much earlier than tumor visualized size and morphology change, but their common measurement strategies such as biopsy suffer from invasive sampling process. In vivo imaging of slight biomolecule expression difference is urgently needed for early cancer detection. Fluorescence of rare earth nanoparticles (RENPs) in second near-infrared (NIR-II) region makes them appropriate tool for in vivo imaging. However, the incapacity to couple with signal amplification strategies, especially programmable signal amplification strategies, limited their application in lowly expressed biomarkers imaging. Here we develop a 980/808 nm NIR programmed in vivo microRNAs (miRNAs) magnifier by conjugating activatable DNAzyme walker set to RENPs, which achieves more effective NIR-II imaging of early stage tumor than size monitoring imaging technique. Dye FD1080 (FD1080) modified substrate DNA quenches NIR-II downconversion emission of RENPs under 808 nm excitation. The miRNA recognition region in DNAzyme walker is sealed by a photo-cleavable strand to avoid “false positive” signal in systemic circulation. Upconversion emission of RENPs under 980 nm irradiation activates DNAzyme walker for miRNA recognition and amplifies NIR-II fluorescence recovery of RENPs via DNAzyme catalytic reaction to achieve in vivo miRNA imaging. This strategy demonstrates good application potential in the field of early cancer detection.     

Noninvasive Early Diagnosis of Allograft Rejection by a Granzyme B Protease Responsive NIR-II Bioimaging Nanosensor

Early diagnosis of allograft rejection helps to improve the immune-related management of transplant recipients. The clinically-used core needle biopsy method is invasive and subject to sampling error. In vivo fluorescence imaging for monitoring immune-related processes has the advantages of non-invasiveness, fast feedback and high sensitivity. Herein, we report a responsive second near-infrared (NIR-II) fluorescent nanosensor (ErGZ) to detect early allograft rejection. ErGZ allows ratiometric in vivo fluorescence sensing of granzyme B, which is overexpressed in recipients’ T cells during the onset of rejection. The sensor demonstrates efficacious detection of allograft rejection with high sensitivity and specificity, which accomplishes non-invasive diagnosis of rejection in skin and deep buried islets transplant mice models 2 d and 5 d earlier than biopsy, by in vivo fluorescence imaging and urinary detection, respectively, providing a valuable approach for therapeutical management.     

NIR-II fluorescent nanophosphors for bio-imaging

The design of nanoprobes in the second window near-infrared region has grasped a substantial amount of attention due to the flexible emission in the second near-infrared region (NIR-II) region (1,000–1,700 nm). In addition, this region provides the advantage of reduced photon scattering with less autofluorescence for improvement during in vivo fluorescence imaging. NIR-II nanoprobes such as quantum dots, AIEgens, carbon nanotubes, and polymers are in a constant state of evolution for improved NIR-II emission. Among these probes, lanthanides are explored the most for NIR-II imaging applications. Moreover, nanophosphors, although in their nascent form, are interesting compounds due to their good luminescence properties with efficient energy transfer processes. Our review aims to give insight into nanophosphors, mainly for biological imaging applications. We will also provide a comparative study of lanthanides and nanophosphors for understanding the mechanism and importance of nanophosphors in the future bio-imaging field.     

Tuning molecular aggregation to achieve highly bright AIE dots for NIR-II fluorescence imaging and NIR-I photoacoustic imaging

Currently, bright aggregation-induced emission luminogens (AIEgens) with high photoluminescence quantum yields (PLQYs) in the NIR-II region are still limited, and thus an efficient strategy to enhance NIR-II fluorescence performance through tuning molecular aggregation is proposed here. The synthesized donor–acceptor tailored AIEgen (DTPA-TBZ) not only exhibits an excellent absorptivity in the NIR-I region, but also good fluorescence signals in the NIR-II region with an emission extending to 1200 nm. Benefiting from such improved intramolecular restriction and aggregation, a significant absolute PLQY value of 8.98% was obtained in solid DTPA-TBZ. Encouragingly, the resulting AIE dots also exhibit a high relative PLQY of up to 11.1% with IR 26 as the reference (PLQY = 0.5%). Finally, the AIE dots were applied in high performance NIR-II fluorescence imaging and NIR-I photoacoustic (PA) imaging: visualization of abdominal vessels, hind limb vasculature, and cerebral vessels with high signal to background ratios was performed via NIR-II imaging; Moreover, PA imaging has also been performed to clearly observe tumors in vivo. These results demonstrate that by finely tuning molecular aggregation in DTPA-TBZ, a good NIR-I absorptivity and a highly emissive fluorescence in the NIR-II region can be achieved simultaneously, finally resulting in a promising dual-modal imaging platform for real-world applications to achieve precise cancer diagnostics.

A highly efficient dual-modal imaging platform by using bright AIE dots was constructed to achieve precise cancer diagnostics.     

Ag+-Coupled Black Phosphorus Vesicles with Emerging NIR-II Photoacoustic Imaging Performance for Cancer Immune-Dynamic Therapy and Fast Wound Healing

A silver-ion-coupled black phosphorus (BP) vesicle (BP Ve-Ag⁺) with a second near infrared (NIR-II) window photoacoustic (PA) imaging capability was firstly constructed to maximize the potential of BP quantum dot (QD) in deeper bioimaging and diversified therapy. The embedded Ag⁺ could improve the relatively large band gap of BP QD via intense charge coupling based on theoretical simulation results, subsequently leading to the enhanced optical absorption capability, accompanied with the occurrence of the strong NIR-II PA signal. Guiding by NIR-II PA bioimaging, the hidden Ag⁺ could be precisely released with the disassembly of Ve during photodynamic therapy process and captured by macrophages located in lesion region for arousing synergistic cancer photodynamic/Ag⁺ immunotherapy. BP Ve-Ag⁺ can contrapuntally kill pathogenic bacteria and accelerate wound healing monitored by NIR-II PA imaging.     

Engineering the Protein Corona Structure on Gold Nanoclusters Enables Red-Shifted Emissions in the Second Near-infrared Window for Gastrointestinal Imaging

The application of NIR-II emitters for gastrointestinal (GI) tract imaging remains challenging due to fluorescence quenching in the digestive microenvironment. Herein, we report that red-shifting of the fluorescence emission of Au nanoclusters (AuNCs) into NIR-II region with improved quantum yields (QY) could be achieved by engineering a protein corona structure consisting of a ribonuclease-A (RNase-A) on the particle surfaces. RNase-A-encapsulated AuNCs (RNase-A@AuNCs) displayed emissions at 1050 nm with a 1.9 % QY. Compared to rare earth and silver-based NIR-II emitters, RNase-A@AuNCs had excellent biocompatibility, showing >50-fold higher sensitivity in GI tract, and migrated homogenously during gastrointestinal peristalsis to allow visualization of the detailed structures of the GI tract. RNase-A@AuNCs could successfully examine intestinal tumor mice from healthy mice, indicating a potential utility for early diagnosis of intestinal tumors.     

An Extended NIR-II Superior Imaging Window from 1500 to 1900 nm for High-Resolution In Vivo Multiplexed Imaging Based on Lanthanide Nanocrystals

High-resolution in vivo optical multiplexing in second near-infrared window (NIR-II, 1000–1700 nm) is vital to biomedical research. Presently, limited by bio-tissue scattering, only luminescent probes located at NIR-IIb (1500–1700 nm) window can provide high-resolution in vivo multiplexed imaging. However, the number of available luminescent probes in this narrow NIR-IIb region is limited, which hampers the available multiplexed channels of in vivo imaging. To overcome the above challenges, through theoretical simulation we expanded the conventional NIR-IIb window to NIR-II long-wavelength (NIR-II-L, 1500–1900 nm) window on the basis of photon-scattering and water-absorption. We developed a series of novel lanthanide luminescent nanoprobes with emission wavelengths from 1852 nm to 2842 nm. NIR-II-L nanoprobes enabled high-resolution in vivo dynamic multiplexed imaging on blood vessels and intestines, and provided multi-channels imaging on lymph tubes, tumors and intestines. The proposed NIR-II-L probes without mutual interference are powerful tools for high-contrast in vivo multiplexed detection, which holds promise for revealing physiological process in living body.     

Real-time identification of gut microbiota with aminopeptidase N using an activable NIR fluorescent probe

A NIR fluorescent probe (DDAA) derived from fluorophore DDAO with alanine as the recognition group was developed for sensing aminopeptidase N (APN) in gut microbiota. Using DDAA as the real-time guidance tool for the fluorescence imaging of intestinal microorganism, target bacteria and saccharomycete possessing active APN were identified successfully from human feces.     

Technetium-99m-based simple and convenient radiolabeling of Escherichia coli for in vivo tracking of microorganisms

Journal of Radioanalytical and Nuclear Chemistry - We herein report a convenient radiolabeling method capable of real-time in vivo imaging and biodistribution of bacteria in a living subject....     

Application of prodrugs to inflammatory diseases of the gut

Oral delivery is the most common and preferred route of drug administration although the digestive tract exhibits several obstacles to drug delivery including motility and intraluminal pH profiles. The gut milieu represents the largest mucosal surface exposed to microorganisms with 10(10-12) colony forming bacteria/g of colonic content. Approximately, one third of fecal dry matter is made of bacteria/ bacterial components. Indeed, the normal gut microbiota is responsible for healthy digestion of dietary fibers (polysaccharides) and fermentation of short chain fatty acids such as acetate and butyrate that provide carbon sources (fuel) for these bacteria. Inflammatory bowel disease (IBD) results in breakage of the mucosal barrier, an altered microbiota and dysregulated gut immunity. Prodrugs that are chemically constructed to target colonic release or are degraded specifically by colonic bacteria, can be useful in the treatment of IBD. This review describes the progress in digestive tract prodrug design and delivery in light of gut metabolic activities.     

Organic Spherical Nucleic Acids for the Transport of a NIR-II-Emitting Dye Across the Blood–Brain Barrier

DNA nanotechnology plays an increasingly important role in the biomedical field; however, its application in the design of organic nanomaterials is underexplored. Herein, we report the use of DNA nanotechnology to transport a NIR-II-emitting nanofluorophore across the blood–brain barrier (BBB), facilitating non-invasive imaging of brain tumors. Specifically, the DNA block copolymer, PS-b-DNA, is synthesized through a solid-phase click reaction. We demonstrate that its self-assembled structure shows exceptional cluster effects, among which BBB-crossing is the most notable. Therefore, PS-b-DNA is utilized as an amphiphilic matrix to fabricate a NIR-II nanofluorephore, which is applied in in vivo bioimaging. Accordingly, the NIR-II fluorescence signal of the DNA-based nanofluorophore localized at a glioblastoma is 3.8-fold higher than the NIR-II fluorescence signal of the PEG-based counterpart. The notably increased imaging resolution will significantly benefit the further diagnosis and therapy of brain tumors.