Bioorthogonal Conjugation Directed by a Sugar-Sorting Pathway for Continual Tracking of Stressed Organelles

Late-Stage Functionalization of Living Organisms: Rethinking Selectivity in Biology

With unlimited selectivity, full post-translational chemical control of biology would circumvent the dogma of genetic control. The resulting direct manipulation of organisms would enable atomic-level precision in "editing" of function. We argue that a key aspect that is still missing in our ability to do this (at least with a high degree of control) is the selectivity of a given chemical reaction in a living organism. In this Review, we systematize existing illustrative examples of chemical selectivity, as well as identify needed chemical selectivities set in a hierarchy of anatomical complexity: organismo- (selectivity for a given organism over another), tissuo- (selectivity for a given tissue type in a living organism), cellulo- (selectivity for a given cell type in an organism or tissue), and organelloselectivity (selectivity for a given organelle or discrete body within a cell). Finally, we analyze more traditional concepts such as regio-, chemo-, and stereoselective reactions where additionally appropriate. This survey of late-stage biomolecule methods emphasizes, where possible, functional consequences (i.e., biological function). In this way, we explore a concept of late-stage functionalization of living organisms (where "late" is taken to mean at a given state of an organism in time) in which programmed and selective chemical reactions take place in life. By building on precisely analyzed notions (e.g., mechanism and selectivity) we believe that the logic of chemical methodology might ultimately be applied to increasingly complex molecular constructs in biology. This could allow principles developed at the simple, small-molecule level to progress hierarchically even to manipulation of physiology.

Bioorthogonal Chemistry in Cellular Organelles

While bioorthogonal reactions are routinely employed in living cells and organisms, their application within individual organelles remains limited. In this review, we highlight diverse examples of bioorthogonal reactions used to investigate the roles of biomolecules and biological processes as well as advanced imaging techniques within cellular organelles. These innovations hold great promise for therapeutic interventions in personalized medicine and precision therapies. We also address existing challenges related to the selectivity and trafficking of subcellular dynamics. Organelle-targeted bioorthogonal reactions have the potential to significantly advance our understanding of cellular organization and function, provide new pathways for basic research and clinical applications, and shape the direction of cell biology and medical research.

Biocapture-Directed Chemical Labeling for Discerning Stressed States of Organelles

Lysosomal rupture engaged in diverse diseases remains poorly discerned from lysosomal membrane permeabilization (LMP). We herein reported biocapture-directed chemical labeling (BCCL) for the discern of lysosomal rupture by tracking the release of optically labeled cathepsins from damaged lysosomes into the cytosol. BCCL entails covalent anchoring of an azide-tagged suicide substrate (Epo-LeuTyr^Az) to the enzyme active site and bioorthogonal ligation of the introduced azide with ^DBCORC, a ratiometric sensor featuring an acidity-reporting red emissive X-rhodamine-lactam (ROX), blue emissive coumarin (CM) inert to pH, and DBCO reactive to azide. Aided with fluorescein isocyanate-labeled sialic acid (FITC-Sia), a probe remained in pH-elevated lysosomes but dissipated from LMP⁺ lysosomes, BCCL enables optical discern of four states of lysosomes: ruptured lysosomes (blue in cytosol), LMP⁺ lysosomes (blue in lysosomes), pH-elevated lysosomes (blue and green in lysosomes), and physiological lysosomes (blue, green and red in lysosomes). This approach could find applicability to study lysosome rupture over LMP in diseases and to evaluate lysosome rupture-inducing drugs.

In cellulo synthesis of dendrimeric sensors for fluorescence-on imaging of bacterial phagocytosis

Methods for optical tracking of pathogen-host interactions are of biomedical significance. We herein have reported a high molecular weight pH sensor (Den-pH) that is assembled in bacteria and then stably trapped in bacteria irrespective of bacterial membrane potentials. Endowed with acidity-triggered red fluorescence, Den-pH allows signal-on tracking of S. aureus in phagocytosis by macrophages. Intra-bacterial formation of multifunctional optical probes, which offers the advantage of overcoming the liability of conventional potential-sensitive dyes to dissipate from stressed bacteria, offers a new tool to study stressed pathogens.

An organelle-directed chemical ligation approach enables dual-color detection of mitophagy

Dysfunctional organelles and defective turnover of organelles are engaged in multiple human diseases, but are elusive to image with conventional organelle probes. To overcome this, we developed intra-mitochondrial CLICK to assess mitophagy (IMCLAM), using a pair of conventional ΔΨm probes, where each probe alone fails to track dysfunctional mitochondria. The in situ formed optical triad is stably trapped in mitochondria without resorting to ΔΨm. Utilizing an acidity-responsive ΔΨm probe, IMCLAM enabled fluorescence-on detection of mitophagy by sensing pH acidification upon delivery of mitochondria into lysosomes. Moreover, we applied IMCLAM to assay mitophagy induced by pharmacological compounds in living cells and wild-type zebrafish embryos. Thus, IMCLAM offers a simplified tool to study mitochondria and mitophagy and provide a basis for screening mitophagy-inducing compounds. Abbreviations: CCCP, carbonyl cyanide m-chlorophenylhydrazone; IMCLAM, intra-mitochondrial CLICK to assess mitophagy; ROX, X-rhodamine; SPAAC, stain-promoted azide-alkyne Click Chemistry; TPP, triphenylphosphonium.

Installation of high-affinity Siglec-1 ligand on tumor surface for macrophage-engaged tumor suppression

Siglecs that binds cell surface sialoglycans are a family of immunomodulatory receptors, of which, Siglec-7 expressed on natural killer (NK) cells promotes tumor immunoevation while the role of Siglec-1 expressed on macrophages on tumor development remains largely unexplored. Herein, we selectively introduced high affinity sialoside ligands of Siglec-1 and Siglec-7 to tumor cell surface via in vivo Strain-promoted Azide-Alkyne cyclization of ^TCCSiaα2,3-Lactose or ^FITCSiaα2,6-Lactose with 9-azido sialic acid (^AzSia) metabolically installed on tumor cell surface. We found that ^TCCSiaα2,3-Lactose conjugated on tumor surface moderately inhibited tumor growth while ^FITCSiaα2,6-Lactose promote tumor growth. These results suggest high-affinity ligand of Siglec-1 dispalyed on tumors surface provide a new perspective for tumor immunotherapy.

Galectin Trafficking Pathway-Enabled Color-Switchable Detection of Lysosomal Membrane Permeabilization

Lysosomal membrane permeabilization (LMP) engaged in multiple human diseases is accompanied by relocation of cytosolic galectin into LMP⁺ lysosomes. We herein reported a galectin trafficking-targeted method to image LMP using two kinds of glyco-dendrimers, a sialic acid-terminated dendrimer labeled with pH-inert rhodamine and a lactose-terminated dendrimer labeled with fluorescein that becomes green-emissive in pH-elevated lysosomes. Albeit both accumulated in physiological lysosomes, the former is released from LMP⁺ lysosomes while the latter binds to galectin accumulated in LMP⁺ lysosomes and thus trapped in LMP⁺ lysosomes. Accordingly, LMP⁺ lysosomes exhibit loss of red fluorescence and turn-on green fluorescence due to loss of lysosomal acidity. This red-to-green color switch enables discernment of LMP⁺ lysosomes from physiological lysosomes and pH-elevated lysosomes and can be further utilized to detect LMP in distinct cell death pathways. These results suggest the utility of galectin trafficking pathway-integrated synthetic probes for detection of LMP, a key factor for diseased cells.

Organelle-Directed Metabolic Glycan Labeling and Optical Tracking of Dysfunctional Lysosomes Thereof

Metabolic glycan labeling (MGL) has been employed for diverse purposes, such as cell surface glycan imaging and tumor surface engineering. We herein reported organelle-specific MGL (OMGL) for selective tagging of the inner limiting membrane of lysosomes over the cell surface. This is operated via acidity-promoted accumulation of optical probes in lysosomes and bioorthogonal ligation of the trapped probes with 9-azidosialic acid (AzSia) metabolically installed on lysosomal membrane proteins. Overcoming the limitation of classical organelle probes to dissipate from stressed organelles, OMGL enables optical tracking of pH-elevated lysosomes in exocytosis and membrane-permeabilized lysosomes in different cell death pathways. Thus, OMGL offers a new tool to study lysosome biology.

Organelle-Partitioned Sugar-Rhodamine Diad for In Vivo Tumor Imaging

Current tumor imaging agents are often limited by their liability to dissipate from tumor tissues. As cell sugar sorting enables exogenous sugars to be delivered into predetermined subcellular locations, we synthesized sialic acid (Sia) derivatives with rhodamine-X conjugated at C-9 (^ROXSia), which hitchhikes cell sialic acid sorting to target tumor cell lysosomes, exhibiting pH-independent long-term probe retention in lysosomes. ^ROXSia gives selective, bright, and endured fluorescence signals in subcutaneous tumors and orthotopic tumors in mice models. These results indicate the potential of ^ROXSia as a lysosome-targeted optical agent for fluorescence-guided tumor resection.

In vivo real-time tracking of tumor-specific biocatalysis in cascade nanotheranostics enables synergistic cancer treatment

Glucose oxidase (GOD)-based synergistic cancer therapy has aroused great research interest in the context of cancer treatment due to the inherent biocompatibility and biodegradability. However, this emerging therapeutic system still lacks a strategy to predict and regulate the in vivo biocatalytic behavior of GOD in real time to minimize the side effects on normal tissues. Herein, we developed a tumor-specific cascade nanotheranostic system (BNG) that combines GOD-catalyzed oxidative stress and dual-channel fluorescent sensing, significantly improving the synergistic therapeutic efficacy with real-time feedback information. The nanotheranostic system remains completely silent in the blood circulatory system and selectively releases GOD enzymes in the tumor site, with enhanced near-infrared (NIR) fluorescence at 825 nm. Subsequently, GOD catalyzes H2O2 production, triggering cascade reactions with NIR fluorescence at 650 nm as an optical output, along with GSH depletion, enabling synergistic cancer treatment. The designed nanotheranostic system, integrated with tumor-activated cascade reactions and triggering a dual-channel output at each step, represents an insightful paradigm for precise cooperative cancer therapy.

Imaging stressed organellesviasugar-conjugated color-switchable pH sensors

Sugar-conjugated pH sensors discriminate stressed lysosomes in different cell starvation conditionsviared-to-green fluorescence switch.

Organelle-Redirected Chameleon Sensor-Enabled Live Cell Imaging of Mitochondrial DNA

Mitochondrial DNA (mtDNA) plays important roles in diverse physiological processes and myriad diseases. We herein report mtDNA imaging with a chameleon sensor containing a cationic rhodamine B (RB) entity for mitochondria targeting and a fluorogenic SYBR Green-I (SG) entity for DNA sensing. SG-RB selectively binds to mtDNA and gives green SG fluorescence in mitochondria of living cells but gives red RB fluorescence upon delivery of mitochondria into lysosomes in mitophagy. With the dual-color imaging, mtDNA aggregation and elevated mitophagy were identified in HeLa cells stressed with anticancer doxorubicin. These results suggest the utility of organelle-redirected DNA sensors for live cell imaging of mtDNA involved in myriad pathological disorders.

Regioselective Single-Electron Tsuji-Trost Reaction of Allylic Alcohols: A Photoredox/Nickel Dual Catalytic Approach

A radical-mediated functionalization of allyl alcohol derived partners with a variety of alkyl 1,4-dihydropyridines via photoredox/nickel dual catalysis is described. This transformation transpires with high linear and E-selectivity, avoiding the requirement of harsh conditions (e.g., strong base, elevated temperature). Additionally, using aryl sulfinate salts as radical precursors, allyl sulfones can also be obtained. Kinetic isotope effect experiments implicated oxidative addition of the nickel catalyst to the allylic electrophile as the turnover-limiting step, supporting previous computational studies.

An in cellulo-activated multicolor cell labeling approach used to image dying cell clearance

Dying cell clearance is critical for myriad biological processes such as tissue homeostasis.

Senescence-associated sialidase revealed by an activatable fluorescence-on labeling probe

A fluorescence-quenched substrate of sialidase enables fluorescence-on live cell imaging of sialidases, revealing up-regulation of lysosome-associated sialidase in cell senescence.