Biology subjects

Cheng, J.-X.

Publications and source records attributed to Cheng, J.-X..

At least 37 records · Page 2Linked to original sources

bioRxiv2023

Nanoscale Structural Mapping of Protein Aggregates in Live Cells Modeling Huntington's Disease

Protein aggregation, in the form of amyloid fibrils, is intimately correlated with many neurodegenerative diseases. Despite recent advances in structural biology, it remains challenging to acquire structural information of proteins in live cells. Tagging with fluorescent proteins, like green fluorescent protein (GFP), is routinely used for protein visualization. Yet, this method alone cannot provide detailed structural information on the protein system of interest, and tagging proteins has the potential to perturb native structure and function. Here, by fluorescence-detected as well as label-free scattering-based mid-infrared photothermal (MIP) microscopy, we demonstrate nanoscale mapping of secondary structure of protein aggregates in a yeast model of Huntingtons disease. We first used GFP as a highly sensitive photothermal reporter to validate {beta}-sheet enrichment in huntingtin (htt) protein aggregates. We then obtained label-free structural maps of protein aggregates. Our data showed that the fluorescent protein tag indeed perturbed the secondary structure of the aggregate, evident by a spectral shift. Live cell MIP spectroscopy further revealed the fine spatial distribution of structurally distinct components in protein aggregates, featuring a 246-nm diameter core highly enriched in {beta}-sheet surrounded by a [a]-helix-rich shell. Interestingly, this structural partition exists only in presence of the [RNQ+] prion, a prion that acts to facilitate the formation of other amyloid prions. Indeed, when htt is induced to aggregate in the absence of this prion ([rnq-] state), it forms non-toxic amyloid aggregates exclusively. These results showcase the potential of MIP for unveiling detailed and subtle structural information on protein systems in live cells. SignificanceProtein aggregation is a hallmark of neurodegenerative diseases, such as Huntingtons Disease. Understanding the nature of neurotoxic aggregates could lead to better therapeutic approaches. The limited progress in this direction is partly due to the lack of tools for extracting structural information in the physiological context of the aggregates. Here, we report a photothermally detected mid-infrared micro-spectroscopy technique able to dissect the secondary structure of aggregates of the huntingtin protein in live cells. We describe for the first time a nanoscale partition of secondary structures between {beta}-rich core and [a]-rich shell of the aggregates. This work demonstrates the potential of mid-infrared photothermal microscopy for structural and functional mapping of proteins in live cells.

biophysics↗

bioRxiv2023

Stimulated Raman Photothermal Microscopy towards Ultrasensitive Chemical Imaging

Stimulated Raman scattering (SRS) microscopy has shown enormous potential in revealing molecular structures, dynamics and couplings in complex systems. However, the sensitivity of SRS is fundamentally limited to milli-molar level due to the shot noise and the small modulation depth. To overcome this barrier, we revisit SRS from the perspective of energy deposition. The SRS process pumps molecules to their vibrationally excited states. The thereafter relaxation heats up the surrounding and induces refractive index changes. By probing the refractive index changes with a laser beam, we introduce stimulated Raman photothermal (SRP) microscopy, where a >500-fold boost of modulation depth is achieved. Versatile applications of SRP microscopy on viral particles, cells, and tissues are demonstrated. SRP microscopy opens a new way to perform vibrational spectroscopic imaging with ultrahigh sensitivity. One-Sentence SummaryWe demonstrate a new spectroscopic imaging method that improves the signal intensity by >500-fold.

bioengineering↗

bioRxiv2023

Video-rate Mid-infrared Photothermal Imaging by Single Pulse Photothermal Detection per Pixel

By optically sensing the mid-infrared absorption induced photothermal effect, midinfrared photothermal (MIP) microscope enables super-resolution IR imaging and scrutinizing of biological systems in an aqueous environment. However, the speed of current lock-in based sample-scanning MIP system is limited to 1.0 millisecond or longer per pixel, which is insufficient for capturing dynamics inside living systems. Here, we report a single pulse laserscanning MIP microscope that dramatically increases the imaging speed by three orders of magnitude. We harness a lock-in free demodulation scheme which uses high-speed digitization to resolve single IR pulse induced contrast at nanosecond time scale. To realize single pulse photothermal detection at each pixel, we employ two sets of galvo mirrors for synchronized scanning of mid-infrared and probe beams to achieve an imaging line rate over 2 kHz. With video-rate imaging capability, we observed two types of distinct dynamics of lipids in living cells. Furthermore, by hyperspectral imaging, we chemically dissected a single cell wall at nanometer scale. Finally, with a uniform field of view over 200 by 200 m2 and 2 Hz frame rate, we mapped fat storage in free-moving C. elegans and live embryos.

bioengineering↗

bioRxiv2022

Fingerprint SRS Imaging Unveils Ergosteryl Ester as a Metabolic Signature of Azole-Resistant Candida albicans

Candida albicans (C. albicans), a major fungal pathogen, causes life-threatening infections in immunocompromised individuals. Fluconazole (FLC) is recommended as first-line therapy for treatment of invasive fungal infections. Yet, the widespread use of FLC has resulted in increased antifungal resistance among different strains of Candida, especially C. albicans, which is a leading source of hospital-acquired infections. Here, by hyperspectral stimulated Raman scattering (hSRS) imaging of single fungal cells in the fingerprint window and pixel-wise spectral unmixing, we report aberrant ergosteryl ester accumulation in azole-resistant C. albicans compared to azole-susceptible species. This accumulation was a consequence of de novo lipogenesis. Lipid profiling by mass spectroscopy identified ergosterol oleate to be the major species stored in azole-resistant C. albicans. Blocking ergosterol esterification by oleate and suppressing sterol synthesis by FLC synergistically suppressed the viability of C. albicans in vitro and limited the growth of biofilm on mouse skin in vivo. Our findings highlight a metabolic marker and a new therapeutic strategy for targeting azole-resistant C. albicans by interrupting the esterified ergosterol biosynthetic pathway. Significance StatementInvasive fungal infections and increasing antifungal resistance are emerging threats to public health with high morbidity and mortality. Despite the advances in azole resistance mechanisms, it remains unclear why some fungal species are intrinsically resistant to or easily acquire resistance to multiple antifungal drugs. Here, using fingerprint SRS microscopy, we uncovered a molecular signature, aberrant ergosteryl ester accumulation, linked to the azole resistance of Candida species. An antifungal treatment strategy combining oleate (inhibitor of ersgosteryl esterification) and azole significantly attenuates the azole resistance and the viability of C. albicans in vitro and in vivo. Our work opens a new way to detect and treat azole-resistant fungal infections by targeting ergosterol metabolism.

microbiology↗

bioRxiv2022

High-precision neural stimulation by a highly efficient candle soot fiber optoacoustic emitter

Highly precise neuromodulation with a high efficacy poses great importance in neuroscience. Here, we developed a candle soot fiber optoacoustic emitter (CSFOE), capable of generating a high pressure of over 10 MPa, enabling highly efficient neuromodulation in vitro. The design of the fiber optoacoustic emitter, including the choice of the material and the thickness of the layered structure, was optimized in both simulations and experiments. The optoacoustic conversion efficiency of the optimized CSFOE was found to be ten times higher than the other carbon-based fiber optoacoustic emitters. Driven by a single laser, the CSFOE can perform dual-site optoacoustic activation of neurons, confirmed by calcium (Ca) imaging. Our work opens potential avenues for more complex and programmed control in neural circuits using a simple design for multisite neuromodulation in vivo.

neuroscience↗

bioRxiv2022

Wireless Neuromodulation at Submillimeter Precision via a Microwave Split-Ring Resonator

Microwaves, with wavelengths on the order of millimeters, have centimeter-scale penetration depth and have been shown to reversibly inhibit neuronal activity. Yet, microwaves alone do not provide sufficient spatial precision to modulate target neurons without affecting surrounding tissues. Here, we report an implantable split-ring resonator (SRR) that generates a localized and enhanced microwave field at the gap site with submillimeter spatial precision. The SRR breaks the microwave diffraction limit and greatly enhances the efficiency of microwave inhibition. With the SRR, microwaves at dosages below the safe exposure limit are shown to inhibit neurons within 1 mm from the gap site. Application of the microwave SRR to suppress seizures in an in vivo model of epilepsy is demonstrated.

bioengineering↗

bioRxiv2022

Visualization of a Limonene Synthesis Metabolon inside Living Bacteria by Hyperspectral SRS Microscopy

Metabolons consisting of cellular structure elements and sequential metabolic enzymes are expected to be involved in diverse biological processes. However, direct visualization of metabolons in prokaryotic cells is still challenging. In this study, we report direct visualization of concentrated subcellular regions of limonene synthesis inside single engineered Escherichia coli by using hyperspectral stimulated Raman scattering (hSRS) microscopy. Equipped with spectral unmixing, hSRS imaging provides a reliable method to quantify intracellular limonene content. In E. coli strains with a complete limonene synthesis pathway, intracellular limonene is found locally concentrated and colocalized with proteins. Furthermore, dual-modality SRS and two-photon fluorescence imaging showed colocalization of limonene and GFP-fused limonene synthase. Significance StatementMonitoring biosynthesis activity at the single-cell level is key to metabolic engineering but is still difficult to achieve in a label-free manner. Using hyperspectral stimulated Raman scattering imaging in the 670-900 cm-1 region, we visualized localized limonene synthesis inside engineered E. coli. The colocalization of limonene and GFP-fused limonene synthase was confirmed by co-registered stimulated Raman scattering and two-photon fluorescence images. Our finding suggests a limonene synthesis metabolon with a polar distribution inside the cells. This finding expands our knowledge of de novo limonene biosynthesis in engineered bacteria and highlights the potential of SRS chemical imaging in metabolic engineering research.

biophysics↗

bioRxiv2022

Single-shot Volumetric Chemical Imaging by Mid- Infrared Photothermal Fourier Light Field Microscopy

Three-dimensional molecular imaging of living organisms and cells plays a significant role in modern biology. Yet, current volumetric imaging modalities are largely fluorescence-based and thus lack chemical content information. Mid-infrared photothermal microscopy as a new chemical imaging technology provides infrared spectroscopic information at sub-micrometer spatial resolution. Here, by harnessing thermosensitive fluorescent dyes to sense the mid-infrared photothermal effect, we demonstrate mid-infrared photothermal Fourier light field (MIP-FLF) microscopy for single-shot volumetric infrared spectroscopic imaging at the speed of 8 volumes per second and sub-micron spatial resolution. Protein contents in bacteria and lipid droplets in living pancreatic cancer cells are visualized. Altered lipid metabolism in drug-resistant pancreatic cancer cells is observed with the MIP-FLF microscope.

biochemistry↗

bioRxiv2022

The Balance between Saturated and Unsaturated Fatty Acids Regulates Ovarian Cancer Cell Fate

Fatty acids are an important source of energy and a key component of phospholipids in membranes and organelles. Saturated (SFAs) are converted into unsaturated fatty acids (UFAs) by stearoyl Co-A desaturase (SCD), an enzyme highly active in cancer. Here we studied how the balance between SFAs and UFAs maintained by SCD impacts cancer cell survival and tumor progression. SCD depletion or inhibition caused lower levels of UFAs vs. SFAs and altered fatty acyl chain plasticity, as demonstrated by lipidomics and stimulated Raman spectroscopy (SRS). Further, the loss of equilibrium between UFAs and SFAs resulting from SCD knock down triggered endoplasmic reticulum (ER) stress response with brisk activation of IRE1/XBP1 and PERK/eIF2/ATF4 axes. Stiff and disorganized ER membrane was visualized by electron microscopy and SRS imaging in cells in which SCD was knocked down. The induction of long-term mild ER stress or short-time severe ER stress by the increased levels of SFAs and loss of UFAs led to cell death. However, ER stress and apoptosis could be readily rescued by supplementation with UFAs and re-equilibration of SFA/UFA levels. The effects of SCD knockdown or inhibition observed in vitro, translated into suppression of intraperitoneal tumor growth in xenograft models. Furthermore, a combined intervention using an SCD inhibitor and an SFA enriched diet, initiated ER stress in tumors growing in vivo and potently blocked their dissemination. In all, our data support SCD as a key regulator of the cancer cell fate under metabolic stress and point to new treatment strategies targeting the lipid balance. Significance StatementWe show that the balance between saturated and unsaturated fatty acids tightly regulated by the desaturase SCD impacts the survival of cancer cells; increased levels of unsaturation being protective against ER stress induced apoptosis. Decreasing fatty acid unsaturation, either through SCD depletion or through SCD inhibition coupled with a dietary intervention blocks tumor progression in vivo. Our findings support the concept of targeting the lipid balance as a new target in cancer.

cancer biology↗

bioRxiv2022

LIPA-driven hydrolysis of cholesteryl arachidonate promotes cancer metastasis via NF-κB

Cholesteryl ester (CE) is an established marker in many types of aggressive cancers. Yet, the function of CE homeostasis during cancer progression is largely unknown. Here, enabled by Raman spectromicroscopy, pan-cancer bioinformatic analysis, and biocompatible Raman probe of cholesterol, LIPA was identified as the key regulator of CE hydrolysis in cancer cells. LIPA inhibition induced aberrant accumulation of CE-rich lipid droplet at single cell level. LIPA-driven CE hydrolysis was directly visualized by stimulated Raman scattering imaging of alkyne-tagged cholesterol. Cholesteryl arachidonate was identified as a dominant substrate that is rapidly hydrolyzed by LIPA. Inhibition of LIPA effectively suppressed cancer metastasis both in vitro and in vivo. Mechanistically, LIPA inhibition suppresses NF-{kappa}B signaling, while the NF-{kappa}B members positively regulate the expression level of LIPA, indicating regulation of CE homeostasis by a LIPA-CE-NF{kappa}B feedback loop. Collectively, our findings reveal that LIPA drives CE hydrolysis during cancer progression and is an important metabolic target for cancer therapy.

cancer biology↗

bioRxiv2021

Photoinactivation of catalase sensitizes Candida albicans and Candida auris to ROS-producing agents and immune cells

Nearly all organisms found in nature have evolved and developed their own specific strategies to cope with reactive oxygen species (ROS). Catalase, a heme-containing tetramer protein expressed in a broad range of aerobic fungi, has been utilized as an essential enzymatic ROS detoxifying mechanism, and shows remarkable efficiency in degrading hydrogen peroxide (H2O2) for fungal cell survival and host invasion. Here, we demonstrate that catalase inactivation with blue light renders fungal cells highly susceptible to ROS attack, thus resembling a strength-to-weakness optical switch. To unveil catalase as the underlying molecular target of blue light and its inactivation mechanism, we systematically compared wild-type Candida albicans to a catalase-deficient mutant strain for susceptibility to ROS in the absence/presence of 410 nm treatment. Upon testing on a wide range of fungal species and strains, we found that intracellular catalase could be effectively and universally inactivated by 410 nm blue light. We find that the photoinactivation of catalase in combination with ROS-generating agents is highly effective and potent in achieving full eradication of multiple fungal species and strains, including multiple clinical strains of Candida auris, the causative agent of the global fungal epidemic. In addition, photoinactivation of catalase is shown to facilitate macrophage killing of intracellular Candida albicans. The antifungal efficacy of catalase photoinactivation is further validated using a Candida albicans-induced mouse model of skin abrasion. Taken together, our findings offer a novel catalase-photoinactivation approach to address multidrug-resistant Candida infections.

microbiology↗

bioRxiv2021

Single-cell chemical imaging of engineered strains reveals heterogeneity in fatty acid production

Understanding metabolic heterogeneity is critical for optimizing microbial production of valuable chemicals, but requires tools that can quantify metabolites at the single-cell level over time. Here, we develop longitudinal hyperspectral stimulated Raman scattering (SRS) chemical imaging to directly visualize free fatty acids in engineered Escherichia coli over many cell cycles. We also develop compositional analysis to determine the chain length and unsaturation of the fatty acids in living cells. Our method reveals substantial heterogeneity in fatty acid production among and within colonies that emerges over the course of many generations. Interestingly, the strains display distinct types of production heterogeneity in an enzyme-dependent manner. By pairing time-lapse and SRS imaging, we examine the relationship between growth and production at the single-cell level. Single-cell quantification does not show a significant growth-production tradeoff in a strain that exhibits high production heterogeneity. Our results demonstrate that cell-to-cell production heterogeneity is pervasive and provide a means to link single-cell and population-level production.

synthetic biology↗

bioRxiv2021

SRS-FISH: High-Throughput Platform Linking Microbiome Function to Identity at the Single Cell Level

One of the biggest challenges in microbiome research in environmental and medical samples is to better understand functional properties of microbial community members at a single cell level. Single cell isotope probing has become a key tool for this purpose, but the currently applied detection methods for measuring isotope incorporation into single cells do not allow high-throughput analyses. Here, we report on the development of an imaging-based approach termed stimulated Raman scattering - two-photon fluorescence in situ hybridization (SRS-FISH) for high-throughput structure-function analyses of microbial communities with single cell resolution. SRS-FISH has an imaging speed of 10 to 100 milliseconds per cell, which is two to three orders of magnitude faster than spontaneous Raman-FISH. Using this technique, we delineated metabolic responses of thirty thousand individual cells to various mucosal sugars in the human gut microbiome via incorporation of deuterium from heavy water as an activity marker. Application of SRS-FISH to investigate the utilization of host-derived nutrients by two major human gut microbiome taxa revealed that response to mucosal sugars tends to be dominated by Bacteroidales, with an unexpected finding that Clostridia can outperform Bacteroidales at foraging fucose.

microbiology↗

bioRxiv2021

Photoinactivation of Catalase Sensitizes Wide-Ranging Bacteria to ROS-Producing Agents and Immune Cells

Bacteria have evolved to cope with the detrimental effects of reactive oxygen species (ROS) using their essential molecular components. Catalase, a heme-containing tetramer protein expressed universally in most of the aerobic bacteria, plays an indispensable role in scavenging excess hydrogen peroxide (H2O2). Here, through utilization of wild-type and catalase-deficient mutants, we identified catalase as an endogenous therapeutic target of 400-420 nm blue light. Catalase residing in bacteria could be effectively inactivated by blue light, subsequently rendering the pathogens extremely vulnerable to H2O2 and H2O2-producing agents. As a result, photoinactivation of catalase and H2O2 synergistically eliminate a wide range of catalase-positive planktonic bacteria and P. aeruginosa inside biofilms. In addition, photoinactivation of catalase is shown to facilitate macrophages to defend against intracellular pathogens. The antimicrobial efficacy of catalase photoinactivation is further validated using a Pseudomonas aeruginosa-induced mice abrasion model. Taken together, our findings offer a catalase-targeting phototherapy against multidrug-resistant bacterial infections.

microbiology↗

bioRxiv2021

Metabolic Reprogramming from Glycolysis to Fatty Acid Uptake and beta-Oxidation in Platinum-Resistant Cancer Cells

Increased aerobic glycolysis is widely considered as a hallmark of cancer. Yet, cancer cell metabolic reprograming during development of therapeutic resistance is under-studied. Here, through high-throughput stimulated Raman scattering imaging and single cell analysis, we found that cisplatin-resistant cells exhibit increased uptake of exogenous fatty acids, accompanied with decreased glucose uptake and de novo lipogenesis, indicating a reprogramming from glucose and glycolysis dependent to fatty acid uptake and beta-oxidation dependent anabolic and energy metabolism. A metabolic index incorporating measurements of glucose derived anabolism and fatty acid uptake correlates linearly to the level of resistance to cisplatin in ovarian cancer cell lines and in primary cells isolated from ovarian cancer patients. Mechanistically, the increased fatty acid uptake facilitates cancer cell survival under cisplatin-induced oxidative stress by enhancing energy production through beta-oxidation. Consequently, blocking fatty acid beta-oxidation by a small molecule inhibitor in combination with cisplatin or carboplatin synergistically suppressed ovarian cancer proliferation in vitro and growth of patient-derived xenograft in vivo. Collectively, these findings support a new way for rapid detection of cisplatin-resistance at single cell level and a new strategy for treatment of cisplatin-resistant tumors.

cancer biology↗

bioRxiv2020

Frizzled-7 Identifies Platinum Tolerant Ovarian Cancer Cells Susceptible to Ferroptosis

Defining traits of platinum tolerant cancer cells could expose new treatment vulnerabilities. Here, new markers associated with platinum tolerant cells and tumors were identified by using in vitro and in vivo ovarian cancer (OC) models treated repetitively with carboplatin and validated in human specimens. Platinum-tolerant cells and tumors were found to be enriched in ALDH (+) cells, formed more spheroids, and expressed increased levels of stemness-related transcription factors compared to parental cells. Additionally, platinum-tolerant cells and tumors highly expressed the Wnt receptor, Frizzled 7 (FZD7). FZD7 knock down improved sensitivity to platinum, decreased spheroid formation, and delayed tumor initiation. The molecular signature distinguishing FZD7(+) from FZD7(-) cells included epithelial-to-mesenchymal (EMT), stemness, and oxidative phosphorylation enriched gene sets. Overexpression of FZD7 activated the oncogenic factor Tp63, driving upregulation of glutathione metabolism pathways, including glutathione peroxidase 4 (GPX4), which protects cells from chemotherapy-induced oxidative stress. FZD7(+) platinum-tolerant OC cells were more sensitive and underwent ferroptosis after treatment with GPX4 inhibitors. FZD7, Tp63 and glutathione metabolism gene sets were strongly correlated in the OC Tumor Cancer Genome Atlas (TCGA) database and in human OC specimens residual after chemotherapy. These results support the existence of a platinum-tolerant cell population with partial stem cell features, characterized by FZD7 expression and dependent on FZD7-{beta}-catenin-Tp63-GPX4 pathway for survival. The findings reveal a novel therapeutic vulnerability of platinum tolerant cancer cells and provide new insight into a potential "persister cancer cell" phenotype.

cancer biology↗

bioRxiv2020

Neural Stimulation in vitro and in vivo by Photoacoustic Nanotransducers

Neuromodulation is an invaluable approach for study of neural circuits and clinical treatment of neurological diseases. Here, we report semiconducting polymer nanoparticles based photoacoustic nanotransducers (PANs) for neural stimulation. Our PANs strongly absorb light in the near-infrared second window and generate localized acoustic waves. PANs can also be surface-modified to selectively bind onto neurons. PAN-mediated activation of primary neurons in vitro is achieved with ten 3-nanosecond laser pulses at 1030 nm over a 3 millisecond duration. In vivo neural modulation of mouse brain activities and motor activities is demonstrated by PANs directly injected into brain cortex. With millisecond-scale temporal resolution, sub-millimeter spatial resolution and negligible heat deposition, PAN stimulation is a new non-genetic method for precise control of neuronal activities, opening potentials in non-invasive brain modulation.

neuroscience↗

bioRxiv2020

A Thermodynamic Interpretation of the Stimulated Raman Spectroscopic Signature to Action Potential in Single Neurons

It has previously been suggested that the plasma membrane condenses and melts reversibly during an action potential in a neuron, analogous to an acoustic wave travelling in the compressive membrane region. If true it has fundamental consequences for our understanding of the regulation of biological functions during an action potential. It has long been known that the electrical dipoles in the neuronal membrane reorient during an action potential, observed through a variety of optical methods. However, this information has been insufficient to confirm if and how the collective thermodynamic state of the neuronal membrane changes during an action potential. Here, we show that hyperspectral stimulated Raman spectroscopy (SRS) can resolve the thermodynamic state of the neuronal membranes in a single neuron during an action potential. These measurements indicate that the system becomes ordered and compressed during the de-polarisation phase and disordered and expanded during hyper polarisation Therefore, the observation is consistent with the acoustic hypothesis and SRS provides a powerful tool to not only further validate the hypothesis in future, but also explore the role of membrane thermodynamics during an action potential.

biophysics↗