Physicochemical and Antioxidative Properties of Protein Hydrolysates from Residual Goat Placenta Extract by Two Different Methods.

Protein hydrolysates from the goat placenta provide multiple benefits, such as immune system enhancement, antioxidant activities, and reductions in uric acid levels. Despite these benefits, their industrial applications have been underexplored. This study aimed to prepare extract protein hydrolysates (GPERPs) from residual goat placenta extract (GPER) and assess their functional properties, focusing on how different drying methods influence these properties.

Liquid Biopsy-Based Accurate Diagnosis and Genomic Profiling of Hard-to-Biopsy Tumors via Parallel Single-Cell Genomic Sequencing of Exfoliated Tumor Cells.

Liquid biopsy provides a convenient and safer procedure for the diagnosis and genomic profiling of tumors that are inaccessible to biopsy by analyzing exfoliated tumor cells (ETCs) or tumor-derived cell-free DNA (cfDNA). However, its primary challenge lies in its limited accuracy in comparison to tissue-based approaches. We report a parallel single-ETC genomic sequencing (Past-Seq) method for the accurate diagnosis and genomic profiling of hard-to-biopsy tumors such as cholangiocarcinoma (CCA) and upper tract urothelial carcinoma (UTUC).

Single-cell low-pass whole genome sequencing accurately detects circulating tumor cells for liquid biopsy-based multi-cancer diagnosis.

Accurate detection of circulating tumor cells (CTCs) in blood and non-blood body fluids enables generation of deterministic cancer diagnosis and represent a less invasive and safer liquid biopsy approach. Although genomic alternations have been widely used in circulating tumor DNA (ctDNA) analysis, studies on cell-based genomic alternations profiling for CTC detection are rare due to major technical limitations in single-cell whole genome sequencing (WGS) including low throughput, low accuracy and high cost. We report a single-cell low-pass WGS-based protocol (scMet-Seq) for sensitive and accurate CTC detection by combining a metabolic function-associated marker Hexokinase 2 (HK2) and a Tn5 transposome-based WGS method with improved cell fixation strategy.

Recent advances in high-throughput single-cell transcriptomics and spatial transcriptomics.

Single-cell RNA sequencing (scRNA-seq) has been developed for characterizing the transcriptome of cells that are rare but of biological significance. With cell barcoding and microchip technologies, a suite of high-throughput scRNA-seq protocols enable transcriptome profiling in thousands of individual cells at single-cell resolution for classifying cell types, discovering novel cell populations, investigating cellular heterogeneity and elucidating lineage trajectories. Microchip technologies including microfluidics- and microwell-based platforms play a major role in high-throughput scRNA-seq.

Proteomics Evidence of the Role of TDMQ20 in the Cholinergic System and Synaptic Transmission in a Mouse Model of Alzheimer's Disease.

The interaction between copper ions and amyloid peptide Aβ has been reported to be involved in Alzheimer's disease (AD) pathology. Based on copper coordination biochemistry, we designed specific copper chelators [tetradentate monoquinolines (TDMQs)] in order to regulate copper homeostasis in the AD brain and inhibit the deleterious oxidative stress catalyzed by copper-Aβ complexes. We previously reported that TDMQ20, a highly selective copper chelator selected as a drug candidate, was able to extract copper from the Cu-Aβ complex and restore cognitive and behavioral deficits in AD mouse models.

Detection and surveillance of circulating tumor cells in osteosarcoma for predicting therapy response and prognosis.

Objective: Osteosarcoma (OS) is an aggressive, highly metastatic, relatively drug-resistant bone tumor with poor long-term survival rates. The presence and persistence of circulating tumor cells (CTCs) in the peripheral blood are believed to be associated with treatment inefficiency and distant metastases. A blood-based CTC test is thus greatly needed for monitoring disease progression and predicting clinical outcomes.

A Multicancer Malignant Pleural Effusion Diagnostic Test Using Hexokinase 2 and Single-Cell Sequencing.

Background: Malignant pleural effusion (MPE) represents advanced malignant disease with poor prognosis. To date, pleural effusion cytology remains the best test to diagnose MPE but suffers from limited diagnostic sensitivity and high variation. We report a hexokinase 2-based method (HK2-seq) as a novel diagnostic method for multicancer MPE diagnosis.

Single-Cell Genomics-Based Molecular Algorithm for Early Cancer Detection.

As one of the prime applications of liquid biopsy, the detection of tumor-derived whole cells and molecular markers is enabled in a noninvasive means before symptoms or hints from imaging procedures used for cancer screening. However, liquid biopsy is not a diagnostic test of malignant diseases because it fails to establish a definitive cancer diagnosis. Although single-cell genomics provides a genome-wide genetic alternation landscape, it is technologically challenging to confirm cell malignancy of a suspicious cell in body fluids due to unknown technical noise of single-cell sequencing and genomic variation among cancer cells, especially when tumor tissues are unavailable for sequencing as the reference.

Hexokinase 2 discerns a novel circulating tumor cell population associated with poor prognosis in lung cancer patients.

Unlike other epithelial cancer types, circulating tumor cells (CTCs) are less frequently detected in the peripheral blood of non-small cell lung cancer (NSCLC) patients using epithelial marker-based detection approaches despite the aggressive nature of NSCLC. Here, we demonstrate hexokinase-2 (HK2) as a metabolic function-associated marker for the detection of CTCs. In 59 NSCLC patients bearing cytokeratin-positive (CK) primary tumors, HK2 enables resolving cytokeratin-negative (HK2/CK) CTCs as a prevalent population in about half of the peripheral blood samples with positive CTC counts.

Advances in single-cell whole genome sequencing technology and its application in biomedicine.

The advent and development of single-cell whole-genome sequencing (scWGS) technology has shed lights on the genomic heterogeneities within biosamples at the single-cell resolution. The technology is particularly well-established in the recent decade and witnesses a variety of clinical applications, such as circulating tumor cell (CTC) detection and preimplantation genetic diagnosis/screening (PGD/PGS). In this review, we summarize the latest practical breakthroughs of scWGS in the field of biomedicine, with the hope of providing a guideline to apply single-cell genomic sequencing in clinical researches.

Insights Into the Mechanism of Tyrosine Nitration in Preventing β-Amyloid Aggregation in Alzheimer's Disease.

Nitration of tyrosine at the tenth residue (Tyr10) in amyloid-β (Aβ) has been reported to reduce its aggregation and neurotoxicity in our previous studies. However, the exact mechanism remains unclear. Here, we used Aβ peptide with differently modified forms at Tyr10 to investigate the molecular mechanism to fill this gap.

TDMQ20, a Specific Copper Chelator, Reduces Memory Impairments in Alzheimer's Disease Mouse Models.

Besides targeting amyloid or tau metabolisms, regulation of redox metal ions is a recognized therapeutic target for Alzheimer's disease (AD). Based on the bioinorganic chemistry of copper, we designed specific chelators of copper(II) (TDMQs) insight to regulate copper homeostasis in the brain and to inhibit the deleterious oxidative stress catalyzed by copper-amyloid complexes. An oral treatment by TDMQ20 was able to fully reverse the cognitive and behavioral impairment in three different murine models, two nontransgenic models mimicking the early stage of AD and a transgenic model representing a more advanced stage of AD.

Metabolic regulation of prostate cancer heterogeneity and plasticity.

Metabolic reprogramming is one of the main hallmarks of cancer cells. It refers to the metabolic adaptations of tumor cells in response to nutrient deficiency, microenvironmental insults, and anti-cancer therapies. Metabolic transformation during tumor development plays a critical role in the continued tumor growth and progression and is driven by a complex interplay between the tumor mutational landscape, epigenetic modifications, and microenvironmental influences.

Single-Cell Sequencing-Enabled Hexokinase 2 Assay for Noninvasive Bladder Cancer Diagnosis and Screening by Detecting Rare Malignant Cells in Urine.

Bladder cancer (BC) is among the most common tumors with a high recurrence rate, necessitating noninvasive and sensitive diagnostic methods. Accurate detection of exfoliated tumor cells (ETCs) in urine is crucial for noninvasive BC diagnosis but suffers from limited sensitivity when ETCs are rare and confounded by reactive, regenerative, or reparative cells. Single-cell sequencing (SCS) enables accurate detection of ETCs by surveying oncogenic driver mutations or genome-wide copy number alternations.

Genetic Fate Mapping of Transient Cell Fate Reveals N-Cadherin Activity and Function in Tumor Metastasis.

Genetic lineage tracing unravels cell fate and plasticity in development, tissue homeostasis, and diseases. However, it remains technically challenging to trace temporary or transient cell fate, such as epithelial-to-mesenchymal transition (EMT) in tumor metastasis. Here, we generated a genetic fate-mapping system for temporally seamless tracing of transient cell fate.

Dysregulated lncRNA-miRNA-mRNA Network Reveals Patient Survival-Associated Modules and RNA Binding Proteins in Invasive Breast Carcinoma.

Breast cancer is the most common cancer in women, but few biomarkers are effective in clinic. Previous studies have shown the important roles of non-coding RNAs in diagnosis, prognosis, and therapy selection for breast cancer and have suggested the significance of integrating molecules at different levels to interpret the mechanism of breast cancer. Here, we collected transcriptome data including long non-coding RNA (lncRNA), microRNA (miRNA), and mRNA for ~1,200 samples, including 1079 invasive breast carcinoma samples and 104 normal samples, from The Cancer Genome Atlas (TCGA) project.

Liquid Biopsy Based Single-Cell Transcriptome Profiling Characterizes Heterogeneity of Disseminated Tumor Cells from Lung Adenocarcinoma.

The advent of rapid and inexpensive sequencing technology allows scientists to decipher intra-tumor heterogeneity spatially and temporally for resolving the evolutionary history of tumor and the underlying mechanism. However, studies on characterizing heterogeneity of disseminated tumor cells (DTCs) in liquid biopsies are rare because of the rarity and low viability of DTCs as well as a large number of non-tumor cells. Here, high-throughput single-cell transcriptome sequencing technology and rare DTC enrichment method are employed to decipher the heterogeneity and distinct molecular signatures of DTCs in malignant pleural effusion (MPE) from lung adenocarcinoma.

Liquid biopsy-based single-cell metabolic phenotyping of lung cancer patients for informative diagnostics.

Accurate prediction of chemo- or targeted therapy responses for patients with similar driver oncogenes through a simple and least-invasive assay represents an unmet need in the clinical diagnosis of non-small cell lung cancer. Using a single-cell on-chip metabolic cytometry and fluorescent metabolic probes, we show metabolic phenotyping on the rare disseminated tumor cells in pleural effusions across a panel of 32 lung adenocarcinoma patients. Our results reveal extensive metabolic heterogeneity of tumor cells that differentially engage in glycolysis and mitochondrial oxidation.

Highly multiplexed profiling of cell surface proteins on single circulating tumor cells based on antibody and cellular barcoding.

Circulating tumor cells (CTCs) are extraordinarily rare in blood samples and represent a real-time "liquid biopsy" of tumors. Although genetic and transcriptional sequencing of single CTCs has been reported, these methods fail to provide phenotypic and functional information of CTCs such as protein levels of surface proteins. Studies of single-cell proteomic assays of CTCs have been rare because of a lack of single-cell proteomic methods to handle and analyze rare cells in a high background of non-target cells with high sensitivity, throughput, and multiplexing capacity.

Establishment and characterization of a patient-derived circulating lung tumor cell line in vitro and in vivo.

Background: Circulating tumor cells (CTCs) have been described as a population of cells that may seed metastasis, which is a reliable target for the prevention of metastases in lung cancer patients at the early stage. The culturing of CTCs in vitro can be used to study the mechanism of lung cancer metastasis and to screen antimetastasis drugs. This study aims to establish CTC cell line in vitro and explore the potential mechanism of its metastasis.

Single-Cell Proteomics for Cancer Immunotherapy.

Cancer immunotherapy fights against cancer by modulating the immune response and is delivering encouraging results in clinical treatments. However, it is challenging to achieve durable response in all cancer patients during treatment due to the diversity and dynamic nature of immune system as well as inter- and intratumor heterogeneity. A comprehensive assessment of system immunity and tumor microenvironment is crucial for effective and safe cancer therapy, which can potentially be resolved by single-cell proteomic analysis.

A microfluidic chip with double-sided herringbone microstructures for enhanced capture of rare tumor cells.

A microfluidic chip with single-sided herringbone microstructure has been developed to isolate circulating tumor cells (CTCs) from blood samples of cancer patients. Here, we describe a new double-sided herringbone chip in which staggered herringbone micromixers are placed on both top and bottom surfaces of microchannels. The double-sided herringbone structure enables a high CTC capture efficiency of whole blood samples without depletion of red blood cells because of the effects of leukocyte margination and plasma skimming.

Microchip-based single-cell functional proteomics for biomedical applications.

Cellular heterogeneity has been widely recognized but only recently have single cell tools become available that allow characterizing heterogeneity at the genomic and proteomic levels. We review the technological advances in microchip-based toolkits for single-cell functional proteomics. Each of these tools has distinct advantages and limitations, and a few have advanced toward being applied to address biological or clinical problems that traditional population-based methods fail to address.

High-throughput screening of rare metabolically active tumor cells in pleural effusion and peripheral blood of lung cancer patients.

Malignant pleural effusion (MPE), the presence of malignant cells in pleural fluid, is often the first sign of many cancers and occurs in patients with metastatic malignancies. Accurate detection of tumor cells in pleural fluid is crucial because the presence of MPE denotes an advanced stage of disease and directs a switch in clinical managements. Cytology, as a traditional diagnostic tool, has limited sensitivity especially when tumor cells are not abundant, and may be confounded by reactive mesothelial cells in the pleural fluid.

Single cell proteomics in biomedicine: High-dimensional data acquisition, visualization, and analysis.

New insights on cellular heterogeneity in the last decade provoke the development of a variety of single cell omics tools at a lightning pace. The resultant high-dimensional single cell data generated by these tools require new theoretical approaches and analytical algorithms for effective visualization and interpretation. In this review, we briefly survey the state-of-the-art single cell proteomic tools with a particular focus on data acquisition and quantification, followed by an elaboration of a number of statistical and computational approaches developed to date for dissecting the high-dimensional single cell data.