Biobanks in chronic disease management: A comprehensive review of strategies, challenges, and future directions.

Biobanks, through the collection and storage of patient blood, tissue, genomic, and other biological samples, provide unique and rich resources for the research and management of chronic diseases such as cardiovascular diseases, diabetes, and cancer. These samples contain valuable cellular and molecular level information that can be utilized to decipher the pathogenesis of diseases, guide the development of novel diagnostic technologies, treatment methods, and personalized medical strategies. This article first outlines the historical evolution of biobanks, their classification, and the impact of technological advancements. Subsequently, it elaborates on the significant role of biobanks in revealing molecular biomarkers of chronic diseases, promoting the translation of basic research to clinical applications, and achieving individualized treatment and management. Additionally, challenges such as standardization of sample processing, information privacy, and security are discussed. Finally, from the perspectives of policy support, regulatory improvement, and public participation, this article provides a forecast on the future development directions of biobanks and strategies to address challenges, aiming to safeguard and enhance their unique advantages in supporting chronic disease prevention and treatment.

Single-cell transcriptomic profiling reveals immune cell heterogeneity in acute myeloid leukaemia peripheral blood mononuclear cells after chemotherapy.

PURPOSE: Acute myeloid leukaemia (AML) is a heterogeneous disease characterised by the rapid clonal expansion of abnormally differentiated myeloid progenitor cells residing in a complex microenvironment. However, the immune cell types, status, and genome profile of the peripheral blood mononuclear cell (PBMC) microenvironment in AML patients after chemotherapy are poorly understood. In order to explore the immune microenvironment of AML patients after chemotherapy, we conducted this study for providing insights into precision medicine and immunotherapy of AML. METHODS: In this study, we used single-cell RNA sequencing (scRNA-seq) to analyse the PBMC microenvironment from five AML patients treated with different chemotherapy regimens and six healthy donors. We compared the cell compositions in AML patients and healthy donors, and performed gene set enrichment analysis (GSEA), CellPhoneDB, and copy number variation (CNV) analysis. RESULTS: Using scRNA-seq technology, 91,772 high quality cells of 44,950 PBMCs from AML patients and 46,822 PBMCs from healthy donors were classified as 14 major cell clusters. Our study revealed the sub-cluster diversity of T cells, natural killer (NK) cells, monocytes, dendritic cells (DCs), and haematopoietic stem cell progenitors (HSC-Prog) in AML patients under chemotherapy. NK cells and monocyte-DCs showed significant changes in transcription factor expression and chromosome copy number variation (CNV). We also observed significant heterogeneity in CNV and intercellular interaction networks in HSC-Prog cells. CONCLUSION: Our results elucidated the PBMC single-cell landscape and provided insights into precision medicine and immunotherapy for treating AML.

Gold drugs as colistin adjuvants in the fight against MCR-1 producing bacteria.

The emergence and rapid spread of the mobile colistin resistance gene mcr-1 among bacterial species and hosts significantly challenge the efficacy of "last-line" antibiotic colistin. Previously, we reported silver nitrate and auranofin serve as colistin adjuvants for combating mcr-1-positive bacteria. Herein, we uncovered more gold-based drugs and nanoparticles, and found that they exhibited varying degree of synergisms with colistin on killing mcr-1-positive bacteria. However, pre-activation of the drugs by either glutathione or N-acetyl cysteine, thus releasing and accumulating gold ions, is perquisite for their abilities to substitute zinc cofactor from MCR-1 enzyme. X-ray crystallography and biophysical studies further supported the proposed mechanism. This study not only provides basis for combining gold-based drugs and colistin for combating mcr-1-positive bacterial infections, but also undoubtedly opens a new horizon for metabolism details of gold-based drugs in overcoming antimicrobial resistance.

Knockdown of ARL5B Induces Mitochondrial-mediated Apoptosis and Inhibits Glycolysis in Breast Cancer Cells by Activating MDA5 Signaling.

AIM: Mitochondria are essential for energy metabolism in the tumor microenvironment and the survival of cancer cells. BACKGROUND: ADP-ribosylation factor-like GTPase 5b (ARL5B) has been found to be associated with mitochondrial dysfunction and breast cancer (BC) progression, but the underlying mechanism needs to be further understood. OBJECTIVE: We investigated the effects of ARL5B on the apoptosis and glycolysis of breast cancer cells and its underlying mechanisms. METHODS: Quantitative reverse transcription-PCR (qRT-PCR) and western blot assays were used to detect the expression of ARL5B in breast cancer tissues and cells. An ARL5B loss-of-function assay was performed to verify its role in BC development. RESULTS: ARL5B was upregulated in breast cancer tissues and cell lines. ARL5B knockdown induced apoptosis and activated the mitochondrial pathway in breast cancer cells. Interestingly, the inhibition of ARL5B repressed the aerobic glycolysis of breast cancer cells. The role of ARL5B in breast cancer cells was exerted by mediating the activation of viral RNA sensor MDA5-evoked signaling. Silencing ARL5B triggered MDA5 signaling by upregulating the key proteins involved in the MDA5 pathway. Importantly, MDA5 silencing reversed the effects of ARL5B knockdown on mitochondrial-mediated apoptosis and glycolysis, whereas poly (I:C), as a ligand for MDA5, further enhanced ARL5B knockdown- facilitated mitochondrial apoptosis and the inhibition of glycolysis. CONCLUSION: The knockdown of ARL5B activated MDA5 signaling and thus led to the enhanced mitochondrial- mediated apoptosis and glycolysis inhibition in breast cancer cells. Our study suggested that ARL5B might be a potential therapy target for BC.

Arsenic trioxide targets Hsp60, triggering degradation of p53 and survivin.

The mechanisms of action of arsenic trioxide (ATO), a clinically used drug for the treatment of acute promyelocytic leukemia (APL), have been actively studied mainly through characterization of individual putative protein targets. There appear to be no studies at a system level. Herein, we integrate metalloproteomics through a newly developed organoarsenic probe, As-AC (C20H17AsN4O3S2) with quantitative proteomics, allowing 37 arsenic binding and 250 arsenic regulated proteins to be identified in NB4, a human APL cell line. Bioinformatics analysis reveals that ATO disrupts multiple physiological processes, in particular, chaperone-related protein folding and cellular response to stress. Furthermore, we discover heat shock protein 60 (Hsp60) as a vital target of ATO. Through biophysical and cell-based assays, we demonstrate that ATO binds to Hsp60, leading to abolishment of Hsp60 refolding capability. Significantly, the binding of ATO to Hsp60 disrupts the formation of Hsp60-p53 and Hsp60-survivin complexes, resulting in degradation of p53 and survivin. This study provides significant insights into the mechanism of action of ATO at a systemic perspective, and serves as guidance for the rational design of metal-based anticancer drugs.

The study of antiviral drugs targeting SARS-CoV-2 nucleocapsid and spike proteins through large-scale compound repurposing.

Contributing to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) clinical treatment, a drug library encompassing approximately 3,142 clinical-stage or FDA-approved small molecules is profiled to identify the candidate therapeutic inhibitors targeting nucleocapsid protein (N) and spike protein (S) of SARS-CoV-2. 16 screened candidates with higher binding affinity are evaluated via virtual screening. Comparing to those under trial/temporarily used antivirus drugs (i.e., umifenovir, lopinavir), ceftriaxone, cefotaxime, and cefuroxime show higher binding affinities to the N-terminal domain of N protein (N-NTD), C-terminal domain of N protein (N-CTD), and receptor-binding domain of S protein (S-RBD). Cefotaxime and cefuroxime have high binding affinities towards S-RBD with angiotensin-converting enzyme 2 (ACE2) complex via influence the critical interface sites at the interface of S-RBD (Arg403, Tyr453, Trp495, Gly496, Phe497, Asn501and Tyr505) and ACE2 (Asn33, His34, Glu37, Asp38, Lys353, Ala386, Ala387, Gln388, Pro389, Phe390 and Arg393) complex.

One step further into the blackbox: a pilot study of how to build more confidence around an AI-based decision system of breast nodule assessment in 2D ultrasound.

OBJECTIVES: To investigate how a DL model makes decisions in lesion classification with a newly defined region of evidence (ROE) by incorporating "explainable AI" (xAI) techniques. METHODS: A data set of 785 2D breast ultrasound images acquired from 367 females. The DenseNet-121 was used to classify whether the lesion is benign or malignant. For performance assessment, classification results are evaluated by calculating accuracy, sensitivity, specificity, and receiver operating characteristic for experiments of both coarse and fine regions of interest (ROIs). The area under the curve (AUC) was evaluated, and the true-positive, false-positive, true-negative, and false-negative results with breakdown in high, medium, and low resemblance on test sets were also reported. RESULTS: The two models with coarse and fine ROIs of ultrasound images as input achieve an AUC of 0.899 and 0.869, respectively. The accuracy, sensitivity, and specificity of the model with coarse ROIs are 88.4%, 87.9%, and 89.2%, and with fine ROIs are 86.1%, 87.9%, and 83.8%, respectively. The DL model captures ROE with high resemblance of physicians' consideration as they assess the image. CONCLUSIONS: We have demonstrated the effectiveness of using DenseNet to classify breast lesions with limited quantity of 2D grayscale ultrasound image data. We have also proposed a new ROE-based metric system that can help physicians and patients better understand how AI makes decisions in reading images, which can potentially be integrated as a part of evidence in early screening or triaging of patients undergoing breast ultrasound examinations. KEY POINTS: • The two models with coarse and fine ROIs of ultrasound images as input achieve an AUC of 0.899 and 0.869, respectively. The accuracy, sensitivity, and specificity of the model with coarse ROIs are 88.4%, 87.9%, and 89.2%, and with fine ROIs are 86.1%, 87.9%, and 83.8%, respectively. • The first model with coarse ROIs is slightly better than the second model with fine ROIs according to these evaluation metrics. • The results from coarse ROI and fine ROI are consistent and the peripheral tissue is also an impact factor in breast lesion classification.

S-Dimethylarsino-glutathione (darinaparsin®) targets histone H3.3, leading to TRAIL-induced apoptosis in leukemia cells.

Histone H3.3 was identified as an arsenic-binding protein of S-dimethylarsino-glutathione (ZIO-101, darinaparsin®) in leukemia cells by GE-ICP-MS. Such a binding results in TRAIL-induced apoptosis. We further validate histone H3.3 as a vital target for ZIO-101, offering new information on the mode of action of arsenic-based anticancer agents.

Multi-omics and temporal dynamics profiling reveal disruption of central metabolism in Helicobacter pylori on bismuth treatment.

Integration of multi-omics enables uncovering cellular responses to stimuli or the mechanism of action of a drug at a system level. Bismuth drugs have long been used for the treatment of Helicobacter pylori infection and their antimicrobial activity was attributed to dysfunction of multiple proteins based on previous proteome-wide studies. Herein, we investigated the response of H. pylori to a bismuth drug at transcriptome and metabolome levels. Our multi-omics data together with bioassays comprehensively reveal the impact of bismuth on a diverse array of intracellular pathways, in particular, disruption of central carbon metabolism is systematically evaluated as a primary bismuth-targeting system in H. pylori. Through temporal dynamics profiling, we demonstrate that bismuth initially perturbs the TCA cycle and then urease activity, followed by the induction of oxidative stress and inhibition of energy production, and in the meantime, induces extensive down-regulation in H. pylori metabolome. The present study thus expands our knowledge on the inhibitory actions of bismuth and provides a novel systematic perspective of H. pylori in response to a clinical drug that sheds light on enhanced therapeutic methodologies.

On-line coupling of continuous-flow gel electrophoresis with inductively coupled plasma-mass spectrometry to quantitatively evaluate intracellular metal binding properties of metallochaperones HpHypA and HpHspA in E. coli cells.

On-line coupling of gel electrophoresis with inductively coupled plasma-mass spectrometry (GE-ICP-MS) offers a strategy to monitor intracellular metals and their associated proteins simultaneously. Herein, we examine the feasibility of the GE-ICP-MS system in the quantitative analysis of intracellular metal binding properties using two Helicobacter pylori metallochaperones HypA and HspA overexpressed in E. coli cells as showcases. We show that parallel detection of metal and sulfur signals allows accurate quantification of intracellular metal-protein stoichiometries, even for metalloproteins that bind metal ions with micromolar affinities. Using this approach, we demonstrate that only a trace amount of Ni(2+) is associated with HpHypA in cells, distinct from the in vitro observation of stoichiometric binding, while HpHypA exhibits high fidelity towards its structural metal Zn(2+) with stoichiometric Zn(2+) binding. In contrast, HpHspA associates with Zn(2+), Ni(2+), Cu(2+) and Co(2+) from an essential metal pool with ca. 0.5 molar equivalents of total metals bound per HpHspA monomer. The metal binding properties of both HpHypA and HpHspA were altered by Bi(3+). The binding of both Zn(2+) and Ni(2+) to HpHypA was suppressed under the stress of Bi(3+) in cells, different from in vitro studies that showed that Bi(3+) interfered with Zn(2+) but not Ni(2+) binding. This study provides an analytical approach to investigate the intracellular metal selectivity of overexpressed metalloproteins.

Structural elucidation and in vitro antioxidant activities of a new heteropolysaccharide from Litchi chinensis.

Two polysaccharides, LCP70S-1 and LCP70W, were isolated from the pulp tissues of Litchi chinensis by anion-exchange chromatography and gel-filtration chromatography, while the structure of LCP70S-1 was elucidated and its physico-chemical properties was analyzed. The results demonstrated that LCP70S-1 is composed of L-rhamnose, L-arabinose and D-galactose in the ratio of 1.06:6.39:4.21, and the main chain of the heteropolysaccharide possess (1→3,6)-linked galactopyranosyl branches at O-6. The three branches consist of (1→3)-linked rhamnopyranosyl residues, (1→3,6)-linked galactopyranosyl and (1→5)-linked arabinopyranosyl residues, and terminated with (1→)-linked arabinopyranosyl residues, respectively. The two polysaccharides were further evaluated with 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging activities and their reducing power in vitro. The results showed that LCP70W and LCP70S-1 possessed significant antioxidant activities, especially for LCP70S-1. As such, LCP70S-1 could potentially serve as an antioxidant and would value further study for human healthcare.

Structural characterization of a novel polysaccharide from pulp tissues of Litchi chinensis and its immunomodulatory activity.

A novel polysaccharide (LCP50W) with a molecular weight of 4.72 × 10(4) Da was isolated from the pulp tissues of Litchi chinensis . The chemical structure of LCP50W was characterized using physicochemical and instrumental analyses. The results indicated that the main chain of LCP50W consisted of (1→3)-linked ß-L-rhamnopyranosyl, (1→6)-linked α-D-glucopyranosyl, and (1→2,6)-linked α-D-glucopyranosyl residues, which branched at O-6. The three branches consisted of (1→2)-linked α-L-rhamnopyranosyl, (1→3)-linked α-D-galactopyranosyl, and (1→3)-linked α-L-mannopyranosyl residues, terminated with (1→)-linked α-L-arabinopyranosyl residues, respectively. The in vitro immunomodulatory assay revealed that LCP50W promoted the proliferation of mouse splenocytes and enhanced the cytotoxicity of NK cells. LCP50W boosted the secretion of Th1 cytokine IFN-γ while it inhibited the secretion of Th2 cytokine IL-4; it also enhanced the expression of T-bet while it inhibited the expression of GATA-3. Additionally, LCP50W promoted the development of cell cycle toward the S phase.

Structure characterization and antioxidant activity of a novel polysaccharide isolated from pulp tissues of Litchi chinensis.

A novel polysaccharide (LCP50S-2) with antioxidant activity was isolated from Litchi chinensis Sonn. The structure of LCP50S-2 was elucidated on the basis of physicochemical and instrumental analyses, and its average molecular weight was determined by gel permeation chromatography to be 2.19 × 10(2) kDa. The backbone of LCP50S-2 was composed of (1→3)-linked ß-L-rhamnopyranosyl residues, (1→4)-linked α-D-xylopyranosyl residues, (1→4)-linked ß-D-glucopyranosyl residues, and (1→4)-linked α-D-glucopyranosyl residues which branched at O-6. The two branches consisted of α-L-arabinopyranosyl residues and (1→6)-linked ß-D-galactopyranosyl residues terminated with α-L-arabinopyranosyl residues, respectively. In the in vitro antioxidant assay, LCP50S-2 was found to possess DPPH radical-scavenging activity and hydroxyl radical-scavenging activity with IC(50) values of 220 and 266 µg/mL, respectively.

[The purification and characterization of polysaccharides isolated from Ginkgo biloba and their in vitro antioxidant activities].

OBJECTIVE: To isolate and identify the polysaccharides of Ginkgo biloba and determine their antioxidant activities in vitro. METHODS: Used hot extraction and alcohol precipitation to get the crude polysaccharides, removed protein with Sevag method, further purify by column chromatography packed with DEAE-52 and DEAE-Sepharose Fast Flow. The homogeneity and molecular weights were evaluated, configuration and monosaccharide composition were measured by IR and high performance ion chromatography analysis, the scavenging activities of GBPB-S on hydroxyl radical and DPPH were measured. RESULTS: The molecular weights of GBPB-W and GBPB-S were 26 300 and 19 100, and both of them were composed of rhamnose, arabinose, galactose, glucose and mannose with the ratios of (3.48: 8.47:3.73: 1.76: 1) and (5.34: 5.37: 5.27: 1:1.68). GBPB-S had certain scavenging effect on hydroxyl radical and DPPH. CONCLUSION: The polysaccharide isolated from Ginkgo biloba has a direct antioxidant activities in vitro.