Protein Corona Gold Nanoparticles Fingerprinting Reveals a Profile of Blood Coagulation Proteins in the Serum of HER2-Overexpressing Breast Cancer Patients

Omics-Enhanced Nanomedicine for Cancer Therapy

Cancer nanomedicine has emerged as a promising approach to overcome the limitations of conventional cancer therapies, offering enhanced efficacy and safety in cancer management. However, the inherent heterogeneity of tumors presents increasing challenges for the application of cancer nanomedicine in both diagnosis and treatment. This heterogeneity necessitates the integration of advanced and high-throughput analytical techniques to tailor nanomedicine strategies to individual tumor profiles. Omics technologies, encompassing genomics, epigenomics, transcriptomics, proteomics, metabolomics, and more, provide unparalleled insights into the molecular and cellular mechanisms underlying cancer. By dissecting tumor heterogeneity across multiple levels, these technologies offer robust support for the development of personalized and precise cancer nanomedicine strategies. In this review, the principles, techniques, and applications of key omics technologies are summarized. Especially, the synergistic integration of omics and nanomedicine in cancer therapy is explored, focusing on enhanced diagnostic accuracy, optimized therapeutic strategies and the assessment of nanomedicine-mediated biological responses. Moreover, this review addresses current challenges and outlines future directions in the field of omics-enhanced nanomedicine. By offering valuable insights and guidance, this review aims to advance the integration of omics with nanomedicine, ultimately driving improved diagnostic and therapeutic strategies for cancer.

Leveraging single-cell transcriptomic data to uncover immune suppressive cancer cell subsets in triple-negative canine breast cancers

Introduction

Single-cell RNA sequencing (scRNA-seq) has become an essential tool for uncovering the complexities of various physiological and immunopathological conditions in veterinary medicine. However, there is currently limited information on immune-suppressive cancer subsets in canine breast cancers. In this study, we aimed to identify and characterize immune-suppressive subsets of triple-negative canine breast cancer (TNBC) by utilizing integrated scRNA-seq data from published datasets.

Methods

Published scRNA-seq datasets, including data from six groups of 30 dogs, were subjected to integrated bioinformatic analysis.

Results

Immune modulatory TNBC subsets were identified through functional enrichment analysis using immune-suppressive gene sets, including those associated with anti-inflammatory and M2-like macrophages. Key immune-suppressive signaling, such as viral infection, angiogenesis, and leukocyte chemotaxis, was found to play a role in enabling TNBC to evade immune surveillance. In addition, interactome analysis revealed significant interactions between distinct subsets of cancer cells and effector T cells, suggesting potential T-cell suppression.

Discussion

The present study demonstrates a versatile and scalable approach to integrating and analyzing scRNA-seq data, which successfully identified immune-modulatory subsets of canine TNBC. It also revealed potential mechanisms through which TNBC promotes immune evasion in dogs. These findings are crucial for advancing the understanding of the immune pathogenesis of canine TNBC and may aid in the development of new immune-based therapeutic strategies.

Biomolecular Corona of Gold Nanoparticles: The Urgent Need for Strong Roots to Grow Strong Branches

Gold nanoparticles (GNPs) are largely employed in diagnostics/biosensors and are among the most investigated nanomaterials in biology/medicine. However, few GNP-based nanoformulations have received FDA approval to date, and promising in vitro studies have failed to translate to in vivo efficacy. One key factor is that biological fluids contain high concentrations of proteins, lipids, sugars, and metabolites, which can adsorb/interact with the GNP's surface, forming a layer called biomolecular corona (BMC). The BMC can mask prepared functionalities and target moieties, creating new surface chemistry and determining GNPs' biological fate. Here, the current knowledge is summarized on GNP-BMCs, analyzing the factors driving these interactions and the biological consequences. A partial fingerprint of GNP-BMC analyzing common patterns of composition in the literature is extrapolated. However, a red flag is also risen concerning the current lack of data availability and regulated form of knowledge on BMC. Nanomedicine is still in its infancy, and relying on recently developed analytical and informatic tools offers an unprecedented opportunity to make a leap forward. However, a restart through robust shared protocols and data sharing is necessary to obtain "stronger roots". This will create a path to exploiting BMC for human benefit, promoting the clinical translation of biomedical nanotools.

Designed Nanomaterials-Assisted Proteomics and Metabolomics Analysis for In Vitro Diagnosis

In vitro diagnosis (IVD) is pivotal in modern medicine, enabling early disease detection and treatment optimization. Omics technologies, particularly proteomics and metabolomics, offer profound insights into IVD. Despite its significance, omics analyses for IVD face challenges, including low analyte concentrations and the complexity of biological environments. In addition, the direct omics analysis by mass spectrometry (MS) is often hampered by issues like large sample volume requirements and poor ionization efficiency. Through manipulating their size, surface charge, and functionalization, as well as the nanoparticle-fluid incubation conditions, nanomaterials have emerged as a promising solution to extract biomolecules and enhance the desorption/ionization efficiency in MS detection. This review delves into the last five years of nanomaterial applications in omics, focusing on their role in the enrichment, separation, and ionization analysis of proteins and metabolites for IVD. It aims to provide a comprehensive update on nanomaterial design and application in omics, highlighting their potential to revolutionize IVD.

Fixation and Visualization of Full Protein Corona on Lipid Surface of Composite Nanoconstruction

Spontaneous sorption of proteins on the nanoparticles' surface leads to the fact that nanoparticles in biological media are always enveloped by a layer of proteins-the protein corona. Corona proteins affect the properties of nanoparticles and their behavior in a biological environment. In this regard, knowledge about the composition of the corona is a necessary element for the development of nanomedicine. Because proteins have different sorption efficacy, isolating particles with a full corona and characterizing the full corona is challenging. In this study, we propose a photo-activated cross-linker for full protein corona fixation. We believe that the application of our proposed approach will make it possible to capture and visualize the full corona on nanoparticles coated with a lipid shell.

Gold Nanoparticles in Triple-Negative Breast Cancer Therapeutics

BACKGROUND

Triple-negative breast cancer (TNBC) is the most aggressive type of breast cancer with enhanced metastasis and poor survival. Though chemotherapy, radiotherapy, photothermal therapy (PTT), photodynamic therapy (PDT), and gene delivery are used to treat TNBC, various side effects limit these therapeutics against TNBC. In this review article, we have focused on the mechanism of action of gold nanoparticles (AuNPs) to enhance the efficacy of therapeutics with targeted delivery on TNBC cells.

METHODS

Research data were accumulated from PubMed, Scopus, Web of Science, and Google Scholar using searching criteria "gold nanoparticles and triple-negative breast cancer" and "gold nanoparticles and cancer". Though we reviewed many old papers, the most cited papers were from the last ten years.

RESULTS

Various studies indicate that AuNPs can enhance bioavailability, site-specific drug delivery, and efficacy of chemotherapy, radiotherapy, PTT, and PDT as well as modulate gene expression. The role of AuNPs in the modulation of TNBC therapeutics through the inhibition of cell proliferation, progression, and metastasis has been proved in vitro and in vivo studies. As these mechanistic actions of AuNPs are most desirable to develop drugs with enhanced therapeutic efficacy against TNBC, it might be a promising approach to apply AuNPs for TNBC therapeutics.

CONCLUSION

This article reviewed the mechanism of action of AuNPs and their application in the enhancement of therapeutics against TNBC. Much more attention is required for studying the role of AuNPs in developing them either as a single or synergistic anticancer agent against TNBC.

Nano-omics: nanotechnology-based multidimensional harvesting of the blood-circulating cancerome

Over the past decade, the development of 'simple' blood tests that enable cancer screening, diagnosis or monitoring and facilitate the design of personalized therapies without the need for invasive tumour biopsy sampling has been a core ambition in cancer research. Data emerging from ongoing biomarker development efforts indicate that multiple markers, used individually or as part of a multimodal panel, are required to enhance the sensitivity and specificity of assays for early stage cancer detection. The discovery of cancer-associated molecular alterations that are reflected in blood at multiple dimensions (genome, epigenome, transcriptome, proteome and metabolome) and integration of the resultant multi-omics data have the potential to uncover novel biomarkers as well as to further elucidate the underlying molecular pathways. Herein, we review key advances in multi-omics liquid biopsy approaches and introduce the 'nano-omics' paradigm: the development and utilization of nanotechnology tools for the enrichment and subsequent omics analysis of the blood-circulating cancerome.

Gold Nanoparticles Contact with Cancer Cell: A Brief Update

The fine-tuning of the physicochemical properties of gold nanoparticles has facilitated the rapid development of multifunctional gold-based nanomaterials with diagnostic, therapeutic, and therapeutic applications. Work on gold nanoparticles is increasingly focusing on their cancer application. This review provides a summary of the main biological effects exerted by gold nanoparticles on cancer cells and highlights some critical factors involved in the interaction process (protein corona, tumor microenvironment, surface functionalization). The review also contains a brief discussion of the application of gold nanoparticles in target discovery.

Chemical and Biophysical Signatures of the Protein Corona in Nanomedicine

An inconvenient hurdle in the practice of nanomedicine is the protein corona, a spontaneous collection of biomolecular species by nanoparticles in living systems. The protein corona is dynamic in composition and may entail improved water suspendability and compromised delivery and targeting to the nanoparticles. How much of this nonspecific protein ensemble is determined by the chemistry of the nanoparticle core and its surface functionalization, and how much of this entity is dictated by the biological environments that vary spatiotemporally in vivo? How do we "live with" and exploit the protein corona without significantly sacrificing the efficacy of nanomedicines in diagnosing and curing human diseases? This article discusses the chemical and biophysical signatures of the protein corona and ponders challenges ahead for the field of nanomedicine.

Circulating Proteins Associated with Response and Resistance to Neoadjuvant Chemotherapy in HER2-Positive Breast Cancer

Simple Summary

The goal of this study was to find circulating proteins that can be easily sampled and incorporated into a clinical setting to improve predictive treatment response in HER2-positive breast cancer patients receiving neoadjuvant chemotherapy. We looked for potential biomarkers in serum, which we identified using two proteomics techniques: qualitative LC-MS/MS and a quantitative assay that assessed protein expression between responders and non-responders HER2-positive breast cancer patients to neoadjuvant chemotherapy.

Abstract

Despite the increasing use of neoadjuvant chemotherapy (NAC) in HER2-positive breast cancer (BC) patients, the clinical problem of predicting individual treatment response remains unanswered. Furthermore, the use of ineffective chemotherapeutic regimens should be avoided. Serum biomarker levels are being studied more and more for their ability to predict therapy response and aid in the development of personalized treatment regimens. This study aims to identify effective protein networks and biomarkers to predict response to NAC in HER2-positive BC patients through an exhaustive large-scale LC-MS/MS-based qualitative and quantitative proteomic profiling of serum samples from responders and non-responders. Serum samples from HER2-positive BC patients were collected before NAC and were processed by three methods (with and without nanoparticles). The qualitative analysis revealed differences in the proteomic profiles between responders and non-responders, mainly in proteins implicated in the complement and coagulation cascades and apolipoproteins. Qualitative analysis confirmed that three proteins (AFM, SERPINA1, APOD) were correlated with NAC resistance. In this study, we show that serum biomarker profiles can predict treatment response and outcome in the neoadjuvant setting. If these findings are further developed, they will be of significant clinical utility in the design of treatment regimens for individual BC patients.

Nanoparticle protein corona evolution: from biological impact to biomarker discovery

Nanoparticles exposed to biological fluids such as blood, quickly interact with their surrounding milieu resulting in a biological coating that results in large part as a function of the physicochemical properties of the nanomaterial. The large nanoparticle surface area-to-volume ratio further augments binding of biological molecules and the resulting biomolecular or protein corona, once thought of as problematic biofouling, is now viewed as a rich source of biological information that can guide the development of nanomedicines. This review gives an overview of the utility of the protein corona in proteomic profiling and discusses how a better understanding of nano-bio interactions can accelerate the clinical translation of nanomedicines and facilitate the identification of disease-specific biomarkers. With the FDA requirement of the protein corona analysis of nanoparticles in place, it is envisaged that analyzing the protein corona of nanoparticles on a case-by-case basis can provide highly valuable nano-bio interface information that can aid and improve their clinical translation.

Detection of Circulating Serum Protein Biomarkers of Non-Muscle Invasive Bladder Cancer after Protein Corona-Silver Nanoparticles Analysis by SWATH-MS

Because cystoscopy is expensive and invasive, a new method of detecting non-invasive muscular bladder cancer (NMIBC) is needed. This study aims to identify potential serum protein markers for NMIBC to improve diagnosis and to find treatment approaches that avoid disease progression to a life-threatening phenotype (muscle-invasive bladder cancer, MIBC). Here, silver nanoparticles (AgNPs, 9.73 ± 1.70 nm) as a scavenging device together with sequential window acquisition of all theoretical mass spectra (SWATH-MS) were used to quantitatively analyze the blood serum protein alterations in two NMIBC subtypes, T1 and Ta, and they were compared to normal samples (HC). NMIBC’s analysis of serum samples identified three major groups of proteins, the relative content of which is different from the HC content: proteins implicated in the complement and coagulation cascade pathways and apolipoproteins. In conclusion, many biomarker proteins were identified that merit further examination to validate their useful significance and utility within the clinical management of NMIBC patients.

Tear Proteomics in Keratoconus: A Quantitative SWATH-MS Analysis

Purpose

To elucidate dysregulated proteins in keratoconus (KC) to provide a better understanding of the molecular mechanisms that lead to the development of the disease using sequential window acquisition of all theoretical mass spectra (SWATH-MS) as a protein quantification tool of the tear proteomic profile.

Methods

Prospective cross-sectional study that includes 25 keratoconic eyes and 25 healthy eyes. All participants underwent a clinical, tomographic, and aberrometric exam. Tear sample was collected using Schirmer strips and analyzed by liquid chromatography with tandem mass spectrometry. SWATH-MS was used as a quantification tool of the tear proteomic profile. The expression of the quantified proteins was compared between groups, and the biological and molecular functions of the dysregulated proteins as well as their functional relationships were studied by in silico analysis.

Results

A total of 203 proteins were quantified in tear samples of patients with KC and control participants, of which 18 showed differential expression between groups (P < 0.05). An increase in the expression of 7 proteins and a decrease in the expression of 11 proteins were observed. Protein–protein interactions and gene ontology analysis showed the involvement of these dysregulated proteins in structural, inflammatory-immune, iron homeostasis, oxidative stress, and extracellular matrix proteolysis processes.

Conclusions

Tear protein quantification has revealed the dysregulation of proteins involved in biological processes previously associated with KC. Among them, iron homeostasis should be highlighted as a relevant pathway in the KC pathophysiology, and it should be taken into account in the development of therapeutic targets to cope with tissue damage derived from iron accumulation and toxicity.

Blood-based protein biomarkers in bladder urothelial tumors

Bladder cancer (BC) is the fifth most common cancer with a high prevalence rate. It is classically classified in two groups, namely non-muscle invasive (NMIBC) and muscle invasive (MIBC). NMIBC accounts for 75% of cases and has a better prognosis than MIBC. However, 30-50% of the NMIBC patients will show recurrences throughout their lives, and about 10-20% of them will progress to MIBC, with frequent metastasis and a reduced survival rate. The diagnosis of bladder cancer is confirmed by direct visualization of the tumour and other mucosal abnormalities with endoscopic excision using cystoscopy and transurethral resection of the bladder (TURBT). An adequate TURBT requires complete resection of all visible tumour with appropriate sampling of the bladder to assess the depth of invasion. However, for many years, researchers have attempted to identify and utilise urinary markers for bladder cancer detection. Voided urine cytology has been the mainstay of urine-based diagnosis of bladder cancer since originally described by Papanicolau and Marshall. Nonetheless, urine cytology has several drawbacks, including a poor sensitivity for low-grade/stage tumours, a lack of interobserver consistency and a variable range of readings (e.g., atypical, atypical-suspicious, non-diagnostic). These shortcomings have inspired the search for more sensitive bladder cancer biomarkers. To bring precision medicine to genitourinary oncology, the analysis of the plasma/serum wide genome and proteome offers promising possibilities.

Qualitative and Quantitative Comparison of Plasma Exosomes from Neonates and Adults

Exosomes are extracellular vesicles that contain nucleic acids, lipids and metabolites, and play a critical role in health and disease as mediators of intercellular communication. The majority of extracellular vesicles in the blood are platelet-derived. Compared to adults, neonatal platelets are hyporeactive and show impaired granule release, associated with defects in Soluble N-ethylmaleimide-sensitive fusion Attachment protein REceptor (SNARE) proteins. Since these proteins participate in biogenesis of exosomes, we investigated the potential differences between newborn and adult plasma-derived exosomes. Plasma-derived exosomes were isolated by ultracentrifugation of umbilical cord blood from full-term neonates or peripheral blood from adults. Exosome characterization included size determination by transmission electron microscopy and quantitative proteomic analysis. Plasma-derived exosomes from neonates were significantly smaller and contained 65% less protein than those from adults. Remarkably, 131 proteins were found to be differentially expressed, 83 overexpressed and 48 underexpressed in neonatal (vs. adult) exosomes. Whereas the upregulated proteins in plasma exosomes from neonates are associated with platelet activation, coagulation and granule secretion, most of the underexpressed proteins are immunoglobulins. This is the first study showing that exosome size and content change with age. Our findings may contribute to elucidating the potential “developmental hemostatic mismatch risk” associated with transfusions containing plasma exosomes from adults.