Quest for Multifunctionality: Current Progress in the Characterization of Heterometallic Metal-Organic Frameworks.

Metal-organic frameworks (MOFs) are a class of porous, crystalline materials that have been systematically developed for a broad range of applications. Incorporation of two or more metals into a single crystalline phase to generate heterometallic MOFs has been shown to lead to synergistic effects, in which the whole is oftentimes greater than the sum of its parts. Because geometric proximity is typically required for metals to function cooperatively, deciphering and controlling metal distributions in heterometallic MOFs is crucial to establish structure-function relationships. However, determination of short- and long-range metal distributions is nontrivial and requires the use of specialized characterization techniques. Advancements in the characterization of metal distributions and interactions at these length scales is key to rapid advancement and rational design of functional heterometallic MOFs. This perspective summarizes the state-of-the-art in the characterization of heterometallic MOFs, with a focus on techniques that allow metal distributions to be better understood. Using complementary analyses, in conjunction with computational methods, is critical as this field moves toward increasingly complex, multifunctional systems.

Encoding Multilayer Complexity in Anti-Counterfeiting Heterometallic MOF-Based Optical Tags.

Optical tags provide a way to quickly and unambiguously identify valuable assets. Current tag fluorophore options lack the tunability to allow combined methods of encoding in a single material. Herein we report a design strategy to encode multilayer complexity in a family of heterometallic rare-earth metal-organic frameworks based on highly connected nonanuclear clusters. To impart both intricacy and security, a synergistic approach was implemented resulting in both overt (visible) and covert (near-infrared, NIR) properties, with concomitant multi-emissive spectra and tunable luminescence lifetimes. Tag authentication is validated with a variety of orthogonal detection methodologies. Importantly, the effect induced by subtle compositional changes on intermetallic energy transfer, and thus on the resulting photophysical properties, is demonstrated. This strategy can be widely implemented to create a large library of highly complex, difficult-to-counterfeit optical tags.

Protocells: Modular Mesoporous Silica Nanoparticle-Supported Lipid Bilayers for Drug Delivery.

Mesoporous silica nanoparticle-supported lipid bilayers, termed 'protocells,' represent a potentially transformative class of therapeutic and theranostic delivery vehicle. The field of targeted drug delivery poses considerable challenges that cannot be addressed with a single 'magic bullet'. Consequently, the protocell has been designed as a modular platform composed of interchangeable biocompatible components. The mesoporous silica core has variable size and shape to direct biodistribution and a controlled pore size and surface chemistry to accommodate diverse cargo. The encapsulating supported lipid bilayer can be modified with targeting and trafficking ligands as well as polyethylene glycol (PEG) to effect selective binding, endosomal escape of cargo, drug efflux prevention, and potent therapeutic delivery, while maintaining in vivo colloidal stability. This review describes the individual components of the platform, including the mesoporous silica nanoparticle core and supported lipid bilayer, their assembly (by multiple techniques) into a protocell, and the combined, often synergistic, performance of the protocell based on in vitro and in vivo studies, including the assessment of biocompatibility and toxicity. In closing, the many emerging variations of the protocell theme and the future directions for protocell research are commented on.

Performance characteristics of the AmpliSeq Cancer Hotspot panel v2 in combination with the Ion Torrent Next Generation Sequencing Personal Genome Machine.

Next-Generation Sequencing is a rapidly advancing technology that has research and clinical applications. For many cancers, it is important to know the precise mutation(s) present, as specific mutations could indicate or contra-indicate certain treatments as well as be indicative of prognosis. Using the Ion Torrent Personal Genome Machine and the AmpliSeq Cancer Hotspot panel v2, we sequenced two pancreatic cancer cell lines, BxPC-3 and HPAF-II, alone or in mixtures, to determine the error rate, sensitivity, and reproducibility of this system. The system resulted in coverage averaging 2000× across the various amplicons and was able to reliably and reproducibly identify mutations present at a rate of 5%. Identification of mutations present at a lower rate was possible by altering the parameters by which calls were made, but with an increase in erroneous, low-level calls. The panel was able to identify known mutations in these cell lines that are present in the COSMIC database. In addition, other, novel mutations were also identified that may prove clinically useful. The system was assessed for systematic errors such as homopolymer effects, end of amplicon effects and patterns in NO CALL sequence. Overall, the system is adequate at identifying the known, targeted mutations in the panel.

Silver nanoparticles: correlating nanoparticle size and cellular uptake with genotoxicity.

The focus of this research was to develop a better understanding of the pertinent physico-chemical properties of silver nanoparticles (AgNPs) that affect genotoxicity, specifically how cellular uptake influences a genotoxic cell response. The genotoxicity of AgNPs was assessed for three potential mechanisms: mutagenicity, clastogenicity and DNA strand-break-based DNA damage. Mutagenicity (reverse mutation assay) was assessed in five bacterial strains of Salmonella typhimurium and Echerichia coli, including TA102 that is sensitive to oxidative DNA damage. AgNPs of all sizes tested (10, 20, 50 and 100nm), along with silver nitrate (AgNO3), were negative for mutagenicity in bacteria. No AgNPs could be identified within the bacteria cells using transmission electron microscopy (TEM), indicating these bacteria lack the ability to actively uptake AgNPs 10nm or larger. Clastogenicity (flow cytometry-based micronucleus assay) and intermediate DNA damage (DNA strand breaks as measured in the Comet assay) were assessed in two mammalian white blood cell lines: Jurkat Clone E6-1 and THP-1. It was observed that micronucleus and Comet assay end points were inversely correlated with AgNP size, with smaller NPs inducing a more genotoxic response. TEM results indicated that AgNPs were confined within intracellular vesicles of mammalian cells and did not penetrate the nucleus. The genotoxicity test results and the effect of AgNO3 controls suggest that silver ions may be the primary, and perhaps only, cause of genotoxicity. Furthermore, since AgNO3 was not mutagenic in the gram-negative bacterial Ames strains tested, the lack of bacterial uptake of the AgNPs may not be the major reason for the lack of genotoxicity observed.

Label-Free, Noninvasive Bone Cell Classification by Hyperspectral Confocal Raman Microscopy.

Characterizing and identifying cells in multicellular in vitro models remain a substantial challenge. Here, we utilize hyperspectral confocal Raman microscopy and principal component analysis coupled with linear discriminant analysis to form a label-free, noninvasive approach for classifying bone cells and osteosarcoma cells. Through the development of a library of hyperspectral Raman images of the K7M2-wt osteosarcoma cell lines, 7F2 osteoblast cell lines, RAW 264.7 macrophage cell line, and osteoclasts induced from RAW 264.7 macrophages, we built a linear discriminant model capable of correctly identifying each of these cell types. The model was cross-validated using a k-fold cross validation scheme. The results show a minimum of 72% accuracy in predicting cell type. We also utilize the model to reconstruct the spectra of K7M2 and 7F2 to determine whether osteosarcoma cancer cells and normal osteoblasts have any prominent differences that can be captured by Raman. We find that the main differences between these two cell types are the prominence of the ß-sheet protein secondary structure in K7M2 versus the α-helix protein secondary structure in 7F2. Additionally, differences in the CH2 deformation Raman feature highlight that the membrane lipid structure is different between these cells, which may affect the overall signaling and functional contrasts. Overall, we show that hyperspectral confocal Raman microscopy can serve as an effective tool for label-free, nondestructive cellular classification and that the spectral reconstructions can be used to gain deeper insight into the differences that drive different functional outcomes of different cells.

Orthogonal luminescence lifetime encoding by intermetallic energy transfer in heterometallic rare-earth MOFs.

Lifetime-encoded materials are particularly attractive as optical tags, however examples are rare and hindered in practical application by complex interrogation methods. Here, we demonstrate a design strategy towards multiplexed, lifetime-encoded tags via engineering intermetallic energy transfer in a family of heterometallic rare-earth metal-organic frameworks (MOFs). The MOFs are derived from a combination of a high-energy donor (Eu), a low-energy acceptor (Yb) and an optically inactive ion (Gd) with the 1,2,4,5 tetrakis(4-carboxyphenyl) benzene (TCPB) organic linker. Precise manipulation of the luminescence decay dynamics over a wide microsecond regime is achieved via control over metal distribution in these systems. Demonstration of this platform's relevance as a tag is attained via a dynamic double encoding method that uses the braille alphabet, and by incorporation into photocurable inks patterned on glass and interrogated via digital high-speed imaging. This study reveals true orthogonality in encoding using independently variable lifetime and composition, and highlights the utility of this design strategy, combining facile synthesis and interrogation with complex optical properties.

Lipid-coated mesoporous silica nanoparticles for anti-viral applications via delivery of CRISPR-Cas9 ribonucleoproteins.

Emerging and re-emerging viral pathogens present a unique challenge for anti-viral therapeutic development. Anti-viral approaches with high flexibility and rapid production times are essential for combating these high-pandemic risk viruses. CRISPR-Cas technologies have been extensively repurposed to treat a variety of diseases, with recent work expanding into potential applications against viral infections. However, delivery still presents a major challenge for these technologies. Lipid-coated mesoporous silica nanoparticles (LCMSNs) offer an attractive delivery vehicle for a variety of cargos due to their high biocompatibility, tractable synthesis, and amenability to chemical functionalization. Here, we report the use of LCMSNs to deliver CRISPR-Cas9 ribonucleoproteins (RNPs) that target the Niemann-Pick disease type C1 gene, an essential host factor required for entry of the high-pandemic risk pathogen Ebola virus, demonstrating an efficient reduction in viral infection. We further highlight successful in vivo delivery of the RNP-LCMSN platform to the mouse liver via systemic administration.

Bridging the In Vitro to In Vivo gap: Using the Chick Embryo Model to Accelerate Nanoparticle Validation and Qualification for In Vivo studies.

We postulate that nanoparticles (NPs) for use in therapeutic applications have largely not realized their clinical potential due to an overall inability to use in vitro results to predict NP performance in vivo. The avian embryo and associated chorioallantoic membrane (CAM) has emerged as an in vivo preclinical model that bridges the gap between in vitro and in vivo, enabling rapid screening of NP behavior under physiologically relevant conditions and providing a rapid, accessible, economical, and more ethical means of qualifying nanoparticles for in vivo use. The CAM is highly vascularized and mimics the diverging/converging vasculature of the liver, spleen, and lungs that serve as nanoparticle traps. Intravital imaging of fluorescently labeled NPs injected into the CAM vasculature enables immediate assessment and quantification of nano-bio interactions at the individual NP scale in any tissue of interest that is perfused with a microvasculature. In this review, we highlight how utilization of the avian embryo and its CAM as a preclinical model can be used to understand NP stability in blood and tissues, extravasation, biocompatibility, and NP distribution over time, thereby serving to identify a subset of NPs with the requisite stability and performance to introduce into rodent models and enabling the development of structure-property relationships and NP optimization without the sacrifice of large populations of mice or other rodents. We then review how the chicken embryo and CAM model systems have been used to accelerate the development of NP delivery and imaging agents by allowing direct visualization of targeted (active) and nontargeted (passive) NP binding, internalization, and cargo delivery to individual cells (of relevance for the treatment of leukemia and metastatic cancer) and cellular ensembles (e.g., cancer xenografts of interest for treatment or imaging of cancer tumors). We conclude by showcasing emerging techniques for the utilization of the CAM in future nano-bio studies.

Programmable Photoluminescence via Intrinsic and DNA-Fluorophore Association in a Mixed Cluster Heterometallic MOF.

A rapid and facile design strategy to create a highly complex optical tag with programmable, multimodal photoluminescent properties is described. This was achieved via intrinsic and DNA-fluorophore hidden signatures. As a first covert feature of the tag, an intricate novel heterometallic near-infrared (NIR)-emitting mesoporous metal-organic framework (MOF) was designed and synthesized. The material is constructed from two chemically distinct, homometallic hexanuclear clusters based on Nd and Yb. Uniquely, the Nd-based cluster is observed here for the first time in a MOF and consists of two staggered Nd µ3-oxo trimers. To generate controlled, multimodal, and tailorable emission with difficult to counterfeit features, the NIR-emissive MOF was post-synthetically modified via a fluorescent DNA oligo labeling design strategy. The surface attachment of several distinct fluorophores, including the simultaneous attachment of up to three distinct fluorescently labeled oligos was achieved, with excitation and emission properties across the visible spectrum (480-800 nm). The DNA inclusion as a secondary covert element in the tag was demonstrated via the detection of SYBR Gold dye association. Importantly, the approach implemented here serves as a rapid and tailorable way to encrypt distinct information in a facile and modular fashion and provides an innovative technology in the quest toward complex optical tags.

Covert MOF-Based Photoluminescent Tags via Tunable Linker Energetics.

Optical anticounterfeiting tags utilize the photoluminescent properties of materials to encode unique patterns, enabling identification and validation of important items and assets. These tags must combine optical complexity with ease of production and authentication to both prevent counterfeiting and to remain practical for widespread use. Metal-organic frameworks (MOFs) based on polynuclear, rare earth clusters are ideal materials platforms for this purpose, combining fine control over structure and composition, with tunable, complex energy transfer mechanisms via both linker and metal components. Here we report the design and synthesis of a set of heterometallic MOFs based on combinations of Eu, Nd, and Yb with the tetratopic linker 1,3,6,8-tetrakis(4-carboxyphenyl)pyrene. The energetics of this linker facilitate the intentional concealment of the visible emissions from Eu while retaining the infrared emissions of Nd and Yb, creating an optical tag with multiple covert elements. Unique to the materials system reported herein, we document the occurrence of a previously not observed 11-metal cluster correlated with the presence of Yb in the MOFs, coexisting with a commonly encountered 9-metal cluster. We demonstrate the utility of these materials as intricate optical tags with both rapid and in-depth screening techniques, utilizing orthogonal identifiers across composition, emission spectra, and emission decay dynamics. This work highlights the important effect of linker selection in controlling the resulting photoluminescent properties in MOFs and opens an avenue for the targeted design of highly complex, multifunctional optical tags.

Upregulation of CD14 in mesenchymal stromal cells accelerates lipopolysaccharide-induced response and enhances antibacterial properties.

Mesenchymal stromal cells (MSCs) have broad-ranging therapeutic properties, including the ability to inhibit bacterial growth and resolve infection. However, the genetic mechanisms regulating these antibacterial properties in MSCs are largely unknown. Here, we utilized a systems-based approach to compare MSCs from different genetic backgrounds that displayed differences in antibacterial activity. Although both MSCs satisfied traditional MSC-defining criteria, comparative transcriptomics and quantitative membrane proteomics revealed two unique molecular profiles. The antibacterial MSCs responded rapidly to bacterial lipopolysaccharide (LPS) and had elevated levels of the LPS co-receptor CD14. CRISPR-mediated overexpression of endogenous CD14 in MSCs resulted in faster LPS response and enhanced antibacterial activity. Single-cell RNA sequencing of CD14-upregulated MSCs revealed a shift in transcriptional ground state and a more uniform LPS-induced response. Our results highlight the impact of genetic background on MSC phenotypic diversity and demonstrate that overexpression of CD14 can prime these cells to be more responsive to bacterial challenge.

Singleplex, multiplex and pooled sample real-time RT-PCR assays for detection of SARS-CoV-2 in an occupational medicine setting.

For workplaces which cannot operate as telework or remotely, there is a critical need for routine occupational SARS-CoV-2 diagnostic testing. Although diagnostic tests including the CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel (CDC Diagnostic Panel) (EUA200001) were made available early in the pandemic, resource scarcity and high demand for reagents and equipment necessitated priority of symptomatic patients. There is a clearly defined need for flexible testing methodologies and strategies with rapid turnaround of results for (1) symptomatic, (2) asymptomatic with high-risk exposures and (3) asymptomatic populations without preexisting conditions for routine screening to address the needs of an on-site work force. We developed a distinct SARS-CoV-2 diagnostic assay based on the original CDC Diagnostic Panel (EUA200001), yet, with minimum overlap for currently employed reagents to eliminate direct competition for limited resources. As the pandemic progressed with testing loads increasing, we modified the assay to include 5-sample pooling and amplicon target multiplexing. Analytical sensitivity of the pooled and multiplexed assays was rigorously tested with contrived positive samples in realistic patient backgrounds. Assay performance was determined with clinical samples previously assessed with an FDA authorized assay. Throughout the pandemic we successfully tested symptomatic, known contact and travelers within our occupational population with a ~ 24-48-h turnaround time to limit the spread of COVID-19 in the workplace. Our singleplex assay had a detection limit of 31.25 copies per reaction. The three-color multiplexed assay maintained similar sensitivity to the singleplex assay, while tripling the throughput. The pooling assay further increased the throughput to five-fold the singleplex assay, albeit with a subtle loss of sensitivity. We subsequently developed a hybrid 'multiplex-pooled' strategy to testing to address the need for both rapid analysis of samples from personnel at high risk of COVID infection and routine screening. Herein, our SARS-CoV-2 assays specifically address the needs of occupational healthcare for both rapid analysis of personnel at high-risk of infection and routine screening that is essential for controlling COVID-19 disease transmission. In addition to SARS-CoV-2 and COVID-19, this work demonstrates successful flexible assays developments and deployments with implications for emerging highly transmissible diseases and future pandemics.

Detection of breast cancer cells using targeted magnetic nanoparticles and ultra-sensitive magnetic field sensors.

INTRODUCTION: Breast cancer detection using mammography has improved clinical outcomes for many women, because mammography can detect very small (5 mm) tumors early in the course of the disease. However, mammography fails to detect 10 - 25% of tumors, and the results do not distinguish benign and malignant tumors. Reducing the false positive rate, even by a modest 10%, while improving the sensitivity, will lead to improved screening, and is a desirable and attainable goal. The emerging application of magnetic relaxometry, in particular using superconducting quantum interference device (SQUID) sensors, is fast and potentially more specific than mammography because it is designed to detect tumor-targeted iron oxide magnetic nanoparticles. Furthermore, magnetic relaxometry is theoretically more specific than MRI detection, because only target-bound nanoparticles are detected. Our group is developing antibody-conjugated magnetic nanoparticles targeted to breast cancer cells that can be detected using magnetic relaxometry. METHODS: To accomplish this, we identified a series of breast cancer cell lines expressing varying levels of the plasma membrane-expressed human epidermal growth factor-like receptor 2 (Her2) by flow cytometry. Anti-Her2 antibody was then conjugated to superparamagnetic iron oxide nanoparticles using the carbodiimide method. Labeled nanoparticles were incubated with breast cancer cell lines and visualized by confocal microscopy, Prussian blue histochemistry, and magnetic relaxometry. RESULTS: We demonstrated a time- and antigen concentration-dependent increase in the number of antibody-conjugated nanoparticles bound to cells. Next, anti Her2-conjugated nanoparticles injected into highly Her2-expressing tumor xenograft explants yielded a significantly higher SQUID relaxometry signal relative to unconjugated nanoparticles. Finally, labeled cells introduced into breast phantoms were measured by magnetic relaxometry, and as few as 1 million labeled cells were detected at a distance of 4.5 cm using our early prototype system. CONCLUSIONS: These results suggest that the antibody-conjugated magnetic nanoparticles are promising reagents to apply to in vivo breast tumor cell detection, and that SQUID-detected magnetic relaxometry is a viable, rapid, and highly sensitive method for in vitro nanoparticle development and eventual in vivo tumor detection.

Markers of fibrosis and epithelial to mesenchymal transition demonstrate field cancerization in histologically normal tissue adjacent to breast tumors.

Previous studies have shown that a field of genetically altered but histologically normal tissue extends 1 cm or more from the margins of human breast tumors. The extent, composition and biological significance of this field are only partially understood, but the molecular alterations in affected cells could provide mechanisms for limitless replicative capacity, genomic instability and a microenvironment that supports tumor initiation and progression. We demonstrate by microarray, qRT-PCR and immunohistochemistry a signature of differential gene expression that discriminates between patient-matched, tumor-adjacent histologically normal breast tissues located 1 cm and 5 cm from the margins of breast adenocarcinomas (TAHN-1 and TAHN-5, respectively). The signature includes genes involved in extracellular matrix remodeling, wound healing, fibrosis and epithelial to mesenchymal transition (EMT). Myofibroblasts, which are mediators of wound healing and fibrosis, and intra-lobular fibroblasts expressing MMP2, SPARC, TGF-ß3, which are inducers of EMT, were both prevalent in TAHN-1 tissues, sparse in TAHN-5 tissues, and absent in normal tissues from reduction mammoplasty. Accordingly, EMT markers S100A4 and vimentin were elevated in both luminal and myoepithelial cells, and EMT markers α-smooth muscle actin and SNAIL were elevated in luminal epithelial cells of TAHN-1 tissues. These results identify cellular processes that are differentially activated between TAHN-1 and TAHN-5 breast tissues, implicate myofibroblasts as likely mediators of these processes, provide evidence that EMT is occurring in histologically normal tissues within the affected field and identify candidate biomarkers to investigate whether or how field cancerization contributes to the development of primary or recurrent breast tumors.

Expanding the ZIFs Repertoire for Biological Applications with the Targeted Synthesis of ZIF-20 Nanoparticles.

Owing to their facile synthesis, tailorable porosity, diverse compositions, and low toxicity, zeolitic imidazolate framework (ZIF) nanoparticles (NPs) have emerged as attractive platforms for a variety of biologically relevant applications. To date, a small subset of ZIFs representing only two topologies and very few linker chemistries have been studied in this realm. We seek to expand the bio-design space for ZIF NPs through the targeted synthesis of a hierarchically complex ZIF based on two types of cages, ZIF-20, with lta topology. This study demonstrates the rapid synthesis and size tunability of ZIF-20 particles across the micro and nanoregimes via microwave heating and the use of a modulating agent. To evaluate the utility of ZIF particles for biological applications, we examine their stability in biologically relevant media and demonstrate biocompatibility with A549 human epithelial cells. Further, the ability to encapsulate and release methylene blue, a therapeutic and bioimaging agent, is validated. Importantly, ZIF-20 NPs display a unique behavior relative to previously studied ZIFs based on their specific structural and chemical features. This finding highlights the need to expand the design space across the broader ZIFs family, to exploit a wider range of relevant properties for biological applications and beyond.

Gene editing and CRISPR in the clinic: current and future perspectives.

Genome editing technologies, particularly those based on zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and CRISPR (clustered regularly interspaced short palindromic repeat DNA sequences)/Cas9 are rapidly progressing into clinical trials. Most clinical use of CRISPR to date has focused on ex vivo gene editing of cells followed by their re-introduction back into the patient. The ex vivo editing approach is highly effective for many disease states, including cancers and sickle cell disease, but ideally genome editing would also be applied to diseases which require cell modification in vivo. However, in vivo use of CRISPR technologies can be confounded by problems such as off-target editing, inefficient or off-target delivery, and stimulation of counterproductive immune responses. Current research addressing these issues may provide new opportunities for use of CRISPR in the clinical space. In this review, we examine the current status and scientific basis of clinical trials featuring ZFNs, TALENs, and CRISPR-based genome editing, the known limitations of CRISPR use in humans, and the rapidly developing CRISPR engineering space that should lay the groundwork for further translation to clinical application.

Antibody Targeted Metal-Organic Frameworks for Bioimaging Applications.

We report on the availability and chemical utility of primary amines within metal-organic frameworks (MOFs) for cell targeting. Primary amine groups represent one of the most versatile chemical moieties for conjugation to biologically relevant molecules, including antibodies and enzymes. Specifically, we used two different chemical conjugations schemes, utilizing the amino functionality on the organic linker: first, carbodiimide chemistry was used to link the primary amine to available carboxyl groups on the protein neutravidin; second, sulfhydryl cross-linking chemistry was used via Traut's reagent scheme. Importantly, this is the first report that documents this methodology implemented with MOF systems. Finally, the ability of the EpCAM antibody targeted MOFs to bind to a human epithelial cell line (A549), a common target for imaging studies, was confirmed with confocal microscopy.

Heterogeneous partition of cellular blood-borne nanoparticles through microvascular bifurcations.

Blood flowing through microvascular bifurcations has been an active research topic for many decades, while the partitioning pattern of nanoscale solutes in the blood remains relatively unexplored. Here we demonstrate a multiscale computational framework for direct numerical simulation of the nanoparticle (NP) partitioning through physiologically relevant vascular bifurcations in the presence of red blood cells (RBCs). The computational framework is established by embedding a particulate suspension inflow-outflow boundary condition into a multiscale blood flow solver. The computational framework is verified by recovering a tubular blood flow without a bifurcation and validated against the experimental measurement of an intravital bifurcation flow. The classic Zweifach-Fung (ZF) effect is shown to be well captured by the method. Moreover, we observe that NPs exhibit a ZF-like heterogeneous partition in response to the heterogeneous partition of the RBC phase. The NP partitioning prioritizes the high-flow-rate daughter branch except for extreme (large or small) suspension flow partition ratios under which the complete phase separation tends to occur. By analyzing the flow field and the particle trajectories, we show that the ZF-like heterogeneity in the NP partition can be explained by the RBC-entrainment effect caused by the deviation of the flow separatrix preceded by the tank treading of RBCs near the bifurcation junction. The recovery of homogeneity in the NP partition under extreme flow partition ratios is due to the plasma skimming of NPs in the cell-free layer. These findings, based on the multiscale computational framework, provide biophysical insights to the heterogeneous distribution of NPs in microvascular beds that are observed pathophysiologically.