Distinct network patterns emerge from Cartesian and XOR epistasis models: a comparative network science analysis.

Background: Epistasis, the phenomenon where the effect of one gene (or variant) is masked or modified by one or more other genes, significantly contributes to the phenotypic variance of complex traits. Traditionally, epistasis has been modeled using the Cartesian epistatic model, a multiplicative approach based on standard statistical regression. However, a recent study investigating epistasis in obesity-related traits has identified potential limitations of the Cartesian epistatic model, revealing that it likely only detects a fraction of the genetic interactions occurring in natural systems.

Distinct Network Patterns Emerge from Cartesian and XOR Epistasis Models: A Comparative Network Science Analysis.

Background: Epistasis, the phenomenon where the effect of one gene (or variant) is masked or modified by one or more other genes, can significantly contribute to the observed phenotypic variance of complex traits. To date, it has been generally assumed that genetic interactions can be detected using a Cartesian, or multiplicative, interaction model commonly utilized in standard regression approaches. However, a recent study investigating epistasis in obesity-related traits in rats and mice has identified potential limitations of the Cartesian model, revealing that it only detects some of the genetic interactions occurring in these systems.

Interaction models matter: an efficient, flexible computational framework for model-specific investigation of epistasis.

Purpose: Epistasis, the interaction between two or more genes, is integral to the study of genetics and is present throughout nature. Yet, it is seldom fully explored as most approaches primarily focus on single-locus effects, partly because analyzing all pairwise and higher-order interactions requires significant computational resources. Furthermore, existing methods for epistasis detection only consider a Cartesian (multiplicative) model for interaction terms.

Cluster Analysis reveals Socioeconomic Disparities among Elective Spine Surgery Patients.

This work demonstrates the use of cluster analysis in detecting fair and unbiased novel discoveries. Given a sample population of elective spinal fusion patients, we identify two overarching subgroups driven by insurance type. The Medicare group, associated with lower socioeconomic status, exhibited an over-representation of negative risk factors.

Aliro: an automated machine learning tool leveraging large language models.

Motivation: Biomedical and healthcare domains generate vast amounts of complex data that can be challenging to analyze using machine learning tools, especially for researchers without computer science training.

Results: Aliro is an open-source software package designed to automate machine learning analysis through a clean web interface. By infusing the power of large language models, the user can interact with their data by seamlessly retrieving and executing code pulled from the large language model, accelerating automated discovery of new insights from data.

Plasticity of circulating tumor cells in small cell lung cancer.

Small cell lung cancer (SCLC) is an aggressive neuroendocrine tumor with low five-year survival rates. Recently described molecular phenotypes of SCLC exhibit differential vulnerabilities heralding potential for stratified treatment. Whilst tumor biopsy in SCLC is challenging, circulating tumor cells in the liquid biopsy are prevalent and can be repeatedly sampled accommodating the dynamic plasticity of SCLC phenotypes.

Characterization of BCMA Expression in Circulating Rare Single Cells of Patients with Plasma Cell Neoplasms.

B-cell maturation antigen (BCMA), a key regulator of B-cell proliferation and survival, is highly expressed in almost all cases of plasma cell neoplasms and B-lymphoproliferative malignancies. BCMA is a robust biomarker of plasma cells and a therapeutic target with substantial clinical significance. However, the expression of BCMA in circulating tumor cells of patients with hematological malignancies has not been validated for the detection of circulating plasma and B cells.

Multianalyte liquid biopsy to aid the diagnostic workup of breast cancer.

Breast cancer (BC) affects 1 in every 8 women in the United States and is currently the most prevalent cancer worldwide. Precise staging at diagnosis and prognosis are essential components for the clinical management of BC patients. In this study, we set out to evaluate the feasibility of the high-definition single cell (HDSCA) liquid biopsy (LBx) platform to stratify late-stage BC, early-stage BC, and normal donors using peripheral blood samples.

Modular mixing of benzene-1,3,5-tricarboxamide supramolecular hydrogelators allows tunable biomimetic hydrogels for control of cell aggregation in 3D.

Few synthetic hydrogels can mimic both the viscoelasticity and supramolecular fibrous structure found in the naturally occurring extracellular matrix (ECM). Furthermore, the ability to control the viscoelasticity of fibrous supramolecular hydrogel networks to influence cell culture remains a challenge. Here, we show that modular mixing of supramolecular architectures with slow and fast exchange dynamics can provide a suitable environment for multiple cell types and influence cellular aggregation.

Identification of epithelial and mesenchymal circulating tumor cells in clonal lineage of an aggressive prostate cancer case.

Little is known about the complexity and plasticity of circulating tumor cell (CTC) biology in different compartments of the fluid microenvironment during tumor metastasis. Here we integrated phenomics, genomics, and targeted proteomics to characterize CTC phenotypic and genotypic heterogeneity in paired peripheral blood (PB) and bone marrow aspirate (BMA) from a metastatic prostate cancer patient following the rapid disease progression, using the High-Definition Single Cell Assay 3.0 (HDSCA3.

Enrichment-Free Single-Cell Detection and Morphogenomic Profiling of Myeloma Patient Samples to Delineate Circulating Rare Plasma Cell Clones.

Multiple myeloma is an incurable malignancy that initiates from a bone marrow resident clonal plasma cell and acquires successive mutational changes and genomic alterations, eventually resulting in tumor burden accumulation and end-organ damage. It has been recently recognized that myeloma secondary genomic events result in extensive sub-clonal heterogeneity both in localized bone marrow areas and circulating peripheral blood plasma cells. Rare genomic subclones, including myeloma initiating cells, could be the drivers of disease progression and recurrence.

Platelet-Coated Circulating Tumor Cells Are a Predictive Biomarker in Patients with Metastatic Castrate-Resistant Prostate Cancer.

Metastatic castration-resistant prostate cancer (mCRPC) includes a subset of patients with particularly unfavorable prognosis characterized by combined defects in at least two of three tumor suppressor genes: , , and as aggressive variant prostate cancer molecular signature (AVPC-MS). We aimed to identify circulating tumor cells (CTC) signatures that could inform treatment decisions of patients with mCRPC with cabazitaxel-carboplatin combination therapy versus cabazitaxel alone. Liquid biopsy samples were collected prospectively from 79 patients for retrospective analysis.

Large Extracellular Vesicle Characterization and Association with Circulating Tumor Cells in Metastatic Castrate Resistant Prostate Cancer.

Liquid biopsies hold potential as minimally invasive sources of tumor biomarkers for diagnosis, prognosis, therapy prediction or disease monitoring. We present an approach for parallel single-object identification of circulating tumor cells (CTCs) and tumor-derived large extracellular vesicles (LEVs) based on automated high-resolution immunofluorescence followed by downstream multiplexed protein profiling. Identification of LEVs >6 µm in size and CTC enumeration was highly correlated, with LEVs being 1.

PEG Analogs Synthesized by Ring-Opening Metathesis Polymerization for Reversible Bioconjugation.

Poly(ethylene glycols) (PEGs) with protein-reactive end-groups are widely utilized in bioconjugation reactions. Herein, we describe the use of ring-opening metathesis polymerization (ROMP) to synthesize unsaturated protein-reactive PEG analogs. These ROMP PEGs (rPEGs) contained terminal aldehyde functionality and ranged in molecular weight from 6 to 20 kDa.

Polymorphism in Benzene-1,3,5-tricarboxamide Supramolecular Assemblies in Water: A Subtle Trade-off between Structure and Dynamics.

In biology, polymorphism is a well-known phenomenon by which a discrete biomacromolecule can adopt multiple specific conformations in response to its environment. The controlled incorporation of polymorphism into noncovalent aqueous assemblies of synthetic small molecules is an important step toward the development of bioinspired responsive materials. Herein, we report on a family of carboxylic acid functionalized water-soluble benzene-1,3,5-tricarboxamides (BTAs) that self-assemble in water to form one-dimensional fibers, membranes, and hollow nanotubes.

Dynamic diversity of synthetic supramolecular polymers in water as revealed by hydrogen/deuterium exchange.

Numerous self-assembling molecules have been synthesized aiming at mimicking both the structural and dynamic properties found in living systems. Here we show the application of hydrogen/deuterium exchange (HDX) mass spectrometry (MS) to unravel the nanoscale organization and the structural dynamics of synthetic supramolecular polymers in water. We select benzene-1,3,5-tricarboxamide (BTA) derivatives that self-assemble in HO to illustrate the strength of this technique for supramolecular polymers.

Exposing Differences in Monomer Exchange Rates of Multicomponent Supramolecular Polymers in Water.

The formation of multicomponent and bioactive supramolecular polymers is a promising strategy for the formation of biomaterials that match the dynamic and responsive nature of biological systems. In order to fully realize the potential of this strategy, knowledge of the location and behavior of bioactive components within the system is crucial. By employing synthetic strategies to create multifunctional monomers, coupled with FRET and STORM techniques, we have investigated the formation and behavior of a bioactive and multicomponent supramolecular polymer.

Dual pH- and Temperature-Responsive Protein Nanoparticles.

Multiply responsive protein nanoparticles are interesting for a variety of applications. Herein, we describe the synthesis of a vault nanoparticle that responds to both temperature and pH. Specifically, poly(-isopropylacrylamide--acrylic acid) with a pyridyl disulfide end group was prepared by reversible addition-fragmentation chain transfer (RAFT) polymerization.

Synthesis of Nanogel-Protein Conjugates.

The covalent conjugation of bovine serum albumin (BSA) to disulfide cross-linked polymeric nanogels is reported. Polymeric nanogel precursors were synthesized via a reversible addition-fragmentation chain transfer (RAFT) random copolymerization of poly(ethylene glycol) methyl ether methacrylate (PEGMA) and pyridyl disulfide methacrylate (PDSMA). Reaction of the p(PEGMA--PDSMA) with dithiothreitol resulted in the formation of nanogels.

Smart vaults: thermally-responsive protein nanocapsules.

Synthetic modification of a recombinant protein cage called a vault with stimuli-responsive smart polymers provides access to a new class of biohybrid materials; the polymer nanocapsules retain the structure of the protein cage and exhibit the responsive nature of the polymer. Vaults are naturally occurring ubiquitous ribonucleoprotein particles 41 × 41 × 72.5 nm composed of a protein shell enclosing multiple copies of two proteins and multiple copies of one or more small untranslated RNAs.

Aminooxy and Pyridyl Disulfide Telechelic Poly(Polyethylene Glycol Acrylate) by RAFT Polymerization.

An efficient method to synthesize telechelic, bio-reactive polymers is described. Homotelechelic polymers were synthesized by reversible addition-fragmentation chain transfer (RAFT) polymerization in one step by employing bifunctional chain transfer agents (CTAs). A bis-carboxylic acid CTA was coupled to -BOC-aminooxy ethanol or pyridyl disulfide ethanol resulting in a bis--BOC-aminooxy CTA and a bis-pyridyl disulfide CTA, respectively.

Synthesis of Michael Acceptor Ionomers of Poly(4-Sulfonated Styrene-co-Poly(Ethylene Glycol) Methyl Ether Acrylate).

Ionomers containing sodium 4-styrene sulfonate (4SS) and poly(ethylene glycol) methyl ether acrylate (PEGA) were synthesized by reversible addition-fragmentation chain transfer (RAFT) polymerization. The polymerization was mediated by 1-phenylethyl dithiobenzoate chain transfer agent in a dimethylformamide/water solvent system. Well-defined copolymers of pPEGA-co-4SS were produced with molecular weights ranging from 10 kDa to 40 kDa and polydispersity indices (PDIs) of 1.