Active-quiescent switching occurs in biological populations in which growth is confined to a proliferative active state, while cells may reversibly enter a nonproliferative quiescent state. Experiments often observe only part of this process, through active-state markers, aggregate population measurements, or aggregate data supplemented by sparse active-state observations. Such measurements arise when marker panels are limited, active-state assays require fixation or endpoint sampling, or only total cell number, optical density, tumor burden, or aggregate fluorescence is reported. These observation choices complicate sparse regression methods such as sparse identification of nonlinear dynamics (SINDy), because the measured variable may satisfy a different equation from the underlying active-quiescent system. A library chosen for the wrong observable may therefore fit a trajectory without preserving mechanistic interpretation or transferability. We study this issue using a two-compartment ordinary differential equation model. We define observable reduction as the elimination of hidden states to obtain the differential equation satisfied by the measured variable. For several biologically relevant growth laws, we derive observation-specific reductions and use them to construct sparse-regression libraries. Using synthetic data, we compare these structured libraries with standard polynomial SINDy. Polynomial libraries can match training trajectories while failing coefficient-relation and transfer tests, whereas reduction-guided libraries recover interpretable coefficient maps when the observed regime is informative. These results show that interpretable equation learning in hidden-compartment systems requires matching both the regression target and candidate library to the observation process.

Triple-Negative Breast Cancer (TNBC) presents a significant clinical challenge due to its heterogeneity and lack of targeted treatment options, with chemotherapy and immunotherapy combinations currently serving as the main therapeutic strategy. Efforts to address TNBC heterogeneity have largely focused on classifying intrinsic cancer subtypes based on differential tumor mRNA expression, a strategy that has proven effective in hormone receptor-positive breast cancers but has yet to yield a clinically useful predictor of survival or treatment response in TNBC. We hypothesize that both the intrinsic characteristics of TNBC and the surrounding immune microenvironment influence treatment outcomes and that immune cell infiltration affects TNBC subtype classification and response variability. To explore this hypothesis, we compared the predictive and prognostic capabilities of cancer subtype-based (TNBC-type) gene signatures and immune cell deconvolution methods (CIBERSORT) within the same TNBC datasets. We found that immune cell abundance outperformed TNBC subtype-signatures and multicellular immune cell aggregates showed the highest performance of all. More specifically, aggregate immune cells associated with tertiary lymphoid structures and tumor associated macrophages/monocytes demonstrated statistically significant predictive value. These findings were confirmed in an independent cohort of 67 TNBC patients treated with neoadjuvant chemotherapy. Further, single-cell RNA sequencing analysis revealed that the predictive power of cancer-subtype could be partially explained by immune- and stromal features. Examination of single-cell resolution spatial transcriptomic data confirmed presence of TLS-like, TAM- and cancer-stromal niches within TNBC biopsy samples that were associated with treatment response. Overall, our results highlight that immune cell aggregates, which capture the spatial organization of the TME, outperform cell-type specific gene signatures in predicting TNBC outcomes. Our novel approach provides a robust framework for interpreting spatial relationships in bulk RNA-seq data, offering a pathway for reconciling past data with current advancements in spatial profiling technologies. This work paves the way for future studies to leverage the multi-cellular complexity of TNBC, enhancing diagnostic precision and facilitating the development of therapies that strategically modulate the tumor microenvironment for improved anti-cancer responses.

Tumors grow because the total number of cancer cells increases without limit. The prevailing explanation is that each proliferating cancer cell has acquired unlimited replicative capacity, yet this does not explain why the overwhelming majority of cancer cells fail to initiate tumors on transplantation, why the cancer stem cell fraction of serially passaged cultures remains nearly constant, or why the measured cell loss factor of human tumors is so high. This review proposes an alternative reading of these observations. Non-stem cancer cells may possess a replicative lifespan that is set not by telomere attrition but by the progressive accumulation of damaged proteins, protein aggregates and dysfunctional mitochondria, so that each lineage eventually terminates in growth arrest or death. Persistent expansion would then depend on th e rate at which non-stem cancer cells are converted back into stem cells. Work on transforming growth factor-β associated molecules, including TMEPAI/PMEPA1, MAFK-GPNMB and THG-1, is reviewed in this light, together with evidence from budding yeast and mammalian stem cells that damage is partitioned asymmetrically at division. Established observations, reasonable inferences and untested assumptions are distinguished explicitly, and experimental tests are proposed.

Neurodegenerative diseases (NDs) affect more than 55 million people worldwide, with this number projected to exceed 139 million by 2050 due to population aging. Alzheimer's disease (AD) accounts for 60-70% of dementia cases, while Parkinson's disease (PD) affects over 10 million individuals globally, highlighting the growing clinical and socioeconomic burden of these progressive neurological disorders. Effective treatment of AD, PD, amyotrophic lateral sclerosis (ALS), and related central nervous system disorders remains hindered by the blood-brain barrier (BBB), poor brain accumulation, rapid systemic clearance, and off-target toxicity. RVG29, a 29-amino-acid peptide derived from rabies virus glycoprotein, has emerged as a promising brain-targeting ligand because of its high affinity for nicotinic acetylcholine receptors expressed on neuronal and brain endothelial cells. This review critically examines the mechanisms underlying RVG29-mediated receptor-dependent BBB transcytosis, intracellular trafficking, and neuronal uptake. Furthermore, it comprehensively evaluates RVG29-functionalized lipid nanoparticles, polymeric nanoparticles, exosomes, biomimetic nanocarriers, micelles, inorganic nanostructures, and hybrid systems with respect to their physicochemical characteristics, targeting efficiency, therapeutic efficacy, and safety. Collectively, these nanocarriers demonstrate enhanced BBB penetration, increased drug accumulation in diseased brain regions, and efficient delivery of small molecules, genes, mRNA, and siRNA. By modulating oxidative stress, neuroinflammation, protein aggregation, ferroptosis, and mitochondrial dysfunction, RVG29-engineered nanocarriers provide significant neuroprotection with favorable biocompatibility and minimal immunogenicity. Despite these advances, challenges related to large-scale manufacturing, peptide stability, regulatory approval, and long-term biosafety must be addressed to facilitate their clinical translation as precision neurotherapeutics.

The subcutaneous (SC) route of administration for therapeutic proteins (TPs) offers advantages such as patient convenience, reduced delivery complexity, and self-administration leading to enhanced adherence. Although SC delivery may be perceived to have higher immunogenicity risk than intravenous (IV) administration due to longer antigen exposure and proximity to resident professional immune cells, recent data suggest that immunogenicity rates of TPs are comparable between SC and IV administration routes. Factors thought to contribute to immunogenicity risk encompass dosing regimen (route of administration), and patient and product-related elements. Product related factors include liabilities related to protein sequence, critical quality attributes that may occur during process development and manufacturing such as post-translational modifications, propensity to aggregate, presence of impurities, and the drug's mechanism of action. Advances in formulation, delivery systems, molecular design and associated biophysical characterization can help mitigate some of these risks. The Immunogenicity Sub team of the Subcutaneous Drug Development & Delivery Consortium, held a workshop at the 2023 PEGS Boston meeting, focused on delineating the immunogenicity risk factors carried by SC administration. In this paper, the team presents the outcome of the workshop and discusses the most recent clinical examples of SC administration which highlight that the SC route is not inherently more immunogenic than IV administration and requires context-specific evaluation. Additionally, the paper provides an overview of the current landscape in non-clinical immunogenicity risk assessment focused on novel in vivo and in vitro models, together with identified gaps and opportunities for further improvement of immunogenicity prediction as it relates to SC route.

Desmin-related cardiomyopathy (DRC) is an inherited disorder characterized by progressive conduction abnormalities, arrhythmias, and heart failure. Although desmin aggregation is a defining pathological feature, the downstream signaling mechanisms driving disease progression remain poorly understood. In this study, whole-exome sequencing identified a heterozygous DES p.S13F variant in a multigenerational pedigree with a highly penetrant cardiac phenotype, and its pathogenic mechanisms were investigated using clinical data, zebrafish and mouse models, and cellular experiments. DES p.S13F expression induced desmin aggregation, cytoskeletal-associated protein abnormalities, mitochondrial dysfunction, oxidative stress, cardiomyocyte apoptosis, and adverse cardiac remodeling. Transcriptomic and protein analyses consistently revealed impaired canonical Notch signaling, with reduced NICD1 abundance in DES p.S13F-expressing mouse hearts and cardiomyocytes, providing a biochemical readout supporting impaired canonical NOTCH1 activation. Pharmacological Notch inhibition aggravated cardiac and cellular abnormalities, whereas Jagged1-mediated pathway activation ameliorated cardiac phenotypes in zebrafish and partially restored cytoskeletal-associated protein abundance while attenuating oxidative stress and apoptosis in DES p.S13F-expressing cardiomyocytes. Genetic NICD1 overexpression produced concordant protective effects, further supporting the functional involvement of canonical Notch signaling. Collectively, these findings identify Notch signaling insufficiency as a functionally relevant disease-modifying mechanism in DES p.S13F-associated cardiomyopathy and suggest that restoration of canonical Notch signaling may represent a potential therapeutic strategy for desmin-related cardiomyopathy.

Tripartite motif-containing protein 10β (TRIM10β) is a primate-specific isoform whose expression is restricted in most human tissues and regulated in a lineage- and stage-specific manner during erythropoiesis. However, the organelle-level mechanisms underlying the cytotoxic effects of dysregulated TRIM10β remain unclear. Here, we show that TRIM10β expression coincides with p38-p21 activation during late erythroid differentiation. Ectopic TRIM10β expression increased p38 phosphorylation and p21 expression in both erythroid and non-erythroid cells, whereas TRIM10β depletion attenuated late-stage p21 induction in differentiating erythroid cells. Proteomic analysis identified the mitochondrial carrier adenine nucleotide translocase 1 (ANT1) as a TRIM10β-interacting protein. Consistent with this interaction, TRIM10β localized to mitochondria, reduced ANT1-VDAC1 association and cellular ATP levels, and altered fission-associated signaling and mitochondrial membrane potential. In parallel, TRIM10β formed centrosome-proximal aggregates associated with defective centrosome organization, altered cell-cycle progression, γH2AX accumulation, and nuclear envelope deformation. These findings identify TRIM10β as a stage-restricted modulator of erythroid p38-p21 signaling and show that its dysregulated expression perturbs mitochondrial and centrosomal homeostasis, providing a mechanistic basis for its cytotoxicity.

Protein tyrosine nitration is a post-translational modification associated with conditions of oxidative and inflammatory stress, driven by the production of reactive oxygen and nitrogen species (ROS and RNS). Once considered primarily a footprint of oxidative damage, tyrosine nitration is increasingly recognized as a selective modification that, in specific biological contexts, can alter protein structure, stability, enzymatic activity, and interaction networks. Mechanistically, nitration occurs through peroxynitrite-dependent and heme-peroxidase-dependent pathways and preferentially targets specific tyrosine residues based on local protein structure, solvent accessibility, and microenvironmental chemistry. Accumulating evidence has identified disease-specific nitration signatures across multiple pathological contexts. In neurodegenerative disorders, including Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis, nitration of proteins such as tau, α-synuclein, manganese superoxide dismutase, ATP synthase, glyceraldehyde-3-phosphate dehydrogenase, heat shock proteins, and cytoskeletal components contributes to mitochondrial dysfunction, protein aggregation, metabolic failure, and neuronal loss. Similarly, in cardiovascular and pulmonary diseases, protein tyrosine nitration disrupts vascular and epithelial homeostasis by impairing endothelial signaling, fibrinolysis, lipid metabolism, and barrier integrity through modification of key regulatory proteins. By influencing phosphorylation-dependent signaling, enzymatic function, and protein-protein interactions, tyrosine nitration contributes to the connection between redox imbalance and progressive cellular and tissue dysfunction. This review summarizes current mechanistic insights into site-specific protein tyrosine nitration, highlights the emerging disease-associated nitroproteome, and discusses how advances in analytical and structural approaches are redefining nitration as a functional regulatory modification. Understanding the molecular determinants and consequences of tyrosine nitration may enable the development of targeted diagnostics and therapeutic strategies across diverse human diseases.

Despite extensive characterization of cytosolic and nuclear acetylation, the functional relevance of luminal ER-Nε-lysine acetylation in the nervous system remains poorly understood. This modification is mediated by a coordinated metabolic-secretory axis involving acetyl-CoA availability and the ER-resident acetyltransferases ATase-1 (NAT8B) and ATase-2 (NAT8), which depend on acetyl-CoA import into the ER via the transporter SLC33A1 (AT-1). Upstream, the citrate transporters SLC25A1 and SLC13A5 contribute to shaping the cytosolic acetyl-CoA pool. Emerging evidence identifies this pathway as a key regulator of proteostasis within the early secretory pathway, linking cellular metabolism to protein processing, trafficking, and degradation. Recent studies in neurological disease models suggest that excessive activation of this machinery may exert pathogenic effects through distinct mechanisms. In experimental models of autism spectrum disorder (ASD), increased ER acetylation is associated with altered secretory pathway flux, impaired synaptic proteostasis, and abnormal neuronal connectivity, ultimately leading to ASD-like phenotypes. In Alzheimer's disease (AD) models, excessive ER-Nε-lysine acetylation appears to suppress reticulophagic clearance of aggregation-prone proteins within the secretory pathway, whereas genetic or pharmacological reduction of AT-1/ATase activity enhances proteostatic clearance and confers protective effects. In this opinion article, we discuss ER-Nε-lysine acetylation as a context-dependent regulator of proteostasis in neurodevelopmental and neurodegenerative disease models. We highlight key unresolved questions regarding acetylation substrates, relevance to human biology, and future therapeutic opportunities. We further consider its potential relevance to additional disorders, including multiple sclerosis, where its contribution remains largely unexplored.

Microglia are the primary immune cells of the brain, but their role in Parkinson's disease is not fully understood. Chronic microglial activation is toxic to neurons, but in the early stages of pathology, microglia also exert beneficial functions. We used induced pluripotent stem cell (iPSC)-derived coculture models to investigate how human microglia respond to α-synuclein aggregates that form de novo inside human dopaminergic neurons with α-synuclein gene triplication or are triggered by fibrils. We found that microglia cleared Ser129-phosphorylated α-synuclein aggregates through a contact-dependent mechanism. This process was fine-tuned by sensing (P2RY12) and inhibitory (CD22) signals and involved selective phagocytosis of neuronal subcompartments (trogocytosis), independently of TREM2 or phosphatidylserine. In the presence of intraneuronal α-synuclein aggregates, microglia exhibited morphological and transcriptional changes indicative of activation. Using single-cell sequencing, we identified a cluster of disease-associated microglia (DAM) responsible for this beneficial phenotype and the Parkinson's disease GWAS candidate glycoprotein nonmetastatic melanoma protein B (GPNMB) as a key effector of aggregate clearance by microglial lysosomes. GPNMB interacted with Ser129-phosphorylated α-synuclein in iPSC-derived microglia exposed to aggregate-laden dopaminergic neurons and was up-regulated in substantia nigra microglia of individuals with incidental Lewy bodies or Parkinson's disease. Microglia-specific GPNMB knockdown using CRISPRi reduced intraneuronal aggregate clearance. GPNMB-mediated trogocytosis was negatively regulated by an autocrine IL-10 signaling loop, whereas IL-10 receptor blockade enhanced the phagocytic response. Together, our study identifies a subtype of human microglia capable of removing intraneuronal aggregates and potential therapeutic targets.

Near-infrared (NIR) photocatalysis promises deep-tissue compatibilities but remains fundamentally constrained by two bottlenecks: insufficient photon energy and rapid charge recombination. Here, we report packing-accelerated consecutive excitation (PACE), a mechanism enabling low energy near-infrared (NIR) photons to drive high energy single electron transfer (SET) reactions. We design a self-assembling ruthenium complex, Ru-3, that forms densely packed nanoaggregates exhibiting aggregation-stabilized excited states, a pronounced excited state absorption band at ∼1315 nm, and nanosecond scale triplet lifetimes. Under dual NIR-I/IIa irradiation (808 nm/1310 nm), Ru-3 nanoparticles exhibit photophysical behavior consistent with consecutive photon harvesting and access to a higher-energy reactive state that supports efficient SET catalysis under aqueous conditions. This PACE-driven reactivity enables robust oxidation of mitochondrial NADH to NAD+, disrupting electron-transport homeostasis, inducing cGAS-STING dependent pyroptosis, and reprogramming tumor-associated macrophages toward an M1 phenotype. In multiple murine tumor models, PACE-mediated photocatalysis elicits strong antitumor immunity and leads to tumor regression with minimal systemic toxicity. This work establishes PACE as a new photochemical paradigm that overcomes the intrinsic energy and charge-separation limits of NIR photoredox chemistry, opening a route toward high-energy photocatalysis in complex biological environments.