This book chapter presents a proteomics-driven study focused on defining protein marker panels to monitor the quality of human induced pluripotent stem cells (hiPSCs) during large-scale manufacturing. Using mass spectrometry and comparative protein profiling, the authors identified over 300 differentially expressed proteins associated with apoptosis, metabolic pathways, RNA processing, and cell signaling in overgrown hiPSC populations.

Changes in pluripotency and differentiation marker expression were tracked across embryoid body formation. The findings contribute to the development of analytical tools for identity, purity, and potency assessment, supporting GMP-compliant hiPSC production, regulatory CMC strategy for cell-based therapies, and standardized quality control methods in regenerative medicine. »»

Allogeneic chimeric antigen receptor natural killer (CAR-NK) cell therapies are gaining rapid momentum as off-the-shelf alternatives to autologous CAR T cell therapies. These platforms combine the innate cytotoxicity of NK cells with engineered specificity, offering promise for scalable manufacturing and reduced risk of graft-versus-host disease.

However, the regulatory landscape for allogeneic CAR-NK products is complex, given the diverse mechanisms of action, source variability (e.g., iPSC-derived NKs), and genome editing components. To navigate these intricacies, regulatory professionals must strategically interpret existing FDA guidance documents on gene therapy, genome editing, potency, and overall CMC practices for IND and BLA.

This article summarizes key considerations across core guidance documents, offering a harmonized view of regulatory expectations for CAR-NK development at clinical stage. »»

This study presents two methods for identifying stable, detergent-resistant protein aggregates: semi-denaturing agarose gel electrophoresis and tandem mass spectrometry.

These techniques allow for the detection of prions and amyloid-forming proteins in yeast, supporting protein characterization workflows relevant to aggregation analysis, impurity profiling, and structural stability assessment in biologic products. »»

Through global proteome analysis and quantitative mass spectrometry, this study identified a consistent panel of 22 protein markers for hiPSC characterization.

Comparing iPSC lines from different somatic sources to embryonic and primary cells, the work supports cell identity verification and quality control standards used in cell therapy development and CMC documentation. »»

The study is focused on RNA-binding protein, KSHV ORF57 and defines its structural domains that regulate its stability through phosphorylation and homodimer formation.

By identifying residues and domains critical to proteasome resistance, it informs viral protein design, expression control, and vector optimization strategies relevant to gene therapy manufacturing and regulatory evaluation. »»

This study introduced a proteomics-based method to isolate and identify amyloid-forming proteins from cell lysates without genetic tagging. Mass spectrometry was used to detect endogenous yeast prions and disease-related polyglutamine aggregates in mammalian cells.

The approach enabled unbiased identification of protein assemblies, contributing to workflows in protein conformation analysis and aggregate profiling in quality and safety assessments of biologic products. »»

Using Macaca fascicularis and Cercopithecus aethiops, this study evaluated primate models for preclinical testing of vaccines and therapeutics against tick-borne encephalitis virus and Omsk hemorrhagic fever virus. Inactivated vaccines showed protective immune responses, with measurable viral clearance in lymphoid and neural tissues.

The model supports efficacy testing aligned with vaccine development standards and viral pathogenesis research in biologics programs. »»

In this Nuclear Acid Testing (NAT) study authors developed a novel multiplex PCR array for simultaneous detection of eight clinically relevant viruses critical for human cell and tissue transplantation products (HCT/P) listed in 21CFR 1271.85, including HIV-1, HIV-2, HBV, HCV, HTLV-1/2, WNV, and Vaccinia.

Primer sets were fully optimized, multiplex PCR planform used SYBR Green chemistry and was validated across diverse viral strains. The array demonstrated high sensitivity in human plasma samples, offering a rapid molecular tool applicable to donor screening, biosafety, and analytical validation processes in CMC testing. »»

This study is focused on RNA-protein interactions and revealed how the KSHV ORF57 protein enhances the expression of viral and human IL-6 by stabilizing mRNA and interfering with microRNA-mediated silencing. Using a genome-wide CLIP assay, the authors identified ORF57 binding motifs that block RISC targeting.

These mechanisms are relevant to gene regulation and expression stability in viral systems, informing strategies in vector design and molecular therapeutic development. »»

This Nuclear Acid Testing (NAT) study used nested PCR to detect murine leukemia virus (MLV)-related gag gene sequences in peripheral blood mononuclear cells from patients with chronic fatigue syndrome. A high detection rate was observed in patient samples compared to healthy controls, and sequence analysis revealed a diverse group of MLV-like viruses.

These findings raised considerations related to blood safety and pathogen screening, areas relevant to viral detection methods and molecular assay validation. »»

This non-clinical study evaluated neurovirulence and replication of a chimeric Langat/Dengue 4 flavivirus vaccine candidate in mice and monkeys. The chimera demonstrated strong attenuation in murine models and limited CNS involvement in primates, with occasional pathologic effects.

The work supports safety testing protocols and animal model selection in live vaccine development and preclinical evaluation of attenuated viral products. »»

This publication demonstrated that KSHV RNA-binding protein, ORF57, enhances splicing and expression of intron-containing viral genes by associating with spliceosomal complexes. ORF57 localized with splicing factors in nuclear speckles and directly bound viral pre-mRNAs, influencing alternative splicing outcomes.

These findings contribute to understanding viral gene expression mechanisms and splicing regulation relevant to viral vector design and transcript engineering. »»

By disrupting the ORF57 gene within the KSHV genome, this study showed that loss of ORF57 severely impaired expression of key lytic genes and blocked production of infectious virus particles. Partial rescue of replication was achieved with ectopic ORF57 expression.

These results highlight ORF57 as essential for posttranscriptional regulation and functional viral reactivation, with implications for lytic-phase control in gene-modified virus platforms. »»

This study evaluated cardiac oxidative damage following acute total body gamma radiation exposure in rats. Protein carbonylation was assessed through redox proteomics to identify early post-exposure changes and long-term cardiac injury.

The findings highlight mechanisms of radiation-induced damage and support use of oxidative markers in preclinical safety assessments and biomarker validation studies. »»

This research used mass spectrometry to examine protein carbonylation patterns resulting from metal-catalyzed oxidation. Sequence specificity and structural context influenced modification outcomes, with implications for identifying oxidative hotspots.

The results contribute to understanding degradation pathways in biologics and oxidative stress as a factor in therapeutic protein stability. »»

Scientific Reports, 2017

This study developed cell-based assays to detect innate immune response–modulating impurities (IIRMIs) in interferon-β (IFNβ) products. The authors found that certain IFNβ formulations (e.g., Betaseron/Extavia) contained trace IIRMIs that activated NF-κB via TLR2/TLR4 and MyD88, upregulating inflammatory mediators, whereas other products (Rebif/Avonex) did not. In IFNAR-knockout systems, the stimulatory effects were attributed to impurities rather than IFNβ itself.

The work highlights how subtle manufacturing differences can introduce TLR-stimulating contaminants that may contribute to product immunogenicity. »»

This publication compared how different metal-catalyzed oxidative systems affect carbonylation patterns and structural integrity in therapeutic proteins.

The study revealed system-specific residue targeting and degradation pathways, aiding in the assessment of protein oxidation, formulation robustness, and analytical control strategies in biologic drug development. »»

This study investigated how mitochondrial-targeted therapies induce oxidative stress and compromise mitochondrial DNA stability. Excessive superoxide production and membrane depolarization were linked to impaired mtDNA integrity.

These findings inform safety evaluation of oxidative mechanisms and support the development of mitochondrial biomarkers relevant to early-stage therapeutic screening and drug-induced toxicity profiling. »»

This study explored how traumatic brain injury triggers hepatic expression of serum amyloid A1 (SAA1), and how the drug telmisartan modulates this response.

Protein aggregation and systemic inflammatory pathways were examined, linking neurologic trauma to peripheral biomarker expression.

The work contributes to biomarker discovery and systemic response modeling for translational research. »»

Human Molecular Genetics, 2013

Using Drosophila and neuronal cell models, the authors show that the RNA-binding capacity of FUS is essential for the neurodegenerative phenotypes associated with ALS-linked FUS mutations. Disrupting four phenylalanine residues to abolish RNA binding prevented neurodegeneration and reduced cytoplasmic mislocalization/inclusion of FUS.

RNA-binding–deficient FUS remained predominantly nuclear, and incorporation of mutant FUS into stress granules depended on RNA binding. These findings position RNA interaction as a key driver of FUS-mediated toxicity in ALS. »»

Using a proteomic screen, this study showed that intrinsically disordered domain-containing proteins are more likely to be sequestered into polyglutamine aggregates.

The results highlight protein interaction preferences during misfolding and aggregation, relevant to understanding protein stability and aggregate-related impurity mechanisms in therapeutic protein production. »»

This study used a mass spectrometry-based approach to identify amyloid-forming proteins in yeast and mammalian cells without relying on genetic markers.

The method uncovered diverse endogenous prions and polyglutamine aggregates, supporting proteomic workflows used in structural integrity assessment, aggregate profiling, and biologic product impurity evaluation. »»

This study developed a yeast model to study optineurin-linked proteinopathies, demonstrating a distinct aggregation pattern that impaired endocytic trafficking and autophagy.

The work supports the use of yeast for modeling neurodegenerative disease mechanisms and analyzing aggregation-prone proteins relevant to quality control and degradation pathways in biologic development. »»

This review highlights yeast-based models for studying ALS and frontotemporal lobar degeneration-related protein aggregation.

It emphasizes the system’s value in rapidly evaluating aggregation behavior and toxicity, supporting high-throughput screening and protein characterization efforts that parallel regulatory testing of therapeutic proteins. »»

Using solid-state NMR, this study defined the parallel in-register β-sheet architecture of Ure2p prion fibrils, with the N-terminal domain forming the amyloid core.

These structural insights are essential for understanding prion templating mechanisms and inform approaches to analyzing aggregation in biologic and biosimilar comparability assessments. »»

The study examined how Hsp104, a protein disaggregase, facilitates the de novo formation of prions in yeast.

By modulating prion nucleation and propagation, Hsp104 provides insights into protein folding quality control and chaperone-assisted aggregate management, relevant to manufacturing controls in recombinant protein production. »»

This work demonstrated that the Sup35NM domain from yeast forms prions in mammalian cells, revealing cross-species propagation of amyloid structures.

It supports the universality of amyloid mechanisms and offers a model for prion-like behavior applicable to both basic research and the evaluation of aggregate-related risks in biologic therapies. »»

This study showed that Hsp70 nucleotide exchange factors are essential for maintaining the [URE3] prion state in yeast.

It highlights the role of chaperone systems in prion propagation and protein homeostasis, offering mechanistic insights that align with protein folding management in cell-based biologic production. »»