Enabling Clinical Adoption of Omics: Fit-for-Purpose Validation and a Spatial Biomarker Case Study
Over the past two decades, omics technologies have steadily expanded from discovery research into translational and clinical development, offering unprecedented insights into biology, disease mechanisms, and therapeutic response. Advances in genomics, transcriptomics, proteomics, metabolomics, and, more recently, spatial and multi-omics platforms have created powerful opportunities to identify predictive biomarkers, refine patient stratification, and accelerate drug development. The added value of omics lies in their ability to capture complex, system-level biology that traditional single-analyte assays cannot address, thereby bridging the gap between exploratory research and precision medicine.
Yet this rapid progress has also highlighted a critical challenge: how to validate omics data in a way that is scientifically rigorous but also practical. Current analytical validation paradigms were largely developed for conventional assays such as ELISA or qPCR, which measure one or a handful of targets at a time. Applying the same frameworks directly to high-dimensional omics assays often results in processes that are overly burdensome, expensive, and poorly aligned with the dynamic nature of omics platforms.
Moving forward, the field needs more efficient and adaptive validation processes, aligned with the specific purpose of each omics application. This involves applying full rigor when data will inform regulatory submissions or clinical decisions, while using streamlined, fit-for-purpose approaches for exploratory research and mechanistic studies.
In this presentation, Aliri R&D Director and Spatial-Omics Expert, Corinne Ramos, Ph.D., illustrates these challenges and opportunities through a spatial multi-omics use case, where paired patient biopsies were profiled with spatial transcriptomics and proteomics to uncover mechanistic insights, identify predictive biomarkers, and generate regulatory-ready evidence for clinical development.
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Maximizing Reproducibility and Sensitivity in qPCR for Detecting Transcripts Over a Broad Dynamic Range in Response to Anti-PD-1 Therapy
This study aims to optimize and validate a qPCR workflow for the reproducible and sensitive quantification of immune checkpoint transcripts (PD-1,PD-L1, CTLA-4) in FFPE lung cancer tissues. By refining tissue preparation, RNA input, and assay conditions, we establish a robust method for detecting gene expression across a broad dynamic range, enabling reliable assessment of immunotherapy response and supporting biomarker-driven patient stratification.
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Development and Validation of a Sensitive LC-MS/MS Method for the Quantification of SGR-1505 in Human Plasma to Support Clinical Pharmacokinetic Studies
MALT1 is a key mediator of NF-κB signaling and an emerging therapeutic target in B-cell malignancies and autoimmune diseases. SGR-1505, a potent MALT1 inhibitor, is being clinically evaluated for its therapeutic potential. In this study, we developed and validated a reliable and high-throughput LC-MS/MS method for the quantitation of SGR-1505 in human plasma (K₂EDTA) to support clinical pharmacokinetic studies. This work exemplifies the critical role of CRO-led bioanalysis in bridging early discovery and clinical development of emerging therapeutics.
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Development of Total ASO method in Mouse Plasma and Tissues Using LC-FD and LC-MS Platforms
Bioanalytical methods are needed to analyze protein conjugated antisense oligonucleotides (POCs) to accurately quantify the active antisense oligonucleotide (ASO) payloads, assess its pharmacokinetics and biodistribution in plasma and tissues, and ensure patient safety by evaluating potential immunogenicity and toxicity. Because the conjugate, the free ASO, and the linked ASO fragment can all be present, specialized techniques are required to differentiate and quantify these components, which is essential for supporting the development of these complex biotherapeutics. The unique properties of POCs present significant analytical challenges that necessitate specialized methods.
We set out to develop a methodology for quantifying total ASO in POCs that could be universally applied across similar POCs. The
study compared mass spectrometry and fluorescence detection platforms to determine optimal sensitivity, selectivity,
and adaptability. Additionally, it aimed to establish a single extraction method suitable for both plasma and tissue
analysis.
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Precision Bioanalysis for the Development of Dermal Therapies
In this application note, we outline next-generation spatial bioanalysis and spatial omics approaches for detecting and quantifying drug substance within dermal tissue, including human skin, reconstructed skin, nails, tape strips, and hair.
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Ophthalmic Support
Aliri has extensive experience supporting the precision bioanalysis of ophthalmic therapies including:
- Method demonstration, development, optimization, fit-for-purpose & GLP validation, and regulatory sample analysis
of ocular tissue and supporting matrices - Challenging large and small molecule ophthalmic drugs, including, prostaglandin analogs, peptides,
hormones, polysaccharides, allergen biomarkers, siRNA, oligonucleotidesWhole-eye spatial imaging using Quantitative
Mass Spectrometry Imaging (QMSI) to visually understand how your molecule performs in the microenvironment.
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Meet CyTOF: Simultaneous Inflammatory Response Monitoring & Cell Population Characterization
Say goodbye to PBMC processing, cold-chain shipping, and multiple assays, and experience the power of a single assay which combines cellular phenotyping directly with the level of activation.
Inflammation plays a critical role in numerous disease processes, including autoimmune disorders, infectious diseases, and immune-related adverse effects in immunotherapy. The ability to accurately assess inflammation is critical for understanding disease mechanisms, monitoring treatment efficacy, and identifying novel therapeutic targets. Traditional cytokine assays often lack the cellular context necessary for fully understanding immune activation and regulation. Inflammatory responses are shaped by intricate cytokine networks and immune cell interactions, which demand a more integrated, high-resolution analytical approach to provide meaningful insights.
Through the development of a proprietary next-generation inflammatory response assay that analyzes 46 markers off the shelf, Aliri can bridge this gap by simultaneously measuring cytokines and immune cell phenotypes, delivering a multi-dimension multi-dimensional dataset to enhance translational research and clinical decision-making.
Audience Takeaways
- How CyTOF works
- Advantages of CyTOF over Flow Cytometry and kit-based LBAs
- Case Study of Aliri’s proprietary Inflammatory Response Assay in Action
Bioanalysis and Spatial Imaging of Dermal Tissue
In this application note, we dive into the different bioanalytical and spatial imaging methods for detecting and quantifying drug substance within dermal tissue, including human skin, reconstructed skin, nails, tape strips, and hair.
Explore our advanced platforms and their applications:
- MALDI Imaging
- QMSI Evaluation of Human Toenail Clippings
- LC-MS/MS
- Penetration Profiling & Penetration Pathway
- Target Exposure
- Hyaluronic Acid by QMSI
- Elemental Imaging by QMSI
- Multiplex in situ profiling
- Platforms Combinations
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Considerations for Probe Selection for Oligonucleotide Hybridization LC/MS Workflows
Recently, while developing an assay for a siRNA complex using the LNA approach, we observed interferences from the probe to the antisense strand when it was analyzed by mass spectrometry. We modified the melting temperature to release the streptavidin/biotinylated hybridized to avoid releasing most of the biotinylated probe/antisense complex, but the limited release still had enough of the probe in the final extracts to cause interferences in the LLOQ samples. Modifying LC conditions helped to resolve the interference, but those changes were not entirely successful due to peak shape issues with the internal standard. After reviewing the probe design, we implemented an alternate PNA probe with the intention that any residual PNA probe would be easier to resolve chromatographically.
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Selection and Evaluation of Hybridization Capture Probes for LC/MS Analysis of Oligonucleotides
LC/MS bioanalysis of oligonucleotides has had its historical challenges in all areas of the workflow including extraction, liquid chromatography, and mass spectrometry detection. Among the primary pain points for the extraction of oligonucleotides is poor recovery from nonspecific binding or poor extraction efficiency using the most common extraction approaches. Recent publications of a more specific biotinylated probe hybridization approach have addressed these challenges, however, there hasn’t been much presented on the specific advantages for different probe types that can be used for this hybridization work. Although there has been a focus on DNA, LNA, and PNA probe design with research to demonstrate the specific attributes each offers, there has been limited discussion on the overall impact on recovery and interference from these different probes. Biotinylated probe design has been focused on limiting self-hybridization of the probe while maintaining a complimentary sequence with a sufficiently high score to out-compete any interferences from matrix or from the sense strand in siRNA modalities while keeping the melting temperature (Tm) of the hybridized duplex low enough to ensure recovery from the streptavidin beads. Recently, while developing an assay for a siRNA complex using the LNA approach, we observed interferences from the probe to the antisense strand when it was analyzed by mass spectrometry. We modified the melting temperature to release the streptavidin/biotinylated hybridized to avoid releasing most of the biotinylated probe/antisense complex, but the limited release still had enough of the probe in the final extracts to cause interferences in the LLOQ samples. Modifying LC conditions helped to resolve the interference, but those changes were not entirely successful due to peak shape issues with the internal standard. After reviewing the probe design, we implemented an alternate PNA probe with the intention that any residual PNA probe would be easier to resolve chromatographically.
Download our poster to learn more.