Figure 1: Schematic overview of the LITOSeek™ platform, illustrating liquid biopsy multiomics workflow for precision medicine
INTRODUCTION
Traditional tumor biopsy techniques, while informative, face limitations due to tumor heterogeneity and accessibility challenges at various metastatic sites throughout a patient’s treatment journey. Advances in next-generation sequencing technology (NGS) have enabled the development of non-invasive methods for blood-based biomarker detection, commonly referred to as a liquid biopsy (LBx). Novigenix’s pioneering liquid biopsy technology platform LITOSeek™ (Liquid ImmunoTranscriptOmics) leverages whole-blood LBx RNA-sequencing to capture patient-specific transcriptomic profiles. By integrating next-generation sequencing and AI technologies, LITOSeek™ excels in discovering robust blood-based RNA biomarkers and creating precise, specialized predictive models. Furthermore, the platform integrates LBx genomic mutations (ctDNA) for multimodal assessment of disease with unprecedented predictive capabilities, and it is compatible with other omics data such as methylation and proteomics for comprehensive assessment of patient profiles.
LITOSeek™ Translational Medicine
A number of liquid biopsy solutions have been developed and validated on the LITOSeek™ platform for precision development of novel therapeutics. These solutions can be readily implemented in global clinical trials with the convenience of a routine blood draw.
LBx Solutions for Precision Development of Novel Therapeutics
✓ Immuno pharmaco-dynamics (ImmunoPD) response markers
✓ Predictive biomarkers of response and resistance to therapy
✓ Mechanisms of action and mechanisms of resistance to therapy
✓ Discovery of safety biomarkers
✓ Digital cytometry and cellular deconvolution overcoming logistical hurdles of flow cytometry and CyTOF
Case Study #1:
LITOSeek™ LBx for Early Prediction of Durable Clinical Benefit
Traditional tumor biopsy techniques, while informative, face limitations due to tumor heterogeneity and accessibility challenges at various metastatic sites throughout a patient’s treatment journey. Advances in next-generation sequencing technology (NGS) have enabled the development of non-invasive methods for blood-based biomarker detection, commonly referred to as a liquid biopsy (LBx). Novigenix’s pioneering liquid biopsy technology platform LITOSeek™ (Liquid ImmunoTranscriptOmics) leverages whole-blood LBx RNA-sequencing to capture patient-specific transcriptomic profiles. By integrating next-generation sequencing and AI technologies, LITOSeek™ excels in discovering robust blood-based RNA biomarkers and creating precise, specialized predictive models. Furthermore, the platform integrates LBx genomic mutations (ctDNA) for multimodal assessment of disease with unprecedented predictive capabilities, and it is compatible with other omics data such as methylation and proteomics for comprehensive assessment of patient profiles.
A total of 93 metastatic bladder cancer patients underwent immunotherapy, and clinical responses were evaluated by RECIST criteria six months after therapy initiation. Whole-blood PAXgene® Blood RNA
Tubes were collected before treatment and on-treatment (either after the first or second cycle), and RNA-seq data was generated to identify gene expression signatures predictive of durable clinical benefits to immunotherapy, and to characterize immune modulation upon treatement.
The LITOSeek™ NoviScore univariant and multivariant models were used to accurately pinpoint the most significant biomarkers distinguishing transcriptomic profiles for discovery of key biomarkers indicative of immune changes associated with effective response to therapy. The resulting gene signatures were further analyzed with NoviContext using
multiple knowledge-based bioinformatic approaches, such as protein- interaction network analysis, and biological pathway analysis, to characterize central pathways related to transcriptomic modulations.
Biomarker contextualization identified modulation of key pathways of antigen processing and presentation,
T-cell mediated immunity, and cell cycle in patients with durable clinical benefit. These biomarkers provide deep insights into the immune system´s dynamic response to immunotherapy. The results are consistent with multiple other studies concluding that response to immunotherapy is driven by systemic cell responses, with a major role played by T cells which can be predictive of clinical benefit (Fairfax et al., Nature Medicine 2020; Valpione et al, Nature Cancer 2020; Hiam-Galvez, K.J. et al., Nat Rev Cancer, 2021).
Find out more:
Sandra van Wilpe et. al. “Multimodal integration of blood RNA and ctDNA reflects response to immunotherapy in metastatic urothelial cancer”, JCI Insight; 10.1172/jci.insight.186062
LITOSeek™ Predictive Modeling: Early Prediction of Clinical Benefit
LITOSeek™ NoviSig feature reduction machine-learning algorithms identified a set of 10 genes related to relevant group comparisons and central biological pathways for downstream modeling. Predictive models developed based on these 10 early-response biomarkers were trained with NoviSig algorithms, and their performance was evaluated in the confirmation and blinded, independent validation cohort. The Kaplan-Meier curve illustrates the predictive power of LITOSeek™ in stratification of patients into those with clinical benefit (CB) and those without (N-CB).
Blinded Validation cohort
AUC=0.77, specificity=67%, sensitivity=67%
Blinded Validation cohort
AUC=0.77, specificity=67%, sensitivity=67%
These results highlight the platform´s capabilities in identifying highly accurate RNA biomarkers of therapeutic response where other traditional biomarkers such as PD-L1 Score and Tumor Mutational Burden fail to have predictive power.
One of the key advantages of LITOSeek™ is its multimodal assessment of patient populations for more accurate assessment of disease and therapeutic intervention. Integration of RNA gene signature models with matched circulating tumor DNA (ctDNA) data from the same patient time-point were used to develop a multiomic model for prediction of clinical benefit. This approach provides a holistic assessment of patient response to therapeutic intervention with significant improvement of model performance for precise prediction of patient clinical benefit:
Confirmation cohort
Specificity=100%, sensitivity=71%
Blinded Validation cohort
Specificity=100%, sensitivity=79%
Case Study #2:
LITOSeek™ Unveils Dynamic Systemic Immune Modulation Along Colorectal Cancer Progression
Colorectal cancer (CRC) is the second leading cause of cancer-related deaths worldwide. Lifestyle-driven prevention and early diagnosis are the best strategies to reduce the mortality of CRC. Liquid biopsies measuring ctDNA are emerging as an alternaive to the invasive colonoscopy for CRC detection. However, the tumor-signal-dependent nature of this approach results in low sensitivity in precancerous and early CRC stages. In contrast, the immune system is highly sensitive to the emergence of cancer (Hiam-Galvez, K.J. et al., Nat Rev Cancer, 2021). In fact, activation of innate immunity is already detectable in the peripheral blood of individuals with pre-malignant advanced adenomas. This immune response is followed by signs of transient B-cell activation and sustained inhibition of T-cell responses along CRC progression, whereby at late stages, protumoral myeloid cells, wound healing and coagulation processes prevail. These results provide precision immune intelligence in the CRC patient journey and have paved the way for the development of a diagnostic test with high sensitivity for early detection of CRC.
Find out more:
Martinez-Usatorre A. et al. Human blood cell transcriptomics unveils dynamic systemic immune modulation along colorectal cancer progression.
Journal for ImmunoTherapy of Cancer 2024;12:e009888. doi:10.1136/ jitc-2024-009888 jitc-2024-009888
Conclusions
The LITOSeek™ platform has demonstrated a broad range of applicability in precision oncology, offering Precise & Predictive Patient Profiling for development of novel therapeutics. The ISO 13485 certified platform is currently used in a number of FDA clinical trials across therapeutic modalities including:
✓ Antibody-Drug Conjugates (ADC)
✓ Targeted Radionuclide Therapy
✓ Therapeutic Vaccines
✓ Cellular Therapies
✓ Immunotherapies
Contact us to explore how LITOSeek™ can accelerate your clinical development programs.