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Oncogene/Tumor Suppressor Proximity Profiling & Transcription Interference Assessment Service

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Background Service What We Can Offer Workflow Highlights FAQs Contact

Despite the clinical promise of gene therapies, accurately assessing the risk of insertional oncogenesis, particularly proximity to critical oncogenic control regions and physical distance to nearest transcription start sites, remains a major challenge. We introduce the Oncogene/Tumor Suppressor Proximity Profiling & Transcription Interference Assessment Services, a dedicated analytical platform that maps vector integration sites and quantifies promoter insertion or enhancer activation effects. Our service leverages high-resolution benchmarking of insertional risk profiles across diverse in vivo CAR-T delivery systems, including lentivirus, retrovirus, AAV, and LNP/mRNA mediated transposon platforms. By precisely determining whether a vector integrates into high-risk genomic regions and assessing transcriptional interference, we empower you with critical safety and efficacy data to guide safer vector design and regulatory decision-making.

Introduction

Oncogenes and tumor suppressors drive cancer hallmarks by regulating EV formation, cargo sorting, and release dynamics across disease progression, thus remodeling the surrounding stroma and immune landscape. Incorporating their activity states into CAR T cell engineering presents dual challenges, including possible EV shuttling of growth signals into modified T cells or dampening of cytotoxic responses, alongside potential gains in T cell homing, longevity, and defense against suppressive tumor cues.

Fig.1 The roles of oncogenes and tumor suppressors at multiple levels of cancer extracellular vesicle shedding and cargo acquisition. (OA Literature) Fig.1 The functions of oncogenes and tumor suppressors during distinct phases of extracellular vesicle release and cargo packaging in cancer.¹

Our Service

Our Oncogene/Tumor Suppressor Proximity Profiling & Transcription Interference Assessment Services directly map physical interactions and transcriptional conflicts between oncogenes and tumor suppressors at endogenous chromatin loci. By integrating high-resolution proximity-dependent crosslinking with real-time elongation assays, we reveal how oncogenic signaling silences suppressor genes or disrupts their feedback loops. This empowers precise mechanism-driven immunotherapy and combination target discovery.

What We Can Offer

We offer comprehensive oncogenomic safety assessment for your gene therapy vectors, precisely mapping integration sites, quantifying proximity to high-risk oncogenic regions and TSS, and evaluating promoter insertion, enhancer activation, and transcriptional interference risks.

Featured services of oncogene/tumor suppressor proximity profiling & transcription interference assessment services at Creative Biolabs. (Creative Biolabs Original)

Our Service Process

Required Starting Materials:

Transduced Cells: Genomic DNA extracted from target cells (e.g., primary T cells, CAR-T products) after transduction with viral vectors (Lentivirus, Retrovirus, AAV) or transfection with transposon systems (LNP/mRNA).
Reference Sequences: Vector backbone map (LTRs, promoter, enhancer elements) and host reference genome.

Workflow of oncogene/tumor suppressor proximity profiling & transcription interference assessment services at Creative Biolabs. (Creative Biolabs Original)

Final Deliverables

Integration Site Landscape Report: A comprehensive table listing all insertion loci, chromosome positions, distance to nearest TSS, and proximity to high-risk oncogenic control regions.
Insertional Oncogenesis Risk Profile: A heatmap or ranking scoring each delivery system based on proximity to oncogenes/tumor suppressors and transcriptional interference potential.

Key Advantages

Single-Nucleotide Resolution Risk Mapping: We achieve base-precise localization of vector integration sites, enabling definitive identification of insertions within high-risk oncogenic regions.
Integrated Multi-Parametric Safety Profiling: We concurrently evaluate TSS proximity, promoter insertion, enhancer activation, and transcriptional interference to deliver a comprehensive safety assessment.
Cross-Platform Analytical Versatility: Our service is compatible with lentivirus, retrovirus, AAV, and LNP/mRNA transposon systems, facilitating direct comparative benchmarking.

FAQ

Q1: Can your service be applied to non-viral delivery systems (e.g., LNP mRNA transposons)?

A1: Yes, our platform agnostic pipeline supports lentivirus, retrovirus, AAV, Sleeping Beauty transposons, and LNP/mRNA-based systems, enabling direct safety benchmarking across modalities.

Q2: Can you detect integration events that occur in quiescent or non-dividing cells (e.g., HSCs or neurons)?

A2: Yes, our ligation mediated PCR and targeted capture protocols are independent of cell proliferation, allowing detection of stable insertions in both dividing and non-dividing primary human cells, including CD34+ HSPCs and post mitotic neurons.

Why Choose Us?

Our integrated platform uniquely combines proximity profiling with transcription interference assessment to directly map oncogene and tumor suppressor crosstalk at chromatin level. We resolve physical interactions and functional transcriptional conflicts in native cellular contexts, offering mechanistic clarity essential for targeted cancer immunotherapy and checkpoint regulation studies. Fast, reproducible, and tailored to your immune-oncology models.

Customer Reviews

"Using Creative Biolabs' Oncogene/Tumor Suppressor Proximity Profiling & Transcription Interference Assessment Services, we were able to map the MYC p53 interaction landscape at sub-nanometer resolution. The proximity profiling service revealed unexpected spatial clustering of MYC near p53 responsive promoters, while the transcription interference assessment clearly quantified how MYC overexpression blocks p53's recruitment of RNA Pol II." Dr. El*a.

"Our team applied Creative Biolabs' services to study KRAS-driven transcriptional conflict with FOXO3. The proximity profiling identified physical tethering of mutant KRAS to FOXO3 binding sites, and the transcription interference service directly measured decreased FOXO3 target gene elongation." Dr. S* O*.

"The Oncogene/Tumor Suppressor Proximity Profiling & Transcription Interference Assessment Services were transformative for our study on mutant p53 gain-of-function. Proximity profiling revealed that mutant p53 physically associates with the BRD4 controlled super-enhancer of MYC, and the transcription interference service directly measured how this interaction interferes with MYC's own negative feedback loop." Dr. H*P* R*.

How to contact us?

Ready to resolve oncogene and tumor suppressor crosstalk in your immunotherapy models? Reach out to our scientific team directly through the inquiry form on this page. We provide rapid feasibility assessments, detailed service proposals, and expert consultation to tailor each assay to your specific cancer targets and transcriptional questions.

Reference

Bebelman, Maarten P et al. "The forces driving cancer extracellular vesicle secretion." Neoplasia (New York, N.Y.) vol. 23,1 (2021): 149-157. Distributed under Open Access License CC BY 4.0, without modification. https://doi.org/10.1016/j.neo.2020.11.011.

All products and services are For Research Use Only and CANNOT be used in the treatment or diagnosis of disease.