CRISPR mediated lncRNA Knockout Screening Service
Introduction
Creative Biolabs' CRISPR mediated lncRNA Knockout Screening Service uses an unbiased high-throughput platform with advanced CRISPR/Cas systems like Cas13 (CasRx). It maps essential lncRNA dependencies in disease models, accelerating therapeutic target discovery and confirming druggability. As a trusted partner, we deliver causative data on lncRNA essentiality and MoA, transforming speculative hits into validated targets and de-risking your non-coding drug development pipeline.
CRISPR mediated lncRNA Knockout Screening Service
Background of LncRNA and Therapeutic Potential
LncRNAs, which constitute the majority of the non-coding RNAome, are often tissue-specific and act as scaffolds, decoys, or guides. Their dysregulation is a common feature in complex diseases, especially cancer, where they drive oncogenesis and drug resistance. Because they are often disease-specific and non-protein-coding, they offer a unique therapeutic opportunity for developing highly selective drugs, such as ASOs or RNA-structure-targeting small molecules, potentially with reduced systemic toxicity compared to broad protein kinase inhibitors.
Screening Purpose
The primary purpose of the CRISPR mediated lncRNA Knockout Screening Service is to perform a genome-scale loss-of-function screen to identify lncRNAs whose ablation leads to a significant negative phenotype, such as cell death or loss of proliferation (a "dropout" screen).
- DNA-Targeting Approach (Cas9): Uses paired guide RNAs (pgRNAs) to permanently delete the lncRNA locus, providing a definitive assessment of the gene's essentiality.
- RNA-Targeting Approach (Cas13/CasRx): Uses CasRx to directly cleave the lncRNA transcript in the cytoplasm. This is vital because many lncRNA loci overlap with protein-coding genes, where a Cas9 knockout would cause confounding, non-specific protein loss. CasRx ensures the observed phenotype is genuinely linked to the lncRNA transcript itself.
Subsequent Application of Hits
Identified lncRNA hits, once validated, open up multiple avenues for drug development:
- Lead Identification: The validated target (e.g., RP11-350G8.5) is moved forward for ASO design or high-throughput small molecule screening against its functional mechanisms or structural features (G-quadruplexes).
- Resistance Mitigation: LncRNAs found to be essential in drug-resistant cell models (e.g., Bortezomib-resistant MM cells) can be targeted in combination therapies to overcome established clinical resistance mechanisms.
- Biomarker Development: Differential expression of essential lncRNAs can serve as powerful prognostic or predictive biomarkers for patient stratification.
Workflow
Our detailed, multi-stage workflow ensures robust data generation and comprehensive target validation, suitable for visualization as a clear flowchart.
| Stage | Activity Description |
|---|---|
| Required Starting Materials | Provide (1) Cell line(s) of interest (e.g., established tumor lines, primary patient samples, or resistant clones), (2) Preliminary lncRNA target list (or bulk RNA-Seq/expression data for prioritization), and (3) Disease-relevant selection criteria (e.g., specific drug concentration for dropout screening). |
| Library Design & Prep | We utilize our proprietary pan-cancer-optimized gRNA libraries (including the Cas13-based Albarossa design) or design custom gRNA/pgRNA libraries targeting your specific lncRNA set, ensuring guides avoid genomic overlap with coding regions where possible. |
| High-Throughput Screen | Cas9 or Cas13 (CasRx) is stably expressed in the cell line(s). The gRNA library is transduced, and cells undergo the designated dropout selection (e.g., proliferative competition or drug challenge) over 10–21 days. |
| Deep Sequencing & Analysis | Genomic DNA is isolated, and gRNA sequences are amplified and sequenced (NGS). Data is processed using the MAGeCK robust rank aggregation (RRA) algorithm. |
| Target Prioritization | We integrate functional hit lists with patient data (prognostic and transcriptional profiles) via our Bioinformatic Prioritization Pipeline to rank candidates based on clinical relevance. |
| 5. Validation & MoA Study | Individual lncRNA candidates are validated using orthogonal assays (siRNA knockdown, qRT-PCR) and molecular studies (RNA-FISH for localization, RNA-Seq for pathway analysis, biophysical assays). |
| Final Deliverables | (1) Prioritized Target List and Rationale Report, (2) Raw and Processed NGS Data, and (3) Functional Validation Report (including viability data, pathway analysis, and structural characteristics). |
| Estimated Timeframe | The typical timeframe for this service ranges from 10 to 16 weeks, depending on the complexity of the cell models and the scope of the target validation and structural characterization requested. |
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What We Can Offer
Our CRISPR mediated lncRNA Knockout Screening Service is a comprehensive, customizable solution designed to maximize the success rate of your non-coding RNA drug discovery program. Creative Biolabs ensures maximum precision and clinical relevance at every stage of target identification.
Customized Library Design and Screening
Offering bespoke guide RNA (gRNA) or paired gRNA (pgRNA) libraries optimized for your specific target list, from focused screens of under 100 lncRNAs to large, transcriptome-wide, pan-cancer screens using the advanced Cas13-based Albarossa design.
Integrated Dual-Platform Precision
The ability to execute both DNA-targeting Cas9 (for definitive locus knockout) and RNA-targeting Cas13d (CasRx) systems to eliminate ambiguity caused by gene overlap and confirm transcript-specific function.
Intelligent Bioinformatic Prioritization
Seamless integration of high-throughput functional screening results with patient prognostic and expression data through our proprietary Bioinformatic Prioritization Pipeline, ensuring the targets are highly actionable and clinically relevant.
Comprehensive Downstream Validation
Efficient delivery of detailed Mechanism-of-Action (MoA) studies, including pathway analysis (e.g., UPR, ICD) and functional localization (e.g., RNA-FISH), minimizing your internal validation burden.
Structural Characterization for Druggability
Dedicated biophysical analysis to identify critical secondary structures (e.g., G-quadruplexes) that provide concrete, immediate design inputs for developing targeted ASO or small molecule therapeutics.
Flexible Project Scope and Delivery
We provide flexible, one-stop project execution from initial consultation and design through final data reports, allowing you to choose endpoints that perfectly align with your current research phase.
Customer Reviews
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FAQs
What is the benefit of your "Bioinformatic Prioritization Pipeline" over standard hit ranking?
Standard ranking often prioritizes the lncRNA that causes the fastest cell death. Our proprietary pipeline integrates your functional screening data with publicly available clinical data (e.g., prognostic markers from MM or other cancer patient databases). This ensures the lncRNAs we deliver are not just active in vitro, but are also highly correlated with poor patient outcomes or drug resistance in vivo, maximizing the clinical relevance of your discovery efforts.
Can Creative Biolabs target lncRNAs localized only in the cell nucleus, or only those in the cytoplasm?
Yes, we can target both. We use the Cas9-based system (KO/CRISPRi) primarily to target lncRNAs that function in the nucleus by disrupting transcription or genomic structure. The Cas13 (CasRx) system, which degrades the mature transcript, is highly effective for both nuclear and cytoplasmic lncRNAs, depending on the lncRNA stability and export dynamics. Our approach is tailored to the localization and function of your specific target.
What final evidence of "druggability" do you provide after a successful screen?
Beyond functional validation (viability, MoA), we offer structural characterization using biophysical assays (e.g., circular dichroism, NMR). We identify key secondary structures like G-quadruplexes and hairpin regions. These structures are ideal for targeting by ASOs designed to bind specific loops, or by small molecules designed to stabilize or destabilize the RNA structure—providing a concrete starting point for drug design.
I have a list of 50 lncRNAs. What is the most cost-effective way to determine their functional relevance?
For a focused set of 50 candidates, the most efficient and powerful strategy is a multiplexed Cas9/CasRx dropout screen using a streamlined custom library, followed by immediate prioritization and targeted validation. This strategy is faster and more cost-effective than screening them individually. Contact us to design a rapid, focused screen that minimizes unnecessary validation time.
Creative Biolabs offers the most advanced and comprehensive solution for navigating the complex non-coding genome. Our CRISPR mediated lncRNA Knockout Screening Service provides an integrated, end-to-end pipeline, moving you seamlessly from unbiased discovery to clinically relevant, structurally characterized therapeutic candidates. We are committed to accelerating your drug development pipeline with high-confidence functional genomic data.
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