Part Collection
Parts we created for LiRA

Platform Overview

The LiRA parts collection offers a comprehensive, modular platform for programmable dual-biomarker detection and targeted therapeutic delivery in hepatitis B virus-associated hepatocellular carcinoma using the RADAR system. This platform addresses a fundamental challenge in precision oncology: single biomarkers often lack the specificity needed to distinguish cancer cells from healthy tissue, leading to off-target effects in therapeutic applications. By implementing Boolean AND-gate logic that requires simultaneous detection of both viral integration markers (HBx) and tumor-associated biomarkers (GPC3, AKR1B10), LiRA improves targeting specificity while maintaining the flexibility to adapt to different patient tumor profiles.

This enables researchers to detect disease-specific transcriptomic signatures and translate them into controlled therapeutic responses within living cells. The system operates through complementary sensor-trigger pairs: sensor plasmids contain engineered stop codons that block output protein translation, while trigger plasmids express reverse complement sequences that form double-stranded RNA complexes with their corresponding sensors. When both are present in a cell, ADAR enzymes edit the sensor stop codons, allowing output protein expression.

This post-transcriptional logic mechanism operates entirely through endogenous cellular machinery without requiring genome editing, offering a safer alternative for therapeutic applications. The platform was developed through iterative design-build-test cycles combining computational sensor design with experimental validation in mammalian cell models, yielding a collection of well-characterized parts with quantified performance metrics.

All parts have been submitted to The iGEM Parts Registry. On this page, we provide a detailed description of our parts, organized by functional modules. For more detailed information, visit the corresponding parts pages on The iGEM Parts Registry or our Engineering, Experiments, and Results wiki pages.

The LiRA Parts Collection Categories

Independent RADAR Sensors for HBV-HCC Biomarker Detection (Table 1) include our experimentally validated sensor-trigger pairs that detect individual disease biomarkers through ADAR-mediated stop codon editing.

AND-Gated Split GFP System for Dual-Biomarker Detection (Table 2) comprises our Boolean logic implementation parts that demonstrate proof-of-concept for tumor-selective therapeutic targeting.

Therapeutic Split IL-2 Platform for Targeted Cancer Immunotherapy (Table 3) translates the validated sensor-logic architecture into clinical application by replacing diagnostic GFP with split interleukin-2 cytokine fragments.

Independent RADAR Sensors for HBV-HCC Biomarker Detection

Module Type Designer Code Name Length (bp) Function and Description
Sensor Coding Noor El Kereamy BBa_25RYF076 Glypican-3 (GPC3) Sensor Plasmid Insert 1921 Sensor insert targeting GPC3 3'UTR transcripts overexpressed in hepatocellular carcinoma. Contains mCherry reporter (708 bp), engineered GPC3 sensor sequence with TAG stop codon (231 bp), and eGFP output (714 bp). Requires RADAR plasmid backbone for ADAR-mediated activation upon target detection.
Sensor Coding Noor El Kereamy BBa_259468A4 Aldo-Keto Reductase Family 1 Member B10 (AKR1B10) Sensor Plasmid Insert 1843 Sensor insert detecting AKR1B10 metabolic enzyme upregulated in HCC tumor environments. Contains mCherry reporter (708 bp), AKR1B10 5'UTR sensor sequence with TAG stop codon (153 bp), and eGFP output (714 bp). Requires RADAR plasmid backbone for signal activation.
Sensor Coding Noor El Kereamy BBa_25QMONLE Hepatitis B Virus X Antigen (HBx) Broad Sensor Plasmid Insert 1777 Sensor insert targeting highly conserved HBx sequences across integrated HBV genomes. Contains mCherry reporter (708 bp), HBx sensor sequence with TAG stop codon (87 bp) derived from conserved regions between viral start codons, and eGFP output (714 bp). Requires RADAR plasmid backbone for viral integration detection across genotypes.
Sensor Coding Noor El Kereamy BBa_259QGXXB Hepatitis B Virus X Antigen (HBx) Hep3B Cell Line-Specific Sensor Plasmid Insert 1783 Sensor insert derived from Hep3B cell line viral integration for testing sequence variant tolerance. Contains mCherry reporter (708 bp), Hep3B-specific HBx sensor with TAG stop codon (93 bp) including one editable mismatch plus seven additional mismatched bases, and eGFP output (714 bp). Validates sensor robustness with 5% mismatch tolerance in RADAR plasmid backbone.
Trigger Coding Noor El Kereamy BBa_25GUSBL6 Glypican-3 (GPC3) Trigger Plasmid Insert 1045 Trigger insert expressing reverse complement of GPC3 sensor sequence for experimental validation. Contains mTagBFP reporter and GPC3 trigger sequence (231 bp) that forms complementary dsRNA with sensor. Requires CMV promoter backbone for constitutive expression as positive control.
Trigger Coding Noor El Kereamy BBa_255DROWF Aldo-Keto Reductase Family 1 Member B10 (AKR1B10) Trigger Plasmid Insert 967 Trigger insert containing reverse complement of AKR1B10 sensor sequence for controlled laboratory validation. Contains mTagBFP reporter and AKR1B10 trigger sequence (153 bp) enabling dsRNA formation. Requires CMV promoter backbone for constitutive expression.
Trigger Coding Noor El Kereamy BBa_25C91P4O Hepatitis B Virus X Antigen (HBx) Broad Trigger Plasmid Insert 901 Trigger insert expressing consensus HBx sequence representing conserved viral antigen across isolates. Contains mTagBFP2 reporter and HBx broad trigger sequence (87 bp). Requires CMV promoter backbone and demonstrates strong activation of both broad and cell line-specific sensors.

AND-Gated Split GFP System for Dual-Biomarker Detection

Module Type Designer Code Name Length (bp) Function and Description
Sensor Measurement Melwin Cheng Choon Lei BBa_253Y381H GPC3-spGFP1-10 Sensor Plasmid Insert 1872 AND-gate sensor insert producing split GFP first fragment upon GPC3 3'UTR detection. Contains mCherry reporter, GPC3 sensor sequence with TAG stop codon (231 bp), and spGFP1-10 fragment (639 bp). Requires RADAR plasmid backbone and HBx-spGFP11 sensor for functional fluorescence output.
Sensor Measurement Melwin Cheng Choon Lei BBa_25DYNBRE HBx-spGFP11 Sensor Plasmid Insert 1731 AND-gate sensor insert producing split GFP second fragment upon HBx viral integration detection. Contains mCherry reporter, HBx sensor with TAG stop codon (87 bp), and spGFP11 fragment with three repeats (237 bp). Completes Boolean logic circuit when assembled in RADAR plasmid backbone.
Control Measurement Melwin Cheng Choon Lei BBa_2562CLUA Constitutive spGFP1-10 Control Insert 1462 Control insert validating split GFP reconstitution independent of sensor activation. Contains mScarlet3 reporter and constitutively expressed spGFP1-10 fragment (639 bp). Requires CMV promoter backbone for baseline split protein assembly measurements.
Control Measurement Melwin Cheng Choon Lei BBa_25PYP692 Constitutive spGFP11 Control Insert 1486 Control insert confirming split GFP fragment compatibility and assembly conditions. Contains mTagBFP2 reporter and constitutively expressed spGFP11 with three repeats (237 bp). Requires CMV promoter backbone for validating optimal fragment assembly.

Therapeutic Split IL-2 Platform for Targeted Cancer Immunotherapy

Module Type Designer Code Name Length (bp) Function and Description
Sensor Therapeutic Melwin Cheng Choon Lei BBa_25NIOP62 GPC3-Neo2A IL-2 Sensor Plasmid Insert 1578 Therapeutic AND-gate sensor insert producing first IL-2 fragment with leucine zipper upon GPC3 tumor biomarker detection. Contains mCherry reporter, GPC3 sensor with TAG stop codon (231 bp), and Neo2A_H1 with signal peptide and SynZip17 (351 bp). Requires RADAR plasmid backbone and remains non-functional until combined with second IL-2 fragment.
Sensor Therapeutic Melwin Cheng Choon Lei BBa_2562D1QC HBx-Neo2B IL-2 Sensor Plasmid Insert 1578 Therapeutic AND-gate sensor insert producing second IL-2 fragment upon HBx viral integration detection. Contains mCherry reporter, HBx sensor with TAG stop codon (87 bp), and Neo2B_H234 with SynZip18 and signal peptide (495 bp). Completes therapeutic Boolean logic when assembled in RADAR plasmid backbone for functional cytokine assembly.
Control Therapeutic Melwin Cheng Choon Lei BBa_25GU0O5Z Constitutive Neo2A IL-2 Control Insert 1159 Control insert validating first IL-2 fragment expression and assembly independent of sensor systems. Contains mScarlet3 reporter and constitutively expressed Neo2A_H1 with signal peptide and SynZip17 (351 bp). Requires CMV promoter backbone for testing split cytokine functionality.
Control Therapeutic Melwin Cheng Choon Lei BBa_25RY2FP1 Constitutive Neo2B IL-2 Control Insert 1326 Control insert confirming second IL-2 fragment reconstitution and cytokine functionality. Contains mTagBFP2 reporter and constitutively expressed Neo2B_H234 with SynZip18 and signal peptide (495 bp). Requires CMV promoter backbone for validating therapeutic protein assembly.