Tar­get­ing the Dark Mat­ter of Can­cer with AI-Designed Mini Binder

Direct­ing chimeric anti­gen recep­tor (CAR) T cell immunother­a­pies against intra­cel­lu­lar or secret­ed tumour spe­cif­ic neoanti­gens remains a sig­nif­i­cant chal­lenge, lim­it­ing the poten­tial can­cer tar­get reper­toire clin­i­cal­ly. To address this, we have lever­aged AI-based pro­tein design to gen­er­ate pep­tide-MHC class I‑specific minibinders that mim­ic T‑cell recep­tor (TCR) recog­ni­tion, inte­grat­ed into a CAR plat­form. Using immunopep­tidomics, we have a iden­ti­fied a HLA‑A*02 restrict­ed pep­tide derived from IGFBPL‑1, fre­quent­ly expressed by small-cell lung can­cer cells.

To exper­i­men­tal­ly iden­ti­fy func­tion­al TCR-mimet­ic minibinders, we imple­ment­ed a high-through­put library screen­ing strat­e­gy. Select­ed TCR-mimet­ic minibinders were incor­po­rat­ed as bind­ing mod­ules into sec­ond gen­er­a­tion CAR T cell con­structs. Pep­tide-spe­cif­ic acti­va­tion of T cells express­ing IGFBPL1 minibinder-CAR was detect­ed upon co-cul­ture with IGFBPL1 pep­tide-pulsed HLA class I‑matched tar­get cells, demon­strat­ing func­tion­al tumor recognition.

We sub­se­quent­ly demon­strat­ed tar­get spe­cif­ic acti­va­tion of our IGBFPL1 minibinder-CAR against endoge­nous expres­sion of IGFBPL1 pep­tide on mul­ti­ple HLA‑A*02 SCLC cell lines. Ongo­ing exper­i­ments are fur­ther char­ac­ter­iz­ing CAR func­tion­al­i­ty and cyto­tox­i­c­i­ty, with opti­mi­sa­tion con­tin­u­ing in both the refine­ment of the arti­fi­cial IGFBPL1 spe­cif­ic minibinders and the opti­mal CAR recep­tor con­struct pairing.

Over­all, this AI-based plat­form rep­re­sents a sig­nif­i­cant advance in tar­get­ing pre­vi­ous­ly inac­ces­si­ble intra­cel­lu­lar onco­pro­teins and neoanti­gens with CAR T cells, as well as poten­tial­ly oth­er modal­i­ties like T cell engagers in the future.

Direct­ing chimeric anti­gen recep­tor (CAR) T cell immunother­a­pies against intra­cel­lu­lar or secret­ed tumour spe­cif­ic neoanti­gens remains a sig­nif­i­cant chal­lenge, lim­it­ing the poten­tial can­cer tar­get reper­toire clin­i­cal­ly. To address this, we have lever­aged AI-based pro­tein design to gen­er­ate pep­tide-MHC class I‑specific minibinders that mim­ic T‑cell recep­tor (TCR) recog­ni­tion, inte­grat­ed into a CAR plat­form. Using immunopep­tidomics, we have a iden­ti­fied a HLA‑A*02 restrict­ed pep­tide derived from IGFBPL‑1, fre­quent­ly expressed by small-cell lung can­cer cells.

To exper­i­men­tal­ly iden­ti­fy func­tion­al TCR-mimet­ic minibinders, we imple­ment­ed a high-through­put library screen­ing strat­e­gy. Select­ed TCR-mimet­ic minibinders were incor­po­rat­ed as bind­ing mod­ules into sec­ond gen­er­a­tion CAR T cell con­structs. Pep­tide-spe­cif­ic acti­va­tion of T cells express­ing IGFBPL1 minibinder-CAR was detect­ed upon co-cul­ture with IGFBPL1 pep­tide-pulsed HLA class I‑matched tar­get cells, demon­strat­ing func­tion­al tumor recognition.

We sub­se­quent­ly demon­strat­ed tar­get spe­cif­ic acti­va­tion of our IGBFPL1 minibinder-CAR against endoge­nous expres­sion of IGFBPL1 pep­tide on mul­ti­ple HLA‑A*02 SCLC cell lines. Ongo­ing exper­i­ments are fur­ther char­ac­ter­iz­ing CAR func­tion­al­i­ty and cyto­tox­i­c­i­ty, with opti­mi­sa­tion con­tin­u­ing in both the refine­ment of the arti­fi­cial IGFBPL1 spe­cif­ic minibinders and the opti­mal CAR recep­tor con­struct pairing.

Over­all, this AI-based plat­form rep­re­sents a sig­nif­i­cant advance in tar­get­ing pre­vi­ous­ly inac­ces­si­ble intra­cel­lu­lar onco­pro­teins and neoanti­gens with CAR T cells, as well as poten­tial­ly oth­er modal­i­ties like T cell engagers in the future.

Targeting the Dark Matter of Cancer with AI-Designed Mini Bind
Targeting the Dark Matter of Cancer with AI-Designed Mini Bind
Targeting the Dark Matter of Cancer with AI-Designed Mini Bind

Tobias Bald

Tobias Bald, PhD, serves as Pro­fes­sor for Tumor Immuno­bi­ol­o­gy at the Insti­tute for Exper­i­men­tal Oncol­o­gy at the Uni­ver­si­ty Hos­pi­tal Bonn, Ger­many. He obtained his PhD with high­est hon­ors from the Fac­ul­ty of Med­i­cine at the Uni­ver­si­ty of Bonn in 2015, focus­ing on the role of inflam­ma­to­ry respons­es in melanoma pro­gres­sion and the sig­nif­i­cance of the type I IFN sys­tem in can­cer immunother­a­py effi­ca­cy. Fol­low­ing the receipt of an EMBO Long-term Fel­low­ship, dr. Bald joined dr. Mark Smyth’s lab at the Queens­land Insti­tute for Med­ical Research, Bris­bane, Aus­tralia, in 2016. 

In 2018, he was grant­ed an ear­ly career fel­low­ship, enabling him to estab­lish a junior group to inves­ti­gate the impact of the Nectin-Net­work in the tumor microen­vi­ron­ment. In 2020, dr. Bald became a mem­ber of the DFG clus­ter of excel­lence ImmunoSen­sa­tion and found­ed the Lab­o­ra­to­ry for Tumor Immuno­bi­ol­o­gy (www​.bald​lab​.com) at the Uni­ver­si­ty Hos­pi­tal Bonn. His research focus­es on under­stand­ing the reg­u­la­tion of tumor-infil­trat­ing immune cells to devel­op inno­v­a­tive can­cer therapies. 

More about Dr. Tobias Bald.

Tobias Bald, PhD, serves as Pro­fes­sor for Tumor Immuno­bi­ol­o­gy at the Insti­tute for Exper­i­men­tal Oncol­o­gy at the Uni­ver­si­ty Hos­pi­tal Bonn, Ger­many. He obtained his PhD with high­est hon­ors from the Fac­ul­ty of Med­i­cine at the Uni­ver­si­ty of Bonn in 2015, focus­ing on the role of inflam­ma­to­ry respons­es in melanoma pro­gres­sion and the sig­nif­i­cance of the type I IFN sys­tem in can­cer immunother­a­py effi­ca­cy. Fol­low­ing the receipt of an EMBO Long-term Fel­low­ship, dr. Bald joined dr. Mark Smyth’s lab at the Queens­land Insti­tute for Med­ical Research, Bris­bane, Aus­tralia, in 2016. 

In 2018, he was grant­ed an ear­ly career fel­low­ship, enabling him to estab­lish a junior group to inves­ti­gate the impact of the Nectin-Net­work in the tumor microen­vi­ron­ment. In 2020, dr. Bald became a mem­ber of the DFG clus­ter of excel­lence ImmunoSen­sa­tion and found­ed the Lab­o­ra­to­ry for Tumor Immuno­bi­ol­o­gy (www​.bald​lab​.com) at the Uni­ver­si­ty Hos­pi­tal Bonn. His research focus­es on under­stand­ing the reg­u­la­tion of tumor-infil­trat­ing immune cells to devel­op inno­v­a­tive can­cer therapies. 

Tobias Bald | Targeting the Dark Matter of Cancer with AI-Designed Mini Binder
Tobias Bald, Uni­ver­si­ty of Bonn, DEUTSCHLAND

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