Biology subjects

Rieger, L.

Publications and source records attributed to Rieger, L..

5 recordsLinked to original sources

bioRxiv2024

Engineering de novo binder CAR-T cell therapies with generative AI

Chimeric antigen receptor T cell (CAR-T) therapies have revolutionized cancer treatment, with six CAR-T products currently in clinical use1-4. Despite their success, high resistance rates due to antigen escape remain a major challenge5,6. In silico design of de novo binders (DNBs) has the potential to accelerate the development of new binding domains for CAR-T, possibly enabling personalized therapies for cancer resistance7,8. Here, we show that DNBs can be used for CAR-T, targeting clinically relevant cancer antigens. Using a DNB against the epidermal growth factor receptor (EGFR), we demonstrate comparable cytotoxicity, cytokine secretion, long-term proliferation, and lysis of primary patient-derived cancer organoids with single-chain variable fragment (scFv)-based and DNB-based CAR-T cells. Moreover, we use generative artificial intelligence (AI) guided binder design with RFdiffusion9 to target the B cell maturation antigen (BCMA), a key antigen in multiple myeloma treatment10-17. We confirmed the activity of our AI-designed BCMA CAR-T in short- and long-term effector readouts, including a xenograft mouse model of multiple myeloma. Notably, our AI-guided CAR-T approach also successfully targets a mutated BCMA protein variant resistant to the clinically used bispecific antibody teclistamab. In sum, we demonstrate a proof-of-concept for engineering new, bespoke cellular immunotherapies targeting cancer resistance with the help of generative AI. This approach may further accelerate the development of new CAR-T therapies addressing cancer resistance.

bioengineering↗

bioRxiv2019

Integrated Low-Energy and Low Carbon Shortcut Nitrogen removal with Biological Phosphorus Removal for Sustainable Mainstream Wastewater Treatment

While enhanced biological phosphorus removal (EBPR) is widely utilized for phosphorus (P) removal from wastewater, understanding of efficient process alternatives that allow combined biological P removal and shortcut nitrogen (N) removal, such as nitritation-denitritation, is limited. Here, we demonstrate efficient and reliable combined total N, P, and chemical oxygen demand removal (70%, 83%, and 81%, respectively) in a sequencing batch reactor (SBR) treating real mainstream wastewater (primary effluent) at 20{degrees}C. Anaerobic - aerobic cycling (with intermittent oxic/anoxic periods during aeration) was used to achieve consistent removal rates, nitrite oxidizing organism (NOO) suppression, and high effluent quality. Importantly, high resolution process monitoring coupled to ex situ batch activity assays demonstrated that robust biological P removal was coupled to energy and carbon efficient nitritation-denitritation, not simultaneous nitrification-denitrification, for the last >400 days of 531 total days of operation. Nitrous oxide emissions of 2.2% relative to the influent TKN (or 5.2% relative to total inorganic nitrogen removal) were similar to those measured in other shortcut N bioprocesses. No exogenous chemicals were needed to achieve consistent process stability and high removal rates in the face of frequent wet weather flows and highly variable influent concentrations. Process modeling reproduced the performance observed in the SBR and confirmed that nitrite drawdown via denitritation contributed to suppression of NOO activity.

bioengineering↗

bioRxiv2019

A time resolved interaction analysis of Bem1 reconstructs the flow of Cdc42 during polar growth

Cdc42 organizes cellular polarity and directs the formation of cellular structures in many organisms. By locating Cdc24, the source of active Cdc42, to the growing edge of the yeast cell, the scaffold protein Bem1 is instrumental in shaping the cellular gradient of Cdc42. This gradient instructs bud formation, bud growth, or cytokinesis through the actions of a diverse set of effector proteins. To address how Bem1 participates in this transformation we systematically mapped its protein interactions in time and space. SPLIFF analysis defined a unique ensemble of Bem1 interaction-states for each cell cycle stage. The characterization of mutants of Bem1 that interact with a discrete subset of the interaction partners allowed to assign specific functions to different interaction states and identified the determinants for their cellular distributions. The analysis characterizes Bem1 as a cell cycle specific shuttle that distributes active Cdc42 from its source to its effectors and helps to convert the PAKs Cla4 and Ste20 into their active conformation.

cell biology↗

bioRxiv2019

An actin nucleation complex catalyzes filament formation at sites of exocytosis

Due to the local enrichment of factors that influence its formation, dynamics, and organization, the actin cytoskeleton displays different shapes and functions within the same cell. In yeast cells post-Golgi vesicles ride on long actin cables to the bud tip. The scaffold proteins Boi1 and Boi2 participate in tethering and docking these vesicles to the plasma membrane. Here we show that Boi1/2 also recruit nucleation and elongation factors to form actin filaments at sites of exocytosis. Disrupting the physical connection between Boi1/2 and the nucleation factor Bud6 impairs filament formation in the bud, reduces the directed movement of the vesicles to the tip, and shortens their tethering time at the cortex. Artificially transplanting Boi1 from the bud tip to the peroxisomal membrane partially redirects the actin cytoskeleton and the vesicular flow towards the peroxisome, and creates an alternative, rudimentary vesicle-docking zone. We conclude that Boi1/2 is sufficient to induce the formation of a cortical actin structure that receives and aligns incoming vesicles before fusing with the membrane.

cell biology↗

bioRxiv2017

The Cell Polarity Proteins Boi1p And Boi2p Stimulate Vesicle Fusion At The Plasma Membrane Of Yeast Cells

Eukaryotic cells can direct secretion to defined regions of their plasma membrane. These regions are distinguished by an elaborate architecture of proteins and lipids that are specialized to capture and fuse post-Golgi vesicles. Here we show that the proteins Boi1p and Boi2p are important elements of this area of active exocytosis at the tip of growing yeast cells. Cells lacking Boi1p and Boi2p accumulate secretory vesicles in their bud. The essential PH domains of Boi1p and Boi2p interact with Sec1p, a protein required for SNARE complex formation and vesicle fusion. Sec1p loses its tip localization in cells depleted of Boi1p and Boi2p but can partially compensate for their loss upon overexpression. The capacity to simultaneously bind phospholipids, Sec1p, multiple subunits of the exocyst, Cdc42p, and the module for generating active Cdc42p identify Boi1p and Boi2p as essential mediators between exocytosis and polar growth.\n\nSummary statementA novel protein complex connects vesicle fusion with Cdc42p activation. Genetic and protein interaction data suggest that its central members Boi1p and Boi2p chaperone the formation of the docking complex.

cell biology↗