Biology subjects

de Almeida, M.

Publications and source records attributed to de Almeida, M..

3 recordsLinked to original sources

bioRxiv2026

CRISPR screens establish regulatory maps of immunosuppressive surface molecules in cancer

Cancer cells can evade immune surveillance by triggering inhibitory checkpoint responses in tumor-associated T cells through the expression of immunosuppressive surface molecules. While therapeutic blockade of such receptors has emerged as a pillar of cancer therapy, tumor cell-intrinsic mechanisms controlling their expression remain incompletely understood. Fluorescence-activated cell sorting (FACS)-based genetic screens can be used to decipher regulatory pathways, but conventional screening approaches are biased towards regulators that are dispensable for cancer cell proliferation and survival. Here, we used a tetracycline-inducible Cas9 system enabling fully time-controllable CRISPR-based mutagenesis to gain a more comprehensive and comparative survey of regulators controlling the expression of four major immunosuppressive surface molecules, PD-L1 (CD274), CD47, CD276 and HLA-E, as well as CD151, a candidate surface target associated with tumor growth and invasion. As a prominent hit, our screens identify the membrane-trafficking factor DNAJC13 as a regulator of PD-L1 and CD276. Among DNAJC13-controlled surface proteins, we identify other known and proposed immune-checkpoint molecules. Based on this function, suppression of DNAJC13 strongly increases the sensitivity of human cancer cells to T-cell attack in vitro and prolongs survival of mice bearing pancreatic tumors. Together, our study establishes regulatory maps of major immune-modulatory surface molecules and identifies DNAJC13 as a potential target for the coordinated inhibition of multiple immunosuppressive signals.

molecular biology↗

bioRxiv2024

A multivalent adaptor mechanism drives the nuclear import of proteasomes

Nuclear protein homeostasis, including the turnover of transcription factors, critically depends on nuclear proteasomes. After each cell division, proteasomes need to be re-imported into the newly formed nucleus in a highly dynamic process that requires the largely unstructured protein AKIRIN2. However, how AKIRIN2 orchestrates this process and, more generally, how large protein complexes are translocated into the nucleus remains poorly understood. Here, we have used an integrated approach combining protein-wide saturation mutagenesis screens, cryoEM, and biochemical reconstitution to characterize AKIRIN2 as a scaffold protein that coordinates the stepwise assembly of an importin cluster around the proteasome. Through surveying every possible single amino acid substitution in AKIRIN2 using FACS- and microscopy-based genetic screens, we establish a comprehensive map of functionally relevant residues and binding interfaces in structured and disordered protein regions. Integrating these results with cryoEM analysis reveals a wing helix in a disordered region of AKIRIN2 that plays a crucial role in stabilizing proteasome interactions. Upon primary binding, AKIRIN2 homodimers recruit the importin IPO9, which in turn facilitates the binding of a second AKIRIN2 homodimer that recruits additional importins. Together, this multivalent molecular assembly amplifies the number of nuclear localisation signals and, thereby, triggers efficient proteasome translocation into the nucleus. Inside the nucleus, RanGTP rapidly dissociates importins, and AKIRIN2 is degraded by the proteasome in a ubiquitin-independent manner. Beyond mechanistically resolving the nuclear import of proteasomes, we propose that multivalent adaptor proteins like AKIRIN2 orchestrate the import of other macromolecular complexes and thereby dynamically control the composition of the nuclear proteome.

molecular biology↗

bioRxiv2022

SPOP targets the immune transcription factor IRF1 for proteasomal degradation

Adaptation of the functional proteome is essential to counter pathogens during infection, yet precisely timed degradation of these response proteins after pathogen clearance is likewise key to preventing autoimmunity. Interferon Regulatory Factor 1 (IRF1) plays an essential role as a transcription factor in driving the expression of immune response genes during infection. The striking difference in functional output with other IRFs, is that IRF1 also drives the expression of various cell cycle inhibiting factors, making it an important tumor suppressor. Thus, it is critical to regulate the abundance of IRF1 to achieve a "Goldilocks" zone in which there is sufficient IRF1 to prevent tumorigenesis, yet not too much which could drive excessive immune activation. Using genetic screening, we identified the E3 ligase receptor Speckle Type BTB/POZ Protein (SPOP) to mediate IRF1 proteasomal turnover. We identified four S/T-rich degrons in IRF1 required for its SPOP MATH domain-dependent turnover. In the absence of SPOP, increased IRF1 protein levels functionally drive increased transcription of IRF1-response-genes, underpinning the biological significance of SPOP in curtailing IRF1 protein abundance.

cell biology↗