Biology subjects

Bakin, A. V.

Publications and source records attributed to Bakin, A. V..

3 recordsLinked to original sources

bioRxiv2025

A Sequential Triple-Drug Strategy for Selective Targeting of p53-Mutant Cancers

The tumor suppressor TP53 gene (p53) is mutated in most human malignancies; however, existing treatment options are largely ineffective, lack selectivity, and cause toxic side effects. To address these clinical problems, we developed a sequential triple-drug strategy for p53 mutant cancer cells. Here we show that a combination of a thymidine analogue (TAS102) plus PARP inhibitor (PARPi) promotes formation of DNA double-strand breaks (DSBs) and G2-arrest specifically in p53 mutant cancer cells. Transcriptome analysis revealed that TAS102-PARPi treatment of p53 mutant cells did not repress DNA replication but activated DSB repair and blocked the mitotic program, consistent with G2-arrest. In contrast, TAS102-PARPi treatment of normal p53 wild-type cells resulted in a temporal G1-arrest and rapid recovery of cell cycle capacity after drug withdrawal. In p53 mutant cancer cells, subsequent blocking of a G2-checkpoint kinase, such as WEE1, released these G2-arrested cells into mitosis, leading to massive cell death. Delayed administration of a G2-kinase inhibitor provides time for p53 wild-type cells to repair DNA, thereby minimizing toxicity to normal tissues. This sequential triple-drug strategy exhibited robust efficacy in preclinical models of colorectal and pancreatic cancers and was well tolerated in mice. Together, our findings illustrate a promising triple-drug strategy for targeting p53 mutant malignancies.

cancer biology↗

bioRxiv2025

BOGO: A Proteome-Wide Gene Overexpression Platform for Discovering Rational Cancer Combination Therapies

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/673780v2_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@19d5d7dorg.highwire.dtl.DTLVardef@64f7eborg.highwire.dtl.DTLVardef@d08b75org.highwire.dtl.DTLVardef@173c448_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG Cancer drug resistance remains a major barrier to durable treatment success, often leading to relapse despite advances in precision oncology. While combination therapies are being increasingly investigated, such as chemotherapy with small molecule inhibitors, predicting drug response and identifying rational drug combinations based on resistance mechanisms remain major challenges. Therefore, a proteome-wide, single-gene overexpression screening platform is essential for guiding rational therapy selection. Here, we present BOGO (Bxb1-landing pad human ORFeome-integrated system for a proteome-wide Gene Overexpression), a robust, scalable, and reproducible screening platform that enables single-copy, site-specific integration and overexpression of [~]19,000 human open across cancer cell models. Using BOGO, we identified drug-specific response drivers for 16 chemotherapeutic agents and integrated clinical datasets to uncover proliferation and resistance-associated genes with prognostic potential. Drug response similarity networks revealed both shared and unique mechanisms, highlighting key pathways such as autophagy, apoptosis, and Wnt signaling, and notable resistance-associated genes including BCL2, POLD2, and TRADD. In particular, we proposed a synergistic combination of the BCL2 family inhibitor ABT-263 (Navitoclax(R)) and the DNA analog TAS-102 (Lonsurf(R)), which revealed that lysosomal modulation is a key mechanism driving DNA analog resistance. This combination therapy selectively enhanced cytotoxicity in colorectal and pancreatic cancer cells in vitro, and demonstrated therapeutic benefit in vivo in both cell line-derived xenograft (CDX) and patient-derived xenograft (PDX) models. Together, these findings establish BOGO as a powerful gene overexpression perturbation platform for systematically identifying chemoresistance and chemosensitization drivers, and for discovering rational combination therapies. Its scalability and reproducibility position BOGO as a broadly applicable tool for functional genomics and therapeutic discovery beyond cancer resistance.

systems biology↗

bioRxiv2025

p38 blockade reverses the immune suppressive tumor microenvironment in metastatic breast cancer

Metastatic breast cancer (MBC) is a life-threatening disease with limited therapeutic options. The immune suppressive tumor microenvironment (TME) limits the potency of the antitumor immune response and facilitates disease progression and metastasis. Our current study demonstrates that p38 is a druggable target in the TME that regulates the outcome of the immune-tumor interaction. The study revealed that systemic blockade of p38 reduces metastasis, and this anti-metastatic response is negated by depletion of CD8+ T cells. Single-cell transcriptomic analysis of the immune-TME showed that pharmacological p38 inhibition (p38i) or tumor-specific inactivation of p38 by CRISPR/Cas9 (p38KO) resulted in a less exhausted and more activated CD8+ T cell phenotype. Immunophenotyping analyses demonstrated that p38 blockade reduced the expression of multiple inhibitory receptors on CD8+ T cells (i.e., PD-1, LAG-3, CTLA-4), indicating a reversal of immune exhaustion and enhanced immune activation systemically and in the TME. In contrast, p38 blockade did not exhibit inhibitory effects on T cells in proliferation assays in vitro and did not affect the proportion of regulatory T cells in vivo. The major negative impact of p38 blockade in vivo was on the myeloid populations, such as myeloid-derived suppressor cells (MDSCs) and tumor-associated macrophages (TAMs). Further, tumor p38 activity was required for the expression of cytokines/chemokines and tumor-derived exosomes with high chemotactic capacity for myeloid cells. Altogether, this study highlights a previously unrecognized p38-driven pathway that promotes an immune suppressive TME and metastasis, and that therapeutic blockade of p38 has important implications for improving antitumor immunity and patient outcomes. STATEMENT OF SIGNIFICANCEThis study highlights a previously unrecognized p38-driven tumor pathway that promotes an immune suppressive microenvironment and metastasis, and that therapeutic blockade of p38 has important implications for improving antitumor immunity and patient outcomes.

cancer biology↗