Biology subjects

Sangfelt, O.

Publications and source records attributed to Sangfelt, O..

4 recordsLinked to original sources

bioRxiv2026

De novo Design of Macrocyclic Molecular Glues

The engineering of induced proximity has transformed drug discovery, yet the development of molecular glues remains largely serendipitous and restricted to the retrospective optimisation of accidental discoveries. Here, we present EvoBind-multimer, a deep learning framework for the de novo design of molecular glues directly from protein sequences. Unlike structure-based docking, our method generates small macrocyclic peptides that bridge user-defined protein pairs without requiring prior interface knowledge or existing ligands. We applied this framework to recruit the E3 ligase VHL to two challenging oncoproteins: KRAS and BRD4. Live-cell NanoBRET demonstrated robust design-induced proximity for both pairs. Mechanistic validation demonstrated that the generated macrocycles form functional VHL-target ternary complexes capable of driving Cullin-RING ligase-dependent proteasomal degradation and downstream signalling shutdown. Finally, evaluation in patient-derived xenograft neuroblastoma tumoroids revealed that ternary complex processing is deeply context-dependent: identical macrocycles acted as potent degraders in one patient model, yet functioned as stabilising "LOCKTACs" in another, driving VHL-dependent target sequestration without turnover. By enabling the de novo design of induced proximity from sequence alone, EvoBind-multimer provides a route towards designing new protein functions.

bioinformatics↗

bioRxiv2023

Sequential drug treatment targeting cell cycle and cell fate regulatory programs blocks non-genetic cancer evolution in acute lymphoblastic leukemia

Targeted therapies exploiting vulnerabilities of cancer cells hold promise for improving patient outcome and reducing side-effects of chemotherapy. However, efficacy of precision therapies is limited in part because of the cellular heterogeneity of tumors. A better mechanistic understanding of how drug effect is linked to cancer cell state diversity is crucial for identifying effective combination therapies that can overcome the heterogeneity to prevent disease recurrence. Here, we characterized at the level of gene regulatory networks and at single-cell resolution the effect of G2/M cell cycle checkpoint inhibition in acute lymphoblastic leukemia (ALL) and demonstrate that WEE1 targeted therapy impinges on cell fate decision regulatory circuits. We found highest inhibition of recovery of proliferation in ALL cells with KMT2A-rearrangment (KMT2A-r), compared to cells of other leukemia subgroups. Single-cell transcriptome and chromatin accessibility profiling of (KMT2A::AFF1) RS4;11 cells treated with the WEE1 inhibitor AZD1775 revealed diversification of cell states at the fate decision points, with a fraction of cells exhibiting strong activation of p53-driven processes linked to induction of apoptosis and senescence, and disruption of a core KMT2A-RUNX1-MYC regulatory network through CDK1-mediated RUNX1 degradation. In RS4;11 cells and in patient-derived xenograft (PDX) model, we uncovered that in this cell state diversification induced by WEE1 inhibition, a subpopulation transitioned to a cell state characterized by activation of transcription factors regulating pre-B cell fate, lipid metabolism and pre-BCR signaling which supported a drug tolerance. Sequential treatment targeting the drug tolerant subpopulation with BCR-signaling inhibitors dasatinib, ibrutinib, or perturbing metabolism by fatostatin or AZD2014 after AZD1775 administration, effectively counteracted drug tolerance that drove recovery of leukemic cells. Collectively, our findings provide new insights into the tight connectivity of gene regulatory programs associated with cell cycle and cell fate regulation, and a rationale for sequential administration of WEE1 inhibitors with low toxicity inhibitors of pre-BCR signaling or metabolism.

cancer biology↗

bioRxiv2020

Single cell characterization of B-lymphoid differentiation and leukemic cell states during chemotherapy in ETV6-RUNX1 positive pediatric leukemia identifies drug-targetable transcription factor activities

Tight regulatory loops orchestrate commitment to B-cell fate within bone marrow. Genetic lesions in this gene regulatory network underlie the emergence of the most common childhood cancer, acute lymphoblastic leukemia (ALL). The initial genetic hits, including the common translocation that fuses ETV6 and RUNX1 genes, lead to arrested cell differentiation. Here, we aimed to characterize transcription factor activities along the B-lineage differentiation trajectory as a reference to characterize the aberrant cell states present in leukemic bone marrow, and to identify those transcription factors that maintain cancer-specific cell states for more precise therapeutic intervention. We compared normal B-lineage differentiation and in vivo leukemic cell states using single cell RNA-sequencing (scRNA-seq) and several complementary genomics profiles. Based on statistical tools for scRNA-seq, we benchmarked a workflow to resolve transcription factor activities and gene expression distribution changes in healthy bone marrow lymphoid cell states. We compared these to ALL bone marrow at diagnosis and in vivo during chemotherapy, focusing on leukemias carrying the ETV6-RUNX1 fusion. We show that lymphoid cell transcription factor activities uncovered from bone marrow scRNA-seq have high correspondence with independent ATAC- and ChIP-seq data. Using this comprehensive reference for regulatory factors coordinating B-lineage differentiation, our analysis of ETV6-RUNX1-positive ALL cases revealed elevated activity of multiple ETS-transcription factors in leukemic cells states, including the leukemia genome-wide association study hit ELK3. The accompanying gene expression changes associated with natural killer cell inactivation and depletion in the leukemic immune microenvironment. Moreover, our results suggest that the abundance of G1 cell cycle state at diagnosis and lack of differentiation-associated regulatory network changes during induction chemotherapy represent features of chemoresistance. To target the leukemic regulatory program and thereby overcome treatment-resistance, we show that selective inhibitors of ETS-transcription factors could effectively reduce cell viability. Our data provide a detailed picture of the transcription factor activities that characterize both normal B-lineage differentiation and those acquired in leukemic bone marrow and provide a rational basis for new treatment strategies targeting the immune microenvironment and the active regulatory network in leukemia.

cancer biology↗

bioRxiv2020

PTENP1-AS contributes to BRAF inhibitor resistance and is associated with adverse clinical outcome in stage III melanoma

Approximately 50% of human cutaneous melanomas carry activating mutations in the serine/threonine protein kinase BRAF. BRAF inhibitors (BRAFi) selectively target the oncogenic BRAFV600E/K and are effective in approximately 80% of patients carrying the mutation. However, resistance to BRAFi is common and emerges within a median time of 6-7 months of treatment and is prolonged to 11 months when combined with MEK inhibitors. Better characterization of the underlying molecular processes is therefore needed to further improve treatments. Inactivation of the tumor suppressor gene PTEN has been suggested to occur during melanomagenesis and drug resistance development. We recently demonstrated that transcription of PTEN is negatively regulated by an antisense RNA from the PTEN pseudogene (PTENP1-AS) and here set out to investigate the impact of this molecular pathway on the resistance to BRAFi and clinical outcome. We used a panel of BRAFi resistant A375 sublines, and observed increased levels of PTENP1-AS associated with reduced expression of PTEN. Furthermore, this loss of PTEN expression was correlated to increased recruitment of Enhancer of zeste homolog 2 (EZH2) and formation of the transcriptional repression mark H3K27me3 at the PTEN promoter in the resistant cells. We demonstrated that targeting of PTENP1-AS was able to re-activate the expression of PTEN and sensitize resistant melanoma cells to BRAFi. Finally, we showed that PTENP1-AS is a promising prognostic marker for clinical outcome in melanoma patients as high expression of PTENP1-AS in regional lymph node metastases from stage III melanoma patients correlated with poor survival.

cancer biology↗