Goñi-Salaverri, A. (Ainhoa)
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- In vivo screening characterizes chromatin factor functions during normal and malignant hematopoiesis(2023) Calvo, I.A. (Isabel A.); Torrea, N. (Natalia); Navarro-Alonso, M. (Mar); Fortelny, N. (Nikolaus); López, A. (Andrés); Taylor-King, J.P. (Jake P.); Lopez, C.K. (Cecile K.); Valle, C. (Cynthia) del; Gross, T. (Torsten); Beinortas, T. (Tumas); Lara-Astiaso, D. (David); Aguado-Álvaro, L.P. (Laura Pilar); Narayan, N. (Nisha); Alignani, D. (Diego); Zazpe, J. (Jon); Giotopoulos, G. (George); Marchese, F.P. (Francesco P.); Goñi-Salaverri, A. (Ainhoa); Prosper-Cardoso, F. (Felipe); Mendieta-Esteban, J. (Julen); Huntly, B.J.P. (Brian J. P.); Saez, B. (Borja)Bulk ex vivo and single-cell in vivo CRISPR knockout screens are used to characterize 680 chromatin factors during mouse hematopoiesis, highlighting lineage-specific and normal and leukemia-specific functions. Cellular differentiation requires extensive alterations in chromatin structure and function, which is elicited by the coordinated action of chromatin and transcription factors. By contrast with transcription factors, the roles of chromatin factors in differentiation have not been systematically characterized. Here, we combine bulk ex vivo and single-cell in vivo CRISPR screens to characterize the role of chromatin factor families in hematopoiesis. We uncover marked lineage specificities for 142 chromatin factors, revealing functional diversity among related chromatin factors (i.e. barrier-to-autointegration factor subcomplexes) as well as shared roles for unrelated repressive complexes that restrain excessive myeloid differentiation. Using epigenetic profiling, we identify functional interactions between lineage-determining transcription factors and several chromatin factors that explain their lineage dependencies. Studying chromatin factor functions in leukemia, we show that leukemia cells engage homeostatic chromatin factor functions to block differentiation, generating specific chromatin factor-transcription factor interactions that might be therapeutically targeted. Together, our work elucidates the lineage-determining properties of chromatin factors across normal and malignant hematopoiesis.
- The phospholipid transporter PITPNC1 links KRAS to MYC to prevent autophagy in lung and pancreatic cancer(2023) Halberg, N. (Nils); Vicent, S. (Silvestre); Vallejo-Blanco, A. (Adrián); Cueto-Ureña, C. (Cristina); Entrialgo-Cadierno, R. (Rodrigo); Vera, L. (Laura); Ambrogio, C. (Chiara); Vietti-Michelina, S. (Sandra); Cortés-Dominguez, I. (Iván); Scaparone, P. (Pietro); Lara-Astiaso, D. (David); Erice, O. (Oihane); Macaya, I. (Irati); Darbo, E. (Elodie); Feliu, I. (Iker); Morales-Urteaga, X. (Xabier); Guruceaga, E. (Elizabeth); Moreno, H. (Haritz); Goñi-Salaverri, A. (Ainhoa); Lecanda, F. (Fernando); Welch, C. (Connor); Lopez, I. (Inés)BackgroundThe discovery of functionally relevant KRAS effectors in lung and pancreatic ductal adenocarcinoma (LUAD and PDAC) may yield novel molecular targets or mechanisms amenable to inhibition strategies. Phospholipids availability has been appreciated as a mechanism to modulate KRAS oncogenic potential. Thus, phospholipid transporters may play a functional role in KRAS-driven oncogenesis. Here, we identified and systematically studied the phospholipid transporter PITPNC1 and its controlled network in LUAD and PDAC.MethodsGenetic modulation of KRAS expression as well as pharmacological inhibition of canonical effectors was completed. PITPNC1 genetic depletion was performed in in vitro and in vivo LUAD and PDAC models. PITPNC1-deficient cells were RNA sequenced, and Gene Ontology and enrichment analyses were applied to the output data. Protein-based biochemical and subcellular localization assays were run to investigate PITPNC1-regulated pathways. A drug repurposing approach was used to predict surrogate PITPNC1 inhibitors that were tested in combination with KRASG12C inhibitors in 2D, 3D, and in vivo models.ResultsPITPNC1 was increased in human LUAD and PDAC, and associated with poor patients' survival. PITPNC1 was regulated by KRAS through MEK1/2 and JNK1/2. Functional experiments showed PITPNC1 requirement for cell proliferation, cell cycle progression and tumour growth. Furthermore, PITPNC1 overexpression enhanced lung colonization and liver metastasis. PITPNC1 regulated a transcriptional signature which highly overlapped with that of KRAS, and controlled mTOR localization via enhanced MYC protein stability to prevent autophagy. JAK2 inhibitors were predicted as putative PITPNC1 inhibitors with antiproliferative effect and their combination with KRASG12C inhibitors elicited a substantial anti-tumour effect in LUAD and PDAC.ConclusionsOur data highlight the functional and clinical relevance of PITPNC1 in LUAD and PDAC. Moreover, PITPNC1 constitutes a new mechanism linking KRAS to MYC, and controls a druggable transcriptional network for combinatorial treatments.
- Correction: The phospholipid transporter PITPNC1 links KRAS to MYC to prevent autophagy in lung and pancreatic cancer(2023) Halberg, N. (Nils); Vicent, S. (Silvestre); Vallejo-Blanco, A. (Adrián); Cueto-Ureña, C. (Cristina); Entrialgo-Cadierno, R. (Rodrigo); Vera, L. (Laura); Ambrogio, C. (Chiara); Vietti-Michelina, S. (Sandra); Cortés-Dominguez, I. (Iván); Scaparone, P. (Pietro); Lara-Astiaso, D. (David); Erice, O. (Oihane); Macaya, I. (Irati); Darbo, E. (Elodie); Feliu, I. (Iker); Morales-Urteaga, X. (Xabier); Guruceaga, E. (Elizabeth); Moreno, H. (Haritz); Goñi-Salaverri, A. (Ainhoa); Lecanda, F. (Fernando); Welch, C. (Connor); Lopez, I. (Inés)
- Functional study of chromatin factors uncovers strong lineage determining roles and divergent behaviours between normal and malignant haematopoiesis(Universidad de Navarra, 2024-01-18) Goñi-Salaverri, A. (Ainhoa); Pineda-Lucena, A. (Antonio); Lara-Astiaso, D. (David)Haematopoiesis relies on the coordinated activities of transcription and chromatin factors (TFs and CFs), which interact to form Genome Regulatory Complexes (GRCs). These dynamic complexes precisely control lineage-specific transcriptional patterns and steer cellular phenotypes. Furthermore, the significance of TFs and CFs is strongly supported by a wealth of evidence from recent studies, which consistently reveal the high recurrence and almost ubiquitous presence of mutations affecting TFs and CFs in haematological malignancies, including acute myeloid leukaemia (AML). During the last decade, researchers in the field of haematopoiesis have greatly benefited from a comprehensive understanding of normal differentiation roadmaps and the transformation events occurring in malignancies. However, our understanding of CFs contribution to haematopoiesis remains limited. We have yet to determine the main factors (CFs and TFs) within GRCs that govern haematopoietic differentiation, unravel their intricate functional interactions and whether CFs have specific roles or redundantly contribute to lineage determination. Furthermore, we still need to discern which epigenetic mechanisms are disrupted in leukaemia and determine their impact on disease initiation and/or maintenance. We hypothesised that CFs within GRCs exert distinct roles during haematopoietic lineage determination and that specific CF disruption might contribute to the initiation and/or maintenance of AML. Firstly, we systematically assessed the lineage-specifying potential of chromatin regulators (CFs and TFs) in murine haematopoietic differentiation trajectories, both ex vivo and in vivo. Ex vivo bulk results unveiled the nuanced and stage-specific roles of GRCs involved in fundamental epigenetic processes during haematopoietic differentiation, including COMPASS methyl-transferases and BAF remodellers. However, a higher level of functional consistency was observed among epigenetic repressor complexes and corepressors. Consistent with the ex vivo effects, in vivo findings at single-cell resolution revealed pronounced lineage-specific trends and functional variability for COMPASS and BAF subcomplexes and suggested that multiple epigenetic repressors, like NuRD, ISWI and N-CoR, help maintain progenitor diversity and balanced lineage distribution by mitigating excessive myelopoiesis. Our second goal was to unveil the potential interactions amongst TFs and CFs to unravel the composition of key GRCs, shifting the current regulatory paradigm from a single factor to a protein complex-centric view. We examined the dynamic patterns of chromatin accessibility upon TF/CF disruptions and selected representative TF motifs of haematopoietic cell fates to analyse global TF footprints upon every knockout. Disruption of COMPASS and BAF showed downregulation of myeloid TF motif accessibility. In contrast, NuRD and other repressors induced increased accessibility of myeloid TFs associated with inflammatory responses upon knockout. Lastly, we aimed to dissect the corruption of CFs function in a Npm1c/Flt3-ITD leukaemia model and provide leukaemic-specific vulnerabilities that suggest potential epigenetic therapeutic avenues. scRNA-seq and CITE-seq analyses unveiled leukaemia transcriptomic heterogeneity, with distinct subpopulations exhibiting varying degrees of growth potential. Afterwards, Perturb-seq analysis of the chromatin regulators loss of function across leukaemia clusters confirmed tumour vulnerabilities upon specific perturbations, facilitating the transition of AML-infected cells towards leukaemic differentiated populations with limited cell proliferation and fitness capacities. These observations revealed that leukaemias subvert the function of CFs involved in homeostatic differentiation by aberrantly blocking these processes to sustain their malignant state.