Biology subjects

Khacho, M.

Publications and source records attributed to Khacho, M..

4 recordsLinked to original sources

bioRxiv2026

eIF4A inhibition disrupts resistance-associated translational and metabolic programs in BRAF-mutant melanoma

Acquired resistance to mitogen-activated protein kinase (MAPK) pathway inhibitors remains a major barrier to durable control of BRAF-mutant melanoma. Although resistance mechanisms are heterogeneous, they converge on adaptive programs that support survival, phenotypic plasticity, and metabolic fitness. We asked whether eukaryotic translation initiation factor 4A (eIF4A)-dependent mRNA translation represents a shared vulnerability of kinase inhibitor-resistant melanoma. Using matched BRAFV600E A375 and BRAF inhibitor-resistant A375R cells together with additional melanoma models, we integrated pharmacological and functional assays with polysome-associated RNA sequencing, quantitative proteomics, bioenergetic profiling, metabolomics, [U-13C5]glutamine tracing, and xenograft studies. Melanoma cells remained sensitive to multiple eIF4A inhibitors regardless of their responsiveness to BRAF inhibition. The eIF4A inhibitor CR-1-31-B rapidly reduced nascent protein synthesis when used alone in A375 cells and when added to the BRAF inhibitor PLX4032 in A375R cells; it also reduced BCL-2, CDK4, and cyclin D3 abundance, suppressed clonogenic growth, and induced apoptosis. Integrated analysis showed that acquired resistance involved broad RNA-abundance remodeling with superimposed changes in translational efficiency and buffering, affecting survival, extracellular-matrix and plasticity programs, and mitochondrial and metabolic functions. In resistant cells, CR-1-31-B induced early transcript-selective translational changes, accompanied at later time points by RNA-abundance and proteome remodeling. Publicly annotated 5' untranslated regions (5'UTRs) of CR-1-31-B-sensitive transcripts were enriched for purine-rich sequence architecture and local structural complexity. eIF4A inhibition preferentially attenuated the expression of proteins acquired during resistance and imposed a lower-output metabolic state in sensitive and resistant cells, reducing tricarboxylic-acid-cycle and pentose-phosphate-pathway metabolite pools and restricting intracellular glutamine-carbon transfer downstream of uptake. In A375 xenografts, CR-1-31-B delayed tumor growth, while its combination with PLX4720 produced deeper and more sustained tumor control and prolonged tumor endpoint-free survival compared with PLX4720 alone. These findings show that multiple resistance-associated programs spanning signaling, cell survival, and metabolism share a dependency on eIF4A-dependent translation and provide a preclinical rationale to test whether adding eIF4A inhibition can prolong responses to MAPK-targeted therapy in melanoma.

cancer biology↗

bioRxiv2026

LOSS OF PARKIN DISRUPTS NUCLEAR AND MITOCHONDRIAL PROGRAMS REQUIRED FOR MUSCLE REGENERATION

Skeletal muscle stem cells (MuSCs) rely on precisely coordinated metabolic and nuclear transitions to exit quiescence, enter the cell cycle, and regenerate tissue. How these processes are coupled remains poorly defined. Here, we identify PARKIN as a critical integrator of mitochondrial quality control and nuclear RNA processing programs that together enable balanced MuSC lineage progression. Using a MuSC-specific, inducible Park2 knockout model, we show that PARKIN supports mitophagy in quiescent MuSCs, and its loss triggers premature mitochondrial polarization and fragmentation -- hallmarks of metabolic activation -- that compromise appropriate self-renewal and fate specification. Unexpectedly, MuSCs harbor a constitutive nuclear pool of PARKIN that rises rapidly upon activation and localizes to interchromatin regions, with focal association with nuclear speckles. Park2-deficient MuSCs exhibit transcriptomic signatures consistent with widespread RNA isoform switching and intron retention, particularly affecting splicing machinery components, accompanied by altered nuclear speckle organization and impaired cell cycle progression. These findings reveal that PARKIN safeguards both mitochondrial homeostasis and the RNA processing architecture essential for activation, thereby coordinating metabolic and nuclear reprogramming during early MuSC state transitions. Our work positions PARKIN as a dual compartment regulator required for robust skeletal muscle regeneration.

cell biology↗

bioRxiv2023

PINK1 Deficiency Alters Muscle Stem Cell Fate Decision And Muscle Regenerative Capacity.

Maintenance of optimal mitochondrial function plays a crucial role in the regulation of muscle stem cell (MuSC) behavior, but the underlying maintenance mechanisms remain ill defined. In this study, we explored the importance of mitophagy, as a mitochondrial quality control regulator, in MuSCs and the role this process plays in maintaining optimal muscle regenerative capacity. Here we show that MuSCs exhibit dynamic alterations in mitophagy under different physiological myogenic states. In particular, quiescent MuSCs exhibit high levels of PINK1/Parkin-dependent mitophagy, which is rapidly decreased upon transition to an early activation state. Genetic disruption of this pathway using Pink1 knockout mice reduced mitophagy in quiescent MuSCs, which was accompanied by increased mitochondrial ROS release and mitochondrial network fragmentation. These abnormalities led to hampered self-renewal of MuSCs which ultimately translated in a progressive loss of muscle regeneration following repetitive injury. However, proliferation and differentiation capacity were unaltered in the absence of PINK1, indicating that altered fate decisions is the main mechanism underlying impaired muscle regeneration. Impaired fate decisions in PINK1 deficient MuSCs could be restored by scavenging excess mitochondrial ROS. Together, these data shed new light on the regulation of mitophagy during MuSC state transitions and position the PINK1-dependent pathway as an important regulator of MuSC mitochondrial properties and fate decisions.

cell biology↗

bioRxiv2020

A broad response to intracellular long-chain polyphosphate in human cells

Polyphosphates (PolyP) are composed of long chains of inorganic phosphates linked together by phosphoanhydride bonds. They are found in all kingdoms of life, playing roles in cell growth, infection, and blood coagulation. A resurgence in interest in polyP has shown links to diverse aspects of human disease. However, unlike in bacteria and lower eukaryotes, the mammalian enzymes responsible for polyP metabolism are not known. Many studies have resorted to adding polyP to cell culture media, but it is not clear if externally applied polyP enters the cell to impact signaling events or whether their effect is mediated exclusively by extracellular receptors. For the first time, we use RNA-seq and mass spectrometry to define a broad impact of polyP produced inside of mammalian cells via ectopic expression of the E. coli polyP synthetase Ppk1. RNA-seq demonstrates that Ppk1 expression impacts expression of over 350 genes enriched for processes related to transcription and cell motility. Analysis of proteins via label-free mass spectrometry identified over 100 changes with functional enrichment in cell migration. Follow up work suggests a role for internally-synthesized polyP in promoting activation of mTOR and ERK1/2-EGR1 signaling pathways implicated in cell growth and stress. Finally, fractionation analysis shows that polyP accumulated in multiple cellular compartments and was associated with the relocalization several nuclear/cytoskeleton proteins, including chromatin bound proteins DEK, TAF10, GTF2I and translation initiation factor eIF5b. Our work is the first to demonstrate that internally produced polyP can activate diverse signaling pathways in human cells. Significance StatementFor many years following its discovery in 1890, polyphosphates (polyP) were dismissed as evolutionary fossils. Best understood for its role in bacteria and yeast, our understanding of polyP in mammals remains rudimentary because the enzymes that synthesize and degrade polyP in mammalian systems are currently unknown. In our work, we carried out large-scale transcriptome and proteome approaches on human cells designed to accumulate internally produced polyP via ectopic expression of a bacterial polyP synthetase. Our work is the first to systematically assess the impact of increased intracellular polyP.

molecular biology↗