Biology subjects

Arsenian-Henriksson, M.

Publications and source records attributed to Arsenian-Henriksson, M..

5 recordsLinked to original sources

bioRxiv2026

Identifying cancer cell-state transitions from multimodal single-cell data

Phenotypic plasticity allows cancer cells to evade therapy, yet the transient nature of state transitions has made their molecular drivers difficult to define. Here, we present a single-cell framework that leverages the temporal delays between mRNA and protein accumulation to directly capture cells undergoing phenotypic switching. We show that differentiation-associated delays between transcript and protein accumulation are detectable in multimodal single-cell data as discordant mRNA and surface-protein levels. Applying this strategy to the K562 leukemia model, which alternates between differentiated CD24- and progenitor-like CD24+ states, we identify transitioning cells and derive a transcriptional signature linking cell-cycle progression and mitochondrial remodeling to plasticity. Genome-wide CRISPR screening confirms key regulators of plasticity, including BCR-ABL1 and mitochondrial homeostasis genes. We summarize the transition-associated program into a score that predicts imatinib response in chronic myeloid leukemia, stratifies survival in acute myeloid leukemia, and retains prognostic value across 31 TCGA tumor types. Spatial transcriptomics reveals localized plasticity hotspots in solid tumors. Together, this framework exposes the molecular basis of cancer plasticity and enables its quantification across tumors.

cancer biology↗

bioRxiv2025

Complex I Drives Glutamine-Dependent TCA Cycle to Support Viability of MYChigh Breast Cancer Cells

In many cancers, stably elevated MYC levels drive persistent and concerted activation of cell growth promoting anabolic programs and the cell cycle in ways that are distinct from normal cells. Therefore, synthetic-lethal strategies to target MYC reprograming of these pathways may identify new selective anticancer therapies for the treatment of MYChigh tumors. Here, we identify enhanced mitochondrial respiration as a hallmark of MYC overexpressing cancer cells. Mitochondrial respiration sustains the TCA cycle by regenerating NAD+ through complex I-mediated oxidation of NADH. Metabolic carbon tracing analysis revealed that MYC shifts TCA cycles carbon source from glucose to glutamine. Inhibition of the glutamine-fueled TCA cycle using NAD+-depleting complex I inhibitors resulted in MYC-dependent synthetic lethality in breast cancer cells. In mouse models of MYChigh tumors, persistent inhibition of tumor growth was achieved through combined inhibition of complex I and glutaminolysis. Our results suggest that the high respiration rate observed in MYChigh cells supports glutamine carbon-enriched TCA cycle, rendering MYChigh tumors selectively vulnerable to inhibitors of mitochondrial respiration and glutaminolysis.

cancer biology↗

bioRxiv2023

Co-inhibition of topoisomerase 1 and BRD4-mediated pause release selectively kills pancreatic cancer via readthrough transcription

Pancreatic carcinoma is one of the most lethal cancers and the absence of efficient therapeutic strategies results in poor prognosis. Transcriptional dysregulation due to alterations in KRAS and MYC impacts initiation, development, and survival of this tumor type. Using patient-derived xenografts of pancreatic carcinoma driven by KRAS and MYC oncogenic transcription, we show that co-inhibition of Topoisomerase 1 (TOP1) and bromodomain containing protein 4 (BRD4) synergistically induce tumor regression through targeting promoter pause-release, a rate-limiting step in transcription elongation. By comparing the nascent transcriptome with the recruitment of elongation and termination factors along genes, we found that co-inhibition of TOP1 and BRD4, while globally impairing RNA production, disturbs recruitment of proteins involved in termination. Thus, RNA polymerases continue transcribing downstream of genes for hundreds of kilobases leading to readthrough transcription. This pervasive transcription also occurs during replication, perturbing replisome progression and leading to DNA damage. The synergistic effect of TOP1 and BRD4 inhibition is specific for cancer cells leaving normal cells unharmed, highlighting the sensitivity of the tumor to these transcriptional defects. This preclinical study provides a mechanistic understanding of the benefit of combining TOP1 and BRD4 inhibitors to treat pancreatic carcinomas addicted to oncogenic drivers of high transcription and replication. One Sentence SummaryTOP1 and BRD4 inhibitors synergize to selectively kill pancreatic cancer in vivo via readthrough transcription without emergence of drug resistance

cancer biology↗

bioRxiv2022

A grappling hook interaction balances self-assembly and chaperone activity of Nucleophosmin 1

How the self-assembly of partially disordered proteins generates functional compartments in the cytoplasm and particularly in the nucleus is poorly understood. Nucleophosmin 1 (NPM1) is an abundant nucleolar protein that forms large oligomers which provide the scaffold for ribosome assembly but also prevent protein aggregation as part of the cellular stress response. Examining the relationship between the self-assembly and chaperone activity of NPM1, we find that oligomerization of full-length NPM1 modulates its ability to retard amyloid formation in vitro. Machine learning and cryo-electron microscopy reveal fuzzy interactions between the disordered region and the C-terminal nucleotide-binding domain that cross-link NPM1 pentamers into oligomers. Ribosomal peptides mediate in a tighter association within the oligomers, reducing their capacity to prevent amyloid formation. We conclude that NPM1 uses a "grappling hook" interaction to form a network-like structure whose chaperone activity is tuned by basic proteins, suggesting a regulatory mechanism for the nucleolar stress response.

biophysics↗

bioRxiv2019

Lactate potentiates differentiation and expansion of cytotoxic T cells

Exercise has a range of effects on metabolism. In animal models, repeated exertion reduces malignant tumour progression, and clinically, exercise can improve outcome for cancer patients. The etiology of the effect of exercise on tumour progression is unclear, as are the cellular actors involved. We show here that exercise-induced reduction in tumour growth is dependent on CD8+ T cells and that lactate, which is produced at high levels during exertion, increases proliferative capacity and cytotoxicity of CD8+ T cells. We found that at elevated levels lactate is used as a fuel during T cell activation. We further found that injection of lactate into animals can reduce malignant tumour growth in a dose-and CD8+ T cell-dependent manner. These data demonstrate that lactate can act to increase the anti-tumour activity of cytotoxic T cells, and in so doing, reduce cancer progression.

immunology↗