Biology subjects

Mall, M.

Publications and source records attributed to Mall, M..

10 recordsLinked to original sources

bioRxiv2025

A spatiotemporal cancer cell trajectory underlies glioblastoma heterogeneity

Cancer cells display highly heterogeneous and plastic states in glioblastoma, an incurable brain tumour. However, how these malignant states arise and whether they follow defined cellular trajectories across tumours is poorly understood. Here, we generated a deep single cell and spatial multi-omic atlas of human glioblastoma that pairs transcriptomic, epigenomic and genomic profiling of 12 tumours across multiple regions. We identify that glioblastoma heterogeneity is driven by spatially-patterned transitions of cancer cells from developmental-like states towards those defined by a glial injury response and hypoxia. This cellular trajectory regionalises tumours into distinct tissue niches and manifests in a molecularly conserved manner across tumours as well as genetically distinct tumour subclones. Moreover, using a new deep learning framework to map cancer cell states jointly with clones in situ, we show that tumour subclones are finely spatially intermixed through glioblastoma tissue niches. Finally, we show that this cancer cell trajectory is intimately linked to myeloid heterogeneity and unfolds across regionalised myeloid signalling environments. Our findings define a stereotyped trajectory of cancer cells in glioblastoma and unify glioblastoma tumour heterogeneity into a tractable cellular and tissue framework.

cancer biology↗

bioRxiv2025

Decoding Plasticity Regulators and Transition Trajectories in Glioblastoma with Single-cell Multiomics

Glioblastoma (GB) is one of the most lethal human cancers, marked by profound intratumoral heterogeneity and near-universal treatment resistance. Cellular plasticity, the capacity of cancer cells to transition between phenotypic states, drives GB progression and resistance. However, the regulatory logic that permits or restricts specific state transitions remains poorly understood. Here, we integrated single-nucleus RNA and chromatin accessibility multi-ome profiles from over one million cells across primary IDH-wildtype GBs and developed scDORI, a scalable deep-learning framework to infer enhancer-driven gene regulatory networks (eGRNs) at single-cell resolution. Our analysis revealed a structured hierarchy of GB cell states governed by distinct regulatory programs, with marked variability in epigenetic plasticity that enables or constrains transitions. Neuronal-like tumor cells emerge as a low plasticity state that deploys active repression, in contrast to more permissive progenitor-like and astrocytic states. We identified the neuronal-like state-specific repressor MYT1L as a key regulator that silences master transcription factors of alternative states. MYT1L gain-of-function in patient-derived GB cells reduced chromatin accessibility, induced neuronal-like identity, and restricted proliferation and invasion in vivo, whereas loss-of-function reactivated plasticity and accelerated malignant features. Our findings delineate the epigenetic architecture and associated transcriptional master regulators that shape GB state trajectories, and establish safeguard repressors such as MYT1L as potential therapeutic targets to constrain malignant plasticity.

cancer biology↗

bioRxiv2025

The glutamine-aspartate metabolic tradeoff between fast growth and metabolic flexibility.

Cancer cells develop unique addictions to nutrients, offering attractive opportunities for clinical intervention. However, how cancer cells orchestrate and benefit from metabolic rewiring remain fundamental open questions. Here, we developed a systematic framework to investigate nutrient dependencies and applied it to study glutamine addiction. By measuring metabolite exchange rates across 54 cancer cell lines with different levels of dependency on extracellular glutamine and in human stem cells, we discovered that a dualistic regulation of glutamate biosynthesis from glutamine or aspartate, driven by the tissue of origin, generates a tradeoff between fast growth and metabolic flexibility. Monitoring dynamic metabolic adaptation to glutamine deprivation showed that the role of glutamine as limiting substrate in purine biosynthesis is not responsible for glutamine dependency. Rather, growth arrest is mediated by glutamine as a signaling molecule. Our approach opens new opportunities to map, mechanistically investigate and pharmacologically interfere with metabolic dependencies, beyond glutamine addiction.

cancer biology↗

bioRxiv2024

Differential KEAP1/NRF2 mediated signaling widens the therapeutic window of redox-targeting drugs in SCLC therapy

Small cell lung cancer (SCLC) patients frequently experience a remarkable response to first-line therapy. Follow up maintenance treatments aim to control residual tumor cells, but generally fail due to cross-resistance, inefficient targeting of tumor vulnerabilities, or dose-limiting toxicity, resulting in relapse and disease progression. Here, we show that SCLC cells, similar to their cells of origin, pulmonary neuroendocrine cells (PNECs), exhibit low activity in pathways protecting against reactive oxygen species (ROS). When exposed to a novel thioredoxin reductase 1 (TXNRD1) inhibitor, these cells quickly exhaust their ROS-scavenging capacity, regardless of their molecular subtype or resistance to first-line therapy. Importantly, unlike non-cancerous cells, SCLC cells cannot adapt to drug-induced ROS stress due to the suppression of ROS defense mechanisms by multiple layers of epigenetic and transcriptional regulation. By exploiting this difference in oxidative stress management, we safely increased the therapeutic dose of TXNRD1 inhibitors in vivo by pharmacological activation of the NRF2 stress response pathway. This resulted in improved tumor control without added toxicity to healthy tissues. These findings underscore the therapeutic potential of TXNRD1 inhibitors for maintenance therapy in SCLC. Graphical summary O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=72 SRC="FIGDIR/small/621846v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@2a7336org.highwire.dtl.DTLVardef@f21de9org.highwire.dtl.DTLVardef@189d062org.highwire.dtl.DTLVardef@cff38b_HPS_FORMAT_FIGEXP M_FIG C_FIG Pharmacological induction of NRF2 leads to differential cyto-protection against TXNRD1 inhibitors in normal tissue but not in SCLC tumor cells. This results in a reduction of adverse effects, allowing to increase the therapeutic dose.

cancer biology↗

bioRxiv2024

Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumourigenesis

Cell fate plasticity enables development, yet unlocked plasticity is a cancer hallmark. Regulating cell identity requires gene activation and repression. While master regulators induce lineage-specific genes to restrict plasticity, it remains unclear whether unwanted plasticity is actively suppressed by lineage-specific repressors. Here, we computationally predict so-called safeguard repressors for 18 cell types that block phenotypic plasticity lifelong. We validated hepatocyte-specific candidates using reprogramming, revealing that Prospero homeobox protein 1 (PROX1) enhanced hepatocyte identity by direct repression of alternate fate master regulators. In mice, Prox1 was required for efficient hepatocyte regeneration after injury and acted as a tumour suppressor in multiple liver cancer models. In line with patient data, Prox1 depletion caused hepatocyte fate loss in vivo, and promoted transition of hepatocellular carcinoma to cholangiocarcinoma, conversely, overexpression promoted cholangiocarcinoma to hepatocellular carcinoma transdifferentiation. Our findings provide mechanistic evidence for PROX1 as a hepatocyte-specific safeguard and support a model where individual cell type-specific repressors actively suppress plasticity throughout life to safeguard lineage choice and prevent disease.

cancer biology↗

bioRxiv2023

Dextromethorphan inhibits collagen transport in the endoplasmic reticulum eliciting an anti-fibrotic response in ex-vivo and in vitro models of pulmonary fibrosis

Excessive deposition of fibrillar collagen in the interstitial extracellular matrix (ECM) of human lung tissue causes fibrosis, which can ultimately lead to organ failure. Despite our understanding of the molecular mechanisms underlying the disease, a cure for pulmonary fibrosis has not yet been found. In this study, we screened an FDA-approved drug library containing 712 drugs and found that Dextromethorphan (DXM), a cough expectorant, significantly reduces the amount of excess fibrillar collagen deposited in the ECM in in-vitro cultured primary human lung fibroblasts (NHLF) and ex-vivo cultured human precision-cut lung slice (hPCLS) models of lung fibrosis. Reduced extracellular fibrillar collagen levels in the ECM upon DXM treatment are due to a reversible trafficking inhibition of collagen type I (COL1) in the endoplasmic reticulum (ER) in TANGO1 and HSP47 positive structures. Mass spectrometric analysis shows that DXM causes hyper-hydroxylation of proline and lysine residues on Collagen (COL1, COL3, COL4, COL5, COL7, COL12) and Latent-transforming growth factor beta-binding protein (LTBP1 and LTBP2) peptides coinciding with their secretion block. In addition, thermal proteome profiling of cells treated with DXM shows increased thermal stability of prolyl-hydroxylases such as P3H2, P3H3, P3H4, P4HA1 and P4HA2, suggesting a change in activity. Transcriptome analysis of pro-fibrotic stimulated NHLFs and hPCLS upon DXM treatment showed activation of an anti-fibrotic program via regulation of pathways such as those involved in the MMP-ADAMTS axis, WNT, and fibroblast-to-myofibroblast differentiation. Taken together, the data obtained from both in-vitro and ex-vivo models of fibrogenesis show that Dextromethorphan has potent anti-fibrotic activity by efficient inhibition of COL1 membrane trafficking in the ER.

cell biology↗

bioRxiv2021

Post-entry, spike-dependent replication advantage of B.1.1.7 and B.1.617.2 over B.1 SARS-CoV-2 in an ACE2-deficient human lung cell line

Epidemiological data demonstrate that SARS-CoV-2 variants of concern (VOC) B.1.1.7 and B.1.617.2 are more transmissible and infections are associated with a higher mortality than non-VOC virus infections. Phenotypic properties underlying their enhanced spread in the human population remain unknown. B.1.1.7 virus isolates displayed inferior or equivalent spread in most cell lines and primary cells compared to an ancestral B.1 SARS-CoV-2, and were outcompeted by the latter. Lower infectivity and delayed entry kinetics of B.1.1.7 viruses were accompanied by inefficient proteolytic processing of spike. B.1.1.7 viruses failed to escape from neutralizing antibodies, but slightly dampened induction of innate immunity. The bronchial cell line NCI-H1299 supported 24- and 595-fold increased growth of B.1.1.7 and B.1.617.2 viruses, respectively, in the absence of detectable ACE2 expression and in a spike-determined fashion. Superior spread in NCI-H1299 cells suggests that VOCs employ a distinct set of cellular cofactors that may be unavailable in standard cell lines.

microbiology↗

bioRxiv2021

MEOX2 homeobox gene promotes growth of malignant gliomas

Glioblastoma (GBM) is an aggressive tumor that frequently exhibits gain of chromosome 7, loss of chromosome 10 and aberrantly activated receptor tyrosine kinase signaling pathways. Here, we identify mesenchyme homeobox 2 (MEOX2) on chromosome 7 with increased expression in GBM as a salient oncogenic transcription factor. Specifically, we show that MEOX2 overexpression leads to increased ERK phosphorylation, and we identify a phosphorylation site on MEOX2 that regulates its transcriptional activity by altering its subnuclear localization. We show that MEOX2 overexpression can lead to increased growth in GBM implantation models and cooperates with loss of p53 and PTEN in cerebral organoid models of human malignant gliomas to induce cell proliferation. Furthermore, using high-throughput genomics, we identify transcriptional target genes of MEOX2 in patient-derived GBM tumorsphere models and a fresh frozen GBM tumor. These analyses show that MEOX2 activates several oncogenic pathways involved in MAPK signaling and extracellular matrix organization. Furthermore, MEOX2 binds to oncogenic ETS factors and known glioma oncogenes such as FABP7. In total, we reveal a novel role for MEOX2 in GBM initiation and progression and demonstrate that MEOX2 can enhance ERK signaling through a feed-forward mechanism. Significance StatementGlioblastoma (GBM) harbors gain of chromosome 7 as an early driver event. In this study, we show that mesenchyme homeobox 2 (MEOX2), an aberrantly upregulated transcription factor on chromosome 7, is an oncogene in human glioblastoma. In contrast to GBM, MEOX2 expression is very low in normal brain. We show that MEOX2 cooperates with p53 and PTEN loss to promote tumor initiation in cerebral organoid models. In addition, we identify direct and indirect molecular targets of MEOX2 and demonstrate its role in activating the ERK signaling cascade. These findings identify a novel oncogene in GBM and highlight the transcriptional networks hijacked by these tumors to activate signaling pathways central to GBM biology.

cancer biology↗

bioRxiv2020

THE DYNAMIC INTERPLAY BETWEEN HOMEODOMAIN TRANSCRIPTION FACTORS AND CHROMATIN ENVIRONMENT REGULATES PRONEURAL FACTOR OUTCOMES

Generation of neurons of vast diversity involves early spatial and temporal patterning of the neuronal precursors by morphogenic gradients and combinatorial expression of transcription factors. While the proneuronal function of the basic-helix-loop-helix (bHLH) transcription factor Ngn2 is well established, its role in neuronal subtype specification remains unclear. Here, we found that coexpressing NGN2 with the forebrain homeobox factor EMX1 converts human pluripotent stem cells into a highly homogeneous glutamatergic forebrain neurons without partial cholinergic and monoaminergic gene programs observed in cells infected with NGN2 only. Our molecular characterization revealed that transcriptional output and genomic targeting of Ngn2 is altered by co-factors such as EMX1 explaining the more focused subtype specification. Ngn2 function is less modified by the chromatin environment and does not affect regionalization of pre-patterned neural progenitors. These results enable improved strategies for generating a plethora of defined neuronal subpopulations from pluripotent stem cells for therapeutic or disease-modeling purposes. HighlightsO_LINGN2 converts human ES cells into glutamatergic neurons some of which co-express a partial cholinergic program C_LIO_LINGN2 directly binds to and activates ISL1 in ES cells which together with PHOX2A/B induce cholinergic genes C_LIO_LIAnterior-posterior regionalization affects NGN2 binding and transcriptional output but does not focus subtype specification C_LIO_LIForebrain homeobox factors including EMX1 and FOXG1 redirect NGN2 chromatin binding and repress posterior and cholinergic genes, resulting in homogeneous forebrain excitatory neurons C_LI

genomics↗

bioRxiv2019

Nuclear lamin B is crucial to the nuclear envelope integrity and extracellular trap release in neutrophils

Its not clear how nuclear envelope (NE) is ruptured for chromatin externalization during NETosis. The membrane rupture during neutrophil NET release was described as a membrane lysis process, this notion, however, has been questioned. Here, we found that lamin B, the structural NE component, was involved in NETosis. Unexpectedly, lamin B was not fragmented by destructive proteolysis, but rather disassembled into its intact full-length molecule, in NETotic cells with ruptured NE. In the mechanistic study, our experiments demonstrated that cytosolic PKC translocated to the nucleus, where it serves as a NETotic lamin kinase to induce lamin B phosphorylation, following by lamina disassembly and NE rupture. To determine causality, we found that decreasing lamin B phosphorylation, by PKC inhibition or genetic deletion, or mutation at the PKC consensus phosphorylation sites of lamin B, attenuated extracellular trap formation. Importantly, strengthening NE by lamin B overexpression attenuated neutrophil NETosis in vivo and alleviated exhibition of NET-associated inflammatory cytokines in UVB irradiated skin of lamin B transgenic mice. These findings advance our understanding of NETosis process and elucidate a cellular mechanism that PKC-mediated lamin B phosphorylation drives nuclear envelope rupture for NET release in neutrophils.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC=\"FIGDIR/small/647529v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (49K):\norg.highwire.dtl.DTLVardef@7bd231org.highwire.dtl.DTLVardef@124bf6dorg.highwire.dtl.DTLVardef@19396ecorg.highwire.dtl.DTLVardef@9989cb_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗