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bioRxiv2025

Beyond synthetic lethality in large-scale metabolic and regulatory network models via genetic minimal intervention sets

MotivationThe integration of genome-scale metabolic and regulatory networks has received significant interest in the field of Cancer Systems Biology. However, the identification of lethal genetic interventions in these integrated models remains a substantially challenge due to the combinatorial explosion of potential solutions. To address this issue, we previously developed the genetic Minimal Cut Set (gMCS) framework, which is capable of computing synthetic lethal interactions - minimal sets of gene knockouts that are lethal for cellular proliferation- in genome-scale metabolic networks with signed directed acyclic regulatory pathways. Here, we present a novel formulation to calculate genetic Minimal Intervention Sets, gMISs, which incorporate interventions with both gene knockouts and knock-ins. ResultsWith our gMIS approach, we assessed the landscape of lethal genetic interactions in human cells and the impact of gene knock-in perturbations, which enable us to capture for the first-time genetic interventions beyond synthetic lethality, particularly synthetic dosage lethality and tumor suppressor gene complexes. We applied the concept of synthetic dosage lethality to predict essential genes in cancer and demonstrated a significant increase in sensitivity when compared to large-scale gene knockout screen data. Moreover, we conducted a tumor suppressor analysis in cancer cell lines and identified single gene knock-in strategies that block cellular proliferation. Finally, we illustrate the ability of our gMIS approach to elucidate potential targets for cancer research with several examples in hematological malignancies Availability and implementationThe Python package gMCSpy has been updated to include the functionalities to calculate gMISs. It can be accessed here: https://github.com/PlanesLab/gMCSpy.

systems biology↗

bioRxiv2022

Proteomic profiling identifies co-regulated expression of splicing factors as a characteristic feature of intravenous leiomyomatosis

Intravenous leiomyomatosis (IVLM) is a rare benign smooth muscle tumour that is characterised by intravenous growth in the uterine and pelvic veins. Previous DNA copy number and transcriptomic studies have shown that IVLM harbours unique genomic and transcriptomic alterations when compared to uterine leiomyoma (uLM), which may account for their distinct clinical behaviour. Here we undertake the first comparative proteomic analysis of IVLM and other smooth muscle tumours (comprising uLM, soft tissue leiomyoma and benign metastasising leiomyoma) utilising data-independent acquisition mass spectrometry. We show that, at the protein level, IVLM is defined by the unique co-regulated expression of splicing factors. In particular, IVLM is enriched in two clusters composed of co-regulated proteins from the hnRNP, LSm, SR and Sm classes of the spliceosome complex. One of these clusters (Cluster 3) is associated with key biological processes including nascent protein translocation and cell signalling by small GTPases. Taken together, our study provides evidence of co-regulated expression of splicing factors in IVLM compared to other smooth muscle tumours which suggests a possible role for alternative splicing in the pathogenesis of IVLM.

cancer biology↗

bioRxiv2026

Persistent Malignant Stem Cells Drive Relapse After Transplantation in the Myelodysplastic Neoplasms

The myelodysplastic neoplasms (MDS) are initiated in hematopoietic stem cells (HSCs). Allogeneic transplantation is the only curative treatment, but relapse remains common. To detect rare MDS HSCs, we developed an ultra-low-input DNA sequencing assay and applied it to a multicenter post-transplant cohort. HSC mutation detection preceded relapse by a mean of 98 days and strongly predicted relapse (95.7% vs. 30.3%; hazard ratio, 8.8; P=1.5e-7). Mutations detected only in unfractionated marrow did not predict relapse. We developed methods to measure donor-host HSC chimerism, improving relapse prediction sensitivity. Single-cell protein, DNA, and RNA analyses with mitochondrial lineage tracing confirmed MDS cell enrichment within immunophenotypically- and transcriptionally-defined HSCs, identifying shared ribosomal gene downregulation and candidate mechanisms of venetoclax sensitivity. Venetoclax/azacytidine depleted detectable MDS HSCs in longitudinally evaluated patients. These findings establish that HSC mutation detection predicts post-transplant relapse, provide a rationale for preemptive intervention, and define shared biological features of transplant-resistant MDS HSCs.

cancer biology↗

bioRxiv2026

Genomic classification and immune profiling define mucosal melanoma

Mucosal melanoma is a rare, lethal melanoma subtype with distinct genetics and limited benefit from immunotherapy. To define features associated with mucosal melanoma clinical outcomes, we assembled a large, multimodally profiled cohort spanning primary and metastatic disease. Compared with cutaneous melanoma, primary mucosal melanoma showed greater genomic heterogeneity, ploidy and aneuploidy, and a more dedifferentiated, proliferative transcriptional state. Analysis of genomic sequencing of 339 patients with mucosal melanoma identified four mutually exclusive genomic subtypes: CDK4/MDM2/CCND1, SF3B1-mutated, TP53/ATRX, and mucosal melanoma Triple WT, associated with distinct anatomic sites but similar outcomes. In the tumor microenvironment, we observed reduced T cell infiltration and increased CD163+ tumor-associated macrophages in mucosal melanoma relative to cutaneous melanoma. In matched longitudinal samples, CD163+ tumor-associated macrophages increased with disease progression and immunotherapy resistance. CD163+ tumor-associated macrophages engaged non-regulatory T cells through GAL9-TIM-3 interactions, nominating TIM-3 blockade as a therapeutic strategy for mucosal melanoma. These findings define the distinct aggressive biology of mucosal melanoma and highlight potential therapeutic targets and mechanisms of immune resistance.

cancer biology↗

bioRxiv2020

Selective Vulnerability of Senescent Glioblastoma Cells to Bcl-XL Inhibition

Despite decades of research and numerous basic science advances, there have only marginal gains in improving glioblastoma multiforme survival. Therefore, new ideas and approaches for treating this aggressive disease are essential to drive progress forward. Conventional therapies, such as radiation and Temozolomide (TMZ), function to cause oxidative stress and DNA damage yielding a senescent-like state of replicative arrest in susceptible cells. However, increasing evidence demonstrates malignant cells can escape senescence leading to tumor recurrence. Ablation of non-replicating senescent tumor cells after radiation and chemotherapy may be an avenue to reduce the rates of tumor recurrence. Senolytic agents have been developed that selectively target senescent cells, but it remains unknown whether senolytics might be utilized against senescent-like glioma cells. We employed radiation or TMZ to induce a functionally senescent state in human glioblastoma cells. Viable cells that survive these treatments were then utilized to screen candidate senolytic drugs, to identify those selectively effective at ablating senescent-like cells over naive non-tumor and proliferative cells. Among 10 candidate senolytic drugs evaluated, only Bcl-XL inhibitors demonstrated reproducible senolytic activity in radiated or TMZ-treated glioma across the majority of GBM cell lines evaluated. Conversely, Bcl-2 inhibitors and other established senolytic drugs failed to show any consistent senolytic activity. In agreement with these data, Bcl-XL knockdown selectively reduced the viability of senescent-like GBM cells, whereas knockdown of Bcl-2 or Bcl-W yielded no senolytic effect. These findings demonstrate the potential to harness radiation-induced biology to ablate latent surviving cells and highlight Bcl-XL dependency as a potential vulnerability of surviving GBM cells after exposure to radiation or TMZ.

cancer biology↗

bioRxiv2020

A Mild Keratin 1 Decrease Leads to Cell Death and Increased Oxidative Stress in B16-F10 Melanoma Cell Lines

Keratins play multiple significant biological roles in epithelium. K1 / keratin 10 (K10) heterodimer is a hallmarker for keratinocyte differentiation. While keratins are absent in normal melanocyte, keratins have been found in both melanoma cell lines and human melanoma. The biological significance of the keratins in melanoma cells has remained unclear. In our current study we applied K1 siRNA to investigate the biological significance of the K1 in B16-F10 melanoma cells. We found that as low as a 16% decrease in the K1 level led to significant increases in both apoptosis and necrosis of the cells. Moreover, the mild K1 decrease led to significant increases in both dichlorofluorescein (DCF) and ethidium signals - two indicators of oxidative stress - in the cells. Collectively, our findings have provided the first evidence indicating both a critical role of the K1 in maintaining the survival of melanoma cells and an important role of the K1 in modulating the oxidative stress state of the cells. These findings have exposed new functions of keratins in cancer cells, suggesting that K1 may become a novel therapeutic target for melanoma.

cancer biology↗

bioRxiv2020

Whole genome sequencing provides evidence of two biologically and clinically distinct entities of asymptomatic monoclonal gammopathies: progressive versus stable myeloma precursor condition

Multiple myeloma (MM) is consistently preceded by precursor conditions recognized clinically as monoclonal gammopathy of undetermined significance (MGUS) or smoldering myeloma (SMM). We interrogate, for the first time, the whole genome sequence (WGS) profile of 18 MGUS and compare them with those from 14 SMMs and 80 MMs. We show that cases with a non-progressing, clinically stable myeloma precursor condition (n=15) are characterized by later initiation in the patients life and by the absence of myeloma defining genomic events including: chromothripsis, templated insertions, mutations in driver genes, aneuploidy, and canonical APOBEC mutational activity. This data provides evidence that WGS can be used to recognize two biologically and clinically distinct myeloma precursor entities that are either progressive or stable.

cancer biology↗

bioRxiv2022

Single-cell transcriptomic analysis of human pleura reveals stromal heterogeneity and informs in vitro models of mesothelioma

The pleural lining of the thorax regulates local immunity, inflammation and repair. A variety of conditions, both benign and malignant including pleural mesothelioma, can affect this tissue. A lack of knowledge concerning the mesothelial and stromal cells comprising the pleura has hampered the development of targeted therapies. Here we present the first comprehensive single cell transcriptomic atlas of the human parietal pleura and demonstrate its utility in elucidating pleural biology. We confirm the presence of known universal fibroblasts and describe novel, potentially pleural-specific, fibroblast subtypes. We also present transcriptomic characterisation of multiple in vitro models of benign and malignant mesothelial cells, and characterise these through comparison with in vivo transcriptomic data. While bulk pleural transcriptomes have been reported previously, this is the first study to provide resolution at single cell level. We expect our pleural cell atlas will prove invaluable to those studying pleural biology and disease. For example, it has already enabled us to shed light on the transdifferentiation of mesothelial cells allowing us to develop a simple method for prolonging mesothelial cell differentiation in vitro.

cancer biology↗

bioRxiv2026

Deciphering the Multiscale Morphology of Somatic Oncogenic Alterations in Hepatocellular Carcinoma

Somatic oncogenic mutations are typically defined by their molecular alterations, yet how they reorganize cellular architecture within intact tissues remain largely unknown. Here, we demonstrate that distinct oncogenic drivers produce unique multiscale architectural phenotypes that can be quantitatively resolved in intact liver tissue. Using iterative expansion microscopy, multiscale light-sheet imaging, and three-dimensional morphometric analysis, we systematically mapped structural remodeling from single-cell morphology to mitochondrial architecture in mosaic mouse models of hepatocellular oncogene activation. NRAS and CTNNB1 induced fundamentally different morphological programs. NRAS activation drove extensive remodeling of cell morphology, membrane curvature, and surface irregularity, whereas CTNNB1 activation largely preserved global cell morphology while selectively altering mitochondrial organization and shape. We first established a zonation-aware reference state for interpreting oncogene-associated organelle remodeling by resolving mitochondrial differences between periportal and pericentral hepatocytes. Within this framework, CTNNB1 activation shifted mitochondrial features toward a pericentral-like state, consistent with the role of Wnt/{beta}-catenin signaling in hepatic zonation and metabolic identity. Furthermore, integrating cellular morphology, membrane geometry, and mitochondrial architecture improved discrimination of oncogenic states beyond any individual structural feature, demonstrating that mutation-specific phenotypes arise through coordinated remodeling across multiple biological scales. Together, these findings establish multiscale structural phenotyping as a framework for linking oncogenic genotype to three-dimensional cellular organization and reveal that distinct oncogenic drivers remodel different architectural compartments during liver oncogene activation.

cancer biology↗

bioRxiv2025

Rewiring DNA repair with PARP-based chemical inducers of proximity

Chemical inducers of proximity (CIPs) can elicit durable--and often neomorphic--biological effects through the formation of a ternary complex, even at low equilibrium occupancy of their targets. This "event-driven" pharmacology is exemplified by CIPs that promote targeted protein degradation, but other applications remain underexplored. We developed a generalizable strategy to discover event-driven CIPs by tracking the cellular effects of heterobifunctional small molecules alongside quantitative measures of intracellular target engagement. Using this approach, we discovered PCIP-1, which inhibits DNA repair by recruiting BET proteins to PARP2. Unlike conventional PARP inhibitors, PCIP-1 activity is observed at low equilibrium occupancy of PARP1/2 and without inhibition of PARP-catalyzed PARylation, yet it retains synthetic lethality in cancer cells with homologous recombination deficiencies. PARP1 knockout, which confers resistance to conventional PARP drugs, increases sensitivity to PCIP-1, offering a potential new mechanism to overcome clinical resistance. Through these studies, we demonstrate that DNA repair can be rewired by CIPs and introduce a new form of event-driven pharmacology.

cancer biology↗

bioRxiv2025

Unique epigenomic signatures identify biologically significant subtypes of MDS and predict response to azacitidine

Myelodysplastic syndromes (MDS) are characterized by aberrant DNA methylation, and mutations in epigenetic modifiers are frequently found in these patients. Although DNA methyltransferase inhibitors (DNMTi) are used to treat MDS, response variability remains a challenge in the clinic, with limited predictive markers. Through comprehensive genomic, epigenomic, and transcriptomic analyses, we have gained valuable insights into the intricate interplay between genetic and epigenetic alterations in MDS. We describe aberrantly hyper and hypomethylated regions in MDS, extending beyond promoter regions and affecting long-distance regulatory elements. Using these aberrant DNA methylation patterns, we classified MDS patients into epigenetic subtypes correlated with known molecular drivers. This epigenetic classification includes a novel group of patients characterized only by their shared DNA methylation profile and lacking any genetic drivers. Furthermore, we identified a robust DNA methylation signature capable of distinguishing DNMTi responders from non-responders prior to receiving treatment. Leveraging these DMRs, we developed robust classifiers capable of predictive response to DNMTi by integrating DNA methylation, gene expression, mutations, and laboratory parameters. Our findings highlight the potential of epigenetic-based classifiers for personalized treatment approaches for MDS patients. Key PointsDNA methylation patterns define biologically meaningful MDS subtypes and uncover a new group lacking known mutations. A methylation-based signature at diagnosis predicts azacitidine response, supporting its use in guiding personalized MDS therapy.

cancer biology↗

bioRxiv2024

Advantage of the F(ab)'2 fragment over IgG for RIT and PRIT

Radioimmunotherapy (RIT) has proved clinically effective in the treatment of relapsed or consolidating NHL after chemotherapy. However, it is still at the clinical trial stage for the treatment of solid tumors. The efficacy of the treatment on this type of tumor is limited by hematological toxicity, which restricts the activities injected. Pre-targeted radioimmunotherapy (PRIT) enables radiolabeling to be carried out in vivo at a time when the quantities of antigen-targeted vector reach a maximum level in the tumor, but have largely decayed in the bloodstream, thus limiting hematological toxicity. This therapeutic approach would make it possible to use higher radiopharmaceutical activities than those used in RIT, thereby increasing the doses deposited in the tumor and the therapeutic response. Despite encouraging preclinical trials, this approach has failed to live up to expectations in terms of clinical applications. In the context of PRIT using the Inverse Electron Demand Diels Alder (IEDDA) reaction as a method for radiolabeling tumor-targeted vectors, a major research effort has been made to improve the quality of in vivo radiolabeling using tetrazine (Tz) and transcycloctene (TCO) variants whose stability and reactivity have been optimized. Most trials in this field have been carried out using antibodies which, thanks to their long biological half-life, enable prolonged irradiation of tumors. Low-molecular-weight vectors such as affinity proteins or antigen-specific antibody fragments (VHH,scFv, F(ab)) have the advantage of being rapidly eliminated from circulation by renal filtration, but on the other hand, the quantities and residence times of these vectors in the tumor are reduced compared with IgG. F(ab)2 antibody fragments have properties intermediate between those of IgG and low-molecular-weight vectors that could be suitable for PRIT approaches, but they have not yet been evaluated in PRIT using IEDDA. In preparation for a preclinical trial of radioimmunotherapy of triple-negative breast cancer in spontaneously affected dogs, we compared the biodistribution of IgG and its F(ab)2 fragment targeting canine CD138 in a xenogeneic model of canine breast cancer and in a mouse model of colon cancer expressing human ACE antigen. This analysis shows that the use of F(ab)2 fragments improves the therapeutic index compared with IgG. F(ab)2 fragments seem particularly well suited to tumor targeting in PRIT using short-lived isotopes such as 211At.

cancer biology↗

bioRxiv2022

Clonally resolved single-cell multi-omics identifies routes of cellular differentiation in acute myeloid leukemia

Inter-patient variability and the similarity of healthy and leukemic stem cells have impeded the characterization of leukemic stem cells (LSCs) in acute myeloid leukemia (AML), and their differentiation landscape. Here, we introduce CloneTracer, a novel method that adds clonal resolution to single-cell RNA-seq datasets. Applied to samples from 19 AML patients, CloneTracer revealed routes of leukemic differentiation. While residual healthy cells dominated the dormant stem cell compartment, active leukemic stem cells resembled their healthy counterpart and retained erythroid capacity. By contrast, downstream myeloid progenitors were highly aberrant and constituted the disease-defining compartment: Their gene expression and differentiation state determined both chemotherapy response and the leukemias ability to differentiate to transcriptomically normal monocytes. Finally, we demonstrated the potential of CloneTracer to identify surface markers mis-regulated specifically in leukemic cells by intra-patient comparisons. Taken together, CloneTracer revealed a differentiation landscape that mimics its healthy counterpart and determines biology and therapy response in AML.

cancer biology↗

bioRxiv2016

Exploiting Homeostatic Repopulation to Increase DC Vaccine Efficacy in Multiple Myeloma

Standard of care for multiple myeloma involves autologous hematopoietic cell transplant (AHCT), which can extend life by a year; however the disease remains incurable. A dendritic cell vaccine developed at Moffitt will be used both immediately before and after AHCT, with the aim of achieving complete response. Data will be collected during the trial to test the biological activity of the vaccine. This data will parameterize a model that facilitates the exploration of outcomes when varying the timing of vaccination. This calibrated model will also inform the design of a follow-up trial, which will include vaccination in conjunction with other immunotherapies.

Cancer Biology↗

bioRxiv2021

The genetic history of Mayotte and Madagascar cattle breeds mirrors the complex pattern of human exchanges in Western Indian Ocean

Despite their central economic and cultural role, the origin of cattle populations living in Indian Ocean islands still remains poorly documented. Here, we unravel the demographic and adaptive histories of the extant Zebus from the Mayotte and Madagascar islands using high-density SNP genotyping data. We found that these populations are very closely related and both display a predominant indicine ancestry. They diverged in the 16th century at the arrival of European people who transformed the trade network in the area. Their common ancestral cattle population originates from an admixture between an admixed African zebu population and an Indian zebu that occurred around the 12th century at the time of the earliest contacts between human African populations of the Swahili corridor and Austronesian people from Southeast Asia in Comoros and Madagascar. A steep increase of the estimated population sizes from the beginning of the 16th to the 17th century coincides with the expansion of the cattle trade. By carrying out genome scans for recent selection in the two cattle populations from Mayotte and Madagascar, we identified sets of candidate genes involved in biological functions (cancer, skin structure and UV-protection, nervous system and behavior, organ development, metabolism and immune response) broadly representative of the physiological adaptation to tropical conditions. Overall, the origin of the cattle populations from Western Indian Ocean islands mirrors the complex history of human migrations and trade in this area.

evolutionary biology↗

bioRxiv2022

Plasma proteomic biomarkers identify non-responders and reveal biological insights about the tumor microenvironment in melanoma patients after PD1 blockade

Most patients treated with immune checkpoint blockade (ICB) do not have durable treatment responses. Therefore, there is a critical need to identify early non-invasive biomarkers of response. We performed plasma proteomic analysis (>700 proteins) at three timepoints on 174 metastatic melanoma patients treated with ICB. We leverage independent training and testing cohorts to build a predictor of immunotherapy response that outperforms several tissue-based approaches. We found 217 differentially expressed proteins between ICB responders (R) and non-responders (NR), including a co-regulated module of proteins enriched in certain NR patients. By analyzing single-cell RNA-sequencing data of tumor biopsies from 32 patients, we dissected the relative contribution of cells in the tumor to proteins in circulation. The majority of proteins in the co-regulated NR module derived from tumor and myeloid cells. Amongst myeloid cells, we identified a subset of tumor-associated macrophages (TAMs) with a suppressive phenotype that expressed high levels of the co-regulated NR module, thus suggesting they are key drivers of non-response signatures. Together, our data demonstrates the utility of plasma proteomics in biomarker discovery and in understanding the biology of host response to tumors.

cancer biology↗

bioRxiv2023

H2AX promotes replication fork degradation and chemosensitivity in BRCA-deficient tumours

Histone H2AX plays a key role in DNA damage signalling in the surrounding regions of DNA double-strand breaks (DSBs)1,2. In response to DNA damage, H2AX becomes phosphorylated on serine residue 139 (known as {gamma}H2AX), resulting in the recruitment of the DNA repair effectors 53BP1 and BRCA13-6. Here, by studying resistance to poly(ADP-ribose) polymerase (PARP) inhibitors in BRCA1/2-deficient mammary tumours7,8, we identify a novel function for {gamma}H2AX in orchestrating drug-induced replication fork degradation. Mechanistically, {gamma}H2AX-dependent replication fork degradation is elicited by the inhibition of CtIP-mediated fork protection. As a result, H2AX loss restores replication fork stability and increases chemoresistance in BRCA1/2-deficient tumour cells without restoring homology-directed DNA repair, as highlighted by the lack of DNA damage-induced RAD51 foci. Furthermore, in the attempt to discover acquired genetic vulnerabilities, we find that ATM inhibition overcomes PARP inhibitor (PARPi) resistance in H2AX-deficient tumours by interfering with CtIP-mediated fork protection of stalled forks. In summary, our results demonstrate a novel role for H2AX in replication fork biology in BRCA-deficient tumours and establish a function of H2AX separable from its classical role in DNA damage signalling and DSB repair.

cancer biology↗

bioRxiv2025

Integrated multi-omics profiling reveals the role of the DNA methylation landscape in shaping biological heterogeneity and clinical behaviour of metastatic melanoma

The biological and clinical relevance of the DNA methylation landscape in metastatic melanoma (MM) remains underexplored. In a retrospective cohort of 191 MM lesions from 165 AJCC Stage III and IV patients (EPICA cohort) we identified four tumor subsets (i.e. DEMethylated, LOW, INTermediate and CIMP) with progressively increasing levels of DNA methylation. These findings were validated in the TCGA MM. In EPICA, patients with LOW methylation tumors exhibited a significantly longer survival and a lower progression rate to more advanced AJCC stages, compared to patients with CIMP tumors. Furthermore, in an independent adjuvant immune checkpoint blockade MM cohort, patients with DEM/LOW pre-therapy lesions showed significantly longer relapse-free survival compared to those with INT/CIMP lesions. RNA-seq data analysis revealed that LOW and CIMP EPICA tumors showed opposite activation of master molecules influencing prognostic target genes, and differential expression of immunotherapy response and melanoma differentiation signatures. Compared to CIMP tumors, LOW lesions showed enrichment for pre-exhausted and exhausted T cells and more frequent retention of HLA Class I antigens. The differentiation and immune-related transcriptional features associated with LOW vs CIMP lesions were tumor-intrinsic programs retained in-vitro by melanoma cell lines. Consistently, treatment of differentiated melanoma cell lines with a DNMT inhibitor induced global DNA de-methylation, promoted de-differentiation and upregulated viral mimicry and IFNG predictive signatures of immunotherapy response. These findings underscore the role of DNA methylation in driving MM biological and clinical heterogeneity and support exploration of methylome targeting strategies for precision immunotherapy in melanoma.

cancer biology↗