Biology subjects

Amend, S. R.

Publications and source records attributed to Amend, S. R..

15 recordsLinked to original sources

bioRxiv2026

Indirect genomic effects shape cancer risk across species

Tumour prevalence varies dramatically throughout the animal kingdom despite broadly conserved cellular and developmental processes, raising the question of how evolution has shaped susceptibility 1,2. Here, we link macroevolutionary variation in tumour prevalence to gene-level selection by integrating comparative genomics data from 109 species of birds and mammals using a Bayesian phylogenetic framework to estimate pangenome-wide rates of genetic evolution across >150 million years of evolutionary change. We identify 3,206 genes in which natural selection is associated with shifts in tumour prevalence, with more than 80% of which are linked to reduced prevalence, suggesting pervasive selection for cancer suppression. Using causal phylogenetic inference, we show that genes associated with reduced tumour prevalence act predominantly through indirect effects on body size, revealing growth as a key mediator of cancer risk across species. In contrast, genes associated with increased tumour prevalence exert direct effects independent of body size. Finally, at the species-level, we demonstrate that exceptionally low rates of benign tumours do not necessarily coincide with reduced malignancy, revealing that benign and malignant tumour processes are evolutionarily decoupled. Together, these results reveal how natural selection has fine-tuned the link between genotype, phenotype, and cancer risk across species.

evolutionary biology↗

bioRxiv2026

Drug-tolerant persister cells reallocate carbon sources to fuel antioxidant metabolism for survival

Therapy resistance is the leading cause of cancer-related deaths. Drug-tolerant persister cells (DTPs) represent a major barrier to cancer cure, mediating resistance through adaptive cell state transitions and driving tumor progression. Here, we investigate metabolic differences between DTPs and drug-sensitive cancer cells using integrated fluxomics. Proteomic profiling and extracellular flux analyses revealed that DTPs upregulate glycolysis and gluconeogenesis while reducing oxidative phosphorylation, indicating a shift in central carbon metabolism. Isotope tracing and metabolic modeling demonstrate that DTPs utilize glucose to fuel the pentose phosphate pathway (PPP) to generate NADPH and metabolize glutamine to provide carbons for the PPP via gluconeogenesis. Integrating our multi-omic datasets into a genome-scale model identified that DTPs sustain antioxidant metabolism by decreasing fluxes of other NADPH-consuming reactions upon in silico PPP knockout. These findings reveal a systems-level shift in DTP metabolism that maintains antioxidant activity for cell survival, highlighting potential new targets and treatment paradigms to overcome therapy resistance.

cancer biology↗

bioRxiv2025

Mitotic bypass and endocycling promote cancer cell survival after genotoxic chemotherapy

Genotoxic chemotherapies are central components of the treatment regimen for most cancers but are rarely curative. Drug-tolerant persister cells (DTPs) evade cell death during these treatments by accessing transient adaptive states and can contribute to cancer progression after treatment. Here, we demonstrate that cancer cells can survive genotoxic chemotherapy-induced stress by accessing a DTP state wherein stress-induced bypass of mitosis precipitates continued endocycling which promotes survival by allowing cells to evade mitotic catastrophe and cell death. Mechanistic studies indicate that persistent DNA damage signaling in endocycling persister cells triggers sustained p53-independent CDK1 inhibition by WEE1 and Myt1. Continued survival in endocycling persisters is dependent on activation of this G2 checkpoint, and disrupting WEE1 or Myt1 activity using clinical-stage small molecule inhibitors is sufficient to drive CDK1 reactivation, forcing mitotic entry, catastrophe, and cell death. Our results define endocycling DTPs as targetable mediators of cancer cell persistence after genotoxic therapy.

cell biology↗

bioRxiv2025

Cancer cells surviving cisplatin chemotherapy increase stress-induced OMA1 activity and mitochondrial fragmentation

Cancer is one of the leading causes of deaths worldwide. Once cancer cells acquire therapy resistance, they become the main driver of cancer lethality in patients. Thus, mechanisms of therapy resistance must be investigated to improve patient outcomes. Mitochondria are critical organelles in the cellular stress responses, undergoing dynamic morphological and functional changes in response to external stimuli. We and others have identified a chemotherapy-resistant cancer cell state where cells that survive treatment exhibit a dramatic increase in cell size and remain non-proliferative for weeks. In this study, we demonstrate that cancer cells that enter this resistant cell state in response to cisplatin increase OMA1 activity and decrease mitochondrial fusion and function to combat oxidative stress. These findings contribute to further understanding the role of the mitochondrial stress responses in therapy resistance in cancer and provide a potential therapeutic avenue to targeting cancer cells that enter this chemotherapy-resistant cell state.

cancer biology↗

bioRxiv2025

HIF-1α and RhoA Drive Enhanced Motility and Aerotaxis of Polyaneuploid Prostate Cancer Cells in Hypoxia

Most cancer deaths result from metastasis, yet only a rare subset of tumor cells can complete this process. Among these, polyaneuploid cancer cells (PACCs), which arise via endoreplication under stressors such as hypoxia, are implicated as metastatic drivers, but how they acquire this potential is poorly understood. Here, we show that prostate cancer-derived PACCs exhibit features predictive of invasion and intravasation. Time-lapse fluorescence microscopy and single-cell tracking under hypoxia revealed that PACCs migrated significantly farther than Non-PACCs, consistent with local invasion. PACC trajectories showed a strong tendency to migrate toward oxygen, consistent with aerotaxis and predictive of intravasation. siRNA-mediated knockdown demonstrated that the enhanced motility and aerotaxis of hypoxic PACCs require both HIF-1and RhoA, with RhoA expression suppressed upon HIF-1 inhibition. Altogether, we propose a HIF-1[->] RhoA [->] motility/aerotaxis mechanism enabling PACCs to escape hypoxic cores, invade tissue, and access vasculature, highlighting them as a uniquely invasive subpopulation with implications for anti-metastatic therapies.

cancer biology↗

bioRxiv2024

Dysregulation of cellular iron predisposes chemotherapy resistant cancer cells to ferroptosis

Despite centuries of research, metastatic cancer remains incurable due to resistance against all conventional cancer therapeutics. Alternative strategies leveraging non-proliferative vulnerabilities in cancer are required to overcome cancer recurrence. Ferroptosis is an iron dependent cell death pathway that has shown promising pre-clinical activity in several contexts of therapeutic resistant cancer. However, ferroptosis sensitivity is highly variable across tissue types and cell state posing a challenge for clinical translation. We describe a convergent phenotype induced by chemotherapy where cells surviving chemotherapy have similar transcriptomic signatures and dysregulated iron homeostasis, regardless of initial cell type or chemotherapy used. Elevated labile iron levels are counteracted by NRF2 signaling that does not alleviate the amount of labile iron. Selectively inhibiting GPX4 leads to uniform susceptibility to ferroptosis in surviving cells, highlighting the common reliance on lipid peroxidation defenses. Cellular iron dysregulation is a vulnerability of chemoresistant cancer cells that can be leveraged by triggering ferroptosis. STATEMENT OF SIGNIFICANCEWe show that cells surviving chemotherapy are uniformly sensitive to ferroptosis, despite different sensitivity in untreated cells. Ferroptosis sensitivity surprisingly occurs alongside NRF2 signaling, likely due to loss of PCBP1 and accumulated labile iron. Labile iron accumulation as a driver of ferroptosis sensitivity constitutes another starting point for translation of ferroptosis.

cancer biology↗

bioRxiv2024

Polyploid cancer cells reveal signatures of chemotherapy resistance

Therapeutic resistance in cancer significantly contributes to mortality, with many patients eventually experiencing recurrence after initial treatment responses. Recent studies have identified therapy-resistant large polyploid cancer cells in patient tissues, particularly in late-stage prostate cancer, linking them to advanced disease and relapse. Here, we analyzed bone marrow aspirates from 44 advanced prostate cancer patients and found the presence of circulating tumor cells with increased genomic content (CTC-IGC) was significantly associated with poorer progression- free survival. Single cell copy number profiling of CTC-IGC displayed clonal origins with typical CTCs, suggesting complete polyploidization. Induced polyploid cancer cells from PC3 and MDA-MB-231 cell lines treated with docetaxel or cisplatin were examined through single cell DNA sequencing, RNA sequencing, and protein immunofluorescence. Novel RNA and protein markers, including HOMER1, TNFRSF9, and LRP1, were identified as linked to chemotherapy resistance. These markers were also present in a subset of patient CTCs and associated with recurrence in public gene expression data. This study highlights the prognostic significance of large polyploid tumor cells, their role in chemotherapy resistance, and their expression of markers tied to cancer relapse, offering new potential avenues for therapeutic development.

cancer biology↗

bioRxiv2024

Cells in the Polyaneuploid Cancer Cell State are Pro-Metastatic

There remains a large need for a greater understanding of the metastatic process within the prostate cancer field. Our research aims to understand the adaptive - ergo potentially metastatic - responses of cancer to changing microenvironments. Emerging evidence has implicated a role of the Polyaneuploid Cancer Cell (PACC) state in metastasis, positing the PACC state as capable of conferring metastatic competency. Mounting in vitro evidence supports increased metastatic potential of cells in the PACC state. Additionally, our recent retrospective study of prostate cancer patients revealed that PACC presence in the prostate at the time of radical prostatectomy was predictive of future metastatic progression. To test for a causative relationship between PACC state biology and metastasis, we leveraged a novel method designed for flow-cytometric detection of circulating tumor cells (CTCs) and disseminated tumor cells (DTCs) in subcutaneous, caudal artery, and intracardiac mouse models of metastasis. This approach provides both quantitative and qualitative information about the number and PACC-status of recovered CTCs and DTCs. Collating data from all models, we found that 74% of recovered CTCs and DTCs were in the PACC state. In vivo colonization assays proved PACC populations can regain proliferative capacity at metastatic sites following dormancy. Additional direct and indirect mechanistic in vitro analyses revealed a PACC-specific partial Epithelial-to-Mesenchymal-Transition phenotype and a pro-metastatic secretory profile, together providing preliminary evidence that PACCs are mechanistically linked to metastasis. Statement of SignificanceWe provide the first evidence that cells in the polyaneuploid cancer cell state contribute to increased metastatic competency in vivo.

cancer biology↗

bioRxiv2024

Oncogenic signaling in the adult Drosophila prostate-like accessory gland leads to activation of a conserved pro-tumorigenic program, in the absence of proliferation.

Drosophila models for tumorigenesis and metastasis have revealed conserved mechanisms of signaling that are also involved in mammalian cancer. Many of these models use the proliferating tissues of the larval stages of Drosophila development, when tissues are highly mitotically active, or stem cells are abundant. Fewer Drosophila tumorigenesis models use adult animals to initiate tumor formation when many tissues are largely terminally differentiated and postmitotic. The Drosophila accessory glands are prostate-like tissues and a model for some aspects of prostate tumorigenesis using this tissue has been explored. In this model, oncogenic signaling was induced during the proliferative stage of accessory gland development, raising the question of how oncogenic activity would impact the terminally differentiated and postmitotic adult tissue. Here, we show that oncogenic signaling in the adult Drosophila accessory gland leads to activation of a conserved pro-tumorigenic program, similar to that observed in mitotic larval tissues, but in the absence of proliferation. Oncogenic signaling in the adult postmitotic gland leads to tissue hyperplasia with nuclear anaplasia and aneuploidy through endoreduplication, which increases polyploidy and occasionally results in non-mitotic neoplastic-like extrusions. We compare gene expression changes in our Drosophila model with that of endocycling prostate cancer cells induced by chemotherapy, which potentially mediate tumor recurrence after treatment. Similar signaling pathways are activated in the Drosophila gland and endocycling cancer cells, suggesting the adult accessory glands provide a useful model for aspects of prostate cancer progression that do not involve cellular proliferation.

developmental biology↗

bioRxiv2024

Punctuational evolution is pervasive in distal site metastatic colonization

The evolution of metastasis represents a lethal stage of cancer progression. Yet, the evolutionary kinetics of metastatic disease remain unresolved. Here, using single cell CRISPR-Cas9 lineage tracing data, we show that in metastatic disease, gradual molecular evolution is punctuated by episodes of rapid evolutionary change associated with lineage divergence. By measuring punctuational effects across the metastatic cascade, we show that punctuational effects contribute more to the molecular diversity at distal site metastases compared to the paired primary tumor, suggesting qualitatively different modes of evolution may drive primary and metastatic tumor progression. This is the first empirical evidence for distinct patterns of molecular evolution at early and late stages of metastasis and demonstrates the complex interplay of cell intrinsic and extrinsic factors that shape lethal cancer.

cancer biology↗

bioRxiv2023

Multiparameter flow cytometric detection and analysis of rare cells in in vivo models of cancer metastasis

Rapid and reliable circulating tumor cell (CTC) and disseminated tumor cell (DTC) detection forms a major underpinning of rigorous in vivo metastasis research. While many cancer cells initiate metastasis, very few can complete it. Clinical data evidences that each successive step of metastatic cascade presents increasing barriers to metastatic success, limiting the number of successful metastatic cells to fewer than 1 in 1,500,000,000. As such, it is critical to employ metastasis research approaches that allow scientists to discern which step(s) of the cascade present metastatic barriers to their model systems, and in which steps their model systems might display competency. Here, we present a novel flow-cytometry based method that allows for the simultaneous comparison of multiple steps of the cascade within one model system via the co-identification of CTC and DTCs from single animals. This approach is not only highly reliable and reproducible, but also broadly applicable and highly adaptable to a wide range of scientific inquiries.

cancer biology↗

bioRxiv2022

Exploration of mechanisms of drug resistance by polyaneuploid cancer cells in a microfluidic device and patient tissues

Chemoresistance is a major cause of treatment failure in many cancers. However, the life cycle of cancer cells as they respond to and survive environmental and therapeutic stress is understudied. In this study, we utilized a microfluidic device to induce the development of doxorubicin-resistant (DOXR) cells from triple negative breast cancer (TNBC) cells within 11 days by generating gradients of DOX and medium. In vivo chemoresistant xenograft models, an unbiased genome-wide transcriptome analysis, and a patient data/tissue analysis all showed that chemoresistance arose from failed epigenetic control of the nuclear protein-1 (NUPR1)/histone deacetylase 11 (HDAC11) axis, and high Nupr1 expression correlated with poor clinical outcomes. These results suggest that the chip can rapidly induce resistant cells that increase tumor heterogeneity and chemoresistance, highlighting the need for further studies on the epigenetic control of the NUPR1/HDAC11 axis in TNBC.

cancer biology↗

bioRxiv2022

Cells in the Polyaneuploid Cancer Cell (PACC) state have increased metastatic potential

Although metastasis is the leading cause of cancer deaths, it is quite rare at the cellular level. Only a rare subset of cancer cells ([~]1 in 1.5 billion) can complete the entire metastatic cascade: invasion, intravasation, survival in the circulation, extravasation, and colonization (i.e. are metastasis competent). We propose that cells engaging a Polyaneuploid Cancer Cell (PACC) phenotype are metastasis competent. PACCs are enlarged, non-dividing cells with increased genomic content that form in response to stress. Single-cell tracking using time-lapse microscopy reveals that PACCs are more motile than nonPACCs. Additionally, PACCs exhibit increased capacity for environment-sensing and directional migration in chemotactic environments, predicting successful invasion. Magnetic Twisting Cytometry and Atomic Force Microscopy reveal that cells in the PACC state display hyper-elastic properties like increased peripheral deformability and maintained peri-nuclear cortical integrity that predict successful intravasation and extravasation. Furthermore, four orthogonal methods reveal that PACCs have increased expression of Vimentin, a known hyper-elastic biomolecule. Lastly, anoikis-resistance assays and detection of PACCs in the blood of a patient with metastatic castrate-resistant prostate cancer using a selection- free circulating tumor cell detection platform reveal that PACCs are capable of surviving in the circulation. Taken together with the knowledge that PACCs are capable of eventual depolyploidization and progeny formation (as a potential route to colonization), these data support PACCs as candidate metastasis-competent cells worthy of further analysis.

cancer biology↗

bioRxiv2022

Nuclear morphology and functional characteristics that enable survival of cells in the polyaneuploid cancer cell state following cytotoxic chemotherapy

In this study, we characterized nuclear morphology and function as cancer cells underwent recovery following chemotherapeutic treatment to identify the unique characteristics associated with treatment resistance and successful survival. Cells that survived following treatment and resisted therapy-induced cell death were predominantly mononucleated with increased nuclear/cellular size, enabled by continuous endocycling. We found that cells that survive after therapy release likely employ more efficient DNA damage repair and exhibit a distinct nucleolar phenotype - fewer but larger nucleoli - and increased rRNA levels. These data support a paradigm where soon after therapy release, the treated population mostly contains cells with a high level of widespread and catastrophic DNA damage that leads to apoptosis, while the minority of cells that have successful DDR are more likely to access a pro-survival state. These findings suggest that one way cancer cells can survive systemic therapy is to enter the polyaneuploid cancer cell (PACC) state, a recently-described mechanism of therapy resistance. Cancer cells in this state are physically enlarged, undergo whole-genome doubling resulting in polyaneuploid genomes, and are associated with worse prognosis in cancer patients. The PACC state is accessed when a cancer cell experiences external stress, such as genotoxic chemotherapy; after a period of recovery, cells exit the PACC state and resume proliferation to repopulate the tumor cell pool. Our findings demonstrate the fate of cancer cells following chemotherapy treatment and define key characteristics of the resistant PACC state. This work is essential for understanding and, ultimately, targeting, cancer resistance and recurrence.

cancer biology↗

bioRxiv2021

Optimized Data-Independent Acquisition Approach for Proteomic Analysis at Single-Cell Level

Single-cell proteomic analysis provides valuable insights into cellular heterogeneity allowing the characterization of the cellular microenvironment which is difficult to accomplish in bulk proteomic analysis. Currently, single-cell proteomic studies utilize data-dependent acquisition (DDA) mass spectrometry (MS) coupled with a TMT labelled carrier channel. Due to the extremely imbalanced MS signals among the carrier channel and other TMT reporter ions, the quantification is compromised. Thus, data-independent acquisition (DIA)-MS should be considered as an alternative approach towards single-cell proteomic study since it generates reproducible quantitative data. However, there are limited reports on the optimal workflow for DIA-MS-based single-cell analysis. Herein, we report an optimized DIA workflow for single-cell proteomics using Orbitrap Lumos Tribrid instrument. We utilized a breast cancer cell line (MDA-MB-231) and induced drug resistant polyaneuploid cancer cells (PACCs) to evaluate our established workflow. We found that a short LC gradient was preferable for peptides extracted from single cell level with less than 2 ng sample amount. The total number of co-searching peptide precursors was also critical for protein and peptide identifications at nano- and sub-nano-gram levels. Post-translationally modified peptides could be identified from a nano-gram level of peptides. Using the optimized workflow, up to 1,500 protein groups were identified from a single PACC corresponding to 0.2 ng of peptides. Furthermore, about 200 peptides with phosphorylation, acetylation, and ubiquitination were identified from global DIA analysis of 100 cisplatin resistant PACCs (20 ng). Finally, we used this optimized DIA approach to compare the whole proteome of MDA-MB-231 parental cells and induced PACCs at a single-cell level. We found the single-cell level comparison could reflect real protein expression changes and identify the protein copy number. Our results demonstrate that the optimized DIA pipeline can serve as a reliable quantitative tool for single-cell as well as sub-nano-gram proteomic analysis.

systems biology↗