Supplementary figures and figure legends

Abstract The metastatic cascade is a critical component of cancer evolution. Understanding the rewired metabolism in organ-specific metastasis in breast cancer could help identify strategies to improve the treatment and prevention of metastatic disease. Here, we used a systems biology approach to assess the evolution of metabolic fluxes from parental breast cancer cells to their brain- and lung-homing metastatic derivatives. We found that divergent lineages had distinct, heritable metabolic fluxes. Lung-homing cells maintained adaptations for high glycolytic flux despite low levels of glycolytic intermediates, constitutively activating a pathway sink into lactate. This exacerbated Warburg effect –– stronger than the Warburg effect in the primary tumor –– was associated with a high ratio of lactate dehydrogenase (LDH) to pyruvate dehydrogenase (PDH) expression, a signature which correlated with lung metastasis in patients with breast cancer. While feature classification models trained on clinical characteristics alone were unable to predict tropism, the LDH/PDH ratio was a significant predictor of a patient's future metastasis to the lung but not to other organs, independent of other transcriptomic signatures. Lung- and brain-homing lineages had differential selection patterns in acidic metabolic microenvironments. High lactate efflux was also a trait in lung-homing metastatic pancreatic cancer cells, suggesting that lactate production may be a convergent phenotype in lung metastasis. Together, these analyses highlight the essential role that metabolic evolution plays in organ-specific cancer metastasis and identify a putative biomarker for predicting lung metastasis in breast cancer patients. Citation Format: Deepti Mathur, Chen Liao, Wendy Lin, Alessandro La Ferlita, Salvatore Alaimo, Samuel Taylor, Yi Zhong, Christine Iacobuzio-Donahue, Alfredo Ferro, Joao Xavier. Metabolic evolution in breast cancer predicts organ-specific metastasis [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr A039.

Potato (Solanum tuberosum) is a significant non-grain food crop in terms of global production. However, its yield potential might be raised by identifying means to release bottlenecks within photosynthetic metabolism, from the capture of solar energy to the synthesis of carbohydrates. Recently, engineered increases in photosynthetic rates in other crops have been directly related to increased yield - how might such increases be achieved in potato? To answer this question, we derived the photosynthetic parameters V-cmax and J(max) to calibrate a kinetic model of leaf metabolism (e-Photosynthesis) for potato. This model was then used to simulate the impact of manipulating the expression of genes and their protein products on carbon assimilation rates in silico through optimizing resource investment among 23 photosynthetic enzymes, predicting increases in photosynthetic CO2 uptake of up to 67%. However, this number of manipulations would not be practical with current technologies. Given a limited practical number of manipulations, the optimization indicated that an increase in amounts of three enzymes - Rubisco, FBP aldolase, and SBPase - would increase net assimilation. Increasing these alone to the levels predicted necessary for optimization increased photosynthetic rate by 28% in potato.

Abstract Understanding the rewired metabolism underlying organ-specific metastasis in breast cancer could help identify strategies to improve the treatment and prevention of metastatic disease. Here, we used a systems biology approach to compare metabolic fluxes used by parental breast cancer cells and their brain- and lung-homing derivatives. Divergent lineages had distinct, heritable metabolic fluxes. Lung-homing cells maintained high glycolytic flux despite low levels of glycolytic intermediates, constitutively activating a pathway sink into lactate. This strong Warburg effect was associated with a high ratio of lactate dehydrogenase (LDH) to pyruvate dehydrogenase (PDH) expression, which correlated with lung metastasis in patients with breast cancer. Although feature classification models trained on clinical characteristics alone were unable to predict tropism, the LDH/PDH ratio was a significant predictor of metastasis to the lung but not to other organs, independent of other transcriptomic signatures. High lactate efflux was also a trait in lung-homing metastatic pancreatic cancer cells, suggesting that lactate production may be a convergent phenotype in lung metastasis. Together, these analyses highlight the essential role that metabolism plays in organ-specific cancer metastasis and identify a putative biomarker for predicting lung metastasis in patients with breast cancer. Significance: Lung-homing metastatic breast cancer cells express an elevated ratio of lactate dehydrogenase to pyruvate dehydrogenase, indicating that ratios of specific metabolic gene transcripts have potential as metabolic biomarkers for predicting organ-specific metastasis.

The fitness costs of reproduction by clonal growth can include a limited ability to adapt to environmental and temporal heterogeneity. Paradoxically, some facultatively clonal species are not only able to survive, but colonize, thrive and expand in heterogeneous environments. This is likely due to the capacity for acclimation (sensu stricto) that compensates for the fitness costs and complements the ecological advantages of clonality. Introduced Phragmites australis demonstrates great phenotypic plasticity in response to temperature, nutrient availability, geographic gradient, water depths, habitat fertility, atmospheric CO2, interspecific competition and intraspecific competition for light. However, no in situ comparative subspecies studies have explored the difference in plasticity between the non-invasive native lineage and the highly invasive introduced lineage. Clonality of the native and introduced lineages makes it possible to control for genetic variation, making P. australis a unique system for the comparative study of plasticity. Using previously identified clonal genotypes, we investigated differences in their phenotypic plasticity through measurements of the lengths and densities of stomata on both the abaxial (lower) and adaxial (upper) surfaces of leaves, and synthesized these measurements to estimate impacts on maximum stomatal conductance to water (g(wmax)). Results demonstrated that at three marsh sites, invasive lineages have consistently greater g(wmax) than their native congeners, as a result of greater stomatal densities and smaller stomata. Our analysis also suggests that phenotypic plasticity, determined as within-genotype variation in g(wmax), of the invasive lineage is similar to, or exceeds, that shown by the native lineage.

In addition to the well-established effector functions of IgGs, including direct cytotoxicity and antibody-dependent cellular cytotoxicity, some populations of IgGs may exert anti-inflammatory effects. Here, we describe a population of antibodies that form in the natural course of metastatic cancer and contain glycans that terminate with sialic acid. We demonstrate that both the titer of these antibodies and their level of sialylation are relatively stable throughout the progression of metastatic melanoma. The sialylation pattern of these antibodies somehow correlates with their specificity for tumor-associated antigens, as IgGs targeting several antigens associated with infectious agents are relatively poor of sialic acid. We also show that some antibodies targeting the melanoma-associated antigen NY-ESO-1 bind to the human C-type lectin CD209 (DC-SIGN). We propose that these antibodies are candidate anti-inflammatory antibodies. The presence of anti-inflammatory antibodies in cancer patients may explain, at least in part, why tumors persist and spread in the host despite strong tumor-specific humoral responses. The elucidation of the cellular and molecular pathways involved in the induction of anti-inflammatory antibodies specific for tumor-associated antigens and their function may yield important insights into how tumors evade immune detection and progress.

Variation in phloem sap composition is important in determining aphid performance and is known to occur at both diurnal timescales and in response to plant age. For field grown potato plants, Solanum tuberosum L. (Solanaceae), we determined diurnal variation in components of phloem sap, measured by ethylene diamine tetra-acetate exudation, and tested for impacts of plant age. The effects of plant age and diurnal cycles on honeydew production by Macrosiphum euphorbiae (Thomas) and Myzus persicae (Sulzer) (both Hemiptera: Aphididae) were also quantified. Both the ratio of sucrose to amino acids and the composition of amino acids in phloem sap varied significantly with time of day. Dietary essential amino acids contributed a smaller proportion of amino acids in the phloem sap of older plants and during early phases of the diurnal cycle. The only significant effect on aphid honeydew production was of the diurnal cycle for Ma. euphorbiae, although increased honeydew production during the day when compared with the production at night, was consistent across the two species. In contrast with studies carried out at seasonal scales, we found limited evidence for variation in phloem sap composition in response to plant age, consistent with our results for honeydew production. These data highlight the need for improved understanding of how seasonal and diurnal physiology of plants influence performance in phloem sap feeding insects.

• The evolution of C(4) photosynthesis in plants has allowed the maintenance of high CO(2) assimilation rates despite lower stomatal conductances. This underpins the greater water-use efficiency in C(4) species and their tendency to occupy drier, more seasonal environments than their C(3) relatives. • The basis of interspecific variation in maximum stomatal conductance to water (g(max) ), as defined by stomatal density and size, was investigated in a common-environment screening experiment. Stomatal traits were measured in 28 species from seven grass lineages, and comparative methods were used to test for predicted effects of C(3) and C(4) photosynthesis, annual precipitation and habitat wetness on g(max) . • Novel results were as follows: significant phylogenetic patterns exist in g(max) and its determinants, stomatal size and stomatal density; C(4) species consistently have lower g(max) than their C(3) relatives, associated with a shift towards smaller stomata at a given density. A direct relationship between g(max) and precipitation was not supported. However, we confirmed associations between C(4) photosynthesis and lower precipitation, and showed steeper stomatal size-density relationships and higher g(max) in wetter habitats. • The observed relationships between stomatal patterning, photosynthetic pathway and habitat provide a clear example of the interplay between anatomical traits, physiological innovation and ecological adaptation in plants.

ABSTRACTPhylogenetic analyses show that C4 grasses typically occupy drier habitats than their C3 relatives, but recent experiments comparing the physiology of closely related C3 and C4 species have shown that advantages of C4 photosynthesis can be lost under drought. We tested the generality of these paradoxical findings in grass species representing the known evolutionary diversity of C4 NADP‐me and C3 photosynthetic types. Our experiment investigated the effects of drought on leaf photosynthesis, water potential, nitrogen, chlorophyll content and mortality. C4 grasses in control treatments were characterized by higher CO2 assimilation rates and water potential, but lower stomatal conductance and nitrogen content. Under drought, stomatal conductance declined more dramatically in C3 than C4 species, and photosynthetic water‐use and nitrogen‐use efficiency advantages held by C4 species under control conditions were each diminished by 40%. Leaf mortality was slightly higher in C4 than C3 grasses, but leaf condition under drought otherwise showed no dependence on photosynthetic‐type. This phylogenetically controlled experiment suggested that a drought‐induced reduction in the photosynthetic performance advantages of C4 NADP‐me relative to C3 grasses is a general phenomenon.

C4 photosynthesis is an important example of convergent evolution in plants, having arisen in eudicots, monocots and diatoms. Comparisons between such diverse groups are confounded by phylogenetic and ecological differences, so that only broad generalisations can be made about the role of C4 photosynthesis indetermining ecophysiological traits. However, 60% of C4 species occur in the grasses (Poaceae) and molecular phylogenetic techniques confirm that there are between 8 and 17 independent origins of C4 photosynthesis in the Poaceae. In a screening experiment, we compared leaf physiology and growth traits across several majorindependent C3 & C4 groups within the Poaceae, asking 1) which traits differ consistently between photosynthetictypes and 2) which traits differ consistently between clades within each photosynthetic type.