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Quantitative phase imaging (QPI) measures the growth rate of individual cells by quantifying changes in mass versus time. Here, we use the breast cancer cell lines MCF-7, BT-474, and MDA-MB-231 to validate QPI as a multiparametric approach for determining response to single-agent therapies. Our method allows for rapid determination of drug sensitivity, cytotoxicity, heterogeneity, and time of response for up to 100,000 individual cells or small clusters in a single experiment. We find that QPI EC 50 values are concordant with CellTiter-Glo (CTG), a gold standard metabolic endpoint assay. In addition, we apply multiparametric QPI to characterize cytostatic/cytotoxic and rapid/slow responses and track the emergence of resistant subpopulations. Thus, QPI reveals dynamic changes in response heterogeneity in addition to average population responses, a key advantage over endpoint viability or metabolic assays. Overall, multiparametric QPI reveals a rich picture of cell growth by capturing the dynamics of single-cell responses to candidate therapies. The authors developed a real-time and label-free approach based on quantitative phase imaging to determine drug sensitivity with significant advantages over endpoint viability or metabolic assays, and which reveals single cell response heterogeneity.

Background Acral melanoma (AM) is an aggressive melanoma variant that arises from palmar, plantar, and nail unit melanocytes. Compared to non-acral cutaneous melanoma (CM), AM is biologically distinct, has an equal incidence across genetic ancestries, typically presents in advanced stage disease, is less responsive to therapy, and has an overall worse prognosis. Methods An independent analysis of published sequencing data was performed to evaluate the frequency of receptor tyrosine kinase (RTK) ligands and adapter protein gene variants and expression. To target these genetic variants, a zebrafish acral melanoma model and preclinical patient-derived xenograft (PDX) mouse models were treated with a panel of RTK inhibitors. Residual PDX tumors were evaluated for changes in proliferation, vasculature, necrosis, and ferroptosis by histology and immunohistochemistry. Results RTK ligands and adapter proteins are frequently amplified, translocated, and/or overexpressed in AM. Dual FGFR/VEGFR inhibitors decrease acral-analogous melanocyte proliferation and migration in zebrafish, and the potent pan-FGFR/VEGFR inhibitor, Lenvatinib, uniformly induces tumor regression in AM PDX tumors but only slows tumor growth in CM models. Unlike other multi-RTK inhibitors, Lenvatinib is not directly cytotoxic to dissociated AM PDX tumor cells and instead disrupts tumor architecture and vascular networks. Conclusion Considering the great difficulty in establishing AM cell culture lines, these findings suggest that AM may be more sensitive to microenvironment perturbations than CM. In conclusion, dual FGFR/VEGFR inhibition may be a viable therapeutic strategy that targets the unique biology of AM.

Infants born with intrauterine growth restriction (IUGR) have up to a five-fold higher risk of learning and memory impairment than those with normal growth. Using a mouse model of hypertensive diseases of pregnancy (HDP) to replicate uteroplacental insufficiency (UPI), we have previously shown that UPI causes premature embryonic hippocampal dentate gyrus (DG) neurogenesis in IUGR offspring. The DG is a brain region that receives the first cortical information for memory formation. In the current study, we examined the postnatal DG neuron morphology one month after delivery (P28) using recombinant adeno-associated viral labeling of neurons. We also examined DG microglia’s morphology using immunofluorescent histochemistry and defined the hippocampal cytokine/chemokine milieu using Luminex xMAP technology. We found that IUGR preserved the principal dendrite lengths but decreased the dendritic branching and volume of DG neurons. IUGR augmented DG microglial number and cell size. Lastly, IUGR altered the hippocampal cytokine/chemokine profile in a sex-specific manner. We conclude that the prematurely-generated neuronal progenitors develop abnormal morphologies postnatally in a cell-autonomous manner. Microglia appear to modulate neuronal morphology by interacting with dendrites amidst a complex cytokine/chemokine environment that could ultimately lead to adult learning and memory deficits in our mouse model.

Models that recapitulate the complexity of human tumors are urgently needed to develop more effective cancer therapies. We report a bank of human patient-derived xenografts (PDXs) and matched organoid cultures from tumors that represent the greatest unmet need: endocrine-resistant, treatment-refractory and metastatic breast cancers. We leverage matched PDXs and PDX-derived organoids (PDxO) for drug screening that is feasible and cost-effective with in vivo validation. Moreover, we demonstrate the feasibility of using these models for precision oncology in real time with clinical care in a case of triple-negative breast cancer (TNBC) with early metastatic recurrence. Our results uncovered a Food and Drug Administration (FDA)-approved drug with high efficacy against the models. Treatment with this therapy resulted in a complete response for the individual and a progression-free survival (PFS) period more than three times longer than their previous therapies. This work provides valuable methods and resources for functional precision medicine and drug development for human breast cancer.

Recurrence of metastatic breast cancer stemming from acquired endocrine and chemotherapy resistance remains a health burden for women with luminal (ER + ) breast cancer. Disseminated ER + tumor cells can remain viable but quiescent for years to decades. Contributing factors to metastatic spread include the maintenance and expansion of breast cancer stem cells (CSCs). Breast CSCs frequently exist as a minority population in therapy resistant tumors. In this study, we show that cytoplasmic complexes composed of steroid receptor (SR) co-activators, PELP1 and SRC-3, modulate breast CSC expansion through upregulation of the HIF-activated metabolic target genes PFKFB3 and PFKFB4 . Seahorse metabolic assays demonstrated that cytoplasmic PELP1 influences cellular metabolism by increasing both glycolysis and mitochondrial respiration. PELP1 interacts with PFKFB3 and PFKFB4 proteins, and inhibition of PFKFB3 and PFKFB4 kinase activity blocks PELP1-induced tumorspheres and protein–protein interactions with SRC-3. PFKFB4 knockdown inhibited in vivo emergence of circulating tumor cell (CTC) populations in mammary intraductal (MIND) models. Application of PFKFB inhibitors in combination with ER targeted therapies blocked tumorsphere formation in multiple models of advanced breast cancer including tamoxifen (TamR) and paclitaxel (TaxR) resistant models, murine tumor cells, and ER + patient-derived organoids (PDxO). Together, our data suggest that PELP1, SRC-3, and PFKFBs cooperate to drive ER + tumor cell populations that include CSCs and CTCs. Identifying non-ER pharmacological targets offers a useful approach to blocking metastatic escape from standard of care ER/estrogen (E2)-targeted strategies to overcome endocrine and chemotherapy resistance.

BackgroundHeterogeneous tumors exhibit impaired immune responses1–3 and inferior responses to immune checkpoint inhibitors.1 4 5 To understand the mechanisms by which heterogenous tumors evade immune control, our lab previously established a novel model of tumor heterogeneity in which we implant mice with tumors comprised of multiple fluorescently labeled tumor populations.6 Using the fluorescent tags to track the spatial locations of specific tumor cell populations, we have demonstrated that tumor cells profoundly impact the organization of the immune microenvironment in their spatial vicinity. Building on this work, we here investigate the mechanisms tumor cells use to shape their local tumor microenvironment.MethodsWe implanted mice with heterogeneous tumors comprised of 1:1 mixes of fluorescently tagged tumor cells, using two ‘immune hot’ squamous cell skin carcinoma tumor lines (CIT18 and CIT6, tagged RFP+ and YFP+), or with homogeneous tumors comprised of a single population. Tumors were manually dissected into RFP+ and YFP+ regions. T cells in each region were analyzed by flow cytometry or by single cell RNAseq + TCRseq of sorted T cells. Chemokines and cytokines in each region were assayed by a 64-plex ELISA-based array. To complement these approaches, immune cells in each RFP+ and YFP+ regions were analyzed by immunofluorescence microscopy across multiple timepoints.ResultsWe find that the chemokine microenvironment within a heterogeneous tumor is dictated by the local tumor cells. Specifically, in mixed CIT6:CIT18 tumors, spatial regions occupied by CIT18 tumor cells had a chemokine milieu characterized by high levels of pro-inflammatory chemokines CXCL10, CCL5, CXCL11, CCL17 and CCL22, matching homogeneous CIT18 tumors. By contrast, regions of the same heterogeneous tumors occupied by CIT6 tumors lacked this signature, mirroring homogeneous CIT6 tumors. The inflammatory chemokine-rich tumor regions exhibited elevated numbers of CD4+ T cells, whose abundance was significantly correlated with elevated effector function (IFNγ+) of CD8+ T cells. Both T cell metrics were diminished in regions lacking the inflammatory chemokine signature. Using single-cell TCRseq analysis, we additionally mapped the distribution of expanded T cell clonotypes across multiple spatial regions of a single tumor.ConclusionsWe demonstrate that within heterogeneous tumors, local tumor cells dictate the cytokine and chemokine milieu within their spatial vicinity. This provides a mechanistic underpinning explaining the ability of tumor cells to shape their immune microenvironment on a localized level. Further, we link regions of diminished CD4+ infiltration and effector CD8+ T cell function to spatial regions where tumor cells enforce decreased levels of inflammatory chemokines.ReferencesWolf Y, Bartok O, Patkar S, Eli GB, Cohen S, Litchfield K, et al. UVB-Induced Tumor Heterogeneity Diminishes Immune Response in Melanoma. Cell. 2019;179:219-235.e21.Westcott PMK, Muyas F, Hauck H, Smith OC, Sacks NJ, Ely ZA, et al. Mismatch repair deficiency is not sufficient to elicit tumor immunogenicity. Nat Genet. 2023;55:1686–95.Nguyen KB, Roerden M, Copeland CJ, Backlund CM, Klop-Packel NG, Remba T, et al. Decoupled neoantigen cross-presentation by dendritic cells limits anti-tumor immunity against tumors with heterogeneous neoantigen expression. eLife. 2023;12:e85263.McGranahan N, Furness AJS, Rosenthal R, Ramskov S, Lyngaa R, Saini SK, et al. Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade. Science. 2016;351:1463–9.Liu D, Schilling B, Liu D, Sucker A, Livingstone E, Jerby-Arnon L, et al. Integrative molecular and clinical modeling of clinical outcomes to PD1 blockade in patients with metastatic melanoma. Nat Med. 2019;25:1916–27.Tanaka M, Lum L, Hu KH, Chaudhary P, Hughes S, Ledezma-Soto C, et al. Tumor cell heterogeneity drives spatial organization of the intratumoral immune response. J Exp Med. 2025;222:e20242282.Ethics ApprovalAll animal experiments were approved by the by the University of Utah Office of Comparative Medicine (IACUC #22-02003).

Recurrence of metastatic breast cancer stemming from acquired endocrine and chemotherapy resistance remains a health burden for women with luminal (ER.sup.+) breast cancer. Disseminated ER.sup.+ tumor cells can remain viable but quiescent for years to decades. Contributing factors to metastatic spread include the maintenance and expansion of breast cancer stem cells (CSCs). Breast CSCs frequently exist as a minority population in therapy resistant tumors. In this study, we show that cytoplasmic complexes composed of steroid receptor (SR) co-activators, PELP1 and SRC-3, modulate breast CSC expansion through upregulation of the HIF-activated metabolic target genes PFKFB3 and PFKFB4. Seahorse metabolic assays demonstrated that cytoplasmic PELP1 influences cellular metabolism by increasing both glycolysis and mitochondrial respiration. PELP1 interacts with PFKFB3 and PFKFB4 proteins, and inhibition of PFKFB3 and PFKFB4 kinase activity blocks PELP1-induced tumorspheres and protein-protein interactions with SRC-3. PFKFB4 knockdown inhibited in vivo emergence of circulating tumor cell (CTC) populations in mammary intraductal (MIND) models. Application of PFKFB inhibitors in combination with ER targeted therapies blocked tumorsphere formation in multiple models of advanced breast cancer including tamoxifen (TamR) and paclitaxel (TaxR) resistant models, murine tumor cells, and ER.sup.+ patient-derived organoids (PDxO). Together, our data suggest that PELP1, SRC-3, and PFKFBs cooperate to drive ER.sup.+ tumor cell populations that include CSCs and CTCs. Identifying non-ER pharmacological targets offers a useful approach to blocking metastatic escape from standard of care ER/estrogen (E2)-targeted strategies to overcome endocrine and chemotherapy resistance.

A Correction to this paper has been published: https://doi.org/10.1038/s41588-021-00811-4.

Recurrence of metastatic breast cancer stemming from acquired endocrine and chemotherapy resistance remains a health burden for women with luminal (ER+) breast cancer. Disseminated ER+ tumor cells can remain viable but quiescent for years to decades. Contributing factors to metastatic spread include the maintenance and expansion of breast cancer stem cells (CSCs). Breast CSCs are poorly proliferative and frequently exist as a minority population in therapy resistant tumors. Our objective is to define novel signaling pathways that govern therapy resistance in ER+ breast cancer. In this study, we show that cytoplasmic complexes composed of steroid receptor (SR) co-activators, PELP1 and SRC-3, modulate breast CSC expansion through upregulation of the HIF-activated metabolic target genes PFKFB3 and PFKFB4. Seahorse metabolic assays demonstrated that cytoplasmic PELP1 influences cellular metabolism by increasing both glycolysis and mitochondrial respiration. PELP1 interacts with PFKFB3 and PFKFB4 proteins, and inhibition of PFKFB3 and PFKFB4 kinase activity blocks PELP1-induced tumorspheres and protein-protein interactions with SRC-3. PFKFB4 knockdown inhibited in vivo emergence of circulating tumor cell (CTC) populations in ER+ mammary intraductal (MIND) xenografts. Application of PFKFB inhibitors in combination with ER targeted therapies blocked tumorsphere formation in multiple models of advanced breast cancer, including tamoxifen (TamR) and paclitaxel (TaxR) resistant models and ER+ patient-derived organoids (PDxO). Together, our data suggest that PELP1, SRC-3, and PFKFBs cooperate to drive ER+ tumor cells that include CSCs and CTCs. Identifying non-ER pharmacological targets offers a useful approach to blocking metastatic escape from standard of care ER/estrogen (E2)-targeted strategies to overcome endocrine and chemotherapy resistance in ER+ breast cancer.

Functional precision oncology seeks to match patients with effective therapies by empirically testing patient-derived samples for drug sensitivity in the laboratory. However, existing approaches require significant sample expansion time and expense prior to analysis, rendering them impractical for routine clinical testing. Quantitative phase imaging (QPI) provides a potential path forward by directly measuring responses at single cell resolution without the need for extensive sample expansion. In previous work, we demonstrated that multiple, independent parameters of cellular response to therapeutic agents can be derived from QPI data, an approach we call multiparametric QPI (mQPI). Here, we demonstrate application of mQPI using cells from patient derived xenograft organoid (PDxO) models, as well as cells viably frozen direct from patients. Using mQPI with breast cancer PDxO models, we uncover distinct drug responses for cells originating from different anatomic sites in the same patient and resolve cellular heterogeneity of response in a model of acquired therapeutic resistance. We also show that mQPI can detect drug responses in viably frozen primary patient samples, either direct from thaw or after a short term expansion of only 2 weeks. Overall, these data provide proof-of-principle for application of mQPI to a range of sample types, including cryopreserved material direct from patients. This underscores the clinical potential of mQPI as a time- and materials-efficient alternative to current methods in functional precision oncology.