Modeling Therapeutic Antibody-Small Molecule Drug-Drug Interactions Using a Three-Dimensional Perfusable Human Liver Coculture Platform

Traditional in vitro human liver cell culture models lose key hepatic functions such as metabolic activity during short-term culture. Advanced three-dimensional (3D) liver coculture platforms offer the potential for extended hepatocyte functionality and allow for the study of more complex biologic interactions, which can improve and refine human drug safety evaluations. Here, we use a perfusion flow 3D microreactor platform for the coculture of cryopreserved primary human hepatocytes and Kupffer cells to study the regulation of cytochrome P450 3A4 isoform (CYP3A4) activity by chronic interleukin 6 (IL-6)-mediated inflammation over 2 weeks. Hepatocyte cultures remained stable over 2 weeks, with consistent albumin production and basal IL-6 levels. Direct IL-6 stimulation that mimics an inflammatory state induced a dose-dependent suppression of CYP3A4 activity, an increase in C-reactive protein (CRP) secretion, and a decrease in shed soluble interleukin-6 receptor (IL-6R) levels, indicating expected hepatic IL-6 bioactivity. Tocilizumab, an anti-IL-6R monoclonal antibody used to treat rheumatoid arthritis, has been demonstrated clinically to impact small molecule drug pharmacokinetics by modulating cytochrome P450 enzyme activities, an effect not observed in traditional hepatic cultures. We have now recapitulated the clinical observation in a 3D bioreactor system. Tocilizumab was shown to desuppress CYP3A4 activity while reducing the CRP concentration after 72 hours in the continued presence of IL-6. This change in CYP3A4 activity decreased the half-life and area under the curve up to the last measurable concentration (AUClast) of the small molecule CYP3A4 substrate simvastatin hydroxy acid, measured before and after tocilizumab treatment. We conclude that next-generation in vitro liver culture platforms are well suited for these types of long-term treatment studies and show promise for improved drug safety assessment.

Circulating immune cell phenotype dynamics reflect the strength of tumor-immune cell interactions in patients during immunotherapy

The extent to which immune cell phenotypes in the peripheral blood reflect within-tumor immune activity prior to and early in cancer therapy is unclear. To address this question, we studied the population dynamics of tumor and immune cells, and immune phenotypic changes, using clinical tumor and immune cell measurements and single-cell genomic analyses. These samples were serially obtained from a cohort of advanced gastrointestinal cancer patients enrolled in a trial with chemotherapy and immunotherapy. Using an ecological population model, fitted to clinical tumor burden and immune cell abundance data from each patient, we find evidence of a strong tumor-circulating immune cell interaction in responder patients but not in those patients that progress on treatment. Upon initiation of therapy, immune cell abundance increased rapidly in responsive patients, and once the peak level is reached tumor burden decreases, similar to models of predator-prey interactions; these dynamic patterns were absent in nonresponder patients. To interrogate phenotype dynamics of circulating immune cells, we performed single-cell RNA sequencing at serial time points during treatment. These data show that peripheral immune cell phenotypes were linked to the increased strength of patients' tumor-immune cell interaction, including increased cytotoxic differentiation and strong activation of interferon signaling in peripheral T cells in responder patients. Joint modeling of clinical and genomic data highlights the interactions between tumor and immune cell populations and reveals how variation in patient responsiveness can be explained by differences in peripheral immune cell signaling and differentiation soon after the initiation of immunotherapy.

A mutation in Ampd2 is associated with nephrotic syndrome and hypercholesterolemia in mice

Background

Previously, we identified three loci affecting HDL-cholesterol levels in a screen for ENU-induced mutations in mice and discovered two mutated genes. We sought to identify the third mutated gene and further characterize the mouse phenotype.

Methods

We engaged, DNA sequencing, gene expression profiling, western blotting, lipoprotein characterization, metabolomics assessment, histology and electron microscopy in mouse tissues.

Results

We identify the third gene as Ampd2, a liver isoform of AMP Deaminase (Ampd), a central component of energy and purine metabolism pathways. The causative mutation was a guanine-to-thymine transversion resulting in an A341S conversion in Ampd2. Ampd2 homozygous mutant mice exhibit a labile hypercholesterolemia phenotype, peaking around 9 weeks of age (251 mg/dL vs. wildtype control at 138 mg/dL), and was evidenced by marked increases in HDL, VLDL and LDL. In an attempt to determine the molecular connection between Ampd2 dysfunction and hypercholesterolemia, we analyzed hepatic gene expression and found the downregulation of Ldlr, Hmgcs and Insig1 and upregulation of Cyp7A1 genes. Metabolomic analysis confirmed an increase in hepatic AMP levels and a decrease in allantoin levels consistent with Ampd2 deficiency, and increases in campesterol and β-sitosterol. Additionally, nephrotic syndrome was observed in the mutant mice, through proteinuria, kidney histology and effacement and blebbing of podocyte foot processes by electron microscopy.

Conclusion

In summary we describe the discovery of a novel genetic mouse model of combined transient nephrotic syndrome and hypercholesterolemia, resembling the human disorder.

Electronic supplementary material

The online version of this article (doi:10.1186/1476-511X-13-167) contains supplementary material, which is available to authorized users.

A `one-two punch' therapy strategy to target chemoresistance in estrogen receptor positive breast cancer

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Patient tumor subclones that survive chemotherapy acquire primitive cell traits.

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HDAC inhibitors can reverse chemo-acquired stemness states and abolish self-renewal abilities.

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Belinostat promotes stem cell differentiation and inhibits HDAC and MYC pathways.

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A ‘one-two punch’, chemotherapy-HDAC inhibitor combination strategy reverses chemo-induced resistant phenotypes.

Cancer cell phenotypes evolve during a tumor's treatment. In some cases, tumor cells acquire cancer stem cell-like (CSL) traits such as resistance to chemotherapy and diminished differentiation; therefore, targeting these cells may be therapeutically beneficial. In this study we show that in progressive estrogen receptor positive (ER+) metastatic breast cancer tumors, resistant subclones that emerge following chemotherapy have increased CSL abundance. Further, in vitro organoid growth of ER+ patient cancer cells also shows that chemotherapy treatment leads to increased abundance of ALDH+/CD44+ CSL cells. Chemotherapy induced CSL abundance is blocked by treatment with a pan-HDAC inhibitor, belinostat. Belinostat treatment diminished both mammosphere formation and size following chemotherapy, indicating a decrease in progenitor CSL traits. HDAC inhibitors specific to class IIa (HDAC4, HDAC5) and IIb (HDAC6) were shown to primarily reverse the chemo-resistant CSL state. Single-cell RNA sequencing analysis with patient samples showed that HDAC targets and MYC signaling were promoted by chemotherapy and inhibited upon HDAC inhibitor treatment. In summary, HDAC inhibition can block chemotherapy-induced drug resistant phenotypes with ‘one-two punch’ strategy in refractory breast cancer cells.

Serial single-cell genomics reveals convergent subclonal evolution of resistance as early-stage breast cancer patients progress on endocrine plus CDK4/6 therapy

Combining cyclin-dependent kinase (CDK) inhibitors with endocrine therapy improves outcomes for metastatic estrogen receptor positive (ER+) breast cancer patients but its value in earlier stage patients is unclear. We examined evolutionary trajectories of early-stage breast cancer tumors, using single cell RNA sequencing (scRNAseq) of serial biopsies from the FELINE clinical trial (#NCT02712723) of endocrine therapy (letrozole) alone or combined with the CDK inhibitor ribociclib. Despite differences in subclonal diversity evolution across patients and treatments, common resistance phenotypes emerged. Resistant tumors treated with combination therapy showed accelerated loss of estrogen signaling with convergent up-regulation of JNK signaling through growth factor receptors. In contrast, cancer cells maintaining estrogen signaling during mono- or combination therapy showed potentiation of CDK4/6 activation and ERK upregulation through ERBB4 signaling. These results indicate that combination therapy in early-stage ER+ breast cancer leads to emergence of resistance through a shift from estrogen to alternative growth signal-mediated proliferation.

Evolution of core archetypal phenotypes in progressive high grade serous ovarian cancer

The evolution of resistance in high-grade serous ovarian cancer (HGSOC) cells following chemotherapy is only partially understood. To understand the selection of factors driving heterogeneity before and through adaptation to treatment, we profile single-cell RNA-sequencing (scRNA-seq) transcriptomes of HGSOC tumors collected longitudinally during therapy. We analyze scRNA-seq data from two independent patient cohorts to reveal that HGSOC is driven by three archetypal phenotypes, defined as oncogenic states that describe the majority of the transcriptome variation. Using a multi-task learning approach to identify the biological tasks of each archetype, we identify metabolism and proliferation, cellular defense response, and DNA repair signaling as consistent cell states found across patients. Our analysis demonstrates a shift in favor of the metabolism and proliferation archetype versus cellular defense response archetype in cancer cells that received multiple lines of treatment. While archetypes are not consistently associated with specific whole-genome driver mutations, they are closely associated with subclonal populations at the single-cell level, indicating that subclones within a tumor often specialize in unique biological tasks. Our study reveals the core archetypes found in progressive HGSOC and shows consistent enrichment of subclones with the metabolism and proliferation archetype as resistance is acquired to multiple lines of therapy.

Exploiting collateral sensitivity controls growth of mixed culture of sensitive and resistant cells and decreases selection for resistant cells in a cell line model

Background

CDK4/6 inhibitors such as ribociclib are becoming widely used targeted therapies in hormone-receptor-positive (HR+) human epidermal growth factor receptor 2-negative (HER2-) breast cancer. However, cancers can advance due to drug resistance, a problem in which tumor heterogeneity and evolution are key features.

Methods

Ribociclib-resistant HR+/HER2- CAMA-1 breast cancer cells were generated through long-term ribociclib treatment. Characterization of sensitive and resistant cells were performed using RNA sequencing and whole exome sequencing. Lentiviral labeling with different fluorescent proteins enabled us to track the proliferation of sensitive and resistant cells under different treatments in a heterogeneous, 3D spheroid coculture system using imaging microscopy and flow cytometry.

Results

Transcriptional profiling of sensitive and resistant cells revealed the downregulation of the G2/M checkpoint in the resistant cells. Exploiting this acquired vulnerability; resistant cells exhibited collateral sensitivity for the Wee-1 inhibitor, adavosertib (AZD1775). The combination of ribociclib and adavosertib achieved additional antiproliferative effect exclusively in the cocultures compared to monocultures, while decreasing the selection for resistant cells.

Conclusions

Our results suggest that optimal antiproliferative effects in heterogeneous cancers can be achieved via an integrative therapeutic approach targeting sensitive and resistant cancer cell populations within a tumor, respectively.

RAGE Inhibitors as Alternatives to Dexamethasone for Managing Cerebral Edema Following Brain Tumor Surgery

Resection of brain tumors frequently causes injury to the surrounding brain tissue that exacerbates cerebral edema by activating an inflammatory cascade. Although corticosteroids are often utilized peri-operatively to alleviate the symptoms associated with brain edema, they increase operative morbidities and suppress the efficacy of immunotherapy. Thus, novel approaches to minimize cerebral edema caused by neurosurgical procedures will have significant utility in the management of patients with brain tumors. We have studied the role of the receptor for advanced glycation end products (RAGE) and its ligands on inflammatory responses to neurosurgical injury in mice and humans. Blood-brain barrier (BBB) integrity and neuroinflammation were characterized by Nanostring, flow cytometry, qPCR, and immunoblotting of WT and RAGE knockout mice brains subjected to surgical brain injury (SBI). Human tumor tissue and fluid collected from the resection cavity of patients undergoing craniotomy were also analyzed by single-cell RNA sequencing and ELISA. Genetic ablation of RAGE significantly abrogated neuroinflammation and BBB disruption in the murine SBI model. The inflammatory responses to SBI were associated with infiltration of S100A9-expressing myeloid-derived cells into the brain. Local release of pro-inflammatory S100A9 was confirmed in patients following tumor resection. RAGE and S100A9 inhibitors were as effective as dexamethasone in attenuating neuroinflammation. However, unlike dexamethasone and S100A9 inhibitor, RAGE inhibition did not diminish the efficacy of anti-PD-1 immunotherapy in glioma-bearing mice. These observations confirm the role of the RAGE axis in surgically induced neuroinflammation and provide an alternative therapeutic option to dexamethasone in managing post-operative cerebral edema.

ONC201/TIC10 enhances durability of mTOR inhibitor everolimus in metastatic ER+ breast cancer

The mTOR inhibitor, everolimus, is an important clinical management component of metastatic ER+ breast cancer (BC). However, most patients develop resistance and progress on therapy, highlighting the need to discover strategies that increase mTOR inhibitor effectiveness. We developed ER+ BC cell lines, sensitive or resistant to everolimus, and discovered that combination treatment of ONC201/TIC10 with everolimus inhibited cell growth in 2D/3D in vitro studies. We confirmed increased therapeutic response in primary patient cells progressing on everolimus, supporting clinical relevance. We show that ONC201/TIC10 mechanism in metastatic ER+ BC cells involves oxidative phosphorylation inhibition and stress response activation. Transcriptomic analysis in everolimus resistant breast patient tumors and mitochondrial functional assays in resistant cell lines demonstrated increased mitochondrial respiration dependency, contributing to ONC201/TIC10 sensitivity. We propose that ONC201/TIC10 and modulation of mitochondrial function may provide an effective add-on therapy strategy for patients with metastatic ER+ BCs resistant to mTOR inhibitors.

Abstract SP012: Convergent evolution of resistance pathways during early stage breast cancer treatment with combination cell cycle (CDK) and endocrine signaling inhibitors

Combining cyclin-dependent kinase (CDK) inhibitors with endocrine therapy improves outcomes for metastatic estrogen receptor positive (ER+), HER2 negative, breast cancer patients. However, the value of this combination in potentially curable earlier stage patients is not clear. Using single cell transcriptomic profiling, we examined the evolutionary trajectories of early stage breast cancer tumors using serial tumor biopsies from a clinical trial of preoperative endocrine therapy alone (letrozole) or in combination with the cell cycle inhibitor ribociclib. Applying hierarchical regression and Gaussian process mathematical modelling, we classified each tumor by whether it shrinks or persists with therapy and determined cancer phenotypes related to evolution of resistance and cell cycle transcriptional rewiring. We found that all patients’ tumors undergo subclonal evolution during therapy, irrespective of the clinical response. However, tumors subjected to endocrine therapy alone showed reduced diversity over time, those facing combination therapy exhibited increased diversity. Despite different diversity, single nuclei RNA sequencing uncovered common phenotypic changes in tumor cells that persist following treatment. In these tumors, accelerated loss of estrogen signaling is convergent with up-regulation of the JNK pathway, while persistent tumors that maintain estrogen signaling during therapy show potentiation of CDK4/6 activation consistent with ERBB4 and ERK signaling up-regulation. Cell cycle reconstruction identified that these tumors can rebound during combination therapy treatment, indicating stronger selection and promotion of a proliferative state. These results indicate that combination therapy in early stage ER+ breast cancers with ER and CDK inhibition drives rapid evolution of resistance via a shift from estrogen signaling to alternative growth factor receptor mediated proliferation and JNK signaling activation, concordant with a bypass in the G1 checkpoint.

Citation Format: JI Griffiths, J Chen, PA Cosgrove, A O'Dea, P Sharma, CX Ma, M Trivedi, K Kalinsky, KB Wisinski, R O'Reagan, I Makhoul, LM Spring, A Bardia, FR Adler, AL Cohen, JT Chang, QJ Khan, AH Bild. Convergent evolution of resistance pathways during early stage breast cancer treatment with combination cell cycle (CDK) and endocrine signaling inhibitors [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr SP012.

Experimentally induced ocular chlamydial infection in infant pig-tailed macaques

Four Macaca nemestrina monkeys were inoculated in the conjunctiva with Chlamydia trachomatis (strain E) at 6 weeks of age. A fifth monkey was inoculated with HeLa cell materials only. Ten weeks later, all monkeys were reinoculated with either strain E or strain C. All inoculated monkeys were susceptible to infection with C. trachomatis as documented by fluorescent antibody staining of smears and reisolation of the organism from conjunctival and nasopharyngeal swab specimens. Rectal and vaginal swab specimens remained negative throughout the study. Three of four inoculated animals responded with IgM titers reaching a peak of 1:16 (M#3) and 1:32 (M#1, M#4) 2 weeks after the primary inoculation. IgG appeared in all inoculated animals and titers rose to peak levels of 1:64 (M#2), 1:128 (M#1, M#3), and 1:256 (M#4). Histopathology documented a dramatic difference in immunological response following secondary inoculation. Primary inoculation elicited a typical inflammatory response characterized by moderate stromal infiltration of polymorphonuclear and mononuclear leukocytes. Plasma cells appeared by week 3 postinoculation (pi). Following a secondary inoculation, classic follicle formation was evident by 1 week pi. Mononuclear markers identified a germinal center composed of B cells and a T cell cap. Epithelial thinning near the cap of the follicle was accompanied by a complete loss of goblet cells. This model may be useful for studying the immunopathology of infant chlamydial infections.

Abstract 388: Acquired sensitivity to ONC201/TIC10 in ER+ breast cancer progressing on the mTOR inhibitor everolimus

The mTOR inhibitor everolimus has become an important component for clinical management of metastatic ER+ breast cancer. Despite the improved patient outcomes, progression and resistance will still develop. Therefore, it is important to research strategies that can increase response durability and effectiveness of this therapy. Here we developed everolimus resistance models and performed pre-clinical evaluation of the small molecule ONC201/TIC10, a drug candidate showing promising results in clinical trials with advanced cancer patients. ONC201/TIC10 targets mitochondrial function and metabolism and activates stress response, however its efficacy has not been studied in everolimus resistant breast cancer. Transcriptomic analysis in everolimus resistant tumors identified sustained mitochondrial oxidative phosphorylation activity suggesting increased sensitivity to ONC201/TIC10. Our results show that combination treatment of ONC201/TIC10 with everolimus inhibits the growth of sensitive as well as everolimus resistant cells in 2D and 3D in vitro studies. The increased response to combination therapy was confirmed in primary cells from patients progressing on endocrine and mTOR therapy, supporting clinical relevance. We further show that the mechanism of ONC201/TIC10 anti-proliferative activity involves disruption of mitochondrial function and increased levels of the pro-apoptotic transcription factors CHOP and ATF4. Importantly, several resistant cell lines demonstrated increased dependency on mitochondrial respiration compared to sensitive cells which contributes to a vulnerability to ONC201/TIC10. In conclusion, we used pre-clinical models to characterize acquired sensitivity to mTOR inhibition. Combining patient derived data with resistant cell line driven experiments, our study provides validated findings in various settings strengthening the potential for clinical applications of ONC201/TIC10. We propose that ONC201/TIC10 and modulation of mitochondrial function is effective in drug resistant cancer cells and can enhance the anti-tumor activity of standard of care therapy in progressing patients.

Citation Format: Eleni Farmaki, Rena Emond, Aritro Nath, Vince K. Grolmusz, Patrick A. Cosgrove, Andrea H. Bild. Acquired sensitivity to ONC201/TIC10 in ER+ breast cancer progressing on the mTOR inhibitor everolimus [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 388.

Experimental trachoma in subcutaneous conjunctival autografts in macaques

To study chlamydial conjunctivitis, conjunctival autografts subcutaneously implanted in pockets on the abdomens of rhesus (Macaca mulatta) and pig-tailed (M. nemestrina) monkeys were inoculated percutaneously (4-10 X 10(4) inclusion-forming units per pocket) with trachoma strains of Chlamydia trachomatis (serovars B & C). These conjunctival pockets were removed on days 2, 3, 4, 5, 6, 7, 8, 10, 14 and 16 post-inoculation (pi). Tissues (at least two samples at each time interval) were prepared either for reisolation of the organisms by cell culture or histologic examination by light and electron microscopy. Control tissue, inoculated with either HeLa cell material or UV-inactivated organisms, were prepared in parallel. Bloods were drawn and tear strips taken at weekly intervals for 8 weeks. A total of 221 bulbar and 99 palpebral conjunctival pockets were established over time with the success rate of 75% and 88%, respectively, in six rhesus and ten pig-tailed monkeys. Histological examination revealed widespread infiltration of mixed polymorphonuclear and mononuclear cells on days 2 and 3 pi. By day 5 pi, lymphocytes had migrated into the thinned epithelial layer. Patches of inflammatory infiltrate similar to trachoma follicles were observed, although distinct germinal centers were absent. Surface morphologies of normal and infected pocket conjunctiva were examined by scanning electron microscopy. Normal tissue was characterized by a regular mosaic pattern of closely packed epithelial cells containing numerous microvilli. Infected tissue was edematous, and the continuity of the mucosal surface had been altered. Chlamydiae were reisolated from the pockets on days 2, 3, 6, 8 and 10 pi.(ABSTRACT TRUNCATED AT 250 WORDS)

Abstract 4318: Cancer cell communication with macrophages prevents T cell activation during emergence of cell cycle therapy resistance

By corrupting signals for growth and survival, evolving cancer cells can engineer the tumor microenvironment (TME) to promote treatment resistance. However, the specific interactions between malignant and non-malignant cells that predispose drug resistance and their changes during treatment remain widely unknown. Here we examine the composition, communication, and phenotypic diversity of tumor-associated cell populations in serial biopsies from early-stage ER+ breast cancers. We used single-cell RNA sequencing to profile over 400 thousand malignant and non-malignant cells from patient tumor samples obtained before, during and after treatment. The patients received either endocrine therapy (letrozole) alone or in combination with a CDK4/6 cell cycle inhibitor (ribociclib). Our analyses reveal that cancer cells from ribociclib-resistant tumors stimulate macrophage differentiation towards an immune-suppressive phenotype through upregulation of a diversity of cytokines and growth factors. The macrophage phenotype shift leads to reduced crosstalk with cytotoxic T-cells via IL-2/15/18 receptors, diminishing T-cell activation and recruitment. These results indicate that cancer communications promoting an immune-cold TME predispose tumors to develop CDK4/6 cell cycle inhibitor resistance, and that the beneficial effects of blocking cancer cell proliferation must be balanced against their inhibitory effect on immune cell division and activation. An optimal treatment strategy will require coupling the prevention of cancer division with activation of an effective cytotoxic T-cell response.

Citation Format: Jason I. Griffiths, Patrick A. Cosgrove, Eric Medina Castaneda, Aritro Nath, Jinfeng Chen, Frederick R. Adler, Jeffrey T. Chang, Qamar J. Khan, Andrea H. Bild. Cancer cell communication with macrophages prevents T cell activation during emergence of cell cycle therapy resistance. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4318.

Predicting clinical response to everolimus in ER+ breast cancers using machine-learning

Endocrine therapy remains the primary treatment choice for ER+ breast cancers. However, most advanced ER+ breast cancers ultimately develop resistance to endocrine. This acquired resistance to endocrine therapy is often driven by the activation of the PI3K/AKT/mTOR signaling pathway. Everolimus, a drug that targets and inhibits the mTOR complex has been shown to improve clinical outcomes in metastatic ER+ breast cancers. However, there are no biomarkers currently available to guide the use of everolimus in the clinic for progressive patients, where multiple therapeutic options are available. Here, we utilized gene expression signatures from 9 ER+ breast cancer cell lines and 23 patients treated with everolimus to develop and validate an integrative machine learning biomarker of mTOR inhibitor response. Our results show that the machine learning biomarker can successfully distinguish responders from non-responders and can be applied to identify patients that will most likely benefit from everolimus treatment.

Cellular interactions within the immune microenvironment underpins resistance to cell cycle inhibition in breast cancers

Immune evasion by cancer cells involves reshaping the tumor microenvironment (TME) via communication with non-malignant cells. However, resistance-promoting interactions during treatment remain lesser known. Here we examine the composition, communication, and phenotypes of tumor-associated cells in serial biopsies from stage II and III high-risk estrogen receptor positive (ER+ ) breast cancers of patients receiving endocrine therapy (letrozole) as single agent or in combination with ribociclib, a CDK4/6-targeting cell cycle inhibitor. Single-cell RNA sequencing analyses on longitudinally collected samples show that in tumors overcoming the growth suppressive effects of ribociclib, first cancer cells upregulate cytokines and growth factors that stimulate immune-suppressive myeloid differentiation, resulting in reduced myeloid cell- CD8 + T-cell crosstalk via IL-15/18 signaling. Subsequently, tumors growing during treatment show diminished T-cell activation and recruitment. In vitro, ribociclib does not only inhibit cancer cell growth but also T cell proliferation and activation upon co-culturing. Exogenous IL-15 improves CDK4/6 inhibitor efficacy by augmenting T-cell proliferation and cancer cell killing by T cells. In summary, response to ribociclib in stage II and III high-risk ER +  breast cancer depends on the composition, activation phenotypes and communication network of immune cells.

Single-Cell Transcriptomics Sheds Light on Tumor Evolution: Perspectives from City of Hope's Clinical Trial Teams

Tumor heterogeneity is a significant factor influencing cancer treatment effectiveness and can arise from genetic, epigenetic, and phenotypic variations among cancer cells. Understanding how tumor heterogeneity impacts tumor evolution and therapy response can lead to more effective treatments and improved patient outcomes. Traditional bulk genomic approaches fail to provide insights into cellular-level events, whereas single-cell RNA sequencing (scRNA-seq) offers transcriptomic analysis at the individual cell level, advancing our understanding of tumor growth, progression, and drug response. However, implementing single-cell approaches in clinical trials involves challenges, such as obtaining high-quality cells, technical variability, and the need for complex computational analysis. Effective implementation of single-cell genomics in clinical trials requires a collaborative "Team Medicine" approach, leveraging shared resources, expertise, and workflows. Here, we describe key technical considerations in implementing the collection of research biopsies and lessons learned from integrating scRNA-seq into City of Hope's clinical trial design, highlighting collaborative efforts between computational and clinical teams across breast, brain, and ovarian cancer studies to understand the composition, phenotypic state, and underlying resistance mechanisms within the tumor microenvironment.