Academic Appointments

Honors & Awards

  • Translational Research and Applied Medicine Pilot Grant, Stanford Medicine (2019-2021)
  • Leopold Casper-Promotionspreis, awarded for the best Ph.D. thesis in the field of Urology in Germany, German Association for Urology/Deutsche Gesselschaft fuer Urologie (DGU) (2016)
  • Postdoctoral Fellowship, Fritz Thyssen Foundation, Germany (2015-2017)
  • Scotland's Saltire Scholarship, British Council on behalf of the Scottish government (2010-2011)

Professional Education

  • Bachelor of Med & Surgery (MBBS), B. J. Medical College, Maharashtra University of Health Sciences, Pune, India (2010)
  • Masters of research (MRes), University of Glasgow, Glasgow, U.K (2011)
  • Doctor of Philosophy (Ph.D.), Technische Universität München, Munich, Germany (2015)

Current Research and Scholarly Interests

I am interested in understanding the determinants of therapeutic resistance in cancer. I investigate the composition of the tumor microenvironment and adaptive responses to therapy using single-cell RNA sequencing.

All Publications

  • Direct measurement of engineered cancer mutations and their transcriptional phenotypes in single cells. Nature biotechnology Kim, H. S., Grimes, S. M., Chen, T., Sathe, A., Lau, B. T., Hwang, G. H., Bae, S., Ji, H. P. 2023


    Genome sequencing studies have identified numerous cancer mutations across a wide spectrum of tumor types, but determining the phenotypic consequence of these mutations remains a challenge. Here, we developed a high-throughput, multiplexed single-cell technology called TISCC-seq to engineer predesignated mutations in cells using CRISPR base editors, directly delineate their genotype among individual cells and determine each mutation's transcriptional phenotype. Long-read sequencing of the target gene's transcript identifies the engineered mutations, and the transcriptome profile from the same set of cells is simultaneously analyzed by short-read sequencing. Through integration, we determine the mutations' genotype and expression phenotype at single-cell resolution. Using cell lines, we engineer and evaluate the impact of >100 TP53 mutations on gene expression. Based on the single-cell gene expression, we classify the mutations as having a functionally significant phenotype.

    View details for DOI 10.1038/s41587-023-01949-8

    View details for PubMedID 37697151

    View details for PubMedCentralID 8018281

  • Follicular lymphoma evolves with a surmountable dependency on acquired glycosylation motifs in the B cell receptor. Blood Haebe, S. E., Day, G., Czerwinski, D. K., Sathe, A., Grimes, S. M., Chen, T., Long, S. R., Martin, B. A., Ozawa, M. G., Ji, H. P., Shree, T., Levy, R. 2023


    An early event in the genesis of follicular lymphoma (FL) is the acquisition of new glycosylation motifs in the B cell receptor (BCR) due to gene rearrangement and/or somatic hypermutation. These N-linked glycosylation motifs (N-motifs) contain mannose-terminated glycans and can interact with lectins in the tumor microenvironment, activating the tumor BCR pathway. N-motifs are stable during FL evolution suggesting that FL tumor cells are dependent on them for their survival. Here, we investigated the dynamics and potential impact of N-motif prevalence in FL at the single cell level across distinct tumor sites and over time in 17 patients. While most patients had acquired at least one N-motif as an early event, we also found (i) cases without N-motifs in the heavy or light chains at any tumor site or timepoint and (ii) cases with discordant N-motif patterns across different tumor sites. Inferring phylogenetic trees for the patients with discordant patterns, we observed that both N-motif-positive and N-motif-negative tumor subclones could be selected and expanded during tumor evolution. Comparing N-motif-positive to N-motif-negative tumor cells within a patient revealed higher expression of genes involved in the BCR pathway and inflammatory response, while tumor cells without N-motifs had higher activity of pathways involved in energy metabolism. In conclusion, while acquired N-motifs likely support FL pathogenesis through antigen-independent BCR signaling in most FL patients, N-motif-negative tumor cells can also be selected and expanded and may depend more heavily on altered metabolism for competitive survival.

    View details for DOI 10.1182/blood.2023020360

    View details for PubMedID 37683139

  • Single-cell multi-gene identification of somatic mutations and gene rearrangements in cancer. NAR cancer Grimes, S. M., Kim, H. S., Roy, S., Sathe, A., Ayala, C. I., Bai, X., Almeda-Notestine, A. F., Haebe, S., Shree, T., Levy, R., Lau, B. T., Ji, H. P. 2023; 5 (3): zcad034


    In this proof-of-concept study, we developed a single-cell method that provides genotypes of somatic alterations found in coding regions of messenger RNAs and integrates these transcript-based variants with their matching cell transcriptomes. We used nanopore adaptive sampling on single-cell complementary DNA libraries to validate coding variants in target gene transcripts, and short-read sequencing to characterize cell types harboring the mutations. CRISPR edits for 16 targets were identified using a cancer cell line, and known variants in the cell line were validated using a 352-gene panel. Variants in primary cancer samples were validated using target gene panels ranging from 161 to 529 genes. A gene rearrangement was also identified in one patient, with the rearrangement occurring in two distinct tumor sites.

    View details for DOI 10.1093/narcan/zcad034

    View details for PubMedID 37435532

    View details for PubMedCentralID PMC10331933

  • Single Cell Transcriptomic Analysis of Human Extra- and Intra-Hepatic Cholangiocarcinoma Ayala, C. I., Sathe, A., Grimes, S., Bae, X., Dua, M., Poultsides, G., Visser, B., Ji, H. SPRINGER. 2023: S177-S178
  • Activating Immune Effectors and Dampening Immune Suppressors Generates Successful Therapeutic Cancer Vaccination in Patients with Lymphoma Shree, T., Haebe, S., Czerwinski, D. K., Eckhert, E., Day, G., Sathe, A., Grimes, S. M., Frank, M. J., Maeda, L. S., Alizadeh, A. A., Advani, R. H., Hoppe, R., Long, S. R., Martin, B., Ozawa, M. G., Khodadoust, M. S., Ji, H. P., Levy, R. AMER SOC HEMATOLOGY. 2022: 6450-6451
  • Prevalence of Acquired N-Glycosylation Sites at the Single Cell Level in Follicular Lymphoma Haebe, S., Shree, T., Day, G., Czerwinski, D. K., Sathe, A., Grimes, S. M., Long, S. R., Martin, B., Ozawa, M. G., Ji, H. P., Levy, R. AMER SOC HEMATOLOGY. 2022: 9211-9212
  • Colorectal cancer metastases in the liver establish immunosuppressive spatial networking between tumor associated SPP1+ macrophages and fibroblasts. Clinical cancer research : an official journal of the American Association for Cancer Research Sathe, A., Mason, K., Grimes, S. M., Zhou, Z., Lau, B. T., Bai, X., Su, A., Tan, X., Lee, H., Suarez, C. J., Nguyen, Q., Poultsides, G., Zhang, N. R., Ji, H. P. 2022


    The liver is the most frequent metastatic site for colorectal cancer (CRC). Its microenvironment is modified to provide a niche that is conducive for CRC cell growth.This study focused on characterizing the cellular changes in the metastatic CRC (mCRC) liver tumor microenvironment (TME).We analyzed a series of microsatellite stable (MSS) mCRCs to the liver, paired normal liver tissue and peripheral blood mononuclear cells using single cell RNA-seq (scRNA-seq). We validated our findings using multiplexed spatial imaging and bulk gene expression with cell deconvolution.We identified TME-specific SPP1-expressing macrophages with altered metabolism features, foam cell characteristics and increased activity in extracellular matrix (ECM) organization. SPP1+ macrophages and fibroblasts expressed complementary ligand receptor pairs with the potential to mutually influence their gene expression programs. TME lacked dysfunctional CD8 T cells and contained regulatory T cells, indicative of immunosuppression. Spatial imaging validated these cell states in the TME. Moreover, TME macrophages and fibroblasts had close spatial proximity, which is a requirement for intercellular communication and networking.In an independent cohort of mCRCs in the liver, we confirmed the presence of SPP1+ macrophages and fibroblasts using gene expression data. An increased proportion of TME fibroblasts was associated with a worst prognosis in these patients.We demonstrated that mCRC in the liver is characterized by transcriptional alterations of macrophages in the TME. Intercellular networking between macrophages and fibroblasts supports CRC growth in the immunosuppressed metastatic niche in the liver. These features can be used to target immune checkpoint resistant MSS tumors.

    View details for DOI 10.1158/1078-0432.CCR-22-2041

    View details for PubMedID 36239989

  • Reconstructing the spatial evolution of cancer through subclone detection on copy number profiles in tumor sequencing data. Wu, C., Hess, P. R., Sathe, A., Rong, J., Lau, B. T., Grimes, S. M., Ji, H. P., Zhang, N. R. AMER ASSOC CANCER RESEARCH. 2022
  • A single-cell solution for solid tumors to detect mutations and quantify copy number variations. Wu, C., Hess, P. R., Sathe, A., Rong, J., Lau, B. T., Grimes, S. M., Ji, H. P., Zhang, N. R. AMER ASSOC CANCER RESEARCH. 2022
  • Reconstructing the spatial evolution of cancer through subclone detection on copy number profiles in tumor sequencing data Wu, C., Hess, P. R., Sathe, A., Rong, J., Lau, B. T., Grimes, S. M., Ji, H. P., Zhang, N. R. AMER ASSOC CANCER RESEARCH. 2022
  • Mucinous Epithelial Cell Secretion Drives Mucinous Ascites Formation in Pseudomyxoma Peritonei Patients Ayala, C., Sathe, A., Grimes, S., Zhao, L., Bai, X., Poultsides, G., Lee, B., Ji, H. SPRINGER. 2022: 520-521
  • In Situ Vaccination Induces Changes in Follicular Lymphoma Tumor Cells That Correlate with Abscopal Clinical Regressions Haebe, S., Shree, T., Day, G., Sathe, A., Czerwinski, D. K., Grimes, S. M., Long, S. R., Martin, B., Hoppe, R., Ji, H. P., Levy, R. AMER SOC HEMATOLOGY. 2021
  • Therapeutic and Immunologic Responses Elicited By in Situ Vaccination with CpG, Ibrutinib, and Low-Dose Radiation Shree, T., Haebe, S., Czerwinski, D. K., Day, G., Sathe, A., Khodadoust, M. S., Frank, M. J., Beygi, S., Hoppe, R., Long, S. R., Martin, B., Ji, H. P., Levy, R. AMER SOC HEMATOLOGY. 2021
  • Integrative single-cell analysis of allele-specific copy number alterations and chromatin accessibility in cancer. Nature biotechnology Wu, C., Lau, B. T., Kim, H. S., Sathe, A., Grimes, S. M., Ji, H. P., Zhang, N. R. 2021


    Cancer progression is driven by both somatic copy number aberrations (CNAs) and chromatin remodeling, yet little is known about the interplay between these two classes of events in shaping the clonal diversity of cancers. We present Alleloscope, a method for allele-specific copy number estimation that can be applied to single-cell DNA- and/or transposase-accessible chromatin-sequencing (scDNA-seq, ATAC-seq) data, enabling combined analysis of allele-specific copy number and chromatin accessibility. On scDNA-seq data from gastric, colorectal and breast cancer samples, with validation using matched linked-read sequencing, Alleloscope finds pervasive occurrence of highly complex, multiallelic CNAs, in which cells that carry varying allelic configurations adding to the same total copy number coevolve within a tumor. On scATAC-seq from two basal cell carcinoma samples and a gastric cancer cell line, Alleloscope detected multiallelic copy number events and copy-neutral loss-of-heterozygosity, enabling dissection of the contributions of chromosomal instability and chromatin remodeling to tumor evolution.

    View details for DOI 10.1038/s41587-021-00911-w

    View details for PubMedID 34017141

  • An expanded universe of cancer targets. Cell Hahn, W. C., Bader, J. S., Braun, T. P., Califano, A., Clemons, P. A., Druker, B. J., Ewald, A. J., Fu, H., Jagu, S., Kemp, C. J., Kim, W., Kuo, C. J., McManus, M., B Mills, G., Mo, X., Sahni, N., Schreiber, S. L., Talamas, J. A., Tamayo, P., Tyner, J. W., Wagner, B. K., Weiss, W. A., Gerhard, D. S., Cancer Target Discovery and Development Network, Dancik, V., Gill, S., Hua, B., Sharifnia, T., Viswanathan, V., Zou, Y., Dela Cruz, F., Kung, A., Stockwell, B., Boehm, J., Dempster, J., Manguso, R., Vazquez, F., Cooper, L. A., Du, Y., Ivanov, A., Lonial, S., Moreno, C. S., Niu, Q., Owonikoko, T., Ramalingam, S., Reyna, M., Zhou, W., Grandori, C., Shmulevich, I., Swisher, E., Cai, J., Chan, I. S., Dunworth, M., Ge, Y., Georgess, D., Grasset, E. M., Henriet, E., Knutsdottir, H., Lerner, M. G., Padmanaban, V., Perrone, M. C., Suhail, Y., Tsehay, Y., Warrier, M., Morrow, Q., Nechiporuk, T., Long, N., Saultz, J., Kaempf, A., Minnier, J., Tognon, C. E., Kurtz, S. E., Agarwal, A., Brown, J., Watanabe-Smith, K., Vu, T. Q., Jacob, T., Yan, Y., Robinson, B., Lind, E. F., Kosaka, Y., Demir, E., Estabrook, J., Grzadkowski, M., Nikolova, O., Chen, K., Deneen, B., Liang, H., Bassik, M. C., Bhattacharya, A., Brennan, K., Curtis, C., Gevaert, O., Ji, H. P., Karlsson, K. A., Karagyozova, K., Lo, Y., Liu, K., Nakano, M., Sathe, A., Smith, A. R., Spees, K., Wong, W. H., Yuki, K., Hangauer, M., Kaufman, D. S., Balmain, A., Bollam, S. R., Chen, W., Fan, Q., Kersten, K., Krummel, M., Li, Y. R., Menard, M., Nasholm, N., Schmidt, C., Serwas, N. K., Yoda, H. 2021; 184 (5): 1142–55


    The characterization of cancer genomes has provided insight into somatically altered genes across tumors, transformed our understanding of cancer biology, and enabled tailoring of therapeutic strategies. However, the function of most cancer alleles remains mysterious, and many cancer features transcend their genomes. Consequently, tumor genomic characterization does not influence therapy for most patients. Approaches to understand the function and circuitry of cancer genes provide complementary approaches to elucidate both oncogene and non-oncogene dependencies. Emerging work indicates that the diversity of therapeutic targets engendered by non-oncogene dependencies is much larger than the list of recurrently mutated genes. Here we describe a framework for this expanded list of cancer targets, providing novel opportunities for clinical translation.

    View details for DOI 10.1016/j.cell.2021.02.020

    View details for PubMedID 33667368

  • Single Cell Analysis Can Define Distinct Evolution of Tumor Sites in Follicular Lymphoma. Blood Haebe, S. E., Shree, T. n., Sathe, A. n., Day, G. n., Czerwinski, D. K., Grimes, S. n., Lee, H. n., Binkley, M. S., Long, S. R., Martin, B. A., Ji, H. P., Levy, R. n. 2021


    Tumor heterogeneity complicates biomarker development and fosters drug resistance in solid malignancies. In lymphoma, our knowledge of site-to-site heterogeneity and its clinical implications is still limited. Here, we profiled two nodal, synchronously-acquired tumor samples from ten follicular lymphoma patients using single cell RNA, B cell receptor (BCR) and T cell receptor sequencing, and flow cytometry. By following the rapidly mutating tumor immunoglobulin genes, we discovered that BCR subclones were shared between the two tumor sites in some patients, but in many patients the disease had evolved separately with limited tumor cell migration between the sites. Patients exhibiting divergent BCR evolution also exhibited divergent tumor gene expression and cell surface protein profiles. While the overall composition of the tumor microenvironment did not differ significantly between sites, we did detect a specific correlation between site-to-site tumor heterogeneity and T follicular helper (Tfh) cell abundance. We further observed enrichment of particular ligand-receptor pairs between tumor and Tfh cells, including CD40 and CD40LG, and a significant correlation between tumor CD40 expression and Tfh proliferation. Our study may explain discordant responses to systemic therapies, underscores the difficulty of capturing a patient's disease with a single biopsy, and furthers our understanding of tumor-immune networks in follicular lymphoma.

    View details for DOI 10.1182/blood.2020009855

    View details for PubMedID 33728464

  • Identify biomarkers associated with immunotoxicities using single-cell RNAseq. Chen, J., Pflieger, L., Sathe, A., Grimes, S., Brems, M., Pattison, T., Christensen, B., Rhodes, T., Ji, H. AMER ASSOC CANCER RESEARCH. 2020: 32
  • Joint single cell DNA-seq and RNA-seq of gastric cancer cell lines reveals rules of in vitro evolution. NAR genomics and bioinformatics Andor, N. n., Lau, B. T., Catalanotti, C. n., Sathe, A. n., Kubit, M. n., Chen, J. n., Blaj, C. n., Cherry, A. n., Bangs, C. D., Grimes, S. M., Suarez, C. J., Ji, H. P. 2020; 2 (2): lqaa016


    Cancer cell lines are not homogeneous nor are they static in their genetic state and biological properties. Genetic, transcriptional and phenotypic diversity within cell lines contributes to the lack of experimental reproducibility frequently observed in tissue-culture-based studies. While cancer cell line heterogeneity has been generally recognized, there are no studies which quantify the number of clones that coexist within cell lines and their distinguishing characteristics. We used a single-cell DNA sequencing approach to characterize the cellular diversity within nine gastric cancer cell lines and integrated this information with single-cell RNA sequencing. Overall, we sequenced the genomes of 8824 cells, identifying between 2 and 12 clones per cell line. Using the transcriptomes of more than 28 000 single cells from the same cell lines, we independently corroborated 88% of the clonal structure determined from single cell DNA analysis. For one of these cell lines, we identified cell surface markers that distinguished two subpopulations and used flow cytometry to sort these two clones. We identified substantial proportions of replicating cells in each cell line, assigned these cells to subclones detected among the G0/G1 population and used the proportion of replicating cells per subclone as a surrogate of each subclone's growth rate.

    View details for DOI 10.1093/nargab/lqaa016

    View details for PubMedID 32215369

    View details for PubMedCentralID PMC7079336

  • Single cell genomic characterization reveals the cellular reprogramming of the gastric tumor microenvironment. Clinical cancer research : an official journal of the American Association for Cancer Research Sathe, A. n., Grimes, S. M., Lau, B. T., Chen, J. n., Suarez, C. n., Huang, R. J., Poultsides, G. A., Ji, H. P. 2020


    The tumor microenvironment (TME) consists of a heterogenous cellular milieu that can influence cancer cell behavior. Its characteristics havean impact on treatments such as immunotherapy. These features can be revealed with single-cell RNA sequencing (scRNA-seq). We hypothesized that scRNA-seq analysis ofgastric cancer (GC) together with paired normal tissue and peripheral blood mononuclear cells (PBMCs) would identify critical elements of cellular deregulation not apparent with other approaches.scRNA-seq was conducted on seven patients with GC and one patient with intestinal metaplasia. We sequenced 56,167 cells comprising GC (32,407 cells), paired normal tissue (18,657 cells) and PBMCs (5,103 cells). Protein expression was validated by multiplex immunofluorescence.Tumor epithelium had copy number alterations, a distinct gene expression program from normal, with intra-tumor heterogeneity. GC TME was significantly enriched for stromal cells, macrophages, dendritic cells (DCs) and Tregs. TME-exclusive stromal cells expressed distinct extracellular matrix components than normal. Macrophages were transcriptionally heterogenous and did not conform to a binary M1/M2 paradigm. Tumor-DCs had a unique gene expression program compared to PBMC DCs. TME-specific cytotoxic T cells were exhausted with two heterogenous subsets. Helper, cytotoxic T, Treg and NK cells expressed multiple immune checkpoint or costimulatory molecules. Receptor-ligand analysis revealed TME-exclusive inter-cellular communication.Single-cell gene expression studies revealed widespread reprogramming across multiple cellular elements in the GC TME. Cellular remodeling was delineated by changes in cell numbers, transcriptional states and inter-cellular interactions. This characterization facilitates understanding of tumor biology and enables identification of novel targets including for immunotherapy.

    View details for DOI 10.1158/1078-0432.CCR-19-3231

    View details for PubMedID 32060101

  • Site to Site Comparison of Follicular Lymphoma Biopsies By Single Cell RNA Sequencing Haebe, S., Shree, T., Sathe, A., Day, G., Lee, H., Czerwinski, D. K., Grimes, S., Ji, H., Levy, R. AMER SOC HEMATOLOGY. 2019
  • Dynamic Immune Modulation Seen By Single Cell RNA-Sequencing of Serial Lymphoma Biopsies in Patients Undergoing in Situ Vaccination Shree, T., Haebe, S., Sathe, A., Day, G., Lee, H., Czerwinski, D. K., Grimes, S., Ji, H., Levy, R. AMER SOC HEMATOLOGY. 2019
  • Functional genomics identifies predictive markers and clinically actionable resistance mechanisms to CDK4/6 inhibition in bladder cancer JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH Tong, Z., Sathe, A., Ebner, B., Qi, P., Veltkamp, C., Gschwend, J. E., Holm, P., Nawroth, R. 2019; 38: 322


    CDK4/6 inhibitors are a promising treatment strategy in tumor therapy but are hampered by resistance mechanisms. This study was performed to reveal predictive markers, mechanisms of resistance and to develop rational combination therapies for a personalized therapy approach in bladder cancer.A genome-scale CRISPR-dCas9 activation screen for resistance to the CDK4/6 inhibitor Palbociclib was performed in the bladder cancer derived cell line T24. sgRNA counts were analyzed using next generation sequencing and MAGeCK-VISPR. Significantly enriched sgRNAs were cloned and validated on a molecular and functional level for mediating resistance to Palbociclib treatment. Analysis was done in vitro and in vivo in the chorioallantois membrane model of the chicken embryo. Comparison of screen hits to signaling pathways and clinically relevant molecular alterations was performed using DAVID, Reactome, DGIdb and cBioPortal.In the screen, 1024 sgRNAs encoding for 995 genes were significantly enriched indicative of mediators of resistance. 8 random sgRNAs were validated, revealing partial rescue to Palbociclib treatment. Within this gene panel, members of Receptor-Tyrosine Kinases, PI3K-Akt, Ras/MAPK, JAK/STAT or Wnt signaling pathways were identified. Combination of Palbociclib with inhibitors against these signaling pathways revealed beneficial effects in vitro and in in vivo xenografts.Identification of potential predictive markers, resistance mechanisms and rational combination therapies could be achieved by applying a CRISPR-dCas9 screening approach in bladder cancer.

    View details for DOI 10.1186/s13046-019-1322-9

    View details for Web of Science ID 000476806800002

    View details for PubMedID 31331377

    View details for PubMedCentralID PMC6647307

  • Single cell RNA sequencing of serial tumor and blood biopsies from lymphoma patients undergoing in situ vaccination Shree, T., Sathe, A., Ji, H., Levy, R. AMER ASSOC CANCER RESEARCH. 2019
  • Comprehensive characterization of gastric cancer at single-cell resolution Chen, J., Sathe, A., Grimes, S., Greer, S., Lau, B., Renschler, A., Poultsides, G., Suarez, C., Ji, H. AMER ASSOC CANCER RESEARCH. 2019
  • scPred: accurate supervised method for cell-type classification from single-cell RNA-seq data. Genome biology Alquicira-Hernandez, J. n., Sathe, A. n., Ji, H. P., Nguyen, Q. n., Powell, J. E. 2019; 20 (1): 264


    Single-cell RNA sequencing has enabled the characterization of highly specific cell types in many tissues, as well as both primary and stem cell-derived cell lines. An important facet of these studies is the ability to identify the transcriptional signatures that define a cell type or state. In theory, this information can be used to classify an individual cell based on its transcriptional profile. Here, we present scPred, a new generalizable method that is able to provide highly accurate classification of single cells, using a combination of unbiased feature selection from a reduced-dimension space, and machine-learning probability-based prediction method. We apply scPred to scRNA-seq data from pancreatic tissue, mononuclear cells, colorectal tumor biopsies, and circulating dendritic cells and show that scPred is able to classify individual cells with high accuracy. The generalized method is available at

    View details for DOI 10.1186/s13059-019-1862-5

    View details for PubMedID 31829268

  • Single Cell RNA Sequencing of Serial Tumor and Blood Biopsies from Lymphoma Patients on an in Situ Vaccination Clinical Trial Shree, T., Sathe, A., Czerwinski, D. K., Long, S. R., Ji, H., Levy, R. AMER SOC HEMATOLOGY. 2018
  • Targeting the PI3K/AKT/mTOR Pathway in Bladder Cancer. Methods in molecular biology (Clifton, N.J.) Sathe, A., Nawroth, R. 2018; 1655: 335-350


    The PI3K/AKT/mTOR signaling pathway shows frequent molecular alterations and increased activity in cancer. Given its role in the regulation of cell growth, survival and metastasis, molecules within this pathway are promising targets for pharmacologic intervention. Metastatic bladder cancer (BLCA) continues to have few treatment options. Although various molecular alterations in PI3K/AKT/mTOR signaling have been described in BLCA, clinical trials with small molecule inhibitors have not met their endpoints. In this article, we summarize results from preclinical studies and clinical trials that examined PI3K pathway inhibitors in BLCA focusing on technical challenges that might result in contradictory findings in preclinical studies. Based on published data from our group, we also address challenges that need to be overcome to optimize PI3K inhibition in BLCA and enable its successful translation into the clinic.

    View details for DOI 10.1007/978-1-4939-7234-0_23

    View details for PubMedID 28889395

  • Characterization of colorectal liver metastasis at single-cell resolution reveals dynamic interplay in the tumor microenvironment Sathe, A., Chen, J., Wood-Bouwens, C., Almeda, A., Lau, B., Grimes, S. M., Poultsides, G. A., Ji, H. AMER ASSOC CANCER RESEARCH. 2018
  • Integrated single-cell DNA and RNA analysis of intratumoral heterogeneity and immune lineages in colorectal and gastric tumor biopsies Lau, B., Andor, N., Sathe, A., Wood-Bouwens, C., Poultsides, G., Ji, H. AMER ASSOC CANCER RESEARCH. 2018
  • Parallel PI3K, AKT and mTOR inhibition is required to control feedback loops that limit tumor therapy. PloS one Sathe, A., Chalaud, G., Oppolzer, I., Wong, K. Y., von Busch, M., Schmid, S. C., Tong, Z., Retz, M., Gschwend, J. E., Schulz, W. A., Nawroth, R. 2018; 13 (1): e0190854


    Targeting the PI3K pathway has achieved limited success in cancer therapy. One reason for the disappointing activity of drugs that interfere with molecules that are important player in this pathway is the induction of multiple feedback loops that have been only partially understood. To understand these limitations and develop improved treatment strategies, we comprehensively characterized molecular mechanisms of PI3K pathway signaling in bladder cancer cell lines upon using small molecule inhibitors and RNAi technologies against all key molecules and protein complexes within the pathway and analyzed functional and molecular consequences. When targeting either mTORC1, mTOR, AKT or PI3K, only S6K1 phosphorylation was affected in most cell lines examined. Dephosphorylation of 4E-BP1 required combined inhibition of PI3K and mTORC1, independent from AKT, and resulted in a robust reduction in cell viability. Long-term inhibition of PI3K however resulted in a PDK1-dependent, PIP3 and mTORC2 independent rephosphorylation of AKT. AKT rephosphorylation could also be induced by mTOR or PDK1 inhibition. Combining PI3K/mTOR inhibitors with AKT or PDK1 inhibitors suppressed this rephosphorylation, induced apoptosis, decreased colony formation, cell viability and growth of tumor xenografts. Our findings reveal novel molecular mechanisms that explain the requirement for simultaneous targeting of PI3K, AKT and mTORC1 to achieve effective tumor growth inhibition.

    View details for DOI 10.1371/journal.pone.0190854

    View details for PubMedID 29357370

  • Applying the chicken embryo chorioallantoic membrane assay to study treatment approaches in urothelial carcinoma. Urologic oncology Skowron, M. A., Sathe, A., Romano, A., Hoffmann, M. J., Schulz, W. A., van Koeveringe, G. A., Albers, P., Nawroth, R., Niegisch, G. 2017


    Rapid development of novel treatment options demands valid preclinical screening models for urothelial carcinoma (UC). The translational value of high-throughput drug testing using 2-dimensional (2D) cultures is limited while for xenograft models handling efforts and costs often become prohibitive for larger-scale drug testing. Therefore, we investigated to which extent the chicken chorioallantoic membrane (CAM) assay might provide an alternative model to study antineoplastic treatment approaches for UC.The ability of 8 human UC cell lines (UCCs) to form tumors after implantation on CAMs was investigated. Epithelial-like RT-112 and mesenchymal-like T-24 UCCs in cell culture or as CAM tumors were treated with cisplatin alone or combined with histone deacetylase inhibitors (HDACi) romidepsin and suberanilohydroxamic acid. Tumor weight, size, and bioluminescence activity were monitored; tumor specimens were analyzed by histology and immunohistochemistry. Western blotting and quantitative real time polymerase chain reaction were used to measure protein and mRNA expression.UCCs were reliably implantable on the CAM, but tumor development varied among cell lines. Expression of differentiation markers (E-cadherin, vimentin, CK5, CK18, and CK20) was similar in CAM tumors and 2D cultures. Cellular phenotypes also remained stable after recultivation of CAM tumors in 2D cultures. Bioluminescence images correlated with tumor weight. Cisplatin and HDACi decreased weight and growth of CAM tumors in a dose-dependent manner, but HDACi treatment acted less efficiently as in 2D cultures, especially on its typically associated molecular markers. Synergistic effects of HDACi and subsequent cisplatin treatment on UCCs were neither detected in 2D cultures nor detected in CAM tumors.Our results demonstrate that the CAM assay is a useful tool for studying tumor growth and response to conventional anticancer drugs under 3D conditions, especially cytotoxic drugs as cisplatin. With some limitations, it might serve as a cost- and time-effective preclinical screening assay for novel therapeutic approaches before further assessment in expensive and cumbersome animal models.

    View details for DOI 10.1016/j.urolonc.2017.05.003

    View details for PubMedID 28551413

  • Wntless promotes bladder cancer growth and acts synergistically as a molecular target in combination with cisplatin. Urologic oncology Schmid, S. C., Sathe, A., Guerth, F., Seitz, A. K., Heck, M. M., Maurer, T., Schwarzenböck, S. M., Krause, B. J., Schulz, W. A., Stoehr, R., Gschwend, J. E., Retz, M., Nawroth, R. 2017


    To analyze the contribution of Wnt signaling pathway to bladder cancer growth in order to identify suitable target molecules for therapy.Expression of Wnt 2/4/7, LRP5/6, TCF1/2/4, LEF-1, and β-actin was detected by reverse transcription polymerase chain reaction in a panel of 9 and for Wntless (WLS) in 17 bladder cancer cell lines. Protein expression of WLS was detected in 6 cell lines. Wnt/β-catenin activity was analyzed using the TOPflash/FOPflash luciferase reporter assay. Expression level of β-catenin, WIF1, Dickkopf proteins (DKK), HSulf-2, sFRP4, and WLS was modulated by transfecting or infecting cells transiently or stably with respective shRNAs, siRNAs, or cDNAs. For protein detection, whole cell lysates were applied to sodium dodecyl sulfate polyacrylamide gel electrophoresis followed by immunoblots. Effects on cell growth were determined by cell viability assays and BrdU/APC incorporation/staining. For 3-dimensional tumor growth, the chicken chorioallantoic membrane model was used. Tumor growth was characterized by weight.Expression of molecular components and activation of the Wnt signaling pathway could be detected in all cell lines. Expression level of β-catenin, WIF1, DKK, WLS, and HSulf-2 influenced Wnt activity. Expression of WLS was confirmed in 17 cell lines by reverse transcription polymerase chain reaction and in 6 cell lines by immunoblotting. WLS positively regulates Wnt signaling, cell proliferation, and tumor growth in vitro and in vivo. These effects could be reversed by the expression of the Wnt antagonist WIF1 and DKK. Synergistic activity of cisplatin and WLS inactivation by genetic silencing could be observed on cell viability.The Wnt signaling pathway is ubiquitously activated in bladder cancer and regulates tumor growth. WLS might be a target protein for novel therapies in combination with established chemotherapy regimens.

    View details for DOI 10.1016/j.urolonc.2017.04.015

    View details for PubMedID 28501564

  • CDK4/6 Inhibitors in Cancer Therapy: A Novel Treatement Strategy for Bladder Cancer. Bladder cancer (Amsterdam, Netherlands) Pan, Q., Sathe, A., Black, P. C., Goebell, P. J., Kamat, A. M., Schmitz-Draeger, B., Nawroth, R. 2017; 3 (2): 79-88


    Patients with metastatic bladder cancer (mBC) treated with cisplatin-based chemotherapy have a limited median survival of only around 14 months [1]. Despite over 30 years of basic and clinical research, until recently no therapeutic options beyond cisplatin-based therapy had entered clinical routine and, at least in the US, none of the tested agents had been approved for second-line treatment. This has changed with the advent of immune checkpoint blockade, including especially PD-1/PD-L1 inhibitors. The high response rates of 24% over a 14.4 month follow up led to the first US Food and Drug Administration (FDA) approval for a second line therapy for these patients, and it is likely that this marks the beginning of a new era in the systemic treatment of muscle-invasive bladder cancer [2-4]. The strong clinical need to improve the medical management of this disease for those patients, not responding to current therapy has led to an increased molecular understanding of bladder cancer and has forstered the development of many potential molecular manipulations and targeted strategies beyond the new immune-oncologic approaches. Among the molecular alterations indentified in bladder cancer, cell cycle deregulation appears to be a key driver of disease progression. Target-directed therapy against CDK4/6 is an emerging strategy to regain control of cell cycle deregulation. Here, we provide an overview of the current status of CDK4/6 inhibitors in cancer therapy, their potential use in mBC and the challenges for their clinical use.

    View details for DOI 10.3233/BLC-170105

    View details for PubMedID 28516152

  • CDK4/6 Inhibition Controls Proliferation of Bladder Cancer and Transcription of RB1 JOURNAL OF UROLOGY Sathe, A., Koshy, N., Schmid, S. C., Thalgott, M., Schwarzenboeck, S. M., Krause, B. J., Holm, P. S., Gschwend, J. E., Retz, M., Nawroth, R. 2016; 195 (3): 771-779


    The retinoblastoma signaling network is frequently altered in advanced bladder cancer. We investigated the potential of CDK4/6 as a therapeutic target and determined biomarkers for patient stratification.Genetic alterations were analyzed using public databases, including TCGA (The Cancer Genome Atlas), COSMIC (Catalogue of Somatic Mutations in Cancer) and CCLE (Cancer Cell Line Encyclopedia). Effects of the CDK4/6-inhibitor PD-0332991 or LY2835219 were examined in 10 bladder cancer cell lines by immunoblot, cell viability, apoptosis and cell cycle progression. Efficacy of the PD-0332991 and cisplatin combination was analyzed using the combination index. Gene expression level was determined by quantitative polymerase chain reaction. Cytomegalovirus promoter regulated recombinant retinoblastoma was used for reconstitution. Three-dimensional xenografts were grown on chicken chorioallantoic membrane and analyzed by measuring tumor weight and immunohistochemical expression of total retinoblastoma and Ki-67.PD-0332991 treatment decreased the proliferation of retinoblastoma positive bladder cancer cell lines and was synergistic in combination with cisplatin. PD-0332991 or LY2835219 treatment decreased the phosphorylation, total protein and transcript level of retinoblastoma. Treatment resulted in a decrease in E2F target gene expression (CCNA2 and CCNE2) and cell cycle progression from G0/G1 to the S-phase but did not affect apoptosis. In retinoblastoma negative cells reconstituted with recombinant retinoblastoma PD-0332991 affected only phosphorylation and not the total retinoblastoma level. These cells remained resistant to treatment. In 3-dimensional retinoblastoma xenografts, treatment resulted in reduced tumor weight and decreased expression of total retinoblastoma and Ki-67.We provide preclinical evidence that CDK4/6 inhibition is a potential therapeutic strategy for retinoblastoma positive bladder cancer that probably acts by negatively regulating retinoblastoma transcription.

    View details for DOI 10.1016/j.juro.2015.08.082

    View details for Web of Science ID 000370054500090

    View details for PubMedID 26318986

  • Mutant PIK3CA controls DUSP1-dependent ERK 1/2 activity to confer response to AKT target therapy BRITISH JOURNAL OF CANCER Sathe, A., Guerth, F., Cronauer, M. V., Heck, M. M., Thalgott, M., Gschwend, J. E., Retz, M., Nawroth, R. 2014; 111 (11): 2103-2113


    Alterations in the phosphoinositide 3-kinase/AKT/mammalian target of rapamycin (PI3K/AKT/mTOR) signalling pathway are frequent in urothelial bladder cancer (BLCA) and thus provide a potential target for novel therapeutic strategies. We investigated the efficacy of the AKT inhibitor MK-2206 in BLCA and the molecular determinants that predict therapy response.Biochemical and functional effects of the AKT inhibitor MK-2206 were analysed on a panel of 11 BLCA cell lines possessing different genetic alterations. Cell viability (CellTiter-Blue, cell counts), apoptosis (caspase 3/7 activity) and cell cycle progression (EdU incorporation) were analysed to determine effects on cell growth and proliferation. cDNA or siRNA transfections were used to manipulate the expression of specific proteins such as wild-type or mutant PIK3CA, DUSP1 or CREB. For in vivo analysis, the chicken chorioallantoic membrane model was utilised and tumours were characterised by weight and biochemically for the expression of Ki-67 and AKT phosphorylation.Treatment with MK-2206 suppressed AKT and S6K1 but not 4E-BP1 phosphorylation in all cell lines. Functionally, only cell lines bearing mutations in the hotspot helical domain of PIK3CA were sensitive to the drug, independent of other genetic alterations in the PI3K or MAPK signalling pathway. Following MK-2206 treatment, the presence of mutant PIK3CA resulted in an increase in DUSP1 expression that induced a decrease in ERK 1/2 phosphorylation. Manipulating the expression of mutant or wild-type PIK3CA or DUSP1 confirmed that this mechanism is responsible for the induction of apoptosis and the inhibition of tumour proliferation in vitro and in vivo, to sensitise cells to AKT target therapy.Conclusion or interpretation:PIK3CA mutations confer sensitivity to AKT target therapy in BLCA by regulating DUSP1 expression and subsequent ERK1/2 dephosphorylation and can potentially serve as a stratifying biomarker for treatment.

    View details for DOI 10.1038/bjc.2014.534

    View details for Web of Science ID 000345597700010

    View details for PubMedID 25349966

    View details for PubMedCentralID PMC4260039