High-throughput CRISPR-mediated 3D enrichment platform for functional interrogation of chemotherapeutic resistance

Cancer is a disease of somatic mutations. These cellular mutations compete to dominate their microenvironment and dictate the disease outcome. While a therapeutic approach to target-specific oncogenic driver mutations helps to manage the disease, subsequent molecular evolution of tumor cells threatens to overtake therapeutic progress. There is a need for rapid, high-throughput, unbiased in vitro discovery screening platforms that capture the native complexities of the tumor and rapidly identify mutations that confer chemotherapeutic drug resistance. Taking the example of the CDK4/6 inhibitor (CDK4/6i) class of drugs, we show that the pooled in vitro CRISPR screening platform enables rapid discovery of drug resistance mutations in a three-dimensional (3D) setting. Gene-edited cancer cell clones assembled into an organotypic multicellular tumor spheroid (MCTS), exposed to CDK4/6i caused selection and enrichment of the most drug-resistant phenotypes, detectable by next-gen sequencing after a span of 28 days. The platform was sufficiently sensitive to enrich for even a single drug-resistant cell within a large, drug-responsive complex 3D tumor spheroid. The genome-wide 3D CRISPR-mediated knockout screen (>18,000 genes) identified several genes whose disruptions conferred resistance to CDK4/6i. Furthermore, multiple novel candidate genes were identified as top hits only in the microphysiological 3D enrichment assay platform and not the conventional 2D assays. Taken together, these findings suggest that including phenotypic 3D resistance profiling in decision trees could improve discovery and reconfirmation of drug resistance mechanisms and afford a platform for exploring noncell autonomous interactions, selection pressures, and clonal competition.

Abstract 310: Immunophenotyping tumors by novel multiplex immunofluorescence and AQUA (Automated Quantitative Analyses) algorithms to guide development of immunotherapies

Purpose: Deeper understanding of immune landscape of the tumor microenvironment is critical for exploring and development of next generation immunotherapies. Multiplex fluorescence immunohistochemistry (mFIHC) combined with hypothesis driven spatial profiling algorithms (e.g., AQUA Technology) was found to provide the most powerful predictors of immunotherapies in a systematic meta-analyses of over 8000 patients treated with PD1/L1 pathway blockers (Lu et al., JAMA Oncol 2019).

Study Design: To guide clinical development of next generation and/or combination immunotherapies, we built four novel mFIHC assays to simultaneously explore presence of major immune cell lineages, their spatial relationships and functional attributes. The first assay incorporates antibodies to identify major immune cells lineages (e.g., T-, B-, NK-/T- and subtypes of myeloid cells), the second assay is designed to understand T-cell proliferation (via co-expression of Ki67) or suppression (via co-expression of FoxP3), the third method is focused on quantifying the expression of immune checkpoint inhibitors (e.g., LAG3, PD1 and PD-L1), while, the final assay is designed to explore the IFNγ mediated adaptive resistance and immunosuppression (via co-expression of HLA-DR and IDO1). We will describe the successful development of these clinical grade mFIHC assays that utilize automated staining (Leica Bond RX), imaging (Vectra Polaris) and analyses (AQUA® Technology) workflows on tissue microarrays (TMAs) representing multiple regions of interest including tumor, tumor margin, tumor-associated fibrosis, various adjacent normal tissues, lymphoid structures and/or associated inflammation, and metastatic lesions collected from 100 colorectal, and pancreatic cancer patients.

Results: Sensitivity, accuracy and specificity were confirmed for all mFIHC assays on known positive and negative controls. Excellent reproducibility (less than 35% CV) and precision were observed across instruments, operators and independent experiments for all markers. TMA work is underway and the latest results will be presented.

Conclusion: The validated mFIHC assays helped classify unique immune phenotypes and their interactions. These assays, combined with comprehensive selection of tissues from the tumor microenvironment across multiple cancer subtypes, are expected to enable clinical development of next generation cancer therapies.

Citation Format: Ju Young Kim, John Hoerter, Nathan Roscoe, John Fathman, James Santos, Lori Iaconis, Justin Santos, Minhua Qiu, Jacob Levy, Valerie Tolley, Emmanuel Pacia, Tom Carolan, Xun Li, Patrizia Barzaghi-Rinaudo, Brian Schwartz, Robbin Newlin, Karyn Colman, Andy Schumacher, Deborah Knee, Steven Bender, Margaret McLaughlin, Alexander Savchenko, Thai Tran, Shabnam Tangri, Naveen Dakappagari, Jennifer Bordeaux. Immunophenotyping tumors by novel multiplex immunofluorescence and AQUA (Automated Quantitative Analyses) algorithms to guide development of immunotherapies [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 310.

RAGE, carboxylated glycans and S100A8/A9 play essential roles in colitis-associated carcinogenesis

Patients with inflammatory bowel diseases are at increased risk for colorectal cancer, but the molecular mechanisms linking inflammation and cancer are not well defined. We earlier showed that carboxylated N-glycans expressed on receptor for advanced glycation end products (RAGE) and other glycoproteins mediate colitis through activation of nuclear factor kappa B (NF-κB). Because NF-κB signaling plays a critical role in the molecular pathogenesis of colitis-associated cancer (CAC), we reasoned that carboxylated glycans, RAGE and its ligands might promote CAC. Carboxylated glycans are expressed on a subpopulation of RAGE on colon cancer cells and mediate S100A8/A9 binding to RAGE. Colon tumor cells express binding sites for S100A8/A9 and binding leads to activation of NF-κB and tumor cell proliferation. Binding, downstream signaling and tumor cell proliferation are blocked by mAbGB3.1, an anti-carboxylate glycan antibody, and by anti-RAGE. In human colon tumor tissues and in a mouse model of CAC, we found that myeloid progenitors expressing S100A8 and S100A9 infiltrate regions of dysplasia and adenoma. mAbGB3.1 administration markedly reduces chronic inflammation and tumorigenesis in the mouse model of CAC and RAGE-deficient mice are resistant to the onset of CAC. These findings show that RAGE, carboxylated glycans and S100A8/A9 play essential roles in tumor–stromal interactions, leading to inflammation-associated colon carcinogenesis.

Carboxylated glycans mediate colitis through activation of NF-kappa B

The role of carbohydrate modifications of glycoproteins in leukocyte trafficking is well established, but less is known concerning how glycans influence pathogenesis of inflammation. We previously identified a carboxylate modification of N-linked glycans that is recognized by S100A8, S100A9, and S100A12. The glycans are expressed on macrophages and dendritic cells of normal colonic lamina propria, and in inflammatory infiltrates in colon tissues from Crohn's disease patients. We assessed the contribution of these glycans to the development of colitis induced by CD4(+)CD45RB(high) T cell transfer to Rag1(-/-) mice. Administration of an anti-carboxylate glycan Ab markedly reduced clinical and histological disease in preventive and early therapeutic protocols. Ab treatment reduced accumulation of CD4(+) T cells in colon. This was accompanied by reduction in inflammatory cells, reduced expression of proinflammatory cytokines and of S100A8, S100A9, and receptor for advanced glycation end products. In vitro, the Ab inhibited expression of LPS-elicited cytokines and induced apoptosis of activated macrophages. It specifically blocked activation of NF-kappaB p65 in lamina propria cells of colitic mice and in activated macrophages. These results indicate that carboxylate-glycan-dependent pathways contribute to the early onset of colitis.

Changes in finances, insurance, employment, and lifestyle among persons diagnosed with hairy cell leukemia

BACKGROUND

While being cured of cancer generally leads to a life expectancy similar to that of the general population, the extent to which other aspects of life are affected is unknown. To address these concerns, patients with hairy cell leukemia, a cancer with a very high cure rate, were queried about employment, insurance, finances, and lifestyle during and following their treatment.

METHODS

Study participants (n = 31) ranging in age from 24 to 73 years at the time of diagnosis (median, 49 years) were surveyed regarding changes in health and life insurance, employment, out-of-pocket medical costs, exercise, diet, and use of mental and alternative health services that occurred during or following hairy cell leukemia treatment.

RESULTS

Following a diagnosis of hairy cell leukemia, 61.3% of the respondents paid for some aspect of medical care in spite of having health insurance coverage at the time of diagnosis. Four respondents (12.9%) could not obtain health insurance following treatment, and the occupational choices of several individuals or their spouses were based in large part on a desire to obtain or maintain comprehensive health insurance. Of the 13 individuals who attempted to purchase life insurance, 10 had difficulty obtaining a policy or were denied coverage. Lifestyle changes were noted by 40% to 60% of respondents, and included reports of more frequent exercise, adoption of a healthier diet, and having a greater appreciation for life, loved ones, and physical health.

CONCLUSIONS

While hairy cell leukemia is a highly curable malignancy, cancer survivors' lives and lifestyles are altered substantially after receiving treatment for the illness.