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Supplementary Table from Dissecting the Oncogenic Roles of Keratin 17 in the Hallmarks of Cancer

Endogenous expression of K17 in cervical cancer cell lines and knockdown efficiency by siRNAs and shRNAs against K17 in SiHa and CaSki cells (S1); K17 knockdown induces cell-cycle arrest at G1 (S2); K17 knockdown induces p27KIP1 nuclear accumulation (S3); p27KIP1-ubiquitin ligases expression is not altered by K17 knockdown (S4); K17 interacts with p27KIP1 in the nucleus (S5).

Comparison between discovery- and validation-datasets (S1); Comparison between the hazard ratio and survival probability estimated for the discovery, validation and combined datasets on K17 as a prognostic marker in squamous cell carcinomas of the cervix (S2); Primers and probes used for qRT-PCR (S3); Primary antibodies used for western blotting (S4); Failure hazard for cervical cancer patients stratified by K17 status, p27KIP1 status, and combined status using a Cox proportional hazards model (S5).

Video showing the proposed model: K17 promotes nuclear export and subsequent degradation of tumor-suppressor p27KIP1, promoting sustained proliferation and tumor growth.

There is an unmet need to identify and validate tumor-specific therapeutic targets to enable more effective treatments for cancer. Heterogeneity in patient clinical characteristics as well as biological and genetic features of tumors present major challenges for the optimization of therapeutic interventions, including the development of novel and more effective precision medicine. The expression of keratin 17 (K17) is a hallmark of the most aggressive forms of cancer across a wide range of anatomical sites and histological types. K17 correlates with shorter patient survival, predicts resistance to specific chemotherapeutic agents, and harbors functional domains that suggest it could be therapeutically targeted. Here, we explore the role of K17 in the hallmarks of cancer and summarize evidence to date for K17-mediated mechanisms involved in each hallmark, elucidating functional roles that warrant further investigation to guide the development of novel therapeutic strategies.

Pancreatic ductal adenocarcinoma (PDAC), the most common histological subtype of pancreatic cancer, has one of the highest case fatality rates of all known solid malignancies. Over the past decade, several landmark studies have established mutations in KRAS and TP53 as the predominant drivers of PDAC pathogenesis and therapeutic resistance, though treatment options for PDACs and other tumors with these mutations remain extremely limited. Hampered by late tumor discovery and diagnosis, clinicians are often faced with using aggressive and non-specific chemotherapies to treat advanced disease. Clinically meaningful responses to targeted therapy are often limited to the minority of patients with susceptible PDACs, and immunotherapies have routinely encountered roadblocks in effective activation of tumor-infiltrating immune cells. Alternative RNA splicing (ARS) has recently gained traction in the PDAC literature as a field from which we may better understand and treat complex mechanisms of PDAC initiation, progression, and therapeutic resistance. Here, we review PDAC pathogenesis as it relates to fundamental ARS biology, with an extension to implications for PDAC patient clinical management.

Keratin 17 (K17), an oncofetal intermediate filament protein, is one of the most abundantly expressed proteins in pancreatic ductal adenocarcinomas (PDACs) of the most aggressive molecular subtype. The mechanistic roles of this protein in malignancy, however, are largely unexplored. Here we show that K17 expression and disassembly enhances tumor growth and metastatic potential and shortens survival. Using mass spectrometry in K17 isolated from patient’s tumors, we identified a hotspot phosphorylation site in serines 10-13. Site-mutagenesis revealed that phosphorylation of this hotspot is sufficient to disassemble K17 and promote its nuclear translocation. In silico and pharmacologic inhibition studies uncovered the role of the PKC/MEK/RSK pathway in the phosphorylation and disassembly of K17. Murine models bearing tumors expressing phosphomimetic mutations at the serine hotspot displayed enhanced metastases, compared to mice bearing tumors expressing wild-type K17 or phosphorylation-resistant K17. Lastly, we found that detergent-soluble nuclear K17 promotes the expression of metastasis promoting genes in both patient and murine tumors. These results suggest that phosphorylation at specific serines is sufficient to promote pancreatic cancer metastasis and shorter survival, and that these sites could provide novel, druggable therapeutic domains to enhance PDAC patient survival.

Pancreatic ductal adenocarcinoma (PDAC) is a leading cause of cancer death. We previously reported keratin 17 (K17) as a novel negative prognostic and predictive biomarker, whose overexpression confers the resistance to chemotherapies. Here, we investigated the mechanisms of chemoresistance and tumor-specific vulnerabilities that can be exploited for targeted therapies for K17-expressing PDAC. Unbiased metabolomic studies in isogenic PDAC models identified several key metabolic pathways that are upregulated in the presence of K17. We demonstrate that K17 increases pyrimidine biosynthesis, a pathway that has been linked to chemoresistance. Patient dataset analysis revealed that K17 expression and enzymes involved in pyrimidine, but not purine, de novo biosynthesis is associated with shorter patient survival. Rescue experiments showed that deoxycytidine (dC) and deoxythymidine (dT) were sufficient to promote resistance to Gemcitabine (a dC analog) and 5-fluorouracil (a dT analog), respectively. Furthermore, K17-expressing cells were more sensitive to Brequinar, a specific inhibitor of dihydroorotate dehydrogenase (DHODH), the rate-limiting enzyme in de novo pyrimidine biosynthetic pathway. Targeting DHODH by small interfering RNA or by Brequinar with Gemcitabine synergistically inhibited the viability of K17-positive PDAC cells. Importantly, the combination of Gemcitabine and Brequinar significantly inhibited the growth of K17-expressing tumors and extended survival of mice bearing K17-expressing PDACs. Overall, we identified a novel pathway of chemoresistance and a metabolic target of which could lead to the development of a biomarker-based therapy for K17-expressing PDAC.

Pancreatic ductal adenocarcinoma (PDAC) is predicted to become the second leading cause of cancer‐related deaths in the United States by 2020, due in part to innate resistance to widely used chemotherapeutic agents and limited knowledge about key molecular factors that drive tumor aggression. We previously reported a novel negative prognostic biomarker, keratin 17 (K17), whose overexpression in cancer results in shortened patient survival. In this study, we aimed to determine the predictive value of K17 and explore the therapeutic vulnerability in K17‐expressing PDAC, using an unbiased high‐throughput drug screen. Patient‐derived data analysis showed that K17 expression correlates with resistance to gemcitabine (Gem). In multiple in vitro and in vivo models of PDAC, spanning human and murine PDAC cells, and orthotopic xenografts, we determined that the expression of K17 results in a more than twofold increase in resistance to Gem and 5‐fluorouracil, key components of current standard‐of‐care chemotherapeutic regimens. Furthermore, through an unbiased drug screen, we discovered that podophyllotoxin (PPT), a microtubule inhibitor, showed significantly higher sensitivity in K17‐positive compared to K17‐negative PDAC cell lines and animal models. In the clinic, another microtubule inhibitor, paclitaxel (PTX), is used in combination with Gem as a first‐line chemotherapeutic regimen for PDAC. Surprisingly, we found that when combined with Gem, PPT, but not PTX, was synergistic in inhibiting the viability of K17‐expressing PDAC cells. Importantly, in preclinical models, PPT in combination with Gem effectively decreased tumor growth and enhanced the survival of mice bearing K17‐expressing tumors. This provides evidence that PPT and its derivatives could potentially be combined with Gem to enhance treatment efficacy for the ~ 50% of PDACs that express high levels of K17. In summary, we reported that K17 is a novel target for developing a biomarker‐based personalized treatment for PDAC., Keratin 17, a signature gene overexpressed in the most lethal subtype of pancreatic ductal adenocarcinoma (PDAC), is both prognostic and predictive, and it directly promotes chemoresistance. We discover a novel therapeutic regimen that provides higher efficacy for Keratin 17‐expressing PDAC. These studies bring us closer to the frontline of translational research to develop a biomarker‐based targeted therapy for cancers.

Summary Keratin 17 (K17) has been established as a negative prognostic biomarker in cervical and ovarian cancers but has not previously been evaluated as a prognostic biomarker in endometrial adenocarcinoma. The association of K17 with decreased patient survival may be explained in part by the discovery that K17 drives tumor aggression by serving as a nuclear shuttle of p27, leading to cell cycle progression and tumor growth. The current study tests the hypothesis that K17 mRNA and protein levels correlate with decreased survival of patients with high-grade endometrial cancer. Gene expression data (mRNA) from The Cancer Genome Atlas were analyzed for 271 high-grade endometrial carcinomas and K17 immunohistochemistry (IHC) was performed on a separate cohort of 119 high-grade endometrial cancer cases from two academic medical centers. Survival analyses were determined by Cox proportional hazards regression. High K17 mRNA and IHC correlated with decreased overall survival (HR: 1.8, P = .0101, HR: 1.8, P = .0488, respectively). K17 was positive in malignant glandular cells of the endometrium but not in other tissues, including endometrial stroma, myometrium and uterine sarcoma. These results support the conclusion that K17 is a negative prognostic biomarker in high-grade endometrial carcinoma and that K17 IHC test results could be used to inform decisions related to therapeutic intervention.

SF3B1 is the most commonly mutated RNA splicing factor in cancer1–4, but the mechanisms by which SF3B1 mutations promote malignancy are poorly understood. Here we integrated pan-cancer splicing analyses with a positive-enrichment CRISPR screen to prioritize splicing alterations that promote tumorigenesis. We report that diverse SF3B1 mutations converge on repression of BRD9, which is a core component of the recently described non-canonical BAF chromatin-remodelling complex that also contains GLTSCR1 and GLTSCR1L5–7. Mutant SF3B1 recognizes an aberrant, deep intronic branchpoint within BRD9 and thereby induces the inclusion of a poison exon that is derived from an endogenous retroviral element and subsequent degradation of BRD9 mRNA. Depletion of BRD9 causes the loss of non-canonical BAF at CTCF-associated loci and promotes melanomagenesis. BRD9 is a potent tumour suppressor in uveal melanoma, such that correcting mis-splicing of BRD9 in SF3B1-mutant cells using antisense oligonucleotides or CRISPR-directed mutagenesis suppresses tumour growth. Our results implicate the disruption of non-canonical BAF in the diverse cancer types that carry SF3B1 mutations and suggest a mechanism-based therapeutic approach for treating these malignancies. A range of SF3B1 mutations promote tumorigenesis through the repression of BRD9, a core component of the non-canonical BAF complex, and correcting BRD9 mis-splicing in these SF3B1-mutant cells suppresses tumour growth.

Although the overall five-year survival of patients with pancreatic ductal adenocarcinoma (PDAC) is dismal, there are survival differences between cases with clinically and pathologically indistinguishable characteristics, suggesting that there are uncharacterized properties that drive tumor progression. Recent mRNA sequencing studies reported gene-expression signatures that define PDAC molecular subtypes that correlate with differences in survival. We previously identified Keratin 17 (K17) as a negative prognostic biomarker in other cancer types. Here, we set out to determine if K17 is as accurate as molecular subtyping of PDAC to identify patients with the shortest survival. K17 mRNA was analyzed in two independent PDAC cohorts for discovery (n = 124) and validation (n = 145). Immunohistochemical localization and scoring of K17 immunohistochemistry (IHC) was performed in a third independent cohort (n = 74). Kaplan-Meier and Cox proportional-hazard regression models were analyzed to determine cancer specific survival differences in low vs. high mRNA K17 expressing cases. We established that K17 expression in PDACs defines the most aggressive form of the disease. By using Cox proportional hazard ratio, we found that increased expression of K17 at the IHC level is also associated with decreased survival of PDAC patients. Additionally, within PDACs of advanced stage and negative surgical margins, K17 at both mRNA and IHC level is sufficient to identify the subgroup with the shortest survival. These results identify K17 as a novel negative prognostic biomarker that could inform patient management decisions.

Approximately, 70% of pancreatic ductal adenocarcinomas (PDACs) have mutations in the TP53 gene; however, it is still unknown if gain- or loss- of function mutations in TP53 provide differential prognostic value to guide therapy. To fill this gap, we assessed the potential effect of wild-type, missense (gain-of-function) and truncating (loss-of-function) TP53 mutations in patient survival, in two independent clinical cohorts (The Cancer Genome Atlas cohort=141, and the Memorial Sloan Kettering–Integrated Mutation Profiling of Actionable Cancer Targets cohort=376 PDACs). We employed multivariable Cox proportional hazards regression models adjusting for patient demographic (age at diagnosis, sex, race/ethnicity) and tumor characteristics (presence of distant metastasis at diagnosis). Additionally, we conducted stratified analyses by the status of “druggable” (DNA repair gene mutations) and other driver mutations (SMAD4 and CDKN2A genes). We found that PDACs with missense TP53 mutations were associated with a worse patient survival compared to tumors with wild-typeTP53 (HR = 1.47, 95% CI: 1.00-2.17; p=0.051). Similarly, patients with truncating mutations in TP53 had a trend to worse OS (HR=1.11, 95% CI, 0.70-1.76; p=0.654) compared to patients with wild-type TP53, however, these associations were not significant. Furthermore, we found that mutations in DNA repair genes, SMAD4 and CDKN2A genes did not show any prognostic value. Our findings suggest that molecular characterization of specific TP53 mutations may help to determine differences in patient prognosis and potentially guide future clinical management of patients. Citation Format: Carlos M. Mejia Arbelaez, Xining Shan, Tseng Robert, Marie E. Robert, Xiaomei Ma, Luisa F. Escobar-Hoyos. Prognostic effects of different TP53 mutations in pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr A024.

Background: Clinically and histologically identical pancreatic ductal adenocarcinomas (PDACs) differ in response to treatment, disease progression, and survival. Clinical trials are testing the use of either keratin 17 (K17) or GATA6 as surrogate prognostic and predictive biomarkers of PDAC. Still, there is a need to contrast their expression and prognostic value in the same cohort of cases. K17, a biomarker of the most aggressive subtype of PDAC, promotes tumor growth and chemoresistance. GATA6 is a transcription factor necessary for normal pancreatic development, and a surrogate marker of the classical subtype of PDAC, associated with longer-term survival. Our goal was to test the hypothesis that there is a reciprocal relationship between K17 and GATA6 expression and that their detection informs prognostic stratification. Methods: Stony Brook University Hospital PDAC patients were selected, and representative sections were processed for dual-staining by indirect immunoperoxidase methods using antibodies to K17 (KDx Diagnostics) and GATA6 (R&D Systems AF1700). Manual scoring of the proportion of cells with strong (2+) nuclear and/or cytoplasmic staining was determined for K17 versus nuclear staining for GATA6 (PathSQ). Automated image analysis of GATA6 expression was further scored using QuPath v0.3.2 on annotated PDAC sections. Cut-off values for the best COX model for each marker were established to stratify for survival. Results: K17 expression was observed in cancer epithelial cells and in few benign proliferative ducts of chronic pancreatitis but no staining was detected in stromal or acinar cells. By contrast, GATA6 was detected in the nuclei of most cancer epithelial cells and was also consistently detected in benign ductal cells, acinar cells, and stromal cells. Defining high K17 cases as those with staining in ≥10% of tumor cells, high K17 correlated with shorter overall survival (p=0.03), supporting its use as a negative prognostic biomarker. Due to the high level of expression of GATA6 in PDAC cells (range 60-100% of tumor cells across all cases), however, no threshold was found to provide prognostic value. By dual-color IHC, K17 positive cells almost always had strong GATA6 nuclear staining but GATA6 was also detected in all K17-negative tumor cells. Computational analysis demonstrated 98% concordance with manual scoring for high GATA6 and 90% concordance with manual scoring for low GATA6. Conclusions: GATA6 was expressed in most PDAC tumor cells, as well as in benign stromal and epithelial cells. However, K17 expression was focal, relatively tumor cell-specific, and was not detected in most benign cellular components. Although high K17 status identified cases with relatively short survival, a survival threshold for GATA6 could not be detected. Contradiction in our observations of GATA6 compared to previous reports could result from differences in case selection or immunohistochemical protocol. Thus, further work is needed to explore the relationship between K17 and GATA6 as complementary biomarkers of PDAC patient survival. Citation Format: Michael Horowitz, Lyanne Oblein, Jaymie Oentoro, Saumya Kasliwal, Natalia D. Marchenko, Luisa F. Escobar-Hoyos, Kenneth R. Shroyer. Comparison of keratin 17 and GATA6 as prognostic markers in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr B049.

Background: There is an urgent need to understand why patients with clinically and histologically identical pancreatic ductal adenocarcinomas (PDACs) differ in response to treatment, disease progression, and survival. Although two standard chemotherapies are available, predictive biomarkers to guide regimen selection have not been defined. We previously reported that keratin 17 (K17) expression is a hallmark of PDAC cases with shortest patient survival. Furthermore, K17, explored using in vitro and in vivo murine models, drives resistance to gemcitabine and 5-fluorouracil, the most common chemotherapeutic agents in the two chemotherapies. Here, we aimed to validate the prognostic value of K17 and to further explore its role as a predictive biomarker. Methods: We used a cohort of 305 cases, with localized disease and who had gone tumor resection. An indirect immunoperoxidase method was used to detect K17 expression on surgical specimens, as previously described. Survival was plotted using the Kaplan–Meier method and hazard ratios (HRs) were calculated using Cox proportional hazard regressions for both, overall survival (OS) and progression-free survival (PFS). Results: Patients in the high-K17 expression group had shorter overall survival [median=25 mo., HR=1.511, p=0.0338] than those in the low-K17 expression group (median=42 mo.). In addition, high K17 expression was associated with shorter median OS (p=0.0280) and PFS (p=0.0434) in patients who were treated with gemcitabine (GEM) or with Gemcitabine/nab-Paclitaxel (GEMTAX) therapy (OS p=0.1959, PFS p=0.0724), compared to low-K17 counterparts. When we further separated our cohort by K17 level of expression and compared GEM and GEMTAX responses, we found that patients with tumors with high K17 expression do not benefit from GEMTAX adjuvant therapy (p=0.0356). Of note, K17 expression within the responder group was significantly lower than in tumors within the non-responder group for both Gem and GEMTAX (p Citation Format: Lyanne Oblein, Lucia Roa-Peña, Sruthi Babu, Felicia D. Allard, Natalia D. Marchenko, Luisa F. Escobar-Hoyos, Kenneth R. Shroyer. Keratin 17 is a negative prognostic and predictive biomarker in pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr A042.

Background: Keratin 17 (K17) is a negative prognostic biomarker, overexpressed in the biologically most aggressive forms of pancreatic ductal adenocarcinoma (PDAC). In other anatomic sites and disease processes, K17 expression also correlates with immune cell infiltrates and could block T-cell infiltration. Thus, we hypothesized that K17 expression correlates with the inflammatory microenvironment in PDAC. In this study, we aimed to determine the relationship between the stromal immune cell infiltrates and K17 expression, using multiplexed immunohistochemistry (mIHC) and our suite of deep learning tools to quantitatively evaluate the expression of four biomarkers of T-cells and macrophages in PDAC. Methods: mIHC was performed on representative sections of 201 primary PDACs from Stony Brook University Hospital, Thomas Jefferson University Hospital, Cedars Sinai Medical Center, and from a national cohort (KYT, Pancreatic Cancer Action Network, and Perthera). Antibodies for CD4 (helper T-cells), CD8 (cytotoxic T-cells), CD16 (pan-macrophage), CD163 (M2 macrophages), pancytokeratin, and K17 were provided by Roche Diagnostics Corporation through a sponsored research agreement. mIHC was performed on a Discovery Ultra Autostainer (Roche), using horseradish peroxidase (HRP) and alkaline phosphatase (AP)-based protocols with multiple chromogens (Red: CD4, Purple: CD8, Yellow: CD16, Green: CD163, Teal: pancytokeratin, and Brown: K17) to enable multispectral imaging of diverse immune cell populations within the cancer microenvironment. A deep learning analysis workflow was used to detect and classify stromal inflammatory cells, in whole slide images (WSIs), generated using an Olympus VS120 digital microscope (Olympus, Tokyo, Japan). Pixel-wise predictions from a color auto-encoder (ColorAE) union UNET anchor UNET model were combined to create multi-class masks that were further analyzed to perform detection and classification. Results: The analysis of the inflammatory microenvironment focused on defining immune cell infiltrates located within 25 microns of the closest K17-positive versus K17-negative tumor cell in each representative section. Across the sum of K17-positive and negative zones/section, CD4 cell counts ranged from 0-10,617 (mean 2,709), CD8 cell counts ranged from 63-28,596 (mean 6,745), CD16 cell counts ranged from 4-7,797 (mean 3,024), and CD163 cell counts ranged from 35-34,696 (mean 14,968). CD4 T-helper cells, CD8 cytotoxic T cells, and CD16 macrophages were more numerous (respectively, p=0.0012; p= Citation Format: Lyanne Oblein, Michael Horowitz, Mahmudul Hasan, Sruthi Babu, Mariana Torrente-Goncalves, Lucia Roa, Jaymie Oentoro, Jason Harper, Xin Yao Zheng, Wei Jiang, Andrew Hendifar, Natalie Moshayedi, Brent Larson, Veronica Placencio-Hickok, Edik Blais, Emmanuel Petricoin, Joel Saltz, Natalia D. Marchenko, Luisa F. Escobar-Hoyos, Kenneth Shroyer. Keratin 17 excludes CD8-positive T cells and recruits CD163-positive macrophages in pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr C071.

Objectives The microscopic features of urine cytology specimens are subjective and may not reliably distinguish between benign urothelial cells and low-grade urothelial carcinoma (UC). Prior studies demonstrated that keratin 17 (K17) detection in biopsies is highly sensitive for UC. The current study aimed to define K17 diagnostic test performance for initial screening and detect recurrent UC in urine specimens. Methods K17 was detected by immunocytochemistry (ICC) in consecutively collected urine specimens (2018-2019). A qualitative score for the K17 test was determined in 81 samples (discovery cohort) and validated in 98 samples (validation cohort). K17 sensitivity and specificity were analyzed in both cohorts across all grades of UC. Results Based on the discovery cohort, the presence of 5 or more K17 immunoreactive urothelial cells (area under the curve = 0.90; P < .001) was the optimal threshold to define a K17-positive test. The sensitivity of the K17 ICC test for biopsy-confirmed UC was 35 of 36 (97%) and 18 of 21 (86%) in the discovery and validation cohorts, respectively. K17 was positive in 16 of 19 (84%) specimens with biopsy-confirmed low-grade UC and in 34 of 34 (100%) of specimens with high-grade UC. Conclusions K17 ICC is a highly sensitive diagnostic test for initial screening and detection of recurrence across all grades of UC.

Background Although pancreatic ductal adenocarcinoma (PDAC) has one of the lowest 5-year survival rates of all cancers, differences in survival exist between patients with clinically identical characteristics. The authors previously demonstrated that keratin 17 (K17) expression in PDAC, measured by RNA sequencing or immunohistochemistry (IHC), is an independent negative prognostic biomarker. Only 20% of cases are candidates for surgical resection, but most patients are diagnosed by needle aspiration biopsy (NAB). The aims of this study were to determine whether there was a correlation in K17 scores detected in matched NABs and surgical resection tissue sections and whether K17 IHC in NAB cell block specimens could be used as a negative prognostic biomarker in PDAC. Methods K17 IHC was performed for a cohort of 70 patients who had matched NAB cell block and surgical resection samples to analyze the correlation of K17 expression levels. K17 IHC was also performed in cell blocks from discovery and validation cohorts. Kaplan-Meier and Cox proportional hazards regression models were analyzed to determine survival differences in cases with different levels of K17 IHC expression. Results K17 IHC expression correlated in matched NABs and resection tissues. NAB samples were classified as high for K17 when ≥80% of tumor cells showed strong (2+) staining. High-K17 cases, including stage-matched cases, had shorter survival. Conclusions K17 has been identified as a robust and independent prognostic biomarker that stratifies clinical outcomes for cases that are diagnosed by NAB. Testing for K17 also has the potential to inform clinical decisions for optimization of chemotherapeutic interventions.

Pancreatic adenosquamous carcinoma (PASC) is an aggressive cancer whose mutational origins are poorly understood. An early study reported high-frequency somatic mutations affecting UPF1, a nonsense-mediated mRNA decay (NMD) factor, in PASC, but subsequent studies did not observe these lesions. The corresponding controversy about whether UPF1 mutations are important contributors to PASC has been exacerbated by a paucity of functional studies. Here, we modeled two UPF1 mutations in human and mouse cells to find no significant effects on pancreatic cancer growth, acquisition of adenosquamous features, UPF1 splicing, UPF1 protein, or NMD efficiency. We subsequently discovered that 45% of UPF1 mutations reportedly present in PASCs are identical to standing genetic variants in the human population, suggesting that they may be non-pathogenic inherited variants rather than pathogenic mutations. Our data suggest that UPF1 is not a common functional driver of PASC and motivate further attempts to understand the genetic origins of these malignancies., eLife digest Cancer is a group of complex diseases in which cells grow uncontrollably and spread into surrounding tissues and other parts of the body. All types of cancers develop from changes – or mutations – in the genes that affect the pathways involved in controlling the growth of cells. Different cancers possess unique sets of mutations that affect specific genes, and often, it is difficult to determine which of them play the most important role in a particular type of cancer. For example, pancreatic adenosquamous carcinoma, a rare and aggressive form of pancreatic cancer, is a devastating disease with a poor chance of survival – patients rarely live longer than one year after diagnosis. While the cells of this particular cancer display distinct features that separate them from other forms of pancreatic cancer, the genetic causes of these features are unclear. Using new technologies, some researchers have reported mutations in a ‘quality control’ gene called ‘UPF1’, which is responsible for destroying faulty forms of genetic material. However, subsequent studies did not find such mutations. To clarify the role of UPF1 in pancreatic adenosquamous carcinoma, Polaski et al. used mouse and human cancer cells with UPF1 mutations and monitored their effects on tumour growth and the development of features unique to this disease. Polaski et al. first injected mice with mouse pancreatic cancer cells containing mutations in UPF1 (mutated cells) and cancer cells without. Both groups of mice developed pancreatic tumours but there was no difference in tumour growth between the mutated and non-mutated cells, and neither cell type displayed distinct features. The researchers then generated human mutated cells, which were also found to lack any specific characteristics. Further analysis showed that the mutations did not stop UPF1 from working, in fact, over 40% of these mutations occurred naturally in humans without causing cancer. This suggests that UPF1 does not seem to be involved in pancreatic adenosquamous carcinoma. Further investigation is needed to illuminate key genetic players in the development of this type of cancer, which will be vital for improving treatments and outcomes for patients suffering from this disease.

An amendment to this paper has been published and can be accessed via the original article.

RNA splicing, the enzymatic process of removing segments of premature RNA to produce mature RNA, is a key mediator of proteome diversity and regulator of gene expression. Increased systematic sequencing of the genome and transcriptome of cancers has identified a variety of means by which RNA splicing is altered in cancer relative to normal cells. These findings, in combination with the discovery of recurrent change-of-function mutations in splicing factors in a variety of cancers, suggest that alterations in splicing are drivers of tumorigenesis. Greater characterization of altered splicing in cancer parallels increasing efforts to pharmacologically perturb splicing and early-phase clinical development of small molecules that disrupt splicing in patients with cancer. Here we review recent studies of global changes in splicing in cancer, splicing regulation of mitogenic pathways critical in cancer transformation, and efforts to therapeutically target splicing in cancer.

Pancreatic adenosquamous carcinoma (PASC) is a rare and aggressive subtype of pancreatic cancer whose mutational origins are poorly understood. An early study reported somatic mutations in UPF1, which encodes a core component of the nonsense-mediated mRNA decay (NMD) pathway, as a common signature of PASC, but subsequent studies did not observe these lesions in other PASC cohorts. The corresponding controversy about whether UPF1 mutations are important contributors to PASC has been exacerbated by a paucity of functional studies of these lesions. Here, we systematically assessed the potential roles of UPF1 mutations in PASC. We modeled two reported UPF1 mutations to find no consistent effects on pancreatic cancer growth, acquisition of adenosquamous features, UPF1 splicing, UPF1 protein levels, or NMD efficiency. We subsequently discovered that ~40% of UPF1 mutations reportedly present in PASCs are identical to standing genetic variation in the human population, suggesting that they are likely non-pathogenic inherited variation rather than pathogenic mutations. Our data suggest that UPF1 is not a common functional driver of PASC and motivate further attempts to identify unique genetic features defining these malignancies.

Background Multiplex immunohistochemistry (mIHC) permits the labeling of six or more distinct cell types within a single histologic tissue section. The classification of each cell type requires detection of uniquely colored chromogens localized to cells expressing biomarkers of interest. The most comprehensive and reproducible method to evaluate such slides is to employ digital pathology and image analysis pipelines to whole-slide images (WSIs). Our suite of deep learning tools quantitatively evaluates the expression of six biomarkers in mIHC WSIs. These methods address the current lack of readily available methods to evaluate more than four biomarkers and circumvent the need for specialized instrumentation to spectrally separate different colors. The use case application for our methods is a study that investigates tumor immune interactions in pancreatic ductal adenocarcinoma (PDAC) with a customized mIHC panel. Methods Six different colored chromogens were utilized to label T-cells (CD3, CD4, CD8), B-cells (CD20), macrophages (CD16), and tumor cells (K17) in formalin-fixed paraffin-embedded (FFPE) PDAC tissue sections. We leveraged pathologist annotations to develop complementary deep learning-based methods: (1) ColorAE is a deep autoencoder which segments stained objects based on color; (2) U-Net is a convolutional neural network (CNN) trained to segment cells based on color, texture and shape; and (3) ensemble methods that employ both ColorAE and U-Net, collectively referred to as ColorAE:U-Net. We assessed the performance of our methods using: structural similarity and DICE score to evaluate segmentation results of ColorAE against traditional color deconvolution; F1 score, sensitivity, positive predictive value, and DICE score to evaluate the predictions from ColorAE, U-Net, and ColorAE:U-Net ensemble methods against pathologist-generated ground truth. We then used prediction results for spatial analysis (nearest neighbor). Results We observed that (1) the performance of ColorAE is comparable to traditional color deconvolution for single-stain IHC images (note: traditional color deconvolution cannot be used for mIHC); (2) ColorAE and U-Net are complementary methods that detect six different classes of cells with comparable performance; (3) combinations of ColorAE and U-Net in ensemble methods outperform ColorAE and U-Net alone; and (4) ColorAE:U-Net ensemble methods can be employed for detailed analysis of the tumor microenvironment (TME). Summary We developed a suite of scalable deep learning methods to analyze 6 distinctly labeled cell populations in mIHC WSIs. We evaluated our methods and found that they reliably detected and classified cells in the PDAC tumor microenvironment. We also utilized the ColorAE:U-Net ensemble method to analyze 3 mIHC WSIs with nearest neighbor spatial analysis. We demonstrate a proof of concept that these methods can be employed to quantitatively describe the spatial distribution of immune cells within the tumor microenvironment. These complementary deep learning methods are readily deployable for use in clinical research studies.

Multiplex immunohistochemistry (mIHC) is an innovative and cost-effective method that simultaneously labels multiple biomarkers in the same tissue section. Current platforms support labeling six or more cell types with different colored stains that can be visualized with brightfield light microscopy. However, analyzing and interpreting multi-colored images comprised of thousands of cells is a challenging task for both pathologists and current image analysis methods. We propose a novel deep learning based method that predicts the concentration of different stains at every pixel of a whole slide image (WSI). Our method incorporates weak annotations as training data: manually placed dots labelling different cell types based on color. We compare our method with other approaches and observe favorable performance on mIHC images.

Pancreatic ductal adenocarcinoma (PDAC) is characterized by two molecular subtypes, of which the basal-like subtype is associated with the worst survival and is highly resistant to first-line chemotherapy. We previously reported that keratin 17 (K17), a component of the molecular signature of the basal-like subtype, is a negative prognostic and predictive biomarker, whose overexpression results in chemoresistance and shortened patient survival. Here, we aimed to uncover the mechanistic role of K17 in driving cancer aggression and explore the therapeutic opportunities in K17-expressing PDAC. Beyond its role as a cytoskeletal protein, K17 can solubilize from the filamentous form and translocate into the nucleus, where it impacts multiple cellular properties. Previous reports suggest that nuclear K17 regulates cell-cycle progression and gene expression. However, the detailed mechanisms through which K17 modulates gene expression remains unexplored. Through domain-prediction analyses, we identified a novel chromatin-remodeling (SANT) domain in K17 that may interact with histones to regulate chromatin structure. The assay for transposase-accessible chromatin using sequencing (ATAC-seq) revealed that K17 positive cells had comparably accessible regions relative to K17 negative cells. However, the deletion of the K17 SANT domain (dSANT) decreased chromatin accessibility, suggesting that nuclear K17 impacts chromatin structure via the SANT domain. With RNA sequencing (RNA-seq) pathway enrichment analysis, we found that K17 positive cells had differential expressed genes that are associated with cell signaling, immune regulation, and metabolic pathways. More specifically, by comparing wild type K17 and dSANT K17-expressing cells, we found that the SANT domain impacts a wide variety of immune regulatory pathways, many of which affect the tumor microenvironment. We are now performing chromatin immunoprecipitation sequencing (ChIP-seq) with acetylation of lysine 27 on histone H3 protein subunit (H3K27ac), to reveal differential bindings that are impacted by K17 and the SANT domain. Importantly, mice bearing orthotopic xenografts of PDACs with K17-SANT deletion showed survival comparable to those with K17 negative tumors and had significantly longer survival than those with wild-type K17. In summary, we identified a novel chromatin remodeling domain in K17 that could be explored as a target for the development of a biomarker-based treatment for PDAC. Citation Format: Chun-Hao Pan, Robert Tseng, Simon J. Hogg, Gabriella Baraks, Cindy V. Leiton, Lucia Roa-Peña, Natalia Marchenko, Kenneth R. Shroyer, Luisa F. Escobar-Hoyos. A novel chromatin remodeling domain of keratin 17 regulates transcription and promotes tumor aggression in pancreatic cancer [abstract]. In: Proceedings of the AACR Virtual Special Conference on Pancreatic Cancer; 2021 Sep 29-30. Philadelphia (PA): AACR; Cancer Res 2021;81(22 Suppl):Abstract nr PO-048.

Objectives Previous work in our laboratory identified keratin 17 (K17) as a specific and sensitive biomarker for high-grade squamous intraepithelial lesions and cervical squamous cell carcinoma (SCC). K17, however, has not been previously evaluated in endocervical glandular neoplasia. Based on the similar pathogenesis of squamous and glandular lesions of the cervix, we hypothesized that K17 overexpression could also be a diagnostic and/or prognostic biomarker for endocervical neoplasia. Methods Cases of endocervical adenocarcinoma (n = 90), adenocarcinoma in situ (AIS) (n = 32), benign glandular lesions (n = 36), and normal endocervical mucosa (n = 5) were selected from Stony Brook Medicine and the University of Massachusetts from 2002 to 2013. Immunohistochemical staining for K17 was performed by an indirect immunoperoxidase method and was scored based on the proportion of cells that showed strong (2+) staining. Results K17 was highly expressed in 21 (65.6%) of 32 AIS and in 75 (83.0%) of 90 adenocarcinoma cases. In adenocarcinomas, K17 staining was detected in a mean of 33.9% of malignant cells. Staining tended to be strongest at the periphery of pseudoglandular groups and at the invasive front of tumors. K17 was not detected in the epithelial cells of benign glandular lesions, but groups of cuboidal cells, residing beneath the epithelial layer of benign glands, were frequently positive for K17, especially in cases of microglandular hyperplasia. High levels of K17 expression were significantly associated with decreased patient survival. Conclusions K17 is highly expressed in most cases of both invasive adenocarcinoma and in AIS and is a powerful, negative prognostic marker for patient survival.

The major roles of keratin 17 (K17) as a prognostic biomarker have been highlighted in a range of human malignancies. However, its relevance to esophageal squamous cell carcinoma (ESCC) remains unexplored. In this study, the relationship between K17 expression and clinicopathologic parameters and survival were determined by RNA sequencing (RNA-Seq) in 90 ESCCs and by immunohistochemistry (IHC) in 68 ESCCs. K17 expression was significantly higher in ESCC than in paired normal tissues at both the messenger RNA and protein levels. K17 messenger RNA and staining by IHC were significantly correlated with aggressive characteristics, including advanced clinical stage, invasion depth, and lymph node metastases; and were predictive of poor prognosis in advanced disease patients. Furthermore, K17 expression was detected by IHC in high-grade premalignant lesions of the esophageal mucosa, suggesting that K17 could also be a biomarker of dysplasia of the esophageal mucosa. Overall, this study established that K17 is a negative prognostic biomarker for the most common subtype of esophageal cancer.

Pancreatic ductal adenocarcinoma (PDAC) includes two molecular subtypes, of which the basal-like subtype is associated with the shortest survival and is highly resistant to chemotherapy. The basal-like subtype is defined by a 25-gene signature; however, the role of these genes in promoting tumor aggression remains unexplored. Here, we set out to uncover the mechanisms of chemoresistance and explore targeted therapies for this subtype. We focused on studying an oncofetal antigen, keratin 17 (K17), which is the most overexpressed hallmark gene of the basal-like PDAC. We manipulated the expression of K17 and found that in multiple in vitro and in vivo models of PDAC, spanning human and murine PDAC cells and orthotopic xenografts, K17 expression resulted in a greater than two-fold increase in resistance to Gemcitabine (Gem) and 5-fluorouracil, the major chemotherapeutic agents in standard-of-care treatments. To uncover the mechanisms associated with K17-induced chemoresistance, we performed unbiased metabolomic studies in isogenic PDAC cell lines and found that compared to control cells, K17 increases intracellular levels of deoxycytidine (dC) by four-fold that promote Gem (dC analogue) resistance. Based on previous findings that K17 enters nucleus to regulate gene expression, we explored whether K17 triggers metabolic reprogramming at the transcriptional level and found that enzymes involved in pyrimidine biosynthesis are positively correlated with K17 expression in PDAC cells. Given that it is still poorly understood how K17 regulates gene expression, we performed domain-prediction analyses. We discovered and validated a novel chromatin remodeling domain on K17 that is required for metabolic reprogramming. We are now performing ChIP-Seq and RNA-Seq to understand how this domain alters pyrimidine biosynthesis. To identify small molecules that could target K17-expressing PDACs potentially by disrupting metabolic reprograming, we performed an unbiased high-throughput drug screen and found that Podophyllotoxin (PPT), a microtubule inhibitor, significantly and selectively killed K17-positive compared to K17-negative PDAC cells. In the clinic, another microtubule inhibitor, Paclitaxel (PTX), is used in combination with Gem as a first line chemotherapy. Surprisingly, when combined with Gem, PPT but not PTX, was synergistic in inhibiting the viability of K17-expressing PDAC cells and enhanced survival of mice bearing K17-expressing PDACs. Currently, we are exploring the role of PPT in regulating pyrimidine biosynthesis. In summary, we identified a novel pathway of chemoresistance and a compound that could result in developing a biomarker-based personalized therapy. Citation Format: Chun-Hao Pan, Yuka Otsuka, BanuPriya Sridharan, Melissa Woo, Cindy V. Leiton, Sruthi Babu, Mariana Torrente Gonçalves, Ryan R. Kawalerski, Ji Dong K. Bai, Richard A. Moffitt, Jiang Zhao, David K. Chang, Andrew V. Biankin, Tim Duong, Pankaj K. Singh, Louis Scampavia, Timothy Spicer, Kenneth R. Shroyer, Luisa F. Escobar-Hoyos. Targeting a novel rewired pathway of nucleotide metabolism that drives chemoresistance in the most lethal molecular subtype of pancreatic cancer [abstract]. In: Proceedings of the AACR Virtual Special Conference on Pancreatic Cancer; 2020 Sep 29-30. Philadelphia (PA): AACR; Cancer Res 2020;80(22 Suppl):Abstract nr PO-023.

CLINICAL NEED & OBJECTIVES: There is an unmet need for the discovery and development of novel therapeutic approaches for PDAC. Molecular subtyping, however, has recently uncovered potential biomarkers that, subject to further investigation, may be druggable to extend PDAC patient survival. Expression of Keratin 17 (K17), an oncofetal intermediate filament (IF) protein and hallmark of the most aggressive subtype, associates negatively with survival and drives chemotherapy resistance in PDAC. This suggests a functional role of K17 in PDAC, though the underlying mechanisms are unknown. Nuclear localization, however, has been suggested as a part of the overarching processes through which K17 promotes tumor growth. In related keratins, post-translational modifications (PTM) such as phosphorylation drive IF dissociation (solubilization) and can contribute to migration and metastatic dissemination. Thus, we hypothesized that K17 may harbor PTM- and/or solubilization-dependent oncogenic functions that could reveal new PDAC therapeutic options. METHODS & RESULTS: Using isogenic murine PDAC models, we found that K17 expression enhances tumor growth and metastatic potential. Furthermore, K17 solubility was associated with shorter survival, independent of total K17 expression or cell proliferation in both murine and human PDACs. To identify K17 PTMs potentially driving solubilization, we performed liquid chromatography mass spectrometry to sequence K17 isolated from patient PDACs and identified phosphorylation of a conserved N-terminal region (Ser 10-13) as the predominant PTMs. To determine if Ser 10-13 phosphorylation regulates K17 solubility, we generated mutants that mimic K17 Ser 10-13 phosphorylation and found that this was sufficient to solubilize K17 and promote nuclear localization. Building on these findings, we used kinase inhibitors to show that the PKC-MEK-RSK signaling pathway is involved in phosphorylation of K17 Ser 10-13. To assess the impact of K17 Ser 10-13 phosphorylation on tumors, nude mice were implanted orthotopically with isogenic human PDAC cell lines expressing either wild type (WT), loss of function (LOF) Ser 10-13 mutants, or Ser 10-13 phosphorylation gain of function (GOF) mutants. Compared to tumors expressing WT K17, GOF tumors resulted in increased metastases, and LOF mutants abrogated these characteristics. CONCLUSION: These results suggest that enhanced K17 solubility by phosphorylation at Ser 10-13 is sufficient to impact PDAC metastasis and survival and reveal novel druggable sites on K17. These results motivate future studies to uncover K17 phosphorylation targeting approaches for PDAC. If successful, they will be coupled with the identification of PDAC patients by tumor K17 expression, providing the basis of a potential precision medicine strategy. Citation Format: Ryan R. Kawalerski, Mariana T. Gonçalves, Lucia Roa-Peña, Cindy V. Leiton, Chun-Hao Pan, Luke A. Torre-Healy, Taryn Boyle, Natasha T. Snider, Kenneth R. Shroyer, Luisa F. Escobar-Hoyos. Solubilization of keratin 17 promotes the metastatic dissemination of the most lethal form of pancreatic cancer [abstract]. In: Proceedings of the AACR Virtual Special Conference on Pancreatic Cancer; 2020 Sep 29-30. Philadelphia (PA): AACR; Cancer Res 2020;80(22 Suppl):Abstract nr PO-050.

The purpose of this study is to launch a novel biomarker-based targeted therapy that may result in improved precision and efficacy for the treatment of pancreatic ductal adenocarcinoma (PDAC). We discovered that Keratin 17 (K17), an oncofetal intermediate filament and nuclear oncoprotein expressed in 50% of PDAC cases, is a biomarker of the most aggressive and treatment-resistant form of PDAC. We set out to validate K17 as a druggable target and to identify K17-targeting mechanisms. In pre-clinical mouse models, animals bearing K17+ PDACs display the shortest survival, suggesting that K17 drives tumor aggression and should be explored as a potential therapeutic target. We used the following two approaches aimed to inhibit K17 nuclear shuttle functions, in order to identify therapeutic strategies: 1) Targeting K17 functional domains: By protein-sequence modeling analyses and site-directed mutagenesis, we identified functional domains in K17 (K17-FDs) that bind to, shift the subcellular localization of, and promote the degradation of nuclear tumor suppressors (e.g. p27). Using SILAC mass spectrometry of nuclear proteomes from isogenic human cells, we found that 80% of the nuclear proteome is altered by K17, that half of these proteins encode the domain targeted by the K17-FDs, and that a large proportion of these proteins are involved in gene expression. Animals harboring tumors with mutated K17-FDs lived two-times longer than control animals bearing K17+ PDACs, suggesting that the K17-FDs may be therapeutic targets. We are currently testing small molecule and peptide inhibitors to target the K17-FDs in vitro and in vivo, as a discovery approach to design small-molecule inhibitors of K17. 2) Targeting K17 nuclear export: K17 impacts the nuclear export of ~50% of the proteome and depends on exportin-1 (XPO1). We found that K17+ PDAC cells were more sensitive to Selective Inhibitor of Nuclear Export (SINE) therapy, leading to a 2-fold increase in cell death compared to control cells, suggesting that nuclear export by K17 in PDAC cells could be therapeutically targeted. SINE therapy is currently FDA-approved for treatment of other cancer types and repurposing for the treatment of K17-positive PDACs may result in enhanced therapeutic efficacy. In conclusion, these studies provide the basis for the development of novel biomarker-based therapeutic approaches using small-molecule inhibitors, to target K17 active sites or the pathways altered by this protein in PDAC. Citation Format: Cindy V. Leiton, Chun-Hao Pan, Ji Dong Bai, Lucia Roa-Peña, Sruthi Babu, Alex Penson, Nashaat Turkman, Richard Moffitt, Markus Seeliger, David Talmage, Kenneth R. Shroyer, Luisa F. Escobar-Hoyos. Therapeutic targeting of keratin 17 functional domains and nuclear export uncover therapeutic vulnerabilities of pancreatic cancer [abstract]. In: Proceedings of the AACR Virtual Special Conference on Pancreatic Cancer; 2020 Sep 29-30. Philadelphia (PA): AACR; Cancer Res 2020;80(22 Suppl):Abstract nr PO-040.

Introduction: Cytology and cystoscopy have limited sensitivity and specificity for the diagnosis of urothelial carcinoma (UC), due to inflammatory atypia, sampling errors, and other clinicopathologic factors that may obscure test results. Therefore, there remains a clinical need to identify biomarkers to improve the diagnostic accuracy to detect UC. Keratin 17 (K17) is an embryologic cytokeratin that functions as an oncoprotein to promote the degradation of tumor suppressors that drive tumorigenesis. Published work from our group established that K17 is highly expressed in UC and confirmed specificity for UC by immunohistochemical localization of K17 in tissue biopsies of both low-grade and high-grade UCs (Babu et al., Mod Pathol, 2018). Objective: The objective of the current study was to develop an immunocytochemical (ICC) assay to determine K17 is a sensitive and specific biomarker to enhance diagnostic accuracy for UC in urine cytology. Methods: 80 ThinPrep CytoLyt-fixed urine specimens, collected at Stony Brook Medicine in 2018, including 39 with a clinicopathologic diagnosis of UC based on current cytologic diagnosis, and/or a history of biopsy confirmed UC within one year (+/-) of urine cytology specimen collection. K17 ICC was performed by indirect immunoperoxidase methods and K17 test results were scored based on the detection of immunoreactive urothelial cells and not on an assessment of cytologic atypia. The sensitivity and specificity of urine K17 ICC for detection of urothelial neoplasia was calculated by comparison of ICC test results with the cytologic diagnosis and/or the histologic diagnosis of positive cystoscopic biopsy specimens (papillary urothelial neoplasm of low malignant potential [PUNLMP, n=1] or greater). Samples that had no history of abnormal urine cytologic or biopsy diagnosis were categorized as negative for urothelial neoplasia. Results: Relative to the final clinicopathologic diagnosis of UC (n=38) or PUNLMP (n=1), K17 ICC had a sensitivity of 100% (95% CI: 91-100%) and specificity of 90% (95% CI: 77-96%). The positive predictive value was 90% (95% Cl: 78-96%) and the negative predictive value was 100% (95% Cl: 90-100%). Comparing ICC test results to cytologic and biopsy diagnoses, K17 ICC was positive in 9/23 (39%) cases with negative urine cytology. Of these 9 cases, 4 cases had biopsy confirmed UC. K17 ICC was positive in 4/11 (36%) of cases with inflammatory/reactive changes. Of these 4 cases, 3 had biopsy-confirmed UC. K17 ICC was positive in 14/30 (46%) of cases with mild atypia. Of these 14 cases, 12 had biopsy-confirmed UC and 1 had PUNLMP. K17 ICC was positive in 16/16 (100%) of cases with moderate atypia (n=8), severe atypia (n=3), or UC (n=5), all with biopsy-confirmed UC. Conclusions: K17 ICC is a novel and highly sensitive and specific diagnostic test for underlying biopsy-confirmed UC among samples with inflammatory/reactive changes, cytologic atypia, or positive urine cytology. Thus, the K17 test could serve as an adjunct to guide the clinical management of UC cases. Citation Format: Sruthi Babu, Lucia Roa-Peña, Ina Chan, Nam W. Kim, Sholeh Jahanfard, Luisa F. Escobar-Hoyos, Kenneth R. Shroyer. Validation of a novel cytologic biomarker for urothelial carcinoma [abstract]. In: Proceedings of the AACR Special Conference on Bladder Cancer: Transforming the Field; 2019 May 18-21; Denver, CO. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(15_Suppl):Abstract nr B01.

Pancreatic ductal adenocarcinoma (PDAC) is driven by co-existing mutations in KRAS and TP53. However, how these mutations collaborate to promote this cancer is unknown. Here, we uncover sequence-specific changes in RNA splicing enforced by mutant p53 which enhance KRAS activity. Mutant p53 increases expression of splicing regulator hnRNPK to promote inclusion of cytosine-rich exons within GTPase-activating proteins (GAPs), negative regulators of RAS family members. Mutant p53-enforced GAP isoforms lose cell membrane association, leading to heightened KRAS activity. Preventing cytosine-rich exon inclusion in mutant KRAS/p53 PDACs decreases tumor growth. Moreover, mutant p53 PDACs are sensitized to inhibition of splicing via spliceosome inhibitors. These data provide insight into co-enrichment of KRAS and p53 mutations and therapeutics targeting this mechanism in PDAC.

There is a clinical need to identify novel biomarkers to improve diagnostic accuracy for the detection of urothelial tumors. The current study aimed to evaluate keratin 17 (K17), an oncoprotein that drives cell cycle progression in cancers of multiple anatomic sites, as a diagnostic biomarker of urothelial neoplasia in bladder biopsies and in urine cytology specimens. We evaluated K17 expression by immunohistochemistry in formalin-fixed, paraffin embedded tissue specimens of non-papillary invasive urothelial carcinoma (UC) (classical histological cases), high grade papillary UC (PUC-LG), low grade papillary UC (PUC-HG), papillary urothelial neoplasia of low malignant potential (PUNLMP), and normal bladder mucosa. A threshold was established to dichotomize K17 status in tissue specimens as positive vs. negative, based on the proportion of cells that showed strong staining. In addition, K17 immunocytochemistry was performed on urine cytology slides, scoring positive test results based on the detection of K17 in any urothelial cells. Mann–Whitney and receiver operating characteristic analyses were used to compare K17 expression between histologic diagnostic categories. The median proportion of K17 positive tumor cells was 70% (range 20–90%) in PUNLMP, 30% (range 5–100%) in PUC-LG, 20% (range 1–100%), in PUC-HG, 35% (range 5–100%) in UC but staining was rarely detected (range 0–10%) in normal urothelial mucosa. Defining cases in which K17 was detected in ≥10% of cells were considered positive, the sensitivity of K17 in biopsies was 89% (95% CI: 80–96%) and the specificity was 88% (95% CI: 70–95%) to distinguish malignant lesions (PUC-LG, PUC-HG, and UC) from normal urothelial mucosa. Furthermore, K17 immunocytochemistry had a sensitivity of 100% and a specificity of 96% for urothelial carcinoma in 112 selected urine specimens. Thus, K17 is a sensitive and specific biomarker of urothelial neoplasia in tissue specimens and should be further explored as a novel biomarker for the cytologic diagnosis of urine specimens.

Keratins that are overexpressed selectively in human carcinomas may offer diagnostic and prognostic utility. In this study, we show that high expression of keratin-17 (K17) predicts poor outcome in patients with cervical cancer, at early or late stages of disease, surpassing in accuracy either tumor staging or loss of p27KIP1 as a negative prognostic marker in this setting. We investigated the mechanistic basis for the biologic impact of K17 through loss- and gain-of-function experiments in human cervix, breast, and pancreatic cancer cells. Specifically, we determined that K17 functions as an oncoprotein by regulating the subcellular localization and degradation of p27KIP1. We found that K17 was released from intermediate filaments and translocated into the nucleus via a nuclear localization signal (NLS), specific among keratins, where it bound p27KIP1 during G1 phase of the cell cycle. p27KIP1 lacks a nuclear export signal (NES) and requires an adaptor for CRM1 binding for nuclear export. In K17, we defined and validated a leucine-rich NES that mediated CRM1 binding for export. Cervical cancer cells expressing K17 mutations in its NLS or NES signals exhibited an increase in levels of nuclear p27KIP1, whereas cells expressing wild-type K17 exhibited a depletion in total endogenous p27KIP1. In clinical specimens of cervical cancer, we confirmed that the expressions of K17 and p27KIP1 were inversely correlated, both across tumors and within individual tumors. Overall, our findings establish that K17 functions specially among keratins as an oncoprotein by controlling the ability of p27KIP1 to influence cervical cancer pathogenesis. Cancer Res; 75(17); 3650–62. ©2015 AACR.

Sufficient epidemiologic evidence has established an etiologic link between bladder cancer risk and occupational exposure as a painter to organic solvents. Currently, it remains to be established whether gene-specific promoter methylation contributes to bladder cancer development, including by enhancing chromosome breakage or loss. We investigated the effect of chronic exposure to organic solvents and paints on DNA methylation profiles in the promoter regions of four genes (GSTP1, p16(INK4a), APC and CDH1) and micronucleus (MN) frequency in exfoliated urothelial cells from voided urine from Colombian male non-smoking car painters and age-matched unexposed individuals. The exposed group had a higher percentage of individuals with2 MNs/2000 cells compared with the unexposed group (P=0.04). Gene-specific analysis showed a significantly higher percentage of individuals with methylated GSTP1, p16(INK4a) and APC in the exposed group. Poisson regression analysis indicated that exposed individuals with methylated GSTP1 and p16(INK4a) promoters were more than twofold more likely to have an increase in MN frequency as compared with the reference. Finally, among exposed individuals with GSTP1 and p16(INK4a) methylated promoters, those with a greater age had a higher RR of increased MN frequency compared with younger exposed individuals with methylated promoters. These results support the conclusion that gene-specific promoter methylation may increase MN frequency in a dependent or independent interaction with occupational exposure to organic solvents.

Background Overexpression of keratin 17 (K17) is highly associated with poor prognosis in squamous cell carcinoma (SCC) of the cervix. This study was performed to (1) determine whether K17 may be a prognostic biomarker in head and neck squamous cell carcinoma (HNSCC) and (2) to establish if K17 expression is associated with human papillomavirus (HPV) status. Methods Immunohistochemical staining was performed for K17 of oral, oropharyngeal, and laryngeal SCCs, and normal oropharyngeal mucosa. The HPV status was determined using polymerase chain reaction (PCR). Results Elevated K17 expression was significantly associated with an overall decreased patient survival (P = .02) and, more specifically, in patients with oropharyngeal SCC (P = .01). When controlling for HPV status and tumor location K17 was still a significant predictor of survival (P = .01). Conclusion Therefore, K17 is a novel prognostic biomarker of poor survival for patients with HNSCCs, controlling for anatomic site and HPV status.

Clinical Need and Objectives: Our previous reports suggest that keratin 17 (K17), an intermediate filament (IF), is an oncoprotein and biomarker of the most aggressive and treatment-resistant form of pancreatic ductal adenocarcinoma (PDAC). Importantly, K17 transitions from its “insoluble” IF form to a “soluble” form that can regulate cell cycle progression and gene expression, though the mechanisms that mediate K17 solubilization are yet unknown. Determining these mechanisms may uncover new keratin 17-specific PDAC therapeutic vulnerabilities. Methods and Results: We found that in human and murine PDAC models, the soluble fraction of K17 exists in the full-length form (flK17) and as a caspase-cleaved peptide (ccK17), each with potential roles as biomarkers and/or functional drivers of PDAC aggression. In a PDAC tumor mouse model and human samples, we show, independent of total K17 protein amount, that the percent of soluble and ccK17 in tumor cells is negatively prognostic. We sequenced both the soluble and cytoskeletal insoluble forms of K17 from primary PDACs using liquid chromatography mass spectrometry (LC-MS) and identified that K17 is phosphorylated on several N-terminal serine residues, some of which identify a semiconserved IF motif that may regulate caspase cleavage and solubilization. Serine phosphatase inhibition in vitro demonstrated that phosphorylation is necessary to trigger K17 solubilization followed by nuclear translocation. Mutagenesis of N-terminal serine sites demonstrated that phosphorylation of three serine residues is sufficient to solubilize K17 from its filamentous state, and that phosphorylation of K17 by a PKC-RSK signaling pathway is likely to induce solubilization. In vitro and in vivo experiments are ongoing to address the functional role of this mechanism in regulating PDAC pathogenesis. Conclusion: Phosphorylation is an important regulator of K17 dynamics in PDAC, promoting solubilization and, in some cases, caspase cleavage. Our results suggest that soluble K17 may have a functional role in promoting tumor aggression. Inhibiting RSK or PKC kinases that phosphorylate K17 could impact tumor growth by blocking K17 solubilization/cleavage, and this line of research could accelerate the development of more effective treatments, coupled to soluble K17 testing as a predictive biomarker for PDAC. Citation Format: Ryan R. Kawalerski, Lucia Roa-Pena, Luke A. Torre-Healy, Taryn Boyle, Cindy V. Leiton, Natasha T. Snider, Kenneth R. Shroyer, Luisa F. Escobar-Hoyos. Oncogenic mechanism of soluble keratin 17 offers potential therapeutic vulnerability in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2019 Sept 6-9; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2019;79(24 Suppl):Abstract nr C26.

The purpose of this study is to launch a novel biomarker-based targeted therapy that may result in improved precision and personalized medicine for pancreatic ductal adenocarcinoma (PDAC). We discovered that keratin 17 (K17), an intermediate filament (IF), is a nuclear oncoprotein found in 50% of PDAC cases, identifying the most aggressive and treatment-resistant form of PDAC and functioning as a biomarker. We set out to validate K17 as a druggable target and to identify K17-targeting mechanisms. In preclinical mouse models, animals bearing K17-expressing PDACs display the shortest survival interval, suggesting that K17 drives tumor aggression and is a potential therapeutic target. We used the following two approaches aimed to inhibit K17 nuclear shuttle functions in order to identify potential therapeutic strategies. 1) Targeting K17 functional domains: By protein-sequence modeling analyses and site-directed mutagenesis, we identified functional domains in K17 (K17-FDs) that bind to, shift the subcellular localization of, and promote the degradation of nuclear tumor suppressors (i.e., p27). Using SILAC mass spectrometry analysis of nuclear proteomes from isogenic human cells, we found that 80% of the nuclear proteome is altered by K17, that half of these proteins encode the domain targeted by the K17-FDs, and that a large proportion of these proteins are involved in gene expression. Animals harboring tumors with mutated K17-FDs lived two times longer than control animals, suggesting that the K17-FDs may be therapeutic targets. We are currently testing small-molecule and peptide inhibitors to target the K17-FDs in vitro and in vivo, as a discovery approach to design small-molecule inhibitors of K17. 2) Targeting K17 nuclear export: K17 impacts the export of ~50% of the proteome and depends on exportin-1 (XPO1) for nuclear export. We found that PDAC cells expressing K17 were more sensitive to Selective Inhibitor of Nuclear Export (SINE) therapy, leading to a 2-fold increase in cell death compared to control cells, suggesting that nuclear export is a necessary oncogenic pathway exploited by K17 in PDAC cells. SINE therapy is currently FDA approved for treatment of other cancer types, and repurposing for the treatment of K17-positive PDACs may result in enhanced therapeutic efficacy. In conclusion, these studies provide the basis for novel biomarker-based therapeutic approaches for the most aggressive PDAC cases using small-molecule inhibitors that directly target K17 active sites or the pathways altered by this protein. Citation Format: Cindy V. Leiton, Chun-Hao Pan, Ji Dong Bai, Lucia Roa-Peña, Sruthi Babu, Alex Penson, Nashaat Turkman, Richard Moffitt, Markus Seeliger, David Talmage, Kenneth R. Shroyer, Luisa F. Escobar-Hoyos. Therapeutic targeting of keratin 17 and nuclear export uncover therapeutic vulnerabilities of pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2019 Sept 6-9; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2019;79(24 Suppl):Abstract nr C32.

Our aims are to uncover the molecular mechanisms through which keratin 17 (K17), a prognostic biomarker, drives tumor aggression and to target these mechanisms to provide more effective treatment for pancreatic ductal adenocarcinoma (PDAC). In murine orthotopic xenografts, we found that K17-positve PDACs survive for a shorter interval than controls. Prompted by previous reports that post-translational modifications (PTMs) regulate intermediate filament dynamics, we established in vitro that phosphorylated K17 detaches from the cytoskeleton and enters the nucleus, where it promotes tumor growth by targeting tumor suppressor proteins, including p27, for nuclear export and degradation. To further understand the events that control K17 solubilization, we sequenced K17 from primary PDACs by liquid chromatography-mass spectrometry and identified serine sites within the N-terminus that are phosphorylated only in soluble K17. Furthermore, phosphorylation is required to maintain K17 solubility and soluble K17 accumulates in the nucleus of PDAC cells. By an unbiased screen of 80 small-molecule kinase inhibitors in PDAC, we determined that SYK kinase inhibitors, already in clinical trials for other malignancies, abrogated K17 solubilization. Prompted by our finding that K17 serves as a nuclear shuttle of p27, we identified two amino acid sequences in K17 that have similar polarity to sequences that are used by cyclins to dock to p27. Point mutations in two of these domain key residues blocked K17-mediated degradation of nuclear p27, and we identified similar effects in the background of wild-type and oncogenic KrasG12D PDAC cells. Current studies are under way to find additional protein and RNA targets for potential therapeutic intervention. Using patient-derived organoids, human and murine PDAC cells, we determined that K17-expressing PDAC cells are more than twice as resistant as isogenic K17-negative cells to gemcitabine (Gem) and 5-fluorouracil (5-FU), two key components of current chemotherapeutic regimens. By unbiased liquid chromatography-coupled tandem mass spectrometry metabolomics, RNA-sequencing analyses (TCGA), and in vivo magnetic resonance spectroscopy, we found that K17 induces metabolic reprogramming by increasing glycolysis and pyrimidine biosynthesis, pathways that have been linked to chemoresistance. We are extending this work to determine if disruption of K17-mediated metabolic rewiring by small-molecule inhibitors will resensitize tumor cells to pyrimidine analogues. In conclusion, K17 undergoes key post-translational modifications that enable solubilization and nuclear translocation, the targeting of tumor suppressor proteins, and enhanced pyrimidine biosynthesis to drive chemoresistance. Uncovering these mechanisms could ultimately lead to the identification of novel approaches to target the oncogenic functions of K17, and thereby, to enable the development of more effective treatment options for PDAC. Citation Format: Kenneth R. Shroyer, Luisa Escobar-Hoyos, Cindy Leiton, Chun-Hao Pan, Ryan Kawalerski, Lucia Roa-Peña, Sruthi Babu. Keratin 17 drives tumor aggression and could be targeted for treatment of pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2019 Sept 6-9; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2019;79(24 Suppl):Abstract nr B50.

Pancreatic ductal adenocarcinoma (PDAC) is characterized by two molecular subtypes, of which the basal-like subtype is associated with the worst survival and is highly resistant to the currently available first-line chemotherapy. Our laboratory has identified that keratin 17 (K17) is a novel negative prognostic biomarker, as accurate as molecular subtyping in predicting patient survival. Patient-derived data analysis suggests that K17 expression correlates with increased resistance to chemotherapeutic agents. The goal of this study is to determine the role of K17 in chemoresistance, and to identify novel therapeutic approaches for around 50% of PDAC patients with tumors that express high levels of K17. In multiple in vivo and in vitro models of PDAC, spanning human and murine PDAC cells, patient-derived organoids, and orthotopic xenograft models, we determined that K17 expression causes more than two-fold increase in resistance to gemcitabine (Gem) and 5-fluorouracil (5-FU), key components of the current standard-of-care chemotherapeutic regimens. To uncover the mechanism associated to K17-induced chemoresistance, we performed unbiased metabolomic studies in isogenic PDAC cell lines and found that K17 reprograms several key metabolic pathways. In particular, K17 increases pyrimidine biosynthesis, a pathway has been linked to chemoresistance. Rescue experiments showed that deoxycytidine (dC) was sufficient to promote Gem (dC analogue) resistance in K17-nonexpressing PDAC cells, suggesting that upregulation of pyrimidine synthesis by K17 underlies resistance to chemotherapeutic agents. Through unbiased RNA-sequencing studies, we identified that gene expression of enzymes involved in pyrimidine biosynthesis was increased specifically in high K17-expressing cells. Previous reports from our group and others suggest that nuclear K17 regulates cell-cycle progression and gene expression. Through domain-prediction analyses, we discovered a novel domain on K17 involved in transcriptional regulation that is required for metabolic reprogramming. Currently, we are testing the role of this domain in metabolic reprograming. In addition, are pursuing two approaches to determine the “druggability” of these findings. First, we are testing if interrupting K17-mediated nucleotide metabolism, by means of small-molecule inhibitors, resensitizes tumor cells to pyrimidine analogues. Second, we are validating the results of a large-scale small-molecule inhibitor screen of FDA-approved, pharma-developed tools to identify compounds that target DNA metabolism and transcription in K17-expressing PDAC cells. In summary, we identified a novel and potentially druggable pathway of chemoresistance that could ultimately result in developing novel therapeutic strategies to enhance patient survival. Citation Format: Chun-Hao Pan, Cindy V. Leiton, Lucia Roa-Peña, Ryan R. Kawalerski, Richard A. Moffitt, Jiang Zhao, Timothy Spicer, Peter Bailey, David K. Chang, Andrew Biankin, Tim Duong, Pankaj K. Singh, Kenneth R. Shroyer, Luisa F. Escobar-Hoyos. A novel rewired pathway of nucleotide metabolism drives chemoresistance in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2019 Sept 6-9; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2019;79(24 Suppl):Abstract nr C39.