CDK12 Loss Promotes Prostate Cancer Development While Exposing Vulnerabilities to Paralog-Based Synthetic Lethality

Biallelic loss of cyclin-dependent kinase 12 (CDK12) defines a unique molecular subtype of metastatic castration-resistant prostate cancer (mCRPC). It remains unclear, however, whether CDK12 loss per se is sufficient to drive prostate cancer development-either alone, or in the context of other genetic alterations-and whether CDK12-mutant tumors exhibit sensitivity to specific pharmacotherapies. Here, we demonstrate that tissue-specific Cdk12 ablation is sufficient to induce preneoplastic lesions and robust T cell infiltration in the mouse prostate. Allograft-based CRISPR screening demonstrated that Cdk12 loss is positively associated with Trp53 inactivation but negatively associated with Pten inactivation-akin to what is observed in human mCRPC. Consistent with this, ablation of Cdk12 in prostate organoids with concurrent Trp53 loss promotes their proliferation and ability to form tumors in mice, while Cdk12 knockout in the Pten-null prostate cancer mouse model abrogates tumor growth. Bigenic Cdk12 and Trp53 loss allografts represent a new syngeneic model for the study of androgen receptor (AR)-positive, luminal prostate cancer. Notably, Cdk12/Trp53 loss prostate tumors are sensitive to immune checkpoint blockade. Cdk12-null organoids (either with or without Trp53 co-ablation) and patient-derived xenografts from tumors with CDK12 inactivation are highly sensitive to inhibition or degradation of its paralog kinase, CDK13. Together, these data identify CDK12 as a bona fide tumor suppressor gene with impact on tumor progression and lends support to paralog-based synthetic lethality as a promising strategy for treating CDK12-mutant mCRPC.

Pigment cell progenitor heterogeneity and reiteration of developmental signaling underlie melanocyte regeneration in zebrafish

Tissue-resident stem and progenitor cells are present in many adult organs, where they are important for organ homeostasis and repair in response to injury. However, the signals that activate these cells and the mechanisms governing how these cells renew or differentiate are highly context-dependent and incompletely understood, particularly in non-hematopoietic tissues. In the skin, melanocyte stem and progenitor cells are responsible for replenishing mature pigmented melanocytes. In mammals, these cells reside in the hair follicle bulge and bulb niches where they are activated during homeostatic hair follicle turnover and following melanocyte destruction, as occurs in vitiligo and other skin hypopigmentation disorders. Recently, we identified melanocyte progenitors in adult zebrafish skin. To elucidate mechanisms governing melanocyte progenitor renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for progenitors, deciphered transcriptional changes and intermediate cell states during regeneration, and analyzed cell-cell signaling changes to discover mechanisms governing melanocyte regeneration. We identified KIT signaling via the RAS/MAPK pathway as a regulator of melanocyte progenitor direct differentiation and asymmetric division. Our findings show how activation of different subpopulations of mitfa-positive cells underlies cellular transitions required to properly reconstitute the melanocyte pigmentary system following injury.

Abstract 5324: Drug repurposing and genetic screening strategies for effective treatment discovery in soft-tissue sarcomas

Treatment advances for soft-tissue sarcomas have been slow. This is, in part, due to their rarity (accounting for 0.7% of all cancers) and heterogeneity (over 50 different diseases fall under this category). Moreover, preclinical models are scarce, often exhibiting slow growth kinetics, which limits their study by large genetic and pharmacological libraries. Here, we present an update on our efforts to harness the power of patient-partnered research to create a platform for rare cancer drug target discovery as a broadly available community resource. We developed a patient-partnered tissue donation pipeline to enable patients anywhere in the United States to participate and piloted our approach for CTNNB1-driven desmoid tumors. To overcome challenges in tissue heterogeneity during ex vivo culture, we optimized a multiplexed sequencing protocol to quantitatively track changes in tumor cell fraction across hundreds of media formulations. Following this strategy, we were able to verify and expand three cell lines that preserve the CTNNB1 mutations at high purity. To identify potential therapeutics, we completed a 6,750-drug repurposing screen, at 2.5uM in duplicate, in two verified cell line models. After extensive quality control assessments and data integration steps to leverage the power of other large scale drug screens, we selected 263 compounds for follow-up based on potency, selectivity, and association with molecular features associated with desmoid tumors. Approximately 70% of selected compounds were validated by an 8-point, 2-fold dilution, dose-response format with a top concentration of 10uM. Of the confirmed active compounds, 80 showed a strong pattern of selectivity, 20 are FDA approved drugs and 13 investigational compounds show a statistical association with CTNNB1 hotspot mutation status or transcriptomic features associated with desmoid tumors. To prioritize potential therapeutic targets, we tested an efficient CRISPR/Cas9 all-in-one library design. The reduction of the CRISPR/Cas9 library size was achieved via multiple gene- and guide-level strategies, which enables statistically powered gene essentiality interrogation in slow-growing patient-derived models. We tested several plating and infection parameters and developed an optimized pipeline for the rapid introduction of this library into early patient-derived samples. Established cell lines of mesenchymal and non-mesenchymal origin, which have previously been tested by genome-wide libraries, were used to control for library and lineage effects. We are developing a biologist-friendly web portal that will enable the research community to easily interact with models and data produced by this effort. Our study provides evidence that a systematic patient-powered approach can facilitate discovery of therapeutic hypotheses for these understudied diseases.

Citation Format: Mushriq Al-Jazrawe, Kathryn Cebula, Elisabeth A. Abeyta, Haley S. Curtis, Jane K. McIninch, Jaime H. Cheah, James Berstler, Lisa Miller, James Neiswender, Lisa Brenan, Mike Burger, Francisca Vazquez, Jesse S. Boehm. Drug repurposing and genetic screening strategies for effective treatment discovery in soft-tissue sarcomas. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5324.

Abstract A052: Systematic dissection of transcriptional states in pancreatic cancer

Transcriptional states in pancreatic cancer can stratify patients by response to chemotherapy and clinical outcomes. These include the classical and basal-like states as well as a newly identified neural-like progenitor (NRP) state, which we have previously found to be enriched in primary patient tumors treated with neoadjuvant chemotherapy and radiotherapy. While several transcription factor drivers of classical and basal-like identity have been described, key regulators of the NRP state are unknown. Through in silico approaches, we identified candidate transcription factors of the NRP state, including GLIS3, a Krüppel-like zinc finger protein that mediates neuroendocrine fate during pancreatic development and differentiation of human embryonic stem cells into posterior neural progenitor cells. Our understanding of biologic and clinically-relevant attributes of transcriptional cell states remains limited by state-specific biases in various preclinical models. Existing human cell lines maintained as two-dimensional cultures tend to preferentially represent the basal-like state, whereas human three-dimensional organoid models grown in standard culture conditions best reflect the classical state. These phenotypes are therefore impacted by culture conditions as well as underlying genetic features. Furthermore, most murine pancreatic cancer models do not fully reflect the classical vs. basal-like state heterogeneity observed in humans. To enable systematic study of the classical, basal-like and NRP phenotypes, we developed isogenic KP (KrasG12D/+;Trp53FL/FL) murine organoids with a germline dCas9-VPR system to enable facile overexpression of state-specific transcription factors through CRISPR activation approaches. Quantitative PCR, RNA-sequencing, and proteomics confirmed Gata6, deltaN Trp63, and Glis3 as drivers of classical, basal-like, and NRP identity, respectively. DeltaN Trp63 organoids were further differentiated by loss of luminal morphology. Pairwise comparisons of global transcriptional alterations suggest the greatest similarities between the Gata6- and Glis3-overexpressed models, which is consistent with enhanced associations between classical and NRP states in patient tumors. Finally, although basal-like and NRP states are associated with poorer response to multi-agent chemotherapy, state-specific therapeutic sensitivities to other treatments remain incompletely defined. We therefore performed drug sensitivity assays with a panel of targeted therapies and unveiled state-specific sensitivities. These data were corroborated by drug sensitivity profiling of human patient-derived organoids and cell lines. Taken together, these results suggest a framework for defining cell state-specific vulnerabilities that may aid in stratifying and treating pancreatic cancer patients with new therapies.

Citation Format: Jimmy A. Guo, Jennifer Su, Ananya Jambhale, Julien Dilly, Connor J. Hennessey, Carina Shiau, Patrick Yu, Steven Wang, Junning Wang, Laleh Abbassi, James Neiswender, Tate Bertea, Annan Yang, Qijia Yu, Peter Westcott, Jason Schenkel, Daniel Y. Kim, Hannah I. Hoffman, Grissel Cervantes Jaramillo, Giselle A. Uribe, Westley W. Wu, Arnav Mehta, David Ting, Julian A. Pacheco, Amy Deik, Clary Clish, Francisca Vazquez, Brian Wolpin, Aviv Regev, William A. Freed-Pastor, Joseph D. Mancias, Tyler Jacks, William L. Hwang, Andrew J. Aguirre. Systematic dissection of transcriptional states 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 A052.

Intracranial AAV-IFN-β gene therapy eliminates invasive xenograft glioblastoma and improves survival in orthotopic syngeneic murine model

The highly invasive property of glioblastoma (GBM) cells and genetic heterogeneity are largely responsible for tumor recurrence after the current standard‐of‐care treatment and thus a direct cause of death. Previously, we have shown that intracranial interferon‐beta (IFN‐β) gene therapy by locally administered adeno‐associated viral vectors (AAV) successfully treats noninvasive orthotopic glioblastoma models. Here, we extend these findings by testing this approach in invasive human GBM xenograft and syngeneic mouse models. First, we show that a single intracranial injection of AAV encoding human IFN‐β eliminates invasive human GBM8 tumors and promotes long‐term survival. Next, we screened five AAV‐IFN‐β vectors with different promoters to drive safe expression of mouse IFN‐β in the brain in the context of syngeneic GL261 tumors. Two AAV‐IFN‐β vectors were excluded due to safety concerns, but therapeutic studies with the other three vectors showed extensive tumor cell death, activation of microglia surrounding the tumors, and a 56% increase in median survival of the animals treated with AAV/P2‐Int‐mIFN‐β vector. We also assessed the therapeutic effect of combining AAV‐IFN‐β therapy with temozolomide (TMZ). As TMZ affects DNA replication, an event that is crucial for second‐strand DNA synthesis of single‐stranded AAV vectors before active transcription, we tested two TMZ treatment regimens. Treatment with TMZ prior to AAV‐IFN‐β abrogated any benefit from the latter, while the reverse order of treatment doubled the median survival compared to controls. These studies demonstrate the therapeutic potential of intracranial AAV‐IFN‐β therapy in a highly migratory GBM model as well as in a syngeneic mouse model and that combination with TMZ is likely to enhance its antitumor potency.

Loss of 5-hydroxymethylcytosine is an epigenetic hallmark of melanoma

DNA methylation at the 5 position of cytosine (5-mC) is a key epigenetic mark that is critical for various biological and pathological processes. 5-mC can be converted to 5-hydroxymethylcytosine (5-hmC) by the ten-eleven translocation (TET) family of DNA hydroxylases. Here, we report that "loss of 5-hmC" is an epigenetic hallmark of melanoma, with diagnostic and prognostic implications. Genome-wide mapping of 5-hmC reveals loss of the 5-hmC landscape in the melanoma epigenome. We show that downregulation of isocitrate dehydrogenase 2 (IDH2) and TET family enzymes is likely one of the mechanisms underlying 5-hmC loss in melanoma. Rebuilding the 5-hmC landscape in melanoma cells by reintroducing active TET2 or IDH2 suppresses melanoma growth and increases tumor-free survival in animal models. Thus, our study reveals a critical function of 5-hmC in melanoma development and directly links the IDH and TET activity-dependent epigenetic pathway to 5-hmC-mediated suppression of melanoma progression, suggesting a new strategy for epigenetic cancer therapy.

Production of the antifungal compounds phenazine and pyrrolnitrin from Pseudomonas chlororaphis O6 is differentially regulated by glucose

AIMS

To determine whether glucose in growth medium affects secondary metabolite production and biocontrol efficacy of Pseudomonas chlororaphis O6.

METHODS AND RESULTS

The secondary metabolites pyrrolnitrin and phenazines antagonize phytopathogenic fungi. The expression of the prnA gene encoding tryptophan halogenase, the first step in pyrrolnitrin biosynthesis, required the stationary-phase sigma factor, RpoS. Mutations in rpoS and prnA in Ps. chlororaphis O6 eliminated antifungal activity against Rhizoctonia solani and Fusarium graminearum. Pyrrolnitrin production was reduced by glucose in growth media, whereas phenazine levels were increased. The efficacy of Ps. chlororaphis O6 in the biocontrol of tomato late blight was reduced by addition of glucose to the growth medium.

CONCLUSIONS

Regulation by glucose of pyrrolnitrin production influenced the efficacy of the biocontrol of tomato leaf blight.

SIGNIFICANCE AND IMPACT OF THE STUDY

The nutritional regulation of secondary metabolite production from a soil pseudomonad may account, at least in part, for the variability of biocontrol under field conditions.

Unit or service standards

As competition in the health-care market increases, issues such as accountability, patient satisfaction, and evaluation after quality of patient care have become progressively more important. This article describes the evaluation of a quality assurance program from a centralized, retrospective system to a unit-based, concurrent review process. Issues related to problem management, research, and education are identified.