Cyclin-dependent Kinase 9 Inhibitor Research Articles

PFKFB3 mediates tubular cell death in cisplatin nephrotoxicity by activating CDK4

Nephrotoxicity is a major side effect of cisplatin, a widely used cancer therapy drug. However, the mechanism of cisplatin nephrotoxicity remains unclear and no effective kidney protective strategies are available. Here, we report the induction of 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3) in both in vitro cell culture and in vivo mouse models of cisplatin nephrotoxicity. Notably, PFKFB3 was mainly induced in the nucleus of kidney tubular cells, suggesting a novel function other than its canonical role in glycolysis. Both pharmacological inhibition and genetic silencing of PFKFB3 led to the suppression of cisplatin-induced apoptosis in cultured renal proximal tubular cells (RPTCs). Moreover, cisplatin-induced kidney injury or nephrotoxicity was ameliorated in renal proximal tubule-specific PFKFB3 knockout mice. Mechanistically, we demonstrated the interaction of PFKFB3 with cyclin-dependent kinase 4 (CDK4) during cisplatin treatment, resulting in CDK4 activation and consequent phosphorylation and inactivation of retinoblastoma tumor suppressor (Rb). Inhibition of CDK4 reduced cisplatin-induced apoptosis in RPTCs and kidney injury in mice. Collectively, this study unveils a novel pathological role of PFKFB3 in cisplatin nephrotoxicity through the activation of the CDK4/Rb pathway, suggesting a new kidney protective strategy for cancer patients by blocking PFKFB3.

SNS-032 attenuates liver fibrosis by anti-active hepatic stellate cells via inhibition of cyclin dependent kinase 9.

Liver fibrosis is a common pathological process of all chronic liver diseases. Hepatic stellate cells (HSCs) play a central role in the development of liver fibrosis. Cyclin-dependent kinase 9 (CDK9) is a cell cycle kinase that regulates mRNA transcription and elongation. A CDK9 inhibitor SNS-032 has been reported to have good effects in anti-tumor. However, the role of SNS-032 in the development of liver fibrosis is unclear. In this study, SNS-032 was found to alleviate hepatic fibrosis by inhibiting the activation and inducing the apoptosis of active HSCs in carbon tetrachloride-induced model mice. In vitro, SNS-032 inhibited the activation and proliferation of active HSCs and induced the apoptosis of active HSCs by downregulating the expression of CDK9 and its downstream signal transductors, such phosphorylated RNA polymerase II and Bcl-2. CDK9 short hairpin RNA was transfected into active HSCs to further elucidate the mechanism of the above effects. Similar results were observed in active HSCs after CDK9 knockdown. In active HSCs with CDK9 knockdown, the expression levels of CDK9, phosphorylated RNA polymerase II, XIAP, Bcl-2, Mcl-1, and ɑ-SMA significantly decreased, whereas those of cleaved-PARP1 and Bax decreased prominently. These results indicated that SNS-032 is a potential drug and CDK9 might be a new prospective target for the treatment of liver fibrosis.

Antileukemic activity of YPN-005, a CDK7 inhibitor, inducing apoptosis through c-MYC and FLT3 suppression in acute myeloid leukemia

Acute myeloid leukemia (AML) is an aggressive blood cancer with a high rate of relapse associated with adverse survival outcomes, especially in elderly patients. An aberrant expression of cyclin dependent kinase 7 (CDK7) is associated with poor outcomes and CDK7 inhibition has showed antitumor activities in various cancers. We investigated the efficacy of YPN-005, a CDK7 inhibitor in AML cell lines, xenograft mouse model, and primary AML cells. YPN-005 effectively inhibited the proliferation of AML cells by inducing apoptosis and reducing phosphorylation of RNA polymerase II. The c-MYC expression decreased with treatment of YPN-005, and the effect of YPN-005 was negatively correlated with c-MYC expression. YPN-005 also showed antileukemic activities in primary AML cells, especially those harboring FMS-like tyrosine kinase 3–internal tandem duplication (FLT3-ITD) mutation and in in vivo mouse model. Phosphorylated FLT3/Signal transducer and activator of transcription 5 (STAT5) was decreased and FLT3/STAT5 was downregulated with YPN-005 treatment. Our data suggest that YPN-005 has a role in treating AML by suppressing c-MYC and FLT3.

120 (PB110) - Modeling of cell cycle response to cyclin-dependent kinase 12 (CDK12) inhibition

Background: In vitro studies have shown that CDK12 inhibition (CDK12i) leads to DNA damage accumulation, cell cycle arrest, and mitotic defects which result in antiproliferation. In vitro modeling and translation to in vivo can elucidate the PK-PD-efficacy relationship of CDK12i and subsequently simulate the efficacy of new dosing regimens. The goal of this work was to develop a mechanistic model to describe the effect of CDK12i on in vitro proliferation using H1048 cells, and subsequently translate the model to predict in vivo tumor growth inhibition (TGI) in an H1048 CDX (Cell Line-Derived Xenograft) model.

CDK7 is a prognostic biomarker for non-small cell lung cancer.

AimNon-small cell lung cancer (NSCLC) remains the leading cause of cancer-related death globally despite promising progress of personalized therapy approaches. Cyclin-dependent kinase 7 (CDK7) is a kinase involved in transcription, overexpressed in a broad spectrum of cancer types and found to be associated with an unfavourable prognosis. In this study, we aimed to investigate the protein expression of CDK7 in a large cohort of NSCLC incorporating adenocarcinomas (adNSCLC) and squamous cell carcinomas (sqNSCLC) and to correlate its expression with clinicopathological data.MethodsWe performed immunohistochemical staining of CDK7 on our cohort of NSCLC including 258 adNSCLC and 101 sqNSCLC and measured protein expression via a semi-automated read out. According to the median value of CDK7 the cohort was stratified in a CDK7 high and low expressing group, respectively, and results were correlated with clinico-pathological data.ResultsCDK7 was significantly higher expressed in sqNSCLC than in adNSCLC. In the group of sqNSCLC, CDK7 expression was significantly higher in sqNSCLC with lymph node metastases than in sqNSCLC with N0 stage. We found a significantly worse overall survival and disease-free survival for patients with CDK7 high expressing NSCLC.ConclusionSince a high CDK7 expression seems to be linked with a poor prognosis it might serve as a promising novel prognostic biomarker and its assessment could be implied in future routine diagnostic workup of NSCLC samples. Considering that CDK7 inhibitors are currently tested in several trials for advanced solid malignancies, it may also be a new target for future anti-cancer therapy.

Abstract A019: Phase 1, first-in-human, dose-expansion study of oral TP-1287, a cyclin dependent kinase 9 (CDK9) inhibitor, in patients with sarcoma

Abstract Background: CDK9 blockade inhibits tumor growth and progression by impairing the transcription of key oncogenes, such as MCL1 and MYC. TP-1287 is an orally delivered phosphate prodrug of the CDK9 inhibitor alvocidib. The anti-tumor activity of alvocidib has previously been shown in vitro in a Ewing sarcoma cell line and in vivo in a mouse Ewing sarcoma xenograft model. TP-1287 is being investigated in a phase 1 dose escalation and dose expansion study in patients with solid tumors (escalation) and sarcoma (expansion) (NCT03604783). The design of the expansion part of the phase 1 study in patients with sarcoma is herein described. Methods: Thirty patients with sarcoma will be enrolled. Key eligibility criteria are age ≥18 years (≥16 years if ≥40 kg); histologically confirmed locally advanced or metastatic unresectable Ewing sarcoma, dedifferentiated liposarcoma, or synovial sarcoma (10 patients each); 1–3 prior lines of therapy (including an anthracycline); Eastern Cooperative Oncology Group performance status of ≤1; acceptable liver and renal function, and acceptable hematologic and coagulation status. Exclusion criteria include a history of certain cardiovascular diseases (including heart failure and myocardial infarction [≤6 months]); seizure disorder requiring anticonvulsant therapy; presence of symptomatic central nervous system metastatic disease or disease that requires local therapy ≤2 weeks; severe chronic obstructive pulmonary disease with hypoxemia; active infections; or treatment with surgery, chemotherapy, or investigational therapy within 28 days or 5 half-lives (whichever occurs first). Patients will be treated at the recommended phase 2 dose established during dose escalation (11 mg twice daily orally, continuous dosing) and will continue to receive treatment with the same dose/schedule if they successfully complete a 28-day treatment cycle without significant treatment-related toxicity or progressive disease. Assessments will be performed on Day 1 and Day 15 of each cycle. Assessments for response and tumor burden will be done after Cycle 2 and at the end of every other cycle thereafter. The primary objective is objective response rate; secondary objectives are progression-free survival at 16 and 24 weeks and safety; and exploratory objectives are systemic exposure, antitumor activity (by objective radiographic assessment), and pharmacodynamics. Tumor tissue concentrations may be measured in patients who consent to optional tumor biopsies. Statistical analysis for all safety and efficacy parameters will be primarily descriptive in nature; time-to-event variables will be summarized via Kaplan-Meier. The dose expansion cohort is currently recruiting in the United States. Results: N/A. Conclusions: N/A. Citation Format: Andrew J. Wagner, Gregory M. Cote, Donald Richards, Nicholas J. Vogelzang, William J. Edenfield, Mitchell E. Gross, Lynn Mar, Gil D. Fine, Edward Dow, John A. Charlson. Phase 1, first-in-human, dose-expansion study of oral TP-1287, a cyclin dependent kinase 9 (CDK9) inhibitor, in patients with sarcoma [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr A019.

THZ1 targeting CDK7 suppresses c-KIT transcriptional activity in gastrointestinal stromal tumours

BackgroundGastrointestinal stromal tumours (GISTs) are the most common mesenchymal tumours of the gastrointestinal tract and are characterized by activating mutations of c-KIT or PDGFRa receptor tyrosine kinases (RTKs). Despite the clinical success of tyrosine kinase inhibitors (TKIs), more than half of GIST patients develop resistance due to a second mutation. Cyclin-dependent kinase 7 (CDK7) is the catalytic subunit of CDK-activating kinase (CAK), and it plays an important role in the regulation of cell cycle transitions and gene transcription. THZ1, a CDK7 inhibitor, exhibits a dose-dependent inhibitory effect in various cancers.MethodsData from the public GEO database and tissue microarray were used to analyse the gene expression levels of CDKs in GISTs. The impact of CDK7 knockdown and the CDK7 inhibitor THZ1 on GIST progression was investigated in vitro using CCK-8, colony formation, and flow cytometry assays and in vivo using a xenograft mouse model. RNA sequencing was performed to investigate the mechanism of GIST cell viability impairment mediated by THZ1 treatment.ResultsOur study demonstrated that CDK7 is relatively overexpressed in high-risk GISTs and predicts a poor outcome. A low concentration of THZ1 exhibited a pronounced antineoplastic effect in GIST cells in vivo and in vitro. Moreover, THZ1 exerted synergistic anticancer effects with imatinib. THZ1 treatment resulted in transcriptional modulation by inhibiting the phosphorylation of Ser2, Ser5, and Ser7 within RNA polymerase II (RNAPII). c-KIT, an oncogene driver of GIST, was transcriptionally repressed by THZ1 treatment or CDK7 knockdown. Transcriptome sequencing analysis showed that OSR1 acts as a downstream target of CDK7 and regulates c-KIT expression. Taken together, our results highlight elevated CDK7 expression as a predictor of poor outcome in GIST and present the combination of CDK7 and RTK inhibitors as a potent therapeutic strategy to improve the efficacy of GIST treatment.3dK7zp1xpFMvfXo5mnDRH-Video abstract

Abstract A06: Strategies to circumvent resistance to cyclin-dependent kinase-9 inhibition (CDK9i) in non-Hodgkin lymphoma (NHL)

Abstract Introduction Oncogenic programs are facilitated by activators of transcriptional machinery, including certain CDKs. CDK9, a component of the positive transcription elongation factor b (pTEFb) complex, has arisen as an attractive target due to its regulation of MYC and MCL1 transcription (Hashiguchi et al, 2019). Nevertheless, we and others have observed resistance to CDK9i in vitro and in vivo. Here we studied the effects of CDK9 inhibition using the novel selective CDK9 inhibitor AZD4573, currently under evaluation in clinical trials. Methods A panel of NHL cell lines (OCI-LY3/19, SUDHL4/10/16, VAL, U2932) and primary NHL cells were employed. Response to CDK9i was characterized using LC-MS proteomic analysis, RNA-Seq, and CRISPR-Cas9 Screening. Results NHL cells treated with AZD4573 for 6h exhibited a dose dependent reduction in phospho-RNAPIISer2, as well as loss of MYC and Mcl-1. CDK9i potently inhibited proliferation and induced apoptosis in a panel of NHL cell lines (IC50 range 5-30 nM). Two DLBCL cell lines underwent LC-MS proteomic analysis following AZD4573 treatment (30 nM, 3h). Treated cells exhibited rapid loss of MYC, Mcl-1, PIM3 and JUNB protein levels. We observed broad transcriptional repression via RNA-seq, including downregulation of PIM3 and JUNB (30 nM, 3h). However, a subset of genes, including MYC, PIM1 and JUNB underwent early transcriptional recovery, confirmed by immunoblotting, thus identifying candidate genes which may account for resistance to CDK9i. PIM kinases cooperate with the PI3K/ATK signaling pathway, and have been proposed as therapeutic targets in cancer. We next used SGI1776 (PIM1 specific) and AZD1208 (pan-PIM) in combination with AZD4573, and found synergy between them in a panel of 4 cell lines and primary samples. OCI-LY3 xenograft mice treated with a combination of AZD4573 (15 mg/kg; IP; once weekly) and AZD1208 (30 mg/kg; oral gavage, twice weekly) demonstrated restricted tumor growth and increased survival compared to control. To further understand pathways mediating resistance to CDK9i, we carried out a genome-wide loss of function CRISPR-Cas9 library screen. Two Cas9-expressing NHL cell lines were transduced with a CRISPR library comprised of ~5 unique sgRNA per gene. Loss of AKT, RPTOR, or mTOR, among others, sensitized cells to AZD4573. Concurrent treatment with PI3K inhibitors synergistically suppressed proliferation of NHL cell lines and primary cells treated with AZD4573 in vitro. OCI-LY3 xenograft mice were treated with AZD4573 (15 mg/kg; IP; once weekly), Copanlisib (15 mg/kg; IP; twice weekly), or a combination of both. Combo treatment restricted tumor growth and prolonged survival to a greater extent than either drug alone. Conclusions CDK9i with AZD4573 downregulated numerous oncoproteins. However, a subset of genes including MYC and PIM3 recovered transcription. PI3K/AKT pathway was implicated in resistance to CDK9i in CRISPR library screens. Concurrent targeting of pro-survival pathways (e.g., PIM, PI3K) partially reversed resistance to CDK9i. Citation Format: Elana Thieme, Duanchen Sun, Nur Bruss, Geeta Sharma, Tingting Liu, Daniel Coleman, Tamilla Nechiporuk, Daniel Bottomly, Shannon McWeeney, Patrick Pirrotte, Zheng Xia, Alexey Danilov. Strategies to circumvent resistance to cyclin-dependent kinase-9 inhibition (CDK9i) in non-Hodgkin lymphoma (NHL) [abstract]. In: Proceedings of the Third AACR International Meeting: Advances in Malignant Lymphoma: Maximizing the Basic-Translational Interface for Clinical Application; 2022 Jun 23-26; Boston, MA. Philadelphia (PA): AACR; Blood Cancer Discov 2022;3(5_Suppl):Abstract nr A06.

Ligand- and structure-based identification of novel CDK9 inhibitors for the potential treatment of leukemia

Cyclin-dependent kinase 9 (CDK9) plays a vital role in controlling cell transcription and has been an attractive target for cancer treatment. Herein, ten predictive models derived from 1330 unique molecules against CDK9 were constructed based on molecular fingerprints and graphs using two conventional machine learning and four deep learning methods. The evaluation results showed that FP-GNN deep learning architecture performed best for CDK9 inhibitors prediction with the highest BA and F1 values of 0.681 and 0.912 for testing set. We then performed virtual screening to identify new CDK9 inhibitors by incorporating the optimal established predictive model and molecular docking. Five compounds were identified to show broad anticancer activity against various cancer cell lines through bioassays. For example, C9 exhibited antiproliferative activities against HeLa, MOLM-13 and MDA-MB-231 with IC50 values of 2.53, 3.92 and 11.65 μM. Kinase inhibition assay results demonstrated that these compounds displayed submicromolar (214 ∼ 504 nM) inhibitory activities against CDK9. Further cellular mechanism evaluation revealed that C9 suppressed the activity of CDK9 and interfered with the expression of Mcl-1 and cleaved PARP in MOLM-13 cells, resulting in the induction of cellular apoptosis. In addition, C9 displayed a good stability in rat liver microsomes, artificial gastrointestinal fluid and plasm. An online platform (called DEEPCDK9Pred) was developed based on the FP-GNN models to predict or design new CDK9 inhibitors. Collectively, our findings demonstrated that FP-GNN algorithm can achieve accurate prediction of CDK9 inhibitors and the subsequent discovery of C9 as a new potential CDK9 inhibitor deserves further structural modification for the treatment of leukemia.

Elevation of effective p53 expression sensitizes wild-type p53 breast cancer cells to CDK7 inhibitor THZ1

BackgroundThe cyclin-dependent kinase 7 (CDK7) inhibitor THZ1 represses multiple cancer cells. However, its tumor-repressive efficiency in wild-type p53 breast cancer cells remains controversial.MethodsWe conducted various assays, including CCK8, colony formation, flow cytometry, western blotting, and lactate dehydrogenase release detection, to clarify whether p53 elevation sensitizes breast cancer cells to THZ1.ResultsWe found that upregulating functional p53 contributes to the increased sensitivity of breast cancer cells to THZ1. Increased THZ1 sensitivity requires active p53 and an intact p53 pathway, which was confirmed by introducing exogenous wild-type p53 and the subsequent elevation of THZ1-mediated tumor suppression in breast cancer cells carrying mutant p53. We confirmed that p53 accumulates in the nucleus and mitochondria during cell death. Furthermore, we identified extensive transcriptional disruption, rather than solely CDK7 inhibition, as the mechanism underlying the nutlin-3 and THZ1-induced death of breast cancer cells. Finally, we observed the combined nutlin-3 and THZ1 treatment amplified gasdermin E cleavage.ConclusionEnhanced sensitivity of breast cancer cells to THZ1 can be achieved by increasing effective p53 expression. Our approach may serve as a potential treatment for patients with breast cancer resistant to regular therapies.FBBFZg_5FsQzh51uphycMCVideo

CDK9 binds and activates SGK3 to promote cardiac repair after injury via the GSK-3β/β-catenin pathway.

The mammalian heart possesses entire regeneration capacity after birth, which is lost in adulthood. The role of the kinase network in myocardial regeneration remains largely elusive. SGK3 (threonine-protein kinase 3) is a functional kinase we identified previously with the capacity to promote cardiomyocyte proliferation and cardiac repair after myocardial infarction. However, the upstream signals regulating SGK3 are still unknown. Based on the quantitative phosphoproteomics data and pulldown assay, we identified cyclin-dependent kinase 9 (CDK9) as a novel therapeutic target in regeneration therapy. The direct combination between CDK9 and SGK3 was further confirmed by co-immunoprecipitation (Co-IP). CDK9 is highly expressed in the newborn period and rarely detected in the adult myocardium. In vitro, the proliferation ratio of primary cardiomyocytes was significantly elevated by CDK9 overexpression while inhibited by CDK9 knockdown. In vivo, inhibition of CDK9 shortened the time window of cardiac regeneration after apical resection (AR) in neonatal mice, while overexpression of CDK9 significantly promoted mature cardiomyocytes (CMs) to re-enter the cell cycle and cardiac repair after myocardial infarction (MI) in adult mice. Mechanistically, CDK9 promoted cardiac repair by directly activating SGK3 and downstream GSK-3β/β-catenin pathway. Consequently, our study indicated that CDK9 might be a novel target for MI therapy by stimulating myocardial regeneration.

Overexpression of gamma glutamyl hydrolase predicts extranodal extension in squamous cell carcinoma of the oral cavity

Extranodal extension (ENE) is an important prognostic factor in oral squamous cell carcinoma (OSCC). However, ENE is only confirmed postoperatively by histologic assessment of the lymph nodes after neck dissection. Accurate identification of ENE preoperatively would help in management of OSCC. We determined the expression of molecular markers gamma glutamyl hydrolase (GGH), cyclin-dependent kinase inhibitor-3 (CDKN3), and chromobox homolog-7 (CBX7) using immunohistochemistry in OSCC clinical samples (n=35). The intensity of staining was scored using a semiquantitative index (HSCORE). The association between clinicopathologic parameters and expression of molecular markers with ENE status was analyzed using chi-square test. The number of positive nodes and the highest anatomic level of nodal involvement significantly correlated with ENE (P < .05). High GGH expression was significantly associated with ENE (P < .05), with an increased risk for ENE (odds ratio [OR] 9.9, 95% CI 1.08-91.47, P=.04), whereas no significant association was seen for CDKN3 and CBX7 expression with ENE. However, a trend toward significance was observed with a high level of CDKN3 and a low level of CBX7 expression with ENE. Gamma glutamyl hydrolase offers potential as a predictor for ENE in OSCC, whereas the role of CDKN3 and CBX7 need to be validated in a larger sample.

CDK7 inhibition augments response to multidrug chemotherapy in pancreatic cancer

BackgroundPancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer with a dismal prognosis. Although combined treatment with gemcitabine and albumin-bound paclitaxel has improved the prognosis of PDAC, both intrinsic and acquired chemoresistance remain as severe hurtles towards improved prognosis. Thus, new therapeutic targets and innovative strategies are urgently needed.MethodsIn this study, we used the KPC mouse model-derived PDAC cell line TB32047 to perform kinome-wide CRISPR-Cas9 loss-of-function screening. Next-generation sequencing and MAGeCK-VISPR analysis were performed to identify candidate genes. We then conducted cell viability, clonogenic, and apoptosis assays and evaluated the synergistic therapeutic effects of cyclin-dependent kinase 7 (CDK7) depletion or inhibition with gemcitabine (GEM) and paclitaxel (PTX) in a murine orthotopic pancreatic cancer model. For mechanistic studies, we performed genome enrichment analysis (GSEA) and Western blotting to identify and verify the pathways that render PDAC sensitive to GEM/PTX therapy.ResultsWe identified several cell cycle checkpoint kinases and DNA damage-related kinases as targets for overcoming chemoresistance. Among them, CDK7 ranked highly in both screenings. We demonstrated that both gene knockout and pharmacological inhibition of CDK7 by THZ1 result in cell cycle arrest, apoptosis induction, and DNA damage at least predominantly through the STAT3-MCL1-CHK1 axis. Furthermore, THZ1 synergized with GEM and PTX in vitro and in vivo, resulting in enhanced antitumor effects.ConclusionsOur findings support the application of CRISPR-Cas9 screening in identifying novel therapeutic targets and suggest new strategies for overcoming chemoresistance in pancreatic cancer.

Identification of cell cycle-associated and -unassociated regulators for expression of a hepatocellular carcinoma oncogene cyclin-dependent kinase inhibitor 3

Human cyclin-dependent kinase inhibitor 3 (CDKN3) is a known oncogene in hepatocellular carcinoma (HCC) and its expression is promoted during tumor development. CDKN3 serves as a cell cycle regulator and its dysregulation is considered to be a causal factor for tumor progression. However, the molecular basis of the regulation of CDKN3 expression remains largely elusive. Using in silico approach, we identified CDKN3SE, a super enhancer (SE), and enhancer RNA (eRNA) candidates transcribed from this SE. Among the eRNA candidates, the expression of CDKN3eRNA was detected in the human HCC model cell line HepG2, and was found to facilitate the expression of CDKN3 without affecting the cell proliferation rate. In silico screening revealed two DNA-binding transcription factors, upstream stimulatory factor (USF) 1 and 2, involved in the regulation of CDKN3eRNA expression on CDKN3SE. A knock-down of USF1/USF2 expression in the HepG2 cells did not affect CDKN3eRNA expression, while the expression of CDKN3 was down-regulated. In a USF2 dominant negative HepG2 cell line generated by genome editing, a drastically altered cell shape and lowered cell proliferation rate were found; however, the expression of CDKN3eRNA appeared unaffected. Thus, the present study illustrated two regulators for CDKN3 expression: USF2, as a cell cycle-associated protein regulator, and CDKN3eRNA, as a cell cycle-unassociated RNA regulator.

Intra-articular injection of flavopiridol-loaded microparticles for treatment of post-traumatic osteoarthritis

Rapid joint clearance of small molecule drugs is the major limitation of current clinical approaches to osteoarthritis and its subtypes, including post-traumatic osteoarthritis (PTOA). Particulate systems such as nano/microtechnology could provide a potential avenue for improved joint retention of small molecule drugs. One drug of interest for PTOA treatment is flavopiridol, which inhibits cyclin-dependent kinase 9 (CDK9). Herein, polylactide-co-glycolide microparticles encapsulating flavopiridol were formulated, characterized, and evaluated as a strategy to mitigate PTOA-associated inflammation through the inhibition of CDK9. Characterization of the microparticles, including the drug loading, hydrodynamic diameter, stability, and release profile was performed. The mean hydrodynamic diameter of flavopiridol particles was ∼15 µm, indicating good syringeability and low potential for phagocytosis. The microparticles showed no cytotoxicity in-vitro, and drug activity was maintained after encapsulation, even after prolonged exposure to high temperatures (60 °C). Flavopiridol-loaded microparticles or blank (unloaded) microparticles were administered by intraarticular injection in a rat knee injury model of PTOA. We observed significant joint retention of flavopiridol microparticles compared to the soluble flavopiridol, confirming the sustained release behavior of the particles. Matrix metalloprotease (MMP) activity, an indicator of joint inflammation, was significantly reduced by flavopiridol microparticles 3 days post-injury. Histopathological analysis showed that flavopiridol microparticles reduced PTOA severity 28 days post-injury. Taken altogether, this work demonstrates a promising biomaterial platform for sustained small molecule drug delivery to the joint space as a therapeutic measure for post-traumatic osteoarthritis. Statement of significancePost-traumatic osteoarthritis (PTOA) begins with the deterioration of subchondral bone and cartilage after acute injuries. In spite of the prevalence of PTOA and its associated financial and psychological burdens, therapeutic measures remain elusive. A number of small molecule drugs are now under investigation to replace FDA-approved palliative measures, including cyclin-dependent kinase 9 (CDK9) inhibitors which work by targeting early inflammatory programming after injury. However, the short half-life of these drugs is a major hurdle to their success. Here, we show that biomaterial encapsulation of Flavopiridol (CDK9 inhibitor) in poly (lactic-co-glycolic acid) microparticles is a promising route for direct delivery and improved drug retention time in the knee joint. Moreover, administration of the flavopiridol microparticles reduced the severity of PTOA.

P1269: VIP152 IS A NOVEL CDK9 INHIBITOR WITH IMPROVED SELECTIVITY, TARGET MODULATION, AND CARDIAC SAFETY IN PATIENTS WITH LYMPHOMA

Background: Cyclin dependent kinase 9 (CDK9) controls transcriptional elongation, its inhibition may be effective in controlling cancer. To date, no drugs specifically targeting CDK9 have been approved due to challenges with therapeutic window. VIP152 was designed to be a highly potent and selective CDK9 inhibitor with favorable pharmacokinetic (PK) and pharmacodynamic (PD) effects to improve efficacy in patients with lymphoma. Aims: - To demonstrate the pharmacodynamic effects and safety profile associated with a selective CDK9 inhibitor with a favorable pharmacokinetic profile. - To demonstrate the utility of a selective CDK9 inhibitor for treatment of hematologic patients with an unmet medical need such as high-grade B cell lymphoma (HGBL) and chronic lymphocytic leukemia who relapse or are refractory to ibrutinib and venetoclax (R/R CLL). Methods: VIP152, fadraciclib, alvocidib (flavopiridol), KB-0742, and AZD4573 are evaluated in a CDK9/Cyclin T assay in the presence of low and high ATP and in a kinome scan at 1 µM. Differential expression (DE) analysis from VIP152, atuveciclib and KB-0742 treatment of 2 lymphoma cell lines by RNA seq is compared to DE of samples from 7 VIP152 treated HGBL patients. VIP152 cytotoxicity is evaluated in CRISPR/Cas9 edited HG-3 CLL cell line with homozygous TP53 edits R175H or R248Q, and in samples from 8 R/R CLL patients who relapsed or were refractory to ibrutinib and venetoclax. Results: In the presence of low ATP, the IC50 for VIP152 is 4.5 nM where others have IC50s from 3.2-29.4 nM. With high ATP, VIP152, AZD4573 and alvocidib maintain potency in low nM range, while fadraciclib and KB-0742 have 760 nM-1.7 µM IC50s. The kinome scan shows VIP152, KB-0742 and fadraciclib have the least number of hits. Kd values show VIP152 is the most selective CDK9 inhibitor versus all other CDKs. In patients at the current clinical dose of 30 mg administered once weekly, the average VIP152 unbound plasma concentration over a 24h period is 18 nM. The VIP152 IC50 of 4.5 nM unbound is maintained for 15h indicating target coverage. VIP152 PK exposure is dose-linear and proportional with low intra/inter-subject variability. Analysis of triplicate ECG data from 58 solid and heme cancer patients demonstrates that VIP152 does not prolong QTc interval after single or multiple doses (5-30 mg). DE analysis of MYC+ DLBLC cell lines with VIP152, atuveciclib or KB-0742 1µM treatment indicate that 85%, 76% or 68% of DE genes are downregulated, respectively and only VIP152 and atuveciclib achieve significant DE of MYC. DE is reproducible in HGBL patients’ whole blood at Cycle 1 Day 1 and Day 15 (r=0.9627) and findings will be validated in the ongoing clinical trial. VIP152 treatment demonstrates significant cytotoxicity in both WT and TP53 mutant CLL lines. R/R CLL samples treated with VIP152 showed a significant reduction in viability in a concentration-dependent manner. Summary/Conclusion: VIP152 is a potent and selective CDK9 inhibitor currently in development with a favorable cardiac safety profile. PK/PD demonstrates unbound plasma concentrations exceed in vitro IC50. Selective transcriptional downregulation is observed with 30mg IV weekly. Samples from patients with DLBCL or CLL are sensitive to VIP152 and updated PK, PD and ctDNA dynamics from the ongoing phase 1 trials (NCT02635672, NCT04978779) will be presented.

O-GlcNAc transferase maintains metabolic homeostasis in response to CDK9 inhibition.

Co-targeting of O-GlcNAc transferase (OGT) and the transcriptional kinase cyclin-dependent kinase 9 (CDK9) is toxic to prostate cancer cells. As OGT is an essential glycosyltransferase, identifying an alternative target showing similar effects is of great interest. Here, we used a multiomics approach (transcriptomics, metabolomics, and proteomics) to better understand the mechanistic basis of the combinatorial lethality between OGT and CDK9 inhibition. CDK9 inhibition preferentially affected transcription. In contrast, depletion of OGT activity predominantly remodeled the metabolome. Using an unbiased systems biology approach (weighted gene correlation network analysis), we discovered that CDK9 inhibition alters mitochondrial activity/flux, and high OGT activity is essential to maintain mitochondrial respiration when CDK9 activity is depleted. Our metabolite profiling data revealed that pantothenic acid (vitamin B5) is the metabolite that is most robustly induced by both OGT and OGT+CDK9 inhibitor treatments but not by CDK9 inhibition alone. Finally, supplementing prostate cancer cell lines with vitamin B5 in the presence of CDK9 inhibitor mimics the effects of co-targeting OGT and CDK9.

Abstract 2564: CDK9 inhibition via KB-0742 is a potential strategy to treat transcriptionally addicted cancers

Abstract Lineage-specific transcriptional networks drive cellular differentiation and development. Disruption of these specific cell programs can result in cancer and create a subset of tumors that are “transcriptionally addicted.” Sarcomas, for example, are characterized by an oncogenic fusion protein consisting of a FET family RNA-binding protein fused to a transcription factor (TF). The oncogenic fusions result in a restructuring of the transcriptome promoting cancer. In chordoma, TBXT (brachyury)—normally involved in notochord differentiation—is aberrantly expressed, resulting in promotion of cancer. As these oncogenic TFs are difficult to target directly, we and others have proposed targeting associated transcriptional regulators to inhibit their activity. Cyclin-dependent kinase 9 (CDK9) interacts with TFs to promote activation of target genes and promotes transcription elongation through phosphorylation of RNA polymerase II. We have developed a potent, selective, and orally bioavailable CDK9 inhibitor, KB-0742. Here we present the preclinical activity of KB-0742 in models of sarcoma and chordoma. We first evaluated KB-0742 activity in sarcoma in a 300-immortalized cell line screen containing 18 soft tissue sarcoma cell lines. The median IC50 of the cell lines in the study was 0.8705 µM. Sarcoma cell lines were enriched for sensitivity to KB-0742 with 61% (11/18) of the lines with an IC50 below the median. The 11 cell lines had a median IC50 of 0.679 µM. We then evaluated the activity of KB-0742 in 5 patient-derived cell line (PDC) models, with all 5 showing a cytotoxic response to treatment as measured by negative GRmax values. Last, a single patient-derived organoid (PDO) model of adult rhabdomyosarcoma was evaluated. KB-0742 treatment resulted in an IC50 of 2.75 µM and a max inhibition rate of 98.61%. For chordoma we examined the activity of KB-0742 in vivo using 2 patient-derived xenograft (PDX) models. In model CF466, we observed a dose-dependent response with increased TGI and greater reductions in RNA polymerase II phosphorylation in tumors treated with KB-0742 at 60 mg/kg as compared to 30 mg/kg. We then evaluated KB-0742 as a single agent and in combination with afatinib in the model CF539. KB-0742 as a single agent showed similar TGI activity as afatinib, whereas the combination showed increased response as compared to the two single-agent arms. These data show that transcriptionally addicted tumors are sensitive to CDK9 inhibition via KB-0742 treatment, and support the continued development of our compound to potentially treat sarcoma and chordoma. KB-0742 is currently being evaluated in a phase 1/2 clinical trial (NCT04718675) for relapsed or refractory solid tumors or non-Hodgkin lymphoma. Once a recommended phase 2 dose is established, expansion cohorts for patients with sarcoma, chordoma, and other transcriptionally addicted tumors may be opened. Citation Format: Melinda A. Day, Douglas C. Saffran, Tressa Hood, Nikolaus Obholzer, Akanksha Pandey, Charles Y. Lin, Pavan Kumar, Daniel M. Freed, Jorge DiMartino. CDK9 inhibition via KB-0742 is a potential strategy to treat transcriptionally addicted cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2564.

Abstract 3955: Targeting transcription elongation via CDK9 in mantle cell lymphoma patients with dual resistance to BTK inhibition and CAR T therapy

Abstract Introduction Clinical relapse following CD19 CAR T therapy after failure to BTK inhibitors (BTKi) is a novel and fast growing medical challenge in treating patients with mantle cell lymphoma (MCL). Thus, developing a novel therapy to overcome this BTKi-CAR T dual resistance (Dual-R) is an urgent need. Our unpublished data revealed MYC targets and cyclin-dependent kinase 9 (CDK9) are highly upregulated in the Dual-R compared to BTKi-R samples. CDK9 is a critical component of the positive transcription elongation factor b (P-TEFb) complex. Its inhibition induces acute decline of short-lived mRNA and proteins, especially MYC and MCL-1, in acute myeloid leukemia and diffuse large B-cell lymphoma. Therefore, we hypothesize that targeting CDK9 may turn off MYC-driven tumor survival and drug resistance. BAY-1251152 is a novel selective CDK9 inhibitor with nanomolar potency. However, whether it has the potential to overcome BTKi-CAR T dual resistance has not been assessed. Methods To validate the correlation of MYC and CDK9 with drug resistance and clinical outcome, we performed whole transcriptomic profiling using primary patient samples. To assess the in vitro efficacy of BAY-1251152, we performed cell viability assay and cell apoptosis assay using MCL cell lines and primary patient samples and followed up with functional studies. furthermore, we assessed its in vivo efficacy using patient-derived xenograft (PDX) models derived from MCL patients including one with Dual-R. Results The expression of MYC oncogene associates with ibrutinib resistance and Dual-R, and poor clinical outcome. CDK9 expression does not correlates with ibrutinib resistance but it does associate with Dual-R and poor clinical outcome in CAR T-relapsed patients. CDK9 inhibition by BAY-1251152 is highly potent in anti-MCL activity in MCL cell lines with low nanomolar range of IC50 (59.6-172.3 nM) by inducing robust cell apoptosis. BAY-1251152 induces dose and time-dependent CDK9 inhibition. A rapid decline of phosphorylation of RNA polymerase II, MYC, MCL-1, and Cyclin D1 can be observed as early as 2 hours. Furthermore, BAY-1251152 (10mg/kg, QW) significantly inhibited tumor growth (p = 0.000003) in a PDX model derived from a Dual-R patient without causing apparent toxicity in NSG mice. In addition, BAY-1251152 also significantly suppressed tumor growth in the PDX models derived from a BTKi-R patient (p=0.00015) and a BTKi-venetoclax dual-resistant patient (p=0.009). Conclusion Our findings showed that targeting CDK9 by its specific inhibitor BAY-1251152 led to potent in vitro anti-MCL activity. BAY-1251152 induces fast CDK9 inhibition and rapid decline of MYC, MCL-1 and Cyclin D1 to induce robust cell death. BAY-1251152 is also potent in inhibiting tumor growth in PDX models. These data support that CDK9 is a promising target to overcome BTKi-CAR T dual resistance in MCL, which is in urgent need. Citation Format: Vivian Changying Jiang, Lingzhi Li, Alexa Jordan, Yu Xue, Fangfang Yan, Joseph McIntosh, Yang Liu, Yuxuan Che, Yijing Li, Qingsong Cai, Angela Leeming, Lukas Simon, Zhongming Zhao, Jia Zhou, Michael Wang. Targeting transcription elongation via CDK9 in mantle cell lymphoma patients with dual resistance to BTK inhibition and CAR T therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3955.

Abstract 3931: TGN-1062 inhibits CDK7 and augments the effects of gemcitabine and nab-paclitaxel in pancreatic cancer models

Abstract Purpose: Overexpression of Cyclin-Dependent Kinase 7 (CDK7) is linked to poor clinical outcomes in a variety of cancer types including AML, breast, ovarian, pancreatic, and lung cancers. CDK7 plays a dual role in tumor progression by regulating the cell cycle via phosphorylation of members of the CDK family and stimulation of transcription via phosphorylation of RNA Polymerase II. CDK7 has also been shown to be associated with super-enhancers which can lead to overexpression of oncogenic driver genes such as BCL2, GFI1, and MYC. The development of a selective inhibitor of CDK7 is a promising strategy to control expression of these oncogenic genes in patients’ tumors. Previously, we described the design and synthesis of a potent and selective small molecule inhibitor of CDK7, TGN-1062, which was designed to bind to the catalytic ATP pocket. We showed efficacy in both AML and ovarian in vitro and in vivo models with correlative biomarker data. Here, we have generated further data on the effect and safety of TGN-1062 in pancreatic cancer cell line (CDX) and patient derived xenograft (PDX) models, both as a single agent and in combination with standard of care (SOC) therapies. Methods: In vivo efficacy studies were conducted in mice engrafted with pancreatic CDX and PDX tumors and treated with TGN-1062 with and without SOC therapies. Tumors were measured to determine tumor growth inhibition (TGI) and correlating drug accumulation levels were measured in both tumors and plasma using mass spectrometry. Immunohistochemistry (IHC) was performed on tumors to determine changes in cleaved Caspase-3, MYC, Ki67, and RNA Pol II. Rats were dosed with TGN-1062 to assess plasma exposures and preliminary tolerability. Results: In a pancreatic CDX model (MIA PaCa-2), TGN-1062 showed 38% TGI as a single agent and 121% TGI when in combination with gemcitabine and nab-paclitaxel, which on its own showed 37% TGI. In a pancreatic PDX model, TGN-1062 did not exhibit single agent effect, but combination with gemcitabine and nab-paclitaxel showed 95% TGI compared to 79% TGI with gemcitabine/nab-paclitaxel alone. Drug accumulation, biomarker analysis, and IHC from CDX and PDX tumors, showed that TGN-1062 treatment decreased RNA Pol II phosphorylation and MYC expression, and induced apoptosis. Rat pharmacokinetics indicated 100% oral bioavailability. Conclusion: Our potent and selective small molecule inhibitor of CDK7, TGN-1062, shows promise in pancreatic cancer models as a single or in combination with SOC. Preliminary data suggests that TGN-1062 can be developed further in multiple cancer indications. Citation Format: Alexis Weston, Trason Thode, Ryan Rodriguez del Villar, Serina Ng, Samuel Sampson, Shelby Rheinschmidt, Tithi Ghosh Halder, Raffaella Soldi, Mohan Kaadige, Srinivas Kasibhatla, Haiyong Han, Justin Moser, Vincent Chung, Joseph Chao, Victoria Villaflor, Daniel Von Hoff, Sunil Sharma. TGN-1062 inhibits CDK7 and augments the effects of gemcitabine and nab-paclitaxel in pancreatic cancer models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3931.