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Overview of the regulation of CAK and the role of CDK7 in regulating the cell cycle (a) and transcription (b). CAK = CDK activating kinase, CDK = cyclin-dependent kinase, CK2 = protein kinase CK2, G1 = gap phase 1, G2 = gap phase 2, M = mitosis, P = phosphate, PKCι = protein kinase C iota, Pol II = RNA polymerase II, S = synthesis, TFIIH = transcription factor II H
Source publication
Cyclin-dependent kinase 7 (CDK7), along with cyclin H and MAT1, forms the CDK-activating complex (CAK), which directs progression through the cell cycle via T-loop phosphorylation of cell cycle CDKs. CAK is also a component of the general transcription factor, TFIIH. CDK7-mediated phosphorylation of RNA polymerase II (Pol II) at active gene promote...
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Structural studies of the initiation-elongation transition of RNA polymerase II (pol II) transcription were previously facilitated by the use of synthetic oligonucleotides. Here we report structures of initiation complexes de novo converted from pre-initiation complex (PIC) through catalytic activities and stalled at different template positions. C...
During transcription initiation, the general transcription factor TFIIH marks RNA polymerase II by phosphorylating Ser5 of the carboxyl-terminal domain (CTD) of Rpb1, which is followed by extensive modifications coupled to transcription elongation, mRNA processing, and histone dynamics. We have determined a 3.5-Å resolution cryo–electron microscopy...
Citations
... Additionally, CDK7 activates the CDK9/cyclin T1 complex (TFEB) to promote the elongation process [21]. While CDK7 and CDK9 pathways have recently been targeted in cancer treatment [22,23], further elucidation is required regarding their involvement in the paraptotic program. ...
Background
Paraptosis is a programmed cell death characterized by cytoplasmic vacuolation, which has been explored as an alternative method for cancer treatment and is associated with cancer resistance. However, the mechanisms underlying the progression of paraptosis in cancer cells remain largely unknown.
Methods
Paraptosis-inducing agents, CPYPP, cyclosporin A, and curcumin, were utilized to investigate the underlying mechanism of paraptosis. Next-generation sequencing and liquid chromatography-mass spectrometry analysis revealed significant changes in gene and protein expressions. Pharmacological and genetic approaches were employed to elucidate the transcriptional events related to paraptosis. Xenograft mouse models were employed to evaluate the potential of paraptosis as an anti-cancer strategy.
Results
CPYPP, cyclosporin A, and curcumin induced cytoplasmic vacuolization and triggered paraptosis in cancer cells. The paraptotic program involved reactive oxygen species (ROS) provocation and the activation of proteostatic dynamics, leading to transcriptional activation associated with redox homeostasis and proteostasis. Both pharmacological and genetic approaches suggested that cyclin-dependent kinase (CDK) 7/9 drive paraptotic progression in a mutually-dependent manner with heat shock proteins (HSPs). Proteostatic stress, such as accumulated cysteine-thiols, HSPs, ubiquitin-proteasome system, endoplasmic reticulum stress, and unfolded protein response, as well as ROS provocation primarily within the nucleus, enforced CDK7/CDK9–Rpb1 (RNAPII subunit B1) activation by potentiating its interaction with HSPs and protein kinase R in a forward loop, amplifying transcriptional regulation and thereby exacerbating proteotoxicity leading to initiate paraptosis. The xenograft mouse models of MDA-MB-231 breast cancer and docetaxel-resistant OECM-1 head and neck cancer cells further confirmed the induction of paraptosis against tumor growth.
Conclusions
We propose a novel regulatory paradigm in which the activation of CDK7/CDK9–Rpb1 by nuclear proteostatic stress mediates transcriptional regulation to prime cancer cell paraptosis.
Graphical Abstract
... Proteolysis-targeting chimeras (PROTACs) can selectively hijack BRD4, CDKs and TFs into the ubiquitin-proteasome system to elicit its degradation, resulting to interruption of SE-driven transcriptional program. CRISPR/Cas9-mediated genetic perturbation can directly targeting individual components within SEs an integral component of TF IIH (TFIIH), mediating the phosphorylation of RNA Pol II C-terminal domain (CTD) heptapeptide repeats at serine 5 (Ser5) and serine 7 (Ser7) residues to initiate transcription [167]. In addition, CDK7 phosphates to CDK9, a part of the positive transcription elongation factor b (P-TEFb), which then phosphorylates serine 2 (Ser2) residues within the RNA Pol II CTD to promote transcriptional elongation [168]. ...
Metastasis remains the principal cause of cancer-related lethality despite advancements in cancer treatment. Dysfunctional epigenetic alterations are crucial in the metastatic cascade. Among these, super-enhancers (SEs), emerging as new epigenetic regulators, consist of large clusters of regulatory elements that drive the high-level expression of genes essential for the oncogenic process, upon which cancer cells develop a profound dependency. These SE-driven oncogenes play an important role in regulating various facets of metastasis, including the promotion of tumor proliferation in primary and distal metastatic organs, facilitating cellular migration and invasion into the vasculature, triggering epithelial-mesenchymal transition, enhancing cancer stem cell-like properties, circumventing immune detection, and adapting to the heterogeneity of metastatic niches. This heavy reliance on SE-mediated transcription delineates a vulnerable target for therapeutic intervention in cancer cells. In this article, we review current insights into the characteristics, identification methodologies, formation, and activation mechanisms of SEs. We also elaborate the oncogenic roles and regulatory functions of SEs in the context of cancer metastasis. Ultimately, we discuss the potential of SEs as novel therapeutic targets and their implications in clinical oncology, offering insights into future directions for innovative cancer treatment strategies.
... Cyclin-dependent kinase 7 (CDK7) plays two primary roles in regulating the cell cycle and transcription factors [6]. During cell cycle progression, CDK7 activates CDK1 and CDK2 during the S/G2 phases and CDK4/6 during the G1 phase via phosphorylation [7]. ...
... During transcription, CDK7 phosphorylates serine 5 (Ser5) and Ser7 in the RNA polymerase II (Pol II)-C-terminal domain (CTD) and CDK9, which induces Ser2 phosphorylation of the Pol II CTD [6]. CDK7/9 regulate cell division, gene transcription, and other important biological processes in normal cells; however, they are overexpressed in most carcinomas [8][9][10]. ...
... The development of therapies targeting CDK7 is ongoing for various cancers [6,13,14]. However, early CDK7 inhibitors were not initially CDK7-specific but instead acted as multi-CDK inhibitors. ...
Triple-negative breast cancer (TNBC) accounts for approximately 15–20% of all breast cancer types, indicating a poor survival prognosis with a more aggressive biology of metastasis to the lung and a short response duration to available therapies. Ibulocydine (IB) is a novel (cyclin-dependent kinase) CDK7/9 inhibitor prodrug displaying potent anti-cancer effects against various cancer cell types. We performed in vitro and in vivo experiments to determine whether IB inhibits metastasis and eventually overcomes the poor drug response in TNBC. The result showed that IB inhibited the growth of TNBC cells by inducing caspase-mediated apoptosis and blocking metastasis by reducing MMP-9 expression in vitro. Concurrently, in vivo experiments using the metastasis model showed that IB inhibited metastasis of MDA-MB-231-Luc cells to the lung. Collectively, these results demonstrate that IB inhibited the growth of TNBC cells and blocked metastasis by regulating MMP-9 expression, suggesting a novel therapeutic agent for metastatic TNBC.
... Preclinical investigations have consistently revealed robust anti-tumour effects across a range of cancer types, for example osteosarcoma [24], multiple myeloma [25], and breast carcinoma [26]. SY-1365, a modified variant of THZ1 and a CDK7 inhibitor, started its phase I clinical trial for the treatment of ovarian and breast carcinomas in 2017 [27,28]. ...
Chordomas are very rare malignant neoplasms of the bone occurring almost exclusively along the spine. As the tumours are thought to arise from notochordal remnants, the vast majority of chordomas express the TBXT gene, resulting in detectable nuclear amounts of its gene product brachyury. This T-Box transcription factor is commonly recognised as being essential in chordoma cells, and limiting TBXT expression is thought to be the key factor in controlling this tumour. Although the tumour is rare, distinct molecular differences and vulnerabilities have been described with regard to its location and the progression status of the disease, rendering it mandatory for novel cell lines to reflect all relevant chordoma subtypes. Here, we describe a novel chordoma cell line arising from the pleural effusion of a disseminated, poorly differentiated chordoma. This cell line, U-CH22, represents a highly aggressive terminal chordoma and, therefore, fills a relevant gap within the panel of available cell culture models for this orphan disease. CDK7 and CDK9 inhibition was lately identified as being effective in reducing viability in four chordoma cell lines, most likely due to a reduction in brachyury levels. In this study, we determined the capability of the CDK7 inhibitor THZ1 and the CDK1/2/5/9 inhibitor dinaciclib to reduce TBXT expression at mRNA and protein levels in a broad range of nine cell lines that are models of primary, recurrent, and metastasised chordoma of the clivus and the sacrum.
... Two oncogenes promoting progression from G2 to M phase (CDK7 and CDC25B) show a similar mismatch of expression profiles after CRNDE silencing. The expression of the former is significantly reduced, which is consistent with the observed decrease in the expression of cyclin H (the CDK7 protein forms a complex with this cyclin, which promotes cell division [35]). However, at the same time, the concentration of the CDC25B gene transcript increases significantly, which in turn should exert an opposite, pro-proliferative physiological effect [36]. ...
CRNDE is considered an oncogene expressed as long non-coding RNA. Our previous paper is the only one reporting CRNDE as a micropeptide-coding gene. The amino acid sequence of this micropeptide (CRNDEP) has recently been confirmed by other researchers. This study aimed at providing a mass spectrometry (MS)-based validation of the CRNDEP sequence and an investigation of how the differential expression of CRNDE(P) influences the metabolism and chemoresistance of ovarian cancer (OvCa) cells. We also assessed cellular localization changes of CRNDEP, looked for its protein partners, and bioinformatically evaluated its RNA-binding capacities. Herein, we detected most of the CRNDEP sequence by MS. Moreover, our results corroborated the oncogenic role of CRNDE, portraying it as the gene impacting carcinogenesis at the stages of DNA transcription and replication, affecting the RNA metabolism, and stimulating the cell cycle progression and proliferation, with CRNDEP being detected in the centrosomes of dividing cells. We also showed that CRNDEP is located in nucleoli and revealed interactions of this micropeptide with p54, an RNA helicase. Additionally, we proved that high CRNDE(P) expression increases the resistance of OvCa cells to treatment with microtubule-targeted cytostatics. Furthermore, altered CRNDE(P) expression affected the activity of the microtubular cytoskeleton and the formation of focal adhesion plaques. Finally, according to our in silico analyses, CRNDEP is likely capable of RNA binding. All these results contribute to a better understanding of the CRNDE(P) role in OvCa biology, which may potentially improve the screening, diagnosis, and treatment of this disease.
... A compelling candidate in this context is CDK7, a cyclin-dependent kinase-activating kinase that is integral to cell cycle progression and gene transcription [7]. Targeting CDK7 via various modalities, such as small interfering RNA (siRNA) or pharmacological inhibitors, has yielded encouraging antineoplastic results [8,9]. Recent advancements have ushered in a cadre of CDK7 inhibitors into phase I/II clinical trials for breast cancer [10]. ...
Cyclin-dependent kinase 7 (CDK7) serves as a pivotal regulator in orchestrating cellular cycle dynamics and gene transcriptional activity. Elevated expression levels of CDK7 have been ubiquitously documented across a spectrum of malignancies and have been concomitantly correlated with adverse clinical outcomes. This review delineates the biological roles of CDK7 and explicates the molecular pathways through which CDK7 exacerbates the oncogenic progression of breast cancer. Furthermore, we synthesize the extant literature to provide a comprehensive overview of the advancement of CDK7-specific small-molecule inhibitors, encapsulating both preclinical and clinical findings in breast cancer contexts. The accumulated evidence substantiates the conceptualization of CDK7 as a propitious therapeutic target in breast cancer management.
... In addition, other studies have indicated that cyclindependent kinase 7 (CDK7) inhibitors have become one of the most powerful candidates to target oncogenic SEs [84]. CDK7, along with cyclin H and MAT1, forms the CDK-activating complex (CAK), which dirves progression via cell cycle and transcription initiation [85,86]. ...
... Preclinical studies have shown that CDK7 inhibitors execute anti-cancer function partly depending on the repression of transcription, particularly transcription of super-enhancer-associated genes in cancer [87]. CDK7 inhibitors include THZ1, THZ2, SY-1365, LDC4297, BS-181, ICEC0942 (CT7001), SY-5609 and LY3405105, and some of them are now under Phase I/II clinical trials [84,[88][89][90]. As a covalent inhibitor of CDK7, THZ1 inhibited transcription by eliminating CDK7-dependent phosphorylation of RNA Pol II-carboxy terminal domain (CTD) on Ser-5 and Ser-7 [91,92]. ...
Super enhancers (SEs) consist of clusters of enhancers, harboring an unusually high density of transcription factors, mediator coactivators and epigenetic modifications. SEs play a crucial role in the maintenance of cancer cell identity and promoting oncogenic transcription. Super enhancer lncRNAs (SE-lncRNAs) refer to either transcript from SEs locus or interact with SEs, whose transcriptional activity is highly dependent on SEs. Moreover, these SE-lncRNAs can interact with their associated enhancer regions in cis and modulate the expression of oncogenes or key signal pathways in cancers. Inhibition of SEs would be a promising therapy for cancer. In this review, we summarize the research of SE-lncRNAs in different kinds of cancers so far and decode the mechanism of SE-lncRNAs in carcinogenesis to provide novel ideas for the cancer therapy.
... Additionally, CDK7 activates the CDK9/cyclin T1 complex (TFEB) to promote the elongation process [21]. While CDK7 and CDK9 pathways have recently been targeted in cancer treatment [22,23], further elucidation is required regarding their involvement in the paraptotic program. ...
The mechanisms underlying progression in cell paraptosis are largely unknown. CPYPP, cyclosporin A, and curcumin incited cytoplasmic vacuolization and induced paraptosis in breast cancer cells. The paraptotic program evolved with reactive oxygen species (ROS) provocation and overactivation of proteostatic dynamics to elicit transcriptional regulation involved in redox homeostasis and proteostasis. Pharmacological and genetic approaches suggested that cyclin-dependent kinase (CDK) 7/9 drives paraptotic progression in a reciprocally-dependent manner with heat shock proteins (HSPs). Proteostatic stress as accumulated cysteine-thiols, HSPs, ubiquitin-proteasome system, endoplasmic reticulum stress, and unfolding protein response, as well as ROS provocation primarily within the nucleus enforced CDK7/CDK9-Rpb1 (RNAPII subunit B1) activation by potentiating its interaction with HSPs and protein kinase R (PKR) in a forward loop to amplify the transcriptional regulation and thereby exacerbate proteotoxicity leading to overt paraptosis. Xenograft mouse with OECM-1 cells further confirmed the paraptotic induction against tumor growth. A novel regulatory paradigm that activation of CDK7/CDK9-Rpb1 by nuclear proteostatic stress mediates transcriptional regulation to prime cancer cell paraptosis therefore was concluded.
Citation Format: Ling-Chu Chang, Shih-Kai Chiang, Shuen-Ei Chen. CDK7/CDK9 mediates transcriptional regulation to prime cancer cell paraptosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4326.
... CDK7i can cause cell cycle arrest, apoptosis, and transcriptional repression, especially in super-enhancer-related genes in cancer, and has demonstrated its potential to overcome cancer treatment resistance. Four CDK7i, ICEC0942 (CT7001), SY-1365, SY-5609, and LY3405105 are now in Phase I/II clinical trials [52]. Inhibition of CDK7 by BS-181 significantly hinders the development of collagen-induced arthritis in mice [37]. ...
Colorectal cancer is a global malignancy with a high incidence and mortality rate. THZ2, a small inhibitor targeted CDK7, could inhibit multiple human tumor growths including small cell lung cancer, triple-negative breast cancer, ovarian cancer. However, the effect of THZ2 on inflammation, especially on colitis-associated colorectal cancer, is still unknown. In this study, we assessed the anti-inflammatory and anti-tumor effect of THZ2 in the mouse models of dextran sulfate sodium (DSS)-induced acute colitis and azoxymethane (AOM)/DSS-induced colitis-associated colorectal cancer. We found that THZ2 ameliorated inflammatory symptoms, including bleeding and diarrhea, in mouse models of DSS-induced acute colitis and AOM/DSS-induced colorectal cancer. The results of Western blot and immunohistochemistry showed that THZ2 rescued the up-regulated expression of COX2, IL-6, β-catenin, and snail in the mouse models. Moreover, THZ2 inhibits the development of colorectal cancer in the mouse model of AOM/DSS-induced colitis-associated colorectal cancer. Generally, THZ2 not only can inhibit DSS-induced colitis, but also can hinder AOM/DSS-induced colorectal cancer.
... It regulates transcription initiation and the cell cycle by phosphorylating RNA polymerase II and cyclin-dependent kinases, respectively. Due to this central role in cellular physiology, the CAK has been identified as a promising target for cancer therapeutics 3 and it is a possible target for antivirals 4 . Several groups have discovered specific inhibitors of the CAK 4-9 , including high-affinity inhibitors that occupy the active site to compete with adenosine-nucleotide binding, and covalent inhibitors that modify a cysteine residue in the vicinity of the active site. ...
Rational design of next-generation therapeutics can be facilitated by high-resolution structures of drug targets bound to small-molecule inhibitors. However, application of structure-based methods to macromolecules refractory to crystallization has been hampered by the often-limiting resolution and throughput of cryogenic electron microscopy (cryo-EM). Here, we use high-resolution cryo-EM to determine structures of the CDK-activating kinase, a master regulator of cell growth and division, in its free and nucleotide-bound states and in complex with 15 inhibitors at up to 1.8 Å resolution. Our structures provide detailed insight into inhibitor interactions and networks of water molecules in the active site of cyclin-dependent kinase 7 and provide insights into the mechanisms contributing to inhibitor selectivity, thereby providing the basis for rational design of next-generation therapeutics. These results establish a methodological framework for the use of high-resolution cryo-EM in structure-based drug design.
