1
|
Kiri S, Ryba T. Cancer, metastasis, and the epigenome. Mol Cancer 2024; 23:154. [PMID: 39095874 PMCID: PMC11295362 DOI: 10.1186/s12943-024-02069-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 07/22/2024] [Indexed: 08/04/2024] Open
Abstract
Cancer is the second leading cause of death worldwide and disease burden is expected to increase globally throughout the next several decades, with the majority of cancer-related deaths occurring in metastatic disease. Cancers exhibit known hallmarks that endow them with increased survival and proliferative capacities, frequently as a result of de-stabilizing mutations. However, the genomic features that resolve metastatic clones from primary tumors are not yet well-characterized, as no mutational landscape has been identified as predictive of metastasis. Further, many cancers exhibit no known mutation signature. This suggests a larger role for non-mutational genome re-organization in promoting cancer evolution and dissemination. In this review, we highlight current critical needs for understanding cell state transitions and clonal selection advantages for metastatic cancer cells. We examine links between epigenetic states, genome structure, and misregulation of tumor suppressors and oncogenes, and discuss how recent technologies for understanding domain-scale regulation have been leveraged for a more complete picture of oncogenic and metastatic potential.
Collapse
Affiliation(s)
- Saurav Kiri
- College of Medicine, University of Central Florida, 6850 Lake Nona Blvd., Orlando, 32827, Florida, USA.
| | - Tyrone Ryba
- Department of Natural Sciences, New College of Florida, 5800 Bay Shore Rd., Sarasota, 34243, Florida, USA.
| |
Collapse
|
2
|
Peng S, Xie Z, Jiang H, Zhang G, Chen N. Revealing the characteristics of SETD2-mutated clear cell renal cell carcinoma through tumor heterogeneity analysis. Front Genet 2024; 15:1447139. [PMID: 39119581 PMCID: PMC11306021 DOI: 10.3389/fgene.2024.1447139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 07/08/2024] [Indexed: 08/10/2024] Open
Abstract
Background Renal cell carcinoma (RCC) is the most prevalent type of malignant kidney tumor in adults, with clear cell renal cell carcinoma (ccRCC) comprising about 75% of all cases. The SETD2 gene, which is involved in the modification of histone proteins, is often found to have alterations in ccRCC. Yet, our understanding of how these SETD2 mutations affect ccRCC characteristics and behavior within the tumor microenvironment is still not fully understood. Methods We conducted a detailed analysis of single-cell RNA sequencing (scRNA-seq) data from ccRCC. First, the data was preprocessed using the Python package, "scanpy." High variability genes were pinpointed through Pearson's correlation coefficient. Dimensionality reduction and clustering identification were performed using Principal Component Analysis (PCA) and the Leiden algorithm. Malignant cell identification was conducted with the "InferCNV" R package, while cell trajectories and intercellular communication were depicted using the Python packages "VIA" and "cellphoneDB." We then employed the R package "Deseq2" to determine differentially expressed genes (DEGs) between groups. Using high-dimensional weighted gene correlation network analysis (hdWGCNA), co-expression modules were identified. We intersected these modules with DEGs to establish prognostic models through univariate Cox and the least absolute shrinkage and selection operator (LASSO) method. Results We identified 69 and 53 distinctive cell clusters, respectively. These were classified further into 12 unique cell types. This analysis highlighted the presence of an abnormal tumor sub-cluster (MT + group), identified by high mitochondrial-encoded protein gene expression and an indication of unfavorable prognosis. Investigation of cellular interactions spotlighted significant interactions between the MT + group and endothelial cells, macrophaes. In addition, we developed a prognostic model based on six characteristic genes. Notably, risk scores derived from these genes correlated significantly with various clinical features. Finally, a nomogram model was established to facilitate more accurate outcome prediction, incorporating four independent risk factors. Conclusion Our findings provide insight into the crucial transcriptomic characteristics of ccRCC associated with SETD2 mutation. We discovered that this mutation-induced subcluster could stimulate M2 polarization in macrophages, suggesting a heightened propensity for metastasis. Moreover, our prognostic model demonstrated effectiveness in forecasting overall survival for ccRCC patients, thus presenting a valuable clinical tool.
Collapse
Affiliation(s)
- Shansen Peng
- Meizhou Clinical Institute of Shantou University Medical College, Meizhou, China
- Department of Urology, Meizhou People’s Hospital, Meizhou Academy of Medical Sciences, Meizhou, China
| | - Zhouzhou Xie
- Meizhou Clinical Institute of Shantou University Medical College, Meizhou, China
- Department of Urology, Meizhou People’s Hospital, Meizhou Academy of Medical Sciences, Meizhou, China
| | - Huiming Jiang
- Meizhou Clinical Institute of Shantou University Medical College, Meizhou, China
- Department of Urology, Meizhou People’s Hospital, Meizhou Academy of Medical Sciences, Meizhou, China
| | - Guihao Zhang
- Meizhou Clinical Institute of Shantou University Medical College, Meizhou, China
- Department of Urology, Meizhou People’s Hospital, Meizhou Academy of Medical Sciences, Meizhou, China
| | - Nanhui Chen
- Meizhou Clinical Institute of Shantou University Medical College, Meizhou, China
- Department of Urology, Meizhou People’s Hospital, Meizhou Academy of Medical Sciences, Meizhou, China
| |
Collapse
|
3
|
Maldonado E, Rathmell WK, Shapiro GI, Takebe N, Rodon J, Mahalingam D, Trikalinos NA, Kalebasty AR, Parikh M, Boerner SA, Balido C, Krings G, Burns TF, Bergsland EK, Munster PN, Ashworth A, LoRusso P, Aggarwal RR. A Phase II Trial of the WEE1 Inhibitor Adavosertib in SETD2-Altered Advanced Solid Tumor Malignancies (NCI 10170). CANCER RESEARCH COMMUNICATIONS 2024; 4:1793-1801. [PMID: 38920407 PMCID: PMC11264598 DOI: 10.1158/2767-9764.crc-24-0213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/16/2024] [Accepted: 06/20/2024] [Indexed: 06/27/2024]
Abstract
We sought to evaluate the efficacy of WEE1 inhibitor adavosertib in patients with solid tumor malignancies (cohort A) and clear cell renal cell carcinoma (ccRCC; cohort B). NCT03284385 was a parallel cohort, Simon two-stage, phase II study of adavosertib (300 mg QDAY by mouth on days 1-5 and 8-12 of each 21-day cycle) in patients with solid tumor malignancies harboring a pathogenic SETD2 mutation. The primary endpoint was the objective response rate. Correlative assays evaluated the loss of H3K36me3 by IHC, a downstream consequence of SETD2 loss, in archival tumor tissue. Eighteen patients were enrolled (9/cohort). The median age was 60 years (range 45-74). The median duration of treatment was 1.28 months (range 0-24+). No objective responses were observed in either cohort; accrual was halted following stage 1. Minor tumor regressions were observed in 4/18 (22%) evaluable patients. Stable disease (SD) was the best overall response in 10/18 (56%) patients, including three patients with SD > 4 months. One patient with ccRCC remains on treatment for >24 months. The most common adverse events of any grade were nausea (59%), anemia (41%), diarrhea (41%), and neutropenia (41%). Nine patients (50%) experienced a Grade ≥3 adverse event. Of eight evaluable archival tissue samples, six (75%) had a loss of H3K36me3 by IHC. Adavosertib failed to exhibit objective responses in SETD2-altered ccRCC and other solid tumor malignancies although prolonged SD was observed in a subset of patients. Combination approaches may yield greater depth of tumor response. SIGNIFICANCE WEE1 inhibition with adavosertib monotherapy demonstrated limited clinical activity in patients with SETD2-altered solid tumors despite compelling preclinical data indicating a synthetic lethal effect, which did not translate into robust tumor regression. Loss of the H3K36me3 trimethylation mark caused by SETD2-deficiency was confirmed in the majority of evaluable tumors. A subset of patients derived clinical benefit as manifested by minor tumor regressions and prolonged SD.
Collapse
Affiliation(s)
- Edward Maldonado
- University of California, San Francisco, San Francisco, California.
| | | | | | | | - Jordi Rodon
- Investigational Cancer Therapeutics, MD Anderson Cancer Center, Houston, Texas.
| | | | | | | | - Mamta Parikh
- University of California, Davis, Davis, California.
| | | | - Celene Balido
- University of California, San Francisco, San Francisco, California.
| | - Gregor Krings
- University of California, San Francisco, San Francisco, California.
| | - Timothy F. Burns
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania.
| | | | | | - Alan Ashworth
- University of California, San Francisco, San Francisco, California.
| | | | | |
Collapse
|
4
|
Wong EWP, Sahin M, Yang R, Lee U, Zhan YA, Misra R, Tomas F, Alomran N, Polyzos A, Lee CJ, Trieu T, Fundichely AM, Wiesner T, Rosowicz A, Cheng S, Liu C, Lallo M, Merghoub T, Hamard PJ, Koche R, Khurana E, Apostolou E, Zheng D, Chen Y, Leslie CS, Chi P. TAD hierarchy restricts poised LTR activation and loss of TAD hierarchy promotes LTR co-option in cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.31.596845. [PMID: 38895201 PMCID: PMC11185511 DOI: 10.1101/2024.05.31.596845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Transposable elements (TEs) are abundant in the human genome, and they provide the sources for genetic and functional diversity. The regulation of TEs expression and their functional consequences in physiological conditions and cancer development remain to be fully elucidated. Previous studies suggested TEs are repressed by DNA methylation and chromatin modifications. The effect of 3D chromatin topology on TE regulation remains elusive. Here, by integrating transcriptome and 3D genome architecture studies, we showed that haploinsufficient loss of NIPBL selectively activates alternative promoters at the long terminal repeats (LTRs) of the TE subclasses. This activation occurs through the reorganization of topologically associating domain (TAD) hierarchical structures and recruitment of proximal enhancers. These observations indicate that TAD hierarchy restricts transcriptional activation of LTRs that already possess open chromatin features. In cancer, perturbation of the hierarchical chromatin topology can lead to co-option of LTRs as functional alternative promoters in a context-dependent manner and drive aberrant transcriptional activation of novel oncogenes and other divergent transcripts. These data uncovered a new layer of regulatory mechanism of TE expression beyond DNA and chromatin modification in human genome. They also posit the TAD hierarchy dysregulation as a novel mechanism for alternative promoter-mediated oncogene activation and transcriptional diversity in cancer, which may be exploited therapeutically.
Collapse
|
5
|
Wang Y, Peng J, Yang D, Xing Z, Jiang B, Ding X, Jiang C, Ouyang B, Su L. From metabolism to malignancy: the multifaceted role of PGC1α in cancer. Front Oncol 2024; 14:1383809. [PMID: 38774408 PMCID: PMC11106418 DOI: 10.3389/fonc.2024.1383809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/16/2024] [Indexed: 05/24/2024] Open
Abstract
PGC1α, a central player in mitochondrial biology, holds a complex role in the metabolic shifts seen in cancer cells. While its dysregulation is common across major cancers, its impact varies. In some cases, downregulation promotes aerobic glycolysis and progression, whereas in others, overexpression escalates respiration and aggression. PGC1α's interactions with distinct signaling pathways and transcription factors further diversify its roles, often in a tissue-specific manner. Understanding these multifaceted functions could unlock innovative therapeutic strategies. However, challenges exist in managing the metabolic adaptability of cancer cells and refining PGC1α-targeted approaches. This review aims to collate and present the current knowledge on the expression patterns, regulators, binding partners, and roles of PGC1α in diverse cancers. We examined PGC1α's tissue-specific functions and elucidated its dual nature as both a potential tumor suppressor and an oncogenic collaborator. In cancers where PGC1α is tumor-suppressive, reinstating its levels could halt cell proliferation and invasion, and make the cells more receptive to chemotherapy. In cancers where the opposite is true, halting PGC1α's upregulation can be beneficial as it promotes oxidative phosphorylation, allows cancer cells to adapt to stress, and promotes a more aggressive cancer phenotype. Thus, to target PGC1α effectively, understanding its nuanced role in each cancer subtype is indispensable. This can pave the way for significant strides in the field of oncology.
Collapse
Affiliation(s)
- Yue Wang
- Department of Surgery, Nanjing Central Hospital, Nanjing, China
| | - Jianing Peng
- Division of Biosciences, University College London, London, United Kingdom
| | - Dengyuan Yang
- Department of Surgery, Nanjing Central Hospital, Nanjing, China
| | - Zhongjie Xing
- Department of Surgery, Nanjing Central Hospital, Nanjing, China
| | - Bo Jiang
- Department of General Surgery, Nanjing Drum Tower Hospital, Clinical College of Nanjing Medical University, Nanjing, China
| | - Xu Ding
- Department of Surgery, Nanjing Central Hospital, Nanjing, China
| | - Chaoyu Jiang
- Department of General Surgery, Nanjing Drum Tower Hospital, Clinical College of Nanjing Medical University, Nanjing, China
| | - Bing Ouyang
- Department of Surgery, Nanjing Central Hospital, Nanjing, China
| | - Lei Su
- Department of General Surgery, Nanjing Drum Tower Hospital, Clinical College of Nanjing Medical University, Nanjing, China
- Department of General Surgery, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| |
Collapse
|
6
|
Lyskjær I, Iisager L, Axelsen CT, Nielsen TK, Dyrskjøt L, Fristrup N. Management of Renal Cell Carcinoma: Promising Biomarkers and the Challenges to Reach the Clinic. Clin Cancer Res 2024; 30:663-672. [PMID: 37874628 PMCID: PMC10870122 DOI: 10.1158/1078-0432.ccr-23-1892] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/23/2023] [Accepted: 09/27/2023] [Indexed: 10/25/2023]
Abstract
The incidence of renal cell carcinoma (RCC) is increasing worldwide, yet research within this field is lagging behind other cancers. Despite increased detection of early disease as a consequence of the widespread use of diagnostic CT scans, 25% of patients have disseminated disease at diagnosis. Similarly, around 25% progress to metastatic disease following curatively intended surgery. Surgery is the cornerstone in the treatment of RCC; however, when the disease is disseminated, immunotherapy or immunotherapy in combination with a tyrosine kinase inhibitor is the patient's best option. Immunotherapy is a potent treatment, with durable treatment responses and potential to cure the patient, but only half of the patients benefit from the administered treatment, and there are currently no methods that can identify which patients will respond to immunotherapy. Moreover, there is a need to identify the patients in greatest risk of relapsing after surgery for localized disease and direct adjuvant treatment there. Even though several molecular biomarkers have been published to date, we are still lacking routinely used biomarkers to guide optimal clinical management. The purpose of this review is to highlight some of the most promising biomarkers, discuss the efforts made within this field to date, and describe the barriers needed to be overcome to have reliable and robust predictive and prognostic biomarkers in the clinic for renal cancer.
Collapse
Affiliation(s)
- Iben Lyskjær
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Laura Iisager
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | | | | | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Niels Fristrup
- Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
| |
Collapse
|
7
|
Takeda K, Bastacky S, Dhir R, Mohebnasab M, Quiroga-Garza GM. Morphological characteristics of SETD2-mutated locally advanced clear cell renal cell carcinoma: Comparison with BAP1-mutated clear cell renal cell carcinoma. Ann Diagn Pathol 2024; 68:152223. [PMID: 37976977 DOI: 10.1016/j.anndiagpath.2023.152223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023]
Abstract
SET-domain containing 2 (SETD2) and BRCA1-associated protein 1 (BAP1), both chromatin remodeling genes, are frequently mutated in clear cell renal cell carcinoma (ccRCC) and involved in tumor progression and metastasis. Herein, we studied clinicopathologic features of 7 cases of locally advanced ccRCC with single SETD2 mutation, and compared to 7 cases of locally advanced ccRCC with single BAP1 mutation. SETD2-mutated ccRCC showed high-grade transformation, comprising of enlarged tumor cells with voluminous clear cytoplasm, enlarged irregular nuclei with prominent nucleoli, eosinophilic cytoplasmic granules, arranged in various architectural patterns such as large nested, tubular, tubulopapillary and solid. 71 % (5 of 7 cases) of SETD2-mutated ccRCC showed a rhabdoid morphology. SETD2-mutated ccRCC have striking propensity for invasive growth; all cases have vascular invasion and perirenal (extracapsular) adipose tissue invasion. After nephrectomy, distant metastasis was found in 67 % (4 of 7 cases) of patients with SETD2-mutated ccRCC. The most common metastatic site was the lung (3 cases), followed by precaval lymph nodes (1 case). BAP1-mutated ccRCC also showed a similar high-grade morphology, with rhabdoid and/or sarcomatoid features. Their high-grade features mostly overlapped with those of SETD2-mutated ccRCC, which makes difficult to predict the presence of BAP1 or SETD2 mutation solely from morphology. These findings justify the use of molecular testing to detect these mutations, especially when we encounter high-grade ccRCC. Detecting SETD2 and BAP1 mutation in ccRCC is useful for risk stratification and proper therapeutic strategy.
Collapse
Affiliation(s)
- Kotaro Takeda
- Department of Pathology, Genitourinary Pathology Center of Excellence, University of Pittsburgh Medical Center, Pittsburgh, USA.
| | - Sheldon Bastacky
- Department of Pathology, Genitourinary Pathology Center of Excellence, University of Pittsburgh Medical Center, Pittsburgh, USA
| | - Rajiv Dhir
- Department of Pathology, Genitourinary Pathology Center of Excellence, University of Pittsburgh Medical Center, Pittsburgh, USA
| | - Maedeh Mohebnasab
- Department of Pathology, Division of Molecular Genetics Pathology, University of Pittsburgh Medical Center, Pittsburgh, USA
| | - Gabriela M Quiroga-Garza
- Department of Pathology, Genitourinary Pathology Center of Excellence, University of Pittsburgh Medical Center, Pittsburgh, USA
| |
Collapse
|
8
|
Wang T, Wagner RT, Hlady RA, Pan X, Zhao X, Kim S, Wang L, Lee J, Luo H, Castle EP, Lake DF, Ho TH, Robertson KD. SETD2 loss in renal epithelial cells drives epithelial-to-mesenchymal transition in a TGF-β-independent manner. Mol Oncol 2024; 18:44-61. [PMID: 37418588 PMCID: PMC10766198 DOI: 10.1002/1878-0261.13487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/25/2023] [Accepted: 07/04/2023] [Indexed: 07/09/2023] Open
Abstract
Histone-lysine N-methyltransferase SETD2 (SETD2), the sole histone methyltransferase that catalyzes trimethylation of lysine 36 on histone H3 (H3K36me3), is often mutated in clear cell renal cell carcinoma (ccRCC). SETD2 mutation and/or loss of H3K36me3 is linked to metastasis and poor outcome in ccRCC patients. Epithelial-to-mesenchymal transition (EMT) is a major pathway that drives invasion and metastasis in various cancer types. Here, using novel kidney epithelial cell lines isogenic for SETD2, we discovered that SETD2 inactivation drives EMT and promotes migration, invasion, and stemness in a transforming growth factor-beta-independent manner. This newly identified EMT program is triggered in part through secreted factors, including cytokines and growth factors, and through transcriptional reprogramming. RNA-seq and assay for transposase-accessible chromatin sequencing uncovered key transcription factors upregulated upon SETD2 loss, including SOX2, POU2F2 (OCT2), and PRRX1, that could individually drive EMT and stemness phenotypes in SETD2 wild-type (WT) cells. Public expression data from SETD2 WT/mutant ccRCC support the EMT transcriptional signatures derived from cell line models. In summary, our studies reveal that SETD2 is a key regulator of EMT phenotypes through cell-intrinsic and cell-extrinsic mechanisms that help explain the association between SETD2 loss and ccRCC metastasis.
Collapse
Affiliation(s)
- Tianchu Wang
- Molecular Pharmacology and Experimental Therapeutics Graduate Program, Mayo Clinic Graduate School of Biomedical SciencesMayo ClinicRochesterMNUSA
- Department of Molecular Pharmacology and Experimental TherapeuticsMayo ClinicRochesterMNUSA
| | - Ryan T. Wagner
- Department of Molecular Pharmacology and Experimental TherapeuticsMayo ClinicRochesterMNUSA
| | - Ryan A. Hlady
- Department of Molecular Pharmacology and Experimental TherapeuticsMayo ClinicRochesterMNUSA
| | - Xiaoyu Pan
- Department of Molecular Pharmacology and Experimental TherapeuticsMayo ClinicRochesterMNUSA
| | - Xia Zhao
- Department of Molecular Pharmacology and Experimental TherapeuticsMayo ClinicRochesterMNUSA
| | - Sungho Kim
- Department of Molecular Pharmacology and Experimental TherapeuticsMayo ClinicRochesterMNUSA
| | - Liguo Wang
- Division of Biomedical Statistics and Informatics, Department of Health Science ResearchMayo ClinicRochesterMNUSA
| | - Jeong‐Heon Lee
- Epigenomics Development LaboratoryMayo ClinicRochesterMNUSA
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterMNUSA
| | - Huijun Luo
- Division of Hematology and OncologyMayo Clinic ArizonaPhoenixAZUSA
| | | | | | - Thai H. Ho
- Division of Hematology and OncologyMayo Clinic ArizonaPhoenixAZUSA
| | - Keith D. Robertson
- Department of Molecular Pharmacology and Experimental TherapeuticsMayo ClinicRochesterMNUSA
| |
Collapse
|
9
|
Pascual G, Majem B, Benitah SA. Targeting lipid metabolism in cancer metastasis. Biochim Biophys Acta Rev Cancer 2024; 1879:189051. [PMID: 38101461 DOI: 10.1016/j.bbcan.2023.189051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 11/29/2023] [Accepted: 12/04/2023] [Indexed: 12/17/2023]
Abstract
This review delves into the most recent research on the metabolic adaptability of cancer cells and examines how their metabolic functions can impact their progression into metastatic forms. We emphasize the growing significance of lipid metabolism and dietary lipids within the tumor microenvironment, underscoring their influence on tumor progression. Additionally, we present an outline of the interplay between metabolic processes and the epigenome of cancer cells, underscoring the importance regarding the metastatic process. Lastly, we examine the potential of targeting metabolism as a therapeutic approach in combating cancer progression, shedding light on innovative drugs/targets currently undergoing preclinical evaluation.
Collapse
Affiliation(s)
- Gloria Pascual
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
| | - Blanca Majem
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Salvador Aznar Benitah
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
| |
Collapse
|
10
|
Contreras Yametti GP, Robbins G, Chowdhury A, Narang S, Ostrow TH, Kilberg H, Greenberg J, Kramer L, Raetz E, Tsirigos A, Evensen NA, Carroll WL. SETD2 mutations do not contribute to clonal fitness in response to chemotherapy in childhood B cell acute lymphoblastic leukemia. Leuk Lymphoma 2024; 65:78-90. [PMID: 37874744 DOI: 10.1080/10428194.2023.2273752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 10/14/2023] [Indexed: 10/26/2023]
Abstract
Mutations in genes encoding epigenetic regulators are commonly observed at relapse in B cell acute lymphoblastic leukemia (B-ALL). Loss-of-function mutations in SETD2, an H3K36 methyltransferase, have been observed in B-ALL and other cancers. Previous studies on mutated SETD2 in solid tumors and acute myelogenous leukemia support a role in promoting resistance to DNA damaging agents. We did not observe chemoresistance, an impaired DNA damage response, nor increased mutation frequency in response to thiopurines using CRISPR-mediated knockout in wild-type B-ALL cell lines. Likewise, restoration of SETD2 in cell lines with hemizygous mutations did not increase sensitivity. SETD2 mutations affected the chromatin landscape and transcriptional output that was unique to each cell line. Collectively our data does not support a role for SETD2 mutations in driving clonal evolution and relapse in B-ALL, which is consistent with the lack of enrichment of SETD2 mutations at relapse in most studies.
Collapse
Affiliation(s)
- Gloria P Contreras Yametti
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Gabriel Robbins
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Ashfiyah Chowdhury
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Sonali Narang
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Talia H Ostrow
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Harrison Kilberg
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Joshua Greenberg
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Lindsay Kramer
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Elizabeth Raetz
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Aristotelis Tsirigos
- Departments of Pediatrics and Pathology, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Nikki A Evensen
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - William L Carroll
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
- Department of Pathology, NYU Langone Health, New York, NY, USA
| |
Collapse
|
11
|
Xu W, Lu J, Tian X, Ye S, Wei S, Wang J, Anwaier A, Qu Y, Liu W, Chang K, Zhang H, Ye D. Unveiling the impact of tertiary lymphoid structures on immunotherapeutic responses of clear cell renal cell carcinoma. MedComm (Beijing) 2024; 5:e461. [PMID: 38222314 PMCID: PMC10784869 DOI: 10.1002/mco2.461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 11/23/2023] [Accepted: 12/05/2023] [Indexed: 01/16/2024] Open
Abstract
Tertiary lymphoid structures (TLS) are organized aggregates of immune cells that form under pathological conditions. However, the predictive value of TLS in clear cell renal cell carcinoma (ccRCC) for immunotherapies remains unclear. We comprehensively assessed the implications for prognosis and immunological responses of the TLS spatial and maturation heterogeneity in 655 ccRCC patients. A higher proportion of early-TLS was found in peritumoral TLS, while intratumoral TLS mainly comprised secondary follicle-like TLS (SFL-TLS), indicating markedly better survival. Notably, presence of TLS, especially intratumoral TLS and SFL-TLS, significantly correlated with better survival and objective reflection rate for ccRCC patients receiving anti-Programmed Cell Death Protein-1 (PD-1)/Programmed Cell Death-Ligand-1 (PD-L1) immunotherapies. In peritumoral TLS cluster, primary follicle-like TLS, the proportion of tumor-associated macrophages, and Treg infiltration in the peritumoral regions increased prominently, suggesting an immunosuppressive tumor microenvironment. Interestingly, spatial transcriptome annotation and multispectral fluorescence showed that an abundance of mature plasma cells within mature TLS has the capacity to produce IgA and IgG, which demonstrate significantly higher objective response rates and a superior prognosis for ccRCC patients subjected to immunotherapy. In conclusion, this study revealed the implications of TLS spatial and maturation heterogeneity on the immunological status and clinical responses, allowing the improvement of precise immunotherapies of ccRCC.
Collapse
Affiliation(s)
- Wenhao Xu
- Department of UrologyFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteShanghaiChina
| | - Jiahe Lu
- Department of UrologyFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteShanghaiChina
- School of Cellular and Molecular MedicineUniversity of BristolBristolUK
| | - Xi Tian
- Department of UrologyFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteShanghaiChina
| | - Shiqi Ye
- Department of UrologyFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteShanghaiChina
| | - Shiyin Wei
- Affiliated Hospital of Youjiang Medical University for NationalitiesBaiseChina
| | - Jun Wang
- State Key Laboratory of Oncology in South ChinaCollaborativeInnovation Center for Cancer MedicineDepartment of UrologySun Yat‐sen University Cancer CenterGuangzhouChina
| | - Aihetaimujiang Anwaier
- Department of UrologyFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteShanghaiChina
| | - Yuanyuan Qu
- Department of UrologyFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteShanghaiChina
| | - Wangrui Liu
- Renji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Kun Chang
- Department of UrologyFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteShanghaiChina
| | - Hailiang Zhang
- Department of UrologyFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteShanghaiChina
| | - Dingwei Ye
- Department of UrologyFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteShanghaiChina
| |
Collapse
|
12
|
Zheng X, Luo Y, Xiong Y, Liu X, Zeng C, Lu X, Wang X, Cheng Y, Wang S, Lan H, Wang K, Weng Z, Bi W, Gan X, Jia X, Wang L, Wang Y. Tumor cell-intrinsic SETD2 inactivation sensitizes cancer cells to immune checkpoint blockade through the NR2F1-STAT1 pathway. J Immunother Cancer 2023; 11:e007678. [PMID: 38056895 PMCID: PMC10711831 DOI: 10.1136/jitc-2023-007678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2023] [Indexed: 12/08/2023] Open
Abstract
BACKGROUND Cancer immunotherapies can induce durable tumor regression, but most patients do not respond. SETD2 mutation has been linked to the efficacy of immune checkpoint inhibitors (ICIs) immunotherapy. The functional importance of the SETD2 inactivation and how to modulate immunotherapy response remains unclear. METHODS To explore the function of SETD2 in immunotherapy, knockout and subsequent functional experiments were conducted. Bulk RNA-seq, ATAC-seq, Chip-seq and single-cell RNA-seq were performed to dissect the mechanism and explore the immune microenvironment of mouse tumor. Flow cytometry was used to assess cell surface antigen and intratumoral T cell levels. RESULTS We comprehensively determine the effect of SETD2 inactivation in ICIs therapy and elucidate the mechanistic impact on tumor immunity. Murine syngeneic tumors harboring Setd2 inactivation are sensitive to ICIs. By bulk and single-cell RNA-seq, we further reveal that SETD2 inactivation reprograms intratumoral immune cells and inflames the tumor microenvironment, which is characterized by high infiltration of T cells and enhanced antigen presentation to activate CD8+ T cell-mediated killing. Mechanistically, via an integrated multiomics analysis using ATAC-seq, ChIP-seq and RNA-seq, we demonstrate that SETD2 inactivation reduces NR2F1 transcription by impairing H3K36me3 deposition and chromatin accessibility, which activates the STAT1 signaling pathway to promote chemokines and programmed cell death protein-1 (PD-1) expression and enhance antigen presentation. All these regulatory mechanisms synergistically promote the effects of anti-programmed cell death ligand 1 immunotherapy in Setd2-knockout syngeneic mouse models. The SETD2-NR2F1-STAT1 regulatory axis is conserved in human and murine cancers. Finally, cancer patients harboring SETD2 mutations who received ICIs show increased durable clinical benefits and survival. CONCLUSIONS These findings provide novel insights into the biology of SETD2 inactivation regulation and reveal a new potential therapeutic biomarker for ICIs immunotherapy in various refractory cancers.
Collapse
Affiliation(s)
- Xufen Zheng
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yuxiang Luo
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yangjie Xiong
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoxiao Liu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chunling Zeng
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiaojing Lu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiaofang Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yumei Cheng
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Simin Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Haoqi Lan
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Kai Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhonghui Weng
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wenbo Bi
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xinxin Gan
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Xiaona Jia
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Linhui Wang
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Yuexiang Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| |
Collapse
|
13
|
Janin M, Davalos V, Esteller M. Cancer metastasis under the magnifying glass of epigenetics and epitranscriptomics. Cancer Metastasis Rev 2023; 42:1071-1112. [PMID: 37369946 PMCID: PMC10713773 DOI: 10.1007/s10555-023-10120-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023]
Abstract
Most of the cancer-associated mortality and morbidity can be attributed to metastasis. The role of epigenetic and epitranscriptomic alterations in cancer origin and progression has been extensively demonstrated during the last years. Both regulations share similar mechanisms driven by DNA or RNA modifiers, namely writers, readers, and erasers; enzymes responsible of respectively introducing, recognizing, or removing the epigenetic or epitranscriptomic modifications. Epigenetic regulation is achieved by DNA methylation, histone modifications, non-coding RNAs, chromatin accessibility, and enhancer reprogramming. In parallel, regulation at RNA level, named epitranscriptomic, is driven by a wide diversity of chemical modifications in mostly all RNA molecules. These two-layer regulatory mechanisms are finely controlled in normal tissue, and dysregulations are associated with every hallmark of human cancer. In this review, we provide an overview of the current state of knowledge regarding epigenetic and epitranscriptomic alterations governing tumor metastasis, and compare pathways regulated at DNA or RNA levels to shed light on a possible epi-crosstalk in cancer metastasis. A deeper understanding on these mechanisms could have important clinical implications for the prevention of advanced malignancies and the management of the disseminated diseases. Additionally, as these epi-alterations can potentially be reversed by small molecules or inhibitors against epi-modifiers, novel therapeutic alternatives could be envisioned.
Collapse
Affiliation(s)
- Maxime Janin
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), IJC Building, Germans Trias I Pujol, Ctra de Can Ruti, Cami de Les Escoles S/N, 08916 Badalona, Barcelona, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
| | - Veronica Davalos
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), IJC Building, Germans Trias I Pujol, Ctra de Can Ruti, Cami de Les Escoles S/N, 08916 Badalona, Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), IJC Building, Germans Trias I Pujol, Ctra de Can Ruti, Cami de Les Escoles S/N, 08916 Badalona, Barcelona, Spain.
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain.
- Institucio Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain.
| |
Collapse
|
14
|
Lu X, Vano YA, Su X, Helleux A, Lindner V, Mouawad R, Spano JP, Rouprêt M, Compérat E, Verkarre V, Sun CM, Bennamoun M, Lang H, Barthelemy P, Cheng W, Xu L, Davidson I, Yan F, Fridman WH, Sautes-Fridman C, Oudard S, Malouf GG. Silencing of genes by promoter hypermethylation shapes tumor microenvironment and resistance to immunotherapy in clear-cell renal cell carcinomas. Cell Rep Med 2023; 4:101287. [PMID: 37967556 PMCID: PMC10694769 DOI: 10.1016/j.xcrm.2023.101287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/21/2023] [Accepted: 10/19/2023] [Indexed: 11/17/2023]
Abstract
The efficacy of immune checkpoint inhibitors varies in clear-cell renal cell carcinoma (ccRCC), with notable primary resistance among patients. Here, we integrate epigenetic (DNA methylation) and transcriptome data to identify a ccRCC subtype characterized by cancer-specific promoter hypermethylation and epigenetic silencing of Polycomb targets. We develop and validate an index of methylation-based epigenetic silencing (iMES) that predicts primary resistance to immune checkpoint inhibition (ICI) in the BIONIKK trial. High iMES is associated with VEGF pathway silencing, endothelial cell depletion, immune activation/suppression, EZH2 activation, BAP1/SETD2 deficiency, and resistance to ICI. Combination therapy with hypomethylating agents or tyrosine kinase inhibitors may benefit patients with high iMES. Intriguingly, tumors with low iMES exhibit increased endothelial cells and improved ICI response, suggesting the importance of angiogenesis in ICI treatment. We also develop a transcriptome-based analogous system for extended applicability of iMES. Our study underscores the interplay between epigenetic alterations and tumor microenvironment in determining immunotherapy response.
Collapse
Affiliation(s)
- Xiaofan Lu
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400 Illkirch, France
| | - Yann-Alexandre Vano
- Department of Medical Oncology, Hôpital Européen Georges Pompidou, Institut du Cancer Paris CARPEM, AP-HP, Université Paris Cité, Paris, France; Centre de Recherche Cordeliers, INSERM 1138, Université de Paris Cité, Sorbonne Université, Equipe labellisée Ligue contre le Cancer, 75006 Paris, France
| | - Xiaoping Su
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexandra Helleux
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400 Illkirch, France
| | - Véronique Lindner
- Department of Pathology, Strasbourg University Hospital, Strasbourg, France
| | - Roger Mouawad
- Department of Medical Oncology, Sorbonne University, AP-HP, Hôpital Pitié-Salpêtrière, Paris, France
| | - Jean-Philippe Spano
- Department of Medical Oncology, Sorbonne University, AP-HP, Hôpital Pitié-Salpêtrière, Paris, France
| | - Morgan Rouprêt
- Sorbonne University, GRC 5 P, UKredictive Onco-Uro, AP-HP, Urology, Pitié-Salpêtrière Hospital, 75013 Paris, France
| | - Eva Compérat
- Department of Pathology, Sorbonne University, AP-HP, Hôpital Tenon, Paris, France
| | - Virginie Verkarre
- Department of Pathology, Hôpital Européen Georges Pompidou, Institut du Cancer Paris CARPEM, AP-HP, Université Paris Cité, Paris, France
| | - Cheng-Ming Sun
- Centre de Recherche Cordeliers, INSERM 1138, Université de Paris Cité, Sorbonne Université, Equipe labellisée Ligue contre le Cancer, 75006 Paris, France
| | - Mostefa Bennamoun
- Department of Medical Oncology, Institut Mutualiste Montsouris, Paris, France
| | - Hervé Lang
- Department of Urology, Strasbourg University Hospital, Strasbourg, France
| | - Philippe Barthelemy
- Department of Medical Oncology, Strasbourg University, Institut de Cancérologie de Strasbourg, Strasbourg, France
| | - Wenxuan Cheng
- Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, P.R. China
| | - Li Xu
- Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, P.R. China
| | - Irwin Davidson
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400 Illkirch, France
| | - Fangrong Yan
- Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, P.R. China
| | - Wolf Hervé Fridman
- Centre de Recherche Cordeliers, INSERM 1138, Université de Paris Cité, Sorbonne Université, Equipe labellisée Ligue contre le Cancer, 75006 Paris, France
| | - Catherine Sautes-Fridman
- Centre de Recherche Cordeliers, INSERM 1138, Université de Paris Cité, Sorbonne Université, Equipe labellisée Ligue contre le Cancer, 75006 Paris, France
| | - Stéphane Oudard
- Centre de Recherche Cordeliers, INSERM 1138, Université de Paris Cité, Sorbonne Université, Equipe labellisée Ligue contre le Cancer, 75006 Paris, France
| | - Gabriel G Malouf
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400 Illkirch, France; Department of Medical Oncology, Strasbourg University, Institut de Cancérologie de Strasbourg, Strasbourg, France.
| |
Collapse
|
15
|
Rao H, Liu C, Wang A, Ma C, Xu Y, Ye T, Su W, Zhou P, Gao WQ, Li L, Ding X. SETD2 deficiency accelerates sphingomyelin accumulation and promotes the development of renal cancer. Nat Commun 2023; 14:7572. [PMID: 37989747 PMCID: PMC10663509 DOI: 10.1038/s41467-023-43378-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 11/07/2023] [Indexed: 11/23/2023] Open
Abstract
Patients with polycystic kidney disease (PKD) encounter a high risk of clear cell renal cell carcinoma (ccRCC), a malignant tumor with dysregulated lipid metabolism. SET domain-containing 2 (SETD2) has been identified as an important tumor suppressor and an immunosuppressor in ccRCC. However, the role of SETD2 in ccRCC generation in PKD remains largely unexplored. Herein, we perform metabolomics, lipidomics, transcriptomics and proteomics within SETD2 loss induced PKD-ccRCC transition mouse model. Our analyses show that SETD2 loss causes extensive metabolic reprogramming events that eventually results in enhanced sphingomyelin biosynthesis and tumorigenesis. Clinical ccRCC patient specimens further confirm the abnormal metabolic reprogramming and sphingomyelin accumulation. Tumor symptom caused by Setd2 knockout is relieved by myriocin, a selective inhibitor of serine-palmitoyl-transferase and sphingomyelin biosynthesis. Our results reveal that SETD2 deficiency promotes large-scale metabolic reprogramming and sphingomyelin biosynthesis during PKD-ccRCC transition. This study introduces high-quality multi-omics resources and uncovers a regulatory mechanism of SETD2 on lipid metabolism during tumorigenesis.
Collapse
Affiliation(s)
- Hanyu Rao
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute for Personalized Medicine and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Changwei Liu
- State Key Laboratory of Systems Medicine for Cancer, Institute for Personalized Medicine and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Aiting Wang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute for Personalized Medicine and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Chunxiao Ma
- State Key Laboratory of Systems Medicine for Cancer, Institute for Personalized Medicine and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Yue Xu
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Tianbao Ye
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenqiong Su
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute for Personalized Medicine and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Peijun Zhou
- Division of Kidney Transplant, Department of Urology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wei-Qiang Gao
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Li Li
- State Key Laboratory of Systems Medicine for Cancer, Institute for Personalized Medicine and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China.
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200127, China.
| | - Xianting Ding
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
- State Key Laboratory of Systems Medicine for Cancer, Institute for Personalized Medicine and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China.
| |
Collapse
|
16
|
Zhou X, Sekino Y, Li HT, Fu G, Yang Z, Zhao S, Gujar H, Zu X, Weisenberger DJ, Gill IS, Tulpule V, D’souza A, Quinn DI, Han B, Liang G. SETD2 Deficiency Confers Sensitivity to Dual Inhibition of DNA Methylation and PARP in Kidney Cancer. Cancer Res 2023; 83:3813-3826. [PMID: 37695044 PMCID: PMC10843145 DOI: 10.1158/0008-5472.can-23-0401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 07/18/2023] [Accepted: 09/06/2023] [Indexed: 09/12/2023]
Abstract
SETD2 deficiency alters the epigenetic landscape by causing depletion of H3K36me3 and plays an important role in diverse forms of cancer, most notably in aggressive and metastatic clear-cell renal cell carcinomas (ccRCC). Development of an effective treatment scheme targeting SETD2-compromised cancer is urgently needed. Considering that SETD2 is involved in DNA methylation and DNA repair, a combination treatment approach using DNA hypomethylating agents (HMA) and PARP inhibitors (PARPi) could have strong antitumor activity in SETD2-deficient kidney cancer. We tested the effects of the DNA HMA 5-aza-2'-dexoxydytidine (DAC), the PARPi talazoparib (BMN-673), and both in combination in human ccRCC models with or without SETD2 deficiency. The combination treatment of DAC and BMN-673 synergistically increased cytotoxicity in vitro in SETD2-deficient ccRCC cell lines but not in SETD2-proficient cell lines. DAC and BMN-673 led to apoptotic induction, increased DNA damage, insufficient DNA damage repair, and increased genomic instability. Furthermore, the combination treatment elevated immune responses, upregulated STING, and enhanced viral mimicry by activating transposable elements. Finally, the combination effectively suppressed the growth of SETD2-deficient ccRCC in in vivo mouse models. Together, these findings indicate that combining HMA and PARPi is a promising potential therapeutic strategy for treating SETD2-compromised ccRCC. SIGNIFICANCE SETD2 deficiency creates a vulnerable epigenetic status that is targetable using a DNA hypomethylating agent and PARP inhibitor combination to suppress renal cell carcinoma, identifying a precision medicine-based approach for SETD2-compromised cancers.
Collapse
Affiliation(s)
- Xinyi Zhou
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Urology, Xiangya Hospital, Central South University, Hunan, Changsha 410008, China
| | - Yohei Sekino
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Urology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Hong-Tao Li
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Guanghou Fu
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Zhi Yang
- Department of Surgery, Keck School of Medicine of USC, Los Angeles, California; Department of Surgery and Biomedical Engineering, Keck School of Medicine USC, Los Angeles, CA, USA
| | - Shuqing Zhao
- Department of Surgery, Keck School of Medicine of USC, Los Angeles, California; Department of Surgery and Biomedical Engineering, Keck School of Medicine USC, Los Angeles, CA, USA
| | - Hemant Gujar
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Xiongbing Zu
- Department of Urology, Xiangya Hospital, Central South University, Hunan, Changsha 410008, China
| | - Daniel J Weisenberger
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Inderbir S. Gill
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Varsha Tulpule
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Anishka D’souza
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - David I Quinn
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Bo Han
- Department of Surgery, Keck School of Medicine of USC, Los Angeles, California; Department of Surgery and Biomedical Engineering, Keck School of Medicine USC, Los Angeles, CA, USA
| | - Gangning Liang
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| |
Collapse
|
17
|
Wu W, Chang F, Zhang J, Tang S, Lv Z, Chen F. A novel coagulation-related lncRNA predicts the prognosis and immune of clear cell renal cell carcinoma. Sci Rep 2023; 13:16302. [PMID: 37770494 PMCID: PMC10539335 DOI: 10.1038/s41598-023-43065-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/19/2023] [Indexed: 09/30/2023] Open
Abstract
Renal cell cancer is associated with the coagulation system. Long non-coding RNA (lncRNA) expression is closely associated with the development of clear cell renal cell carcinoma (ccRCC). The aim of this study was to build a novel lncRNA model to predict the prognosis and immunological state of ccRCC. The transcriptomic data and clinical data of ccRCC were retrieved from TCGA database, subsequently, the lasso regression and lambda spectra were used to filter prognostic lncRNAs. ROC curves and the C-index were used to confirm the predictive effectiveness of this model. We also explored the difference in immune infiltration, immune checkpoints, tumor mutation burden (TMB) and drug sensitivity between the high- and low-risk groups. We created an 8 lncRNA model for predicting the outcome of ccRCC. Multivariate Cox regression analysis showed that age, tumor grade, and risk score are independent prognostic factors for ccRCC patients. ROC curve and C-index revealed the model had a good performance in predicting prognosis of ccRCC. GO and KEGG analysis showed that coagulation related genes were related to immune response. In addition, high risk group had greater TMB level and higher immune checkpoints expression. Sorafenib, Imatinib, Pazopanib, and etoposide had higher half maximal inhibitory concentration (IC50) in the high risk group whereas Sunitinib and Bosutinib had lower IC50. This novel coagulation-related long noncoding RNAs model could predict the prognosis of patients with ccRCC, and coagulation-related lncRNA may be connected to the tumor microenvironment and gene mutation of ccRCC.
Collapse
Affiliation(s)
- Wensong Wu
- Department of Urology, The Third Central Clinical College of Tianjin Medical University, Tianjin, China, 300170
| | - Fan Chang
- Department of Urology, The Third Central Hospital of Tianjin, 83 Jintang Road, Tianjin, China, 300170
- Department of Urology, Nankai University Afnity the Third Central Hospital, Tianjin, China, 300170
| | - Jianghui Zhang
- Department of Urology, The Third Central Hospital of Tianjin, 83 Jintang Road, Tianjin, China, 300170
- Department of Urology, Nankai University Afnity the Third Central Hospital, Tianjin, China, 300170
| | - Shuai Tang
- Department of Urology, The Third Central Hospital of Tianjin, 83 Jintang Road, Tianjin, China, 300170
- Department of Urology, Nankai University Afnity the Third Central Hospital, Tianjin, China, 300170
| | - Zhen Lv
- Department of Urology, The Third Central Hospital of Tianjin, 83 Jintang Road, Tianjin, China, 300170
- Department of Urology, Nankai University Afnity the Third Central Hospital, Tianjin, China, 300170
| | - Fangmin Chen
- Department of Urology, The Third Central Hospital of Tianjin, 83 Jintang Road, Tianjin, China, 300170.
- Department of Urology, Nankai University Afnity the Third Central Hospital, Tianjin, China, 300170.
| |
Collapse
|
18
|
Zhang Y, Guo W, Feng Y, Yang L, Lin H, Zhou P, Zhao K, Jiang L, Yao B, Feng N. Identification of the H3K36me3 reader LEDGF/p75 in the pancancer landscape and functional exploration in clear cell renal cell carcinoma. Comput Struct Biotechnol J 2023; 21:4134-4148. [PMID: 37675289 PMCID: PMC10477754 DOI: 10.1016/j.csbj.2023.08.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/18/2023] [Accepted: 08/25/2023] [Indexed: 09/08/2023] Open
Abstract
Lens epithelium-derived growth factor (LEDGF/p75) is a reader of epigenetic marks and a potential target for therapeutic intervention. Its involvement in human immunodeficiency virus (HIV) integration and the development of leukemia driven by MLL (also known as KMT2A) gene fusion make it an attractive candidate for drug development. However, exploration of LEDGF/p75 as an epigenetic reader of H3K36me3 in tumors is limited. Here, for the first time, we analyze the role of LEDGF/p75 in multiple cancers via multiple online databases and in vitro experiments. We used pancancer bulk sequencing data and online tools to analyze correlations of LEDGF/p75 with prognosis, genomic instability, DNA damage repair, prognostic alternative splicing, protein interactions, and tumor immunity. In summary, the present study identified that LEDGF/p75 may serve as a prognostic predictor for tumors such as adrenocortical carcinoma, kidney chromophobe, liver hepatocellular carcinoma, pancreatic adenocarcinoma, skin cutaneous melanoma, and clear cell renal cell carcinoma (ccRCC). In addition, in vitro experiments and gene microarray sequencing were performed to explore the function of LEDGF/p75 in ccRCC, providing new insights into the pathogenesis of the nonmutated SETD2 ccRCC subtype.
Collapse
Affiliation(s)
- Yuwei Zhang
- Nantong University Medical School, Nantong, China
- Department of Urology, Jiangnan University Medical Center, Wuxi, China
| | - Wei Guo
- Department of Urology, Jiangnan University Medical Center, Wuxi, China
| | - Yangkun Feng
- Nantong University Medical School, Nantong, China
| | - Longfei Yang
- Nantong University Medical School, Nantong, China
- Department of Urology, Jiangnan University Medical Center, Wuxi, China
| | - Hao Lin
- Department of Urology, Jiangnan University Medical Center, Wuxi, China
| | - Pengcheng Zhou
- Department of Medical Genetics, Nanjing Medical University, Nanjing, China
| | - Kejie Zhao
- Department of Medical Genetics, Nanjing Medical University, Nanjing, China
| | - Lin Jiang
- Department of Endocrinology and Metabolism, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Bing Yao
- Department of Medical Genetics, Nanjing Medical University, Nanjing, China
| | - Ninghan Feng
- Nantong University Medical School, Nantong, China
- Department of Urology, Jiangnan University Medical Center, Wuxi, China
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| |
Collapse
|
19
|
Chen R, Wu J, Liu S, Sun Y, Liu G, Zhang L, Yu Q, Xu J, Meng L. Immune-related risk prognostic model for clear cell renal cell carcinoma: Implications for immunotherapy. Medicine (Baltimore) 2023; 102:e34786. [PMID: 37653791 PMCID: PMC10470711 DOI: 10.1097/md.0000000000034786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 09/02/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is associated with complex immune interactions. We conducted a comprehensive analysis of immune-related differentially expressed genes in patients with ccRCC using data from The Cancer Genome Atlas and ImmPort databases. The immune-related differentially expressed genes underwent functional and pathway enrichment analysis, followed by COX regression combined with LASSO regression to construct an immune-related risk prognostic model. The model comprised 4 IRGs: CLDN4, SEMA3G, CAT, and UCN. Patients were stratified into high-risk and low-risk groups based on the median risk score, and the overall survival rate of the high-risk group was significantly lower than that of the low-risk group, confirming the reliability of the model from various perspectives. Further comparison of immune infiltration, tumor mutation load, and immunophenoscore (IPS) comparison between the 2 groups indicates that the high-risk group could potentially demonstrate a heightened sensitivity towards immunotherapy checkpoints PD-1, CTLA-4, IL-6, and LAG3 in ccRCC patients. The proposed model not only applies to ccRCC but also shows potential in developing into a prognostic model for renal cancer, thus introducing a novel approach for personalized immunotherapy in ccRCC.
Collapse
Affiliation(s)
- Ronghui Chen
- Clinical Medical College of Weifang Medical University, Weifang, China
| | - Jun Wu
- Department of Oncology, People’s Hospital of Rizhao, Rizhao, China
| | - Shan Liu
- Department of Oncology, People’s Hospital of Rizhao, Rizhao, China
| | - Yefeng Sun
- Department of Emergency, People’s Hospital of Rizhao, Rizhao, China
| | - Guozhi Liu
- Jining Medical University, Jining, China
| | - Lin Zhang
- Jining Medical University, Jining, China
| | - Qing Yu
- Clinical Medical College of Weifang Medical University, Weifang, China
| | - Juan Xu
- Clinical Medical College of Weifang Medical University, Weifang, China
| | - Lingxin Meng
- Department of Oncology, People’s Hospital of Rizhao, Rizhao, China
| |
Collapse
|
20
|
Dan J, Du Z, Zhang J, Chen T. The interplay between H3K36 methylation and DNA methylation in cancer. Cancer Biol Med 2023; 20:j.issn.2095-3941.2023.0234. [PMID: 37602556 PMCID: PMC10476472 DOI: 10.20892/j.issn.2095-3941.2023.0234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 07/25/2023] [Indexed: 08/22/2023] Open
Affiliation(s)
- Jiameng Dan
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming 650500, China
| | - Zeling Du
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming 650500, China
| | - Jinghong Zhang
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming 650500, China
| | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston 77030, USA
- Programs in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston 77030, USA
| |
Collapse
|
21
|
Yin J, Qi TF, Li L, Wang Y. Targeted Profiling of Epitranscriptomic Reader, Writer, and Eraser Proteins Regulated by H3K36me3. Anal Chem 2023; 95:9672-9679. [PMID: 37296074 PMCID: PMC10372775 DOI: 10.1021/acs.analchem.3c01552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Trimethylation of lysine 36 on histone H3 (H3K36me3), an epigenetic mark associated with actively transcribed genes, plays an important role in multiple cellular processes, including transcription elongation, DNA methylation, DNA repair, etc. Aberrant expression and mutations of the main methyltransferase for H3K36me3, i.e., SET domain-containing 2 (SETD2), were shown to be associated with various cancers. Here, we performed targeted profiling of 154 epitranscriptomic reader, writer, and eraser (RWE) proteins using a scheduled liquid chromatography-parallel-reaction monitoring (LC-PRM) method coupled with the use of stable isotope-labeled (SIL) peptides as internal standards to investigate how H3K36me3 modulates the chromatin occupancies of epitranscriptomic RWE proteins. Our results showed consistent changes in chromatin occupancies of RWE proteins upon losses of H3K36me3 and H4K16ac and a role of H3K36me3 in recruiting METTL3 to chromatin following induction of DNA double-strand breaks. In addition, protein-protein interaction network and Kaplan-Meier survival analyses revealed the importance of METTL14 and TRMT11 in kidney cancer. Taken together, our work unveiled cross-talks between histone epigenetic marks (i.e., H3K36me3 and H4K16ac) and epitranscriptomic RWE proteins and uncovered the potential roles of these RWE proteins in H3K36me3-mediated biological processes.
Collapse
Affiliation(s)
- Jiekai Yin
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403, United States
| | - Tianyu F Qi
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403, United States
| | - Lin Li
- Deparment of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403, United States
- Deparment of Chemistry, University of California, Riverside, California 92521-0403, United States
| |
Collapse
|
22
|
El Khoury LY, Pan X, Hlady RA, Wagner RT, Shaikh S, Wang L, Humphreys MR, Castle EP, Stanton ML, Ho TH, Robertson KD. Extensive intratumor regional epigenetic heterogeneity in clear cell renal cell carcinoma targets kidney enhancers and is associated with poor outcome. Clin Epigenetics 2023; 15:71. [PMID: 37120552 PMCID: PMC10149001 DOI: 10.1186/s13148-023-01471-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/21/2023] [Indexed: 05/01/2023] Open
Abstract
BACKGROUND Clear cell renal cell cancer (ccRCC), the 8th leading cause of cancer-related death in the US, is challenging to treat due to high level intratumoral heterogeneity (ITH) and the paucity of druggable driver mutations. CcRCC is unusual for its high frequency of epigenetic regulator mutations, such as the SETD2 histone H3 lysine 36 trimethylase (H3K36me3), and low frequency of traditional cancer driver mutations. In this work, we examined epigenetic level ITH and defined its relationships with pathologic features, aspects of tumor biology, and SETD2 mutations. RESULTS A multi-region sampling approach coupled with EPIC DNA methylation arrays was conducted on a cohort of normal kidney and ccRCC. ITH was assessed using DNA methylation (5mC) and CNV-based entropy and Euclidian distances. We found elevated 5mC heterogeneity and entropy in ccRCC relative to normal kidney. Variable CpGs are highly enriched in enhancer regions. Using intra-class correlation coefficient analysis, we identified CpGs that segregate tumor regions according to clinical phenotypes related to tumor aggressiveness. SETD2 wild-type tumors overall possess greater 5mC and copy number ITH than SETD2 mutant tumor regions, suggesting SETD2 loss contributes to a distinct epigenome. Finally, coupling our regional data with TCGA, we identified a 5mC signature that links regions within a primary tumor with metastatic potential. CONCLUSION Taken together, our results reveal marked levels of epigenetic ITH in ccRCC that are linked to clinically relevant tumor phenotypes and could translate into novel epigenetic biomarkers.
Collapse
Affiliation(s)
- Louis Y El Khoury
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Xiaoyu Pan
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Ryan A Hlady
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Ryan T Wagner
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Shafiq Shaikh
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Liguo Wang
- Division of Biomedical Statistics and Informatics, Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
| | | | - Erik P Castle
- Department of Urology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Melissa L Stanton
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Phoenix, AZ, USA
| | - Thai H Ho
- Division of Hematology and Medical Oncology, Mayo Clinic Arizona, Scottsdale, AZ, USA.
| | - Keith D Robertson
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA.
| |
Collapse
|
23
|
Martínez-Ruiz C, Black JRM, Puttick C, Hill MS, Demeulemeester J, Larose Cadieux E, Thol K, Jones TP, Veeriah S, Naceur-Lombardelli C, Toncheva A, Prymas P, Rowan A, Ward S, Cubitt L, Athanasopoulou F, Pich O, Karasaki T, Moore DA, Salgado R, Colliver E, Castignani C, Dietzen M, Huebner A, Al Bakir M, Tanić M, Watkins TBK, Lim EL, Al-Rashed AM, Lang D, Clements J, Cook DE, Rosenthal R, Wilson GA, Frankell AM, de Carné Trécesson S, East P, Kanu N, Litchfield K, Birkbak NJ, Hackshaw A, Beck S, Van Loo P, Jamal-Hanjani M, Swanton C, McGranahan N. Genomic-transcriptomic evolution in lung cancer and metastasis. Nature 2023; 616:543-552. [PMID: 37046093 PMCID: PMC10115639 DOI: 10.1038/s41586-023-05706-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/04/2023] [Indexed: 04/14/2023]
Abstract
Intratumour heterogeneity (ITH) fuels lung cancer evolution, which leads to immune evasion and resistance to therapy1. Here, using paired whole-exome and RNA sequencing data, we investigate intratumour transcriptomic diversity in 354 non-small cell lung cancer tumours from 347 out of the first 421 patients prospectively recruited into the TRACERx study2,3. Analyses of 947 tumour regions, representing both primary and metastatic disease, alongside 96 tumour-adjacent normal tissue samples implicate the transcriptome as a major source of phenotypic variation. Gene expression levels and ITH relate to patterns of positive and negative selection during tumour evolution. We observe frequent copy number-independent allele-specific expression that is linked to epigenomic dysfunction. Allele-specific expression can also result in genomic-transcriptomic parallel evolution, which converges on cancer gene disruption. We extract signatures of RNA single-base substitutions and link their aetiology to the activity of the RNA-editing enzymes ADAR and APOBEC3A, thereby revealing otherwise undetected ongoing APOBEC activity in tumours. Characterizing the transcriptomes of primary-metastatic tumour pairs, we combine multiple machine-learning approaches that leverage genomic and transcriptomic variables to link metastasis-seeding potential to the evolutionary context of mutations and increased proliferation within primary tumour regions. These results highlight the interplay between the genome and transcriptome in influencing ITH, lung cancer evolution and metastasis.
Collapse
Affiliation(s)
- Carlos Martínez-Ruiz
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - James R M Black
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Clare Puttick
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Mark S Hill
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Jonas Demeulemeester
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
- Integrative Cancer Genomics Laboratory, Department of Oncology, KU Leuven, Leuven, Belgium
- VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium
| | - Elizabeth Larose Cadieux
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
- Medical Genomics, University College London Cancer Institute, London, UK
| | - Kerstin Thol
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Thomas P Jones
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | | | - Antonia Toncheva
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Paulina Prymas
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Andrew Rowan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Sophia Ward
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - Laura Cubitt
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - Foteini Athanasopoulou
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - Oriol Pich
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Takahiro Karasaki
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
| | - David A Moore
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - Roberto Salgado
- Department of Pathology, ZAS Hospitals, Antwerp, Belgium
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Emma Colliver
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Carla Castignani
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
- Medical Genomics, University College London Cancer Institute, London, UK
| | - Michelle Dietzen
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Ariana Huebner
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Maise Al Bakir
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Miljana Tanić
- Medical Genomics, University College London Cancer Institute, London, UK
- Experimental Oncology, Institute for Oncology and Radiology of Serbia, Belgrade, Serbia
| | - Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Emilia L Lim
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Ali M Al-Rashed
- Centre for Nephrology, Division of Medicine, University College London, London, UK
| | - Danny Lang
- Scientific Computing STP, Francis Crick Institute, London, UK
| | - James Clements
- Scientific Computing STP, Francis Crick Institute, London, UK
| | - Daniel E Cook
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Rachel Rosenthal
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Gareth A Wilson
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Alexander M Frankell
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | | | - Philip East
- Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Nnennaya Kanu
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Kevin Litchfield
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
| | - Nicolai J Birkbak
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Allan Hackshaw
- Cancer Research UK & UCL Cancer Trials Centre, London, UK
| | - Stephan Beck
- Medical Genomics, University College London Cancer Institute, London, UK
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
- Department of Medical Oncology, University College London Hospitals, London, UK
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK.
- Department of Medical Oncology, University College London Hospitals, London, UK.
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
| |
Collapse
|
24
|
Xie Y, Sahin M, Wakamatsu T, Inoue-Yamauchi A, Zhao W, Han S, Nargund AM, Yang S, Lyu Y, Hsieh JJ, Leslie CS, Cheng EH. SETD2 regulates chromatin accessibility and transcription to suppress lung tumorigenesis. JCI Insight 2023; 8:e154120. [PMID: 36810256 PMCID: PMC9977508 DOI: 10.1172/jci.insight.154120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 01/18/2023] [Indexed: 02/23/2023] Open
Abstract
SETD2, a H3K36 trimethyltransferase, is the most frequently mutated epigenetic modifier in lung adenocarcinoma, with a mutation frequency of approximately 9%. However, how SETD2 loss of function promotes tumorigenesis remains unclear. Using conditional Setd2-KO mice, we demonstrated that Setd2 deficiency accelerated the initiation of KrasG12D-driven lung tumorigenesis, increased tumor burden, and significantly reduced mouse survival. An integrated chromatin accessibility and transcriptome analysis revealed a potentially novel tumor suppressor model of SETD2 in which SETD2 loss activates intronic enhancers to drive oncogenic transcriptional output, including the KRAS transcriptional signature and PRC2-repressed targets, through regulation of chromatin accessibility and histone chaperone recruitment. Importantly, SETD2 loss sensitized KRAS-mutant lung cancer to inhibition of histone chaperones, the FACT complex, or transcriptional elongation both in vitro and in vivo. Overall, our studies not only provide insight into how SETD2 loss shapes the epigenetic and transcriptional landscape to promote tumorigenesis, but they also identify potential therapeutic strategies for SETD2 mutant cancers.
Collapse
Affiliation(s)
- Yuchen Xie
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, New York, USA
| | - Merve Sahin
- Computational and Systems Biology Program, MSKCC, New York, New York, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, New York, USA
| | - Toru Wakamatsu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Akane Inoue-Yamauchi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Wanming Zhao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Song Han
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Amrita M. Nargund
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Shaoyuan Yang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Yang Lyu
- Molecular Oncology, Department of Medicine, Washington University, St. Louis, Missouri, USA
| | - James J. Hsieh
- Molecular Oncology, Department of Medicine, Washington University, St. Louis, Missouri, USA
| | | | - Emily H. Cheng
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
- Department of Pathology and Laboratory Medicine, MSKCC, New York, New York, USA
- Weill Cornell Medical College, New York, New York, USA
| |
Collapse
|
25
|
Yu M, Qian K, Wang G, Xiao Y, Zhu Y, Ju L. Histone methyltransferase SETD2: An epigenetic driver in clear cell renal cell carcinoma. Front Oncol 2023; 13:1114461. [PMID: 37025591 PMCID: PMC10070805 DOI: 10.3389/fonc.2023.1114461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 03/09/2023] [Indexed: 04/08/2023] Open
Abstract
SET domain-containing 2 (SETD2) is a lysine methyltransferase that catalyzes histone H3 lysine36 trimethylation (H3K36me3) and has been revealed to play important roles in the regulation of transcriptional elongation, RNA splicing, and DNA damage repair. SETD2 mutations have been documented in several cancers, including clear cell renal cell carcinoma (ccRCC). SETD2 deficiency is associated with cancer occurrence and progression by regulating autophagy flux, general metabolic activity, and replication fork speed. Therefore, SETD2 is considered a potential epigenetic therapeutic target and is the subject of ongoing research on cancer-related diagnosis and treatment. This review presents an overview of the molecular functions of SETD2 in H3K36me3 regulation and its relationship with ccRCC, providing a theoretical basis for subsequent antitumor therapy based on SETD2 or H3K36me3 targets.
Collapse
Affiliation(s)
- Mengxue Yu
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kaiyu Qian
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Gang Wang
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
- Human Genetic Resources Preservation Center of Hubei Province, Wuhan, China
| | - Yu Xiao
- Human Genetic Resources Preservation Center of Hubei Province, Wuhan, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
| | - Yuan Zhu
- Human Genetic Resources Preservation Center of Hubei Province, Wuhan, China
- *Correspondence: Yuan Zhu, ; Lingao Ju,
| | - Lingao Ju
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
- Medical Research Institute, Wuhan University, Wuhan, China
- *Correspondence: Yuan Zhu, ; Lingao Ju,
| |
Collapse
|
26
|
Rappold PM, Vuong L, Leibold J, Chakiryan NH, Curry M, Kuo F, Sabio E, Jiang H, Nixon BG, Liu M, Berglund AE, Silagy AW, Mascareno A, Golkaram M, Marker M, Reising A, Savchenko A, Millholland J, Chen YB, Russo P, Coleman J, Reznik E, Manley BJ, Ostrovnaya I, Makarov V, DiNatale RG, Blum KA, Ma X, Chowell D, Li MO, Solit DB, Lowe SW, Chan TA, Motzer RJ, Voss MH, Hakimi AA. A Targetable Myeloid Inflammatory State Governs Disease Recurrence in Clear-Cell Renal Cell Carcinoma. Cancer Discov 2022; 12:2308-2329. [PMID: 35758895 PMCID: PMC9720541 DOI: 10.1158/2159-8290.cd-21-0925] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 04/22/2022] [Accepted: 06/22/2022] [Indexed: 11/16/2022]
Abstract
It is poorly understood how the tumor immune microenvironment influences disease recurrence in localized clear-cell renal cell carcinoma (ccRCC). Here we performed whole-transcriptomic profiling of 236 tumors from patients assigned to the placebo-only arm of a randomized, adjuvant clinical trial for high-risk localized ccRCC. Unbiased pathway analysis identified myeloid-derived IL6 as a key mediator. Furthermore, a novel myeloid gene signature strongly correlated with disease recurrence and overall survival on uni- and multivariate analyses and is linked to TP53 inactivation across multiple data sets. Strikingly, effector T-cell gene signatures, infiltration patterns, and exhaustion markers were not associated with disease recurrence. Targeting immunosuppressive myeloid inflammation with an adenosine A2A receptor antagonist in a novel, immunocompetent, Tp53-inactivated mouse model significantly reduced metastatic development. Our findings suggest that myeloid inflammation promotes disease recurrence in ccRCC and is targetable as well as provide a potential biomarker-based framework for the design of future immuno-oncology trials in ccRCC. SIGNIFICANCE Improved understanding of factors that influence metastatic development in localized ccRCC is greatly needed to aid accurate prediction of disease recurrence, clinical decision-making, and future adjuvant clinical trial design. Our analysis implicates intratumoral myeloid inflammation as a key driver of metastasis in patients and a novel immunocompetent mouse model. This article is highlighted in the In This Issue feature, p. 2221.
Collapse
Affiliation(s)
- Phillip M. Rappold
- Department of Surgery, Urology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lynda Vuong
- Department of Surgery, Urology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, MSKCC, New York, NY, USA
| | - Josef Leibold
- Cancer Biology and Genetics Program, MSKCC, New York, NY, USA
- Department of Medical Oncology & Pneumology (Internal Medicine VIII), University Hospital Tuebingen, Tuebingen 72076, Germany
- DFG Cluster of Excellence 2180 Image-Guided and Functional Instructed Tumor Therapy (iFIT), University of Tuebingen, Tuebingen 72076, Germany
| | - Nicholas H. Chakiryan
- Department of Genitourinary Oncology, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Michael Curry
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fengshen Kuo
- Department of Surgery, Urology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, MSKCC, New York, NY, USA
| | - Erich Sabio
- Human Oncology and Pathogenesis Program, MSKCC, New York, NY, USA
| | - Hui Jiang
- Department of Surgery, Urology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, MSKCC, New York, NY, USA
| | - Briana G. Nixon
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ming Liu
- Legend Biotech USA Inc, NJ, USA
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anders E. Berglund
- Department of Biostatistics and Bioinformatics, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Andrew W. Silagy
- Department of Surgery, Urology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ankur Mascareno
- Department of Surgery, Urology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, MSKCC, New York, NY, USA
| | - Mahdi Golkaram
- Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, USA
| | | | | | | | | | | | - Paul Russo
- Department of Surgery, Urology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jonathan Coleman
- Department of Surgery, Urology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ed Reznik
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brandon J. Manley
- Department of Genitourinary Oncology, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA Integrated Mathematical Oncology Department, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Irina Ostrovnaya
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Vladimir Makarov
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH, USA
| | - Renzo G. DiNatale
- Department of Surgery, Urology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kyle A. Blum
- Department of Surgery, Urology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xiaoxiao Ma
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH, USA
| | - Diego Chowell
- Department of Oncological Sciences, The Precision Immunology Institute, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ming O. Li
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David B. Solit
- Human Oncology and Pathogenesis Program, MSKCC, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, MSKCC, New York, NY, USA
| | - Scott W. Lowe
- Cancer Biology and Genetics Program, MSKCC, New York, NY, USA
| | - Timothy A. Chan
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH, USA
| | - Robert J. Motzer
- Department of Medicine, Genitourinary Oncology, MSKCC, New York, NY, USA
| | - Martin H. Voss
- Department of Medicine, Genitourinary Oncology, MSKCC, New York, NY, USA
| | - A. Ari Hakimi
- Department of Surgery, Urology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| |
Collapse
|
27
|
The SWI/SNF chromatin remodeling factor DPF3 regulates metastasis of ccRCC by modulating TGF-β signaling. Nat Commun 2022; 13:4680. [PMID: 35945219 PMCID: PMC9363427 DOI: 10.1038/s41467-022-32472-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 08/02/2022] [Indexed: 12/23/2022] Open
Abstract
DPF3, a component of the SWI/SNF chromatin remodeling complex, has been associated with clear cell renal cell carcinoma (ccRCC) in a genome-wide association study. However, the functional role of DPF3 in ccRCC development and progression remains unknown. In this study, we demonstrate that DPF3a, the short isoform of DPF3, promotes kidney cancer cell migration both in vitro and in vivo, consistent with the clinical observation that DPF3a is significantly upregulated in ccRCC patients with metastases. Mechanistically, DPF3a specifically interacts with SNIP1, via which it forms a complex with SMAD4 and p300 histone acetyltransferase (HAT), the major transcriptional regulators of TGF-β signaling pathway. Moreover, the binding of DPF3a releases the repressive effect of SNIP1 on p300 HAT activity, leading to the increase in local histone acetylation and the activation of cell movement related genes. Overall, our findings reveal a metastasis-promoting function of DPF3, and further establish the link between SWI/SNF components and ccRCC. The functional role of DPF3, a component of the SWI/SNF chromatin remodelling complex associated with clear cell renal cell carcinoma (ccRCC), remains unknown. Here, the authors characterise the mechanism by which DPF3 promotes metastasis via the activation of the TGF-β signalling pathway in ccRCC.
Collapse
|
28
|
Leung W, Teater M, Durmaz C, Meydan C, Chivu AG, Chadburn A, Rice EJ, Muley A, Camarillo JM, Arivalagan J, Li Z, Flowers CR, Kelleher NL, Danko CG, Imielinski M, Dave SS, Armstrong SA, Mason CE, Melnick AM. SETD2 Haploinsufficiency Enhances Germinal Center-Associated AICDA Somatic Hypermutation to Drive B-cell Lymphomagenesis. Cancer Discov 2022; 12:1782-1803. [PMID: 35443279 PMCID: PMC9262862 DOI: 10.1158/2159-8290.cd-21-1514] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/08/2022] [Accepted: 04/18/2022] [Indexed: 01/26/2023]
Abstract
SETD2 is the sole histone methyltransferase responsible for H3K36me3, with roles in splicing, transcription initiation, and DNA damage response. Homozygous disruption of SETD2 yields a tumor suppressor effect in various cancers. However, SETD2 mutation is typically heterozygous in diffuse large B-cell lymphomas. Here we show that heterozygous Setd2 deficiency results in germinal center (GC) hyperplasia and increased competitive fitness, with reduced DNA damage checkpoint activity and apoptosis, resulting in accelerated lymphomagenesis. Impaired DNA damage sensing in Setd2-haploinsufficient germinal center B (GCB) and lymphoma cells associated with increased AICDA-induced somatic hypermutation, complex structural variants, and increased translocations including those activating MYC. DNA damage was selectively increased on the nontemplate strand, and H3K36me3 loss was associated with greater RNAPII processivity and mutational burden, suggesting that SETD2-mediated H3K36me3 is required for proper sensing of cytosine deamination. Hence, Setd2 haploinsufficiency delineates a novel GCB context-specific oncogenic pathway involving defective epigenetic surveillance of AICDA-mediated effects on transcribed genes. SIGNIFICANCE Our findings define a B cell-specific oncogenic effect of SETD2 heterozygous mutation, which unleashes AICDA mutagenesis of nontemplate strand DNA in the GC reaction, resulting in lymphomas with heavy mutational burden. GC-derived lymphomas did not tolerate SETD2 homozygous deletion, pointing to a novel context-specific therapeutic vulnerability. This article is highlighted in the In This Issue feature, p. 1599.
Collapse
Affiliation(s)
- Wilfred Leung
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, New York
- Department of Biomedical Sciences, Cornell University, Ithaca, New York
| | - Matt Teater
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, New York
| | - Ceyda Durmaz
- Graduate Program of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, New York
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, New York
| | - Alexandra G Chivu
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Edward J Rice
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Ashlesha Muley
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, New York
| | - Jeannie M Camarillo
- Departments of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois
| | - Jaison Arivalagan
- Departments of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois
| | - Ziyi Li
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Christopher R Flowers
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Neil L Kelleher
- Departments of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Marcin Imielinski
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
- New York Genome Center, New York, New York
- Caryl and Israel Englander Institute for Precision Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, New York
| | - Sandeep S Dave
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, North Carolina
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, New York
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York
| | - Ari M Melnick
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, New York
| |
Collapse
|
29
|
Molenaar TM, van Leeuwen F. SETD2: from chromatin modifier to multipronged regulator of the genome and beyond. Cell Mol Life Sci 2022; 79:346. [PMID: 35661267 PMCID: PMC9167812 DOI: 10.1007/s00018-022-04352-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/09/2022] [Accepted: 05/05/2022] [Indexed: 12/13/2022]
Abstract
Histone modifying enzymes play critical roles in many key cellular processes and are appealing proteins for targeting by small molecules in disease. However, while the functions of histone modifying enzymes are often linked to epigenetic regulation of the genome, an emerging theme is that these enzymes often also act by non-catalytic and/or non-epigenetic mechanisms. SETD2 (Set2 in yeast) is best known for associating with the transcription machinery and methylating histone H3 on lysine 36 (H3K36) during transcription. This well-characterized molecular function of SETD2 plays a role in fine-tuning transcription, maintaining chromatin integrity, and mRNA processing. Here we give an overview of the various molecular functions and mechanisms of regulation of H3K36 methylation by Set2/SETD2. These fundamental insights are important to understand SETD2’s role in disease, most notably in cancer in which SETD2 is frequently inactivated. SETD2 also methylates non-histone substrates such as α-tubulin which may promote genome stability and contribute to the tumor-suppressor function of SETD2. Thus, to understand its role in disease, it is important to understand and dissect the multiple roles of SETD2 within the cell. In this review we discuss how histone methylation by Set2/SETD2 has led the way in connecting histone modifications in active regions of the genome to chromatin functions and how SETD2 is leading the way to showing that we also have to look beyond histones to truly understand the physiological role of an ‘epigenetic’ writer enzyme in normal cells and in disease.
Collapse
|