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Trejo-Villegas OA, Heijink IH, Ávila-Moreno F. Preclinical evidence in the assembly of mammalian SWI/SNF complexes: Epigenetic insights and clinical perspectives in human lung disease therapy. Mol Ther 2024; 32:2470-2488. [PMID: 38910326 DOI: 10.1016/j.ymthe.2024.06.026] [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: 12/11/2023] [Revised: 04/18/2024] [Accepted: 06/20/2024] [Indexed: 06/25/2024] Open
Abstract
The SWI/SNF complex, also known as the BRG1/BRM-associated factor (BAF) complex, represents a critical regulator of chromatin remodeling mechanisms in mammals. It is alternatively referred to as mSWI/SNF and has been suggested to be imbalanced in human disease compared with human health. Three types of BAF assemblies associated with it have been described, including (1) canonical BAF (cBAF), (2) polybromo-associated BAF (PBAF), and (3) non-canonical BAF (ncBAF) complexes. Each of these BAF assemblies plays a role, either functional or dysfunctional, in governing gene expression patterns, cellular processes, epigenetic mechanisms, and biological processes. Recent evidence increasingly links the dysregulation of mSWI/SNF complexes to various human non-malignant lung chronic disorders and lung malignant diseases. This review aims to provide a comprehensive general state-of-the-art and a profound examination of the current understanding of mSWI/SNF assembly processes, as well as the structural and functional organization of mSWI/SNF complexes and their subunits. In addition, it explores their intricate functional connections with potentially dysregulated transcription factors, placing particular emphasis on molecular and cellular pathogenic processes in lung diseases. These processes are reflected in human epigenome aberrations that impact clinical and therapeutic levels, suggesting novel perspectives on the diagnosis and molecular therapies for human respiratory diseases.
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Affiliation(s)
- Octavio A Trejo-Villegas
- Lung Diseases and Functional Epigenomics Laboratory (LUDIFE), Biomedicine Research Unit (UBIMED), Facultad de Estudios Superiores-Iztacala (FES-Iztacala), Universidad Nacional Autónoma de México (UNAM), Avenida de los Barrios #1, Colonia Los Reyes Iztacala, Tlalnepantla de Baz, 54090, Estado de México, México
| | - Irene H Heijink
- Departments of Pathology & Medical Biology and Pulmonology, GRIAC Research Institute, University Medical Center Groningen, University of Groningen, 9713 Groningen, the Netherlands
| | - Federico Ávila-Moreno
- Lung Diseases and Functional Epigenomics Laboratory (LUDIFE), Biomedicine Research Unit (UBIMED), Facultad de Estudios Superiores-Iztacala (FES-Iztacala), Universidad Nacional Autónoma de México (UNAM), Avenida de los Barrios #1, Colonia Los Reyes Iztacala, Tlalnepantla de Baz, 54090, Estado de México, México; Research Unit, Instituto Nacional de Enfermedades Respiratorias (INER), Ismael Cosío Villegas, 14080, Ciudad de México, México; Research Tower, Subdirección de Investigación Básica, Instituto Nacional de Cancerología (INCan), 14080, Ciudad de México, México.
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Haugh AM, Osorio RC, Francois RA, Tawil ME, Tsai KK, Tetzlaff M, Daud A, Vasudevan HN. Targeted DNA Sequencing of Cutaneous Melanoma Identifies Prognostic and Predictive Alterations. Cancers (Basel) 2024; 16:1347. [PMID: 38611025 PMCID: PMC11011039 DOI: 10.3390/cancers16071347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND Cutaneous melanoma (CM) can be molecularly classified into four groups: BRAF mutant, NRAS mutant, NF1 mutant and triple wild-type (TWT) tumors lacking any of these three alterations. In the era of immune checkpoint inhibition (ICI) and targeted molecular therapy, the clinical significance of these groups remains unclear. Here, we integrate targeted DNA sequencing with comprehensive clinical follow-up in CM patients. METHODS This was a retrospective cohort study that assessed clinical and molecular features from patients with localized or metastatic CM who underwent targeted next-generation sequencing as part of routine clinical care. A total of 254 patients with CM who had a CLIA-certified targeted sequencing assay performed on their tumor tissue were included. RESULTS Of the 254 patients with cutaneous melanoma, 77 were BRAF mutant (30.3%), 77 were NRAS mutant (30.3%), 47 were NF1 mutant (18.5%), 33 were TWT (13.0%) and the remaining 20 (7.9%) carried mutations in multiple driver genes (BRAF/NRAS/NF1 co-mutated). The majority of this co-mutation group carried mutations in NF1 (n = 19 or 90%) with co-occurring mutations in BRAF or NRAS, often with a weaker oncogenic variant. Consistently, NF1 mutant tumors harbored numerous significantly co-altered genes compared to BRAF or NRAS mutant tumors. The majority of TWT tumors (n = 29, 87.9%) harbor a pathogenic mutation within a known Ras/MAPK signaling pathway component. Of the 154 cases with available TMB data, the median TMB was 20 (range 0.7-266 mutations/Mb). A total of 14 cases (9.1%) were classified as having a low TMB (≤5 mutations/Mb), 64 of 154 (41.6%) had an intermediate TMB (>5 and ≤20 mutations/Mb), 40 of 154 (26.0%) had a high TMB (>20 and ≤50 mutations/Mb) and 36 of 154 (23.4%) were classified as having a very high TMB (>50 mutations/Mb). NRAS mutant melanoma demonstrated significantly decreased overall survival on multivariable analysis (HR for death 2.95, 95% CI 1.13-7.69, p = 0.027, log-rank test) compared with other TCGA molecular subgroups. Of the 116 patients in our cohort with available treatment data, 36 received a combination of dual ICI with anti-CTLA4 and anti-PD1 inhibition as first-line therapy. Elevated TMB was associated with significantly longer progression-free survival following dual-agent ICI (HR 0.26, 95% CI 0.07-0.90, p = 0.033, log-rank test). CONCLUSIONS NRAS mutation in CMs correlated with significantly worse overall survival. Elevated TMB was associated with increased progression-free survival for patients treated with a combination of dual ICI, supporting the potential utility of TMB as a predictive biomarker for ICI response in melanoma.
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Affiliation(s)
- Alexandra M. Haugh
- Department of Medicine, Division of Hematology/Oncology, Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94142, USA; (A.M.H.); (K.K.T.); (A.D.)
| | - Robert C. Osorio
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA 94143, USA (M.E.T.)
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94143, USA
| | - Rony A. Francois
- Department of Dermatology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Michael E. Tawil
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA 94143, USA (M.E.T.)
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94143, USA
| | - Katy K. Tsai
- Department of Medicine, Division of Hematology/Oncology, Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94142, USA; (A.M.H.); (K.K.T.); (A.D.)
| | - Michael Tetzlaff
- Department of Dermatology, University of California San Francisco, San Francisco, CA 94143, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Adil Daud
- Department of Medicine, Division of Hematology/Oncology, Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94142, USA; (A.M.H.); (K.K.T.); (A.D.)
| | - Harish N. Vasudevan
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA 94143, USA (M.E.T.)
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94143, USA
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Akinjiyan FA, Nassief G, Phillipps J, Adeyelu T, Elliott A, Abdulla F, Zhou AY, Souroullas G, Kim KB, Vanderwalde A, Park SJ, Ansstas G. ARID2 mutations may relay a distinct subset of cutaneous melanoma patients with different outcomes. Sci Rep 2024; 14:3444. [PMID: 38341515 PMCID: PMC10858967 DOI: 10.1038/s41598-024-54136-3] [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: 12/06/2023] [Accepted: 02/08/2024] [Indexed: 02/12/2024] Open
Abstract
ARID genes encode subunits of SWI/SNF chromatin remodeling complexes and are frequently mutated in human cancers. We investigated the correlation between ARID mutations, molecular features, and clinical outcomes in melanoma patients. Cutaneous melanoma samples (n = 1577) were analyzed by next-generation sequencing. Samples were stratified by pathogenic/likely pathogenic mutation in ARID genes (ARID1A/2/1B/5B). PD-L1 expression was assessed using IHC (SP142; positive (+): ≥ 1%). Tumor mutation burden (TMB)-high was defined as ≥ 10 mutations/Mb. Transcriptomic signatures predictive of response to immune checkpoint inhibitors-interferon gamma and T-cell inflamed score were calculated. Real-world overall survival (OS) information was obtained from insurance claims data, with Kaplan-Meier estimates calculated from time of tissue collection until last date of contact. Mann-Whitney U, Chi-square, and Fisher exact tests were applied where appropriate, with p values adjusted for multiple comparisons. ARID2 mutations were more prevalent in cutaneous melanoma compared to ARID1A (11.0%: n = 451 vs 2.8%: n = 113), with concurrent ARID1A/ARID2 mutation in 1.1% (n = 46) of samples. ARID mutations were associated with a high prevalence of RAS pathway mutations-NF1 (ARID1A, 52.6%; ARID2, 48.5%; ARID1A/2, 63.6%; and ARID-WT, 13.3%; p < 0.0001) and KRAS (ARID1A, 3.5%; ARID2, 3.1%; ARID1A/2, 6.5%; and ARID-WT, 1.0%; p = 0.018)), although BRAF mutations were less common in ARID-mutated cohorts (ARID1A, 31.9%; ARID2, 35.6%; ARID1A/2, 26.1%; and ARID-WT, 50.4%; p < 0.0001). TMB-high was more common in ARID-mutated samples (ARID1A, 80.9%; ARID2, 89.9%; ARID1A/2, 100%; and ARID-WT, 49.4%; p < 0.0001), while PD-L1 positivity was similar across subgroups (ARID1A, 43.8%; ARID2, 51.1%; ARID1A/2, 52.5%; and ARID-WT, 44.9%; p = 0.109). Patients with ARID1A mutations had a higher prevalence of dMMR/MSI-H compared to those with ARID-WT (2.7% vs 0.2%, p = 0.030). Median IFN-γ and T-cell signatures were higher in ARID2-mutated samples compared to ARID-WT (IFN-γ: - 0.15 vs - 0.21, p = 0.0066; T-cell: 23.5 vs - 18.5, p = 0.041). ARID2-mutated patients had improved survival compared to ARID-WT; (HR: 1.22 (95% CI 1.0-1.5), p = 0.022). No additional OS benefit was observed with anti-PD-1 therapy for ARID2 mutation compared to ARID-WT. Melanoma patients with ARID mutations exhibited higher prevalence of markers associated with ICI response, including TMB-H, and immune-related signatures. Our data also suggests improved survival outcome in patients with ARID2 mutations, irrespective of anti-PD1 therapy.
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Affiliation(s)
- Favour A Akinjiyan
- Division of Medical Oncology, Department of Medicine, Washington University in Saint Louis, 4921 Parkview Place, Saint Louis, MO, 63110, USA
| | - George Nassief
- Division of Medical Oncology, Department of Medicine, Washington University in Saint Louis, 4921 Parkview Place, Saint Louis, MO, 63110, USA
| | - Jordan Phillipps
- Division of Medical Oncology, Department of Medicine, Washington University in Saint Louis, 4921 Parkview Place, Saint Louis, MO, 63110, USA
| | | | | | | | - Alice Y Zhou
- Division of Medical Oncology, Department of Medicine, Washington University in Saint Louis, 4921 Parkview Place, Saint Louis, MO, 63110, USA
| | - George Souroullas
- Division of Medical Oncology, Department of Medicine, Washington University in Saint Louis, 4921 Parkview Place, Saint Louis, MO, 63110, USA
| | - Kevin B Kim
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | | | - Soo J Park
- Division of Hematology/Oncology, Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - George Ansstas
- Division of Medical Oncology, Department of Medicine, Washington University in Saint Louis, 4921 Parkview Place, Saint Louis, MO, 63110, USA.
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Chen R, Zhang G, Sun K, Chen AF. Aging-Associated ALKBH5-m 6A Modification Exacerbates Doxorubicin-Induced Cardiomyocyte Apoptosis Via AT-Rich Interaction Domain 2. J Am Heart Assoc 2024; 13:e031353. [PMID: 38156523 PMCID: PMC10863816 DOI: 10.1161/jaha.123.031353] [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: 06/11/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023]
Abstract
BACKGROUND Chemotherapy-induced cardiovascular disease is a growing concern in the elderly population who have survived cancer, yet the underlying mechanism remains poorly understood. We investigated the role of ALKBH5 (AlkB homolog 5), a primary N6-methyladenosine (m6A) demethylase, and its involvement in m6A methylation-mediated regulation of targets in aging-associated doxorubicin-induced cardiotoxicity. METHODS AND RESULTS To validate the relationship between doxorubicin-induced cardiotoxicity and aging, we established young and old male mouse models. ALKBH5 expression was modulated through adeno-associated virus 9 (in vivo), Lentivirus, and siRNAs (in vitro) to examine its impact on cardiomyocyte m6A modification, doxorubicin-induced cardiac dysfunction, and remodeling. We performed mRNA sequencing, methylated RNA immunoprecipitation sequencing, and molecular assays to unravel the mechanism of ALKBH5-m6A modification in doxorubicin-induced cardiotoxicity. Our data revealed an age-dependent increase in doxorubicin-induced cardiac dysfunction, remodeling, and injury. ALKBH5 expression was elevated in aging mouse hearts, leading to reduced global m6A modification levels. Through mRNA sequencing and methylated RNA immunoprecipitation sequencing analyses, we identified ARID2 (AT-rich interaction domain 2) as the downstream effector of ALKBH5-m6A modulation in cardiomyocytes. Further investigations revealed that ARID2 modulates DNA damage response and enhances doxorubicin-induced cardiomyocyte apoptosis. CONCLUSIONS Our findings provide insights into the role of ALKBH5-m6A modification in modulating doxorubicin-induced cardiac dysfunction, remodeling, and cardiomyocyte apoptosis in male mice. These results highlight the potential of ALKBH5-targeted treatments for elderly patients with cancer in clinical settings.
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Affiliation(s)
- Runtai Chen
- Center for Vascular Disease and Translational MedicineThe Third Xiangya Hospital of Central South UniversityChangshaHunanChina
- Department of CardiologyThe Third Xiangya Hospital of Central South UniversityChangshaHunanChina
| | - Guogang Zhang
- Center for Vascular Disease and Translational MedicineThe Third Xiangya Hospital of Central South UniversityChangshaHunanChina
- Department of CardiologyThe Third Xiangya Hospital of Central South UniversityChangshaHunanChina
| | - Kun Sun
- Institute for Developmental and Regenerative Cardiovascular Medicine, Xinhua Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Alex F. Chen
- Center for Vascular Disease and Translational MedicineThe Third Xiangya Hospital of Central South UniversityChangshaHunanChina
- Department of CardiologyThe Third Xiangya Hospital of Central South UniversityChangshaHunanChina
- Institute for Developmental and Regenerative Cardiovascular Medicine, Xinhua Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
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Lopedote P, Nawaiseh AA, Malek A, Faller G, Hattar M, Dow E, Kozyreva O. Early progression and transformation of a splenic diffuse red pulp small B-cell lymphoma with NOTCH1, ARID2, CREBBP, and TNFRSF14 gene mutations. Leuk Res Rep 2023; 20:100384. [PMID: 37664441 PMCID: PMC10471916 DOI: 10.1016/j.lrr.2023.100384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/28/2023] [Accepted: 08/21/2023] [Indexed: 09/05/2023] Open
Abstract
Splenic diffuse red pulp small B-cell lymphoma (SDRPL) is a rare entity. Diagnosis is typically achieved with splenectomy and most patients remain in remission after this intervention. Hemoglobin value less than 10 g/dL and NOTCH1, TP53, and MAP2K1 gene mutations at diagnosis have been associated with worse outcome. Progression after splenectomy of SDRPL is possible, although transformation to aggressive lymphoma has rarely been reported. We herein report the case of a patient formerly diagnosed with SDRPL with gene mutations involving CREBBP, NOTCH1, ARID2, and TNFRSF14 who transformed to diffuse large B-cell lymphoma six months after splenectomy.
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Affiliation(s)
- Paolo Lopedote
- Department of Medicine, St Elizabeth's Medical Center, Boston University, Boston, MA, United States
| | - Ahmad Al Nawaiseh
- Department of Medicine, St Elizabeth's Medical Center, Boston University, Boston, MA, United States
| | - Anita Malek
- Department of Pathology, St Elizabeth's Medical Center, Boston, MA, United States
| | - Garrey Faller
- Department of Pathology, Good Samaritan Medical Center, Brockton, MA, United States
| | - Mariana Hattar
- Department of Medicine, St Elizabeth's Medical Center, Boston University, Boston, MA, United States
| | - Edward Dow
- Norfolk Center for Cancer Care, Brockton, MA, United States
| | - Olga Kozyreva
- Department of Medical Oncology, St Elizabeth's Medical Center, Dana Farber Cancer Institute, Boston, MA, United States
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Shi Y, Shin DS. Dysregulation of SWI/SNF Chromatin Remodelers in NSCLC: Its Influence on Cancer Therapies including Immunotherapy. Biomolecules 2023; 13:984. [PMID: 37371564 DOI: 10.3390/biom13060984] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/30/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Lung cancer is the leading cause of cancer death worldwide. Molecularly targeted therapeutics and immunotherapy revolutionized the clinical care of NSCLC patients. However, not all NSCLC patients harbor molecular targets (e.g., mutated EGFR), and only a subset benefits from immunotherapy. Moreover, we are lacking reliable biomarkers for immunotherapy, although PD-L1 expression has been mainly used for guiding front-line therapeutic options. Alterations of the SWI/SNF chromatin remodeler occur commonly in patients with NSCLC. This subset of NSCLC tumors tends to be undifferentiated and presents high heterogeneity in histology, and it shows a dismal prognosis because of poor response to the current standard therapies. Catalytic subunits SMARCA4/A2 and DNA binding subunits ARID1A/ARID1B/ARID2 as well as PBRM1 were identified to be the most commonly mutated subunits of SWI/SNF complexes in NSCLC. Mechanistically, alteration of these SWI/SNF subunits contributes to the tumorigenesis of NSCLC through compromising the function of critical tumor suppressor genes, enhancing oncogenic activity as well as impaired DNA repair capacity related to genomic instability. Several vulnerabilities of NSCLCS with altered SWI/SNF subunits were detected and evaluated clinically using EZH2 inhibitors, PROTACs of mutual synthetic lethal paralogs of the SWI/SNF subunits as well as PARP inhibitors. The response of NSCLC tumors with an alteration of SWI/SNF to ICIs might be confounded by the coexistence of mutations in genes capable of influencing patients' response to ICIs. High heterogenicity in the tumor with SWI/SNF deficiency might also be responsible for the seemingly conflicting results of ICI treatment of NSCLC patients with alterations of SWI/SNF. In addition, an alteration of each different SWI/SNF subunit might have a unique impact on the response of NSCLC with deficient SWI/SNF subunits. Prospective studies are required to evaluate how the alterations of the SWI/SNF in the subset of NSCLC patients impact the response to ICI treatment. Finally, it is worthwhile to point out that combining inhibitors of other chromatin modulators with ICIs has been proven to be effective for the treatment of NSCLC with deficient SWI/SNF chromatin remodelers.
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Affiliation(s)
- Yijiang Shi
- Division of Hematology/Oncology, Department of Medicine, Los Angeles, CA 90073, USA
- Division of Hematology/Oncology, Department of Medicine, VA Greater Los Angeles Healthcare System, 11301 Wilshire Blvd, Los Angeles, CA 90073, USA
| | - Daniel Sanghoon Shin
- Division of Hematology/Oncology, Department of Medicine, Los Angeles, CA 90073, USA
- Division of Hematology/Oncology, Department of Medicine, VA Greater Los Angeles Healthcare System, 11301 Wilshire Blvd, Los Angeles, CA 90073, USA
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Reddy D, Bhattacharya S, Workman JL. (mis)-Targeting of SWI/SNF complex(es) in cancer. Cancer Metastasis Rev 2023; 42:455-470. [PMID: 37093326 PMCID: PMC10349013 DOI: 10.1007/s10555-023-10102-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/05/2023] [Indexed: 04/25/2023]
Abstract
The ATP-dependent chromatin remodeling complex SWI/SNF (also called BAF) is critical for the regulation of gene expression. During the evolution from yeast to mammals, the BAF complex has evolved an enormous complexity that contains a high number of subunits encoded by various genes. Emerging studies highlight the frequent involvement of altered mammalian SWI/SNF chromatin-remodeling complexes in human cancers. Here, we discuss the recent advances in determining the structure of SWI/SNF complexes, highlight the mechanisms by which mutations affecting these complexes promote cancer, and describe the promising emerging opportunities for targeted therapies.
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Affiliation(s)
- Divya Reddy
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | | | - Jerry L Workman
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA.
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Hsu CY, Yanagi T, Maeda T, Nishihara H, Miyamoto K, Kitamura S, Tokuchi K, Ujiie H. Eribulin inhibits growth of cutaneous squamous cell carcinoma cell lines and a novel patient-derived xenograft. Sci Rep 2023; 13:8650. [PMID: 37244956 DOI: 10.1038/s41598-023-35811-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/24/2023] [Indexed: 05/29/2023] Open
Abstract
Advanced cutaneous squamous cell carcinoma (cSCC) is treated with chemotherapy and/or radiotherapy, but these typically fail to achieve satisfactory clinical outcomes. There have been no preclinical studies to evaluate the effectiveness of eribulin against cSCC. Here, we examine the effects of eribulin using cSCC cell lines and a novel cSCC patient-derived xenograft (PDX) model. In the cSCC cell lines (A431 and DJM-1 cells), eribulin was found to inhibit tumor cell proliferation in vitro as assessed by cell ATP levels. DNA content analysis by fluorescence-activated cell sorting (FACS) showed that eribulin induced G2/M cell cycle arrest and apoptosis. In xenograft models of cSCC cell lines, the administration of eribulin suppressed tumor growth in vivo. We also developed a cSCC patient-derived xenograft (PDX) which reproduces the histological and genetic characteristics of a primary tumor. Pathogenic mutations in TP53 and ARID2 were detected in the patient's metastatic tumor and in the PDX tumor. The cSCC-PDX responded well to the administration of eribulin and cisplatin. In conclusion, the present study shows the promising antineoplastic effects of eribulin in cSCC. Also, we established a novel cSCC-PDX model that preserves the patient's tumor. This PDX could assist researchers who are exploring innovative therapies for cSCC.
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Affiliation(s)
- Che-Yuan Hsu
- Department of Dermatology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15 W7, Kita-Ku, Sapporo, 060-8638, Japan
| | - Teruki Yanagi
- Department of Dermatology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15 W7, Kita-Ku, Sapporo, 060-8638, Japan.
| | - Takuya Maeda
- Department of Dermatology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15 W7, Kita-Ku, Sapporo, 060-8638, Japan
| | - Hiroshi Nishihara
- Genomics Unit, Keio Cancer Center, Keio University School of Medicine, Tokyo, Japan
| | - Kodai Miyamoto
- Department of Dermatology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15 W7, Kita-Ku, Sapporo, 060-8638, Japan
| | - Shinya Kitamura
- Department of Dermatology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15 W7, Kita-Ku, Sapporo, 060-8638, Japan
| | - Keiko Tokuchi
- Department of Dermatology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15 W7, Kita-Ku, Sapporo, 060-8638, Japan
| | - Hideyuki Ujiie
- Department of Dermatology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15 W7, Kita-Ku, Sapporo, 060-8638, Japan
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Simeoni F, Loukas I, Wilson TS, Scaffidi P. CRISPR-based large-scale modeling of loss-of-function mutations to investigate mechanisms of stress resistance in cancer. STAR Protoc 2023; 4:102097. [PMID: 36853711 PMCID: PMC9947008 DOI: 10.1016/j.xpro.2023.102097] [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: 11/23/2022] [Revised: 12/17/2022] [Accepted: 01/19/2023] [Indexed: 02/13/2023] Open
Abstract
Dissecting mechanisms driving subclone expansion in primary cancers has been challenging. Here, we present a protocol to systematically disrupt entire gene networks and assess the functional impact of this perturbation on cancer cell fitness. By combining arrayed CRISPR libraries and high-content microscopy, we describe steps to identify classes of genes whose inactivation promotes resistance to environmental challenges faced by cancer cells during tumor growth or upon therapy. A proof-of-principle interrogation of the epigenetic regulatory network is described. For complete details on the use and execution of this protocol, please refer to Loukas et al. (2022).1.
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Affiliation(s)
- Fabrizio Simeoni
- Cancer Epigenetics Laboratory, The Francis Crick Institute, NW1 1AT London, UK.
| | - Ioannis Loukas
- Cancer Epigenetics Laboratory, The Francis Crick Institute, NW1 1AT London, UK
| | | | - Paola Scaffidi
- Cancer Epigenetics Laboratory, The Francis Crick Institute, NW1 1AT London, UK; Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy.
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Aguirre-Vázquez A, Castorena-Torres F, Silva-Ramírez B, Peñuelas-Urquides K, Camacho-Moll ME, Salazar-Olivo LA, Velasco I, Bermúdez de León M. Cell-type dependent regulation of pluripotency and chromatin remodeling genes by hydralazine. Stem Cell Res Ther 2023; 14:42. [PMID: 36927767 PMCID: PMC10021945 DOI: 10.1186/s13287-023-03268-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 03/08/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND The generation of induced pluripotent stem cells has opened the field of study for stem cell research, disease modeling and drug development. However, the epigenetic signatures present in somatic cells make cell reprogramming still an inefficient process. This epigenetic memory constitutes an obstacle in cellular reprogramming. Here, we report the effect of hydralazine (HYD) and valproic acid (VPA), two small molecules with proven epigenetic activity, on the expression of pluripotency genes in adult (aHF) and neonatal (nbHF) human fibroblasts. METHODS aHF and nbHF were treated with HYD and/or VPA, and viability and gene expression assays for OCT4, NANOG, c-MYC, KLF4, DNMT1, TET3, ARID1A and ARID2 by quantitative PCR were performed. aHF and nbHF were transfected with episomal plasmid bearing Yamanaka factors (OCT4, SOX2, KLF4 and c-MYC) and exposed to HYD and VPA to determine the reprogramming efficiency. Methylation sensitive restriction enzyme (MSRE) qPCR assays were performed on OCT4 and NANOG promoter regions. Immunofluorescence assays were carried out for pluripotency genes on iPSC derived from aHF and nbHF. RESULTS HYD upregulated the expression of OCT4 (2.5-fold) and NANOG (fourfold) genes but not c-Myc or KLF4 in aHF and had no significant effect on the expression of all these genes in nbHF. VPA upregulated the expression of NANOG (twofold) in aHF and c-MYC in nbHF, while it downregulated the expression of NANOG in nbHF. The combination of HYD and VPA canceled the OCT4 and NANOG overexpression induced by HYD in aHF, while it reinforced the effects of VPA on c-Myc expression in nbHF. The HYD-induced overexpression of OCT4 and NANOG in aHDF was not dependent on demethylation of gene promoters, and no changes in the reprogramming efficiency were observed in both cell populations despite the downregulation of epigenetic genes DNMT1, ARID1A, and ARID2 in nbHF. CONCLUSIONS Our data provide evidence that HYD regulates the expression of OCT4 and NANOG pluripotency genes as well as ARID1A and ARID2 genes, two members of the SWI/SNF chromatin remodeling complex family, in normal human dermal fibroblasts.
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Affiliation(s)
- Alain Aguirre-Vázquez
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, 64720, Monterrey, Nuevo León, Mexico.,Depto. de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, 78216, San Luis Potosí, S.L.P., Mexico
| | | | - Beatriz Silva-Ramírez
- Departamento de Inmunogenética, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, 64720, Monterrey, Nuevo León, Mexico
| | - Katia Peñuelas-Urquides
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, 64720, Monterrey, Nuevo León, Mexico
| | - María Elena Camacho-Moll
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, 64720, Monterrey, Nuevo León, Mexico
| | - Luis A Salazar-Olivo
- Depto. de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, 78216, San Luis Potosí, S.L.P., Mexico
| | - Iván Velasco
- Instituto de Fisiología Celular-Neurociencias, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico.,Laboratorio de Reprogramación Celular, Instituto Nacional de Neurología y Neurocirugía "Manuel Velasco Suárez", 14269, Mexico City, Mexico
| | - Mario Bermúdez de León
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, 64720, Monterrey, Nuevo León, Mexico.
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11
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Vanni I, Pastorino L, Tanda ET, Andreotti V, Dalmasso B, Solari N, Mascherini M, Cabiddu F, Guadagno A, Coco S, Allavena E, Bruno W, Pietra G, Croce M, Gangemi R, Piana M, Zoppoli G, Ferrando L, Spagnolo F, Queirolo P, Ghiorzo P. Whole-Exome Sequencing and cfDNA Analysis Uncover Genetic Determinants of Melanoma Therapy Response in a Real-World Setting. Int J Mol Sci 2023; 24:ijms24054302. [PMID: 36901733 PMCID: PMC10002464 DOI: 10.3390/ijms24054302] [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: 12/20/2022] [Revised: 02/16/2023] [Accepted: 02/19/2023] [Indexed: 02/24/2023] Open
Abstract
Although several studies have explored the molecular landscape of metastatic melanoma, the genetic determinants of therapy resistance are still largely unknown. Here, we aimed to determine the contribution of whole-exome sequencing and circulating free DNA (cfDNA) analysis in predicting response to therapy in a consecutive real-world cohort of 36 patients, undergoing fresh tissue biopsy and followed during treatment. Although the underpowered sample size limited statistical analysis, samples from non-responders had higher copy number variations and mutations in melanoma driver genes compared to responders in the BRAF V600+ subset. In the BRAF V600- subset, Tumor Mutational Burden (TMB) was twice that in responders vs. non-responders. Genomic layout revealed commonly known and novel potential intrinsic/acquired resistance driver gene variants. Among these, RAC1, FBXW7, GNAQ mutations, and BRAF/PTEN amplification/deletion were present in 42% and 67% of patients, respectively. Both Loss of Heterozygosity (LOH) load and tumor ploidy were inversely associated with TMB. In immunotherapy-treated patients, samples from responders showed higher TMB and lower LOH and were more frequently diploid compared to non-responders. Secondary germline testing and cfDNA analysis proved their efficacy in finding germline predisposing variants carriers (8.3%) and following dynamic changes during treatment as a surrogate of tissue biopsy, respectively.
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Affiliation(s)
- Irene Vanni
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Lorenza Pastorino
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132 Genoa, Italy
| | - Enrica Teresa Tanda
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132 Genoa, Italy
- Medical Oncology 2, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Virginia Andreotti
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Bruna Dalmasso
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Nicola Solari
- Surgical Oncology, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Matteo Mascherini
- Surgical Clinic Unit 1, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Francesco Cabiddu
- Anatomic Pathology Unit, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Antonio Guadagno
- Anatomic Pathology Unit, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Simona Coco
- Lung Cancer Unit, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Eleonora Allavena
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132 Genoa, Italy
| | - William Bruno
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132 Genoa, Italy
| | - Gabriella Pietra
- IRCCS Ospedale Policlinico San Martino, U.O. Immunologia, 16132 Genoa, Italy
- Department of Experimental Medicine (DiMES), University of Genoa, 16132 Genoa, Italy
| | - Michela Croce
- Bioterapie, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Rosaria Gangemi
- Bioterapie, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Michele Piana
- Dipartimento di Matematica (MIDA), University of Genoa, 16132 Genoa, Italy
- Life Science Computational Laboratory (LISCOMP), IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Gabriele Zoppoli
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132 Genoa, Italy
- Clinica di Medicina Interna a Indirizzo Oncologico, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Lorenzo Ferrando
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132 Genoa, Italy
- Clinica di Medicina Interna a Indirizzo Oncologico, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Francesco Spagnolo
- Medical Oncology 2, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
- Dipartimento di Scienze Chirurgiche e Diagnostiche Integrate (DISC), University of Genoa, 16132 Genoa, Italy
| | - Paola Queirolo
- Melanoma, Sarcoma & Rare Tumors Division, European Institute of Oncology (IEO), 20141 Milan, Italy
| | - Paola Ghiorzo
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132 Genoa, Italy
- Correspondence: ; Tel.: +39-010-5557255
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12
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Cao HJ, Jiang H, Ding K, Qiu XS, Ma N, Zhang FK, Wang YK, Zheng QW, Xia J, Ni QZ, Xu S, Zhu B, Ding XF, Chen TW, Qiu L, Chen W, Li ZG, Zhou B, Feng WM, Xie D, Li JJ. ARID2 mitigates hepatic steatosis via promoting the ubiquitination of JAK2. Cell Death Differ 2023; 30:383-396. [PMID: 36396719 PMCID: PMC9950479 DOI: 10.1038/s41418-022-01090-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 10/25/2022] [Accepted: 11/04/2022] [Indexed: 11/18/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) has become a growing public health problem. However, the complicated pathogenesis of NAFLD contributes to the deficiency of effective clinical treatment. Here, we demonstrated that liver-specific loss of Arid2 induced hepatic steatosis and this progression could be exacerbated by HFD. Mechanistic study revealed that ARID2 repressed JAK2-STAT5-PPARγ signaling pathway by promoting the ubiquitination of JAK2, which was mediated by NEDD4L, a novel E3 ligase for JAK2. ChIP assay revealed that ARID2 recruited CARM1 to increase H3R17me2a level at the NEDD4L promoter and activated the transcription of NEDD4L. Moreover, inhibition of Jak2 by Fedratinib in liver-specific Arid2 knockout mice alleviated HFD-induced hepatic steatosis. Downregulation of ARID2 and the reverse correlation between ARID2 and JAK2 were also observed in clinical samples. Therefore, our study has revealed an important role of ARID2 in the development of NAFLD and provided a potential therapeutic strategy for NAFLD.
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Affiliation(s)
- Hui-Jun Cao
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Hao Jiang
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
- Department of Biomedical Informatics, School of Life Sciences, Central South University, Changsha, 410013, China
| | - Kai Ding
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xiao-Song Qiu
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Ning Ma
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
- Department of Thoracic Surgery, Section of Esophageal Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Feng-Kun Zhang
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yi-Kang Wang
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Qian-Wen Zheng
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Ji Xia
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Qian-Zhi Ni
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, 200433, China
| | - Sheng Xu
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Bing Zhu
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xu-Fen Ding
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Tian-Wei Chen
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Lin Qiu
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Wei Chen
- Cancer Institute of Integrated Traditional Chinese and Western Medicine, Tongde Hospital of Zhejiang Province, Hangzhou, 310012, Zhejiang, China
| | - Zhi-Gang Li
- Department of Thoracic Surgery, Section of Esophageal Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Bin Zhou
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Wen-Ming Feng
- Department of Surgery, The First Affiliated Hospital of Huzhou University, Huzhou, 313000, Zhejiang, China
| | - Dong Xie
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100022, China.
| | - Jing-Jing Li
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
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13
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D’Agosto S, Fiorini E, Pezzini F, Delfino P, Simbolo M, Vicentini C, Andreani S, Capelli P, Rusev B, Lawlor RT, Bassi C, Landoni L, Pea A, Luchini C, Scarpa A, Corbo V. Long-term organoid culture of a small intestinal neuroendocrine tumor. Front Endocrinol (Lausanne) 2023; 14:999792. [PMID: 37082125 PMCID: PMC10112019 DOI: 10.3389/fendo.2023.999792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 03/02/2023] [Indexed: 04/22/2023] Open
Abstract
Gastroenteropancreatic neuroendocrine tumors (GEP-NETs) are rare and highly heterogeneous neoplasms whose incidence has markedly increased over the last decades. A grading system based on the tumor cells' proliferation index predicts high-risk for G3 NETs. However, low-to-intermediate grade (G1/G2) NETs have an unpredictable clinical course that varies from indolent to highly malignant. Cultures of human cancer cells enable to perform functional perturbation analyses that are instrumental to enhance our understanding of cancer biology. To date, no tractable and reliable long-term culture of G1/G2 NET has been reported to permit disease modeling and pharmacological screens. Here, we report of the first long-term culture of a G2 metastatic small intestinal NET that preserves the main genetic drivers of the tumor and retains expression patterns of the endocrine cell lineage. Replicating the tissue, this long-term culture showed a low proliferation index, and yet it could be propagated continuously without dramatic changes in the karyotype. The model was readily available for pharmacological screens using targeted agents and as expected, showed low tumorigenic capacity in vivo. Overall, this is the first long-term culture of NETs to faithfully recapitulate many aspects of the original neuroendocrine tumor.
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Affiliation(s)
- Sabrina D’Agosto
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Elena Fiorini
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Francesco Pezzini
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Pietro Delfino
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Michele Simbolo
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Caterina Vicentini
- Centre for Applied Research on Cancer (ARC-Net) Research Centre, University of Verona, Verona, Italy
| | - Silvia Andreani
- Centre for Applied Research on Cancer (ARC-Net) Research Centre, University of Verona, Verona, Italy
| | - Paola Capelli
- Azienda Ospedaliera Integrata dell’Università di Verona, Verona, Italy
| | - Borislav Rusev
- Centre for Applied Research on Cancer (ARC-Net) Research Centre, University of Verona, Verona, Italy
| | - Rita T. Lawlor
- Centre for Applied Research on Cancer (ARC-Net) Research Centre, University of Verona, Verona, Italy
| | - Claudio Bassi
- Pancreas Institute, Department of Surgery, University and Hospital Trust of Verona, Verona, Italy
| | - Luca Landoni
- Pancreas Institute, Department of Surgery, University and Hospital Trust of Verona, Verona, Italy
| | - Antonio Pea
- Pancreas Institute, Department of Surgery, University and Hospital Trust of Verona, Verona, Italy
| | - Claudio Luchini
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
- Centre for Applied Research on Cancer (ARC-Net) Research Centre, University of Verona, Verona, Italy
| | - Vincenzo Corbo
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
- Centre for Applied Research on Cancer (ARC-Net) Research Centre, University of Verona, Verona, Italy
- *Correspondence: Vincenzo Corbo,
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14
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Li W, An N, Wang M, Liu X, Mei Z. Downregulation of AT-rich interaction domain 2 underlies natural killer cell dysfunction in oral squamous cell carcinoma. Immunol Cell Biol 2023; 101:78-90. [PMID: 36269235 DOI: 10.1111/imcb.12602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 09/15/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022]
Abstract
The immune system plays a significant role in controlling oral squamous cell carcinoma (OSCC) initiation and progression. Natural killer (NK) cells actively participate in antitumor immunity but become dysfunctional or exhausted in the tumor microenvironment. To explore the mechanisms of NK cell dysfunction in OSCC, we characterized the expression and function of AT-rich interaction domain 2 (ARID2) in NK cells in a murine OSCC model. ARID2 was downregulated in tongue NK cells compared with splenic NK cells. Notably, ARID2 was significantly decreased in NK cells with an exhausted phenotype and weakened antitumor function. ARID2 knockdown resulted in the upregulation of programmed cell death protein 1 (PD-1) and downregulation of interferon-gamma (IFN-γ), tumor necrosis factor (TNF), granzyme B and perforin in NK cells. As a result, ARID2 knockdown impaired NK cell cytotoxicity. Besides, ARID2 overexpression suppressed the expression of PD-1 and lymphocyte-activation gene 3, and promoted the expression of IFN-γ, TNF, granzyme B and perforin in NK cells which were adoptively transferred into OSCC-bearing mice. Taken together, our study implies that the OSCC microenvironment triggers ARID2 downregulation in intratumoral NK cells. In turn, ARID2 downregulation results in PD-1 upregulation on NK cells and subsequently impairs NK cell cytotoxicity. Therefore, we uncovered a novel mechanism of NK cell dysfunction in OSCC.
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Affiliation(s)
- Wei Li
- Department of Head and Neck Surgery, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ning An
- Department of Head and Neck Surgery, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mingwei Wang
- Department of Pathology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiguo Liu
- Department of Head and Neck Surgery, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhidan Mei
- Department of Head and Neck Surgery, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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15
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USP2 Inhibits Lung Cancer Pathogenesis by Reducing ARID2 Protein Degradation via Ubiquitination. BIOMED RESEARCH INTERNATIONAL 2022; 2022:1525216. [PMID: 36567903 PMCID: PMC9779997 DOI: 10.1155/2022/1525216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 11/19/2022] [Accepted: 11/22/2022] [Indexed: 12/23/2022]
Abstract
Background Ubiquitination is an important regulator in physiological and pathological conditions. Ubiquitin-specific protease 2 (USP2), as a member of the USP family, exhibits oncogenic effects in multiple malignancies. However, the exact role of USP2 has not been well clarified in lung cancer pathogenesis and progression. Therefore, we aimed to further investigate the regulatory roles of USP2 in lung cancer in this study. Methods Firstly, immunoprecipitation-Mass Spectrometry (IP-MS), Co-immunoprecipitation (Co-IP), combined with immunofluorescent colocalization method, was conducted for USP2 protein interaction analysis in lung cancer cell lines. qRT-PCR, Western blot, and immunohistochemistry assays explored the USP2 expression pattern and USP2/ARID2- (AT-rich interactive domain 2-) specific shRNAs and overexpression vectors. Co-IP assays were designed to validate USP2-ARID2 protein interaction. Further functional studies including CHX chase assay, transwell assay, and wound healing assay were subsequently applied to evaluate the impact of USP2 modulation on lung cancer cells. Results USP2 suppression was characteristic in lung cancer cell line models and lung cancer samples. USP2 and ARID2 demonstrated protein-protein interaction and overlapping localization in cancer cell models. Functional experiments suggested USP2 inhibited lung cancer cell invasion and migration by reducing ARID2 protein degradation. Subsequent ubiquitination assays indicated ARID2 protein degradation via the ubiquitination was significantly reduced by USP2 interaction. Conclusions Our study provided novel insight that USP2 might suppress lung cancer by reducing ARID2 protein degradation via ubiquitination.
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ARID2 suppression promotes tumor progression and upregulates cytokeratin 8, 18 and β-4 integrin expression in TP53-mutated tobacco-related oral cancer and has prognostic implications. Cancer Gene Ther 2022; 29:1908-1917. [PMID: 35869277 DOI: 10.1038/s41417-022-00505-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 06/16/2022] [Accepted: 07/06/2022] [Indexed: 01/25/2023]
Abstract
Mutations in ARID2 and TP53 genes are found to be implicated in the tobacco related tumorigeneses. However, the effect of loss of ARID2 in the TP53 mutated background in tobacco related cancer including oral cancer has not been investigated yet. Hence, in this study we knockdown ARID2 using shRNA mediated knockdown strategy in TP53 mutated oral squamous cell carcinoma (OSCC) cell line and studied its tumorigenic role. Our study revealed that suppression of ARID2 in TP53 mutated oral cancer cells increases cell motility and invasion, induces drastic morphological changes and leads to a marked increase in the expression levels of cytokeratins, and integrins, CK8, CK18 and β4-Integrin, markers of cell migration/invasion in oral cancer. ARID2 suppression also showed early onset and increased tumorigenicity in-vivo. Interestingly, transcriptome profiling revealed differentially expressed genes associated with migration and invasion in oral cancer cells including AKR1C2, NCAM2, NOS1, ADAM23 and genes of S100A family in ARID2 knockdown TP53 mutated oral cancer cells. Pathway analysis of differentially regulated genes identified "cancer pathways" and "PI3K/AKT Pathway" to be significantly dysregulated upon suppression of ARID2 in TP53 mutated OSCC cells. Notably, decreased ARID2 expression and increased CK8, CK18 expression leads to poor prognosis in Head and Neck cancer (HNSC) patients as revealed by Pan-Cancer TCGA data analysis. To conclude, our study is the first to demonstrate tumor suppressor role of ARID2 in TP53 mutated background indicating their cooperative role in OSCC, and also highlights its prognostic implications suggesting ARID2 as an important therapeutic target in OSCC.
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Li Y, Yang X, Zhu W, Xu Y, Ma J, He C, Wang F. SWI/SNF complex gene variations are associated with a higher tumor mutational burden and a better response to immune checkpoint inhibitor treatment: a pan-cancer analysis of next-generation sequencing data corresponding to 4591 cases. Cancer Cell Int 2022; 22:347. [DOI: 10.1186/s12935-022-02757-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 10/20/2022] [Indexed: 11/15/2022] Open
Abstract
Abstract
Background
Genes related to the SWItch/sucrose nonfermentable (SWI/SNF) chromatin remodeling complex are frequently mutated across cancers. SWI/SNF-mutant tumors are vulnerable to synthetic lethal inhibitors. However, the landscape of SWI/SNF mutations and their associations with tumor mutational burden (TMB), microsatellite instability (MSI) status, and response to immune checkpoint inhibitors (ICIs) have not been elucidated in large real-world Chinese patient cohorts.
Methods
The mutational rates and variation types of six SWI/SNF complex genes (ARID1A, ARID1B, ARID2, SMARCA4, SMARCB1, and PBRM1) were analyzed retrospectively by integrating next-generation sequencing data of 4591 cases covering 18 cancer types. Thereafter, characteristics of SWI/SNF mutations were depicted and the TMB and MSI status and therapeutic effects of ICIs in the SWI/SNF-mutant and SWI/SNF-non-mutant groups were compared.
Results
SWI/SNF mutations were observed in 21.8% of tumors. Endometrial (54.1%), gallbladder and biliary tract (43.4%), and gastric (33.9%) cancers exhibited remarkably higher SWI/SNF mutational rates than other malignancies. Further, ARID1A was the most frequently mutated SWI/SNF gene, and ARID1A D1850fs was identified as relatively crucial. The TMB value, TMB-high (TMB-H), and MSI-high (MSI-H) proportions corresponding to SWI/SNF-mutant cancers were significantly higher than those corresponding to SWI/SNF-non-mutant cancers (25.8 vs. 5.6 mutations/Mb, 44.3% vs. 10.3%, and 16.0% vs. 0.9%, respectively; all p < 0.0001). Furthermore, these indices were even higher for tumors with co-mutations of SWI/SNF genes and MLL2/3. Regarding immunotherapeutic effects, patients with SWI/SNF variations showed significantly longer progression-free survival (PFS) rates than their SWI/SNF-non-mutant counterparts (hazard ratio [HR], 0.56 [95% confidence interval {CI} 0.44–0.72]; p < 0.0001), and PBRM1 mutations were associated with relatively better ICI treatment outcomes than the other SWI/SNF gene mutations (HR, 0.21 [95% CI 0.12–0.37]; p = 0.0007). Additionally, patients in the SWI/SNF-mutant + TMB-H (HR, 0.48 [95% CI 0.37–0.54]; p < 0.0001) cohorts had longer PFS rates than those in the SWI/SNF-non-mutant + TMB-low cohort.
Conclusions
SWI/SNF complex genes are frequently mutated and are closely associated with TMB-H status, MSI-H status, and superior ICI treatment response in several cancers, such as colorectal cancer, gastric cancer, and non-small cell lung cancer. These findings emphasize the necessity and importance of molecular-level detection and interpretation of SWI/SNF complex mutations.
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Zhang FL, Li DQ. Targeting Chromatin-Remodeling Factors in Cancer Cells: Promising Molecules in Cancer Therapy. Int J Mol Sci 2022; 23:12815. [PMID: 36361605 PMCID: PMC9655648 DOI: 10.3390/ijms232112815] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/12/2022] [Accepted: 10/19/2022] [Indexed: 03/28/2024] Open
Abstract
ATP-dependent chromatin-remodeling complexes can reorganize and remodel chromatin and thereby act as important regulator in various cellular processes. Based on considerable studies over the past two decades, it has been confirmed that the abnormal function of chromatin remodeling plays a pivotal role in genome reprogramming for oncogenesis in cancer development and/or resistance to cancer therapy. Recently, exciting progress has been made in the identification of genetic alteration in the genes encoding the chromatin-remodeling complexes associated with tumorigenesis, as well as in our understanding of chromatin-remodeling mechanisms in cancer biology. Here, we present preclinical evidence explaining the signaling mechanisms involving the chromatin-remodeling misregulation-induced cancer cellular processes, including DNA damage signaling, metastasis, angiogenesis, immune signaling, etc. However, even though the cumulative evidence in this field provides promising emerging molecules for therapeutic explorations in cancer, more research is needed to assess the clinical roles of these genetic cancer targets.
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Affiliation(s)
- Fang-Lin Zhang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Cancer Institute, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Da-Qiang Li
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Cancer Institute, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Department of Breast Surgery, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Shanghai Key Laboratory of Breast Cancer, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
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19
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He X, Xu J, Niu N, Xu G, Zhu H, Liu Z, Mou Y, Qian Z, Wang H, Hu J, Ma T, Ma J, Tao H. PBRM1 presents a potential prognostic marker and therapeutic target in duodenal papillary carcinoma. Clin Transl Med 2022; 12:e1062. [PMID: 36178086 PMCID: PMC9523678 DOI: 10.1002/ctm2.1062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Due to its rarity, duodenal papillary carcinoma (DPC) is seldom studied as a unique disease and no specific molecular features or treatment guidelines are provided. METHODS Whole-exome sequencing was performed to gain new insights into the DPC mutation landscape and to identify potential signalling pathways and therapeutic targets. Mechanistically, immunohistochemistry (IHC), immunofluorescence, RNA-seq, ATAC-seq and in vitro cell function experiments were performed to confirm the underlying mechanisms. RESULTS We described the mutational landscape of DPC for the first time as a group of rare tumours with a high frequency of dysregulation in the chromatin remodelling pathway, particularly PBRM1-inactivating mutations that are significantly higher than duodenal adenocarcinomas and ampullary adenocarcinoma (27% vs. 0% vs. 7%, p < .01). In vitro cell experiments showed that downregulation of PBRM1 expression could significantly promote the cancer progression and epithelial-to-mesenchymal transition via the PBRM1-c-JUN-VIM axis. The IHC data indicated that PBRM1 deficiency (p = .047) and c-JUN expression (p < .001) were significantly associated with poor prognosis. Meanwhile, the downregulation of PBRM1 expression in HUTU-80 cells was sensitive to radiation, which may be due to the suppression of c-JUN by irradiation. CONCLUSIONS Our findings define a novel molecular subgroup of PBRM1-inactivating mutations in DPC. PBRM1 play an important role in DPC progression and may serve as a potential therapeutic target and prognostic indicator.
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Affiliation(s)
- Xujun He
- Key Laboratory of Gastroenterology of Zhejiang ProvinceZhejiang Provincial People's Hospital (Affiliated People's HospitalHangzhou Medical College)HangzhouZhejiangChina,Department of Genetic and Genome MedicineZhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College)HangzhouZhejiangChina,Department of Gastrointestinal and Pancreatic SurgeryZhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College)HangzhouZhejiangChina
| | - Ji Xu
- Key Laboratory of Gastroenterology of Zhejiang ProvinceZhejiang Provincial People's Hospital (Affiliated People's HospitalHangzhou Medical College)HangzhouZhejiangChina,Department of Gastrointestinal and Pancreatic SurgeryZhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College)HangzhouZhejiangChina
| | - Nan Niu
- The Second Clinical Medical College of Zhejiang Chinese Medical UniversityHangzhouZhejiangChina
| | - Guoxi Xu
- Department of Gastrointestinal SurgeryJinjiang HospitalQuanzhouFujianChina
| | - Honglin Zhu
- Genetron Health (Beijing) TechnologyCo. Ltd.BeijingChina
| | - Zhengchuang Liu
- Key Laboratory of Gastroenterology of Zhejiang ProvinceZhejiang Provincial People's Hospital (Affiliated People's HospitalHangzhou Medical College)HangzhouZhejiangChina
| | - Yiping Mou
- Key Laboratory of Gastroenterology of Zhejiang ProvinceZhejiang Provincial People's Hospital (Affiliated People's HospitalHangzhou Medical College)HangzhouZhejiangChina,Department of Gastrointestinal and Pancreatic SurgeryZhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College)HangzhouZhejiangChina
| | - Zhengyuan Qian
- Key Laboratory of Gastroenterology of Zhejiang ProvinceZhejiang Provincial People's Hospital (Affiliated People's HospitalHangzhou Medical College)HangzhouZhejiangChina,Department of Gastrointestinal and Pancreatic SurgeryZhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College)HangzhouZhejiangChina
| | - Huiju Wang
- Key Laboratory of Gastroenterology of Zhejiang ProvinceZhejiang Provincial People's Hospital (Affiliated People's HospitalHangzhou Medical College)HangzhouZhejiangChina,Department of Gastrointestinal and Pancreatic SurgeryZhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College)HangzhouZhejiangChina
| | - Junfeng Hu
- Key Laboratory of Gastroenterology of Zhejiang ProvinceZhejiang Provincial People's Hospital (Affiliated People's HospitalHangzhou Medical College)HangzhouZhejiangChina,Department of Gastrointestinal and Pancreatic SurgeryZhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College)HangzhouZhejiangChina
| | - Tonghui Ma
- Genetron Health (Beijing) TechnologyCo. Ltd.BeijingChina
| | - Jie Ma
- Department of PathologyZhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College)HangzhouZhejiangChina
| | - Houquan Tao
- Key Laboratory of Gastroenterology of Zhejiang ProvinceZhejiang Provincial People's Hospital (Affiliated People's HospitalHangzhou Medical College)HangzhouZhejiangChina,Department of Gastrointestinal and Pancreatic SurgeryZhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College)HangzhouZhejiangChina
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20
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Role of SWI/SNF chromatin remodeling genes in lung cancer development. Biochem Soc Trans 2022; 50:1143-1150. [PMID: 35587173 DOI: 10.1042/bst20211084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 04/26/2022] [Accepted: 05/03/2022] [Indexed: 11/17/2022]
Abstract
SWI/SNF family of chromatin remodeling complexes uses the energy of ATP to change the structure of DNA, playing key roles in DNA regulation and repair. It is estimated that up to 25% of all human cancers contain alterations in SWI/SNF, although the precise molecular mechanisms for their involvement in tumor progression are largely unknown. Despite the improvements achieved in the last decades on our knowledge of lung cancer molecular biology, it remains the major cause of cancer-related deaths worldwide and it is in urgent need for new therapeutic alternatives. We and others have described recurrent alterations in different SWI/SNF genes in nearly 20% of lung cancer patients, some of them with a significant association with worse prognosis, indicating an important role of SWI/SNF in this fatal disease. These alterations might be therapeutically exploited, as it has been shown in cellular and animal models with the use of EGFR inhibitors, DNA-damaging agents and several immunotherapy approaches. Therefore, a better knowledge of the molecular mechanisms regulated by SWI/SNF alterations in lung cancer might be translated into a therapeutic improvement of this frequently lethal disease. In this review, we summarize all the evidence of SWI/SNF alterations in lung cancer, the current knowledge about the potential mechanisms involved in their tumorigenic role, as well as the results that support a potential exploitation of these alterations to improve the treatment of lung cancer patients.
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21
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Dreier MR, de la Serna IL. SWI/SNF Chromatin Remodeling Enzymes in Melanoma. EPIGENOMES 2022; 6:epigenomes6010010. [PMID: 35323214 PMCID: PMC8947417 DOI: 10.3390/epigenomes6010010] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/07/2022] [Accepted: 03/14/2022] [Indexed: 11/16/2022] Open
Abstract
Melanoma is an aggressive malignancy that arises from the transformation of melanocytes on the skin, mucosal membranes, and uvea of the eye. SWI/SNF chromatin remodeling enzymes are multi-subunit complexes that play important roles in the development of the melanocyte lineage and in the response to ultraviolet radiation, a key environmental risk factor for developing cutaneous melanoma. Exome sequencing has revealed frequent loss of function mutations in genes encoding SWI/SNF subunits in melanoma. However, some SWI/SNF subunits have also been demonstrated to have pro-tumorigenic roles in melanoma and to affect sensitivity to therapeutics. This review summarizes studies that have implicated SWI/SNF components in melanomagenesis and have evaluated how SWI/SNF subunits modulate the response to current therapeutics.
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22
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He F, Song K, Guan G, Huo J, Xin Y, Li T, Liu C, Zhu Q, Fan N, Guo Y, Wu L. The Phenomenon of Gene Rearrangement is Frequently Associated with TP53 Mutations and Poor Disease-Free Survival in Hepatocellular Carcinoma. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2021; 14:723-736. [PMID: 34188519 PMCID: PMC8233541 DOI: 10.2147/pgpm.s313848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/03/2021] [Indexed: 01/05/2023]
Abstract
Purpose Gene rearrangements (GRs) have been reported to be related to adverse prognosis in some tumours, but the relationship in hepatocellular carcinoma (HCC) remains less studied. The objective of our study was to explore the clinicopathological characteristics and prognosis of HCC patients (HCCs) with GRs (GR-HCCs). Patients and Methods This retrospective study included 297 HCCs who underwent hepatectomy and had their tumours sequenced by next-generation sequencing. Categorical variables between groups were compared by the chi-square test. The impact of variables on disease-free survival (DFS) and survival after relapse (SAR) was analysed by the Kaplan–Meier method and Cox regression. Results We observed four repetitive GR events in 297 HCCs: BRD9/TERT, ARID2/intergenic, CDKN2A/intergenic and OBSCN truncation. GR-HCCs frequently presented with low tumour differentiation, tumour necrosis, microvascular invasion, elevated AFP and gene mutations (TP53, NTRK3 and BRD9). The 1-, 2-, and 3-year cumulative DFS rates in GR-HCCs were 45.1%, 31.9%, 31.9%, respectively, which were significantly lower than those of GR-negative HCCs (NGR-HCCs) (72.5%, 57.9%, and 49.0%, respectively; P = 0.001). GR was identified as an independent risk factor for inferior DFS in HCCs (HR = 1.980, 95% CI = 1.246–3.147; P = 0.004). However, there was no significant difference in SAR between GR-HCCs and NGR-HCCs receiving targeted therapy or immunotherapy. Conclusion GR is frequently associated with TP53 mutations and significantly affects DFS following radical resection for HCC. We recommend that GR-HCCs should be closely followed up as a high-risk group for postoperative recurrence.
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Affiliation(s)
- Fu He
- Liver Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, People's Republic of China.,Department of Clinical Medicine, Qingdao University, Qingdao, 266071, Shandong, People's Republic of China
| | - Kangjian Song
- Liver Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, People's Republic of China.,Department of Clinical Medicine, Qingdao University, Qingdao, 266071, Shandong, People's Republic of China
| | - Ge Guan
- Organ Transplant Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, People's Republic of China
| | - Junyu Huo
- Liver Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, People's Republic of China.,Department of Clinical Medicine, Qingdao University, Qingdao, 266071, Shandong, People's Republic of China
| | - Yang Xin
- Liver Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, People's Republic of China
| | - Tianxiang Li
- Organ Transplant Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, People's Republic of China
| | - Chao Liu
- Liver Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, People's Republic of China
| | - Qingwei Zhu
- Liver Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, People's Republic of China.,Department of Clinical Medicine, Qingdao University, Qingdao, 266071, Shandong, People's Republic of China
| | - Ning Fan
- Liver Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, People's Republic of China
| | - Yuan Guo
- Liver Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, People's Republic of China
| | - Liqun Wu
- Liver Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, People's Republic of China
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