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Agdanowski MP, Castells-Graells R, Sawaya MR, Cascio D, Yeates TO, Arbing MA. X-ray crystal structure of a designed rigidified imaging scaffold in the ligand-free conformation. Acta Crystallogr F Struct Biol Commun 2024; 80:107-115. [PMID: 38767964 PMCID: PMC11134730 DOI: 10.1107/s2053230x2400414x] [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: 02/22/2024] [Accepted: 05/06/2024] [Indexed: 05/22/2024] Open
Abstract
Imaging scaffolds composed of designed protein cages fused to designed ankyrin repeat proteins (DARPins) have enabled the structure determination of small proteins by cryogenic electron microscopy (cryo-EM). One particularly well characterized scaffold type is a symmetric tetrahedral assembly composed of 24 subunits, 12 A and 12 B, which has three cargo-binding DARPins positioned on each vertex. Here, the X-ray crystal structure of a representative tetrahedral scaffold in the apo state is reported at 3.8 Å resolution. The X-ray crystal structure complements recent cryo-EM findings on a closely related scaffold, while also suggesting potential utility for crystallographic investigations. As observed in this crystal structure, one of the three DARPins, which serve as modular adaptors for binding diverse `cargo' proteins, present on each of the vertices is oriented towards a large solvent channel. The crystal lattice is unusually porous, suggesting that it may be possible to soak crystals of the scaffold with small (≤30 kDa) protein cargo ligands and subsequently determine cage-cargo structures via X-ray crystallography. The results suggest the possibility that cryo-EM scaffolds may be repurposed for structure determination by X-ray crystallography, thus extending the utility of electron-microscopy scaffold designs for alternative structural biology applications.
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Affiliation(s)
- Matthew P. Agdanowski
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Roger Castells-Graells
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
- UCLA–DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Michael R. Sawaya
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
- UCLA–DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Duilio Cascio
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
- UCLA–DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Todd O. Yeates
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
- UCLA–DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Mark A. Arbing
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
- UCLA–DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095, USA
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2
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Chen S, Xu D, Huang R, Lin Y, Li L. Correlation of BARD1 gene polymorphisms with risk of neuroblastoma: a meta-analysis. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2024:1-19. [PMID: 38619196 DOI: 10.1080/15257770.2024.2336215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 03/21/2024] [Indexed: 04/16/2024]
Abstract
BRCA1-associated RING domain protein 1 (BARD1) gene polymorphisms may be associated with neuroblastoma (NB) susceptibility. However, the results remain controversial. Relevant studies were identified by searching PubMed, Web of Science, Embase, China National Knowledge Infrastructure databases up to March 5, 2023. The strength of the association between BARD1 polymorphisms and susceptibility of NB was assessed by calculating odds ratios (ORs) and 95% confidence intervals (95% CIs) through the fixed- or random-effects model. Eight articles involving 12 studies were finally included. We found that rs6435862 T > G, rs3768716 A > G, rs17487792 C > T and rs7587476 C > T variant increase the risk of NB in allelic, dominant, recessive, homozygous and heterozygous genetic models, while rs7585356 G > A variant appeared protective against NB. When stratified by ethnicity, subgroup analysis indicated that the above association remained significant in Caucasian populations in all genetic models, except for rs7585356G > A polymorphism in Asians. In Asian populations, we found the similar results in the allelic and dominant model of rs6435862 T > G, rs3768716 A > G, rs17487792 C > T and rs7587476 C > T as in Caucasians, while there lacked a significant association in the other three model. In addition, rs7585356 G > A was not associated with an increased risk of NB in the Asian population. After Bonferroni correction, significant associations for rs7585356 G > A disappeared in both Asian and Caucasian populations, with no significant association found for rs7587476 in the allelic and dominant models among Asians. BARD1 polymorphisms might be significantly associated with NB susceptibility. It is crucial that these finding should be further confirmed through extensive and well-planned studies.
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Affiliation(s)
- Shan Chen
- Department of Laboratory, Fuzhou Second General Hospital, Fuzhou, Fujian, China
| | - Di Xu
- Department of Pediatric Surgery, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, Fujian, China
| | - Rongdong Huang
- Fujian Center for Disease Control and Prevention, Fuzhou, Fujian, China
| | - Yang Lin
- Department of Pediatric Surgery, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, Fujian, China
| | - Lizhi Li
- Department of Pediatric Surgery, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, Fujian, China
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3
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Albarakati N, Al-Ghamdi H, Al-Sowayan B, Alshareeda A. Homologous recombination mRNAs (RAD21, RAD50 and BARD1) have a potentially poor prognostic role in ERBB2-low bladder cancer patients. Sci Rep 2023; 13:11738. [PMID: 37474724 PMCID: PMC10359419 DOI: 10.1038/s41598-023-38923-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/17/2023] [Indexed: 07/22/2023] Open
Abstract
Human epidermal growth factor receptor 2 (HER2/ERBB2) factor is known to be implicated in many malignancies and the potential of it as a prognostic biomarker was reported years ago. Molecular subtypes of HER2/ERBB2 negative and positive with distinct clinical outcomes have been identified in recent years; however, it is still under investigation for bladder cancer. This study evaluates the biological and prognostic significance of RAD21, RAD50 and BARD1 (homologous recombination biomarkers) mRNA levels with ERBB2 low and high expression to explore their impact on bladder cancer patient survival and cancer aggressiveness. The expression of ERBB2, RAD21, RAD50 and BARD1 mRNA levels was assessed in The Cancer Genome Atlas (TCGA) bladder cancer dataset along with four validation cohorts. Outcome analysis was evaluated using disease-free survival (DFS) and overall survival (OS). Univariate and multivariate analysis were used to evaluate the relationship between RAD21, RAD50, BARD1 and ERBB2 expression and clinicopathological variables. A significant increase in mRNA expression levels of RAD21, RAD50 and BARD1 was noticed in ERBB2-low patients compared to ERBB2-high patients. This overexpression of the homologous recombination repair transcripts was associated with poor outcome in ERBB2-low tumors, not in ERBB2-high tumors. Furthermore, the combined expression of high RAD21/RAD50, high RAD21/BARD1 or high RAD50/BARD1 were significantly associated with worse DFS and a better outcome for those with low co-expression in the ERBB2-low cohort. High expression of either RAD21/RAD50 or RAD21/BARD1 in ERBB2-low cohort associated with higher chance of metastasis. In addition, gene expression of BARD1 alone or in combination with RAD50 acted as an independent prognostic factor for worst survival. The data presented in this study reveal a connection between RAD21, RAD50, BARD1 and ERBB2 and patient survival. Importantly, it provided novel findings and potential prognostic markers, particularly in ERBB2-low bladder cancer.
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Affiliation(s)
- Nada Albarakati
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Jeddah, Kingdom of Saudi Arabia.
- King Saud Bin Abdulaziz University for Health Sciences, Ministry of the National Guard-Health Affairs, Riyadh, Saudi Arabia.
| | - Hanin Al-Ghamdi
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Jeddah, Kingdom of Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Ministry of the National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - Batla Al-Sowayan
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Ministry of the National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - Alaa Alshareeda
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Ministry of the National Guard-Health Affairs, Riyadh, Saudi Arabia
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4
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Carrera S, Rodríguez-Martínez AB, Garin I, Sarasola E, Martínez C, Maortua H, Callejo A, Ruiz de Lobera A, Muñoz A, Miñambres N, Jiménez-Labaig P. Germline heterozygous exons 8-11 pathogenic BARD1 gene deletion reported for the first time in a family with suspicion of a hereditary colorectal cancer syndrome: more than an incidental finding? Hered Cancer Clin Pract 2023; 21:2. [PMID: 36709314 PMCID: PMC9883939 DOI: 10.1186/s13053-023-00246-4] [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: 10/21/2022] [Accepted: 01/24/2023] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is a highly prevalent disease in developed countries. Inherited Mendelian causes account for approximately 5% of CRC cases, with Lynch syndrome and familial adenomatous polyposis being the most prevalent forms. Scientific efforts are focused on the discovery of new candidate genes associated with CRC and new associations of phenotypes with well-established cancer-related genes. BRCA1-associated ring domain (BARD1) gene deleterious germline variants are associated with a moderate increase in the relative risk of breast cancer, but their association with other neoplasms, such as CRC, remains unclear. CASE PRESENTATION We present the case of a 49-year-old male diagnosed with rectal adenocarcinoma whose maternal family fulfilled Amsterdam clinical criteria for Lynch syndrome. Genetic test confirmed the presence in heterozygosis of a germline pathogenic deletion of exons 8-11 in BARD1 gene. The predictive genetic study of the family revealed the presence of this pathogenic variant in his deceased cancer affected relatives, confirming co-segregation of the deletion with the disease. CONCLUSIONS To the best of our knowledge, this is the first published work in which this BARD1 deletion is detected in a family with familial colorectal cancer type X (FCCTX) syndrome, in which the clinical criteria for Lynch syndrome without alteration of the DNA mismatch repair (MMR) system are fulfilled. Whether this incidental germline finding is the cause of familial colorectal aggregation remains to be elucidated in scientific forums. Patients should be carefully assessed in specific cancer genetic counseling units to account for hypothetical casual findings in other genes, in principle unrelated to the initial clinical suspicion, but with potential impact on their health.
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Affiliation(s)
- Sergio Carrera
- grid.411232.70000 0004 1767 5135Hereditary Cancer Genetic Counseling Unit- Medical Oncology Department, Cruces University Hospital, Plaza de Cruces S/N. 48903, Baracaldo, Bizkaia Spain
| | | | - Intza Garin
- grid.411232.70000 0004 1767 5135Molecular Genetics Laboratory, Cruces University Hospital, Baracaldo, Spain
| | - Esther Sarasola
- grid.414269.c0000 0001 0667 6181Molecular Genetics Laboratory, Basurto University Hospital, Bilbao, Spain
| | - Cristina Martínez
- grid.411232.70000 0004 1767 5135Molecular Genetics Laboratory, Cruces University Hospital, Baracaldo, Spain
| | - Hiart Maortua
- grid.411232.70000 0004 1767 5135Molecular Genetics Laboratory, Cruces University Hospital, Baracaldo, Spain
| | - Almudena Callejo
- grid.411232.70000 0004 1767 5135Medical Oncology Department, Cruces University Hospital, Baracaldo, Spain
| | - Abigail Ruiz de Lobera
- grid.411232.70000 0004 1767 5135Medical Oncology Department, Cruces University Hospital, Baracaldo, Spain
| | - Alberto Muñoz
- grid.411232.70000 0004 1767 5135Medical Oncology Department, Cruces University Hospital, Baracaldo, Spain
| | - Nagore Miñambres
- grid.411232.70000 0004 1767 5135Medical Oncology Department, Cruces University Hospital, Baracaldo, Spain
| | - Pablo Jiménez-Labaig
- grid.411232.70000 0004 1767 5135Medical Oncology Department, Cruces University Hospital, Baracaldo, Spain
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5
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Hawsawi YM, Shams A, Theyab A, Abdali WA, Hussien NA, Alatwi HE, Alzahrani OR, Oyouni AAA, Babalghith AO, Alreshidi M. BARD1 mystery: tumor suppressors are cancer susceptibility genes. BMC Cancer 2022; 22:599. [PMID: 35650591 PMCID: PMC9161512 DOI: 10.1186/s12885-022-09567-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/14/2022] [Indexed: 12/24/2022] Open
Abstract
The full-length BRCA1-associated RING domain 1 (BARD1) gene encodes a 777-aa protein. BARD1 displays a dual role in cancer development and progression as it acts as a tumor suppressor and an oncogene. Structurally, BARD1 has homologous domains to BRCA1 that aid their heterodimer interaction to inhibit the progression of different cancers such as breast and ovarian cancers following the BRCA1-dependant pathway. In addition, BARD1 was shown to be involved in other pathways that are involved in tumor suppression (BRCA1-independent pathway) such as the TP53-dependent apoptotic signaling pathway. However, there are abundant BARD1 isoforms exist that are different from the full-length BARD1 due to nonsense and frameshift mutations, or deletions were found to be associated with susceptibility to various cancers including neuroblastoma, lung, breast, and cervical cancers. This article reviews the spectrum of BARD1 full-length genes and its different isoforms and their anticipated associated risk. Additionally, the study also highlights the role of BARD1 as an oncogene in breast cancer patients and its potential uses as a prognostic/diagnostic biomarker and as a therapeutic target for cancer susceptibility testing and treatment.
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Affiliation(s)
- Yousef M Hawsawi
- King Faisal Specialist Hospital and Research Center- Research Center, KFSH&RC, MBC-J04, P.O. Box 40047, Jeddah, 21499, Saudi Arabia. .,College of Medicine, Al-Faisal University, P.O. Box 50927, Riyadh, 11533, Saudi Arabia.
| | - Anwar Shams
- Department of Pharmacology, College of Medicine, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Abdulrahman Theyab
- College of Medicine, Al-Faisal University, P.O. Box 50927, Riyadh, 11533, Saudi Arabia.,Department of Pharmacology, College of Medicine, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia.,Department of Laboratory Medicine, Security Forces Hospital, Mecca, Kingdom of Saudi Arabia
| | - Wed A Abdali
- King Faisal Specialist Hospital and Research Center- Research Center, KFSH&RC, MBC-J04, P.O. Box 40047, Jeddah, 21499, Saudi Arabia
| | - Nahed A Hussien
- Department of Zoology, Faculty of Science, Cairo University, Giza, 12613, Egypt.,Department of Biology, College of Science, Taif University, P.O Box 11099, Taif, 21944, Saudi Arabia
| | - Hanan E Alatwi
- Department of Biology, Faculty of Sciences, University of Tabuk, Tabuk, Kingdom of Saudi Arabia.,Genome and Biotechnology Unit, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - Othman R Alzahrani
- Department of Biology, Faculty of Sciences, University of Tabuk, Tabuk, Kingdom of Saudi Arabia.,Genome and Biotechnology Unit, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - Atif Abdulwahab A Oyouni
- Department of Biology, Faculty of Sciences, University of Tabuk, Tabuk, Kingdom of Saudi Arabia.,Genome and Biotechnology Unit, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - Ahmad O Babalghith
- Medical genetics Department, College of Medicine, Umm Alqura University, Makkah, Saudi Arabia
| | - Mousa Alreshidi
- Departement of biology, College of Science, University of Hail, Hail, Saudi Arabia.,Molecular Diagnostic and Personalized Therapeutic Unit, University of Hail, Hail, Saudi Arabia
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6
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Maurer LM, Daley JD, Mukherjee E, Venier RE, Julian CM, Bailey NG, Jacobs MF, Kumar-Sinha C, Raphael H, Periyapatna N, Weiss K, Janeway KA, Mody R, Lucas PC, McAllister-Lucas LM, Bailey KM. BRCA1-associated RING domain-1 (BARD1) loss and GBP1 expression enhance sensitivity to DNA damage in Ewing sarcoma. CANCER RESEARCH COMMUNICATIONS 2022; 2:220-232. [PMID: 36187937 PMCID: PMC9524505 DOI: 10.1158/2767-9764.crc-21-0047] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ewing sarcoma is a fusion oncoprotein-driven primary bone tumor. A subset of patients (~10%) with Ewing sarcoma are known to harbor germline variants in a growing number of genes involved in DNA damage repair. We recently reported our discovery of a germline mutation in the DNA damage repair protein BARD1 (BRCA1-associated RING domain-1) in a patient with Ewing sarcoma. BARD1 is recruited to the site of DNA double stranded breaks via the poly(ADP-ribose) polymerase (PARP) protein and plays a critical role in DNA damage response pathways including homologous recombination. We thus questioned the impact of BARD1 loss on Ewing cell sensitivity to DNA damage and the Ewing sarcoma transcriptome. We demonstrate that PSaRC318 cells, a novel patient-derived cell line harboring a pathogenic BARD1 variant, are sensitive to PARP inhibition and by testing the effect of BARD1 depletion in additional Ewing sarcoma cell lines, we confirm that BARD1 loss enhances cell sensitivity to PARP inhibition plus radiation. Additionally, RNA-seq analysis revealed that loss of BARD1 results in the upregulation of GBP1 (guanylate-binding protein 1), a protein whose expression is associated with variable response to therapy depending on the adult carcinoma subtype examined. Here, we demonstrate that GBP1 contributes to the enhanced sensitivity of BARD1 deficient Ewing cells to DNA damage. Together, our findings demonstrate the impact of loss-of function mutations in DNA damage repair genes, such as BARD1, on Ewing sarcoma treatment response.
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Affiliation(s)
- Lisa M Maurer
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Jessica D Daley
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Elina Mukherjee
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Rosemarie E Venier
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | - Claire M Julian
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Nathanael G Bailey
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Michelle F Jacobs
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI
| | | | - Haley Raphael
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Nivitha Periyapatna
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Kurt Weiss
- Department of Orthopedic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Katherine A Janeway
- Pediatric Oncology, Dana-Farber / Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | - Rajen Mody
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI
| | - Peter C Lucas
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | | | - Kelly M Bailey
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA
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7
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Quintanilha JC, Wang J, Sibley AB, Xu W, Espin-Garcia O, Jiang C, Etheridge AS, Ratain MJ, Lenz HJ, Bertagnolli M, Kindler HL, Dickler MN, Venook A, Liu G, Owzar K, Lin D, Innocenti F. Genome-wide association studies of survival in 1520 cancer patients treated with bevacizumab-containing regimens. Int J Cancer 2022; 150:279-289. [PMID: 34528705 PMCID: PMC8627468 DOI: 10.1002/ijc.33810] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/13/2021] [Accepted: 08/23/2021] [Indexed: 01/17/2023]
Abstract
Germline variants might predict cancer progression. Bevacizumab improves overall survival (OS) in patients with advanced cancers. No biomarkers are available to identify patients that benefit from bevacizumab. A meta-analysis of genome-wide association studies (GWAS) was conducted in 1,520 patients from Phase III trials (CALGB 80303, 40503, 80405 and ICON7), where bevacizumab was randomized to treatment without bevacizumab. We aimed to identify genes and single nucleotide polymorphisms (SNPs) associated with survival independently of bevacizumab treatment or through interaction with bevacizumab. A cause-specific Cox model was used to test the SNP-OS association in both arms combined (prognostic), and the effect of SNPs-bevacizumab interaction on OS (predictive) in each study. The SNP effects across studies were combined using inverse variance. Findings were tested for replication in advanced colorectal and ovarian cancer patients from The Cancer Genome Atlas (TGCA). In the GWAS meta-analysis, patients with rs680949 in PRUNE2 experienced shorter OS compared to patients without it (P = 1.02 × 10-7 , hazard ratio [HR] = 1.57, 95% confidence interval [CI] 1.33-1.86), as well as in TCGA (P = .0219, HR = 1.58, 95% CI 1.07-2.35). In the GWAS meta-analysis, patients with rs16852804 in BARD1 experienced shorter OS compared to patients without it (P = 1.40 × 10-5 , HR = 1.51, 95% CI 1.25-1.82) as well as in TCGA (P = 1.39 × 10-4 , HR = 3.09, 95% CI 1.73-5.51). Patients with rs3795897 in AGAP1 experienced shorter OS in the bevacizumab arm compared to the nonbevacizumab arm (P = 1.43 × 10-5 ). The largest GWAS meta-analysis of bevacizumab treated patients identified PRUNE2 and BARD1 (tumor suppressor genes) as prognostic genes of colorectal and ovarian cancer, respectively, and AGAP1 as a potentially predictive gene that interacts with bevacizumab with respect to patient survival.
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Affiliation(s)
- Julia C.F. Quintanilha
- UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jin Wang
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Alexander B. Sibley
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Wei Xu
- Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network and Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Osvaldo Espin-Garcia
- Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network and Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Chen Jiang
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Amy S. Etheridge
- UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Mark J. Ratain
- University of Chicago Comprehensive Cancer Center, Chicago, Illinois, USA
| | - Heinz-Josef Lenz
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | | | - Hedy L. Kindler
- University of Chicago Comprehensive Cancer Center, Chicago, Illinois, USA
| | | | - Alan Venook
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, USA
| | - Geoffrey Liu
- Division of Medical Oncology and Hematology, Department of Medicine, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, ON, Canada
| | - Kouros Owzar
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA,Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina, USA
| | - Danyu Lin
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Federico Innocenti
- UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA,Correspondence: Federico Innocenti, MD, PhD. University of North Carolina at Chapel Hill, UNC Eshelman School of Pharmacy, Genetic Medicine Bldg. 120 Mason Farm Rd, Campus Box 7361, Chapel Hill, NC 27599-7361, Tel 919-966-9422 Fax 919-966-5863,
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8
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Russi M, Marson D, Fermeglia A, Aulic S, Fermeglia M, Laurini E, Pricl S. The fellowship of the RING: BRCA1, its partner BARD1 and their liaison in DNA repair and cancer. Pharmacol Ther 2021; 232:108009. [PMID: 34619284 DOI: 10.1016/j.pharmthera.2021.108009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 08/22/2021] [Accepted: 09/20/2021] [Indexed: 12/12/2022]
Abstract
The breast cancer type 1 susceptibility protein (BRCA1) and its partner - the BRCA1-associated RING domain protein 1 (BARD1) - are key players in a plethora of fundamental biological functions including, among others, DNA repair, replication fork protection, cell cycle progression, telomere maintenance, chromatin remodeling, apoptosis and tumor suppression. However, mutations in their encoding genes transform them into dangerous threats, and substantially increase the risk of developing cancer and other malignancies during the lifetime of the affected individuals. Understanding how BRCA1 and BARD1 perform their biological activities therefore not only provides a powerful mean to prevent such fatal occurrences but can also pave the way to the development of new targeted therapeutics. Thus, through this review work we aim at presenting the major efforts focused on the functional characterization and structural insights of BRCA1 and BARD1, per se and in combination with all their principal mediators and regulators, and on the multifaceted roles these proteins play in the maintenance of human genome integrity.
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Affiliation(s)
- Maria Russi
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Domenico Marson
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Alice Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Suzana Aulic
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Maurizio Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Erik Laurini
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Sabrina Pricl
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy; Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland.
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9
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Ando K, Nakagawara A. Acceleration or Brakes: Which Is Rational for Cell Cycle-Targeting Neuroblastoma Therapy? Biomolecules 2021; 11:biom11050750. [PMID: 34069817 PMCID: PMC8157238 DOI: 10.3390/biom11050750] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/09/2021] [Accepted: 05/12/2021] [Indexed: 11/27/2022] Open
Abstract
Unrestrained proliferation is a common feature of malignant neoplasms. Targeting the cell cycle is a therapeutic strategy to prevent unlimited cell division. Recently developed rationales for these selective inhibitors can be subdivided into two categories with antithetical functionality. One applies a “brake” to the cell cycle to halt cell proliferation, such as with inhibitors of cell cycle kinases. The other “accelerates” the cell cycle to initiate replication/mitotic catastrophe, such as with inhibitors of cell cycle checkpoint kinases. The fate of cell cycle progression or arrest is tightly regulated by the presence of tolerable or excessive DNA damage, respectively. This suggests that there is compatibility between inhibitors of DNA repair kinases, such as PARP inhibitors, and inhibitors of cell cycle checkpoint kinases. In the present review, we explore alterations to the cell cycle that are concomitant with altered DNA damage repair machinery in unfavorable neuroblastomas, with respect to their unique genomic and molecular features. We highlight the vulnerabilities of these alterations that are attributable to the features of each. Based on the assessment, we offer possible therapeutic approaches for personalized medicine, which are seemingly antithetical, but both are promising strategies for targeting the altered cell cycle in unfavorable neuroblastomas.
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Affiliation(s)
- Kiyohiro Ando
- Research Institute for Clinical Oncology, Saitama Cancer Center, 818 Komuro, Ina, Saitama 362-0806, Japan
- Correspondence: (K.A.); (A.N.); Tel.: +81-48-722-1111 (K.A.); +81-942-50-8829 (A.N.)
| | - Akira Nakagawara
- Saga International Carbon Particle Beam Radiation Cancer Therapy Center, Saga HIMAT Foundation, 3049 Harakoga-Machi, Saga 841-0071, Japan
- Correspondence: (K.A.); (A.N.); Tel.: +81-48-722-1111 (K.A.); +81-942-50-8829 (A.N.)
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10
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McDougall LI, Powell RM, Ratajska M, Lynch-Sutherland CF, Hossain SM, Wiggins GAR, Harazin-Lechowska A, Cybulska-Stopa B, Motwani J, Macaulay EC, Reid G, Walker LC, Ryś J, Eccles MR. Differential Expression of BARD1 Isoforms in Melanoma. Genes (Basel) 2021; 12:320. [PMID: 33672422 PMCID: PMC7927127 DOI: 10.3390/genes12020320] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/12/2021] [Accepted: 02/20/2021] [Indexed: 12/11/2022] Open
Abstract
Melanoma comprises <5% of cutaneous malignancies, yet it causes a significant proportion of skin cancer-related deaths worldwide. While new therapies for melanoma have been developed, not all patients respond well. Thus, further research is required to better predict patient outcomes. Using long-range nanopore sequencing, RT-qPCR, and RNA sequencing analyses, we examined the transcription of BARD1 splice isoforms in melanoma cell lines and patient tissue samples. Seventy-six BARD1 mRNA variants were identified in total, with several previously characterised isoforms (γ, φ, δ, ε, and η) contributing to a large proportion of the expressed transcripts. In addition, we identified four novel splice events, namely, Δ(E3_E9), ▼(i8), IVS10+131▼46, and IVS10▼176, occurring in various combinations in multiple transcripts. We found that short-read RNA-Seq analyses were limited in their ability to predict isoforms containing multiple non-contiguous splicing events, as compared to long-range nanopore sequencing. These studies suggest that further investigations into the functional significance of the identified BARD1 splice variants in melanoma are warranted.
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Affiliation(s)
- Lorissa I. McDougall
- Department of Pathology, Otago Medical School, Dunedin Campus, University of Otago, Dunedin 9010, New Zealand; (L.I.M.); (R.M.P.); (M.R.); (C.F.L.-S.); (S.M.H.); (J.M.); (E.C.M.); (G.R.)
| | - Ryan M. Powell
- Department of Pathology, Otago Medical School, Dunedin Campus, University of Otago, Dunedin 9010, New Zealand; (L.I.M.); (R.M.P.); (M.R.); (C.F.L.-S.); (S.M.H.); (J.M.); (E.C.M.); (G.R.)
| | - Magdalena Ratajska
- Department of Pathology, Otago Medical School, Dunedin Campus, University of Otago, Dunedin 9010, New Zealand; (L.I.M.); (R.M.P.); (M.R.); (C.F.L.-S.); (S.M.H.); (J.M.); (E.C.M.); (G.R.)
- Department of Biology and Medical Genetics, Medical University of Gdansk, 80-211 Gdansk, Poland
| | - Chi F. Lynch-Sutherland
- Department of Pathology, Otago Medical School, Dunedin Campus, University of Otago, Dunedin 9010, New Zealand; (L.I.M.); (R.M.P.); (M.R.); (C.F.L.-S.); (S.M.H.); (J.M.); (E.C.M.); (G.R.)
| | - Sultana Mehbuba Hossain
- Department of Pathology, Otago Medical School, Dunedin Campus, University of Otago, Dunedin 9010, New Zealand; (L.I.M.); (R.M.P.); (M.R.); (C.F.L.-S.); (S.M.H.); (J.M.); (E.C.M.); (G.R.)
| | - George A. R. Wiggins
- Department of Pathology and Biomedical Science, University of Otago, Christchurch 8011, New Zealand; (G.A.R.W.); (L.C.W.)
| | - Agnieszka Harazin-Lechowska
- Department of Tumour Pathology, Maria Sklodowska-Curie National Research Institute of Oncology, Cracow Branch, 8011 Cracow, Poland; (A.H.-L.); (J.R.)
| | - Bożena Cybulska-Stopa
- Department of Clinical Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, Cracow Branch, 8011 Cracow, Poland;
| | - Jyoti Motwani
- Department of Pathology, Otago Medical School, Dunedin Campus, University of Otago, Dunedin 9010, New Zealand; (L.I.M.); (R.M.P.); (M.R.); (C.F.L.-S.); (S.M.H.); (J.M.); (E.C.M.); (G.R.)
| | - Erin C. Macaulay
- Department of Pathology, Otago Medical School, Dunedin Campus, University of Otago, Dunedin 9010, New Zealand; (L.I.M.); (R.M.P.); (M.R.); (C.F.L.-S.); (S.M.H.); (J.M.); (E.C.M.); (G.R.)
| | - Glen Reid
- Department of Pathology, Otago Medical School, Dunedin Campus, University of Otago, Dunedin 9010, New Zealand; (L.I.M.); (R.M.P.); (M.R.); (C.F.L.-S.); (S.M.H.); (J.M.); (E.C.M.); (G.R.)
| | - Logan C. Walker
- Department of Pathology and Biomedical Science, University of Otago, Christchurch 8011, New Zealand; (G.A.R.W.); (L.C.W.)
| | - Janusz Ryś
- Department of Tumour Pathology, Maria Sklodowska-Curie National Research Institute of Oncology, Cracow Branch, 8011 Cracow, Poland; (A.H.-L.); (J.R.)
| | - Michael R. Eccles
- Department of Pathology, Otago Medical School, Dunedin Campus, University of Otago, Dunedin 9010, New Zealand; (L.I.M.); (R.M.P.); (M.R.); (C.F.L.-S.); (S.M.H.); (J.M.); (E.C.M.); (G.R.)
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1010, New Zealand
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11
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Jasiak A, Krawczyńska N, Iliszko M, Czarnota K, Buczkowski K, Stefanowicz J, Adamkiewicz-Drożyńska E, Cichosz G, Iżycka-Świeszewska E. Expression of BARD1 β Isoform in Selected Pediatric Tumors. Genes (Basel) 2021; 12:genes12020168. [PMID: 33530592 PMCID: PMC7911681 DOI: 10.3390/genes12020168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/18/2021] [Accepted: 01/23/2021] [Indexed: 12/20/2022] Open
Abstract
Currently, many new possible biomarkers and mechanisms are being searched and tested to analyse pathobiology of pediatric tumours for the development of new treatments. One such candidate molecular factor is BARD1 (BRCA1 Associated RING Domain 1)—a tumour-suppressing gene involved in cell cycle control and genome stability, engaged in several types of adult-type tumours. The data on BARD1 significance in childhood cancer is limited. This study determines the expression level of BARD1 and its isoform beta (β) in three different histogenetic groups of pediatric cancer—neuroblastic tumours, and for the first time in chosen germ cell tumours (GCT), and rhabdomyosarcoma (RMS), using the qPCR method. We found higher expression of beta isoform in tumour compared to healthy tissue with no such changes concerning BARD1 full-length. Additionally, differences in expression of BARD1 β between histological types of neuroblastic tumours were observed, with higher levels in ganglioneuroblastoma and ganglioneuroma. Furthermore, a higher expression of BARD1 β characterized yolk sac tumours (GCT type) and RMS when comparing with non-neoplastic tissue. These tumours also showed a high expression of the TERT (Telomerase Reverse Transcriptase) gene. In two RMS cases we found deep decrease of BARD1 β in post-chemotherapy samples. This work supports the oncogenicity of the beta isoform in pediatric tumours, as well as demonstrates the differences in its expression depending on the histological type of neoplasm, and the level of maturation in neuroblastic tumours.
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Affiliation(s)
- Anna Jasiak
- Department of Biology and Medical Genetics, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland; (A.J.); (M.I.); (G.C.)
- Laboratory of Clinical Genetics, University Clinical Centre, 17 Smoluchowskiego St., 80-210 Gdansk, Poland
| | - Natalia Krawczyńska
- Department of Biology and Medical Genetics, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland; (A.J.); (M.I.); (G.C.)
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, 407S Goodwin Ave, Urbana, IL 61801, USA;
| | - Mariola Iliszko
- Department of Biology and Medical Genetics, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland; (A.J.); (M.I.); (G.C.)
- Laboratory of Clinical Genetics, University Clinical Centre, 17 Smoluchowskiego St., 80-210 Gdansk, Poland
| | - Katarzyna Czarnota
- Department of Pathology and Neuropathology, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland; (K.C.); (K.B.)
| | - Kamil Buczkowski
- Department of Pathology and Neuropathology, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland; (K.C.); (K.B.)
- Department of Pathomorphology, Copernicus Hospitals, 1-6 Nowe Ogrody St., 80-803 Gdansk, Poland
| | - Joanna Stefanowicz
- Department of Pediatrics, Hematology, Oncology, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland; (J.S.); (E.A.-D.)
| | - Elżbieta Adamkiewicz-Drożyńska
- Department of Pediatrics, Hematology, Oncology, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland; (J.S.); (E.A.-D.)
| | - Grzegorz Cichosz
- Department of Biology and Medical Genetics, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland; (A.J.); (M.I.); (G.C.)
| | - Ewa Iżycka-Świeszewska
- Department of Pathology and Neuropathology, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland; (K.C.); (K.B.)
- Department of Pathomorphology, Copernicus Hospitals, 1-6 Nowe Ogrody St., 80-803 Gdansk, Poland
- Correspondence:
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12
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The cross-talk between signaling pathways, noncoding RNAs and DNA damage response: Emerging players in cancer progression. DNA Repair (Amst) 2021; 98:103036. [PMID: 33429260 DOI: 10.1016/j.dnarep.2020.103036] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 12/11/2020] [Indexed: 02/06/2023]
Abstract
The DNA damage response (DDR) pathway's primary purpose is to maintain the genome structure's integrity and stability. A great deal of effort has done to understand the exact molecular mechanisms of non-coding RNAs, such as lncRNA, miRNAs, and circRNAs, in distinct cellular and genomic processes and cancer progression. In this regard, the ncRNAs possible regulatory role in DDR via modulation of key components expression and controlling repair signaling pathway activation is validated. Therefore, in this article, we will discuss the latest developments of ncRNAs contribution in different aspects of DNA repair through regulation of ATM-ATR, P53, and other regulatory signaling pathways.
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