Assessment of DNA-damage repair in breast cancer

Background: Current evidence indicates that DNA damage response (DDR) is a highly complex process that involves various pathways working in an orchestrated and interwoven manner in response to different types of damage to DNA. Although specific defects of DDR remain to be deciphered in cancer as a general, there is certainly an undeniable relationship between a particular dysfunction of DDR and the phenotype of tumour [1, 2]. It has been demonstrated that familial forms of breast and ovarian cancer are characterised by defects in one of the main mechanisms of DDR homologous recombination (HR) as a result of germline loss-of-function mutations in one of HR modifying genes, such as BRCA1 and BRCA2 [1, 3, 4]. Defects of genes involved in other DDR pathways are also associated with specific types of cancers; for instance hereditary non polyposis colorectal cancer (HNPCC) is strongly associated with specific mutations in the DNA mismatch repair pathway. Several previous studies have demonstrated that impaired DDR play a fundamental role in the pathogenesis and behaviour of breast cancer (BC). However, characterisation of this complex process, the expression and co-expression of the key proteins involved in the various DDR pathways and their prognostic significance in BC remain to be defined. In BC, it is reported that genes involved in DNA double strand breaks (DSB) repair are the most important. Two main pathways are involved in the repair of DNA-DSB; HR and Non Homologous End Joining (NHEJ) [3]. The common characteristics of global DDR are multiple genes induction directly associated with sensing and repair of DNA, arrest of cell cycle, and cell division inhibition. As a result DDR process does not only include genes activation involved in damage sensing as well as repair but additionally genes involved in control of cell-cycle [5]. Despite the fact that DDR may possibly involve activation of several pathways (such as SUMOylation (SUMO)) [6, 7] and many genes are engaged in different overlapping mechanisms, each pathway is characterised by activation and expression of a unique set of genes. This could allow discovering the active or aberrant pathway in a given tumour [1, 4, 5]. This study explores the hypothesis that investigation of alterations in the different pathways of DNA-DSB, may contribute to the characteristics of BC. Therefore, the aim was to perform a comprehensive profiling of key proteins involved in the different DNA-DSB repair pathways in the different molecular classes of BC. This approach aims to address the inherent problems arising from the complexity of DDR mechanism in BC with the potential of discovering a key pathway that is active or inactive in specific forms of BC that can be helpful to identify DNA repair status in individual BC patients. Method: The study cohort comprises three BC groups: A) Large series of unselected primary sporadic operable invasive tumours (n=1904) in addition to B) 386 cases of oestrogen receptor (ER) negative tumours and C) a well-characterised series of BC from patients with known BRCA1 germline mutations (n=24). The proteins investigated in this study are known to participate in different DNA-DSB repair pathways including, DNA damage sensors (ATM and ATR), HR repair (BRCA1, BARD1, Rad51, γH2AX and SMC6L1), DNA damage checkpoint signalling protein (CHK1 and CHK2), NHEJ repair (KU70/KU80, and DNA-PK), and SUMO (PIAS1, PIAS4, and UBC9). Because subcellular localisation of DDR proteins may affect their function, two markers that have role in nuclear transport in the cell were examined (NPM and KPNA2). The expression of these proteins was assessed using the well-established immunohistochemical technique utilising tissue microarray technology. The expression of proteins was further evaluated in various cell lines; BRCA1 deficient HeLaSilenciX® cells, and control BRCA1 proficient HeLaSilenciX®, MDA-MB-436 (BRCA1 deficient), and MCF-7 (BRCA1 proficient and ER+) using Reverse Phase Protein Microarray (RPPA). Results: Both cytoplasmic and nuclear expression was observed for expression of Rad51, SMC6L1, BRCA1, BARD1; (HR markers), PIAS1, UBC9 (SUMO markers), γH2AX (DNA-DSB marker) and CHK1 (checkpoint signalling protein). In contrast, both NHEJ markers and most of the DNA damage sensors (ATM and ATR), CHK2 and PIAS4 were mainly expressed in the nucleus. Generally, tumours that showed positive cytoplasmic/negative nuclear expression such as CHK1, PIAS1, Rad51, and BRCA1, and positive nuclear NHEJ markers showed an association with a poor outcome and adverse prognostic characteristics including high histologic grade, high mitotic frequency, high nuclear pleomorphism and larger tumour size in addition to ER negativity, and triple negative breast cancer (TNBC). Conversely, nuclear+/cytoplasmic- expression showed an association the better outcome. Interestingly, ATM protein expression showed no association with the expression of the two NHEJ markers, whereas ATR showed an association with cytoplasmic expression of BRCA1 and BARD1 and was positively associated with NHEJ markers. In non-TNBC, tumours showing BRCA1-/KU70/KU80- phenotype had worse breast cancer specific survival (BCSS) than positive expression (P<0.0001), whereas in the TN cohort,complex of KU70/KU80-&DNA-PK+ had the worst BCSS (P=0.001), and both are independent prognostic markers for BC. KPNA2, but not NPM was highly associated with poor BCSS (P<0.0001). At least one of nucleocytoplasmic transport markers (NPM or KPNA2) was significantly associated with the subcellular localisation of the most of the markers that showed cytoplasmic expression including SMC6L1, γH2AX, BRCA1, BARD1, UBC9, PIAS1 ,Rad51 and CHK1. RPPA was used to investigate the protein expression in different cell lines, although the correlation between RPPA and IHC was not significant, the results of RPPA were consistent with that demonstrated by IHC further supporting the finding of the current study. Conclusion: This study highlight the complexity of DDR related proteins and the overlap between different pathways involved in DDR. The finding of this study may help in the classification of BC and therefore, targeting active pathways in the development of drugs would enhance better patients’ outcomes. Major prognostic and predictive variables can be very important in choosing suitable treatment plans, identifying the risk of recurrence and classifying patients for clinical trials. Our results show that the HR- repair marker Rad51, complex of HR and NHEJ repair markers (BRCA1&KU70/KU80) in non-TNBC, and a complex of NHEJ markers (KU70/KU80&DNA-PK) are all independent prognostic markers for BC. In addition to expression, subcellular localisation of DDR proteins appeared to be a major factor in their role. Particularly, HR repair markers (but not NHEJ) showed worse features of cytoplasmic location of expression, whereas nuclear expression was associated with more favourable features. Finally, the results of this study provide further evidence to support combined use of IHC with the parallel analytic capability of protein microarray RPPA to investigate protein alterations in human tumours

Assessment of DNA-damage repair in breast cancer

Background: Current evidence indicates that DNA damage response (DDR) is a highly complex process that involves various pathways working in an orchestrated and interwoven manner in response to different types of damage to DNA. Although specific defects of DDR remain to be deciphered in cancer as a general, there is certainly an undeniable relationship between a particular dysfunction of DDR and the phenotype of tumour [1, 2]. It has been demonstrated that familial forms of breast and ovarian cancer are characterised by defects in one of the main mechanisms of DDR homologous recombination (HR) as a result of germline loss-of-function mutations in one of HR modifying genes, such as BRCA1 and BRCA2 [1, 3, 4]. Defects of genes involved in other DDR pathways are also associated with specific types of cancers; for instance hereditary non polyposis colorectal cancer (HNPCC) is strongly associated with specific mutations in the DNA mismatch repair pathway. Several previous studies have demonstrated that impaired DDR play a fundamental role in the pathogenesis and behaviour of breast cancer (BC). However, characterisation of this complex process, the expression and co-expression of the key proteins involved in the various DDR pathways and their prognostic significance in BC remain to be defined. In BC, it is reported that genes involved in DNA double strand breaks (DSB) repair are the most important. Two main pathways are involved in the repair of DNA-DSB; HR and Non Homologous End Joining (NHEJ) [3]. The common characteristics of global DDR are multiple genes induction directly associated with sensing and repair of DNA, arrest of cell cycle, and cell division inhibition. As a result DDR process does not only include genes activation involved in damage sensing as well as repair but additionally genes involved in control of cell-cycle [5]. Despite the fact that DDR may possibly involve activation of several pathways (such as SUMOylation (SUMO)) [6, 7] and many genes are engaged in different overlapping mechanisms, each pathway is characterised by activation and expression of a unique set of genes. This could allow discovering the active or aberrant pathway in a given tumour [1, 4, 5]. This study explores the hypothesis that investigation of alterations in the different pathways of DNA-DSB, may contribute to the characteristics of BC. Therefore, the aim was to perform a comprehensive profiling of key proteins involved in the different DNA-DSB repair pathways in the different molecular classes of BC. This approach aims to address the inherent problems arising from the complexity of DDR mechanism in BC with the potential of discovering a key pathway that is active or inactive in specific forms of BC that can be helpful to identify DNA repair status in individual BC patients. Method: The study cohort comprises three BC groups: A) Large series of unselected primary sporadic operable invasive tumours (n=1904) in addition to B) 386 cases of oestrogen receptor (ER) negative tumours and C) a well-characterised series of BC from patients with known BRCA1 germline mutations (n=24). The proteins investigated in this study are known to participate in different DNA-DSB repair pathways including, DNA damage sensors (ATM and ATR), HR repair (BRCA1, BARD1, Rad51, γH2AX and SMC6L1), DNA damage checkpoint signalling protein (CHK1 and CHK2), NHEJ repair (KU70/KU80, and DNA-PK), and SUMO (PIAS1, PIAS4, and UBC9). Because subcellular localisation of DDR proteins may affect their function, two markers that have role in nuclear transport in the cell were examined (NPM and KPNA2). The expression of these proteins was assessed using the well-established immunohistochemical technique utilising tissue microarray technology. The expression of proteins was further evaluated in various cell lines; BRCA1 deficient HeLaSilenciX® cells, and control BRCA1 proficient HeLaSilenciX®, MDA-MB-436 (BRCA1 deficient), and MCF-7 (BRCA1 proficient and ER+) using Reverse Phase Protein Microarray (RPPA). Results: Both cytoplasmic and nuclear expression was observed for expression of Rad51, SMC6L1, BRCA1, BARD1; (HR markers), PIAS1, UBC9 (SUMO markers), γH2AX (DNA-DSB marker) and CHK1 (checkpoint signalling protein). In contrast, both NHEJ markers and most of the DNA damage sensors (ATM and ATR), CHK2 and PIAS4 were mainly expressed in the nucleus. Generally, tumours that showed positive cytoplasmic/negative nuclear expression such as CHK1, PIAS1, Rad51, and BRCA1, and positive nuclear NHEJ markers showed an association with a poor outcome and adverse prognostic characteristics including high histologic grade, high mitotic frequency, high nuclear pleomorphism and larger tumour size in addition to ER negativity, and triple negative breast cancer (TNBC). Conversely, nuclear+/cytoplasmic- expression showed an association the better outcome. Interestingly, ATM protein expression showed no association with the expression of the two NHEJ markers, whereas ATR showed an association with cytoplasmic expression of BRCA1 and BARD1 and was positively associated with NHEJ markers. In non-TNBC, tumours showing BRCA1-/KU70/KU80- phenotype had worse breast cancer specific survival (BCSS) than positive expression (P<0.0001), whereas in the TN cohort,complex of KU70/KU80-&DNA-PK+ had the worst BCSS (P=0.001), and both are independent prognostic markers for BC. KPNA2, but not NPM was highly associated with poor BCSS (P<0.0001). At least one of nucleocytoplasmic transport markers (NPM or KPNA2) was significantly associated with the subcellular localisation of the most of the markers that showed cytoplasmic expression including SMC6L1, γH2AX, BRCA1, BARD1, UBC9, PIAS1 ,Rad51 and CHK1. RPPA was used to investigate the protein expression in different cell lines, although the correlation between RPPA and IHC was not significant, the results of RPPA were consistent with that demonstrated by IHC further supporting the finding of the current study. Conclusion: This study highlight the complexity of DDR related proteins and the overlap between different pathways involved in DDR. The finding of this study may help in the classification of BC and therefore, targeting active pathways in the development of drugs would enhance better patients’ outcomes. Major prognostic and predictive variables can be very important in choosing suitable treatment plans, identifying the risk of recurrence and classifying patients for clinical trials. Our results show that the HR- repair marker Rad51, complex of HR and NHEJ repair markers (BRCA1&KU70/KU80) in non-TNBC, and a complex of NHEJ markers (KU70/KU80&DNA-PK) are all independent prognostic markers for BC. In addition to expression, subcellular localisation of DDR proteins appeared to be a major factor in their role. Particularly, HR repair markers (but not NHEJ) showed worse features of cytoplasmic location of expression, whereas nuclear expression was associated with more favourable features. Finally, the results of this study provide further evidence to support combined use of IHC with the parallel analytic capability of protein microarray RPPA to investigate protein alterations in human tumours

Hidden regulators: the emerging roles of lncRNAs in brain development and disease

Long non-coding RNAs (lncRNAs) have emerged as critical players in brain development and disease. These non-coding transcripts, which once considered as “transcriptional junk,” are now known for their regulatory roles in gene expression. In brain development, lncRNAs participate in many processes, including neurogenesis, neuronal differentiation, and synaptogenesis. They employ their effect through a wide variety of transcriptional and post-transcriptional regulatory mechanisms through interactions with chromatin modifiers, transcription factors, and other regulatory molecules. Dysregulation of lncRNAs has been associated with certain brain diseases, including Alzheimer’s disease, Parkinson’s disease, cancer, and neurodevelopmental disorders. Altered expression and function of specific lncRNAs have been implicated with disrupted neuronal connectivity, impaired synaptic plasticity, and aberrant gene expression pattern, highlighting the functional importance of this subclass of brain-enriched RNAs. Moreover, lncRNAs have been identified as potential biomarkers and therapeutic targets for neurological diseases. Here, we give a comprehensive review of the existing knowledge of lncRNAs. Our aim is to provide a better understanding of the diversity of lncRNA structure and functions in brain development and disease. This holds promise for unravelling the complexity of neurodevelopmental and neurodegenerative disorders, paving the way for the development of novel biomarkers and therapeutic targets for improved diagnosis and treatment

Transcriptomic and Protein Expression Analysis Reveals Clinicopathological Significance of Bloom Syndrome Helicase (BLM) in Breast Cancer

BLM has key roles in homologous recombination repair, telomere maintenance and DNA replication. Germ-line mutation in the BLM gene causes Bloom’s syndrome, a rare disorder characterised by premature aging and predisposition to multiple cancers including breast cancer. The clinicopathological significance of BLM in sporadic breast cancers is unknown. We investigated BLM mRNA expression in the Molecular Taxonomy of Breast Cancer International Consortium cohort (n=1950) and validated in an external dataset of 2413 tumours. BLM protein level was evaluated in the Nottingham Tenovus series comprising 1650 breast tumours. High BLM mRNA expression was highly significantly associated with high histological grade, larger tumour size, ER negative, PgR negative and triple negative phenotypes (ps<0.0001). High BLM mRNA expression was also linked to aggressive molecular phenotypes including PAM50.Her2 (p<0.0001), PAM50.Bas al (p<0.0001) and PAM50.LumB (p<0.0001) and Genufu subtype (ER+/Her2-/High proliferation) (p<0.0001). PAM50.LumA tumours and Genufu subtype (ER+/Her2-/low proliferation) were more likely to express low levels of BLM mRNA (ps<0.0001). Integrative molecular clusters (intClust) intClust.1 (p<0.0001), intClust.5 (p<0.0001), intClust.9 (p<0.0 001) and intClust.10 (p<0.0001) were also more likely in tumours with high BLM mRNA expression. High BLM mRNA expression was associated with poor breast cancer specific survival (BCSS) (ps<0.000001). At the protein level, altered sub-cellular localisation with high cytoplasmic BLM and low nuclear BLM was linked to aggressive phenotypes. In multivariate analysis, BLM mRNA and BLM protein levels independently influenced BCSS ( p=0.03). This is the first and the largest study to provide evidence that BLM is a promising biomarker in breast cancer

Clinical and biological significance of RAD51 expression in breast cancer: a key DNA damage response protein

Impaired DNA damage response (DDR) may play a fundamental role in the pathogenesis of breast cancer (BC). RAD51 is a key player in DNA double-strand break repair. In this study, we aimed to assess the biological and clinical significance of RAD51 expression with relevance to different molecular classes of BC and patients’ outcome. The expression of RAD51 was assessed immunohistochemically in a well-characterised annotated series (n = 1184) of early-stage invasive BC with long-term follow-up. A subset of cases of BC from patients with known BRCA1 germline mutations was included as a control group. The results were correlated with clinicopathological and molecular parameters and patients’ outcome. RAD51 protein expression level was also assayed in a panel of cell lines using reverse phase protein array (RPPA). RAD51 was expressed in the nuclei (N) and cytoplasm (C) of malignant cells. Subcellular colocalisation phenotypes of RAD51 were significantly associated with clinicopathological features and patient outcome. Cytoplasmic expression (RAD51C+) and lack of nuclear expression (RAD51 N-) were associated with features of aggressive behaviour, including larger tumour size, high grade, lymph nodal metastasis, basal-like, and triple-negative phenotypes, together with aberrant expression of key DDR biomarkers including BRCA1. All BRCA1-mutated tumours had RAD51C+/N- phenotype. RPPA confirmed IHC results and showed differential expression of RAD51 in cell lines based on ER expression and BRCA1 status. RAD51 N+ and RAD51C+ tumours were associated with longer and shorter breast cancer-specific survival (BCSS), respectively. The RAD51 N+ was an independent predictor of longer BCSS (P<0.0001). Lack of RAD51 nuclear expression is associated with poor prognostic parameters and shorter survival in invasive BC patients. The significant associations between RAD51 subcellular localisation and clinicopathological features, molecular subtype and patients’ outcome suggest that the trafficking of DDR proteins between the nucleus and cytoplasm might play a role in the development and progression of BC

Cytoplasmic localization of alteration/deficiency in activation 3 (ADA3) predicts poor clinical outcome in breast cancer patients.

Transcriptional activation by estrogen receptor (ER) is a key step to breast oncogenesis. Given previous findings that ADA3 is a critical component of HAT complexes that regulate ER function and evidence that overexpression of other ER coactivators such as SRC-3 is associated with clinical outcomes in breast cancer, the current study was designed to assess the potential significance of ADA3 expression/localization in human breast cancer patients. In this study, we analyzed ADA3 expression in breast cancer tissue specimens and assessed the correlation of ADA3 staining with cancer progression and patient outcome. Tissue microarrays prepared from large series of breast cancer patients with long-term follow-ups were stained with anti-ADA3 monoclonal antibody using immunohistochemistry. Samples were analyzed for ADA3 expression followed by correlation with various clinicopathological parameters and patients\u27 outcomes. We report that breast cancer specimens show predominant nuclear, cytoplasmic, or mixed nuclear + cytoplasmic ADA3 staining patterns. Predominant nuclear ADA3 staining correlated with ER+ status. While predominant cytoplasmic ADA3 staining negatively correlated with ER+ status, but positively correlated with ErbB2, EGFR, and Ki67. Furthermore, a positive correlation of cytoplasmic ADA3 was observed with higher histological grade, mitotic counts, Nottingham Prognostic Index, and positive vascular invasion. Patients with nuclear ADA3 and ER positivity have better breast cancer specific survival and distant metastasis free survival. Significantly, cytoplasmic expression of ADA3 showed a strong positive association with reduced BCSS and DMFS in ErbB2+/EGFR+ patients. Although in multivariate analyses ADA3 expression was not an independent marker of survival, predominant nuclear ADA3 staining in breast cancer tissues correlates with ER+ expression and together serves as a marker of good prognosis, whereas predominant cytoplasmic ADA3 expression correlates with ErbB2+/EGFR+ expression and together is a marker of poor prognosis. Thus, ADA3 cytoplasmic localization together with ErbB2+/EGFR+ status may serve as better prognostic marker than individual proteins to predict survival of patients

Biological and clinical significance of PARP1 protein expression in breast cancer

Poly(ADP-ribose) polymerase-1 (PARP1) is a key facilitator of DNA repair. PARP inhibitors have gained recent attention as promising therapeutic agents for the treatment of solid tumours including breast cancer (BC). However, the biological and clinical significance of PARP1 expression in BC and its role in DNA-damage response (DDR) remain to be defined. We investigated the expression of PARP1 expression, cleaved (PARP1c) and non-cleaved (PAR1nc) forms, in a large and well-characterised cohort of clinically annotated stage I–III operable BCs (n = 1,269) and 43 BRCA1-mutated BCs using immunohistochemistry. PARP1 expression was correlated to clinicopathological variables, outcome and expression of other key DNA repair proteins (BRCA1, RAD51, Ku70/80, PIASγ and CHK1). Expression of PARP1 was exclusively nuclear. 49 and 85 % of sporadic BC showed expression PARP1nc and PARP1c, respectively. In BRCA1-mutated tumours, PARP1nc/PARP1c was highly expressed (95 and 79 %, respectively). PARP1nc expression was positively associated with premenopausal younger age patients, larger size and higher tumour grade. PARP1 was positively associated with DDR-proteins; RAD51, BRCA1, CHK1 and PIASγ (p < 0.001). Negative association was found between PARP1nc and Ki67. PARP1c was associated with ER (p < 0.001). Different associations between PARP1 and DDR-proteins were observed when stratified based on ER/BRCA1 status. PARP1 was not an independent predictor of outcome in sporadic or BRCA1-mutated BC. Our results demonstrate a potential biological role for PARP1c and PARP1nc in DNA repair in BC based on the significant association with other key DNA damage repair proteins. These associations were not restricted to ER-negative or triple-negative subgroup

Preparing the Bone Tissue Regeneration Ground by Exosomes: From Diagnosis to Therapy

Bone tissue engineering employs acellular scaffolds or scaffolds, along with cells and growth factors, to provide the mechanical support needed, as well as serve as a delivery vehicle for bioactive molecules to the injury sites. As tissue engineering continues to evolve, it has integrated two emerging fields: stem cells and nanotechnology. A paracrine factor that is found to be responsible for the major regenerative effect in stem cell transplantation is an extracellular vesicle called an ‘exosome’. Recent advances in nanotechnology have allowed the ‘exosome’ to be distinguished from other extracellular vesicles and be polymerized into a well-defined concept. Scientists are now investigating exosome uses in clinical applications. For bone-related diseases, exosomes are being explored as biomarkers for different bone pathologies. They are also being explored as a therapeutic agent where progenitor cell-derived exosomes are used to regenerate damaged bone tissue. In addition, exosomes are being tested as immune modulators for bone tissue inflammation, and finally as a delivery vehicle for therapeutic agents. This review discusses recently published literature on the clinical utilization of exosomes in bone-related applications and the correlated advantages. A particular focus will be placed on the potential utilization of regenerative cell-derived exosomes as a natural biomaterial for tissue regeneration.</jats:p

Scaffold-Free 3-D Cell Sheet Technique Bridges the Gap between 2-D Cell Culture and Animal Models

Various tissue engineering techniques have been created in research spanning two centuries, resulting in new opportunities for growing cells in culture and the creation of 3-D tissue-like constructs. These techniques are classified as scaffold-based and scaffold-free techniques. Cell sheet, as a scaffold-free technique, has attracted research interest in the context of drug discovery and tissue repair, because it provides more predictive data for in vivo testing. It is one of the most promising techniques and has the potential to treat degenerative tissues such as heart, kidneys, and liver. In this paper, we argue the advantages of cell sheets as a scaffold-free approach, compared to other techniques, including scaffold-based and scaffold-free techniques such as the classic systemic injection of cell suspension.</jats:p