Expression and methylation patterns partition luminal-A breast tumors into distinct prognostic subgroups

Background

Breast cancer is a heterogeneous disease comprising several biologically different types, exhibiting diverse responses to treatment. In the past years, gene expression profiling has led to definition of several “intrinsic subtypes” of breast cancer (basal-like, HER2-enriched, luminal-A, luminal-B and normal-like), and microarray based predictors such as PAM50 have been developed. Despite their advantage over traditional histopathological classification, precise identification of breast cancer subtypes, especially within the largest and highly variable luminal-A class, remains a challenge. In this study, we revisited the molecular classification of breast tumors using both expression and methylation data obtained from The Cancer Genome Atlas (TCGA).

Methods

Unsupervised clustering was applied on 1148 and 679 breast cancer samples using RNA-Seq and DNA methylation data, respectively. Clusters were evaluated using clinical information and by comparison to PAM50 subtypes. Differentially expressed genes and differentially methylated CpGs were tested for enrichment using various annotation sets. Survival analysis was conducted on the identified clusters using the log-rank test and Cox proportional hazards model.

Results

The clusters in both expression and methylation datasets had only moderate agreement with PAM50 calls, while our partitioning of the luminal samples had better five-year prognostic value than the luminal-A/luminal-B assignment as called by PAM50. Our analysis partitioned the expression profiles of the luminal-A samples into two biologically distinct subgroups exhibiting differential expression of immune-related genes, with one subgroup carrying significantly higher risk for five-year recurrence. Analysis of the luminal-A samples using methylation data identified a cluster of patients with poorer survival, characterized by distinct hyper-methylation of developmental genes. Cox multivariate survival analysis confirmed the prognostic significance of the two partitions after adjustment for commonly used factors such as age and pathological stage.

Conclusions

Modern genomic datasets reveal large heterogeneity among luminal breast tumors. Our analysis of these data provides two prognostic gene sets that dissect and explain tumor variability within the luminal-A subgroup, thus, contributing to the advancement of subtype-specific diagnosis and treatment.

Electronic supplementary material

The online version of this article (doi:10.1186/s13058-016-0724-2) contains supplementary material, which is available to authorized users.

Tissue specific DNA methylation in normal human breast epithelium and in breast cancer

Cancer is a heterogeneous and tissue-specific disease. Thus, the tissue of origin reflects on the natural history of the disease and dictates the therapeutic approach. It is suggested that tissue differentiation, mediated mostly by epigenetic modifications, could guide tissue-specific susceptibility and protective mechanisms against cancer. Here we studied breast specific methylation in purified normal epithelium and its reflection in breast cancers. We established genome wide methylation profiles of various normal epithelial tissues and identified 110 genes that were differentially methylated in normal breast epithelium. A number of these genes also showed methylation alterations in breast cancers. We elaborated on one of them, TRIM29 (ATDC), and showed that its promoter was hypo-methylated in normal breast epithelium and heavily methylated in other normal epithelial tissues. Moreover, in breast carcinomas methylation increased and expression decreased whereas the reverse was noted for multiple other carcinomas. Interestingly, TRIM29 regulation in breast tumors clustered according to the PAM50 classification. Thus, it was repressed in the estrogen receptor positive tumors, particularly in the more proliferative luminal B subtype. This goes in line with previous reports indicating tumor suppressive activity of TRIM29 in estrogen receptor positive luminal breast cells in contrast to oncogenic function in pancreatic and lung cancers. Overall, these findings emphasize the linkage between breast specific epigenetic regulation and tissue specificity of cancer.

Serum DNA methylation for monitoring response to neoadjuvant chemotherapy in breast cancer patients

Patients with large or nonoperable breast cancers often receive neoadjuvant chemotherapy to facilitate full resection of the tumor and enable conservation of the breast. However, currently available methods for evaluation of response during therapy are limited and the actual effect of the treatment is only recognized at surgery upon completion of chemotherapy. Timely assessment of response could allow individual tailoring of the treatment and save noneffective drugs and unnecessary toxicity. Here, we suggest that tumor derived DNA methylation in the serum may reflect changes in tumor burden and allow early recognition of responders versus nonresponders. In this pilot study, we collected 7 consecutive serum samples from 52 patients with locally advanced breast cancer during neoadjuvant chemotherapy. We selected RASSF1, which was methylated in more than 80% of the tumors, for serum analysis. Using the "methylation sensitive PCR and high resolution melting," we detected RASSF1 methylation in the serum of 21 patients prior to therapy. In four patients who achieved complete pathological response, RASSF1 methylation in the serum became undetectable early during therapy. In contrast, in 17 patients that had partial or minimal pathological response, serum RASSF1 methylation persisted longer or throughout the treatment (complete versus partial response p = 0.02). These findings support further development of this assay for monitoring response during neoadjuvant therapy.

Searching for the right word: performance on four word-retrieval tasks across childhood

Word retrieval was assessed in 207 normally developing Hebrew-speaking children aged 8-17 through four tasks: picture naming, phonemic fluency, semantic fluency, and homophone meaning generation (HMGT). Scores on all tests correlated positively and significantly with participant age. Yet, age effects and the correlation between age and test scores were weakest for the naming test and strongest for the HMGT. We discuss the nature of the word search involved in each task and suggest that the more executive demands required by a test the steeper the slope of performance increase on this test.

A similar cell-specific pattern of HOXA methylation in normal and in cancer tissues

HOX genes are developmental genes that determine anterior-posterior embryonic pattern and govern the process of differentiation. Inappropriate expression of HOX genes has been implicated in developmental abnormalities and hematopoietic malignancies. In addition, HOX genes silencing by DNA methylation has been reported in cancers and related to disease aggressiveness and outcome. On the other hand, accumulating evidence suggests that epigenetic changes at HOX genes are linked to normal development and differentiation. To better understand the relationship between HOXA methylation and cancer, we analyzed the methylation pattern of HOXA genes in human primary breast and colon carcinomas, normal tissues, and normal white blood cells. Genome-wide methylation arrays of breast cancers and white blood cells demonstrated similar methylation patterns. Quantitative methylation analysis of seven representative HOXA genes revealed various levels of methylation in both normal tissues and cancers. Analysis of epithelial-enriched normal breast tissue and stroma indicated that the stroma was the major origin of HOXA methylation. Furthermore, in selected dense breast cancers, minimal increase in methylation of several HOXA genes did not correlate with the predominance of malignant epithelial cells in these tumors. Our results suggest that methylation of the HOXA cluster may be a normal developmental and cell type specific process rather than a cancer specific mechanism.

Effects of short-term awareness interventions on children's attitudes toward peers with a disability

The purpose of this study was to explore the effect of two awareness activities on children's attitudes towards peers with a disability. The Children's Attitudes towards Peers with Disability scale including cognitive, behavioral and emotional subscales was administered before and after two types of short-term interventions. The first included 75 children from grades 7-9, who actively participated in the workshop simulating movement activities. The second intervention included 121 students of the 10th grade, who observed their peers participating in a wheelchair-basketball activity together with elite wheelchair-basketball players. Results indicated significant effects in the cognitive and behavioral domains. Post-test findings confirmed that intervention bridged the difference in the cognitive domain observed between those with and without previous contact at pretest.

How does the homophone meaning generation test associate with the phonemic and semantic fluency tests? A quantitative and qualitative analysis

The current study examines whether the Homophone Meaning Generation Test (HMGT; Warrington, 2000) is correlated with the phonemic and/or the semantic fluency tests and compares its association with the number of switches and clusters and the mean cluster size of these two tasks. One hundred healthy Hebrew speakers (18-35 years of age; mean = 24.9) generated meanings for 24 homophones and provided words beginning in three different letters, as well as words belonging to three semantic categories. Results show that the HMGT score correlated significantly and similarly with the total score of both the phonemic and the semantic fluency tests. There was a significant correlation between the HMGT and the number of phonemic switches and clusters, but not between the HMGT and the mean phonemic cluster size. The HMGT correlated with the number of semantic switches and clusters, as well as with the mean semantic cluster size. The findings suggest that the relationship between these tests is mediated by a shared executive component, attesting to the HMGT's utility in tapping into mechanisms of shifting and mental flexibility.

A Novel Synthetic Cannabinoid Derivative Inhibits Inflammatory Liver Damage via Negative Cytokine Regulation

The therapeutic potential of cannabinoids has been described previously for several inflammatory diseases, but the molecular mechanisms underlying the anti-inflammatory properties of cannabinoids are not well understood. In this study, we investigated the mechanism of action of a novel synthetic cannabinoid, [(+)(6aS,10aS)-6,6-Dimethyl-3-(1,1-dimethylheptyl)-1-hydroxy-9-(1H-imidazol-2-ylsulfanylmethyl]-6a,7,10,10a-tetrahydro-6H-dibenzo[b,d]pyran (PRS-211,092) that has no psychotropic effects but exhibits immunomodulatory properties. Treatment with PRS-211,092 significantly decreased Concanavalin A-induced liver injury in mice that was accompanied by: 1) promotion of early gene expression of interleukin (IL)-6 and IL-10 that play a protective role in this model; 2) induction of early gene expression of the suppressors of cytokine signaling (SOCS-1 and 3), followed by 3) inhibition of several pro-inflammatory mediators, including IL-2, monocyte chemoattractant protein-1 (MCP-1), IL-1beta, interferon-gamma, and tumor necrosis factor alpha. Based on these results, we propose a mechanism by which PRS-211,092 stimulates the expression of IL-6, IL-10 and the SOCS proteins that, in turn, negatively regulates the expression of pro-inflammatory cytokines. Negative regulation by PRS-211,092 was further demonstrated in cultured T cells, where it inhibited IL-2 production and nuclear factor of activated T cells activity. These findings suggest that this cannabinoid derivative is an immunomodulator that could be developed as a potential drug for hepatitis as well as for other short- or long-term inflammatory diseases.

A matched controlled study of Kielland's forceps for transverse arrest of the fetal vertex

This study attempted to determine whether delivery with Kielland's forceps for deep transverse arrest is less favourable than other instruments. One hundred and forty-six women who underwent rotation and delivery with Kielland's forceps between 1994 and 1997 were matched by parity and birth weight to one of two control groups: delivery by non-rotational forceps or the vacuum extractor. No significant differences were found in maternal or neonatal outcome (vaginal lacerations, 3rd- or 4th-degree perineal tears, postpartum haemorrhage, fever, blood transfusion, duration of hospitalisation, Apgar score, asphyxia, scalp trauma, admission to the intensive care unit or neonatal hospitalisation). The incidence of heart rate abnormalities prior to instrumental delivery was similar. The 'failure to deliver' rate (8.9% after Kielland's forceps) was not different to the 7.5% and 6.8% found in each control group. These data indicate that the outcome after Kielland's forceps delivery is similar to other instrumental deliveries if performed by experienced obstetricians.

Determination of fetal occiput position by ultrasound during the second stage of labor

OBJECTIVE

To investigate whether ultrasonography is superior to vaginal examination for determination of fetal occiput position during the second stage of labor.

METHODS

We conducted a prospective cohort study of 44 parturients. During the second stage of labor, an attending obstetrician performed a vaginal examination to detect fetal occiput position. This was followed by combined abdominal and perineal ultrasound examination. The two methods were compared to the true position. Results were analyzed using Student's t test for quantitative parameters. McNemar's and Fisher's exact tests were applied in order to examine differences between the study groups.

RESULTS

The error rate in detecting fetal occiput position was significantly lower using the ultrasound technique (6.8%) compared to vaginal examination (29.6%, p = 0.011). Parity, maternal body mass index or fetal weight had no influence on the error rate.

CONCLUSIONS

Ultrasonographic determination of the fetal position is an accurate technique and is superior to vaginal examination.

Immobilization of recombinant heparinase I fused to cellulose-binding domain

Immobilization of biologically active proteins is of great importance to research and industry. Cellulose is an attractive matrix and cellulose-binding domain (CBD) an excellent affinity tag protein for the purification and immobilization of many of these proteins. We constructed two vectors to enable the cloning and expression of proteins fused to the N- or C-terminus of CBD. Their usefulness was demonstrated by fusing the heparin-degrading protein heparinase I to CBD (CBD-HepI and HepI-CBD). The fusion proteins were over-expressed in Escherichia coli under the control of a T7 promoter and found to accumulate in inclusion bodies. The inclusion bodies were recovered by centrifugation, the proteins were refolded and recovered on a cellulose column. The bifunctional fusion protein retained its abilities to bind to cellulose and degrade heparin. C-terminal fusion of heparinase I to CBD was somewhat superior to N-terminal fusion: Although specific activities in solution were comparable, the latter exhibited impaired binding capacity to cellulose. CBD-HepI-cellulose bioreactor was operated continuously and degraded heparin for over 40 h without any significant loss of activity. By varying the flow rate, the mean molecular weight of the heparin oligosaccharide produced could be controlled. The molecular weight distribution profiles, obtained from heparin depolymerization by free heparinase I, free CBD-HepI, and cellulose-immobilized CBD-HepI, were compared. The profiles obtained by free heparinase I and CBD-HepI were indistinguishable, however, immobilized CBD-HepI produced much lower molecular weight fragments at the same percentage of depolymerization. Thus, CBD can be used for the efficient production of bioreactors, combining purification and immobilization into essentially a single step.

Co-stimulation-dependent activation of a JNK-kinase in T lymphocytes

Previously we implicated c-Jun N-terminal kinase (JNK) as an element that is involved in signal integration during co-stimulation of T lymphocytes. This pathway has now been traced to an upper level, comprising MAPKK SEK1/MKK4/JNKK1 which, similarly to JNK, must receive input both from the TCR and CD28. A large portion of this input is probably integrated at the level of the Rho-family protein CDC42 which, here, activates SEK1 and JNK to the level reached by TCR and CD28 stimulation. We have identified another putative SEK/ JNK pathway regulator, PKCtheta, which in contrast to CDC42, activates SEK and JNK maximally only in conjunction with a calcium signal delivered through calcineurin. Signals originating at the TCR and CD28 may travel down the JNK pathway via PKCtheta, calcineurin, CDC42, MEKK1 and SEK1.

Molecular follow-up of disease progression and interferon therapy in chronic myelocytic leukemia

We previously reported that the abl promoter (Pa) undergoes de novo DNA methylation in the course of chronic myelocytic leukemia (CML). The clinical implications of this finding are the subject of the present study in which samples of CML patients, including a group treated with interferon alpha (IFNalpha) were surveyed. The methylation status of the abl promoter was monitored by polymerase chain reaction (PCR) amplification of the Pa region after digestion with several site-methylation sensitive restriction enzymes. Some 74% of the DNA samples from blood and marrow drawn in the chronic phase were nonmethylated, similar to control samples from non-CML patients. The remaining 26% were partially methylated in the abl Pa region. The latter samples were derived from patients who were indistinguishable from the others on the basis of clinical presentation. Methylated samples were mostly derived from patients known to have a disease of longer duration (26 months v 7.5 months, P = .01). Samples of 30 IFNalpha-treated patients were sequentially analyzed in the course of treatment. Fifteen patients with no evidence of Pa methylation before treatment remained methylation-free. The remainder, who displayed Pa methylation before treatment, reverted to the methylation-free status. The outcome is attributed to IFNalpha therapy, as the Pa methylation status was not reversed in any of the patients treated with hydroxyurea. Methylation of the abl promoter indicates a disease of long-standing, most likely associated with a higher probability of imminent blastic transformation. It appears to predict the outcome of IFNalpha therapy far better than the cytogenetic response.

Costimulation requirement for AP-1 and NF-kappa B transcription factor activation in T cells

The transcriptional activity of the IL-2 promoter requires T-cell costimulation delivered by the TCR and the auxiliary receptor CD28. Several transcription factors participate in IL-2 promoter activation, among which are AP-1-like factors and NF-kappa B. Protein phosphorylation has an important role in the regulation of these two factors: (1) it induces the transactivating capacity of the AP-1 protein c-Jun; and (2) it is involved in the release of the cytoplasmic inhibitor, I kappa B, from NF-kappa B, allowing translocation of the latter into the nucleus. We have recently shown that both phosphorylation processes require T-cell costimulation. Furthermore, in activated T cells, the kinetics of the two phosphorylation events are essentially similar. According to our results, however, the kinases responsible for the two processes are distinct entities. Whereas TPCK inhibits phosphorylation of I kappa B and, consequently, activation of NF-kappa B, it markedly enhances the activity of JNK, the MAP kinase-related kinase that phosphorylates the transactivation domain of c-Jun. We, therefore, propose the activation scheme presented in FIGURE 3 for T-cell costimulation. Costimulation results in the activation of a signaling pathway that leads to the simultaneous induction of the two transcription factors, AP-1 and NF-kappa B. Integration of the signals generated by TCR and CD28 engagement occurs along this pathway, which then bifurcates to induce I kappa B phosphorylation and NF-kappa B activation on the one hand, and JNK activation and c-Jun phosphorylation on the other. We are currently engaged in defining where the two signals integrate along the AP-1/NF-kappa B pathway.

In vivo stimulation of I kappa B phosphorylation is not sufficient to activate NF-kappa B

NF-kappa B is a major inducible transcription factor in many immune and inflammatory reactions. Its activation involves the dissociation of the inhibitory subunit I kappa B from cytoplasmic NF-kappa B/Rel complexes, following which the Rel proteins are translocated to the nucleus, where they bind to DNA and activate transcription. Phosphorylation of I kappa B in cell-free experiments results in its inactivation and release from the Rel complex, but in vivo NF-kappa B activation is associated with I kappa B degradation. In vivo phosphorylation of I kappa B alpha was demonstrated in several recent studies, but its role is unknown. Our study shows that the T-cell activation results in rapid phosphorylation of I kappa B alpha and that this event is a physiological one, dependent on appropriate lymphocyte costimulation. Inducible I kappa B alpha phosphorylation was abolished by several distinct NF-kappa B blocking reagents, suggesting that it plays an essential role in the activation process. However, the in vivo induction of I kappa B alpha phosphorylation did not cause the inhibitory subunit to dissociate from the Rel complex. We identified several protease inhibitors which allow phosphorylation of I kappa B alpha but prevent its degradation upon cell stimulation, presumably through inhibition of the cytoplasmic proteasome. In the presence of these inhibitors, phosphorylated I kappa B alpha remained bound to the Rel complex in the cytoplasm for an extended period of time, whereas NF-kappa B activation was abolished. It appears that activation of NF-kappa B requires degradation of I kappa B alpha while it is a part of the Rel cytoplasmic complex, with inducible phosphorylation of the inhibitory subunit influencing the rate of degradation.

Progressive de novo DNA methylation at the bcr-abl locus in the course of chronic myelogenous leukemia

De novo methylation of CpG islands is a rare event in mammalian cells. It has been observed in the course of developmental processes, such as X chromosome inactivation and genomic imprinting. The methylation of DNA, an important factor in the epigenetic control of gene expression, may also be involved in tumorigenesis. After the t(9;22) chromosomal translocation and generation of the Philadelphia chromosome, the initiating event in chronic myelogenous leukemia (CML), most of the abl coding sequence is fused to the 5' region of the bcr gene. Expression of the hybrid bcr-abl gene is, therefore, regulated by the bcr promoter. In most cases of CML, one of the two abl promoters (Pa) is nested within the bcr-abl transcriptional unit and should be able to transcribe the type Ia 6-kb normal abl mRNA from the Philadelphia chromosome. However, we have found that the 6-kb transcript is present only in CML cell lines containing a normal abl allele and that the apparent inactivation of the nested Pa promoter is associated with allele-specific methylation. Furthermore, we have noticed that the Pa promoter is contained within a CpG island and undergoes progressive de novo methylation in the course of the disease. This is attested to by the fact that DNA samples from CML patients that are methylation-free at the time of diagnosis invariably become methylated in advanced CML. Since tumor progression in CML cannot always be inferred from the clinical presentation, assessment of de novo CpG methylation may prove to be of critical value in management of the disease. It could herald blastic transformation at a stage when bone marrow transplantation, the only potentially curative therapeutic procedure in CML, is still effective.

Serum thyroglobulin and iodine-131 whole-body scan in the diagnosis and assessment of treatment for metastatic differentiated thyroid carcinoma

Because of the limitations of periodic 131I whole-body scans, including suspension of substitution therapy, questionable sensitivity and low yield in detecting metastases in patients who have undergone thyroidectomy, serum thyroglobulin and 131I whole-body scans were evaluated for sensitivity in detecting local, regional or distant metastases in 261 patients with differentiated thyroid carcinoma after total thyroidectomy and ablation.

METHODS

A noncompetitive immunoradiometric assay was used for serum thyroglobulin determination. An 131I whole-body scan was obtained after replacement therapy had been suspended for 6 wk or when TSH reached levels higher than 50 microU/ml. In patients who underwent radiological procedures with iodinated contrast media, the waiting period before the 131I whole-body scan was no less than 10 wk.

RESULTS

Of the 58 patients with proven metastases who were followed for 12 yr (mean 7 +/- 3.3 yr), 51 (88.4%) had high serum thyroglobulin assays performed while under full replacement therapy and 32 (55%) showed clear 131I whole-body scan localization. There were no instances of positive whole-body scans and negative serum thyroglobulin.

CONCLUSION

In patients treated with 131I, serum thyroglobulin assay was an excellent method to assess treatment. Patients with metastatic disease and negative whole-body scans with or without serum thyroglobulin exhibited a trend toward higher mortality. This trend may also indicate that the lack of 131I trapping and low thyroglobulin is a sign of metabolic dedifferentiation of otherwise histologically differentiated thyroid tumors.

Hashimoto's thyroiditis and carcinoma of the thyroid gland

Seven cases of Hashimoto's disease (HT) occurring in association with carcinoma of the thyroid gland are presented. The diagnosis of HT was not reached before surgery in any of the cases; it was an incidental histopathological finding. There was no case of pure papillary cancer: two specimens showed mixed papillary and follicular cancers, four revealed follicular carcinomas (one of them with anaplastic areas) and one medullary neoplasm. Other authors, however, have reported that pure papillary carcinoma occurred with significantly greater frequency in thyroids also displaying Hashimoto's disease. Total thyroidectomy was performed in all seven patients and one patient with anaplastic follicular cancer also received external irradiation. TSH suppressive therapy was given postoperatively. All these patients are alive with no evidence of further disease after seven to 17 years of follow-up study, whereas the mortality in our total series of thyroid cancers, even in patients with low-grade malignancy, was about 9%. Thus the prognosis of patients with carcinoma of the thyroid gland with coexisting Hashimoto's disease is better than that of patients with carcinoma of the thyroid gland alone. Hashimoto's thyroiditis does not seem to be a premalignant lesion. There was no evidence suggesting that thyroid carcinoma originated in the proliferating epithelium of Hashimoto's thyroiditis. It would appear that thyroid carcinoma stimulates the development of HT in some patients and that the presence of the autoimmune inflammatory reaction and the circulating antibodies retard growth and dissemination of carcinoma of the thyroid gland.