Discussion
This is the first comprehensive study examining the whole HSP family in breast cancer patients. The HSP family, characterized by 95 genes and one pseudogene, represents only 0.46% of the 20,531 analysed genes. In this study, we found that in BRCA almost 30% of the total genes were deregulated (19.45% upregulated and 10.5% downregulated), where the HSP family accounts for 0.39% of this deregulation (0.32% of the upregulated genes and 0.52% of the downregulated). Several reasons have been mentioned to explain HSP misregulation in cancer: by the stressful situations found in cancer tissues [
4], to increase the stabilization of transcription factors, receptors, protein kinases and other proteins that lie along the pathways of normal to cancer transition [
24], and by the oncogenic agents/events that directly affect the heat shock response [
25]. The activation of Heat Shock factors (HSF) during cancer progression can in turn explain the activation of the HSPs molecular chaperones [
26,
27]. Therefore, considering that cancer tissues are subjected to several stressful situations we expected to see more upregulated HSPs (
n = 13) and fewer downregulated (
n = 11). At this point we have to say that the expression levels of several HSPs were very close to the cut-point used (log
2 fold-change = ±1), this happened for example with the HSPC family which codes for the HSP90 (all appeared with a certain level of upregulation, see Fig.
3). In any case, it is evident that in BRCA the expression levels of several HSP family members are affected. Upregulation was noted mainly in the CHAP and HSPC family members while the greatest downregulation was observed in most HSPB members (Fig.
3 and Additional file
9). The downregulation of the small HSPs agrees with a recent report [
28]. The HSP70 superfamily (which includes the HSP70 and HSP110 or HSPH family) and the DNAJ members showed variable results with ups and downs.
The present study revealed that deregulation of the HSPs varied according to the BRCA molecular subtype. Of importance at this point is: what are the functional implications of the up- and down-regulation of the HSP genes in each breast cancer subtypes? This is not an easy point to address because in the present report we are finding alterations in HSP genes that are little known to be linked with breast cancer; moreover others like DNAJB3 (increased in HER2 subtype), DNAJB13 and DNAJC22 (increased in Luminal and Basal subtypes), and SACS (increased in all subtypes) have not been related with any cancer type. Let’s begin with the Chaperonin family. The members of this group can be divided into three distinct subgroups: Type I chaperonins, established by HSPE1 and HSPD1 genes (also known by their bacterial names GroES and GroEL or HSP10 and HSP60 respectively), type II chaperonins forming the T-complex protein-1 ring complex (TRiC) which is formed by a double ring structure with eight distinct subunits (TCP1 and CCT genes) working as an ATP dependent protein folding machinery [
29], and finally the BBS group of genes (BBS10, BBS12 and MKKS) that in conjunction with the TRiC complex mediate the BBSome assembly [
30]. Of this group of genes, HSPD1, HSPE1, CCT3 and CCT5 were overexpressed in Basal, HER2 and Luminal B subtypes (more aggressive BRCA tumours). HSPD1 and HSPE1 are located on chromosome 2 arranged in a head-to-head orientation and both are implicated in macromolecular protein assembly and mitochondrial protein import, while CCT3 and CCT5 form a protein complex folding various proteins including actin and tubulin upon ATP hydrolysis and, as part of the BBS/CCT complex, they are involved in the assembly of the BBSome, which in turn is implicated in ciliogenesis regulating transports vesicles to the cilia [
30]. At this point we have to remember that breast cancer cells, mainly stem cells, have primary cilia (a non-motile microtubule based cell-surface organelle) that acts as a cellular antenna for receiving signaling pathways involved in the regulation of cell proliferation, differentiation and migration [
31,
32]. Therefore our study adds evidence to an important role of CCT3 and CCT5 in the more aggressive BRCA tumours: Basal, HER2 and Luminal B subtypes. CCT3 has been involved in mitosis progression and associated with poor prognosis in hepatocellular carcinoma [
33], has been implicated in osteosarcoma tumorigenesis [
34], and appeared as a candidate biomarker in epithelial ovarian cancer [
35] and in cholangiocarcinoma patients [
36]. CCT3 was found differentially expressed in colon and other epithelial cancers [
37] and its expression has been associated with drug resistance in a squamous lung cancer cell line [
38]. CCT5 was found upregulated in p53-mutated breast tumours and might be implicated in resistance to docetaxel treatment [
39]. Of notice, all the other TRiC genes except CCT6B were also among the most highly expressed in cancer and upregulated accordingly in the different subtypes, suggesting an important role of the TRiC complex specifically in BRCA as previously suggested [
40]. TRiC has an essential role in cell proteostasis in physiological conditions but also in oncogenesis and cancer progression [
41] and is known to regulate the proper folding of several others genes involved in cancer such as actin, tubulin [
42], p53 [
43] and protoncogene STAT3 [
44]. In our study, HSP-Clust II (enriched with Basal-like tumours) presented high expression levels of the TRiC complex genes. The current standard of treatment of triple-negative (TNBC) tumours is systemic neoadjuvant chemotherapy that typically include taxanes which inhibit tubulin depolymerization [
45]. We hypothesize that the measurement of the TRiC complex genes along with the classification of tumour samples in the different HSP-Clusts could be used as an important tool to predict taxane response, even though further studies are needed to validate this assumption.
Coming back to HSPE1, in a previous proteomic analysis this protein appeared with altered expression in MDA-MB-231 breast cancer cells (triple negative highly aggressive cells) [
46] and both HSPD1/HSPE1 have also been found upregulated in other cancer types associated with tumour cell transformation [
47]. Interestingly, both TRiC genes and HSPD1/HSPE1 were co-expressed and were associated with worst prognosis individually and had high expression in the HSP-Clust II and III of our study (Additional file
10 B). All this data together suggest that not only the TRiC complex has a protagonist role in cancer behaviour but also that the HSPD1/HSPE1 complex is involved tightly with TRiC in proteostasis regulation, an association that is poorly understood in breast cancer and should be further studied. On the other hand, BBS12 was underexpressed in the HER2 subtype predominantly and along with BBS10, both showed decreased expression levels in all subtypes. MKKS gene (also known as BBS6) was not altered. Therefore, our study reveals specific chaperones that participate in the assembly of the BBSome altered in BRCA.
The HSP70 family is a group of evolutionary conserved and ubiquitously expressed genes that in conjunction with the DNAJ family act as a protein folding regulatory network that also protects the cell against stressful conditions [
48]. Several members of the HSP70 family were found highly expressed (HSPA8, HSPA5, HSPA1A) or upregulated in BRCA. We found that HSPA6 expression appeared elevated mainly in Luminal A, Luminal B and Basal subtypes. In a previous study high levels of this protein were associated with recurrence in hepatocellular carcinoma [
49]. HYOU1 also known as oxygen-regulated protein 150 (ORP150) was upregulated in HER2 and Basal subtypes and the protein has been implicated with tumour progression in different cancers [
50‐
53]. HSPA5 was found highly expressed in all subtypes, and especially upregulated in Basal tumours in our study, and has been associated with endoplasmic reticulum stress response (ERSR), inhibition of apoptosis and autophagy in several studies [
54‐
56]. HSPA8 was the most expressed gene of the HSP70 family and one of the genes with the strongest association with survival in our study. This gene is constitutively expressed and has been largely associated with the protein folding and stress response [
57,
58]. Interestingly, DNAJC12, a gene strongly upregulated in Luminal A and B tumours, was found to interact with HSPA8 under ERSR [
59].
Only one HSP appeared upregulated in the four subtypes considered: the protein encoded by DNAJC5B, which is implicated in protein processing at the level of the endoplasmic reticulum [
60]. This protein has been found in secretory vesicles as well as in synaptic and clathrin-coated vesicles in neuroendocrine, exocrine and nervous cells. Of interest is that this member of the DNAJ family has been found upregulated in human bladder carcinoma, gastric adenocarcinoma, and glioblastoma cell lines by the OCT4B1 variant (octamer-binding transcription factor 4 B1 variant) which is expressed by pluripotent normal and cancer stem cell lines and linked to anti-apoptosis [
61]. In addition, these authors found that the OCT4B1 variant is also linked to upregulation of the chaperonin DNAJC11 which is complexed with mitofilin in the mitochondrial membrane [
62] and has been associated with neuromuscular diseases and lymphoid abnormalities [
63]. In this study, DNAJC11 appeared slightly upregulated in Luminal B, HER2 and Basal subtypes. No attention has been directed to these proteins (DNAJC5B and DNAJC11) in BRCA. It is now evident that further studies must be directed to clarify the role of these proteins. DNAJC9 appeared upregulated in Basal, HER2 and Luminal B, and in previous studies has been found upregulated in node-positive uterine cervical carcinoma [
64].
Our study revealed HSPs that appeared both deregulated and not well studied in BRCA; for example, DNAJB3 appeared with high levels of upregulation only in HER2 BRCA subtype. Close gene location with HER2 gene cannot explain upregulation of DNAJB3 since this gene is located on chromosome 2 while HER2 (amplified in HER2 subtype) is located on chromosome 17. Little is known about the protein encoded by this gene, and its role in cancer in general and in breast cancer in particular is not known. DNAJB3 has been reported downregulated in obese human subjects, DNAJB3 over-expression in adipose cell lines caused: a) reduction in JNK (Jun N-terminal kinase) improving insulin sensitivity and enhancing glucose uptake and b) mediated PI3K/AKT pathway activation [
65]. Of interest here is that the PI3K/Akt signalling pathway is negatively regulated by PTEN and we have reported that PTEN is downregulated by HSPB1 (HSP27), both proteins have been implicated in HER2-positive tumours [
66]. Therefore, it will be of interest to study the role of DNAJB3 in HER2 BRCA. However, we have to take into account that the upregulation levels of this gene might appear statistically significant, but the number of RNA molecules could be relatively low. Therefore, an upregulated gene could have few RNA copy numbers and we ignore if the encoded protein has biological significance. Nevertheless, this entire complex HSP70/DNAJ landscape suggests an intricate regulatory interaction between these genes that remains to be untangled.
Finally, among the upregulated small heat shock proteins, HSPB1 stands out as the highest expressed of the group and appeared upregulated in Luminal A, Luminal B, and HER2 (close to the cut-point in Basal); the protein encoded by this gene has been well studied in breast cancer [
4,
67].
Many of these upregulated genes and proteins have been reported as associated with tumour progression in different cancer types and in several opportunities with poor prognosis. In concordance, we have found that some of these genes appeared upregulated mainly in aggressive breast cancer subtypes that were clustered in the HSP-Clust III group. Moreover, the complexity of the regulation of the HSPs in BRCA is further increased when we consider the high number of client proteins that are associated with the HSPs [
11].
Another interesting observation from the present study is that several HSPs were downregulated in all breast cancer subtypes: DNAJB4, DNAJC18, HSPA12A, HSPA12B, HSPB2, HSPB6, and HSPB7. DNAJB4 is a member of the DNAJ family and is described as a tumour suppressor [
68], which is in agreement with our results; increased expression of DNAJB4 has been implicated in the stabilization of wild-type E-cadherin (but not the mutant) stimulating the anti-invasive function of E-cadherin in gastric cancer cells [
68]. Little is known about the protein coded by DNAJC18, but a polymorphic variant has been associated with aggressive bladder carcinoma [
69]. HSPA12A encodes a protein of the HSP70 family that seems to act like a protective factor in gastric cancer [
70]. We found high levels of suppression in several members of the HSPB family (CRYAB, HSPB2, HSPB6 and HSPB7) (Fig.
3); in an integrated genomic and epigenomic analysis the ATM, HSPB2 and CRYAB (this last downregulated in Luminal A, Luminal B and Basal) genes were found commonly deleted and underexpressed in patients with breast cancer brain metastasis [
71]. The role of CRYAB gene (Alpha B-crystallin HSPB5) is controversial in cancer [
72‐
79], its expression has been associated with aggressive breast cancer subtypes. In agreement with our results, HSPB6 and HSPB7 have been found downregulated in several tumour types [
80‐
85], and we report here this downregulation in all subtypes of BRCA is possibly supporting a role as tumour suppressor genes. In our analyses we compared tumour tissue with normal breast tissue, but displacement of stroma in the tumour samples could be affecting the results. Nevertheless, in a recent publication none of the HSP genes were found altered by the confounding effect of tumour purity [
86]. The HSPs expression patterns of the molecular subtypes are still heterogeneous [
15] and the results of the present study contribute to the characterization of these subtypes. We are now completing the study of the methylation status of the HSP genes as well as the mutations, amplifications and deletions in these genes.
Of importance, we have to mention that some genes evaluated in this work presented clinically and biologically meaningful characteristics already described, but some others genes are totally unknown at the moment [
87]. The clinically important genes DNAJB5, HSCB, HSPA2 (usually differentially overexpressed in Luminal A and B), DNAJC4, and HSPA12B (downregulated in BRCA) presented a significant FDR value in the Cox’s proportional hazard model presenting negative coefficients (their expression was associated with a good prognosis). In contrast, the genes with high expression levels significantly associated with poor prognosis were: CCT6A, HSPA14, DNAJC6 (upregulated in Basal), CCT2 (upregulated in Luminal B), CCT5, HSPD1 (upregulated in Basal, Luminal B and HER2), SEC63 (upregulated in HER2), TCP1, CCT4, CCT7, CCT8 (upregulated in HER2 and Basal), HSP90AA1 (upregulated with a near 0.9 log
2 fold-change in Luminal B, HER2 and Basal), HSPH1 (upregulated in Luminal B, HER2), DNAJA2, HSPA9, HSPA4, DNAJC13, and HSPA8. Many of which were previously mentioned (HSP90AA1, TRiC, HSPD1/HSPE1, HSP70 family) and others for which their role in BRCA has not been exhaustively studied.
An important point of this study is the finding of three discrete HSPs expression profiles with prognostic significance (
P = 0.0022) that we called HSP-Clust I, II and III. These HSP clusters groups were reproduced in an independent dataset using the METABRIC cohort and a single sample predictor was trained to classify unknown samples into one of the three HSP-Clusts with robust results. Importantly, TCGA and METABRIC datasets were developed using different RNA measurement technologies but the clusters found showed striking similarities and had significant impact on disease outcome. An interesting point to address is that the HSP-Clust II (predominantly basal-like) in METABRIC is much more clearly associated with a poor prognosis than the same signatures in the TCGA, a plausible explanation might be found in the survival differences of Basal-like tumours in each cohort (Additional file
12). Even though HSP-Clusts survival is highly related to PAM50 subtypes as expected, it is important to notice that the overlap between groups is not complete. Regarding Luminal tumours, HSP-Clust I presented mainly Luminal A tumours while HSP-Clust III presented mixed proportions of Luminal A and Luminal B subtypes. These findings could be reflecting differences in the biology of Luminal A tumours from HSP-Clust I with respect to Luminal A tumours of HSP-Clust III. Also, since HSPs have been long related with drug resistance, it would be of interest to test if the different HSP-Clust are related with different chemotherapy response profiles, which in turn, could imply a differential treatment for each HSP-Clust group. Further studies will be necessary to turn this classification useful for clinical practice and to better characterize the prognostic and treatment for these groups of patients. Since we used a combination of all HSP genes to evaluate survival, this could add superfluous information that can reduce the performance of the study. It will be interesting to reduce the number of HSP genes in order to increase the potential of the HSPs expression patterns as a prognostic factor. For instance, the clinical subset of HSP genes with clinical importance could be used as a genetic signature to develop prognostic tests or as a base for future research of predictive assays based on immunohistochemistry, microarray or rPCR.