Iam comparing them according to the DNA repair Capacity and gene expression involvrd in DNA repair .... trying to understand the behaviour and the repair Capicity in those cell lines and I see some overlap between these cell lines in DNA repair capacity ...... so, I need an expert Opinion because I read on the leterature that those Luminal B especially have an overlap with TNBC in gene expression. Thanks in advance

Thanks for your help

We have been working on canine mammary tumours which is considered as a naturally occurring animal model of human breast cancer. In our studies we have also classified canine mammary tumours on the basis of molecular subtyping ( un published data) we have also observed overlapping of luminal and basal subtypes. For further classification one needs an elaborate panel of markers. There are several articles on this aspect in human and canine mammary neoplasia.

Best of luck and go ahead.

Kuldip :::: This is amazing .... can you recommend some of this Articles to me ... I will approciate that so much :) :)

Triple negative breast cancers are more aggressive than Luminal breast cancers and they have worst prognosis among all groups of breast cancer. You can compare any breast cancer cell line based on the gene signatures irrespective of their origin.

Thanks Sandeep

Hi Hamed, The first seminal paper that people often cite is by Sorlie et al. I have attached it here for your reference.

There is also a PLOS paper which looks at lots of breast cancer cell lines - also attached here for your reference but in next post!. I wish you all the best.

Here is the plos paper....

Thanks Charles .... I approciate your help

Hamed:

TALE OF TWO GENERATIONS OF MOLECULAR CLASSIFICATION OF BREAST CANCER

The facts are considerably more complicated than so far suggested, although the contributions above are a good start for what is now, in hindsight, seen as the first generation of molecular classification, that is, molecular "taxonomy" of breast cancer into distinct subclasses, pioneered by the Charles Perou and Therese Sørlie team at Stanford University almost a decade and a half ago. But we are already almost five years into the second generation of what I call breast cancer MOLECULAR ARCHITECTURE, the era of breast cancer SUBTYPING (as opposed to first generation SUBCLASSING or subgrouping) developed by Brain Lehmann and his team at the Vanderbilt-Ingram Cancer Center of Vanderbilt University in late 2010, and first published in 2011. This leads to the era of TNBC SUBTYPING for triple negative breast cancer, now well-validated through gene expression profiling, and with, as I will show, validated clinical relevance to the treatment of TNBC disease.

So being a specialist in triple negative breast cancer, I will here try to provide a more complete and up-to-date account of the architecture of TNBC. The first thing to recognize is that although the Perou/Sørlie team in its original seminal classification of breast cancer molecular subtypes [1] did not identify other than an luminal A and luminal B subgroups of the luminal class/subtype, they later [2] suggested a third luminal subgroup, the luminal C tumors. However a subsequent and more definitive analysis [3] of the expanded dataset by the same team wholly failed to support the existence of this third subgroup (luminal C), and without any confirming data to date, the classification of the luminal C subgroup must be considered abandoned as it has been by the authors themselves, as witness in their recent work [4] which now only identifies these breast cancer intrinsic subclasses (and as this paper [4] supersedes - and even contradicts - their previous papers, I would advise using only it, and their later papers (2011 and on) and not the earlier articles):

(1) LUMINAL A (ER+/PR+/HER2-),

(2) LUMINAL B (triple-positive: ER+/PR+/HER2+),

(3) HER2 (ER-/PR-/HER2+),

(4) BASAL (proximately mapped to triple negative: ER-/PR-/HER2- but with defining EGFR+, CK 5/6, and high Ki-67),

(5) CLAUDIN-LOW (triple negativity but with defining E-cadherin, claudin-3, claudinin-4 and claudinin-7 low, and low Ki-67), and I note that this claudin-low subtype has the genomic characteristics of a cancer stem cell-like (CSC) phenotype [5].

(a classification that has been further refined by other investigators).

But the second issue is to note a mistranslation here: preclinical in vitro/in vivo research has typically failed to distinguish between basal tumors, which are proximately mapped to triple negative: ER-/PR-/HER2-, on the one hand, and claudin-low tumors on the other, yet these behave differentially clinically and perhaps also prognostically. Thus, compared to basal-like tumors, claudin-low tumors appear to have lower rates of pCR [6], and so cannot be casually, and carelessly, lumped into "TNBC" cell lines like MB-MDA-231 and others.

THE PROBLEMS OF PRECLINICAL RESEARCH VERSUS MOLECULAR SUBCLASSES

One final example will serve to suggest the vast scope and potential of mistranslations: Many studies on potentially active agents for triple negative breast cancer disease have been conducted using, indifferently, either MDA-MB-231 or MD-MD-468 cells. However MDA-MB-468 cells most closely map basal tumors (EGFR-positivity and cytokeratins 5/6) while MDA-MB-231 closely map the new claudin-low molecular subtype [6], and clearly these are significantly different in molecular and phenotypic behavior, with MDA-MB-468 being highly proliferative and prognostically highly compromised relative to MDA-MB-231, so it matters gravely which cancer cell line is chosen, and it will also matter as to outcome obtained from any given preclinical study trying to determine the efficacy and responsivity of a particular therapeutic agent against one versus the other cell line, yet basic scientists often slur these together as "triple-negative" cell lines.

Furthermore, MDA-MB-231 cells are characterized more critically by claudin-3 and claudinin-4 downregulation, by low expression of the Ki-67 proliferation marker, enrichment for markers associated with EMT, and, importantly, the expression of features associated with mammary cancer stem cells (CSCs) like the CD44+CD24-/low phenotype. But these features are not shared with MDA-MB-468 [9.10] so we would expect that MDA-MB-468 would be differentially responsive to MEK protein kinase inhibitors among other molecular pathway targeting agents, but not so for MDA-MD-231. What a difference a cell line makes! So we must always make explicit recognition of the fact that MDA-MB-468 is a basal BC cell line versus MDA-MB-231 which is now known to be a claudin-low, not basal, cell line.

THE SECOND GENERATION: THE ERA OF TNBC SUBTYPING

But the third issue is the most critical: we are now in the second generation of TNBC molecular architecture, where the triple negative breast cancer (TNBC) subclass/subgroup is itself decomposed into six distinct subtypes [7,8]:

- two basal-like subtypes, BL1 and BL2, involving cell cycle and DNA damage response genes;

- two mesenchymal subtypes, M and MSL, driven by genes involved in cell differentiation and growth factor pathways;

- an immunomodulatory (IM) type driven by immune system genes, plus

- a luminal subgroup subtype, LAR (luminal androgen receptor ), driven by signaling of the male sex hormone androgen receptor (AR)

CLINICAL IMPLICATIONS OF THE NEW TNBC SUBTYPING MOLECULAR ARCHITECTURE

So the lesson to learn is that preclinical and clinical studies need to become aware of these subgroups. For example, the M and MSL subtypes respond to Src inhibition using dasatinib (Sprycel), in contrast to the BL1 and BL2 subtypes which are not similarly responsive, but rather exhibit some responsivity to the platinum cisplatin. In contrast, the LAR TNBC subtype is responsive to the AR (androgen receptor) antagonist bicalutamide (Casodex) which is showing significant clinical promise outside of metastatic prostate cancer, for AR-positive breast cancer.

But there is another even more critical lesson: the objective response rate (ORR), particularly pCR (pathological complete response) can be vastly different between TNBC subtypes. This was demonstrated in a recent retrospective analysis [11] where it where it was found that although the overall pCR response from neoadjuvant chemotherapy was 28% in a TNBC population, the actual subtype-specific responses differed significantly: thus, pCR was 0% for patients with the BL2 subtype, and just 10% for those with LAR tumors and 23% for MSL subtypes, but in stark contrast the BL1 subtype achieved the highest pCR rate at an exceptional 52%. In addition, a patient's TNBC subtype was demonstrated to be an independent predictor of pCR status under likelihood ratio test.

Thus, we now are beginning to see true clinical relevance emerge from the TNBC molecular subtyping architecture, of both prognostic and therapy-response predictive value, and several other validating clinical studies are currently in press.

HOW TO SUBTYPE TNBC USING THE TNBCtype TOOL

As I deal extensively with advanced disease TNBC patients, I use the TNBCtype subtyping tool - when of course gene expression profiles are available - to capture and map to the true reality of the human molecular level for TNBC and basal subtypes and their subgroups. This freely accessible TNBCtype tool is a rare public service from the Vanderbilt University team that ushered in the TNBC Subtyping Molecular era I briefly described above, and what it provides is a determination TNBC molecular subtype from gene expression profile input, entered as a genome-wide gene expression matrix in the form of a .csv (derivable from Excel and other Office programs) file on the user-friendly web interface TNBCtype website at:

http://cbc.mc.vanderbilt.edu/tnbc/.

Comprehensive instructions for how to input data into the TNBCtype tool is available, and any residual questions are kindly answered by Stephen Chen (email him at: [email protected]). Before using the tool, I would strongly advise reading Stephen's paper [8] on TNBCtype, as well as Brian Lehmann's paper on TNBC molecular subtyping [7].

Truly, we've come a long way from the relatively naive early pre-molecular immunohistochemical (IHC) receptor-based classification of TNBC, through the first generation of breast cancer molecular subclassing courtesy of the genius of Charles Perou and Therese Sørlie Stanford University team, and finally through the innovate, ground-breaking TNBC molecular subtyping architecture brought to us by the forward-thinking Vanderbilt University team of Brain Lehmann and Stephen Chen. So in any research project exploring and comparing the luminal (A and B) breast cancer subclasses with TNBC cell lines must be aware and take into account these new and critical facts of TNBC molecular architectures, down to the deep subtyping level.

REFERENCES

1. Perou CM, Sorlie T, Eisen MB, van de Rijn M, Jeffrey SS, et al. (2000) Molecular portraits of human breast tumours. Nature 406: 747–752. doi: 10.1038/35021093.

2. Sorlie T, Perou CM, Tibshirani R, Aas T, Geisler S, et al. (2001) Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci U S A 98: 10869–10874.

3. Sorlie T, Tibshirani R, Parker J, Hastie T, Marron JS, et al. (2003) Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci U S A 100: 8418–8423.

4. Prat A, Perou CM. Deconstructing the molecular portraits of breast cancer. Mol Oncol 2011; 5(1):5-23.

5. Hennessy, B.T. et al. Characterization of a naturally occurring breast cancer subset enriched in epithelial-to-mesenchymal transition and stem cell characteristics. 2009, Cancer Res., 69, 4116.

6. Prat A, Parker J, Karginova O, Fan C, Livasy C, Herschkowitz JI, He X, Perou CM: Phenotypic and molecular characterization of the claudin-low intrinsic subtype of breast cancer. Breast Cancer Res 2010, 12:R68.

7. Lehmann BD, Bauer JA, Chen X, et al. Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies. J Clin Invest 2011 Jul 1; 121(7):2750-67.

8. Chen X, Li J, Gray WH, et al. TNBCtype: A Subtyping Tool for Triple-Negative Breast Cancer. Cancer Inform 2012; 11:147-56.

9. Sheridan C, Kishimoto H, Fuchs RK, et al. CD44+/CD24- breast cancer cells exhibit enhanced invasive properties: an early step necessary for metastasis. Breast Cancer Res 2006; 8(5):R59.

10. Jaggupilli A, Elkord E. Significance of CD44 and CD24 as cancer stem cell markers: an enduring ambiguity. Clin Dev Immunol 2012; 2012:708036.

11. Masuda H, Baggerly KA, Wang Y, et al. Differential response to neoadjuvant chemotherapy among seven triple-negative breast cancer molecular subtypes. Clin Cancer Res 2013; 19(19): 5533–5540.