In a distributed storage system, code symbols are dispersed across space in nodes or storage units as opposed to time. In settings such as that of a large data center, an important consideration is the efficient repair of a failed node. Efficient repair calls for erasure codes that in the face of node failure, are efficient in terms of minimizing the amount of repair data transferred over the network, the amount of data accessed at a helper node as well as the number of helper nodes contacted. Coding theory has evolved to handle these challenges by introducing two new classes of erasure codes, namely regenerating codes and locally recoverable codes as well as by coming up with novel ways to repair the ubiquitous Reed-Solomon code. This survey provides an overview of the efforts in this direction that have taken place over the past decade. I. INTRODUCTIONThis survey article deals with the use of erasure coding for the reliable and efficient storage of large amounts of data in settings such as that of a data center. The amount of data stored in a single data center can run into tens or hundreds of petabytes. Reliability of data storage is ensured in part by introducing redundancy in some form, ranging from simple replication to the use of more sophisticated erasure-coding schemes such as Reed-Solomon codes. Minimizing the storage overhead that comes with ensuring reliability is a key consideration in the choice of erasure-coding scheme. More recently a second problem has surfaced, namely, that of node repair.In [1], [2] the authors study the Facebook warehouse cluster and analyze the frequency of node failures as well as the resultant network traffic relating to node repair. It was observed in [1] that a median of 50 nodes are unavailable per day and that a median of 180TB of cross-rack traffic is generated as a result of node unavailability. It was also reported that 98.08% of the cases have exactly one block missing in a stripe. The erasure code that was deployed in this instance was an [n = 14, k = 10] Reed Solomon (RS) code. Here n denotes the block length of the code and k the dimension. The conventional repair of an [n, k] RS code is inefficient in that the repair of a single node, calls for contacting k other (helper) nodes and downloading k times the amount of data stored in the failed node, which is clearly inefficient. Thus there is significant practical interest in the design of erasure-coding techniques that offer both low overhead and which can also be repaired efficiently.Coding theorists have responded to this need by coming up with two new classes of codes, namely ReGenerating (RG) and Locally Recoverable (LR) codes. The focus in a RG code is on minimizing the amount of data download needed to repair a failed node, termed the repair bandwidth while LR codes seek to minimize the number of helper nodes contacted for node repair, termed the repair degree. In a different direction, coding theorists have also re-examined the problem of node repair in RS codes and have come up with new and more efficient ...

BackgroundThe Bmi1 polycomb ring finger oncogene, a transcriptional repressor belonging to the Polycomb group of proteins plays an important role in the regulation of stem cell self-renewal and is elevated in several cancers. In the current study, we have explored the role of Bmi1 in regulating the stemness and drug resistance of breast cancer cells.MethodsUsing real time PCR and immunohistochemistry primary breast tissues were analyzed. Retro- and lentiviruses were utilized to overexpress and knockdown Bmi1, RT-PCR and Western blot was performed to evaluate mRNA and protein expression. Stemness properties were analyzed by flow cytometry and sphere-formation and tumor formation was determined by mouse xenograft experiments. Dual luciferase assay was employed to assess promoter activity and MTT assay was used to analyze drug response.ResultsWe found Bmi1 overexpression in 64% of grade III invasive ductal breast adenocarcinomas compared to normal breast tissues. Bmi1 overexpression in immortalized and transformed breast epithelial cells increased their sphere-forming efficiency, induced epithelial to mesenchymal transition (EMT) with an increase in the expression of stemness-related genes. Knockdown of Bmi1 in tumorigenic breast cells induced epithelial morphology, reduced expression of stemness-related genes, decreased the IC50 values of doxorubicin and abrogated tumor-formation. Bmi1-high tumors showed elevated Nanog expression whereas the tumors with lower Bmi1 showed reduced Nanog levels. Overexpression of Bmi1 increased Nanog levels whereas knockdown of Bmi1 reduced its expression. Dual luciferase promoter-reporter assay revealed Bmi1 positively regulated the Nanog and NFκB promoter activity. RT-PCR analysis showed that Bmi1 overexpression activated the NFκB pathway whereas Bmi1 knockdown reduced the expression of NFκB target genes, suggesting that Bmi1 might regulate Nanog expression through the NFκB pathway.ConclusionsOur study showed that Bmi1 is overexpressed in several high-grade, invasive ductal breast adenocarcinomas, thus supporting its role as a prognostic marker. While Bmi1 overexpression increased self-renewal and promoted EMT, its knockdown reversed EMT, reduced stemness, and rendered cells drug sensitive, thus highlighting a crucial role for Bmi1 in regulating the stemness and drug response of breast cancer cells. Bmi1 may control self-renewal through the regulation of Nanog expression via the NFκB pathway.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2407-14-785) contains supplementary material, which is available to authorized users.

IntroductionMatrix detachment triggers anoikis, a form of apoptosis, in most normal epithelial cells, while acquisition of anoikis resistance is a prime requisite for solid tumor growth. Of note, recent studies have revealed that a small population of normal human mammary epithelial cells (HMECs) survive in suspension and generate multicellular spheroids termed ‘mammospheres’. Therefore, understanding how normal HMECs overcome anoikis may provide insights into breast cancer initiation and progression.MethodsPrimary breast tissue-derived normal HMECs were grown as adherent monolayers or mammospheres. The status of AMP-activated protein kinase (AMPK) and PEA15 signaling was investigated by immunoblotting. Pharmacological agents and an RNA interference (RNAi) approach were employed to gauge their roles in mammosphere formation. Immunoprecipitation and in vitro kinase assays were undertaken to evaluate interactions between AMPK and PEA15. In vitro sphere formation and tumor xenograft assays were performed to understand their roles in tumorigenicity.ResultsIn this study, we show that mammosphere formation by normal HMECs is accompanied with an increase in AMPK activity. Inhibition or knockdown of AMPK impaired mammosphere formation. Concomitant with AMPK activation, we detected increased Ser116 phosphorylation of PEA15, which promotes its anti-apoptotic functions. Inhibition or knockdown of AMPK impaired PEA15 Ser116 phosphorylation and increased apoptosis. Knockdown of PEA15, or overexpression of the nonphosphorylatable S116A mutant of PEA15, also abrogated mammosphere formation. We further demonstrate that AMPK directly interacts with and phosphorylates PEA15 at Ser116 residue, thus identifying PEA15 as a novel AMPK substrate. Together, these data revealed that AMPK activation facilitates mammosphere formation by inhibition of apoptosis, at least in part, through Ser116 phosphorylation of PEA15. Since anoikis resistance plays a critical role in solid tumor growth, we investigated the relevance of these findings in the context of breast cancer. Significantly, we show that the AMPK-PEA15 axis plays an important role in the anchorage-independent growth of breast cancer cells both in vitro and in vivo.ConclusionsOur study identifies a novel AMPK-PEA15 signaling axis in the anchorage-independent growth of both normal and cancerous mammary epithelial cells, suggesting that breast cancer cells may employ mechanisms of anoikis resistance already inherent within a subset of normal HMECs. Thus, targeting the AMPK-PEA15 axis might prevent breast cancer dissemination and metastasis.Electronic supplementary materialThe online version of this article (doi:10.1186/s13058-014-0420-z) contains supplementary material, which is available to authorized users.

Cell detachment from the extracellular matrix triggers anoikis. Disseminated tumor cells must adapt to survive matrix deprivation, while still retaining the ability to attach at secondary sites and reinitiate cell division. In this study, we illuminate mechanisms that enable reversible matrix attachment by breast cancer cells. Matrix deprival triggered AMPK activity and concomitantly inhibited AKT activity by upregulating the AKT phosphatase PHLPP2. The resultant pAMPK high /pAKT low state was critical for cell survival in suspension, as PHLPP2 silencing also increased anoikis while impairing autophagy and metastasis. In contrast, matrix re-attachment led to AKT-mediated AMPK inactivation via PP2C-α-mediated restoration of the pAKT high /pAMPK low state. Clinical specimens of primary and metastatic breast cancer displayed an AKT-associated gene expression signature, whereas circulating breast tumor cells displayed an elevated AMPKdependent gene expression signature. Our work establishes a double-negative feedback loop between AKT and AMPK to control the switch between matrix-attached and matrix-detached states needed to coordinate cell growth and survival during metastasis.Significance: Findings reveal a molecular switch that regulates cancer cell survival during metastatic dissemination, with the potential to illuminate targets to prevent metastasis in breast cancer.

Metastasis is clinically the most challenging and lethal aspect of breast cancer. While animal-based xenograft models are expensive and time-consuming, conventional two-dimensional (2D) cell culture systems fail to mimic in vivo signaling. In this study we have developed a three-dimensional (3D) scaffold system that better mimics the topography and mechanical properties of the breast tumor, thus recreating the tumor microenvironment in vitro to study breast cancer metastasis. Porous poly(ε-caprolactone) (PCL) scaffolds of modulus 7.0 ± 0.5 kPa, comparable to that of breast tumor tissue were fabricated, on which MDA-MB-231 cells proliferated forming tumoroids. A comparative gene expression analysis revealed that cells growing in the scaffolds expressed increased levels of genes implicated in the three major events of metastasis, viz., initiation, progression, and the site-specific colonization compared to cells grown in conventional 2D tissue culture polystyrene (TCPS) dishes. The cells cultured in scaffolds showed increased invasiveness and sphere formation efficiency in vitro and increased lung metastasis in vivo. A global gene expression analysis revealed a significant increase in the expression of genes involved in cell-cell and cell-matrix interactions and tissue remodeling, cancer inflammation, and the PI3K/Akt, Wnt, NF-kappaB, and HIF1 signaling pathways-all of which are implicated in metastasis. Thus, culturing breast cancer cells in 3D scaffolds that mimic the in vivo tumor-like microenvironment enhances their metastatic potential. This system could serve as a comprehensive in vitro model to investigate the manifold mechanisms of breast cancer metastasis.