Comparative transcriptome of normal and cancer-associated fibroblasts.

BACKGROUND: The characteristics of a tumor are largely determined by its interaction with the surrounding micro-environment (TME). TME consists of both cellular and non-cellular components. Cancer-associated fibroblasts (CAFs) are a major component of the TME. They are a source of many secreted factors that influence the survival and progression of tumors as well as their response to drugs. Identification of markers either overexpressed in CAFs or unique to CAFs would pave the way for novel therapeutic strategies that in combination with conventional chemotherapy are likely to have better patient outcome. METHODS: Fibroblasts have been derived from Benign Prostatic Hyperplasia (BPH) and prostate cancer. RNA from these has been used to perform a transcriptome analysis in order to get a comparative profile of normal and cancer-associated fibroblasts. RESULTS: The study has identified 818 differentially expressed mRNAs and 17 lincRNAs between normal and cancer-associated fibroblasts. Also, 15 potential lincRNA-miRNA-mRNA combinations have been identified which may be potential biomarkers. CONCLUSIONS: This study identified differentially expressed markers between normal and cancer-associated fibroblasts that would help in targeted therapy against CAFs/derived factors, in combination with conventional therapy. However, this would in future need more experimental validation.

microRNA profile of endometrial cancer from Indian patients-identification of potential biomarkers for prognosis.

Endometrial cancer is one of the major cancers in women throughout the world. If diagnosed early, these cancers are treatable and the prognosis is usually good. However, one major problem in treating endometrial cancer is accurate diagnosis and staging. Till date, the choice method for diagnosis and staging is histopathology. Although there are few molecular markers identified, they are not always sufficient in making accurate diagnosis and deciding on therapeutic strategy. As a result, very often patients are under treated or over treated. In this study, our group has profiled microRNAs from Indian patients using NGS-based approach. We have identified 212 differentially expressed microRNAs in endometrial cancer. Among these, there are 17 novel miRNAs. Since this data represents only Indian cohort and also lacks survival data, validation across other populations is necessary before being considered as biomarkers. As one approach towards this, these microRNAs have also been compared to data from TCGA, which represent other populations and also correlated to relevance in overall survival. Using in-silico approaches, mRNA targets of the miRNAs have been predicted. After comparing with TCGA, we have identified 16 miRNA-mRNA pairs which could be potential prognostic biomarkers for endometrial cancer. This is the first miRNA profiling report from Indian cohort and one of the very few studies which have identified potential biomarkers of prognosis in endometrial cancer.

Gene expression signature of castrate resistant prostate cancer.

Prostate gland is a highly androgen dependent gland and hence the first line of treatment for metastatic prostate cancer happens to be androgen ablation. This is achieved by multiple non-surgical methods. However, most of these cancers although respond well initially, become resistant to androgen ablation sooner or later. These cancers then become extremely aggressive and difficult to treat, thereby drastically affect the patient prognosis. Identification of a gene expression signature for castrate resistant prostate cancer may aid in identification of mechanisms responsible for castrate resistance, which in turn would help in better management of the disease. METHODS: Patient samples belonging to a. Control group; b. Castrate Sensitive group and c. Castrate Resistant group were collected. Gene expression profiling was performed on these samples using RNA-seq. Differentially expressed genes between control and castrate sensitive as well as control and castrate resistant groups were identified. This data was compared with data from The Cancer Genome Atlas (TCGA) in order to get relevance in prognosis. RESULTS: We have identified 481 differentially expressed genes between control and castrate sensitive groups; and 446 genes differentially expressed between control and castrate resistant groups. We have also identified 364 genes which are expressed in the castrate resistant group alone, which is of interest since these may have an implication in evolution of castrate resistance and also prognosis. When compared to prostate cancer data from TCGA, 763 genes were found in common to our dataset. With this, a CaS and CaR signature was defined. Using criteria such as overall survival, disease-free survival, progression-free survival and biochemical recurrence, we have identified genes that may have relevance in progression to castrate resistance and in prognosis. Functional annotation of these genes may give an insight into the mechanism of development of castrate resistance.

Emerging role of gut microbiota dysbiosis in neuroinflammation and neurodegeneration.

Alzheimer's disease (AD), is a chronic age-related progressive neurodegenerative disorder, characterized by neuroinflammation and extracellular aggregation of Aß peptide. Alzheimer's affects every 1 in 14 individuals aged 65 years and above. Recent studies suggest that the intestinal microbiota plays a crucial role in modulating neuro-inflammation which in turn influences Aß deposition. The gut and the brain interact with each other through the nervous system and chemical means via the blood-brain barrier, which is termed the Microbiota Gut Brain Axis (MGBA). It is suggested that the gut microbiota can impact the host's health, and numerous factors, such as nutrition, pharmacological interventions, lifestyle, and geographic location, can alter the gut microbiota composition. Although, the exact relationship between gut dysbiosis and AD is still elusive, several mechanisms have been proposed as drivers of gut dysbiosis and their implications in AD pathology, which include, action of bacteria that produce bacterial amyloids and lipopolysaccharides causing macrophage dysfunction leading to increased gut permeability, hyperimmune activation of inflammatory cytokines (IL-1ß, IL-6, IL-8, and NLRP3), impairment of gut- blood brain barrier causing deposition of Aß in the brain, etc. The study of micro-organisms associated with dysbiosis in AD with the aid of appropriate model organisms has recognized the phyla Bacteroidetes and Firmicutes which contain organisms of the genus Escherichia, Lactobacillus, Clostridium, etc., to contribute significantly to AD pathology. Modulating the gut microbiota by various means, such as the use of prebiotics, probiotics, antibiotics or fecal matter transplantation, is thought to be a potential therapeutic intervention for the treatment of AD. This review aims to summarize our current knowledge on possible mechanisms of gut microbiota dysbiosis, the role of gut brain microbiota axis in neuroinflammation, and the application of novel targeted therapeutic approaches that modulate the gut microbiota in treatment of AD.

To block or not to block-hormonal signaling in the treatment of cancers.

The breast and prostate glands are the two major organs that are highly dependent on the gonadal steroid hormones for their development and homeostasis. The cancers of these organs also show a large dependence on steroid hormones and have formed the basis of endocrine therapy. Estrogen deprivation by oophorectomy has been in active practice since the 1970s, and androgen deprivation therapy for prostate cancer was a major breakthrough in medicine in 1941. Since then, several improvisations have happened in these modes of therapy. However, the development of resistance to this deprivation and the emergence of hormone independence are major problems in both cancers. The lessons learned from rodent models have made it clear that the male hormone has a role in females and vice versa. Also, the metabolic products of these hormones may have unintentional effects including proliferative conditions in both sexes. Hence, administering estrogen as a method of chemical castration in males and administering DHT in females may not be the ideal scenario. It would be important to consider the status of the opposite sex hormone signaling and its effects and come up with a combinatorial regime to strike a balance between androgen and estrogen signaling. This review summarizes the current understanding and developments in this field in the context of prostate cancer.

Non-canonical Estrogen Signaling in Endocrine Resistance.

Breast cancer is one of the leading causes of cancer related deaths in women worldwide. The disease is extremely heterogenous. A large percentage of the breast cancers are dependent on estrogen signaling and hence respond to endocrine therapies which essentially block the estrogen signaling. However, many of these tumors emerge as endocrine resistant tumors. Many mechanisms have been proposed to explain the emergence of endocrine resistance, which include mutations in the estrogen receptors, cross-talk with other signaling pathways, cancer stem cells etc. This review is focused on the role of non-canonical estrogen receptor signaling in endocrine resistance. Most of the therapeutics which are used currently are targeting the major receptor of estrogen namely ER-α. Last two decades has witnessed the discovery of alternate forms of ER-α, as well as other receptors for estrogen such as ERRgamma, GPER-1 as well as ER-ß, which are activated not only by estrogen, but also by the therapeutic agents such as tamoxifen that are routinely used in treatment of breast cancer. However, when the alternate receptors are activated, they result in activation of membrane signaling which subsequently activates pathways such as MAPK and GPCR leading to cell-proliferation. This renders the anticipated anti-estrogenic effects of tamoxifen less effective or ineffective. Future research in this area has to focus on the alternate mechanisms and develop a combinatorial strategy, which can complement the existing therapeutics to get better outcome of endocrine therapies.

Notch Represses Transcription by PRC2 Recruitment to the Ternary Complex.

It is well established that Notch functions as a transcriptional activator through the formation of a ternary complex that comprises Notch, Maml, and CSL. This ternary complex then serves to recruit additional transcriptional cofactors that link to higher order transcriptional complexes. The mechanistic details of these events remain unclear. This report reveals that the Notch ternary complex can direct the formation of a repressor complex to terminate gene expression of select target genes. Herein, it is demonstrated that p19Arf and Klf4 are transcriptionally repressed in a Notch-dependent manner. Furthermore, results indicate that Notch recruits Polycomb Repressor Complex 2 (PRC2) and Lysine Demethylase 1 (KDM1A/LSD1) to these promoters, which leads to changes in the epigenetic landscape and repression of transcription. The demethylase activity of LSD1 is a prerequisite for Notch-mediated transcriptional repression. In addition, a stable Notch transcriptional repressor complex was identified containing LSD1, PRC2, and the Notch ternary complex. These findings demonstrate a novel function of Notch and provide further insight into the mechanisms of Notch-mediated tumorigenesis.Implications: This study provides rationale for the targeting of epigenetic enzymes to inhibit Notch activity or use in combinatorial therapy to provide a more profound therapeutic response. Mol Cancer Res; 15(9); 1173-83. ©2017 AACR.

Notch signaling drives stemness and tumorigenicity of esophageal adenocarcinoma.

Esophageal adenocarcinoma ranks sixth in cancer mortality in the world and its incidence has risen dramatically in the Western population over the last decades. Data presented herein strongly suggest that Notch signaling is critical for esophageal adenocarcinoma and underlies resistance to chemotherapy. We present evidence that Notch signaling drives a cancer stem cell phenotype by regulating genes that establish stemness. Using patient-derived xenograft models, we demonstrate that inhibition of Notch by gamma-secretase inhibitors (GSI) is efficacious in downsizing tumor growth. Moreover, we demonstrate that Notch activity in a patient's ultrasound-assisted endoscopic-derived biopsy might predict outcome to chemotherapy. Therefore, this study provides a proof of concept that inhibition of Notch activity will have efficacy in treating esophageal adenocarcinoma, offering a rationale to lay the foundation for a clinical trial to evaluate the efficacy of GSI in esophageal adenocarcinoma treatment.

NACK is an integral component of the Notch transcriptional activation complex and is critical for development and tumorigenesis.

The Notch signaling pathway governs many distinct cellular processes by regulating transcriptional programs. The transcriptional response initiated by Notch is highly cell context dependent, indicating that multiple factors influence Notch target gene selection and activity. However, the mechanism by which Notch drives target gene transcription is not well understood. Herein, we identify and characterize a novel Notch-interacting protein, Notch activation complex kinase (NACK), which acts as a Notch transcriptional coactivator. We show that NACK associates with the Notch transcriptional activation complex on DNA, mediates Notch transcriptional activity, and is required for Notch-mediated tumorigenesis. We demonstrate that Notch1 and NACK are coexpressed during mouse development and that homozygous loss of NACK is embryonic lethal. Finally, we show that NACK is also a Notch target gene, establishing a feed-forward loop. Thus, our data indicate that NACK is a key component of the Notch transcriptional complex and is an essential regulator of Notch-mediated tumorigenesis and development.

Protumorigenic actions of S100A2 involve regulation of PI3/Akt signaling and functional interaction with Smad3.

S100 family of calcium-binding proteins is commonly upregulated in a variety of tumor types and is often associated with tumor progression. Among several S100 members, altered expression of S100A2 is a potential diagnostic and prognostic marker in cancer. Several reports suggest a role for S100A2 in metastasis. Earlier, our studies established regulation of S100A2 by transforming growth factor-ß (TGF-ß) and its involvement in TGF-ß-mediated cancer cell invasion and migration. However, the molecular mechanisms of S100A2 protumorigenic actions remain unexplored. In the present study, we demonstrate that overexpression of S100A2 in A549 lung cancer cells induced epithelial-mesenchymal transition (EMT) followed by increased invasion, loose colony morphology in soft agar and enhanced Akt phosphorylation (Ser-473). Furthermore, overexpression of S100A2 led to increased tumor growth in immunocompromised mice. In agreement, immunohistochemical examination of resected xenograft tumors established inverse correlation between S100A2 and E-cadherin expression together with activated Akt signaling. Interestingly, our study demonstrates a strong dependence of S100A2 and Smad3 in TGF-ß-induced Hep3B cell EMT and invasion. Most importantly, we demonstrate that these effects of S100A2 are manifested through functional interaction with Smad3, which is enhanced in the presence of high calcium and TGF-ß. S100A2 stabilizes Smad3 and binds to its C-terminal MH2 domain. Additionally, loss of S100A2 attenuates the transcription of TGF-ß/Smad3 target genes involved in tumor promotion, such as PA1-1 and vimentin. Collectively, our findings present the first mechanistic details of S100A2 protumorigenic actions and its involvement in TGF-ß-mediated cancer cell invasion and EMT.

Triple negative breast cancer initiating cell subsets differ in functional and molecular characteristics and in γ-secretase inhibitor drug responses.

Increasing evidence suggests that stem-like cells mediate cancer therapy resistance and metastasis. Breast tumour-initiating stem cells (T-ISC) are known to be enriched in CD44(+) CD24(neg/low) cells. Here, we identify two T-ISC subsets within this population in triple negative breast cancer (TNBC) lines and dissociated primary breast cancer cultures: CD44(+) CD24(low+) subpopulation generates CD44(+) CD24(neg) progeny with reduced sphere formation and tumourigenicity. CD44(+) CD24(low+) populations contain subsets of ALDH1(+) and ESA(+) cells, yield more frequent spheres and/or T-ISC in limiting dilution assays, preferentially express metastatic gene signatures and show greater motility, invasion and, in the MDA-MB-231 model, metastatic potential. CD44(+) CD24(low+) but not CD44(+) CD24(neg) express activated Notch1 intracellular domain (N1-ICD) and Notch target genes. We show N1-ICD transactivates SOX2 to increase sphere formation, ALDH1+ and CD44(+) CD24(low+) cells. Gamma secretase inhibitors (GSI) reduced sphere formation and xenograft growth from CD44(+) CD24(low+) cells, but CD44(+) CD24(neg) were resistant. While GSI hold promise for targeting T-ISC, stem cell heterogeneity as observed herein, could limit GSI efficacy. These data suggest a breast T-ISC hierarchy in which distinct pathways drive developmentally related subpopulations with different anti-cancer drug responsiveness.

Regulation of S100A2 expression by TGF-ß-induced MEK/ERK signalling and its role in cell migration/invasion.

S100A2, an EF hand calcium-binding protein, is a potential biomarker in several cancers and is also a TGF-ß (transforming growth factor-ß)-regulated gene in melanoma and lung cancer cells. However, the mechanism of S100A2 regulation by TGF-ß and its significance in cancer progression remains largely unknown. In the present study we report the mechanism of S100A2 regulation by TGF-ß and its possible role in TGF-ß-mediated tumour promotion. Characterization of the S100A2 promoter revealed an AP-1 (activator protein-1) element at positions -1161 to -1151 as being the most critical factor for the TGF-ß1 response. Chromatin immunoprecipitation and electrophoretic mobility-shift assays confirmed the functional binding of the AP-1 complex, predominantly JunB, to the S100A2 promoter in response to TGF-ß1 in HaCaT keratinocytes. JunB overexpression markedly stimulated the S100A2 promoter which was blocked by the dominant-negative JunB and MEK1 [MAPK (mitogen-activated protein kinase)/ERK (extracellular-signal-regulated kinase) kinase 1] inhibitor, PD98059. Intriguingly, despite the presence of a putative SMAD-binding element, S100A2 regulation by TGF-ß1 was found to be SMAD3 independent. Interestingly, p53 protein and TGF-ß1 show synergistic regulation of the S100A2 promoter. Finally, knockdown of S100A2 expression compromised TGF-ß1-induced cell migration and invasion of Hep3B cells. Together our findings highlight an important link between the TGF-ß1-induced MAPK and p53 signalling pathways in the regulation of S100A2 expression and pro-tumorigenic actions.

Hierarchical phosphorylation within the ankyrin repeat domain defines a phosphoregulatory loop that regulates Notch transcriptional activity.

The Notch signal transduction pathway mediates important cellular functions through direct cell-to-cell contact. Deregulation of Notch activity can lead to an altered cell proliferation and has been linked to many human cancers. Casein kinase 2 (CK2), a ubiquitous kinase, regulates several cellular processes by phosphorylating proteins involved in signal transduction, gene expression, and protein synthesis. In this report we identify Notch(ICD) as a novel target of phosphorylation by CK2. Using mapping and mutational studies, we identified serine 1901, located in the ankyrin domain of Notch, as the target amino acid. Interestingly, phosphorylation of serine 1901 by CK2 appears to generate a second phosphorylation site at threonine 1898. Furthermore, threonine 1898 phosphorylation only occurs when Notch forms a complex with Mastermind and CSL. Phosphorylation of both threonine 1898 and serine 1901 resulted in decreased binding of the Notch-Mastermind-CSL ternary complex to DNA and consequently lower transcriptional activity. These data indicate that the phosphorylation of serine 1901 and threonine 1898 negatively regulates Notch function by dissociating the complex from DNA. This study identifies a new component involved in regulation of Notch(ICD) transcriptional activity, reinforcing the notion that a precise and tight regulation is required for this essential signaling pathway.

Notch signalling in solid tumours: a little bit of everything but not all the time.

The discovery of Notch in Drosophila melanogaster nearly a century ago opened the door to an ever-widening understanding of cellular processes that are controlled or influenced by Notch signalling. As would be expected with such a pleiotropic pathway, the deregulation of Notch signalling leads to several pathological conditions, including cancer. A role for Notch is well established in haematological malignancies, and more recent studies have provided evidence for the importance of Notch activity in solid tumours. As it is thought to act as an oncogene in some cancers but as a tumour suppressor in others, the role of Notch in solid tumours seems to be highly context dependent.

Molecular alterations in exocrine neoplasms of the pancreas.

CONTEXT: Pancreatic cancer is one of the leading causes of cancer-related deaths. Most cases are diagnosed at an advanced stage when the disease is beyond surgical intervention. Molecular studies during the past decade have contributed greatly to our understanding of this disease. Various germ-line and somatic mutations associated with pancreatic cancers have been characterized, along with abnormal variations in the gene expression patterns. A thorough characterization of molecular alterations such as genetic and epigenetic changes, alterations in the expression of genes and changes in proteins, and posttranslational modifications in pancreatic cancer could lead to a better understanding of its pathogenesis. OBJECTIVE: To provide an overview of the various molecular alterations in pancreatic cancer and the methodologies used to catalog such alterations. DATA SOURCES: Published studies about various molecular alterations at the genomic, epigenetic, transcriptomic, and proteomic levels in pancreatic cancer. CONCLUSIONS: The available data from pancreatic cancer suggests that there are a large number of molecular alterations at genomic, epigenetic, transcriptomic, and proteomic levels. It is now possible to initiate a systems approach to studying pancreatic cancer especially in light of newer initiatives to dissect the pancreatic cancer genome.

Human Protein Reference Database--2009 update.

Human Protein Reference Database (HPRD--http://www.hprd.org/), initially described in 2003, is a database of curated proteomic information pertaining to human proteins. We have recently added a number of new features in HPRD. These include PhosphoMotif Finder, which allows users to find the presence of over 320 experimentally verified phosphorylation motifs in proteins of interest. Another new feature is a protein distributed annotation system--Human Proteinpedia (http://www.humanproteinpedia.org/)--through which laboratories can submit their data, which is mapped onto protein entries in HPRD. Over 75 laboratories involved in proteomics research have already participated in this effort by submitting data for over 15,000 human proteins. The submitted data includes mass spectrometry and protein microarray-derived data, among other data types. Finally, HPRD is also linked to a compendium of human signaling pathways developed by our group, NetPath (http://www.netpath.org/), which currently contains annotations for several cancer and immune signaling pathways. Since the last update, more than 5500 new protein sequences have been added, making HPRD a comprehensive resource for studying the human proteome.