Methyl-CpG binding domain protein 2 (Mbd2) drives breast cancer progression through the modulation of epithelial-to-mesenchymal transition

Methyl-CpG-binding domain protein 2 (Mbd2), a reader of DNA methylation, has been implicated in different types of malignancies, including breast cancer. However, the exact role of Mbd2 in various stages of breast cancer growth and progression in vivo has not been determined. To test whether Mbd2 plays a causal role in mammary tumor growth and metastasis, we performed genetic knockout (KO) of Mbd2 in MMTV-PyMT transgenic mice and compared mammary tumor progression kinetics between the wild-type (PyMT-Mbd2+/+) and KO (PyMT-Mbd2-/-) groups. Our results demonstrated that deletion of Mbd2 in PyMT mice impedes primary tumor growth and lung metastasis at the experimental endpoint (postnatal week 20). Transcriptomic and proteomic analyses of primary tumors revealed that Mbd2 deletion abrogates the expression of several key determinants involved in epithelial-to-mesenchymal transition, such as neural cadherin (N-cadherin) and osteopontin. Importantly, loss of the Mbd2 gene impairs the activation of the PI3K/AKT pathway, which is required for PyMT-mediated oncogenic transformation, growth, and survival of breast tumor cells. Taken together, the results of this study provide a rationale for further development of epigenetic therapies targeting Mbd2 to inhibit the progression of breast cancer.

Impact of eIF2α phosphorylation on the translational landscape of mouse embryonic stem cells

The integrated stress response (ISR) is critical for cell survival under stress. In response to diverse environmental cues, eIF2α becomes phosphorylated, engendering a dramatic change in mRNA translation. The activation of ISR plays a pivotal role in the early embryogenesis, but the eIF2-dependent translational landscape in pluripotent embryonic stem cells (ESCs) is largely unexplored. We employ a multi-omics approach consisting of ribosome profiling, proteomics, and metabolomics in wild-type (eIF2α+/+) and phosphorylation-deficient mutant eIF2α (eIF2αA/A) mouse ESCs (mESCs) to investigate phosphorylated (p)-eIF2α-dependent translational control of naive pluripotency. We show a transient increase in p-eIF2α in the naive epiblast layer of E4.5 embryos. Absence of eIF2α phosphorylation engenders an exit from naive pluripotency following 2i (two chemical inhibitors of MEK1/2 and GSK3α/β) withdrawal. p-eIF2α controls translation of mRNAs encoding proteins that govern pluripotency, chromatin organization, and glutathione synthesis. Thus, p-eIF2α acts as a key regulator of the naive pluripotency gene regulatory network.

mRNA translation in astrocytes controls hippocampal long-term synaptic plasticity and memory

Activation of neuronal protein synthesis upon learning is critical for the formation of long-term memory. Here, we report that learning in the contextual fear conditioning paradigm engenders a decrease in eIF2α (eukaryotic translation initiation factor 2) phosphorylation in astrocytes in the hippocampal CA1 region, which promotes protein synthesis. Genetic reduction of eIF2α phosphorylation in hippocampal astrocytes enhanced contextual and spatial memory and lowered the threshold for the induction of long-lasting plasticity by modulating synaptic transmission. Thus, learning-induced dephosphorylation of eIF2α in astrocytes bolsters hippocampal synaptic plasticity and consolidation of long-term memories.

Radiology reporting of incidental osteoporotic vertebral fragility fractures present on CT studies: results of UK national re-audit

AIM

To describe a UK-wide re-audit of the 2019 Royal College of Radiologists (RCR) audit evaluating patient-related data and organisational infrastructure in the radiological reporting of vertebral fragility fractures (VFFs) on computed tomography (CT) studies and to assess the impact of a series of RCR interventions, initiated to raise VFF awareness, on reporting practice and outcomes.

MATERIALS AND METHODS

Patient specific and organisational questionnaires largely replicated those utilised in 2019. The patient questionnaire involved retrospective analysis of between 50 and 100 consecutive, non-traumatic CT studies which included the thoracolumbar spine. All RCR radiology audit leads were invited to participate. Data collection commenced from 1 April 2022.

RESULTS

Data were supplied by 129/194 (67%) departments. One thousand five hundred and eighty-six of 7,316 patients (21.7%) had a VFF on auditor review. Overall improvements were demonstrated in key initial/provisional reporting results; comment on spine/bone (93.2%, 14.4% improvement, p<0.0002); fracture severity assessment (34.7%, 8.5% improvement, p=0.0007); use of recommended terminology (67.8%, 7.5% improvement, p=0.0034); recommendations for further management (11.7%, 9.1% improvement, p<0.0002).

CONCLUSIONS

The 2022 national re-audit confirms improvements in diagnostic performance and practice in VFF reporting. Continuing work is required to build on this improvement and to further embed best practice.

Methyl-CpG binding domain 2 (Mbd2) is an epigenetic regulator of autism-risk genes and cognition

The Methyl-CpG-Binding Domain Protein family has been implicated in neurodevelopmental disorders. The Methyl-CpG-binding domain 2 (Mbd2) binds methylated DNA and was shown to play an important role in cancer and immunity. Some evidence linked this protein to neurodevelopment. However, its exact role in neurodevelopment and brain function is mostly unknown. Here we show that Mbd2-deficiency in mice (Mbd2-/-) results in deficits in cognitive, social and emotional functions. Mbd2 binds regulatory DNA regions of neuronal genes in the hippocampus and loss of Mbd2 alters the expression of hundreds of genes with a robust down-regulation of neuronal gene pathways. Further, a genome-wide DNA methylation analysis found an altered DNA methylation pattern in regulatory DNA regions of neuronal genes in Mbd2-/- mice. Differentially expressed genes significantly overlap with gene-expression changes observed in brains of Autism Spectrum Disorder (ASD) individuals. Notably, downregulated genes are significantly enriched for human ortholog ASD risk genes. Observed hippocampal morphological abnormalities were similar to those found in individuals with ASD and ASD rodent models. Hippocampal Mbd2 knockdown partially recapitulates the behavioral phenotypes observed in Mbd2-/- mice. These findings suggest that Mbd2 is a novel epigenetic regulator of genes that are associated with ASD in humans. Mbd2 loss causes behavioral alterations that resemble those found in ASD individuals.

Fibrinolytic System and Cancer: Diagnostic and Therapeutic Applications

Fibrinolysis is a crucial physiological process that helps to maintain a hemostatic balance by counteracting excessive thrombosis. The components of the fibrinolytic system are well established and are associated with a wide array of physiological and pathophysiological processes. The aberrant expression of several components, especially urokinase-type plasminogen activator (uPA), its cognate receptor uPAR, and plasminogen activator inhibitor-1 (PAI-1), has shown a direct correlation with increased tumor growth, invasiveness, and metastasis. As a result, targeting the fibrinolytic system has been of great interest in the field of cancer biology. Even though there is a plethora of encouraging preclinical evidence on the potential therapeutic benefits of targeting the key oncogenic components of the fibrinolytic system, none of them made it from “bench to bedside” due to a limited number of clinical trials on them. This review summarizes our existing understanding of the various diagnostic and therapeutic strategies targeting the fibrinolytic system during cancer.

Enhanced Anticancer Effect of a Combination of S-adenosylmethionine (SAM) and Immune Checkpoint Inhibitor (ICPi) in a Syngeneic Mouse Model of Advanced Melanoma

Immune checkpoint inhibitors (ICPi) targeting the PD-1/PD-L1 pathway have shown marked success in patients with advanced melanoma. However, 60-70% of patients fail to respond, warranting a therapeutic intervention that could increase response rates. We and others have shown that S-adenosylmethionine (SAM), a universal methyl donor, has significant anticancer effects in numerous cancers previously; however, its effect on melanoma progression has not been evaluated. Interestingly, SAM was reported to be essential for T cell activation and proliferation and, thus, could potentially cooperate with ICPi and block melanoma progression. In this study, we examined the antitumor effects of SAM and ICPi alone and in combination in a well-established melanoma mouse model wherein syngeneic C57BL/6 mouse were subcutaneously (orthotopic) injected with B16-F1 cells. Treatment of mice with either SAM or anti-PD-1 antibody alone resulted in significant reduction in tumor volumes and weights; effects that were highest in mice treated with a combination of SAM+anti-PD-1. RNA-sequencing analysis of the primary tumors showed numerous differentially expressed genes (DEGs) following treatment with SAM+anti-PD-1, which was shown to downregulate cancer, MAPK, and tyrosine kinase pathways. Indeed, SAM+anti-PD-1 reversed the aberrant expression of some known melanoma genes. Tumor immunophenotyping revealed the SAM+anti-PD-1 combination was significantly more effective than either SAM or anti-PD-1 as the CD8⁺ T cells had higher activation, proliferation, and cytokine production compared to all other groups. This study shows that the combination of currently approved agents SAM and ICPi can effectively block melanoma via alteration of key genes/pathways implicated in cancer and immune response pathways, providing the rationale for the initiation of clinical trials with SAM and ICPi.

S-adenosylmethionine in combination with decitabine shows enhanced anti-cancer effects in repressing breast cancer growth and metastasis

Abnormal DNA methylation orchestrates many of the cancer‐related gene expression irregularities such as the inactivation of tumour suppressor genes through hypermethylation as well as activation of prometastatic genes through hypomethylation. The fact that DNA methylation abnormalities can be chemically reversed positions the DNA methylation machinery as an attractive target for anti‐cancer drug development. However, although in vitro studies suggested that targeting concordantly hypo‐ and hypermethylation is of benefit in suppressing both oncogenic and prometastatic functions of breast cancer cells, this has never been tested in a therapeutic setting in vivo. In this context, we investigated the combined therapeutic effects of an approved nutraceutical agent S‐adenosylmethionine (SAM) and FDA‐approved hypomethylating agent decitabine using the MDA‐MB‐231 xenograft model of breast cancer and found a pronounced reduction in mammary tumour volume and lung metastasis compared to the animals in the control and monotherapy treatment arms. Immunohistochemical assessment of the primary breast tumours showed a significantly reduced expression of proliferation (Ki‐67) and angiogenesis (CD31) markers following combination therapy as compared to the control group. Global transcriptome and methylome analyses have revealed that the combination therapy regulates genes from several key cancer‐related pathways that are abnormally expressed in breast tumours. To our knowledge, this is the first preclinical study demonstrating the anti‐cancer therapeutic potential of using a combination of methylating (SAM) and demethylating agent (decitabine) in vivo. Results from this study provide a molecularly founded rationale for clinically testing a combination of agents targeting the epigenome to reduce the morbidity and mortality from breast cancer.

An enhanced chemopreventive effect of methyl donor S-adenosylmethionine in combination with 25-hydroxyvitamin D in blocking mammary tumor growth and metastasis

Therapeutic targeting of metastatic breast cancer still remains a challenge as the tumor cells are highly heterogenous and exploit multiple pathways for their growth and metastatic spread that cannot always be targeted by a single-agent monotherapy regimen. Therefore, a rational approach through simultaneous targeting of several pathways may provide a better anti-cancer therapeutic effect. We tested this hypothesis using a combination of two nutraceutical agents S-adenosylmethionine (SAM) and Vitamin D (Vit. D) prohormone [25-hydroxyvitamin D; '25(OH)D'] that are individually known to exert distinct changes in the expression of genes involved in tumor growth and metastasis. Our results show that both SAM and 25(OH)D monotherapy significantly reduced proliferation and clonogenic survival of a panel of breast cancer cell lines in vitro and inhibited tumor growth, lung metastasis, and breast tumor cell colonization to the skeleton in vivo. However, these effects were significantly more pronounced in the combination setting. RNA-Sequencing revealed that the transcriptomic footprint on key cancer-related signaling pathways is broader in the combination setting than any of the monotherapies. Furthermore, comparison of the differentially expressed genes from our transcriptome analyses with publicly available cancer-related dataset demonstrated that the combination treatment upregulates genes from immune-related pathways that are otherwise downregulated in bone metastasis in vivo. Since SAM and Vit. D are both approved nutraceuticals with known safety profiles, this combination treatment may serve as a novel strategy to reduce breast cancer-associated morbidity and mortality.

uPAR antibody (huATN-658) and Zometa reduce breast cancer growth and skeletal lesions

Urokinase plasminogen activator receptor (uPAR) is implicated in tumor growth and metastasis due to its ability to activate latent growth factors, proteases, and different oncogenic signaling pathways upon binding to different ligands. Elevated uPAR expression is correlated with the increased aggressiveness of cancer cells, which led to its credentialing as an attractive diagnostic and therapeutic target in advanced solid cancer. Here, we examine the antitumor effects of a humanized anti-uPAR antibody (huATN-658) alone and in combination with the approved bisphosphonate Zometa (Zoledronic acid) on skeletal lesion through a series of studies in vitro and in vivo. Treatment with huATN-658 or Zometa alone significantly decreased human MDA-MB-231 cell proliferation and invasion in vitro, effects which were more pronounced when huATN-658 was combined with Zometa. In vivo studies demonstrated that huATN-658 treatment significantly reduced MDA-MB-231 primary tumor growth compared with controls. In a model of breast tumor-induced bone disease, huATN-658 and Zometa were equally effective in reducing skeletal lesions. The skeletal lesions were significantly reduced in animals receiving the combination of huATN-658 + Zometa compared with monotherapy treatment. These effects were due to a significant decrease in osteoclastic activity and tumor cell proliferation in the combination treatment group. Transcriptome analysis revealed that combination treatment significantly changes the expression of genes from signaling pathways implicated in tumor progression and bone remodeling. Results from these studies provide a rationale for the continued development of huATN-658 as a monotherapy and in combination with currently approved agents such as Zometa in patients with metastatic breast cancer.

DNA Methylation Readers and Cancer: Mechanistic and Therapeutic Applications

DNA methylation is a major epigenetic process that regulates chromatin structure which causes transcriptional activation or repression of genes in a context-dependent manner. In general, DNA methylation takes place when methyl groups are added to the appropriate bases on the genome by the action of "writer" molecules known as DNA methyltransferases. How these methylation marks are read and interpreted into different functionalities represents one of the main mechanisms through which the genes are switched "ON" or "OFF" and typically involves different types of "reader" proteins that can recognize and bind to the methylated regions. A tightly balanced regulation exists between the "writers" and "readers" in order to mediate normal cellular functions. However, alterations in normal methylation pattern is a typical hallmark of cancer which alters the way methylation marks are written, read and interpreted in different disease states. This unique characteristic of DNA methylation "readers" has identified them as attractive therapeutic targets. In this review, we describe the current state of knowledge on the different classes of DNA methylation "readers" identified thus far along with their normal biological functions, describe how they are dysregulated in cancer, and discuss the various anti-cancer therapies that are currently being developed and evaluated for targeting these proteins.

Targeting DNA Hypomethylation in Malignancy by Epigenetic Therapies

DNA methylation is a chemically reversible epigenetic modification that regulates the chromatin structure and gene expression, and thereby takes part in various cellular processes like embryogenesis, genomic imprinting, X-chromosome inactivation, and genome stability. Alterations in the normal methylation levels of DNA may contribute to the development of pathological conditions like cancer. Even though both hypo- and hypermethylation-mediated abnormalities are prevalent in the cancer genome, the field of cancer epigenetics has been more focused on targeting hypermethylation. As a result, DNA hypomethylation-mediated abnormalities remained relatively less explored, and currently, there are no approved drugs that can be clinically used to target hypomethylation. Understanding the precise role of DNA hypomethylation is not only crucial from a mechanistic point of view but also for the development of pharmacological agents that can reverse the hypomethylated state of the DNA. This chapter focuses on the causes and impact of DNA hypomethylation in the development of cancer and describes the possible ways to pharmacologically target it, especially by using a naturally occurring physiologic agent S-adenosylmethionine (SAM).

Identification of an Epigenetic Signature of Osteoporosis in Blood DNA of Postmenopausal Women

Osteoporosis is one of the most common age-related progressive bone diseases in elderly people. Approximately one in three women and one in five men are predisposed to developing osteoporosis. In postmenopausal women, a reduction in BMD leads to an increased risk of fractures. In the current study, we delineated the DNA methylation signatures in whole blood samples of postmenopausal osteoporotic women. We obtained whole blood DNA from 22 normal women and 22 postmenopausal osteoporotic women (51 to 89 years old) from the Canadian Multicenter Osteoporosis Study (CaMos) cohort. These DNA samples were subjected to Illumina Infinium human methylation 450 K analysis. Illumina 450K raw data were analyzed by Genome Studio software. Analysis of the female participants with early and advanced osteoporosis resulted in the generation of a list of 1233 differentially methylated CpG sites when compared with age-matched normal women. T test, ANOVA, and post hoc statistical analyses were performed, and 77 significantly differentially methylated CpG sites were identified. From the 13 most significant genes, ZNF267, ABLIM2, RHOJ, CDKL5, and PDCD1 were selected for their potential role in bone biology. A weighted polygenic DNA methylation score of these genes predicted osteoporosis at an early stage with high sensitivity and specificity and correlated with measures of bone density. Pyrosequencing analysis of these genes was performed to validate the results obtained from Illumina 450 K methylation analysis. The current study provides proof of principal for the role of DNA methylation in osteoporosis. Using whole blood DNA methylation analysis, women at risk of developing osteoporosis can be identified before a diagnosis of osteoporosis is made using BMD as a screening method. Early diagnosis will help to select patients who might benefit from early therapeutic intervention. © 2018 American Society for Bone and Mineral Research.

Abstract 1388: Pharmacologic targeting of DNA methylation blocks breast cancer growth and metastasis

Abnormal DNA methylation is a hallmark of cancer which orchestrates changes in gene transcription seen in cancer. Both hypermethylation-mediated inactivation of tumor suppressor genes and hypomethylation-mediated activation of pro-metastatic genes are common attributes of cancer cells which make the methylome an attractive anti-cancer therapeutic target. Interestingly, in contrast to genetic changes, DNA methylation-mediated epigenetic changes are potentially reversible by either dietary supplements or therapeutic strategies. Consequently, a wide variety of epigenetic drugs primarily targeting DNA hypermethylation has been shown to be effective in preclinical and clinical settings. Pioneering works done by us have shown that treatment of various human cell lines (breast, prostate, osteosarcoma) with a methylating agent S-adenosyl methionine (SAM) can block tumor growth and metastasis in vivo. At the molecular level, SAM treatment induces hypermethylation of promoters of key pro-metastatic genes; and thereby inhibits their expression. However, the anti-cancer effect of SAM has never been examined. Based on the heterogeneity of tumor cells which are at different stages of tumor invasiveness, we hypothesized that treatment with demethylating (Decitabine) and methylating agents (SAM) would collectively lead to the activation of tumor suppressor genes and suppression of pro-metastatic genes to block cancer growth and metastasis.

In the current study, we first investigated the effects of Decitabine and SAM alone and in combination to prevent breast cancer development, growth, and metastasis using the MDA-MB-231 xenograft model of breast cancer. Our data showed that treatment with Decitabine and SAM resulted in a significant delay in the progression of mammary tumors in experimental animals compared to controls, effects which were significantly more pronounced when Decitabine and SAM were administered in a combination setting. Gene expression analysis of the cancer cells revealed that SAM-treatment repressed the expression of several key genes involved in cancer progression. In addition, immunohistochemical analysis of primary tumors revealed that the combination treatment (Decitabine, SAM) reduced the number of Ki67 positive cells as well reduced the expression of angiogenesis marker CD-31. Further studies examining the effects of combined therapy on genome-wide gene expression changes as well as any potential side effects on animal behavior and toxicity will be presented and discussed.

Results from this study will provide compelling evidence and rationale for the initiation of clinical trials with SAM alone as a monotherapy and in combination with currently approved epigenetic drugs (Decitabine) to reduce breast cancer-associated morbidity and mortality.

Citation Format: Niaz Mahmood, Ani Arakelian, William J. Muller, Moshe Szyf, Shafaat A. Rabbani. Pharmacologic targeting of DNA methylation blocks breast cancer growth and metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1388.

Liquid metals: fundamentals and applications in chemistry

Post-transition elements, together with zinc-group metals and their alloys belong to an emerging class of materials with fascinating characteristics originating from their simultaneous metallic and liquid natures. These metals and alloys are characterised by having low melting points (i.e. between room temperature and 300 °C), making their liquid state accessible to practical applications in various fields of physical chemistry and synthesis. These materials can offer extraordinary capabilities in the synthesis of new materials, catalysis and can also enable novel applications including microfluidics, flexible electronics and drug delivery. However, surprisingly liquid metals have been somewhat neglected by the wider research community. In this review, we provide a comprehensive overview of the fundamentals underlying liquid metal research, including liquid metal synthesis, surface functionalisation and liquid metal enabled chemistry. Furthermore, we discuss phenomena that warrant further investigations in relevant fields and outline how liquid metals can contribute to exciting future applications.

DNA methylation signatures of breast cancer in peripheral T-cells

BACKGROUND

Immune surveillance acts as a defense mechanism in cancer, and its disruption is involved in cancer progression. DNA methylation reflects the phenotypic identity of cells and recent data suggested that DNA methylation profiles of T cells and peripheral blood mononuclear cells (PBMC) are altered in cancer progression.

METHODS

We enrolled 19 females with stage 1 and 2, nine with stage 3 and 4 and 9 age matched healthy women. T cells were isolated from peripheral blood and extracted DNA was subjected to Illumina 450 K DNA methylation array analysis. Raw data was analyzed by BMIQ, ChAMP and ComBat followed by validation of identified genes by pyrosequencing.

RESULTS

Analysis of data revealed ~ 10,000 sites that correlated with breast cancer progression and established a list of 89 CG sites that were highly correlated (p < 0.01, r > 0.7, r < - 0.7) with breast cancer progression. The vast majority of these sites were hypomethylated and enriched in genes with functions in the immune system.

CONCLUSIONS

The study points to the possibility of using DNA methylation signatures as a noninvasive method for early detection of breast cancer and its progression which need to be tested in clinical studies.

Multifaceted Role of the Urokinase-Type Plasminogen Activator (uPA) and Its Receptor (uPAR): Diagnostic, Prognostic, and Therapeutic Applications

The plasminogen activator (PA) system is an extracellular proteolytic enzyme system associated with various physiological and pathophysiological processes. A large body of evidence support that among the various components of the PA system, urokinase-type plasminogen activator (uPA), its receptor (uPAR), and plasminogen activator inhibitor-1 and -2 (PAI-1 and PAI-2) play a major role in tumor progression and metastasis. The binding of uPA with uPAR is instrumental for the activation of plasminogen to plasmin, which in turn initiates a series of proteolytic cascade to degrade the components of the extracellular matrix, and thereby, cause tumor cell migration from the primary site of origin to a distant secondary organ. The components of the PA system show altered expression patterns in several common malignancies, which have identified them as ideal diagnostic, prognostic, and therapeutic targets to reduce cancer-associated morbidity and mortality. This review summarizes the various components of the PA system and focuses on the role of uPA-uPAR in different biological processes especially in the context of malignancy. We also discuss the current state of knowledge of uPA-uPAR-targeted diagnostic and therapeutic strategies for various malignancies.

Methyl donor S-adenosylmethionine (SAM) supplementation attenuates breast cancer growth, invasion, and metastasis in vivo; therapeutic and chemopreventive applications

DNA hypomethylation coordinately targets various signaling pathways involved in tumor growth and metastasis. At present, there are no approved therapeutic modalities that target hypomethylation. In this regard, we examined the therapeutic plausibility of using universal methyl group donor S-adenosylmethionine (SAM) to block breast cancer development, growth, and metastasis through a series of studies in vitro using two different human breast cancer cell lines (MDA-MB-231 and Hs578T) and in vivo using an MDA-MB-231 xenograft model of breast cancer. We found that SAM treatment caused a significant dose-dependent decrease in cell proliferation, invasion, migration, anchorage-independent growth and increased apoptosis in vitro. These results were recapitulated in vivo where oral administration of SAM reduced tumor volume and metastasis in green fluorescent protein (GFP)-tagged MDA-MB-231 xenograft model. Gene expression analyses validated the ability of SAM to decrease the expression of several key genes implicated in cancer progression and metastasis in both cell lines and breast tumor xenografts. SAM was found to be bioavailable in the serum of experimental animals as determined by enzyme-linked immunosorbent assay and no notable adverse side effects were seen including any change in animal behavior. The results of this study provide compelling evidence to evaluate the therapeutic potential of methylating agents like SAM in patients with breast cancer to reduce cancer-associated morbidity and mortality.

Abstract A09: Development of epigenetic-based strategies for blocking breast cancer growth, invasion, and metastasis in vitro and in vivo

DNA hypomethylation has been implicated in the coordinated targeting of various signaling pathways involved in tumor growth and metastasis. In the current study, through various in vitro and in vivo assays, we have examined the plausibility of using universal methyl donor S-adenosyl methionine (SAM) to block breast cancer development, growth, and metastasis in our xenograft and transgenic models of breast cancer. Treatment of highly invasive human triple-negative breast cancer (TNBC) cell lines MDA-MB-231 and Hs578T with SAM resulted in a significant dose-dependent decrease in cell proliferation, invasion, migration, colony formation, and increased apoptosis in vitro. Affymetrix gene expression array and real-time PCR (qPCR) validated the ability of SAM to decrease the expression of several genes implicated in cancer progression in MDA-MB-231 cells. For the in vivo studies, MDA-MB-231 cells expressing green fluorescent protein (MDA-MB-231-GFP) were inoculated into female CD-1 nude mice via mammary fat pad. From day three post tumor cell inoculation, animals were treated with SAM (0.8-1.6 mg/day) or vehicle alone as control via daily oral gavage, and tumor volume was determined at weekly intervals for 10 weeks. SAM treatment caused a significant dose-dependent decrease in tumor volume and GFP-positive metastasis to lungs, liver, and spleen in experimental animals compared to vehicle-treated controls. Analysis of RNA from primary tumors by qPCR showed the ability of SAM to cause a marked decrease in the expression of several prometastatic and EMT pathway genes. Pyrosequencing of tumoral DNA from control and experimental animals showed that SAM treatment causes a significant increase in the percentage of CpG methylation at the promoter region of several cancer-related genes which were seen to be downregulated in the qPCR assay.

We next determined the effect of SAM in MMTV-PyMT transgenic mouse model of breast cancer where SAM treatment resulted in a significant delay in the development of mammary tumors and decreased tumor growth in experimental animals as compared to vehicle-treated controls. SAM was found to bioavailable in the serum of experimental animals as determined by mass spectrometry and no notable adverse side effects were seen, including any change in animal behavior.

Results from these studies provide compelling evidence for the therapeutic potential of SAM in breast cancer to provide the rationale for initiating clinical trials with SAM in patients with breast and other common cancers as monotherapy or in combination setting with current therapeutic agents to reduce cancer-associated morbidity and mortality.

Note: This abstract was not presented at the conference.

Citation Format: Niaz Mahmood, David Cheishvili, Ani Arakelian, William J. Muller, Imrana Tanveer, Haseeb Khan, Moshe Szyf, Shafaat A. Rabbani. Development of epigenetic-based strategies for blocking breast cancer growth, invasion, and metastasis in vitro and in vivo [abstract]. In: Proceedings of the AACR International Conference held in cooperation with the Latin American Cooperative Oncology Group (LACOG) on Translational Cancer Medicine; May 4-6, 2017; São Paulo, Brazil. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(1_Suppl):Abstract nr A09.

Evolution of 2D tin oxides on the surface of molten tin

The exfoliation of two dimensional (2D) oxides, established on the surface of specific liquid metals, has recently been introduced.

Abstract 4346: S-Adenosyl methionine (SAM) blocks breast cancer growth, invasion and metastasis in vitro and in vivo

DNA hypomethylation has been implicated in the coordinated targeting of various signaling pathways involved in tumor growth and metastasis. In the current study through various in vitro and in vivo assays, we have examined the plausibility of using universal methyl donar S-adenosyl methionine (SAM) for its ability to block breast cancer development, growth and metastasis in our xenograft and transgenic models of breast cancer. Treatment of highly invasive human triple negative breast cancer (TNBC) cell lines MDA-MB-231 and Hs578T with SAM resulted in a significant dose-dependent decrease in cell proliferation, invasion, migration, colony formation and increased apoptosis in vitro. Affymetrix gene expression array and real time PCR (qPCR) validated showed the ability of SAM to decrease the expression several genes implicated in cancer progression in MDA-MB-231 cells. For the in vivo studies, MDA-MB-231 cells expressing green fluorescent protein (MDA-MB-231-GFP) were inoculated into female CD-1 nude mice via mammary fat pad. From day three post tumor cell inoculation, animals were treated with SAM (0.8-1.6 mg/day) or vehicle alone as control via daily oral gavage and tumor volume was determined at weekly intervals for 10 weeks. SAM treatment caused a significant dose dependent decrease in tumor volume and GFP positive metastasis to lungs, liver and spleen in experimental animals compared to vehicle-treated controls. Analysis of RNA from primary tumors by qPCR showed the ability of SAM to cause a marked decrease in the expression of several pro-metastatic and EMT pathway genes. Pyrosequencing of tumoral DNA from control and experimental animals showed that SAM treatment causes a significant increase in the percentage of CpG methylation at the promoter region of several cancer-related genes which were seen to be downregulated in the qPCR assay. We next determined the effect of SAM in MMTV-PyMT transgenic mouse model of breast cancer where SAM treatment resulted in a significant delay in the development of mammary tumors and decreased tumor growth in experimental animals as compared to vehicle treated controls. SAM was found to bioavailable in the serum of experimental animals as determined by mass spectrometry and no notable adverse side effects were seen including any change in animal behavior. Results from these studies provide compelling evidence for the therapeutic potential of SAM in breast cancer to provide the rationale for initiating clinical trials with SAM in patients with breast and other common cancers as monotherapy or in combination setting with current therapeutic agents to reduce cancer associated morbidity and mortality.

Citation Format: Niaz Mahmood, David Cheishvili, Ani Arakelian, William J. Muller, Moshe Szyf, Shafaat A. Rabbani. S-Adenosyl methionine (SAM) blocks breast cancer growth, invasion and metastasis in vitro and in vivo [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4346. doi:10.1158/1538-7445.AM2017-4346

Gastric specimens for diagnosing tuberculosis in adults unable to expectorate in Rawalpindi, Pakistan

Setting: Adult pulmonary tuberculosis (TB) patients unable to expectorate quality sputum represent a diagnostic challenge. A private hospital in Pakistan routinely performs gastric aspiration in adults with difficulties expectorating. Objective: To assess the usefulness of gastric specimens (GS) in diagnosing pulmonary TB (PTB) and drug-resistant TB in adult presumptive TB patients unable to expectorate, and to compare the diagnostic yield and sensitivity of smear, culture and the Xpert^® MTB/RIF assay. Design: This was a comparative cross-sectional study based on retrospective record review. Results: Of 900, 885 and 877 GS tested by smear, Xpert and culture, respectively, interpretable results were obtained for respectively 900 (100%), 859 (97.1%) and 754 (86.0%), with a diagnostic yield of respectively 23.6%, 30.3% and 24.9%. The yield was significantly higher for Xpert in previously treated patients. There were 313 patients with definite TB, defined as positive on Xpert and/or culture. The 82.8% sensitivity of Xpert was significantly higher than that of smear (61.0%) and culture (67.8%). Conclusion: GS obtained by aspiration under routine programme conditions is useful for detecting TB and drug-resistant TB in adult patients unable to expectorate. Xpert, with its rapid testing, high proportion of interpretable results and better sensitivity, can substantially improve the diagnosis of bacteriologically confirmed TB and rifampicin resistance.

Comparative genomics of two jute species and insight into fibre biogenesis

Jute (Corchorus sp.) is one of the most important sources of natural fibre, covering ∼80% of global bast fibre production¹. Only Corchorus olitorius and Corchorus capsularis are commercially cultivated, though there are more than 100 Corchorus species² in the Malvaceae family. Here we describe high-quality draft genomes of these two species and their comparisons at the functional genomics level to support tailor-designed breeding. The assemblies cover 91.6% and 82.2% of the estimated genome sizes for C. olitorius and C. capsularis, respectively. In total, 37,031 C. olitorius and 30,096 C. capsularis genes are identified, and most of the genes are validated by cDNA and RNA-seq data. Analyses of clustered gene families and gene collinearity show that jute underwent shared whole-genome duplication ∼18.66 million years (Myr) ago prior to speciation. RNA expression analysis from isolated fibre cells reveals the key regulatory and structural genes involved in fibre formation. This work expands our understanding of the molecular basis of fibre formation laying the foundation for the genetic improvement of jute.

Antibiotic susceptibility in Streptococcus pneumoniae, Haemophilus influenzae and Streptococcus pyogenes in Pakistan: a review of results from the Survey of Antibiotic Resistance (SOAR) 2002-15

OBJECTIVES

To investigate changes in the antibiotic susceptibility of Streptococcus pneumoniae, Haemophilus influenzae and Streptococcus pyogenes from the Survey of Antibiotic Resistance (SOAR) in community-acquired respiratory tract infections (CA-RTIs) between 2002 and 2015 in Pakistan.

METHODS

This is a review based on previously published studies from 2002-03, 2004-06 and 2007-09 and also new data from 2014-15. Susceptibility was determined by Etest(®) or disc diffusion according to CLSI and pharmacokinetic/pharmacodynamic (PK/PD) breakpoints.

RESULTS

A total of 706 isolates from CA-RTIs comprising 381 S. pneumoniae, 230 H. influenzae and 95 S. pyogenes were collected between 2002 and 2015 and tested against a range of antibiotics. Antibiotic resistance in S. pneumoniae rose steeply from 2002 to 2009, with isolates non-susceptible to penicillin and macrolides increasing from 10% to 34.1% and from 13%-14% to 29.7%, respectively. Susceptibility to amoxicillin/clavulanic acid (and by inference amoxicillin) remained between 99.4% and 100% from 2002 to 2015. Over the years, the prevalence of susceptibility to cefuroxime was 98%-100% among S. pneumoniae. Resistance in S. pneumoniae to some older antibiotics between 2007 and 2009 was high (86.8% for trimethoprim/sulfamethoxazole and 57.2% for tetracycline). Between 2002 and 2015, ampicillin resistance (β-lactamase-positive strains) among H. influenzae has remained low (between 2.6% and 3.2%) and almost unchanged over the years (H. influenzae was not tested during 2004-06). For S. pyogenes isolates, macrolide resistance reached 22%; however, susceptibility to penicillin, amoxicillin/clavulanic acid and cefuroxime remained stable at 100%.

CONCLUSIONS

In S. pneumoniae from Pakistan, there has been a clear reduction in susceptibility to key antibiotics since 2002, but not to amoxicillin/clavulanic acid (amoxicillin) or cefuroxime. However, susceptibility in H. influenzae has remained stable. Local antibiotic susceptibility/resistance data are essential to support informed prescribing for CA-RTIs and other infections.

Constituents of Cuscuto Reflexa are anti-HIV Agents

Crude water extracts of Cuscuta reflexa exhibited anti-HIV activity. Fractionation of the crude extract led to the isolation of nine pure compounds with closely related structures, showing interesting structure activity relationships. 3,5,7,4′-Tetrahydroxyflavanone (aromadendrin) inhibited infection by binding to V3 loop of gp 120 and inhibiting its interaction with CD4, whereas 3,5,7,3′,4′-pentahydroxyflavanone (taxifolin), with an extra OH group in the 3′ position in ring B was less specific and exhibited less selectivity in cell cultures. In general, flavanones containing an extra OH group in the 3′ position (taxifolin, taxifolin-7-O-β-D-glucopyranoside and coccinoside B) were less specific and inhibited viral protease, reverse transcriptase, CD4 /gp120 interaction in vitro and bound to non specific proteins. Other compounds isolated from C reflexa were derivatives of quinic acids; 3,4-O-dicaffeoylquinic acid was more active than 3-O-caffeoyl quinic acid. The anti-HIV activity of crude extract may be the result of combinatory effects with compounds of different modes of action.

Alkyl Hydrogen Phosphonate Derivatives of the anti-HIV Agent AZT may be Less Toxic than the Parent Nucleoside Analogue

Novel alkyl hydrogen phosphonate derivatives of the anti-HIV nucleoside analogue AZT have been prepared by phosphorochloridite chemistry. These materials are designed to act as labile membrane-soluble prodrugs of the bioactive free nucleotides. In vitro evaluation has revealed the compounds to have a pronounced and selective antiviral action. Short-chain (C1-C7) alkyl derivatives are more potent than the parent hydrogen phosphonate, whilst one long-chain (C18) compound is less active. In an assay that demonstrates the toxicity of the parent drug AZT, the alkyl H-phosphonates appear to be less cytotoxic, whilst retaining full antiviral activity. Lastly, the compounds are all poorly active in a cell line (JM) that is poorly responsive to AZT, indicating that they act as depot forms of the nucleoside rather than of the free nucleotide.

Inhibitory Effects of Novel Mannose-Binding Lectins on HIV-Infectivity and Syncytium Formation

Several new lectins were isolated and characterized with respect to their composition and sugar binding specificities and their ability to prevent HIV-1 infection. Twelve of the 13 mannose-specific lectins were inhibitory to varying degrees. The most effective were Machaerium biovulatum agglutinin (MBA) and M. lunatus agglutinin (MLA) which at 0.4 μg ml−1 prevented the cytopathic effect of the virus. Lower protection was obtained with Bowringia mildbraedii agglutinin (BMA), Galanthus nivalis agglutinin (GNA), Lablab niger agglutinin (LNA) and Dolichos lablab agglutinin (DLA). All these lectins are more protective than Con A while MBA is nearly 10 times more potent than any previously reported lectin. In each case the selective antiviral activity appears to be due to interaction with virus and not with some component on the target cell. MBA and GNA immobilized on Sepharose specifically bound gp120.

Studies of binding to glycoproteins confirmed the recognition of particular isomers of high mannose oligosaccharides Man9 to Man7GlcNAc2 by BMA and of Man5GlcNAc2 glycopeptides by GNA. By contrast, MBA did not bind oligomannosidic structures but did interact with ovalbumin, a glycoprotein rich in hybrid-type glycans.

Inhibition of the Production of HIV-1 from Chronically Infected H9 Cells by Metal Compounds and Their Complexes with L-cysteine or N-acetyl-L-cysteine

A number of metal compounds and their complexes with cysteine and N-acetyl-cysteine (NAC) were tested for their ability to inhibit HIV replication in vitro, specifically in chronically infected H9 cells (which produce virus continuously). Out of seven metal compounds tested, only bismuth nitrate and bismuth sodium tartrate inhibited virus production in chronically infected H9 cells. The complexes made with metals and cysteine or NAC had slightly improved selective indices.

Synthesis and Evaluation of Some Symmetrical Phosphate Dimer Derivatives of 3′-Modified Nucleosides as Potential anti-HIV Agents

Novel symmetrical nucIeotide-(5′,5′)-dimers of 3′-O-acetylthymidine, 3′-O-methylthymidine, 3′-O-ethylthymidine, 3′-O-n-propylthymidine and 3′-azido-3′-deoxythymidine (AZT) were synthesized as membrane soluble pro-drugs. These were prepared using phosphorodichloridate chemistry and were characterised by spectroscopic and analytical data. In-vitro evaluation of the derivatives in cells acutely infected with the human immunodeficiency virus (HIV-1) demonstrated a range of activities. These derivatives were generally found to display poor inhibition of HIV proliferation. Derivatives containing AZT moieties were found to be potent, but such compounds were less active than the parent nucleoside. The data indicated that the AZT-containing compounds act primarily via the release of the free nucleoside. However, in some cases, the dimers of certain inactive nucleoside analogues were found to be active. In these cases, release of the nucleoside alone cannot account for the activity.

Inhibition of HIV Infection by Caffeoylquinic Acid Derivatives

The caffeoylquinic acids 3,4,5-tri-O-caffeoylquinic acid (1) and 4,5-di-O-caffeoylquinic acid (2), as well as caffeic acid (4) and synapoic acid (5) were isolated from the plant Securidaka longipedunculata (polygalaceae). 1 exhibited a greater selective inhibition of HIV replication than 2 which had an anti-HIV activity similar to that of 3,4,5-tri-O-galloylquinic acid (3), isolated from Guiera senegalensis (combretaceae); 4 and 5 were ineffective and the structurally related compound rosmarinic acid (6) had only slight anti-HIV activity. Studies of the actions of these compounds suggest that inhibition of the viral reverse transcriptase in vitro is non-specific and that they act by specific binding to gp120 which prevents its interaction with CD4 on T-lymphocytes and thus inactivates virus infectivity.

Antiviral Activity of 2-Hydroxy Fatty Acids

Following an earlier demonstration of an antiviral effect against varicella-zoster virus (VZV, human herpesvirus 3) using 2-hydroxymyristic acid (2-hydroxytetradecanoic acid; 2-HM), an inhibitor of protein myristoylation, both 2-HM and 2-hydroxypalmitic acid (2-hydroxyhexadecanoic acid; 2-HP) have been tested against a range of viruses. Although both compounds inhibit the replication of varicella-zoster virus (VZV; human herpesvirus 3) they do not inhibit the replication of closely related herpesviruses. They do, however, inhibit the replication of both poliovirus (a member of the Picornaviridae) and the human immunodeficiency virus type 1 (HIV-1; a member of the Retroviridae). Neither compound is toxic to adherent cells by dye uptake assay, although limited toxicity is apparent to non-adherent cell lines at high concentrations. The mechanisms underlying these effects are discussed. A diminished effect of 2-hydroxymyristic acid when the compound is dissolved in dimethyl sulphoxide (DMSO) rather than ethanol is reported, and the implications for the use of DMSO as a ‘universal solvent’ for compound screening noted. Finally, it is suggested that targeting of ‘virus-essential’ cellular functions may provide an alternative route for inhibiting viral replication.

Antiviral Activity of N4-Aminocytidine Derivatives Related to AZT

A number of N4-hydroxy and N4-amino derivatives of 3′-azido-2′,3′-dideoxy-5-methylcytidine have been synthesized and tested for antiviral activity against HIV-1 and HIV-2. The N4-phenylamino and N4-dimethylamino analogues show marked anti-HIV activity which is comparable to that of AZT.

Screening of Compounds for Activity against HIV: A Collaborative Study

The collaborative study was undertaken to examine the sensitivity of a range of tests used in assessing the antiviral activities of compounds against human immunodeficiency virus (HIV). A panel of 20 compounds with diverse antiviral activities against HIV were tested under code at three antiviral testing centres supported by the Medical Research Council's AIDS Directed Programme and at the European Community Centralised Facility (ECCF) for New Antiviral Compounds against AIDS in Belgium. Compounds known to have major anti-HIV activity ranked high in all assays, with the exception of the glucosidase inhibitors and certain nucleoside analogues. Results of two assays based on MT4 cells (centre IV) showed a high degree of similarity, despite the use of distinct HIV-1 (HTLV-IIIB) and HIV-2 (ROD) viruses. Considerable similarity was also observed between the assays based on HTLV-IIIRF in C8166 cells (centres I and II). Other assays performed at centre II and at centre III had enhanced sensitivity for glycosidase inhibitors. The differences in anti-HIV activity that were observed may be attributable to specific properties of the cell lines used and particular testing methodologies. The use of more than one type of assay is advisable in order not to miss compounds with low to moderate activity against HIV.

The Enzymatic Synthesis and Anti-HIV Activity of 9-β-D-2-Deoxy and 9-β-D-2′,3′-Dideoxynucleossdes of 2-Aminopurine

The 9-β-D-2′-deoxy and 9-β-D-2′,3′-dideoxyribonucleosides of 2-aminopurine have been prepared using crude nucleoside N-deoxyribosyltransferases (E.C. 2.4.2.6) from Lactobacillus leichmannii in the presence of 10% ethylene glycol to inhibit degradation of the product nucleosides. The 2′,3′-dideoxynucleoside of 2-aminopurine is an inhibitor of the replication of HIV-1, HIV-2, and SIV with EC50 values in the range 8–100 μM depending on the cell line used and has low in vitro toxicity at its effective concentrations.

Antiviral Activity of Bicyclic Pyrimidine Nucleosides

A number of pyrimidine nucleosides, which may show two hydrogen bonding modes, have been prepared and tested for antiviral activity against a series of viruses. Whilst none of the compounds described showed significant activity against human immunodeficiency virus (HIV), the bicyclic 2′-deoxynucleoside, [2], derived from the base 6H,8H-3,4-dihydropyrimido[4,5-c][1,2]oxazin-7-one, was shown to inhibit herpes simplex virus type 1 (HSV-1) at similar concentrations as BVDU1 and ACV. Compounds 13, 6-(2-deoxyribofuranosyl)-6H,8H-2-methyl-3,4-dihydropyrimido[4,5-c][1,2]oxazin-7-one, and 14, N4-hydroxy-5-(2-chloroethyl)-2′-deoxyuridine, were as active as ACV against varicella-zoster virus (VZV).

Increased stability of heterogeneous ribonucleoproteins by a deacetylase inhibitor

Splicing factors are often influenced by various signaling pathways, contributing to the dynamic changes of protein isoforms in cells. Heterogeneous ribonucleoproteins (hnRNPs) regulate many steps of RNA metabolism including pre-mRNA splicing but their control by cell signaling particularly through acetylation and ubiquitination pathways remains largely unknown. Here we show that TSA, a deacetylase inhibitor, reduced the ratio of Bcl-x splice variants Bcl-xL/xS in MDA-MB-231 breast cancer cells. This TSA effect was independent of TGFβ1; however, only in the presence of TGFβ1 was TSA able to change the splicing regulators hnRNP F/H by slightly reducing their mRNA transcripts but strongly preventing protein degradation. The latter was also efficiently prevented by lactacystin, a proteasome inhibitor, suggesting their protein stability control by both acetylation and ubiquitination pathways. Three lysines K87, K98 and K224 of hnRNP F are potential targets of the mutually exclusive acetylation or ubiquitination (K(Ac/Ub)) in the protein modification database PhosphoSitePlus. Mutating each of them but not a control non-K(Ac/Ub) (K68) specifically abolished the TSA enhancement of protein stability. Moreover, mutating K98 (K98R) and K224 (K224R) also abolished the TSA regulation of alternative splicing of a Bcl-x mini-gene. Furthermore, about 86% (30 of 35) of the multi-functional hnRNP proteins in the database contain lysines that are potential sites for acetylation/ubiquitination. We demonstrate that the degradation of three of them (A1, I and L) are also prevented by TSA. Thus, the deacetylase inhibitor TSA enhances hnRNP F stability through the K(Ac/Ub) lysines, with some of them essential for its regulation of alternative splicing. Such a regulation of protein stability is perhaps common for a group of hnRNPs and RNA metabolism.

Food Processing and Maillard Reaction Products: Effect on Human Health and Nutrition

Maillard reaction produces flavour and aroma during cooking process; and it is used almost everywhere from the baking industry to our day to day life to make food tasty. It is often called nonenzymatic browning reaction since it takes place in the absence of enzyme. When foods are being processed or cooked at high temperature, chemical reaction between amino acids and reducing sugars leads to the formation of Maillard reaction products (MRPs). Depending on the way the food is being processed, both beneficial and toxic MRPs can be produced. Therefore, there is a need to understand the different types of MRPs and their positive or negative health effects. In this review we have summarized how food processing effects MRP formation in some of the very common foods.

An endogenous 'non-specific' protein detected by a His-tag antibody is human transcription regulator YY1

Histidine-tags have been used for a wide variety of experiments including protein purification, Western blots, immunoprecipitation and immunohistochemistry. In our previous studies, we have repeatedly detected a ‘non-specific’ endogenous protein of about 60 kD in Western blots of protein lysates from HEK293T or HeLa cells using the anti-His-tag antibody (His-probe (H3), catalogue #, SC-8036, Santa Cruz Biotech. Co.) (Yu et al., J. Biol. Chem. 284 (2009) 1505–1513). Here we have immunoprecipitated the protein from HeLa nuclear extracts using the anti-His-tag antibody, excised the 60 kD band and subjected it to LC–MS/MS (Fig. 1). The deduced sequences of two peptides of the protein match the human transcriptional regulator YY1 (Yin and Yang 1, UniProt ID, P25490, Fig. 2), which contains 11 histidine residues in a stretch (from amino acid 70 to 80) at its NH₂-terminal region without known functions (Lee et al., Nucleic Acids Res. 23 (1995) 925–931; Bushmeyer et al., J. Biol. Chem. 270 (1995) 30213–30220). Since genes encoding other Histidine-repeat proteins also exist in the genome (Salichs et al., PLoS Genet. 5 (2009) e1000397), it is possible that YY1 might not be the only endogenous protein that could be expressed and recognized by the antibody in different sources of samples in future experiments. The presence of various endogenous histidine-repeat proteins suggests that data from experiments particularly immunostaining using His-tag antibodies need to be interpreted with caution. This might also be useful to the broader scientific community by providing an example for the interpretation of ‘non-specific’ bands in Western blots.

Evolutionarily emerged G tracts between the polypyrimidine tract and 3' AG are splicing silencers enriched in genes involved in cancer

Background

The 3′ splice site (SS) at the end of pre-mRNA introns has a consensus sequence (Y)_nNYAG for constitutive splicing of mammalian genes. Deviation from this consensus could change or interrupt the usage of the splice site leading to alternative or aberrant splicing, which could affect normal cell function or even the development of diseases. We have shown that the position “N” can be replaced by a CA-rich RNA element called CaRRE1 to regulate the alternative splicing of a group of genes.

Results

Taking it a step further, we searched the human genome for purine-rich elements between the -3 and -10 positions of the 3′ splice sites of annotated introns. This identified several thousand such 3′SS; more than a thousand of them contain at least one copy of G tract. These sites deviate significantly from the consensus of constitutive splice sites and are highly associated with alterative splicing events, particularly alternative 3′ splice and intron retention. We show by mutagenesis analysis and RNA interference that the G tracts are splicing silencers and a group of the associated exons are controlled by the G tract binding proteins hnRNP H/F. Species comparison of a group of the 3′SS among vertebrates suggests that most (~87%) of the G tracts emerged in ancestors of mammals during evolution. Moreover, the host genes are most significantly associated with cancer.

Conclusion

We call these elements together with CaRRE1 regulatory RNA elements between the Py and 3′AG (REPA). The emergence of REPA in this highly constrained region indicates that this location has been remarkably permissive for the emergence of de novo regulatory RNA elements, even purine-rich motifs, in a large group of mammalian genes during evolution. This evolutionary change controls alternative splicing, likely to diversify proteomes for particular cellular functions.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1143) contains supplementary material, which is available to authorized users.

Emerging Roles of Branched-Chain Amino Acid Supplementation in Human Diseases

The branched-chain amino acids (BCAAs), namely, valine, leucine, and isoleucine, are indispensable amino acids required for body protein synthesis. Unlike other amino acids, the BCAAs are primarily catabolised in the extrahepatic tissues. The BCAAs play role in regulation of protein synthesis and turnover as well as maintenance of the body glutamate-glutamine level. In strenuous and traumatic conditions, the BCAAs are oxidized which limits their availability in tissues. Such condition affects the body glutamate-glutamine pool and protein synthesis mechanisms. Thus BCCA supplementation is emerging as a nutritional strategy for treating many diseases. Many studies have found that BCAA administration is able to improve the health status of the patients suffering from different diseases even though there are conditions where they do not exert any effect. There are also some reports where elevated BCAAs have been shown to be associated with the pathogenesis of diseases. In this review, we have discussed the implication of BCAA supplementation in different pathological conditions and their relevant outcomes.

IL-10 gene promoter and intron polymorphisms and changes in IL-10 secretion in women with idiopathic recurrent miscarriage

STUDY QUESTION

Is recurrent pregnancy loss (RPL) associated with polymorphisms in the promoter and intron regions of the interleukin-10 (IL-10) gene?

SUMMARY ANSWER

IL-10 rs1518111 was found to be associated with RPL but the commonly studied promoter variants rs1800872, rs1800871 and 1800896 were not.

WHAT IS KNOWN ALREADY

Reduced expression of IL-10 is implicated in RPL, due to defective maternal immune tolerance (causing early miscarriages) or placental vascular insufficiency (causing late losses). IL-10 production is in part inherited, and IL-10 gene variants associated with reduced IL-10 expression have been analyzed for their association with RPL, often with inconclusive results.

STUDY DESIGN, SIZE, DURATION

A retrospective case-control study was performed between January 2011 and April 2012. The subjects comprised 296 RPL cases and 305 control women.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Genotyping of the IL-10 intron (rs1878672, rs3024492, rs1554286, rs1518111, rs3024491, rs3024490) and promoter (rs1800872, rs1800871, rs1800896) variants was done by real-time PCR, with defined clusters.

MAIN RESULTS AND THE ROLE OF CHANCE

A higher minor allele frequency (MAF) of rs1518111 (P = 0.03) was in seen RPL cases; but the MAFs of the remaining SNPs were comparable between cases and controls. Setting the homozygous major allele genotype (1/1) as the reference, significantly higher frequencies of heterozygous rs1554286 and rs1800872, and homozygous rs1800896 genotype carriers, and a reduced frequency of homozygous rs1518111 genotype carriers, were seen in RPL cases, while the distribution of the remaining genotypes were comparable between cases and controls. Serum IL-10 levels were significantly reduced in RPL cases compared with control women (P = 0.002), and this correlated with rs1518111 and rs1800871 genotypes in both groups, and with the rs1800872 genotype among control women. A nine-locus (rs1878672, rs3024492, rs1554286, rs1518111, rs3024491, rs3024490, rs1800872, rs1800871 and rs1800896) haploview analysis demonstrated an increased frequency of haplotype 112112121 in RPL cases, thus conferring a disease susceptibility nature to this haplotype.

LIMITATIONS, REASONS FOR CAUTION

The main limitation of this study was that it was limited to Bahraini Arabs, thereby necessitating parallel studies of other ethnic groups. Another limitation is the study design, which prompts speculation on whether it is a cause-effect relationship.

WIDER IMPLICATIONS OF THE FINDINGS

While the lack of association of the various IL-10 promoter variants with RPL was in agreement with reports from varied ethnic groups, this is the first study to confirm the association between IL-10 rs151811 intronic variant and RPL.

STUDY FUNDING/COMPETING INTEREST(S)

The study was funded by grants from the Arabian Gulf University Research Fund. None of the authors report any competing interests.

Xyloglucan endotransglycosylase/hydrolase genes from a susceptible and resistant jute species show opposite expression pattern following Macrophomina phaseolina infection

Two of the most widely and intensively cultivated jute species, Corchorus capsularis and Corchorus olitorius, suffer severely from a stem rot disease caused by the fungus Macrophomina phaseolina. Wild jute species, C. trilocularis, shows resistance to this pathogenic fungus. In this study, the technique of differential display was applied to identify genes which are differentially expressed, under both infected and un-infected conditions, between C. trilocularis and C. olitorius var O-72. Two xyloglucan endotransglycosylase/hydrolase (XTH) genes designated CoXTH1 (from Corchorus olitorius) and CtXTH1 (from C.trilocularis) were identified from each of the two species which show different expression patterns upon fungal infection. A steady rise in the expression of CtXTH1 in response to infection was observed by quantitative real time PCR whereas the expression of CoXTH1 was found to be downregulated. Full length sequences of these two genes were determined using primer based gene walking and RACE PCR. This study confirms the involvement of XTH in molecular interactions between M. phaseolina and jute. However, it remains to be explored whether XTH is an essential component of the signaling pathway involved in plant-fungal interaction.

Abstract P6-07-13: Local relapse and survival

Aim: Local recurrence may precede distant relapse and death. Many factors which predict local recurrence also predict death. Few studies have investigated the contribution of local recurrence to mortality independent of prior prognostic factors such as nodal status. We wished to estimate the extent to which overall survival is affected specifically by local recurrence.

Methods: 114 of of 2945 patients aged 19 to 94 years (mean 58.3) who had either mastectomy or breast conservation for breast cancer between 1991 and 2011 subsequently suffered an ipsilateral local recurrence. We matched, with one exception (due to extreme young age), each patient who had a local recurrence with 2 controls matched for calendar year of presentation, age, nodal status, grade, and tumour size. A Cox regression analysis of survival from the first therapeutic operation was done on the case matched subset with local recurrence coded dichotomously and age coded continuously as the absolute deviation from the population mean (as both young and old age affect survival adversely) as predictors. To confirm independence of the effect of local recurrence on the hazard of death a further Cox regression analysis of survival as above was done for the whole series with local recurrence, Grade 3, &gt;3 nodes involved, tumour diameter &gt;40mm, coded dichotomously, and age coded as above as independent variables.

Results: The results of the analyses are given in the table below.