New-Onset Diabetes Mellitus After Transplantation in a Cynomolgus Macaque (Macaca fasicularis)

A 5.5-y-old intact male cynomolgus macaque (Macaca fasicularis) presented with inappetence and weight loss 57 d after heterotopic heart and thymus transplantation while receiving an immunosuppressant regimen consisting of tacrolimus, mycophenolate mofetil, and methylprednisolone to prevent graft rejection. A serum chemistry panel, a glycated hemoglobin test, and urinalysis performed at presentation revealed elevated blood glucose and glycated hemoglobin (HbA1c) levels (727 mg/dL and 10.1%, respectively), glucosuria, and ketonuria. Diabetes mellitus was diagnosed, and insulin therapy was initiated immediately. The macaque was weaned off the immunosuppressive therapy as his clinical condition improved and stabilized. Approximately 74 d after discontinuation of the immunosuppressants, the blood glucose normalized, and the insulin therapy was stopped. The animal''s blood glucose and HbA1c values have remained within normal limits since this time. We suspect that our macaque experienced new-onset diabetes mellitus after transplantation, a condition that is commonly observed in human transplant patients but not well described in NHP. To our knowledge, this report represents the first documented case of new-onset diabetes mellitus after transplantation in a cynomolgus macaque.Abbreviations: NODAT, new-onset diabetes mellitus after transplantationNew-onset diabetes mellitus after transplantation (NODAT, formerly known as posttransplantation diabetes mellitus) is an important consequence of solid-organ transplantation in humans.^{7-10,15,17,19,21,25-28,31,33,34,37,38,42} A variety of risk factors have been identified including increased age, sex (male prevalence), elevated pretransplant fasting plasma glucose levels, and immunosuppressive therapy.^{7-10,15,17,19,21,25-28,31,33,34,37,38,42} The relationship between calcineurin inhibitors, such as tacrolimus and cyclosporin, and the development of NODAT is widely recognized in human medicine.^{7-10,15,17,19,21,25-28,31,33,34,37,38,42} Cynomolgus macaques (Macaca fasicularis) are a commonly used NHP model in organ transplantation research. Cases of natural and induced diabetes of cynomolgus monkeys have been described in the literature;^14,43,45 however, NODAT in a macaque model of solid-organ transplantation has not been reported previously to our knowledge.     

Characterization of the Possible Roles for B Class MADS Box Genes in Regulation of Perianth Formation in Orchid

To investigate sepal/petal/lip formation in Oncidium Gower Ramsey, three paleoAPETALA3 genes, O. Gower Ramsey MADS box gene5 (OMADS5; clade 1), OMADS3 (clade 2), and OMADS9 (clade 3), and one PISTILLATA gene, OMADS8, were characterized. The OMADS8 and OMADS3 mRNAs were expressed in all four floral organs as well as in vegetative leaves. The OMADS9 mRNA was only strongly detected in petals and lips. The mRNA for OMADS5 was only strongly detected in sepals and petals and was significantly down-regulated in lip-like petals and lip-like sepals of peloric mutant flowers. This result revealed a possible negative role for OMADS5 in regulating lip formation. Yeast two-hybrid analysis indicated that OMADS5 formed homodimers and heterodimers with OMADS3 and OMADS9. OMADS8 only formed heterodimers with OMADS3, whereas OMADS3 and OMADS9 formed homodimers and heterodimers with each other. We proposed that sepal/petal/lip formation needs the presence of OMADS3/8 and/or OMADS9. The determination of the final organ identity for the sepal/petal/lip likely depended on the presence or absence of OMADS5. The presence of OMADS5 caused short sepal/petal formation. When OMADS5 was absent, cells could proliferate, resulting in the possible formation of large lips and the conversion of the sepal/petal into lips in peloric mutants. Further analysis indicated that only ectopic expression of OMADS8 but not OMADS5/9 caused the conversion of the sepal into an expanded petal-like structure in transgenic Arabidopsis (Arabidopsis thaliana) plants.The ABCDE model predicts the formation of any flower organ by the interaction of five classes of homeotic genes in plants (Yanofsky et al., 1990; Jack et al., 1992; Mandel et al., 1992; Goto and Meyerowitz, 1994; Jofuku et al., 1994; Pelaz et al., 2000, 2001; Theißen and Saedler, 2001; Pinyopich et al., 2003; Ditta et al., 2004; Jack, 2004). The A class genes control sepal formation. The A, B, and E class genes work together to regulate petal formation. The B, C, and E class genes control stamen formation. The C and E class genes work to regulate carpel formation, whereas the D class gene is involved in ovule development. MADS box genes seem to have a central role in flower development, because most ABCDE genes encode MADS box proteins (Coen and Meyerowitz, 1991; Weigel and Meyerowitz, 1994; Purugganan et al., 1995; Rounsley et al., 1995; Theißen and Saedler, 1995; Theißen et al., 2000; Theißen, 2001).The function of B group genes, such as APETALA3 (AP3) and PISTILLATA (PI), has been thought to have a major role in specifying petal and stamen development (Jack et al., 1992; Goto and Meyerowitz, 1994; Krizek and Meyerowitz, 1996; Kramer et al., 1998; Hernandez-Hernandez et al., 2007; Kanno et al., 2007; Whipple et al., 2007; Irish, 2009). In Arabidopsis (Arabidopsis thaliana), mutation in AP3 or PI caused identical phenotypes of second whorl petal conversion into a sepal structure and third flower whorl stamen into a carpel structure (Bowman et al., 1989; Jack et al., 1992; Goto and Meyerowitz, 1994). Similar homeotic conversions for petal and stamen were observed in the mutants of the AP3 and PI orthologs from a number of core eudicots such as Antirrhinum majus, Petunia hybrida, Gerbera hybrida, Solanum lycopersicum, and Nicotiana benthamiana (Sommer et al., 1990; Tröbner et al., 1992; Angenent et al., 1993; van der Krol et al., 1993; Yu et al., 1999; Liu et al., 2004; Vandenbussche et al., 2004; de Martino et al., 2006), from basal eudicot species such as Papaver somniferum and Aquilegia vulgaris (Drea et al., 2007; Kramer et al., 2007), as well as from monocot species such as Zea mays and Oryza sativa (Ambrose et al., 2000; Nagasawa et al., 2003; Prasad and Vijayraghavan, 2003; Yadav et al., 2007; Yao et al., 2008). This indicated that the function of the B class genes AP3 and PI is highly conserved during evolution.It has been thought that B group genes may have arisen from an ancestral gene through multiple gene duplication events (Doyle, 1994; Theißen et al., 1996, 2000; Purugganan, 1997; Kramer et al., 1998; Kramer and Irish, 1999; Lamb and Irish, 2003; Kim et al., 2004; Stellari et al., 2004; Zahn et al., 2005; Hernandez-Hernandez et al., 2007). In the gymnosperms, there was a single putative B class lineage that duplicated to generate the paleoAP3 and PI lineages in angiosperms (Kramer et al., 1998; Theißen et al., 2000; Irish, 2009). The paleoAP3 lineage is composed of AP3 orthologs identified in lower eudicots, magnolid dicots, and monocots (Kramer et al., 1998). Genes in this lineage contain the conserved paleoAP3- and PI-derived motifs in the C-terminal end of the proteins, which have been thought to be characteristics of the B class ancestral gene (Kramer et al., 1998; Tzeng and Yang, 2001; Hsu and Yang, 2002). The PI lineage is composed of PI orthologs that contain a highly conserved PI motif identified in most plant species (Kramer et al., 1998). Subsequently, there was a second duplication at the base of the core eudicots that produced the euAP3 and TM6 lineages, which have been subject to substantial sequence changes in eudicots during evolution (Kramer et al., 1998; Kramer and Irish, 1999). The paleoAP3 motif in the C-terminal end of the proteins was retained in the TM6 lineage and replaced by a conserved euAP3 motif in the euAP3 lineage of most eudicot species (Kramer et al., 1998). In addition, many lineage-specific duplications for paleoAP3 lineage have occurred in plants such as orchids (Hsu and Yang, 2002; Tsai et al., 2004; Kim et al., 2007; Mondragón-Palomino and Theißen, 2008, 2009; Mondragón-Palomino et al., 2009), Ranunculaceae, and Ranunculales (Kramer et al., 2003; Di Stilio et al., 2005; Shan et al., 2006; Kramer, 2009).Unlike the A or C class MADS box proteins, which form homodimers that regulate flower development, the ability of B class proteins to form homodimers has only been reported in gymnosperms and in the paleoAP3 and PI lineages of some monocots. For example, LMADS1 of the lily Lilium longiflorum (Tzeng and Yang, 2001), OMADS3 of the orchid Oncidium Gower Ramsey (Hsu and Yang, 2002), and PeMADS4 of the orchid Phalaenopsis equestris (Tsai et al., 2004) in the paleoAP3 lineage, LRGLOA and LRGLOB of the lily Lilium regale (Winter et al., 2002), TGGLO of the tulip Tulipa gesneriana (Kanno et al., 2003), and PeMADS6 of the orchid P. equestris (Tsai et al., 2005) in the PI lineage, and GGM2 of the gymnosperm Gnetum gnemon (Winter et al., 1999) were able to form homodimers that regulate flower development. Proteins in the euAP3 lineage and in most paleoAP3 lineages were not able to form homodimers and had to interact with PI to form heterodimers in order to regulate petal and stamen development in various plant species (Schwarz-Sommer et al., 1992; Tröbner et al., 1992; Riechmann et al., 1996; Moon et al., 1999; Winter et al., 2002; Kanno et al., 2003; Vandenbussche et al., 2004; Yao et al., 2008). In addition to forming dimers, AP3 and PI were able to interact with other MADS box proteins, such as SEPALLATA1 (SEP1), SEP2, and SEP3, to regulate petal and stamen development (Pelaz et al., 2000; Honma and Goto, 2001; Theißen and Saedler, 2001; Castillejo et al., 2005).Orchids are among the most important plants in the flower market around the world, and research on MADS box genes has been reported for several species of orchids during the past few years (Lu et al., 1993, 2007; Yu and Goh, 2000; Hsu and Yang, 2002; Yu et al., 2002; Hsu et al., 2003; Tsai et al., 2004, 2008; Xu et al., 2006; Guo et al., 2007; Kim et al., 2007; Chang et al., 2009). Unlike the flowers in eudicots, the nearly identical shape of the sepals and petals as well as the production of a unique lip in orchid flowers make them a very special plant species for the study of flower development. Four clades (1–4) of genes in the paleoAP3 lineage have been identified in several orchids (Hsu and Yang, 2002; Tsai et al., 2004; Kim et al., 2007; Mondragón-Palomino and Theißen, 2008, 2009; Mondragón-Palomino et al., 2009). Several works have described the possible interactions among these four clades of paleoAP3 genes and one PI gene that are involved in regulating the differentiation and formation of the sepal/petal/lip of orchids (Tsai et al., 2004; Kim et al., 2007; Mondragón-Palomino and Theißen, 2008, 2009). However, the exact mechanism that involves the orchid B class genes remains unclear and needs to be clarified by more experimental investigations.O. Gower Ramsey is a popular orchid with important economic value in cut flower markets. Only a few studies have been reported on the role of MADS box genes in regulating flower formation in this plant species (Hsu and Yang, 2002; Hsu et al., 2003; Chang et al., 2009). An AP3-like MADS gene that regulates both floral formation and initiation in transgenic Arabidopsis has been reported (Hsu and Yang, 2002). In addition, four AP1/AGAMOUS-LIKE9 (AGL9)-like MADS box genes have been characterized that show novel expression patterns and cause different effects on floral transition and formation in Arabidopsis (Hsu et al., 2003; Chang et al., 2009). Compared with other orchids, the production of a large and well-expanded lip and five small identical sepals/petals makes O. Gower Ramsey a special case for the study of the diverse functions of B class MADS box genes during evolution. Therefore, the isolation of more B class MADS box genes and further study of their roles in the regulation of perianth (sepal/petal/lip) formation during O. Gower Ramsey flower development are necessary. In addition to the clade 2 paleoAP3 gene OMADS3, which was previously characterized in our laboratory (Hsu and Yang, 2002), three more B class MADS box genes, OMADS5, OMADS8, and OMADS9, were characterized from O. Gower Ramsey in this study. Based on the different expression patterns and the protein interactions among these four orchid B class genes, we propose that the presence of OMADS3/8 and/or OMADS9 is required for sepal/petal/lip formation. Further sepal and petal formation at least requires the additional presence of OMADS5, whereas large lip formation was seen when OMADS5 expression was absent. Our results provide a new finding and information pertaining to the roles for orchid B class MADS box genes in the regulation of sepal/petal/lip formation.     

Plasma membrane poration by opioid neuropeptides: a possible mechanism of pathological signal transduction

Neuropeptides induce signal transduction across the plasma membrane by acting through cell-surface receptors. The dynorphins, endogenous ligands for opioid receptors, are an exception; they also produce non-receptor-mediated effects causing pain and neurodegeneration. To understand non-receptor mechanism(s), we examined interactions of dynorphins with plasma membrane. Using fluorescence correlation spectroscopy and patch-clamp electrophysiology, we demonstrate that dynorphins accumulate in the membrane and induce a continuum of transient increases in ionic conductance. This phenomenon is consistent with stochastic formation of giant (~2.7 nm estimated diameter) unstructured non-ion-selective membrane pores. The potency of dynorphins to porate the plasma membrane correlates with their pathogenic effects in cellular and animal models. Membrane poration by dynorphins may represent a mechanism of pathological signal transduction. Persistent neuronal excitation by this mechanism may lead to profound neuropathological alterations, including neurodegeneration and cell death.Neuropeptides are the largest and most diverse family of neurotransmitters. They are released from axon terminals and dendrites, diffuse to pre- or postsynaptic neuronal structures and activate membrane G-protein-coupled receptors. Prodynorphin (PDYN)-derived opioid peptides including dynorphin A (Dyn A), dynorphin B (Dyn B) and big dynorphin (Big Dyn) consisting of Dyn A and Dyn B are endogenous ligands for the κ-opioid receptor. Acting through this receptor, dynorphins regulate processing of pain and emotions, memory acquisition and modulate reward induced by addictive substances.^{1, 2, 3, 4} Furthermore, dynorphins may produce robust cellular and behavioral effects that are not mediated through opioid receptors.^{5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29} As evident from pharmacological, morphological, genetic and human neuropathological studies, these effects are generally pathological, including cell death, neurodegeneration, neurological dysfunctions and chronic pain. Big Dyn is the most active pathogenic peptide, which is about 10- to 100-fold more potent than Dyn A, whereas Dyn B does not produce non-opioid effects.^{16, 17, 22, 25} Big Dyn enhances activity of acid-sensing ion channel-1a (ASIC1a) and potentiates ASIC1a-mediated cell death in nanomolar concentrations^{30, 31} and, when administered intrathecally, induces characteristic nociceptive behavior at femtomolar doses.^{17, 22} Inhibition of endogenous Big Dyn degradation results in pathological pain, whereas prodynorphin (Pdyn) knockout mice do not maintain neuropathic pain.^{22, 32} Big Dyn differs from its constituents Dyn A and Dyn B in its unique pattern of non-opioid memory-enhancing, locomotor- and anxiolytic-like effects.²⁵Pathological role of dynorphins is emphasized by the identification of PDYN missense mutations that cause profound neurodegeneration in the human brain underlying the SCA23 (spinocerebellar ataxia type 23), a very rare dominantly inherited neurodegenerative disorder.^{27, 33} Most PDYN mutations are located in the Big Dyn domain, demonstrating its critical role in neurodegeneration. PDYN mutations result in marked elevation in dynorphin levels and increase in its pathogenic non-opioid activity.^{27, 34} Dominant-negative pathogenic effects of dynorphins are not produced through opioid receptors.ASIC1a, glutamate NMDA (N-methyl-d-aspartate) and AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid)/kainate ion channels, and melanocortin and bradykinin B2 receptors have all been implicated as non-opioid dynorphin targets.^{5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 35, 36} Multiplicity of these targets and their association with the cellular membrane suggest that their activation is a secondary event triggered by a primary interaction of dynorphins with the membrane. Dynorphins are among the most basic neuropeptides.^{37, 38} The basic nature is also a general property of anti-microbial peptides (AMPs) and amyloid peptides that act by inducing membrane perturbations, altering membrane curvature and causing pore formation that disrupts membrane-associated processes including ion fluxes across the membrane.³⁹ The similarity between dynorphins and these two peptide groups in overall charge and size suggests a similar mode of their interactions with membranes.In this study, we dissect the interactions of dynorphins with the cell membrane, the primary event in their non-receptor actions. Using fluorescence imaging, correlation spectroscopy and patch-clamp techniques, we demonstrate that dynorphin peptides accumulate in the plasma membrane in live cells and cause a profound transient increase in cell membrane conductance. Membrane poration by endogenous neuropeptides may represent a novel mechanism of signal transduction in the brain. This mechanism may underlie effects of dynorphins under pathological conditions including chronic pain and tissue injury.     

Induction of COX-2-PGE2 synthesis by activation of the MAPK/ERK pathway contributes to neuronal death triggered by TDP-43-depleted microglia

Neuroinflammation is a striking hallmark of amyotrophic lateral sclerosis (ALS) and other neurodegenerative disorders. Previous studies have shown the contribution of glial cells such as astrocytes in TDP-43-linked ALS. However, the role of microglia in TDP-43-mediated motor neuron degeneration remains poorly understood. In this study, we show that depletion of TDP-43 in microglia, but not in astrocytes, strikingly upregulates cyclooxygenase-2 (COX-2) expression and prostaglandin E2 (PGE2) production through the activation of MAPK/ERK signaling and initiates neurotoxicity. Moreover, we find that administration of celecoxib, a specific COX-2 inhibitor, greatly diminishes the neurotoxicity triggered by TDP-43-depleted microglia. Taken together, our results reveal a previously unrecognized non-cell-autonomous mechanism in TDP-43-mediated neurodegeneration, identifying COX-2-PGE2 as the molecular events of microglia- but not astrocyte-initiated neurotoxicity and identifying celecoxib as a novel potential therapy for TDP-43-linked ALS and possibly other types of ALS.Amyotrophic lateral sclerosis (ALS) is an adult-onset neurodegenerative disease characterized by the degeneration of motor neurons in the brain and spinal cord.¹ Most cases of ALS are sporadic, but 10% are familial. Familial ALS cases are associated with mutations in genes such as Cu/Zn superoxide dismutase 1 (SOD1), TAR DNA-binding protein 43 (TARDBP) and, most recently discovered, C9orf72. Currently, most available information obtained from ALS research is based on the study of SOD1, but new studies focusing on TARDBP and C9orf72 have come to the forefront of ALS research.^{1, 2} The discovery of the central role of the protein TDP-43, encoded by TARDBP, in ALS was a breakthrough in ALS research.^{3, 4, 5} Although pathogenic mutations of TDP-43 are genetically rare, abnormal TDP-43 function is thought to be associated with the majority of ALS cases.¹ TDP-43 was identified as a key component of the ubiquitin-positive inclusions in most ALS patients and also in other neurodegenerative diseases such as frontotemporal lobar degeneration,^{6, 7} Alzheimer''s disease (AD)^{8, 9} and Parkinson''s disease (PD).^{10, 11} TDP-43 is a multifunctional RNA binding protein, and loss-of-function of TDP-43 has been increasingly recognized as a key contributor in TDP-43-mediated pathogenesis.^{5, 12, 13, 14}Neuroinflammation, a striking and common hallmark involved in many neurodegenerative diseases, including ALS, is characterized by extensive activation of glial cells including microglia, astrocytes and oligodendrocytes.^{15, 16} Although numerous studies have focused on the intrinsic properties of motor neurons in ALS, a large amount of evidence showed that glial cells, such as astrocytes and microglia, could have critical roles in SOD1-mediated motor neuron degeneration and ALS progression,^{17, 18, 19, 20, 21, 22} indicating the importance of non-cell-autonomous toxicity in SOD1-mediated ALS pathogenesis.Very interestingly, a vital insight of neuroinflammation research in ALS was generated by the evidence that both the mRNA and protein levels of the pro-inflammatory enzyme cyclooxygenase-2 (COX-2) are upregulated in both transgenic mouse models and in human postmortem brain and spinal cord.^{23, 24, 25, 26, 27, 28, 29} The role of COX-2 neurotoxicity in ALS and other neurodegenerative disorders has been well explored.^{30, 31, 32} One of the key downstream products of COX-2, prostaglandin E2 (PGE2), can directly mediate COX-2 neurotoxicity both in vitro and in vivo.^{33, 34, 35, 36, 37} The levels of COX-2 expression and PGE2 production are controlled by multiple cell signaling pathways, including the mitogen-activated protein kinase (MAPK)/ERK pathway,^{38, 39, 40} and they have been found to be increased in neurodegenerative diseases including AD, PD and ALS.^{25, 28, 32, 41, 42, 43, 44, 45, 46} Importantly, COX-2 inhibitors such as celecoxib exhibited significant neuroprotective effects and prolonged survival or delayed disease onset in a SOD1-ALS transgenic mouse model through the downregulation of PGE2 release.²⁸Most recent studies have tried to elucidate the role of glial cells in neurotoxicity using TDP-43-ALS models, which are considered to be helpful for better understanding the disease mechanisms.^{47, 48, 49, 50, 51} Although the contribution of glial cells to TDP-43-mediated motor neuron degeneration is now well supported, this model does not fully suggest an astrocyte-based non-cell autonomous mechanism. For example, recent studies have shown that TDP-43-mutant astrocytes do not affect the survival of motor neurons,^{50, 51} indicating a previously unrecognized non-cell autonomous TDP-43 proteinopathy that associates with cell types other than astrocytes.Given that the role of glial cell types other than astrocytes in TDP-43-mediated neuroinflammation is still not fully understood, we aim to compare the contribution of microglia and astrocytes to neurotoxicity in a TDP-43 loss-of-function model. Here, we show that TDP-43 has a dominant role in promoting COX-2-PGE2 production through the MAPK/ERK pathway in primary cultured microglia, but not in primary cultured astrocytes. Our study suggests that overproduction of PGE2 in microglia is a novel molecular mechanism underlying neurotoxicity in TDP-43-linked ALS. Moreover, our data identify celecoxib as a new potential effective treatment of TDP-43-linked ALS and possibly other types of ALS.     

TRAF2 is a biologically important necroptosis suppressor

Tumor necrosis factor α (TNFα) triggers necroptotic cell death through an intracellular signaling complex containing receptor-interacting protein kinase (RIPK) 1 and RIPK3, called the necrosome. RIPK1 phosphorylates RIPK3, which phosphorylates the pseudokinase mixed lineage kinase-domain-like (MLKL)—driving its oligomerization and membrane-disrupting necroptotic activity. Here, we show that TNF receptor-associated factor 2 (TRAF2)—previously implicated in apoptosis suppression—also inhibits necroptotic signaling by TNFα. TRAF2 disruption in mouse fibroblasts augmented TNFα–driven necrosome formation and RIPK3-MLKL association, promoting necroptosis. TRAF2 constitutively associated with MLKL, whereas TNFα reversed this via cylindromatosis-dependent TRAF2 deubiquitination. Ectopic interaction of TRAF2 and MLKL required the C-terminal portion but not the N-terminal, RING, or CIM region of TRAF2. Induced TRAF2 knockout (KO) in adult mice caused rapid lethality, in conjunction with increased hepatic necrosome assembly. By contrast, TRAF2 KO on a RIPK3 KO background caused delayed mortality, in concert with elevated intestinal caspase-8 protein and activity. Combined injection of TNFR1-Fc, Fas-Fc and DR5-Fc decoys prevented death upon TRAF2 KO. However, Fas-Fc and DR5-Fc were ineffective, whereas TNFR1-Fc and interferon α receptor (IFNAR1)-Fc were partially protective against lethality upon combined TRAF2 and RIPK3 KO. These results identify TRAF2 as an important biological suppressor of necroptosis in vitro and in vivo.Apoptotic cell death is mediated by caspases and has distinct morphological features, including membrane blebbing, cell shrinkage and nuclear fragmentation.^{1, 2, 3, 4} In contrast, necroptotic cell death is caspase-independent and is characterized by loss of membrane integrity, cell swelling and implosion.^{1, 2, 5} Nevertheless, necroptosis is a highly regulated process, requiring activation of RIPK1 and RIPK3, which form the core necrosome complex.^{1, 2, 5} Necrosome assembly can be induced via specific death receptors or toll-like receptors, among other modules.^{6, 7, 8, 9} The activated necrosome engages MLKL by RIPK3-mediated phosphorylation.^{6, 10, 11} MLKL then oligomerizes and binds to membrane phospholipids, forming pores that cause necroptotic cell death.^{10, 12, 13, 14, 15} Unchecked necroptosis disrupts embryonic development in mice and contributes to several human diseases.^{7, 8, 16, 17, 18, 19, 20, 21, 22}The apoptotic mediators FADD, caspase-8 and cFLIP suppress necroptosis.^{19, 20, 21, 23, 24} Elimination of any of these genes in mice causes embryonic lethality, subverted by additional deletion of RIPK3 or MLKL.^{19, 20, 21, 25} Necroptosis is also regulated at the level of RIPK1. Whereas TNFα engagement of TNFR1 leads to K63-linked ubiquitination of RIPK1 by cellular inhibitor of apoptosis proteins (cIAPs) to promote nuclear factor (NF)-κB activation,²⁶ necroptosis requires suppression or reversal of this modification to allow RIPK1 autophosphorylation and consequent RIPK3 activation.^{2, 23, 27, 28} CYLD promotes necroptotic signaling by deubiquitinating RIPK1, augmenting its interaction with RIPK3.²⁹ Conversely, caspase-8-mediated CYLD cleavage inhibits necroptosis.²⁴TRAF2 recruits cIAPs to the TNFα-TNFR1 signaling complex, facilitating NF-κB activation.^{30, 31, 32, 33} TRAF2 also supports K48-linked ubiquitination and proteasomal degradation of death-receptor-activated caspase-8, curbing apoptosis.³⁴ TRAF2 KO mice display embryonic lethality; some survive through birth but have severe developmental and immune deficiencies and die prematurely.^{35, 36} Conditional TRAF2 KO leads to rapid intestinal inflammation and mortality.³⁷ Furthermore, hepatic TRAF2 depletion augments apoptosis activation via Fas/CD95.³⁴ TRAF2 attenuates necroptosis induction in vitro by the death ligands Apo2L/TRAIL and Fas/CD95L.³⁸ However, it remains unclear whether TRAF2 regulates TNFα-induced necroptosis—and if so—how. Our present findings reveal that TRAF2 inhibits TNFα necroptotic signaling. Furthermore, our results establish TRAF2 as a biologically important necroptosis suppressor in vitro and in vivo and provide initial insight into the mechanisms underlying this function.     

RNA Silencing of Exocyst Genes in the Stigma Impairs the Acceptance of Compatible Pollen in Arabidopsis

Initial pollen-pistil interactions in the Brassicaceae are regulated by rapid communication between pollen grains and stigmatic papillae and are fundamentally important, as they are the first step toward successful fertilization. The goal of this study was to examine the requirement of exocyst subunits, which function in docking secretory vesicles to sites of polarized secretion, in the context of pollen-pistil interactions. One of the exocyst subunit genes, EXO70A1, was previously identified as an essential factor in the stigma for the acceptance of compatible pollen in Arabidopsis (Arabidopsis thaliana) and Brassica napus. We hypothesized that EXO70A1, along with other exocyst subunits, functions in the Brassicaceae dry stigma to deliver cargo-bearing secretory vesicles to the stigmatic papillar plasma membrane, under the pollen attachment site, for pollen hydration and pollen tube entry. Here, we investigated the functions of exocyst complex genes encoding the remaining seven subunits, SECRETORY3 (SEC3), SEC5, SEC6, SEC8, SEC10, SEC15, and EXO84, in Arabidopsis stigmas following compatible pollinations. Stigma-specific RNA-silencing constructs were used to suppress the expression of each exocyst subunit individually. The early postpollination stages of pollen grain adhesion, pollen hydration, pollen tube penetration, seed set, and overall fertility were analyzed in the transgenic lines to evaluate the requirement of each exocyst subunit. Our findings provide comprehensive evidence that all eight exocyst subunits are necessary in the stigma for the acceptance of compatible pollen. Thus, this work implicates a fully functional exocyst complex as a component of the compatible pollen response pathway to promote pollen acceptance.In flowering plants, sexual reproduction occurs as a result of constant communication between the male gametophyte and the female reproductive organ, from the initial acceptance of compatible pollen to final step of successful fertilization (for review, see Beale and Johnson, 2013; Dresselhaus and Franklin-Tong, 2013; Higashiyama and Takeuchi, 2015). In the Brassicaceae, the stigmas that present a receptive surface for pollen are categorized as dry and covered with unicellular papillae (Heslop-Harrison and Shivanna, 1977). Communication is initiated rapidly following contact of a pollen grain with a stigmatic papilla, as the role of the papillae is to regulate the early cellular responses leading to compatible pollen germination. The basal compatible pollen recognition response also presents a barrier to foreign pollen or is inhibited with self-incompatible pollen (for review, see Dickinson, 1995; Hiscock and Allen, 2008; Chapman and Goring, 2010; Indriolo et al., 2014b).The initial adhesive interaction between the pollen grain and the papilla cell in the Brassicaceae is mediated by the exine of the pollen grain and the surface of the stigmatic papilla (Preuss et al., 1993; Zinkl et al., 1999). A stronger connection results between the adhered pollen grain and the stigmatic papilla with the formation of a lipid-protein interface (foot) derived from the pollen coat and the stigmatic papillar surface (Mattson et al., 1974; Stead et al., 1980; Gaude and Dumas, 1986; Elleman and Dickinson, 1990; Elleman et al., 1992; Preuss et al., 1993; Mayfield et al., 2001). It is at this point that a Brassicaceae-specific recognition of compatible pollen is proposed to occur (Hülskamp et al., 1995; Pruitt, 1999), though the nature of this recognition system is not clearly defined. Two stigma-specific Brassica oleracea glycoproteins, the S-Locus Glycoprotein and S-Locus Related1 (SLR1) protein, play a role in compatible pollen adhesion (Luu et al., 1997, 1999), potentially through interactions with the pollen coat proteins, PCP-A1 and SLR1-BP, respectively (Doughty et al., 1998; Takayama et al., 2000). The simultaneous recognition of self-incompatible pollen would also take place at this stage (for review, see Dresselhaus and Franklin-Tong, 2013; Indriolo et al., 2014b; Sawada et al., 2014). Thus, this interface not only provides a strengthened bond between the pollen grain and stigmatic papilla, but likely facilitates the interaction of signaling proteins from both partners to promote specific cellular responses in the stigmatic papilla toward the pollen grain.One response regulated by these interactions is the release of water from the stigmatic papilla to the adhered compatible pollen grain to enable the pollen grain to rehydrate, germinate, and produce a pollen tube (Zuberi and Dickinson, 1985; Preuss et al., 1993). Upon hydration, the pollen tube emerges at the site of pollen-papilla contact and penetrates the stigma surface between the plasma membrane and the overlaying cell wall (Elleman et al., 1992; Kandasamy et al., 1994). Pollen tube entry into the stigmatic surface represents a second barrier, selecting compatible pollen tubes. Subsequently, the compatible pollen tubes traverse down to the base of the stigma, enter the transmitting tract, and grow intracellularly toward ovules for fertilization. Pollen-pistil interactions at these later stages are also highly regulated (for review, see Beale and Johnson, 2013; Dresselhaus and Franklin-Tong, 2013; Higashiyama and Takeuchi, 2015).EXO70A1, a subunit of the exocyst, was identified as a factor involved in early pollen-stigma interactions, where it is required in the stigma for the acceptance of compatible pollen and inhibited by the self-incompatibility response (Samuel et al., 2009). Stigmas from the Arabidopsis (Arabidopsis thaliana) exo70A1 mutant display constitutive rejection of wild-type-compatible pollen (Samuel et al., 2009; Safavian et al., 2014). This stigmatic defect was rescued by the stigma-specific expression of an Red Fluorescent Protein (RFP):EXO70A1 transgene (Samuel et al., 2009) or partially rescued by providing a high relative humidity environment (Safavian et al., 2014). In addition, the stigma-specific expression of an EXO70A1 RNA interference construct in Brassica napus ‘Westar’ resulted in impaired compatible pollen acceptance and a corresponding reduction in seed production compared with compatible pollinations with wild-type B. napus ‘Westar’ pistils (Samuel et al., 2009). From these studies, EXO70A1 was found to be a critical component in stigmatic papillae to promote compatible pollen hydration and pollen tube entry through the stigma surface. One of the functions of the exocyst is to mediate polar secretion (for review, see Heider and Munson, 2012; Zárský et al., 2013; Synek et al., 2014). Consistent with this, previous studies have observed vesicle-like structures in proximity to the stigmatic papillar plasma membrane in response to compatible pollen in both Brassica spp. and Arabidopsis species (Elleman and Dickinson, 1990, 1996; Dickinson, 1995; Safavian and Goring, 2013; Indriolo et al., 2014a). The secretory activity is predicted to promote pollen hydration and pollen tube entry. As well, consistent with the proposed inhibition of EXO70A1 by the self-incompatibility pathway (Samuel et al., 2009), a complete absence or a significant reduction of vesicle-like structures at the stigmatic papillar plasma membrane was observed in the exo70A1 mutant and with self-incompatible pollen (Safavian and Goring, 2013; Indriolo et al., 2014a).The exocyst is a well-defined complex in yeast (Saccharomyces cerevisiae) and animal systems, consisting of eight subunits, SEC3, SEC5, SEC6, SEC8, SEC10, SEC15, EXO70, and EXO84 (TerBush et al., 1996; Guo et al., 1999). Exocyst subunit mutants were first identified in yeast as secretory mutants displaying a cytosolic accumulation of secretory vesicles (Novick et al., 1980). Subsequent work defined roles for the exocyst in vesicle docking at target membranes in processes such as regulated secretion, polarized exocytosis, and cytokinesis to facilitate membrane fusion by Soluble NSF Attachment protein Receptor (SNARE) complexes (for review, see Heider and Munson, 2012; Liu and Guo, 2012). In plants, genes encoding all eight exocyst subunits have been identified, and many of these genes exist as multiple copies. For example, the Arabidopsis genome contains single copy genes for SEC6 and SEC8, two copies each for SECRETORY3 (SEC3), SEC5, SEC10, and SEC15, three EXO84 genes, and 23 EXO70 genes (Chong et al., 2010; Cvrčková et al., 2012; Vukašinović et al., 2014). Ultrastructural studies using electron tomography uncovered the existence of a structure resembling the exocyst in Arabidopsis (Otegui and Staehelin, 2004; Seguí-Simarro et al., 2004). Localization studies of specific Arabidopsis exocyst subunits also supported conserved roles in polarized exocytosis and cytokinesis in plants. Localization studies have shown EXO70, SEC6, and SEC8 at the growing tip of pollen tubes (Hála et al., 2008), EXO70A1 at the stigmatic papillar plasma membrane (Samuel et al., 2009), SEC3a, SEC6, SEC8, SEC15b, EXO70A1, and EXO84b at the root epidermal cell plasma membrane and developing cell plate (Fendrych et al., 2010, 2013; Wu et al., 2013; Zhang et al., 2013; Rybak et al., 2014), and SEC3a at the plasma membrane in the embryo and root hair (Zhang et al., 2013). Similar to the yeast exocyst mutants, vesicle accumulation has also been observed in the exo70A1 and exo84b mutants (Fendrych et al., 2010; Safavian and Goring, 2013). Taken together, these findings strongly support that plant exocyst subunits function in vivo in vesicle docking at sites of polarized secretion and cytokinesis (for review, see Zárský et al., 2013). In support of this, a recent study investigating Transport Protein Particle (TRAPP)II and exocyst complexes during cytokinesis in Arabidopsis has identified all eight exocyst components in immunoprecipitated complexes (SEC3a/SEC3b, SEC5a, SEC6, SEC8, SEC10, SEC15b, EXO70A1, EXO70H2, and EXO84b; Rybak et al., 2014).Several plant exocyst subunit genes have been implicated in biological processes that rely on regulated vesicle trafficking, where corresponding mutants have displayed a range of growth defects. At the cellular level, these phenotypes have been associated with decreased cell elongation and polar growth (Cole et al., 2005, 2014; Wen et al., 2005; Synek et al., 2006), defects in cytokinesis and cell plate formation (Fendrych et al., 2010; Wu et al., 2013; Rybak et al., 2014), and disrupted Pin-Formed (PIN) auxin efflux carrier recycling and polar auxin transport (Drdová et al., 2013). Several Arabidopsis subunit mutants display strong growth defects such as the sec3a mutant with an embryo-lethal phenotype (Zhang et al., 2013), sec6, sec8, and exo84b mutants with severely dwarfed phenotypes and defects in root growth (Fendrych et al., 2010; Wu et al., 2013; Cole et al., 2014), and exo70A1 with a milder dwarf phenotype (Synek et al., 2006). The Arabidopsis exo70A1 mutant has also been reported to have defects in root hair elongation, hypocotyl elongation, compatible pollen acceptance, seed coat deposition, and tracheary element differentiation (Synek et al., 2006; Samuel et al., 2009; Kulich et al., 2010; Li et al., 2013). Essential roles for other exocyst subunits include Arabidopsis SEC5a/SEC5b, SEC6, SEC8, and SEC15a/SEC15b in male gametophyte development and pollen tube growth (Cole et al., 2005; Hála et al., 2008; Wu et al., 2013), SEC8 in seed coat deposition (Kulich et al., 2010), SEC5a, SEC8, EXO70A1, and EXO84b in root meristem size and root cell elongation (Cole et al., 2014), and a maize (Zea mays) SEC3 homolog in root hair elongation (Wen et al., 2005). Finally, the Arabidopsis EXO70B1, EXO70B2, and EXO70H1 subunits have been implicated in plant defense responses (Pecenková et al., 2011; Stegmann et al., 2012; Kulich et al., 2013; Stegmann et al., 2013).Even with these detailed studies on the functions of exocyst subunits in plants, a systematic demonstration of the requirement of all eight exocyst subunits in a specific plant biological process is currently lacking. EXO70A1 was previously identified as an essential factor in the stigma for compatible pollen-pistil interactions in Arabidopsis and B. napus (Samuel et al., 2009), and we hypothesized that this protein functions as part of the exocyst complex to tether post-Golgi secretory vesicles to stigmatic papillar plasma membrane (Safavian and Goring, 2013). To provide support for the proposed biological role of the exocyst in the stigma for compatible pollen acceptance, we investigated the roles of the remaining seven subunits, SEC3, SEC5, SEC6, SEC8, SEC10, SEC15, and EXO84, in Arabidopsis stigmatic papillae. Given that some Arabidopsis exocyst subunits were previously determined to be essential at earlier growth stages, stigma-specific RNA-silencing constructs were used for each exocyst subunit, and the early postpollination stages were analyzed for these transgenic lines. Our collective data demonstrates that all eight exocyst subunits are required in the stigma for the early stages of compatible pollen-pistil interactions.     

Characterization of the β-Carotene Hydroxylase Gene DSM2 Conferring Drought and Oxidative Stress Resistance by Increasing Xanthophylls and Abscisic Acid Synthesis in Rice

Drought is a major limiting factor for crop production. To identify critical genes for drought resistance in rice (Oryza sativa), we screened T-DNA mutants and identified a drought-hypersensitive mutant, dsm2. The mutant phenotype was caused by a T-DNA insertion in a gene encoding a putative β-carotene hydroxylase (BCH). BCH is predicted for the biosynthesis of zeaxanthin, a carotenoid precursor of abscisic acid (ABA). The amounts of zeaxanthin and ABA were significantly reduced in two allelic dsm2 mutants after drought stress compared with the wild type. Under drought stress conditions, the mutant leaves lost water faster than the wild type and the photosynthesis rate, biomass, and grain yield were significantly reduced, whereas malondialdehyde level and stomata aperture were increased in the mutant. The mutant is also hypersensitive to oxidative stresses. The mutant had significantly lower maximal efficiency of photosystem II photochemistry and nonphotochemical quenching capacity than the wild type, indicating photoinhibition in photosystem II and decreased capacity for eliminating excess energy by thermal dissipation. Overexpression of DSM2 in rice resulted in significantly increased resistance to drought and oxidative stresses and increases of the xanthophylls and nonphotochemical quenching. Some stress-related ABA-responsive genes were up-regulated in the overexpression line. DSM2 is a chloroplast protein, and the response of DSM2 to environmental stimuli is distinctive from the other two BCH members in rice. We conclude that the DSM2 gene significantly contributes to control of the xanthophyll cycle and ABA synthesis, both of which play critical roles in the establishment of drought resistance in rice.Abiotic stresses such as drought, salinity, and adverse temperatures are major limiting factors for plant growth and reproduction. To respond to environmental cues, plants have evolved a variety of biochemical and physiological mechanisms to adapt to adverse conditions during their growth and development (Boyer, 1982). Abscisic acid (ABA) has been recognized as a stress hormone that coordinates the complex networks of stress responses. Under drought or salt stress conditions, plant endogenous ABA level can rise to about 40-fold, triggering the closure of stomata and accumulating reactive oxygen species (ROS), dehydrins, and late embryogenesis abundant proteins for osmotic adjustment (Verslues et al., 2006). The endogenous ABA level is determined by ABA biosynthesis, catabolism, and release of ABA from ABA-Glc conjugates (Nambara and Marion-Poll, 2005; Lee et al., 2006). Therefore, identification of all the components affecting active ABA content is essential for a complete understanding of the action of the hormone.Numerous ABA biosynthetic genes have been identified through mutant analysis, such as maize (Zea mays) viviparous mutants vp2, vp5, vp7, vp9, vp14, w3, y3, and y9 (Schwartz et al., 1997; Hable et al., 1998; Singh et al., 2003); rice (Oryza sativa) preharvest-sprouting mutants psh1, psh2, psh3, and psh4 (Fang et al., 2008); sunflower (Helianthus annuus) nondormant mutant nd-1 (Conti et al., 2004); Arabidopsis (Arabidopsis thaliana) ABA- and nonphotochemical quenching (NPQ)-deficient mutants aba1, aba2, aba3, aba4, npq1, npq2, b1, b2, and nced3 (Havaux et al., 2000; Xiong et al., 2001; Tian et al., 2003; Barrero et al., 2005; Kim and DellaPenna, 2006; North et al., 2007); and tomato (Solanum lycopersicum) white-flower mutant wf (Galpaz et al., 2006; Supplemental Fig. S1). The mutants unable to biosynthesize carotenoid precursors for endogenous ABA synthesis often produced preharvest-sprouting seeds and wilted or white leaves (Gubler et al., 2005; Nambara and Marion-Poll, 2005; Finch-Savage and Leubner-Metzger, 2006).ABA biosynthesis initiates with the synthesis of a C5 building block, isopentenyl pyrophosphate, and its isomer dimethylallyl pyrophosphate through a plastid methylerythritol phosphate pathway (Eisenreich et al., 2001; Hunter, 2007). The three isopentenyl pyrophosphate molecules are then added to dimethylallyl pyrophosphate by geranylgeranyl diphosphate synthase to produce C20 geranylgeranyl diphosphate. Two geranylgeranyl diphosphates are condensed by a committing enzyme, phytoene synthase, to produce colorless C40 carotenoid phytoene, which is then desaturated and isomerized into red-colored lycopene by phytoene desaturase (PDS), ζ-carotene desaturase (ZDS), and Z-ISO and CRTISO isomerases in plants (Isaacson et al., 2002; Park et al., 2002). Subsequently, several cyclization and hydroxylation reactions take place to yield α-carotene and β-carotene (Li et al., 1996; Hable et al., 1998; Park et al., 2002; Miki and Shimamoto, 2004; Fang et al., 2008). Heme-type cytochrome P450-type CYP97 and non-heme-type β-carotene hydroxylase (BCH) are primarily responsible for the hydroxylation of α-carotene and β-carotene to produce lutein and zeaxanthin, respectively. Zeaxanthin, an important component of the xanthophyll cycle, is epoxidated by zeaxanthin epoxidase to produce violaxanthin, and this reaction can be reversed by violaxanthin deepoxidase to increase the xanthophyll cycle for plants to adapt to high-light stress (Johnson et al., 2008). Neoxanthin synthase converts violaxanthin into neoxanthin (North et al., 2007). In chloroplast, 9-cis-epoxycarotenoid dioxygenase (NCED) cleaves violaxanthin and neoxanthin to produce xanthoxin, the direct substrate for ABA synthesis via ABA aldehyde (Schwartz et al., 1997, 2003; Xiong and Zhu, 2003). Increasing evidence suggest that the endogenous ABA level is fine-tuned by differential regulation of the multiple steps of ABA biosynthesis (Seo and Koshiba, 2002; Nambara and Marion-Poll, 2005; Destefano-Beltrán et al., 2006; Thompson et al., 2007; Rodríguez-Gacio et al., 2009; Supplemental Fig. S1).The xanthophyll cycle (light-dependent reversible conversion between violaxanthin and zeaxanthin) is involved in photoprotection in PSII by regulating the nonradiative dissipation of excess absorbed light energy as heat (Gilmore et al., 1994). Mutants with defects in the xanthophyll cycle exhibit a weak photoprotective ability and produce ROS such as hydrogen peroxide (H₂O₂) when the absorption of light energy exceeds that consumed for photosynthesis (Niyogi, 1999). Under dehydration stress, electrons at a high energy state can easily form ROS, which are toxic to proteins, DNA, and lipids (Mittler, 2002; Apel and Hirt, 2004). However, plants have evolved a variety of biochemical and physiological mechanisms to scavenge ROS, thus maintaining a balance between ROS production and scavenging (Mittler et al., 2004).An association between the xanthophyll cycle and stress tolerance has been reported in plants. In Arabidopsis, overexpression of a bacterial BCH gene caused a specific 2-fold increase in the size of the xanthophyll cycle and enhanced photooxidative tolerance (Davison et al., 2002). Constitutive overexpression of a bacterial BCH gene, crtZ, in tobacco (Nicotiana tabacum) led to increased zeaxanthin synthesis and enhanced UV light tolerance (Götz et al., 2002). In Arabidopsis, zeaxanthin synthesis can be catalyzed by both heme-type CYP97 hydroxylases LUT1 and LUT5 and non-heme-type hydroxylases BCH1 and BCH2, and these two types exhibit some overlapping activities (Tian et al., 2003, 2004; Kim and DellaPenna, 2006). In contrast to the intensive molecular and genetic studies of BCH in Arabidopsis, the counterpart in economically important crops such as rice has not been identified.In this study, we characterized the rice drought-sensitive mutant dsm2, impaired in the gene DSM2 encoding a BCH. Our results demonstrate that DSM2 acts as a putative enzyme catalyzing the biosynthesis of zeaxanthin, one of the precursors of ABA that participates in the process of NPQ. Decreases of NPQ, maximal efficiency of PSII photochemistry (F_v/F_m), xanthophylls, and ABA in the dsm2 mutant suggest that the drought hypersensitivity of dsm2 is due to the combination of impairments in the xanthophyll cycle and ABA synthesis under drought stress conditions. DSM2 overexpression lines, possessing high F_v/F_m and NPQ, showed significantly improved drought resistance at both seedling and reproductive stages. Furthermore, our results imply that DSM2 may be the major member of the BCH family in rice for controlling zeaxanthin synthesis in response to dehydration stresses.     

Restoration of miR-101 suppresses lung tumorigenesis through inhibition of DNMT3a-dependent DNA methylation

The deregulation of miR-101 and DNMT3a has been implicated in the pathogenesis of multiple tumor types, but whether and how miR-101 silencing and DNMT3a overexpression contribute to lung tumorigenesis remain elusive. Here we show that miR-101 downregulation associates with DNMT3a overexpression in lung cancer cell lines and patient tissues. Ectopic miR-101 expression remarkably abrogated the DNMT3a 3′-UTR luciferase activity corresponding to the miR-101 binding site and caused an attenuated expression of endogenous DNMT3a, which led to a reduction of global DNA methylation and the re-expression of tumor suppressor CDH1 via its promoter DNA hypomethylation. Functionally, restoration of miR-101 expression suppressed lung cancer cell clonability and migration, which recapitulated the DNMT3a knockdown effects. Interestingly, miR-101 synergized with decitabine to downregulate DNMT3a and to reduce DNA methylation. Importantly, ectopic miR-101 expression was sufficient to trigger in vivo lung tumor regression and the blockage of metastasis. Consistent with these phenotypes, examination of xenograft tumors disclosed an increase of miR-101, a decrease of DNMT3a and the subsequent DNA demethylation. These findings support that the loss or suppression of miR-101 function accelerates lung tumorigenesis through DNMT3a-dependent DNA methylation, and suggest that miR-101-DNMT3a axis may have therapeutic value in treating refractory lung cancer.Owing to a high propensity for recurrence and a high rate of metastasis at the advanced stages,^{1, 2, 3} lung cancer remains the leading cause of cancer-related mortality. DNA methylation is a major epigenetic rule controlling chromosomal stability and gene expression.^{4, 5} It is under control of DNA methyltransferases (DNMTs), whose overexpression in lung cancer cells predicts worse outcomes.^{6, 7} It is postulated that DNMT overexpression induces DNA hypermethylation and silencing of tumor suppressor genes (TSGs), leading to an aggressive lung cancer. Indeed, enforced expression of DNMT1 or DNMT3a increases DNA methylation, while the abolition of DNMT expression by genetic depletion, microRNAs (miRs) or small molecules reduces genome-wide and gene-specific DNA methylation and restores TSG expression.^{8, 9, 10, 11, 12, 13} As TSGs are the master controllers for cell multiplicity and their silencing predicts poor prognosis,^{14, 15} TSG re-expression via promoter DNA hypomethylation inhibits cell proliferation and induces cell differentiation.^{13, 16} Thus, DNMT gene abundance could serve as a target for anticancer therapy, but how DNMT upregulation occurs in lung cancer is incompletely understood.MiRs are small non-coding RNAs that crucially regulate target gene expression. Up to 30% of all protein-coding genes are predicted to be targeted by miRs,^{17, 18} supporting the key roles of miRs in controlling cell fate.^{19, 20, 21, 22} Research is showing that certain miRs are frequently dysregulated in cancers, including lung cancer.^{7, 23, 24} As miR targets can promote or inhibit cancer cell expansion, miRs have huge potential for acting as bona fide oncogenes (i.e., miR-21) or TSGs (i.e., miR-29b).^{7, 25} We and others demonstrated that the levels of DNMT1 or DNMT3a or DNMT3b are regulated by miR-29b, miR-148, miR-152 or miR-30c,^{7, 13, 26, 27} and overexpression of these miRs results in DNA hypomethylation and TSG reactivation with the concurrent blockage of cancer cell proliferation.^{7, 13} These findings underscore the importance of miRs as epigenetic modulators and highlight their therapeutic applications.MiR-101 is frequently silenced in human cancers^{28, 29, 30, 31} and, importantly, exhibits antitumorigenic properties when overexpressed. Mechanistically, miR-101 inactivation by genomic loss causes the overexpression of EZH2, a histone methyltransferase, via 3′-UTR targeting, which is followed by histone hypermethylation and aggressive tumorigenesis.^{29, 30, 32} However, whether and how miR-101 silencing contributes to DNA hypermethylation patterning in lung cancer is unclear. In this study, we explore the role of miR-101 in regulating DNMT3a expression and the impacts of miR-101-DNMT3a nexus on lung cancer pathogenesis. We showed that the expression of miR-101 and DNMT3a was negatively correlated in lung cancer. We presented evidence that ectopic miR-101 expression decreased DNMT3a levels, reduced global DNA methylation and upregulated CDH1 via its promoter DNA demethylation. The biological significance of miR-101-mediated DNA hypomethylation and CDH1 re-expression was evident by its inhibition of lung tumor cell growth in vitro and in vivo. Thus, our findings mechanistically and functionally link miR-101 silencing to DNA hypermethylation in lung cancer cells.     

Unraveling the Complex Trait of Crop Yield With Quantitative Trait Loci Mapping in Brassica napus

Yield is the most important and complex trait for the genetic improvement of crops. Although much research into the genetic basis of yield and yield-associated traits has been reported, in each such experiment the genetic architecture and determinants of yield have remained ambiguous. One of the most intractable problems is the interaction between genes and the environment. We identified 85 quantitative trait loci (QTL) for seed yield along with 785 QTL for eight yield-associated traits, from 10 natural environments and two related populations of rapeseed. A trait-by-trait meta-analysis revealed 401 consensus QTL, of which 82.5% were clustered and integrated into 111 pleiotropic unique QTL by meta-analysis, 47 of which were relevant for seed yield. The complexity of the genetic architecture of yield was demonstrated, illustrating the pleiotropy, synthesis, variability, and plasticity of yield QTL. The idea of estimating indicator QTL for yield QTL and identifying potential candidate genes for yield provides an advance in methodology for complex traits.YIELD is the most important and complex trait in crops. It reflects the interaction of the environment with all growth and development processes that occur throughout the life cycle (Quarrie et al. 2006). Crop yield is directly and multiply determined by yield-component traits (such as seed weight and seed number). Yield-related traits (such as biomass, harvest index, plant architecture, adaptation, resistance to biotic and abiotic constraints) may also indirectly affect yield by affecting the yield-component traits or by other, unknown mechanisms. Increasing evidence suggests that “fine-mapped” quantitative trait loci (QTL) or genes identified as affecting crop yield involve diverse pathways, such as seed number (Ashikari et al. 2005; Tian et al. 2006b; Burstin et al. 2007; Xie et al. 2008; Xing et al. 2008; Xue et al. 2008), seed weight (Ishimaru 2003; Song et al. 2005; Shomura et al. 2008; Wang et al. 2008; Xie et al. 2006, 2008; Xing et al. 2008; Xue et al. 2008), flowering time (Cockram et al. 2007; Song et al. 2007; Xie et al. 2008; Xue et al. 2008), plant height (Salamini 2003; Ashikari et al. 2005; Xie et al. 2008; Xue et al. 2008), branching (Clark et al. 2006; Burstin et al. 2007; Xing et al. 2008), biomass yield (Quarrie et al. 2006; Burstin et al. 2007), resistance and tolerance to biotic and abiotic stresses (Khush 2001; Brown 2002; Yuan et al. 2002; Waller et al. 2005; Zhang 2007; Warrington et al. 2008), and root architecture (Hochholdinger et al. 2008).Many experiments have explored the genetic basis of yield and yield-associated traits (yield components and yield-related traits) in crops. Summaries of identified QTL have been published for wheat (MacCaferri et al. 2008), barley (Von Korff et al. 2008), rice, and maize (http://www.gramene.org/). The results show several common patterns. First, QTL for yield and yield-associated traits tend to be clustered in the genome, which suggests that the QTL of the yield-associated traits have pleiotropic effects on yield. Second, this kind of pleiotropy has not been well analyzed genetically. The QTL for yield (complicated factor), therefore, have not been associated with any yield-associated traits (relatively simple factors, such as plant height). Therefore, they are unlikely to predict accurately potential candidate genes for yield. Third, only a few loci (rarely >10) have been found for each of these traits. Thus, the genetic architecture of yield has remained ambiguous. Fourth, trials were carried out in a few environments and how the mode of expression of QTL for these complex traits might respond in different environments is unclear.In this study, the genetic architecture of crop yield was analyzed through the QTL mapping of seed yield and eight yield-associated traits in two related populations of rapeseed (Brassica napus) that were grown in 10 natural environments. The complexity of the genetic architecture of seed yield was demonstrated by QTL meta-analysis. The idea of estimating indicator QTL (QTL of yield-associated traits, which are defined as the potential genetic determinants of the colocalized QTL for yield) for yield QTL in conjunction with the identification of candidate genes is described.     

Nontransgenic Genome Modification in Plant Cells

Zinc finger nucleases (ZFNs) are a powerful tool for genome editing in eukaryotic cells. ZFNs have been used for targeted mutagenesis in model and crop species. In animal and human cells, transient ZFN expression is often achieved by direct gene transfer into the target cells. Stable transformation, however, is the preferred method for gene expression in plant species, and ZFN-expressing transgenic plants have been used for recovery of mutants that are likely to be classified as transgenic due to the use of direct gene-transfer methods into the target cells. Here we present an alternative, nontransgenic approach for ZFN delivery and production of mutant plants using a novel Tobacco rattle virus (TRV)-based expression system for indirect transient delivery of ZFNs into a variety of tissues and cells of intact plants. TRV systemically infected its hosts and virus ZFN-mediated targeted mutagenesis could be clearly observed in newly developed infected tissues as measured by activation of a mutated reporter transgene in tobacco (Nicotiana tabacum) and petunia (Petunia hybrida) plants. The ability of TRV to move to developing buds and regenerating tissues enabled recovery of mutated tobacco and petunia plants. Sequence analysis and transmission of the mutations to the next generation confirmed the stability of the ZFN-induced genetic changes. Because TRV is an RNA virus that can infect a wide range of plant species, it provides a viable alternative to the production of ZFN-mediated mutants while avoiding the use of direct plant-transformation methods.Methods for genome editing in plant cells have fallen behind the remarkable progress made in whole-genome sequencing projects. The availability of reliable and efficient methods for genome editing would foster gene discovery and functional gene analyses in model plants and the introduction of novel traits in agriculturally important species (Puchta, 2002; Hanin and Paszkowski, 2003; Reiss, 2003; Porteus, 2009). Genome editing in various species is typically achieved by integrating foreign DNA molecules into the target genome by homologous recombination (HR). Genome editing by HR is routine in yeast (Saccharomyces cerevisiae) cells (Scherer and Davis, 1979) and has been adapted for other species, including Drosophila, human cell lines, various fungal species, and mouse embryonic stem cells (Baribault and Kemler, 1989; Venken and Bellen, 2005; Porteus, 2007; Hall et al., 2009; Laible and Alonso-González, 2009; Tenzen et al., 2009). In plants, however, foreign DNA molecules, which are typically delivered by direct gene-transfer methods (e.g. Agrobacterium and microbombardment of plasmid DNA), often integrate into the target cell genome via nonhomologous end joining (NHEJ) and not HR (Ray and Langer, 2002; Britt and May, 2003).Various methods have been developed to indentify and select for rare site-specific foreign DNA integration events or to enhance the rate of HR-mediated DNA integration in plant cells. Novel T-DNA molecules designed to support strong positive- and negative-selection schemes (e.g. Thykjaer et al., 1997; Terada et al., 2002), altering the plant DNA-repair machinery by expressing yeast chromatin remodeling protein (Shaked et al., 2005), and PCR screening of large numbers of transgenic plants (Kempin et al., 1997; Hanin et al., 2001) are just a few of the experimental approaches used to achieve HR-mediated gene targeting in plant species. While successful, these approaches, and others, have resulted in only a limited number of reports describing the successful implementation of HR-mediated gene targeting of native and transgenic sequences in plant cells (for review, see Puchta, 2002; Hanin and Paszkowski, 2003; Reiss, 2003; Porteus, 2009; Weinthal et al., 2010).HR-mediated gene targeting can potentially be enhanced by the induction of genomic double-strand breaks (DSBs). In their pioneering studies, Puchta et al. (1993, 1996) showed that DSB induction by the naturally occurring rare-cutting restriction enzyme I-SceI leads to enhanced HR-mediated DNA repair in plants. Expression of I-SceI and another rare-cutting restriction enzyme (I-CeuI) also led to efficient NHEJ-mediated site-specific mutagenesis and integration of foreign DNA molecules in plants (Salomon and Puchta, 1998; Chilton and Que, 2003; Tzfira et al., 2003). Naturally occurring rare-cutting restriction enzymes thus hold great promise as a tool for genome editing in plant cells (Carroll, 2004; Pâques and Duchateau, 2007). However, their wide application is hindered by the tedious and next to impossible reengineering of such enzymes for novel DNA-target specificities (Pâques and Duchateau, 2007).A viable alternative to the use of rare-cutting restriction enzymes is the zinc finger nucleases (ZFNs), which have been used for genome editing in a wide range of eukaryotic species, including plants (e.g. Bibikova et al., 2001; Porteus and Baltimore, 2003; Lloyd et al., 2005; Urnov et al., 2005; Wright et al., 2005; Beumer et al., 2006; Moehle et al., 2007; Santiago et al., 2008; Shukla et al., 2009; Tovkach et al., 2009; Townsend et al., 2009; Osakabe et al., 2010; Petolino et al., 2010; Zhang et al., 2010). Here too, ZFNs have been used to enhance DNA integration via HR (e.g. Shukla et al., 2009; Townsend et al., 2009) and as an efficient tool for the induction of site-specific mutagenesis (e.g. Lloyd et al., 2005; Zhang et al., 2010) in plant species. The latter is more efficient and simpler to implement in plants as it does not require codelivery of both ZFN-expressing and donor DNA molecules and it relies on NHEJ—the dominant DNA-repair machinery in most plant species (Ray and Langer, 2002; Britt and May, 2003).ZFNs are artificial restriction enzymes composed of a fusion between an artificial Cys₂His₂ zinc-finger protein DNA-binding domain and the cleavage domain of the FokI endonuclease. The DNA-binding domain of ZFNs can be engineered to recognize a variety of DNA sequences (for review, see Durai et al., 2005; Porteus and Carroll, 2005; Carroll et al., 2006). The FokI endonuclease domain functions as a dimer, and digestion of the target DNA requires proper alignment of two ZFN monomers at the target site (Durai et al., 2005; Porteus and Carroll, 2005; Carroll et al., 2006). Efficient and coordinated expression of both monomers is thus required for the production of DSBs in living cells. Transient ZFN expression, by direct gene delivery, is the method of choice for targeted mutagenesis in human and animal cells (e.g. Urnov et al., 2005; Beumer et al., 2006; Meng et al., 2008). Among the different methods used for high and efficient transient ZFN delivery in animal and human cell lines are plasmid injection (Morton et al., 2006; Foley et al., 2009), direct plasmid transfer (Urnov et al., 2005), the use of integrase-defective lentiviral vectors (Lombardo et al., 2007), and mRNA injection (Takasu et al., 2010).In plant species, however, efficient and strong gene expression is often achieved by stable gene transformation. Both transient and stable ZFN expression have been used in gene-targeting experiments in plants (Lloyd et al., 2005; Wright et al., 2005; Maeder et al., 2008; Cai et al., 2009; de Pater et al., 2009; Shukla et al., 2009; Tovkach et al., 2009; Townsend et al., 2009; Osakabe et al., 2010; Petolino et al., 2010; Zhang et al., 2010). In all cases, direct gene-transformation methods, using polyethylene glycol, silicon carbide whiskers, or Agrobacterium, were deployed. Thus, while mutant plants and tissues could be recovered, potentially without any detectable traces of foreign DNA, such plants were generated using a transgenic approach and are therefore still likely to be classified as transgenic. Furthermore, the recovery of mutants in many cases is also dependent on the ability to regenerate plants from protoplasts, a procedure that has only been successfully applied in a limited number of plant species. Therefore, while ZFN technology is a powerful tool for site-specific mutagenesis, its wider implementation for plant improvement may be somewhat limited, both by its restriction to certain plant species and by legislative restrictions imposed on transgenic plants.Here we describe an alternative to direct gene transfer for ZFN delivery and for the production of mutated plants. Our approach is based on the use of a novel Tobacco rattle virus (TRV)-based expression system, which is capable of systemically infecting its host and spreading into a variety of tissues and cells of intact plants, including developing buds and regenerating tissues. We traced the indirect ZFN delivery in infected plants by activation of a mutated reporter gene and we demonstrate that this approach can be used to recover mutated plants.