Developmental Upregulation of an Alternative Form of pcp2 with Reduced GDI Activity

The pcp2/L7 gene is characterized by its very cell type-specific expression restricted to cerebellar Purkinje cells and retinal bipolar neurons. Although remarkable progress as to the biochemical properties of the encoded protein has been made, knowledge on its physiological functions remains sparse. While characterizing a pcp2-driven transgenic strain, we observed the presence of a longer, so far unknown, pcp2 transcript. Different from another recently discovered splice variant, ret-pcp2, expression of this novel transcript is observed in bipolar as well as cerebellar Purkinje cells of mid-postnatal mice. The protein encoded by our novel variant appears to be less efficient in binding to Gα subunits compared to the original L7/pcp2 protein and it is also less inhibitory with respect to GTPγ binding. Its expression in the eye appears to be independent from eye opening in postnatal mice

Rekombinase vermittelter Kassettenaustausch im Mausgenom

Sequenz-spezifische DNA-Rekombination (SSR) bewirkende Systeme aus niederen Organismen, wie z.B. das Cre/loxP-System aus dem P1-Phagen oder das Flp/FRT-System aus Hefe, sind in den letzten Jahren als wichtige und weitverbreitete Werkzeuge zur Modifikation des Säugergenoms etabliert worden. Dies hängt unter anderem mit der Vielfalt an Reaktionen zusammen, welche diese Systeme in der Lage sind durchzuführen. Dazu zählen Exzisions/Deletions-, Integrations-, Inversions- und Translokationsreaktionen. Die hier vorgestellte Arbeit fokussiert auf die Integrationsreaktion, welche aus thermodynamischen Gründen bisher keine breite Anwendung finden konnte, und ihren Einsatz bei der Etablierung allelischer Serien in embryonalen Stammzellen (ES Zellen) oder frühen Embryonen der Maus. Eine solche Methodik wäre ideal für Fragestellungen zu Funktionen von Genen in vivo (Functional Genomics) geeignet. Zur Anwendung kam ein als „Rekombinase vermittelter Kassettenaustausch“ (recombinase-mediated cassette exchange, RMCE) bezeichnetes Verfahren. RMCE ist ein Zwei-Schritt-Verfahren: Zuerst wird der interessierende Genort durch homologe Rekombination derart verändert, daß 5’ und 3’ des Genlocus SSR-Erkennungsstellen eingeführt werden. Durch das Einbringen eines die gleichen Erkennungsstellen tragenden Austauschplasmides und die Bereitstellung der entsprechenden Rekombinase kann die im Genom residierende gegen die eingebrachte Kassette (von Erkennungsstellen flankiertes DNA-Segment) ausgetauscht werden. In dieser Arbeit werden zwei verschiedene Ansätze für RMCE vorgestellt: Der erste Ansatz basiert auf der Verwendung heterospezifischer lox-Sequenzen, welche sich in einer Base unterscheiden (lox511/loxP). Diese Mutation sollte eine effektive Integration durch Verhinderung der Exzision gewährleisten. Es konnte hier gezeigt werden, daß RMCE unter Verwendung einer solchen Methodologie in ES Zellen und frühen Mausembryonen effizient möglich ist, daß das Produkt der Integration jedoch instabil ist und nachfolgender Exzision unterliegt. Diese Deletionsreaktionen sind durch promiskuitive Rekombination der verwendeten lox511 und loxP bedingt. Aus diesen Erkenntnissen wurde ein zweiter Ansatz entwickelt, welcher auf dem simultanen Einsatz des Cre/lox- und des Flp/FRT-Systems basiert. Diese Methodik umgeht die Nachteile promiskuitiver Erkennungssequenzen und ihre Anwendbarkeit, Funktionsfähigkeit und Effizienz in ES Zellen konnten demonstriert werden. Ein solches Verfahren, welches sowohl in Zellkultur als auch in frühen Mausembryonen zum Einsatz kommen könnte, bietet insbesondere im Hinblick auf zukünftige Bedürfnisse in der Functional Genomics viele Optionen

Genetic variations regulate alternative splicing in the 5' untranslated regions of the mouse glioma-associated oncogene 1, Gli1

<p>Abstract</p> <p>Background</p> <p>Alternative splicing is one of the key mechanisms that generate biological diversity. Even though alternative splicing also occurs in the 5' and 3' untranslated regions (UTRs) of mRNAs, the understanding of the significance and the regulation of these variations is rather limited.</p> <p>Results</p> <p>We investigated 5' UTR mRNA variants of the mouse Gli1 oncogene, which is the terminal transcriptional effector of the Hedgehog (HH) signaling pathway. In addition to identifying novel transcription start sites, we demonstrated that the expression ratio of the Gli1 splice variants in the 5' UTR is regulated by the genotype of the mouse strain analyzed. The GT allele, which contains the consensus intronic dinucleotides at the 5' splice site of intron 1B, favors exon 1B inclusion, while the GC allele, having a weaker 5' splice site sequence, promotes exon 1B skipping. Moreover, the alternative Gli1 5' UTRs had an impact on translational capacity, with the shorter and the exon 1B-skipped mRNA variants being most effective.</p> <p>Conclusions</p> <p>Our findings implicate novel, genome-based mechanisms as regulators of the terminal events in the mouse HH signaling cascade.</p

Bi-objective branch-and-cut algorithms based on LP-relaxation and bound sets

Most real-world optimization problems are multi-objective by nature, with conflicting and incomparable objectives. Solving a multi-objective optimization problem requires a method which can generate all rational compromises between the objectives. This paper proposes two distinct bound set based branch-and-cut algorithms for general bi-objective combinatorial optimization problems, based on implicit and explicit lower bound sets, respectively. The algorithm based on explicit lower bound sets computes, for each branching node, a lower bound set and compares it to an upper bound set. The other fathoms branching nodes by generating a single point on the lower bound set for each local nadir point. We outline several approaches for fathoming branching nodes and we propose an updating scheme for the lower bound sets that prevents us from solving the bi-objective LP-relaxation of each branching node. To strengthen the lower bound sets, we propose a bi-objective cutting plane algorithm that adjusts the weights of the objective functions such that different parts of the feasible set are strengthened by cutting planes. In addition, we suggest an extension of the branching strategy "Pareto branching". We prove the effectiveness of the algorithms through extensive computational results

In vitro functional assays to assess the reciprocal interplay between tumor cells and macrophages.

Tumor-associated macrophages (TAMs) are integral components of the tumor microenvironment. They are involved in various aspects of tumor cell biology, driving pathological processes such as tumor cell proliferation, metastasis, immunosuppression, and resistance to therapy. TAMs exert their tumorigenic effects by secreting growth factors, cytokines/chemokines, metabolites, and other soluble bioactive molecules. These mediators directly promote tumor cell proliferation and modulate interactions with immune and stromal cells, facilitating further tumor growth. As research into therapies targeting TAMs intensifies, there is a growing need for reliable methods to comprehend the impact of TAMs on cancer progression and to validate novel therapeutics directed at TAMs. The traditional "M1-M2" macrophage classification based on transcriptional profiles of TAMs is not only too simplistic to describe their physiological roles, it also does not explain differences observed between mouse and human macrophages. In this context, methods that assess how TAMs influence tumor or immune cells, either through direct contact or the release of soluble factors, offer a more promising approach. We describe here comprehensive protocols for in vitro functional assays to study TAMs, specifically regarding their impact on the growth of lung cancer cells. We have applied these methods to both mouse and human macrophages, achieving similar outcomes in promoting the proliferation of cancer cells. This methodology can serve as a standardized approach for testing novel therapeutic approaches, targeting TAMs with novel immunotherapeutic compounds, or utilizing gene-editing techniques. Taken together, the described methodology may contribute to our understanding of complex macrophage-tumor interactions and support the development of innovative therapeutic strategies

Class Frizzled GPCRs in GtoPdb v.2021.3

Receptors of the Class Frizzled (FZD, nomenclature as agreed by the NC-IUPHAR subcommittee on the Class Frizzled GPCRs [175]), are GPCRs originally identified in Drosophila [19], which are highly conserved across species. While SMO shows structural resemblance to the 10 FZDs, it is functionally separated as it mediates effects in the Hedgehog signaling pathway [175]. FZDs are activated by WNTs, which are cysteine-rich lipoglycoproteins with fundamental functions in ontogeny and tissue homeostasis. FZD signalling was initially divided into two pathways, being either dependent on the accumulation of the transcription regulator &#946;-catenin or being &#946;-catenin-independent (often referred to as canonical vs. non-canonical WNT/FZD signalling, respectively). WNT stimulation of FZDs can, in cooperation with the low density lipoprotein receptors LRP5 (O75197) and LRP6 (O75581), lead to the inhibition of a constitutively active destruction complex, which results in the accumulation of &#946;-catenin and subsequently its translocation to the nucleus. &#946;-catenin, in turn, modifies gene transcription by interacting with TCF/LEF transcription factors. WNT/&#946;-catenin-independent signalling can also be activated by FZD subtype-specific WNT surrogates [133]. &#946;-catenin-independent FZD signalling is far more complex with regard to the diversity of the activated pathways. WNT/FZD signalling can lead to the activation of heterotrimeric G proteins [33, 178, 150], the elevation of intracellular calcium [184], activation of cGMP-specific PDE6 [2] and elevation of cAMP as well as RAC-1, JNK, Rho and Rho kinase signalling [56]. Novel resonance energy transfer-based tools have allowed the study of the GPCR-like nature of FZDs in greater detail. Upon ligand stimulation, FZDs undergo conformational changes and signal via heterotrimeric G proteins [239, 240, 102, 174]. Furthermore, the phosphoprotein Dishevelled constitutes a key player in WNT/FZD signalling towards planar-cell-polarity-like pathways. Importantly, FZDs exist in at least two distinct conformational states that regulate pathway selection [240]. As with other GPCRs, members of the Frizzled family are functionally dependent on the arrestin scaffolding protein for internalization [22], as well as for &#946;-catenin-dependent [13] and -independent [89, 14] signalling. The pattern of cell signalling is complicated by the presence of additional ligands, which can enhance or inhibit FZD signalling (secreted Frizzled-related proteins (sFRP), Wnt-inhibitory factor (WIF), sclerostin or Dickkopf (DKK)), as well as modulatory (co)-receptors with Ryk, ROR1, ROR2 and Kremen, which may also function as independent signalling proteins

Class Frizzled GPCRs (version 2019.4) in the IUPHAR/BPS Guide to Pharmacology Database

Receptors of the Class Frizzled (FZD, nomenclature as agreed by the NC-IUPHAR subcommittee on the Class Frizzled GPCRs [156]), are GPCRs originally identified in Drosophila [17], which are highly conserved across species. While SMO shows structural resemblance to the 10 FZDs, it is functionally separated as it mediates effects in the Hedgehog signaling pathway [156]. FZDs are activated by WNTs, which are cysteine-rich lipoglycoproteins with fundamental functions in ontogeny and tissue homeostasis. FZD signalling was initially divided into two pathways, being either dependent on the accumulation of the transcription regulator &#946;-catenin or being &#946;-catenin-independent (often referred to as canonical vs. non-canonical WNT/FZD signalling, respectively). WNT stimulation of FZDs can, in cooperation with the low density lipoprotein receptors LRP5 (O75197) and LRP6 (O75581), lead to the inhibition of a constitutively active destruction complex, which results in the accumulation of &#946;-catenin and subsequently its translocation to the nucleus. &#946;-Catenin, in turn, modifies gene transcription by interacting with TCF/LEF transcription factors. &#946;-Catenin-independent FZD signalling is far more complex with regard to the diversity of the activated pathways. WNT/FZD signalling can lead to the activation of heterotrimeric G proteins [28, 159, 135], the elevation of intracellular calcium [164], activation of cGMP-specific PDE6 [2] and elevation of cAMP as well as RAC-1, JNK, Rho and Rho kinase signalling [48]. Novel resonance energy transfer-based tools have allowed the study of the GPCR-like nature of FZDs in greater detail. Upon ligand stimulation, FZDs undergo conformational changes and signal via heterotrimeric G proteins [213, 214]. Furthermore, the phosphoprotein Dishevelled constitutes a key player in WNT/FZD signalling. Importantly, FZDs exist in at least two distinct conformational states that regulate the pathway selection [214]. As with other GPCRs, members of the Frizzled family are functionally dependent on the arrestin scaffolding protein for internalization [19], as well as for &#946;-catenin-dependent [12] and -independent [80, 13] signalling. The pattern of cell signalling is complicated by the presence of additional ligands, which can enhance or inhibit FZD signalling (secreted Frizzled-related proteins (sFRP), Wnt-inhibitory factor (WIF), sclerostin or Dickkopf (DKK)), as well as modulatory (co)-receptors with Ryk, ROR1, ROR2 and Kremen, which may also function as independent signalling proteins

Class Frizzled GPCRs in GtoPdb v.2023.1

Receptors of the Class Frizzled (FZD, nomenclature as agreed by the NC-IUPHAR subcommittee on the Class Frizzled GPCRs [180]), are GPCRs originally identified in Drosophila [20], which are highly conserved across species. While SMO shows structural resemblance to the 10 FZDs, it is functionally separated as it is involved in the Hedgehog signaling pathway [180]. SMO exerts its effects by activating heterotrimeric G proteins or stabilization of GLI by sequestering catalytic PKA subunits [186, 6, 58]. While SMO itself is bound by sterols and oxysterols [27, 94], FZDs are activated by WNTs, which are cysteine-rich lipoglycoproteins with fundamental functions in ontogeny and tissue homeostasis. FZD signalling was initially divided into two pathways, being either dependent on the accumulation of the transcription regulator &#946;-catenin or being &#946;-catenin-independent (often referred to as canonical vs. non-canonical WNT/FZD signalling, respectively). WNT stimulation of FZDs can, in cooperation with the low density lipoprotein receptors LRP5 (O75197) and LRP6 (O75581), lead to the inhibition of a constitutively active destruction complex, which results in the accumulation of &#946;-catenin and subsequently its translocation to the nucleus. &#946;-catenin, in turn, modifies gene transcription by interacting with TCF/LEF transcription factors. WNT/&#946;-catenin-dependent signalling can also be activated by FZD subtype-specific WNT surrogates [138]. &#946;-catenin-independent FZD signalling is far more complex with regard to the diversity of the activated pathways. WNT/FZD signalling can lead to the activation of heterotrimeric G proteins [34, 183, 155], the elevation of intracellular calcium [189], activation of cGMP-specific PDE6 [2] and elevation of cAMP as well as RAC-1, JNK, Rho and Rho kinase signalling [57]. Novel resonance energy transfer-based tools have allowed the study of the GPCR-like nature of FZDs in greater detail. Upon ligand stimulation, FZDs undergo conformational changes and signal via heterotrimeric G proteins [244, 245, 107, 179, 104]. Furthermore, the phosphoprotein Dishevelled constitutes a key player in WNT/FZD signalling towards planar-cell-polarity-like pathways. Importantly, FZDs exist in at least two distinct conformational states that regulate pathway selection [245]. As with other GPCRs, members of the Frizzled family are functionally dependent on the arrestin scaffolding protein for internalization [23], as well as for &#946;-catenin-dependent [14] and -independent [91, 15] signalling. The pattern of cell signalling is complicated by the presence of additional ligands, which can enhance or inhibit FZD signalling (secreted Frizzled-related proteins (sFRP), Wnt-inhibitory factor (WIF), sclerostin or Dickkopf (DKK)), as well as modulatory (co)-receptors with Ryk, ROR1, ROR2 and Kremen, which may also function as independent signalling proteins

Class Frizzled GPCRs in GtoPdb v.2025.3

Receptors of the Class Frizzled (FZD, nomenclature as agreed by the NC-IUPHAR subcommittee on the Class Frizzled GPCRs [184]), are GPCRs highly conserved across species and were originally identified in Drosophila [21]. While SMO shows structural resemblance to the 10 FZDs, it is functionally separated as it is involved in Hedgehog signaling [184]. SMO exerts its effects by activating heterotrimeric G proteins or stabilization of GLI by sequestering catalytic PKA subunits [191, 6, 62]. While SMO itself is bound by sterols and oxysterols [28, 96], FZDs are activated by WNTs, which are cysteine-rich lipoglycoproteins with fundamental functions in ontogeny and tissue homeostasis. FZD signaling was initially divided into two pathways, being either dependent on the accumulation of the transcription regulator &#946;-catenin or being &#946;-catenin-independent (often referred to as canonical vs. non-canonical WNT/FZD signaling, respectively). Nevertheless, it makes pharmacologically more sense to define downstream signaling by transducer coupling to either DVL or heterotrimeric G proteins [185]. WNT stimulation of FZDs can, in cooperation with the low density lipoprotein receptors LRP5 (O75197) and LRP6 (O75581), lead to the inhibition of a constitutively active destruction complex, which results in the accumulation of &#946;-catenin and subsequently its translocation to the nucleus. &#946;-catenin, in turn, modifies gene transcription by interacting with TCF/LEF transcription factors. WNT/&#946;-catenin-dependent signalling can also be activated by FZD subtype-specific WNT surrogates [142]. &#946;-catenin-independent FZD signalling is far more complex with regard to the diversity of the activated pathways. WNT/FZD signalling can lead to the activation of heterotrimeric G proteins [35, 188, 159], the elevation of intracellular calcium [194], activation of cGMP-specific PDE6 [2] and elevation of cAMP as well as RAC-1, JNK, Rho and Rho kinase signalling [61]. Novel resonance energy transfer-based tools have allowed the study of the GPCR-like nature of FZDs in greater detail. Upon ligand stimulation, FZDs undergo conformational changes and signal via heterotrimeric G proteins [248, 249, 110, 183, 108, 56, 13]. Furthermore, the phosphoprotein Dishevelled constitutes a key transducer in WNT/FZD signaling towards planar-cell-polarity-like pathways. Importantly, FZDs adopt distinct conformational landscapes that regulate pathway selection [249, 54]. As with other GPCRs, members of the Frizzled family are functionally dependent on the arrestin scaffolding protein for internalization [24], as well as for &#946;-catenin-dependent [15] and -independent [93, 16] signalling. The pattern of cell signalling is complicated by the presence of additional ligands, which can enhance or inhibit FZD signalling (secreted Frizzled-related proteins (sFRP), Wnt-inhibitory factor (WIF), sclerostin or Dickkopf (DKK)), as well as modulatory (co)-receptors with Ryk, ROR1, ROR2 and PTK7, which may also function as independent signaling proteins. An important FZD4-selective non-WNT agonist is the norrin cysteine knot protein, which is a key player in FZD4-mediated vascularization for example in the retina and which is functionally related to familial exudative vitreoretinopathy (FEVR)

Inhibition of heat shock protein 90 with AUY922 represses tumor growth in a transgenic mouse model of islet cell neoplasms

Background: This study was designed to evaluate the role of heat shock protein 90 (HSP90) in tumor progression of murine islet cell tumors. Blockade of HSP90 has recently been proposed as a therapeutic target, but effects in models of islet cell tumors with AUY922, a newly developed HSP90 inhibitor, have not been examined. Material and Methods: The carcinoid cell line BON-1 and the HSP90 inhibitor AUY922 were used to determine effects on signaling and growth in vitro. In vivo transgenic RIP1-Tag2 mice, which develop islet cell neoplasms, were treated with vehicle or AUY922 (25 mg/kg/twice per week) from week 5 until death. The resected pancreata were evaluated macroscopically and microscopically by immunohistochemistry. Quantitative real-time PCR was performed for HSP90 targets with RNA from islets isolated from treated and untreated RIP1-Tag2 mice. Results: HSP90 blockade impaired constitutive and growth factor-induced signaling in vitro. Moreover, HSP90 inhibition attenuated in vitro cell growth in a dose-dependent manner. In vivo, AUY922 significantly reduced tumor volume by 92% compared to untreated controls (p = 0.000), and median survival in the used transgenic mouse model was prolonged (110 vs. 119 days; p = 0.75). Quantitative real-time PCR for downstream target genes of HSP90 demonstrated significant downregulation in the islet cell tumors of RIP1-Tag2 mice treated with AUY922, confirming our ability to achieve effective pharmacologic levels of AUY922 within the desired tissue site in vivo. Conclusion: This is the first study to show that the HSP90 antagonist AUY922 may provide a new option for therapy of islet cell neoplasms