# Patent

## Title
Archease as RNA ligaes complex member

## Abstract

The present invention relates to the use of Archease proteins as RNA ligase enhancer, methods of ligating RNA molecules, kits for these methods and uses and transgenic cells.

## Background
CROSS-REFERENCE TO RELATED APPLICATION
This application relates to and claims the benefit of priority from European Patent Application No. 12165153.3, filed on Apr. 23, 2012, the entire disclosure of which is incorporated herein by reference.
The present invention relates to the field of cell and molecular biology tools, in particular to enzyme complexes with RNA ligase activity, said complexes or their parts for analysis and therapeutics.
The Endoplasmic Reticulum (ER) maintains homeostasis in protein folding, modification and secretion by sensing and responding to stress conditions leading to the accumulation of unfolded proteins in the ER lumen. The Unfolded Protein Response (UPR) signals from the ER to the nucleus through three stress-responsive signalling pathways in mammals. The most conserved UPR signalling pathway is initiated by Ire1, an ER resident transmembrane protein that responds to unfolded proteins in the ER lumen by dimerisation, autophosphorylation and activation of a cytoplasmic nuclease domain. Ire1 cleaves the mRNA encoding the transcription factor Xbp1 removing a 26 nt intron in the ORF. Religation of the exon halves by an unknown RNA ligase causes a frameshift, which allows translation to proceed past a stop codon. The resulting full-length protein (referred to as Xbp1s) moves to the nucleus and activates downstream target genes to help restore ER homeostasis.
In yeast, both tRNA splicing and non-conventional mRNA splicing during the UPR are executed by the tRNA ligase Trl1 through a 5′P dependent ligation pathway. This is possible because mRNA cleavage by Ire1 and pre-tRNA cleavage by the Sen endonuclease complex (TSEN) both generate 2′-3′ cyclic phosphate and 5′hydroxyl termini amenable for Trl1. The mammalian tRNA ligase recently identified as a pentameric protein complex with HSPC117 as the catalytic component (Popow et al., 2011), required similar termini but ligates through a different mechanism.
Previously, the inventors have identified HSPC177 as RNA ligase (WO 2012/028606 A1). Splicing of several human pre-tRNAs requires the removal of introns and the ligation of the generated 5′ and 3′ exons by HSPC117 homologous proteins found in bacteria, archaea and vertebrates but generally not in plants and fungi.
It is a goal to identify ligases or their cofactors involved in non-conventional splicing induced by the Unfolded Protein Response (UPR), a stress response caused by misfolded proteins in cells, especially in the ER.
The present invention is based on the finding that Archease, while not being sufficient for splicing activity on its own, is required for efficient ligation of nucleic acids. Although ligases may be active on their own, Archease is able to strongly boost ligase activity. The invention thus provides the use of Archease for enhancing the ligase activity of a ligase enzyme. The invention also encompasses inhibition of Archease to reduce splicing activity, especially upon UPR, in a cell, which may cause cell death, e.g. by apoptosis or breakdown of cell metabolism, or reduction of cell growth or protein production. The invention is further defined by the subject matter of the claims.
Despite years of intense study, the identity of the ligation process in non-conventional splicing has eluded discovery in mammalian cells. While HSPC117 is the likely candidate for this splicing activity, it has been shown herein with certainty that ligation is dependent on Archease for stimulation of ligase activity. It is assumed that a few ligase complexes (possibly associated with the ER membrane) may suffice to induce non-conventional splicing upon induction of stress response as long as Archease is present to stimulate enzymatic rate.
Archease has been sequenced (e.g. Genbank ACC NO: NP_848642) and has been previously characterized as a protein with two SHS2 domains with one inserted into another. It usually has a three layer beta-alpha-beta sandwich domain similar to those found in chaperones. Archease proteins form a cluster of orthologous genes (KOG4528) with no detectable representatives in the plant or fungal model organisms. As used herein the expression “Archease” or “Archease protein” refers to any homologous or orthologous molecule in this cluster which has now been identified to enhance ligase reactions, especially RNA ligase reaction of e.g. spicing ligases like HSPC117. Example sequences of such Archease proteins are given in FIG. 5 as SEQ ID NO: 24 to SEQ ID NO: 44. Most Archease enzymes share the catalytic residues corresponding to D39 and/or K144 of SEQ ID NO: 28.
The ligase enhanced by the Archease can be used to catalyze the transfer of a first polynucleotide to a second polynucleotide. The ends of both polynucleotides can be connected by the ligase. This connection is usually a covalent connection of a phosphodiester bond between both polynucleotides. In particular, one polynucleotide may comprise a 3′ phosphate, in particular in form of a 2′,3′-cyclic phosphate, and the other may comprise a 5′-OH terminus.
In general, the polynucleotide ligation can be an inter- or intra-strand ligation. Two separate polynucleotide strands may be connected on the 3′ and 5′ end, respectively. Furthermore, in an intra-strand ligation, the 5′ and 3′ end of one polynucleotide molecule is connected.
In a further embodiment of the present invention the polynucleotide is double-stranded. In particular, the first and/or second polynucleotide molecule connected by the ligase enhanced by the Archease may comprise a double-stranded section or is fully double-stranded or alternatively single-stranded. In particular preferred, the 3′ end mentioned above as well as the 5′ terminus of the other polynucleotide end, which are connected by the ligase reaction, may be double-stranded. Further portions of the polynucleotide can also be single-stranded, in the case of RNA splicing there is usually a single-stranded 3′ overhang of a pre-tRNA. Also, the 5′ and/or 3′ ends, which are connected by the ligase reaction may be single-stranded—as is usually the case in pre-tRNA processing. Double-strandedness may be a base pairing between the first and the second polynucleotide molecules, or alternatively may be base pairing to further polynucleotide strands.
In preferred embodiments the ligase is an RNA ligase. The first and/or second polynucleotide may be RNA. In particular preferred embodiments the present ligase enhanced by the Archease is used for RNA splicing. In an RNA splicing reaction an intron section is removed between two exons, which are connected by the ligase. A typical splicing reaction is the reaction of an exon1-intronexon2 sequence to exon1-exon2. Other splicing reactions may remove several introns and, optionally also exons between these intron sections.
The polynucleotides that are connected by the inventive use of the ligase may be of any length. Example polynucleotide lengths are 2 to 3000 nucleotides or base pairs in length. In special embodiments, the first polynucleotide or the second polynucleotide may be more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 40, 45, 50, 60, 70, 80, 90 or more than 100 nucleotides or base pairs in length. Alternatively or in addition thereto, the polynucleotide, either the first polynucleotide or second polynucleotide or both, may be up to 3000, 2000, 1500, 1200, 1000, 900, 800, 700, 600, 500, 400, 300, 200, 100, 80, 70, 60 or up to 50 nucleotides or base pairs in length.
In preferred embodiments the ligase enzyme is HSPC117. HSPC117 has been characterized previously as RNA ligase (WO 2012/028606 A1, incorporated herein by reference). The same definitions of HSPC117 molecules are used herein. In particular, the present invention relates to the use of a HSPC117 molecule as RNA ligase as a molecular biology tool and in therapeutics. HSPC117 has been sequenced (e.g. Genbank ACC NO: NP_055121 or CAG33456), and located at chromosome 22 orf 28 (“C220RF28”). HSPC117 is the human homolog of the bacterial/archaeal RtcB gene family characterised by a highly conserved domain of unknown function (UPF0027) and a unique protein fold. UPF0027 proteins form a cluster of orthologous genes (KOG3833) with no detectable representatives in the plant or fungal model organisms. This phyletic distribution is highly reminiscent of the exclusive occurrence of RNA>p ligase activity in animals and archaea. HSPC117 is also referred herein as HSPC117/C220RF28 or RtcB/HSPC117. As used herein the expression “HSPC117 molecule” refers to any homologous or orthologous molecule in this cluster which has now been identified to catalyze an RNA ligase reaction. Example sequences of such “HSPC117 molecules” are given in SEQ ID NOs: 1 to 11, 13, 15, 17, 19, 21, and 23. All HSPC117 molecules have been found to contain the catalytic cysteine residue corresponding to C122 of SEQ ID NO: 1.
In preferred embodiments, the HSPC117 molecule is set forth as in any one of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 15, 17, 19, 21, or 23. The Homo sapiens HSPC117 is encoded by the mRNA sequence of SEQ ID NO: 46 (NCBI database accession number NM_014306) or by the coding sequence of SEQ ID NO: 12. The mRNA can be targeted by siRNA molecules for inhibition.
In preferred embodiments the inventive ligase, e.g. HSPC117, is of an animal or archaea, in particular of a mammal, such as a primate, including human, or rodent, in particular mouse or rat.
The inventive HSPC117 molecule may be further modified by one or more amino acid substitution or deletion. Furthermore, the inventive HSPC117 molecule may be expressed as part of a fusion protein and may comprise further additional amino acids or polypeptide sequences. In particular preferred, the inventive HSPC117 molecule has a sequence identity of at least 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90% or at least 95% to any one of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 21, SEQ ID NO: 23. In preferred embodiments the sequence identity is related to SEQ ID NO: 1. Sequence identities are usually calculated over the whole length sequences of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 21, SEQ ID NO: 23. Of course such a HSPC117 molecule variant maintains the RNA ligase activity as mentioned above as can be easily determined by standard assays as known in the art, e.g. in WO 2012/028606 A1, or as shown in the example section herein. In particular of importance is that the HSPC117 molecule maintains catalytically important residues, such as cysteine 122 of SEQ ID NO: 1. Variants of the inventive HSPC117 molecules are e.g. described in US 2007/0204352 A1 (especially SEQ ID NOs: 15, 16, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78 thereof), incorporated herein by reference as SEQ ID NOs: 12 to 23, and can be used for the inventive purposes.
Preferred Archease proteins are set forth as in any one of SEQ ID NOs: 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, or 44. SEQ ID NOs: 24 to 43 are provided in an alignment in FIG. 5 with corresponding amino acids aligned to each other. SEQ ID NO: 44 is a further expression variant with 12 additional N-terminal amino acids of the Homo sapiens Archease of SEQ ID NO: 28. The Homo sapiens Archease is encoded by the mRNA sequence of SEQ ID NO: 45 (NCBI database accession number NM_178547). The mRNA can be targeted by siRNA molecules for inhibition.
Most Archease enzymes share the catalytic residues corresponding to D39 and/or K144 of SEQ ID NO: 28. Preferably the Archease comprises the sequence portion (E or D or V)-(I or V or P)-K-(A or S)-(V or I or P or M or A or L). Amino acid alternatives given in brackets; The K in said sequence portion corresponds to K144 of SEQ ID NO: 28. Alternatively or in addition, the Archease may comprise the sequence portion (D or E or P)-(H or T or I)-(T or P or M)-A-D-(I or V or A or L). Amino acid alternatives given in brackets; The D in said sequence portion corresponds to D39 of SEQ ID NO: 28. Such sequence portions are present in the sequences given in FIG. 5 for SEQ ID NO: 24 to 43, which are preferred forms of such sequence portions.
In preferred embodiments the inventive Archease is of an animal or archaea, in particular of a mammal, such as a primate, including human, or rodent, in particular mouse or rat.
The inventive Archease may be further modified by one or more amino acid substitution or deletion. Furthermore, the inventive Archease may be expressed as part of a fusion protein and may comprise further additional amino acids or polypeptide sequences. In particular preferred, the inventive Archease has a sequence identity of at least 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90% or at least 95% to any one of SEQ ID NOs: 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, or 44. In preferred embodiments the sequence identity is related to SEQ ID NO: 28. Sequence identities are usually calculated over the whole length sequences of SEQ ID NOs: 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, or 44. Of course such an Archease variant maintains the ligase enhancing activity as mentioned above as can be easily determined by standard ligase assays as known in the art, e.g. in WO 2012/028606 A1, or as shown in the example section herein.
In the case of amino acid substitution (of both the Archease or the ligase), in preferred embodiments at least 50%, at least 60%, at least 70%, at least 80%, at least 90% or at least 95% of the substitutions are conserved amino acid substitutions. Conserved substitutions are mutations within an amino acid group. Amino acids are usually grouped according to their polarity, charge and/or size. The following groups are noteworthy: basic amino acids: arginine, histidine, lysine; acidic amino acids: aspartic acid, glutamic acid; polar amino acids: asparagine, glutamine; small amino acids: alanine, serine, threonine, methionine, glycine; aromatic amino acids: phenylalanine, tryptophan, tyrosine, histidine; hydrophobic amino acids: leucine, isoleucine, valine. Cysteine is a special case, as it may usually be conservatively substituted with serine and any other polar uncharged sidechain and vice versa. Glycine may be used as substituent for any amino acid. Glycin can be substituted usually by a small sidechain such as by alanine, serine, threonine. Proline may be usually substituted, or used as substituent for glycin.
In a further aspect, the present invention relates to the method of ligating at least two polynucleotide molecules—as e.g. described above—using an Archease and a ligase as described above. Herein, the expressions “use . . . as ligase” and “method of ligating polynucleotide molecules” are used interchangeably.
In preferred embodiments the inventive use or method may comprise contacting at least two polynucleotide molecules with the ligase and the Archease in a cell. The invention also relates to the use of recombinant ligase and/or Archease. Recombinant ligase and Archease (including any homologs or orthologs as mentioned above) can be readily obtained by expression of genetic constructs comprising one or more ligase or Archease DNA sequences operable linked to regulatory DNA sequences (which may be heterologuous regulatory sequences), such as promoters or enhancers, in host cells. Example host cells are bacterial, archaea, fungal (including yeast), plant or animal (including insect or mammalian) cells. In such constructs, the design of which is described in common laboratory manuals and is routine to a skilled practitioner, the regulatory sequences may be operably linked to a polynucleotide encoding the ligase or an active variant thereof having ligase activity and the Archease or an active variant thereof having ligase enhancing activity. Especially for but not limiting to in vitro purposes, the Archease and/or ligase may be provided in isolated and/or purified form.
The inventive Archease (and the ligase) may be used in vivo such as in a cell, e.g. artificially provided therein or recombinantly expressed in the cell. Two polynucleotide molecules may be ligated in said cell according to an embodiment of the present invention. The cell may be any cell as described above, preferably a non-human cell or an isolated human cell.
In a further embodiment the polynucleotide molecules may be contacted with a ligase and the Archease in vitro or in situ such as e.g. including outside a cell or in a cell free solution. With the inventive Archease and ligase it is possible to ligate polynucleotide molecules in an isolated fashion, ex vivo.
According to the present invention the Archease protein may be provided per se. Alternatively, Archease proteins may be used or provided as a component of a kit.
Thus, in a further aspect the invention relates to a kit that contains an Archease. The kit may further comprise a ligase reaction buffer comprising buffer components and one or more metal ions selected from Mg2+, Mn2+, Ni2+ or mixtures thereof. In preferred embodiments the metal ions are included in an amount for use in a final concentration range of ca 0.1-20 mM, preferably 1-10 mM, in particular preferred 2-5 mM.
Besides the above-mentioned metal ions, the buffer of the kit may contain the usual buffer components that are well known in the art. Such buffers may e.g. include phosphate, Hepes, Tris-HCl components. Preferably the buffer is in the range of physiological pH values of e.g. pH 6 to pH 9, preferably pH 7-8, especially preferred about pH 7.4. The buffer may comprise tonic substances or salts ranging from about 10-200 mM KCl or NaCl. Furthermore, the buffer may contain non-ionic tonicity substances such as glycerol.
In the form of a test kit, the kit may further comprise a polynucleotide, especially a RNA molecule, that is a substrate of ligase enhanced by the Archease, especially a polynucleotide with a 2′,3′ cyclic phosphate. The kit may also comprise GTP, which is used by the Archease in guanylation reactions. This polynucleotide or the GTP may e.g. further comprise a label such as a radioactive label or fluorescent label to detect the polynucleotide molecule before or after the ligase reaction or to detect GTP binding to the Archease or to detect transfer of a G residue to a ligase.
The kit preferably comprises a ligase, especially preferred as described above, e.g. a RNA ligase such as HSPC117. Such a kit is useful for all types of reactions and to monitor polynucleotide processing or hybridisation. The inventive Archease or kit may be especially used for ligation or splicing studies or for obtaining Archease inhibitors, especially by the methods described below. The Archease may be immobilized for ease of phase separation and/or comprise a label. Said label may be used to immobilize the Archease. Example labels include a His-tag or a FLAG-label.
The present invention in a further aspect relates to a transgenic cell comprising an exogenously expressed Archease protein. The cell may be a cell line or comprised in an animal model, in particular a non-human animal model. A cell line may be also a human cell line that stably expresses Archease proteins.
Stable expression of the exogenously expressed Archease protein is achieved by inserting an Archease DNA, under the control of a promoter, preferably an inducible promoter, into the cell. In certain embodiments this DNA can be inserted in the genome of the cell, which can be achieved by conventional methods such as commercially available systems like the tetracycline-inducible system such as the t-REx system (invitrogen). Such cells are useful in combination with RNA that can be ligated, especially RNA with 2′,3′ cyclic phosphate or 5′-OH to ligate the RNA molecules.
The cell or cell line may further express an exogenously expressed ligase enzyme, e.g. as described above, preferably with an inducible promoter.
The present invention further relates to methods of reducing ligase activity, in particular RNA ligase activity, e.g. RNA>p ligase activity, in a cell comprising inhibiting a Archease molecule in a cell, preferably by knock-out or RNAi. RNA>p ligase activity, as mentioned above, relates to RNA ligase reactions using 2′,3′-cyclic phosphate terminated RNA as substrate. Such a method can be used to reduce tRNA production or processing in said cell. Further or alternatively, such a method can be used to reduce Unfolded Protein Response (UPR) in a cell. A reduction of Archease can be achieved by administering a ligand to Archease that binds, segregates or generally inactivates Archease in said cell or by inhibiting Archease expression. Such a binding inhibitor is e.g. an Archease antibody, which is e.g. commercially available. An “Archease-antibody” includes any functional equivalents and derivatives thereof, including antibody fragments such as Fab, F(ab)2, Fv, or single chain antibodies (scAb) that binds Archease. In preferred embodiments the inhibition is achieved by reducing expression of an Archease, preferably an endogenous Archease, in said cell. A suitable inhibitor to reduce Archease expression is an Archease siRNA molecule to induce RNAi.
Preferred methods of inhibiting Archease expression are knock-out or RNAi. For a knock-out, a genomic Archease is modified to prevent or reduce expression, transcription or translation of a functional Archease. Such modifications may include large stretch deletion of e.g. up to 200 or more nucleotides or selective modifications (deletions or substitutions) in the catalytic centre. E.g. a modification in the catalytic D39 and/or K144 according to the human Archease sequence of SEQ ID NO:28 is sufficient to prevent expression of a functional molecule. Of course the skilled man in the art can readily select alternative modifications, which are within the routine ability of a molecular cell biologist.
A further preferred method is RNAi (RNA interference). For antagonizing cellular Archease expression preferably siRNA molecules are administered to reduce the expression and function. RNA interference is a mechanism to suppress gene expression in a sequence-specific manner. RNA interference is a highly effective methodology for suppression of specific gene function in eukaryotic cells. When applied to cells and organisms, RNAi entails the degradation of target mRNA upon transfection of short interfering RNA (siRNA) oligos or short-hairpin RNA (shRNA) encoding vectors. Various methods of RNAi have been described and are generally known for altering gene expression in plant cells, drosophila and human melanoma cells as is described for example in US 2002/0162126 and US 2002/0173478. The siRNA for use in the methods and compositions of the invention are selected to target Archease. In this manner they are targeted to various RNAs or portions thereof corresponding to the Archease gene or mRNA (SEQ ID NO: 45). It is understood by one of skill in the art that the siRNA as herein described may also include altered siRNA that is a hybrid DNA/RNA construct or any equivalent thereof, double-stranded RNA, microRNA (miRNA), as well as siRNA forms such as siRNA duplications, small hairpin RNA (shRNA) in viral and non-viral vectors and siRNA or shRNA in carriers. Example siRNA molecules are provided as SEQ ID NO: 47 and 48 herein and are further commercially available.
In a further embodiment the invention relates to an Archease knock-out cell or cell with reduced or inhibited endogenous Archease expression.
In preferred embodiments said cell further has a knock-out of a ligase, e.g. RNA ligase like HSPC117, or reduced or inhibited expression of said ligase. Ligase inhibition can be performed similarly as described above for Archease, e.g. by knock-outs, inhibitor administration like anti-ligase antibodies or siRNA. siRNAs may target the ligase gene or mRNA, e.g. the mRNA of HSPC117 as set forth in SEQ ID NO: 46 or any homolog or ortholog variant thereof as expressed in said cell.
Such cell lines can be further used in polynucleotide ligation or splicing studies, i.e. to study the function of polynucleotide ligation. Further, the cell lines can be used to study UPR responses. In a transgenic cell wherein Archease is under control of an inducible promoter this allows specific on/off studies of the ligase enhancement and UPR responses and is a useful tool to control the ligase activity, be it only for splicing studies, for UPR studies or as a cellular biochemical engineering tool. Therefore, in a preferred embodiment, the invention relates to an Archease knock-out cell that does not express endogenous Archease but is in addition exogenously transfected with an Archease polynucleotide under control of an inducible promoter. In preferred embodiments the cell is a mammal cell, especially preferred a cell of a primate, in particular of a human or of a rodent such as a mouse cell. These cells, including cells with increased or decreased Archease expression as described above, can be used for ligation, splicing or UPR studies, in particular to identify inhibitors or enhancers of UPR that act on Archease.
Said cell may be in a non-human model animal, which may similarly be used to study Archease, ligase action, splicing and especially UPR in said animal. The animal may conditionally express Archease by using a suitable conditional promoter as known in the art. Thus the invention also relates to such model animals.
The inventive method of reducing RNA ligase activity in a cell comprising inhibiting an Archease in the cell, e.g. by knock-out or RNAi, preferably reduces the expression of Archease, preferably an endogenous Archease, in said cell. This method can be used to reduce the Unfolded Protein Response (UPR) in said cell.
The method may further comprise inducing stress in said cell, whereby unfolded proteins accumulate in said cell. Stress—be it by temperature increase, increased metabolism (such as in cancer cells) or by chemicals—can cause an increased production of proteins that are not properly folded. The UPR is activated in response to an accumulation of unfolded or misfolded proteins in the lumen of the endoplasmic reticulum. The UPR has two primary aims: initially to restore normal function of the cell by halting protein translation and activate the signaling pathways that lead to increasing the production of molecular chaperones involved in protein folding. If these objectives are not achieved within a certain time lapse or the disruption is prolonged, the UPR aims towards apoptosis. Thus the inventive Archease inhibition can be used to induce apoptosis in a cell. The inventive method or uses of Archease also include the prevention (or reducing the risk) of apoptosis in a cell due to unfolded protein accumulation, said method comprising increasing Archease protein amounts or expression levels in said cell, whereby an unfolded protein response in said cell is increased.
One of the primary functions of the ER is to exert quality control on the proteins it makes: Only properly folded proteins are packaged into ER exit vesicles and allowed to move onward to be displayed on the cell surface. For this purpose, the lumen of the endoplasmic reticulum (ER) provides an oxidative compartment wherein proteins destined for secretion or insertion into cellular membranes are co-translationally modified with sugar moieties and folded. Stresses that compromise the ER environment impair maturation resulting in the accumulation of misfolded proteins and activation of a stress response termed the unfolded protein response (UPR). Environmental stresses that reduce carbon source availability (glucose), and oxygen, which occurs under pathogenic conditions such as cancer and viral infection, also have a direct impact on secretory homeostasis and thereby trigger the UPR. During UPR, inhibition of protein synthesis serves to lower the overall rate of protein traffic into the ER, but the fact that this process is counterbalanced by an increased synthesis of ER chaperones highlights the specificity of the UPR.
Prolonged activity of the UPR, an indication that ER stress cannot be mitigated and homeostasis cannot be reestablished, correlates with cell death. This suggests that the commitment to apoptosis in this context may have evolved to protect the organism from rogue cells that lack the capacity to ascertain the fidelity of their signaling components. A life-or-death decision, based on an assessment of whether ER stress can be mitigated in a timely fashion, explains the UPR's central role in numerous human diseases. Examples include protein-misfolding diseases such as retinitis pigmentosa, an inherited form of blindness in which the retina degenerates by apoptotic cell death when a misfolded mutant rhodopsin is produced during retinal development. Another example is type II diabetes, in which pancreatic beta cells are compromised by excessive demand for insulin production. Certain types of cancer, especially those that arise in secretory tissues, such as multiple myeloma, use the cytoprotective role of the UPR to sustain their rapid growth.
In a further aspect the present invention relates to the treatment of diseases with abnormal tRNA processing or diseases dependent on (increased) tRNA processing. This treatment is tied to the ability of Archease to strongly modify the activity of RNA ligases like HSPC117. Moreover, the present invention relates to the treatment of diseases with causing a deficiency in UPR or diseases causing increased UPR or disorders associated with the UPR. The inventive treatment may not necessarily relate to a treatment in a curative sense but may also be a reduction of disease symptoms. The inventive treatment may also be a prophylactic treatment to reduce the risk of disease occurrence or symptom occurrences.
“Prevention” as used here shall not be construed as an absolute preventive effect but as a relative term, that is used to express the reduction of the risk of disease or disease symptom development. Treatments for prevention are prophylactic treatments.
In preferred embodiments the inventive treatment targeting Archease is combined with a treatment targeting an RNA ligase, like HSPC117. In preferred embodiments, Archease inhibition or inhibitors are combined with RNA ligase, e.g HSPC117, inhibition or inhibitors. In further embodiments, Archease enzyme activators are combined with RNA ligase, e.g HSPC117, activators. Such activators are e.g. the enzymes themselves or polynucleotides, e.g. vectors, encoding said enzymes.
In particular embodiments the invention provides the use of an Archease as an polynucleotide ligase enhancer or a method of inhibiting an Archease, with the proviso that methods for treatment of the human or animal body by therapy are excluded, or the use of an Archease or Archease inhibitor for use as medicament. An Archease inhibitor is any molecule that reduces Archease activity or expression as described above, preferably an Archease antibody or Archease siRNA.
It was found that Archease is required for the splicing of the Xbp1 mRNA. Archease thus has potential as a therapeutic target, for instance in the form of inhibitors to impair splicing (the case of multiple myeloma) or by enhancing Archease expression when UPR needs to be boosted. It is worth to note that, hitting the UPR pathway downstream of the endonuclease IRE1, more precisely at the ligation step, should not affect IRE1's mRNA decay function. Potent inhibitors of IRE1 have been identified as salicylaldehyde analogs (U.S. Pat. No. 7,858,666 and US 2009/0291857 A1).
In diabetes, the ultimate cell fate decision of life or death is dependent on the nature and severity of ER stress to which the β-cell is exposed. Thus, there are two types of ER stress conditions: resolvable and unresolvable. When ER stress can be resolved, the UPR promotes β-cell survival, whereas under unresolvable ER stress conditions, the UPR activates death effectors, leading to β-cell apoptosis. When β-cells are exposed to conditions that induce mild ER stress (e.g. physiological exposure to glucose fluctuations after a meal), the ER can facilitate stress mitigation and restore protein homeostasis, thus ‘priming’ cells for future ER stress insult and promoting cell survival. This situation also benefits from a more efficient UPR, which could be achieved by overexpressing a tRNA ligase (e.g. HSPC117) and/or Archease. Thus the present invention also provides a method of treating diabetes or preventing the risk of diabetes progression comprising administering an Archease agonist, e.g. an Archease enzyme or Archease encoding polynucleotide such as a suitable vector, to said patient. Preferably the Archease agonist is administered in combination with a HSPC117 agonist, e.g. HSPC117 or a HSPC117 encoding polynucleotide such as a HSPC117 encoding vector.
XBP1 has also been identified as a cellular transcription factor that binds to an enhancer in the promoter of the T cell leukemia virus type 1 promoter. Thus the invention also provides the treatment of T cell leukemia virus infections with an Archease inhibitor that reduced expression of XBP1 as shown herein. The generation of XBP1s during plasma cell differentiation also seems to be the cue for Kaposi's sarcoma-associated herpesvirus and Epstein Barr virus reactivation from latency. Thus the invention also relates to the treatment or prevention of these diseases with an Archease inhibitor.
A further disease condition which benefits from Archease activity is Alzheimer's disease. It is therapeutically beneficial to activate the UPR in such a way where neuronal cells survive the apoptotic effects due to unfolded aggregates of [beta]-amyloid protein. Thus the invention further includes the treatment of Alzheimer's disease with an Archease agonist as described above.
Diseases such as cancer, inflammation, and viral infection may be therapeutically modulated by inhibition of the UPR. In these types of conditions, cellular survival due to corruption of the UPR is impacted. Protein folding in the ER is negatively impacted by such conditions in the tumor microenvironment as hypoxia, glucose starvation, amino acid deprivation, acidosis and mutant malfolded and oncogenic proteins. Additionally chemo-, bio-, and radiotherapy can lead to protein folding stress. It is possible to induce apoptosis in these conditions by inhibiting the anti-apoptotic effects of the UPR. Myeloma derived from neoplastic antibody secreting plasma cells provides an example of a condition in which this approach can be applied.
Enveloped viruses must use and corrupt the UPR to ensure production of progeny from infected cells. Viruses often produce vast quantities of viral membrane glycoproteins which are folded and modified in the ER. Therefore, activation of the UPR by the virus for this purpose as a survival mechanism is common. It is therefore logical that inhibition of the UPR during viral infection can impact the outcome of the disease in a beneficial way.
Only specialized secretory cells and diseased cells activate the UPR for their own benefit. Most cells are not under such protein folding stress and therefore would not be impacted by a UPR inhibitor. Thus, “disorders associated with the UPR” as used herein means conditions for which pathogenesis can be advantageously impacted by inhibition of the UPR. In various embodiments of the invention such inhibition of the UPR is accomplished through inhibition of Archease.
In some embodiments, the Archease inhibitors are useful to treat or ameliorate a symptom of a B cell autoimmune disease, certain cancers, and infections of enveloped viruses that use the endoplasmic reticulum as a viral factory for expressing viral surface and spike proteins for budding and infection. Archease inhibitors can be used as single agents or in combination therapies.
B-cell autoimmune diseases which can be treated include, but are not limited to, Addison's disease, antiphospholipid syndrome, aplastic anemia, autoimmune hemolytic anemias, autoimmune hepatitis, autoimmune hypophysitis, autoimmune lymphoproliferative disorders, autoimmune myocarditis, Churg-Strauss syndrome, epidermolysis bullosa acquisita, giant cell arteritis, Goodpasture's syndrome, Graves' disease, Guillain-Barré syndrome. Hashimoto's thyroiditis, idiopathic thrombocytopenic purpura, IgA nephropathy, myasthenia gravis, pemphigus foliaceous, pemphigus vulgaris, polyarteritis nodosa, polymyositis/dermatomyositis, rheumatoid arthritis, scleroderma, Sjögren's syndrome, systemic lupus erythematosus, Takayasu's arteritis, and Wegener's granulomatosis.
Cancers which can be treated include solid tumors, such as tumors of the breast, bone, prostate, lung, adrenal gland (e.g., adrenocortical tumors), bile duct, bladder, bronchus, nervous tissue (including neuronal and glial tumors), gall bladder, stomach, salivary gland, esophagus, small intestine, cervix, colon, rectum, liver, ovary, pancreas, pituitary adenomas, and secretory adenomas. Methods of the invention are particularly useful for treating drug- or radiation-resistant solid tumors.
Cancers of the blood (e.g., lymphomas and leukemias) also can be treated including, but not limited to, multiple myeloma, Hodgkin's lymphoma, non-Hodgkin's lymphomas (e.g., cutaneous T cell lymphomas such as Sezary syndrome and Mycosis fungoides, diffuse large cell lymphoma, HTLV-1 associated T cell lymphoma, nodal peripheral T cell lymphoma, extranodal peripheral T cell lymphoma, central nervous system lymphoma, and AIDS-related lymphoma). Leukemias include acute and chronic types of both lymphocytic and myelogenous leukemia (e.g., acute lymphocytic or lymphoblastic leukemia, acute myelogenous leukemia, acute myeloid leukemia, chronic myelogenous leukemia, chronic lymphocytic leukemia, T cell prolymphocytic leukemia, adult T cell leukemia, and hairy cell leukemia). Monoclonal gammopathy of undetermined significance (MGUS), the precursor of myeloma, also can be treated.
Viral infections which can be treated include infections of enveloped viruses which utilize the unfolded protein response pathway when they replicate and form infectious progeny (e.g., measles, pox viruses, Ebola, etc.). Infections also include those of Epstein Barr virus (EBV), cytomegalovirus (CMV), Flaviviruses (e.g., Japanese Encephalitis Virus and West Nile Virus), and Hepatitis C virus (HCV).
Archease inhibition may have therapeutic effect in several diseases. Such diseases include proliferative diseases, in particular cancer. By reducing tRNA processing the proliferative activity can be greatly decreased resulting in reduced cell growth. Therefore the present invention provides a method of reducing tumor cell growth comprising administering an Archease inhibitor to said cell. It is known that tumor cells have abnormally high rates of Polymerase (Pol) III transcription (Marshall & White, 2008). Since Pol III synthesizes tRNAs, targeting the tRNA ligase will turn (high) tRNA production rate-limiting in cancer cells. The importance of tRNA splicing components for proliferation is e.g. disclosed in the WO2004/087884 A2 (incorporated herein by reference).
In a further aspect the present invention provides the treatment of a disease or infection dependent on host polymerases, such as hepatitis delta virus infection comprising administering an Archease inhibitor to said cell. The human hepatitis delta virus is the only animal virus known to replicate its RNA genome using a host polymerase. Host factors involved in the replication of the virus are elusive. A ligase-host factor in circularizing the viral genome during replication is implicated (Reid & Lazinski, 2000). In a combined proteomic-RNAi screen identified more than 100 proteins associated to the hepatitis delta antigens. A portion of the identified proteins has roles in RNA metabolism, and two of those are the ligase HSPC117 and also its complex partner DDX1. Combined this suggests that Archease is a decisive target for treating a hepatitis delta virus infection.
Furthermore the present invention relates to a method of treating a disease in a subject associated with dysfunctional tRNA splicing, in particular being deficient in a tRNA ligation by RNA>p ligase, preferably pontocerebellar hypoplasia, comprising administering an Archease molecule to said subject. A link has been established between the tRNA splicing pathway and Pontocerebellar hypoplasia. This disease belongs to a group of degenerative autosomal recessive disorders with prenatal onset, atrophy or hypoplasia of the cerebellum and other motor impairments. Mechanistically these diseases are associated with aberrant removal of introns and ligation of exons during tRNA splicing. Therefore administration of a functional Archease can restore normal splicing and intron removal and treat the disease, while it is also well known, but not understood at a molecular level, that tRNA metabolism has a special impact on brain function.
Cells respond to oxidative stress by secreting Angiogenin, a factor that displays ribonuclease activity besides its known role in angiogenesis. Angiogenin cleaves mature tRNAs at the anticodon loop, thereby generating tRNA fragments known as tiRNAs, for tRNA-derived stress-induced RNAs. tiRNA accumulation impairs protein synthesis and is therefore detrimental to cell health and function. Inactivating the human tRNA ligase HSPC117 leads to an increase in tiRNAs in cultured cells. Increased HSPC117 reverts Angiogenin cleavage and reduces tiRNA levels. HSPC117 therefore may have a distinct role in re-ligating Angiogenin-cleaved tRNA. This angiogenin reaction cannot be reverted upon inhibition of HSPC117 molecule. In turn HSPC117 activity is enhanced by Archease as shown herein. In the absence of Archease, HSPC117 has only a low residual activity. Thus, the present invention also relates to a method of modulating tiRNA amounts in a cell, such as by increasing or decreasing Archease activity in a cell.
Various types of physiological stress induce the unfolded protein response including, but not limited to, hypoxia, nutrient starvation, acidosis, and genetic damage resulting in mutant or over-expressed misfolded proteins (oncogenic stress). One or more of these conditions are manifest in cancer cells, which may in part be mediated by the microenviroment of the tumor. It is likely that the cytoprotective arm of the unfolded protein response (UPR) plays an anti-apototic role in tumor survival. In addition, bio- and chemotherapeutic drugs and radiation treatments may further impact the protein folding and degradation cycle in the ER thereby inducing the UPR as a protective resistance mechanism. Patients succumb to cancer because either the tumor is resistant to conventional therapies or returns in a resistant form after an initial response to treatment and, therefore, new treatments and treatment combinations are needed.
Angiogenesis inhibitors block tumor growth by inhibiting new blood vessel formation, a process that would enhance the stress effects of the tumor microenvironment. A promising approach to further reduce tumor burden would be to administer anti-angiogenesis agents in combination with Archease inhibitors.
Interference with UPR may sensitize cancer cells to various chemotherapeutics that elevate the cellular stress and thus, Archease inhibitors may become important therapies in conjunction with current and future standard of care in cancer.
In some embodiments an Archease inhibitor is administered in combination with a cancer therapeutic agent, for example radiation therapy or a cancer therapeutic agent (e.g., a chemotherapeutic agent or a biotherapeutic agent). The cancer therapeutic agent can be administered separately or together with the Archease inhibitor. The cancer therapeutic agent can be administered at essentially the same time as the Archease inhibitor or can be administered either before or after the Archease inhibitor.
In a further aspect, the present invention provides a pharmaceutical composition comprising an Archease expressing nucleic acid, preferably in form of an expression vector, or an Archease inhibitor, preferably an antibody or siRNA or variant thereof as described above. Such a composition can be a ready to use composition, e.g. for the treatment of any disease described above. Pharmaceutical compositions or formulations for therapeutic or prophylactic use may comprise a pharmaceutically acceptable diluent, carrier, solubilizer, emulsifier and/or preservative. The invention also provides for pharmaceutical compositions comprising a therapeutically effective amount of an Archease inhibitor or expression nucleic acid. The term “therapeutically effective amount” means an amount which provides a therapeutic effect for a specified condition and route of administration. The composition may be in a liquid or lyophilized form and comprises a diluent (Tris, acetate or phosphate buffers) having various pH values and ionic strengths, solubilizer such as Tween or Polysorbate, carriers such as human serum albumin or gelatin, preservatives such as thimerosal or benzyl alcohol, and antioxidants such as ascorbic acid or sodium metabisulfite. Selection of a particular composition will depend upon a number of factors, including the condition being treated, the route of administration and the pharmacokinetic parameters desired. Nucleic acids and siRNA formulations are preferably administered in liposome formulations. Compositions of the invention may be administered by injection, either subcutaneous, intravenous or intramuscular, or by oral, nasal, pulmonary or rectal administration. The route of administration eventually chosen will depend upon a number of factors and may be ascertained by one skilled in the art. Preferably intracellular administration is facilitated by use of suitable vehicles like liposomes or microsomes.
The invention further provides a method of obtaining an Archease inhibitor, comprising contacting Archease with a candidate inhibitor determining the activity of a RNA ligase in contact with said Archease, wherein an inhibitor is obtained when said activity of said ligase is reduced in comparison to Archease that has not been treated with said inhibitor. Such a ligase is e.g. HSPC117. Tests to determine the ligase activity are known in the art, as e.g. described in WO 2012/028606 A1 or as described herein, and involve the ligation of two RNA molecules under suitable conditions as described herein. A preferred test is shown in example 12. In general, the Archease activity test monitors the activity of an Archease-dependent RNA ligase, such as RtcB/HSPC117, in the presence of Archease and its substrates with and without the inhibitor. Apart from the presence or absence of the inhibitor the conditions of the assay should be the same. The ligation test can also be a splicing test together with a splicing endonuclease. Said contacting step and/or the ligase activity determination can be in vitro (e.g. of isolated enzymes), in a cell or cell line or in a model non-human animal, e.g. as described above. The inhibitor can be used in the above described methods of treatment, especially in the pharmaceutical formulations as mentioned above. Inhibitors are e.g. antibodies, siRNAs, small organic molecules but also inactive forms of Archease, like the mutant forms with mutations in amino acids corresponding to D39 and/or K144 of SEQ ID NO: 28 (e.g. corresponding to D39A and K144A mutations), which render said mutated Archease inactive and inhibit wild-type Archease, which would otherwise be active. Preferred inhibitors are non-hydrolysable GTP analogues, such as GMPCPP. Non-hydrolysable GTP analogues may act as competitive inhibitors for the guanylation of RtcB proteins. Preferably the inhibitor is tested according to the test method described above. Such an inhibitor or any inhibitor described herein can be used in any one of the inventive uses, methods or kits requiring an Archease inhibitor.
Archease and the ligase may also be used in combination during contacting with the candidate inhibitor. Thus, the invention also provides the inventive method of obtaining an inhibitor comprising contacting Archease with a candidate inhibitor, wherein the Archease is in combination with a RNA ligase, such as HSPC117, and determining the activity of the RNA ligase, wherein an inhibitor is obtained when said activity of said ligase is reduced in comparison to an Archease-ligase combination that has not been treated with said inhibitor. In such a combination the Archease and the ligase may co present coincidentally in a test container, cell or model animal as described above.
As shown herein, Archease acts on ligases like HSPC117 by promoting the formation of an HSPC117-guanylate adduct, probably by releasing the GMP associated after an initial round of catalysis. Thus the inventive method of obtaining an Archease inhibitor can also be adapted by determining loss of guanylation activity of the Archease, e.g. by determining a transfer of a G residue to the ligase.
In said methods, the substrate of the reaction, e.g. GTP or polynucleotides, may be labeled for determining the activity. Example labels include radioactive labels, fluorescent, or chemical. The Archease and/or the ligase may be immobilized to allow easy separation from the test solutions.
The present invention is further illustrated by the following figures and examples, without being limited to these specific embodiments of the present invention.



FIGURES
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee. 
FIG. 1: The human tRNA ligase apparently catalyses a limited number of substrate turnovers. A) Affinity purified, FLAG-tagged HSPC117 associates with the proteins DDX1, FAM98B, ASW and CGI-99. B) Affinity purified FLAG-tagged HSPC117 processes tRNA exon halves into mature tRNAs and circularizes the linear intron released by the tRNA endonuclease. C) Varying amounts of affinity purified tRNA ligase complex were incubated with the isolated linear intron and the formation of ligated species was monitored by gel electrophoresis followed by phosphorimaging. The signals corresponding to concatemerized intron were quantified and plotted as fraction of the total signal detectable in the respective lane.
FIG. 2: HSPC117 and Archease share their taxonomic coverage. RtcB/HSPC117 proteins are widely distributed in bacteria, archaea and vertebrates but not in plants and fungi. The taxonomic coverage of Archease proteins correlates with the occurrence of RtcB/HSPC117.
FIG. 3: Archease boosts RNA ligation by the human tRNA ligase complex. A) Time-course ligation assay with affinity-purified tRNA ligase complex and pre-cleaved tRNA substrates in absence or presence of recombinant Archease. B) Time course ligation assay with affinity purified tRNA ligase complex and isolated linear introns (2.5 μM) in absence or presence of recombinant Archease (8.5 μM) expressed in E. coli. The signals corresponding to the concatemerized intron were quantified and plotted as fraction of the total signal detectable in the respective lane.
FIG. 4: Archease neither exhibits RNA ligase activity nor co-purifies with the human RNA ligase complex. A) Coomassie Blue stained preparations of FLAG-tagged Archease and HSPC117 affinity purified at 150 mM NaCl. B) RNA ligase activity assay of FLAG-HSPC117 and FLAG-Archease using pre-cleaved tRNA substrates. Extracts of HEK 293 cells were used as a negative control. * Indicates unspecific products.
FIG. 5: Alignment of various Archease protein sequences. From top to bottom SEQ ID NO: 24 to 43. Highly conserved amino acids (D39 and K144, numbered according to the human protein sequence, SEQ ID NO: 28) mutagenized in this study are highlighted by black triangles.
FIG. 6: The point mutations D39A and K144A abolish the function of Archease in RNA ligation. A) Time-course of ligation activity of FLAG-HSPC117 complexes upon addition of recombinant wild-type or mutant Archease (15 μM). B) SDS-PAGE analysis of purified recombinant wild-type and mutant Archease.
FIG. 7: HSPC117 and Archease both contribute to the maturation of pre-tRNA transcripts in processing assays. A) HeLa cell extracts depleted of Archease and/or HSPC117 by RNA interference show impaired formation of mature tRNA in pre-tRNA splicing assays. Both proteins appear to contribute equally to tRNA ligase activity in these extracts. B) Quantification of the reduction of mRNA levels of Archease and HSPC117 upon transfection of siRNAs by real time PCR. Comparable depletion efficiencies were attained for both transcripts. Depletion of either factor does not lead to a substantial reduction of the other. C) The defect in tRNA maturation observed in extracts depleted of Archease by RNAi can be restored by over-expressing wild-type, but not mutant versions of the protein. D) Western Blots showing levels of over-expressed wild-type and mutant Archease. Ctrl. indicates a control plasmid, EV an empty vector.
FIG. 8: The human tRNA ligase HSPC117 and Archease are both required for non-conventional splicing of Xbp1 mRNA during the Unfolded Protein Response (UPR). A) Experimental outline for in vitro splicing assay. B) An internally labeled fragment of Xbp1 mRNA was pre-cleaved with recombinant Ire1 endonuclease and supplemented with buffer or HeLa whole-cell extract (wce) for the indicated time points to allow ligation of exon halves. Formation of splice product is specific to the presence of both Ire1 and cell extract. Lanes marked “unspliced” and “spliced” contain control transcripts to mark the size of the splice product. C) HSPC117 and Archease both contribute to non-conventional splicing. 3′ end labeled Xbp1 was pre-cleaved with Ire1 and supplemented with whole-cell extract from HeLa cells treated with siRNAs as indicated above the lanes. Cell extracts were harvested 72 hrs post transfection. D) Ligase activity for non-conventional splicing resides in HSPC117 but not in Archease. In vitro splicing assay using 3′end labeled Xbp1 carried out using whole cell extract (input) or FLAG-IP from HEK293 cells stably expressing FLAG-HSPC117, FLAG-Archease or FLAG-DDX1. Ligation activity is only found in IPs of integral members of the tRNA ligase complex. E) Non-conventional splicing activity is stimulated by addition of Archease. Splicing assay using 3′ end labeled Xbp1 carried out as above with addition of buffer or recombinant protein as indicated above the lanes. D39A and K144A represent Archease mutagenized at highly conserved amino acid positions rendering the protein inactive. Bovine Serum Albumine (BSA) was included as control.
FIG. 9: Time course for 5′ end and 3′ end labelled Xbp1: In vitro splicing assay produces identical splice product irrespective of the position of the radioactive label.
FIG. 10: In vitro ligation activity is proportional to amount of cell extract added.
FIG. 11: Depletion of HSPC117 and Archease using siRNAs reduces non-conventional splicing of endogenous Xbp1 mRNA in HeLa cells.
A. RT-PCR for Xbp1 spliced forms. Total RNA was isolated from siRNA-treated cells 120 hrs post-transfection. Stress induced by treating cells with 2 mM DTT for 4 hrs.
B. Q-PCR for total Xbp1 mRNA levels following siRNA-mediated KD and stress induction.
C. Upregulation of Xbp1 target genes is impaired upon depletion of HSPC11 and Archease. Q-PCR for DNAJB9, EDEM1 and HSPA5 carried out using same cDNA as above. Error bars represent standard deviation; all experiments were carried out in triplicates.
FIG. 12: Depletion of HSPC117 and Archease ablates Xbp1S accumulation upon stress induction.
HeLa cells stably expressing FLAG-mXbp1U (WT) or FLAG-mXbp1s (constitutively spliced) were transfected with siRNA for 72 hrs prior to stress-induction with 0.3 uM thapsigargin (TG). Cells were lysed in RIPA buffer (ThermoScientific) and analysed by Western blotting.
FIG. 13: Guanylation of HSPC117 within the human tRNA ligase complex by Archease. A. Affinity purified FLAG-HSPC117 was incubated with wild-type or mutant versions of Archease or buffer as a control in the presence of [α-32P]GTP or [α-32P]ATP, full circles indicate inclusion, empty circles indicate omission from reaction mixtures. Reaction mixtures were resolved by SDS PAGE and radiolabeled protein species visualized by phosphorimaging. B. Equal loading was confirmed by Coomassie staining.
FIG. 14: Assay to monitor inhibition of RNA ligase activity. The figure shows the ligation activity of FLAG-RTCB, the catalytic subunit of the human tRNA ligase, in the presence of wildtype or mutant (D39A) Archease and GTP or the non-hydrolyzable analog GMPcPP. The linear substrate (second from bottom to top) is converted into a circular product (bottom) or a concatemer (top), which is further circularized (third from bottom to top). Ligation only took place with wild-type Archease and GTP. The addition of non-hydrolysable GMPCPP inhibits the reaction.
FIG. 15: Knockdown of RTCB and Archease in HeLa cells. The figure shows RTCB (A) and Archease (B) mRNA expression levels upon stable knockdown in HeLa cells by means of short hairpin RNAs (shRNAs). Both in control and knockdown cells, mRNA expression levels vary upon induction of the UPR with tunicamycin (Tm). However, decreased mRNA expression levels are observed throughout the entire experimental period.
FIG. 16: Reduced XBP1 splicing activity and EDEM1 induction after knockdown of Archease in HeLa cells. The figure shows expression levels of total Xbp1 mRNA (unspliced and spliced, A); spliced Xbp1 mRNA (Xbp1s, B) and Edem1 (C) as revealed by qPCR. Compared to control cells, knockdown of Archease leads to a decrease in mRNA Xbp1 splicing as seen by reduced levels of Xbp1s mRNA. This impacts on the expression levels of both total Xbp1 and Edem1 mRNAs.
FIG. 17: Knockdown of RTCB and Archease in H929 cells. The figure shows decreased mRNA expression levels of RTCB (A) and Archease (B) upon stable knockdown in H929 cells by means of shRNAs.



EXAMPLES
Example 1
Reduced Activity of HSPC117 Complex without Archease
It was found that the HSPC117 complex (FIG. 1A) exhibits RNA ligase activity (FIG. 1B) which, in a time course analysis, does not seem to progress over time after an initial burst of activity (FIG. 1C). This result suggests a lack of turnover in the enzymatic reaction and that additional factors are required to attain full activity.
Example 2
Archease is Required for Efficient RNA Ligation by the Human RNA Ligase Complex In Vitro
Addition of Archaease influences ligase activity of affinity purified human tRNA ligase complexes. As shown in FIGS. 3A and B, addition of recombinant Archease boosts ligation activity to a great extent (including circularization of the intron).
Example 3
Archease Neither Exhibits RNA Ligase Activity Nor Co-Purifies with the Human RNA Ligase Complex
Stable cell lines expressing a FLAG-tagged version of Archease and HSPC117 were generated to perform immuno-precipitations. Fluted FLAG-Archease was assayed for tRNA ligation in parallel with FLAG-HSPC117, which contains the entire tRNA ligase complex. As shown in FIG. 4A, affinity-purified FLAG-tagged Archease neither associated with components of the tRNA ligase complex, nor did the tRNA ligase complex co-purify with Archease. RNA ligase activity was only detectable in reactions containing affinity-purified RNA ligase complex but not FLAG-tagged Archease (FIG. 4B).
Example 4
The Point Mutations D39a and K144A Abolish the Function of Archease in RNA Ligation
To study the function of Archease the available NMR structure from the euryarchaeote Methanothermobacter thermautotrophicus (Yee et al., 2002) (36% identical to human protein) was used and aspartic acid (D) 39 and lysine (K) 144, both extremely conserved residues, were replaced by alanines (D39A; K144A) (FIG. 5). Wild-type and mutant versions of Archease were over-expressed in HeLa cells and tRNA ligase activity was measured. As seen in FIG. 6A, addition of recombinant wild-type Archease led to an increase in RNA ligase activity while neither of the mutant versions of Archease stimulated the low levels of ligation achieved in its absence. FIG. 6B confirms equal concentrations of recombinant proteins added to the reactions.
Example 5
Archease is Required for Efficient In Vitro Splicing of Pre-tRNA Substrates in Human Cell Extracts
It was also tested whether depletion of Archease would impair tRNA splicing activity in cell extracts. HeLa extracts depleted of Archease by RNAi were incubated with an internally labeled pre-tRNA substrate and the appearance of mature tRNA was monitored (FIG. 7A). To silence HSPC117 a commercially available mixture of siRNA duplexes was used (Dharmacon Cat. No. L-017647-00-0005). To silence Archease a single siRNA duplex of the sequence 5′-UGA CAU UUA AGA CAC CAA A[dT][dT]-3′ (sense strand; SEQ ID NO: 47) and 5′-UUU GGU GUC UUA AAU GUC A[dT][dT]-3′ (antisense strand; SEQ ID NO: 48) was used. The obtained results were confirmed using a commercially available mixture of siRNA duplexes (Dharmacon Cat. No. L-017915-01-0005).
For the splicing assay RNA was prepared by T7-transcrition from PCR product containing spliced and unspliced form of human Xbp1. Substrates were labelled internally using a-GTP and at the 3′end using ligation to pCp. Substrate was pre-cleaved with recombinant Ire1 for 5 mins in tRNA ligation buffer with subsequent addition of protein extract of FLAG-IP eluate to total volume of 5 μl. Samples were treated with proteinase K and phenol-chloroform extracted prior to loading on 10% PAGE gel.
Similar to targeting the tRNA ligase HSPC117 (Popow et al., 2011), depletion of Archease severely impaired tRNA ligation. Transfection of siRNAs targeting Archease efficiently depleted its mRNA (FIG. 7B). In addition, it was confirmed that lack of ligation following the depletion of Archease could not be attributed to destabilization of HSPC117. Ruling out off-target effects, it was possible to restore tRNA maturation in extracts depleted of Archease by simultaneous expression of the wild-type protein but not the point mutants D39A and K144A (FIGS. 7C and D).
Example 6
Archease is Required for Efficient In Vitro Splicing of Xbp1 mRNA During the Unfolded Protein Response
Perturbation of normal ER function causes mis- or unfolded proteins to accumulate leading to activation of the unfolded protein response (UPR). One of three UPR pathway inducers in mammals, the ER transmembrane protein Ire1, cleaves the Xbp1 mRNA specifically to remove a 26 nt intron (FIG. 8A). In vitro splicing assays carried out with a cleaved Xbp1 RNA minimal substrate and HeLa cell extracts depleted of HSPC117 and/or Archease revealed that both proteins are required for efficient ligation of the exons generated by recombinant Ire1 (FIGS. 8B and C). Loss of HSPC117, the catalytic subunit of the mammalian tRNA ligase complex, caused strongly reduced exon-exon ligation. Interestingly, depletion of the newly identified tRNA ligase-activating factor Archease resulted in a comparable loss of ligation activity (FIG. 8C). None of the additional four components of the tRNA ligase complex were required for ligation in agreement with previous findings (WO 2012/28606). As for cleaved pre-tRNA substrates, only affinity purified HSPC117 and DDX1 but not Archease exhibited RNA ligase activity towards cleaved Xbp1 RNA minimal substrates (FIG. 8D). The reduced ligation activity seen in Archease-depleted extracts raised the question whether Archease is an RNA ligase or rather acts to stimulate the ligation activity of other ligases. To address this question stable cell lines expressing FLAG-tagged versions of HSPC117, Archease, and DDX1 (a DEAD-box helicase component of the human tRNA ligase complex) were generated and the Xbp1 ligation assay using FLAG-IPs was performed. As shown in FIG. 8D ligation activity in FLAG-HSPC117 and FLAG-DDX1 IPs were observed while no ligation was detected for FLAG-Archease IP.
Addition of recombinant wild-type Archease but not its mutagenized versions strongly stimulated ligation of Xbp1 RNA minimal substrates by affinity purified human tRNA ligase complex (FIG. 8E). To further address the stimulatory activity of Archease both HSPC117 and Archease were depleted by RNAi and then an Archease rescue-construct containing either WT or MUT Archease was introduced. Although Archease harbours no ligase activity in itself as seen in IP experiments the over-expression of WT Archease is sufficient to partly rescue the in vitro ligation activity in KD extracts showing that its stimulatory activity is strong enough to boost activity of a small amount of HSPC117 remaining. These experiments also show that over-expression of mutant Archease by itself is sufficient to impair in vitro ligation activity despite partial depletion of the catalytic subunit of the tRNA ligase complex.
Interestingly, when Xbp1 mRNA was pre-cleaved with Ire1 prior to addition of cell extract a single fragment appeared resulting from the ligation of the two Xbp1 exon halves. A similar fragment was observed in splicing assays using either 5′- or 3′-endlabelled Xbp1 RNA (FIG. 9), arguing against a contaminating cleavage event. Splicing activity was seen to be proportional to the amount of extract added (FIG. 10).
Example 7
Depletion of HSPC117 and Archease Impairs Non-Conventional Splicing and Prevents Activation of Xbp1 Downstream Targets in Cell Culture
To expand the findings from the in vitro ligation assay in a more physiological setting HSPC117 and Archease were depleted by siRNA transfection in HeLa cells and stress was induced by treating the cells with 1 mM DTT or 0.3 uM thapsigargin for 4 hrs. The accumulation of spliced Xbp1 was monitored by RT-PCR using primers flanking the non-conventional splice site in Xbp1. Surprisingly depletion of HSPC117 alone caused only limited change in Xbp1 splicing upon stress induction, while depletion of Archease impaired splicing significantly (FIG. 11A); both proteins were depleted to comparable levels. Q-PCR for total Xbp1 levels in siRNA-treated cells corroborated the RT-PCR results (FIG. 11B). In control samples the extended stress induction led to elevated levels of Xbp1 mRNA since the Xbp1S protein feeds back on its own promoter, leading to strong transcription of Xbp1 mRNA during the stress response. Depletion of HSPC117 resulted in about 50% reduction in transcript activation while the depletion of Archease abolishes the enhanced production of Xbp1 mRNA altogether (FIG. 11B). These results argue that the stimulatory activity elicited by Archease is sufficient to maintain ligation activity in the presence of reduced amounts of HSPC117.
The accumulation of Xbp1S protein activates transcription of genes that ameliorate ER stress. The lack of UPR ligase function would therefore be expected to impair upregulation of these downstream targets upon stress induction. To measure this Q-PCR for the Xbp1-specific factors EDEM1 and DNAJB9 as well as for the general stress responder HSPA5 (BiP) was performed. The activation of EDEM1 and DNAJB9 was abolished in cells depleted of Archease using siRNAs, while HSPC117 depletion had a minor effect (FIG. 11C). The activation of HSPA5 was only mildly affected by the depletion of both Archease and HSPC117 confirming the specific disruption of the Ire1 signaling pathway upon depletion of non-conventional RNA splicing. The upregulation of down-stream targets mirrors the accumulation of spliced Xbp1 seen in FIG. 11A arguing that impaired Xbp1 mRNA splicing translates directly into loss of Xbp1s protein (FIG. 12 left panel); presumably the mild reduction in Xbp1 splicing seen in HSPC117-depleted cells still leaves enough protein to initiate the activation of down-stream genes. This shows that UPR-activated target genes depend on a functional tRNA ligase machinery for their upregulation upon stress.
Example 8
Depletion of HSPC117 and Archease Impairs Accumulation of Xbp1S
To confirm the RT- and Q-PCR results described above Western blots to detect direct deficiency in Xbp1 protein accumulation upon stress induction in siRNA-treated HeLa cells were performed. Stable cell lines expressing FLAG-tagged mouse Xbp1 were generated. Expression of an Xbp1 mRNA with the non-conventional intron removed (constitutive expression of Xbp1S) was used as a control. Expression level was only 2-3 fold above endogenous Xbp1 as seen by RT-PCR and stress induction led to comparable splicing pattern for endogenous hXbp1 and transgenic FLAG-mXbp1. Stable cell lines were treated with siRNAs for 72 hrs, lysed and analysed by Western blotting (FIG. 12). Similar to results from RT-PCRs depleting HSPC117 had no effect on Xbp1S protein accumulation while depletion of Archease caused a strong drop in protein level compared to the control transfection. Depletion of both proteins showed synergistic effect resulting in an almost complete loss of Xbp1S upon stress induction.
Despite years of intense study the identity of the ligation process in non-conventional Xbp1 splicing has eluded discovery in mammalian cells. While HSPC117 is the likely candidate for this splicing activity, it has been shown herein with certainty that ligation is dependent on Archease for stimulation of ligase activity. It is possible that a few ligase complexes (possibly associated with the ER membrane) may suffice to splice Xbp1 upon induction of stress response as long as Archease is present to stimulate enzymatic rate. This fits with observations from RT-PCR and Q-PCR assays where initially cells were harvested after very short stress exposure to spot kinetic differences in initial splicing. When strategy was changed and stress induction was run for several hours before sample harvesting a differential accumulation of spliced product was detected. Presumably the enhanced number of Xbp1 transcripts requiring splicing caused by the initial pool of Xbp1S makes it harder for the limited amount of HSPC117 in siRNA-treated cells to keep up ligating the available substrates and thereby makes it possible to see a significant difference in amount of spliced Xbp1 mRNA.
Steady-state levels of unspliced Xbp1 mRNA are upregulated in the absence of stress upon a) Archease depletion by RNAi, b) through over-expression of dominant-negative mutant Archease, or c) most strongly seen when both are combined. This phenomenon could be caused by enhanced transcription (through an unknown feedback mechanism) or by stabilisation of the unspliced Xbp1 mRNA (due to altered subcellular localisation).
Example 9
Archease is Required for Guanylation of HSPC117
Since HSPC117 alone does not undergo guanylation in vitro it was tested whether Archease supports RNA ligation by HSPC117 by mediating its guanylation. Affinity purified FLAG-HSPC117 was incubated with wild-type or mutant and inactive variants (D39A; K144A) of Archease or buffer as a control in the presence of [α-32P]GTP or [α-32P]ATP. Reaction mixtures were resolved by SDS PAGE and radiolabeled protein species visualized by phosphorimaging or by Coomassie staining (FIGS. 13 A and B). Guanylation of FLAG-HSPC117 was only detectable in the presence of wild-type but not of mutant versions of Archease.
Example 10
Medical Applications of Inhibitors of Archease and the Human tRNA Ligase Complex
The UPR, and especially the Ire1/Xbp1 branch, is found to be involved in an increasing number of diseases; most strikingly over-expression of Xbp1S in a mouse model was found to predispose animals to the development of multiple myeloma. Several compounds have been designed to impair the activity of Ire1 thereby ablating the over-activation of the pathway which contributes to disease progression; however, since Ire1 also has additional functions in the UPR independent on Xbp1 splicing targeting the ligase or Archease rather than the endonuclease would allow for enhanced specificity in disrupting over-activated Xbp1 signalling.
The implication of Archease and HSPC117 in the ligation of tRNA and mRNA substrates allows interfering with these splicing pathways in order to abolish negative effects associated with increased splicing activity.
Prolonged activity of the UPR, an indication that ER stress cannot be mitigated and homeostasis cannot be reestablished, correlates with cell death, suggesting that the commitment to apoptosis may have evolved to protect the organism from rogue cells that lack the capacity to ascertain the fidelity of their signaling components (Walter and Ron, 2011). A life-or-death decision, based on an assessment of whether ER stress can be mitigated in a timely fashion, nicely explains the UPR's central role in numerous human diseases. When homeostasis fails, the UPR can serve as an apoptotic executor that kills cells that would be beneficial, or as a cytoprotector that safeguards rogue cells to the detriment of the organism. Examples in the first category include retinitis pigmentosa, an inherited form of blindness in which the retina degenerates by apoptotic cell death when a misfolded mutant rhodopsin is produced during retinal development. Another such example is type II diabetes, in which pancreatic beta cells are compromised by excessive demand for insulin production. The second category is exemplified by enveloped virus infections that can exploit the UPR to increase the capacity of the ER to assist in viral replication. Similarly, certain types of cancer—especially those that arise in secretory tissues, such as multiple myeloma (see below)—use the cytoprotective role of the UPR to sustain their rapid growth. Impairing the endonuclease activity of IRE1 compromises the physiological cleavage of several RNA molecules during UPR. Inhibiting the ligase activity of HSPC117 and Archease facilitates this effect. Special targets are diseases where the spliced form of the Xbp1 protein is over-represented, such as multiple myeloma (Carrasco et al., 2007; Papandreou et al., 2011).
Example 11
Archease and UPR in Diabetes
In diabetes, the ultimate cell fate decision of life or death is dependent on the nature and severity of ER stress to which the β-cell is exposed. Thus, there are two types of ER stress conditions: resolvable and unresolvable. When ER stress can be resolved, the UPR promotes β-cell survival, whereas under unresolvable ER stress conditions, the UPR activates death effectors, leading to β-cell apoptosis. When β-cells are exposed to conditions that induce mild ER stress (e.g. physiological exposure to glucose fluctuations after a meal), the ER can facilitate stress mitigation and restore protein homeostasis, thus ‘priming’ cells for future ER stress insult and promoting cell survival. It has been shown that IRE1α and PERK are the primary transducers for regulating insulin production under these conditions, thus promoting activation of UPR prosurvival pathways. Unresolvable ER stress conditions occur when the UPR response is insufficient to restore ER homeostasis, leading to the induction of proapoptotic pathways. This can be attributed to several factors, including genetic mutations, chronic exposure to high glucose, and dysregulation of the UPR itself. This situation also benefits from a more efficient UPR, which could be achieved by overexpressing a tRNA ligase (e.g. HSPC117) and/or Archease. In fact, Fonseca et al. propose that discovering methods that could reduce ER stress to a tolerable state and/or modulating the UPR to preferentially activate survival over death pathways could lead to novel and efficient therapeutic treatments for diabetes.
Example 12
Assay to Monitor Archease Function and Inhibition of RNA Ligase Activity and Inhibitor Assay
The RNA ligation activity of FLAG-RTCB, the catalytic subunit of the human tRNA ligase, was determined in the presence of wildtype or mutant (D39A) Archease with the addition of GTP or non-hydrolysable GMPcPP (5′-guanylylmethylenebisphosphonate). Ligation only takes place with wild-type Archease and in the presence of GTP. GMPcPP strongly inhibits the ligation reaction. The reaction was carried out with FLAG-RTCB purified from HEK293 cells and hexahistidine tagged wild-type or mutant Archease. Furthermore, GTP or GMPcPP were used at 0.5 mM concentration. A linear intron derived from a radioactively labelled pre-tRNA that was transcribed with T7 polymerase and cleaved with recombinant tRNA endonuclease from Methanocaldococcus jannaschii served as substrate. Cleavage products were resolved on preparative denaturing polyacrylamide gels and the linear intron was eluted overnight and recovered by precipitation. With reference to FIG. 14, FLAG-RTCB and wild-type Archease in the presence of GTP are able to convert the linear substrate (second from bottom to top) into a circular product (bottom) or a concatemer (top), which is further circularized (third from bottom to top). This type of assay can be used to validate candidate inhibitors of the Archease or even the ligase or to screen compound libraries in order to find inhibitory molecules.
Example 13
Knockdown of RTCB (HSPC117) and Archease in Therapeutic Models
The expression of RTCB and Archease was reduced in HeLa and H929 cells by means of short hairpin RNAs (shRNAs) following an already established method that uses flanking sequences derived from microRNA-30 (Fellmann et al., Mol. Cell. 41, 733, 2011). Using a retroviral MSCV-based system knockdown constructs were stably expressed in the desired cell line which led to decreased expression levels of RTCB and/or Archease as seen in FIGS. 15-17. Furthermore, this decrease could be maintained when cells were treated with tunicamycin over a time period of 24 h. For this experiment, cells were plated at equal densities and treated with 1 ug/ml of tunicamycin (Tm). Hereafter, RNA was extracted using Trizol and cDNA was synthesized by means of the Maxima First Strand cDNA Synthesis Kit. QPCR was performed in duplicates and beta-actin was used for normalization. Expression levels were normalized to control cells expressing similar shRNA constructs targeting Renilla luciferase.
FIG. 15 illustrates the knockdown of RTCB and Archease in HeLa cells. RTCB and Archease mRNA expression levels were reduced upon stable knockdown in HeLa cells by means of shRNAs. Both in control and knockdown cells, mRNA expression levels vary upon induction of the UPR with tunicamycin. However, decreased mRNA expression levels are observed throughout the entire experimental period.
It has been shown that replication of the hepatitis delta virus (HDV) depends on the presence of components of the human RNA ligase, namely RTCB/HSPC117 and DDX1 (Cao et al., RNA. 2009 November; 15 (11):1971-9). Interfering with the tRNA ligase in human cells—by impairing ligase and/or Archease's activity—has a strong effect on the cycle of the virus. Viruses also depend on a functional XBP1 branch of the unfolded protein response, or UPR (Hassan et al., J Biol Chem. 2012 Feb. 10; 287(7):4679-89). Thus by impairing Archease activity, virus infected cells become susceptible to apoptosis or lead to impaired viral development and thus is a therapeutic approach for treating viral infections.
Regarding cancer, it has been reported that multiple myeloma cells heavily rely on a chronically activated UPR in order to generate high levels of the transcription factor XBP1s through unconventional, cytoplasmic splicing—cleavage and ligation—of Xbp1 mRNA. Cleavage is executed by the endonuclease IRE1. The tRNA ligase and Archease together constitute the ligase required for XBP1 mRNA splicing.
Compounds interfering with the endonuclease activity of IRE1 have been developed (Papandreou et al., Blood. 2011 Jan. 27; 117 (4):1311-4.) but showed only limited anti-myeloma activity. The emergence of the tRNA ligase and in particular Archease as factors required for this splicing process provides a new target for the treatment of multiple myeloma.
In FIGS. 16A and 16B it is shown that using HeLa cells partially depleted of Archease by means of shRNAs, levels of spliced Xbp1 (Xbp1s mRNA) could be reduced in comparison with control cells after induction of the UPR with tunicamycin. Furthermore, reduced levels of total Xbp1 mRNA (unspliced and spliced) were observed as the transcription factor XBP1s induces its own expression as well as of EDEM1 mRNA (FIG. 16C), which is a down-stream target specifically transcribed by the action of XPB1s. Importantly, the Archease inhibition system described above can decrease the expression of RTCB and Archease in H929 multiple myeloma cell lines (FIG. 17). These cells should become impaired in Xbp1 mRNA splicing rendering them sensitive to chemotherapeutic agents, e.g. bortezomib.
REFERENCES


    Cao et al., RNA. 15 (11):1971-9, 2009.
    Carrasco et al. Cancer cell 11, 349-360, 2007.
    Fellmann et al., Mol. Cell 41, 733, 2011.
    Fonseca et al., Trends Endocrinol Metab 22(7): 266-274, 2011
    Hassan et al., J Biol Chem. 10; 287(7):4679-89, 2012.
    Papandreou et al., Blood 117, 1311-1314, 2011.
    Popow et al. Science (New York, N.Y.) 331, 760-764, 2011.
    Popow et al., Cell Mol Life Sci. DOI: 10.1007/s00018-012-0944-2, 2012.
    Walter, P., and Ron, D., Science (New York, N.Y. 334, 1081-1086, 2011.
    Yee et al., Proceedings of the National Academy of Sciences of the United States of America 99, 1825-1830, 2002.

## Claims

1. A method for enhancing the ligase activity of a RNA ligase enzyme, wherein the RNA ligase enzyme is a HSPC117, comprising:
A) providing an Archease protein, and
B) contacting the RNA ligase enzyme with the Archease protein, wherein the Archease protein guanylates the RNA ligase enzyme with a GTP, and
C) transferring a first RNA end of an RNA molecule to a second RNA end of an RNA molecule catalyzed by the RNA ligase enzyme,

wherein one or more selected from the Archease, the RNA ligase, the GTP, the RNA molecule having the first RNA end and the RNA molecule having the second RNA end has a label.

2. The method of claim 1, wherein the Archease protein is set forth as in any one of SEQ ID NOs: 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, or 44.

3. The method of claim 1, wherein the HSPC117 molecule is set forth as in any one of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 15, 17, 19, 21, or 23.

4. The method of claim 1 wherein said RNA molecules are mRNA or tRNA molecules.

5. The method of claim 1, wherein the contacting is during or prior to RNA splicing.

6. A method for treating a disease associated with dysfunctional tRNA splicing or dysfunctional UPR in a subject,
comprising administering a therapeutically effective amount of an Archease molecule to the subject,
wherein the subject has the disease associated with dysfunctional tRNA splicing or dysfunctional UPR,
wherein the Archease molecule enhances the ligase activity of an RNA ligase in the subject.

7. The method of claim 6, further comprising administering a therapeutically effective amount of the RNA ligase to the subject.

8. The method of claim 6, wherein the disease is type-II diabetes.

9. The method of claim 6, wherein the RNA ligase is HSPC117.

10. The method of claim 9, wherein HSPC117 is any one of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 15, 17, 19, 21, or 23.

11. The method of claim 6, wherein the archease molecule is archease protein.

12. The method of claim 11, wherein the archease protein is any one of SEQ ID NOs: 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, or 44.

13. The method of claim 6, wherein the archease molecule is a nucleic acid coding for archease protein.

14. The method of claim 1, wherein the label, for any of the Archease and the RNA ligase, is selected from a His tag or a FLAG tag, and/or wherein the label, for any of the GTP, the RNA molecule having the first RNA end and the RNA molecule having the second RNA end is selected from a radioactive label and a fluorescent label.