TLK2
tousled like kinase 2
Tousled-like kinase 2 is a serine/threonine kinase and as of Oct. 9, 2018, 28 papers were found in a basic search of PubMed using “TLK2” as the search term.
Described Functions or Roles
First described in Arabidopsis thaliana, with mutations leading to defects in flower development, Two members of this family exist in humans (TLK1 and TLK2).[1] Both TLK1 and TLK2 localize to the nucleus, with activity linked to DNA replication and maximal activity during the S phase. DNA double-strand breaks induce rapid inhibition of activity, suggesting a role in checkpoint regulation. Histone H3 along with H3-H4 chaperone Asf1A/B have been shown to be substrates of TLKs, establishing a link with chromatin assembly.[2-5] TLK2 activity has been specifically identified as being responsible for recovery from DNA damage checkpoint arrest during G2, with absence of TLK2 preventing recovery.[6] While there has been indications that TLK1 and TLK2 share functions, there has been more recent evidence that TLK2 performs unique functions after DNA damage, with both kinase performing similar functions in non-damaged cells.[6] TLK2 appears to be widely expressed in tissues, with the greatest expression in the testes.
Physiology, Phenotypes and Disease
Cancer
From public TCGA data sets, a significant number of missense mutations have
been observed in TLK2 for cholangiocarcinoma (bile duct cancer). In addition,
high expression is observed in testicular germ cell tumors along with high copy
number variation in kidney chromophobe (deletion) and kidney renal papillary
cell carcinoma (amplification). [DKK] A related study of TCGA data has suggested
that TLK2 is significantly over-expressed in 37% of luminal breast cancer tumors
and associated with poor survival in these patients.[7] The authors further hypothesize that TLK2 may act “as a context-dependent driver of ER-positive/luminal tumours in the absence of PIK3CA expression.”
Neurodevelopment
Inherited heterozygous mutations in TLK2 showed a consistent set of neruodevelopmental disorder phenotypes in affected individuals (40 total) including mild neurodevelopment delays, a variety of behavioral disorders, significant gastro-intestinal problems along with facial dysmorphism. Further analysis of cell lines from affected individuals indicated that at least two variants act through haploinsufficiency (heterozygous loss-of-function).[4]
Resources
TLK2-specific PRM peptides have been identified and are provided on the DKK.
References
[1] Silljé HH, Takahashi K, Tanaka K, Van Houwe G, Nigg EA. Mammalian homologues of the plant Tousled gene code for cell-cycle-regulated kinases with maximal activities linked to ongoing DNA replication. EMBO J. 1999;18: 5691–5702.
[2] Carrera P, Moshkin YM, Gronke S, Sillje HHW, Nigg EA, Jackle H, et al. Tousled-like kinase functions with the chromatin assembly pathway regulating nuclear divisions. Genes Dev. 2003;17: 2578–2590.
[3] Silljé HH, Nigg EA. Identification of human Asf1 chromatin assembly factors as substrates of Tousled-like kinases. Curr Biol. 2001;11: 1068–1073.
[4] Reijnders MRF, Miller KA, Alvi M, Goos JAC, Lees MM, de Burca A, et al. De Novo and Inherited Loss-of-Function Variants in TLK2: Clinical and Genotype-Phenotype Evaluation of a Distinct Neurodevelopmental Disorder. Am J Hum Genet. 2018;102: 1195–1203.
[5] Klimovskaia IM, Young C, Strømme CB, Menard P, Jasencakova Z, Mejlvang J, et al. Tousled-like kinases phosphorylate Asf1 to promote histone supply during DNA replication. Nat Commun. 2014;5: 3394.
[6] Bruinsma W, van den Berg J, Aprelia M, Medema RH. Tousled-like kinase 2 regulates recovery from a DNA damage-induced G2 arrest. EMBO Rep. 2016;17: 659–670.
[7] Srihari S, Singla J, Wong L, Ragan MA. Inferring synthetic lethal interactions from mutual exclusivity of genetic events in cancer. Biol Direct. 2015;10: 57.
Tousled-like kinase 2 is a serine/threonine kinase and as of Oct. 9, 2018, 28 papers were found in a basic search of PubMed using “TLK2” as the search term.
Described Functions or Roles
First described in Arabidopsis thaliana, with mutations leading to defects in flower development, Two members of this family exist in humans (TLK1 and TLK2).[1] Both TLK1 and TLK2 localize to the nucleus, with activity linked to DNA replication and maximal activity during the S phase. DNA double-strand breaks induce rapid inhibition of activity, suggesting a role in checkpoint regulation. Histone H3 along with H3-H4 chaperone Asf1A/B have been shown to be substrates of TLKs, establishing a link with chromatin assembly.[2-5] TLK2 activity has been specifically identified as being responsible for recovery from DNA damage checkpoint arrest during G2, with absence of TLK2 preventing recovery.[6] While there has been indications that TLK1 and TLK2 share functions, there has been more recent evidence that TLK2 performs unique functions after DNA damage, with both kinase performing similar functions in non-damaged cells.[6] TLK2 appears to be widely expressed in tissues, with the greatest expression in the testes.
Physiology, Phenotypes and Disease
Cancer
From public TCGA data sets, a significant number of missense mutations have been observed in TLK2 for cholangiocarcinoma (bile duct cancer). In addition, high expression is observed in testicular germ cell tumors along with high copy number variation in kidney chromophobe (deletion) and kidney renal papillary cell carcinoma (amplification). [DKK] A related study of TCGA data has suggested that TLK2 is significantly over-expressed in 37% of luminal breast cancer tumors and associated with poor survival in these patients.[7] The authors further hypothesize that TLK2 may act “as a context-dependent driver of ER-positive/luminal tumours in the absence of PIK3CA expression.”
Neurodevelopment
Inherited heterozygous mutations in TLK2 showed a consistent set of neruodevelopmental disorder phenotypes in affected individuals (40 total) including mild neurodevelopment delays, a variety of behavioral disorders, significant gastro-intestinal problems along with facial dysmorphism. Further analysis of cell lines from affected individuals indicated that at least two variants act through haploinsufficiency (heterozygous loss-of-function).[4]
Resources
TLK2-specific PRM peptides have been identified and are provided on the DKK.
References
[1] Silljé HH, Takahashi K, Tanaka K, Van Houwe G, Nigg EA. Mammalian homologues of the plant Tousled gene code for cell-cycle-regulated kinases with maximal activities linked to ongoing DNA replication. EMBO J. 1999;18: 5691–5702.
[2] Carrera P, Moshkin YM, Gronke S, Sillje HHW, Nigg EA, Jackle H, et al. Tousled-like kinase functions with the chromatin assembly pathway regulating nuclear divisions. Genes Dev. 2003;17: 2578–2590.
[3] Silljé HH, Nigg EA. Identification of human Asf1 chromatin assembly factors as substrates of Tousled-like kinases. Curr Biol. 2001;11: 1068–1073.
[4] Reijnders MRF, Miller KA, Alvi M, Goos JAC, Lees MM, de Burca A, et al. De Novo and Inherited Loss-of-Function Variants in TLK2: Clinical and Genotype-Phenotype Evaluation of a Distinct Neurodevelopmental Disorder. Am J Hum Genet. 2018;102: 1195–1203.
[5] Klimovskaia IM, Young C, Strømme CB, Menard P, Jasencakova Z, Mejlvang J, et al. Tousled-like kinases phosphorylate Asf1 to promote histone supply during DNA replication. Nat Commun. 2014;5: 3394.
[6] Bruinsma W, van den Berg J, Aprelia M, Medema RH. Tousled-like kinase 2 regulates recovery from a DNA damage-induced G2 arrest. EMBO Rep. 2016;17: 659–670.
[7] Srihari S, Singla J, Wong L, Ragan MA. Inferring synthetic lethal interactions from mutual exclusivity of genetic events in cancer. Biol Direct. 2015;10: 57.
These figures show a summary of data collected by the cancer genome atlas for TLK2. The mutations heatmaps shows the fraction samples with each type of genetic mutation, while the copy number variation shows the percentage of samples where a deletion or amplication was dectected. Finally, the mRNA expression tab shows the amount of mRNA detected on a log-2 scale for each cancer type. The X-axis cancer type abbreviations are described here. This summary of the cancer genome atlas (TCGA) was collated from firebrowse developed by the Broad Institute. The code used to produce these figures is available through github.
Kinase Domain Structure:
- Title: TLK2 kinase domain from human
- Resolution: 2.86
Associated Compounds:
- PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
View This Structure on RCSB PDB
This data stems from the differentiation of neural stem cells into fully functional neurons and glia, which requires precise regulation of diverse molecular pathways over time and space. As part of the Harvard Medical School Library of Integrated Network-based Cellular Signatures (LINCS) Program (NIH grant U54 HL127365, lincs.hms.harvard.edu), we used phospho-proteomics to assess changes during ReN VM cell differentiation. Depicted is the dark kinase of interest (black) and two reference kinases (blue and green) to aid interpretation of the values. More information on this work can be found on Synapse.
INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system drawing from natural language processing systems and structured databases. It collects mechanistic and causal assertions, represents them in a standardized form (INDRA Statements), and assembles them into various modeling formalisms including causal graphs and dynamical models. More information on this work can be found on Github. In this particular figure, several interaction-types are depicted; physical complexes (blue), phosphorylation (black), and general up- or downregulation (green and red, respectively). Biomacromolecules are represented as squares, small molecule as circles, and biological processes and diamonds. The thickness of each line reflects a confidence score, with thicker lines higher in confidence.
Affinity Purification - Mass Spectrometry
The calibration reverse curve plot with linear robust regression analysis is shown [1]. The observed concentrations of the stable isotopically labeled peptide surrogate was obtained for each peptide using LC-MS in parallel reaction mode with a constant quantity of natural isotope abundance peptide as the internal standard (25 fmol/µL) [2]. The analyte matrix was a tryptic digest of pooled patient derived xenografts (1 µg/µL) that was prepared according to CPTAC-SOP. Each of the three most intense peptide fragment ions is depicted as a different symbol. The measurements from replicate LC-MS analyses are depicted as the same symbol [3] The LOD was determined using a non-parametric method with eight LC-MS analyses without added analyte [4]. The LOQ was generated from the LOD [5]. The plots are dimensioned such that the theoretical line is at a 45° angle to facilitate assessment of peptide recovery and performance. The LOD, LOQ, and regression parameters are summarize in the Table.
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2855883/
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3494192/
- https://proteomics.cancer.gov/sites/default/files/assay-characterization-guidance-document.pdf
- http://clinchem.aaccjnls.org/content/50/4/732
- “Algorithms, Routines and S Functions for Robust Statistics” (CRC Press, Boca Raton, Florida, USA, 1993)
View Peptide Parameters
The calibration reverse curve plot with linear robust regression analysis is shown [1]. The observed concentrations of the stable isotopically labeled peptide surrogate was obtained for each peptide using LC-MS in parallel reaction mode with a constant quantity of natural isotope abundance peptide as the internal standard (25 fmol/µL) [2]. The analyte matrix was a tryptic digest of pooled patient derived xenografts (1 µg/µL) that was prepared according to CPTAC-SOP. Each of the three most intense peptide fragment ions is depicted as a different symbol. The measurements from replicate LC-MS analyses are depicted as the same symbol [3] The LOD was determined using a non-parametric method with eight LC-MS analyses without added analyte [4]. The LOQ was generated from the LOD [5]. The plots are dimensioned such that the theoretical line is at a 45° angle to facilitate assessment of peptide recovery and performance. The LOD, LOQ, and regression parameters are summarize in the Table.
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2855883/
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3494192/
- https://proteomics.cancer.gov/sites/default/files/assay-characterization-guidance-document.pdf
- http://clinchem.aaccjnls.org/content/50/4/732
- “Algorithms, Routines and S Functions for Robust Statistics” (CRC Press, Boca Raton, Florida, USA, 1993)
View Peptide Parameters
The expression of kinases varies widely across the human tissues assayed by the GTEx project and the Human Proteome Map. To gain a better understanding of the kinase tissue distribution, we've created an application that describes and summarizes the expression of each dark kinase in the context of the rest of the kinome. This interactive window onto the full applications shows the data associated with TLK2. The graph summarizes the expression of the kinase across all the organ systems.
The full application can further explored at the Kinase Expression Data Application.
The Reactome Knowledgebase of Human Biological Pathways and Processes is a curated and peer-reviewed knowledgebase available online as an open access resource that can be freely used and distributed by all members of the biological research community. This view of the reactome database is focused on TLK2 and displays the pathways associated with TLK2.