JCT  Vol.5 No.10 , September 2014
Molecular Profile of Human Serine Palmitoyltransferase-1 Proximate of Chromosome 9 Disease Susceptibility Gene Cluster in Inflammatory Cancer Cell Lines
Abstract: Background: Over 1100 genes have been annotated for human chromosome 9, including disease genes implicated in inflammation, atherosclerosis, cancer and neurodegeneration. The serine palmitoyltransferase-1, SPTLC1, gene is at the 9q22.2 cytogenetic band, a high G+C content region with common genetic alterations sufficient to modify cellular behavior. The sequence is highly conserved among diverse species from bacteria to humans, including a recently discovered 126 nucleotide alternate open reading frame, AltORF. The protein encoded by the reading frames has domains of biological interest and considerable overlapping molecular functions associated with cellular behavior and cancer progression. Methods: Here we examined molecular features of SPTLC1 in a group of inflammation associated cancer cell lines SKN-SH, MDA-PCa, Glioma LN18, PC3 and 647V. Subcellular localization of SPTLC1 was assessed by immunofluorescence microscopy and recombinant green fluorescent protein expression. In addition, PCR, DNA sequencing and bioinformatics analysis were used for molecular profiling of the SPTLC1 genomic and reverse transcribed cDNA fragments. Results: SPTLC1 is detected in all cell lines examined, with intense peri-nuclear staining, consistent with localization in the cytoplasm. Genomic DNA sample, but not the cD NA of SKN cells could be amplified with an AltORF primer set. The PC3 and MDA-PCa cancer cell lines which are both of prostate origin, show differences in SPTLC1 PCR amplification. Similar levels of SPTLC1 AltORF transcripts were detected by quantitative RT-PCR in all cell lines, except the PC3 cell line with low transcript level whose cDNA did not generate nucleotide base sequence information. Conclusions: This is the first reported transcriptional expression of the SPTLC1 AltORF for the inflammation associated human cancer cell lines. Interestingly, it is proximate of oncogenic cancer susceptibility genes and distal of tumor suppressor genes, the high content of short nucleotide repeats in the SPTLC1 AltORF sequence suggesting the region may be genetically unstable. This nominal functional genomics report on the human SPTLC1 AltORF will contribute to compiling a more detailed SPTLC1 gene ontology and is expected to help shed more insight into unique molecular attributes of SPTLC1 in the context of cancer cell behavior, malignant progression and the design of treatment for inflammation associated cancers.
Cite this paper: Yerokun, T. , Neblett, T. and Johnson, C. (2014) Molecular Profile of Human Serine Palmitoyltransferase-1 Proximate of Chromosome 9 Disease Susceptibility Gene Cluster in Inflammatory Cancer Cell Lines. Journal of Cancer Therapy, 5, 885-901. doi: 10.4236/jct.2014.510096.

[1]   Carton, J.M., Uhlinger, D.J., Batheja, A.D., Derian, C., Ho, G., Argenteri, D. and D’Andrea, M.R. (2003) Enhanced Serine Palmitoyltransferase Expression in Proliferating Fibroblasts, Transformed Cell Lines and Human Tumors. Journal of Histochemistry Cytochemistry, 51, 715-726.

[2]   Batheja, A.D., Uhlinger, D.J., Carton, J.M., Ho, G. and D’Andrea, M.R. (2003) Characterization of Serine Palmitoyltransferases in Normal Human Tissues. Journal of Histochemistry Cytochemistry, 51, 687-696.

[3]   Wei, J., Yerokun, T., Leipelt, M., Haynes, C., Radhakrishna, H., Merrill, A.H., et al. (2009) Serine Palmitoyltransferase Subunit 1 Is Present in the Endoplasmic Reticulum, Nucleus and Focal Adhesions, and Functions in Cell Morphology. Biochimica et Biophysica Acta (BBA)—Molecular and Cell Biology of Lipids, 1791, 746-756.

[4]   Bejaoui, K., Wu, C., Scheffler, M.D., Haan, G., Ashby, P., Wu, L., de Jong, P. and Brown Jr., R.H. (2001) SPTLC1 Is Mutated in Hereditary Sensory Neuropathy, Type 1. Nature Genetics, 27, 261-262.

[5]   Dawkins, J.L., Hulme, D.J., Brahmbhatt, S.B., Auer-Grumbach, M. and Nicholson, G.A. (2001) Mutations in SPTLC1, Encoding Serine Palmitoyltransferase, Long Chain Base Subunit-1, Cause Hereditary Sensory Neuropathy Type I. Nature Genetics, 27, 309-312.

[6]   Verhoeven, K., Coen, K., De Vriendt, E., Jacobs, A., Van Gerwen, V., Smouts, I., et al. (2004) SPTLC1 Mutation in Twin Sisters with Hereditary Sensory Neuropathy Type I. Neurology, 62, 1001-1002.

[7]   Hornemann, T., Penno, A., Richard, S., Nicholson, G., van Dijk, F.S., Rotthier, A., Timmerman, V. and von Eckardstein, A. (2009) A Systematic Comparison of All Mutations in Hereditary Sensory Neuropathy Type I (HSAN I) Reveals That the G387A Mutation Is Not Disease Associated. Neurogenetics, 10, 135-143.

[8]   Penno, A., Reilly, M.M., Houlden, H., Laurá, M., Rentsch, K., Niederkofler, V., et al. (2010) Hereditary Sensory Neuropathy Type 1 Is Caused by the Accumulation of Two Neurotoxic Sphingolipids. The Journal of Biological Chemistry, 285, 11178-11187.

[9]   Rotthier, A., Penno, A., Rautenstrauss, B., Auer-Grumbach, M., Stettner, G.M., Asselbergh, B., et al. (2011) Characterization of Two Mutations in the SPTLC1 Subunit of Serine Palmitoyltransferase Associated with Hereditary Sensory and Autonomic Neuropathy Type I. Human Mutation, 32, E2211-E2225.

[10]   Taylor, J.P., Hardy, J. and Fishbeck, K.H. (2002) Toxic Proteins in Neurodegenerative Disease. Science, 296, 1991-1995.

[11]   Auer-Grumbach, M. (2008) Hereditary Sensory Neuropathy Type I. Orphanet Journal of Rare Diseases, 3, 7-13.

[12]   Hannun, Y.A., Luberto, C. and Argraves, K.M. (2001) Enzymes of Sphingolipid Metabolism: From Modular to Integrative Signaling. Biochemistry, 40, 4893-4903.

[13]   Weiss, B. and Stoffell, W. (1997) Human and Murine Serine-Palmitoyl-CoA Transferase—Cloning, Expression and Characterization of the Key Enzyme in Sphingolipid Synthesis. European Journal of Biochemistry, 249, 239-247.

[14]   Yerokun, T. and Stewart, J. (2006) Novel Functional Association of Serine Palmitoyltransferase Subunit 1-A Peptide in Sphingolipid Metabolism with Cytochrome P4501A1 Transactivation and Proliferative Capacity of the Human Glioma LN18 Brain Tumor Cell Line. International Journal of Environmental Research and Public Health, 3, 252-261.

[15]   Humphray, S.J., Oliver, K., Hunt, A.R., Plumb, R.W., Loveland, J.E., Howe, K.L., et al. (2004) DNA Sequence and Analysis of Human Chromosome 9. Nature, 429, 369-374.

[16]   Crespo, I., Vital, A.L., Nieto, A.B., Rebelo, O., Tao, H., Lopes, M.C., et al. (2011) Detailed Characterization of Alterations of Chromosomes 7, 9, and 10 in Glioblastoma as Assessed by Single-Nucleotide Polymorphism Arrays. Journal of Molecular Diagnostics, 13, 634-647.

[17]   Leo, C. and Chen, J.D. (2000) The SRC Family of Nuclear Receptor Coactivators. Gene, 245, 1-11.

[18]   Liu, J., Liao, Z., Camden, J., Griffin, K.D., Garrad, R.C., Santiago-Perez, L.I., González, F.A., Seye, C.I., Weisman, G.A. and Erb, L. (2004) Src Homology 3 Binding Sites in the P2Y2 Nucleotide Receptor Interact with Src and Regulate Activities of Src, Pyk2, and Growth Factor Receptors. Journal of Biological Chemistry, 279, 8212-8218.

[19]   Oyama, M., Itagaki, C., Hata, H., Suzuki, Y., Izumi, T., Natsume, T., Isobe, T. and Sugano, S. (2004) Analysis of Small Human Proteins Reveals the Translation of Upstream Open Reading Frames of mRNAs. Genome Research, 14, 2048-2052.

[20]   Oyama, M., Kozuka-Hata, H., Suzuki, Y., Semba, K., Yamamoto, T. and Sugano, S. (2007) Diversity of Translation Start Sites May Define Increased Complexity of the Human Short ORFeome. Molecular & Cellular Proteomics, 6, 1000-1006.

[21]   Vanderperre, B., Lucier, J.F. and Roucou, X. (2012) HAltORF: A Database of Predicted Out-of-Frame Alternative Open Reading Frames in Human. Database (Oxford), 2012, bas025.

[22]   Futerman, A.H. and Hannun, Y.A. (2004) The Complex Life of Simple Sphingolipids. EMBO Reports, 5, 777-782.

[23]   Hornemann, T., Wei, Y. and von Eckardstein, A. (2007) Is the Mammalian Serine Palmitoyltransferase a High-Mole- cular-Mass Complex? Biochemical Journal, 405, 157-164.

[24]   Tamehiro, N., Zhou, S., Okuhira, K., Benita, Y., Brown, C.E., Zhuang, D.Z., Latz, E., Hornemann, T., von Eckardstein, A., Xavier, R.J., Freeman, M.W. and Fitzgerald, M.L. (2008) SPTLC1 Binds ABCA1 to Negatively Regulate Trafficking and Cholesterol Efflux Activity of the Transporter. Biochemistry, 47, 6138-6147.

[25]   Chang, H.Y., Sneddon, J.B., Alizadeh, A.A., Sood, R., West, R.B., Montgomery, K., Chi, J.T., van de Rijn, M., Botstein, D. and Brown, P.O. (2004) Gene Expression Signature of Fibroblast Serum Response Predicts Human Cancer Progression: Similarities between Tumors and Wounds. PLoS Biology, 2, Article ID: e7.

[26]   Rangarajan, E.S. and Izard, T. (2012) The Cytoskeletal Protein α-Catenin Unfurls upon Binding to Vinculin. Journal of Biological Chemistry, 287, 18492-18499.

[27]   Ewing, R.M., Chu, P., Elisma, F., Li, H., Taylor, P., Climie, S., et al. (2007) Large-Scale Mapping of Human Protein-Protein Interactions by Mass Spectrometry. Molecular Systems Biology, 3, 89.

[28]   Abramow-Newerly, M., Roy, A.A., Nunn, C. and Chidiac, P. (2006) RGS Proteins Have a Signaling Complex: Interactions between RGS Proteins and GPCRs, Effectors, and Auxiliary Proteins. Cellular Signalling, 18, 579-591.

[29]   Riker, A.I., Enkemann, S.A., Fodstad, O., Liu, S., Ren, S., Morris, C., et al. (2008) The Gene Expression Profiles of Primary and Metastatic Melanoma Yield a Transition Point of Tumor Progression and Metastasis. BMC Medical Genomics, 1, 13.

[30]   Tamehiro, N., Mujawar, Z., Zhou, S., Zhuang, D.Z., Hornemann, T., von Eckardstein, A. and Fitzgerald, M.L. (2009) Cell Polarity Factor Par3 Binds SPTLC1 and Modulates Monocyte Serine Palmitoyltransferase Activity and Chemotaxis. Journal of Biological Chemistry, 284, 24881-24890.

[31]   Hirose, T., Karasawa, M., Sugitani, Y., Fujisawa, M., Akimoto, K., Ohno, S. and Noda, T. (2006) PAR3 Is Essential for Cyst-Mediated Epicardial Development by Establishing Apical Cortical Domains. Development, 133, 1389-1398.

[32]   Sfakianos, J., Togawa, A., Maday, S., Hull, M., Pypaert, M., Cantley, L., Toomre, D. and Mellman, I. (2007) Par3 Functions in the Biogenesis of the Primary Cilium in Polarized Epithelial Cells. Journal of Cell Biology, 179, 1133-1140.

[33]   Marcil, M., Brooks-Wilson, A., Clee, S.M., Roomp, K., Zhang, L.H., Yu, L., et al. (1999) Mutations in the ABC1 Gene in Familial HDL Deficiency with Defective Cholesterol Efflux. Lancet, 354, 1341-1346.

[34]   Luciani, M.F., Denizot, F., Savary, S., Mattei, M.G. and Chimini, G. (1994) Cloning of Two Novel ABC Transporters Mapping on Human Chromosome 9. Genomics, 21, 150-159.

[35]   Maruno, M., Yoshimine, T., Muhammad, A.K., Tokiyoshi, K. and Hayakawa, T. (1996) Loss of Heterozygosity of Microsatellite Loci on Chromosome 9p in Astrocytic Tumors and Its Prognostic Implications. Journal of Neuro-Oncology, 30, 19-24.

[36]   Bulashevska, S., Szakacs, O., Brors, B., Eils, R. and Kovacs, G. (2004) Pathways of Urothelial Cancer Progression Suggested by Bayesian Network Analysis of Allelotyping Data. International Journal of Cancer, 110, 850-856.

[37]   Gudmundsson, J., Sulem, P., Gudbjartsson, D.F., Jonasson, J.G., Sigurdsson, A., Bergthorsson, J.T., et al. (2009) Common Variants on 9q22.33 and 14q13.3 Predispose to Thyroid Cancer in European Populations. Nature Genetics, 41, 460-464.

[38]   Jones, A.M., Howarth, K.M., Martin, L., Gorman, M., Mihai, R., Moss, L., et al. (2012) Thyroid Cancer Susceptibility Polymorphisms: Confirmation of Loci on Chromosomes 9q22 and 14q13, Validation of a Recessive 8q24 Locus and Failure to Replicate a Locus on 5q24. Journal of Medical Genetics, 49, 158-163.

[39]   Warren, H., Dudbridge, F., Fletcher, O., Orr, N., Johnson, N., Hopper, J.L., et al. (2012) 9q31.2-rs865686 as a Susceptibility Locus for Estrogen Receptor-Positive Breast Cancer: Evidence from the Breast Cancer Association Consortium. Cancer Epidemiology, Biomarkers & Prevention, 21, 1783-1791.

[40]   Sinha, S., Singh, R.K., Alam, N., Roy, A., Roychoudhury, S. and Panda, C.K. (2008) Alterations in Candidate Genes PHF2, FANCC, PTCH1 and XPA at Chromosomal 9q22.3 Region: Pathological Significance in Early- and Late-Onset Breast Carcinoma. Molecular Cancer, 7, 84.

[41]   Byrom, J., Mudaliar, V., Redman, C.W., Jones, P., Strange, R.C. and Hoban, P.R. (2004) Loss of Heterozygosity at Chromosome 9q22-31 Is a Frequent and Early Event in Ovarian Tumors. International Journal of Oncology, 24, 1271-1277.

[42]   Kemp, Z.E., Carvajal-Carmona, L.G., Barclay, E., Gorman, M., Martin, L., Wood, W., et al. (Colorectal Tumour Gene Identification Study Consortium) (2006) Evidence of Linkage to Chromosome 9q22.33 in Colorectal Cancer Kindreds from the United Kingdom. Cancer Research, 66, 5003-5006.

[43]   Majewski, T., Lee, S., Jeong, J., Yoon, D.S., Kram, A., Kim, M.S., et al. (2008) Understanding the Development of Human Bladder Cancer by Using a Whole-Organ Genomic Mapping Strategy. Laboratory Investigation, 88, 694-721.

[44]   Takuwa, Y., Takuwa, N. and Sugimoto, N. (2002) The Edg Family G Protein-Coupled Receptors for Lysophospholipids: Their Signaling Properties and Biological Activities. Journal of Biochemistry, 131, 767-771.

[45]   Bussemakers, M.J., van Bokhoven, A., Verhaegh, G.W., Smit, F.P., Karthaus, H.F., Schalken, J.A., Debruyne, F.M., Ru, N. and Isaacs, W.B. (1999) DD3: A New Prostate-Specific Gene, Highly Overexpressed in Prostate Cancer. Cancer Research, 59, 5975-5979.

[46]   Vaananen, R.M., Lilja, H., Cronin, A., Kauko, L., Rissanen, M., Kauko, O., Kekki, H., Vidback, S., Nurmi, M., Alanen, K. and Pettersson, K. (2013) Association of Transcript Levels of 10 Established or Candidate-Biomarker Gene Targets with Cancerous versus Non-Cancerous Prostate Tissue from Radical Prostatectomy Specimens. Clinical Biochemistry, 46, 670-674.

[47]   Wang, Y.Q., Qi, X.W., Wang, F., Jiang, J. and Guo, Q.N. (2012) Association between TGFBR1 Polymorphisms and Cancer Risk: A Meta-Analysis of 35 Case-Control Studies. PLoS ONE, 7, Article ID: e42899.

[48]   Sirvent, A., Benistant, C. and Roche, S. (2008) Cytoplasmic Signalling by the c-Abl Tyrosine Kinase in Normal and Cancer Cells. Biology of the Cell, 100, 617-631.

[49]   Fletcher, O., Johnson, N., Orr, N., Hosking, F.J., Gibson, L.J., Walker, K., et al. (2011) Novel Breast Cancer Susceptibility Locus at 9q31.2: Results of a Genome-Wide Association Study. Journal of the National Cancer Institute, 103, 425-435.

[50]   Antoniou, A.C., Kuchenbaecker, K.B., Soucy, P., Beesley, J., Chen, X., McGuffog, L., et al. (2012) Common Variants at 12p11, 12q24, 9p21, 9q31.2 and in ZNF365 Are Associated with Breast Cancer Risk for BRCA1 and/or BRCA2 Mutation Carriers. Breast Cancer Research, 14, R33.

[51]   Uhlen, M., Oksvold, P., Fagerberg, L., Lundberg, E., Jonasson, K., Forsberg, M., Zwahlen, M., Kampf, C., Wester, K., Hober, S., Wernerus, H., Bjorling, L. and Ponten, F. (2012) Towards a Knowledge-Based Human Protein Atlas. Nature Biotechnology, 28, 1248-1250.

[52]   Speicher, M.R. (1995) Microsatellite Instability in Human Cancer. Oncology Research, 7, 267-275.

[53]   Sigrist, C.J., de Castro, E., Cerutti, L., Cuche, B.A., Hulo, N., Bridge, A., Bougueleret, L. and Xenarios, I. (2013) New and Continuing Developments at PROSITE. Nucleic Acids Research, 41, D344-D347.

[54]   Mukherjee, J.J. and Dekker, E.E. (1990) 2-amino-3-Ketobutyrate CoA Ligase of Escherichia coli: Stoichiometry of Pyridoxal Phosphate Binding and Location of the Pyridoxyllysine Peptide in the Primary Structure of the Enzyme. Biochimica et Biophysica Acta, 1037, 24-29.

[55]   Yasuda, S., Nishijima, M. and Hanada, K. (2003) Localization, Topology and Function of the LCB1 Subunit of Serine Palmitoyltransferase in Mammalian Cells. Journal of Biological Chemistry, 278, 4176-4183.

[56]   Batada, N.N., Urrutia, A.O. and Hurst, L.D. (2007) Chromatin Remodelling Is a Major Source of Coexpression of Linked Genes in Yeast. Trends in Genetics, 23, 480-484.

[57]   Xu, C., Bailly-Maitre, B. and Reed, J.C. (2005) Endoplasmic Reticulum Stress: Cell Life and Death Decisions. Journal of Clinical Investigation, 115, 2656-2664.

[58]   Moenner, M., Pluquet, O., Bouchecareilh, M. and Chevet, E. (2007) Integrated Endoplasmic Reticulum Stress Responses in Cancer. Cancer Research, 67, 10631-10634.

[59]   Kaklamani, V.G. and Pasche, B. (2004) Role of TGF-β in Cancer and the Potential for Therapy and Prevention. Expert Review of Anticancer Therapy, 4, 649-661.

[60]   Magrassi, L., Marziliano, N., Inzani, F., Cassini, P., Chiaranda, I., Skrap, M., Pizzolito, S., Arienta, C. and Arbustini, E. (2010) EDG3 and SHC3 on Chromosome 9q22 Are Co-Amplified in Human Ependymomas. Cancer Letters, 290, 36-42.

[61]   Contos, J.J., Ishii, I. and Chun, J. (2000) Lysophosphatidic Acid Receptors. Molecular Pharmacology, 58, 1188-1196.

[62]   Hecht, J.H., Weiner, J.A., Post, S.R. and Chun, J. (1996) Ventricular Zone Gene-1 (vzg-1) Encodes a Lysophosphatidic Acid Receptor Expressed in Neurogenic Regions of the Developing Cerebral Cortex. Journal of Cell Biology, 135, 1071-1083.

[63]   Chun, J., Hla, T., Lynch, K.R., Spiegel, S. and Moolenaar, W.H. (2010) International Union of Basic and Clinical Pharmacology. LXXVIII. Lysophospholipid Receptor Nomenclature. Pharmacological Reviews, 62, 579-587.

[64]   Blaho, V.A. and Hla, T. (2011) Regulation of Mammalian Physiology, Development, and Disease by the Sphingosine 1-Phosphate and Lysophosphatidic Acid Receptors. Chemical Reviews, 111, 6299-6320.

[65]   Fei, D.L., Sanchez-Mejias, A., Wang, Z., Flaveny, C., Long, J., Singh, S., et al. (2012) Hedgehog Signaling Regulates Bladder Cancer Growth and Tumorigenicity. Cancer Research, 72, 4449-4458.

[66]   Thornton, M., Aslam, M.A., Tweedle, E.M., Ang, C., Campbell, F., Jackson, R., Costello, E., Rooney, P.S., Vlatkovi?, N. and Boyd, M.T. (2013) The Unfolded Protein Response Regulator GRP78 Is a Novel Predictive Biomarker in Colorectal Cancer. International Journal of Cancer, 133, 1408-1418.

[67]   Albano, F., Zagaria, A., Anelli, L., Coccaro, N., Impera, L., Minervini, C.F., et al. (2013) Gene Expression Profiling of Chronic Myeloid Leukemia with Variant t(9;22) Reveals a Different Signature from Cases with Classic Translocation. Molecular Cancer, 12, 36.

[68]   Qiu, Z., Cang, Y. and Goff, S.P. (2010) c-Abl Tyrosine Kinase Regulates Cardiac Growth and Development. Proceedings of the National Academy of Sciences of the United States of America, 107, 1136-1141.

[69]   Taouji, S., Higa, A., Delom, F., Palcy, S., Mahon, F.X., Pasquet, J.M., Bossé, R., Ségui, B. and Chevet, E. (2013) Phosphorylation of Serine Palmitoyltransferase Long Chain-1 (SPTLC1) on Tyrosine 164 Inhibits Its Activity and Promotes Cell Survival. Journal of Biological Chemistry, 288, 17190-17201.

[70]   Rangé, H., Poitou, C., Boillot, A., Ciangura, C., Katsahian, S., Lacorte, J.M., Czernichow, S., Meilhac, O., Bouchard, P. and Chaussain, C. (2013) Orosomucoid, a New Biomarker in the Association between Obesity and Periodontitis. PLoS ONE, 8, Article ID: e57645.

[71]   Breslow, D.K., Collins, S.R., Bodenmiller, B., Aebersold, R., Simons, K., Shevchenko, A., Ejsing, C.S. and Weissman, J.S. (2010) Orm Family Proteins Mediate Sphingolipid Homeostasis. Nature, 463, 1048-1053.