Research Article: Characterization of Alstrom Syndrome 1 (ALMS1) Transcript Variants in Hodgkin Lymphoma Cells

Date Published: January 30, 2017

Publisher: Public Library of Science

Author(s): Katarina Braune, Ines Volkmer, Martin S. Staege, Francesco Bertolini.


The Alstrom syndrome gene (ALMS1) is one of the largest disease associated genes identified today in the human genome and is implicated in cell cycle control, ciliogenesis, endosome recycling and intracellular transport mechanisms. ALMS1 mutations cause Alstrom syndrome, a rare genetic disorder. However, its function is not completely understood. DNA microarray analysis suggested that ALMS1 might be differentially expressed between Hodgkin lymphoma (HL) cells and normal tissues. By using reverse transcription-polymerase chain reaction (RT-PCR) we detected low but variable expression of ALMS1 in HL cell lines with highest expression in KM-H2 cells. Immunofluorescence indicated centrosomal accumulation of ALMS1 protein in HL cells. Knock-down of ALMS1 in KM-H2 cells had no impact on viability or cytotoxic drug sensitivity of these cells. Sequencing of RT-PCR products from HL cell lines identified three variable regions in ALMS1 transcripts that affect exons 2, 13, and 23. One of these variants was characterized by splicing out of exon 13. The other variants are characterized by two alternative 5 prime ends or alternative 3 prime ends. Structure prediction of the corresponding RNAs and proteins suggest that the different transcript variants might affect posttranscriptional regulation and ligand binding.

Partial Text

Hodgkin lymphoma (HL) is a lymphoproliferative disease of unknown etiology. The prognosis for HL patients steadily improved over the last few decades, particularly with the introduction of combined radio-chemotherapy [1]. With a five-year survival rate of over 90% in Europe and the United States [2,3], Hodgkin lymphoma today has one of the best prognoses among all childhood malignancies. Despite this development, not all patients can be cured with currently established therapy protocols. Furthermore, conventional cancer therapy is associated with numerous side effects and serious long-term complications such as secondary malignancies [4]. By understanding the molecular mechanisms of tumor development, progression and drug resistance, potential candidate genes can be identified as new targets for HL therapy.

Genes with differential expression in tumor cells compared to normal tissues may represent potential targets for cancer therapy. In our previous studies we identified a probe set (214707_x_at) annotated to ALMS1 as differentially expressed between HL cell lines and a panel of normal tissues [6]. This probe set was one of 50 probe sets with very low signal intensities in HL cell lines. Using a larger number of publicly available microarray data sets from normal tissues, normal B cells, HL biopsies and HL cell lines, we reproduced this observation. As shown in Fig 1, the ALMS1 probe set 214707_x_at showed very low signal intensities in HL cell lines in comparison to normal tissues including normal B cells. Interestingly, micro-dissected HL cells from biopsies showed higher signal intensities whereas non-dissected HL biopsies from a different study showed the same low signal intensities as established cell lines (Fig 1). The microarrays used in this study included 5 probe sets related to ALMS1. In addition to the probe set 214707_x_at, the arrays contained two ALMS1 specific probe sets (214220_s_at and 214221_at), one probe set specific for the ALMS1 pseudogene (ALMS1P; probe set 1552576_at), and one probe set specific for the ALMS1 intronic transcript 1 (ALMS1-IT1; probe set 1556911_at). As shown in Fig 1, the signal intensities for these probe sets indicated no down-regulation in HL cell lines. Signal intensities for ALMS1-IT1 were even higher in HL cell lines and micro-dissected HL cells than in normal tissues.

Although the ALMS1 gene is one of the largest disease-associated genes identified today in the human genome, its physiological function and pathological significance both for the etiology of Alstrom syndrome and carcinogenesis remains largely unknown.




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