{"owner": "ArrayExpress Uploader", "pop_total": 0, "species": "human", "factors": [{"GSM1384135": {"PATIENT GENDER": "NA", "MEDICAL HISTORY": "not specified", "TISSUE TYPE": "normal spleen control", "TREATMENT": "not specified", "SITE OF INVOLVEMENT OF LYMPHOMA": "not specified", "KARYOTYPE": "not specified", "PATIENT AGE": "not specified"}}, {"GSM1384135": {"PATIENT GENDER": "NA", "MEDICAL HISTORY": "not specified", "TISSUE TYPE": "normal spleen control", "TREATMENT": "not specified", "SITE OF INVOLVEMENT OF LYMPHOMA": "not specified", "KARYOTYPE": "not specified", "PATIENT AGE": "not specified"}}, {"GSM1384135": {"PATIENT GENDER": "NA", "MEDICAL HISTORY": "not specified", "TISSUE TYPE": "normal spleen control", "TREATMENT": "not specified", "SITE OF INVOLVEMENT OF LYMPHOMA": "not specified", "KARYOTYPE": "not specified", "PATIENT AGE": "not specified"}}, {"GSM1384132": {"PATIENT GENDER": "male", "MEDICAL HISTORY": "kidney Tx for dysplasia", "TISSUE TYPE": "Hepatosplenic T cell Lymphoma", "TREATMENT": "splenectomy, combined CT", "SITE OF INVOLVEMENT OF LYMPHOMA": "S, Pe, BM", "KARYOTYPE": "40-48,XY,+X \u00ef\u00bf\u00bd[3],-5[4],i(7)(q10),+8[5],+10[2],add(11)(q22)[10],inc[cp12].aCGH+8", "PATIENT AGE": "18 yrs"}}, {"GSM138413": {"PATIENT GENDER": "male", "MEDICAL HISTORY": "Crohn\u00e2\u0080\u0099s disease", "TISSUE TYPE": "Hepatosplenic T cell Lymphoma", "TREATMENT": "splenectomy, combined CT, MAB", "SITE OF INVOLVEMENT OF LYMPHOMA": "S", "KARYOTYPE": "46-47,XY,add(4)(p16),i(7)(q10),+8[4],-[20],+mar[2][cp6]", "PATIENT AGE": "52 yrs"}}, {"GSM1384130": {"PATIENT GENDER": "male", "MEDICAL HISTORY": "Budd-Chiari syndrome, liver Tx", "TISSUE TYPE": "Hepatosplenic T cell Lymphoma", "TREATMENT": "splenectomy", "SITE OF INVOLVEMENT OF LYMPHOMA": "S, L, BM", "KARYOTYPE": "45-46,X,-Y,-4,der(7)add(7)(p22)add(7)(q32), i(7)(q10),+i(7)(q10)[2],der(8)t(1;8)(q21; p23),-22,+mar1,+mar2[cp11].aCGH+8", "PATIENT AGE": "33 yrs"}}, {"GSM1384129": {"PATIENT GENDER": "male", "MEDICAL HISTORY": "not specified", "TISSUE TYPE": "Hepatosplenic T cell Lymphoma", "TREATMENT": "splenectomy, allo BMTx", "SITE OF INVOLVEMENT OF LYMPHOMA": "S", "KARYOTYPE": "46-48,XY,r(7),inc[2]", "PATIENT AGE": "26 yrs"}}], "id": 2038, "ownerprofile_id": "arrayexpress_sid", "platform": 4, "summary_wrapped": "Hepatosplenic T-cell lymphoma (HSTL) is an aggressive lymphoma cytogenetically characterized by isochromosome 7q   [i(7)(q10)], of which...", "geo_gse_id": "E-GEOD-57520", "owner_profile": "/profile/8773/arrayexpressuploader", "factor_count": 7, "sample_count": 7, "tags": ["cell", "chromosome", "disease", "lymphoma"], "lastmodified": "Dec.12, 2014", "is_default": false, "geo_gds_id": "", "slug": "expression-data-from-hepatosplenic-t-cell-lymphoma", "geo_id_plat": "E-GEOD-57520_A-AFFY-44", "name": "Expression data from Hepatosplenic T cell lymphoma patient samples and normal spleen as control.", "created": "Jul.10, 2014", "summary": "Hepatosplenic T-cell lymphoma (HSTL) is an aggressive lymphoma cytogenetically characterized by isochromosome 7q   [i(7)(q10)], of which the molecular consequences remain unknown. We report here results of an integrative genomic and transcriptomic (expression microarray and RNA-sequencing) study of six HSTL cases with i(7)(q10) and three cases with ring 7   [r(7)], a rare variant aberration. Using high resolution array CGH, we prove that HSTL is characterized by the common loss of a 34.88 Mb region at 7p22.1p14.1 (3506316-38406226 bp) and duplication/amplification of a 38.77 Mb region at 7q22.11q31.1 (86259620-124892276 bp). Our data indicate that i(7)(q10)/r(7)-associated loss of 7p22.1p14.1 is a critical event in the development of HSTL, while gain of 7q sequences drives progression of the disease and underlies its intrinsic chemoresistance. Loss of 7p22.1p14.1 does not target a postulated tumor suppressor gene but unexpectedly enhances the expression of CHN2 from the remaining 7p allele, resulting in overexpression of \u03b22-chimerin and dysregulation of a pathway involving RAC1 and NFATC2 with a cell proliferation response. Gain of 7q leads to increased expression of critical genes, including RUNDC3B, PPP1R9A and ABCB1, a known multidrug resistance gene. RNA-sequencing did not identify any additional recurrent mutations or gene fusions, suggesting that i(7)(q10) is the only driver event in this tumor. Our study confirms the previously described gene expression profile of HSTL and identifies a set of 24 genes, including three located on chromosome 7 (CHN2, ABCB1 and PPP1R9A), distinguishing HSTL from other malignancies overall design", "source": "http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-57520", "sample_source": "http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-57520/samples/"}