Primary effect of chemotherapy on the transcription profile of AIDS-related Kaposi's sarcoma.
BACKGROUND
Drugs & used in anticancer chemotherapy have severe effects upon the cellular transcription and replication machinery. From in vitro studies it has become clear that these drugs can affect specific genes, as well as have an effect upon the total transcriptome.


METHODS
Total mRNA from two skin lesions from a single AIDS-KS patient was analyzed with the SAGE (Serial Analysis of Gene Expression) technique to assess changes in the transcriptome induced by chemotherapy. SAGE libraries were constructed from material obtained 24 (KS-24) and 48 (KS-48) hrs after combination therapy with bleomycin, doxorubicin and vincristine. KS-24 and KS-48 were compared to SAGE libraries of untreated AIDS-KS, and to libraries generated from normal skin and from isolated CD4+ T-cells, using the programs USAGE and HTM. SAGE libraries were also compared with the SAGEmap database.


RESULTS
In order to assess the primary response of AIDS-related Kaposi's sarcoma (AIDS-KS) to chemotherapy in vivo, we analyzed the transcriptome of AIDS-KS skin lesions from a HIV-1 seropositive patient at two time points after therapy. The mRNA profile was found to have changed dramatically within 24 hours after drug treatment. There was an almost complete absence of transcripts highly expressed in AIDS-KS, probably due to a transcription block. Analysis of KS-24 suggested that mRNA pool used in its construction originated from poly(A) binding protein (PABP) mRNP complexes, which are probably located in nuclear structures known as interchromatin granule clusters (IGCs). IGCs are known to fuse after transcription inhibition, probably affecting poly(A)+RNA distribution.Forty-eight hours after chemotherapy, mRNA isolated from the lesion was largely derived from infiltrating lymphocytes, confirming the transcriptional block in the AIDS-KS tissue.


CONCLUSIONS
These in vivo findings indicate that the effect of anti-cancer drugs is likely to be more global than up- or downregulation of specific genes, at least in this single patient with AIDS-KS. The SAGE results obtained 24 hrs after chemotherapy can be most plausibly explained by the isolation of a fraction of more stable poly(A)+RNA.
van der Kuyl
Antoinette C
AC
Department of Human Retrovirology, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands. a.c.vanderkuyl@amc.uva.nl
van den Burg
Remco
R
Zorgdrager
Fokla
F
Dekker
John T
JT
Maas
Jolanda
J
van Noesel
Carel J M
CJ
Goudsmit
Jaap
J
Cornelissen
Marion
M
D000163:Acquired Immunodeficiency Syndrome / Q000188:drug therapy* / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects*; D015723:Gene Library; D005796:Genes / Q000187:drug effects; D052138:Genes, Neoplasm / Q000187:drug effects; D006801:Humans; D011061:Poly A / Q000032:analysis; D012313:RNA / Q000032:analysis; D012333:RNA, Messenger / Q000032:analysis; D000077278:RNA, Mitochondrial; D012334:RNA, Neoplasm / Q000032:analysis; D012514:Sarcoma, Kaposi / Q000188:drug therapy* / Q000235:genetics*; D012878:Skin Neoplasms / Q000188:drug therapy* / Q000235:genetics*; D013997:Time Factors; D014158:Transcription, Genetic / Q000187:drug effects*
D012333:RNA, Messenger; D000077278:RNA, Mitochondrial; D012334:RNA, Neoplasm; D011061:Poly A; D012313:RNA