Article Figures & Data
Figures
- Figure 1
Northern blot analysis of HNSCC SEREX clones. The expression of clones AU-HN-4 (A), AU-HN-18 (B), AU-HN-25 (C), and AU-HN-6 (D) was assayed in the following normal human tissues: (1) spleen, (2) thymus, (3) prostate, (4) testis, (5) ovary, (6) small intestine, (7) colon, and (8) lymphocytes.
- Figure 2
AU-HN-15 expression in HNSCC tumors. The expression of AU-HN-15 (A) and beta-actin (B) was determined by RT-PCR in the following samples: (1-8) HNSCC tumor tissue; (9-12) HNSCC cell lines: SCC-4 (9), HTB-43 (10), SCC-25 (11) and CCL-30 (12); (13-16) tissue adjacent to HNSCC tumor; (17-18) AU-HN-15 plasmid.
- Figure 3
Quantification of clone AU-HN-15 mRNA in normal and tumor tissues by qRT-PCR. Messenger RNA copy number is expressed as the number of AU-HN-15 molecules in 100 ng of total RNA per 105 molecules of beta-glucoronidase. (A) Normal tissues: (1) brain, (2) testis-1, (3) colon, (4) liver, (5) testis-2, (6) kidney-1, (7) lung, (8) trachea, (9) small intestine, (10) stomach, (11) thymus, (12) heart, (13), spleen, (14) bone marrow, (15) kidney-2. (B) HNSCC tumor tissues (1-11) and HNSCC cell lines (12-15): SCC-25 (12), HTB-4B (13), SCC-4 (14), CCL-30 (15). (C) Paired samples: HNSCC (1, 3, 5) and adjacent mucosae (2, 4, 6) from three primary tumors; HNSCC metastatic to lymph node (7) and paired normal tissue (8).
Tables
- Table 1
HNSCC clones corresponding to known genes.
Functional Group Clone ID No. of Times Isolated Identity Unigene Cluster Previously Identified by SEREX DNA binding/ Transcription AU-HN-2 1 TREX1, 3' repair exonuclease Hs.278408 no AU-HN-4 2 BRAP (BRCA1 associated): Nuclear localization protein Hs.122764 yes AU-HN-5 1 Trim 26 zinc finger domains Hs.1287 no AU-HN-10 1 GTF21 transcription factor. Murine homolog TF11-1 Hs.278589 no AU-HN-11 6 NSEP1 (YB-1) transcription factor Hs.74497 yes AU-HN-16 1 MAZ transcription factor associated with c-myc Hs.7647 yes AU-HN-17 1 SON (DBP-5; KIAA1019; NREBP DNA binding protein) Hs.92909 yes AU-HN-27 1 NACA nascent polypeptide-associated complex Hs.32916 yes AU-HN-37 1 NUBP2 nucleotide binding protein Hs.256549 no RNA processing/ Translation AU-HN-3 1 EEF2 Translation elongation factor 2 Hs.75309 no AU-HN-13 2 GU2 Putative RNA helicase Hs.7392 no AU-HN-30 1 RPLI3A ribosomal protein Hs.119122 no AU-HN-31 1 SFRS21P (CASP11; SIP1; SRRP1290 splicing factor) Hs.51957 no AU-HN-33 1 RPS12 ribosomal protein Hs.339696 no AU-HN-34 1 MGC2835 RNA helicase Hs.70582 no Regulatory AU-HN-18 1 TMF1, TATA modulatory factor Hs.267632 yes AU-HN-23 1 PRC1 regulator of cytokinesis Hs.344037 no Structural AU-HN-22 2 KRT14 keratin 14 Hs.355214 no AU-HN-28 1 Viniculin Hs.75350 yes AU-HN-32 1 H2AFY histone family member Hs.75258 no Apoptosis repressor AU-HN-14 2 SLK (KIAA02304) Ste related kinase Hs.105751 no AU-HN-20 2 NOL3 (ARC) nuclear protein 3, apoptosis repressor Hs.278439 no Molecular chaperone AU-HN-24 1 DNAJA2 member of Hsp40 family Hs.21189 yes AU-HN-35 1 DNAJA1 member of HSP40 family Hs.94 yes Other AU-HN-1 1 LINE-1 retrotransposon No yes AU-HN-6 1 MOG (HSPC 165) Homolog of yeast protein Hs.13605 no AU-HN-12 4 LIMS1 (PINCH): LIM and senescent antigen-like domain Hs.112378, Hs.193700 yes AU-HN-21 2 COPB2 coatomer protein complex subunit protein Hs.75724 no AU-HN-25 1 FLJ22548 hypothetical protein Hs.103267 no AU-HN-26 2 C21orf97; FLJ21324; MGC15873 Hs.4746 yes AU-HN-29 3 SSNA1 Sjogrens syndrome nuclear autoantigen 1 Hs.18528 no - Table 2
Correspondence of HNSCC clones with other SEREX clones.
Clone ID SEREX Clones Tumor Type AU-HN-1 NGO-Lu-8 lung AU-HN-4 P2B-25f, NGO-Br-5, NY-REN-63, MO-BR-100, RMNY-BR-52, MO-OVA-76, NY-CO-6, HOM-TS-GL1-16, TM-92, TE2-7 breast, renal, ovary, colon, normal testis AU-HN-11 HOM-TSOv2.35, HOM-Ts-PMR2-12 normal testis AU-HN-12 NGO-St-79, MO-REN-80, NY-REN-48, NGO-Br-47, NY-ESO-10, UL-AML-4, NGO-Co-8 stomach, renal, breast, esophagus, AML, colon AU-HN-14 MO-BC-1128, se20-9, NGO-Lu-33 lung AU-HN-16 MO-CO-135, MO-CO-2 colon AU-HN-17 NGO-Pr-44 prostate AU-HN-18 NGO-St-29, LONY-BR-81, MO-CO-103 stomach, breast, colon AU-HN-24 NY-REN-14 renal AU-HN-26 NY-CO-18 colon AU-HN-27 NY-CO-2, NW-FW 22, NGO-Lu-27 colon, lung AU-HN-28 NY-BR-101, NGO-Br-52 breast AU-HN-35 NGO-Lu-17, 6-32, 6-25.1, 6-8.1, 6.26.1, 6.27 lung, liver - Table 3
HNSCC SEREX clones corresponding to novel or not fully characterized genes.
Function Clone No. Identity Previously Identified SEREXa Clones Tumor Type Unigene Cluster Regulatory/ DNA binding AU-HN-9 unknown no Hs.95262 AU-HN-15 KIAA0530, zinc finger domain HOM-TSsemA-56, NY-CO-6, MOBr-17 colon, breast, normal testis Hs.173081 TNF-inducible AU-HN-36 rat stannin no Hs.76691 Unknown AU-HN-7 hypothetical protein DKFZp4340032 no Hs.114173 AU-HN-8 human FLJ23089 no Hs.130554 AU-HN-19 PC326 HOM-TSsem4.95, P2A-89, HOM-TSMa4.9, MOVA95, HOM-HCC-27.8, HOM-Br3.40, Mz19-F-45 prostate, liver,melanoma, lung,ovary, normal testis Hs.279882 aSEREX database (36).
- Table 4
Novel antigens identified in HNSCC by SEREX: summary of Northern blot analyses.
Tissue Expressiona of Clone AU-HN- 2 4 6 9 14 15 18 20 23 25 34 Spleen ++ - - + + - - + nt - nt Thymus + - - + + - - + nt (+) nt Prostate ++ - - + + - - + nt + nt Testis + ++ +++ + + - ++ +++ nt +++ nt Lymphocytes ++ - - + + - - + nt (+) nt Ovary + - - + + - - + nt + nt Small intestine + - - + + - - + nt - nt Colon + - - + + - - + - + - Brain nt nt nt nt nt - nt nt - nt + Heart nt nt nt nt nt - nt nt - nt + Kidney nt nt nt nt nt - nt nt ++ nt + Liver nt nt nt nt nt - nt nt ++ nt + Lung nt nt nt nt nt - nt nt - nt - aExpression: +++, high expression; ++, medium expression; +, low expression; (+), very weak; nt, not tested.
- Table 5
Serological screening of the HNSCC screen 5 clones with the individual HNSCC sera making up the pool used for the screening.
Clone No. Identity Serum BT RM DG AU-HN-12 PINCH + + + AU-HN-22 keratin - - + AU-HN-23 human Hsp DNAj (+)a - - AU-HN-25 FLJ22548 - - + AU-HN-26a C21orf97, FDJ21324 (+) - - AU-HN-26b + + - AU-HN-27 NACN, transcription activator - + + AU-HN-28 vinculin - + + AU-HN-29a Sjogren's nuclear antigen NA14 + - + AU-HN-29b (+) - - AU-HN-29c + + + AU-HN-30 L13a ribosomal protein (+) - - AU-HN-31 SFRS21 splicing factor - + - AU-HN-32 H2A.1 histone + - + AU-HN-33 S12 ribosomal protein - + - AU-HN-34 RNA helicase related (+) - - AU-HN-35 human Hsp DNAj (+) - - AU-HN-36 rat stannin related + + - AU-HN-97 laminin receptor + + + a(+) HNSCC clones positive only with BT serum (adenocarcinoma).
- Table 6
Description of SEREX screenings.
Screen No. Tissue Serum (dilution) No. of pfu Screened No. of Clones 1 JKa tumor JKa (1:100) 5 x 105 3 2 normal testis JKa (1:100) 1 x 106 9 4 SCC-25b RLc (1:100) 1 x 106 19 5 RMd tumor pool: RMd (1:100), DGe (1:150) and BTf (1:200) 9 x 105 19 aJK: Right neck dissection, LN with metastatic moderately differentiated keratinizing SCC. bSCC-25: Cell line established from SCC of the tongue. cRL: Neck dissection, metastatic moderately differentiated SCC from primary tongue lesion; large tumor burden. dRM: Left cheek tumor, ulcerating moderately differentiated keratinizing SCC. eDG: HNSCC Stage 4; large tumor burden. fBT: Neck dissection, metastatic adenocarcinoma.
Volume 4, Issue 1
