The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSIBLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.

/pdf/gapped-blast-and-psi-blast-a-new-generation-of-protein-2ybl67x5yx.pdf

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

Increased generation of reactive oxygen species (ROS) and an altered redox status have long been observed in cancer cells, and recent studies suggest that this biochemical property of cancer cells can be exploited for therapeutic benefits. Cancer cells in advanced stage tumours frequently exhibit multiple genetic alterations and high oxidative stress, suggesting that it might be possible to preferentially eliminate these cells by pharmacological ROS insults. However, the upregulation of antioxidant capacity in adaptation to intrinsic oxidative stress in cancer cells can confer drug resistance. Abrogation of such drug-resistant mechanisms by redox modulation could have significant therapeutic implications. We argue that modulating the unique redox regulatory mechanisms of cancer cells might be an effective strategy to eliminate these cells.

Targeting cancer cells by ROS-mediated mechanisms: a radical therapeutic approach?

Transcription factor Nrf2 is essential for the antioxidant responsive element (ARE)-mediated induction of phase II detoxifying and oxidative stress enzyme genes. Detailed analysis of differential Nrf2 activity displayed in transfected cell lines ultimately led to the identification of a new protein, which we named Keap1, that suppresses Nrf2 transcriptional activity by specific binding to its evolutionarily conserved amino-terminal regulatory domain. The closest homolog of Keap1 is a Drosophila actin-binding protein called Kelch, implying that Keap1 might be a Nrf2 cytoplasmic effector. We then showed that electrophilic agents antagonize Keap1 inhibition of Nrf2 activity in vivo, allowing Nrf2 to traverse from the cytoplasm to the nucleus and potentiate the ARE response. We postulate that Keap1 and Nrf2 constitute a crucial cellular sensor for oxidative stress, and together mediate a key step in the signaling pathway that leads to transcriptional activation by this novel Nrf2 nuclear shuttling mechanism. The activation of Nrf2 leads in turn to the induction of phase II enzyme and antioxidative stress genes in response to electrophiles and reactive oxygen species.

/pdf/keap1-represses-nuclear-activation-of-antioxidant-responsive-4szbzl5y9i.pdf

Keap1 represses nuclear activation of antioxidant responsive elements by Nrf2 through binding to the amino-terminal Neh2 domain

https://aasldpubs.onlinelibrary.wiley.com/doi/pdf/10.1053/jhep.2001.29401

Chronic hepatitis B

https://aasldpubs.onlinelibrary.wiley.com/doi/epdf/10.1002/hep.23190

Chronic hepatitis B: Update 2009

867 restoration of mir-517a expression induces cell apoptosis in bladder cancer cell lines

PROBLEM TO BE SOLVED: To provide a method for identifying lung cancer metastasized to lymph node. SOLUTION: The method for identifying lung cancer metastasized to lymph node comprises detecting the expression of a gene in a gene set determined by the following steps (i) to (v): (i) Standardizing the expression data of a gene group expressed specifically to lung cancer metastasized to lymph node. (ii) Preparing a gene list with high-identification ability by sequencing genes with high-identification ability. (iii) Selecting gene sets from the above gene list. (iv) Evaluating the identification ability of the gene sets in the step (iii). (v) Determining the gene set having the ability to identify the lung cancer. COPYRIGHT: (C)2007,JPO&INPIT

Gene set for identifying lymph node metastasis of lung cancer

176 oncogenic lasp1 is directly regulated by the tumor suppressive micrornas (mir-1, mir-218, and mir-133a) in bladder cancer

Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC

BACKGROUND: Head and neck squamous cell carcinoma (HNSCC) is the sixth most common malignancy worldwide. In spite of considerable advances in multimodality therapy including surgery, radiotherapy and chemotherapy, the overall five-year survival rate for patients with HNSCC is around 40%. Understanding of the molecular pathway underlying HNSCC could significantly improve diagnosis, therapy, and disease prevention. Recent our microRNA (miRNA) expression signature revealed that the expression of microRNA-218 (miR-218) was reduced in cancer tissues, suggesting a candidate of tumor suppressor in HNSCC. In this study, we investigated the functional significance of miR-218 and its mediated molecular pathways in HNSCC.

METHODS: XTT, migration and invasion assays were performed following transient transfection of miR-218 in HNSCC cell lines (FaDu and SAS). Genome-wide gene expression analysis and GeneCodis software were used to analyze the pathways regulated by miR-218 or LAMB3. The expressions of miR-218 and lamini-332 genes were verified using qRT-PCR in HNSCC cells lines and clinical specimens. The luciferase reporter assay was used to identify the actual binding site of miR-218 in target gene.

RESULTS: Restoration of miR-218 in cancer cells led to significant inhibition of cell migration and invasion activities in HNSCC cell lines (FaDu and SAS). Genome-wide gene expression analysis of miR-218 transfectants and in silico database analysis showed that focal adhesion pathway was a promising candidate of miR-218 target pathway. The laminins are an important and biologically active part of the basal lamina, the function of that are various such as influencing cell differentiation, migration and adhesion as well as proliferation and cell survival. Interestingly, all components of laminin-332 (LAMA3, LAMB3 and LAMC2) were downregulated and listed on the candidate genes in focal adhesion pathway. Furthermore, we focused on LAMB3 which has a miR-218 target site and gene expression studies and luciferase reporter assays showed that LAMB3 was directly regulated by miR-218. Silencing study of LAMB3 demonstrated significant inhibition of cell migration and invasion in HNSCC cells. In clinical specimens with HNSCC, the expression levels of laminin-332 were significantly upregulated in cancer tissues compared to adjacent non-cancerous tissues.

CONCLUSIONS: These data showed that tumor suppressive miR-218 contributes to cancer cell migration and invasion through regulating focal adhesion pathway, especially laminin-332. Tumor suppressive miRNA-mediated novel cancer pathways provide new insights into the potential mechanisms of HNSCC oncogenesis.

Citation Format: Takashi Kinoshita, Toyoyuki Hanazawa, Nijiro Nohata, Naoko Kikkawa, Noriko Yamamoto, Hideki Enokida, Hirofumi Yoshino, Takeshi Yamasaki, Hideo Hidaka, Masayuki Nakagawa, Yoshitaka Okamoto, Naohiko Seki. Tumor suppressive microRNA-218 inhibits cancer cell migration and invasion through targeting laminin-332 in head and neck squamous cell carcinoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3102A. doi:10.1158/1538-7445.AM2013-3102A

Abstract 3102A: Tumor suppressive microRNA-218 inhibits cancer cell migration and invasion through targeting laminin-332 in head and neck squamous cell carcinoma.

Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL

(Background) Bladder cancer (BC) is the fourth most common tumor diagnosed and the second most common cancer of the genitourinary tract in Japan Though there have been significant advances in treatment, including surgical technique and adjuvant chemotherapy, approximately 70% of first diagnosed BC recurs after treatment, and 10% to 15% of recurrent tumors proceed to muscle invasion and metastasis Therefore, it is crucial to find a new strategy for BC diagnosis and treatment based on recent genome analysis in BC oncogenesis Our expression signatures of human cancer including bladder cancer (BC) revealed that the expression of microRNA-1 (miR-1) and microRNA-133a (miR-133a) were significantly reduced in cancer cells In human genome, miR-1 and miR-133a located same chromosomal regions (miR-1-2 and miR-133a-1 on 18q112, and miR-1-1 and miR-133a-2 on 20q1333) called cluster In this study, we investigated the functional significance of miR-1 and miR-133a and identify the novel molecular targets regulated by miR-1 and miR-133a commonly in BC (Methods) Cell proliferation, invasion, migration and apoptosis assay was performed by restoration of mature miR-1 and/or miR-133a in BC cell lines Genome-wide gene expression analysis was performed to identify the molecular networks of miR-1 and miR-133a by microarray technique A luciferase reporter assay was used to identify the actual binding site between miR-1 and miR-133a and its candidate target genes Cell proliferation, invasion, migration and apoptosis assays were performed to investigate the targets genes in BC cell lines To investigate of expression of target genes, immunohistochemistry was performed by using BC tissue microarray (Results) Restoration of miR-1 and/or miR-133a significantly inhibited cell proliferation migration and invasion in cancer cells Apoptosis assay showed that significant apoptotic cells were induced by miR-1 and/or miR-133a transfection Genome-wide molecular targets search and luciferase reporter assay showed that Transgelin2 (TAGLN2), prothymosin-alpha (PTMA) and purine nucleoside phosphorylase (PNP) were directly regulated by miR-1 and miR-133a commonly Silencing of the target genes studies demonstrated significant inhibition of cell proliferation and invasion, and increase of apoptosis in BC cells Immunohistochemistry showed that TAGLN2 and PTMA expression level was significantly higher in BC than normal bladder epitheliums (Conclusions) miR-1 and miR-133a function as tumor suppressor in BC TAGLN2, PTMA and PNP were directly regulated by tumor suppressive miR-1 and miR-133a commonly These genes may function as oncogenes contributed to cell proliferation and invasion in BC Tumor suppressive miR-1 and miR-133a mediates novel molecular targets provide new insights into the potential mechanisms of BC oncogenesis

Citation Format: {Authors} {Abstract title} [abstract] In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1103 doi:1538-7445AM2012-1103

Naohiko Seki

Papers

867 restoration of mir-517a expression induces cell apoptosis in bladder cancer cell lines

Gene set for identifying lymph node metastasis of lung cancer

176 oncogenic lasp1 is directly regulated by the tumor suppressive micrornas (mir-1, mir-218, and mir-133a) in bladder cancer

Abstract 3102A: Tumor suppressive microRNA-218 inhibits cancer cell migration and invasion through targeting laminin-332 in head and neck squamous cell carcinoma.

Abstract 1103: Molecular targets regulated by tumor suppressivemicroRNA-1andmicroRNA-133ain bladder cancer