16 Works

Comparative genomic and transcriptomic analyses of trans-kingdom pathogen Fusarium solani species complex reveal degrees of compartmentalization

Daphne Z. Hoh, Hsin-Han Lee, Naohisa Wada, Wei-An Liu, Min R. Lu, Cheng-Kuo Lai, Huei-Mien Ke, Pei-Feng Sun, Sen-Lin Tang, Wen-Hsin Chung, Ying-Lien Chen, Chia-Lin Chung & Isheng Jason Tsai
Abstract Background The Fusarium solani species complex (FSSC) comprises fungal pathogens responsible for mortality in a diverse range of animals and plants, but their genome diversity and transcriptome responses in animal pathogenicity remain to be elucidated. We sequenced, assembled and annotated six chromosome-level FSSC clade 3 genomes of aquatic animal and plant host origins. We established a pathosystem and investigated the expression data of F. falciforme and F. keratoplasticum in Chinese softshell turtle (Pelodiscus sinensis)...

Additional file 2 of Circulating CD8+CD122+ T cells as a prognostic indicator of pancreatic cancer

Katsuhito Teramatsu, Takamasa Oono, Koki Oyama, Nao Fujimori, Masatoshi Murakami, Sho Yasumori, Akihisa Ohno, Kazuhide Matsumoto, Ayumu Takeno, Kohei Nakata, Masafumi Nakamura & Yoshihiro Ogawa
Additional file 2.

Circulating CD8+CD122+ T cells as a prognostic indicator of pancreatic cancer

Katsuhito Teramatsu, Takamasa Oono, Koki Oyama, Nao Fujimori, Masatoshi Murakami, Sho Yasumori, Akihisa Ohno, Kazuhide Matsumoto, Ayumu Takeno, Kohei Nakata, Masafumi Nakamura & Yoshihiro Ogawa
Abstract Purpose The distribution of tissue infiltrating lymphocytes has been shown to affect the prognosis of patients with pancreatic cancer in some previous studies. However, the role of peripheral lymphocytes in pancreatic cancer remains debated. The purpose of this study was to analyze the peripheral subtypes of T lymphocytes, and establish their association with the prognosis of patients with pancreatic cancer. Methods Blood and tissue samples were collected from patients with metastatic pancreatic cancer (n...

Additional file 3 of Comparative genomic and transcriptomic analyses of trans-kingdom pathogen Fusarium solani species complex reveal degrees of compartmentalization

Daphne Z. Hoh, Hsin-Han Lee, Naohisa Wada, Wei-An Liu, Min R. Lu, Cheng-Kuo Lai, Huei-Mien Ke, Pei-Feng Sun, Sen-Lin Tang, Wen-Hsin Chung, Ying-Lien Chen, Chia-Lin Chung & Isheng Jason Tsai
Additional file 3. Extended Results and Methods.

Additional file 3 of Comparative genomic and transcriptomic analyses of trans-kingdom pathogen Fusarium solani species complex reveal degrees of compartmentalization

Daphne Z. Hoh, Hsin-Han Lee, Naohisa Wada, Wei-An Liu, Min R. Lu, Cheng-Kuo Lai, Huei-Mien Ke, Pei-Feng Sun, Sen-Lin Tang, Wen-Hsin Chung, Ying-Lien Chen, Chia-Lin Chung & Isheng Jason Tsai
Additional file 3. Extended Results and Methods.

Additional file 1 of Circulating CD8+CD122+ T cells as a prognostic indicator of pancreatic cancer

Katsuhito Teramatsu, Takamasa Oono, Koki Oyama, Nao Fujimori, Masatoshi Murakami, Sho Yasumori, Akihisa Ohno, Kazuhide Matsumoto, Ayumu Takeno, Kohei Nakata, Masafumi Nakamura & Yoshihiro Ogawa
Additional file 1.

Additional file 1 of Circulating CD8+CD122+ T cells as a prognostic indicator of pancreatic cancer

Katsuhito Teramatsu, Takamasa Oono, Koki Oyama, Nao Fujimori, Masatoshi Murakami, Sho Yasumori, Akihisa Ohno, Kazuhide Matsumoto, Ayumu Takeno, Kohei Nakata, Masafumi Nakamura & Yoshihiro Ogawa
Additional file 1.

Circulating CD8+CD122+ T cells as a prognostic indicator of pancreatic cancer

Katsuhito Teramatsu, Takamasa Oono, Koki Oyama, Nao Fujimori, Masatoshi Murakami, Sho Yasumori, Akihisa Ohno, Kazuhide Matsumoto, Ayumu Takeno, Kohei Nakata, Masafumi Nakamura & Yoshihiro Ogawa
Abstract Purpose The distribution of tissue infiltrating lymphocytes has been shown to affect the prognosis of patients with pancreatic cancer in some previous studies. However, the role of peripheral lymphocytes in pancreatic cancer remains debated. The purpose of this study was to analyze the peripheral subtypes of T lymphocytes, and establish their association with the prognosis of patients with pancreatic cancer. Methods Blood and tissue samples were collected from patients with metastatic pancreatic cancer (n...

Serum immunoglobulin G as a discriminator of infection in follicular lymphoma patients undergoing chemotherapy with bendamustine in combination with rituximab

Akie Hirata, Kaname Miyashita, Takafumi Tanaka, Kiyoko Hirata, Taisuke Narazaki, Hayato Utsunomiya, Hirofumi Ohno, Eriko Nakashima, Yoshimichi Tachikawa, Ilseung Choi, Kenichi Taguchi & Youko Suehiro
Chemotherapy, including bendamustine, usually causes lymphocytopaenia and hypogammaglobulinaemia as side effects in patients with haematological malignancies. Therefore, the possibility has been considered that these immunological adverse events induced by bendamustine may lead to infectious diseases. However, lymphocytopaenia and/or hypogammaglobulinaemia have not yet been shown to have a statistically significant association with infection in cancer patients who receive bendamustine. We retrospectively studied 27 patients with relapsed or refractory indolent follicular lymphoma who were treated with bendamustine...

Additional file 1 of Comparative genomic and transcriptomic analyses of trans-kingdom pathogen Fusarium solani species complex reveal degrees of compartmentalization

Daphne Z. Hoh, Hsin-Han Lee, Naohisa Wada, Wei-An Liu, Min R. Lu, Cheng-Kuo Lai, Huei-Mien Ke, Pei-Feng Sun, Sen-Lin Tang, Wen-Hsin Chung, Ying-Lien Chen, Chia-Lin Chung & Isheng Jason Tsai
Additional file 1: Table S1. Read summary of genome assemblies from each sequencing platform. Table S2. Fusarium genomes and an outrgroup genome used in the phylogenomic analysis and comparative studies. Table S3. Scaffold assembly completeness. Table S4. FSSC genome assemblies used to compare N90. Table S5. Number of genes with predicted signal peptide and effector using SignalP and EffectorP, respectively. Table S6. Number of genes with predicted carbohydrate-active enzymes (CAZymes) and its categories using dbCAN2....

Additional file 1 of Comparative genomic and transcriptomic analyses of trans-kingdom pathogen Fusarium solani species complex reveal degrees of compartmentalization

Daphne Z. Hoh, Hsin-Han Lee, Naohisa Wada, Wei-An Liu, Min R. Lu, Cheng-Kuo Lai, Huei-Mien Ke, Pei-Feng Sun, Sen-Lin Tang, Wen-Hsin Chung, Ying-Lien Chen, Chia-Lin Chung & Isheng Jason Tsai
Additional file 1: Table S1. Read summary of genome assemblies from each sequencing platform. Table S2. Fusarium genomes and an outrgroup genome used in the phylogenomic analysis and comparative studies. Table S3. Scaffold assembly completeness. Table S4. FSSC genome assemblies used to compare N90. Table S5. Number of genes with predicted signal peptide and effector using SignalP and EffectorP, respectively. Table S6. Number of genes with predicted carbohydrate-active enzymes (CAZymes) and its categories using dbCAN2....

Comparative genomic and transcriptomic analyses of trans-kingdom pathogen Fusarium solani species complex reveal degrees of compartmentalization

Daphne Z. Hoh, Hsin-Han Lee, Naohisa Wada, Wei-An Liu, Min R. Lu, Cheng-Kuo Lai, Huei-Mien Ke, Pei-Feng Sun, Sen-Lin Tang, Wen-Hsin Chung, Ying-Lien Chen, Chia-Lin Chung & Isheng Jason Tsai
Abstract Background The Fusarium solani species complex (FSSC) comprises fungal pathogens responsible for mortality in a diverse range of animals and plants, but their genome diversity and transcriptome responses in animal pathogenicity remain to be elucidated. We sequenced, assembled and annotated six chromosome-level FSSC clade 3 genomes of aquatic animal and plant host origins. We established a pathosystem and investigated the expression data of F. falciforme and F. keratoplasticum in Chinese softshell turtle (Pelodiscus sinensis)...

Serum immunoglobulin G as a discriminator of infection in follicular lymphoma patients undergoing chemotherapy with bendamustine in combination with rituximab

Akie Hirata, Kaname Miyashita, Takafumi Tanaka, Kiyoko Hirata, Taisuke Narazaki, Hayato Utsunomiya, Hirofumi Ohno, Eriko Nakashima, Yoshimichi Tachikawa, Ilseung Choi, Kenichi Taguchi & Youko Suehiro
Chemotherapy, including bendamustine, usually causes lymphocytopaenia and hypogammaglobulinaemia as side effects in patients with haematological malignancies. Therefore, the possibility has been considered that these immunological adverse events induced by bendamustine may lead to infectious diseases. However, lymphocytopaenia and/or hypogammaglobulinaemia have not yet been shown to have a statistically significant association with infection in cancer patients who receive bendamustine. We retrospectively studied 27 patients with relapsed or refractory indolent follicular lymphoma who were treated with bendamustine...

Additional file 2 of Comparative genomic and transcriptomic analyses of trans-kingdom pathogen Fusarium solani species complex reveal degrees of compartmentalization

Daphne Z. Hoh, Hsin-Han Lee, Naohisa Wada, Wei-An Liu, Min R. Lu, Cheng-Kuo Lai, Huei-Mien Ke, Pei-Feng Sun, Sen-Lin Tang, Wen-Hsin Chung, Ying-Lien Chen, Chia-Lin Chung & Isheng Jason Tsai
Additional file 2: Fig. S1. Genome features in FSSC assemblies. Fig. S2. Multi-locus sequence typing (MLST) phylogeny tree of FSSC. Fig. S3. Genome phylogeny of Fusarium species. Fig. S4. Orthologue sharing amongst Fusarium chromosome. Fig. S5. FSSC genome synteny. Fig. S6. Synteny between F. vanettenii Fs6 and FVANE. Fig. S7. Location of FSSC-specific genes across genomes. Fig. S8. Selection level in FSSC chromosomes. Fig. S9. Orthogroup number comparison between F. falciforme Fu3 and F. oxysporum...

Additional file 2 of Comparative genomic and transcriptomic analyses of trans-kingdom pathogen Fusarium solani species complex reveal degrees of compartmentalization

Daphne Z. Hoh, Hsin-Han Lee, Naohisa Wada, Wei-An Liu, Min R. Lu, Cheng-Kuo Lai, Huei-Mien Ke, Pei-Feng Sun, Sen-Lin Tang, Wen-Hsin Chung, Ying-Lien Chen, Chia-Lin Chung & Isheng Jason Tsai
Additional file 2: Fig. S1. Genome features in FSSC assemblies. Fig. S2. Multi-locus sequence typing (MLST) phylogeny tree of FSSC. Fig. S3. Genome phylogeny of Fusarium species. Fig. S4. Orthologue sharing amongst Fusarium chromosome. Fig. S5. FSSC genome synteny. Fig. S6. Synteny between F. vanettenii Fs6 and FVANE. Fig. S7. Location of FSSC-specific genes across genomes. Fig. S8. Selection level in FSSC chromosomes. Fig. S9. Orthogroup number comparison between F. falciforme Fu3 and F. oxysporum...

Additional file 2 of Circulating CD8+CD122+ T cells as a prognostic indicator of pancreatic cancer

Katsuhito Teramatsu, Takamasa Oono, Koki Oyama, Nao Fujimori, Masatoshi Murakami, Sho Yasumori, Akihisa Ohno, Kazuhide Matsumoto, Ayumu Takeno, Kohei Nakata, Masafumi Nakamura & Yoshihiro Ogawa
Additional file 2.

Registration Year

  • 2022
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Affiliations

  • Kyushu University Hospital
    16
  • Kyushu University
    14
  • National Taiwan Normal University
    8
  • National Taiwan University
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  • Academia Sinica
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  • National Chung Hsing University
    8