Article
Multidisciplinary Sciences
Yun-Tao Liu, David Strugatsky, Wei Liu, Z. Hong Zhou
Summary: Cryo-EM reconstructions of human cytomegalovirus (HCMV) virions reveal host tRNAs associated with the virion's capsid-bound tegument protein, pp150. tRNA recruitment is mediated by interactions specific to HCMV only, suggesting an explanation for the absence of such tRNA densities in related herpesviruses.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Lauren E. Beck, Jasmine Lee, Christopher Cote, Margaret C. Dunagin, Ilya Lukonin, Nikkita Salla, Marcello K. Chang, Alex J. Hughes, Joseph D. Mornin, Zev J. Gartner, Prisca Liberali, Arjun Raj
Summary: This study establishes a framework to quantitatively determine constraints on organoid morphologies and identifies a set of constraints in canine kidney cysts and intestinal organoids. These constraints can vary with cyst age and culture conditions, and may inform future organoid engineering efforts.
Article
Multidisciplinary Sciences
Alexey Stukalov, Virginie Girault, Vincent Grass, Ozge Karayel, Valter Bergant, Christian Urban, Darya A. Haas, Yiqi Huang, Lila Oubraham, Anqi Wang, M. Sabri Hamad, Antonio Piras, Fynn M. Hansen, Maria C. Tanzer, Igor Paron, Luca Zinzula, Thomas Engleitner, Maria Reinecke, Teresa M. Lavacca, Rosina Ehmann, Roman Woelfel, Joerg Jores, Bernhard Kuster, Ulrike Protzer, Roland Rad, John Ziebuhr, Volker Thiel, Pietro Scaturro, Matthias Mann, Andreas Pichlmair
Summary: The study reports a concurrent multi-omics analysis of SARS-CoV-2 and SARS-CoV, revealing both distinct and common molecular mechanisms between these closely related coronaviruses, as well as their impact on the host cell proteome. The results of this study may provide insights into the design of virus- and host-directed therapies for these coronaviruses.
Article
Immunology
Yunhe Liu, Lin Zhang, Xinyi Ju, Sheng Wang, Jingbo Qie
Summary: As one of the most malignant cancers, hepatocellular carcinoma (HCC) exhibits high heterogeneity in its complex ecosystem. Cell communication, especially with macrophages, plays a critical role in HCC development, with a unique interaction identified between macrophages and HCC malignant cells. The study provides insights into immune infiltration and cell communication patterns in the HCC ecosystem through single-cell transcriptome analysis.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Immunology
Lin Lv, Tianyun Zhang, Hanying Jia, Yanyan Zhang, Asif Ahsan, Xiaoyang Zhao, Teng Chen, Zhiqiang Shen, Ning Shen
Summary: This study investigated the temporal viral and host transcriptomes in porcine alveolar macrophages infected with virulent and attenuated African swine fever virus (ASFV) strains. The findings demonstrated that the attenuated ASFV strain HuB20 can quickly activate the host's antiviral immune response, as well as activating genes associated with RNA virus response in addition to the DNA sensing mechanism.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Siwy Ling Yang, Louis DeFalco, Danielle E. Anderson, Yu Zhang, Jong Ghut Ashley Aw, Su Ying Lim, Xin Ni Lim, Kiat Yee Tan, Tong Zhang, Tanu Chawla, Yan Su, Alexander Lezhava, Andres Merits, Lin-Fa Wang, Roland G. Huber, Yue Wan
Summary: The study identified functional structural elements within the SARS-CoV-2 genome, showed differences in RNA folding between wildtype and mutant viruses, and found hundreds of RNA-RNA interactions within the virus genome and between virus and host RNAs. The virus genome strongly binds to mitochondrial and small nucleolar RNAs and undergoes extensive 2'-O-methylation.
NATURE COMMUNICATIONS
(2021)
Article
Oncology
Joann Jung, Sowon Park, Yeonwoo Jang, Sung-Hwan Lee, Yun Seong Jeong, Sun Young Yim, Ju-Seog Lee
Summary: Hepatocellular carcinoma (HCC) is a common cancer that causes a large number of deaths worldwide. Metabolic reprogramming is a key feature of HCC, allowing cancer cells to meet the high energy demands for fast growth. By comparing genomic data from mice and humans, we identified three distinct metabolic subtypes of HCC and found clinical and molecular characteristics associated with each subtype. Notably, we discovered that the high metabolic subtype is resistant to immunotherapy and uncovered a potential mechanism for this resistance.
Article
Multidisciplinary Sciences
Ori Heyman, Dror Yehezkel, Camilla Ciolli Mattioli, Neta Blumberger, Gili Rosenberg, Aryeh Solomon, Dotan Hoffman, Noa Bossel Ben-Moshe, Roi Avraham
Summary: Encounters between host cells and intracellular bacterial pathogens lead to complex phenotypes that determine the outcome of infection. Single-cell RNA sequencing (scRNA-seq) has limited capacity to analyze the role of bacterial factors. The scPAIR-seq method developed in this study enables functional analysis of mutant-dependent changes in host transcriptomes, providing insights into bacterial virulence strategies and their interplay with host defense strategies.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Oncology
Sheng-Han Wang, Shiou-Hwei Yeh, Pei-Jer Chen
Summary: HBV infection is a major risk factor for HCC globally, with chronic hepatitis B generating an inflammatory microenvironment that leads to genetic mutations in hepatocytes predisposing them to cancer. Male dominance in HBV-related HCC highlights the interplay between sex hormones and viral factors influencing carcinogenesis.
Article
Biochemistry & Molecular Biology
Jordi Gomez Borrego, Marc Torrent Burgas
Summary: Adhesion and colonization of host cells by pathogenic bacteria rely on protein-protein interactions (PPIs). This study developed a filtering process to obtain a reliable list of domains and motifs participating in PPIs between bacteria and human cells. Structural analysis revealed that human proteins involved in these interactions are rich in alpha helix and disordered regions. The most significant domain-domain interactions were validated, but verifying domain-motif interactions was more challenging. Post-translational modifications, especially phosphorylation, also play a role in these interactions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Hong-Xia Hou, Dan Zhao, Jin-Hua Xiao, Da-Wei Huang
Summary: This study investigated the gene expression patterns between Wolbachia-infected and noninfected fig wasp species and found divergent interactions between males and females, with males having more differently expressed genes. The upregulated genes in males were mainly related to biosynthesis, signaling pathways, and pathogenesis, while downregulated genes were involved in transport, oxidation-reduction, and cellular responses to stress. Additionally, more genes were up-regulated in males for Wolbachia's gene expression.
Article
Plant Sciences
Miguel Correa Marrero, Sylvain Capdevielle, Weijie Huang, Ali M. Al-Subhi, Marco Busscher, Jacqueline Busscher-Lange, Froukje van Der Wal, Dick de Ridder, Aalt D. J. van Dijk, Saskia A. Hogenhout, Richard G. H. Immink
Summary: This study generated a protein-protein interaction network between phytoplasma effectors and Arabidopsis thaliana transcription factors. The results showed widespread interactions between phytoplasma effectors and host transcription factors, especially those involved in host developmental processes. Comparison with other host-pathogen protein interaction networks revealed that phytoplasma effectors have unusual targets, indicating a unique and unusual infection strategy employed by phytoplasmas.
Article
Microbiology
Rachel P. J. Lai, Teresa Cortes, Suzaan Marais, Neesha Rockwood, Melissa L. Burke, Acely Garza-Garcia, Stuart Horswell, Abdul K. Sesay, Anne O'Garra, Douglas B. Young, Robert J. Wilkinson
Summary: This study used RNA sequencing to analyze the transcriptome of sputum from tuberculosis patients, revealing upregulated inflammatory responses and metabolic shifts in the host, as well as alterations in commensal bacterial populations and functional gene expression. The study also found that M. tuberculosis in sputum showed similarities to aerobic replication, cholesterol metabolism, and propionate detoxification pathways, indicating potential extracellular location and zinc deprivation.
Article
Multidisciplinary Sciences
Di Chen, Arghyashree Roychowdhury-Sinha, Pragya Prakash, Xiao Lan, Wenmin Fan, Akira Goto, Jules A. Hoffmann
Summary: The injection of oncogenic RasV12 cells into adult male flies led to massive proliferation, causing the flies to die after 2 to 3 weeks. The early injection induced a transcriptomic response involving over 100 genes encoding chemoreceptors. Furthermore, the flies exhibited intense catabolic activities, active tracheogenesis, cuticulogenesis, as well as stress and inflammation-type responses.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Virology
Arpita Kar, Abhisekh Samanta, Soumyadeep Mukherjee, Subhasis Barik, Avik Biswas
Summary: Hepatitis B virus (HBV) is a major cause of hepatocellular carcinoma (HCC), the most common primary liver malignancy. The study of HBV-host interactions has identified various mechanisms involved in the development and progression of HBV-associated HCC. This review provides a comprehensive summary of the existing knowledge on HBV-host interplay and highlights new therapeutic strategies for HBV-induced HCC.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Surgery
Daisuke Asano, Atsushi Kudo, Keiichi Akahoshi, Aya Maekawa, Yoshiki Murase, Kosuke Ogawa, Hiroaki Ono, Daisuke Ban, Shinji Tanaka, Minoru Tanabe
Summary: The study aims to elucidate the role of surgery in patients with high-grade neuroendocrine neoplasms (hg-NENs) and Ki-67 more than 20%. Through a retrospective analysis, the study found that surgery was beneficial for patients with low Ki-67 value, regardless of tumor differentiation.
Review
Gastroenterology & Hepatology
Daisuke Ban, Giovanni Maria Garbarino, Yoshiya Ishikawa, Goro Honda, Jin-Young Jang, Chang Moo Kang, Aya Maekawa, Yoshiki Murase, Yuichi Nagakawa, Hitoe Nishino, Takao Ohtsuka, Anusak Yiengpruksawan, Itaru Endo, Akihiko Tsuchida, Masafumi Nakamura
Summary: Minimally invasive distal pancreatectomy (MIDP) is now being used for a wider range of conditions, including pancreatic malignancies. While a standardized stepwise procedure has been shown to improve surgical outcomes, studies have yet to compare different approaches to splenic vessels in MIDP. An understanding of anatomy is crucial for ensuring the safety and success of MIDP procedures.
JOURNAL OF HEPATO-BILIARY-PANCREATIC SCIENCES
(2022)
Review
Gastroenterology & Hepatology
Hitoe Nishino, Giuseppe Zimmitti, Takao Ohtsuka, Mohammed Abu Hilal, Brian K. P. Goh, David A. Kooby, Yoshiharu Nakamura, Shailesh V. Shrikhande, Yoo-Seok Yoon, Daisuke Ban, Yuichi Nagakawa, Kohei Nakata, Itaru Endo, Akihiko Tsuchida, Masafumi Nakamura
Summary: This review evaluated the literature regarding peripancreatic vascular anatomy, emphasizing its importance in safe MIDP. While few articles specifically studied the relationship between anatomical variations and surgical outcomes of MIDP, further detailed anatomical analyses and descriptions are needed to benefit surgeons and patients.
JOURNAL OF HEPATO-BILIARY-PANCREATIC SCIENCES
(2022)
Article
Oncology
Aya Maekawa, Atsushi Kudo, Mitsuhiro Kishino, Yoshiki Murase, Shuichi Watanabe, Yoshiya Ishikawa, Hiroki Ueda, Keiichi Akahoshi, Kosuke Ogawa, Hiroaki Ono, Shinji Tanaka, Yuko Kinowaki, Minoru Tanabe
Summary: Hormonal tumor mapping showed variation in hormone production between primary and metastatic tumors of GEP-NENs. Minimally invasive treatment guided by hormonal mapping could be a promising alternative to traditional cytoreduction.
JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY
(2022)
Article
Oncology
Toshihiko Masui, Tetsuhide Ito, Izumi Komoto, Shinsuke Kojima, Yosuke Kasai, Minoru Tanabe, Kazuo Hara, Satoshi Hirano, Takuji Okusaka, Yasushi Ichikawa, Yusuke Kinugasa, Norihiro Kokudo, Atsushi Kudo, Akihiro Sakurai, Kenichi Sugihara, Hiroshi Date, Ken Haruma, Susumu Hijioka, Koichi Hirata, Hiroo Yamano, Motohiro Sakamine, Takashi Kikuchi, Masanori Fukushima, Masayuki Imamura, Shinji Uemoto
Summary: This study analyzed a registry cohort of neuroendocrine neoplasms (NEN) in Japan, providing crucial clinical data for understanding the characteristics of this disease and facilitating further research.
INTERNATIONAL JOURNAL OF CLINICAL ONCOLOGY
(2022)
Article
Gastroenterology & Hepatology
Daisuke Ban, Hitoe Nishino, Takao Ohtsuka, Yuichi Nagakawa, Mohammed Abu Hilal, Horacio J. Asbun, Ugo Boggi, Brian K. P. Goh, Jin He, Goro Honda, Jin-Young Jang, Chang Moo Kang, Michael L. Kendrick, David A. Kooby, Rong Liu, Yoshiharu Nakamura, Kohei Nakata, Chinnusamy Palanivelu, Shailesh Shrikhande, Kyoichi Takaori, Chung-Ngai Tang, Shin-E Wang, Christopher L. Wolfgang, Anusak Yiengpruksawan, Yoo-Seok Yoon, Ruben Ciria, Giammauro Berardi, Giovanni Maria Garbarino, Ryota Higuchi, Naoki Ikenaga, Yoshiya Ishikawa, Shingo Kozono, Aya Maekawa, Yoshiki Murase, Yusuke Watanabe, Giuseppe Zimmitti, Filipe Kunzler, Zi-Zheng Wang, Leon Sakuma, Hiroaki Osakabe, Chie Takishita, Itaru Endo, Masao Tanaka, Hiroki Yamaue, Minoru Tanabe, Go Wakabayashi, Akihiko Tsuchida, Masafumi Nakamura
Summary: This study validated the usefulness of anatomy-based approaches for minimally invasive distal pancreatectomy through expert consensus. Four clinical questions were addressed, resulting in 10 recommendations that all reached at least a 75% consensus among experts.
JOURNAL OF HEPATO-BILIARY-PANCREATIC SCIENCES
(2022)
Article
Gastroenterology & Hepatology
Yuichi Nagakawa, Kohei Nakata, Hitoe Nishino, Takao Ohtsuka, Daisuke Ban, Horacio J. Asbun, Ugo Boggi, Jin He, Michael L. Kendrick, Chinnusamy Palanivelu, Rong Liu, Shin-E Wang, Chung-Ngai Tang, Kyoichi Takaori, Mohammed Abu Hilal, Brian K. P. Goh, Goro Honda, Jin-Young Jang, Chang Moo Kang, David A. Kooby, Yoshiharu Nakamura, Shailesh V. Shrikhande, Christopher L. Wolfgang, Anusak Yiengpruksawan, Yoo-Seok Yoon, Yusuke Watanabe, Shingo Kozono, Ruben Ciria, Giammauro Berardi, Giovanni Maria Garbarino, Ryota Higuchi, Naoki Ikenaga, Yoshiya Ishikawa, Aya Maekawa, Yoshiki Murase, Giuseppe Zimmitti, Filipe Kunzler, Zi-Zheng Wang, Leon Sakuma, Chie Takishita, Hiroaki Osakabe, Itaru Endo, Masao Tanaka, Hiroki Yamaue, Minoru Tanabe, Go Wakabayashi, Akihiko Tsuchida, Masafumi Nakamura
Summary: This study aims to provide recommendations for elucidating the anatomy and surgical approaches to minimally invasive pancreatoduodenectomy (MIPD). Through a comprehensive literature search and Delphi voting process, experts developed six recommendations with at least 75% consensus. Preoperative evaluation of anatomical variations and vascular branching patterns, as well as intraoperative confirmation of vascular course based on anatomical landmarks, were highlighted as crucial steps for safe and reliable MIPD.
JOURNAL OF HEPATO-BILIARY-PANCREATIC SCIENCES
(2022)
Article
Gastroenterology & Hepatology
Atsushi Kudo, Ukihide Tateishi, Ryoichi Yoshimura, Junichi Tsuchiya, Kota Yokoyama, Shoko Takano, Noritoshi Kobayashi, Daisuke Utsunomiya, Masaharu Hata, Yasushi Ichikawa, Minoru Tanabe, Makoto Hosono, Seigo Kinuya
Summary: Lu-177-DOTATATE demonstrated remarkable tumor shrinkage and tolerability in Japanese patients with advanced NETs.
JOURNAL OF HEPATO-BILIARY-PANCREATIC SCIENCES
(2022)
Article
Oncology
Hirofumiip Watanabe, Fumiyoshi Fujishima, Izumi Komoto, Masayuki Imamura, Susumu Hijioka, Kazuo Hara, Yasushi Yatabe, Atsushi Kudo, Toshihiko Masui, Takahiro Tsuchikawa, Kazuhiro Sakamoto, Hisashi Shiga, Tomohiro Nakamura, Naoki Nakaya, Fuyuhiko Motoi, Michiaki Unno, Hironobu Sasano
Summary: This study evaluated the significance of SSTR2 immunoreactivity in gastrointestinal neuroendocrine tumors (GI-NETs) using digital image analysis (DIA) and other methods. The results showed that SSTR2 immunoreactivity varied according to the primary sites and was correlated with proliferative activity. Additionally, DIA was found to be a good alternative for predicting response to somatostatin analogues (SSAs) in evaluating SSTR2 immunoreactivity of GI-NETs.
Article
Endocrinology & Metabolism
Minami Miyauchi, Takumi Akashi, Asuka Furukawa, Keisuke Uchida, Tomoki Tamura, Noboru Ando, Susumu Kirimura, Hiroshi Shintaku, Kurara Yamamoto, Takashi Ito, Keiko Miura, Kou Kayamori, Yosuke Ariizumi, Takahiro Asakage, Atsushi Kudo, Minoru Tanabe, Yasuhisa Fujii, Hironori Ishibashi, Kenichi Okubo, Masanori Murakami, Tetsuya Yamada, Akira Takemoto, Yuan Bae, Yoshinobu Eishi, Kenichi Ohashi
Summary: Pheochromocytomas and paragangliomas are tumors originating from the neuroendocrine system. PHOX2B is the most sensitive and specific diagnostic marker for these tumors, especially in the case of parasympathetic/head and neck paragangliomas.
ENDOCRINE PATHOLOGY
(2022)
Article
Oncology
Takeshi Ishii, Yoshimitsu Akiyama, Shu Shimada, Ayano Kabashima, Daisuke Asano, Shuichi Watanabe, Yoshiya Ishikawa, Hiroki Ueda, Keiichi Akahoshi, Kosuke Ogawa, Hiroaki Ono, Atsushi Kudo, Minoru Tanabe, Shinji Tanaka
Summary: This study found that overexpression of histone H3K4 methyltransferase SETD1A is associated with shorter disease-free survival in pancreatic ductal adenocarcinoma (PDAC) patients. SETD1A plays a crucial role in increasing the proliferation and motility of PDAC cells. RUVBL1 was identified as a new downstream target gene of the SETD1A-H3K4me3 pathway and co-expression of SETD1A and RUVBL1 is an important factor for predicting the prognosis of PDAC patients.
Article
Oncology
Hiroaki Ono, Yoshiki Murase, Hironari Yamashita, Tomotaka Kato, Daisuke Asano, Yoshiya Ishikawa, Shuichi Watanabe, Hiroki Ueda, Keiichi Akahoshi, Kosuke Ogawa, Atsushi Kudo, Yoshimitsu Akiyama, Shinji Tanaka, Minoru Tanabe
Summary: The invasiveness and drug resistance of pancreatic cancer are crucial in defining its malignant potential and impacting the microenvironment around the tumor. The upregulation of Ribonucleotide reductase large subunit M1 (RRM1) in gemcitabine-resistant cancer cells is associated with a worse prognosis for pancreatic cancer. This study demonstrates that histone acetylation plays a role in the regulatory mechanism leading to gemcitabine resistance and subsequent RRM1 upregulation. Furthermore, RRM1 activation promotes extracellular matrix remodeling and enhances the migratory and invasive potential of pancreatic cancer cells.
INTERNATIONAL JOURNAL OF ONCOLOGY
(2023)
Article
Gastroenterology & Hepatology
Ryo Saito, Daisuke Ban, Takahiro Mizui, Takeshi Takamoto, Satoshi Nara, Minoru Esaki, Kazuaki Shimada
Summary: This study introduces the concept of oligo-like liver metastasis (OLLM) in post-surgical pancreatic ductal adenocarcinoma (PDAC) patients and suggests that OLLM patients have a better prognosis after recurrence, indicating that surgical intervention may be beneficial.
ANNALS OF GASTROENTEROLOGICAL SURGERY
(2023)
Letter
Health Care Sciences & Services
Koji Morishita, Atsushi Kudo, Tokujiro Uchida, Naoki Kurashima, Mikayo Toba, Kei Ito, Yasuhiro Otomo
JOURNAL OF PATIENT SAFETY
(2022)