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About the Cover

May 2023 | Volume 6, No. 5

Research Articles

  • Tannins amount determines whether tannase-containing bacteria are probiotic or pathogenic in IBD
    Open Access
    Tannins amount determines whether tannase-containing bacteria are probiotic or pathogenic in IBD

    Qiuyue He, Kenan Guo, Lulu Wang, Fei Xie, Qingyuan Zhao, Xianhong Jiang, Zhongming He, Peng Wang, Shiqiang Li, Yan Huang, Cong Zhang, Rongjuan Huang, Yang Liu, Fengchao Wang, Xiaoyang Zhou, Rong Niu, Tao Zuo, Yong Wang, Chuangen Li

    Qiuyue He ... Chuangen Li

    Published 9 February 2023

    TA-induced microbial metabolite GA displays dual effects on IBD. GA exerts its function through two ways: influence bacteria penetration and directly affect epithelial cells. Interaction between diet and microbial enzyme is pivotal in affecting IBD.

  • Dual function of Rab1A in secretion and autophagy: hypervariable domain dependence
    Open Access
    Dual function of Rab1A in secretion and autophagy: hypervariable domain dependence

    Valeriya Gyurkovska, Rakhilya Murtazina, Sarah F Zhao, Sojin Shikano, Yukari Okamoto, Nava Segev

    Valeriya Gyurkovska ... Nava Segev

    Published 13 February 2023

    Gyurkovska et al show that whereas both Rab1A and Rab1B regulate secretion, Rab1A-HVD enables it to localize to autophagosomes and regulate autophagy. This provides a mechanism for a dual functionality of a single Rab in two different cellular pathways.

  • AurkA nuclear localization is promoted by TPX2 and counteracted by protein degradation
    Open Access
    AurkA nuclear localization is promoted by TPX2 and counteracted by protein degradation

    Italia Anna Asteriti, Federica Polverino, Venturina Stagni, Valentina Sterbini, Camilla Ascanelli, Francesco Davide Naso, Anna Mastrangelo, Alessandro Rosa, Alessandro Paiardini, Catherine Lindon, Giulia Guarguaglini

    Italia Anna Asteriti ... Giulia Guarguaglini

    Published 16 February 2023

    This study shows that TPX2 co-overexpression in non-transformed human cells induces AurkA nuclear accumulation and promotes its non-mitotic oncogenic functions.

  • BRG1 HSA domain interactions with BCL7 proteins are critical for remodeling and gene expression
    Open Access
    BRG1 HSA domain interactions with BCL7 proteins are critical for remodeling and gene expression

    Nicholas Dietrich, Kevin Trotter, James M Ward, Trevor K Archer

    Nicholas Dietrich ... Trevor K Archer

    Published 17 February 2023

    Interactions between the BRG1 HSA domain and the B-cell CLL/lymphoma 7 proteins facilitate BRG1-mediated chromatin remodeling and induce changes in the gene expression of essential biological pathways.

  • Activation and inhibition of the C-terminal kinase domain of p90 ribosomal S6 kinases
    Open Access
    Activation and inhibition of the C-terminal kinase domain of p90 ribosomal S6 kinases

    Marlene Uglebjerg Fruergaard, Christine Juul Fælled Nielsen, Cecilia Rosada Kjeldsen, Lars Iversen, Jacob Lauwring Andersen, Poul Nissen

    Marlene Uglebjerg Fruergaard ... Poul Nissen

    Published 20 February 2023

    The design of a constitutively active form of the C-terminal kinase domain of the p90 ribosomal S6 kinase 2 (RSK2) is described, and this is based on a phosphomimetic mutation and a C-terminal truncation, yielding a high kinase activity.

  • Single-cell whole-genome sequencing, haplotype analysis in prenatal diagnosis of monogenic diseases
    Open Access
    Single-cell whole-genome sequencing, haplotype analysis in prenatal diagnosis of monogenic diseases

    Liang Chang, Haining Jiao, Jiucheng Chen, Guanlin Wu, Ping Liu, Rong Li, Jianying Guo, Wenqing Long, Xiaojian Tang, Bingjie Lu, Haibin Xu, Han Wu

    Liang Chang ... Han Wu

    Published 21 February 2023

    cbNIPT by WGS and haplotype analysis predict the inherited genotypes for families with monogenic diseases and provide a potentially better solution for prenatal diagnosis of monogenic diseases.

  • Segregation of pathways leading to pexophagy
    Open Access
    Segregation of pathways leading to pexophagy

    Francesco G Barone, Sylvie Urbé, Michael J Clague

    Francesco G Barone ... Michael J Clague

    Published 21 February 2023

    Pexophagy occurs via distinct NIX- and USP30/NBR1-dependent pathways.

  • Three-dimensional growth reveals fine-tuning of 5-lipoxygenase by proliferative pathways in cancer
    Open Access
    Three-dimensional growth reveals fine-tuning of 5-lipoxygenase by proliferative pathways in cancer

    Tamara Göbel, Bjarne Goebel, Marius Hyprath, Ira Lamminger, Hannah Weisser, Carlo Angioni, Marius Mathes, Dominique Thomas, Astrid S Kahnt

    Tamara Göbel ... Astrid S Kahnt

    Published 27 February 2023

    The expression of 5-lipoxygenase, the key enzyme in leukotriene biosynthesis, is suppressed in proliferating cancer cells by a PI3K/mTORC-2– and MEK-1/ERK-dependent axis involving E2F1 and b-Myb.

  • Disruption of polyhomeotic polymerization decreases nucleosome occupancy and alters genome accessibility
    Open Access
    Disruption of polyhomeotic polymerization decreases nucleosome occupancy and alters genome accessibility

    Adfar Amin, Sangram Kadam, Jakub Mieczkowski, Ikhlak Ahmed, Younus A Bhat, Fouziya Shah, Michael Y Tolstorukov, Robert E Kingston, Ranjith Padinhateeri, Ajazul H Wani

    Adfar Amin ... Ajazul H Wani

    Published 27 February 2023

    Disruption of SAM domain–mediated polymerization of Polycomb Group protein polyhomeotic decreases nucleosome occupancy in Drosophila S2 cells.

  • Novel inhibitors of microtubule organization and phragmoplast formation in diverse plant species
    Open Access
    Novel inhibitors of microtubule organization and phragmoplast formation in diverse plant species

    Yusuke Kimata, Moé Yamada, Takashi Murata, Keiko Kuwata, Ayato Sato, Takamasa Suzuki, Daisuke Kurihara, Mitsuyasu Hasebe, Tetsuya Higashiyama, Minako Ueda

    Yusuke Kimata ... Minako Ueda

    Published 27 February 2023

    Cell division is a crucial step in the development of plants, and the present study reports two novel inhibitors of plant cell division, which affect microtubule organization and cytokinesis.

  • Assessing the impacts of various factors on circular RNA reliability
    Open Access
    Assessing the impacts of various factors on circular RNA reliability

    Trees-Juen Chuang, Tai-Wei Chiang, Chia-Ying Chen

    Trees-Juen Chuang ... Chia-Ying Chen

    Published 27 February 2023

    This study systematically assesses the impacts of numerous factors related to circRNA identification, conservation, biogenesis, and function on circRNA reliability, providing a useful guideline and an important resource for selecting high-confidence circRNAs for further investigations.

  • Regulatory de novo mutations underlying intellectual disability
    Open Access
    Regulatory de novo mutations underlying intellectual disability

    Matias G De Vas, Fanny Boulet, Shweta S Joshi, Myles G Garstang, Tahir N Khan, Goutham Atla, David Parry, David Moore, Inês Cebola, Shuchen Zhang, Wei Cui, Anne K Lampe, Wayne W Lam, Genomics England Research Consortium, Jorge Ferrer, Madapura M Pradeepa, Santosh S Atanur

    Matias G De Vas ... Santosh S Atanur

    Published 28 February 2023

    This study provides suggestive evidence that the de novo mutations in fetal brain-specific enhancers play role in the aetiology of intellectual disability.

  • RAS and PP2A activities converge on epigenetic gene regulation
    Open Access
    RAS and PP2A activities converge on epigenetic gene regulation

    Anna Aakula, Mukund Sharma, Francesco Tabaro, Reetta Nätkin, Jesse Kamila, Henrik Honkanen, Matthieu Schapira, Cheryl Arrowsmith, Matti Nykter, Jukka Westermarck

    Anna Aakula ... Jukka Westermarck

    Published 1 March 2023

    This study reveals a hidden regulatory layer in epigenetic gene expression in cancer by co-operative phosphoregulation by RAS and tumor suppressor phosphatase PP2A.

  • Defibrotide impact on the acute GVHD disease incidence in pediatric hematopoietic stem cell transplant recipients
    Open Access
    Defibrotide impact on the acute GVHD disease incidence in pediatric hematopoietic stem cell transplant recipients

    Domenica Squillaci, Annalisa Marcuzzi, Erika Rimondi, Guglielmo Riccio, Egidio Barbi, Davide Zanon, Natalia Maximova

    Domenica Squillaci ... Natalia Maximova

    Published 6 March 2023

    The prophylactic use of defibrotide in pediatric HSCT recipients significantly reduces the incidence and severity of acute GVHD, with a modification of cytokine pattern, both strongly coherent with the protective drug’s action.

  • Endemic Burkitt lymphoma avatar mouse models for exploring inter-patient tumor variation and testing targeted therapies
    Open Access
    Endemic Burkitt lymphoma avatar mouse models for exploring inter-patient tumor variation and testing targeted therapies

    Priya Saikumar Lakshmi, Cliff I Oduor, Catherine S Forconi, Viriato M’Bana, Courtney Bly, Rachel M Gerstein, Juliana A Otieno, John M Ong’echa, Christian Münz, Micah A Luftig, Michael A Brehm, Jeffrey A Bailey, Ann M Moormann

    Priya Saikumar Lakshmi ... Ann M Moormann

    Published 6 March 2023

    Patient-derived tumor models show promise for evaluating novel cancer treatments that could improve outcomes for African children diagnosed with EBV-associated endemic Burkitt lymphoma.

  • A multiplexed siRNA screen identifies key kinase signaling networks of brain glia
    Open Access
    A multiplexed siRNA screen identifies key kinase signaling networks of brain glia

    Jong-Heon Kim, Jin Han, Ruqayya Afridi, Jae-Hong Kim, Md Habibur Rahman, Dong Ho Park, Won Suk Lee, Gyun Jee Song, Kyoungho Suk

    Jong-Heon Kim ... Kyoungho Suk

    Published 6 March 2023

    This study reports a multiplexed brain glial kinase screen, providing insight into the largely unknown glial intracellular signaling networks controlling neuroinflammation and highlights the therapeutic potential of targeting glial kinases to modulate glial phenotypes and treat neuroinflammatory disorders.

  • Preference of CAMSAP3 for expanded microtubule lattice contributes to stabilization of the minus end
    Open Access
    Preference of CAMSAP3 for expanded microtubule lattice contributes to stabilization of the minus end

    Hanjin Liu, Tomohiro Shima

    Hanjin Liu ... Tomohiro Shima

    Published 9 March 2023

    D2 region in CAMSAP3 preferentially bound to expanded microtubule lattices and also induced lattice expansion, explaining the molecular functions of CAMSAP3.

  • Analysis of context-specific KRAS–effector (sub)complexes in Caco-2 cells
    Open Access
    Analysis of context-specific KRAS–effector (sub)complexes in Caco-2 cells

    Camille Ternet, Philipp Junk, Thomas Sevrin, Simona Catozzi, Erik Wåhlén, Johan Heldin, Giorgio Oliviero, Kieran Wynne, Christina Kiel

    Camille Ternet ... Christina Kiel

    Published 9 March 2023

    We used affinity purification of KRAS in different genetic and growth contexts to determine KRAS-mediated complexes, their rewiring in specific contexts, and their link to functional outcomes.

  • H4K20me1 plays a dual role in transcriptional regulation of regeneration and axis patterning in <em>Hydra</em>
    Open Access
    H4K20me1 plays a dual role in transcriptional regulation of regeneration and axis patterning in Hydra

    Akhila Gungi, Shagnik Saha, Mrinmoy Pal, Sanjeev Galande

    Akhila Gungi ... Sanjeev Galande

    Published 21 March 2023

    H4K20me1 modification by SETD8 methyltransferase is typically associated with repression. In Hydra, it is associated with activation machinery locally at Wnt-responsive promoters indicating its dual role in transcriptional regulation.

  • <em>MiR-532-3p</em> inhibited the methylation of <em>SOCS2</em> to suppress the progression of PC by targeting <em>DNMT3A</em>
    Open Access
    MiR-532-3p inhibited the methylation of SOCS2 to suppress the progression of PC by targeting DNMT3A

    Kaiqiong Wang, Dongwei Gong, Xin Qiao, Jinfang Zheng

    Kaiqiong Wang ... Jinfang Zheng

    Published 21 April 2023

    MiR-532-3p has a low expression in pancreatic cancer, but its overexpression can inhibit the tumor progression via DNMT3A-dependent inhibition of SOCS2 methylation.

Methods

  • Plasma proteome dynamics of COVID-19 severity learnt by a graph convolutional network of multi-scale topology
    Open Access
    Plasma proteome dynamics of COVID-19 severity learnt by a graph convolutional network of multi-scale topology

    Samy Gauthier, Alexy Tran-Dinh, Ian Morilla

    Samy Gauthier ... Ian Morilla

    Published 20 February 2023

    We used a graph convolutional network to model the plasma proteome of 384 COVID-19 patients. The model incorporates clinical data and is able to predict severity. We identified the proteins that shifted most in expression depending on severity.

  • New algorithms for accurate and efficient de novo genome assembly from long DNA sequencing reads
    Open Access
    New algorithms for accurate and efficient de novo genome assembly from long DNA sequencing reads

    Laura Gonzalez-Garcia, David Guevara-Barrientos, Daniela Lozano-Arce, Juanita Gil, Jorge Díaz-Riaño, Erick Duarte, Germán Andrade, Juan Camilo Bojacá, Maria Camila Hoyos-Sanchez, Christian Chavarro, Natalia Guayazan, Luis Alberto Chica, Maria Camila Buitrago Acosta, Edwin Bautista, Miller Trujillo, Jorge Duitama

    Laura Gonzalez-Garcia ... Jorge Duitama

    Published 22 February 2023

    Innovative algorithmic approaches were used to perform assembly of complex genomes across the tree of life, from long DNA sequencing data.

  • Efficient knock-in method enabling lineage tracing in zebrafish
    Open Access
    Efficient knock-in method enabling lineage tracing in zebrafish

    Jiarui Mi, Olov Andersson

    Jiarui Mi ... Olov Andersson

    Published 6 March 2023

    This study introduces a knock-in method in zebrafish that is cloning-free, preserves the endogenous gene, achieves high germline transmission, and useful for both cell labelling and lineage tracing.

  • A protocol for single nucleus RNA-seq from frozen skeletal muscle
    Open Access
    A protocol for single nucleus RNA-seq from frozen skeletal muscle

    Tyler GB Soule, Carly S Pontifex, Nicole Rosin, Matthew M Joel, Sukyoung Lee, Minh Dang Nguyen, Sameer Chhibber, Gerald Pfeffer

    Tyler GB Soule ... Gerald Pfeffer

    Published 13 March 2023

    The authors detail a method to isolate nuclei for single nucleus RNA sequencing from frozen, biobanked human skeletal muscle samples.

Corrections

  • Correction: Chitinase 1 regulates pulmonary fibrosis by modulating TGF-β/SMAD7 pathway via TGFBRAP1 and FOXO3
    Open Access
    Correction: Chitinase 1 regulates pulmonary fibrosis by modulating TGF-β/SMAD7 pathway via TGFBRAP1 and FOXO3

    Chang-Min Lee, Chuan-Hua He, Jin Wook Park, Jae Hyun Lee, Suchitra Kamle, Bing Ma, Bedia Akosman, Roberto Cotez, Emily Chen, Yang Zhou, Erica L Herzog, Changwan Ryu, Xueyan Peng, Ivan O Rosas, Sergio Poli, Carol Feghali Bostwick, Augustine M Choi, Jack A Elias, Chun Geun Lee

    Chang-Min Lee ... Chun Geun Lee

    Published 10 April 2023

    Chitinase 1 (CHIT1) plays a role in the pathogenesis of pulmonary fibrosis by modulating canonical and noncanonical TGF-β signaling via interaction with TGFBRAP1 and FOXO3. These findings highlight the CHIT1/SMAD7 axis as a potential biomarker and therapeutic target of pulmonary fibrosis.

Interviews

  • Michael J Clague: mitophagy, pexophagy, &amp; metabolism
    Open Access
    Michael J Clague: mitophagy, pexophagy, & metabolism

    Michael J Clague

    Michael J Clague

    Published 26 April 2023

    Interview with Michael J Clague

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Volume 6, No. 5
May 2023
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