Biochemistry & Molecular Biology

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Review Biochemistry & Molecular Biology

SARS-CoV-2 Omicron variant: recent progress and future perspectives

Yao Fan, Xiang Li, Lei Zhang, Shu Wan, Long Zhang, Fangfang Zhou

Summary: Since the COVID-19 pandemic began, the Omicron variant (B.1.1.529) of the SARS-CoV-2 virus has emerged as the most mutated and concerning variant. It has shown high transmissibility and immune evasion abilities, rapidly replacing the Delta variant in several regions. However, recent studies suggest that Omicron has reduced pathogenicity and significant resistance to vaccines and antibody therapies. This review summarizes the molecular and clinical characteristics of Omicron, discusses potential therapeutic approaches, and highlights strategies for ending the pandemic.

SIGNAL TRANSDUCTION AND TARGETED THERAPY (2022)

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Article Biochemistry & Molecular Biology

Symptoms and risk factors for long COVID in non-hospitalized adults

Anuradhaa Subramanian, Krishnarajah Nirantharakumar, Sarah Hughes, Puja Myles, Tim Williams, Krishna M. Gokhale, Tom Taverner, Joht Singh Chandan, Kirsty Brown, Nikita Simms-Williams, Anoop D. Shah, Megha Singh, Farah Kidy, Kelvin Okoth, Richard Hotham, Nasir Bashir, Neil Cockburn, Siang Ing Lee, Grace M. Turner, Georgios V. Gkoutos, Olalekan Lee Aiyegbusi, Christel McMullan, Alastair K. Denniston, Elizabeth Sapey, Janet M. Lord, David C. Wraith, Edward Leggett, Clare Iles, Tom Marshall, Malcolm J. Price, Steven Marwaha, Elin Haf Davies, Louise J. Jackson, Karen L. Matthews, Jenny Camaradou, Melanie Calvert, Shamil Haroon

Summary: A retrospective analysis of primary care records in the United Kingdom reveals individual symptoms associated with SARS-CoV-2 infections, which persisted for 12 weeks or more after infection, as well as risk factors associated with developing long COVID.

NATURE MEDICINE (2022)

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Review Biochemistry & Molecular Biology

Ferroptosis in cancer therapy: a novel approach to reversing drug resistance

Chen Zhang, Xinyin Liu, Shidai Jin, Yi Chen, Renhua Guo

Summary: Ferroptosis, an iron-dependent form of cell death, plays a crucial role in tumor suppression and has the potential to reverse cancer therapy resistance.

MOLECULAR CANCER (2022)

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Article Biochemistry & Molecular Biology

Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants

Qian Wang, Sho Lekthan, Zhiten Li, Liyua Liu, Yichen Guo, Yiming Huang, Anthony D. Bowen, Michael Liu, Maple Wang, Jian Yu, Riccardo Valdez, Adam S. Lauring, Zizhang Sheng, Harris H. Wang, Aubree Gordon, Lihong Liu, David D. Ho

Summary: The BQ and XBB subvariants of SARS-CoV-2 Omicron, with additional spike mutations, are rapidly expanding and have altered antibody evasion properties. Neutralization of BQ.1, BQ.1.1, XBB, and XBB.1 by vaccinated individuals and infected persons' sera was significantly impaired, including those boosted with a WA1/BA.5 bivalent mRNA vaccine. The titers against BQ and XBB subvariants were much lower than observed before, indicating that these subvariants pose a serious threat to current COVID-19 vaccines and render all authorized antibodies inactive.

CELL (2023)

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Article Biochemistry & Molecular Biology

Safety, tolerability and viral kinetics during SARS-CoV-2 human challenge in young adults

Ben Killingley, Alex J. Mann, Mariya Kalinova, Alison Boyers, Niluka Goonawardane, Jie Zhou, Kate Lindsell, Samanjit S. Hare, Jonathan Brown, Rebecca Frise, Emma Smith, Claire Hopkins, Nicolas Noulin, Brandon Londt, Tom Wilkinson, Stephen Harden, Helen McShane, Mark Baillet, Anthony Gilbert, Michael Jacobs, Christine Charman, Priya Mande, Jonathan S. Nguyen-Van-Tam, Malcolm G. Semple, Robert C. Read, Neil M. Ferguson, Peter J. Openshaw, Garth Rapeport, Wendy S. Barclay, Andrew P. Catchpole, Christopher Chiu

Summary: This study establishes a new SARS-CoV-2 human challenge model and investigates the viral kinetics during primary infection. The findings have implications for public health recommendations and strategies to control the transmission of SARS-CoV-2.

NATURE MEDICINE (2022)

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Article Biochemistry & Molecular Biology

VFDB 2022: a general classification scheme for bacterial virulence factors

Bo Liu, Dandan Zheng, Siyu Zhou, Lihong Chen, Jian Yang

Summary: The VFDB is a comprehensive knowledge base and analysis platform for bacterial virulence factors, which has recently undergone a reorganization based on extensive literature mining to make it more suitable for future analysis of bacterial virulence factors. Additionally, the web interface of VFDB has been redesigned to ensure global accessibility for users with various client settings.

NUCLEIC ACIDS RESEARCH (2022)

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Article Biochemistry & Molecular Biology

Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays

Ao Chen, Sha Liao, Mengnan Cheng, Kailong Ma, Liang Wu, Yiwei Lai, Xiaojie Qiu, Jin Yang, Jiangshan Xu, Shijie Hao, Xin Wang, Huifang Lu, Xi Chen, Xing Liu, Xin Huang, Zhao Li, Yan Hong, Yujia Jiang, Jian Peng, Shuai Liu, Mengzhe Shen, Chuanyu Liu, Quanshui Li, Yue Yuan, Xiaoyu Wei, Huiwen Zheng, Weimin Feng, Zhifeng Wang, Yang Liu, Zhaohui Wang, Yunzhi Yang, Haitao Xiang, Lei Han, Baoming Qin, Pengcheng Guo, Guangyao Lai, Pura Munoz-Canoves, Patrick H. Maxwell, Jean Paul Thiery, Qing-Feng Wu, Fuxiang Zhao, Bichao Chen, Mei Li, Xi Dai, Shuai Wang, Haoyan Kuang, Junhou Hui, Liqun Wang, Ji-Feng Fei, Ou Wang, Xiaofeng Wei, Haorong Lu, Bo Wang, Shiping Liu, Ying Gu, Ming Ni, Wenwei Zhang, Feng Mu, Ye Yin, Huanming Yang, Michael Lisby, Richard J. Cornall, Jan Mulder, Mathias Uhlen, Miguel A. Esteban, Yuxiang Li, Longqi Liu, Xun Xu, Jian Wang

Summary: Spatially resolved transcriptomic technologies enable us to study complex biological processes such as mammalian embryogenesis. However, current methods have limitations in resolution, gene capture, and field of view, which hinders their systematic application to large and three-dimensional mid- and late-gestation embryos. In this study, we developed Stereo-seq, a spatially enhanced resolution omics-sequencing method, by combining DNA nanoball-patterned arrays and in situ RNA capture. We used Stereo-seq to generate the mouse organogenesis spatiotemporal transcriptomic atlas, MOSTA, which provides single cell resolution and high sensitivity for mapping the kinetics and directionality of transcriptional variation during mouse organogenesis. By utilizing this atlas, we investigated the molecular basis of spatial cell heterogeneity and cell fate specification in developing tissues like the dorsal midbrain. Our panoramic atlas will facilitate in-depth research into long-standing questions about normal and abnormal mammalian development.

CELL (2022)

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Article Biochemistry & Molecular Biology

Targeting COVID-19 (SARS-CoV-2) main protease through active phytochemicals of ayurvedic medicinal plants -Withania somnifera(Ashwagandha),Tinospora cordifolia(Giloy) andOcimum sanctum(Tulsi) - a molecular docking study

Priya Shree, Priyanka Mishra, Chandrabose Selvaraj, Sanjeev Kumar Singh, Radha Chaube, Neha Garg, Yamini Bhusan Tripathi

Summary: By utilizing molecular docking and molecular dynamics simulation, this study identifies potential phytochemicals from medicinal plants that could inhibit SARS-CoV-2 and possess drug-like properties.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2022)

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Review Biochemistry & Molecular Biology

Atherosclerosis: Recent developments

Johan L. M. Bjoerkegren, Aldons J. Lusis

Summary: This article reviews the current understanding of the molecular, cellular, genetic, and environmental contributions to atherosclerosis and highlights recent developments and unexpected biological findings, such as the heterogeneity of inflammatory and smooth muscle cells in lesions, the roles of senescence and clonal hematopoiesis, and the links to the gut microbiome.

CELL (2022)

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Article Biochemistry & Molecular Biology

miRTarBase update 2022: an informative resource for experimentally validated miRNA-target interactions

Hsi-Yuan Huang, Yang-Chi-Dung Lin, Shidong Cui, Yixian Huang, Yun Tang, Jiatong Xu, Jiayang Bao, Yulin Li, Jia Wen, Huali Zuo, Weijuan Wang, Jing Li, Jie Ni, Yini Ruan, Liping Li, Yidan Chen, Yueyang Xie, Zihao Zhu, Xiaoxuan Cai, Xinyi Chen, Lantian Yao, Yigang Chen, Yijun Luo, Shupeng LuXu, Mengqi Luo, Chih-Min Chiu, Kun Ma, Lizhe Zhu, Gui-Juan Cheng, Chen Bai, Ying-Chih Chiang, Liping Wang, Fengxiang Wei, Tzong-Yi Lee, Hsien-Da Huang

Summary: miRTarBase is a large biological database that provides experimentally verified miRNA-target interactions, making it one of the most research-friendly MTI databases with comprehensive and experimentally verified annotations.

NUCLEIC ACIDS RESEARCH (2022)

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Review Biochemistry & Molecular Biology

Role of Phenolic Compounds in Human Disease: Current Knowledge and Future Prospects

Md. Mominur Rahman, Md. Saidur Rahaman, Md. Rezaul Islam, Firoza Rahman, Faria Mannan Mithi, Taha Alqahtani, Mohannad A. Almikhlafi, Samia Qasem Alghamdi, Abdullah S. Alruwaili, Md. Sohel Hossain, Muniruddin Ahmed, Rajib Das, Talha Bin Emran, Md. Sahab Uddin

Summary: Inflammation is a natural protective mechanism, but excessive inflammation can contribute to various diseases. Phenolic compounds can inhibit pro-inflammatory mediators and enzymes, and they also possess antioxidant and anti-inflammatory properties. They have been utilized for the treatment of different human ailments.

MOLECULES (2022)

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Article Biochemistry & Molecular Biology

Dali server: structural unification of protein families

Liisa Holm

Summary: Protein structure is crucial for understanding biological function, and recent advancements in deep learning have revolutionized the field of structural bioinformatics. The Dali server for protein structure comparison has been upgraded to allow searching for foldomes of key organisms in the AlphaFold Database and to provide annotated structural alignments with protein families.

NUCLEIC ACIDS RESEARCH (2022)

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Letter Biochemistry & Molecular Biology

SARS-CoV-2 Omicron RBD shows weaker binding affinity than the currently dominant Delta variant to human ACE2

Leyun Wu, Liping Zhou, Mengxia Mo, Tingting Liu, Chengkun Wu, Chunye Gong, Kai Lu, Likun Gong, Weiliang Zhu, Zhijian Xu

SIGNAL TRANSDUCTION AND TARGETED THERAPY (2022)

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Article Biochemistry & Molecular Biology

Intestinal Akkermansia muciniphila predicts clinical response to PD-1 blockade in patients with advanced non-small-cell lung cancer

Lisa Derosa, Bertrand Routy, Andrew Maltez Thomas, Valerio Iebba, Gerard Zalcman, Sylvie Friard, Julien Mazieres, Clarisse Audigier-Valette, Denis Moro-Sibilot, Francois Goldwasser, Carolina Alves Costa Silva, Safae Terrisse, Melodie Bonvalet, Arnaud Scherpereel, Herve Pegliasco, Corentin Richard, Francois Ghiringhelli, Arielle Elkrief, Antoine Desilets, Felix Blanc-Durand, Fabio Cumbo, Aitor Blanco, Romain Boidot, Sandy Chevrier, Romain Daillere, Guido Kroemer, Laurie Alla, Nicolas Pons, Emmanuelle Le Chatelier, Nathalie Galleron, Hugo Roume, Agathe Dubuisson, Nicole Bouchard, Meriem Messaoudene, Damien Drubay, Eric Deutsch, Fabrice Barlesi, David Planchard, Nicola Segata, Stephanie Martinez, Laurence Zitvogel, Jean-Charles Soria, Benjamin Besse

Summary: In addition to PD-L1 expression, biomarkers for predicting the response to immune checkpoint inhibitors (ICIs) in non-small-cell lung cancer (NSCLC) are needed. This study found that fecal Akkermansia muciniphila (Akk) was associated with clinical benefit of ICI treatment in NSCLC patients, independent of PD-L1 expression and other factors. The relative abundance of Akk in the gut microbiome may serve as a potential biomarker for patient stratification.

NATURE MEDICINE (2022)

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Article Biochemistry & Molecular Biology

Humoral and cellular immune memory to four COVID-19 vaccines

Zeli Zhang, Jose Mateus, Camila H. Coelho, Jennifer M. Dan, Carolyn Rydyznski Moderbacher, Rosa Isela Galvez, Fernanda H. Cortes, Alba Grifoni, Alison Tarke, James Chang, E. Alexandar Escarrega, Christina Kim, Benjamin Goodwin, Nathaniel Bloom, April Frazier, Daniela Weiskopf, Alessandro Sette, Shane Crotty

Summary: Multiple COVID-19 vaccines have successfully protected against symptomatic cases and deaths. Comparisons of T cell, B cell, and antibody responses to different vaccines can provide insights into protective immunity against COVID-19, particularly immune memory. mRNA vaccines and Ad26.COV2.S induced strong T cell responses, while mRNA vaccines showed substantial declines in antibodies.

CELL (2022)

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Article Biochemistry & Molecular Biology

Immune imprinting, breadth of variant recognition, and germinal center response in human SARS-CoV-2 infection and vaccination

Katharina Roltgen, Sandra C. A. Nielsen, Oscar Silva, Sheren F. Younes, Maxim Zaslavsky, Cristina Costales, Fan Yang, Oliver F. Wirz, Daniel Solis, Ramona A. Hoh, Aihui Wang, Prabhu S. Arunachalam, Deana Colburg, Shuchun Zhao, Emily Haraguchi, Alexandra S. Lee, Mihir M. Shah, Monali Manohar, Iris Chang, Fei Gao, Vamsee Mallajosyula, Chunfeng Li, James Liu, Massa J. Shoura, Sayantani B. Sindher, Ella Parsons, Naranjargal J. Dashdorj, Naranbaatar D. Dashdorj, Robert Monroe, Geidy E. Serrano, Thomas G. Beach, R. Sharon Chinthrajah, Gregory W. Charville, James L. Wilbur, Jacob N. Wohlstadter, Mark M. Davis, Bali Pulendran, Megan L. Troxell, George B. Sigal, Yasodha Natkunam, Benjamin A. Pinsky, Kari C. Nadeau, Scott D. Boyd

Summary: During the SARS-CoV-2 pandemic, different vaccines have been used globally. This study compares the antibodies generated by mRNA vaccines, infection, and other types of vaccines. It shows that mRNA vaccines result in a better antibody breadth against viral variants compared to infection. Infection leads to variant-specific antibodies, while mRNA vaccination imprints responses towards the original virus strain. mRNA vaccines also stimulate robust germinal centers in lymph nodes, enhancing the immune response.

CELL (2022)

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Review Biochemistry & Molecular Biology

Notch signaling pathway: architecture, disease, and therapeutics

Binghan Zhou, Wanling Lin, Yaling Long, Yunkai Yang, Huan Zhang, Kongming Wu, Qian Chu

Summary: The NOTCH gene and signaling pathway have been studied for 110 years and play important roles in the development, homeostasis, and related diseases of tissues and organs. However, recent studies have found that the outcomes of NOTCH signaling are context-dependent. In terms of cancer, NOTCH signaling can both promote and inhibit tumor development. NOTCH-targeted therapies in clinical trials have not met expectations, and NOTCH mutations may serve as predictive biomarkers for immune checkpoint blockade therapy in many cancers.

SIGNAL TRANSDUCTION AND TARGETED THERAPY (2022)

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Article Biochemistry & Molecular Biology

UniProt: the Universal Protein Knowledgebase in 2023

Alex Bateman, Maria-Jesus Martin, Sandra Orchard, Michele Magrane, Shadab Ahmad, Emanuele Alpi, Emily H. Bowler-Barnett, Ramona Britto, Austra Cukura, Paul Denny, Tunca Dogan, ThankGod Ebenezer, Jun Fan, Penelope Garmiri, Leonardo Jose da Costa Gonzales, Emma Hatton-Ellis, Abdulrahman Hussein, Alexandr Ignatchenko, Giuseppe Insana, Rizwan Ishtiaq, Vishal Joshi, Dushyanth Jyothi, Swaathi Kandasaamy, Antonia Lock, Aurelien Luciani, Marija Lugaric, Jie Luo, Yvonne Lussi, Alistair MacDougall, Fabio Madeira, Mahdi Mahmoudy, Alok Mishra, Katie Moulang, Andrew Nightingale, Sangya Pundir, Guoying Qi, Shriya Raj, Pedro Raposo, Daniel L. Rice, Rabie Saidi, Rafael Santos, Elena Speretta, James Stephenson, Prabhat Totoo, Edward Turner, Nidhi Tyagi, Preethi Vasudev, Kate Warner, Xavier Watkins, Hermann Zellner, Alan J. Bridge, Lucila Aimo, Ghis-laine Argoud-Puy, Andrea H. Auchincloss, Kristian B. Axelsen, Parit Bansal, Delphine Baratin, Teresa M. Batista Neto, Marie-Claude Blatter, Jerven T. Bolleman, Emmanuel Boutet, Lionel Breuza, Blanca Cabrera Gil, Cristina Casals-Casas, Kamal Chikh Echioukh, Elisabeth Coudert, Beatrice Cuche, Edouard de Castro, Anne Estreicher, Maria L. Famiglietti, Marc Feuermann, Elisabeth Gasteiger, Pascale Gaudet, Sebastien Gehant, Vivienne Gerritsen, Arnaud Gos, Nadine Gruaz, Chantal Hulo, Nevila Hyka-Nouspikel, Florence Jungo, Arnaud Kerhornou, Philippe Le Mercier, Damien Lieberherr, Patrick Masson, Anne Morgat, Venkatesh Muthukrishnan, Salvo Paesano, Ivo Pedruzzi, Sandrine Pilbout, Lucille Pourcel, Sylvain Poux, Monica Pozzato, Manuela Pruess, Nicole Redaschi, Catherine Rivoire, Christian J. A. Sigrist, Karin Sonesson, Cecilia N. Arighi, Leslie Armin-ski, Chuming Chen, Yongxing Chen, Hongzhan Huang, Kati Laiho, Peter McGarvey, Darren A. Natale, Karen Ross, C. R. Vinayaka, Qinghua Wang, Yuqi Wang, Jian Zhang, Hema Bye-A-Jee, Rossana Zaru, Shyamala Sundaram, Cathy H. Wu

Summary: The UniProt Knowledgebase aims to provide comprehensive, high-quality, and freely accessible protein sequences annotated with functional information. The database has expanded its data processing pipeline and website to accommodate the increasing information content, with over 227 million sequences and plans to include a reference proteome for each taxonomic group. Detailed annotations are extracted from the literature to update or create reviewed entries, while unreviewed entries are supplemented with annotations from automated systems. The new website, https://www.uniprot.org/, offers enhanced user experience and easy access to data, including AlphaFold structures and improved protein subcellular localization visualizations.

NUCLEIC ACIDS RESEARCH (2023)

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Article Biochemistry & Molecular Biology

Low neutralization of SARS-CoV-2 Omicron BA.2.75.2, BQ.1.1 and XBB.1 by parental mRNA vaccine or a BA.5 bivalent booster

Chaitanya Kurhade, Jing Zou, Hongjie Xia, Mingru Liu, Hope C. Chang, Ping Ren, Xuping Xie, Pei-Yong Shi

Summary: This study reported on the neutralizing activities of a BA.5 bivalent booster against SARS-CoV-2 Omicron sublineages. The results showed that the BA.5 bivalent booster had good neutralizing efficacy against BA.4/5 but weaker efficacy against BA.2.75.2, BQ.1.1, and XBB.1. Previous infection significantly enhanced the strength and breadth of neutralization induced by the BA.5 bivalent booster. These data support a vaccine update strategy that matches newly emerged SARS-CoV-2 variants.

NATURE MEDICINE (2023)

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Article Biochemistry & Molecular Biology

Genomic characterization of metastatic patterns from prospective clinical sequencing of 25,000 patients

Bastien Nguyen, Christopher Fong, Anisha Luthra, Shaleigh A. Smith, Renzo G. DiNatale, Subhiksha Nandakumar, Henry Walch, Walid K. Chatila, Ramyasree Madupuri, Ritika Kundra, Craig M. Bielski, Brooke Mastrogiacomo, Mark T. A. Donoghue, Adrienne Boire, Sarat Chandarlapaty, Karuna Ganesh, James J. Harding, Christine A. Iacobuzio-Donahue, Pedram Razavi, Ed Reznik, Charles M. Rudin, Dmitriy Zamarin, Wassim Abida, Ghassan K. Abou-Alfa, Carol Aghajanian, Andrea Cercek, Ping Chi, Darren Feldman, Alan L. Ho, Gopakumar Iyer, Yelena Y. Janjigian, Michael Morris, Robert J. Motzer, Eileen M. O'Reilly, Michael A. Postow, Nitya P. Raj, Gregory J. Riely, Mark E. Robson, Jonathan E. Rosenberg, Anton Safonov, Alexander N. Shoushtari, William Tap, Min Yuen Teo, Anna M. Varghese, Martin Voss, Rona Yaeger, Marjorie G. Zauderer, Nadeem Abu-Rustum, Julio Garcia-Aguilar, Bernard Bochner, Abraham Hakimi, William R. Jarnagin, David R. Jones, Daniela Molena, Luc Morris, Eric Rios-Doria, Paul Russo, Samuel Singer, Vivian E. Strong, Debyani Chakravarty, Lora H. Ellenson, Anuradha Gopalan, Jorge S. Reis-Filho, Britta Weigelt, Marc Ladanyi, Mithat Gonen, Sohrab P. Shah, Joan Massague, Jianjiong Gao, Ahmet Zehir, Michael F. Berger, David B. Solit, Samuel F. Bakhoum, Francisco Sanchez-Vega, Nikolaus Schultz

Summary: This study investigates the genomic mechanisms driving metastasis in cancer patients. By analyzing a cohort of over 25,000 patients with metastatic diseases, the researchers identify associations between genomic alterations and patterns of metastatic dissemination across different tumor types. The study highlights the complex role of chromosomal instability in cancer progression and provides valuable insights for further research on metastatic spread.

CELL (2022)

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