Article
Biochemical Research Methods
Brandon G. Roy, Stacy DeBlasio, Yong Yang, Theodore Thannhauser, Michelle Heck, Marc Fuchs
Summary: We investigated changes in the proteome and transcriptome of Nicotiana benthamiana plants infected by grapevine fanleaf virus (GFLV) with an emphasis on vein clearing symptom development. Comparative analyses of plants infected by wildtype GFLV strains and their mutant strains identified host biochemical pathways involved in viral symptom development.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Forestry
Tingting Chen, Yu Sheng, Zhaodong Hao, Xiaofei Long, Fangfang Fu, Yang Liu, Zhonghua Tang, Asif Ali, Ye Peng, Lu Lu, Xiangyang Hu, Jisen Shi, Jinhui Chen
Summary: Through comparative transcriptome and proteome analysis of tetraploid Liriodendron sino-americanum, this study revealed enhanced photosynthetic capacity and molecular changes related to photosynthesis in tetraploids, which may explain the altered phenotype compared with diploid plants.
Article
Cell Biology
Yue Liu, Yangyang Ding, Zhanfa Liu, Qian Chen, Xiaobo Li, Xianglan Xue, Yabin Pu, Yuehui Ma, Qianjun Zhao
Summary: By performing comprehensive analysis of transcriptome and proteome, we identified differentially expressed proteins and pathways related to the wool bending of Zhongwei goats. Validation using PRM method confirmed the reliability of the proteomic data. KRT and collagen alpha family may play important roles in the development of goat hair follicle and wool bending.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Oncology
Chaelin You, Xuan-Mei Piao, Keunsoo Kang, Yong-June Kim, Kyuho Kang
Summary: Approximately 80% of new bladder cancer patients are diagnosed with non-muscle invasive bladder cancer (NMIBC), with about 15% progressing to muscle-invasive bladder cancer (MIBC) associated with poor prognosis. This study identified SKA3 as a potential prognostic marker for NMIBC progression through transcriptome analysis and gene expression profiling. Inhibition of SKA3 could potentially serve as a novel therapeutic approach to improve outcomes in bladder cancer patients.
Article
Dentistry, Oral Surgery & Medicine
Jie Bao, Juan Chen, XiZhao Zhang, Li Xu, YongSheng Fan, XiaoBing Dou
Summary: This study aimed to explore the serum signatures of RAU patients through proteomic and transcriptomic analysis, revealing that complement and coagulation cascade pathway, oxidative stress, and inflammation responses may play vital roles in the pathogenesis of RAU. The study identified key miRNA-protein pairs associated with oxidative stress and inflammation responses, and highlighted the importance of the complement and coagulation cascade pathway in RAU.
Article
Cell Biology
Yi-Rong Jiang, Le Zhu, Lan-Rui Cao, Qiong Wu, Jian-Bo Chen, Yu Wang, Jie Wu, Tian-Yu Zhang, Zhao-Lun Wang, Zhi-Ying Guan, Qin-Qin Xu, Qian-Xi Fan, Shao-Wen Shi, Hui-Feng Wang, Jian-Zhan Pan, Xu-Dong Fu, Yongcheng Wang, Qun Fang
Summary: A new single-cell analysis platform, capable of simultaneously analyzing the transcriptome and proteome, provides an important resource for understanding the relationship between transcription and translation in cells. By applying this platform to mouse oocytes, we investigated the correlation between RNA and protein, as well as the meiosis regulatory network, and identified specific oocyte maturational signatures.
Article
Biochemistry & Molecular Biology
Diana M. Bessa de Sousa, Rodolphe Poupardin, Saul A. Villeda, Adam B. Schroer, Thomas Froehlich, Vanessa Frey, Wolfgang Staffen, Heike Mrowetz, Barbara Altendorfer, Michael S. Unger, Bernhard Iglseder, Bernhard Paulweber, Eugen Trinka, Janne Cadamuro, Martin Drerup, Katharina Schallmoser, Ludwig Aigner, Kathrin M. Kniewallner
Summary: Alzheimer's disease (AD) and aging are associated with platelet hyperactivity, but the mechanisms underlying abnormal platelet function in AD and aging are poorly understood. This study investigated the molecular profile of platelet activation in AD patients, non-demented elderly, and young controls. The results showed increased platelet activation in AD and aged individuals compared to young controls based on proteomic analysis, and dysregulation of proteolytic machinery and autophagy in AD and aging based on transcriptomic profiling.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Plant Sciences
Aliki Xanthopoulou, Theodoros Moysiadis, Christos Bazakos, Evangelos Karagiannis, Ioanna Karamichali, George Stamatakis, Martina Samiotaki, Maria Manioudaki, Michail Michailidis, Panagiotis Madesis, Ioannis Ganopoulos, Athanassios Molassiotis, Georgia Tanou
Summary: The study provides new insights into plant biology through the integration of genomics and proteomics, identifying a large number of genes and proteins in sweet cherries. Analysis reveals differences between gene and protein quantities, key regulators of fruit development, and novel cherry proteins. Additionally, a new protein-level annotation and database were developed for further research in Prunus species.
Article
Engineering, Environmental
Shen Rao, Tian Yu, Xin Cong, Xiaozhuo Lai, Jiqian Xiang, Jie Cao, Xiaoli Liao, Yuanyuan Gou, Wei Chao, Hua Xue, Shuiyuan Cheng, Feng Xu
Summary: Analysis of Cardamine violifolia treated with selenate revealed upregulation of sulfate transporter genes and sulfur assimilatory enzyme genes, as well as downregulation of calcium proteins and cysteine-rich kinases, and upregulation of SBP1 and SDI2. This study offers novel insights into the mechanisms of Se accumulation and tolerance in plants.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Parasitology
Orawan Phuphisut, Akkarin Poodeepiyasawat, Tippayarat Yoonuan, Dorn Watthanakulpanich, Palang Chotsiri, Onrapak Reamtong, Angela Mousley, Geoffrey N. N. Gobert, Poom Adisakwattana
Summary: This study provides comprehensive transcriptome profiles of discrete reproductive tissue samples in Ascaris lumbricoides, revealing the molecular basis of these important tissues. The findings suggest that genes involved in protein phosphorylation, adhesion molecules, G-protein-coupled receptor signaling pathway, SMA genes, and TGF-beta signaling pathway play crucial roles in the reproductive processes of Ascaris. The enriched KEGG pathway analysis identifies Hippo signaling, oxytocin signaling, and tight junction pathways as important players in the male and female reproductive systems of Ascaris.
PARASITES & VECTORS
(2022)
Article
Biochemistry & Molecular Biology
Jing Han, Zengguang Ma, Linjie Chen, Zaizhan Wang, Can Wang, Lina Wang, Chunhua Chen, Zhonghai Ren, Chenxing Cao
Summary: In this study, a cucumber mutant called odd1 was isolated, which exhibited multiple morphological changes. Anatomical and cytological analyses revealed that cell size and number decreased in odd1, and the shoot apical meristem was smaller compared to the wild type. Additionally, odd1 showed female sterility, possibly due to the absence of ovules. Genetic analysis identified odd1 as a recessive single gene mutant located on chromosome 5. Integrated profiling of transcriptome and proteome indicated that differential expression of genes related to hormones and shoot apical meristem maintenance might be responsible for the phenotypic changes in odd1.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Cell Biology
Hewei Zhang, Lijun Kong, Yan Zhang, Cheng Wang, Linxiao Sun
Summary: Maslinic acid has shown anti-tumor activity against pancreatic cancer cells by inhibiting proliferation, migration, and invasion while inducing apoptosis. Key genes and proteins related to its anti-tumor activity were identified through transcriptomics and proteomics analysis. This study highlights the potential of MA as a therapeutic drug for cancer.
Review
Endocrinology & Metabolism
Jeong Joo Pyo, Yongsoo Choi
Summary: Through transcriptome and proteome analysis of nonalcoholic steatohepatitis (NASH) patients and mouse models, we established NASH gene signatures and explored the pathological mechanisms of NASH. The up-regulated genes in NASH were associated with inflammation, steatosis, apoptosis, and extracellular matrix organization, while the down-regulated genes were related to metal ion response and lipid and amino acid metabolism. Cross-species analysis revealed consistently dysregulated genes between human and mouse NASH, and 14 of these genes were further validated at the protein level. Dysregulation of amino acid metabolism was identified as a significant hepatic perturbation in both human and mouse NASH.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Toxicology
Prarthana Shankar, Gloria R. Garcia, Jane K. LaDu, Christopher M. Sullivan, Cheryl L. Dunham, Britton C. Goodale, Katrina M. Waters, Stanislau Stanisheuski, Claudia S. Maier, Preethi Thunga, David M. Reif, Robyn L. Tanguay
Summary: The study reveals the role of wfikkn1 in AHR signaling, suggesting its involvement in skeletal muscle development and neurological pathways. Mutant zebrafish show behavior deficiencies, but the absence of Wfikkn1 does not significantly alter TCDD-induced behavior effects.
TOXICOLOGICAL SCIENCES
(2022)
Article
Medicine, Research & Experimental
Sebastian Virreira Winter, Ozge Karayel, Maximilian T. Strauss, Shalini Padmanabhan, Matthew Surface, Kalpana Merchant, Roy N. Alcalay, Matthias Mann
Summary: The article presents a mass spectrometry-based proteomic workflow for urinary proteome profiling as a valuable strategy for biomarker discovery and patient stratification in Parkinson's disease (PD). The study found significant differences in urinary proteome between PD patients and healthy controls, as well as between LRRK2 G2019S carriers and non-carriers, with lysosomal dysregulation in LRRK2 G2019S mutation carriers. When combined with machine learning, the urinary proteome data alone could effectively classify mutation status and disease manifestation in PD patients.
EMBO MOLECULAR MEDICINE
(2021)
Article
Respiratory System
Maria Sparreman Mikus, Johan Kolmert, Lars Andersson, Jorgen Ostling, Richard G. Knowles, Cristina Gomez, Magnus Ericsson, John-Olof Thorngren, Payam Emami Khoonsari, Barbro Dahlen, Maciej Kupczyk, Bertrand De Meulder, Charles Auffray, Per S. Bakke, Bianca Beghe, Elisabeth H. Bel, Massimo Caruso, Pascal Chanez, Bo Chawes, Stephen J. Fowler, Mina Gaga, Thomas Geiser, Mark Gjomarkaj, Ildiko Horvath, Peter H. Howarth, Sebastian L. Johnston, Guy Joos, Norbert Krug, Paolo Montuschi, Jacek Musial, Ewa Nizankowska-Mogilnicka, Henric K. Olsson, Alberto Papi, Klaus F. Rabe, Thomas Sandstrom, Dominick E. Shaw, Nikolaos M. Siafakas, Mathias Uhlen, John H. Riley, Stewart Bates, Roelinde J. M. Middelveld, Craig E. Wheelock, Kian Fan Chung, Ian M. Adcock, Peter J. Sterk, Ratko Djukanovic, Peter Nilsson, Sven-Erik Dahlen, Anna James
Summary: This study aimed to identify plasma biomarkers associated with asthma phenotypes by analyzing the samples from two well-characterized cohorts of severe and mild-to-moderate asthmatics. The results revealed several proteins that were significantly different between severe and mild-to-moderate asthmatics, and treatment with oral corticosteroids reduced the levels of these proteins. However, differences in protein levels between severe and mild-to-moderate asthmatics remained even after correction for corticosteroid use.
EUROPEAN RESPIRATORY JOURNAL
(2022)
Article
Neurosciences
Anders K. Nilsson, Abdellah Tebani, Daniel Malmodin, Anders Pedersen, Gunnel Hellgren, Chatarina Lofqvist, Ingrid Hansen-Pupp, Mathias Uhlen, Ann Hellstrom
Summary: As an increasing number of extremely premature infants survive, understanding the maturation of their metabolome and its relation to the development of morbidities is crucial. This study used 1H-NMR to analyze the serum metabolic profile of 87 preterm infants and found that the metabolome of extremely premature infants changes substantially in the neonatal period, largely driven by the transition from total parenteral nutrition to full enteral feeding.
FRONTIERS IN NEUROSCIENCE
(2022)
Article
Chemistry, Multidisciplinary
Mujdat Zeybel, Muhammad Arif, Xiangyu Li, Ozlem Altay, Mengnan Shi, Murat Akyildiz, Burcin Saglam, Mehmet Gokhan Gonenli, Buket Yigit, Burge Ulukan, Dilek Ural, Saeed Shoaie, Hasan Turkez, Jens Nielsen, Cheng Zhang, Mathias Uhlen, Jan Boren, Adil Mardinoglu, Hong Yang
Summary: This study characterized MAFLD patients using multiomics data and revealed the impact of dysbiosis in the oral and gut microbiome and host-microbiome interactions on HS. Key features of HS were identified using these data and predicted and validated in a separate cohort.
Correction
Multidisciplinary Sciences
Diana Mahdessian, Anthony J. Cesnik, Christian Gnann, Frida Danielsson, Lovisa Stenstrom, Muhammad Arif, Cheng Zhang, Trang Le, Fredric Johansson, Rutger Schutten, Anna Backstrom, Ulrika Axelsson, Peter Thul, Nathan H. Cho, Oana Carja, Mathias Uhlen, Adil Mardinoglu, Charlotte Stadler, Cecilia Lindskog, Burcu Ayoglu, Manuel D. Leonetti, Fredrik Ponten, Devin P. Sullivan, Emma Lundberg
Article
Multidisciplinary Sciences
Wen Zhong, Swapnali Barde, Nicholas Mitsios, Csaba Adori, Per Oksvold, Kalle von Feilitzen, Liam O'Learyd, Laszlo Csiba, Tibor Hortobagyi, Peter Szocsics, Naguib Mechawar, Zsofia Magloczky, Eva Renner, Miklos Palkovits, Mathias Uhlen, Jan Mulder, Tomas Hokfelt
Summary: This study provides an overview of the distribution of peptidergic systems in the human prefrontal cortex (hPFC) and identifies unique peptide/transmitter-related profiles in different subregions of the hPFC. The results suggest the involvement of neuropeptide signaling in stabilizing circuit connectivity and modulating hPFC functions during health and disease.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Medicine, Research & Experimental
Hasan Turkez, Ozlem Altay, Serkan Yildirim, Xiangyu Li, Hong Yang, Cemil Bayram, Ismail Bolat, Sena Oner, Ozlem Ozdemir Tozlu, Mehmet Enes Arslan, Muhammad Arif, Burak Yulug, Lutfu Hanoglu, Seyda Cankaya, Simon Lam, Halil Aziz Velioglu, Ebru Coskun, Ezgi Idil, Rahim Nogaylar, Ahmet Ozsimsek, Ahmet Hacimuftuoglu, Saeed Shoaie, Cheng Zhang, Jens Nielsen, Jan Boren, Mathias Uhlen, Adil Mardinoglu
Summary: The study indicates that neurodegenerative diseases are associated with metabolic abnormalities. The administration of combined metabolic activators (CMA) improves metabolic disorders in animal models of Alzheimer's disease (AD) and Parkinson's disease (PD). CMA treatment shows promising results in improving neurological and metabolic parameters in NDDs.
Article
Biotechnology & Applied Microbiology
Rosa Lundbye Allesoe, Agnete Troen Lundgaard, Ricardo Hernandez Medina, Alejandro Aguayo-Orozco, Joachim Johansen, Jakob Nybo Nissen, Caroline Brorsson, Gianluca Mazzoni, Lili Niu, Jorge Hernansanz Biel, Valentas Brasas, Henry Webel, Michael Eriksen Benros, Anders Gorm Pedersen, Piotr Jaroslaw Chmura, Ulrik Plesner Jacobsen, Andrea Mari, Robert Koivula, Anubha Mahajan, Ana Vinuela, Juan Fernandez Tajes, Sapna Sharma, Mark Haid, Mun-Gwan Hong, Petra B. Musholt, Federico De Masi, Josef Vogt, Helle Krogh Pedersen, Valborg Gudmundsdottir, Angus Jones, Gwen Kennedy, Jimmy Bell, E. Louise Thomas, Gary Frost, Henrik Thomsen, Elizaveta Hansen, Tue Haldor Hansen, Henrik Vestergaard, Mirthe Muilwijk, Marieke T. Blom, Leen M. T. Hart, Francois Pattou, Violeta Raverdy, Soren Brage, Tarja Kokkola, Alison Heggie, Donna McEvoy, Miranda Mourby, Jane Kaye, Andrew Hattersley, Timothy McDonald, Martin Ridderstrale, Mark Walker, Ian Forgie, Giuseppe N. Giordano, Imre Pavo, Hartmut Ruetten, Oluf Pedersen, Torben Hansen, Emmanouil Dermitzakis, Paul W. Franks, Jochen M. Schwenk, Jerzy Adamski, Mark McCarthy, Ewan Pearson, Karina Banasik, Simon Rasmussen, Soren Brunak
Summary: The application of multiple omics technologies in biomedical cohorts can reveal patient-level disease characteristics and individualized response to treatment. We developed a deep-learning-based framework, MOVE, to integrate and analyze multi-omics data from a cohort of newly diagnosed type 2 diabetes patients. By using in silico perturbations, we identified drug-omics associations in the multi-modal datasets with higher sensitivity than univariate statistical tests.
NATURE BIOTECHNOLOGY
(2023)
Article
Nutrition & Dietetics
Umberto Maria Battisti, Chunixa Gao, Fady Akladios, Woonghee Kim, Hong Yang, Cemil Bayram, Ismail Bolat, Metin Kiliclioglu, Nursena Yuksel, Ozlem Ozdemir Tozlu, Cheng Zhang, Jihad Sebhaoui, Shazia Iqbal, Saeed Shoaie, Ahmet Hacimuftuoglu, Serkan Yildirim, Hasan Turkez, Mathias Uhlen, Jan Boren, Adil Mardinoglu, Morten Grotli
Summary: This study presents a new finding that ellagic acid and its derivatives can selectively and potently inhibit liver pyruvate kinase, which may open up new therapeutic options for non-alcoholic fatty liver disease (NAFLD).
Article
Neurosciences
Burak Yulug, Ozlem Altay, Xiangyu Li, Lutfu Hanoglu, Seyda Cankaya, Simon Lam, Halil Aziz Velioglu, Hong Yang, Ebru Coskun, Ezgi Idil, Rahim Nogaylar, Ahmet Ozsimsek, Cemil Bayram, Ismail Bolat, Sena Oner, Ozlem Ozdemir Tozlu, Mehmet Enes Arslan, Ahmet Hacimuftuoglu, Serkan Yildirim, Muhammad Arif, Saeed Shoaie, Cheng Zhang, Jens Nielsen, Hasan Turkez, Jan Boren, Mathias Uhlen, Adil Mardinoglu
Summary: A clinical trial was conducted to study the effect of combined metabolic activators (CMA) on Alzheimer's disease (AD) patients. The results showed that CMA can improve cognitive functions and clinical parameters associated with AD. This study provides evidence for the use of CMA in the treatment of AD.
TRANSLATIONAL NEURODEGENERATION
(2023)
Article
Mathematical & Computational Biology
Bouchra Ezzamouri, Dorines Rosario, Gholamreza Bidkhori, Sunjae Lee, Mathias Uhlen, Saeed Shoaie
Summary: The human gut microbiome plays a significant role in metabolic disorders, such as type 2 diabetes mellitus. This study investigates the mechanistic role of the gut microbiome in response to metformin treatment, using metagenomics data and genome-scale metabolic modeling. The results demonstrate the commensal and competing behavior of key bacterial species in response to metformin and highlight the impact of different nutritional environments.
NPJ SYSTEMS BIOLOGY AND APPLICATIONS
(2023)
Article
Multidisciplinary Sciences
Andreas Hober, Mirela Rekanovic, Bjorn Forsstrom, Sara Hansson, David Kotol, Andrew J. Percy, Mathias Uhlen, Jan Oscarsson, Fredrik Edfors, Tasso Miliotis
Summary: This study presents a novel quantitative approach to determine the absolute concentration of apo(a) in two microliters of plasma using proteotypic peptides, which meets the requirements for targeted proteomics assays. The assay parameters were optimized, and the LC-SRM/MS results were compared with a commercially available immunoassay.
Article
Multidisciplinary Sciences
Leo Dahl, Ilana B. Kotliar, Annika Bendes, Tea Dodig-Crnkovic, Samuel Fromm, Arne Elofsson, Mathias Uhlen, Thomas P. Sakmar, Jochen M. Schwenk
Summary: A multiplexed immunoassay was developed to test the selectivity of over 400 anti-GPCR antibodies. The results showed that about 61% of the antibodies were selective, 11% bound off-target, and 28% did not bind to any GPCR. It was also found that on-target antibodies had longer, more disordered antigens and were less buried in the interior of GPCR proteins compared to other antibodies.
Editorial Material
Endocrinology & Metabolism
Hong Yang, Cheng Zhang, Hasan Turkez, Mathias Uhlen, Jan Boren, Adil Mardinoglu
Review
Biotechnology & Applied Microbiology
Mathias Uhlen, Stephen R. Quake
Summary: The impact of next-generation sequencing (NGS) is of great significance in the field of life science, contributing to our understanding of human health, disease, biology, and ecology. The majority of NGS systems are based on the concept of 'sequencing by synthesis' (SBS), which uses engineered DNA polymerase for sequential detection of nucleotide incorporation. This review discusses some key concepts leading to the development of NGS technology.
TRENDS IN BIOTECHNOLOGY
(2023)
Article
Oncology
David Kotol, Jakob Woessmann, Andreas Hober, Maria Bueno Alvez, Khue Hua Tran Minh, Fredrik Ponten, Linn Fagerberg, Mathias Uhlen, Fredrik Edfors
Summary: This study utilized mass spectrometry to study proteins in the blood samples of cancer patients and identified potential markers for diagnosing multiple myeloma. By using machine learning and differential expression analysis, a high-accuracy diagnostic model was established, which has significant implications for diagnostic tools in cancer research.