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Multidisciplinary Sciences
Wenqi Hu, Haitao Zeng, Yanan Shi, Chuanchuan Zhou, Jiana Huang, Lei Jia, Siqi Xu, Xiaoyu Feng, Yanyan Zeng, Tuanlin Xiong, Wenze Huang, Peng Sun, Yajie Chang, Tingting Li, Cong Fang, Keliang Wu, Lingbo Cai, Wuhua Ni, Yan Li, Zhiyong Yang, Qiangfeng Cliff Zhang, RiCheng Chian, Zijiang Chen, Xiaoyan Liang, Kehkooi Kee
Summary: This study developed a dual-omics methodology for analyzing the transcriptome and translatome of single-cell oocyte samples. The analysis revealed differences in translational expression patterns between mouse and human oocytes, and identified OOSP2 as an induction factor during human oocyte maturation.
NATURE COMMUNICATIONS
(2022)
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Cell Biology
Keke Xia, Hai-Xi Sun, Jie Li, Jiming Li, Yu Zhao, Lichuan Chen, Chao Qin, Ruiying Chen, Zhiyong Chen, Guangyu Liu, Ruilian Yin, Bangbang Mu, Xiaojuan Wang, Mengyuan Xu, Xinyue Li, Peisi Yuan, Yixin Qiao, Shijie Hao, Jing Wang, Qing Xie, Jiangshan Xu, Shiping Liu, Yuxiang Li, Ao Chen, Longqi Liu, Ye Yin, Huanming Yang, Jian Wang, Ying Gu, Xun Xu
Summary: This study presents a single-cell spatial transcriptome profiling technique called scStereo-seq, which successfully characterized the transcriptomic differences between upper and lower epidermal cells in Arabidopsis leaves. The study also discovered cell-type-specific gene expression gradients and spatial developmental trajectories of vascular cells and guard cells.
DEVELOPMENTAL CELL
(2022)
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Biology
Kyota Ishibashi, Kentaro Ikegami, Takashi Shimbo, Eiji Sasaki, Tomomi Kitayama, Yuzuru Nakamura, Takahiro Tsushima, Yasuyuki Ishibashi, Katsuto Tamai
Summary: This study demonstrates the cell heterogeneity in ACL and MCL ligaments using single-cell analysis. Three types of fibroblasts expressing Col14a1, Col12a1, or Col22a1 are identified. The ligaments show differences in cell composition and gene expression, which also change with age. This research provides a foundation for identifying potential therapeutic targets for ligament injuries.
COMMUNICATIONS BIOLOGY
(2022)
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Hematology
Ziqing Liu, Dana L. Ruter, Kaitlyn Quigley, Natalie T. Tanke, Yuchao Jiang, Victoria L. Bautch
Summary: The study found that endothelial cells exposed to homeostatic laminar flow exhibited overall increased heterogeneity in RNA expression levels, while the heterogeneity in the expression of selected cognate proteins did not closely follow RNA changes. This suggests that endothelial cell homeostasis is post-transcriptionally regulated in response to laminar flow.
ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY
(2021)
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Cell Biology
Xiaoqi Wang, Xiaobin Wu, Pei Zhang, Yuan Zhou, Jun Cai, Ling Jin
Summary: The adaptive immune response mediated by T cells plays a vital role in blood pressure elevation. This study identified four subsets of memory T cells in hypertensive patients and found that CD8 effector memory T cells have more biological functions. Subpopulation 1 of CD8 TEM cells was shown to contribute to blood pressure elevation, and marker genes CKS2, PLIN2, and CNBP were identified.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
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Plant Sciences
Zhanchao Cheng, Changhong Mu, Xiangyu Li, Wenlong Cheng, Miaomiao Cai, Chongyang Wu, Jutang Jiang, Hui Fang, Yucong Bai, Huifang Zheng, Ruiman Geng, Junlei Xu, Yali Xie, Yuping Dou, Juan Li, Shaohua Mu, Jian Gao
Summary: In this study, a modified protocol for protoplast preparation was used to investigate the single-cell transcriptome of the root system in moso bamboo. Four cell types were identified, and new cell-type-specific marker genes for the basal root were defined. The developmental trajectories of the root cap, epidermis, and ground tissues were reconstructed, and key factors regulating cell fate determination were elucidated. Furthermore, the study revealed the divergence of root developmental pathways between moso bamboo and rice and identified key regulatory factors for cell differentiation.
HORTICULTURE RESEARCH
(2023)
Article
Cell Biology
Fulong Ji, Yong Liu, Jinsong Shi, Chunxiang Liu, Siqi Fu, Heng Wang, Bingbing Ren, Dong Mi, Shan Gao, Daqing Sun
Summary: In this study, the researchers characterized the cellular heterogeneity of cavernous hemangiomas using single-cell RNA sequencing. They found a large number of embryonic mesenchymal stem cells (MSCs) in cavernous hemangiomas and proposed that these tumors may originate from embryonic MSCs. Further analysis revealed the involvement of proinflammatory cytokines and related genes in the MSC-induced immune responses in cavernous hemangiomas, as well as the role of UCHL1-induced apoptosis of MSCs in these immune responses. Additionally, marker genes, cell types, and molecular mechanisms associated with the origin, formation, progression, diagnosis, and therapy of cavernous hemangiomas were identified.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Ryan S. Ziffra, Chang N. Kim, Jayden M. Ross, Amy Wilfert, Tychele N. Turner, Maximilian Haeussler, Alex M. Casella, Pawel F. Przytycki, Kathleen C. Keough, David Shin, Derek Bogdanoff, Anat Kreimer, Katherine S. Pollard, Seth A. Ament, Evan E. Eichler, Nadav Ahituv, Tomasz J. Nowakowski
Summary: During mammalian development, differences in chromatin state play a crucial role in cell fate specification and defining cell identity in the developing brain. Through studying chromatin accessibility patterns, it was found that cerebral organoids recapitulate most cell-type-specific enhancer accessibility patterns but lack some open chromatin regions found in vivo. Systematic comparison of chromatin accessibility across brain regions revealed unexpected diversity among neural progenitor cells and highlighted the role of retinoic acid signaling in neuronal lineage specification in the prefrontal cortex.
Article
Biochemistry & Molecular Biology
Desalegn D. Serba, Xiaoxi Meng, James Schnable, Elfadil Bashir, J. P. Michaud, P. V. Vara Prasad, Ramasamy Perumal
Summary: The study used RNA-Seq technology to analyze the effects of sugarcane aphid on moderately resistant and susceptible genotypes, revealing transcriptome differences between the two genotypes at multiple time points after infestation by SCA. The resistant genotype exhibited differential expression of several gene clusters during SCA infestation, while the susceptible genotype showed a series of down-regulated genes on the basis of the resistant genotype.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Cell Biology
Zhimin Chen, Yinshuang Li, Ying Yuan, Kunmei Lai, Keng Ye, Yujiao Lin, Ruilong Lan, Hong Chen, Yanfang Xu
Summary: The study used single-cell sequencing to investigate acute kidney injury induced by different etiologies, and established a kidney cell atlas with 20 cell types. The study identified the characteristics of kidney injury and the cell interactions related to it. This study provides an important resource for understanding the pathogenesis of acute kidney injury.
CELL DEATH & DISEASE
(2023)
Article
Multidisciplinary Sciences
Huy Q. Dinh, Feng Pan, Geng Wang, Qing-Feng Huang, Claire E. Olingy, Zhi-Yong Wu, Shao-Hong Wang, Xin Xu, Xiu-E Xu, Jian-Zhong He, Qian Yang, Sandra Orsulic, Marcela Haro, Li-Yan Li, Guo-Wei Huang, Joshua J. Breunig, H. Phillip Koeffler, Catherine C. Hedrick, Li-Yan Xu, De-Chen Lin, En-Min Li
Summary: This study utilized single-cell RNA sequencing to characterize the heterogeneous microenvironment of ESCC, identifying a tumor-specific subset of CST1(+) myofibroblasts with prognostic values and immunosuppressive features. The analysis of stromal cell types in the ESCC microenvironment provides a rich resource for further understanding of ESCC biology.
NATURE COMMUNICATIONS
(2021)
Article
Cell Biology
Qiuxia Zhou, Changlong Zhao, Zhiyong Yang, Rui Qu, Yunbo Li, Yining Fan, Jinlin Tang, Ting Xie, Zilong Wen
Summary: We used single-cell RNA sequencing to comprehensively profile the heterogeneity of tissue-resident macrophages (TRMs) and dendritic cells (DCs) in adult zebrafish organs. We identified two subtypes of macrophages with different functions in barrier tissues, liver, and heart, as well as conventional dendritic cells (cDCs) and plasmacytoid dendritic cells (pDCs) in these organs. In the brain, we also found a unique population of macrophages/microglia with potent phagocytosis capacity, a population of pDCs, and two distinct populations of cDCs. This study provides valuable insights into the landscape of TRMs and DCs in zebrafish and offers tools for further research.
Article
Biochemistry & Molecular Biology
Yaping Hu, Petr Smarda, Ganping Liu, Beibei Wang, Xiaoge Gao, Qirong Guo
Summary: This study investigates the differences in growth, physiology, and biochemistry between haploid and diploid ginkgo. It establishes a high-depth transcriptome database to reveal their transcriptional differences. The results show that haploid ginkgo exhibits weaker growth potential, lower photosynthesis, and flavonoid accumulation capacity. The study provides important insights into the phenotypic and transcriptional differences of haploid ginkgo.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Cell Biology
Jie Yang, Yongyun Li, Yanping Han, Yiyi Feng, Min Zhou, Chunyan Zong, Xiaoyu He, Renbing Jia, Xiaofang Xu, Jiayan Fan
Summary: This study utilized single-cell RNA sequencing to uncover the cellular heterogeneity and developmental mechanism of human retinoblastoma, identifying two major cell types and 5 different cell states. Cone precursors were found to be the initiating cells of retinoblastoma, while UBE2C was associated with an activation state in the malignant progression of the tumor.
CELL DEATH & DISEASE
(2021)
Article
Multidisciplinary Sciences
Nan Xiang, Hao Xu, Zhou Zhou, Junyu Wang, Pengfei Cai, Li Wang, Zhen Tan, Yingbo Zhou, Tianping Zhang, Jiayuan Zhou, Ke Liu, Songwen Luo, Minghao Fang, Guosheng Wang, Zhuo Chen, Chuang Guo, Xiaomei Li
Summary: This study used single-cell RNA sequencing to investigate cellular heterogeneity in patients with primary Sjogren's syndrome (pSS). The findings suggest that downregulated SOX9 in myoepithelial cells might be associated with impaired epithelial regeneration in pSS. Additionally, an expanded ACKR1(+) endothelial population in pSS patients may play a role in lymphocyte migration. The study also identified expanded IGHD(+) naive B cells in the peripheral blood of pSS patients.
Article
Biochemistry & Molecular Biology
Periklis Makrythanasis, Reza Maroofian, Asbjorg Stray-Pedersen, Damir Musaev, Maha S. Zaki, Iman G. Mahmoud, Laila Selim, Amera Elbadawy, Shalini N. Jhangiani, Zeynep H. Coban Akdemir, Tomasz Gambin, Hanne S. Sorte, Arvid Heiberg, Jennifer McEvoy-Venneri, Kiely N. James, Valentina Stanley, Denice Belandres, Michel Guipponi, Federico A. Santoni, Najmeh Ahangari, Fatemeh Tara, Mohammad Doosti, Justyna Iwaszkiewicz, Vincent Zoete, Paul Hoff Backe, Hanan Hamamy, Joseph G. Gleeson, James R. Lupski, Ehsan Ghayoor Karimiani, Stylianos E. Antonarakis
EUROPEAN JOURNAL OF HUMAN GENETICS
(2018)
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Biochemistry & Molecular Biology
Muhammad Ansar, Hyunglok Chung, Yar M. Waryah, Periklis Makrythanasis, Emilie Falconnet, Ali Raza Rao, Michel Guipponi, Ashok K. Narsani, Ralph Fingerhut, Federico A. Santoni, Emmanuelle Ranza, Ali M. Waryah, Hugo J. Bellen, Stylianos E. Antonarakis
HUMAN MOLECULAR GENETICS
(2018)
Article
Genetics & Heredity
Nelle Lambert, Corinne Dauve, Emmanuelle Ranza, Periklis Makrythanasis, Federico Santoni, Frederique Sloan-Bena, Stefania Gimelli, Jean-Louis Blouin, Michel Guipponi, Armand Bottani, Stylianos E. Antonarakis, Markus M. Kosel, Joel Fluss, Ariane Paoloni-Giacobino
JOURNAL OF HUMAN GENETICS
(2018)
Article
Genetics & Heredity
Muhammad Ansar, Hyung-lok Chung, Rachel L. Taylor, Aamir Nazir, Samina Imtiaz, Muhammad T. Sarwar, Alkistis Manousopoulou, Periklis Makrythanasis, Sondas Saeed, Emilie Falconnet, Michel Guipponi, Constantin J. Pournaras, Maqsood A. Ansari, Emmanuelle Ranza, Federico A. Santoni, Jawad Ahmed, Inayat Shah, Khitab Gul, Graeme C. M. Black, Hugo J. Bellen, Stylianos E. Antonarakis
AMERICAN JOURNAL OF HUMAN GENETICS
(2018)
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Biochemistry & Molecular Biology
Muhammad Ansar, Sohail Aziz Paracha, Alessandro Serretti, Muhammad T. Sarwar, Jamshed Khan, Emmanuelle Ranza, Emilie Falconnet, Justyna Iwaszkiewicz, Sayyed Fahim Shah, Azhar Ali Qaisar, Federico A. Santoni, Vincent Zoete, Andre Megarbane, Jawad Ahmed, Roberto Colombo, Periklis Makrythanasis, Stylianos E. Antonarakis
HUMAN MOLECULAR GENETICS
(2019)
Article
Genetics & Heredity
Atteeq U. Rehman, Maryam Najafi, Marios Kambouris, Lihadh Al-Gazali, Periklis Makrythanasis, Abolfazl Rad, Reza Maroofian, Anna Rajab, Zornitza Stark, Jill V. Hunter, Zeineb Bakey, Mari J. Tokita, Weimin He, Francesco Vetrini, Andrea Petersen, Federico A. Santoni, Hanan Hamamy, Kaman Wu, Fatma Al-Jasmi, Martin Helmstaedter, Sebastian J. Arnold, Fan Xia, Christopher Richmond, Pengfei Liu, Ehsan Ghayoor Karimiani, GholamReza Karami Madani, Sebastian Lunke, Hatem El-Shanti, Christine M. Eng, Stylianos E. Antonarakis, Jozef Hertecant, Magdalena Walkiewicz, Yaping Yang, Miriam Schmidts
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Endocrinology & Metabolism
Caroline Stekelenburg, Karine Gerster, Jean-Louis Blouin, Mariarosaria Lang-Muritano, Michel Guipponi, Federico Santoni, Valerie M. Schwitzgebel
PEDIATRIC DIABETES
(2019)
Article
Genetics & Heredity
Muhammad Ansar, Farid Ullah, Sohail A. Paracha, Darius J. Adams, Abbe Lai, Lynn Pais, Justyna Iwaszkiewicz, Francisca Millan, Muhammad T. Sarwar, Zehra Agha, Sayyed Fahim Shah, Azhar Ali Qaisar, Emilie Falconnet, Vincent Zoete, Emmanuelle Ranza, Periklis Makrythanasis, Federico A. Santoni, Jawad Ahmed, Nicholas Katsanis, Christopher Walsh, Erica E. Davis, Stylianos E. Antonarakis
AMERICAN JOURNAL OF HUMAN GENETICS
(2019)
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Rheumatology
Nikolaos I. Panousis, George K. Bertsias, Halit Ongen, Irini Gergianaki, Maria G. Tektonidou, Maria Trachana, Luciana Romano-Palumbo, Deborah Bielser, Cedric Howald, Cristina Pamfil, Antonis Fanouriakis, Despoina Kosmara, Argyro Repa, Prodromos Sidiropoulos, Emmanouil T. Dermitzakis, Dimitrios T. Boumpas
ANNALS OF THE RHEUMATIC DISEASES
(2019)
Article
Multidisciplinary Sciences
Eleonora Porcu, Sina Rueger, Kaido Lepik, Mawusse Agbessi, Habibul Ahsan, Isabel Alves, Anand Andiappan, Wibowo Arindrarto, Philip Awadalla, Alexis Battle, Frank Beutner, Marc Jan Bonder, Dorret Boomsma, Mark Christiansen, Annique Claringbould, Patrick Deelen, Tonu Esko, Marie-Julie Fave, Lude Franke, Timothy Frayling, Sina A. Gharib, Gregory Gibson, Bastiaan T. Heijmans, Gibran Hemani, Rick Jansen, Mika Kahonen, Anette Kalnapenkis, Silva Kasela, Johannes Kettunen, Yungil Kim, Holger Kirsten, Peter Kovacs, Knut Krohn, Jaanika Kronberg-Guzman, Viktorija Kukushkina, Bernett Lee, Terho Lehtimaki, Markus Loeffler, Urko M. Marigorta, Hailang Mei, Lili Milani, Grant W. Montgomery, Martina Mueler-Nurasyid, Matthias Nauck, Michel Nivard, Brenda Penninx, Markus Perola, Natalia Pervjakova, Brandon L. Pierce, Joseph Powell, Holger Prokisch, Bruce M. Psaty, Olli T. Raitakari, Samuli Ripatti, Olaf Rotzschke, Ashis Saha, Markus Scholz, Katharina Schramm, Ilkka Seppala, Eline P. Slagboom, Coen D. A. Stehouwer, Michael Stumvoll, Patrick Sullivan, Peter A. C. 't Hoen, Alexander Teumer, Joachim Thiery, Lin Tong, Anke Tonjes, Jenny van Dongen, Maarten van Iterson, Joyce van Meurs, Jan H. Veldink, Joost Verlouw, Peter M. Visscher, Uwe Volker, Urmo Vosa, Harm-Jan Westra, Cisca Wijmenga, Hanieh Yaghootkar, Jian Yang, Biao Zeng, Futao Zhang, Marian Beekman, Jan Bot, Joris Deelen, Bert A. Hofman, Jouke J. Hottenga, Aaron Isaacs, P. Mila Jhamai, Szymon M. Kielbasa, Nico Lakenberg, Rene Luijk, Matthijs Moed, Irene Nooren, Rene Pool, Casper G. Schalkwijk, P. Eline Slagboom, H. Eka D. Suchiman, Morris A. Swertz, Ettje F. Tigchelaar, Andre G. Uitterlinden, Leonard H. van den Berg, Ruud van der Breggen, Carla J. H. van der Kallen, Freerk van Dijk, Cornelia M. van Duijn, Michiel van Galen, Marleen M. J. van Greevenbroek, Diana van Heemst, Jeroen van Rooij, Peter Van't Hof, Erik. W. van Zwet, Martijn Vermaat, Michael Verbiest, Marijn Verkerk, Dasha V. Zhernakova, Sasha Zhernakova, Federico A. Santoni, Alexandre Reymond, Zoltan Kutalik
NATURE COMMUNICATIONS
(2019)
Article
Genetics & Heredity
Muhammad Ansar, Hyung-lok Chung, Ali Al-Otaibi, Mohammad Nael Elagabani, Thomas A. Ravenscroft, Sohail A. Paracha, Ralf Scholz, Tayseer Abdel Magid, Muhammad T. Sarwar, Sayyed Fahim Shah, Azhar Ali Qaisar, Periklis Makrythanasis, Paul C. Marcogliese, Erik-Jan Kamsteeg, Emilie Falconnet, Emmanuelle Ranza, Federico A. Santoni, Hesham Aldhalaan, Ali Al-Asmari, Eissa Ali Faqeih, Jawad Ahmed, Hans-Christian Kornau, Hugo J. Bellen, Stylianos E. Antonarakis
AMERICAN JOURNAL OF HUMAN GENETICS
(2019)
Article
Endocrinology & Metabolism
Antoine Rohrbach, Emilie Caron, Rafik Dali, Maxime Brunner, Roxane Pasquettaz, Irina Kolotuev, Federico Santoni, Bernard Thorens, Fanny Langlet
Summary: This study investigated the role of GCK-expressing tanycytes in the regulation of energy balance in mice. The results showed that Gck deletion induced the death of tanycytes and affected adiposity in mice, as well as NPY neuron function.
MOLECULAR METABOLISM
(2021)
Article
Biochemical Research Methods
Melivoia Rapti, Yassine Zouaghi, Jenny Meylan, Emmanuelle Ranza, Stylianos E. Antonarakis, Federico A. Santoni
Summary: CoverageMaster (CoM) is a CNV calling algorithm based on depth-of-coverage maps, capable of accurately detecting and visualizing CNVs of any size, supporting the possibility of replacing probe-based methods with coverage-based approaches.
BRIEFINGS IN BIOINFORMATICS
(2022)