Article
Biology
Ling Zhong, Xiao Yang, Yu Zhou, Jialing Xiao, Huan Li, Jiang Tao, Qian Xi, Chen Chu, Chenglong Li, Xi Yang, Chen Yang, Yi Zhang, Ping Shuai, Yuping Liu, Man Yu, Yi Shi, Jiang Hu, Wei Zhang, Bo Gong, Zhenglin Yang
Summary: Through single-cell RNA sequencing, this study identified cellular heterogeneity and regular networks in multiple myeloma (MM) patients stratified by the Revised International Staging System (R-ISS). The study found different gene expressions and validated specific genes in different stages. Additionally, new signaling pathways and intercellular interaction pairs were discovered. These findings provide significant insights for the prognosis and treatment of MM.
SCIENCE CHINA-LIFE SCIENCES
(2022)
Article
Biology
Mariah Farrell, Heather Fairfield, Michelle Karam, Anastasia D'Amico, Connor S. Murphy, Carolyne Falank, Romanos Sklavenitis Pistofidi, Amanda Cao, Catherine R. Marinac, Julie A. Dragon, Lauren McGuinness, Carlos G. Gartner, Reagan Di Iorio, Edward Jachimowicz, Victoria DeMambro, Calvin Vary, Michaela R. Reagan
Summary: This study identifies the fatty acid binding protein (FABP) family as a potential new target in multiple myeloma. FABP inhibitors demonstrated anti-proliferative and pro-apoptotic effects on multiple myeloma cells, as well as metabolic and DNA methylation changes. High expression of FABP5 in tumor cells was associated with worse overall and progression-free survival in patients.
Article
Biology
Weili Fu, Runze Yang, Jian Li
Summary: Using single-cell and spatial RNA sequencing, a cell atlas of healthy and diseased human tendons was built, revealing the cellular heterogeneity and molecular mechanisms underlying tendinopathy progression. The findings provide new insights into the pathogenesis of tendinopathy and potential strategies for diagnosis and treatment.
Article
Oncology
Zhiyong Zeng, Junfang Lin, Kejie Zhang, Xizhe Guo, Xiaoqiang Zheng, Apeng Yang, Junmin Chen
Summary: This study analyzed single-cell RNA-seq data and bulk gene profiles to reveal a new signature associated with the development of multiple myeloma (MM). The results identified 597 cells divided into 7 clusters based on different risk levels, and established a 20-gene signature that stratifies patients into high and low-risk groups.
CANCER CELL INTERNATIONAL
(2021)
Article
Oncology
Haiyan He, Zifeng Li, Jing Lu, Wanting Qiang, Sihan Jiang, Yaochen Xu, Weijun Fu, Xiaowen Zhai, Lin Zhou, Maoxiang Qian, Juan Du
Summary: The study used single-cell technology to sequence bone marrow samples from multiple myeloma patients, revealing the heterogeneity of the disease and relapse status, and exploring novel biomarkers associated with disease progression and relapse.
CLINICAL AND TRANSLATIONAL MEDICINE
(2022)
Letter
Oncology
Fengjie Jiang, Xiaozhu Tang, Chao Tang, Zhen Hua, Mengying Ke, Chen Wang, Jiamin Zhao, Shengyao Gao, Artur Jurczyszyn, Siegfried Janz, Meral Beksac, Fenghuang Zhan, Chunyan Gu, Ye Yang
Summary: This study identified that HNRNPA2B1 is upregulated in multiple myeloma (MM) patients and negatively correlated with prognosis, playing a role in regulating cell proliferation by modulating AKT3 expression. This suggests that HNRNPA2B1 may act as a potential therapeutic target for MM through the ILF3-dependent pattern.
JOURNAL OF HEMATOLOGY & ONCOLOGY
(2021)
Article
Oncology
Jing Wang, Lili Guo, Chenglan Lv, Min Zhou, Yuan Wan
Summary: This study developed a predictive model for prognosis estimation in newly diagnosed multiple myeloma (MM) patients based on gene expression profiles. Through RNA-seq data and protein-protein interaction network analysis, ten hub genes were identified, and a three-gene (TTK, GINS1, and NCAPG) prognostic model was constructed. This model showed remarkable value in prognostic prediction, and was correlated with various immune cells. Additionally, high-risk MM patients were found to be sensitive to eight drugs.
FRONTIERS IN ONCOLOGY
(2023)
Article
Multidisciplinary Sciences
Richard C. Tyser, Elmir Mahammadov, Shota Nakanoh, Ludovic Vallier, Antonio Scialdone, Shankar Srinivas
Summary: The single-cell transcriptional profile of a human embryo between 16 and 19 days after fertilization shows similarities and differences in gastrulation compared to mouse and non-human primate models. This study provides new insights into human development and offers valuable information for directed differentiation of human cells in vitro.
Article
Multidisciplinary Sciences
Jun Seo Ha, Hyundoo Jeong
Summary: Recent advances in single-cell sequencing techniques have allowed for gene expression profiling at the individual cell level, accelerating biomedical research for complex disease treatment. In this study, we introduce a novel single-cell clustering algorithm, GRACE, which employs ensemble similarity learning and graph autoencoders to accurately classify cells. Through evaluations using real-world single-cell sequencing datasets, we demonstrate that GRACE achieves high assessment metric scores and yields accurate single-cell clustering results.
Article
Biochemistry & Molecular Biology
Dan Guo, Sumei Zhang, Yike Gao, Jinghua Shi, Xiaoxi Wang, Zixin Zhang, Yaran Zhang, Yuming Wang, Kun Zhao, Mei Li, Anqi Wang, Pan Wang, Yanqin Gou, Miao Zhang, Meiyu Liu, Yuhan Zhang, Rui Chen, Jian Sun, Shu Wang, Xunyao Wu, Zhiyong Liang, Jie Chen, Jinghe Lang
Summary: This study characterized and compared tumor heterogeneity and cell-level evolution between ovarian clear cell carcinoma (OCCC) and high-grade serous ovarian carcinoma (HGSC) using single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data. The study identified potential explanations for OCCC chemoresistance, possible pathogenic cell subclusters in OCCC, and novel biomarkers separating OCCC from HGSC. In addition, metabolic pathways were found to be enriched in OCCC samples, and different metabolic pathways were identified as potential targets for inhibiting tumor growth in OCCC and HGSC. The study also analyzed immune cell subsets and provided valuable insights into the cellular and molecular distinctions between OCCC and HGSC for future clinical treatments.
CELL AND BIOSCIENCE
(2023)
Article
Multidisciplinary Sciences
Kai Battenberg, S. Thomas Kelly, Radu Abu Ras, Nicola A. Hetherington, Makoto Hayashi, Aki Minoda
Summary: Single-cell RNA-sequencing analysis has gained popularity, and UniverSC is a universal tool for processing single-cell RNA-seq data on any platform. It provides a command-line tool, docker image, and containerized graphical application for consistent and comprehensive integration, comparison, and evaluation of data from various platforms. Additionally, a cross-platform application with a graphical user interface is available to address the bottleneck of data processing for researchers without bioinformatics expertise.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Malte D. Luecken, M. Buettner, K. Chaichoompu, A. Danese, M. Interlandi, M. F. Mueller, D. C. Strobl, L. Zappia, M. Dugas, M. Colome-Tatche, Fabian J. Theis
Summary: This study benchmarked 68 method and preprocessing combinations on 85 batches of gene expression data, highlighting the importance of highly variable gene selection in improving method performance. When dealing with complex integration tasks, scANVI, Scanorama, scVI, and scGen consistently performed well, while the performance of single-cell ATAC-sequencing integration was strongly influenced by the choice of feature space.
Article
Multidisciplinary Sciences
Peijie Zhou, Shuxiong Wang, Tiejun Li, Qing Nie
Summary: MuTrans is a method based on multiscale reduction technique that can identify the underlying stochastic dynamics governing cell-fate transitions, construct cell-fate dynamical manifold, distinguish stable and transition cells, and quantify transition probabilities between cell states. The method is consistent with Langevin equation and transition rate theory, and has been shown to robustly unravel complex cell fate dynamics induced by transition cells in various systems. It bridges data-driven and model-based approaches for single-cell resolution analysis of cell-fate transitions.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Jacob C. Kimmel, David R. Kelley
Summary: scNym is a semi-supervised adversarial neural network that can transfer cell identity annotations between different experiments by learning rich representations of cell identities from both labeled and unlabeled datasets. It shows superior performance in transferring annotations across experiments and can synthesize information from multiple datasets to improve accuracy. Additionally, scNym models are well calibrated, interpretable, and can be enhanced with saliency methods.
Article
Endocrinology & Metabolism
Ting Yan, Wangwang Qiu, Huaiyu Weng, Youben Fan, Guangwen Zhou, Zhili Yang
Summary: Single-cell transcriptome sequencing revealed that the papillary thyroid carcinoma (PTC) ecosystem is mainly composed of malignant follicular epithelial cells, T cells, B cells, vascular endothelial cells, fibroblasts and cancer-associated fibroblasts. The proportions of different cell types varied between primary tumors, lymph node metastasis, and paracancerous tissue, providing new insights into the progression of PTC.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Article
Hematology
Matthew Ho, Saurabh Zanwar, Francis K. Buadi, Sikander Ailawadhi, Jeremy Larsen, Leif Bergsagel, Moritz Binder, Asher Chanan-Khan, David Dingli, Angela Dispenzieri, Rafael Fonseca, Morie A. Gertz, Wilson Gonsalves, Ronald S. Go, Suzanne Hayman, Prashant Kapoor, Taxiarchis Kourelis, Martha Q. Lacy, Nelson Leung, Yi Lin, Eli Muchtar, Vivek Roy, Taimur Sher, Rahma Warsame, Amie Fonder, Miriam Hobbs, Yi L. Hwa, Robert A. Kyle, S. Vincent Rajkumar, Shaji Kumar
Summary: Patients with multiple myeloma have a lower efficacy from COVID-19 vaccination and a high rate of mortality from COVID-19 in hospitalized patients. The study found a relatively low infection rate but a quarter of the COVID-19 infections were severe. Treatment with CD38 antibody, cardiac and pulmonary comorbidities were independent predictors for ICU admission. Cardiac comorbidity was an independent predictor of mortality, while MM/AL in remission was associated with lower mortality.
AMERICAN JOURNAL OF HEMATOLOGY
(2023)
Article
Oncology
Marco Dicanio, Matteo Giaccherini, Alyssa Clay-Gilmour, Angelica Macauda, Juan Sainz, Mitchell J. Machiela, Malwina Rybicka-Ramos, Aaron D. Norman, Agata Tyczynska, Stephen J. Chanock, Torben Barington, Shaji K. Kumar, Parveen Bhatti, Wendy Cozen, Elizabeth E. Brown, Anna Suska, Eva K. Haastrup, Robert Z. Orlowski, Marek Dudzinski, Ramon Garcia-Sanz, Marcin Kruszewski, Joaquin Martinez-Lopez, Katia Beider, Elzbieta Iskierka-Jazdzewska, Matteo Pelosini, Sonja Berndt, Malgorzata Razny, Krzysztof Jamroziak, S. Vincent Rajkumar, Artur Jurczyszyn, Annette Juul Vangsted, Pilar Garrido Collado, Ulla Vogel, Jonathan N. Hofmann, Mario Petrini, Aleksandra Butrym, Susan L. Slager, Elad Ziv, Edyta Subocz, Graham G. Giles, Niels Frost Andersen, Grzegorz Mazur, Marzena Watek, Fabienne Lesueur, Michelle A. T. Hildebrandt, Daria Zawirska, Lene Hyldahl Ebbesen, Herlander Marques, Federica Gemignani, Charles Dumontet, Judit Varkonyi, Gabriele Buda, Arnon Nagler, Agnieszka Druzd-Sitek, Xifeng Wu, Katalin Kadar, Nicola J. Camp, Norbert Grzasko, Rosalie G. Waller, Celine Vachon, Federico Canzian, Daniele Campa
Summary: The aim of this study was to identify novel pleiotropic variants involved in multiple myeloma (MM) risk. Through analysis of 28,684 single nucleotide polymorphisms (SNPs), DNAJB4-rs34517439-A was found to be associated with an increased risk of developing MM.
INTERNATIONAL JOURNAL OF CANCER
(2023)
Article
Hematology
Karan L. Chohan, Jonas Paludo, Nishanth Vallumsetla, Dirk Larson, Rebecca L. King, Rong He, Wilson Gonsalves, David Inwards, Thomas E. Witzig, Abhisek Swaika, Tania Jain, Nelson Leung, Sikander Ailawadhi, Craig B. Reeder, Martha Q. Lacy, S. Vincent Rajkumar, Shaji Kumar, Robert A. Kyle, Morie A. Gertz, Stephen M. Ansell, Prashant Kapoor
Summary: Waldenstrom macroglobulinemia (WM) is a rare, indolent lymphoma that mostly affects the elderly. A study compared young WM patients to their older counterparts and found that young patients have lower overall survival and higher death attributable to WM. The treatment strategies for WM have not improved the outcome of young patients, and the impact of Bruton tyrosine kinase inhibitors on this patient population is still unknown.
AMERICAN JOURNAL OF HEMATOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Nadine Abdallah, Angela Dispenzieri, Eli Muchtar, Francis K. K. Buadi, Prashant Kapoor, Martha Q. Q. Lacy, Yi L. L. Hwa, Amie Fonder, Miriam A. A. Hobbs, Suzanne R. R. Hayman, Nelson Leung, David Dingli, Ronald S. S. Go, Yi Lin, Wilson I. I. Gonsalves, Moritz Binder, Taxiarchis Kourelis, Rahma Warsame, Robert A. A. Kyle, S. Vincent Rajkumar, Morie A. A. Gertz, Shaji K. K. Kumar
Summary: After long-term follow-up, there is no clear evidence to support the benefit of doxycycline in the post-transplant setting.
AMYLOID-JOURNAL OF PROTEIN FOLDING DISORDERS
(2023)
Article
Genetics & Heredity
Parisa Dashti, Jeroen van de Peppel, Roman Thaler, Christopher R. Paradise, Gary S. Stein, Martin A. Montecino, Johannes P. T. M. van Leeuwen, Bram J. van der Eerden, Amel Dudakovic, Andre J. van Wijnen
Summary: This study found that Smyd2 inhibits proliferation and mineral deposition by osteoblasts, and operates parallel to the suppressive effects of Ezh2 and H3K27 trimethylation on osteoblast differentiation.
Editorial Material
Oncology
Jean-Sebastien Claveau, David L. Murray, Angela Dispenzieri, Prashant Kapoor, Moritz Binder, Francis Buadi, David Dingli, Amie Fonder, Morie Gertz, Wilson Gonsalves, Suzanne Hayman, Miriam Hobbs, Yi Lisa Hwa, Taxiarchis Kourelis, Martha Lacy, Nelson Leung, Yi Lin, Rahma Warsame, Robert A. Kyle, Vincent Rajkumar, Shaji K. Kumar
Editorial Material
Orthopedics
Andre J. van Wijnen, Eric A. Lewallen
JOURNAL OF BONE AND JOINT SURGERY-AMERICAN VOLUME
(2023)
Article
Biochemistry & Molecular Biology
Yeongjun Jang, Liana Fasching, Taejeong Bae, Livia Tomasini, Jeremy Schreiner, Anna Szekely, Thomas Fernandez, James F. Leckman, Flora M. Vaccarino, Alexej Abyzov
Summary: Mosaic mutations can be used to track cell ancestries and reconstruct lineage trees during cancer progression and development. However, analyzing multiple cells' genomes can be redundant and limit scalability. This study presents a cost- and time-efficient strategy using clonal induced pluripotent stem cell lines to reconstruct lineage trees. Shallow sequencing coverage is leveraged to assess clonality, cluster redundant lines, and accurately discover mutations. Only a fraction of lines needs to be sequenced at high coverage.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Oncology
Nelson Leung, S. Vincent Rajkumar
Summary: Light chain cast nephropathy (LCCN) is a significant cause of acute kidney injury (AKI) in patients with multiple myeloma (MM) and is now considered as a defining event of myeloma. While long-term prognosis has improved, short-term mortality remains higher in patients with LCCN if renal failure is not reversed. Rapid reduction of involved serum free light chain is critical for renal function recovery. Treatment algorithm for MM patients with biopsy-proven LCCN or ruling out other causes of AKI is provided based on randomized trial data whenever available. Clinical trial enrollment is recommended prior to following the treatment algorithm.
BLOOD CANCER JOURNAL
(2023)
Article
Oncology
Alexander J. Ryu, Shaji Kumar, Angela Dispenzieri, Robert A. Kyle, S. Vincent Rajkumar, Thomas C. Kingsley
Summary: This study used machine learning and electronic health record data to identify potential drug candidates for modifying the progression risk of MGUS. Various medications were found to be significantly associated with the risk of MGUS progression, which could inform future prospective studies.
BLOOD CANCER JOURNAL
(2023)
Article
Genetics & Heredity
Arijit Panda, Milovan Suvakov, Jessica Mariani, Kristen L. Drucker, Yohan Park, Yeongjun Jang, Thomas M. Kollmeyer, Gobinda Sarkar, Taejeong Bae, Jean J. Kim, Wan Hee Yoon, Robert B. Jenkins, Flora M. Vaccarino, Alexej Abyzov
Summary: The CRISPR-Cas9 system allows precise editing of the genome. Editing experiments involve editing cultured cells and selecting clones with and without intended edits. Whole genome sequencing analysis of three independent experiments revealed minimal off-target edits but hundreds to thousands of unique mutations in each clone after short culture. Copy number alterations (CNAs) also differed among clones and represented the largest source of genomic divergence. The screening of mutations and CNAs acquired in culture is necessary for accurate interpretation of DNA editing experiments and experiments involving clonal lines should compare multiple unedited and edited lines.
Review
Biochemistry & Molecular Biology
Praneet Dara, Zeba Farooqui, Fackson Mwale, Chungyoul Choe, Andre J. van Wijnen, Hee-Jeong Im
Summary: Chronic pain conditions caused by arthritis have devastating effects on both individuals and society. The main objective of pharmacological treatments is to reduce pain, and several types of drugs have been considered. Naltrexone, an oral-activated opioid antagonist, has been shown to have beneficial effects on chronic pain conditions such as fibromyalgia and multiple sclerosis.
Article
Orthopedics
Hayman Lui, Cedryck Vaquette, Janet M. Denbeigh, Randy Bindra, Andre J. van Wijnen, Sanjeev Kakar
Summary: This study aims to assess the use of growth factors (BMP2 and GDF5) for bone and ligament regeneration in a multiphasic scaffold in a rabbit knee model. The addition of BMP2 and GDF5 in the BLB scaffold resulted in heterotopic bone formation and ligament failure.
JOURNAL OF WRIST SURGERY
(2023)
Article
Endocrinology & Metabolism
Stephane Blouin, Farzaneh Khani, Phaedra Messmer, Paul Roschger, Markus A. Hartmann, Andre J. van Wijnen, Roman Thaler, Barbara M. Misof
Summary: Vitamin C is crucial for bone health and low levels of serum Vitamin C increase the risk of skeletal fractures. This study examined the effects of Vitamin C on femoral structure, bone formation, and bone mineralization density distribution in mice. The results showed that Vitamin C depletion significantly reduced cortical thickness and bone volume, as well as diminished the amount of newly formed bone tissue. Additionally, Vitamin C supplementation led to higher calcium concentrations and suggested a longer bone tissue age. Female mice were found to be more sensitive to Vitamin C deficiency. These findings highlight the key role of Vitamin C in bone formation rate and its potential in preventing bone-degenerative diseases, especially in females.
JOURNAL OF BONE AND MINERAL RESEARCH
(2023)
Letter
Oncology
Rahul Banerjee, Bo Wang, Larry D. Anderson, Georgia Mccaughan, Nikita Mehra, Andrew J. Cowan, S. Vincent Rajkumar, Gurbakhash Kaur
BLOOD CANCER JOURNAL
(2023)