Article
Public, Environmental & Occupational Health
Mostafa M. Khodeir, Hassan A. Shabana, Abdullah S. Alkhamiss, Zafar Rasheed, Mansour Alsoghair, Suliman A. Alsagaby, Muhammad Khan, Nelson Fernandez, Waleed Al Abdulmonem
Summary: This study conducted a meta-analysis on different biomarkers to predict the progression of COVID-19 from mild to severe cases. It found that certain biomarkers and risk factors, such as C-reactive protein, interleukin-6, LDH, neutrophil, D-dimer, creatinine, AST, cortisol, age, hypertension, diabetes, and chronic obstructive lung diseases, were significantly correlated with the severity of COVID-19 and its progression. More studies are needed to establish clearer threshold values for predicting progression and guiding proper treatment.
JOURNAL OF INFECTION AND PUBLIC HEALTH
(2021)
Article
Immunology
Andy Y. An, Arjun Baghela, Peter Zhang, Reza Falsafi, Amy H. Lee, Uriel Trahtemberg, Andrew J. Baker, Claudia C. dos Santos, Robert E. W. Hancock
Summary: Transcriptional evidence showed persistent immune dysfunction in both severe COVID-19 and non-COVID-19 septic patients, associated with increased mortality. This highlights the potential for immunomodulatory therapies targeting common mechanisms of immune dysfunction in both diseases.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Radiology, Nuclear Medicine & Medical Imaging
Robin Wang, Zhicheng Jiao, Li Yang, Ji Whae Choi, Zeng Xiong, Kasey Halsey, Thi My Linh Tran, Ian Pan, Scott A. Collins, Xue Feng, Jing Wu, Ken Chang, Lin-Bo Shi, Shuai Yang, Qi-Zhi Yu, Jie Liu, Fei-Xian Fu, Xiao-Long Jiang, Dong-Cui Wang, Li-Ping Zhu, Xiao-Ping Yi, Terrance T. Healey, Qiu-Hua Zeng, Tao Liu, Ping-Feng Hu, Raymond Y. Huang, Yi-Hui Li, Ronnie A. Sebro, Paul J. L. Zhang, Jianxin Wang, Michael K. Atalay, Wei-Hua Liao, Yong Fan, Harrison X. Bai
Summary: This study successfully developed an artificial intelligence system that integrates chest CT and clinical data to predict the risk of future deterioration to critical illness in COVID-19 patients. The AI system accurately triaged patients, identified high-risk individuals, and guided personalized treatment.
EUROPEAN RADIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Anyao Li, Jihong Yang, Jingyang Qian, Xin Shao, Jie Liao, Xiaoyan Lu, Xiaohui Fan
Summary: This study proposes a GCN construction pipeline called scDisProcema, which can track dynamic changes of immune system response during COVID-19 disease progression using single-cell data. By identifying gene modules responsible for different immune cells and explaining the molecular mechanisms underlying cell depletion or proliferation caused by the disease, scDisProcema has great potential in exploring molecular changes during disease progression.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Medicine, General & Internal
Fabio Pisano, Barbara Cannas, Alessandra Fanni, Manuela Pasella, Beatrice Canetto, Sabrina Rita Giglio, Stefano Mocci, Luchino Chessa, Andrea Perra, Roberto Littera
Summary: Introduction:
Few AI models exist for predicting severe forms of COVID-19, hindering early treatment for high-risk individuals. This study developed a machine learning model using demographic, clinical, and immunogenetic markers to predict inherent risk of severe symptoms after contracting SARS-CoV-2. The model achieved high accuracy and sensitivity in identifying individuals at risk for both Alpha and Delta variants.
FRONTIERS IN MEDICINE
(2023)
Article
Immunology
Yiting Wang, Bennan Zhao, Xinyi Zhang, Xia Zhang, Fengjiao Gao, Xiaoyan Yuan, Xiaoxia Ren, Maoquan Li, Dafeng Liu
Summary: This retrospective cohort study investigated the impact of immune breakthroughs on disease progression and prognosis in patients with COVID-19. It found that immune breakthroughs resulting from previous infection or vaccination could decelerate disease progression and enhance prognosis. The immune breakthrough group had lower critical and mortality rates and shorter coronavirus negative conversion time. Additionally, antibody levels and T lymphocyte subsets were negatively related to disease severity, prognosis, and coronavirus negative conversion time.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Radiology, Nuclear Medicine & Medical Imaging
Cheng Wang, Lu Huang, Sa Xiao, Zimeng Li, Chaohui Ye, Liming Xia, Xin Zhou
Summary: The study aimed to predict and visualize the progression of lung lesions in COVID-19 patients in the early stage of illness using chest CT scans. The predicted lesion locations and sizes were in good agreement with the actual findings, showcasing the potential of the extended CTVI method in assisting physicians with treatment planning for COVID-19 pneumonia.
EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING
(2021)
Article
Biochemistry & Molecular Biology
Francesca Sansico, Mattia Miroballo, Daniele Salvatore Bianco, Francesco Tamiro, Mattia Colucci, Elisabetta De Santis, Giovanni Rossi, Jessica Rosati, Lazzaro Di Mauro, Giuseppe Miscio, Tommaso Mazza, Angelo Luigi Vescovi, Gianluigi Mazzoccoli, Vincenzo Giambra
Summary: The research conducted single-cell RNA sequencing analysis revealed that patients with COVID-19 exhibited an increase in COVID-specific surface markers in different subsets of immune cells, while the expression of cell receptors was reduced in response to the viral infection. These results highlight the presence of novel immunoreceptors in COVID-19 patients affecting immune functionality.
Article
Immunology
Zuobing Chen, Qiushi Feng, Tianfang Zhang, Xiaosheng Wang
Summary: This study identified three COVID-19 subtypes based on immune signatures in leukocytes and revealed that the adaptive immune response has a stronger impact on outcomes than the innate immune response. Patients with the highest immune-inciting signatures displayed the best clinical outcomes, suggesting that antiviral immune responses alleviate the severity of COVID-19. Younger individuals exhibited stronger antiviral immune responses, but there was no significant association between sex and immune responses in COVID-19 patients. The type II IFN response signature was found to be an adverse prognostic factor for COVID-19.
INTERNATIONAL IMMUNOPHARMACOLOGY
(2021)
Article
Public, Environmental & Occupational Health
Akshaya Karthikeyan, Akshit Garg, P. K. Vinod, U. Deva Priyakumar
Summary: This study introduces machine learning methods based on blood test data for predicting COVID-19 mortality risk, achieving high accuracy. By analyzing key biomarkers, it provides decision-making solutions for healthcare systems to expedite the decision-making process.
FRONTIERS IN PUBLIC HEALTH
(2021)
Article
Medicine, General & Internal
R. L. Gottlieb, C. E. Vaca, R. Paredes, J. Mera, B. J. Webb, G. Perez, G. Oguchi, P. Ryan, B. U. Nielsen, M. Brown, A. Hidalgo, Y. Sachdeva, S. Mittal, O. Osiyemi, J. Skarbinski, K. Juneja, R. H. Hyland, A. Osinusi, S. Chen, G. Camus, M. Abdelghany, S. Davies, N. Behenna-Renton, F. Duff, F. M. Marty, M. J. Katz, A. A. Ginde, S. M. Brown, J. T. Schiffer, J. A. Hill
Summary: In symptomatic, nonhospitalized high-risk Covid-19 patients, a 3-day course of remdesivir significantly reduced the risk of hospitalization or death compared to placebo, with acceptable safety profile.
NEW ENGLAND JOURNAL OF MEDICINE
(2022)
Article
Multidisciplinary Sciences
Elsa Brunet-Ratnasingham, Sai Priya Anand, Pierre Gantner, Alina Dyachenko, Gael Moquin-Beaudry, Nathalie Brassard, Guillaume Beaudoin-Bussieres, Amelie Pagliuzza, Romain Gasser, Mehdi Benlarbi, Floriane Point, Jeremie Prevost, Annemarie Laumaea, Julia Niessl, Manon Nayrac, Geremy Sannier, Catherine Orban, Marc Messier-Peet, Guillaume Butler-Laporte, David R. Morrison, Sirui Zhou, Tomoko Nakanishi, Marianne Boutin, Jade Descoteaux-Dinelle, Gabrielle Gendron-Lepage, Guillaume Goyette, Catherine Bourassa, Halima Medjahed, Laetitia Laurent, Rose-Marie Rebillard, Jonathan Richard, Mathieu Dube, Remi Fromentin, Nathalie Arbour, Alexandre Prat, Catherine Larochelle, Madeleine Durand, J. Brent Richards, Michael Chasse, Martine Tetreault, Nicolas Chomont, Andres Finzi, Daniel E. Kaufmann
Summary: This study conducted immunovirological assessments on plasma from 279 individuals to identify early predictors of mortality in patients infected with SARS-CoV-2. High vRNA, low specific immunoglobulin G and antibody-dependent cellular cytotoxicity, and elevated cytokines and tissue injury markers were strongly associated with mortality. A three-variable model combining vRNA, age, and sex was able to robustly identify patients with fatal outcomes.
Article
Medicine, General & Internal
Fumin Xu, Xiao Chen, Xinru Yin, Qiu Qiu, Jingjing Xiao, Liang Qiao, Mi He, Liang Tang, Xiawei Li, Qiao Zhang, Yanling Lv, Shili Xiao, Rong Zhao, Yan Guo, Mingsheng Chen, Dongfeng Chen, Liangzhi Wen, Bin Wang, Yongjian Nian, Kaijun Liu
Summary: In this study, predictive models were successfully established based on machine learning, achieving satisfactory predictive performance of disease progression with an optimal feature subset.
INTERNATIONAL JOURNAL OF GENERAL MEDICINE
(2021)
Article
Medicine, Research & Experimental
Chong Wang, Xufang Li, Wanshan Ning, Sitang Gong, Fengxia Yang, Chunxiao Fang, Yu Gong, Di Wu, Muhan Huang, Yujie Gou, Shanshan Fu, Yujie Ren, Ruyi Yang, Yang Qiu, Yu Xue, Yi Xu, Xi Zhou
Summary: The study identified specific alterations in plasma proteomic and metabolomic profiles of children with COVID-19, showing a distinct molecular response compared to adults. This suggests potential differences in pathogenesis and immune response mechanisms between children and adults.
Article
Immunology
Andy Y. An, Arjun Baghela, Peter Zhang, Reza Falsafi, Amy H. Lee, Uriel Trahtemberg, Andrew J. Baker, Claudia C. dos Santos, Robert E. W. Hancock
Summary: This study compared the gene expression trajectories between severe COVID-19 patients and contemporaneous non-COVID-19 severe sepsis patients during hospitalization. COVID-19 patients had 1,215 differentially expressed genes compared to non-COVID-19 sepsis patients at ICU admission, but the number dropped to 9 genes after one week. The findings highlight the importance of early antiviral treatment for COVID-19 and the potential for heme-related therapeutics.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Immunology
Andre F. Rendeiro, Charles Kyriakos Vorkas, Jan Krumsiek, Harjot K. Singh, Shashi N. Kapadia, Luca Vincenzo Cappelli, Maria Teresa Cacciapuoti, Giorgio Inghirami, Olivier Elemento, Mirella Salvatore
Summary: This study investigated the blood metabolomic data of COVID-19 patients using high-throughput targeted nuclear magnetic resonance (NMR) spectroscopy and high-dimensional flow cytometry. The findings showed significant changes in serum metabolome composition associated with disease severity and response to therapy. The study established a clinically annotated, biologically-interpretable space for precise disease monitoring and characterized the temporal dynamics of metabolomic change and treatment response. The results demonstrate that joint immuno-metabolic measurements can be used for patient stratification and early prediction of severe disease.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Lissenya B. Argueta, Lauretta A. Lacko, Yaron Bram, Takuya Tada, Lucia Carrau, Andre Figueiredo Rendeiro, Tuo Zhang, Skyler Uhl, Brienne C. Lubor, Vasuretha Chandar, Cristianel Gil, Wei Zhang, Brittany J. Dodson, Jeroen Bastiaans, Malavika Prabhu, Sean Houghton, David Redmond, Christine M. Salvatore, Yawei J. Yang, Olivier Elemento, Rebecca N. Baergen, Benjamin R. tenOever, Nathaniel R. Landau, Shuibing Chen, Robert E. Schwartz, Heidi Stuhlmann
Summary: The effect of SARS-CoV-2 infection on placental function is still not well understood. Placental analysis showed viral RNA in placentas from women who tested positive at delivery, and high levels of viral RNA were found in placentas from mothers with symptomatic COVID-19. The virus was localized to trophoblasts in direct contact with maternal blood, and transcriptome analysis showed increased expression of chemokines and pathways associated with viral infection and inflammation.
Article
Biochemical Research Methods
Junbum Kim, Samir Rustam, Juan Miguel Mosquera, Scott H. Randell, Renat Shaykhiev, Andre F. Rendeiro, Olivier Elemento
Summary: The UTAG method combines information on cellular phenotypes and physical proximity of cells to identify and quantify microanatomical tissue structures in multiplexed images. It provides a way to detect higher-level architectures, quantify structural differences, and reveal tissue organization patterns.
Article
Immunology
Paoline Laurent, Chao Yang, Andre F. Rendeiro, Benjamin E. Nilsson-Payant, Lucia Carrau, Vasuretha Chandar, Yaron Bram, Benjamin R. tenOever, Olivier Elemento, Lionel B. Ivashkiv, Robert E. Schwartz, Franck J. Barrat
Summary: Lung-infiltrating macrophages play a role in the inflammation and lethality of COVID-19, despite not being infected by the virus. Plasmacytoid dendritic cells (pDCs) in the lungs produce interferons (IFN-I) in response to SARS-CoV-2, leading to macrophage activation. This interaction between pDCs and macrophages may contribute to the severity of the disease.
SCIENCE IMMUNOLOGY
(2022)
Correction
Biochemical Research Methods
Junbum Kim, Samir Rustam, Juan Miguel Mosquera, Scott H. Randell, Renat Shaykhiev, Andre F. Rendeiro, Olivier Elemento
Article
Virology
Chang Wang, Rebekah Honce, Mirella Salvatore, Daniela Chow, Davide Randazzo, Jianjun Yang, Nicholas M. Twells, Lara K. K. Mahal, Stacey Schultz-Cherry, Elodie Ghedin
Summary: Influenza defective interfering (DI) viruses interfere with replication-competent viruses and induce antiviral immunity. This study demonstrates the interferon-independent protection provided by DI viruses against homologous virus infection in mice. The mice treated with DI viruses show reduced viral transcription, less intense inflammatory response, and primed multiciliated cell differentiation in their lungs, even in the absence of type I or III interferons.
JOURNAL OF VIROLOGY
(2023)
Article
Biochemistry & Molecular Biology
Jin-Gyu Cheong, Arjun Ravishankar, Siddhartha Sharma, Christopher N. Parkhurst, Simon A. Grassmann, Claire K. Wingert, Paoline Laurent, Sai Ma, Lucinda Paddock, Isabella C. Miranda, Emin Onur Karakaslar, Djamel Nehar-Belaid, Asa Thibodeau, Michael J. Bale, Vinay K. Kartha, Jim K. Yee, Minh Y. Mays, Chenyang Jiang, Andrew W. Daman, Alexia Martinez de Paz, Dughan Ahimovic, Victor Ramos, Alexander Lercher, Erik Nielsen, Sergio Alvarez-Mulett, Ling Zheng, Andrew Earl, Alisha Yallowitz, Lexi Robbins, Elyse Lafond, Karissa L. Weidman, Sabrina Racine-Brzostek, He S. Yang, David R. Price, Louise Leyre, Andre F. Rendeiro, Hiranmayi Ravichandran, Junbum Kim, Alain C. Borczuk, Charles M. Rice, R. Brad Jones, Edward J. Schenck, Robert J. Kaner, Amy Chadburn, Zhen Zhao, Virginia Pascual, Olivier Elemento, Robert E. Schwartz, Jason D. Buenrostro, Rachel E. Niec, Franck J. Barrat, Lindsay Lief, Joseph C. Sun, Duygu Ucar, Steven Z. Josefowicz
Summary: Inflammation can cause lasting effects on immune and non-immune cells. This study found that the epigenetic programs of hematopoietic stem and progenitor cells (HSPC) were altered for months to a year following severe COVID-19, leading to changes in immune cell activity and gene expression.
Article
Immunology
Katherine A. Drake, Dimitri Talantov, Gary J. Tong, Jack T. Lin, Simon Verheijden, Samuel Katz, Jacqueline M. Leung, Benjamin Yuen, Vinod Krishna, Michelle J. Wu, Alexander M. Sutherland, Sarah A. Short, Pouya Kheradpour, Maxwell R. Mumbach, Kate M. Franz, Vladimir Trifonov, Molly Lucas, James Merson, Charles C. Kim, PRESCO Study Grp
Summary: By analyzing multi-omics data, we identified differences in immune cell composition, cytokine levels, and cell subset-specific transcriptomic and epigenomic signatures between individuals with different disease trajectories. These findings could be used to develop prognostic biomarkers and intervention strategies for the management of severe COVID-19.
CLINICAL IMMUNOLOGY
(2023)
Article
Immunology
Takato Kusakabe, Woan-Yu Lin, Jin-Gyu Cheong, Gagandeep Singh, Arjun Ravishankar, Stephen T. Yeung, Marissa Mesko, Meghan Bialt DeCelie, Guilhermina Carriche, Zhen Zhao, Sophie Rand, Itai Doron, Gregory G. Putzel, Stefan Worgall, Melissa Cushing, Lars Westblade, Giorgio Inghirami, Christopher N. Parkhurst, Chun-Jun Guo, Michael Schotsaert, Adolfo Garcia-Sastre, Steven Z. Josefowicz, Mirella Salvatore, Iliyan D. Iliev
Summary: This study found that patients with severe COVID-19 had elevated levels of Candida albicans immunoglobulin G (IgG) antibodies, intestinal Candida overgrowth, mycobiota dysbiosis, and systemic neutrophilia. Transcriptional changes in antifungal immunity pathways and reprogramming of granulocyte myeloid progenitors (GMPs) were observed in patients with severe COVID-19. Mouse models confirmed the impact of C. albicans colonization on lung neutrophilia and pulmonary NETosis during SARS-CoV-2 infection. Patients treated with tocilizumab experienced sustained reductions in C. albicans IgG antibodies titers and GMP transcriptional changes.
Article
Oncology
Evan K. Noch, Laura N. Palma, Isaiah Yim, Nayah Bullen, Yuqing Qiu, Hiranmayi Ravichandran, Junbum Kim, Andre Rendeiro, Melissa B. Davis, Olivier Elemento, David J. Pisapia, Kevin Zhai, Hongbiao Carl LeKaye, Jason A. Koutcher, Patrick Y. Wen, Keith L. Ligon, Lewis C. Cantley
Summary: This study investigated the critical role of insulin feedback in the poor clinical efficacy of phosphatidylinositol 3-kinase (PI3K) inhibition in cancer and the independent association between hyperglycemia and poor prognosis in glioblastoma (GBM). It was found that combining anti-hyperglycemic therapy with PI3K inhibition improved treatment efficacy in a GBM mouse model. Analysis of clinical trial data revealed that hyperglycemia was independently associated with poor progression-free survival in GBM patients.
Article
Medicine, General & Internal
Chen Chen, Sairam Parthasarathy, Jacqueline M. Leung, Michelle J. Wu, Katherine A. Drake, Vanessa K. Ridaura, Howard C. Zisser, William A. Conrad, Victor F. Tapson, James N. Moy, Christopher R. Defilippi, Ivan O. Rosas, Bellur S. Prabhakar, Mujeeb Basit, Mirella Salvatore, Jerry A. Krishnan, Charles C. Kim
Summary: A longitudinal assessment of symptoms in patients with acute SARS-CoV-2 infection revealed three different phenotypic clusters of Post-acute sequelae of SARS-CoV-2 infection (PASC): remittent, persistent, and incident. The incident phenotype was characterized by the absence of symptoms during acute illness and had a higher proportion of participants with PASC. The administration of systemic corticosteroids during acute infection was associated with PASC at 3 months.
FRONTIERS IN MEDICINE
(2023)
Article
Medicine, Research & Experimental
Hussein Alnajar, Hiranmayi Ravichandran, Andre Figueiredo Rendeiro, Kentaro Ohara, Wael Al Zoughbi, Jyothi Manohar, Noah Greco, Michael Sigouros, Jesse Fox, Emily Muth, Samuel Angiuoli, Bishoy Faltas, Michael Shusterman, Cora N. Sternberg, Olivier Elemento, Juan Miguel Mosquera
Summary: SUC is a rare subtype of UC that usually presents at an advanced stage. Antibodies targeting PD-1 or PD-L1 are approved for use in these cases. This case report provides an important platform for translating these findings to a larger cohort of UC patients.
COLD SPRING HARBOR MOLECULAR CASE STUDIES
(2022)
Article
Cell Biology
Jiwoon Park, Jonathan Foox, Tyler Hether, David C. Danko, Sarah Warren, Youngmi Kim, Jason Reeves, Daniel J. Butler, Christopher Mozsary, Joel Rosiene, Alon Shaiber, Evan E. Afshin, Matthew MacKay, Andre F. Rendeiro, Yaron Bram, Vasuretha Chandar, Heather Geiger, Arryn Craney, Priya Velu, Ari M. Melnick, Iman Hajirasouliha, Afshin Beheshti, Deanne Taylor, Amanda Saravia-Butler, Urminder Singh, Eve Syrkin Wurtele, Jonathan Schisler, Samantha Fennessey, Andre Corvelo, Michael C. Zody, Soren Germer, Steven Salvatore, Shawn Levy, Shixiu Wu, Nicholas P. Tatonetti, Sagi Shapira, Mirella Salvatore, Lars F. Westblade, Melissa Cushing, Hanna Rennert, Alison J. Kriegel, Olivier Elemento, Marcin Imielinski, Charles M. Rice, Alain C. Borczuk, Cem Meydan, Robert E. Schwartz, Christopher E. Mason
Summary: This study reveals the impact of COVID-19 on the body-wide transcriptome and tissue-specific damage. The findings indicate a systemic disruption of canonical cellular and transcriptional pathways in various tissues caused by COVID-19.
CELL REPORTS MEDICINE
(2022)