Article
Public, Environmental & Occupational Health
Shi Zou, Yuting Tan, Yanni Xiang, Yang Liu, Qi Zhu, Songjie Wu, Wei Guo, Mingqi Luo, Ling Shen, Ke Liang
Summary: This study found a significant increase in CD4 and CD8 double-positive (DP) T cells in patients with HIV/TB coinfection. Additionally, these DP T cells also expressed more cytotoxic markers. This suggests that DP T cells may play an important immune role in HIV/TB infection.
FRONTIERS IN PUBLIC HEALTH
(2022)
Article
Immunology
Jiayu He, Yingying Ding, Haijiang Lin, Xing Liu, Xiaoxiao Chen, Weiwei Shen, Sujuan Zhou, Cheng Feng, Miaochen Wang, Jingjing Xia, Na He
Summary: This study aims to analyze and compare genetic variants, mapped genes, and enriched pathways of ECG parameters among people with HIV and HIV-negative controls. It was found that there were 18 novel variants among people with HIV, and these variants had significant interaction with HIV infection. The study suggests that the host genome may influence ECG parameters by interfering with HIV viral infection among people with HIV.
Article
Medicine, General & Internal
Javier Martinez-Sanz, Jorge Diaz-alvarez, Marta Rosas, Raquel Ron, Jose Antonio Iribarren, Enrique Bernal, Felix Gutierrez, Andres Ruiz Sancho, Noemi Cabello, Julian Olalla, Santiago Moreno, Sergio Serrano-Villar
Summary: The study suggests that a low CD4/CD8 ratio during HIV treatment is associated with immunosenescence. Data analysis shows that patients with a CD4/CD8 ratio less than 0.3 in the second year of ART have an increased risk of developing SNAEs in the next five years.
Article
Biology
Severine Menoret, Laurent Tesson, Severine Remy, Victor Gourain, Celine Serazin, Claire Usal, Aude Guiffes, Vanessa Chenouard, Laure-Helene Ouisse, Malika Gantier, Jean-Marie Heslan, Cynthia Fourgeux, Jeremie Poschmann, Carole Guillonneau, Ignacio Anegon
Summary: In this study, a Foxp3-EGFP rat transgenic line was created to genetically tag CD4(+) and CD8(+) FOXP3(+) regulatory T cells. CD4(+)EGFP(+) Treg were found to be 5-10 times more frequent than CD8(+)EGFP(+) Treg. RNAseq analysis provided insights into the transcriptome of CD8(+) Treg, allowing for a better understanding of their phenotype and function.
Article
Infectious Diseases
Maria Jose Brito, Pedro Sequeira, Iryna Silva, Ana Quintas, Catarina Martins, Ana Felix
Summary: This study analyzed cervical lymphocytic populations in HIV+ and HIV- patients, finding an imbalance between CD4(+) and CD8(+) T lymphocytes in HIV+ patients with SIL and SCC. The results showed increased CD8+ infiltrate density with lesion severity, even in patients with immune system recovery under antiretroviral therapy.
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2021)
Article
Immunology
Sebastiaan O. Verboeket, Ferdinand W. Wit, Eveline Verheij, Rosan A. van Zoest, Neeltje A. Kootstra, Marc van der Valk, Jan M. Prins, Maarten F. Schim van der Loeff, Peter Reiss
Summary: In this study, it was found that compared to men who only have sex with women, men who have sex with men have higher CD8(+) counts and lower CD4(+)/CD8(+) ratios, with these differences partly explained by higher CMV seroprevalence.
JOURNAL OF INFECTIOUS DISEASES
(2021)
Article
Biochemistry & Molecular Biology
Yashavanth S. Lakshmanappa, Jamin W. Roh, Niharika N. Rane, Ashok R. Dinasarapu, Daphne D. Tran, Vijayakumar Velu, Anandi N. Sheth, Igho Ofotokun, Rama R. Amara, Colleen F. Kelley, Elaine Waetjen, Smita S. Iyer
Summary: The study found that HIV preferentially infects alpha(4)beta(+)(7) CD4 T cells and enriches genes regulating cell cycle progression and cellular metabolism in the blood. Unlike their blood counterparts, rectal alpha(4)beta(+)(7) CD4 T cells exhibit a core tissue-residency gene expression program.
Article
Virology
Mark A. Pilkinton, Wyatt J. McDonnell, Louise Barnett, Abha Chopra, Rama Gangula, Katie D. White, Shay Leary, Jennifer Currenti, Silvana Gaudieri, Simon A. Mallal, Spyros A. Kalams
Summary: Cellular immune responses to Gag are associated with improved HIV control, with CD8(+) T cell response dominated by a few unique TCRs and CD4(+) T cell response displaying a more diverse TCR repertoire. Greater TCR diversity in CD4(+) T cells may limit HIV genetic diversity during chronic infection.
JOURNAL OF VIROLOGY
(2021)
Article
Biochemistry & Molecular Biology
Sherri L. L. Surman, Jeremy Crawford, Pradyot Dash, Susan L. L. Tonkonogy, Paul G. G. Thomas, Julia L. L. Hurwitz
Summary: The microbiome influences the formation of the T cell receptor repertoire, including its impact on immature thymocytes.
Article
Biology
Wei Wei, Yanjun Su
Summary: In this study, researchers used single cell sequencing technology to investigate T cells in non-small-cell lung cancer patients, identifying specific genes related to immune cell function and inferring the function of three types of T cells. The application of this technology helps to understand the mechanism of lung cancer occurrence and development, discover new diagnostic markers and therapeutic targets, and provide a theoretical reference for precise treatment of lung cancer patients in the future.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Medicine, Research & Experimental
Claire Lhuillier, Nils-Petter Rudqvist, Takahiro Yamazaki, Tuo Zhang, Maud Charpentier, Lorenzo Galluzzi, Noah Dephoure, Cristina C. Clement, Laura Santambrogio, Xi Kathy Zhou, Silvia C. Formenti, Sandra Demaria
Summary: Radiotherapy upregulates the expression of genes containing immunogenic mutations, enhancing the therapeutic efficacy of neoantigen vaccination by promoting the killing of tumor cells through CD8 and CD4 T cells. CD4 T cells produce Th1 cytokines to promote epitope spread, while utilizing radiation to enhance the ability of MHC molecules and death receptors on tumor cells.
JOURNAL OF CLINICAL INVESTIGATION
(2021)
Article
Cell Biology
Menglu Gao, Yili Liu, Mingquan Guo, Qianying Wang, Yan Wang, Jian Fan, Yinzhong Shen, Junjie Hou, Yanmin Wan, Zhaoqin Zhu
Summary: The study found that frequencies of lymphocytes and T cells decreased significantly in COVID-19 patients, while the CD4(+)/CD8(+)T cell ratios increased significantly in patients over 45 years old. Regulatory CD4(+) and CD8(+) T cells may play distinct roles in the pathogenesis of COVID-19, and NK cells might contribute to the lymphopenia associated with COVID-19.
JOURNAL OF LEUKOCYTE BIOLOGY
(2021)
Review
Biotechnology & Applied Microbiology
Eileen J. Murray, Serena B. Gumusoglu, Donna A. Santillan, Mark K. Santillan
Summary: Preeclampsia is a placental disorder characterized by hypertension, proteinuria, and oxidative stress. Immunomodulatory therapies show promise in preventing and treating preeclampsia.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Immunology
Elizabeth Robins, Ming Zheng, Qingshan Ni, Siqi Liu, Chen Liang, Baojun Zhang, Jian Guo, Yuan Zhuang, You-Wen He, Ping Zhu, Ying Wan, Qi-Jing Li
Summary: Recent research has revealed that CD4(+) and CD8(+) T cells in adaptive immunity can exhibit significant lineage plasticity, even undergoing fundamental lineage reprogramming. This shift in functional potential may suggest a new direction for HIV vaccine design.
CELLULAR & MOLECULAR IMMUNOLOGY
(2021)
Article
Genetics & Heredity
Delesa Damena, Francis E. Agamah, Peter O. Kimathi, Ntumba E. Kabongo, Hundaol Girma, Wonderful T. Choga, Lemu Golassa, Emile R. Chimusa
Summary: Recent GWAS studies identified several association variants with severe malaria, but much remains unknown about the biological functions. This study systematically predicted candidate genes and pathways involved in severe malaria resistance, revealing multiple genes enriched in pathogenic pathways and higher minor allele frequencies in endemic populations compared to global populations. These findings suggest the potential for new malaria therapeutics targeting multiple protective host molecular pathways.
FRONTIERS IN GENETICS
(2021)
Article
Neurosciences
Gabriella A. M. Blokland, Jakob Grove, Chia-Yen Chen, Chris Cotsapas, Stuart Tobet, Robert Handa, David St Clair, Todd Lencz, Bryan J. Mowry, Sathish Periyasamy, Murray J. Cairns, Paul A. Tooney, Jing Qin Wu, Brian Kelly, George Kirov, Patrick F. Sullivan, Aiden Corvin, Brien P. Riley, Tonu Esko, Lili Milani, Erik G. Jonsson, Aarno Palotie, Hannelore Ehrenreich, Martin Begemann, Agnes Steixner-Kumar, Pak C. Sham, Nakao Iwata, Daniel R. Weinberger, Pablo Gejman, Alan R. Sanders, Joseph D. Buxbaum, Dan Rujescu, Ina Giegling, Bettina Konte, Annette M. Hartmann, Elvira Bramon, Robin M. Murray, Michele T. Pato, Jimmy Lee, Ingrid Melle, Espen Molden, Roel A. Ophoff, Andrew McQuillin, Nicholas J. Bass, Rolf Adolfsson, Anil K. Malhotra, Nicholas G. Martin, Janice M. Fullerton, Philip B. Mitchell, Peter R. Schofield, Andreas J. Forstner, Franziska Degenhardt, Sabrina Schaupp, Ashley L. Comes, Manolis Kogevinas, Jose Guzman-Parra, Andreas Reif, Fabian Streit, Lea Sirignano, Sven Cichon, Maria Grigoroiu-Serbanescu, Joanna Hauser, Jolanta Lissowska, Fermin Mayoral, Bertram Muller-Myhsok, Thomas G. Schulze, Markus M. Nothen, Marcella Rietschel, John Kelsoe, Marion Leboyer, Stephane Jamain, Bruno Etain, Frank Bellivier, John B. Vincent, Martin Alda, Claire O'Donovan, Pablo Cervantes, Joanna M. Biernacka, Mark Frye, Susan L. McElroy, Laura J. Scott, Eli A. Stahl, Mikael Landen, Marian L. Hamshere, Olav B. Smeland, Srdjan Djurovic, Arne E. Vaaler, Ole A. Andreassen, Bernhard T. Baune, Tracy Air, Martin Preisig, Rudolf Uher, Douglas F. Levinson, Myrna M. Weissman, James B. Potash, Jianxin Shi, James A. Knowles, Roy H. Perlis, Susanne Lucae, Dorret Boomsma, Brenda W. J. H. Penninx, Jouke-Jan Hottenga, Eco J. C. de Geus, Gonneke Willemsen, Yuri Milaneschi, Henning Tiemeier, Hans J. Grabe, Alexander Teumer, Sandra Van der Auwera, Uwe Volker, Steven P. Hamilton, Patrik K. E. Magnusson, Alexander Viktorin, Divya Mehta, Niamh Mullins, Mark J. Adams, Gerome Breen, Andrew M. McIntosh, Cathryn M. Lewis, David M. Hougaard, Merete Nordentoft, Ole Mors, Preben B. Mortensen, Thomas Werge, Thomas D. Als, Anders D. Borglum, Tracey L. Petryshen, Jordan W. Smoller, Jill M. Goldstein
Summary: The study found significant sex-dependent genetic risk in schizophrenia, major depressive disorder, and bipolar disorder, with implications for genes related to neuronal development, immune functions, and vascular functions across and within these disorders. This suggests substantial genetic overlap between sexes in mood and psychotic disorders, with sex-specific effects enriched for genes involved in various physiological functions.
BIOLOGICAL PSYCHIATRY
(2022)
Article
Psychiatry
Antonio F. Pardinas, Sophie E. Smart, Isabella R. Willcocks, Peter A. Holmans, Charlotte A. Dennison, Amy J. Lynham, Sophie E. Legge, Bernhard T. Baune, Tim B. Bigdeli, Murray J. Cairns, Aiden Corvin, Ayman H. Fanous, Josef Frank, Brian Kelly, Andrew McQuillin, Ingrid Melle, Preben B. Mortensen, Bryan J. Mowry, Carlos N. Pato, Sathish Periyasamy, Marcella Rietschel, Dan Rujescu, Carmen Simonsen, David St Clair, Paul Tooney, Jing Qin Wu, Ole A. Andreassen, Kaarina Kowalec, Patrick F. Sullivan, Robin M. Murray, Michael J. Owen, James H. MacCabe, Michael C. O'Donovan, James T. R. Walters
Summary: This study examined the genetic architecture of treatment-resistant schizophrenia (TRS) by reassessing genetic data from schizophrenia studies and validating it in carefully ascertained clinical samples. The results showed that TRS is a polygenic trait with detectable heritability, and it is genetically correlated with traits related to intelligence and cognition. The study also found associations between TRS and a history of taking clozapine.
Article
Transplantation
Yingxin Lin, Armando Teixeira-Pinto, Helen Opdam, Jeremy R. Chapman, Jonathan C. Craig, Natasha Rogers, Henry Pleass, Christopher Davies, Stephen McDonald, Jean Yang, Wai Lim, Germaine Wong
Summary: This study analyzed the data of DCDD donors in Australia and found that donor kidney function and duration of warm ischemia are the key factors for the nonutilization of DCDD kidneys. Strategies to reduce the duration of warm ischemia and improve post-transplant recipient kidney function may reduce rates of nonutilization.
TRANSPLANTATION DIRECT
(2022)
Article
Oncology
Laveniya Satgunaseelan, Dario Strbenac, Cali Willet, Tracy Chew, Rosemarie Sadsad, James Wykes, Tsu-Hui Hubert Low, Wendy A. Cooper, C. Soon Lee, Carsten E. Palme, Jean Y. H. Yang, Jonathan R. Clark, Ruta Gupta
Summary: The prevalence of whole genome duplication (WGD) is high in young patients with oral squamous cell carcinoma (OSCC), and it is associated with adverse pathological characteristics and clinical outcomes. TP53 mutations also occur before WGD.
GENES CHROMOSOMES & CANCER
(2022)
Article
Health Care Sciences & Services
Kevin Y. X. Wang, Gulietta M. Pupo, Varsha Tembe, Ellis Patrick, Dario Strbenac, Sarah-Jane Schramm, John F. Thompson, Richard A. Scolyer, Samuel Muller, Garth Tarr, Graham J. Mann, Jean Y. H. Yang
Summary: In the era of precision medicine, molecular signatures from advanced omics technologies have the potential to guide clinical decisions. However, current approaches are often limited by location-specificity, which hampers the transferability of molecular signatures. To address this issue, the researchers developed a penalised regression model called Cross-Platform Omics Prediction (CPOP), which can predict patient outcomes in a platform-independent manner across time and experiments. CPOP improves upon traditional prediction frameworks by selecting ratio-based features with similar estimated effect sizes. The model demonstrated stable performance across datasets of similar biology, reducing the impact of technical noise generated by omics platforms. The researchers evaluated CPOP using melanoma transcriptomics data and showed its potential in a clinical screening framework for precision medicine. The model's generalization was further demonstrated with ovarian cancer and inflammatory bowel disease studies.
NPJ DIGITAL MEDICINE
(2022)
Article
Biochemical Research Methods
Yue Cao, Yingxin Lin, Ellis Patrick, Pengyi Yang, Jean Yee Hwa Yang
Summary: This study presents a method called scFeatures that creates interpretable cellular and molecular representations of single-cell and spatial data at the sample level. Summarizing a broad collection of features at the sample level is important for understanding disease mechanisms in different experimental studies and accurately classifying disease status of individuals.
Article
Hematology
Angelina J. Lay, Alexander Dupuy, Lejla Hagimola, Jessica Tieng, Mark Larance, Yunwei Zhang, Jean Yang, Yvonne Kong, Joyce Chiu, Emilia Gray, Zihao Qin, Diana Schmidt, Jessica Maclean, Benjamin Hofma, Marc Ellis, Maggie Kalev-Zylinska, Yair Argon, Shaun P. Jackson, Philip Hogg, Freda H. Passam
Summary: This study found that ERp5 plays a negative regulatory role in platelet ER stress response and highlights the importance of disulfide isomerases in platelet ER homeostasis. Furthermore, the study also revealed the close correlation between platelet ER stress and platelet secretion and thrombosis.
Article
Biochemical Research Methods
Jie Hao, Jiawei Zou, Jiaqiang Zhang, Ke Chen, Duojiao Wu, Wei Cao, Guoguo Shang, Jean Y. H. Yang, KongFatt Wong-Lin, Hourong Sun, Zhen Zhang, Xiangdong Wang, Wantao Chen, Xin Zou
Summary: Cell-state transition analysis using single-cell RNA-sequencing can reveal additional information in time-resolved biological phenomena. However, current methods are limited to short-term evolution of cell states based on gene expression derivative. This study presents scSTAR, a method that overcomes this limitation by constructing a paired-cell projection between different biological conditions with arbitrary time spans, leading to more accurate predictions and new discoveries in aging and cancer research.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Yue Cao, Shila Ghazanfar, Pengyi Yang, Jean Yang
Summary: The advancement of scRNA-seq technology has led to its increasing use in large-scale patient cohort studies. This study evaluates the impact of analytical choices on patient outcome prediction using scRNA-seq COVID-19 datasets. The study examines the difference between single-view and multi-view feature spaces, surveys multiple learning platforms, and compares integration approaches. The results highlight the power of ensemble learning, consistency among different learning methods, and the importance of dataset normalization.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biology
Xiaohang Fu, Ellis Patrick, Jean Y. H. Yang, David Dagan Feng, Jinman Kim
Summary: The spatial architecture and phenotypic heterogeneity of tumor cells are associated with cancer prognosis and outcomes. Imaging mass cytometry captures high-dimensional maps of disease-relevant biomarkers at single-cell resolution, which can inform patient-specific prognosis. However, existing methods for survival prediction do not utilize spatial phenotype information at the single-cell level, and there is a lack of end-to-end methods that integrate imaging data with clinical information for improved accuracy. We propose a deep multimodal graph-based network that considers spatial phenotype information and clinical variables to enhance survival prediction, and demonstrate its effectiveness in breast cancer datasets.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Microbiology
Xiangnan Xu, Michal Lubomski, Andrew J. Holmes, Carolyn M. Sue, Ryan L. Davis, Samuel Muller, Jean Y. H. Yang
Summary: The NEMoE model is proposed to analyze the relationship between gut microbiota and health state, taking into account diet-specific variations. Through simulation studies and real-world data analysis, the effectiveness of this approach is demonstrated, showing its potential in designing personalized intervention strategies.
Article
Biochemistry & Molecular Biology
Dantong Zhu, Stephen T. Vernon, Zac D'Agostino, Jingqin Wu, Corey Giles, Adam S. Chan, Katharine A. Kott, Michael P. Gray, Alireza Gholipour, Owen Tang, Habtamu B. Beyene, Ellis Patrick, Stuart M. Grieve, Peter J. Meikle, Gemma A. Figtree, Jean Y. H. Yang
Summary: The current CAD risk scores based on traditional risk factors often fail individuals. We aim to identify lipidomic biomarkers using non-invasive imaging technology and advanced lipidomic measurement to enable intervention before cardiovascular events.
Article
Urology & Nephrology
Yingxin Lin, Armando Teixeira-Pinto, Jonathan C. Craig, Helen Opdam, Jeremy C. Chapman, Henry Pleass, Angus Carter, Natasha M. Rogers, Christopher E. Davies, Stephen McDonald, Jean Yang, Wai H. Lim, Germaine Wong
Summary: The trajectory of blood pressure decline in kidneys donated after circulatory death can predict the risk of delayed graft function. The assessment of haemodynamic changes in donors during the agonal phase may be useful for determining donor suitability and post-transplant outcomes.
CLINICAL KIDNEY JOURNAL
(2023)
Article
Multidisciplinary Sciences
Yingxin Lin, Yue Cao, Elijah Willie, Ellis Patrick, Jean Y. H. Yang
Summary: The emergence of multi-sample multi-condition single-cell multi-cohort studies allows researchers to investigate different cell states. The algorithm scMerge2 enables integration and analysis of large-scale single-cell datasets, revealing accurate signatures of disease progression and removing dataset variability in various single-cell profiling technologies.
NATURE COMMUNICATIONS
(2023)
Review
Mathematical & Computational Biology
Daniel Kim, Andy Tran, Hani Jieun Kim, Yingxin Lin, Jean Yee Hwa Yang, Pengyi Yang
Summary: Inferring gene regulatory networks is crucial in biology, and recent advances in sequencing technology have led to the development of state-of-the-art methods that utilize single-cell multi-omic data for more comprehensive and precise network reconstruction.
NPJ SYSTEMS BIOLOGY AND APPLICATIONS
(2023)