Article
Cell Biology
Tanushree Dangi, Sarah Sanchez, Min Han Lew, Bakare Awakoaiye, Lavanya Visvabharathy, Justin M. Richner, Igor J. Koralnik, Pablo Penaloza-MacMaster
Summary: mRNA vaccines are effective in preventing severe COVID-19, but breakthrough infections, emerging variants, and waning immunity warrant the use of boosters. The extent to which pre-existing immunity influences the efficacy of boosters remains unclear.
Article
Immunology
Tonny J. Owalla, Dianna E. B. Hergott, Annette M. Seilie, Weston Staubus, Chris Chavtur, Ming Chang, James G. Kublin, Thomas G. Egwang, Sean C. Murphy
Summary: Pre-existing and intervening low-density Plasmodium infections have a complex impact on malaria clinical trials. They pose challenges to infection detection endpoints and vaccine-induced immune responses. This paper discusses the implications of these infections on malaria vaccine trials and the methods used to detect them.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Immunology
Josephine R. Giles, Sasikanth Manne, Elizabeth Freilich, Derek A. Oldridge, Amy E. Baxter, Sangeeth George, Zeyu Chen, Hua Huang, Lakshmi Chilukuri, Mary Carberry, Lydia Giles, Nan-Ping P. Weng, Regina M. Young, Carl H. June, Lynn M. Schuchter, Ravi K. Amaravadi, Xiaowei Xu, Giorgos C. Karakousis, Tara C. Mitchell, Alexander C. Huang, Junwei Shi, E. John Wherry
Summary: This study generated an epigenetic and transcriptional atlas of T cell differentiation from healthy humans and applied it to explore disease-specific biology. The study identified molecular regulations of gene expression and chromatin accessibility during T cell differentiation and provided insights into disease biology through three research settings. The study also successfully predicted genome-wide cis-regulatory elements and validated the approach for functional annotation of key effector genes, demonstrating the potential of identifying targets for non-coding cellular engineering.
Article
Virology
Blake Schouest, Alba Grifoni, John Pham, Jose Mateus, John Sydney, James D. Brien, Aruna D. De Silva, Angel Balmaseda, Eva Harris, Alessandro Sette, Daniela Weiskopf
Summary: This study identified ZIKV T cell epitopes in individuals unexposed to ZIKV but living in regions endemic to DENV, confirming the impact of preexisting DENV immunity on ZIKV infection. It also found that cross-reactive T cell populations can be expanded by stimulation with ZIKV peptides, providing insights for understanding natural immunity patterns and developing diagnostic tests and vaccines.
JOURNAL OF VIROLOGY
(2021)
Article
Oncology
Juan A. Hernandez-Aceves, Jacquelynne Cervantes-Torres, Diana Torres-Garcia, Francisco J. Zuniga-Flores, Osiris J. Patino-Chavez, Jorge A. Pena Agudelo, Jose Eduardo Aguayo-Flores, Yonathan Garfias, Laura Montero-Leon, Laura Romero-Romero, Armando Perez-Torres, Gladis Fragoso, Edda Sciutto
Summary: GK-1 has shown anti-tumor and anti-metastatic effects in an experimental model of breast cancer. It can decrease tumor growth, lung and lymph node metastases, and intra-tumor vascular areas. Furthermore, GK-1 prevents T cell exhaustion, enhances cytotoxic activity, and improves the prognosis of triple-negative breast cancer.
CANCER IMMUNOLOGY IMMUNOTHERAPY
(2023)
Article
Immunology
Larissa Henze, Julian Braun, Lil Meyer-Arndt, Karsten Juerchott, Maike Schlotz, Janine Michel, Marica Grossegesse, Maike Mangold, Manuela Dingeldey, Beate Kruse, Pavlo Holenya, Norbert Mages, Ulf Reimer, Maren Eckey, Karsten Schnatbaum, Holger Wenschuh, Bernd Timmermann, Florian Klein, Andreas Nitsche, Claudia Giesecke-Thiel, Lucie Loyal, Andreas Thiel
Summary: Currently available COVID-19 vaccines include inactivated virus, live attenuated virus, mRNA-based, viral vectored and adjuvanted protein-subunit-based vaccines. All of them contain the spike glycoprotein as the main immunogen and result in reduced disease severity upon SARS-CoV-2 infection. However, the effect of vector vaccines in reactivating pre-existing, cross-reactive immunity is still uncertain.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Microbiology
Torben Knuschke, Sebastian Kollenda, Christina Wenzek, Gennadiy Zelinskyy, Philine Steinbach, Ulf Dittmer, Jan Buer, Matthias Epple, Astrid M. Westendorf
Summary: The study demonstrated that therapeutic vaccination with nanoparticles in combination with PD-L1 blockade enhanced virus-specific CD8(+) T cell responses, leading to improved viral clearance during chronic infection. The combination therapy activated CD8(+) T cells, generated new effector cells, and enhanced virus control.
Article
Immunology
Sam M. M. Murray, Azim M. M. Ansari, John Frater, Paul Klenerman, Susanna Dunachie, Eleanor Barnes, Ane Ogbe
Summary: Several studies have reported pre-existing cross-reactive immune responses to SARS-CoV-2 proteins in individuals who have not been infected. The high homology between SARS-CoV-2 and common cold coronaviruses is believed to be a likely source of this cross-reactivity. However, the impact of these cross-reactive responses on the outcome of SARS-CoV-2 infection and vaccination is still uncertain. This review examines the evidence regarding the influence of pre-existing humoral and T cell immune responses on the outcomes of SARS-CoV-2 infection and vaccination, and discusses the importance of conserved coronavirus epitopes for the development of pan-coronavirus vaccines and the potential cross-reactivity of immune responses to ancestral SARS-CoV-2 and SARS-CoV-2 variants in the context of COVID-19 vaccination.
NATURE REVIEWS IMMUNOLOGY
(2023)
Article
Multidisciplinary Sciences
Leo Swadling, Mariana O. Diniz, Nathalie M. Schmidt, Oliver E. Amin, Aneesh Chandran, Emily Shaw, Corinna Pade, Joseph M. Gibbons, Nina Le Bert, Anthony T. Tan, Anna Jeffery-Smith, Cedric C. S. Tan, Christine Y. L. Tham, Stephanie Kucykowicz, Gloryanne Aidoo-Micah, Joshua Rosenheim, Jessica Davies, Marina Johnson, Melanie P. Jensen, George Joy, Laura E. McCoy, Ana M. Valdes, Benjamin M. Chain, David Goldblatt, Daniel M. Altmann, Rosemary J. Boyton, Charlotte Manisty, Thomas A. Treibel, James C. Moon, Lucy van Dorp, Francois Balloux, Aine McKnight, Mahdad Noursadeghi, Antonio Bertoletti, Mala K. Maini
Summary: Research suggests that some individuals can clear potential SARS-CoV-2 infection after exposure, with T cells playing a role in the process. Studying healthcare workers who tested negative for antibodies revealed that they had stronger and more diverse memory T cells, with a focus on RTC.
Article
Immunology
Jiaqi Hu, Chongyin Han, Jiayuan Zhong, Huisheng Liu, Rui Liu, Wei Luo, Pei Chen, Fei Ling
Summary: The study identified CCT6A as a biomarker for pre-exhausted T-cell subpopulation in CRC, while TUBA1B acts as core genes contributing to CD8(+) T cell exhaustion. Additionally, cellular communication between terminally differentiated exhausted T cells and pre-exhausted T cells contributes to exhaustion.
FRONTIERS IN IMMUNOLOGY
(2021)
Review
Immunology
Kehong Zheng, Xiaojun Zheng, Wei Yang
Summary: T-cell exhaustion, caused by metabolic dysfunction, impairs the ability of T cells to eliminate pathogens during chronic viral infections.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Immunology
Alessio Bevilacqua, Zhiyu Li, Ping-Chih Ho
Summary: This article reviews how metabolism affects the differentiation and function of CD8(+) T cells, as well as the principal metabolic dysregulation that leads to the exhausted phenotype. The article also summarizes recent strategies to reprogram impaired metabolic pathways to promote CD8(+) T cell effector function and survival.
EUROPEAN JOURNAL OF IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Natalia Ortega, Marta Ribes, Marta Vidal, Rocio Rubio, Ruth Aguilar, Sarah Williams, Diana Barrios, Selena Alonso, Pablo Hernandez-Luis, Robert A. Mitchell, Chenjerai Jairoce, Angeline Cruz, Alfons Jimenez, Rebeca Santano, Susana Mendez, Montserrat Lamoglia, Neus Rosell, Anna Llupia, Laura Puyol, Jordi Chi, Natalia Rodrigo Melero, Daniel Parras, Pau Serra, Edwards Pradenas, Benjamin Trinite, Julia Blanco, Alfredo Mayor, Sonia Barroso, Pilar Varela, Anna Vilella, Antoni Trilla, Pere Santamaria, Carlo Carolis, Marta Tortajada, Luis Izquierdo, Ana Angulo, Pablo Engel, Alberto L. Garcia-Basteiro, Gemma Moncunill, Carlota Dobano
Summary: Long-term kinetics of antibodies to SARS-CoV-2 were examined in a cohort of health care workers, showing stable levels over time with an increase in anti-spike antibody levels around 150 days post-symptom onset. Additionally, asymptomatic individuals had significantly higher levels of IgG and IgA to HCoV compared to symptomatic individuals, suggesting a potential protective effect of pre-existing cross-reactive HCoVs antibodies against SARS-CoV-2 infection and COVID-19 disease.
NATURE COMMUNICATIONS
(2021)
Article
Oncology
Emanuelle A. Paixao, Luciana R. C. Barros, Artur C. Fassoni, Regina C. Almeida
Summary: The study presents the first mathematical model to describe the multiphasic treatment response in CAR-T cell kinetics, considering the dynamics of CAR-T and tumor cells. The model provides insights into the diverse dynamics of CAR-T cells in different patients and hematological cancers, and suggests potential markers for therapy classification.
Article
Oncology
Yue Liu, Kai Fu, Eric M. Wier, Yifan Lei, Andrea Hodgson, Dongqing Xu, Xue Xia, Dandan Zheng, Hua Ding, Cynthia L. Sears, Jian Yang, Fengyi Wan
Summary: This study identified a novel genotoxin called UshA in attaching/effacing pathogens, which triggers DNA damage and initiates tumorigenic transformation during bacterial infections. Furthermore, it was found that UshA plays a critical role in accelerating colon tumorigenesis in mice. These findings highlight the importance of UshA in the development of colon cancer caused by bacterial infections.
Review
Cell Biology
Alton B. Farris, Juan Vizcarra, Mohamed Amgad, Lee A. D. Cooper, David Gutman, Julien Hogan
Summary: Whole slide imaging (WSI) is an important technique in digital pathology, leading to increased interest in image analysis (IA) techniques, including artificial intelligence (AI) and hypothesis-driven algorithms. Renal pathology, particularly in renal transplant pathology, has seen a rise in research using AI/machine learning for identification of features such as glomeruli. Deep learning methods like artificial neural networks (ANNs)/ convolutional neural networks (CNNs) are commonly employed for analyzing 'big data' in pathology WSIs.
Article
Immunology
S. Thera Lee, Hristo Georgiev, Elise R. Breed, Roland Ruscher, Kristin A. Hogquist
Summary: CD8 α α intestinal intraepithelial lymphocytes (IEL) mainly originate from thymic precursors, with development inhibited by CD80 and CD86, and conventional DCs playing a significant role. Thymic hematopoietic APC show heterogeneity in expression, but exhibit functional redundancy, with no specialized APC subset promoting the CD8 α α IEL fate.
EUROPEAN JOURNAL OF IMMUNOLOGY
(2021)
Editorial Material
Urology & Nephrology
AnnaLisa V. Wilson, Francesca Costigliolo, Alton B. Farris, Rohan Rengen, Lois J. Arend
KIDNEY INTERNATIONAL REPORTS
(2021)
Article
Urology & Nephrology
Alton Brad Farris, Juan Vizcarra, Mohamed Amgad, Lee Alex Donald Cooper, David Gutman, Julien Hogan
Summary: Digital pathology technology allows for automatic detection of glomeruli and selection of cortical regions of interest in kidney allograft biopsy specimens. The automatic fibrosis quantification was moderately correlated with pathologists' assessment, but not significantly associated with eGFR or allograft survival. This pipeline provides a promising method for developing and applying image analysis algorithms in kidney pathology.
KIDNEY INTERNATIONAL REPORTS
(2021)
Article
Oncology
Ivan Borozan, Syed H. Zaidi, Tabitha A. Harrison, Amanda Phipps, Jiayin Zheng, Stephen Lee, Quang M. Trinh, Robert S. Steinfelder, Jeremy Adams, Barbara L. Banbury, Sonja Berndt, Stefanie Brezina, Daniel D. Buchanan, Susan Bullman, Yin Cao, Alton B. Farris, Jane C. Figueiredo, Marios Giannakis, Lawrence E. Heisler, John L. Hopper, Yi Lin, Xuemei Luo, Reiko Nishihara, Elaine R. Mardis, Nickolas Papadopoulos, Conghui Qu, Emma E. G. Reid, Stephen N. Thibodeau, Sophia Harlid, Caroline Y. Um, Li Hsu, Andrea Gsur, Peter T. Campbell, Steven Gallinger, Polly A. Newcomb, Shuji Ogino, Wei Sun, Thomas J. Hudson, Vincent Ferretti, Ulrike Peters
Summary: This study found an association between F. nucleatum and its subspecies animalis with tumor characteristics and colorectal cancer-specific survival. The presence of F. nucleatum, particularly subspecies animalis, was associated with a higher colorectal cancer-specific mortality and specific somatic mutated genes.
CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION
(2022)
Article
Infectious Diseases
Danielle Steed, Jeffrey Collins, Alton B. Farris, Jeannette Guarner, Dilek Yarar, Rachel Friedman-Moraco, Tristan Doane, Stephanie Pouch, G. Marshall Lyon, Michael H. Woodworth
Summary: This article reports a case of bacillary peliosis hepatis and secondary haemophagocytic lymphohistiocytosis in a kidney-transplant recipient with controlled HIV. The patient presented with fever and abdominal pain for two weeks and was found to have hepatomegaly. Laboratory evaluation showed pancytopenia and cholestatic injury. Treatment resulted in excellent clinical response.
LANCET INFECTIOUS DISEASES
(2022)
Article
Immunology
Elise R. Breed, Matous Voboril, Katherine M. Ashby, Ryan J. Martinez, Lily Qian, Haiguang Wang, Oscar C. Salgado, Christine H. O'Connor, Kristin A. Hogquist
Summary: Researchers have identified a subset of thymic dendritic cells that express CD301b and contribute to thymic tolerance. These cells have enhanced antigen processing and presentation, and their activation is induced by type II cytokines. Selective deletion of these cells impairs conventional T cell deletion in the thymus without affecting regulatory T cell selection. These findings highlight the importance of cytokine-induced activation of dendritic cells in central tolerance.
Article
Pathology
Ayse Armutlu, Brian Quigley, Hegyong Choi, Olca Basturk, Gizem Akkas, Burcin Pehlivanoglu, Bahar Memis, Kee-Taek Jang, Mert Erkan, Burcu Erkan, Serdar Balci, Burcu Saka, Pelin Bagci, Alton B. Farris, David A. Kooby, Diego Martin, Bobby Kalb, Shishir K. Maithel, Juan Sarmiento, Michelle D. Reid, N. Volkan Adsay
Summary: The classification of liver cysts is highly conflicting due to definitional variations. Pathological evaluation revealed that most cysts were related to ductal plate malformation, neoplastic conditions, infectious/inflammatory factors, or congenital factors. Liver cysts are more common in women and the majority of them are non-neoplastic.
AMERICAN JOURNAL OF SURGICAL PATHOLOGY
(2022)
Article
Biology
Qiang Li, Fusheng Wang, Yaobing Chen, Hao Chen, Shengdi Wu, Alton B. Farris, Yi Jiang, Jun Kong
Summary: This study constructs a virtual liver tissue volume and develops a virtual needle biopsy sampling method to quantify the sampling bias in liver needle biopsies. The results show significant sampling errors and a correlation between collagen proportionate area and fibrosis stages. This method can be applied to other diseases where needle biopsy sampling bias affects diagnostic results.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Biology
Hanyi Yu, Nima Sharifai, Kun Jiang, Fusheng Wang, George Teodoro, Alton B. Farris, Jun Kong
Summary: Liver fibrosis staging is clinically important for predicting liver disease progression. A new deep learning model called MUSA-UNet has been developed to accurately segment liver portal tract regions in whole-slide images of liver tissue biopsies, which shows promising potential for computational liver disease diagnosis.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Multidisciplinary Sciences
Miriam Manook, Danae Olaso, Imran J. Anwar, Janghoon Yoon, Isabel Delaura, Yeeun Bae, Dimitrios Moris, Brian Shaw, Mingqing Song, Alton B. Farris, Annette Jackson, Jean Kwun, Stuart Knechtle
Summary: This study examined the effectiveness of costimulation blockade and proteasome inhibition for desensitization in female NHPs sensitized by pregnancy alone. The results showed that the addition of belatacept and tacrolimus significantly prolonged graft survival and suppressed the production of donor-specific antibodies.
Meeting Abstract
Immunology
Ryan J. Martinez, Elise Breed, Yosan Worota, Katherine Ashby, Lily Qian, Kristin Ann Hogquist
JOURNAL OF IMMUNOLOGY
(2022)
Meeting Abstract
Pathology
Shu Kwun Lui, Zaid Mahdi, Shelley Caltharp, Jason Wang, Cynthia Cohen, Alton B. Brad Farris
Article
Gastroenterology & Hepatology
Francesca Cingolani, Yunshan Liu, Yang Shen, Jing Wen, Alton B. Farris, Mark J. Czaja
Summary: Activation of ERK1/2 promotes hepatocyte proliferation in response to growth stimuli, with constitutive ERK1/2 signaling playing a critical role in maintaining normal liver homeostasis. Double-knockout of ERK1/2 in mice leads to hepatomegaly, hepatitis, and liver injury, with bile acid synthesis up-regulation being a key mechanism. Inhibition of bile acids prevents liver injury, highlighting the essential physiological function of ERK1/2 in regulating hepatic bile acid synthesis.
HEPATOLOGY COMMUNICATIONS
(2022)
Article
Urology & Nephrology
Federica Genovese, Ahmad Akhgar, Sung Sam Lim, Alton B. Farris, Monica Battle, Jason Cobb, Dominic Sinibaldi, Morten A. Karsdal, Wendy White
Summary: The study confirmed the association of novel extracellular matrix remodeling biomarkers with kidney disease activity and fibrosis in patients with LN, but they were not able to effectively differentiate between patients with LN and those with SLE, as well as other control groups.