Review
Genetics & Heredity
Jonathan Downing, Lloyd D'Orsogna
Summary: Killer immunoglobulin-like receptors (KIR) regulate natural killer cell function through interactions with ligands on cell surfaces. High-resolution determination of KIR allele variation has the potential to optimize clinical outcomes and provide deeper insights into receptor-ligand interactions. This review discusses recently published high-resolution KIR genotyping methods and their application in transplantation and infectious disease control.
Article
Biochemistry & Molecular Biology
Li Song, Gali Bai, X. Shirley Liu, Bo Li, Heng Li
Summary: Killer cell immunoglobulin like receptor (KIR) genes and human leukocyte antigen (HLA) genes are crucial in innate and adaptive immunity, but their genotyping is challenging due to high polymorphism and similarity among genes. Existing tools for HLA genotyping do not work for KIR genes, and specialized KIR genotypers can't resolve all KIR genes either. T1K is a new computational method that accurately infers KIR and HLA alleles from various sequencing data and can identify challenging homologous genes.
Article
Biochemical Research Methods
Jian Yi, Longyun Chen, Yajie Xiao, Zhikun Zhao, Xiaofan Su
Summary: HLA typing is crucial for cancer immunotherapy, and this study found that OptiType demonstrated the highest accuracy in HLA-Ia typing from WES data, potentially providing a superior performance for its clinical application.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Medicine, General & Internal
Vlad Andrei Cianga, Cristina Rusu, Mariana Pavel-Tanasa, Angela Dascalescu, Catalin Danaila, Sebastian Harnau, Carmen-Mariana Aanei, Petru Cianga
Summary: NK cell phenotypes and functions are diverse in AML patients, with lower NK cell counts and maturity but increased hypermature NK cells. Differences in KIR and HLA-C genotypes, as well as inhibitory receptor expressions, are observed in AML. Flow cytometry provides detailed information for evaluating NK cell numbers and phenotypes in AML patients.
FRONTIERS IN MEDICINE
(2023)
Article
Cell Biology
Laia Closa, Francisco Vidal, Maria J. Herrero, Jose L. Caro
Summary: This study analyzed the allele frequencies of HLA-G, HLA-F, MICA, and MICB genes in a population of blood donors in Catalonia, Spain using high-throughput next generation sequencing. The most frequent alleles were identified for each gene, providing important information for further research on the functional role of these genes in different populations and diseases. Strong linkage disequilibrium was observed between MICA and HLA-B, indicating potential genetic associations between these genes.
Article
Genetics & Heredity
Lisanne E. N. Manson, Sander J. Delwig, Jos J. M. Drabbels, Daan J. Touw, Aiko P. J. De Vries, Dave L. Roelen, Henk-Jan Guchelaar
Summary: This study investigates the feasibility and potential impact of repurposing HLA genotype data from kidney transplant patients to prevent drug hypersensitivity reactions.
FRONTIERS IN GENETICS
(2023)
Article
Immunology
Karolina Piekarska, Pawel Radwan, Agnieszka Tarnowska, Andrzej Wisniewski, Michal Radwan, Jacek R. Wilczynski, Andrzej Malinowski, Izabela Nowak
Summary: During early pregnancy, maternal uterine natural killer (NK) cells play a key role in regulating the immune response, with ERAP1 and ERAP2 influencing the HLA class I immunopeptidome formation. This study explores the associations between ERAP1 and ERAP2 polymorphisms, KIR, and HLA-C genes in recurrent implantation failure (RIF), revealing potential impacts of certain ERAP polymorphisms on RIF susceptibility in HLA-C2-positive patients. Moreover, differences in ERAP secretion levels between fertile women and those experiencing IVF procedures suggest potential implications of ERAP1 and ERAP2 in reproductive processes.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Immunology
Sudan Tao, Yanmin He, Katherine M. Kichula, Jielin Wang, Ji He, Paul J. Norman, Faming Zhu
Summary: This study provides a detailed analysis of highly polymorphic KIR and HLA class I genes in Zhejiang Han individuals, highlighting the high frequency of KIR-A haplotypes and C1 KIR ligands in this population. The Zhejiang Han exhibit a greater diversity of inhibitory KIR compared to activating KIR, with numerous centromeric and telomeric haplotypes, as well as some haplotypes containing large-scale duplications or deletions. Additionally, a unique truncated haplotype containing only KIR2DL4 was identified, along with a high frequency of HLA-B*46:01, possibly due to selection pressure from infectious diseases.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Veterinary Sciences
Victor Neira, Cristian Melgarejo, Constanza Urzua-Encina, Felipe Berrios, Valentina Valdes, Sunil Mor, Barbara Brito-Rodriguez, Galia Andrea Ramirez-Toloza
Summary: This study identified and characterized RVA in swine farms in Chile, revealing a high prevalence and genetic evolution of the virus. The results highlight the potential zoonotic nature of RVA circulating in Chilean swine farms.
FRONTIERS IN VETERINARY SCIENCE
(2023)
Article
Immunology
Elena Muraro, Mariangela De Zorzi, Gianmaria Miolo, Davide Lombardi, Simona Scalone, Simon Spazzapan, Samuele Massarut, Tiziana Perin, Riccardo Dolcetti, Agostino Steffan, Valli De Re
Summary: This study investigates the impact of host immune genetics on the response to trastuzumab treatment in HER2-positive breast cancer patients. The results suggest that patients with KIR haplotype tel B have higher ADCC efficiency, while the presence of KIR3DL2/HLA-A03 or A11 is associated with poorer prognosis.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Medicine, Research & Experimental
Yan Zhang, Ada W. C. Yan, Lies Boelen, Linda Hadcocks, Arafa Salam, Daniel Padrosa Gispert, Loiza Spanos, Laura Mora Bitria, Neda Nemat-Gorgani, James A. Traherne, Chrissy Roberts, Danai Koftori, Graham P. Taylor, Daniel Forton, Paul J. Norman, Steven G. E. Marsh, Robert Busch, Derek C. Macallan, Becca Asquith
Summary: Inhibitory killer cell immunoglobulin-like receptors (iKIRs) can modulate T cell responses and affect T cell lifespan. The iKIR-ligand genotype is significantly associated with CD8+ T cell lifespan, with individuals having 4 iKIR-ligand gene pairs having double the lifespan compared to individuals with 2 gene pairs. The iKIR-ligand genotype also alters the immune aging phenotype of CD8+ and CD4+ T cells.
JOURNAL OF CLINICAL INVESTIGATION
(2023)
Article
Immunology
Benjamin D. Solomon, Hong Zheng, Laura W. Dillon, Jason D. Goldman, Christopher S. Hourigan, James R. Heath, Purvesh Khatri
Summary: The human leukocyte antigen (HLA) locus is important for adaptive immune function and clinical applications. This study evaluates computational tools for predicting HLA genotypes using single-cell data and compares them to gold-standard genotyping.
FRONTIERS IN IMMUNOLOGY
(2023)
Review
Immunology
Marina Alexandrova, Diana Manchorova, Tanya Dimova
Summary: Both KIR and HLA are highly variable gene families in the human genome, and play crucial roles in placental development. The interaction between trophoblast cells and maternal immune cells, mediated by KIR-HLA interactions, is essential for the establishment of functional placenta. This review summarizes the recognition of KIR/HLA-C (allo) by decidual NK cells during early human pregnancy and discusses its role in pregnancy disorders and transplacental infections.
IMMUNOLOGICAL REVIEWS
(2022)
Editorial Material
Cell Biology
Maria Loginova, Daria Smirnova, Igor Paramonov
Summary: Next-generation sequencing identified three novel alleles in the Russian population.
Article
Cell Biology
Maria Loginova, Svetlana Druzhinina, Igor Paramonov
Summary: Three novel HLA-DRB1 alleles, HLA-DRB1*07:150, HLA-DRB1*13:345 and HLA-DRB1*14:256, were identified.
Article
Surgery
Evan P. Kransdorf, Marcelo J. Pando, Darren Stewart, Kelsi Lindblad, Robert Bray, Cathi Murphey, Navchetan Kaur, Jignesh K. Patel, Irene Kim, Xiaohai Zhang, Martin Maiers, Jon A. Kobashigawa, Loren Gragert
Summary: The study found that HLA data derived from stem cell donors can generate CPRA values comparable to those from deceased kidney donors, improving upon issues with the current reference panel and enhancing equity in kidney transplant allocation.
AMERICAN JOURNAL OF TRANSPLANTATION
(2021)
Article
Immunology
David Roe, Jonathan Williams, Keyton Ivery, Jenny Brouckaert, Nick Downey, Chad Locklear, Rui Kuang, Martin Maiers
FRONTIERS IN IMMUNOLOGY
(2020)
Article
Immunology
Ray Sajulga, Abeer Madbouly, Stephanie Fingerson, Loren Gragert, Pradeep Bashyal, Yung-Tsi Bolon, Martin Maiers
Summary: This study introduces a DPB1 Prediction Service to improve donor selection in hematopoietic cell transplantation. By leveraging seven-locus haplotype frequencies, the service can accurately predict HLA-DPB1 genotypes and increase donor-recipient match probabilities. Validation using large sample sizes demonstrates the accuracy and utility of this prediction framework, especially for populations of color.
Article
Biotechnology & Applied Microbiology
Nicolas Cardozo, Karen Zhang, Kathryn Doroschak, Aerilynn Nguyen, Zoheb Siddiqui, Nicholas Bogard, Karin Strauss, Luis Ceze, Jeff Nivala
Summary: Detection of specific proteins using nanopores is currently challenging, but the development of NTERs as protein tags has enabled simultaneous detection of up to nine reporter proteins in bacterial or human cells. This multiplexed detection is achieved through the use of protein barcodes measured with nanopores.
NATURE BIOTECHNOLOGY
(2022)
Article
Immunology
Sapir Israeli, Loren Gragert, Martin Maiers, Yoram Louzoun
Summary: A novel multi-region EM implementation that integrates HLA information from different population groups has been developed, showing higher likelihood values and better haplotype recovery than other EM implementations when tested on real and simulated datasets. This approach addresses the need for improved HLA imputation and matching for multi-region populations.
Article
Cell Biology
Kazutoyo Osoegawa, Steven G. E. Marsh, Rhonda Holdsworth, Sebastiaan Heidt, Gottfried Fischer, Cathi Murphey, Martin Maiers, Marcelo A. Fernandez Vina
Summary: HLA serological specificities were defined by the reactivity of HLA molecules with sets of sera and monoclonal antibodies. Many recently identified alleles defined by molecular typing lack their serotype assignment. The correlation between the reactivity of serologic reagents and AA residues was studied, and specific epitopes were identified for different HLA loci. Automated serotype assignments to HLA alleles were developed using HATS software, and additional DEP patterns were identified that do not correspond to any known serologic specificities.
Article
Cell Biology
Zuriya Ansbacher-Feldman, Sapir Israeli, Martin Maiers, Loren Gragert, Dianne De Santis, Moshe Israeli, Yoram Louzoun
Summary: Recently, haplo-identical transplantation with multiple HLA mismatches has become a viable option for stem cell transplants. The detection of haplotype sharing requires the imputation of donor and recipient, which can have errors in high-resolution typing. The proposed graph-based family imputation (GRAMM) method has shown high accuracy in phasing alleles and improving allele imputation accuracy.
Article
Cell Biology
Steven J. Mack, Daniel Schefzyk, Robert P. Millius, Martin Maiers, Jill A. Hollenbach, Jane Pollack, Michael L. Heuer, Loren Gragert, Stephen R. Spellman, Lisbeth A. Guethlein, Joel Schneider, Werner Bochtler, Hans-Peter Eberhard, James Robinson, Steven G. E. Marsh, Alexander H. Schmidt, Jan A. Hofmann, Juergen Sauter
Summary: The Genotype List (GL) String grammar was introduced in 2013 for reporting HLA and KIR genotypes in a text string. Over the past decade, with advancements in genotyping technologies, an extension of the GL String system was needed. The new GL String delimiter ?, introduced in version 1.1, addresses the need to describe ambiguity in gene sequence assignment.
Article
Hematology
Ray Sajulga, Yung-Tsi Bolon, Martin J. Maiers, Effie Peterdori
Summary: HLA-DP is a transplant antigen that plays a role in alloreactivity. This study analyzed the relationship between T-cell epitope diversity and expression levels in HLA-DP and studied the donor search lists for patients undergoing transplantation. The findings highlight the importance of considering both TCE and expression criteria in the selection of candidate donors.
Article
Cell Biology
Steven J. J. Mack, Jurgen Sauter, James Robinson, Kazutoyo Osoegawa, Lloyd McKenzie, Joel Schneider, Martin Maiers, Robert P. P. Milius
Summary: The nomenclatures used to describe HLA and KIR alleles are insufficient for genotyping results as they require terminology beyond allele names. The GL String grammar describes genotyping results, but its accuracy depends on the reference database version. The GL String code (GLSC) system associates each GL String with specific reference context metadata for accurate interpretation of genotyping results.
Article
Hematology
Loren Gragert, Stephen R. Spellman, Bronwen E. Shaw, Martin Maiers
Summary: Matching the HLA at the DPB1 locus between donor and recipient improves the outcomes of hematopoietic stem cell transplantation. Through a DPB1-permissive mismatch model based on T cell epitope reactivity, it is possible to expand the pool of suitable donors. Our models show that the likelihood of finding a DPB1-permissive donor is not significantly lower than the likelihood of an 8/8 match, and only a small number of additional donors need to be typed to find an optimal DPB1-permissive donor. The presence of linkage disequilibrium patterns between the DPB1 locus and other HLA loci suggests that DPB1-permissive donors are easier to identify within minority populations.
TRANSPLANTATION AND CELLULAR THERAPY
(2023)
Article
Oncology
Brent R. Logan, Martin J. Maiers, Rodney A. Sparapani, Purushottam W. Laud, Stephen R. Spellman, Robert E. McCulloch, Bronwen E. Shaw
Summary: The study confirmed the importance of selecting the youngest available MUD for HCT, regardless of patient features. Age was the only donor feature that affected outcomes consistently. By choosing a younger MUD, there is potential for improvement in transplant outcomes.
JCO CLINICAL CANCER INFORMATICS
(2021)
Article
Multidisciplinary Sciences
Richard M. Single, Diogo Meyer, Kelly Nunes, Rodrigo Santos Francisco, Tabita Hunemeier, Martin Maiers, Carolyn K. Hurley, Gabriel Bedoya, Carla Gallo, Ana Magdalena Hurtado, Elena Llop, Maria Luiza Petzl-Erler, Giovanni Poletti, Francisco Rothhammer, Luiza Tsuneto, William Klitz, Andres Ruiz-Linares