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Mikhail Pomaznoy

Mikhail Pomaznoy
Novel-Soft

About

25
Publications
5,271
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469
Citations
Citations since 2017
19 Research Items
449 Citations
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2017201820192020202120222023020406080100120140
2017201820192020202120222023020406080100120140

Publications

Publications (25)
Article
Full-text available
Recent technological advances have made the gathering of comprehensive gene expression datasets a commodity. This has shifted the limiting step of transcriptomic studies from the accumulation of data to their analyses and interpretation. The main problem in analyzing transcriptomics data is that the number of independent samples is typically much l...
Article
Full-text available
Upon Ag encounter, T cells can rapidly divide and form an effector population, which plays an important role in fighting acute infections. In humans, little is known about the molecular markers that distinguish such effector cells from other T cell populations. To address this, we investigated the molecular profile of T cells present in individuals...
Article
Full-text available
The increased incidence of whooping cough worldwide suggests that current vaccination against Bordetella pertussis infection has limitations in quality and duration of protection. The resurgence of infection has been linked to the introduction of acellular vaccines (aP) which has an improved safety profile compared to the previously used whole-cell...
Article
CD8 T cells are considered important contributors to the immune response against Mycobacterium tuberculosis, yet limited information is currently known regarding their specific immune signature and phenotype. In this study, we applied a cell population transcriptomics strategy to define immune signatures of human latent tuberculosis infection (LTBI...
Preprint
Full-text available
Whole-cell inactivated vaccine against Bordetella pertussis (wP) was substituted in many countries by an acellular subunit vaccine (aP) to reduce side effects. Recent epidemiological studies have shown that aP vaccination in infancy induces less durable immunity than wP vaccination. To determine immunological differences associated with aP vs. wP p...
Article
Full-text available
Our recent work has highlighted that care needs to be taken when interpreting single cell data originating from flow cytometry acquisition or cell sorting: We found that doublets of T cells bound to other immune cells are often present in the live singlet gate of human peripheral blood samples acquired by flow cytometry. This hidden “contamination”...
Article
Our recent work highlights that care needs to be taken when interpreting single-cell data originating from flow cytometry acquisition or cell sorting: We found that doublets involving T cells bound to another immune cell are indeed very often present in the live singlet gate of human samples acquired by flow cytometry, in PBMC as well as in tissues...
Article
Full-text available
RNA-seq methods are widely utilized for transcriptomic profiling of biological samples. However, there are known caveats of this technology which can skew the gene expression estimates. Specifically, if the library preparation protocol does not retain RNA strand information then some genes can be erroneously quantitated. Although strand-specific pr...
Preprint
Full-text available
Analysis of transcriptomic data derived from blood samples is complicated by the complex mixture of cell types such samples contain. Transcriptomic signatures derived from such samples are often driven by a particular cell lineage within the mixture. Identifying this most contributing lineage can help to provide a biological interpretation of the s...
Article
Full-text available
Our results highlight for the first time that a significant proportion of cell doublets in flow cytometry, previously believed to be the result of technical artifacts and thus ignored in data acquisition and analysis, are the result of biological interaction between immune cells. In particular, we show that cell:cell doublets pairing a T cell and a...
Article
In the mid-1990s vaccine-related side effects prompted the replacement of the whole Pertussis (wP) by a new acellular Pertussis vaccine (aP). Unexpectedly, whooping cough cases have recently increased, and the switch to the aP vaccine suspected to underlie this rise in morbidity, despite the use of routine boosters. Here we compared the immune resp...
Article
Gene Set Enrichment Analysis (GSEA) and its special case of GO enrichment analysis is a common step in biologically interpretation of gene lists resulting from –omics experiments. A known but under-appreciated aspect of any GSEA is the use of a background gene list, e.g. by discarding genes generally not expressed in the investigated cell type. We...
Article
Here, we applied a cell population transcriptomics strategy to sorted human memory CD8 T cells to define novel immune signatures of latent tuberculosis infection (LTBI) and understand the phenotype of tuberculosis (TB)-specific T cells. We found a 41-gene signature that could discriminate between memory CD8 T cells from healthy LTBI subjects and no...
Article
As part of the Human Immune Project Consortium (HIPC) program, we are aiming to decipher CD4 T cell immune signatures of tuberculosis (TB) in the context of controlled (latent TB) and uncontrolled (active TB) infection. We found commonalities and differences in TB-specific CD4 T cell immune responses of latent TB vs active TB subjects. Both cohorts...
Article
HLA genes are the most polymorphic in the human genome. Specific genetic variants in the HLA locus are frequently associated with diseases and other traits in GWAS studies. How much of those associations are due to functional differences in the peptide binding specificity of the various HLA genes encoded in the locus, vs. how many associations are...
Article
Full-text available
Tuberculosis (TB) is a major infectious disease worldwide, and is associated with several challenges for control and eradication. First, more accurate diagnostic tools that better represent the spectrum of infection states are required; in particular, identify the latent TB infected individuals with high risk of developing active TB. Second, we nee...
Article
Full-text available
Background Biological interpretation of gene/protein lists resulting from -omics experiments can be a complex task. A common approach consists of reviewing Gene Ontology (GO) annotations for entries in such lists and searching for enrichment patterns. Unfortunately, there is a gap between machine-readable output of GO software and its human-interpr...
Preprint
We set out to detect a transcriptional signature in CD4 T cells of individuals at risk of progression to active tuberculosis. We indeed found such a signature which surprisingly could be tracked to a cell population expressing both T cell (CD3) and monocyte (CD14) markers. Imaging experiments revealed that CD3+CD14+ cells included T cell:monocyte c...
Article
Opisthorchis felineus, the trematode belonging to the family Opisthorchiidae, is a causative agent of the infection called opisthorchiasis or liver fluke infection. Being a close relative of O. viverrini and Clonorchis sinensis (oriental liver flukes) it is encountered in northern Eurasia, especially in Russia, Kazakhastan, Belarus, Ukraine, and Ba...
Article
Full-text available
The 3D organization of the genome is tightly connected to its biological function. The Hi-C approach was recently introduced as a method that can be used to identify higher-order chromatin interactions genome-wide. The aim of this study was to determine genome-wide chromatin interaction frequencies using the Hi-C approach in mouse sperm cells and e...
Article
Full-text available
The spatial organization of eukaryotic genome plays an important role in the control of gene expression. The new Hi-C method allows investigation of chromosome contact in the three-dimensional architecture of the whole genome; however, it has not yet been applied to study the spatial configuration of the germ cells genome. Here we describe a protoc...
Preprint
Full-text available
The 3D organization of the genome is tightly connected to its biological function. The Hi-C approach was recently introduced as a method that can be used to identify higher-order chromatin interactions genome-wide. The aim of this study was to determine genome-wide chromatin interaction frequencies using the Hi-C approach in mouse sperm cells and e...

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