BAMboozle removes genetic variation from human sequence data for open data sharing

The risks associated with re-identification of human genetic data are severely limiting open data sharing in life sciences, even in studies where donor-related genetic variant information is not of primary interest. Here, we developed BAMboozle, a versatile tool to eliminate critical types of sensitive genetic information in human sequence data by reverting aligned reads to the genome reference sequence. Applying BAMboozle to functional genomics data, such as single-cell RNA-seq (scRNA-seq) and scATAC-seq datasets, confirmed the removal of donor-related single nucleotide polymorphisms (SNPs) and indels in a manner that did not disclose the altered positions. Importantly, BAMboozle only removes the genetic sequence variants of the sample (i.e., donor) while preserving other important aspects of the raw sequence data. For example, BAMboozled scRNA-seq data contained accurate cell-type associated gene expression signatures, splice kinetic information, and can be used for methods benchmarking. Altogether, BAMboozle efficiently removes genetic variation in aligned sequence data, which represents a step forward towards open data sharing in many areas of genomics where the genetic variant information is not of primary interest.

Urotensin receptor in GtoPdb v.2021.3

The urotensin-II (U-II) receptor (UT, nomenclature as agreed by the NC-IUPHAR Subcommittee on the Urotensin receptor [26, 36, 93]) is activated by the endogenous dodecapeptide urotensin-II, originally isolated from the urophysis, the endocrine organ of the caudal neurosecretory system of teleost fish [7, 92]. Several structural forms of U-II exist in fish and amphibians [93]. The goby orthologue was used to identify U-II as the cognate ligand for the predicted receptor encoded by the rat gene gpr14 [2, 20, 63, 69, 72]. Human urotensin-II, an 11-amino-acid peptide [20], retains the cyclohexapeptide sequence of goby U-II that is thought to be important in ligand binding [61, 53, 10]. This sequence is also conserved in the deduced amino-acid sequence of rat urotensin-II (14 amino-acids) and mouse urotensin-II (14 amino-acids), although the N-terminal is more divergent from the human sequence [19]. A second endogenous ligand for the UT has been discovered in rat [86]. This is the urotensin II-related peptide, an octapeptide that is derived from a different gene, but shares the C-terminal sequence (CFWKYCV) common to U-II from other species. Identical sequences to rat urotensin II-related peptide are predicted for the mature mouse and human peptides [32]. UT exhibits relatively high sequence identity with somatostatin, opioid and galanin receptors [93].

Comparative Analysis Of Orthologous Mast Cell Chymases Active Sites Using Bioinformatics Tools

Mast cells, neutrophils, basophils, natural killer cells, and cytotoxic T cells are among the hematopoietic cell lines originating from immune cells. The importance of mammalian mast cells in innate immunity has piqued the scientific community's interest. cytoplasmic granules of mast cells. Histamine, proteoglycans, proteins, and cytokines are examples of compounds (mediators) that produce mast cell cytoplasmic granules. When external stimuli are received, these granules are released, causing degranulation. Mast cells generate a lot of proteases including chymase, tryptase, and type A carboxypeptidase, among other things. The structure of chymase cma1 was unknown in mice, but it shares 74 percent of its human sequence with chymase CMA1, which was used as a reference. The human CMA1 structure was used to establish and interpret the mouse cma1 structure. Significant residues from the active site, such as catalytic triads and binding residues, were examined. The position of a catalytic triad in human CMA1 chymase and mouse cma1 chymase has been discovered to be similar. Val 175 and Val 197, respectively, replaced two Ala 192 and Gly 214 residues in active site binding residues in target, according to active site residue analysis. We may deduce from this substitution that the cleavage specificity of mouse cma1 chymase varies from that of human CMA1 chymase.

Cloud Computing Based Immunopeptidomics Utilizing Community Curated Variant Libraries Simplifies and Improves Neo-Antigen Discovery in Metastatic Melanoma

Unique peptide neo-antigens presented on the cell surface are attractive targets for researchers in nearly all areas of personalized medicine. Cells presenting peptides with mutated or other non-canonical sequences can be utilized for both targeted therapies and diagnostics. Today’s state-of-the-art pipelines utilize complementary proteogenomic approaches where RNA or ribosomal sequencing data helps to create libraries from which tandem mass spectrometry data can be compared. In this study, we present an alternative approach whereby cloud computing is utilized to power neo-antigen searches against community curated databases containing more than 7 million human sequence variants. Using these expansive databases of high-quality sequences as a reference, we reanalyze the original data from two previously reported studies to identify neo-antigen targets in metastatic melanoma. Using our approach, we identify 79 percent of the non-canonical peptides reported by previous genomic analyses of these files. Furthermore, we report 18-fold more non-canonical peptides than previously reported. The novel neo-antigens we report herein can be corroborated by secondary analyses such as high predicted binding affinity, when analyzed by well-established tools such as NetMHC. Finally, we report 738 non-canonical peptides shared by at least five patient samples, and 3258 shared across the two studies. This illustrates the depth of data that is present, but typically missed by lower statistical power proteogenomic approaches. This large list of shared peptides across the two studies, their annotation, non-canonical origin, as well as MS/MS spectra from the two studies are made available on a web portal for community analysis.

Hematologic and systemic metabolic alterations due to Mediterranean type II G6PD deficiency in a novel murine model

Deficiency of Glucose 6 phosphate dehydrogenase (G6PD) is the single most common enzymopathy, present in approximately 400 million humans (e.g. 5% of humans). Its prevalence is hypothesized to be due to conferring resistance to malaria. However, G6PD deficiency also results in hemolytic sequelae from oxidant stress. Moreover, G6PD deficiency is associated with kidney disease, diabetes, pulmonary hypertension, immunological defects, and neurodegenerative diseases. To date, the only available mouse models have decreased levels of G6PD due to promoter mutations, but with stable G6PD. However, human G6PD mutations are missense mutations that result in decreased enzymatic stability. As such, this results in very low activity in red blood cells and platelets that cannot synthesize new protein. To generate a more accurate model, the human sequence for a severe form of G6PD deficiency (Med -) was knocked into the murine G6PD locus. As predicted, G6PD levels were extremely low in RBCs and deficient mice have increased hemolytic sequalae to oxidant stress. G6PD levels were mildly decreased in non-erythroid organs, consistent with what has been observed in humans. Juxtaposition of G6PD deficient and wild-type mice revealed altered lipid metabolism in multiple organ systems. Together, these findings both establish a new mouse model of G6PD deficiency that more accurately reflects human G6PD deficiency and also advance our basic understanding of altered metabolism in this setting.

Detection and Genome Sequencing of SARS-CoV-2 in a Domestic Cat with Respiratory Signs in Switzerland

Since the emergence of coronavirus disease (COVID-19) in late 2019, domestic cats have been demonstrated to be susceptible to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) under natural and experimental conditions. As pet cats often live in very close contact with their owners, it is essential to investigate SARS-CoV-2 infections in cats in a One-Health context. This study reports the first SARS-CoV-2 infection in a cat in a COVID-19-affected household in Switzerland. The cat (Cat 1) demonstrated signs of an upper respiratory tract infection, including sneezing, inappetence, and apathy, while the cohabiting cat (Cat 2) remained asymptomatic. Nasal, oral, fecal, fur, and environmental swab samples were collected twice from both cats and analyzed by RT-qPCR for the presence of SARS-CoV-2 viral RNA. Both nasal swabs from Cat 1 tested positive. In addition, the first oral swab from Cat 2 and fur and bedding swabs from both cats were RT-qPCR positive. The fecal swabs tested negative. The infection of Cat 1 was confirmed by positive SARS-CoV-2 S1 receptor binding domain (RBD) antibody testing and neutralizing activity in a surrogate assay. The viral genome sequence from Cat 1, obtained by next generation sequencing, showed the closest relation to a human sequence from the B.1.1.39 lineage, with one single nucleotide polymorphism (SNP) difference. This study demonstrates not only SARS-CoV-2 infection of a cat from a COVID-19-affected household but also contamination of the cats’ fur and bed with viral RNA. Our results are important to create awareness that SARS-CoV-2 infected people should observe hygienic measures to avoid infection and contamination of animal cohabitants.

Identifying Primate ACE2 Variants That Confer Resistance to SARS-CoV-2

SARS-CoV-2 infects humans through the binding of viral S-protein (spike protein) to human angiotensin I converting enzyme 2 (ACE2). The structure of the ACE2-S-protein complex has been deciphered and we focused on the 27 ACE2 residues that bind to S-protein. From human sequence databases, we identified nine ACE2 variants at ACE2–S-protein binding sites. We used both experimental assays and protein structure analysis to evaluate the effect of each variant on the binding affinity of ACE2 to S-protein. We found one variant causing complete binding disruption, two and three variants, respectively, strongly and mildly reducing the binding affinity, and two variants strongly enhancing the binding affinity. We then collected the ACE2 gene sequences from 57 nonhuman primates. Among the 6 apes and 20 Old World monkeys (OWMs) studied, we found no new variants. In contrast, all 11 New World monkeys (NWMs) studied share four variants each causing a strong reduction in binding affinity, the Philippine tarsier also possesses three such variants, and 18 of the 19 prosimian species studied share one variant causing a strong reduction in binding affinity. Moreover, one OWM and three prosimian variants increased binding affinity by >50%. Based on these findings, we proposed that the common ancestor of primates was strongly resistant to and that of NWMs was completely resistant to SARS-CoV-2 and so is the Philippine tarsier, whereas apes and OWMs, like most humans, are susceptible. This study increases our understanding of the differences in susceptibility to SARS-CoV-2 infection among primates.

anonymizeBAM: Versatile anonymization of human sequence data for open data sharing

The risks associated with re-identification of human genetic data are severely limiting open data sharing in life sciences. Here, we developed anonymizeBAM, a versatile tool for the anonymization of genetic variant information present in sequence data. Applying anonymizeBAM to single-cell RNA-seq and ATAC-seq datasets confirmed the complete removal of donor-related genetic information. Therefore, the accurate generation of de-identified sequence data will re-enable open sharing in sequencing-based studies for improved transparency, reproducibility, and innovation.