Mitochondrial Variation Research Articles

Loss of Mitochondrial Genetic Diversity despite Population Growth: The Legacy of Past Wolf Population Declines.

Gray wolves (Canis lupus) in the Iberian Peninsula declined substantially in both range and population size in the last few centuries due to human persecution and habitat fragmentation. However, unlike many other western European populations, gray wolves never went extinct in Iberia. Since the minimum number was recorded around 1970, their numbers have significantly increased and then stabilized in recent decades. We analyzed mitochondrial genomes from 54 historical specimens of Iberian wolves from across their historical range using ancient DNA methods. We compared historical and current mitochondrial diversity in Iberian wolves at the 5' end of the control region (n = 17 and 27) and the whole mitochondrial genome excluding the control region (n = 19 and 29). Despite an increase in population size since the 1970s, genetic diversity declined. We identified 10 whole mitochondrial DNA haplotypes in 19 historical specimens, whereas only six of them were observed in 29 modern Iberian wolves. Moreover, a haplotype that was restricted to the southern part of the distribution has gone extinct. Our results illustrate a lag between demographic and genetic diversity changes, and show that after severe population declines, genetic diversity can continue to be lost in stable or even expanding populations. This suggests that such populations may be of conservation concern even after their demographic trajectory has been reversed.

Is the disease risk and penetrance in Leber hereditary optic neuropathy actually low?

Pedigree analysis showed that a large proportion of Leber hereditary optic neuropathy (LHON) family members who carry a mitochondrial risk variant never lose vision. Mitochondrial haplotype appears to be a major factor influencing the risk of vision loss from LHON. Mitochondrial variants, including m.14484T>C and m.11778G>A, have been added to gene arrays, and thus many patients and research participants are tested for LHON mutations. Analysis of the UK Biobank and Australian cohort studies found more than 1 in 1,000 people in the general population carry either the m.14484T>C or the m.11778G>A LHON variant. None of the subset of carriers examined had visual acuity at 20/200 or worse, suggesting a very low penetrance of LHON. Haplogroup analysis of m.14484T>C carriers showed a high rate of haplogroup U subclades, previously shown to have low penetrance in pedigrees. Penetrance calculations of the general population are lower than pedigree calculations, most likely because of modifier genetic factors. This Matters Arising Response paper addresses the Watson etal. (2022) Matters Arising paper, published concurrently in The American Journal of Human Genetics.

Maximizing Small Biopsy Patient Samples: Unified RNA-Seq Platform Assessment of over 120,000 Patient Biopsies.

Despite its wide-ranging benefits, whole-transcriptome or RNA exome profiling is challenging to implement in a clinical diagnostic setting. The Unified Assay is a comprehensive workflow wherein exome-enriched RNA-sequencing (RNA-Seq) assays are performed on clinical samples and analyzed by a series of advanced machine learning-based classifiers. Gene expression signatures and rare and/or novel genomic events, including fusions, mitochondrial variants, and loss of heterozygosity were assessed using RNA-Seq data generated from 120,313 clinical samples across three clinical indications (thyroid cancer, lung cancer, and interstitial lung disease). Since its implementation, the data derived from the Unified Assay have allowed significantly more patients to avoid unnecessary diagnostic surgery and have played an important role in guiding follow-up decisions regarding treatment. Collectively, data from the Unified Assay show the utility of RNA-Seq and RNA expression signatures in the clinical laboratory, and their importance to the future of precision medicine.

Population genomics and subgenome evolution of the allotetraploid frog Xenopus laevis in southern Africa

Allotetraploid genomes have two distinct genomic components called subgenomes that are derived from separate diploid ancestral species. Many genomic characteristics such as gene function, expression, recombination, and transposable element mobility may differ significantly between subgenomes. To explore the possibility that subgenome population structure and gene flow may differ as well, we examined genetic variation in an allotetraploid frog-the African clawed frog (Xenopus laevis)-over the dynamic and varied habitat of its native range in southern Africa. Using reduced representation genome sequences from 91 samples from 12 localities, we found no strong evidence that population structure and gene flow differed substantially by subgenome. We then compared patterns of population structure in the nuclear genome to the mitochondrial genome using Sanger sequences from 455 samples from 183 localities. Our results provide further resolution to the geographic distribution of mitochondrial and nuclear diversity in this species and illustrate that population structure in both genomes corresponds roughly with variation in seasonal rainfall and with the topography of southern Africa.

Maternal genetic diversity of ancient goats in Finland and Estonia and comparison with extant northern European goat breeds.

Countries in the northern Baltic Sea region have been historically linked for thousands of years, and animal husbandry is one of the many information sources that enables the study of historical connections. Although goat husbandry in this part of Europe has been evidenced by scant archaeological materials, zooarchaeological and historical evidence has revealed its continuity, at least since the Late Iron Age. To explore the historical relationship between goat lineages and investigate affinities between the past and present-day populations in the Baltic Sea region, we analysed a 476-bp fragment of the mitochondrial DNA control region in 14 ancient goats from Finland and Estonia and 10 extant goats from Finland. The results revealed high mitochondrial diversity among the ancient goats. Two maternal lineages were shared between the Late Iron Age and medieval individuals from Finland and Estonia. Moreover, ancient Finnish and Estonian goats showed maternal affinity to extant Finngoat and Swedish Landrace breeds. Overall, the analysis of maternal goat lineages confirmed tight historical connections in the region.

Reconstruction of the Major Maternal and Paternal Lineages in the Feral New Zealand Kaimanawa Horses.

New Zealand has the fourth largest feral horse population in the world. The Kaimanawas (KHs) are feral horses descended from various domestic horse breeds released into the Kaimanawa ranges in the 19th and 20th centuries. Over time, the population size has fluctuated dramatically due to hunting, large-scale farming and forestry. Currently, the herd is managed by an annual round-up, limiting the number to 300 individuals to protect the native ecosystem. Here, we genotyped 96 KHs for uniparental markers (mitochondrial DNA, Y-chromosome) and assessed their genetic similarity with respect to other domestic horses. We show that at least six maternal and six paternal lineages contributed unequally to the KH gene pool, and today's KH population possibly represents two sub-populations. Our results indicate that three horse breeds, namely Welsh ponies, Thoroughbreds and Arabian horses had a major influence in the genetic-makeup of the extant KH population. We show that mitochondrial genetic diversity in KHs (π = 0.00687 ± 0.00355) is closer to that of the Sable Island horses (π = 0.0034 ± 0.00301), and less than other feral horse populations around the world. Our current findings, combined with ongoing genomic research, will provide insight into the population-specific genetic variation and inbreeding among KHs. This will largely advance equine research and improve the management of future breeding programs of these treasured New Zealand horse.

Genetic Polymorphism and Phylogenetics of Aedes aegypti from Sudan Based on ND4 Mitochondrial Gene Variations.

This study investigated the genetic differences between Aedes aegypti subspecies (Aedes aegypti aegypti (Aaa) and Aedes aegypti formosus (Aaf)) from Sudan using the NADH dehydrogenase subunit 4 (ND4) mitochondrial gene marker. Nineteen distinct haplotypes of the ND4 were identified in female Aedes aegypti mosquitoes from the study sites. The phylogenetic relationship of the 19 ND4 haplotypes was demonstrated in a median-joining haplotype network tree with Aaa and Aaf populations found to share three haplotypes. The genetic variance (Pairwise FST values) was estimated and found to range from 0.000 to 0.811. Isolation by distance test revealed that geographical distance was correlated to genetic variation (coefficient value (r) = 0.43). The Polar maximum likelihood tree showed the phylogenetic relationship of 91 female Aaa and Aaf from the study sites, with most of the Aaf haplotypes clustered in one group while most of the Aaa haplotypes gathered in another group, but there was an admixture of the subspecies in both clusters, especially the Aaa cluster. The Spatial Analysis of Molecular Variance (SAMOVA) test revealed that the eight populations clustered into two phylogeographic groups/clusters of the two subspecies populations. The 2 Aedes aegypti subspecies seemed not to be totally separated geographically with gene flow among the populations.

The ancient inhabitants of the Chonos Archipelago (~43°–47°S): Characterization of maritime hunter‐gatherers from Western Patagonia using mitochondrial DNA

AbstractBackgroundWithin the southern end of South America, Western Patagonia arises as an intricate region of channels, fjords, and islands. This region holds evidence of human occupation since ca. 14,500 cal years BP, with distinctive maritime adaptations developing around 7300 cal years BP. Historically, three major populations were characterized as part of these maritime traditions: Yámana, Kawésqar, and Chono. The arrival of European population had a profound impact in these communities, affecting their lifestyles, territory and population size and health. The northernmost populations, living within the Chonos Archipelago, were the most affected and the least known communities from Western Patagonia.ObjectivesThis research aims to characterize the mitochondrial DNA diversity of ancient individuals from the Chonos Archipelago, evaluating their genetic affinities with other ancient and present‐day populations from Patagonia.Materials and MethodsA total of 46 individuals from the region were sampled for ancient DNA analysis. Mitochondrial DNA haplogroups were characterized and compared with ancient and present‐day populations from Southern South America.ResultsAll individuals from the Chonos Archipelago belong to C and D haplogroups, particularly to C1b, C1b13, D1, D1g, and D4h3a5. As a group, the individuals from Chonos Archipelago lay closer to ancient individuals from Kawésqar territory, immediately south of them. Using mitogenomes, we characterized two new D4h3a5 lineages almost exclusively associated with populations from Western Patagonia.DiscussionOur results contribute to the understanding of the peopling and human interactions in Western Patagonia, suggesting these unique maritime traditions developed within local populations, genetically associated with earlier terrestrial populations.

Abstract B032: Native sgRNA capture and sequencing (NSC-seq) reveals tumor formation in ApcMin/+ mice and in human colorectal cancer is an oligoclonal process

Abstract CRISPR-Cas9-based technologies have been developed to address a wide range of biological questions, including molecular recording of embryonic development, genetic screening, and tracking tumor evolution at the single-cell resolution. We developed a single-cell lineage tracking platform called native sgRNA Capture and sequencing (NSC-seq) to leverage CRISPR technology for clonal analysis of intestinal tumors in the ApcMin/+ mouse model. We combined CRISPR-induced mutations with spontaneously accumulating mitochondrial variants to enable highly efficient lineage-tracking of single cells. We generated lineage-tracked ApcMin/+ tumors and found that there are more than two independently arising clones within a tumor. We also found oligoclonal tumors within human colorectal specimens using this technology, supporting the oligoclonality of intestinal tumor development across species. Finally, we demonstrated the application of this technology in understanding the rate of loss-of-heterozygosity events in Apc as related to the cellular turnover rates of different intestinal regions. Overall, NSC-seq enables in vivo molecular recording of spontaneous intestinal tumor development at single-cell resolution. Citation Format: Mirazul Islam, Yilin Yang, Vishal M. Shah, Alan J. Simmons, Yanwen Xu, Robert J. Coffey, Ken S. Lau. Native sgRNA capture and sequencing (NSC-seq) reveals tumor formation in ApcMin/+ mice and in human colorectal cancer is an oligoclonal process [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer; 2022 Oct 1-4; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_1):Abstract nr B032.

Association of mitochondrial haplogroups and cognitive impairment in the Amish

AbstractBackgroundMitochondrial dysfunction is an important feature of Alzheimer’s Disease (AD) pathogenesis. Reduced glucose utilization and increased oxidative stress are intermediates through which impaired mitochondria may promote AD‐associated brain changes. Association between groups of variants (“haplogroups”) in the mitochondrial genome and AD have been reported for haplogroups U, J, and K. To test these effects in the Amish, we looked for evidence of association between AD‐associated haplogroups and cognitive impairment in a sample of aged Amish individuals.MethodCognitive status in adult Amish participants (n=670) with whole‐genome sequence (WGS) data was determined based on modified mini‐mental status exam results (3MS). An outcome of cognitively impaired (CI) was assigned to individuals with an education‐adjusted 3MS < 87 at any age. A status of cognitively unimpaired (CU) was assigned to those aged ≥ 75 scoring ≥ 87 on the 3MS. Mitochondrial variants detected by WGS were used to derive broad haplogroups for each sample using Haplogrep2. Mixed model association testing was performed in GENESIS with CI as the outcome, and haplogroup (U, J, or K), APOE ε4 carrier status (ε4 vs no ε4), sex, and age as predictors. Based on reports of sex‐specific haplogroup U effects on AD, a sex‐stratified analysis was conducted. A random‐effect kinship matrix was used to account for relationships.ResultAssociation between mitochondrial haplogroups U, J, or K and CI was not observed at a 5% significance level. The sex‐stratified analysis showed the strongest association of CI with haplogroup U (OR 1.8, 95% CI 0.92‐3.5) among women. Among men, the estimated effect was 0.77 (95% CI 0.37‐1.62). The overall direction of association was opposite in men and women, though neither was statistically significant at 5%.ConclusionAlthough significant evidence of a haplogroup effect on cognitive status was not observed, the moderate sex‐dependent effect of haplogroup U on impairment warrants further examination in an expanded dataset.Previously, haplogroup U was proposed as an AD risk factor among men, whereas it appears as a risk factor for CI in women in the present study.

Mitochondrial genome maintenance - the kinetoplast story.

Mitochondrial DNA replication is an essential process in most eukaryotes. Similar to the diversity in mitochondrial genome size and organization in the different eukaryotic supergroups, there is considerable diversity in the replication process of the mitochondrial DNA. In this review, we summarize the current knowledge of mitochondrial DNA replication and the associated factors in trypanosomes with a focus on Trypanosoma brucei, and provide a new model of minicircle replication for this protozoan parasite. The model assumes the mitochondrial DNA (kinetoplast DNA, kDNA) of T. brucei to be loosely diploid in nature and the replication of the genome to occur at two replication centers at the opposing ends of the kDNA disc (also known as antipodal sites, APS). The new model is consistent with the localization of most replication factors and in contrast to the current model, it does not require the assumption of an unknown sorting and transport complex moving freshly replicated DNA to the antipodal sites. In combination with the previously proposed sexual stages of the parasite in the insect vector, the new model provides a mechanism for maintenance of the mitochondrial genetic diversity.

Comparative structural analysis on the mitochondrial DNAs from various strains of Lentinula edodes.

The evolution of mitochondria through variations in mitochondrial DNA (mtDNA) is one of the intriguing questions in eukaryotic cells. In order to assess the causes of the variations in mitochondria, the mtDNAs of the 21 strains of Lentinula edodes were assembled for this study, and analyzed together with four published mtDNA sequences. The mtDNAs were within the sizes of 117 kb ~ 122 kb. The gene number was observed consistent except for two mtDNAs, which carry a duplicated trnG1-trnG2 unit or a putative gene deletion. The size variation was largely attributed to the number of introns, repeated sequences, transposable elements (TEs), and plasmid-related sequences. Intron loss and gain were found from cox1, rnl, and rns of three mtDNAs. Loss of two introns in cox1 of KY217797.1 reduced its size by 2.7 kb, making it the smallest cox1 gene (8.4 kb) among the cox1s of the 25 mtDNAs, whereas gain of a Group II intron (2.65 kb) and loss of a Group I intron (1.7 kb) in cox1 of MF774813.1 resulted in the longest cox1 (12 kb). In rnl of L. edodes, we discovered four intron insertion consensus sequences which were unique to basidiomycetes but not ascomycetes. Differential incorporation of introns was the primary cause of the rnl size polymorphism. Homing endonucleases (HEGs) were suggestively involved in the mobilization of the introns because all of the introns have HEG genes of the LAGRIDADG or GIY-YIG families with the conserved HEG cleavage sites. TEs contributed to 11.04% of the mtDNA size in average, of which 7.08% was LTR-retrotransposon and 3.96% was DNA transposon, whereas the repeated sequences covered 4.6% of the mtDNA. The repeat numbers were variable in a strain-dependent manner. Both the TEs and repeated sequences were mostly found in the intronic and intergenic regions. Lastly, two major deletions were found in the plasmid-related sequence regions (pol2-pol3 and pol1-atp8) in the five mtDNAs. Particularly, the 6.8 kb-long deletion at pol2-pol3 region made MF774813.1 the shortest mtDNA of all. Our results demonstrate that mtDNA is a dynamic molecule that persistently evolves over a short period of time by insertion/deletion and repetition of DNA segments at the strain level.

Characterization of Mitochondrial Alterations in Aicardi-Goutières Patients Mutated in RNASEH2A and RNASEH2B Genes.

Aicardi-Goutières syndrome (AGS) is a rare encephalopathy characterized by neurological and immunological features. Mitochondrial dysfunctions may lead to mitochondrial DNA (mtDNA) release and consequent immune system activation. We investigated the role of mitochondria and mtDNA in AGS pathogenesis by studying patients mutated in RNASEH2B and RNASEH2A genes. Lymphoblastoid cell lines (LCLs) from RNASEH2A- and RNASEH2B-mutated patients and healthy control were used. Transmission Electron Microscopy (TEM) and flow cytometry were used to assess morphological alterations, reactive oxygen species (ROS) production and mitochondrial membrane potential variations. Seahorse Analyzer was used to investigate metabolic alterations, and mtDNA oxidation and VDAC1 oligomerization were assessed by immunofluorescence. Western blot and RT-qPCR were used to quantify mtTFA protein and mtDNA release. Morphological alterations of mitochondria were observed in both mutated LCLs, and loss of physiological membrane potential was mainly identified in RNASEH2A LCLs. ROS production and 8-oxoGuanine levels were increased in RNASEH2B LCLs. Additionally, the VDAC1 signal was increased, suggesting a mitochondrial pore formation possibly determining mtDNA release. Indeed, higher cytoplasmic mtDNA levels were found in RNASEH2B LCLs. Metabolic alterations confirmed mitochondrial damage in both LCLs. Data highlighted mitochondrial alterations in AGS patients' LCLs suggesting a pivotal role in AGS pathogenesis.

Mitochondrial effects on fertility and longevity in Tigriopus californicus contradict predictions of the mother's curse hypothesis.

Strict maternal inheritance of mitochondria favours the evolutionary accumulation of sex-biased fitness effects, as mitochondrial evolution occurs exclusively in female lineages. The 'mother's curse' hypothesis proposes that male-harming mutations should accumulate in mitochondrial genomes when they have neutral or beneficial effects on female fitness. Rigorous empirical tests have largely focused on Drosophila, where support for the predictions of mother's curse has been mixed. We investigated the impact of mother's curse mutations in Tigriopus californicus, a minute crustacean. Using non-recombinant backcrosses, we introgressed four divergent mitochondrial haplotypes into two nuclear backgrounds and recorded measures of fertility and longevity. We found that the phenotypic effects of mitochondrial mutations were context dependent, being influenced by the nuclear background in which they were expressed, as well as the sex of the individual and rearing temperature. Mitochondrial haplotype effects were greater for fertility than longevity, and temperature effects were greater for longevity. However, in opposition to mother's curse expectations, females had higher mitochondrial genetic variance than males for fertility and longevity, little evidence of sexual antagonism favouring females was found, and the impacts of mitonuclear mismatch harmed females but not males. Together, this indicates that selection on mitochondrial variation has not resulted in the accumulation of male mutation load in Tigriopus californicus.

Precision mitochondrial medicine.

Mitochondria play a key role in cell homeostasis as a major source of intracellular energy (adenosine triphosphate), and as metabolic hubs regulating many canonical cell processes. Mitochondrial dysfunction has been widely documented in many common diseases, and genetic studies point towards a causal role in the pathogenesis of specific late-onset disorder. Together this makes targeting mitochondrial genes an attractive strategy for precision medicine. However, the genetics of mitochondrial biogenesis is complex, with over 1,100 candidate genes found in two different genomes: the nuclear DNA and mitochondrial DNA (mtDNA). Here, we review the current evidence associating mitochondrial genetic variants with distinct clinical phenotypes, with some having clear therapeutic implications. The strongest evidence has emerged through the investigation of rare inherited mitochondrial disorders, but genome-wide association studies also implicate mtDNA variants in the risk of developing common diseases, opening to door for the incorporation of mitochondrial genetic variant analysis in population disease risk stratification.

Selective degradation of tRNASer(AGY) is the primary driver for mitochondrial seryl-tRNA synthetase-related disease.

Mitochondrial translation is of high significance for cellular energy homeostasis. Aminoacyl-tRNA synthetases (aaRSs) are crucial translational components. Mitochondrial aaRS variants cause various human diseases. However, the pathogenesis of the vast majority of these diseases remains unknown. Here, we identified two novel SARS2 (encoding mitochondrial seryl-tRNA synthetase) variants that cause a multisystem disorder. c.654-14T>A mutation induced mRNA mis-splicing, generating a peptide insertion in the active site; c.1519dupC swapped a critical tRNA-binding motif in the C-terminus due to stop codon readthrough. Both mutants exhibited severely diminished tRNA binding and aminoacylation capacities. A marked reduction in mitochondrial tRNASer(AGY) was observed due to RNA degradation in patient-derived induced pluripotent stem cells (iPSCs), causing impaired translation and comprehensive mitochondrial function deficiencies. These impairments were efficiently rescued by wild-type SARS2 overexpression. Either mutation caused early embryonic fatality in mice. Heterozygous mice displayed reduced muscle tissue-specific levels of tRNASers. Our findings elucidated the biochemical and cellular consequences of impaired translation mediated by SARS2, suggesting that reduced abundance of tRNASer(AGY) is a key determinant for development of SARS2-related diseases.

Climate change may cause the extinction of the butterfly Lasiommata petropolitana in the Apennines

Climate change represents a threat to narrow-ranged mountain species living in low-altitude massifs. We studied the disjunct Apennine population of Lasiommata petropolitana (Lepidoptera, Nymphalidae) in the Gran Sasso and Monti della Laga National Park. We quantified the altitudinal shifts undergone in the last decades (1964–2021) in the Alps and Apennines and estimated the local extinction risk due to climate change. We also sequenced the COI mitochondrial marker of seven Apennine specimens, comparing them with those available across the Palearctic. We projected the probability of presence for the species under a future climatic scenario using an ensemble forecasting approach. We found that, despite geographical isolation, the Apennine population of L. petropolitana displays a single widespread COI haplotype also occurring in most European populations. In the Alps and Apennines, this species has shifted uphill an average of 6.3 m per year since 1964. Accordingly, our model predicted a likely extinction in the Apennines by about 2060, due to a reduction of the climatic suitability in this region.Implications for insect conservationImplications for insect conservation Despite its potential loss in the Apennines would not erode mitochondrial diversity, L. petropolitana characterises the butterfly community of the Gran Sasso massif as an alpine enclave. The loss of the Apennine population, together with those of other orophilous butterflies, could trigger a homogenization of alpha and beta diversity and induce a loss of functional diversity in the impoverished high-altitude biotas. As habitat heterogeneity is a key aspect for populations to endure climate change, the maintenance of varied microhabitats, mainly through grazing management, could address the decline of this population.

Genomic architecture of autism from comprehensive whole-genome sequence annotation

Fully understanding autism spectrum disorder (ASD) genetics requires whole-genome sequencing (WGS). We present the latest release of the Autism Speaks MSSNG resource, which includes WGS data from 5,100 individuals with ASD and 6,212 non-ASD parents and siblings (total n= 11,312). Examining a wide variety of genetic variants in MSSNG and the Simons Simplex Collection (SSC; n= 9,205), we identified ASD-associated rare variants in 718/5,100 individuals with ASD from MSSNG (14.1%) and 350/2,419 from SSC (14.5%). Considering genomic architecture, 52% were nuclear sequence-level variants, 46% were nuclear structural variants (including copy-number variants, inversions, large insertions, uniparental isodisomies, and tandem repeat expansions), and 2% were mitochondrial variants. Our study provides a guidebook for exploring genotype-phenotype correlations in families who carry ASD-associated rare variants and serves as an entry point to the expanded studies required to dissect the etiology in the ∼85% of the ASD population that remain idiopathic.

DUPILUMAB REBALANCES IMMUNE RESPONSE IN PEDIATRIC TYPE-2 DISORDERS: IMPACTS ON T-CELL CLONES AND FUNCTIONALITY

<h3>Introduction</h3> Dupilumab demonstrates efficacy in treating a variety of Type-2 disorders refractory to conventional therapies. Improvement in clinical outcomes establishes a need to investigate mechanistic pathways of potential immunomodulation. <h3>Methods</h3> 11 patients, two with moderate-to-severe asthma and 9 with moderate-top-severe AD were recruited to give blood samples pre and three months post-Dupilumab. Longitudinal phenotyping of leukocytes using mass cytometry (CyTOF) and lineage tracing of single-cells using mitochondrial single-cell ATAC-seq (mt-scATAC-seq) was conducted in PBMC and purified T-cells. Clones were inferred using a community-based detection algorithm to cluster cells based on mitochondrial variant allele-frequency (VAF). Gene scores were computed based on open-chromatin regions in the gene and promoter. Differential expression pre- and post-dupilumab was done for each cell cluster population. <h3>Results</h3> CyTOF immunophenotyping showed increased Th1 and Th17 cells following dupilumab, consistent with increased activity of IL-6, TNF, IFNa, and IFNg genes in lymphocytes by mt-scATAC-Seq. Rebalancing of adaptive immunity was accompanied by upregulation of Myc, E2F, MTORC1, PI3K-AKT, and p53 signaling intermediates, and was associated with upregulation of genes controlling apoptosis, unfolded protein response, and oxidative phosphorylation. Changes in frequency of T-cell clonal lineages <i>in vivo</i> were detected following dupilumab. <h3>Conclusion</h3> Data supports clone-specific effects of dupilumab in pediatric Type-2 disorders. This approach enables analysis of changes in gene networks in T-cell clones and populations following treatment. Upregulation of non-Type-2 signaling and changes at the clonal level suggest Dupilumab restores balance to the immune response.

Genetic diversity of whitefly species of the Bemisia tabaci Gennadius (Hemiptera: Aleyrodidae) species complex, associated with vegetable crops in Côte d'Ivoire.

Since several years, whiteflies of the species complex of Bemisia tabaci (Gennadius) are causing several damages on vegetable crops in Côte d'Ivoire. These sap-sucking insects are the main vector of many viruses on tomato and several species of this complex have developed resistances against insecticides. Nevertheless, there is very little information about whitefly species on vegetable crops in Côte d'Ivoire. Here, we investigated the species diversity and their genetic diversity and structuring on samples from vegetable crops in the major tomato production areas of Côte d'Ivoire. To assess this diversity, 535 whitefly samples from different localities and plant species were collected and analysed with nuclear (microsatellite) and mitochondrial (mtCOI) markers. In each site, and ecological data were recorded, including whiteflies abundance and plant species colonised by B. tabaci. The analysis of mtCOI sequences of whiteflies indicated the presence of four cryptic species on tomato and associated crops in Côte d'Ivoire. These were MED ASL, MED Q1, SSA 1 and SSA3. The MED ASL species dominated over all samples in the different regions and plant species. One haplotype of MED ASL out of the 15 identified predominated on most plant species and most sites. These results suggested that MED ASL is probably the main phytovirus vector in the Ivorian vegetable cropping areas. In contrast, only five haplotypes of MED Q1 were identified on vegetables but in the cotton-growing areas of the country. Its low prevalence, low nuclear and mitochondrial diversity might indicate a recent invasion of this species on vegetable crops in Côte d'Ivoire. The Bayesian nuclear analysis indicated the presence of hybrid genotypes between the two main species MED ASL and MED Q1, however in low prevalence (10%). All these results highlight the need to maintain whitefly populations monitoring for a more effective management in Côte d'Ivoire.