Genetic Admixture Research Articles

Sex chromosome turnover in hybridizing stickleback lineages

Abstract Recent discoveries of sex chromosome diversity across the tree of life have challenged the canonical model of conserved sex chromosome evolution and evoked new theories on labile sex chromosomes that maintain less differentiation and undergo frequent turnover. However, theories of labile sex chromosome evolution lack direct empirical support due to the paucity of case studies demonstrating ongoing sex chromosome turnover in nature. Two divergent lineages (viz. WL & EL) of nine-spined sticklebacks (Pungitius pungitius) with different sex chromosomes (linkage group [LG] 12 in the EL, unknown in the WL) hybridize in a natural secondary contact zone in the Baltic Sea, providing an opportunity to study ongoing turnover between coexisting sex chromosomes. In this study, we first identify an 80 kbp genomic region on LG3 as the sex-determining region (SDR) using whole-genome resequencing data of family crosses of a WL population. We then verify this region as the SDR in most other WL populations and demonstrate a potentially ongoing sex chromosome turnover in admixed marine populations where the evolutionarily younger and homomorphic LG3 sex chromosome replaces the older and heteromorphic LG12 sex chromosome. The results provide a rare glimpse of sex chromosome turnover in the wild and indicate the possible existence of additional yet undiscovered sex chromosome diversity in Pungitius sticklebacks.

Genetic Profile of Greek Indigenous Honey Bee Populations, Local Extinctions, Geographical Distinction, and Patterns, by Using mtDNA COI and Nuclear CSD Gene Analysis Markers

Evaluation and conservation of local genetic resources of the domestic honey bee populations is important, especially in regions with high diversity levels as well as high honey bee colony density. Greece is rich in honey bee biodiversity, hosting several subspecies, with the status of them being, though, doubtful. The purpose of the present study was to investigate the genetic relationships of both stationary and movable honey bee populations, originating from many location throughout Greece. Two molecular markers were utilized, namely, the conserved mitochondrial COI gene and the highly variable complementary sex determination (CSD) gene. Samples were collected from nine distant populations: eight populations from colonies that followed the traditional stationary beekeeping model and one following the modern migratory beekeeping model type, where the hives are transferred from place to place according to the season. Regardless the beekeeping model, all populations were characterized by sufficient genetic diversity indicating no signs of inbreeding or any bottleneck effects. Nevertheless, genetic differentiation and phylogenetic analysis in comparison with haplotypes obtained from GenBank revealed a genetic admixture pattern suggesting that movement causes genetic homogeneity, occasionally in the stable reared populations as well. Interestingly, two populations, namely, Kastoria and Protokklisi, belonging to A. m. macedonica population, were significantly differentiated, supporting the maintenance of their genetic integrity. Unfortunately, on the other hand, genetic structure of the populations from Crete (Sasalos population) provided evidence that the indigenous breed from the island, A. m. adami, has probably gone extinct. Future management strategies should focus on the conservation of the local genetic resources in which distinct genetic identity has been sustained.

Exploring the relationship between admixture and genetic susceptibility to attention deficit hyperactivity disorder in two Latin American cohorts

Contemporary research on the genomics of Attention Deficit Hyperactivity Disorder (ADHD) often underrepresents admixed populations of diverse genomic ancestries, such as Latin Americans. This study explores the relationship between admixture and genetic associations for ADHD in Colombian and Mexican cohorts. Some 546 participants in two groups, ADHD and Control, were genotyped with Infinium PsychArray®. Global ancestry levels were estimated using overall admixture proportions and principal component analysis, while local ancestry was determined using a method to estimate ancestral components along the genome. Genome-wide association analysis (GWAS) was conducted to identify significant associations. Differences between Colombia and Mexico were evaluated using appropriate statistical tests. 354 Single-nucleotide polymorphisms (SNPs) and Single-nucleotide variants (SNVs) related to some genes and intergenic regions exhibited suggestive significance (p-value < 5*10e−5) in the GWAS. None of the variants revealed genome-wide significance (p-value < 5*10e−8). The study identified a significant relationship between risk SNPs and the European component of admixture, notably observed in the LOC105379109 gene. Despite differences in risk association loci, such as FOXP2, our findings suggest a possible homogeneity in genetic variation’s impact on ADHD between Colombian and Mexican populations. Current reference datasets for ADHD predominantly consist of samples with high European ancestry, underscoring the need for further research to enhance the representation of reference populations and improve the identification of ADHD risk traits in Latin Americans.

Parallel patterns of genetic diversity and structure in circumboreal species of the Sphagnum capillifolium complex.

Shared geographical patterns of population genetic variation among related species is a powerful means to identify the historical events that drive diversification. The Sphagnum capillifolium complex is a group of closely related peat mosses within the Sphagnum subgenus Acutifolia and contains several circumboreal species whose ranges encompass both glaciated and unglaciated regions across the northern hemisphere. In this paper, we (1) inferred the phylogeny of subg. Acutifolia and (2) investigated patterns of population structure and genetic diversity among five circumboreal species within the S. capillifolium complex. We generated RAD sequencing data from most species of the subg. Acutifolia and samples from across the distribution ranges of circumboreal species within the S. capillifolium complex. We resolved at least 14 phylogenetic clusters within the S. capillifolium complex. Five circumboreal species show some common patterns: One population system comprises plants in eastern North America and Europe, and another comprises plants in the Pacific Northwest or around the Beringian and Arctic regions. Alaska appears to be a hotspot for genetic admixture, genetic diversity, and sometimes endemic subclades. Our results support the hypothesis that populations of five circumboreal species within the S. capillifolium complex survived in multiple refugia during the last glacial maximum. Long-distance dispersal out of refugia, population bottlenecks, and possible adaptations to conditions unique to each refugium could have contributed to current geographic patterns. These results indicate the important role of historical events in shaping the complex population structure of plants with broad distribution ranges.

High clonal diversity and spatial genetic admixture in early prostate cancer and surrounding normal tissue

Somatic copy number alterations (SCNAs) are pervasive in advanced human cancers, but their prevalence and spatial distribution in early-stage, localized tumors and their surrounding normal tissues are poorly characterized. Here, we perform multi-region, single-cell DNA sequencing to characterize the SCNA landscape across tumor-rich and normal tissue in two male patients with localized prostate cancer. We identify two distinct karyotypes: ‘pseudo-diploid’ cells harboring few SCNAs and highly aneuploid cells. Pseudo-diploid cells form numerous small-sized subclones ranging from highly spatially localized to broadly spread subclones. In contrast, aneuploid cells do not form subclones and are detected throughout the prostate, including normal tissue regions. Highly localized pseudo-diploid subclones are confined within tumor-rich regions and carry deletions in multiple tumor-suppressor genes. Our study reveals that SCNAs are widespread in normal and tumor regions across the prostate in localized prostate cancer patients and suggests that a subset of pseudo-diploid cells drive tumorigenesis in the aging prostate.

From sub-Saharan Africa to China: Evolutionary history and adaptation of Drosophila melanogaster revealed by population genomics.

Drosophila melanogaster is a widely used model organism for studying environmental adaptation. However, the genetic diversity of populations in Asia is poorly understood, leaving a notable gap in our knowledge of the global evolution and adaptation of this species. We sequenced genomes of 292 D. melanogaster strains from various ecological settings in China and analyzed them along with previously published genome sequences. We have identified six global genetic ancestry groups, despite the presence of widespread genetic admixture. The strains from China represent a unique ancestry group, although detectable differentiation exists among populations within China. We deciphered the global migration and demography of D. melanogaster, and identified widespread signals of adaptation, including genetic changes in response to insecticides. We validated the effects of insecticide resistance variants using population cage trials and deep sequencing. This work highlights the importance of population genomics in understanding the genetic underpinnings of adaptation, an effort that is particularly relevant given the deterioration of ecosystems.

Genetic diversity among the present Japanese population: evidence from genotyping of human cell lines established in Japan

Japan is often assumed to have a highly homogeneous ethnic population, because it is an island country. This is evident in human cell lines collected from cell banks; however, these genotypes have not been thoroughly characterized. To examine the population genotypes of human cell lines established in Japan, we conducted SNP genotyping on 57 noncancerous cell lines and 43 lung cancer cell lines. Analysis of biogeographic ancestry revealed that 58 cell lines had non-admixed Japanese genotypes, 21 cell lines had an admixture of Japanese and East Asian genotypes, and the remaining 21 cell lines had East Asian genotypes. The proportion of non-admixed Japanese genotypes was similar between lung cancer and noncancerous cell lines, suggesting that patients in Japan may not exclusively have Japanese genotypes. This could influence the incidence of inherited diseases and should be taken into account in personalized medicine tailored to genetic background. The genetic makeup of the present-day Japanese population cannot be fully explained by the ancestral Jomon and Yayoi lineages. Instead, it is necessary to consider a certain level of genetic admixture between Japanese and neighboring Asian populations. Our study revealed genetic variation among human cell lines derived from Japanese individuals, reflecting the diversity present within the Japanese population.

Frequency of Gene Polymorphisms in Admixed Venezuelan Women with Recurrent Pregnancy Loss: Microsomal Epoxy Hydroxylase (rs1051740) and Enos (rs1799983).

Recurrent pregnancy loss (RPL) affects around 2% of women of reproductive age. Primary RPL is defined by ≥2 pregnancy losses and no normal birth delivery. In secondary RPL, the losses are after a normal pregnancy and delivery. Most cases have no clear aetiology, although primary cases are the most complex. Several gene single nucleotide polymorphisms (SNPs) have been associated with RPL. The frequency of some SNPs is increased in women suffering from RLP from Asian or Caucasian races; however, in admixed populations, the information on possible genetic links is scarce and contradictory. This study aimed to assess the frequency of two SNPs present in two different enzymes involved in medical conditions observed during pregnancy. It is a case-control study. Microsomal epoxy hydrolase (mEPH) is involved in detoxifying xenobiotics, is present in the ovaries, and is hormonally regulated. The endothelial nitric oxide synthase (NOS3) that forms nitric is involved in vascular tone. Two SNPs, rs1051740 (mEPH) and rs1799983 (NOS3), were assessed. The study included 50 controls and 63 primary RPL patients. The frequency of mutated alleles in both SNPs was significantly higher in patients (p < 0.05). Double-mutated homozygotes were encountered only in RPL patients (p < 0.05). Genetic polymorphisms rs1051740 and rs1799983 may be involved in primary RPL in the Venezuelan admix population. Genetic studies could provide crucial information on the aetiology of primary RPL.

Demographic characteristics and epigenetic biological aging among post-9/11 veterans: Associations of DunedinPACE with sex, race, and age

Measures of epigenetic aging derived from DNA methylation (DNAm) have enabled the assessment of biological aging in new populations and cohorts. In the present study, we used an epigenetic measure of aging, DunedinPACE, to examine rates of aging across demographic groups in a sample of 2,309 United States military veterans from the VISN 6 MIRECC's Post-Deployment Mental Health Study. As assessed by DunedinPACE, female veterans were aging faster than male veterans (β = 0.39, 95 % CI [0.29, 0.48], p < .001), non-Hispanic Black veterans were aging faster than non-Hispanic White veterans (β = 0.58, 95 % CI [0.50, 0.66], p < .001), and older veterans were biologically aging faster than younger veterans (β = 0.21, 95 % CI [0.18, 0.25], p < .001). In secondary analyses, these differences in rates of aging were not explained by a variety of biopsychosocial covariates. In addition, the percentage of European genetic admixture in non-Hispanic Black veterans was not associated with DunedinPACE. Our findings suggest that female and non-Hispanic Black veterans are at greater risk of accelerated aging among post-9/11 veterans. Interventions that slow aging might provide relatively greater benefit among veterans comprising these at-risk groups.

Abstract LB006: Cell marker-based classification of TNBC subtypes and patient outcomes

Abstract Background: Triple-negative breast cancer (TNBC) is an aggressive BC subtype characterized by significant molecular and clinical heterogeneity, influenced by genetic, phenotypic, and environmental factors, as well as interactions of the tumor with its surrounding milieu. In the recent past, gene expression-based subtyping methods have provided a functional understanding for the observed molecular diversity/heterogeneity. In this study, we propose an approach to reclassifying TNBC while considering the cellular heterogeneity of the tumor as well as the tumor milieu. Methods: RNA-Sequencing data for TNBC cohort of 250 diverse women [European (EA, self-reported race, SRR): 114 and African (AA, SRR): 136)], was obtained from our collaborators at LSUHSC. 38/250 were labeled ERhi via IHC but histologically confirmed to be TNBC patients. We utilized 261 breast specific cell type markers to classify our cohort via hierarchical (HC) and consensus (CC) clustering. Differentially expressed genes (DEGs) were identified at p-adj ≤ 0.05. Endotype specific networks were generated using protein-protein interactions, DEGs, and genes regulated by transcription factor. Survival was assessed via log-rank tests. Genetic admixture was performed on 227/250 patients using method described by Pakstis, A. J. et al. Results: We identified three distinct mechanistic subtypes (endotype, CC1-3) containing nine distinct groups (HC1-9), revealing substantial heterogeneity in cell-type and tissue-state within TNBC. Each subtype exhibited unique biomarkers, reflecting diverse immune, extracellular matrix, adipogenesis, and inflammatory signatures. Endotype specific networks revealed patients in CC1 exhibited upregulation of CD8 T cell activation, interferon and interleukin markers, while CC2 showed upregulation of extracellular matrix genes, and CC3, the subtype containing ERhi patients, showed upregulation of fatty acid regulation, hormone sensitivity, and pro-inflammatory genes. Survival analysis demonstrated favorable outcomes for CC1 and less favorable outcomes for CC2. Additionally, SRR-inferred survival differences highlighted poorer outcomes for CC2 groups. We found SRR-inferred prognostic biomarkers such as TTC6, ANKRD30A, and KRT86 associated with distinct prognostic profiles in CC2. Genetic admixture showed a comparable distribution of SRR and genetic ancestry across subtypes. We developed a user-friendly Shiny App for our subtyping method and validated it using TCGA TNBC data. Conclusion: TNBC subtyping using cellular heterogeneity of biopsied samples provides a mechanistic approach to patient classification. Subtype-specific mechanisms suggest tailored therapeutic strategies and provide survival outcomes specific to each subtype. Our method can be applied to other cohorts using the application developed in this work. Citation Format: Zahra Mesrizadeh, Kavitha Mukund, Fokrul Hossain, Jovanny Zabaleta, Denise Danos, Luis Del Valle, Xiao-Cheng Wu, Chindo Hicks, Yuan Chun Ding, Augusto Ochoa, Lucio Miele, Victoria L. Seewaldt, Shankar Subramaniam. Cell marker-based classification of TNBC subtypes and patient outcomes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB006.

Goffman against DNA: genetic stigma and the use of genetic ancestry tests by white nationalists

How do white nationalists use genetic ancestry tests? This article provides a qualitative analysis of posts from Stormfront, a white nationalist message board, to understand how white nationalists use genetic ancestry tests to advance ideological claims about the threat of genetic admixture. Starting in 2004, members of this message board began discussing the promises and pitfalls of using genetic ancestry tests to prove their whiteness. Using Goffman’s framework of stigma and impression management, we explore how they manage undesirable test results and genetic stigma amongst themselves – when they take genetic tests and discover they are partially non-white. Finally, this article looks at how they simultaneously deploy exclusionary or inclusionary strategies that challenge past concepts of whiteness built on the one-drop rule. Pragmatic concerns often drive their strategic positioning when confronted with undesirable test results, as they are aware that too strict exclusionary policies may impede the group’s demographical survival.

Avanzando Caminos (Leading Pathways): design and procedures of the Hispanic/Latino Cancer Survivorship Study.

Avanzando Caminos (Leading Pathways): The Hispanic/Latino Cancer Survivorship Cohort Study aims to examine the influence of sociocultural, medical, stress-related, psychosocial, lifestyle, behavioral, and biological factors on symptom burden, health-related quality of life, and clinical outcomes among Hispanics/Latinos who have been previously treated for cancer. Avanzando Caminos is a prospective, cohort-based study of 3000 Hispanics/Latinos who completed primary cancer treatment within the past 5 years that is representative of the general Hispanic/Latino population in the United States. Participants will complete self-report measures at baseline (time [T] 1), 6months (T2), 1year (T3), 2years (T4), 3years (T5), 4years (T6), and 5years (T7). Blood samples drawn for assessment of leukocyte gene expression, cardiometabolic markers, and genetic admixture will be collected at baseline (T1), 1year (T3), 3years (T5), and 5years (T7). Medical and cancer characteristics and clinical outcomes will be extracted from the electronic medical record and/or state cancer registry at each time point. Data analysis will include general latent variable modeling and latent growth modeling. Avanzando Caminos will fill critical gaps in knowledge in order to guide future secondary and tertiary prevention efforts to mitigate cancer disparities and optimize health-related quality of life among Hispanic/Latino cancer survivors.

Genetic ancestry and radical prostatectomy findings in Hispanic/Latino patients.

African ancestry is a known factor associated with the presentation and aggressiveness of prostate cancer (PC). Hispanic/Latino populations exhibit varying degrees of genetic admixture across Latin American countries, leading to diverse levels of African ancestry. However, it remains unclear whether genetic ancestry plays a role in the aggressiveness of PC in Hispanic/Latino patients. We explored the associations between genetic ancestry and the clinicopathological data in Hispanic/Latino PC patients from Colombia. We estimated the European, Indigenous and African genetic ancestry, of 230 Colombian patients with localized/regionally advanced PC through a validated panel for genotypification of 106 Ancestry Informative Markers. We examined the associations of the genetic ancestry components with the Gleason Grade Groups (GG) and the clinicopathological characteristics. No association was observed between the genetic ancestry with the biochemical recurrence or Gleason GG; however, in a two groups comparison, there were statistically significant differences between GG3 and GG4/GG5 for European ancestry, with a higher mean ancestry proportion in GG4/GG5. A lower risk of being diagnosed at an advanced age was observed for patients with high African ancestry than those with low African ancestry patients (OR: 0.96, CI: 0.92-0.99, p=0.03). Our findings revealed an increased risk of presentation of PC at an earlier age in patients with higher African ancestry compared to patients with lower African ancestry in our Hispanic/Latino patients.

Genome-wide sequencing reveals geographical variations in the thermal adaptation of an aquaculture species with frequent seedling introductions

Climate change and human activity are essential factors affecting marine biodiversity and aquaculture, and understanding the impacts of human activities on the genetic structure to increasing high temperatures is crucial for sustainable aquaculture and marine biodiversity conservation. As a commercially important bivalve, the Manila clam Ruditapes philippinarum is widely distributed along the coast of China, and it has been frequently introduced from Fujian Province, China, to other regions for aquaculture. In this study, we collected four populations of Manila clams from different areas to evaluate their thermal tolerance by measuring cardiac performance and genetic variations using whole-genome resequencing. The upper thermal limits of the clams showed high variations within and among populations. Different populations displayed divergent genetic compositions, and the admixed population was partly derived from the Zhangzhou population in Fujian Province, implying a complex genomic landscape under the influence of local genetic sources and human introductions. Multiple single nucleotide polymorphisms (SNPs) were associated with the cardiac functional traits, and some of these SNPs can affect the codon usage and the structural stability of the resulting protein. This study shed light on the importance of establishing long-term ecological and genetic monitoring programs at the local level to enhance resilience to future climate change.

Simplified detection of genetic background admixture using artificial intelligence.

Admixture refers to the mixing of genetic ancestry from different populations. Admixture is important for genomic medicine because it can affect how an individual responds to certain medications, how they metabolize drugs, and susceptibility to certain diseases. For example, some genetic variants associated with drug metabolism and response may be more common in certain populations, and individuals with admixed ancestry may have a different frequency of these variants than individuals from the ancestral populations. Understanding the patterns of admixture in a population can also help researchers identify new genetic variants associated with diseases or traits and develop more personalized and targeted treatments. In this study, we compared and classified the known and self-reported genetic backgrounds from 1000 Genomes Project and admixed samples from GTEx projects using supervised, unsupervised and statistical classification methodologies. We developed a novel tool called Admix-AI that uses a one-dimensional convolutional neural network to understand and classify admixed genetic backgrounds using 213 DNA-marker based genetic background labels. Admix-AI can be used to discover admixed proportions in samples and ultimately aid personalized genomic medicine by identifying specific biomarker systems. We compared Admix-AI to the existing admixture categorization software and found our tool to be computationally faster with 2× speedup and streamlined usage. Admix-AI is available as open-source code under GPL version 3.0 license at https://github.com/rpauly/Admix-AI.

Antenatal RHD screening to guide antenatal anti-D immunoprophylaxis in non-immunized D- pregnant women.

In pregnancy, D- pregnant women may be at risk of becoming immunized against D when carrying a D+ fetus, which may eventually lead to hemolytic disease of the fetus and newborn. Administrating antenatal and postnatal anti-D immunoglobulin prophylaxis decreases the risk of immunization substantially. Noninvasive fetal RHD genotyping, based on testing cell-free DNA extracted from maternal plasma, offers a reliable tool to predict the fetal RhD phenotype during pregnancy. Used as a screening program, antenatal RHD screening can guide the administration of antenatal prophylaxis in non-immunized D- pregnant women so that unnecessary prophylaxis is avoided in those women who carry a D- fetus. In Europe, antenatal RHD screening programs have been running since 2009, demonstrating high test accuracies and program feasibility. In this review, an overview is provided of current state-of-the-art antenatal RHD screening, which includes discussions on the rationale for its implementation, methodology, detection strategies, and test performance. The performance of antenatal RHD screening in a routine setting is characterized by high accuracy, with a high diagnostic sensitivity of ≥99.9 percent. The result of using antenatal RHD screening is that 97-99 percent of the women who carry a D- fetus avoid unnecessary prophylaxis. As such, this activity contributes to avoiding unnecessary treatment and saves valuable anti-D immunoglobulin, which has a shortage worldwide. The main challenges for a reliable noninvasive fetal RHD genotyping assay are low cell-free DNA levels, the genetics of the Rh blood group system, and choosing an appropriate detection strategy for an admixed population. In many parts of the world, however, the main challenge is to improve the basic care for D- pregnant women.

The genetic admixture and assimilation of Ahom: a historic migrant from Thailand to India.

The Northeastern region of India is considered a gateway for modern humans' dispersal throughout Asia. This region is a mixture of various ethnic and indigenous populations amalgamating multiple ancestries. One reason for such amalgamation is that, South Asia experienced multiple historic migrations from various parts of the world. A few examples explored genetically are Jews, Parsis and Siddis. Ahom is a dynasty that historically migrated to India during the 12th century. However, this putative migration has not been studied genetically at high resolution. Therefore, to validate this historical evidence, we genotyped autosomal data of the Modern Ahom population residing in seven sister states of India. Principal Component and Admixture analyses haave suggested a substantial admixture of the Ahom population with the local Tibeto-Burman populations. Moreover, the haplotype-based analysis has linked these Ahom individuals mainly with the Kusunda (a language isolated from Nepal) and Khasi (an Austroasiatic population of Meghalaya). Such unexpected presence of widespread population affinities suggests that Ahom mixed and assimilated a wide variety of Trans-Himalayan populations inhabiting this region after the migration. In summary, we observed a significant deviation of Ahom from their ancestral homeland (Thailand) and extensive admixture and assimilation with the local South Asian populations.

Xenografted human microglia display diverse transcriptomic states in response to Alzheimer’s disease-related amyloid-β pathology

Microglia are central players in Alzheimer’s disease pathology but analyzing microglial states in human brain samples is challenging due to genetic diversity, postmortem delay and admixture of pathologies. To circumvent these issues, here we generated 138,577 single-cell expression profiles of human stem cell-derived microglia xenotransplanted in the brain of the AppNL-G-F model of amyloid pathology and wild-type controls. Xenografted human microglia adopt a disease-associated profile similar to that seen in mouse microglia, but display a more pronounced human leukocyte antigen or HLA state, likely related to antigen presentation in response to amyloid plaques. The human microglial response also involves a pro-inflammatory cytokine/chemokine cytokine response microglia or CRM response to oligomeric Aβ oligomers. Genetic deletion of TREM2 or APOE as well as APOE polymorphisms and TREM2R47H expression in the transplanted microglia modulate these responses differentially. The expression of other Alzheimer’s disease risk genes is differentially regulated across the distinct cell states elicited in response to amyloid pathology. Thus, we have identified multiple transcriptomic cell states adopted by human microglia in a multipronged response to Alzheimer’s disease-related pathology, which should be taken into account in translational studies.

Regional European genetic ancestry predicts type I interferon level and risk of severe viral infection.

Viral infection outcomes vary widely between individuals, ranging from mild symptoms to severe organ failure and death, and it is clear that host genetic factors play a role in this variability. Type I interferon (IFN) is a critical anti-viral cytokine, and we have previously noted differences in type I IFN levels between world populations. In this study, we investigate the interrelationship between regional European genetic ancestry, type I IFN levels and severe viral infection outcomes. In cohorts of European ancestry lupus patients living in Europe, we noted higher IFN in the Northwestern populations as compared to Southeastern populations. In an independent cohort of European ancestry lupus patients from the USA with varying proportional regional European genetic admixture, we observed the same Northwest vs. Southeast European ancestry IFN gradient. We developed a model to predict type I IFN level based on regional European ancestry (Area under the curve (AUC) = 0.73, P = 6.1e-6). Examining large databases containing serious viral outcomes data, we found that lower predicted IFN in the corresponding European country was significantly correlated with increased viral infection fatality rate, including Coronavirus Disease 2019 (COVID-19), viral hepatitis and HIV [correlation coefficients: -0.79 (P = 4e-2), -0.94 (P = 6e-3) and -0.96 (P = 8e-2), respectively]. This association between predicted type I IFN level and viral outcome severity suggests a potential causal relationship, as greater intrinsic type I IFN is beneficial in host defense against viruses. Genetic testing could provide insight into individual and population level risk of fatality due to viruses prior to infection, across a wide range of viral pathogens.

Abstract 7609: Potential gene expression meta-signatures predict neoadjuvant chemotherapy response in invasive breast cancer

Abstract Early prediction of Neoadjuvant Chemotherapy (NAC) response is crucial for women with locally advanced breast cancer (BC), given their low response rates. This study aims to identify gene expression patterns and tumor microenvironment (TME) characteristics associated with resistance to NAC, which could significantly impact tumor progression and treatment outcomes. The study encompassed differential gene expression comparing non-responders and responders, enrichment analysis, tumor microenvironment estimation, and cytokines identification from a female patient's cohort with distinct molecular subtypes and candidates to NAC at the Colombian National Cancer Institute. Candidate differentially expressed genes validated with RT-PCR in a larger validation cohort and corroborated in several publicly available databases, including associated treatment drugs. Distinct gene expression profiles were observed between responders and non-responders, emphasizing immune system-related pathways such as IL-17 signaling, B cell receptor signaling, complement and coagulation cascades, natural killer cell-mediated cytotoxicity, and NF-kB signaling. Immune-related genes (AGTR1, APOD, CCL19, CGA, ECEL1, NPY1R, NTNG1, PCSK1, PFDN2, S100B, TPRG1, WDR5B, ZNF385B) were identified as biomarkers correlated with non-response and worse prognosis. Responders showed increased B cell populations, CD4+ and CD8+ effector memory T-cells in lymphoid groups, while non-responders displayed elevated levels of CD8+ naive T-cells. Additionally, responders revealed upregulated myeloid cell populations like macrophages and dendritic cells. Several cytokines like IL1B, IL-2, IL-4, IL-12, IL-21, IL-22, IL-36, and TWEAK showed elevated expression in non-responders. Dexamethasone, Vinblastine, and Streptozocin were candidate drugs that interacted with AGTR1, CGA, and S100B, respectively and are associated with progression and metastasis. Logistic regression revealed that overexpression of CGA showed a higher probability (OR:1.83, p=0.03) while ECEL1 had a lower probability (OR=0.44, p=0.04) in non-responders compared to responders who lacked expression of these genes. Immune-related genes and various subtypes of immune cells within the TME exhibit correlations with response to NAC, and several cell fractions significantly changed before and after NAC. These results suggest meta-signatures that warrant further evaluation as concordance assessment between immunohistochemistry (IHC) and gene expression profiling, in addition to an extensive validation to triage patients before NAC and target personalized interventions. Detection and evaluation of TME components are essential to predict NAC efficacy and avoid disease relapse. Finally, these findings emphasize the importance of assessing admixed populations to facilitate novel findings and alleviate disparities. Citation Format: Hedda Michelle Guevara-Nieto, Rafael S. Parra-Medina, Jovanny Zabaleta, Liliana Lopez-Kleine, Alba L. Combita. Potential gene expression meta-signatures predict neoadjuvant chemotherapy response in invasive breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7609.