IntroductionHippocampal atrophy is frequently observed in neurodegenerative diseases such as Alzheimer’s disease (AD) or hippocampal sclerosis of aging (HS-aging). Volume loss in the hippocampus is described as prodromal stage of dementia and has been associated with AD polygenic risk score (PRS). CA1 and subiculum atrophy have been suggested to be a promising in vivo biomarker for HS-aging. Recent studies suggest that some loci associated with AD may be more related to other brain diseases concomitant with AD. We aimed to find which significant single nucleotide polymorphisms (SNPs) in the latest AD genome wide association studies (GWAS) could be potentially related with early atrophy of specific hippocampal subregions related to HS-aging.Materials and methodsWe used regression models to assess the relation of the AD-PRS, and genome-wide significant AD variants, with CA1 and subiculum volumes assessed by magnetic resonance imaging (MRI) in 1,859 participants without dementia (with mild cognitive impairment or cognitively healthy). Co-regulatory network analyses and over-representation enrichment analyses were conducted to identify biological pathways enriched with co-regulatory networks of genes associated with hippocampal subregion volumes. We meta-analyzed data from seven cohorts to associate their AD-PRS with AD in the presence of concomitant brain pathologies.ResultsReduced volumes of CA1 and subiculum show association with higher levels of AD-PRS and with variant rs5848 in GRN. This variant was enriched in immune-related pathways. AD-PRS showed no significant association with AD pathology alone, but was strongly associated with AD in the presence of concomitant neurodegenerative pathologies, with HS-aging showing the largest effect size.DiscussionSpecific AD-SNPs enriched in immune-brain axis pathways rather than Aβ related processes, were associated with reduced volumes of CA1 and subiculum prior to dementia onset. This supports that AD-PRS may capture genetic susceptibility to concomitant neurodegenerative diseases frequently misdiagnosed as AD. Given that AD-PRS is most strongly associated with AD in cases with HS-aging, and that CA1 and subiculum are promising in vivo biomarker for HS-aging also linked with rs5848 in GRN, our findings are consistent with HS-aging related vulnerability. This insight links early hippocampal subfields atrophy to shared genetic mechanisms and biological pathways of interest.

Recent studies suggest that copy number variants (CNVs) may contribute to the missing heritability of complex diseases such as Alzheimer's disease (AD) and related dementias (ADRD). We performed a CNV analysis using genotyping data (Axiom 815 K Spanish biobank array) from the GR@ACE/DEGESCO dementia dataset (n = 20,067) of the Spanish population. Applying PennCNV and extensive quality control, 8275 controls and 7818 dementia cases were selected for gene-level case/control associations. We identified 43,833 CNVs with deletions (47%) and duplications (53%). No genome-wide significant associations were found, but nominal associations were observed in PKP3-SIGIRR and FBRSL1 loci. CNVs in 2970 genes were exclusive to dementia cases and enriched in vascular-related pathways. Notable findings included 14q11.2 duplication and VPS13B deletions in ADRD cases, the latter confirmed by optical genome mapping. Our findings suggest potential novel genes associated with ADRD in the Spanish population. However, the limited resolution of array-based technologies in detecting CNVs warrants further investigation.

Progressive supranuclear palsy (PSP) is a rare 4-repeat tauopathy that causes behavioural, movement and cognitive abnormalities. We genotyped all available clinical and histopathological PSP cases in Spain and Portugal (N = 522), and conducted the largest PSP GWAS of the Iberian population to date. Genetic burden analysis revealed reduced diagnostic specificity in clinically diagnosed atypical PSP cases—when applying the 2017 MDS criteria—compared to Richardson’s syndrome cases. We independently replicated eight PSP risk variants in seven known loci (MAPT, MOBP, EIF2AK3, STX6, SLCO1A2, DUSP10 and APOE), and identified a novel locus in NFASC/CNTN2 (rs12744678 C: OR[95

BackgroundEarly detection of sepsis is essential for its successful management. Although genome-wide association studies (GWAS) have shown potential in identifying sepsis-related genetic variants, they often involve heterogeneous patient groups and use single-locus analysis methods. Here, we aim to identify new sepsis susceptibility loci in post-surgical patients using an explainable artificial intelligence (XAI) approach applied to GWAS data.MethodsGWAS was performed in 750 post-operative patients with sepsis and 3,500 population controls. We applied a novel XAI-based methodology to GWAS-derived single nucleotide polymorphisms (SNPs) to predict sepsis and prioritize new genetic variants associated with post-operative sepsis susceptibility. We also assessed functional and enrichment effects using empirical data from integrated software tools and datasets, with the top-ranked variants and associated genes.ResultsOur XAI-GWAS approach showed a notable performance in predicting post-surgical sepsis and prioritized SNPs (such as rs17653532, rs1575081785, and rs74707084) with higher contribution to post-operative sepsis prediction. It also facilitated the discovery of post-operative sepsis risk loci with important functional implications related to gene expression regulation, DNA replication, cyclic nucleotide signaling, cell proliferation, and cardiac dysfunction.ConclusionThe combination of GWAS and XAI prioritized loci associated with post-operative sepsis susceptibility. The determination of key genes, such as PRIM2, SYNPR, and RBSN, through pre-operative blood tests could enhance risk stratification, enable early detection of post-operative sepsis, and guide targeted interventions to improve patient outcomes. Further research with additional and ethnically diverse cohorts comprising sepsis and non-sepsis patients undergoing major surgery is needed to validate these exploratory findings.

BACKGROUND:Obesity is a multi-cause chronic disease recognized across the lifespan, with childhood obesity prevalence rising over the past decades. Although exposome-wide association studies have identified early-life environmental drivers of child obesity, and explored the multi-omics signatures of the exposome of children, it is understudied whether the combined effects of multiple exposures are potentially mediated by multi-omics. METHODS:Within the Human Early Life Exposome (HELIX) project, 1041 mother-child pairs were surveyed for a wide range of environmental exposures including over 354 prenatal and childhood exposures. Multi-omics molecular features were measured during childhood, encompassing the blood methylome and transcriptome, plasma proteins and urinary and serum metabolites. Exposome and multi-omics features were integrated into latent factors by Multi-omics Factor Analysis, based on which structural equation modelling was used to assess whether multi-omics mediated associations between exposome and child body mass index (BMI). RESULTS:Key findings included: (i) prenatal nutrition, exercise, and passive smoking influencing BMI via DNA methylation of HOXA5 and Tenascin XB; (ii) childhood exposure to PCBs and phenols linked with BMI through inflammation and coagulation pathways; and (iii) childhood PCB and dietary exposures associated with BMI via immune pathways. CONCLUSIONS:This novel untargeted workflow elucidated biological mechanisms linking environmental exposures to child obesity, potentially supporting targeted public health interventions.

Alzheimer’s disease (AD) is a complex disease with a strong genetic component, yet many genetic risk factors remain unknown. We combined genome-wide association studies (GWAS) on amyloid endophenotypes measured in cerebrospinal fluid (CSF) and positron emission tomography (PET) as surrogates of amyloid pathology, which may provide insights into the underlying biology of the disease. We performed a meta-GWAS of CSF Aβ42 and PET measures combining six independent cohorts (n = 2,076). Given the opposite beta direction of Aβ phenotypes in CSF and PET measures, only genetic signals showing opposite directions were considered for analysis (n = 376,599). We explored the amyloidosis signature in the CSF proteome using SOMAscan proteomics (ACE cohort, n = 1,008), connected it with GWAS loci modulating amyloidosis and performed an enrichment analysis of overlapping hits. Finally, we compared our results with a large meta-analysis using publicly available datasets in CSF (n = 13,409) and PET (n = 13,116). After filtering the meta-GWAS, we observed genome-wide significance in the rs429358-APOE locus and annotated nine suggestive hits. We replicated the APOE loci using the large CSF-PET meta-GWAS, identifying multiple AD-associated genes including the novel GADL1 locus. Additionally, we found 1,387 FDR-significant SOMAscan proteins associated with CSF Aβ42 levels. The overlap among GWAS loci and proteins associated with amyloid burden was minimal (n = 35). The enrichment analysis revealed mechanisms connecting amyloidosis with the plasma membrane’s anchored component, synapse physiology and mental disorders that were replicated in the large CSF-PET meta-analysis. Combining CSF and PET amyloid GWAS with CSF proteome analyses may effectively elucidate causative molecular mechanisms behind amyloid mobilization and AD physiopathology.

The CORDELIA Study (Collaborative Cohorts Reassembled Data to Study Mechanisms and Long-term Incidence of Chronic Diseases) combines 35 Spanish population cohorts to investigate the clinical, environmental, genetic, and omics determinants of cardiovascular disease in the Southern European population. It aims to conduct the largest genome-wide association study to date on cardiovascular disease in this population, improve predictions of cardiovascular incidence using genomic and clinical data, and identify subgroups that would benefit most from targeted pharmacological and lifestyle interventions. CORDELIA includes 196,632 individuals (ages 18–84, 54

INTRODUCTION: Hippocampal sclerosis of aging (HS-aging) is frequently present in individuals over 85 who die with dementia. Recent studies suggest that some loci associated with Alzheimer's disease (AD) may be more related to HS-aging. We aimed to find AD-associated SNPs potentially related to HS-aging. METHODS: We assessed the relation of the AD polygenic risk score (AD-PRS) with hippocampal subfield volumes assessed by magnetic resonance imaging (MRI) as HS-by-proxy in 1,130 non-demented participants. We analyzed 1,708 individuals to associate their AD-PRS (83 variants) with AD alongside HS-aging. RESULTS: HS-by-proxy measures of fimbria and hippocampal body and head show association with AD-PRS, SHARPIN, GRN and TNIP1, also after replication. We replicated the stronger AD-PRS association with AD in the presence of HS-aging compared to AD alone. DISCUSSION: Results show association between some AD-SNPs and HS-proxy, enriched in immune-brain axis pathways, differentiating HS-aging from AD. This insight aids in understanding their interrelationships and identifying specific therapeutic targets. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement The Genome Research @ Ace Alzheimer Center Barcelona project (GR@ACE) is supported by Grifols SA, Fundacion bancaria La Caixa, Ace Alzheimer Center Barcelona and CIBERNED. Ace Alzheimer Center Barcelona is one of the participating centers of the Dementia Genetics Spanish Consortium (DEGESCO). The FACEHBI study is supported by funds from Ace Alzheimer Center Barcelona, Grifols, Life Molecular Imaging, Araclon Biotech, Alkahest, Laboratorio de analisis Echevarne and IrsiCaixa. MB, AR, MM acknowledge the support of the Spanish Ministry of Science and Innovation, Proyectos de Generacion de Conocimiento grants PID2021-122473OA-I00, PID2021-123462OB-I00 and PID2019-106625RB-I00. ISCIII, Accion Estrategica en Salud, integrated in the Spanish National R+D+I Plan and financed by ISCIII Subdireccion General de Evaluacion and the Fondo Europeo de Desarrollo Regional (FEDER Una manera de hacer Europa) grants PI13/02434, PI16/01861, PI17/01474, PI19/00335, PI19/01240, PI19/01301, PI12019/08-1, PI22/01403, PI22/00258 and the ISCIII national grant PMP22/00022, funded by the European Union (NextGenerationEU). The support of CIBERNED (ISCIII) under the grants CB06/05/2004 and CB18/05/00010. The support from the ADAPTED and MOPEAD projects, European Union/EFPIA Innovative Medicines Initiative Joint (grant numbers 115975 and 115985, respectively); from PREADAPT project, Joint Program for Neurodegenerative Diseases (JPND) grant No AC19/00097 and No AC23_2/00038; from HARPONE project, Agency for Innovation and Entrepreneurship (VLAIO) grant No PR067/21 and Janssen. DESCARTES project is funded by German Research Foundation (DFG). Additionally, IdR and CO are supported by the Instituto de Salud Carlos III (ISCIII) under the grant FI20/00215 and FI24/00029 respectively. PGG is supported by CIBERNED employment plan (CNV-304-PRF-866). ACF received support from the ISCIII under the grant Sara Borrell (CD22/00125). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: All protocols of the ACE cohort were approved by the Clinical Research Ethics Commission of the Hospital Clinic (Barcelona, Spain) in accordance with the current Spanish regulations in the field of biomedical research and the Declaration of Helsinki. In accordance with Spain's Data Protection Law, all participants were informed about the study's goals and procedures by a neurologist before signing an informed consent form. Patient privacy and data confidentiality were protected in accordance with applicable laws. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors.

Background:Alzheimer's disease (AD) has a high heritable component characteristic of complex diseases, yet many of the genetic risk factors remain unknown. We combined genome-wide association studies (GWAS) on amyloid endophenotypes measured in cerebrospinal fluid (CSF) and positron emission tomography (PET) as surrogates of amyloid pathology, which may be helpful to understand the underlying biology of the disease. Methods:We performed a meta-analysis of GWAS of CSF Aβ42 and PET measures combining six independent cohorts (n=2,076). Due to the opposite effect direction of Aβ phenotypes in CSF and PET measures, only genetic signals in the opposite direction were considered for analysis (n=376,599). Polygenic risk scores (PRS) were calculated and evaluated for AD status and amyloid endophenotypes. We then searched the CSF proteome signature of brain amyloidosis using SOMAscan proteomic data (Ace cohort, n=1,008) and connected it with GWAS results of loci modulating amyloidosis. Finally, we compared our results with a large meta-analysis using publicly available datasets in CSF (n=13,409) and PET (n=13,116). This combined approach enabled the identification of overlapping genes and proteins associated with amyloid burden and the assessment of their biological significance using enrichment analyses. Results:After filtering the meta-GWAS, we observed genome-wide significance in the rs429358-APOE locus and nine suggestive hits were annotated. We replicated the APOE loci using the large CSF-PET meta-GWAS and identified multiple AD-associated genes as well as the novel GADL1 locus. Additionally, we found a significant association between the AD PRS and amyloid levels, whereas no significant association was found between any Aβ PRS with AD risk. CSF SOMAscan analysis identified 1,387 FDR-significant proteins associated with CSF Aβ42 levels. The overlap among GWAS loci and proteins associated with amyloid burden was very poor (n=35). The enrichment analysis of overlapping hits strongly suggested several signalling pathways connecting amyloidosis with the anchored component of the plasma membrane, synapse physiology and mental disorders that were replicated in the large CSF-PET meta-analysis. Conclusions:The strategy of combining CSF and PET amyloid endophenotypes GWAS with CSF proteome analyses might be effective for identifying signals associated with the AD pathological process and elucidate causative molecular mechanisms behind the amyloid mobilization in AD.

We conducted the largest PSP GWAS of the Iberian population to date (522 cases from 22 Spanish and Portuguese institutions). We independently replicated seven known PSP risk variants, and unveiled a novel locus in NFASC/CNTN2 after meta-analysing our results with a newly available Dutch cohort and publicly available summary statistics. These findings highlight the importance of neuron-oligodendrocyte interactions in PSP etiopathology. ### Competing Interest Statement Vigil Neuroscience and Prevail therapeutics are in a public-private partnerschip research program of Sven J. van der Lee. All funding is paid to his institution. ### Funding Statement This work was funded by CIBERNED (Centro Investigacion Biomedica en Red Enfermedades Neurodegenerativas) 10th internal call for cooperative projects (Register number: 2019/09). Agustin Ruiz, Pascual Sanchez-Juan, Alberto Rabano, and Maria J. Bullido received funding from this convocatory. Pablo Garcia-Gonzalez received support by CIBERNED employment plan CNV-304-PRF-866. CIBERNED is integrated into ISCIII (Instituto de Salud Carlos III). Merce Boada, Marta Marquie and Agustin Ruiz are also supported by national grants PI13/02434, PI16/01861, PI17/01474, PI19/01240. PI19/01301, PI19/00335 and PI22/011403, and CIBERNED grant 2019/08. The Genome Research @ Fundacio ACE project (GR@ACE) is supported by Grifols SA, Fundacion bancaria La Caixa, Fundacio ACE, and CIBERNED. Accion Estrategica en Salud is integrated into the Spanish National R + D + I Plan and funded by ISCIII - Subdireccion General de Evaluacion and the Fondo Europeo de Desarrollo Regional (FEDER - Una manera de hacer Europa). Agustin Ruiz is supported by ISCIII national grant PMP22/00022, funded by the European Union (NextGenerationEU). The genotyping service to generate GR@ACE and PSP/DEGESCO GWAS data was carried out at CEGEN-PRB3-ISCIII; it is supported by grant PT17/0019, of the PE I+D+i 2013-2016, funded by ISCIII and ERDF. Itziar de Rojas received support by a national grant from ISCIII FI20/00215. Amanda Cano acknowledges the support of the Spanish Ministry of Science, Innovation and Universities under the grant Juan de la Cierva (FJC2018-036012-I), the support of ISCIII under the grant Sara Borrell (CD22/00125), Spanish Ministry of Science and Innovation, Proyectos de Generacion de Conocimiento grant PID2021-122473OA-I00, and Fundacion ADEY under the program Proyectos de Investigacion en Salud 2023. Fondo de Investigacion en Salud (Instituto Carlos III) (PI17/00096) in the frame of the European Regional Development Fund (ERDF) and to Fundacio ́ la Marato ́ de TV3 (PI043296 and 202009-10). This work was supported by the Spanish Ministry of Science and Innovation (RTC2019-007150-1), the Instituto de Salud Carlos III (ISCIII) and co-funded by the European Union (PI14/01823, PI16/01575, PI18/01898, PI19/01576, PI21/01875), the Consejeria de Economia, Innovacion, Ciencia y Empleo de la Junta de Andalucia (CVI-02526, CTS-7685, PY20_00896), and the Consejeria de Salud y Bienestar Social de la Junta de Andalucia (PI-0471-2013, PE-0210-2018, PI-0459-2018, PE-0186-2019). Pilar Gomez-Garre was supported by the Nicolas Monardes program (C-0048-2017) from Andalusian Regional Ministry of Health. Laura Munoz-Delgado was supported by the Rio Hortega program [CM21/00051] from the Instituto de Salud Carlos III (ISCIII-FEDER). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Sven J. van der Lee was funded for this study by NWO (#733050512, PROMO-GENODE: a PROspective study of MOnoGEnic causes Of Dementia) a substantial donation by Edwin Bouw Fonds and Dioraphte. SvdL further received funding for the GeneMINDS consortium, which is powered by Health-Holland, Top Sector Life Sciences & Health. Sven J. van der Lee is a recipient of ABOARD, which is a public-private partnership receiving funding from ZonMW (#73305095007) and Health~Holland, Topsector Life Sciences & Health (PPP-allowance; #LSHM20106). More than 30 partners participate in ABOARD. ABOARD also receives funding from Edwin Bouw Fonds and Gieskes-Strijbisfonds. ABOARD also receives funding from de Hersenstichting, Edwin Bouw Fonds and Gieskes-Strijbisfonds. Array genotyping was performed in the context of EADB (European Alzheimer DNA biobank) funded by the JPco-fuND FP-829-029 (ZonMW projectnumber 733051061). This work has been supported by the Queen Sofia Foundation. Pascual Sanchez-Juan is supported by grants from ISCIII (PMP22/00022 and PI20/01011) and TED2021-131676B-100. Luis Miguel Real received support from The absence of seroconversion after exposition to hepatitis C virus is not related to KIR-HLA genotype combinations (GEHEP-012 study). Consejeria de Salud de la Junta de Andalucia (grant number PI-0001/2017) and CIBERINFEC -Consorcio Centro de Investigacion Biomedica en Red de Enfermedades Infecciosas- Instituto de Salud Carlos III, Ministerio de Ciencia e Innovacion y Union Europea (Spain) (NextGeneration EU) (grant number CB21/13/00118). Jose Luis Royo received support from Project 23.04.2021 from Santangela Foundation (Sevilla, Spain). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: For the Iberian cohort, this study was approved by the competent research ethical committee (MED-FACE-2020-01, Universidad Internacional de Catalunya, Sant Cugat del Valles, Spain). For the Dutch cohorts, the local Medical Ethics Committees approved the protocols for the Amsterdam Dementia Cohort (ADC) and the other studies, and all participants of the ADC provided written informed consent. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes The data that support the findings of this study are not openly available due to reasons of sensitivity and are available from the corresponding author upon reasonable request.

The genetic basis of severe COVID-19 has been thoroughly studied, and many genetic risk factors shared between populations have been identified. However, reduced sample sizes from non-European groups have limited the discovery of population-specific common risk loci. In this second study nested in the SCOURGE consortium, we conducted a genome-wide association study (GWAS) for COVID-19 hospitalization in admixed Americans, comprising a total of 4702 hospitalized cases recruited by SCOURGE and seven other participating studies in the COVID-19 Host Genetic Initiative. We identified four genome-wide significant associations, two of which constitute novel loci and were first discovered in Latin American populations ( BAZ2B and DDIAS ). A trans-ethnic meta-analysis revealed another novel cross-population risk locus in CREBBP . Finally, we assessed the performance of a cross-ancestry polygenic risk score in the SCOURGE admixed American cohort. This study constitutes the largest GWAS for COVID-19 hospitalization in admixed Latin Americans conducted to date. This allowed to reveal novel risk loci and emphasize the need of considering the diversity of populations in genomic research.

Background: Microglial dysfunction plays a causative role in Alzheimer’s disease (AD) pathogenesis. Here we focus on a germline insertion/deletion variant mapping SIRPβ1, a surface receptor that triggers amyloid-β(Aβ) phagocytosis via TYROBP. Objective: To analyze the impact of this copy-number variant in SIRPβ1 expression and how it affects AD molecular etiology. Methods: Copy-number variant proxy rs2209313 was evaluated in GERALD and GR@ACE longitudinal series. Hippocampal specimens of genotyped AD patients were also examined. SIRPβ1 isoform-specific phagocytosis assays were performed in HEK393T cells. Results: The insertion alters the SIRPβ1 protein isoform landscape compromising its ability to bind oligomeric Aβ and its affinity for TYROBP. SIRPβ1 Dup/Dup patients with mild cognitive impairment show an increased cerebrospinal fluid t-Tau/Aβ ratio (p = 0.018) and a higher risk to develop AD (OR = 1.678, p = 0.018). MRIs showed that Dup/Dup patients exhibited a worse initial response to AD. At the moment of diagnosis, all patients showed equivalent Mini-Mental State Examination scores. However, AD patients with the duplication had less hippocampal degeneration (p < 0.001) and fewer white matter hyperintensities. In contrast, longitudinal studies indicate that patients bearing the duplication allele show a slower cognitive decline (p = 0.013). Transcriptional analysis also shows that the SIRPβ1 duplication allele correlates with higher TREM2 expression and an increased microglial activation. Conclusions: The SIRPβ1 internal duplication has opposite effects over MCI-to-Dementia conversion risk and AD progression, affecting microglial response to Aβ. Given the pharmacological approaches focused on the TREM2-TYROBP axis, we believe that SIRPβ1 structural variant might be considered as a potential modulator of this causative pathway.

The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, COVID-19) had an estimated overall case fatality ratio of 1.38% (pre-vaccination), being 53% higher in males and increasing exponentially with age. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, we found 133 cases (1.42%) with detectable clonal mosaicism for chromosome alterations (mCA) and 226 males (5.08%) with acquired loss of chromosome Y (LOY). Individuals with clonal mosaic events (mCA and/or LOY) showed a 54% increase in the risk of COVID-19 lethality. LOY is associated with transcriptomic biomarkers of immune dysfunction, pro-coagulation activity and cardiovascular risk. Interferon-induced genes involved in the initial immune response to SARS-CoV-2 are also down-regulated in LOY. Thus, mCA and LOY underlie at least part of the sex-biased severity and mortality of COVID-19 in aging patients. Given its potential therapeutic and prognostic relevance, evaluation of clonal mosaicism should be implemented as biomarker of COVID-19 severity in elderly people.

Hippocampal sclerosis of aging (HS) is one of the most predominant causes of dementia in elder populations and it is often misdiagnosed as Alzheimer’s disease (AD). HS has recently been found to show a hippocampal atrophy pattern that might be key for the differentiation of this pathology from AD in the early stages of dementia. In this study, we aimed to find SNPs associated with AD diagnosis that might be related to HS. To that end, we calculated a polygenic risk score (PRS) combining SNPs associated with AD by Bellenguez et al. (2022) and assessed their relation with HS-by-proxy based on magnetic resonance imaging (MRI) data of hippocampal subfield volumes from 1,130 individuals without dementia syndrome. Our results show a significant association of AD-PRS with fimbria and hippocampal body and head volumes. Association with these hippocampal subfields was also observed on the individual effects of the AD-related variants in the SHARPIN (rs34173062) and TNIP1 (rs871269) genes. Besides, these loci remained consistently associated to HS-aging after increasing the sample size by including an independent cohort of healthy individuals (N = 729). The results presented in this study suggest that some SNPs that have recently been identified as AD variants might be closely related to atrophy in hippocampal subfields instead of AD, and hence, could be instrumental to refine AD and HS pathways, their interrelationships, and to elaborate specific treatment for each condition.

Mosaic loss of chromosome Y (mLOY) is a common ageing-related somatic event and has been previously associated with Alzheimer’s disease (AD). However, mLOY estimation from genotype microarray data only reflects the mLOY degree of subjects at the moment of DNA sampling. Therefore, mLOY phenotype associations with AD can be severely age-confounded in the context of genome-wide association studies. Here, we applied Mendelian randomisation to construct an age-independent mLOY polygenic risk score (mloy-PRS) using 114 autosomal variants. The mloy-PRS instrument was associated with an 80% increase in mLOY risk per standard deviation unit (p = 4.22 × 10−20) and was orthogonal with age. We found that a higher genetic risk for mLOY was associated with faster progression to AD in men with mild cognitive impairment (hazard ratio (HR) = 1.23, p = 0.01). Importantly, mloy-PRS had no effect on AD conversion or risk in the female group, suggesting that these associations are caused by the inherent loss of the Y chromosome. Additionally, the blood mLOY phenotype in men was associated with increased cerebrospinal fluid levels of total tau and phosphorylated tau181 in subjects with mild cognitive impairment and dementia. Our results strongly suggest that mLOY is involved in AD pathogenesis.

Genetic discoveries of Alzheimer’s disease are the drivers of our understanding, and together with polygenetic risk stratification can contribute towards planning of feasible and efficient preventive and curative clinical trials. We first perform a large genetic association study by merging all available case-control datasets and by-proxy study results (discovery n = 409,435 and validation size n = 58,190). Here, we add six variants associated with Alzheimer’s disease risk (near APP, CHRNE, PRKD3/NDUFAF7, PLCG2 and two exonic variants in the SHARPIN gene). Assessment of the polygenic risk score and stratifying by APOE reveal a 4 to 5.5 years difference in median age at onset of Alzheimer’s disease patients in APOE ɛ4 carriers. Because of this study, the underlying mechanisms of APP can be studied to refine the amyloid cascade and the polygenic risk score provides a tool to select individuals at high risk of Alzheimer’s disease.

ABSTRACTMosaic loss of chromosome Y (mLOY) is a common ageing-related somatic event occurring exclusively in men and has been previously associated with Alzheimer’s disease (AD). However, mLOY estimation from genotype microarray data only reflects the mLOY degree of subjects at the moment of DNA sampling. Therefore, mLOY phenotype associations with AD can be severely age-confounded in the context of genome-wide association studies. Here, we applied Mendelian randomization to construct an age-independent polygenic risk score of mLOY (mloy-PRS) using 114 autosomal variants. The mloy-PRS instrument was associated with an 80% increase in mLOY risk per SD unit (p=4.22·10−20) and was orthogonal with age. We found that a higher genetic risk for mLOY was associated with faster progression to AD in males with mild cognitive impairment (HR=1.23; p=0.01). Importantly, mloy-PRS had no effect on AD conversion or risk in the female group. The male-specificity of the observed effects suggests that these associations of mLOY with AD are caused by the inherent loss of the Y chromosome, and not by the increased genomic instability underlying mLOY risk. Additionally, we found that blood mLOY phenotype was associated with increased CSF levels of total tau and phosphorylated tau181 in subjects with mild cognitive impairment and dementia. Our results strongly suggest that mLOY is involved in AD pathogenesis. Furthermore, we encourage researchers to use this mloy-PRS instrument to find unbiased associations between mLOY and ageing-related diseases.

Microglia play an important role in the maintenance of brain homeostasis, and microglial dysfunction plays a causative role in Alzheimer disease pathogenesis. Here we focus on the signal regulatory protein SIRPβ1, a surface receptor expressed on the myeloid cells that triggers amyloid-β and cell debris phagocytosis via TYROBP. We found that a common intragenic duplication alters the SIRPβ1 protein isoform landscape affecting both extracellular and transmembrane domains, which compromise their ability to bind oligomeric Aβ and their affinity for TYROBP. Epidemiological studies show that patients with mild cognitive impairment that are homozygous for the SIRPβ1 duplication allele show an increased cerebrospinal fluid t-Tau/Aβ ratio (p-value=0.018) and a higher risk to develop AD (OR=1.678, p-value=0.018). Magnetic resonance imaging at diagnosis showed that AD patients with the duplication allele exhibited a worse initial response to the disease. At the moment of diagnosis all patients showed equivalent Mini-Mental State Examination scores. However AD patients with the duplication allele had less hippocampal degeneration (Beta= -0.62, p-value < 0.001) and fewer white matter hyperintensities. In contrast, longitudinal studies indicate that patients bearing the duplication allele show a slower cognitive decline after correcting by baseline (p-value = 0.013). Transcriptional analysis of the patients’ hippocampus also shows that the SIRPβ1 duplication allele correlates with higher TREM2 expression and an increased microglial activation. Given the recent pharmacological approaches focused on the TREM2-TYROBP axis, we consider that the presence of this structural variant might be considered as a potential modulator of this causative pathway.### Competing Interest StatementThe authors have declared no competing interest.### Funding StatementThis project did not receive any specific public nor private funding. It has been possible only thanks to the goodwill and the collaborative effort of the researchers and institutions signing this paper. RG acknowledge the support of the Spanish Ministry of Science and Innovation to the EMBL partnership, the Centro de Excelencia Severo Ochoa and the CERCA Programme, Generalitat de Catalunya. RG is principal investigator from grant PGC2018 094017 BI00 from AEI, FEDER, EU. AG is principal investigator of Instituto de Salud Carlos III of Spain grants PI18 01557 and P21 00915 co-financed by the FEDER funds from European Union. JV is principal investigator of ISCIII grants PI18 01556 and PI21 00914 cofinanced by FEDER funds from European Union, and Junta Andalucia grant US 1262734 cofinanced by Programa Operativo FEDER 2014 2020. JJT is principal investigator of PID2019 103921GB I00 from the Spanish Ministerio de Ciencia e Innovacion. JLR is principal investigator of UMA20 FEDERJA 133 from the program FEDER Andalucia 2014 2020, EU. JLR also acknowledges the Centro de Supercomputacion y Bioinformatica (Picasso-server) for computing support I. de Rojas is supported by national grant from the Instituto de Salud Carlos III FI20 00215. CM C was supported by FPU fellowship from the Spanish Ministry of Science, Innovation, and Universities. The Genome Research @ Fundacio ACE project (GR@ACE) is supported by Grifols SA, Fundacion bancaria La Caixa, Fundacio ACE, and CIBERNED. A.R. and M.B. receive support from the European Union EFPIA Innovative Medicines Initiative Joint undertaking ADAPTED and MOPEAD projects, grant numbers 115975 and 115985, respectively. M.B. and A.R. are also supported by national grants PI13 02434, PI16 01861, PI17 01474, PI19 01240 and PI19 01301. Accion Estrategica en Salud is integrated into the Spanish National R + D + I Plan and funded by ISCIII (Instituto de Salud Carlos III) Subdireccion General de Evaluacion and the Fondo Europeo de Desarrollo Regional (FEDER Una manera de hacer Europa).### Author DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below:GR@ACE series was recruted upon de approval from the Ethics Committee H., Clinic I Provincial, Barcelona, Spain. GERALD series was recruited upon de approval from the cometee from the Centro Provincial de Malaga, Malaga, Spain. Human hippocampal autopsy specimens were obtained from the Neurological Tissue Bank of IDIBAPS-Hospital Clinic (Barcelona, Spain). The utilization of post-mortem human samples was approved by the biobank ethic committee (Barcelona, Spain). Control samples were obtained from the National DNA Bank Carlos III University of Salamanca, (Salamanca, Spain) and Hospital Universitario Virgen de Valme (Sevilla, Spain) with the corresponding approval of the Ethical and Scientific Committees. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).YesI have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.YesAll data produced in the present study are available upon reasonable request to the authors upon the approval of the ethic's review board.

Environmental exposures during early life play a critical role in life-course health, yet the molecular phenotypes underlying environmental effects on health are poorly understood. In the Human Early Life Exposome (HELIX) project, a multi-centre cohort of 1301 mother-child pairs, we associate individual exposomes consisting of >100 chemical, outdoor, social and lifestyle exposures assessed in pregnancy and childhood, with multi-omics profiles (methylome, transcriptome, proteins and metabolites) in childhood. We identify 1170 associations, 249 in pregnancy and 921 in childhood, which reveal potential biological responses and sources of exposure. Pregnancy exposures, including maternal smoking, cadmium and molybdenum, are predominantly associated with child DNA methylation changes. In contrast, childhood exposures are associated with features across all omics layers, most frequently the serum metabolome, revealing signatures for diet, toxic chemical compounds, essential trace elements, and weather conditions, among others. Our comprehensive and unique resource of all associations ( https://helixomics.isglobal.org/ ) will serve to guide future investigation into the biological imprints of the early life exposome.