Studies have shown that substance use liability is associated with novelty seeking, anxiety-like behavior, and pain sensitivity. We examined whether common genetic variation in outbred Sprague-Dawley rats explained variation in behavioral measures from three assays with established links to substance use: locomotor response to a novel environment, elevated plus maze, and tail flick. We estimated single-nucleotide polymorphism heritability and performed genome-wide association analyses using permutation-derived significance thresholds (N=534-654 rats across traits). Heritability estimates ranged from 0.14-0.38 across eleven traits. Three independent loci were identified: chromosome 1 for elevated plus maze open-arm behavior (α=0.05), chromosome 14 for elevated plus maze immobility (α=0.10), and chromosome 17 for tail flick latency (α=0.05). Candidate genes included Slc18a2, Gfra1, and Pdzd8 (chromosome 1); Rel and Bcl11a (chromosome 14); and Eci2 and Eci3 (chromosome 17). We compared these loci with our genome wide association study of a F2 intercross of selectively bred high- and low-responder rats, originally derived from Sprague-Dawleys, that model individual differences in externalizing and internalizing behavior. The current loci are distinct from the ones identified in the bred lines. This difference likely reflects selection history in the high- and low-responder F2s, which focused on facets of exploratory locomotion, while loci for anxiety and pain sensitivity traits were identified in the outbreds. This highlights the benefit of using both outbred and selectively bred rats to probe causal variants contributing to individual differences in substance use liability. The current outbred findings implicate monoaminergic signaling, transcriptional control, and lipid metabolism as testable mechanisms for addiction-relevant behaviors.

Differential packaging of vertebrate sperm and egg genomes is evolutionarily conserved for hundreds of millions of years. Unlike oocytes, post-meiotic spermatid nuclei are thought to uniformly replace histones with transition proteins (TNPs) and, ultimately, with protamines, the small non-histone structural proteins. Tracking of endogenously tagged protamines overturns the classical model of paternal chromatin remodeling, revealing a direct histone-to-protamine-1 transition that occurs independently of both TNPs and protamine-2. Stage-resolved chromatin profiling across 26 spermatid datasets reveals that chromatin compaction is a programmed process that requires H4-hyperacetylation but is not instructed by it. Rather, chromatin remodeling is guided by the pre-meiotic 3D-architecture of the spermatid nucleus: i.e., compaction of the A-compartment precedes B-compartment. This compartment-encoded template for sperm nuclear remodeling suggests that male-specific protamine patterns can transmit pre-meiotic structural information to the zygote and may impact embryonic development.

[This corrects the article DOI: 10.3389/fnmol.2025.1469467.].

Cognitive resilience (CR) refers to the continuum from worse to better-than-expected cognition, given the degree of neuropathology. Understanding mechanisms underlying CR could inform discovery of novel targets for dementia prevention; however, specific metabolic pathways underlying CR are yet to be elucidated. Our study included 484 deceased participants (mean age at death =91 years, 70.2% women) from the Religious Orders Study and Rush Memory and Aging Project. Metabolomics profiling was conducted at Metabolon Inc. by a chromatography–mass spectrometry in postmortem dorsolateral prefrontal cortex tissue, yielding 600 known metabolites quantified for analysis. Antemortem cognitive function was assessed annually by 17 neuropsychologic tests through death, and neuropathologies were evaluated in postmortem brain. CR was defined as the residual slope of cognitive decline after controlling for age at death, sex, education, and nine Alzheimer’s disease, other neurodegenerative, and cerebrovascular neuropathologies. We analyzed the associations between individual brain metabolites and CR score using linear regressions. We also constructed co-regulatory networks for metabolites significantly related to CR, and identified key metabolites for CR within each network using recursive conditional analysis. We identified 72 metabolites whose levels in the prefrontal cortex were associated with CR (FDR<0.05), encompassing diverse biochemical categories including 33 amino acids and peptides, 21 lipids, 7 cofactors and vitamins, 6 carbohydrates/energy metabolites, and 5 others. Based on partial correlations, the 72 CR-related metabolites were constructed into 6 co-regulatory networks, each linked to specific biological functions including oxidative stress (key metabolites driving the associations were N-acetylmethionine sulfoxide, ergothioneine, and carotene diol), synaptic function (led by myo-inositol, glycerate, and docosahexaenoyl ethanolamide), neuroinflammation (led by 7-hydroxycholesterol), cell signaling (led by inositol 1-phosphate and gamma-glutamylthreonine), phospholipid metabolism (led by glycerophosphorylcholine), and energy/glucose metabolism (led by UDP-glucose and adenosine monophosphate). The eigenvectors of all 6 co-functional networks were significantly associated with CR (FDR<0.05). We identified brain metabolites implicated in oxidative stress and necroinflammation, synaptic function and cell signaling, and lipid/energy metabolism, associated with rates of cognitive decline after controlling for neuropathologies. These CR-related metabolites may inform the discovery of novel targets for improving cognitive resilience to neuropathology.

Introduction: Despite achievement of complete remission (CR) following chemotherapy, Acute Myelogenous Leukemia (AML) relapses in the majority of adult patients. Molecular and cellular contributors to chemotherapy resistance and to AML expansion and relapse have been identified in genomic, epigenetic and proteomic aberrations, while cellular relapse reservoirs have been identified in leukemia stem cells. Here, we set out to identify and functionally validate genes with consistent expression changes between AML at Diagnosis and Relapse aiming at a better understanding of the gene drivers and biology of AML relapse. Methods: We employed the drop-seq 3' single cell RNA sequencing (scRNA-seq) method (Macosko et al., Cell 2015) to analyze 20 paired AML specimens procured at diagnosis and at relapse from prior CR. We compared the gene expression in pooled (pseudo bulk RNA seq) single hematopoietic stem and progenitor cells (HSPCs) at diagnosis and relapse thus nominating a gene pool with highly concordant UP or DOWN regulation at relapse. We conducted lentiviral CRISPR-Cas9 based gene inactivation screens and cell growth assays using a custom library of ~7200 guides targeting 1550 genes and 1,000 controls. The screens were conducted in three primary human CD34+ non-malignant cell samples and in six primary human AML samples using 30-40 day cultures in stem cell media. A fraction of the genes that accelerated the growth of CD34+ and AML cells were individually re-assayed. Next, we selected 12 novel genes and 2 controls for in vivo studies in AML xenografts. Primary human AML were infected with lentiviral guide pools and following two days of culture injected into irradiated NSG-SGM3 mice. The AML engraftment was monitored serially via blood flow cytometry and bone marrows harvested in weeks 12-16. Guide frequencies in AML xenografts were determined via PCR-based library generation, followed by next generation sequencing and computationally using the MAGeCK software (Li et al., Genome Biology, 2014). Results: The gene with the highest enrichment score (ES) following gene disruption in CD34+ cells was the known AML tumor suppressor DNMT3A (ES 1.64). The expression of DNMT3A was downregulated in AML at relapse, together supporting the conclusion that mutational as well as non-mutational DNMT3A downregulation facilitates stem and progenitor cell expansion in relapsed AML. Further, the AML tumor suppressors SETD2 (ES 1.38, rank 2), RUNX1 (ES 0.73, rank 9) and ETV6 (ES 0.79, rank 26) scored high in this assay. Remarkably, there were 150 genes with a mean enrichment score >0.5 that upon disruption resulted in cell enrichment in all three CD34+ cell samples concordantly. Serially harvested cell samples on days 27 and 40 had high concordance with a Pearson coefficient of R=0.76, p< 2 x 10-15. We measured highly similar effects in pooled day 40 colonies harvested from lentivirally infected cells grown on large MethoCultTM plates. In single gene validation studies, upon genetic disruption of FOXN3, NIN1, TMX1, NCOR2, ODF3B, HMGXB4, GAPT, EHBP1L1, MGAT4B, CSNK1G2, EIF4G3, PCNT and ARHGEF2, we measured significantly increased cell numbers over time. The expression of all thirteen genes were downregulated in CMP-like leukemia cells at Re, and 10/13 of these genes were downregulated in HSC/MPP-like cells. Altogether, so far we experimentally confirmed 57% (17/30) of genes that when downregulated accelerated the growth and survival of human CD34+ stem and progenitor cells. We combined the assays results derived from primary AML day 30 ex vivo growth (N=4 AML) and in vivo AML xenograft assays (N=5 AML) and identified recurrent enrichment for guides targeting the genes: HMGXB4, GAPT, TMX1, ARHGEF2, NIN, FOXN3, and EIF4G3 and additional in vivo AML xenograft experiments are ongoing. Conclusions: The comparative analysis of scRNA-seq data of 20 paired AML specimens procured at diagnosis and relapse, identified frequent and previously unrecognized large-scale changes in gene expression driving leukemia cell growth and relapse. Our experimental findings support a combinatorial role for reduced expression of these genes in leukemic progenitor cell fitness and expansion at relapse and revise current parsimonious models of human AML relapse.

INTRODUCTION:Type 2 diabetes increases the risk of Alzheimer's disease (AD) dementia. Insulin signaling dysfunction exacerbates tau protein phosphorylation, a hallmark of AD pathology. However, the comprehensive impact of diabetes on patterns of AD-related phosphoprotein in the human brain remains underexplored. METHODS:We performed tandem mass tag-based phosphoproteome profiling in post mortem human brain prefrontal cortex samples from 191 deceased older adults with and without diabetes and pathologic AD. RESULTS:Among 7874 quantified phosphosites, microtubule-associated protein tau (MAPT) phosphorylated at T529 and T534 (isoform 8 T212 and T217) were more abundant in AD and showed differential associations with diabetes. Network analysis of co-abundance patterns uncovered synergistic interactions between AD and diabetes, with one module exhibiting higher MAPT phosphorylation (15 MAPT phosphosites) and another displaying lower MAP1B phosphorylation (22 MAP1B phosphosites). DISCUSSION:This study offers phosphoproteomics insights into AD in diabetes, shedding light on mechanisms that can inform the development of therapeutics for dementia. HIGHLIGHTS:The risk of Alzheimer's disease (AD) dementia is increased among older adults living with diabetes. The patterns of AD-related phosphoprotein in the human brain in older adults are differential among older adults living with diabetes. Microtubule-associated protein tau phosphorylated at T529 and T534 (isoform 8 T212 and T217) showed differential associations with diabetes. Phosphosite co-abundance networks of synergistic interactions between AD and diabetes were identified.

The reproductive and endocrine functions of the ovary involve spatially defined interactions among specialized cell populations. Despite the ovary’s importance in fertility and endocrine health, functional attributes of ovarian cells are largely uncharacterized. Here, we profiled >18,000 genes in 257 regions from the ovaries of two premenopausal donors to examine the functional units in the ovary. We also generated single-cell RNA sequencing data for 21,198 cells from three additional donors and identified four major cell types and four immune cell subtypes. Custom selection of sampling areas revealed distinct gene activities for oocytes, theca, and granulosa cells. These data contributed panels of oocyte-, theca-, and granulosa-specific genes, thus expanding the knowledge of molecular programs driving follicle development. Serial samples around oocytes and across the cortex and medulla uncovered previously unappreciated variation of hormone and extracellular matrix remodeling activities. This combined spatial and single-cell atlas serves as a resource for future studies of rare cells and pathological states in the ovary.

Abstract Introduction: CheckMate 914 (CM-914) Part A is a double-blind, phase III randomized trial of the Nivolumab (NIVO) plus Ipilimumab (IPI) vs placebo (PBO) in localized ccRCC. Our prior report from this study suggested a disease-free survival (DFS) benefit for NIVO+IPI among patients with Fuhrman grade 4, TNM stages PT2a and PT4, or sarcomatoid features, although the sample size was limited. It is known that high circulating KIM-1 is associated with worse DFS after nephrectomy. In this exploratory post hoc analysis, we investigated whether high KIM-1 may help identify a subset of patients who benefit from adjuvant NIVO+IPI. Methods: Patients (n=816) with RCC after nephrectomy were randomized in CM-914 Part A to receive NIVO+IPI or PBO as previously described. Assessment of KIM-1 levels was performed using enzyme linked immunoassay (ELISA) on pre-treatment (n=584) and matched on-treatment blood samples (n=584). We used pre-treatment tumor samples to assess PD-L1% tumor cell expression (%TC) in an PD-L1 IHC 28-8 pharm Dx assay. The association between biomarkers and DFS outcomes was investigated by Kaplan-Meier (KM) and Cox proportional hazards analysis. Results: Median baseline serum KIM-1 level was 102 (9.9 - 1055.7) pg/mL. Serum KIM-1 levels were higher in males vs females, ≥65 yrs vs <65 yrs, Asian vs white patients, and patients with partial vs radical nephrectomy. In the PBO arm, subjects with highest quartile of pre-treatment KIM-1 had significantly worse DFS than those from the three lower quartiles. In contrast, this DFS risk among the subjects within the highest KIM-1 quartile was mitigated with NIVO+IPI treatment. Among patients within the highest quartile of pre-treatment KIM-1, there was trend for better DFS for NIVO+IPI versus PBO, HR=0.6 (0.34-1.04). Increase in KIM-1 during study therapy was positively associated with higher DFS rate in both arms. Multivariable analysis showed that PD-L1 %TC was predictive at predefined PD-L1 cutoffs (>=1%, >=5%, and >=10%), associating with improved DFS compared to placebo. Subjects with high PD-L1 expression had a DFS benefit from NIVO+IPI independent of KIM-1. Conclusion: Circulating KIM-1 and tumor PD-L1 expression may enrich for benefit from IO therapy in adjuvant ccRCC and hence holds promise for informing risk stratification and patient inclusion in neoadjuvant or adjuvant clinical trials. Citation Format: Sai Vikram Vemula, Wenxin Xu, Yu Wang, Xiaowen Liu, Jorge Ruiz de Somocurcio, David McDermott, Jun Li, Rupal Bhatt, Chung-Wei Lee, Burcin Simsek, Saurabh Gupta, Robert Motzer. High serum kidney injury marker-1 and high baseline tumor PD-L1 protein expression levels are independently associated with treatment effect in adjuvant nivolumab plus ipilimumab vs placebo in localized clear cell renal cell carcinoma [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 5151.

Subcutaneous white adipose tissue (scWAT) is a dynamic storage and secretory organ that regulates systemic homeostasis, yet the impact of endurance exercise training (ExT) and sex on its molecular landscape is not fully established. Utilizing an integrative multi-omics approach, and leveraging data generated by the Molecular Transducers of Physical Activity Consortium (MoTrPAC), we show profound sexual dimorphism in the scWAT of sedentary rats and in the dynamic response of this tissue to ExT. Specifically, the scWAT of sedentary females displays -omic signatures related to insulin signaling and adipogenesis, whereas the scWAT of sedentary males is enriched in terms related to aerobic metabolism. These sex-specific -omic signatures are preserved or amplified with ExT. Integration of multi-omic analyses with phenotypic measures identifies molecular hubs predicted to drive sexually distinct responses to training. Overall, this study underscores the powerful impact of sex on adipose tissue biology and provides a rich resource to investigate the scWAT response to ExT. Using a multi-omics approach, the authors examine the molecular drivers of sexual dimorphism in the subcutaneous adipose tissue from sedentary and endurance-trained rats. These data provide a valuable resource for adipose tissue-related research.

Introduction: Despite achievement of complete remission (CR) following chemotherapy, Acute Myelogenous Leukemia (AML) relapses in the majority of adult patients. The identification of cellular and molecular mechanisms that underlie resistance, persistence, and competitive regrowth of leukemic cells is of high interest to improve the outcome of AML patients. In this study, we have investigated the consequences of sterile leukemic inflammation on acquired novel properties and therapy resistance in human AML. Methods: Using single cell RNA sequencing we analyzed twenty paired AML specimens procured at diagnosis and at relapse from prior CR, followed by comparative gene expression analyses of selected leukemic cell populations. In addition, we compared the single cell gene expression in leukemic monoblasts/monocytes with pooled normal monocytes of five healthy donors. We used GO analysis, pathway analysis and the database “interferome” to investigate different leukemic cell populations for enrichment of inflammatory and other signatures. We treated human non-malignant CD34+ cells with 1,000 U IFNα and IFNγ for 4h and 24h and detected gene expression changes of selected target genes via qRT-PCR. We measured the expression of IFNα, IFNb and IFNγ together with 3 retrotransposons (LINE elements) and 5 endogenous retroviruses (ERVs) in 6 immature AML (M0, M1, M2) and 8 mature AML (M4, M5a/b) via qRT-PCR. We then incubated 19 primary human AML with 1,000 U IFNα and IFNγ in 20% FBS/RPMI1640 for 4h followed by treatment with escalating doses (1 nM - 10 μM) of Venetoclax for 24 h while IFN was still present. The expression of BCL2 family members BCL2, BCL-xL, MCL1 and BCL2A1 after 4 h IFN pre-stimulation was assayed in 14 AML cases via qRT-PCR and after 24 h, 48 h and 72 h IFN treatment in 8 AML cases using immunoblotting. AML cell lines were pre-incubated with and without 500 nM of the JAK1/2 inhibitors Ruxolitinib or Baricitinib for 2 h followed by 4 h IFN pre-stimulation and measurements of Venetoclax dose responses. Results: We have identified cellular relapse patterns and divergent maturity states of AML at diagnosis (Dx) and at relapse (Re) and found that AML comprising monoblastic/monocytic leukemias aberrantly express many inflammatory and interferon (IFN) stimulated genes. The “inflammatory response” was the most prominent gene set when comparing leukemic monoblasts with non-malignant bone marrow resident monocytes. The correlation of expression of IFN induced genes with survival uncovered extremely poor outcomes for AML patients with the highest quartile expression of the genes IL2RA, INHBA, OPTN, EPSTI1, MX1 or BST2 demonstrating a 1,000-day survival fraction of < 20% (range 4-18%). Using human non-malignant CD34+ cells treated with 1,000 U IFNα and IFNγ, we identified IL2RA, INHBA and BCL2A1 as IFN-induced target genes. We detected blast-intrinsic types I and II IFN production in chemotherapy naive AML specimens that correlated proportionally with the expression of ERVs and retrotransposons, which likely caused the IFN production. Moreover, the mean expression of multiple retroelements was substantially higher in FAB M4/M5 AML compared to M0-M2 AML. We found that one major determinant of very low expression of LINE elements and ERVs was TP53 or TET2 mutated status. Importantly, we uncovered a substantial resistance induction to Venetoclax by IFN and measured transcriptional induction of four anti-apoptotic BCL2 family members in all AML cases tested. On the protein level, we confirmed the induction of MCL1, BCL2A1 and BCL-xL by IFN in multiple AML cases suggesting a combinatorical effect of two or three anti-apoptotic BCL2 family members resulting in IFN-mediated Venetoclax resistance. Of interest, most Venetoclax sensitive AML cases lacked BCL2A1 expression. In line with these results, AML cell lines demonstrated resistance to Venetoclax following IFN stimulation, which was partially or completely reversed after JAK-inhibitor pre-treatment. Conclusions: Our data revealed the importance of sterile inflammation for prognosis and therapy resistance in human AML. We demonstrated that IFN markedly reduces the sensitivity to Venetoclax induced AML cell death via combinatorial upregulation of MCL1, BCL2A1 and BCL-xL. Given that Venetoclax combinations are now major therapies for AML, our findings could improve our biological understanding and the therapy for adult AML.

The seventh iteration of the reference genome assembly for Rattus norvegicus—mRatBN7.2—corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared with its predecessor. Gene annotations are now more complete, improving the mapping precision of genomic, transcriptomic, and proteomics datasets. We jointly analyzed 163 short-read whole-genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined ∼20.0 million sequence variations, of which 18,700 are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats.

The human uterus is a complex and dynamic organ whose lining grows, remodels, and regenerates every menstrual cycle or upon tissue damage. Here, we applied single-cell RNA sequencing to profile more the 50,000 uterine cells from both the endometrium and myometrium of five healthy premenopausal individuals, and jointly analyzed the data with a previously published dataset from 15 subjects. The resulting normal uterus cell atlas contains more than 167K cells, representing the lymphatic endothelium, blood endothelium, stromal, ciliated epithelium, unciliated epithelium, and immune cell populations. Focused analyses within each major cell type and comparisons with subtype labels from prior studies allowed us to document supporting evidence, resolve naming conflicts, and propose a consensus annotation system of 39 subtypes. We release their gene expression centroids, differentially expressed genes, and messenger Ribonucleic Acid (mRNA) patterns of literature-based markers as a shared community resource. We identify multiple potential progenitor cells: compartment-wide progenitors for each major cell type and potential cross-lineage multipotent stromal progenitors that may replenish the epithelial, stromal, and endothelial compartments. Furthermore, many cell types and subtypes exhibit shifts in cell number and transcriptomes across different phases of the menstrual cycle. Finally, comparisons between premenopausal, postpartum, and postmenopausal samples revealed substantial alterations in tissue composition, particularly in the proportions of stromal, endothelial, and immune cells. The cell taxonomy and molecular markers we report here are expected to inform studies of both basic biology of uterine function and its disorders.

Invasive graft biopsies assess the efficacy of immunosuppression through lagging indicators of transplant rejection. We report on a microporous scaffold implant as a minimally invasive immunological niche to assay rejection before graft injury. Adoptive transfer of T cells into Rag2 −/− mice with mismatched allografts induced acute cellular allograft rejection (ACAR), with subsequent validation in wild-type animals. Following murine heart or skin transplantation, scaffold implants accumulate predominantly innate immune cells. The scaffold enables frequent biopsy, and gene expression analyses identified biomarkers of ACAR before clinical signs of graft injury. This gene signature distinguishes ACAR and immunodeficient respiratory infection before injury onset, indicating the specificity of the biomarkers to differentiate ACAR from other inflammatory insult. Overall, this implantable scaffold enables remote evaluation of the early risk of rejection, which could potentially be used to reduce the frequency of routine graft biopsy, reduce toxicities by personalizing immunosuppression, and prolong transplant life.

Brain organoid methods are complicated by multiple rosette structures and morphological variability. We have developed a human brain organoid technique that generates self-organizing, single-rosette cortical organoids (SOSR-COs) with reproducible size and structure at early timepoints. Rather than patterning a 3-dimensional embryoid body, we initiate brain organoid formation from a 2-dimensional monolayer of human pluripotent stem cells patterned with small molecules into neuroepithelium and differentiated to cells of the developing dorsal cerebral cortex. This approach recapitulates the 2D to 3D developmental transition from neural plate to neural tube. Most monolayer fragments form spheres with a single central lumen. Over time, the SOSR-COs develop appropriate progenitor and cortical laminar cell types as shown by immunocytochemistry and single-cell RNA sequencing. At early time points, this method demonstrates robust structural phenotypes after chemical teratogen exposure or when modeling a genetic neurodevelopmental disorder, and should prove useful for studies of human brain development and disease modeling.

Conventional dogma presumes that protamine-mediated DNA compaction in sperm is achieved by electrostatic interactions between DNA and the arginine-rich core of protamines. Phylogenetic analysis reveals several non-arginine residues conserved within, but not across species. The significance of these residues and their post-translational modifications are poorly understood. Here, we investigated the role of K49, a rodent-specific lysine residue in protamine 1 (P1) that is acetylated early in spermiogenesis and retained in sperm. In sperm, alanine substitution (P1(K49A)) decreases sperm motility and male fertility—defects that are not rescued by arginine substitution (P1(K49R)). In zygotes, P1(K49A) leads to premature male pronuclear decompaction, altered DNA replication, and embryonic arrest. In vitro, P1(K49A) decreases protamine–DNA binding and alters DNA compaction and decompaction kinetics. Hence, a single amino acid substitution outside the P1 arginine core is sufficient to profoundly alter protein function and developmental outcomes, suggesting that protamine non-arginine residues are essential for reproductive fitness.

Age-related macular degeneration (AMD) is a leading cause of blindness in older adults. Investigating shared genetic components between metabolites and AMD can enhance our understanding of its pathogenesis. We conduct metabolite genome-wide association studies (mGWASs) using multi-ethnic genetic and metabolomic data from up to 28,000 participants. With bidirectional Mendelian randomization analysis involving 16,144 advanced AMD cases and 17,832 controls, we identify 108 putatively causal relationships between plasma metabolites and advanced AMD. These metabolites are enriched in glycerophospholipid metabolism, lysophospholipid, triradylcglycerol, and long chain polyunsaturated fatty acid pathways. Bayesian genetic colocalization analysis and a customized metabolome-wide association approach prioritize putative causal AMD-associated metabolites. We find limited evidence linking urine metabolites to AMD risk. Our study emphasizes the contribution of plasma metabolites, particularly lipid-related pathways and genes, to AMD risk and uncovers numerous putative causal associations between metabolites and AMD risk.

Common genetic factors likely contribute to multiple psychiatric diseases including mood and substance use disorders. Certain stable, heritable traits reflecting temperament, termed externalizing or internalizing, play a large role in modulating vulnerability to these disorders. To model these heritable tendencies, we selectively bred rats for high and low exploration in a novel environment [bred High Responders (bHR) vs. Low Responders (bLR)]. To identify genes underlying the response to selection, we phenotyped and genotyped 538 rats from an F2 cross between bHR and bLR. Several behavioral traits show high heritability, including the selection trait: exploratory locomotion (EL) in a novel environment. There were significant phenotypic and genetic correlations between tests that capture facets of EL and anxiety. There were also correlations with Pavlovian conditioned approach (PavCA) behavior despite the lower heritability of that trait. Ten significant and conditionally independent loci for six behavioral traits were identified. Five of the six traits reflect different facets of EL that were captured by three behavioral tests. Distance traveled measures from the open field and the elevated plus maze map onto different loci, thus may represent different aspects of novelty-induced locomotor activity. The sixth behavioral trait, number of fecal boli, is the only anxiety-related trait mapping to a significant locus on chromosome 18 within which the Pik3c3 gene is located. There were no significant loci for PavCA. We identified a missense variant in the Plekhf1 gene on the chromosome 1:95 Mb QTL and Fancf and Gas2 as potential candidate genes that may drive the chromosome 1:107 Mb QTL for EL traits. The identification of a locomotor activity-related QTL on chromosome 7 encompassing the Pkhd1l1 and Trhr genes is consistent with our previous finding of these genes being differentially expressed in the hippocampus of bHR vs. bLR rats. The strong heritability coupled with identification of several loci associated with exploratory locomotion and emotionality provide compelling support for this selectively bred rat model in discovering relatively large effect causal variants tied to elements of internalizing and externalizing behaviors inherent to psychiatric and substance use disorders.

PDF file, 6233K, S1: Inference of Aneuploid Genome Proportion and its goodness-of-fit measures; Figure S2: Histolopathological estimates of tumor purities versus AGP; S3: Relationship between AGP and gene expression pattern in ovarian cancer (OV); S4: PCA plots for CNA and CNA-MicroRNA joint analysis; S5: Principal component analyses of gene expression and CNA data for GBM2; S6: Clustering pattern of three data types: PC1 of copy number data, PC1 of expression data, and PC2 of methylation data; S7: Classification of Non-Proneural GBM tumors; S8: Cross-correlation analysis of GBM1-GBM2 at K=3 and 4; S9: Comparison between the revised and the previous GBM classification systems; S10: Cross-correlation analysis between GBM1 and Phillips' dataset at K=2, 3 and 4; S11: PCA plots for 46 Non-Proneural GBM samples in Phillips' dataset; S12: Survival time differences between GBM subtypes, compared between the current and previous classification systems; S13: Cox proportional hazard regression analysis with GBM subtypes as covariates, along with age and Karnofsky performance scores (KPS); S14: Four clusters formed by the 38 reference samples in the Cahoy's dataset.

Abstract Some transmasculine individuals may be interested in pausing gender-affirming testosterone therapy and carrying a pregnancy. The ovarian impact of taking and pausing testosterone is not completely understood. The objective of this study was to utilize a mouse model mimicking transmasculine testosterone therapy to characterize the ovarian dynamics following testosterone cessation. We injected postpubertal 9–10-week-old female C57BL/6N mice once weekly with 0.9 mg of testosterone enanthate or a vehicle control for 6 weeks. All testosterone-treated mice stopped cycling and demonstrated persistent diestrus within 1 week of starting testosterone, while control mice cycled regularly. After 6 weeks of testosterone therapy, one group of testosterone-treated mice and age-matched vehicle-treated diestrus controls were sacrificed. Another group of testosterone-treated mice were maintained after stopping testosterone therapy and were sacrificed in diestrus four cycles after the resumption of cyclicity along with age-matched vehicle-treated controls. Ovarian histological analysis revealed stromal changes with clusters of large round cells in the post testosterone group as compared to both age-matched controls and mice at 6 weeks on testosterone. These clusters exhibited periodic acid–Schiff staining, which has been previously reported in multinucleated macrophages in aging mouse ovaries. Notably, many of these cells also demonstrated positive staining for macrophage markers CD68 and CD11b. Ovarian ribonucleic acid-sequencing found upregulation of immune pathways post testosterone as compared to age-matched controls and ovaries at 6 weeks on testosterone. Although functional significance remains unknown, further attention to the ovarian stroma may be relevant for transmasculine people interested in pausing testosterone to carry a pregnancy. Summary Sentence After testosterone is paused for reproductive purposes in a transgender mouse model, estrous cyclicity resumes, but ovaries demonstrate stromal aberrations and an upregulated inflammatory reaction. Graphical Abstract