Citations

Abstract Background Heart failure (HF) is classified by ejection fraction: reduced EF (<40%) is HFrEF and preserved EF (>50%) is HFpEF. Unlike HFrEF, no therapeutic agent improves mortality in HFpEF. The molecular mechanism that produces HFpEF is not completely understood, but the cascade of pathology that produces HFpEF is thought to begin with changes in vascular reactivity, including a decrease in NO mediated vasodilatation, which coupled with subsequent changes in contractility, energetics and coronary blood flow produce HFpEF. If abnormal vascular reactivity is the initial step in the pathological cascade that produces HFpEF, restoring and/or improving vascular reactivity could represent a novel treatment strategy. Vascular reactivity is primarily regulated by myosin light chain phosphatase, which has catalytic, myosin targeting (MYPT1) and 20kDa subunits. Alternative mRNA splicing of exon24 (E24) of the MYPT1 transcript produces MYPT1 isoforms that differ by the presence or absence of a COOH-terminal leucine zipper (LZ+/LZ-); E24 exclusion produces an NO responsive LZ+ MYPT1, while E24 inclusion produces an NO unresponsive LZ- MYPT. Methods We used the mouse two-hit model of HFpEF (high fat diet and L-NAME) and treated mice with an anti-sense octo-guanidine targeting the 5’ splice site of E24 (ASO-E24) to increase the expression of the NO responsive, LZ+ MYPT1 isoform in vascular smooth muscle. Invasive and noninvasive hemodynamics were used to determine LV function. Results Compared to mice with HFpEF, ASO-E24 treatment maintains LZ+ MYPT1 expression (4.7±0.7au v 1.0±0.4au v 2.0±0.4au, control v HFpEF v ASO-E24 Rx, p<0.05), improves diastolic function; LVEDP (10±1mmHg v 20±4mmHg v 14±3mmHg, p<0.05), dP/dtmin (−8000±300mmHg/s v 6000±500mmHg/s v 8500±700mmHg/s, p<0.05), both early (E; 0.60±0.05m/s v 0.42±0.06m/s v 0.64±0.06m/s, p<0.05) and late diastolic filling (A; 0.38±0.03m/s v 0.24±0.02m/s v 0.47±0.04m/s, p<0.050 and also prevents the increase in lung weight (167±5g v 175±7g v 166±5g, p<0.05). Further, mice treated with ASO-E24 maintained normal relaxation to 8Br-cGMP (65±5% v 44±9% v 72±9%, p=0.05). Conclusion These data demonstrate that maintaining normal LZ+ MYPT1 expression and vascular reactivity prevent the development of HFpEF. These results are consistent with the hypothesis that abnormal vascular reactivity is the initial and primary step in the pathological cascade that produces HFpEF and ASO-E24, which is designed to preserve normal LZ+ MYPT1 expression and vascular reactivity, could represent a novel and effective treatment strategy for HFpEF. Clinical Prospective What is New? In HFpEF, an anti-sense octo-guanidine targeting the 5’ splice site of exon 24 (ASO-E24) of the MYPT1 transcript increases the expression of the NO responsive, LZ+ MYPT1 isoform in vascular smooth muscle. Preserving LZ+ MYPT1 expression and normal vascular reactivity prevents the development of HFpEF. A decrease in LZ+ MYPT1 expression contributes to the development of HFpEF. What are the Clinical Implications? The results of the study demonstrate that abnormal vascular reactivity is an important step in the pathological cascade that produces HFpEF Increasing LZ+ MYPT1 expression could represent a novel treatment strategy for HFpEF.

Abstract Natural killer (NK) cells represent key effectors of antitumor immunity, yet emerging evidence highlights populations with distinct roles in cancer. Despite such expanded diversity within the NK cell repertoire, we lack an understanding of how this heterogeneity affects immune responses and downstream clinical outcomes. Using single-cell RNA sequencing, we systematically profiled NK cells across cancer and uncovered a dichotomous phenotypic and functional landscape of tumor-infiltrating NK cells shaped by opposing intrinsic signaling programs that drive the expression of IFNG or TGFB1. These divergent programs are associated with distinct transcription factor circuits that integrate cues within the tumor microenvironment and skew NK cells toward proinflammatory or suppressive functions. We found that the capacity for NK cells to engage in either functional direction is intrinsically linked to their phenotypic identity. Canonical NK cells recruited from circulation predominantly directed suppressive TGFB1 signals toward effector CD8+ T cells in tumors. Of note, these subsets exhibited higher TGFB1 expression than intratumoral myeloid cells across tumor types. In contrast, a tissue-resident (TR) adaptive subset exhibited exclusively proinflammatory IFNG-driven profiles and was associated with prolonged survival in both primary and metastatic tumor settings. Moreover, these TR adaptive NK cells, but not other subsets, were linked to response to immune checkpoint blockade. Collectively, our study reveals a previously unrecognized regulatory axis in NK cells that shapes NK cell diversity and augments broader antitumor immune responses.

Abstract INTRODUCTION The vascular endothelial growth factor (VEGF) signaling family plays a role in neurodegenerative diseases, including Alzheimer's disease (AD). Previous work has shown widespread effects of the members FLT1 , FLT4 , and VEGFB on AD outcomes. However, these analyses have focused within the non‐Hispanic White (NHW) population. METHODS The goal of this study was to analyze the effects of the VEGF family in underrepresented populations, leveraging large and diverse bulk RNA sequencing and tandem mass tag–mass spectrometry (TMT‐MS) proteomic data. Outcomes included measures of AD pathology and diagnosis. RESULTS Within underrepresented populations, we replicated previously reported effects of FLT1 and FLT4 , whereby higher protein abundance was observed in the AD brain and was associated with higher neuropathology burden. In stratified analyses, these associations were largely consistent across race and ethnicity. DISCUSSION This multi‐omic study on the role of the VEGF family in AD emphasizes the need for more representative studies focused on therapeutic targets for AD. Highlights Vascular endothelial growth factor (VEGF) genes and proteins were quantified in four different brain regions. Samples included participants from four different populations. Previously observed effects were replicated in diverse populations. This study is the largest multi‐omic study of the vascular endothelial growth factor (VEGF) genes among Alzheimer's disease (AD) participants from diverse populations.

Abstract Background Mitochondrial dysfunction in Alzheimer's Disease (AD) is characterized by impaired energy production, oxidative stress, and disrupted calcium homeostasis, which collectively contribute to neuronal damage, synaptic dysfunction, and the progression of AD pathology. A significant knowledge gap in studying mitochondrial dysfunction in Alzheimer's Disease (AD) lies in understanding the precise molecular mechanisms linking mitochondrial metabolic alterations to neuronal damage, particularly how sex‐specific and cell‐type‐specific mitochondrial processes contribute to the progression of AD pathology. Method This study integrates multiple datasets, post‐mortem brain RNAseq from ROSMAP, Mayo Clinic brain bank and Mount Sinai Brain Bank cohort data available via AD Knowledge Portal hosted by Sage Bionetworks), Human Protein Atlas (HPA), MitoCarta3, genome‐scale human metabolic reconstruction, mitochondriome analysis, and brain & blood metabolomics data (data generated by the Alzheimer's Disease Metabolomics Consortium (ADMC)) to identify mitochondrial genes associated with disrupted metabolism in AD. Additionally, biodomain analysis was used to identify key processes associated with pathology. Result A total of 62 common genes were identified across these approaches, highlighting their potential significance in mitochondrial processes. We also developed the framework to perform metabolite‐gene correlation analyses revealing key mitochondrial‐metabolic interactions (eg. homocysteine and MTHFR gene; acetyl‐CoA and PDHA1 gene). Integrated in silico metabolic analysis identified reaction fluxes, uncovering sex‐specific differences in mitochondrial transport and tricarboxylic acid (TCA) cycle subsystems, with notable alterations in females. Biodomain enrichment analysis focused on mitochondrial processes, identifying disruptions in pathways critical for energy production and redox homeostasis. Additionally, we analyzed datasets related to metformin and complex I inhibitors, linking mitochondrial complex I modulation with metabolic alterations in AD. This analysis identified druggable targets and potential therapeutic candidates for mitochondrial metabolic pathways. Conclusion Our findings integrate multiple data sources to provide a systems‐level understanding of mitochondrial metabolism in AD. Sex‐specific differences associated with mitochondrial dysfunction in AD were identified. We identify important mitochondrial transport proteins and metabolites that could potentially be used as druggable targets in AD.

Abstract Pseudouridine (Ψ) is the most prevalent RNA modification in human cells. Although Ψ was among the first post-transcriptional modifications discovered (1951), its biological functions remain poorly understood. More recently, Ψ was incorporated into COVID-19 mRNA vaccine, where it enhances RNA stability and reduces innate immune sensing. However, the precise roles of RNA Ψ in cancer, including leukemia, are largely unknown. Here, we identify RNA Pseudouridine Synthase D4 (RPUSD4) as a novel vulnerability in acute myeloid leukemia (AML) via directly catalyzing mitochondrial RNA (mt-RNA) Ψ formation. We further provide proof-of-concept evidence that targeting RPUSD4 suppresses leukemogenesis and stimulates anti-leukemia immunity. To investigate whether RNA Ψ dysregulation is involved in leukemia, we first compared RNA Ψ levels between primitive CD34+ cells (LSC-enriched) and CD34- bulk cells from multiple primary AML specimens. CD34+ AML cells exhibited significantly elevated RNA Ψ levels. We also examined Ψ levels across various RNA types in AML cells, identifying that mt-RNA contained much higher Ψ levels than other RNA types. These findings imply that RNA Ψ, particularly mt-RNA Ψ, may play a role in LSC biology and leukemogenesis. Further unbiased CRISPR screening revealed RPUSD4 as the most critical Ψ synthase for LSC maintenance. Large-scale transcriptomic and patient data analyses showed that RPUSD4 is highly expressed in AML specimens (P = 3.5 × 10-9), particularly within LSCs (P = 1.4 × 10-18). RPUSD4 knockout (KO) significantly suppressed AML proliferation, reduced mitochondrial OxPhos, and decreased LSC frequency in vitro and substantially delayed AML progression in vivo (MLL-r and FLT3ITD models). Of note, RPUSD4 KO-mediated anti-leukemia effects could be fully rescued by wild-type but not catalytically inactive RPUSD4 both in vitro and in vivo, demonstrating that Ψ synthase activity is essential for its function in leukemia. To profile RPUSD4-dependent Ψ sites, we applied two orthogonal technologies, direct nanopore sequencing and PRAISE sequencing (PMID: 36997645), both capable of detecting Ψ at single-base resolution. These approaches converged on a single RPUSD4-dependent Ψ at position 3,067 on mt-16S rRNA. This Ψ site is essential for maintaining rRNA stability. RPUSD4 KO induced mt-16S rRNA decay, thereby suppressing mitochondrial translation. This led to OxPhos inhibition, growth suppression, and LSC eradication in AML. Mechanistically, RPUSD4 is exclusively localized in mitochondria, where it directly interacts with the mt-RNA exonuclease PNPase. Under physiological conditions, PNPase resides within mitochondria and degrades mt-RNA to prevent accumulation of mitochondrial double-stranded RNA (mt-dsRNA). Upon RPUSD4 depletion, PNPase translocates from mitochondria to the cytosol, resulting in two major consequences: (i) mRNA decay:Cytosolic PNPase degrades mRNAs, particularly the nuclear-encoded mitochondrial mRNAs, such as DHODH(Dihydroorotate dehydrogenase). By retrogradely upregulating DHODH, RPUSD4 promotes de novo pyrimidine synthesis in AML. (ii) Aberrant mt-dsRNA accumulation: The buildup and cytoplasmic release of mt-dsRNA activates “viral mimicry” response that sensitizes AML cells to T cell cytotoxicity. Finally, to therapeutically target RPUSD4, we developed an RNA-based inhibitor, CpG-siRNARPUSD4, by conjugating a specific RPUSD4 siRNA to a Toll-like receptor (TLR9) ligand. CpG-siRNARPUSD4 is specifically internalized by TLR9+ cells, including AML cells, thereby maximizing selectivity and minimizing toxicity. Preclinical studies demonstrate that pharmacologically targeting RPUSD4 significantly prolonged survival across multiple AML models, including patient-derived xenograft (PDX) models, and rendered AML cells more susceptible to T cell–mediated cytotoxicity. Furthermore, the RPUSD4 inhibitor exhibited a promising synergistic effect with DHODH inhibitor in treating relapsed AML in vivo. For instance, in a representative relapsed PDX model, median survival times (in days) were: Ctrl – 28, RPUSD4 inhibitor – 36, DHODH inhibitor – 39, and combination – over 60. In conclusion, our findings uncover a previously unrecognized role of RPUSD4 and mt-RNA Ψ in leukemic metabolism, anti-leukemia immunity, and LSC maintenance. This study also bridges a critical knowledge gap regarding the role of RNA Ψ in leukemogenesis.

Introduction: Previous findings suggest that sirtuin 6 (SIRT6), a nuclear histone deacetylase, is involved in fundamental processes that regulate aging, which include DNA damage repair and maintenance of genomic stability. It remains unclear, however, whether SIRT6 overexpression can mitigate age-related vascular dysfunction due to multiple mechanisms of posttranslational enzyme inactivation (oxidation, ubiquitination-dependent degradation, etc). We hypothesized that overexpression of SIRT6, will improve both endothelium-dependent relaxation and smooth muscle contractile function and improve molecular mechanisms underlying these functions in healthy aged mice. Methods: We used normocholesterolemic mice that were either wild-type for SIRT6 (WT) or overexpressing one copy of SIRT6 (TG) and studied them at either 3 or 18 months of age. We assessed molecular changes in SIRT6 expression, cellular senescence, and vascular contractile protein expression using qPCR, and aortic rings in isolated organ bath chambers to measure endothelium-dependent relaxation to acetylcholine (ACH), endothelium-independent relaxation to sodium nitroprusside (SNP), and contractile responses to serotonin (5HT) and PGF 2α . Results: As expected, overexpression of SIRT6 in TG mice resulted in ~3-fold mRNA expression increase compared to WT mice in aorta. In line with our previous reports, SIRT6 mRNA levels significantly increased with age in aorta. CDKN2A, a cellular senescence marker, increased with aging in WT mice. Surprisingly, SIRT6 overexpression did not attenuate this increase, with TG mice tending to have higher CDKN2A expression than WT at 18m. ACTA2, a contractile protein marker, had modest reductions with age in WT mice, and surprisingly, overexpression of SIRT6 did not alter ACTA2 levels compared to WT at either time point. Finally, overexpression of SIRT6 did not mitigate age-related changes in vascular relaxation or contractile function. Conclusion: Collectively, these data at the surface level suggest that overexpressing SIRT6 does not protect against conduit vessel dysfunction in aged mice and is associated with paradoxical increases in senescent cell markers. It remains elusive whether there are other molecular modulators of aging that offset or alter the activity of SIRT6 with its genetic overexpression. Therefore, future studies investigating molecular determinants of SIRT6 bioactivity and its tissue/context dependence with aging are warranted.

Abstract Osteogenic differentiation is essential for bone development, metabolism, and repair; however, the underlying regulatory relationships among genes remain poorly understood. To elucidate the transcriptomic changes and identify novel regulatory genes involved in osteogenic differentiation, we differentiated mesenchymal stem cells (MSCs) derived from 20 human iPSC lines into preosteoblasts (preOBs) and osteoblasts (OBs). We then performed transcriptome profiling of MSCs, preOBs and OBs. The iPSC-derived MSCs and OBs showed similar transcriptome profiles to those of primary human MSCs and OBs, respectively. Differential gene expression analysis revealed global changes in the transcriptomes from MSCs to preOBs, and then to OBs, including the differential expression of 840 genes encoding transcription factors (TFs). TF regulatory network analysis uncovered a network comprising 451 TFs, organized into five interactive modules. Multiscale embedded gene co-expression network analysis (MEGENA) identified gene co-expression modules and key network regulators (KNRs). From these analyses, KLF16 emerged as an important TF in osteogenic differentiation. We demonstrate that overexpression of Klf16 in vitro inhibited osteogenic differentiation and mineralization, while Klf16+/- mice exhibited increased bone mineral density, trabecular number, and cortical bone area. Our study underscores the complexity of osteogenic differentiation and identifies novel regulatory genes such as KLF16, which plays an inhibitory role in osteogenic differentiation both in vitro and in vivo.

Abstract Osteogenic differentiation is essential for bone development, metabolism, and repair; however, the underlying regulatory relationships among genes remain poorly understood. To elucidate the transcriptomic changes and identify novel regulatory genes involved in osteogenic differentiation, we differentiated mesenchymal stem cells (MSCs) derived from 20 human iPSC lines into preosteoblasts (preOBs) and osteoblasts (OBs). We then performed transcriptome profiling of MSCs, preOBs and OBs. The iPSC-derived MSCs and OBs showed similar transcriptome profiles to those of primary human MSCs and OBs, respectively. Differential gene expression analysis revealed global changes in the transcriptomes from MSCs to preOBs, and then to OBs, including the differential expression of 840 genes encoding transcription factors (TFs). TF regulatory network analysis uncovered a network comprising 451 TFs, organized into five interactive modules. Multiscale embedded gene co-expression network analysis (MEGENA) identified gene co-expression modules and key network regulators (KNRs). From these analyses, KLF16 emerged as an important TF in osteogenic differentiation. We demonstrate that overexpression of Klf16 in vitro inhibited osteogenic differentiation and mineralization, while Klf16+/- mice exhibited increased bone mineral density, trabecular number, and cortical bone area. Our study underscores the complexity of osteogenic differentiation and identifies novel regulatory genes such as KLF16, which plays an inhibitory role in osteogenic differentiation both in vitro and in vivo.

Calcific aortic valve disease (CAVD) is a highly active process, and upregulation of osteogenic signaling is thought to be a major driver to initiation and progression of disease. While previous reports by our group and others demonstrated dysregulation of antioxidants and pro-oxidants in calcified aortic valves, it remains unclear if loss of antioxidant is a causal event driving valvular calcification and dysfunction. We hypothesized that MnSOD deficiency—an essential mitochondrial antioxidant—would result in accelerated reductions of cusp separation distance, increased osteogenic signaling, and augmented calcium deposition in a hypercholesterolemic mouse model of CAVD. We used ldlr -/- / ApoB 100/100 (LA) mice that were either wild-type (LA-MnSOD +/+ ) or MnSOD-deficient (LA-MnSOD +/- ), fed a Western Diet for 3 or 6 months. We used qRT-PCR and immunohistochemistry to measure changes in pro-osteogenic signaling, histopathological analyses of calcium burden (Alizarin Red), and echocardiography to assess aortic valve function. BMP2—a pro-osteogenic marker—increased over time with Western diet feeding, though MnSOD-deficiency did not exacerbate these increases. mRNA levels of pro-osteogenic markers (Runx2, Msx2) were also unchanged with either time on diet or with experimental reduction of MnSOD. Surprisingly, protein levels of late- stage osteoblast marker, osterix, were modestly decreased at the three month time point in in LA-MnSOD +/- mice compared to age-matched wild-type littermates. Consistent with our hypothesis, however, loss of mitochondrial antioxidant capacity substantially increased osterix protein levels and calcium burden at the 6 month time point compared to age-matched wild-type littermates. Functionally, loss of mitochondrial antioxidant capacity did not alter aortic valve cusp separation distance at both 3 and 6 month time points. Collectively, these data suggest that loss of MnSOD does not alter disease initiation but instead augments osteogenic signaling and valvular calcification in established aortic valve disease. Future studies aimed at targeting mitochondrial oxidative stress could elucidate novel strategies to slow progression of established CAVD.

Marfan Syndrome (MFS) is often associated with progressive aortic root dilation, ultimately leading to aortic aneurysm and dissection. While recent work showed increased transforming growth factor beta (TGF-β) signaling contributes to aneurysm formation in aorta, efficacious therapeutic targets remain elusive. Consistent with prior reports of progeroid phenotypes in a subset of Marfan patients we previously demonstrated increased cellular senescence in a MFS mouse model. Here, we sought to determine whether administration of senolytic drugs reduces cellular senescent markers, TGF-β signaling, and aortic root dilation in aged MFS mice by assessing aortic root dimensions by echocardiography and gene expression levels by quantitative real time PCR at 15 months of age following treatment with vehicle (VEH) or the senolytic compound Fisetin for one month. As expected, aortic sinus dimensions were increased dramatically in fibrillin-1 mutant mice compared to wild-type controls and were associated with increased expression of TGF-β1, the senescence marker CDKN2A, the matrix remodeling enzyme MMP2, and the osteogenic and proliferative gene RUNX2. Consistent with previous data from our group, Fisetin treatment dramatically reduced CDKN2A expression in marfanoid mice compared to VEH, which was associated with reductions in TGF-β1, MMP2, and RUNX2. Phenotypically, we observed modest reductions in aortic sinus dimensions compared to VEH, but no substantive change in ascending aortic dilatation. Collectively, these data suggest that senescent cells are significant contributors to molecular changes occurring in MFS and clearance of senescent cells with Fisetin slows the progression aortic root-dilation in fibrillin-1 mutant mice.