Spatial genomics enables multi-modal study of clonal heterogeneity in tissues.

The state and behaviour of a cell can be influenced by both genetic and environmental factors. In particular, tumour progression is determined by underlying genetic aberrations1-4 as well as the makeup of the tumour microenvironment5,6. Quantifying the contributions of these factors requires new technologies that can accurately measure the spatial location of genomic sequence together with phenotypic readouts. Here we developed slide-DNA-seq, a method for capturing spatially resolved DNA sequences from intact tissue sections. We demonstrate that this method accurately preserves local tumour architecture and enables the de novo discovery of distinct tumour clones and their copy number alterations. We then apply slide-DNA-seq to a mouse model of metastasis and a primary human cancer, revealing that clonal populations are confined to distinct spatial regions. Moreover, through integration with spatial transcriptomics, we uncover distinct sets of genes that are associated with clone-specific genetic aberrations, the local tumour microenvironment, or both. Together, this multi-modal spatial genomics approach provides a versatile platform for quantifying how cell-intrinsic and cell-extrinsic factors contribute to gene expression, protein abundance and other cellular phenotypes.

Machine learning to define phenotypes and outcomes of patients hospitalized for heart failure with preserved ejection fraction: Findings from ASCEND-HF.

BACKGROUND: Heart Failure with Preserved Ejection Fraction (HFpEF) is a heterogenous disease with few therapies proven to provide clinical benefit. Machine learning can characterize distinct phenotypes and compare outcomes among patients with HFpEF who are hospitalized for acute HF. METHODS: We applied hierarchical clustering using demographics, comorbidities, and clinical data on admission to identify distinct clusters in hospitalized HFpEF (ejection fraction >40%) in the ASCEND-HF trial. We separately applied a previously developed latent class analysis (LCA) clustering method and compared in-hospital and long-term outcomes across cluster groups. RESULTS: Of 7141 patients enrolled in the ASCEND-HF trial, 812 (11.4%) were hospitalized for HFpEF and met the criteria for complete case analysis. Hierarchical Cluster 1 included older women with atrial fibrillation (AF). Cluster 2 had elevated resting blood pressure. Cluster 3 had young men with obesity and diabetes. Cluster 4 had low resting blood pressure. Mortality at 180 days was lowest among Cluster 3 (KM event-rate 6.2 [95% CI: 3.5, 10.9]) and highest among Cluster 4 (18.8 [14.6, 24.0], P < .001). Twenty four-hour urine output was higher in Cluster 3 (2700 mL [1800, 3975]) than Cluster 4 (2100 mL [1400, 3055], P < .001). LCA also identified four clusters: A) older White or Asian women, B) younger men with few comorbidities, C) older individuals with AF and renal impairment, and D) patients with obesity and diabetes. Mortality at 180 days was lowest among LCA Cluster B (KM event-rate 5.5 [2.0, 10.3]) and highest among LCA Cluster C (26.3 [19.2, 35.4], P < .001). CONCLUSIONS: In patients hospitalized for HFpEF, cluster analysis demonstrated distinct phenotypes with differing clinical profiles and outcomes.

Effects of Sacubitril/Valsartan vs Valsartan in De Novo vs Acute on Chronic HFpEF and HFmrEF.

Background: Decompensated heart failure (HF) can be categorized as de novo or worsening of chronic HF. In PARAGLIDE-HF (Prospective comparison of ARNI with ARB Given following stabiLization In DEcompensated HFpEF), among patients with an ejection fraction >40% that stabilized after worsening HF, sacubitril/valsartan led to a significantly greater reduction in N-terminal pro-B-type natriuretic peptide (NT-proBNP) and was associated with clinical benefit compared to valsartan. Objectives: This prespecified analysis characterized patients with de novo vs worsening chronic HF in PARAGLIDE-HF and assessed the interaction between HF chronicity and the effect of sacubitril/valsartan. Methods: Patients were classified as de novo (first diagnosis of HF) or chronic (known HF prior to the index event). Time-averaged proportional change in NT-proBNP from baseline to weeks 4 and 8 was analyzed using an analysis of covariance model. A win ratio consisting of time to cardiovascular death, number and times of HF hospitalizations during follow-up, number and times of urgent HF visits during follow-up, and time-averaged proportional change in NT-proBNP was assessed for each group. Results: Of the 466 participants, 153 (33%) had de novo HF and 313 (67%) had chronic HF. De novo patients had lower rates of atrial fibrillation/flutter and lower creatinine. There was a nonsignificant reduction in NT-proBNP with sacubitril/valsartan vs valsartan for de novo (0.82; 95% CI: 0.62-1.07) and chronic HF (0.88; 95% CI: 0.73-1.07), interaction P = 0.66. The win ratio was nominally in favor of sacubitril/valsartan for both de novo (1.12; 95% CI: 0.70-1.58) and chronic HF (1.24; 95% CI: 0.89-1.71). Conclusions: There is no interaction between HF chronicity and the effect of sacubitril-valsartan.

In-Hospital Virtual Peer-to-Peer Consultation to Increase Guideline-Directed Medical Therapy for Heart Failure: A Pilot Randomized Trial.

BACKGROUND: Guideline-directed medical therapy (GDMT) for heart failure with reduced ejection fraction (HFrEF) improves clinical outcomes and quality of life. Optimizing GDMT in the hospital is associated with greater long-term use in HFrEF. This study aimed to describe the efficacy of a multidisciplinary virtual HF intervention on GDMT optimization among patients with HFrEF admitted for any cause. METHODS: In this pilot randomized, controlled study, consecutive patients with HFrEF admitted to noncardiology medicine services for any cause were identified at a large academic tertiary care hospital between May to September 2021. Major exclusions were end-stage renal disease, hemodynamic instability, concurrent COVID-19 infection, and current enrollment in hospice care. Patients were randomized to a clinician-level virtual peer-to-peer consult intervention providing GDMT recommendations and information on medication costs versus usual care. Primary end points included (1) proportion of patients with new GDMT initiation or use and (2) changes to HF optimal medical therapy scores which included target dosing (range, 0-9). RESULTS: Of 242 patients identified, 91 (38%) were eligible and randomized to intervention (N=52) or usual care (N=39). Baseline characteristics were similar between intervention and usual care (mean age 63 versus 67 years, 23% versus 26% female, 46% versus 49% Black, mean ejection fraction 33% versus 31%). GDMT use on admission was also similar. There were greater proportions of patients with GDMT initiation or continuation with the intervention compared with usual care. After adjusting for optimal medical therapy score on admission, changes to optimal medical therapy score at discharge were higher for the intervention group compared with usual care (+0.44 versus -0.31, absolute difference +0.75, adjusted estimate 0.86±0.42; P=0.041). CONCLUSIONS: Among eligible patients with HFrEF hospitalized for any cause on noncardiology services, a multidisciplinary pilot virtual HF consultation increased new GDMT initiation and dose optimization at discharge.

Physical Rehabilitation in Older Patients Hospitalized with Acute Heart Failure and Diabetes: Insights from REHAB-HF.

BACKGROUND: Prior studies showed an attenuated response to exercise training among patients with heart failure and type 2 diabetes mellitus. We explored the interaction between diabetes status and a novel, transitional, tailored, progressive rehabilitation intervention that improved physical function compared with usual care in the Rehabilitation Therapy in Older Acute Heart Failure Patients (REHAB-HF) trial. METHODS: The effect of the intervention on 3-month Short Physical Performance Battery (SPPB) (primary endpoint), 6-minute walk distance (6MWD), modified Fried frailty criteria, and quality-of-life scores (Kansas City Cardiomyopathy Questionnaire [KCCQ] and EuroQoL Visual Analogue Scale [VAS]) was compared between participants with and without diabetes. Differences in 6-month clinical outcomes were also explored. RESULTS: Of the 349 participants enrolled in REHAB-HF, 186 (53%) had diabetes. The prevalence of diabetes was higher in the intervention group (59% vs 48%). Participants with diabetes had worse baseline physical function by the SPPB and 6MWD, but similar frailty and quality-of-life scores. There was a consistent improvement with the intervention for 3-month SPPB, 6MWD, and VAS regardless of diabetes status (all interaction P value > .6), but participants with diabetes had significantly less improvement for frailty (P = .021) and a trend toward lower improvement in KCCQ (P = .11). There was no significant interaction by diabetes status for 6-month clinical event outcomes (all interaction P value > .3). CONCLUSIONS: Participants with diabetes had worse baseline physical function but showed similar clinically meaningful improvements from the intervention. There was less benefit for frailty with the intervention in participants with diabetes.

In situ genome sequencing resolves DNA sequence and structure in intact biological samples.

Understanding genome organization requires integration of DNA sequence and three-dimensional spatial context; however, existing genome-wide methods lack either base pair sequence resolution or direct spatial localization. Here, we describe in situ genome sequencing (IGS), a method for simultaneously sequencing and imaging genomes within intact biological samples. We applied IGS to human fibroblasts and early mouse embryos, spatially localizing thousands of genomic loci in individual nuclei. Using these data, we characterized parent-specific changes in genome structure across embryonic stages, revealed single-cell chromatin domains in zygotes, and uncovered epigenetic memory of global chromosome positioning within individual embryos. These results demonstrate how IGS can directly connect sequence and structure across length scales from single base pairs to whole organisms.