Sensory Input, Sex, and Function Shape Hypothalamic Cell Type Development.

Mammalian behavior and physiology undergo dramatic changes in early life. Young animals rely on conspecifics to meet their homeostatic needs, until weaning and puberty initiate nutritional independence and sex-specific social interactions, respectively. How neuronal populations regulating homeostatic functions and social behaviors develop and mature during these transitions remains unclear. We used paired transcriptomic and chromatin accessibility profiling to examine the developmental trajectories of neuronal populations in the hypothalamic preoptic region, where cell types with key roles in physiological and behavioral control have been identified1-6. These data reveal a remarkable diversity of developmental trajectories shaped by the sex of the animal, and the location and behavioral or physiological function of the corresponding cell types. We identify key stages of preoptic development, including the perinatal emergence of sex differences, postnatal maturation and subsequent refinement of signaling networks, and nonlinear transcriptional changes accelerating at the time of weaning and puberty. We assessed preoptic development in various sensory mutants and find a major role for vomeronasal sensing in the timing of preoptic cell type maturation. These results provide novel insights into the development of neurons controlling homeostatic functions and social behaviors and lay ground for examining the dynamics of these functions in early life.

SEACells infers transcriptional and epigenomic cellular states from single-cell genomics data.

Metacells are cell groupings derived from single-cell sequencing data that represent highly granular, distinct cell states. Here we present single-cell aggregation of cell states (SEACells), an algorithm for identifying metacells that overcome the sparsity of single-cell data while retaining heterogeneity obscured by traditional cell clustering. SEACells outperforms existing algorithms in identifying comprehensive, compact and well-separated metacells in both RNA and assay for transposase-accessible chromatin (ATAC) modalities across datasets with discrete cell types and continuous trajectories. We demonstrate the use of SEACells to improve gene-peak associations, compute ATAC gene scores and infer the activities of critical regulators during differentiation. Metacell-level analysis scales to large datasets and is particularly well suited for patient cohorts, where per-patient aggregation provides more robust units for data integration. We use our metacells to reveal expression dynamics and gradual reconfiguration of the chromatin landscape during hematopoietic differentiation and to uniquely identify CD4 T cell differentiation and activation states associated with disease onset and severity in a Coronavirus Disease 2019 (COVID-19) patient cohort.

MACHETE identifies interferon-encompassing chromosome 9p21.3 deletions as mediators of immune evasion and metastasis.

The most prominent homozygous deletions in cancer affect chromosome 9p21.3 and eliminate CDKN2A/B tumor suppressors, disabling a cell-intrinsic barrier to tumorigenesis. Half of 9p21.3 deletions, however, also encompass a type I interferon (IFN) gene cluster; the consequences of this co-deletion remain unexplored. To functionally dissect 9p21.3 and other large genomic deletions, we developed a flexible deletion engineering strategy, MACHETE (molecular alteration of chromosomes with engineered tandem elements). Applying MACHETE to a syngeneic mouse model of pancreatic cancer, we found that co-deletion of the IFN cluster promoted immune evasion, metastasis and immunotherapy resistance. Mechanistically, IFN co-deletion disrupted type I IFN signaling in the tumor microenvironment, leading to marked changes in infiltrating immune cells and escape from CD8+ T-cell surveillance, effects largely driven by the poorly understood interferon epsilon. These results reveal a chromosomal deletion that disables both cell-intrinsic and cell-extrinsic tumor suppression and provide a framework for interrogating large deletions in cancer and beyond.

Determining the rotational orientation of directional deep brain stimulation electrodes using magnetoencephalography.

Objective.The aim of the present study was to evaluate the effect of different electrode configurations on the accuracy of determining the rotational orientation of the directional deep brain stimulation (DBS) electrode with our previously published magnetoencephalography (MEG)-based method.Approach.A directional DBS electrode, along with its implantable pulse generator, was integrated into a head phantom and placed within the MEG sensor array. Predefined bipolar electrode configurations, based on activation of different directional and omnidirectional contacts of the electrode, were set to generate a defined magnetic field during stimulation. This magnetic field was then measured with MEG. Finite element modeling and model fitting approach were used to calculate electrode orientation.Main results.The accuracy of electrode orientation detection depended on the electrode configuration: the vertical configuration (activation of two directional contacts arranged one above the other) achieved an average accuracy of only about 41 ∘. The diagonal configuration (activation of the electrode tip and a single directional contact at the next higher level of the electrode) achieved an accuracy of 13∘, while the horizontal electrode configuration (activation of two adjacent directional contacts at the same electrode level) achieved the best accuracy of 6∘. The accuracy of orientation detection of the DBS electrode depends on the change in spatial distribution of the magnetic field with the rotation of the electrode along its own axis. In the vertical configuration, rotation of the electrode has a small effect on the magnetic field distribution, while in the diagonal or horizontal configuration, electrode rotation has a significant effect on the magnetic field distribution.Significance.Our work suggests that in order to determine rotational orientation of a DBS electrode using MEG, horizontal configuration should be used as it provides the most accurate results compared to other possible configurations.

DBS electrode localization and rotational orientation detection using SQUID-based magnetoencephalography.

Objective.The aim of the present study was to investigate the accuracy of localization and rotational orientation detection of a directional deep brain stimulation (DBS) electrode using a state-of-the-art magnetoencephalography (MEG) scanner.Approach.A directional DBS electrode along with its stimulator was integrated into a head phantom and placed inside the MEG sensor array. The electrode was comprised of six directional and two omnidirectional contacts. Measurements were performed while stimulating with different contacts and parameters in the phantom. Finite element modeling and fitting approach were used to compute electrode position and orientation.Main results.The electrode was localized with a mean accuracy of 2.2 mm while orientation was determined with a mean accuracy of 11∘. The limitation in detection accuracy was due to the lower measurement precision of the MEG system. Considering an ideal measurement condition, these values represent the lower bound of accuracy that can be achieved in patients.Significance.However, a future magnetic measuring system with higher precision will potentially detect location and orientation of a DBS electrode with an even greater accuracy.

Overcoming Challenging Substituent Perturbations with Multisite λ-Dynamics: A Case Study Targeting ß-Secretase 1.

Alchemical free energy calculations have made a dramatic impact upon the field of structure-based drug design by allowing functional group modifications to be explored computationally prior to experimental synthesis and assay evaluation, thereby informing and directing synthetic strategies. In furthering the advancement of this area, a series of 21 ß-secretase 1 (BACE1) inhibitors developed by Janssen Pharmaceuticals were examined to evaluate the ability to explore large substituent perturbations, some of which contain scaffold modifications, with multisite λ-dynamics (MSλD), an innovative alchemical free energy framework. Our findings indicate that MSλD is able to efficiently explore all structurally diverse ligand end-states simultaneously within a single MD simulation with a high degree of precision and with reduced computational costs compared to the widely used approach TI/MBAR. Furthermore, computational predictions were shown to be accurate to within 0.5-0.8 kcal/mol when CM1A partial atomic charges were combined with CHARMM or OPLS-AA-based force fields, demonstrating that MSλD is force field independent and a viable alternative to FEP or TI approaches for drug design.

Landscape of Germline and Somatic Mitochondrial DNA Mutations in Pediatric Malignancies.

Little is known about the spectrum of mitochondrial DNA (mtDNA) mutations across pediatric malignancies. In this study, we analyzed matched tumor and normal whole genome sequencing data from 616 pediatric patients with hematopoietic malignancies, solid tumors, and brain tumors. We identified 391 mtDNA mutations in 284 tumors including 45 loss-of-function mutations, which clustered at four statistically significant hotspots in MT-COX3, MT-ND4, and MT-ND5, and at a mutation hotspot in MT-tRNA-MET. A skewed ratio (4.83) of nonsynonymous versus synonymous (dN/dS) mtDNA mutations with high statistical significance was identified on the basis of Monte Carlo simulations in the tumors. In comparison, opposite ratios of 0.44 and 0.93 were observed in 616 matched normal tissues and in 249 blood samples from children without cancer, respectively. mtDNA mutations varied by cancer type and mtDNA haplogroup. Collectively, these results suggest that deleterious mtDNA mutations play a role in the development and progression of pediatric cancers. SIGNIFICANCE: This pan-cancer mtDNA study establishes the landscape of germline and tumor mtDNA mutations and identifies hotspots of tumor mtDNA mutations to pinpoint key mitochondrial functions in pediatric malignancies.