Biology subjects

Bernstein, B.

Publications and source records attributed to Bernstein, B..

4 recordsLinked to original sources

bioRxiv2026

Brainstem cholinergic cell loss causes slowly-developing motor impairments

Pedunculopontine nucleus (PPN) cholinergic degeneration is a feature of Parkinson's disease (PD), but it is difficult to isolate the symptoms and circuit alterations caused by cholinergic cell loss in PD, where multiple nuclei are simultaneously degenerating. Here we develop a novel mouse model of brainstem cholinergic cell loss to define the timeline of symptom development and map physiological adaptations within the brainstem. Mild motor symptoms, including balance and motor learning deficits reminiscent of early-stage PD, developed after cholinergic lesion with an unexpected long delay. Ex vivo whole-cell recordings showed that cholinergic cell loss increased excitatory synaptic drive onto glutamatergic PPN neurons and increased their intrinsic ability to generate sustained action potential output. In parallel, fiber photometry experiments revealed a slight increase in glutamatergic sensory responsiveness that closely tracked the delayed onset of behavioral symptoms. Together, these results reveal that brainstem cholinergic cell loss triggers the reorganization of motor-related brainstem circuits, providing critical insight into the consequences of non-dopaminergic degeneration in PD.

neuroscience↗

bioRxiv2026

Metastatic Osteosarcoma is Characterized by Loss of Osteoblastic Lineage Fidelity

Osteosarcoma (OS) is a rare and aggressive bone cancer with limited therapeutic progress in several decades. To characterize the transcriptional diversity of malignant cell states in OS, we analyzed single-nucleus RNA sequencing data from 24 tumors, including both primary and metastatic lesions. We identified a canonical osteoblastic cell state that predominated in primary tumor cells, but was dampened in metastases. Integrating tumor data with data from embryonic skeletal development and an experimental osteoblast differentiation model revealed that metastatic OS cells resemble poorly specified mesenchyme enriched for non-osseous programs. Clonal populations in metastatic samples acquired mesenchymal cell states distinct from paired primary tumors. Similar cell state shifts were evident in post-treatment primary tumors relative to paired pre-treatment samples. Our results suggest that localized post-treatment and metastatic OS malignant cells lose osteoblastic lineage fidelity, which may represent a unifying axis of disease evolution and reveal new therapeutic vulnerabilities.

Cancer Biology↗

bioRxiv2025

Enumerating and Exploring the Space of Clonal Trees

Tumor growth is a complex evolutionary process initiated by an abnormal ancestor cell progressively gaining mutations, which eventually results in uncontrolled cell division. Researchers use a structure called a clonal tree-which depicts ancestral relationships between mutated cell populations-to represent a tumors evolutionary history. Numerous methods have been developed to reconstruct a clonal tree from tumor sequencing data. To evaluate the accuracy of such tree inference methods, researchers typically use simulated data where the true evolutionary history is known. However, previous research has not thoroughly analyzed the space of clonal trees under different evolutionary models. Such exploration would help to better understand the underlying structure and characteristics of these spaces of trees and would aid in creation of more appropriate simulated datasets. We analyzed four different categories of clonal trees, each with their own set of assumptions. For each category, we designed and implemented enumeration algorithms that provably generate all such clonal trees with a specified number of mutations. We then used our algorithms to generate several datasets and analyzed the generated trees to discover patterns in the data across different assumptions. We also investigated two tree sampling methods to compare their output with our fully enumerated trees and found that one of the methods does a good job of representing the entire space of trees, while the other does quite poorly. Our findings have important implications for the creation of simulated data commonly used to assess new clonal tree inference methods. Code associated with the project is freely available at: https://bitbucket.org/oesperlab/tree-space/src/main/

bioinformatics↗

bioRxiv2022

A resource for generating and manipulating human microglial states in vitro

Microglia have emerged as key players in the pathogenesis of neurodegenerative conditions such as Alzheimers disease (AD). In response to CNS stimuli, these cells adopt distinct transcriptional and functional subtypes known as states. However, an understanding of the function of these states has been elusive, especially in human microglia, due to lack of tools to model and manipulate this cell-type. Here, we provide a platform for modeling human microglia transcriptional states in vitro. Using single-cell RNA sequencing, we found that exposure of human stem-cell differentiated microglia (iMGLs) to brain-related challenges generated extensive transcriptional diversity which mapped to gene signatures identified in human brain microglia. We identified two in vitro transcriptional clusters that were analogous to human and mouse disease-associated microglia (DAMs), a state enriched in neurodegenerative disease contexts. To facilitate scalable functional analyses, we established a lentiviral approach enabling broad and highly efficient genetic transduction of microglia in vitro. Using this new technology, we demonstrated that MITF (Melanocyte Inducing Transcription Factor), an AD-enriched transcription factor in microglia, drives both a disease-associated transcriptional signature and a highly phagocytic state. Finally, we confirmed these results across iMGLs differentiated from multiple iPSC lines demonstrating the broad utility of this platform. Together, these tools provide a comprehensive resource that enables the manipulation and functional interrogation of human microglial states in both homeostatic and disease-relevant contexts.

neuroscience↗