Biology subjects

Molina, P.

Publications and source records attributed to Molina, P..

5 recordsLinked to original sources

bioRxiv2025

Differential colocalization of cell-type pairs in single-cell spatial omics with DC-SPOMIC

MotivationSpatial omics studies compare cell-cell organization across samples, but most methods model between-sample variability while treating sample-level spatial estimates as error-free. Overlooking within-sample uncertainty can distort inference in heterogeneous cohorts, motivating methods that explicitly quantify and propagate this uncertainty into cohort-level analyses. ResultsWe present PANORAMIC, a hierarchical framework for spatial colocalization analysis that uses edge-corrected neighborhood enrichment to estimate local cell-type colocalization, spatial bootstrapping to quantify within-sample uncertainty, and multilevel random-effects meta-analysis to propagate this uncertainty across samples, patients, and conditions. In simulations, PANORAMIC improved recovery of within-sample uncertainty and between-sample heterogeneity relative to naive estimators across diverse spatial settings and progressive data degradation. Applied to a colorectal cancer tissue microarray profiled by multiplexed immunofluorescence imaging, PANORAMIC identified stronger B- and T-cell colocalization in tumors with Crohns-like reaction than in tumors with diffuse inflammatory infiltration, together with tighter higher-order immune organization consistent with immune aggregates. These results show that propagating within-sample spatial uncertainty can improve cohort-level inference in spatial omics studies. Availability and ImplementationPANORAMIC is released as an open-source R package at https://github.com/plevritis-lab/panoramic. Contact[sylvia.plevritis@stanford.edu]

bioinformatics↗

bioRxiv2025

Non-canonical EGFR signaling is essential for MAPK-mediated apical extrusion of epithelial cells

Individual epithelial cells that acutely express oncogenes such as Ras or Src are extruded apically from monolayers of wildtype cells. Multiple signaling networks have been implicated but the extrusion mechanism is still not fully understood. We examined extrusion of mammary epithelial cells caused by acute induction of oncogenic Ras(Q61L). As reported by others, Ras-dependent extrusion requires downstream activation of ERK but not AKT. Unexpectedly, however, extrusion was completely blocked by Erlotinib, which inhibits Epidermal growth factor receptor (EGFR) activity, or by deletion of the receptor. In pancreatic and lung cancers, EGFR is required for full activation of Ras and consequent ERK activation. However, inhibition or deletion of EGFR had no impact in our system on Ras(Q61L)-GTP levels or ERK phosphorylation. Importantly, receptor function was cell autonomous, because EGFR expression was not required in surrounding WT cells but was essential in the Ras(Q61L) cells, yet did not act through the canonical ERK signaling pathway. Deletion of Ras exchange factors Sos1/2 did not block cell extrusion. Moreover, expression of a constitutively active MEK mutant, instead of Ras, was sufficient to drive extrusion, and EGFR inhibition or knockout in these cells blocked extrusion, with no change in phospho-ERK levels. Notably, acute expression of Ras triggered internalization of E-cadherin, which was partially blocked by inhibition of EGFR. Knockout of E-cadherin was alone sufficient to promote extrusion. Together, these data demonstrate an unanticipated requirement for noncanonical EGFR signaling in cancer cell extrusion, which may act in part through the promotion of E-cadherin endocytosis. Statement of SignificanceApical extrusion of cells acutely expressing oncogenic Ras requires EGFR activity through a noncanonical pathway, independent of ERK and AKT signaling, that promotes E-cadherin internalization from adherens junctions.

cancer biology↗

bioRxiv2024

Scalable single-cell pooled CRISPR screens with conventional knockout vector libraries

Current methods for single-cell RNA profiling of pooled CRISPR screens are limited, either by indirect capture of single guide RNAs (sgRNAs) or by custom modification of plasmid libraries. Here, we present a direct sgRNA capture platform called Native sgRNA Capture and sequencing (NSC-seq) that enables single-cell CRISPR screens using common knockout plasmid libraries, facilitating genotype-phenotype mapping at multiple scales in vitro and in vivo. Additionally, we characterize sgRNA expression in three whole-genome knockout libraries, revealing a substantial subset of truncated (isoform) spacer reads. We provide this dataset as a reference of expressed sgRNA isoforms that may potentially have compromised CRISPR gene editing efficacy and precision.

genomics↗

bioRxiv2023

Temporal recording of mammalian development and precancer

Key to understanding many biological phenomena is knowing the temporal ordering of cellular events, which often require continuous direct observations [1, 2]. An alternative solution involves the utilization of irreversible genetic changes, such as naturally occurring mutations, to create indelible markers that enables retrospective temporal ordering [3-8]. Using NSC-seq, a newly designed and validated multi-purpose single-cell CRISPR platform, we developed a molecular clock approach to record the timing of cellular events and clonality in vivo, while incorporating assigned cell state and lineage information. Using this approach, we uncovered precise timing of tissue-specific cell expansion during murine embryonic development and identified new intestinal epithelial progenitor states by their unique genetic histories. NSC-seq analysis of murine adenomas and single-cell multi-omic profiling of human precancers as part of the Human Tumor Atlas Network (HTAN), including 116 scRNA-seq datasets and clonal analysis of 418 human polyps, demonstrated the occurrence of polyancestral initiation in 15-30% of colonic precancers, revealing their origins from multiple normal founders. Thus, our multimodal framework augments existing single-cell analyses and lays the foundation for in vivo multimodal recording, enabling the tracking of lineage and temporal events during development and tumorigenesis.

developmental biology↗

bioRxiv2023

JZL184 increases anxiety-like behavior and does not reduce alcohol consumption in female rats after repeated mild traumatic brain injury.

Alcohol use disorder (AUD) is highly comorbid with traumatic brain injury (TBI). Previously, using a lateral fluid percussion model (LFP) (an open model of head injury) to generate a single mild to moderate traumatic brain injury (TBI), we showed that TBI produces escalation in alcohol drinking, that alcohol exposure negatively impacts TBI outcomes, and that the endocannabinoid degradation inhibitor (JZL184) confers significant protection from behavioral and neuropathological outcomes in male rodents. In the present study, we used a weight drop model (a closed model of head injury) to produce a repeated mild TBI (rmTBI, 3 TBIs, spaced by 24 hours) to examine the sex-specific effects on alcohol consumption and anxiety-like behavior in rats, and whether systemic treatment with JZL184 would reverse TBI effects on those behaviors in both sexes. In two separate studies, adult male and female Wistar rats were subjected to rmTBI or sham using the weight drop model. Physiological measures of injury severity were collected from all animals. Animals in both studies were allowed to consume alcohol using an intermittent 2-bottle choice procedure (12 pre-TBI sessions and 12 post-TBI sessions). Neurological severity and neurobehavioral scores (NSS and NBS, respectively) were tested 24 hours after the final injury. Anxiety-like behavior was tested at 37-38 days post-injury in Study 1, and 6-8 days post-injury in Study 2. Our results show that females exhibited reduced respiratory rates relative to males with no significant differences between Sham and rmTBI, no effect of rmTBI or sex on righting reflex, and increased neurological deficits in rmTBI groups in both studies. In Study 1, rmTBI increased alcohol consumption in female but not male rats. Male rats consistently exhibited higher levels of anxiety-like behavior than females. rmTBI did not affect anxiety-like behavior 37-38 days post-injury. In Study 2, rmTBI once again increased alcohol consumption in female but not male rats, and repeated systemic treatment with JZL184 did not affect alcohol consumption. Also in Study 2, rmTBI increased anxiety-like behavior in males but not females and repeated systemic treatment with JZL184 produced an unexpected increase in anxiety-like behavior 6-8 days post-injury. In summary, rmTBI increased alcohol consumption in female rats, systemic JZL184 treatment did not alter alcohol consumption, and both rmTBI and sub-chronic systemic JZL184 treatment increased anxiety-like behavior 6-8 days post-injury in males but not females, highlighting robust sex differences in rmTBI effects.

neuroscience↗