Biology subjects

Daniel, M.

Publications and source records attributed to Daniel, M..

8 recordsLinked to original sources

bioRxiv2026

POSH (Plenty of SH3): a novel genetic modifier of Myc function in Drosophila

Abstract: MYC is a conserved transcriptional regulator that coordinates cellular growth, metabolism, and tissue homeostasis through a broad network of downstream effectors. However, the signaling components that translate MYC activity into specific cellular responses remain incompletely defined. Here, using Drosophila melanogaster, we identify Plenty of SH3s (POSH), a conserved RING-domain scaffold protein and regulator of JNK signaling, as a novel genetic interactor of Myc. POSH was identified in a genetic screen for modifiers of a Myc-dependent phenotype in the developing eye. The interaction was independently confirmed using a UAS-Posh transgene. Quantitative analysis showed that reduced Myc primarily decreased ommatidial size, whereas POSH expression predominantly reduced ommatidial number, with this effect becoming more pronounced in Myc-sensitized backgrounds. Myc overexpression also increased Posh transcript levels, and the Posh regulatory region contains a canonical E-box motif, supporting a functional relationship between the two genes while leaving open the question of whether Posh is a direct Myc transcriptional target. Co-expression experiments further revealed a strong morphological interaction between Myc and POSH in the adult eye. Together, these findings identify POSH as a previously unrecognized genetic modifier of Myc function in Drosophila and provide a framework for investigating how Myc interfaces with stress-responsive signaling pathways during tissue development.

genetics↗

bioRxiv2026

Organoid-based colorectal tumor microenvironment model for immuno-oncology research

The development of cancer immunotherapies is hindered by the lack of human-relevant models that accurately translate to patient outcomes. We combine patient-derived colorectal tumor organoids (PDOs) and cancer-associated fibroblasts (CAFs) into floating extracellular matrix drops to form miniature colorectal tumors. These SHaking Organoid CO-cultures (SHOCOs) reproducibly capture key features of the tumor microenvironment (TME), including physiologically relevant ECM, hypoxic regions, and a diversified stromal compartment that captures primary CAF states. Compared with traditional PDO-based co-culture models, SHOCOs maintain immune cells in numbers, states and functional interactions that more closely reflect the physiological tumor microenvironment. The modularity of the system allowed controlled simulation of diverse patient tumor archetypes, and defining how TME components shape therapy response. Immune-rich SHOCOs treated with T-cell bispecific antibodies exhibited robust anti-tumor responses that were stronger and more rapid than their PDO-based counterparts. Stroma-rich tumors, on the other hand, diminished therapy responses by physically hindering both immune cell recruitment and limiting antibody penetration. Thus, SHOCOs enable the construction of modular tumor microenvironments, providing a versatile platform to dissect immune and stromal tumor biology and to catalyze the discovery of novel therapeutic approaches.

cancer biology↗

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↗

bioRxiv2025

Multi-modal image analysis for large scale cancer tissue studies within IMMUcan

MotivationMultiplexed imaging is increasingly used to study tissue architecture in health and disease. To investigate the cancer tumor microenvironment, typically either tissue micro-arrays or small patient cohorts are used to collect and process data. However, studies performed over the course of years, collecting data from thousands of samples are rare and require specialized workflows to ensure sample throughput and reproducibility for data production and processing. Here, we present two such workflows for multiplexed immunofluorescence and imaging mass cytometry of cancer tissues which are applied to a total of roughly 10000 samples from 2500 patients over six years. SummaryIn cancer research, multiplexed imaging allows detailed characterization of the tumor microenvironment (TME) and its link to patient prognosis. The IMMUcan consortium collects multi-modal imaging data from thousands of cancer patients to perform broad molecular and cellular spatial profiling across five cancer indications. Here, we describe two workflows for multiplexed immunofluorescence (mIF) and imaging mass cytometry (IMC) developed within IMMUcan to enable analysis of thousands of cancer tissues. IFQuant supports web-based, user-friendly, and reproducible analysis of mIF data. High sample throughput for IMC is achieved by optimizing experimental protocols and developing a robotic arm for automated slide loading. We provide a resource of 350000 manually labelled cells across 180 cancer samples to accurately annotate cell phenotypes in IMC. All major cell phenotypes and tissue structures correlate well between mIF and IMC. These pipelines form the basis for multiplexed image analysis within IMMUcan and provide computational tools for the larger community.

cancer biology↗

bioRxiv2020

Colormesh: A novel method for quantifying variation in complex color patterns

Color variation is one of the most obvious examples of variation in nature. Objective quantification and interpretation of variation in color and complex patterns is challenging. Assessment of variation in color patterns is limited by the reduction of color into categorical measures and lack of spatial information. We present Colormesh as a novel method for analyzing complex color patterns that offers unique capabilities. Compared to other methods, Colormesh maintains the continuous measure of color at individual sampling points throughout the pattern. This is particularly useful for analyses of variation in color patterns, whether interest is in specific locations or the pattern as a whole. In our approach, the use of Delaunay triangulation to determine sampling location eliminates the need for color patterns to have clearly defined pattern elements, and users are not required to identify discrete color categories. This method is complementary to several other methods available for color pattern quantification, and can be usefully deployed to address a wide range of questions about color pattern variation.

evolutionary biology↗

bioRxiv2020

It is all relative: population estimates enhance kin recognition in the guppy

Kin recognition plays a fundamental role in social evolution, enabling active inbreeding avoidance, nepotism, and promoting cooperative social organization. Many organisms recognize kin based on phenotypic similarity - a process called phenotype matching - by comparing information associated with their own phenotype against the phenotypes of conspecifics. However, recent theory demonstrates that to accurately judge phenotypic similarity (and hence, relatedness), individuals require estimates of the populations distribution of phenotypes as a "frame of reference." Here, I use the Trinidadian guppy (Poecilia reticulata) to provide the first empirical test of this population estimation theory. I varied the phenotypic distributions of the groups in which focal individuals developed and found that, as adults, their patterns of inbreeding avoidance and nepotistic intrasexual competition differed as predicted by population estimation theory. Individuals reared with conspecifics more similar to themselves treated novel conspecifics as less closely related, suggesting a shifted population estimate. Individuals reared with more phenotypically variable conspecifics exhibited less extreme kin discrimination, suggesting a broader population estimate. These results provide experimental evidence that population estimates inform phenotype matching, and are acquired plastically through social experience. By calibrating phenotype matching to the population distribution of phenotypes, population estimation enhances kin recognition, increasing opportunities for the evolution of inbreeding avoidance and nepotism.

evolutionary biology↗

bioRxiv2020

Kin recognition in guppies uses self-referencing on olfactory cues

Kin recognition plays an important role in social evolution, but the proximate mechanisms by which individuals recognize kin remain poorly understood. In many species, individuals form a “kin template” that they compare against conspecifics’ phenotypes to assess phenotypic similarity–and by association, relatedness. Individuals may form a kin template through self-inspection (i.e. self-referencing) and/or by observing their rearing associates (i.e. family-referencing). However, despite much interest, few empirical studies have successfully disentangled self- and family-referencing. Here, we use a novel set of breeding crosses in the Trinidadian guppy (Poecilia reticulata) to definitively disentangle referencing systems by manipulating exposure to kin from conception onwards. We show that guppies discriminate among their full- and maternal half-siblings, which can only be explained by self-referencing. Additional behavioral experiments revealed no evidence that guppies incorporate the phenotypes of their broodmates or mother into the kin template. Finally, by manipulating the format of our behavioral tests, we show that olfactory communication is both necessary and sufficient for kin discrimination. These results demonstrate that individuals recognize kin by comparing the olfactory phenotypes of conspecifics against their own. This study resolves key questions about the proximate mechanisms underpinning kin recognition, with implications for the ontogeny and evolution of social behavior.Competing Interest StatementThe authors have declared no competing interest.View Full Text

animal behavior and cognition↗

bioRxiv2019

Functional connectivity differences in early infancy precede autism symptoms: a multivariate pattern analysis

Functional brain connectivity is altered in children and adults with autism spectrum disorder (ASD). Mapping pre-symptomatic functional disruptions in ASD could identify infants based on neural risk, providing a crucial opportunity to mediate outcomes before behavioral symptoms emerge. Here we quantify functional connectivity using scalable EEG measures of oscillatory phase coherence (6-12Hz). Infants at high and low familial risk for ASD (N=65) underwent an EEG recording at 3 months of age and were assessed for ASD symptoms at 18 months using the Autism Diagnostic Observation Schedule-Toddler Module. Multivariate pattern analysis was used to examine early functional patterns that are associated with later ASD symptoms. Support vector regression (SVR) algorithms accurately predicted observed ASD symptoms at 18 months from EEG data at 3 months (r=0.76, p=0.02). Specifically, lower frontal connectivity and higher right temporo-parietal connectivity predicted higher ASD symptoms. The SVR model did not predict non-verbal cognitive abilities at 18 months (r=0.15, p=0.36), suggesting specificity of these brain alterations to ASD. These data suggest that frontal and temporo-parietal dysconnectivity play important roles in the early pathophysiology of ASD. Early functional differences in ASD can be captured using EEG during infancy and may inform much-needed advancements in the early detection of ASD.

neuroscience↗