Biology subjects

Wood, K. C.

Publications and source records attributed to Wood, K. C..

At least 19 recordsLinked to original sources

bioRxiv2026

Cortical cooling reveals a role for visual cortex in generating visual responses in auditory cortex

Multisensory integration is a fundamental feature of cortical processing, yet the functional pathways that deliver visual signals to the auditory cortex remain poorly understood. While anatomical studies reveal multiple candidate projection routes, demonstrating their causal contribution requires targeted manipulation of neural activity. Here, we used cortical cooling to reversibly inactivate the posteromedial lateral suprasylvian cortex (PMLS) and the adjacent area 21 to determine the functional role of higher-order visual areas in generating visual responses within the auditory cortex of the ferret. Units responsive to sound, light, or combined audiovisual stimuli were found across all sampled auditory fields and cortical depths, with visual responses most prominent within the infragranular layers and the non-tonotopic secondary auditory cortex of the Anterior Ectosylvian Gyrus (AEG). Cortical cooling induced robust, bi-directional, and stimulus-specific modulations of firing rates in AC. Approximately 50% of visually responsive units exhibited a significant decrease or complete elimination of visual activity during cooling, confirming a functional role for visual input from PLMS/area 21 to AC. Surprisingly, cooling also revealed circuit-level complexities: a subset ([~]5%) of units showed enhanced or newly emergent visual responses during inactivation, suggesting that PMLS/area 21 normally exerts a gating influence over alternative visual pathways. Furthermore, contrary to feedforward anatomical predictions, neurons in the AEG--the region most heavily innervated by the cooled visual areas --were less frequently impacted by cooling than those in PEG. Together, these findings demonstrate that higher visual areas causally shape cross-modal processing in the auditory cortex through a complex mixture of direct excitation and network-level modulation.

neuroscience↗

bioRxiv2026

Chromosomal instability and chromosome 17p loss drive convergentNDE1 synthetic lethality in metastatic cancer cells

Recent studies have identified recurrent features of metastatic cancer cells such as their increased chromosomal instability (CIN) and frequent loss of the short arm of chromosome 17 (Chr17p). However, it remains unclear whether these features induce synthetic lethal vulnerabilities that can be used to specifically target metastatic disease. Using whole-genome CRISPR/Cas9 loss-of-function screens performed in matched primary and CIN-high brain-metastatic tumor models, we discovered that brain-metastatic cells exhibit increased sensitivity to the loss of diverse regulators of chromosome segregation. Knockout of one such regulator, NDE1, selectively inhibited the growth of brain-metastatic models in vitro and in vivo, an effect driven by the loss of STAG2 and consequent induction of CIN. Surprisingly, dependence on NDE1 was also highly correlated with loss of Chr17p across hundreds of cancer cell lines in DepMap, the result of losing the NDE1 paralog NDEL1, which resides at this locus. CIN and Chr17p loss are thus independently sufficient to drive NDE1 dependence in brain-metastatic cells, and the presence of both features increases NDE1 dependence additively. These findings demonstrate that metastasis evolution endows cancer cells with specific vulnerabilities, including one that is driven by two recurrently altered molecular features of metastatic disease.

cancer biology↗

bioRxiv2025

CYB5R3 Controls Sex-Specific Stress Erythropoiesis via Heme-Biosynthesis

Cytochrome b5 reductase 3 (CYB5R3) or met-hemoglobin reductase is an oxidoreductase that maintains hemoprotein and cellular redox balance, yet its contribution to erythropoiesis under stress conditions remains unclear. Motivated by prior observations that the hypomorphic CYB5R3 T117S blunts hydroxyurea-induced fetal hemoglobin responses in patients with sickle cell disease, we tested whether CYB5R3 contributes to the regulation of erythropoiesis. Hematopoietic lineage-specific CYB5R3 knockout mice exhibited markedly impaired erythropoietic induction in response to chronic hypoxia compared to controls, with males showing a more pronounced deficit, and splenectomy further exacerbating this impairment. Genetic deletion of CYB5R3 in human CD34 progenitors reduced globin expression and disrupted terminal erythroid differentiation. Meanwhile, CYB5R3 knockdown in K562 cells produced a heme-deficient state whereby only exogenous heme but not hydroxyurea, iron, or upstream precursors restored globin synthesis. Transcriptomic profiling revealed coordinated downregulation of erythroid transcription factors and multiple enzymes in the heme biosynthetic pathway, which was reversed with heme treatment. Together, these results reveal an unexpected function for CYB5R3 beyond met-hemoglobin reduction, positioning it as a central metabolic regulator of sex-specific stress erythropoiesis and unveiling a heme-restricted vulnerability that may augment disease severity in anemia, hemoglobinopathies, and individuals carrying CYB5R3 loss-of-function variants. Key pointsO_LICYB5R3 is required for effective stress erythropoietic induction, with a more pronounced impact in males. C_LIO_LIErythroid-specific CYB5R3 deficiency creates a heme-limited state, impairing erythroblast differentiation and maturation. C_LI

molecular biology↗

bioRxiv2025

Endothelial CYB5R3 couples store-operated calcium entry to TRPV2 activation and vascular fitness

NADH-cytochrome b5 reductase 3 (CYB5R3) is a flavoprotein that governs nitric oxide (NO) signaling and supports NADPH oxidase 4-derived hydrogen peroxide production via coenzyme Q reduction in endothelium. While CYB5R3 expression is decreased during aging, the downstream consequences of CYB5R3 loss are not understood. Here, we demonstrate that depletion of CYB5R3 in primary human aortic endothelial cells activates a Ca2+ influx network characterized by the upregulation of calcium release-activated calcium (CRAC) channel subunits ORAI2 and ORAI3, as well as the non-selective cation channel transient receptor potential vanilloid 2 (TRPV2). When endoplasmic-reticulum Ca2+ stores were depleted, CYB5R3-deficient cells had increased Ca2+ entry through the plasma membrane, part of which was insensitive to classical store-operated Ca2+ entry (SOCE) blockers and was mediated by TRPV2, as demonstrated by genetic knockdown and pharmacologic inhibition. Mechanistically, loss of CYB5R3 increased Ca2+-dependent NO production through elevated CRAC channel activity, which oxidatively inhibited the protein tyrosine phosphatase non-receptor type 1 (PTPN1). This prevented TRPV2 dephosphorylation, thereby maintaining Janus kinase 1 (JAK1)-dependent channel activation downstream of SOCE. It also enhanced the responsiveness of TRPV2 to physiological heat stimuli. Thus, CYB5R3 normally acts as a brake, limiting NO-dependent PTPN1 oxidation and restraining TRPV2 activity. In vivo, endothelial-specific Cyb5r3 deletion enhanced acetylcholine-induced vasorelaxation and improved exercise capacity, demonstrating a physiological function for this pathway in vascular adaptation. Together, these findings identify a CYB5R3-NO-SOCE- PTPN1-TRPV2 signaling axis that couples endothelial redox balance to Ca2+ dynamics and vascular function. SIGNIFICANCEEndothelial cells rely on receptor-regulated Ca2+ signals to produce vasodilators and control vascular function; however, the molecular mechanisms coordinating these pathways are incompletely understood. We identify CYB5R3 as a key redox switch that couples store-operated Ca2+ entry to the non-selective cation channel TRPV2. Loss of CYB5R3 enhances TRPV2 activity downstream of SOCE through NO-dependent oxidative inhibition of the phosphatase PTPN1, sustaining Janus kinase-mediated TRPV2 channel activation. This novel mechanism expands the physiological scope of CYB5R3 by redefining how redox enzymes intersect with Ca2+ signaling, linking endothelial CYB5R3 to vascular relaxation and exercise capacity in vivo. This positions CYB5R3 as a central regulator of vascular function with broad implications for cardiovascular health and disease.

cell biology↗

bioRxiv2025

CDK8 Inhibition Releases the Muscle Differentiation Block in Fusion-driven Alveolar Rhabdomyosarcoma

Alveolar rhabdomyosarcoma (aRMS) is a fusion-driven pediatric cancer with poor survival and limited therapeutic options. To uncover novel vulnerabilities, we employed complex-based analysis of the DepMap functional genomic data, identifying CDK8 as a dependency in aRMS. Both CDK8 knockout and pharmacologic inhibition impaired tumor cell growth and induced myogenic differentiation in vitro and in vivo. Compared to genetic loss, CDK8 inhibition induced more dynamic transcriptional changes. With a genome-scale CRISPR-Cas9 drug modifier screen, we determined that the maximal anti-tumor activity of the CDK8 inhibitor requires the presence of the Mediator kinase module and transcriptional cooperation with the SAGA complex. We further identified SIX4 as a key transcription factor mediating CDK8 inhibitor-induced transcriptional activation of myogenic differentiation genes and tumor cell proliferation. These findings suggest a distinct gain-of-function mechanism of the CDK8 inhibitor and establish a strong rationale for CDK8 inhibition as a differentiation-inducing therapeutic strategy in aRMS. STATEMENT OF SIGNIFICANCEWe provide a framework for uncovering therapeutic targets by network-based analysis of functional genomic screens. We identify CDK8 as a druggable target in aRMS and determine that CDK8 inhibition drives myogenic differentiation and impairs tumor progression via a collaborative mechanism involving the Mediator kinase module, SAGA complex, and SIX4.

cancer biology↗

bioRxiv2025

The role of inhibitory neurons in novelty sound detection in regular and random statistical contexts.

Detecting statistical regularities in sound and responding to violations of these patterns, termed deviance detection, is a core function of the auditory system. In the human brain, studies have shown that deviance responses are enhanced in regular compared to random auditory contexts, but the underlying neuronal circuit mechanisms remain unclear. Here, we examined how inhibitory neurons contribute to context-dependent deviance responses in mouse auditory cortex (AC). Using two-photon calcium imaging in AC of awake head-fixed male and female mice, we recorded neuronal activity during presentation of spectro-temporally rich moving ripple sounds, with deviant ripples embedded in either regular or random ripple sequences. AC neurons exhibited stronger responses to deviant sounds in regular contexts compared to random ones. To identify circuit mechanisms, we selectively inactivated parvalbumin (PV), somatostatin (SST), or vasoactive intestinal polypeptide (VIP) inhibitory neurons during the deviant stimulus presentation. Inactivation of PV and SST neurons broadly increased deviance responses in both contexts. In contrast, VIP inactivation selectively reduced responses to deviant stimuli in the regular, but not random, context, decreasing the context-dependent deviance signal enhancement. At the population level, inactivating all three neuronal subtypes increased detectability of the deviant stimulus, but the effects were context-dependent only for VIP inactivation. These findings reveal a distinct role for VIP neurons in modulating deviance signals based on context regularity, identifying a specific inhibitory neuron type that is critical for context-sensitive auditory processing and predictive coding. SIGNIFICANCE STATEMENTUnderstanding how the brain detects and responds to predictable and unexpected sounds is critical for communication and navigation in complex acoustic environments. Although prior studies have shown that detection of novel sounds is enhanced by regularity in background sound patterns, the underlying circuit mechanisms have remained unknown. Here, we find that neurons in the auditory cortex exhibit stronger deviance responses when the deviant sounds are embedded in regular, predictable sound sequences as compared to random sound sequences. Importantly, we identify a distinct role for specific inhibitory neurons in modulating this context-dependent enhancement. These findings reveal a new insight into how cortical circuits implement predictive coding strategies to optimize sensory processing.

neuroscience↗

bioRxiv2025

Pathway Coessentiality Mapping Reveals Complex II is Required for de novo Purine Biosynthesis in Acute Myeloid Leukemia

Understanding how cellular pathways interact is crucial for treating complex diseases like cancer, yet our ability to map these connections systematically remains limited. Individual gene-gene interaction studies have provided insights1,2, but they miss the emergent properties of pathways working together. To address this challenge, we developed a multi-gene approach to pathway mapping and applied it to CRISPR data from the Cancer Dependency Map3. Our analysis of the electron transport chain revealed certain blood cancers, including acute myeloid leukemia (AML), depend on an unexpected link between Complex II and purine metabolism. Through stable isotope metabolomic tracing, we found that Complex II directly supports de novo purine biosynthesis and exogenous purines rescue AML from Complex II inhibition. The mechanism involves a metabolic circuit where glutamine provides nitrogen to build the purine ring, producing glutamate that Complex II must oxidize to sustain purine synthesis. This connection translated to a metabolic vulnerability whereby increasing intracellular glutamate levels suppresses purine production and sensitizes AML to Complex II inhibition. In mouse models, targeting Complex II triggered rapid disease regression and extended survival in aggressive AML. The clinical relevance of this pathway emerged in human studies, where higher Complex II gene expression correlates with both resistance to mitochondria-targeted therapies and worse survival outcomes specifically in AML patients. These findings establish Complex II as a central regulator of de novo purine biosynthesis and identify it as a promising therapeutic target in AML.

cancer biology↗

bioRxiv2025

Insights into anterograde trafficking and pharmacological chaperoning of Cannabinoid Receptor 2 (CB2)

Cannabinoid Receptor 2 (CB2) is a promising therapeutic target for modulating inflammation. Canonical signalling responses to receptor ligands are critically dependent on cell surface receptor expression. However, it is also now appreciated that intracellular G protein-coupled receptors can contribute to signalling responses and influence functional outcomes. Therefore, understanding how the subcellular distribution of receptors is controlled is also highly pertinent. CB2 is observed to be expressed at the cell surface as well as having a considerable proportion expressed intracellularly. Despite this distribution being well established, little is known about the regulation of CB2 anterograde trafficking and subcellular distribution. We report that sustained treatment with a range of CB2 agonists and inverse agonists stimulates a distinct population of CB2 to be delivered to the cell surface, at various expression levels and despite agonists concurrently internalising cell surface CB2. We present evidence that this ligand-stimulated anterograde trafficking is a result of CB2 agonists, as well as inverse agonists, acting as pharmacological chaperones. We also report that a di-lysine (KK) motif in the CB2 C-terminal tail is required for basal delivery to the cell surface. Corroborating the hypothesis that CB2 ligands can act as pharmacological chaperones, sustained CB2 ligand stimulation induces cell surface expression of the mutated receptor and alters maturation states as measured by western blotting. Our finding that prolonged exposure to CB2 ligands can induce CB2 cell surface delivery via pharmacological chaperoning may well have important implications for optimal design of CB2-targeted therapeutics.

pharmacology and toxicology↗

bioRxiv2025

BRCA1-A and LIG4 complexes mediate ecDNA biogenesis and cancer drug resistance

Extrachromosomal circular DNA (ecDNA) are commonly produced within the nucleus to drive genome dynamics and heterogeneity, enabling cancer cell evolution and adaptation. However, the mechanisms underlying ecDNA biogenesis remain poorly understood. Here using genome-wide CRISPR screening in human cells, we identified the BRCA1-A and the LIG4 complexes mediate ecDNA production. Following DNA fragmentation, the upstream BRCA1-A complex protects DNA ends from excessive resection, promoting end-joining for circularization. Conversely, the MRN complex, which mediates end resection and thus antagonizes the BRCA1-A complex, suppresses ecDNA formation. Downstream, LIG4 conservatively catalyzes ecDNA production in Drosophila and mammals, with patient tumor ecDNA harboring junctions marked by LIG4 activity. Notably, disrupting LIG4 or BRCA1-A in cancer cells impairs ecDNA-mediated adaptation, hindering resistance to both chemotherapy and targeted therapies. Together, our study reveals the roles of the LIG4 and BRCA1-A complexes in ecDNA biogenesis, and uncovers new therapeutic targets to block ecDNA-mediated adaptation for cancer treatment.

cancer biology↗

bioRxiv2023

Integrative PTEN Enhancer Discovery Reveals a New Model of Enhancer Organization

Enhancers possess both structural elements mediating promoter looping and functional elements mediating gene expression. Traditional models of enhancer-mediated gene regulation imply genomic overlap or immediate adjacency of these elements. We test this model by combining densely-tiled CRISPRa screening with nucleosome-resolution Region Capture Micro-C topology analysis. Using this integrated approach, we comprehensively define the cis-regulatory landscape for the tumor suppressor PTEN, identifying and validating 10 distinct enhancers and defining their 3D spatial organization. Unexpectedly, we identify several long-range functional enhancers whose promoter proximity is facilitated by chromatin loop anchors several kilobases away, and demonstrate that accounting for this spatial separation improves the computational prediction of validated enhancers. Thus, we propose a new model of enhancer organization incorporating spatial separation of essential functional and structural components.

genomics↗

bioRxiv2023

Localist versus distributed representation of sounds in the auditory cortex controlled by distinct inhibitory neuronal subtypes

Cortical circuits contain multiple types of inhibitory neurons which shape how information is processed within neuronal networks. Here, we asked whether somatostatin-expressing (SST) and vasoactive intestinal peptide-expressing (VIP) inhibitory neurons have distinct effects on population neuronal responses to noise bursts of varying intensities. We optogenetically stimulated SST or VIP neurons while simultaneously measuring the calcium responses of populations of hundreds of neurons in the auditory cortex of male and female awake, head-fixed mice to sounds. Upon SST neuronal activation, noise bursts representations became more discrete for different intensity levels, relying on cell identity rather than strength. By contrast, upon VIP neuronal activation, noise bursts of different intensity level activated overlapping neuronal populations, albeit at different response strengths. At the single-cell level, SST and VIP neuronal activation differentially modulated the response-level curves of monotonic and nonmonotonic neurons. SST neuronal activation effects were consistent with a shift of the neuronal population responses toward a more localist code with different cells responding to sounds of different intensity. By contrast, VIP neuronal activation shifted responses towards a more distributed code, in which sounds of different intensity level are encoded in the relative response of similar populations of cells. These results delineate how distinct inhibitory neurons in the auditory cortex dynamically control cortical population codes. Different inhibitory neuronal populations may be recruited under different behavioral demands, depending on whether categorical or invariant representations are advantageous for the task. SIGNIFICANCEInformation about sounds is represented in the auditory cortex by neuronal population activity that has a characteristic sparse structure. Cortical neuronal populations comprise multiple types of excitatory and inhibitory neurons. Here, we find that activating different types of inhibitory neurons differentially controls population neuronal representations, with one type of inhibitory neurons increasing the differences in the identity of the cells recruited to represent the different sounds, and another inhibitory neuron type changing the relative activity level of overlapping neuronal populations. Such transformations may be beneficial for different types of auditory behaviors, suggesting that these different types of inhibitory neurons may be recruited under different behavioral constraints in optimizing neuronal representations of sounds.

neuroscience↗

bioRxiv2023

MCB-613 exploits a collateral sensitivity in drug-resistant EGFR-mutant non-small cell lung cancer through covalent inhibition of KEAP1

Targeted therapies have revolutionized cancer chemotherapy. Unfortunately, most patients develop multifocal resistance to these drugs within a matter of months. Here, we used a high-throughput phenotypic small molecule screen to identify MCB-613 as a compound that selectively targets EGFR-mutant, EGFR inhibitor-resistant non-small cell lung cancer (NSCLC) cells harboring diverse resistance mechanisms. Subsequent proteomic and functional genomic screens involving MCB-613 identified its target in this context to be KEAP1, revealing that this gene is selectively essential in the setting of EGFR inhibitor resistance. In-depth molecular characterization demonstrated that (1) MCB-613 binds KEAP1 covalently; (2) a single molecule of MCB-613 is capable of bridging two KEAP1 monomers together; and, (3) this modification interferes with the degradation of canonical KEAP1 substrates such as NRF2. Surprisingly, NRF2 knockout sensitizes cells to MCB-613, suggesting that the drug functions through modulation of an alternative KEAP1 substrate. Together, these findings advance MCB-613 as a new tool for exploiting the selective essentiality of KEAP1 in drug-resistant, EGFR-mutant NSCLC cells.

cancer biology↗

bioRxiv2022

Mediator Kinase Inhibition Impedes Transcriptional Plasticity and Prevents Resistance to ERK/MAPK-Targeted Therapy in KRAS-Mutant Cancers

Acquired resistance remains a major challenge for therapies targeting oncogene activated pathways. KRAS is the most frequently mutated oncogene in human cancers, yet strategies targeting its downstream signaling kinases have failed to produce durable treatment responses. Here, we developed multiple models of acquired resistance to dual-mechanism ERK/MAPK inhibitors across KRAS-mutant pancreatic, colorectal, and lung cancers, and then probed the long-term events enabling survival against this novel class of drugs. These studies revealed that resistance emerges secondary to large-scale transcriptional adaptations that are diverse and tumor-specific. Transcriptional reprogramming extends beyond the well-established early response, and instead represents a dynamic, evolved population-level process that is refined to attain a stably resistant phenotype. Mechanistic and translational studies reveal that resistance to dual-mechanism ERK/MAPK inhibition is broadly susceptible to manipulation of the epigenetic machinery, and that Mediator kinase, in particular, can be co-targeted at a bottleneck point to prevent diverse, tumor-specific resistance programs.

cancer biology↗

bioRxiv2022

Drug dependence in cancer is exploitable by optimally constructed treatment holidays

Recent work in cell culture models, animal models, and human patients indicates that cancers with acquired resistance to a drug can become simultaneously dependent upon the presence of that drug for survival. This drug dependence offers a potential avenue for improving treatments aimed at slowing resistance, yet relatively little is known about the frequency with which drug dependence arises, the mechanisms underlying that dependence, and how drug schedules might be tuned to optimally exploit drug dependence. In this work, we address these open questions using a combination of laboratory evolution, in vitro experiments, and simple mathematical models. First, we used laboratory evolution to select more than 100 resistant BRAF mutant melanoma cell lines with acquired resistance to BRAF, MEK, or ERK inhibitors. We found that nearly half of these lines exhibit drug dependence, and the dependency response is associated with EGFR-driven senescence induction, but not apoptosis, following drug withdrawal. Then, using melanoma populations with evolved resistance to the BRAF inhibitor PLX4720, we showed that drug dependence can be leveraged to dramatically reduce population growth when treatment strategies include optimally chosen drug-free "holidays". On short timescales, the duration of these holidays depends sensitively on the composition of the population, but for sufficiently long treatments it depends only on a single dimensionless parameter ({gamma}) that describes how the growth rates of each cell type depend on the different treatment environments. Experiments confirm that the optimal holiday duration changes in time-with holidays of different durations leading to optimized treatments on different timescales. Furthermore, we find that the presence of "non-dependent" resistant cells does not change the optimal treatment schedule but leads to a net increase in population size. Finally, we show that even in the absence of detailed information about the composition and growth characteristics of cellular clones within a population, a simple adaptive therapy protocol can produce near-optimal outcomes using only measurements of total population size, at least when these measurements are sufficiently frequent. As a whole, these results may provide a stepping-stone toward the eventual development of evolution-inspired treatment strategies for drug dependent cancers.

cancer biology↗

bioRxiv2021

Reversible inactivation of ferret auditory cortex impairs spatial and non-spatial hearing

A key question in auditory neuroscience is to what extent are brain regions functionally specialized for processing specific sound features such as sound location and identity. In auditory cortex, correlations between neural activity and sounds support both the specialization of distinct cortical subfields, and encoding of multiple sound features within individual cortical areas. However, few studies have tested the contribution of auditory cortex to hearing in multiple contexts. Here we determined the role of ferret primary auditory cortex in both spatial and non-spatial hearing by reversibly inactivating the middle ectosylvian gyrus during behavior using cooling (n=2) or optogenetics (n=1). In optogenetic experiments, we utilized the mDLx promoter to express Channelrhodopsin 2 in GABAergic interneurons and confirmed both viral expression (n=2) and light-driven suppression of spiking activity in auditory cortex, recorded using Neuropixels under anesthesia (n=465 units from 2 additional untrained ferrets). Cortical inactivation impaired vowel discrimination in co-located noise, but not in clean conditions, or when the temporally coincident vowel and noise were spatially separated by 180{degrees}. Testing the ferrets implanted with cooling loops in a sound localization task confirmed that deficits in spatial hearing arose from inactivation of the same region of auditory cortex that was implicated in vowel discrimination in noise. Our results are consistent with single unit recordings in primary auditory cortex showing mixed selectivity for spatial and non-spatial features of sound and suggest a contribution of this region to multiple forms of hearing necessary for auditory scene analysis. Significance StatementNeurons in primary auditory cortex are often sensitive to the location and identity of sounds. Here we inactivated auditory cortex during spatial and non- spatial listening tasks using cooling, or optogenetics. Auditory cortical inactivation impaired multiple behaviors, demonstrating a role in both the analysis of sound location and identity and confirming a functional contribution of mixed selectivity observed in neural activity. Parallel optogenetic experiments in two additional untrained ferrets linked behavior to physiology by demonstrating that expression of Channelrhodopsin 2 permitted rapid light-driven suppression of auditory cortical activity recorded under anesthesia.

neuroscience↗

bioRxiv2021

Cortical efficient coding dynamics shape behavioral performance.

Neurons throughout the sensory pathway adapt their responses depending on the statistical structure of the sensory environment. Contrast gain control is a form of adaptation in the auditory cortex, but it is unclear whether the dynamics of gain control reflect efficient adaptation, and whether they shape behavioral perception. Here, we trained mice to detect a target presented in background noise shortly after a change in the contrast of the background. The observed changes in cortical gain and behavioral detection followed the dynamics of a normative model of efficient contrast gain control; specifically, target detection and sensitivity improved slowly in low contrast, but degraded rapidly in high contrast. Auditory cortex was required for this task, and cortical responses were not only similarly affected by contrast but predicted variability in behavioral performance. Combined, our results demonstrate that dynamic gain adaptation supports efficient coding in auditory cortex and predicts the perception of sounds in noise.

neuroscience↗

bioRxiv2021

Cooperative regulation of coupled oncoprotein translation and stability in triple-negative breast cancer by EGFR and CDK12

Evidence has long suggested that epidermal growth factor receptor (EGFR) may play a prominent role in triple-negative breast cancer (TNBC) pathogenesis, but clinical trials of EGFR inhibitors have yielded disappointing results. Using a candidate drug screen, we discovered that inhibition of CDK12 dramatically sensitizes diverse models of TNBC to EGFR blockade. Instead of functioning through CDK12s well-established roles proximal to transcription, this combination therapy drives cell death through the 4E-BP1-dependent suppression of the translation and consequent stability of driver oncoproteins, including MYC. A genome-wide CRISPR/Cas9 screen identified the CCR4-NOT complex as a major determinant of sensitivity to the combination therapy whose loss renders 4E-BP1 unresponsive to drug-induced dephosphorylation, rescuing MYC translational suppression and stability. The central roles of CCR4-NOT and 4E-BP1 in response to the combination therapy were further underscored by the observation of CNOT1 loss and rescue of 4E-BP1 phosphorylation in TNBC cells that naturally evolved therapy resistance. Thus, pharmacological inhibition of CDK12 reveals a long proposed EGFR dependence in TNBC that functions through the cooperative regulation of translation-coupled oncoprotein stability.

cancer biology↗

bioRxiv2021

Comparing instance segmentation methods for analyzing clonal growth of single cells in microfluidic chips

Appropriately tailored segmentation techniques can extract detailed quantitative information from biological image datasets to characterize and better understand sample distributions. Practically, high-resolution characterization of biological samples such as cell populations can provide insights into the sources of variance in biomarker expression, drug resistance, and other phenotypic aspects, but it is still unclear what is the best method for extracting this information from large image-based datasets. We present a software pipeline and comparison of multiple image segmentation methods to extract single-cell morphological and fluorescence quantitation from time lapse images of clonal growth rates using a recently reported microfluidic system. The inputs in all pipelines consist of thousands of unprocessed images and the outputs are the detection of cell counts, chamber identifiers, and individual morphological properties of each clone over time detected through multi-channel fluorescence and bright field imaging. Our conclusion is that unsupervised learning methods for cell segmentation substantially outperform supervised statistical methods with respect to accuracy and have key advantages including individual cell instance detection and flexibility through model training. We expect this system and software to have broad utility for researchers interested in high-throughput single-cell biology.

bioengineering↗