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Biology subjects

Shaw, L. M.

Publications and source records attributed to Shaw, L. M..

13 recordsLinked to original sources

Insulin receptor substrate 2 (IRS2) confers resistance to PI3K pathway inhibition in PIK3CA mutant breast cancer

Activating mutations in PI3K are one of the most frequent mutations in breast cancer and are associated with worse patient outcomes in many breast cancer subtypes. Despite intense interest, cancer treatments that target the PI3K pathway have been only modestly effective due to intrinsic and acquired resistance mechanisms which reactivate PI3K signaling. Here, we characterize a feedback mechanism by which PI3K pathway inhibitors increase insulin receptor substrate 2 (IRS2) abundance and demonstrate the role of IRS2 in promoting resistance to these drugs. In PIK3CA mutant breast tumors and cell lines, there is a significant reduction in IRS2 mRNA and protein abundance which is reversed by PI3K pathway inhibition and mediated by the transcription factor FOXO3. PIK3CA mutations do not alter IRS1 expression. IRS2 confers resistance to PI3K pathway inhibition by sustaining PI3K signaling in PIK3CA mutant, but not wild-type breast cancer cells. Increased IRS2 abundance also correlates with PI3K pathway inhibitor resistance across PI3K mutant cancer cell lines from a variety of tissues. The clinical relevance of these findings is highlighted by the frequency of PI3K mutations in cancer and the identification of a new target to address the challenges associated with prior efforts to block the reactivation of PI3K signaling during PI3K inhibition.

cancer biology↗

Synergistic targeting of MCL1 and caspases for enhanced anti-tumor immunity in breast cancer.

Breast cancer remains largely unresponsive to immunotherapy due to its immunologically "cold" nature, marked by low cytolytic activity and a paucity of neoantigens. To overcome this, we developed a novel therapeutic approach to activate the cGAS-STING pathway, a critical mediator of the type I interferon response essential for effective anti-tumor immunity. We demonstrate that combined inhibition of MCL1 and caspases robustly triggers a type I IFN response in breast cancer cells, effectively remodeling the tumor microenvironment by increasing immune cell infiltration and enhancing antigen presentation. In immunocompetent syngeneic mouse models, this combination therapy significantly suppressed tumor growth, an effect that was reversed upon blockade of the IFN signaling axis. Mechanistically, our findings reveal that co-targeting MCL1 and caspases reprograms the tumor microenvironment enhancing immune surveillance. Given the established safety profiles of both drug classes, this strategy offers a promising and rapidly deployable approach to sensitize breast tumors to immunotherapy.

cancer biology↗

Therapeutic delivery of albumin-binding siRNA targeting IRS2 to diverse cell types reduces mammary tumor growth

Oligonucleotide therapeutics are a new class of drugs that enable robust and sustained modulation of gene expression. However, achieving efficient delivery of siRNAs to tumors is a challenge for therapy. Here, we demonstrate that fully chemically modified siRNAs conjugated with an albumin-binding dendrimer are efficiently delivered to both neoplastic and stromal/immune cells within primary TNBC mammary tumors. siRNAs were designed to selectively target IRS2, a signaling adaptor of insulin and insulin-like growth factor signaling that has been implicated in aggressive breast cancers. These siRNAs reduced Irs2 expression in tumor and stromal cells without causing hyperglycemia, resulting in reduced tumor growth that was associated with decreased vascularization and alterations in macrophage polarization and the expression of EMT proteins. This work demonstrates that siRNAs can be delivered to neoplastic and specific stromal populations in mammary tumors and that they can effectively and specifically silence a driver of aggressive breast cancer.

cancer biology↗

Interaction of IRS2 with PLK1 protects cells from mitotic stress

In this study we identify a role for IRS2 in the protection of cells from mitotic stress through its interaction with PLK1. IRS2 is an adaptor protein for the insulin and IGF-1 receptors that mediates their signaling functions. In this capacity, IRS2 is tyrosine phosphorylated to recruit signaling effectors that control cellular outcomes. A role for IRS2 in mitotic regulation has been reported, but the mechanism of IRS2 action in this regulation has not been determined. Here we report that IRS2 interacts with PLK1 in a CDK1-dependent manner, and they co-localize at centrosomes in mitotic cells. In response to mitotic stress, cells that lack IRS2 or express a PLK1-binding deficient mutant exhibit reduced centrosome separation and a shortened mitotic arrest that leads to reduced tumor cell viability. In contrast, cells expressing an IRS2 mutant that is not tyrosine phosphorylated display normal mitotic function. Together, our findings establish a mechanistic connection between IRS2 and mitotic regulation that is distinct from its function as a signaling adaptor protein.

cell biology↗

Molecular Mechanisms Limiting the Therapeutic Window of AAV Gene Therapy in Mouse Models of Blue Cone Monochromacy

Blue cone monochromacy (BCM) is an X-linked retinal disorder caused by mutations in the OPN1LW/OPN1MW gene locus, resulting in impaired cone function and structural degeneration. We conducted a comparative analysis of AAV-mediated gene therapy in Opn1lw/Opn1mw double knockout (DKO) and Opn1mwC198R/Opn1sw-/- (C198R) BCM mouse models and evaluated the therapeutic window, efficacy, and longevity. Our results demonstrate that the AAV8-Y733F capsid achieved superior cone rescue compared to AAV5. While both DKO and C198R models showed similar therapeutic windows and rescue longevity, treatment efficacy decreased markedly in older mutant mice. Structural analysis revealed that aged cones in both models displayed degenerative changes, including mislocalized mitochondria and compromised connecting cilia. At the molecular level, we observed reduced AAV-mediated transgene expression in DKO and C198R older cones, which may result from decreased transduction efficiency, decreased circular episome stability, genome-wide transcription/translation downregulation, targeted mRNA/protein degradation, or overall cone degeneration. Notably, the cone-specific promoters for Pde6c and Cngb3 maintained robust activity in degenerating cones. These findings suggest that combining an efficient AAV serotype with an optimized cone promoter could be a viable approach to extend the therapeutic window and enhance treatment longevity for BCM patients.

molecular biology↗

Fluorescent tagging of endogenous IRS2 with an auxin-dependent degron to assess dynamic intracellular localization and function

Insulin Receptor Substrate 2 (IRS2) is a signaling adaptor protein for the insulin (IR) and Insulin-like Growth Factor-1 (IGF-1R) receptors. In breast cancer, IRS2 contributes to both initiation of primary tumor growth and establishment of secondary metastases through regulation of cancer stem cell (CSC) function and invasion. However, how IRS2 mediates its diverse functions is not well understood. We used CRISPR/Cas9-mediated gene editing to modify endogenous IRS2 to study the expression, localization, and function of this adaptor protein. A cassette containing an auxin inducible degradation (AID) sequence, 3X-FLAG tag and mNeon-green was introduced at the N-terminus of the IRS2 gene to provide rapid and reversible control of IRS2 protein degradation and analysis of endogenous IRS2 expression and localization. Live fluorescence imaging of these cells revealed that IRS2 shuttles between the cytoplasm and nucleus in response to growth regulatory signals, and deletion of a putative nuclear export sequence in the C-terminal tail promotes nuclear retention of IRS2. Moreover, acute induction of IRS2 degradation reduces CSC function, similar to the constitutive knockout of IRS2. Our data highlight the value of our model of endogenously tagged IRS2 as a tool to elucidate IRS2 localization and function.

cell biology↗

Epistatic interactions between PHOTOPERIOD-1, CONSTANS 1 and CONSTANS 2 modulate the photoperiodic response in wheat

In Arabidopsis, CONSTANS (CO) integrates light and circadian clock signals to promote flowering under long days (LD). In the grasses, a duplication generated two paralogs designated as CONSTANS 1 (CO1) and CONSTANS 2 (CO2). Here we show that in tetraploid wheat plants grown under LD, combined loss-of-function mutations in the A and B-genome homeologs of CO1 and CO2 (co1 co2) result in a small (3 d) but significant (P<0.0001) acceleration of heading time both in PHOTOPERIOD1 (PPD1) sensitive (Ppd-A1b, functional ancestral allele) and insensitive (Ppd-A1a, functional dominant allele) backgrounds. Under short days (SD), co1 co2 mutants headed 13 d earlier than the wild type (P<0.0001) in the presence of Ppd-A1a. However, in the presence of Ppd-A1b, spikes from both genotypes failed to emerge by 180 d. These results indicate that CO1 and CO2 operate mainly as weak heading time repressors in both LD and SD. By contrast, in ppd1 mutants with loss-of-function mutations in both PPD1 homeologs, the wild type Co1 allele accelerated heading time >60 d relative to the co1 mutant allele under LD. We detected significant genetic interactions among CO1, CO2 and PPD1 genes on heading time, which were reflected in complex interactions at the transcriptional and protein levels. Loss-of-function mutations in PPD1 delayed heading more than combined co1 co2 mutations and, more importantly, PPD1 was able to perceive and respond to differences in photoperiod in the absence of functional CO1 and CO2 genes. Similarly, CO1 was able to accelerate heading time in response to LD in the absence of a functional PPD1. Taken together, these results indicate that PPD1 and CO1 are able to respond to photoperiod in the absence of each other, and that interactions between these two photoperiod pathways at the transcriptional and protein levels are important to fine-tune the flowering response in wheat. Author summaryAn understanding of the mechanisms involved in the regulation of wheat heading time is required to engineer more productive varieties better adapted to new or changing environments. A large proportion of wheats natural variation in heading time is determined by differences in genes controlling the photoperiodic response. In this study, we show that the wheat PHOTOPERIOD1 (PPD1) gene has a stronger effect on heading time than CONSTANS1 (CO1) and CO2 in the regulation of the photoperiodic response, and that complex genetic interactions among these genes are important to fine-tune heading time. Using loss-of-function mutants for both CO1 and CO2, we demonstrate that these genes are not required for PPD1 to perceive differences in photoperiod and regulate heading time. Similarly, we show that in the absence of PPD1, CO1 can accelerate heading time more than 60 days in response to long days. Our results indicate that each of these two wheat photoperiod pathways can respond to differences in photoperiod even in the absence of the other one. Differences in the relative importance of these two pathways and in their epistatic interactions have contributed to the diversity of photoperiodic responses observed in different grass species.

plant biology↗

ATN status in amnestic and non-amnestic Alzheimer's disease and frontotemporal lobar degeneration

Under the ATN framework, cerebrospinal fluid analytes provide evidence of the presence or absence of Alzheimers disease pathological hallmarks: amyloid plaques (A), phosphorylated tau (T), and accompanying neurodegeneration (N). Still, differences in cerebrospinal fluid levels across amnestic and non-amnestic variants or due to co-occurring pathologies might lead to misdiagnoses. We assess the diagnostic accuracy of cerebrospinal fluid markers for amyloid, tau, and neurodegeneration in an autopsy cohort of 118 Alzheimers disease patients (98 amnestic; 20 non-amnestic) and 64 frontotemporal lobar degeneration patients (five amnestic; 59 non-amnestic). We calculated between-group differences in cerebrospinal fluid concentrations of amyloid-{beta}1-42 peptide, tau protein phosphorylated at threonine 181, total tau, and the ratio of phosphorylated tau to amyloid-{beta}1-42. Results show that non-amnestic Alzheimers disease patients were less likely to be correctly classified under the ATN framework using independent, published biomarker cutoffs for positivity. Amyloid-{beta}1-42 did not differ between amnestic and non-amnestic Alzheimers disease, and receiver operating characteristic curve analyses indicated that amyloid-{beta}1-42 was equally effective in discriminating both groups from frontotemporal lobar degeneration. However, cerebrospinal fluid concentrations of phosphorylated tau, total tau, and the ratio of phosphorylated tau to amyloid-{beta}1-42 were significantly lower in non-amnestic compared to amnestic Alzheimers disease patients. Receiver operating characteristic curve analyses for these markers showed reduced area under the curve when discriminating non-amnestic Alzheimers disease from frontotemporal lobar degeneration, compared to discrimination of amnestic Alzheimers disease from frontotemporal lobar degeneration. In addition, the ATN framework was relatively insensitive to frontotemporal lobar degeneration, and these patients were likely to be classified as having normal biomarkers or biomarkers suggestive of primary Alzheimers disease pathology. We conclude that amyloid-{beta}1-42 maintains high sensitivity to A status, although with lower specificity, and this single biomarker provides better sensitivity to non-amnestic Alzheimers disease than either the ATN framework or the phosphorylated-tau/amyloid-{beta}1-42 ratio. In contrast, T and N status biomarkers differed between amnestic and non-amnestic Alzheimers disease; standard cutoffs for phosphorylated tau and total tau may thus result in misclassifications for non-amnestic Alzheimers patients. Consideration of clinical syndrome may help improve the accuracy of ATN designations for identifying true non-amnestic Alzheimers disease. Abbreviated SummaryCousins et al. assess the 2018 ATN framework and find that non-amnestic patients with Alzheimers disease (AD) have lower cerebrospinal fluid (CSF) phosphorylated tau and total tau than amnestic AD, while CSF amyloid-{beta} accurately stratifies both non-amnestic and amnestic AD from frontotemporal lobar degeneration.

neuroscience↗

The Alzheimer’s Disease Metabolome: Effects of Sex and APOE ε4 genotype

Recent studies have provided evidence that late-onset Alzheimers disease (AD) can in part be considered a metabolic disease. Besides age, female sex and APOE {varepsilon}4 genotype represent strong risk factors for AD. They also both give rise to large metabolic differences, suggesting that metabolic aspects of AD pathogenesis may differ between males and females and between APOE {varepsilon}4 carriers and non-carriers. We systematically investigated group-specific metabolic alterations by conducting stratified association analyses of 140 metabolites measured in serum samples of 1,517 AD neuroimaging initiative subjects, with AD biomarkers for A{beta} and tau pathology and neurodegeneration. We observed substantial sex differences in effects of 15 metabolites on AD biomarkers with partially overlapping differences for APOE {varepsilon}4 status groups. These metabolites highlighted several group-specific alterations not observed in unstratified analyses using sex and APOE {varepsilon}4 as covariates. Combined stratification by both variables uncovered further subgroup-specific metabolic effects limited to the group with presumably the highest AD risk: APOE {varepsilon}4+ females. Pathways linked to the observed metabolic alterations suggest that females experience more expressed impairment of mitochondrial energy production in AD than males. These findings indicate that dissecting metabolic heterogeneity in AD pathogenesis may enable grading of the biomedical relevance of specific pathways for specific subgroups. Extending our approach beyond simple one- or two-fold stratification may thus guide the way to personalized medicine.\n\nSignificance statementResearch provides substantial evidence that late-onset Alzheimers disease (AD) is a metabolic disease. Besides age, female sex and APOE{varepsilon}4 genotype represent strong risk factors for AD, and at the same time give rise to large metabolic differences. Our systematic investigation of sex and APOE {varepsilon}4 genotype differences in the link between metabolism and measures of pre-symptomatic AD using stratified analysis revealed several group-specific metabolic alterations that were not observed without sex and genotype stratification of the same cohort. Pathways linked to the observed metabolic alterations suggest females are more affected by impairment of mitochondrial energy production in AD than males, highlighting the importance of tailored treatment approaches towards a precision medicine approach.

bioinformatics↗

Serum triglycerides in Alzheimer’s disease: Relation to neuroimaging and CSF biomarkers

ObjectiveTo investigate the association of triglyceride (TG) principal component scores with Alzheimers disease (AD) and the \"A/T/N/V\" (Amyloid, Tau, Neurodegeneration, and Cerebrovascular disease) biomarkers for AD.\n\nMethodsSerum levels of 84 TG species were measured using untargeted lipid profiling of 689 participants from the Alzheimers Disease Neuroimaging Initiative (ADNI) cohort including 190 cognitively normal older adults (CN) and 339 mild cognitive impairment (MCI) and 160 AD. Principal component analysis with factor rotation was used for dimension reduction of TG species. Differences in principal components between diagnostic groups and associations between principal components and AD biomarkers (including CSF, MRI and [18F]FDG-PET) were assessed using a multivariate generalized linear model (GLM) approach. In both cases, the Bonferroni method of adjustment was employed to correct for multiple comparisons.\n\nResultsThe 84 TGs yielded 9 principal components, two of which consisting of long-chain, polyunsaturated fatty acid-containing TGs (PUTGs), were significantly associated with MCI and AD. Lower levels of PUTGs were observed in MCI and AD compared to CN. PUTG principal component scores were also significantly associated with hippocampal volume and entorhinal cortical thickness. In participants carrying APOE {varepsilon}4 allele, these principal components were significantly associated with CSF amyloid-{beta}1-42 values and entorhinal cortical thickness.\n\nConclusionsThis study shows PUTG component scores significantly associated with diagnostic group and AD biomarkers, a finding that was more pronounced in APOE {varepsilon}4 carriers. Replication in independent larger studies and longitudinal follow-up are warranted.

neuroscience↗

Altered Bile Acid Profile in Mild Cognitive Impairment and Alzheimer’s Disease: Relationship to Neuroimaging and CSF Biomarkers

IntroductionBile acids (BAs) are the end products of cholesterol metabolism produced by human and gut microbiome co-metabolism. Recent evidence suggests gut microbiota influence pathological features of Alzheimers disease (AD) including neuroinflammation and amyloid-{beta} deposition.\n\nMethodSerum levels of 20 primary and secondary BA metabolites from the AD Neuroimaging Initiative (n=1562) were measured using targeted metabolomic profiling. We assessed the association of BAs with the \"A/T/N\" (Amyloid, Tau and Neurodegeneration) biomarkers for AD: CSF biomarkers, atrophy (MRI), and brain glucose metabolism ([18F]FDG-PET).\n\nResultsOf 23 BA and relevant calculated ratios, three BA signatures were associated with CSF A{beta}1-42 (\"A\") and three with CSF p-tau181 (\"T\") (corrected p<0.05). Furthermore, three, twelve, and fourteen BA signatures were associated with CSF t-tau, glucose metabolism, and atrophy (\"N\"), respectively (corrected p<0.05).\n\nConclusionThis is the first study to show serum-based BA metabolites are associated with \"A/T/N\" AD biomarkers, providing further support for a role of BA pathways in AD pathophysiology. Prospective clinical observations and validation in model systems are needed to assess causality and specific mechanisms underlying this association.

neuroscience↗

Altered Bile Acid Profile Associates with Cognitive Impairment in Alzheimer’s Disease – An Emerging Role for Gut Microbiome

IntroductionIncreasing evidence suggests a role for the gut microbiome in central nervous system disorders and specific role for the gut-brain axis in neurodegeneration. Bile acids (BA), products of cholesterol metabolism and clearance, are produced in the liver and are further metabolized by gut bacteria. They have major regulatory and signaling functions and seem dysregulated in Alzheimer disease (AD).\n\nMethodsSerum levels of 15 primary and secondary BAs and their conjugated forms were measured in 1,464 subjects including 370 cognitively normal older adults (CN), 284 with early mild cognitive impairment (MCI), 505 with late MCI, and 305 AD cases enrolled in the AD Neuroimaging Initiative. We assessed associations of BA profiles including selected ratios with diagnosis, cognition, and AD-related genetic variants, adjusting for cofounders and multiple testing.\n\nResultsIn AD compared to CN, we observed significantly lower serum concentrations of a primary BA (cholic acid CA) and increased levels of the bacterially produced, secondary BA, deoxycholic acid (DCA), and its glycine and taurine conjugated forms. An increased ratio of DCA:CA, which reflects 7-dehydroxylation of CA by gut bacteria, strongly associated with cognitive decline, a finding replicated in serum and brain samples in the Rush Religious Orders and Memory and Aging Project. Several genetic variants in immune response related genes implicated in AD showed associations with BA profiles.\n\nConclusionWe report for the first time an association between altered BA profile, genetic variants implicated in AD and cognitive changes in disease using a large multicenter study. These findings warrant further investigation of gut dysbiosis and possible role of gut liver brain axis in the pathogenesis of AD.

neuroscience↗

DirtyGenes: significance testing for gene or bacterial population composition changes using the Dirichlet distribution

High throughput sequencing, and quantitative polymerase chain reaction (qPCR), can detect changes in bacterial communities or the genes that they carry, between different environments or treatments. These methods are applied widely to microbiomes in humans, animals, soil and water; an important application is for changes in antimicrobial resistance genes (ARGs). However, at present, there is no statistical method to determine whether observed changes in the overall composition are significant, or result from random variations between samples. Therefore researchers are limited to graphical descriptions. We describe a novel statistical method to determine whether or not observed differences in bacterial populations or their genes are significant. It can be used with data from shotgun metagenomics, 16S characterisation or qPCR. It can also be used for experimental design, to calculate the number of samples needed in future experiments. We show its application to two example data sets. The first is published data on bacterial communities and ARGs in the environment, in which we show that there are significant changes in both ARG and community composition. The second is a new data set on seasonality in bacterial communities and ARGs in hooves from four sheep. While the observed differences are not significant, we show that a minimum group size of eight sheep in a future experiment would provide sufficient power to observe significant changes, should the already observed changes be true. This method has broad uses for statistical testing and experimental design in experiments on changing microbiomes, including for studies on antimicrobial resistance.

bioinformatics↗