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Patil, M.

Publications and source records attributed to Patil, M..

8 recordsLinked to original sources

Cortical Organoid Model of PPP2R5D Genetic Intellectual Disability Models Disease Severity Phenotype

Jordans Syndrome (JS) is a rare, neurodevelopmental disorder caused by de novo missense mutations in protein phosphatase 2 regulatory subunit Bdelta (PPP2R5D). JS is characterized by severe neurological impairments starting in early life. PPP2R5D encodes for B56{delta}, one of the regulatory subunits of protein phosphatase 2A (PP2A). PP2A is a heterotrimeric protein serine/threonine phosphatase that is highly expressed in the brain and the liver. Past studies have focused on PP2As role in liver and little is known about the holoenzymes behavior in neuronal cells. Although B56{delta} is known to play an important role in the substrate specificity of PP2A, the identification of validated downstream substrates in JS remains unclear. To better understand how the mutations affect neuronal cells, we developed cerebral cortical-like organoids from an engineered allele series of the most common JS mutations to characterize the physiological changes throughout different stages of neurodevelopment. Organoids were assessed for transcriptomic, protein, and electrophysiological changes utilizing bulk RNA sequencing, immunocytochemistry, Western Blot, and high-density MicroElectrode Array. The results identify differentially expressed genes and translated proteins, potential neuronal substrates, and significant electrophysiological signatures that suggest mutations in B56{delta} lead to variant-specific dysfunction of PP2A. Overexpression of PPP2R5D through AAV transduction of organoids rescued several phenotypes in the variants, suggesting different pathogenetic etiology underneath. Our findings successfully characterized cerebral cortical-like organoids in JS cell lines and demonstrated its potential as a model for studying neurodevelopmental disorder and for screening therapeutic approaches.

cell biology↗

MNRR1 is required for Triple Negative Breast Cancer growth and metastasis and can be targeted by repurposed drugs.

Despite progress in recent decades, breast cancers remain the most diagnosed malignancies, and second leading cause of cancer death, in women. Although improved screening and systemic and endocrine adjuvant approaches have contributed to major declines in breast cancer mortality, current standard of care drugs are extremely toxic, and many women continue to be overtreated. Although nearly two-thirds of breast cancers are hormone-responsive, aggressive subtypes, particularly Triple Negative Breast Cancer (TNBC), still lack safe oral medications. Recently the roles that mitochondria play in TNBC carcinogenesis, metastasis, and resistance to treatment have garnered a great deal of attention. Contrary to the popular dogma that cancer cells are powered by glycolysis, metastatic breast cancer cells have enhanced mitochondrial function. Our work identified that Mitochondrial Nuclear Retrograde Regulator 1 (MNRR1; also, CHCHD2, PARK22), a key coordinator of mitochondrial-nuclear crosstalk that is physically present in both compartments, is overexpressed in TNBC cells and is an important regulator of metastasis signaling. We have identified Heat Shock Factor 1 (HSF1) as the main transcription factor that activates the MNRR1 promoter in TNBC cell lines. In the mitochondria, MNRR1 protein facilitates ATP production and inhibits apoptosis, whereas in the nucleus it regulates the transcription of stress-responsive genes including several required for epithelial to mesenchymal transition (EMT), metabolic flexibility, and cell growth. Thus, each of the bi-organellar functions of MNRR1 constitutes processes regarded as hallmarks of cancer. For reasons that are not yet fully understood, MNRR1 levels display a significant and robust ancestry bias, showing increased expression in tumor samples from Non-Hispanic Black (NHB) women when compared to disease-matched tumors from Non-Hispanic White (NHW) patients. It is possible that increased levels of MNRR1 may underlie the aggressive metastatic phenotype observed in many NHB patients. In further support of this observation, loss of MNRR1 function, either genetically or by use of inhibitors, reduces TNBC growth and metastasis. MNRR1 therefore is an attractive therapeutic target that could be exploited for design of novel therapies or as adjuncts to existing ones.

cancer biology↗

Novel Gain of Function Mouse Model of KCNT1-Related Epilepsy

KCNT1-related epilepsy is an autosomal dominant neurodevelopmental disorder with at least 64 known human variants, each with unique electrophysiological and epileptic characteristics. A multi-disciplinary collaboration generated a novel mouse model (C57BL/6-Kcnt1em1Bryd) carrying the G269S variant, corresponding to human G288S, located within the coding region of the channel pore. Network excitability of cultured cortical neurons from Kcnt1+/G269S exhibited sustained hyperexcitability and hypersynchronous bursting while Kcnt1G269S/G269S neurons showed early excessive bursting followed by network collapse, suggesting excitotoxicity. Kcnt1+/G269S displayed poor motor coordination, erratic breathing, and increased apneas. Critically, Kcnt1+/G269S were more susceptible to thermal-induced seizures in early life. In summary, these data: (i) provide a novel mouse model of KCNT1-related epilepsy, (ii) provide strong in vitro evidence of neuronal hyperexcitability, (iii) illustrate early-life seizures as a functional outcome measure, and (iv) lay the groundwork for future analysis of neural activity in vivo and modeling circuit level dynamics in vitro and in silico. Significance StatementGain-of-function mutations in the sodium-gated potassium channel KCNT1 have been linked to pediatric epilepsy of varying severity. The human KCNT1 variant G288S (G269S in mice) is linked to Autosomal Dominant Nocturnal Frontal Lobe Epilepsy (ADNFLE), Epilepsy of Infancy with Migrating Focal Seizures (EIMFS), and other severe developmental epileptic encephalopathies. There are currently no therapeutics to prevent the progression of KCNT1-related epilepsy, therefore, the scientific community requires a novel mouse model that is well characterized, in vitro and in vivo, to screen and assess targeted therapeutics. Herein, we engineered a novel mouse to assess developmental and adult phenotypes resulting from the G288S/G269S variant, in vitro and in vivo, to advance translation toward therapeutic testing for individuals with KCNT1-related epilepsy.

neuroscience↗

CAFE: An Integrated Web App for High-Dimensional Analysis and Visualization in Spectral Flow Cytometry

Spectral flow cytometry provides greater insights into cellular heterogeneity by simultaneous measurement of up to 50 markers. However, analyzing such high-dimensional (HD) data is complex through traditional manual gating strategy. To address this gap, we developed CAFE as an open-source Python-based web application with a graphical user interface. Built with Streamlit, CAFE incorporates libraries such as Scanpy for single-cell analysis, Pandas and PyArrow for efficient data handling, and Matplotlib, Seaborn, Plotly for creating customizable figures. Its robust toolset includes density-based down-sampling, dimensionality reduction, batch correction, Leiden-based clustering, cluster merging and annotation. Using CAFE, we demonstrated analysis of a human PBMC dataset of 350,000 cells identifying 16 distinct cell clusters. CAFE can generate publication-ready figures in real time via interactive slider controls and dropdown menus, eliminating the need for coding expertise and making HD data analysis accessible to all. CAFE is licensed under MIT and is freely available at https://github.com/mhbsiam/cafe.

systems biology↗

Cardiolipin deficiency disrupts CoQ redox state and induces steatohepatitis

Metabolic dysfunction-associated steatotic liver disease (MASLD) is a progressive disorder marked by lipid accumulation, leading to metabolic dysfunction-associated steatohepatitis (MASH). A key feature of the transition to MASH involves oxidative stress resulting from defects in mitochondrial oxidative phosphorylation (OXPHOS). Here, we show that pathological alterations in the lipid composition of the inner mitochondrial membrane (IMM) directly instigate electron transfer inefficiency to promote oxidative stress. Specifically, mitochondrial cardiolipin (CL) was downregulated with MASLD/MASH in humans and in mice. Hepatocyte-specific CL synthase knockout (CLS-LKO) led to spontaneous and robust MASH with extensive steatotic and fibrotic phenotype. Loss of CL paradoxically increased mitochondrial respiratory capacity but also promoted electron leak primarily at sites IIIQO and IIF of the electron transport chain, reduced the formation of I+III2+IV respiratory supercomplex, and disrupted the propensity of coenzyme Q (CoQ) to become reduced. Thus, low mitochondrial CL disrupts electron transport chain to promote oxidative stress and contributes to pathogenesis of MASH.

biochemistry↗

Stress Combinations and their Interactions inPlants Database (SCIPDb): A one-stop resource for understanding combined stress responses in plants

We have developed Stress Combinations and their Interactions in Plants Database (SCIPDb; http://www.nipgr.ac.in/scipdb.php), a compendium and interactive platform offering information on both morpho-physio-biochemical (phenome) and molecular (transcriptome) responses of plants to different combinations of stresses. To delineate the effects of various stress combinations/categories on yield in major agricultural crops, global phenome data from 939 studies was analyzed and results showed that yield was affected to the greatest extent under the abiotic-abiotic stress category, followed by the biotic-biotic and abiotic-biotic stress categories. In the abiotic-abiotic stress category, drought-heat, heat-salinity, and ozone-UV are the major stress combinations causing high yield loss in barley, wheat, soybean, and quinoa crops. In the abiotic-biotic stress category, the salinity-weed stress combination causes highest yield loss in rice crop. In the biotic-biotic stress category, the nematode-fungus combination was most detrimental, causing considerable yield losses in potato, groundnut, and sugar beet crops. Transcriptome datasets from 36 studies hosted in SCIPDb identified novel genes. Thus far, these genes have not been known to play a role in combined stress. Integretome analysis under combined drought-heat stress pinpointed carbohydrate, amino acid, and energy metabolism pathways as the crucial metabolic, proteomic, and transcriptional components in plant tolerance to combined stress. These examples illustrate the application of SCIPDb in identifying novel genes and pathways involved in combined stress tolerance. Further, we showed the application of this database in identifying novel candidate genes and pathways for combined drought and pathogen stress tolerance in Arabidopsis and chickpea. To our knowledge, SCIPDb is the only publicly available platform that provides extensive information and paves the way for advancing mechanistic understanding of plant responses to combined stresses.

plant biology↗

CaProDH2-mediated modulation of proline metabolism confers tolerance to Ascochyta in chickpea under drought

Drought and leaf blight caused by the fungus Ascochyta rabiei often co-occur in chickpea (Cicer arietinum)-producing areas. While the responses of chickpea to either drought or A. rabiei infection have been extensively studied, their combined effect on plant defense mechanisms is unknown. Fine modulation of stress-induced signaling pathways under combined stress is an important stress adaptation mechanism that warrants a better understanding. Here we show that drought facilitates resistance against A. rabiei infection in chickpea. The analysis of proline levels and gene expression profiling of its biosynthetic pathway under combined drought and A. rabiei infection revealed the gene encoding proline dehydrogenase (CaProDH2) as a strong candidate conferring resistance to A. rabiei infection. Transcript levels of CaProDH2, pyrroline-5-carboxylate (P5C) quantification, and measurement of mitochondrial reactive oxygen species (ROS) production showed that fine modulation of the proline-P5C cycle determines the observed resistance. In addition, CaProDH2-silenced plants lost basal resistance to A. rabiei infection induced by drought, while overexpression of the gene conferred higher resistance to the fungus. We suggest that the drought-induced accumulation of proline in the cytosol helps maintain cell turgor and raises mitochondrial P5C contents by a CaProDH2-mediated step, which results in ROS production that boosts plant defense responses and confers resistance to A. rabiei infection. Our findings indicate that manipulating the proline-P5C pathway may be a possible strategy for improving stress tolerance in plants suffering from combined drought and A. rabiei infection.

plant biology↗

Neuroendocrine mechanisms governing sex-differences in chronic pain involve prolactin receptor sensory neuron signaling

Many clinical and preclinical studies report higher prevalence and severity of chronic pain in females. We used hyperalgesic priming with interleukin 6 (IL-6) priming and PGE2 as a second stimulus as a model for pain chronicity. Intraplantar IL-6 induced hypersensitivity was similar in magnitude and duration in both males and females, while both paw and intrathecal PGE2 hypersensitivity was more persistent in females. This difference in PGE2 response was dependent on both circulating estrogen and translation regulation signaling in the spinal cord. In males, the duration of hypersensitivity was regulated by testosterone. Since the prolactin receptor (Prlr) is regulated by reproductive hormones and is female-selectively activated in sensory neurons, we evaluated whether Prlr signaling contributes to hyperalgesic priming. Using {Delta}PRL, a competitive Prlr antagonist, and a mouse line with ablated Prlr in the Nav1.8 sensory neuronal population, we show that Prlr in sensory neurons is necessary for the development of hyperalgesic priming in female but not male mice. Overall, sex-specific mechanisms in the initiation and maintenance of chronic pain are regulated by the neuroendocrine system and, specifically, sensory neuronal Prlr signaling. Significance StatementFemales are more likely to experience chronic pain than males, but the mechanisms that underlie this sex difference are not completely understood. Here, we demonstrate that the duration of mechanical hypersensitivity is dependent on circulating sex hormones in mice - where estrogen caused an extension of sensitivity and testosterone was responsible for a decrease in the duration of the hyperalgesic priming model of chronic pain. Additionally, we demonstrated that Prolactin receptor expression in Nav1.8+ neurons was necessary for hyperalgesic priming in female, but not male mice. Our work demonstrates a female-specific mechanism for the promotion of chronic pain involving the neuroendrocrine system and mediated by sensory neuronal prolactin receptor.

neuroscience↗