Biology subjects

Panda, D.

Publications and source records attributed to Panda, D..

9 recordsLinked to original sources

bioRxiv2026

AI-designed nuclease performs robust knock out, base editing and prime editing in plants

Genome-editing applications in biological organisms rely on a limited set of naturally occurring enzymes. Artificial intelligence (AI) is transforming protein design. Here, building on the AI-designed nuclease OpenCRISPR-1, we establish the plant-optimized AI-designed editors (PAiD) as a versatile genome-editing platform in plants. PAiD supports NHEJ-mediated indel generation, adenine and cytosine base editing, and prime editing, with robust performance across multiple loci comparable to SpCas9. These results highlight the translational potential of AI-designed nucleases for plant genome engineering.

plant biology↗

bioRxiv2026

Prime editing of an evolutionarily informed PEPC residue enhances photosynthesis and grain nutrition in C₃ rice

C4 photosynthesis evolved through adaptive changes in key metabolic enzymes that enhance carbon fixation efficiency, yet transferring such traits into C3 crops has met limited success. Using precision prime editing, we introduced an evolutionarily conserved single amino acid substitution (Arg[->]Gly) into phosphoenolpyruvate carboxylase (PEPC) in rice. Edited plants exhibited enhanced PEPC activity in the presence of the feedback inhibitor malate, increased chlorophyll content, elevated photosynthetic rates under ambient CO2, and increased seed size and weight. Remarkably, seeds from the edited lines showed simultaneous enrichment of zinc (Zn), iron (Fe), and protein, hereafter referred to as ZiP rice. This work demonstrates that a single, evolutionarily guided residue change can reprogram core carbon metabolism in a C3 crop, enabling concurrent improvements in photosynthesis and grain nutritional quality.

plant biology↗

bioRxiv2025

Receptor tyrosine kinase AXL regulates Golgi organization and function through an adhesion-Arf1 signaling axis in breast and lung cancers

Cell-matrix adhesion regulates membrane trafficking, Golgi organisation and function. Differential Golgi organisation in cancer cells could drive changes in trafficking and processing of cargoes. A simple screen evaluating Golgi organisation identifies breast (MDAMB231 vs MCF7) and lung cancer (A549 vs CaLu1) cell line pairs with differently organised Golgi, regulated differentially by loss of adhesion. In silico analysis of differentially expressed genes in the CCLE database, evaluated for their association with the Golgi in interaction networks and literature, identified AXL as a putative regulator of Golgi in these cancers. AXL prominently localized at the Golgi, undergoes displacement from the Golgi when inhibited by R428 and knocked down using siRNA, causing the Golgi to disorganize. AXL-dependent regulation of Golgi organisation is also dependent on cell-matrix adhesion. AXL binds active Arf1, whose recruitment to the Golgi is vital for its organisation. On loss of adhesion, loss of AXL and active Arf1 from the Golgi, drives its disorganization to affect Golgi-dependent microtubule acetylation and cell surface glycosylation in MDAMB231 and A549 cells respectively. Together, this validates our screen to identify novel regulators of the Golgi, and identifies AXL-Arf1 crosstalk as a vital mediator of its organisation and function in cancer cells.

cell biology↗

bioRxiv2024

Eliminating Aggressive Cancers via PROTAC-like Inducers of Ferroptosis

Aggressive and therapy-resistant cancers present a significant challenge to treatment and are associated with poor patients survival. Identifying molecular pathways and compounds that target these pathways is critical for improving patient outcomes. RNF4, an E3-ubiquitin ligase, is pivotal in oncoprotein stabilization and DNA repair, enhancing cancer cell survival driving tumorigenesis. Elevated RNF4 levels are associated with poor prognosis in cancer patients. Here, we describe the development of R4VPs, proteolysis-targeted chimeras-like (PROTACs-like). R4VPs promote RNF4 degradation and reduce the levels of its stabilized oncoproteins. Notably, R4VPs induce ferroptotic cell death selectively in cancer cells, sparing non-tumorigenic and primary cells. Surprisingly, R4VPs-induced ferroptosis is independent of RNF4 but preferentially targets tumor-driving mutations, particularly those in the EGFR pathway, while not affecting PI3K-transformed cells. R4VPs effectively induce cell death in therapy-resistant melanoma and sarcomas including patient-derived sarcoma tumor cells. Our findings highlight the potential of ferroptosis inducers such as R4VPs as a therapeutic strategy for therapy resistance, aggressive, and hard-to-treat cancers. TeaserR4VPs induce ferroptotic death of melanoma and sarcoma cells including patient-derived tumor cells sparing non-transomed cells.

cancer biology↗

bioRxiv2024

In vitro anti cancer, anti inflammatory and anti oxidant activity of Celery oil (Apium graveolens)-Myristic acid based microemulsion system: Characterization and Biomedical application

Plant based compounds are frequently modified, developed into drug components to treat different types of cancer. Celery is one of the most used ingredients in daily life, exhibits potential medicinal properties and myristic acid exhibits anti microbial and inflammatory properties making it ideal candidate for combinational therapy. This study demonstrates the formulation of celery oil-myristic acid based microemulsion system with sequence of weight/volume of components to optimize stable microemulsion. the sequence of formulations were performed, optimized through pseudo ternary phase diagram and stability analysis, of which CMA ME 4 formulation were observed to transparent and stable. This CMA ME 4 was analyzed using DLS for particle size which is found to be 14.0{+/-}27.1 and PDI 0.34{+/-}0.46 through 5th day to 30th day. In vitro drug release study has been performed with stimulated physiological condition (pH 5.6) and stimulated tumor tissue (pH 7.4), the microemulsion was withdrawn in time intervals and the kinetic model is constructed to detect the behaviour of the drug release profile. Further, anti inflammatory, anti diabetic and anti obesity assays were performed to analyse the potentiality of CMA ME 4 microemulsion formulation, where the results exhibited from 80 to 90% radical scavenging and inhibition compared with the synthetic drugs. A good cytotoxic activity of CMA ME 4 microemulsion was determined by positive results of the MTT assay performed with HeLa with 80 to 90% cell death, MCF7 with 80 to 90% cell death and HUVECs was used to determine the toxicity level when the microemulsion interacts with the normal cell which is found to be 80 to 90% cell viability over time. These findings more suitably suggest that combination of natural oil with synthetic components can be effective in treatment against diseases.

pharmacology and toxicology↗

bioRxiv2024

Cell-surface glycans are quantitative reporters of Golgi dysfunction in single cells

Complex sugar polymers known as glycans contribute to the high molecular diversity of the eukaryotic cell surface. The types and levels of glycans on one cell can be sensed by other cells using carbohydrate-specific binding proteins such as lectins, enabling glycans to regulate cell-cell interactions. Glycans are covalently assembled onto proteins and lipids as they traverse the secretory pathway, a tightly regulated process known as glycosylation and carried out by Golgi-resident enzymes. Errors in glycosylation due to the dysfunctional trafficking of enzymes and substrates in the Golgi are implicated in human diseases. Here we ask how much information about Golgi dysfunction is encoded by surface glycans in single cells. This task is challenging due to high cell-to-cell variability in glycan levels. We exploited the loss-of-adhesion driven disorganization of the Golgi in mouse fibroblasts to generate a highly reproducible gradient of Golgi morphology phenotypes, by titrating the Arf1 inhibitor Brefeldin A (BFA). We measured the resulting distribution of cell-surface glycans in single cells using two fluorescently tagged lectin probes (ConA and WGA). A mathematical model of intracellular traffic, parameterized against measurements of Golgi fragmentation and endocytosis, quantitatively explains cell-surface lectin levels across time and BFA concentrations. We used this model to construct an optimal Bayesian decoder and showed that singlecell lectin measurements predict Golgi phenotypes with accuracy far greater than chance. By combining signals from two lectins we further improved prediction accuracy and speed. Such multi-lectin information may be exploited during natural cell-cell communication, and in the development of single-cell diagnostics.

cell biology↗

bioRxiv2023

CEP41, a ciliopathy-linked centrosomal protein, regulates microtubule assembly and cell division

Centrosomal proteins play pivotal roles in orchestrating microtubule dynamics, and their dysregulation leads to disorders, including cancer and ciliopathies. Understanding the multifaceted roles of centrosomal proteins is vital to comprehend their involvement in disease development. Here, we report novel cellular functions of CEP41, a centrosomal and ciliary protein implicated in Joubert syndrome. We show that CEP41 is an essential microtubule-associated protein with microtubule-stabilizing activity. Purified CEP41 binds to preformed microtubules, promotes microtubule nucleation, and suppresses microtubule disassembly. When overexpressed in cultured cells, CEP41 localizes to microtubules and promotes microtubule bundling. Conversely, shRNA-mediated knockdown of CEP41 disrupts the interphase microtubule network and delays microtubule reassembly, emphasizing its role in microtubule organization. Further, we demonstrate that CEP41s association with microtubules relies on its conserved rhodanese homology domain (RHOD) and the N-terminal region. Interestingly, a disease-causing mutation in the RHOD domain impairs CEP41-microtubule interaction. Moreover, depletion of CEP41 inhibits cell proliferation and disrupts cell cycle progression, suggesting its potential involvement in cell cycle regulation. These insights into the cellular functions of CEP41 hold promise for unraveling the impact of its mutations in ciliopathies. SummaryA novel role of CEP41 as a microtubule-associated protein that promotes microtubule assembly and regulates cell cycle progression could offer insights into the development of ciliopathies.

biochemistry↗

bioRxiv2021

Altered expression of Api5 affects breast carcinogenesis by modulating FGF2 signalling

Apoptosis or programmed cell death plays a vital role in maintaining homeostasis and, therefore, is a tightly regulated process. Deregulation of apoptosis signalling can favour carcinogenesis. Apoptosis inhibitor 5 (Api5), an inhibitor of apoptosis, is upregulated in cancers. Interestingly, Api5 is shown to regulate both apoptosis and cell proliferation. To address the precise functional significance of Api5 in carcinogenesis here we investigate the role of Api5 in breast carcinogenesis. Consistently, in-silico analysis revealed elevated levels of Api5 transcript in breast cancer patients which correlated with poor prognosis. Overexpression of Api5 in non-tumorigenic breast acinar cultures resulted in increased proliferation and cells exhibited a partial EMT-like phenotype with higher migratory potential and disruption in cell polarity. Furthermore, during acini development, the influence of Api5 is mediated via the combined action of FGF2 activated PDK1-Akt/cMYC signalling and Ras-ERK pathways. Conversely, Api5 knock-down downregulated FGF2 signalling leading to reduced proliferation and diminished in vivo tumorigenic potential of the breast cancer cells. Thus, taken together, our study identifies Api5 as a central player involved in regulating multiple events during breast carcinogenesis.

cancer biology↗

bioRxiv2021

ATR facilitates the degradation of Api5 through the ubiquitin-proteasome pathway via FBXW2 to regulate apoptosis upon DNA damage

Apoptosis inhibitor 5 (Api5) is an inhibitor of apoptosis, which is found to be upregulated in several cancers and promotes invasion as well as metastasis. Over-expression of Api5 is positively co-related with poor survival of cancers and inhibition of DNA damage induced apoptosis in cancerous cells. Acetylation at lysine 251 (K251) on Api5 facilitates the stability of the protein and thus functionally provides resistance to cancer cells against chemotherapeutic or anti-cancerous agents. However, the regulation of Api5 upon DNA damage is not yet known. In this study, we demonstrate that Api5 undergoes degradation following DNA damage via the ubiquitin-proteasome system. Upon DNA damage, ATR was observed to phosphorylate Api5 at serine 138 which led to the cytoplasmic localisation of Api5. The E3-ubiquitin ligase, SCF-FBXW2 ubiquitinates Api5 leading to its proteasomal degradation.

molecular biology↗