Publications by authors named "Karnan Sivasundaram"

Three-dimensional cell culture creates an environment that allows cells to grow and interact with the surrounding extracellular framework. Versican plays a pivotal role in forming the provisional matrix, but it is still unclear how this proteoglycan affects the formation of the extracellular matrix. Here, we established a three-dimensional culture system using fibrin gel, which enables a long-term culture up to a month.

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5' adenosine monophosphate-activated protein kinase-related kinase 5 (ARK5) is involved in mitochondrial ATP production and associated with poor prognosis of multiple myeloma (MM). However, the molecular mechanisms of ARK5 in MM remain largely unknown. This study examined the pathogenic role of ARK5 in mitochondria by using genetically modified isogenic cell clones with or without ARK5 in human myeloma cell lines, KMS-11 and Sachi, which overexpress ARK5.

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  • Research continues to uncover unknowns in cell division mechanisms, leading to the identification of leucine zipper protein 1 (LUZP1) as a novel protein that regulates this process.
  • LUZP1 was found to colocalize with the chromosomal passenger complex (CPC) during specific phases of mitosis and is influenced by CPC activity and kinesin family member 20A (KIF20A).
  • The study reveals that LUZP1 interacts with death-associated protein kinase 3 (DAPK3) and myosin light chain 9 (MYL9), ultimately regulating cytokinesis by affecting the constriction velocity of the contractile ring.
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  • CRISPR/Cas9 is an advanced gene-editing tool known for its ability to create gene knockouts and targeted knock-ins, but efficiency and precision need improvement for broader practical applications.* -
  • This study introduces a method using flow cytometry (FCM) to easily monitor genome editing events in the L1CAM gene across various human cell lines, allowing for quick detection of L1CAM abrogation.* -
  • The L1CAM-based assay is faster and more sensitive than existing methods for measuring targeted knock-in efficiency, helping researchers refine and enhance genome editing techniques.*
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  • Malignant mesothelioma (MMe) is a rare and aggressive cancer with a poor prognosis, despite known genetic factors like BAP1 gene alterations.
  • Researchers created BAP1 knockout human mesothelial cell clones to identify new targeted therapies and discovered that the CAMK2D gene is highly expressed in these cells and in many MMe tissues.
  • They identified the CaMKII inhibitor KN-93 as a promising treatment that effectively reduces tumor growth in models of BAP1-deficient MMe, presenting a potential new approach for therapy.
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Background: Epidermal growth factor receptor (EGFR) is frequently overexpressed in oral squamous cell carcinoma (OSCC), and EGFR-targeting therapeutics have been widely employed to treat patients with a variety of carcinomas including OSCC. Here, we aimed to investigate alternative signaling for OSCC survival under the disruption of EGFR signaling.

Methods: OSCC cell lines, namely HSC-3 and SAS, were utilized to investigate how EGFR disruption affects cell proliferation.

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  • PBK (PDZ-binding kinase) is identified as a poor prognostic factor for cancer, and the study investigates the effects of a specific PBK inhibitor, OTS514, on oral squamous cell carcinoma (OSCC) cells.
  • The research utilized four OSCC cell lines to assess cell survival and apoptosis, with OTS514 reducing cell survival and promoting apoptosis in a dose-dependent manner.
  • Findings suggest OTS514 inhibits OSCC cell growth by downregulating E2F target genes and inducing apoptosis through the p53 signaling pathway, indicating its potential as a targeted cancer therapy.
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Patients with advanced/recurrent mucoepidermoid carcinoma (MEC) have a poor prognosis. This study aimed to establish and characterize human mucoepidermoid carcinoma cell lines from the initial surgical specimen and biopsy specimen upon recurrence from the same patient to provide a resource for MEC research. MEC specimens from the initial surgical procedure and biopsy upon recurrence were used to establish cell lines.

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Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL) is an intractable disease and most cases harbor genetic alterations that activate JAK or ABL signaling. The commonest subtype of Ph-like ALL exhibits a CRLF2 gene rearrangement that brings about JAK1/2-STAT5 pathway activation. However, JAK1/2 inhibition alone is insufficient as a treatment, so combinatorial therapies targeting multiple signals are needed.

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Objective: Moyamoya disease (MMD) is a rare cerebrovascular disease characterized by progressive stenosis of the internal carotid artery (ICA) and secondary formation of collateral vessels. Revascularization surgery is performed in patients with MMD to prevent stroke; however, the pathogenesis of MMD remains unknown. Recently, long noncoding RNAs (lncRNAs) have been found to play a key role in gene regulation and are implicated in various vascular diseases.

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For its cell surface expression, radioprotective 105 (RP105) - an orphan Toll-like receptor - must form a complex with a soluble glycoprotein called myeloid differentiation 1 (MD-1). The number of RP105-negative cells is significantly increased in patients with systemic lupus erythematosus (SLE); however, to elucidate the mechanism underlying this increase, how RP105 is expressed on the cell surface depending on MD-1 should be investigated. We demonstrated that RP105 exhibits two forms depending on MD-1 and its two N-glycosylation sites, N96 and N156.

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  • Targeted knock-in using CRISPR/Cas9 technology holds potential for applications in medical and agricultural research, but it needs improved efficiency and precision for practical use.
  • The researchers developed the CD55 correction assay to monitor gene correction events by creating reporter clones that allow detection of changes in the CD55 gene through flow cytometry.
  • This study validates the CD55 correction assay as a reliable method for quantifying targeted knock-in efficiency, enhancing accuracy in research by addressing biases related to specific cell lines and gene locations.
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is widely distributed in tropical and subtropical countries and is traditionally used for preventing numerous disorders. In this study, a bioguided fractionation of ethyl acetate extract (SE) from root was carried out to target antioxidant and cytotoxic activities. Of the four fractions (SE1-SE4) obtained by column chromatography, SE4 had the strongest anti-radical ability in the DPPH and ABTS assays (IC = 0.

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Versican is a large chondroitin sulfate/dermatan sulfate proteoglycan that plays a key role in the formation of the provisional matrix. Here, we generated dextran sulfate sodium-induced colitis in knockin-mice, R/R, expressing ADAMTS-resistant versican, and investigated the impact of accumulating versican and its turnover in the inflammatory colon mucosa. Histologically, R/R colon showed decreased levels of tissue destruction and an increased number of myofibroblasts and macrophages.

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  • Tandem Paired Nicking (TPN) is a genome editing technique that allows precise targeted knock-ins with minimal interference from DNA damage responses.
  • The method involves using Cas9 nickases to create two specific nicks on a DNA strand, allowing for efficient homology-directed recombination between the genome and donor DNA.
  • This study identifies key factors for optimizing TPN, including using 1700-2000 bp donor DNAs and 20-nt-long spacers for effective cleavage, which enhances the precision and efficiency of targeted knock-in methodologies.
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  • The study focuses on improving targeted knock-in techniques using CRISPR/Cas systems by creating a reporter system based on the PIGP gene, essential for GPI-anchor biosynthesis.
  • Researchers deleted one PIGP allele and introduced a mutation in the other allele in human cell lines, allowing them to monitor knock-in events via flow cytometry by detecting GPI anchors.
  • The findings confirmed the effectiveness of this reporter system in quantifying targeted knock-in efficiency, demonstrating a slight improvement in efficiency using a modified tandem paired nicking procedure.
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Objective: Moyamoya disease (MMD) is a rare cerebrovascular disease characterized by progressive occlusion of the internal carotid artery and the secondary formation of collateral vessels. Patients with MMD have ischemic attacks or intracranial bleeding, but the disease pathophysiology remains unknown. In this study, the authors aimed to identify a gene expression profile specific to the intracranial artery in MMD.

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  • Internal tandem duplication (ITD) of the FLT3 gene is common in acute myeloid leukemia (AML) and often leads to poor patient outcomes; FLT3 inhibitors provide limited benefits.
  • Researchers created a model using CRISPR-Cas9 to investigate how FLT3-ITD affects CD52 expression in K562 leukemia cells and found that FLT3-ITD cells exhibit higher CD52 levels, influenced by STAT5 activation.
  • The study highlights that the anti-CD52 antibody, alemtuzumab, effectively induces cell death in FLT3-ITD cells and suppresses tumor growth in mice, suggesting it as a potential new treatment for AML patients with this mutation.
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Multiple myeloma (MM) cells are derived from mature B cells based on immunoglobulin heavy chain (IgH) gene analysis. The onset of MM is often caused by a reciprocal chromosomal translocation (cTr) between chr 14 with IgH and chr 11 with CCND1. We propose that mature B cells gain potential to transform by reprograming, and then chromosomal aberrations cause the development of abnormal B cells as a myeloma-initiating cell during B cell redifferentiation.

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  • Malignant pleural mesothelioma (MPM) is a deadly cancer affecting the pleura, currently untreatable due to the absence of effective early detection methods and specific therapies.
  • Research on NF2/p16 double-knockout (DKO) cell clones showed that these mutations greatly enhance cell growth and migration in MPM.
  • CD24 was identified as a potential prognostic marker and therapeutic target for MPM, with its high expression linked to poorer patient survival rates and associated with the loss of NF2 and p16 genes.
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Cisplatin is an important drug for the treatment of head and neck squamous cell carcinoma (HNSCC). Determining chemoresistant factors prior to treatment will lead to great benefits for clinicians and patients. Here, we evaluated chemoresistant factors by integrating proteomic and transcriptomic data using HNSCC cell lines to identify a more precise chemoresistant factor in HNSCC.

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  • Multiple myeloma (MM) is a tough cancer to treat, and researchers have found that PDZ binding kinase (PBK) plays a significant role in its growth.
  • Increased levels of interleukin-6 (IL-6) lead to higher PBK expression, which is linked to shorter survival times in MM patients.
  • Targeting PBK through knockout and the use of a specific inhibitor, OTS514, shows promise in reducing tumor growth, suggesting PBK could be a potential new treatment target for MM.
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Unlabelled: The cellular context that integrates gene expression, signaling, and metabolism dictates the oncogenic behavior and shapes the treatment responses in distinct cancer types. Although chimeric fusion proteins involving transcription factors (TF) are hallmarks of many types of acute lymphoblastic leukemia (ALL), therapeutically targeting the fusion proteins is a challenge. In this work, we characterize the core regulatory circuitry (CRC; interconnected autoregulatory loops of TFs) of B-ALL involving MEF2D-fusions and identify MEF2D-fusion and SREBF1 TFs as crucial CRC components.

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  • * FAM46C-disrupted cell lines showed higher cell proliferation and reduced apoptosis, indicated by increased phosphorylated Akt levels and decreased caspase activities compared to wild type (WT) cells.
  • * Inhibition of the PI3K-Akt signaling pathway using specific drugs improved survival in FAM46C mutant cell lines, suggesting that targeting this pathway could be a potential therapeutic strategy for MM with FAM46C abnormalities.
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  • Ameloblastoma is a rare but benign tumor of the head and neck, making up less than 1% of such tumors, with notable BRAF V600E and SMO L412F mutations identified through advanced sequencing techniques.
  • Despite having genomic data, the full molecular signature and characteristics of ameloblastoma cells remain unclear, prompting further investigation in this study.
  • Findings revealed a distinct gene expression pattern in ameloblastoma compared to normal tissues, with activation of KRAS-responsive genes, highlighting the role of IGF2 in cell proliferation and suggesting TLR2 signaling contributes to cell survival, which could lead to improved treatments.
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