Publications by authors named "Arijit Mukhopadhyay"
Article Synopsis
- - Small extracellular vesicles (sEVs) play a key role in cell communication by transporting proteins, lipids, and nucleic acids, which can be non-invasively utilized as disease biomarkers due to their ability to cross barriers like the blood-brain barrier.
- - The study developed a method to isolate sEVs from small quantities of frozen human brain tissue using size exclusion chromatography after obtaining ethical approval and following a series of enzymatic and filtration steps.
- - The effectiveness of the isolation technique was confirmed through various analyses, revealing a good RNA yield for further studies, including qPCR and small RNA sequencing, enhancing the potential for diagnosing diseases using sEVs from brain tissue.
Article Synopsis
- * The study explored the effectiveness of genetic testing, specifically looking at copy number variations (CNVs) in Vietnamese children with ASD, finding a diagnostic success rate of around 6%.
- * Researchers identified 1708 CNVs in total, with 118 being de novo, and highlighted a significant occurrence of deletions in the SHANK3 gene among patients, establishing a basis for developing a CNV-based diagnostic test for ASD in Vietnam.
Article Synopsis
- Glaucoma is a leading cause of irreversible blindness, with a genetic background, and this study investigates new genes linked to familial forms of both primary open-angle glaucoma (POAG) and primary angle closure glaucoma (PACG).
- Whole-exome sequencing was performed on 31 samples from glaucoma-affected families and followed by validation on a larger cohort, identifying rare mutations in critical genes associated with familial glaucoma.
- The research highlighted altered gene expression in specific retinal cells and suggested a connection to extracellular matrix organization, proposing new genetic insights into the development of POAG and PACG.
Introduction: Breast cancer is the most frequently diagnosed cancer globally and is one of the most important contributors to cancer-related deaths. Earlier diagnosis is known to reduce mortality, and better biomarkers are needed. MiRNA clusters often co-express and target mRNAs in a coordinated fashion, perturbing entire pathways; they thus merit further exploration for diagnostic or prognostic use.
View Article and Find Full Text PDFRNA editing is a post-transcriptional modification, which can provide tissue-specific functions not encoded in DNA. Adenosine-to-inosine is the predominant editing event and, along with cytosine-to-uracil changes, constitutes canonical editing. The rest is non-canonical editing.
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- - Autism spectrum disorder (ASD) affects about 1% of the global population, but research is limited in the Vietnamese community; this study explores its genetic factors through whole exome sequencing of 100 affected children and their parents.
- - The study identified 18 unique genetic variants linked to ASD, including both newly discovered variants and previously recognized risk genes, especially noting a high prevalence of X-linked variants found only in affected males.
- - This research enhances understanding of the genetic diversity of ASD and highlights specific genes potentially associated with the disorder, marking the first detailed examination of the genetic landscape of ASD in Vietnamese children.
Article Synopsis
- The study investigates the role of fusion transcripts in the human cortex, identifying 1305 unique fusion events from 59 brain samples and 329 individual cells, focusing on both neurons and astrocytes.
- Most fusion transcripts in the cortex are intra-chromosomal (85%), while those in neurons and astrocytes are mainly inter-chromosomal (80%), with neurons showing significantly more fusions than astrocytes.
- There is an increase in fusion transcripts with age, suggesting contributions to brain plasticity, and differences in transcript profiles between fetal and adult brains indicate varying functions related to neural activity.
Article Synopsis
- The study investigates the role of a specific group of microRNAs, known as the miR-379/miR-656 cluster (C14MC), in oligodendrogliomas (a type of brain tumor), highlighting its previously unexplored clustered effects.
- Researchers found that most miRNAs in this cluster are significantly downregulated in oligodendrogliomas, which is supported by data from The Cancer Genome Atlas.
- The C14MC cluster appears to be regulated by the transcription factor MEF2 and involves epigenetic mechanisms, suggesting its potential role as a tumor suppressor and relevance for developing new cancer therapies.
Article Synopsis
- Clustered miRNAs, particularly from the miR-379/miR-656 cluster (C14MC), are downregulated in diffuse gliomas, correlating with higher tumor grades, suggesting their role in early glioma development.* -
- Analysis shows that higher levels of C14MC miRNAs improve prognosis for glioblastoma, and two internal regulators within this cluster were identified that can induce apoptosis in glioblastoma cells.* -
- Enhanced expression of miR-134 and miR-485-5p in glioblastoma cells reduced cell invasion and proliferation, highlighting their potential as tumor suppressors and possible therapeutic targets.*
Editing in microRNAs, particularly in seed can significantly alter the choice of their target genes. We show that out of 13 different human tissues, different regions of brain showed higher adenosine to inosine (A-to-I) editing in mature miRNAs. These events were enriched in seed sequence (73.
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- Somatic variations in DNA can lead to differences in cell behavior, occurring in both healthy and diseased states.
- A study using exome sequencing found that the normal human brain has about 0.48% somatic variations, with 64% potentially causing non-synonymous changes, mainly G:C>T:A transversions, especially in the frontal cortex.
- The research also noted higher oxidative stress markers in the frontal cortex compared to the corpus callosum, suggesting oxidative stress could play a role in these somatic variations and influence axon guidance-related genes.
Background: Glaucoma is the largest cause of irreversible blindness affecting more than 60 million people globally. The disease is defined as a gradual loss of peripheral vision due to death of Retinal Ganglion Cells (RGC). The RGC death is largely influenced by the rate of aqueous humor production by ciliary processes and its passage through the trabecular meshwork (TM) in the anterior part of the eye.
View Article and Find Full Text PDFRNA editing of miRNAs, especially in the seed region, adds another layer to miRNA mediated gene regulation which can modify its targets, altering cellular signaling involved in important processes such as differentiation. In this study, we have explored the role of miRNA editing in CD4(+) T cell differentiation. CD4(+) T cells are an integral component of the adaptive immune system.
View Article and Find Full Text PDFINK4 locus at chromosome 9p21 has been reported to be associated with primary open angle glaucoma (POAG) and its subtypes along with the associated optic disc parameters across the populations of European, Japanese and African ancestries. The locus encodes three tumor suppressor genes namely CDKN2A, ARF, CDKN2B and a long non-coding RNA CDKN2B-AS1 (also known as ANRIL). Here, we report association study of 34 SNPs from INK4 locus with POAG in a population of Indo-European ancestry from the eastern part of India (350 patients and 354 controls).
View Article and Find Full Text PDFPurpose: Large copy number variations (CNV) can contribute to increased burden for neurodegenerative diseases. In this study, we analyzed the genome-wide burden of large CNVs > 100 kb in primary open angle glaucoma (POAG), a neurodegenerative disease of the eye that is the largest cause of irreversible blindness.
Methods: Genome-wide analysis of CNVs > 100 kb were analyzed in a total of 1720 individuals, including an Indian cohort (347 POAG cases and 345 controls) and a Caucasian cohort (624 cases and 404 controls).
Article Synopsis
- Primary open angle glaucoma (POAG) is a type of eye disease that causes damage to the optic nerve, potentially linked to factors like oxidative stress and mitochondrial problems.
- A study examined the mitochondrial DNA of 101 patients with POAG and 71 healthy controls, finding that patients had a significantly higher mutation rate and unique genetic variations compared to controls.
- Specific mutations were concentrated in genes related to Complex I, which plays a crucial role in energy production and could lead to increased oxidative stress and worsen glaucoma symptoms.
Background: MicroRNAs (miRNAs) are non-uniformly distributed in genomes and ~30% of the miRNAs in the human genome are clustered. In this study we have focused on the imprinted miRNA cluster miR-379/miR-656 on 14q32.31 (hereafter C14) to test their coordinated function.
View Article and Find Full Text PDFHyaluronan (HA) plays a significant role in maintaining aqueous humor outflow in trabecular meshwork, the primary ocular tissue involved in glaucoma. We examined potential association of the single nucleotide polymorphisms (SNPs) of the HA synthesizing gene - hyaluronan synthase 2 (HAS2), hyaluronan binding protein 1 (HABP1) and HA catabolic gene hyaluronidase 3 (HYAL3) in the primary open angle glaucoma (POAG) patients in the Indian population. Thirteen tagged SNPs (6 for HAS2, 3 for HABP1 and 4 for HYAL3) were genotyped in 116 high tension (HTG), 321 non-high tension glaucoma (NHTG) samples and 96 unrelated, age-matched, glaucoma-negative, control samples.
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- Oxidative stress from serum starvation and H2O2 exposure triggers apoptosis in RGC-5 (retinal ganglion cell-5) through the generation of reactive oxygen species (ROS) and activation of apoptotic signals.
- Both conditions led to increased ROS and apoptosis, but distinct differences in nuclear morphology and the JNK1 signaling pathway were observed, indicating different cellular responses.
- Serum starvation resulted in nuclear swelling and higher levels of activated pJNK, while H2O2 exposure inhibited JNK1 activation, suggesting that RGC-5 cells utilize different mechanisms when exposed to these stressors.
Leucine rich repeat kinase 2 (LRRK2) gene defects cause Parkinson's disease (PD). Recently, LRRK2 has also been shown by genome wide association (GWA) studies to be a susceptibility gene for the disease. In India mutations in LRRK2 is a rare cause of PD.
View Article and Find Full Text PDFCopy number variations (CNVs) have provided a dynamic aspect to the apparently static human genome. We have analyzed CNVs larger than 100 kb in 477 healthy individuals from 26 diverse Indian populations of different linguistic, ethnic and geographic backgrounds. These CNVRs were identified using the Affymetrix 50K Xba 240 Array.
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