
Sumit MukherjeeNational Institutes of Health | NIH · National Cancer Institute (NCI): National Institute of Health
Sumit Mukherjee
Doctor of Philosophy
Postdoctoral Research Fellow at Cancer Data Science Lab (CDSL), NCI/NIH
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42
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Introduction
Additional affiliations
November 2021 - October 2022
April 2017 - October 2019
November 2019 - October 2021
Publications
Publications (42)
Summary: Riboswitches are non-coding RNA located in the 5' untranslated regions where they bind a target metabolite used to specify the riboswitch class and control the expression of associated genes. Accurate identification of riboswitches is the first step towards understanding their regulatory and functional roles in the cell. In this paper we d...
Riboswitches are cis-regulatory non-coding genomic segments that control the expression of downstream genes by undergoing conformational change upon ligand binding. We present a comprehensive database of prokaryotic riboswitches that allows the user to search for riboswitches using multiple criteria, extract information about riboswitch location an...
Many human genes are transcribed from both strands and produce sense-antisense gene pairs. Sense-antisense (SAS) chimeric transcripts are produced upon the coalescing of exons/introns from both sense and antisense transcripts of the same gene. SAS chimera was first reported in prostate cancer cells. Subsequently, numerous SAS chimeras have been rep...
Chimeric RNAs are generated by the fusion of the exons or introns of two genes. The generation of chimeric RNAs is important for the functional expansion of cells. Here, we describe the functional implications of chimeric RNAs for generating phenotypic plasticity from an evolutionary perspective.
The standard treatment for melanoma with a BRAF mutation involves Mitogen-Activated Protein Kinase inhibitors (MAPKi), which target the aberrant MAPK signaling pathway. Although patients initially respond well to this therapy, many develop acquired resistance over time. This resistance can be attributed to various altered signaling pathways, includ...
Riboswitches are naturally occurring regulatory segments of RNA molecules that modulate gene expression in response to specific ligand binding. They serve as a molecular ‘switch’ that controls the RNA’s structure and function, typically influencing the synthesis of proteins. Riboswitches are unique because they directly interact with metabolites wi...
Tailoring optimal treatment for individual cancer patients remains a significant challenge. To address this issue, we developed PERCEPTION (PERsonalized Single-Cell Expression-Based Planning for Treatments In ONcology), a precision oncology computational pipeline. Our approach uses publicly available matched bulk and single-cell (sc) expression pro...
The primary therapy for melanoma with a BRAF mutation involves Mitogen-Activated Protein Kinase inhibitors (MAPKi), targeting the dysregulated MAPK signaling pathway. Despite the initial response, many patients often develop acquired resistance. Resistance to MAPKi could be linked to various altered signaling pathways, including reactivation of the...
Riboswitches are conserved structural ribonucleic acid (RNA) sensors that are mainly found to regulate a large number of genes/operons in bacteria. Presently, >50 bacterial riboswitch classes have been discovered, but only the thiamine pyrophosphate riboswitch class is detected in a few eukaryotes like fungi, plants and algae. One of the most impor...
The ongoing COVID-19 pandemic caused by SARS-CoV-2 infections has quickly developed into a global public health threat. COVID-19 patients show distinct clinical features, and in some cases, during the severe stage of the condition, the disease severity leads to an acute respiratory disorder. In spite of several pieces of research in this area, the...
Viral infections can modulate the widespread alternations of cellular splicing, favouring viral replication within the host cells by overcoming host immune responses. However, how SARS‐CoV‐2 induces host cell differential splicing and affects the landscape of transcript alternation in severe COVID‐19 infection remains elusive. Understanding the dif...
Fusions of two genes can lead to the generation of chimeric RNAs, which may have a distinct functional role from their original molecules. Chimeric RNAs could encode novel functional proteins or serve as novel long noncoding RNAs (lncRNAs). The appearance of chimeric RNAs in a cell could help to generate new functionality and phenotypic diversity t...
Breast cancer is the second leading cause of morbidity and mortality in women worldwide. Despite advancements in the clinical application of neoadjuvant chemotherapy (NAC), drug resistance remains a major concern hindering treatment efficacy. Thus, identifying the key genes involved in driving NAC resistance and targeting them with known potential...
Soil bacteria respond rapidly to changes in new environmental conditions. For adaptation to the new environment, they could mutate their genome, which impacts the alternation of the functional and regulatory landscape. Sometimes, these genetic and ecological changes may drive the bacterial evolution and sympatric speciation. Although sympatric spec...
Initial clinical trials and surveillance data have shown that the most commonly administered BNT162b2 COVID-19 mRNA vaccine is effective and safe. However, several cases of mRNA vaccine-induced mild to moderate adverse events were recently reported. Here, we report a rare case of myositis after injection of the first dose of BNT162b2 COVID-19 mRNA...
Fusions of two different genes could lead to the production of chimeric RNAs, which could be translated into novel fusion (or chimeric) proteins. Fusion proteins often act as oncoproteins and drive cancer development, particularly in leukemia and lymphomas. Fusion proteins modify the existing protein-protein interaction (PPI) networks, which could...
During advanced HIV infection, Human Cytomegalovirus (HCMV) has been proven to produce devitalizing end-organ diseases (EOD). The interactive coexistence of HIV and HCMV has been reported by many researchers and has been suggested to be linked with a more aggressive disease state. This study has been designed to bring forward an assessment of the c...
In cancers and other complex diseases, the fusion of two genes can lead to the production of chimeric RNAs, which are associated with disease development. Several recurrent chimeric RNAs are expressed in different cancers and are thus used for clinical cancer diagnosis. Rheumatoid arthritis (RA) is an immune-mediated joint disorder resulting in syn...
Novel pharmaceutical compositions comprising immunogenic peptide and method of using these compositions for immunomodulation, specifically, in prevention and treatment of infections by SARS-CoV-2 virus.
Several recent studies have demonstrated that low plasma 25(OH) vitamin D levels are associated with the risk of COVID-19 infection. The primary source of vitamin D production in humans is environmental UV radiation. In many viral respiratory diseases, peak infection rates are observed during winter due to reduced UV exposure and low temperatures....
Gene fusions can give rise to somatic alterations in cancers. Fusion genes have the potential to create chimeric RNAs, which can generate the phenotypic diversity of cancer cells, and could be associated with novel molecular functions related to cancer cell survival and proliferation. The expression of chimeric RNAs in cancer cells might impact div...
Circulating animal coronaviruses occasionally infect humans. The SARS‐CoV‐2 is responsible for the current worldwide outbreak of COVID‐19 that has resulted in 2 112 844 deaths as of late January 2021. We compared genetic code preferences in 496 viruses, including 34 coronaviruses and 242 corresponding hosts, to uncover patterns that distinguish sin...
The recently emerged SARS-CoV-2 virus is responsible for the ongoing COVID-19 pandemic that has rapidly developed into a global public health threat. Patients severely affected with COVID-19 present distinct clinical features, including acute respiratory disorder, neutrophilia, cytokine storm, and sepsis. In addition, multiple pro-inflammatory cyto...
The recent outbreak of COVID-19 has generated an enormous amount of Big Data. To date, the COVID-19 Open Research Dataset (CORD-19), lists ∼130,000 articles from the WHO COVID-19 database, PubMed Central, medRxiv, and bioRxiv, as collected by Semantic Scholar. According to LitCovid (11 August 2020), ∼40,300 COVID19-related articles are currently li...
Human cytomegalovirus has been implicated as a probable cause for the development of hepatic cholestasis among neonates. our study tried to ascertain the exact demographic, biochemical and immunological markers to differentially diagnose patients with HCMV associated intrahepatic and extrahepatic cholestasis and also decipher the phylogenetic varia...
A new coronavirus infection, COVID-19, has recently emerged, and has caused a global pandemic along with an international public health emergency. Currently, no licensed vaccines are available for COVID-19. The identification of immunodominant epitopes for both Band T-cells that induce protective responses in the host is crucial for effective vacci...
Background: Congenital nephrotic syndrome (CNS) is a rare but serious condition which affects neonates and is caused by monogenic defects of glomerular structural proteins or congenital viral infections. Several reports have established a causal relationship between human cytomegalovirus (HCMV) intrauterine infection and CNS, but thorough study ass...
Salmonella enterica serovar typhi is the causative agent of typhoid fever in human. The available vaccine lacks the effectiveness and further overuse of the antibiotics throughout the past decades lead to the emergence of antibiotic-resistant strains. To reduce the spread of antibiotic resistance, it is essential to develop new vaccines. In this st...
Riboswitches are metabolite or ion sensing cis-regulatory elements that regulate the expression of the associated genes involved in biosynthesis or transport of the corresponding metabolite. Among the nearly 40 different classes of riboswitches discovered in bacteria so far, only the TPP riboswitch has also been found in algae, plants, and in fungi...
Riboswitches are cis-regulatory elements that regulate the expression of genes involved in biosynthesis or transport of a ligand that binds to them. Among the nearly 40 classes of riboswitches discovered so far, three are known to regulate the concentration of biologically encoded amino acids glycine, lysine, and glutamine. While some comparative g...
Gross phylogenomic distribution of lysine riboswitches in Firmicutes.
The length of the red bars in the outer arc of the figure is correlated with the number of lysine riboswitches found in the corresponding species. This number is specified at the top of the bar.
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Generalized model of operon formation and death and its relevance to regulation by lysine riboswitches.
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SMART-BLAST results showing the strong similarity between the lysW gene of S. oneidensis and nhaC genes of other species that belong to the same clade.
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Details of genomes where lysine riboswitches are present, the locations of the riboswitches in the genomic sequences and the corresponding gene/operon information.
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COGs used for the construction of the phylogenetic tree.
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Riboswitches are metabolite-sensing non-coding RNA located in the 5’ untranslated regions of bacteria and controlling gene expression of downstream genes. Their ability to specifically bind metabolites and catalyze reactions lends support to the RNA world hypothesis. Lysine-riboswitch is involved in de novo lysine synthesis in bacteria and contribu...