Arun Kumar’s research while affiliated with Anugrah Narayan College and other places

Human metapneumovirus (HMPV) is a pre-existing negative sense RNA virus of the family Paramyxoviridae, manifesting lower respiratory tract infections in children and adults above the age of 65 years. It replicates in a gradient manner similar to other paramyxovirus and spreads through droplets (released during cough or sneeze) or direct contact with contaminated surfaces. This virus and its history of infections show a characteristic curve with time increasing periodically during the winter, like other respiratory infections such as influenza.

In a recent multicentric, double-blinded, randomized, placebo-controlled trial by Liu et al., involving 328 subjects aged 20–70 years with type 2 diabetes for ~ 6 years and with body mass index >25, dapagliflozin (10 mg/day or placebo) with calorie restriction resulted in a significantly higher rate of remission of diabetes compared with calorie restriction alone. The main objectives evaluated are diabetes remission (characterized as glycated hemoglobin <6.5% and fasting plasma glucose <126 mg/dL without the use of any antidiabetic medications for a minimum of 2 months) while the secondary objectives are variations in body weight, waist size, body fat percentage, blood pressure, glucose levels, and serum lipid levels after 12 months. Dapagliflozin, sold under the brand names Farxiga (US) and Forxiga (EU), is a hypoglycemia medication used to treat type 2 diabetes. Developed by Bristol-Myers Squibb in partnership with AstraZeneca, it is on the World Health Organization’s List of Essential Medicines for diabetes management. Dapagliflozin is a sodium-glucose cotransporter 2 (SGLT2) inhibitor. It blocks SGLT2 in the proximal renal tubules, reducing the reabsorption of filtered glucose. This increases urinary glucose excretion, lowering blood glucose levels. Dapagliflozin also promotes osmotic diuresis and modest weight loss, providing metabolic benefits for patients with type 2 diabetes. Therefore, from this elegant study by Liu et al., we may conclude that this combination of dapagliflozin and calorie restriction led to substantial improvements in systolic blood pressure, body fat percentage, serum triglycerides, and high-density lipoprotein cholesterol levels, suggesting that the integration of dapagliflozin with a structured calorie restriction regimen is both effective and feasible for achieving remission in early-stage type 2 diabetes. We must, however, be aware of the key potential side effects of SGLT2 inhibitors, which involve genital mycotic infections (e.g., yeast infections), Urinary tract infections, Dehydration and volume depletion, Diabetic ketoacidosis, and acute kidney injury. Careful monitoring and patient education are important when prescribing SGLT2 inhibitors. Adjusting dosage, managing hydration, and maintaining close follow-up can help mitigate these adverse effects.

Optical genome mapping (OGM) is an advanced technology that delivers a distinct view of genome structure. It presents numerous benefits compared to conventional sequencing techniques, as well as karyotyping in identifying large-scale structural variations (SVs). SVs refer to significant alterations in the structure of a genome that go beyond the changes of individual nucleotides. These variations can have substantial effects on gene function and are linked to various genetic diseases and disorders. There are several types of SVs, including copy number variations, such as duplications or deletions, translocations, inversions, fusions, and complex rearrangements. OGM has evolved as an innovative technology that offers high-resolution insights into genomic structures. Unlike conventional sequencing techniques such as next-generation sequencing, which concentrate on decoding short DNA segments, OGM allows for the direct visualization of long DNA strands, delivering a comprehensive, large-scale perspective of the genome’s organization. This capability makes it an effective tool for detecting SVs, which may be overlooked by other techniques. Applications of OGM are mostly in cancer genomics to detect chromosomal rearrangements and decode rare genetic disorders. OGM can also be applied in plant science, where large-scale SVs may contribute to traits such as disease. In recent years, a surge in OGM analysis has been witnessed, primarily due to the higher resolution in detecting SVs. Further, with longer reads, OGM helps in the discovery of complex and rare genomic variations.8 OGM protocol employs a paramagnetic disk designed to capture DNA during wash steps, which helps to minimize the shearing forces. Consequently, the resulting DNA fragments range from approximately 150 kilobases (kbp) to megabases (Mbp) in length, which is around 5–10 times longer than the average fragment size obtained through conventional DNA isolation techniques, making them ideal for OGM. To summarize, OGM serves as a robust technology that facilitates the direct observation of extensive SVs within the genome, offering essential insights for genomic research, clinical diagnostics, and the advancement of personalized medicine.

DNA that is found outside the main chromosomes in a cell's nucleus is known as extrachromosomal DNA. This type of DNA is not part of the standard 23 pairs of chromosomes in humans and instead exists as standalone circular or linear DNA structures. Unlike bacterial plasmids, extrachromosomal DNA in human cells contains important genetic material and holds particular significance in cancer cells. Critical characteristics of ecDNA in Cancer is that they frequently harbour amplified versions of oncogenes such as MYC, EGFR, and CCND1. These oncogenes propel the growth and survival of tumors. Cancer cells utilize ecDNA to generate multiple copies of these oncogenes, amplifying their expression without requiring alterations to the chromosomal structure. This amplification grants the cancer cells a competitive edge in growth. ecDNA plays a crucial role in the advancement and growth of cancer, as it amplifies oncogenes, genetic diversity, and resistance to treatments. Its adaptable and ever-changing characteristics empower cancer cells to adjust to external influences such as medication. Gaining insights into ecDNA's operations and impacts could lead to new possibilities for diagnosing and treating cancer, as well as developing therapies aimed at this distinct DNA structure.

DNA that is found outside the main chromosomes in a cell's nucleus is known as extrachromosomal DNA. This type of DNA is not part of the standard 23 pairs of chromosomes in humans and instead exists as standalone circular or linear DNA structures. Unlike bacterial plasmids, extrachromosomal DNA in human cells contains important genetic material and holds particular significance in cancer cells. Critical characteristics of ecDNA in Cancer is that they frequently harbour amplified versions of oncogenes such as MYC, EGFR, and CCND1. These oncogenes propel the growth and survival of tumors. Cancer cells utilize ecDNA to generate multiple copies of these oncogenes, amplifying their expression without requiring alterations to the chromosomal structure. This amplification grants the cancer cells a competitive edge in growth. ecDNA plays a crucial role in the advancement and growth of cancer, as it amplifies oncogenes, genetic diversity, and resistance to treatments. Its adaptable and ever-changing characteristics empower cancer cells to adjust to external influences such as medication. Gaining insights into ecDNA's operations and impacts could lead to new possibilities for diagnosing and treating cancer, as well as developing therapies aimed at this distinct DNA structure.

Enhancer elements are specific DNA sequences that play a crucial role in regulating gene expression. Located upstream or downstream in the genomic context, enhancers enhance the transcription of linked genes. This is achieved by providing binding sites for transcription factors and other proteins, acting as a nucleation point that promotes the assembly of the transcriptional machinery. What makes enhancers unique is that located even thousands of base pairs away, they can exert their function. They can act over long distances, looping to interact with the promoter region of their target genes. Enhancers are often involved in cell type-specific gene expression as different cells express different sets of genes by activating and repressing cell type-specific enhancers. Cancer cells seem to co-opt this mechanism and hijack it for their own survival. In this process, an aberrant enhancer element activates the transcription of oncogenes (genes that have the potential to cause cancer) due to some alterations in genomic structure or regulatory elements that happen in cancer, contributing to tumorigenesis and cancer progression. Enhancer hijacking often occurs through complex genomic rearrangements such as chromosomal translocations and other structural rearrangements such as deletions or amplifications.8 These alterations can bring a usually distant, far-located enhancer into proximity with an oncogene, leading to its inappropriate activation. This is often seen in various cancers, including leukemias and solid tumors. Enhancer hijacking and its effects on gene regulation in cancer are frequently studied using methods such as RNA sequencing, chromatin conformation capture, and CRISPR-Cas9. Finding an enhancer hijacking event may be used to inform treatment choices, especially in precision medicine settings, and may also function as a biomarker for particular cancer types.

Gallbladder cancer (GBC) starts in the epithelial tissue (lining of the bile duct and gallbladder). It is a type of aggressive cancer called adenocarcinoma that can spread to other tissues. Among all cases of biliary tract cancer, 50% is from GBC. It is a deadly cancer with a survival rate of 17.6% between 2007 and 2013. GBC is rarely found in the Western world, but it is commonly found in South Asia. In Southeast Asian countries, GBC plays a significant role in cancer-related morbidity and mortality. GBC incidence exhibits marked regional variability, a rare condition in the western population but having a higher frequency in India, especially the Indo-Gangetic belt and some northeast districts excluding Nagaland. This might be attributed to the differences in environmental factors and genetic predisposition modulating carcinogenesis. In GBC, only 10% of cases are identified in the early stages. The low rate of early detection is due to the lack of screening techniques and the aggressive characteristics of the tumor. Various risk factors are associated with GBC, for example, chronic cholecystitis with or without gallstones, obesity, exposure to heavy metals such as lead and arsenic, bacterial infection, congenital biliary cysts, and abnormal pancreaticobiliary duct junction. The risk factors can cause chronic gallbladder mucosa irritation, leading to dysplasia and neoplasia. GBC can form metaplasia to dysplasia in a time span of 5–15 years, then to carcinoma in situ, and finally to invasive cancer. Dysbiosis is responsible for various diseases, including cancer. Multiple triggers can cause dysbiosis, for example, environmental changes, inflammation, infection, medications, dietary changes, or genetic predisposition. Various researches show that Helicobacter pylori, human papillomavirus, Hepatitis B virus, and Hepatitis C virus microbial species can cause cancer. They are the major species responsible for 90% of infection-associated cancers. Various studies demonstrate that the strains of Salmonella and Helicobacter colonize are linked to developing GBC. While the mechanisms linking gut microbiota to GBC are not fully understood, several studies have suggested a potential association. According to a study, certain gut microbiomes, such as Fusobacterium nucleatum, found glut in GBC tissues, compared to adjacent normal tissues. By evaluating gut microbiome dysbiosis, we can see the potential link between gut microbiome dysbiosis and GBC; it may provide valuable insights into the development and progression of GBC. It could lead to the identification of new diagnostic markers and the development of novel therapeutic strategies. In GBC, the evaluation of gut microbiome dysbiosis (involving evaluating the composition, diversity, and functional capacity of the gut microbiome in patients) has emerged as a promising method for understanding the molecular mechanisms and identifying biomarkers for early prevention and detection of GBC and also investigating the possibility of any link between the gut microbiome and host immune response. In conclusion, evaluating gut microbiome dysbiosis in GBC is a promising direction for identifying potential early detection and prevention biomarkers. Additional investigation is therefore needed to determine the role of gut microbiome dysbiosis in the development and progression of GBC and to identify reliable biomarkers for clinical use.

Enhancer elements are specific DNA sequences that play a crucial role in regulating gene expression. Located upstream or downstream in the genomic context, enhancers enhance the transcription of linked genes. This is achieved by providing binding sites for transcription factors and other proteins, acting as a nucleation point that promotes the assembly of the transcriptional machinery. What makes enhancers unique is that located even thousands of base pairs away, they can exert their function. They can act over long distances, looping to interact with the promoter region of their target genes. Enhancers are often involved in cell type-specific gene expression as different cells express different sets of genes by activating and repressing cell type-specific enhancers. Cancer cells seem to co-opt this mechanism and hijack it for their own survival. In this process, an aberrant enhancer element activates the transcription of oncogenes (genes that have the potential to cause cancer) due to some alterations in genomic structure or regulatory elements that happen in cancer, contributing to tumorigenesis and cancer progression. Enhancer hijacking often occurs through complex genomic rearrangements such as chromosomal translocations and other structural rearrangements such as deletions or amplifications.8 These alterations can bring a usually distant, far-located enhancer into proximity with an oncogene, leading to its inappropriate activation. This is often seen in various cancers, including leukemias and solid tumors. Enhancer hijacking and its effects on gene regulation in cancer are frequently studied using methods such as RNA sequencing, chromatin conformation capture, and CRISPR-Cas9. Finding an enhancer hijacking event may be used to inform treatment choices, especially in precision medicine settings, and may also function as a biomarker for particular cancer types.

Gallbladder cancer (GBC) starts in the epithelial tissue (lining of the bile duct and gallbladder). It is a type of aggressive cancer called adenocarcinoma that can spread to other tissues. Among all cases of biliary tract cancer, 50% is from GBC. It is a deadly cancer with a survival rate of 17.6% between 2007 and 2013. GBC is rarely found in the Western world, but it is commonly found in South Asia. In Southeast Asian countries, GBC plays a significant role in cancer-related morbidity and mortality. GBC incidence exhibits marked regional variability, a rare condition in the western population but having a higher frequency in India, especially the Indo-Gangetic belt and some northeast districts excluding Nagaland. This might be attributed to the differences in environmental factors and genetic predisposition modulating carcinogenesis. In GBC, only 10% of cases are identified in the early stages. The low rate of early detection is due to the lack of screening techniques and the aggressive characteristics of the tumor. Various risk factors are associated with GBC, for example, chronic cholecystitis with or without gallstones, obesity, exposure to heavy metals such as lead and arsenic, bacterial infection, congenital biliary cysts, and abnormal pancreaticobiliary duct junction. The risk factors can cause chronic gallbladder mucosa irritation, leading to dysplasia and neoplasia. GBC can form metaplasia to dysplasia in a time span of 5–15 years, then to carcinoma in situ, and finally to invasive cancer. Dysbiosis is responsible for various diseases, including cancer. Multiple triggers can cause dysbiosis, for example, environmental changes, inflammation, infection, medications, dietary changes, or genetic predisposition. Various researches show that Helicobacter pylori, human papillomavirus, Hepatitis B virus, and Hepatitis C virus microbial species can cause cancer. They are the major species responsible for 90% of infection-associated cancers. Various studies demonstrate that the strains of Salmonella and Helicobacter colonize are linked to developing GBC. While the mechanisms linking gut microbiota to GBC are not fully understood, several studies have suggested a potential association. According to a study, certain gut microbiomes, such as Fusobacterium nucleatum, found glut in GBC tissues, compared to adjacent normal tissues. By evaluating gut microbiome dysbiosis, we can see the potential link between gut microbiome dysbiosis and GBC; it may provide valuable insights into the development and progression of GBC. It could lead to the identification of new diagnostic markers and the development of novel therapeutic strategies. In GBC, the evaluation of gut microbiome dysbiosis (involving evaluating the composition, diversity, and functional capacity of the gut microbiome in patients) has emerged as a promising method for understanding the molecular mechanisms and identifying biomarkers for early prevention and detection of GBC and also investigating the possibility of any link between the gut microbiome and host immune response. In conclusion, evaluating gut microbiome dysbiosis in GBC is a promising direction for identifying potential early detection and prevention biomarkers. Additional investigation is therefore needed to determine the role of gut microbiome dysbiosis in the development and progression of GBC and to identify reliable biomarkers for clinical use.

When it comes to longevity, everyone wants to live for eternity. Longevity research has often led scientists to dark alleys with several candidate molecules responsible for aging. Pioneering genetic studies on model organisms like Caenorhabditis elegans and Drosophila melanogaster discovered the most well-conserved longevity pathways, mainly caloric restriction and the insulin/insulin-like growth factor 1signaling pathways. Apart from these complex molecular circuitries that drive longevity, a recent study published by Zipple et al. (Proceedings of the National Academy of Sciences, 2024) showed that the relationship between mother and grandmother with the child may determine why some animals and humans live longer than expected for their size. Animals that spend more time with their mothers during early life end up living longer but with reduced capacity to produce offspring. This exciting piece of research has far more consequences than just these findings. It implies the importance of the mother in one’s life and the role of parental care in providing longevity and reproductive success.