SKping cell cycle regulation: role of ubiquitin ligase SKP2 in hematological malignancies

SKP2 (S-phase kinase-associated protein 2) is a member of the F-box family of substrate-recognition subunits in the SCF ubiquitin-protein ligase complexes. It is associated with ubiquitin-mediated degradation in the mammalian cell cycle components and other target proteins involved in cell cycle progression, signal transduction, and transcription. Being an oncogene in solid tumors and hematological malignancies, it is frequently associated with drug resistance and poor disease outcomes. In the current review, we discussed the novel role of SKP2 in different hematological malignancies. Further, we performed a limited in-silico analysis to establish the involvement of SKP2 in a few publicly available cancer datasets. Interestingly, our study identified Skp2 expression to be altered in a cancer-specific manner. While it was found to be overexpressed in several cancer types, few cancer showed a down-regulation in SKP2. Our review provides evidence for developing novel SKP2 inhibitors in hematological malignancies. We also investigated the effect of SKP2 status on survival and disease progression. In addition, the role of miRNA and its associated families in regulating Skp2 expression was explored. Subsequently, we predicted common miRNAs against Skp2 genes by using miRNA-predication tools. Finally, we discussed current approaches and future prospective approaches to target the Skp2 gene by using different drugs and miRNA-based therapeutics applications in translational research.

Alterations of the expression of TET2 and DNA 5-hmC predict poor prognosis in Myelodysplastic Neoplasms

BACKGROUND

Myelodysplastic Neoplasms (MDS) are clonal stem cell disorders characterized by ineffective hematopoiesis and progression to acute myeloid leukemia, myelodysplasia-related (AML-MR). A major mechanism of pathogenesis of MDS is the aberration of the epigenetic landscape of the hematopoietic stem cells and/or progenitor cells, especially DNA cytosine methylation, and demethylation. Data on TET2, the predominant DNA demethylator of the hematopoietic system, is limited, particularly in the MDS patients from India, whose biology may differ since these patients present at a relatively younger age. We studied the expression and the variants of TET2 in Indian MDS and AML-MR patients and their effects on 5-hydroxymethyl cytosine (5-hmC, a product of TET2 catalysis) and on the prognosis of MDS patients.

RESULTS

Of the 42 MDS patients, cytogenetics was available for 31 sub-categorized according to the Revised International Prognostic Scoring System (IPSS-R). Their age resembled that of the previous studies from India. Bone marrow nucleated cells (BMNCs) were also obtained from 13 patients with AML-MR, 26 patients with de-novo AML, and 11 subjects with morphologically normal bone marrow. The patients had a significantly lower TET2 expression which was more pronounced in AML-MR and the IPSS-R higher-risk MDS categories. The 5-hmC levels in higher-risk MDS and AML-MR correlated with TET2 expression, suggesting a possible mechanistic role in the loss of TET2 expression. The findings on TET2 and 5-hmC were also confirmed at the tissue level using immunohistochemistry. Pathogenic variants of TET2 were found in 7 of 24 patient samples (29%), spanning across the IPSS-R prognostic categories. One of the variants - H1778R - was found to affect local and global TET2 structure when studied using structural predictions and molecular dynamics simulations. Thus, it is plausible that some pathogenic variants in TET2 can compromise the structure of TET2 and hence in the formation of 5-hmC.

CONCLUSIONS

IPSS-R higher-risk MDS categories and AML-MR showed a reduction in TET2 expression, which was not apparent in lower-risk MDS. DNA 5-hmC levels followed a similar pattern. Overall, a decreased TET2 expression and a low DNA 5-hmC level are predictors of advanced disease and adverse outcome in MDS in the population studied, i.e., MDS patients from India.

Monosodium Glutamate Perturbs Human Trophoblast Invasion and Differentiation through a Reactive Oxygen Species-Mediated Pathway: An In-Vitro Assessment

The overproduction of reactive oxygen species (ROS) has been associated with various human diseases. ROS exert a multitude of biological effects with both physiological and pathological consequences. Monosodium glutamate (MSG), a sodium salt of the natural amino acid glutamate, is a flavor-enhancing food additive, which is widely used in Asian cuisine and is an ingredient that brings out the “umami” meat flavor. MSG consumption in rats is associated with ROS generation. Owing to its consumption as part of the fast-food culture and concerns about its possible effects on pregnancy, we aimed to study the impact of MSG on placental trophoblast cells. MSG exposure influenced trophoblast invasion and differentiation, two of the most critical functions during placentation through enhanced production of ROS. Similar findings were also observed on MSG-treated placental explants, as confirmed by elevated Nrf2 levels. Ultrastructural studies revealed signs of subcellular injury by MSG exposure. Mechanistically, MSG-induced oxidative stress with endoplasmic reticulum stress pathways involving Xbp1s and IRE1α was observed. The effect of MSG through an increased ROS production indicates that its long-term exposure might have adverse health effect by compromising key trophoblast functions.

New immune horizons in therapeutics and diagnostic approaches to Preeclampsia

Hypertensive disorders of pregnancy (HDP) are one of the commonest maladies, affecting 5%-10% of pregnancies worldwide. The American College of Obstetricians and Gynecologists (ACOG) identifies four categories of HDP, namely gestational hypertension (GH), Preeclampsia (PE), chronic hypertension (CH), and CH with superimposed PE. PE is a multisystem, heterogeneous disorder that encompasses 2%-8% of all pregnancy-related complications, contributing to about 9% to 26% of maternal deaths in low-income countries and 16% in high-income countries. These translate to 50 000 maternal deaths and over 500 000 fetal deaths worldwide, therefore demanding high priority in understanding clinical presentation, screening, diagnostic criteria, and effective management. PE is accompanied by uteroplacental insufficiency leading to vascular and metabolic changes, vasoconstriction, and end-organ ischemia. PE is diagnosed after 20 weeks of pregnancy in women who were previously normotensive or hypertensive. Besides shallow trophoblast invasion and inadequate remodeling of uterine arteries, dysregulation of the nonimmune system has been the focal point in PE. This results from aberrant immune system activation and imbalanced differentiation of T cells. Further, a failure of tolerance toward the semi-allogenic fetus results due to altered distribution of Tregs such as CD4+FoxP3+ or CD4+CD25+CD127(low) FoxP3+ cells, thereby creating a cytotoxic environment by suboptimal production of immunosuppressive cytokines like IL-10, IL-4, and IL-13. Also, intracellular production of complement protein C5a may result in decreased FoxP3+ regulatory T cells. With immune system dysfunction as a major driver in PE pathogenesis, it is logical that therapeutic targeting of components of the immune system with pharmacologic agents like anti-inflammatory and immune-modulating molecules are either being used or under clinical trial. Cholesterol synthesis inhibitors like Pravastatin may improve placental perfusion in PE, while Eculizumab (monoclonal antibody inhibiting C5) and small molecular inhibitor of C5a, Zilucoplan are under investigation. Monoclonal antibody against IL-17(Secukinumab) has been proposed to alter the Th imbalance in PE. Autologous Treg therapy and immune checkpoint inhibitors like anti-CTLA-4 are emerging as new candidates in immune horizons for PE management in the future.

Loss of TET2 with reduced genomic 5-hmC is associated with adverse-risk AML

While considerable information exists on the ten-eleven translocation 2 (TET2) mutational landscape in AML, the information on TET2 expression is limiting. So, we aimed to study the TET2 expression at mRNA and protein levels in AML patients compared to healthy controls. To achieve this, we recruited 70 non-M3, de novo AML patients and 20 healthy controls. The expression of TET2 was checked at mRNA and protein levels by qPCR and ELISA respectively and the TET activity was checked by the 5-hmC assay. TET2 mRNA expression was correlated with clinicopathological parameters and overall survival. We found a significant downregulation of TET2 mRNA and protein and significantly lower DNA 5-hmC levels in AML patients compared to controls. TET2 downregulation was more in patients with high blast counts and patients of the adverse-risk ELN category. We also found a significant upregulation of DNMT1 and DNMT3a suggesting a hypermethylation phenotype in de novo AML.

Malaria vaccine: The tale of terror, triumph, tyranny, and trust

Malaria is an endemic disease in a true sense. It is an acute febrile disease caused due to the parasite Plasmodium. However, unlike COVID-19, it failed to raise an international concern or gain the scientific limelight. Most of the 200 million globally affected by malaria, half of them are from Africa. Four of the nations, Nigeria (25%), the Democratic Republic of the Congo (11%), Mozambique (5%), and Uganda (4%), account for half of the world’s malaria burden and is the leading cause of illness and death. In 2019, an estimated 5–6 million people died of malaria – most of them are young children in sub-Saharan Africa. Many of the countries affected by malaria have the lowest economic status. In the malaria-endemic region, the most vulnerable groups are young children and pregnant women. The costs of malaria are enormous to individuals, families, communities, societies, and nations. After a struggle for three decades, the much-awaited malaria vaccine, RTS, S (brand name Mosquirix), was finally launched; but it came with its controversies and allegations. This review explored the different angles of this disease, the vaccine development, and the emerging debates.

The metabolic addiction of cancer stem cells

Cancer stem cells (CSC) are the minor population of cancer originating cells that have the capacity of self-renewal, differentiation, and tumorigenicity (when transplanted into an immunocompromised animal). These low-copy number cell populations are believed to be resistant to conventional chemo and radiotherapy. It was reported that metabolic adaptation of these elusive cell populations is to a large extent responsible for their survival and distant metastasis. Warburg effect is a hallmark of most cancer in which the cancer cells prefer to metabolize glucose anaerobically, even under normoxic conditions. Warburg's aerobic glycolysis produces ATP efficiently promoting cell proliferation by reprogramming metabolism to increase glucose uptake and stimulating lactate production. This metabolic adaptation also seems to contribute to chemoresistance and immune evasion, a prerequisite for cancer cell survival and proliferation. Though we know a lot about metabolic fine-tuning in cancer, what is still in shadow is the identity of upstream regulators that orchestrates this process. Epigenetic modification of key metabolic enzymes seems to play a decisive role in this. By altering the metabolic flux, cancer cells polarize the biochemical reactions to selectively generate "onco-metabolites" that provide an added advantage for cell proliferation and survival. In this review, we explored the metabolic-epigenetic circuity in relation to cancer growth and proliferation and establish the fact how cancer cells may be addicted to specific metabolic pathways to meet their needs. Interestingly, even the immune system is re-calibrated to adapt to this altered scenario. Knowing the details is crucial for selective targeting of cancer stem cells by choking the rate-limiting stems and crucial branch points, preventing the formation of onco-metabolites.

Oncometabolite profiling identifying estrogen-responsive genes in breast cancer

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Background: Metabolomic profiling in breast cancer (BC) is an emerging avenue to identify clinically actionable biomarkers as well as targeted therapeutics. Altered metabolic pathways has been identified in BC. Studies have discovered an association between oncometabolite levels, DNA methylation and other epigenetic changes, with prognosis in BC. Changes in cancer cells metabolism may thus indicate disease aggressiveness and its response to therapy. Methods: An in-silico based oncometabolite profiling was performed in ER +ve and TNBC (ER-/PR-/Her2-) data sets using NCBO-GEO tools. . Inclusion criteria included studies on Human subjects, having at least 2 ER+ PR+ and TNBC samples. After manually filtering the top 250 most significant differentially expressed genes in all studies, those with clear metabolic functions as per the GO category were pooled together, which included both the overexpressed and downregulated genes. 15 unique genes were cherry-picked and taken for further analysis out of which six were downregulated, and nine were upregulated. The identified genes harbouring ERE in their upstream 1000bp region were further analysed to identify CpG islands. In addition, we also performed a Bio-Reader based Text Mining Tool to streamline Pubmed abstracts with the positive strings “oncometabolite,” “breast cancer,” “stem cells” “survival”. We also queried against negative strings “sequencing,” “mutations,” “infections,” “drug-resistance” to develop a list of highly focused abstracts. Results: Novel estrogen-regulated oncometabolite that were differentially expressed in ER+ve vs TNBC BC were identified. Further, we reinforced the fact that 4 out of 7 targets had upstream CpG islands within 1000bp n Both upregulated AMY2A, B3GNT5, PNPLA3 and 2HG whereas and downregulated genes in PLCD4, FBP1 and CA12 along with one target identified from the literature were selectively expressed in ER+ve BC. Conclusions: Our study has identified estrogen-responsive metabolic genes involved in BC. We are currently validating our results in a wet lab setup from breast cancer patient samples. Validated targets may be tested for therapeutic intervention in BC.

The problem with APC and open access: Hurdles in publishing practice

Publish or perish has been the mantra for researchers and scientists. It is an aphorism describing the sheer pressure to publish academic work in order to succeed in an academic career. After all what good one has done if they didn’t even publish an article in a good journal. A good journal is the one with the highest impact factor. The Impact Factor is calculated by dividing the number of citations in the JCR year by the total number of articles published in the two previous years. An Impact Factor of 1.0 means that, on average, the articles published 1 or 2 years ago have been cited one time. While the impact factor metric is very unreliable to judge the quality of the journal or published paper, as numerous unfair and dubious means were frequently adopted to boost the journal impactfactors. But still, the race is on with the psychology to publish in higher impact journals as it is often associated with greater academic rewards. What emerged out of this race is that journals and the publishing houses ramped the article processing charges (APC) to an astronomical level, which was unprecedented before. APC for a few BMC, MDPI, SAGE DOVE press journals on an average exceed 2000 USD, equivalent to few months salary of the Principle Investigtor. Journal publishing house often justifies high APC citing reasons for “open access” such that they are freely available for a wider range of readers free of cost or to meet their operational cost. Although apparently sound like a great initiative, a little more investigation reveals an underlying agenda, which is far from true when we find that a majority of this same. Publishing house ferociously opposes Sci-hub like 3d party platforms which genuinely gives free access to all readers worldwide. Recently, three major academic publishers Elsevier, Wiley, and American Chemical Society filed a copyright infringement suit in the Delhi High Court, India against “Sci-Hub” and “Libgen” which provide free access to millions of research papers/books. This clearly indicates that their intentions are misaligned with what they say. High APC is a means to just earn larger profit margins. Publishing house does mention a fee waiver for low-income countries but is exploited and abused instead of this as a helping gesture. Scientific research can hardly proceed in solo. It needs infrastructure, trained manpower, logistic support, and high-level coordination. Providing fee waivers for publication to countries that hardly can feed its starving populations makes little sense because either way, these countries are far behind to have material to publish or to engage in any credible research. Instead what is happening is what is called “author swapping” wherein the corresponding or co-corresponding authors are cherry-picked from these improvised nations for APC waiver without them anyway participating in the scientific study. This is surely unethical. Journals are also reported extorting authors who fail to pay the APC. There are other flip sides of APC. High APC skew only those rich and affluent labs/groups who may be able to afford them, something getting away even with mediocre articles while genuine data from less affluent labs may never be able to reach these journals. This trend is growing alarmingly high, filtering out publications only from wealthy labs. Though the scientific community is well aware of this, very little is actually done to prevent this as the nexus runs deep benefiting few who can afford it. Unless this chain is broken, future science may just be determined by those who can afford the high APC to get into the highest impact journals, and not by the quality of science.

The innocence of Omicron: Taking the right decision

Rapidly spreading Omicron (B1.1.529) poses a considerable health risk, despite being labeled as a mild SARS-CoV2 variant. The higher transmissibility, immune evasion properties along blunting the effect of vaccine are some of its unique features, a fact that should not be ignored, no matter how benign it might be. We suggest that our knowledge and experience in dealing with Omicron have been very less and its long-term health consequences are still not studied properly. Under these conditions, we must continue to remain vigilant following all safety measures and avoid down-sizing its impact.

How COVID pandemic may end : Co-existence is the key

It has been 2 years plus that the global pandemic has shadowed every aspect of human life. We have witnessed multiple waves of invasion by the different mutated versions of SARS-CoV-2, with each wave specific predominant symptoms and casualties. At present, we are witnessing the rage of Omicron, another mutated version of the virus, carrying 32 alterations in its spike proteins. What makes Omicron unique is its extremely high transmissibility, spreading like wildfire across the globe, with its footprints in over 90 countries infecting over several million. The high mutational burden of Omicron is perhaps the outcome of the selection pressure that this virus has been encountering while infecting its hosts. Added to that is also the effect of vaccination contributing to the emergence of different variants. What is spectacular is that Omicron is relatively less lethal than the previous variants though it contains many more alterations. This may be pointing toward a scenario of mutational exhaustion as well the status of an enhanced host immune surveillance. Under these conditions, it is conceivable that the virus will run out ofall its maximal capacity to mutate. We must accept the fact that the virus and its variants will keep on coming and time and often they might take an upper hand but over years, we will get used to this and learn ways to coexist.We must adjust our vaccine development pipelines and other risk mitigation tools to evade the risk. This has been the case with the influenza virus and it is likely that SARS-CoV-2 will follow the same. Let’s look at the other examples of this kind. How did other pandemics that affect humankind before has ended? The viruses did not go away completely, the modern H1N1, a descendent of the Spanish flu virus, circulates as H3N2 even today. Humans did not completely develop a herd immunity and knocked it off. That simply did not happen. Rather, the viruses became endemic and we will learn to live together. Both sides will develop safety nets so that none affects the other beyond a point of mutual coexistence. A better infectious agent evolves to ensure the survival of its host so that it can sustain itself without killing it. SARS-CoV-2 seems getting educated along these lines too. SARS-CoV-2 evolution to Omicron is perhaps a step in that direction.

Cell to cell hijacking: Role of membrane nanotubes

Cell to Cell communications is the pivot for life processes. Any event that disrupts this leads to the loss of physiological function, eventually leading to cell death. Evolutionarily, cells developed an elaborate mechanism to undertake this paramount responsibility through cell surface glycocalyx, receptors, integrins, and other recognition molecules. Cells also exchange through local acting soluble mediators as well as through vesicles and exosomes. Recent development in this field led to the identification of a spectacular network of membrane process that seems to be the supremo of all that was known about cellular communications. These are called membrane nanotubes or tunneling nanotubes (TNT). Cellular communication can be subdivided into contact and contactless. The former provides more rapid and molecule transfer as compared to the latter. Tunneling nanotubes (TNTs) are a novel type of contact-based communication. TNTs are straight, thin membrane extensions connecting cells over long distances first reported in PC12 cells in 2004. TNT is believed to form from actin-based membrane protrusion. There are three different models of TNT formation. a>Protrusions from one cell grow and extend until it reaches the other cell, followed by a membrane fusion. b> Membrane protrusions grow from both cells until they meet and establish a connection c> TNT formation by cell dislodgement when cells migrate further apart from each other, and during this movement, TNT is formed. It is possible that all these three models may be operational depending on cell types and context. Tunneling nanotubes (TNT) are dynamic connections between cells, representing a novel route for cell-to-cell communication. TNT was reported in various cell types, like epithelial cells, neuronal cells, mesenchyma cells, and immune cells engaged in intercellular exchanges of molecules, subcellular organelles, and pathogen and viruses transport routes. TNT can extend up to 200 µm in length and about 50 nm to 1500 nm in diameter in macrophages. TNT can be established between similar cell types (homo-TNT) or between one cell type and another ( hetro TNT) and thus may be involved in the initiation and growth of cancer as well as dissemination of cancer cells. TNTs are also assumed to play a role in treatment resistance, e.g., in chemotherapy treatment of cancer. Recently, TNT has been used to hijack mitochondria from healthy cells by the cancer cells as a source of energy. TNT was also reported to transport miRNA and other RNA to the surrounding stroma creating an environment suitable for cancer growth. More research in this discipline is needed to understand the full function of these wonderful nanostructures.

The issues and challenges with cancer biomarkers

A biomarker is a measurable indicator used to distinguish precisely/objectively either normal biological state/pathological condition/response to a specific therapeutic intervention. The use of novel molecular biomarkers within evidence-based medicine may improve the diagnosis/treatment of disease, improve health outcomes, and reduce the disease's socio-economic impact. Presently cancer biomarkers are the backbone of therapy, with greater efficacy and better survival rates. Cancer biomarkers are extensively used to treat cancer and monitor the disease's progress, drug response, relapses, and drug resistance. The highest percent of all biomarkers explored are in the domain of cancer. Extensive research using various methods/tissues is carried out for identifying biomarkers for early detection, which has been mostly unsuccessful. The quantitative/qualitative detection of various biomarkers in different tissues should ideally be done in accordance with qualification rules laid down by the Early Detection Research Network (EDRN), Program for the Assessment of Clinical Cancer Tests (PACCT), and National Academy of Clinical Biochemistry. Many biomarkers are presently under investigation, but lacunae lie in the biomarker's sensitivity and specificity. An ideal biomarker should be quantifiable, reliable, of considerable high/low expression, correlate with the outcome progression, cost-effective, and consistent across gender and ethnic groups. Further, we also highlight that these biomarkers' application remains questionable in childhood malignancies due to the lack of reference values in the pediatric population. The development of a cancer biomarker stands very challenging due to its complexity and sensitivity/resistance to the therapy. In past decades, the cross-talks between molecular pathways have been targeted to study the nature of cancer. To generate sensitive and specific biomarkers representing the pathogenesis of specific cancer, predicting the treatment responses and outcomes would necessitate inclusion of multiple biomarkers.

Unveiling the omicron B.1.1. 529: The variant of concern that is rattling the globe

Most viruses–including SARS-CoV-2, seem to have evolved over time. The lack of stringent proofreading mechanisms makes viral DNA/RNA replication error-prone. When a virus replicates, it sometimes changes a little bit, which is called mutations. Any virus with one or more new mutations can be referred to as a “variant” of the original virus. The last 2 years have witnessed the emergence of a large number of variants. Since the pandemic’s beginning, the SARS-CoV-2 coronavirus has mutated extensively, resulting in the emergence of different variants of the virus. One of these is the delta variant (arising from Pango lineage B.1.617.2) that took the word in a storm this year (February-July). The current a variant of concern is the B.1.1.529 (Omicron) variant reported first from South Africa on November 24, 2021. In recent weeks, infections have been widely reported, along with the increased detection of the B.1.1.529 variant. We reviewed the emergence of the new variant (B1.1.529) and its possible outcomes.

The Perils of the Pandemic and India's Child Victims of Covid-19

Aim: The following paper attempts to trace the impact of Covid-19 on the younger generation, mostly from economically underprivileged sections, by focusing on specific themes such as health, education, vulnerability to abuse, and violence. The paper tries to address how the pandemic has affected various dimensions of the lives of these younger generation-children and adolescents, alongside tracing the measures taken by the government in the fight against the virus. Methods: We curated the information based on credible data as published in leading news media, PMC published peer-reviewed materials Conclusions: The paper concludes with recommendations that a coherent government policy and the active participation of NGOs are needed to address the problem. The children's mental health needs to be dealt with utmost care at home, which will pave the way towards a better future for the younger generation during and after the pandemic.

The science of “smell” and the noble for “hugs:” making “sense?”

David Julius and Ardem Patapoutian were jointly awarded the 2021 Nobel Prize in Physiology and Medicine for their discoveries of receptors for temperature and touch. It was a phenomenal moment for the scientific community, more for the discovery that forms the basic fabric of our everyday life—ever imagined how life would have been without feeling the aroma around? Or even the dangers of accidentally touching a heated object. Dr Julius and Dr Patapoutian, independently discovered key mechanisms of how living organisms sense heat, cold, and touch. The journey started when Dr Julius, at the University of California, San Francisco, used a key ingredient in hot chili peppers to identify a protein in nerve cells that respond to these stimuli. Using capsaicin, the pungent component of chili peppers, he provided fundamental insights into mechanisms of pain. Then using a meticulous cDNA library-based functional screening from sensory neurons to search for the gene(s) that could confer capsaicin sensitivity, Dr Julius identified for the first time a novel ion channel (now called transient receptor potential [TRP] vanilloid 1) belonging to the family of TRP ion channels associated with the pain sensitivity. A painful exercise indeed! While Prof Julius was exploring the oceans and skies to hunt for sensory pain pathways, quite independently, Dr Patapoutian of Scripps Research Institute La Jolla, California, was searching for a similar thing that seemed to bother him equally. How do we sense touches? After all, there are so many emotions packaged in this small five-letter word, touch. The mother’s touch is the first sensation that every single of us always cherishes. Dr Patapoutian research is centered around finding candidate genes in a mechanosensitive cell line that could respond to mechanical stimuli. After a thorough search, the team identified two mechanically-activated ion channels, PIEZO1 and PIEZO2, representing an entirely novel class of mechanical sensors-based ion channels. What is fascinating is the idea that discovery of the smell and touch receptor stretches far beyond just touch and temperature sensations only. Mutations in other TRP channels are involved in neurodegenerative disorders and skeletal dysplasia, while mutations in PIEZO channels help control critical functions such as respiration and blood pressure regulation. So now, the mysterious world surrounding us looks more transparent and clearer. The molecular landscape is defined with precision. We now have a chemical entity behind all these emotions and intuition. The warm hug that makes our day is now millions of ions crisscrossing the ion channels. There is a different side to this too. How will the world look if everything is defined as a chemical entity? Won’t we lose the charm? After all, so much within the subtleness remains charmful when wrapped within the veil of ignorance. Knowing too much about something steals the show.

Fault Lines in India's COVID-19 Management: Lessons Learned and Future Recommendations

With about 0.4–0.5 million COVID cases diagnosed every single day in a row over the past three weeks back in May 2021, India was at the epicenter of the global viral rampage. The catastrophe of this crisis was unprecedented, pushing the health care system to its breaking point. Although significant progress has been made in identifying these highly transmissible variants, what is somewhat lacking is the competence to exploit this information for risk mitigation and effective disease management through an integrated nationwide coordinated approach. With a positivity rate of 15–20% (April–May 2021) and the healthcare system pushed to its limit, accompanied by increased mortality, the situation was rather grim then. Though the central command scrambled all its resources and logistics to streamline the supply chain, the efforts were insufficient in response to the ongoing crisis due to a disproportionate rise in the case. We examined the current scenario emerging from this 2nd COVID wave and identified the possible lacunae. We also suggested few recommendations that may be adopted to avoid similar failures in the future.

Spatial transcriptomics: Gene expression in space, time and numbers

Eukaryotic gene expression is an array of complex processes that must fine-tune with cellular needs to maintain homeostasis, yet flexible enough to respond to external cues and signals. Transcriptomics is the average output of cellular gene expression wherein messenger RNA copy the information inscribed in the DNA to instruct protein synthesis by the cellular ribosomes in the cytoplasm. So far, the knowledge gained from the transcriptomic-based studies was similar to the Heisenberg uncertainty dilemma. Information about these transcripts could be quantitated with utmost accuracy at the cost of losing information about their cellular spatial coordinates. In other words, we may quantitate the transcripts by PCR or the modern-day next-generation sequencing but cannot comment on where these transcripts originated or are located in the cells/tissues. Suppose we, however, accurately try to localize these transcripts using in-situ hybridization-like techniques; in that case, we are uncertain about its actual copy numbers due to the semi-quantitative nature of these methods. Its genuinely a Heisenbergian tradeoff that baffled the biologist for a long time until now; an innovative solution seems to be in place. Spatial transcriptomics (ST) is the perfect marriage between localization and quantitation without compromising either. It is a method that allows simultaneous visualization and quantitative analysis of the transcriptome by performing histological sections on glass slides incubated with oligonucleotides containing positional barcodes to generate high-quality cDNA libraries, which may be used for quantitation by RNA-sequencing. Increasingly, the scientific community seems to realize this technology’s full potential, as evidenced by the sheer number of publications in the past 2 years. This technology is the first of its kind to provide an unbiased whole transcriptome analysis with anatomical information from tissue sections where these transcripts are expressed. A time laspse serial longitudinal ST is powerful to identify the temporal transcript oscillations and decay at unprecedented accuracy. Cells of different types are spatially and structurally organized within the tissue matrix to perform their complex functions. Uncovering the complex spatial architecture of heterogenous tissue is crucial for our understanding of the disease’s pathology. Understanding the disease is the primary step towards its remedy, and ST is a powerful tool to address this with precision.

Shaping the Landscape of Eukaryotic Gene Expression: Horizontal Gene Transfer

Horizontal gene transfer (HGT) in prokaryotes refers to the movement of genes and genetic information between two organisms. This usually results in the spread of antibiotic resistance genes among bacteria. Vertical gene transfer(VGT), on the other hand, refers to the flow of genetic information from parents to offsprings. Until recently, HGT was an exclusive prerogative of the prokaryotes. These are obvious due to the distinct nuclear membrane enclosure of eukaryote genomes that are shielded from outside interferences. VGT can cross species barriers and may even allow the transmission of genes across the kingdoms of life. HGT is now an emerging idea in eukaryotic genomes, challenging previous assertions that HGT is restricted to prokaryotes. It is now accepted that HGT can profoundly influence host metabolic pathways and alter gene expressions even in eukaryotes. HGT, is also fundamentally important during development, origin of human diseases, such as cancer, and neurodegenerative disorders. It may also influence therapeutic outcome by promoting resistant phenotypes.  HGT is recently documented in prokaryote to eukaryote HGT is the tardigrade case though an analysis of a draft tardigrade genome suggested that HGT contributed to up to ~17 % of the gene. Further analysis performed after whole genome pair-wise alignments between human genome as well as 53 vertebrate genomes, it was observed that nearly 1500 human genome regions involving 642 known genes, most of which are enriched with ion binding to be conserved with non-mammals than with most mammals. This indicated horizontal gene transfer is more common than we expected in the human genome. It’s a matter of time or maybe a tip of iceberg to know the full extent and implications of HGT. Surprisingly its seems that the eukaryotic genome has many more ways to update itself to vastly expand its repertoire of expression and usability. HGT is just another feather in the crown.

Cancer immunotherapy: Recent advances and challenges

Immunotherapy is a treatment that uses specific components of a person's immune system to fight diseases. This is usually done by stimulating or assisting one's immune system is attacking the offending agent - for instance, in the case of cancer - the target of immunotherapy will be cancer cells. Some types of immunotherapy are also called biologic therapy or biotherapy. One of the fundamental challenges that a living cell encounters are to accurately copy its genetic material to daughter cells during every single cell cycle. When this process goes haywire, genomic instability ensues, and genetic alterations ranging from nucleotide changes to chromosomal translocations and aneuploidy occur. Genomic instability arising out of DNA structural changes (indels, rearrangements, etc.,) can give rise to mutations predisposing to cancer. Cancer prevention refers to actions taken to mitigate the risk of getting cancer. The past decade has encountered an explosive rate of development of anticancer therapy ranging from standard chemotherapy to novel targeted small molecules that are nearly cancer specific, thereby reducing collateral damage. However, a new class of emerging therapy aims to train the body's defense system to fight against cancer. Termed as "cancer immunotherapy" is the new approach that has gained worldwide acceptance. It includes using antibodies that bind to and inhibit the function of proteins expressed by cancer cells or engineering and boosting the person's own T lymphocytes to target cancer. In this review, we summarized the recent advances and developments in cancer immunotherapy along with their shortcoming and challenges.

Menopause and COVID19 severity: The missing link

COVID-19 pandemic has far-reaching consequences on people with comorbidities like Diabetes Mellitus (DM), asthma, cardiovascular disease, and cancer. What seems unusual is an isolated observation that emerged from several independent studies worldwide. Postmenopausal females seem to suffer from severe COVID symptoms. Few of them also show an extended COVID symptom, also “LONG COVID.” Though the association appears strong, there are not enough credible studies to pin it down to the exact cause. We explored the possibility to see if postmenopausal females are at a higher risk for severe COVID and unravel this observation’s molecular pathogenesis. Research performed at King’s College London found that as estrogen levels in females drop in pre-menopause and menopause, they become vulnerable to COVID19 infection, suggesting that high estrogen levels may have a protective effect against the severity of COVID-19. This concept originated from the immune-modulatory and immune suppressive role of estradiol. Although both male and female sex steroids act primarily on the reproductive tissues and modulate their functions, increasing evidence suggests that sex steroids can also work on non-reproductive tissues like the CNS, immune systems, cardiovascular and skeletal systems, etc.Further, estrogen has an enormous effect both on the innate (macrophages/monocytes, neutrophils, NK cells, complement systems, APC-like dendritic cells (DC)], as well as on the adaptive (B and T cells) immune system. There are reports that estrogen may exhibit a pro-inflammatory response, whereas testosterone counteracts it. This could possibly be through an estrogen-mediated production of inflammatory cytokines like IFNγ, interleukin (IL) 6, TNF α. However, estrogen also has a profound anti-inflammatory effect. We need to remember that many of these observations are context and cell-type-specific with a delicate balance between pro and anti-inflammatory responses. There needs a deeper understanding of the reproductive events in females. Perimenopause, menopause, and postmenopause define the end of a woman’s reproductive years. These are the time when her monthly period stops. Whole perimenopause marks the beginning of this process, starting 8- 12 years before menopause. Menopause is the stage when her menstrual periods completely ceases for at least 12 months. Postmenopause is the stage after menopause that continues thereafter. Starting from perimenopause, menopause is marked by declining levels of estrogen((estrone (E1), 17β-estradiol (E2), estriol (E3)), and progesterone. However, there are complex hormonal and cytokine undercurrents to this rather simplistic profile. LH and FSH, however, seem to surge during this period. It currently not know what this LH/FSH surge means for the immune system. With the approach of menopause, there is the release of extracellular vesicles containing inflammasomes, which may be responsible for low-grade systemic inflammation.This cascade may build up significantly and contribute to a hyper-inflammatory environment. According to a survey by Global Health 50/50, though an equal number of males and females were tested positive for COVID-19, the males were largely presented with severe symptoms, thereby implying that the female hormones may have a protective role in the pathophysiology of COVID-19. Further clinical studies performed on the females showed that pre-menopausal females have a relatively mild disease, while menopausal females had moderate to severe illness. The menopausal group also has significantly more requirements for oxygen, ventilation support, and progression-to-severe disease with a prolonged hospital stay and mortality. This is further reinforced by the fact that estradiol modulates the immune cells, which could play an essential role in explaining why a lower incidence of COVID-19 is observed among women than in men. Even been a nuclear hormone, estrogen has cytoplasmic targets. The cytoplasmic activity of estrogen-activated ERα leads to PI3K induction. This, in turn, prevents the nuclear shuttling and transport of NF Menopause kB, resulting in reduced inflammation. The estrogen axis for inflammation is enormously complex, riddled by the different receptor types usage and post-receptor events. The presence of estrogen receptors (ESRs), ERα and ERβ, is of prime importance since the net outcome depends on ER subtypes in use. It seems that a preferential engagement of ERbeta promotes inflammation while ERalpha dampens it. It was further demonstrated that hypoxia, associated with inflammatory conditions, could also downregulate the expression of ERα, tipping the balance in favor of inflammation. Then there are interferon genes that cross talks with Estrogen receptor (ESR) signaling. Estrogen can also polarize toward a TH2 response eliciting a protective humoral response in addition to its capacity for activation of NK cells. Further, a wide variety of immune-modulatory roles is under estrogenic control. This involves the antigen-presenting dendritic cells, CD4+ and CD8+ T cell populations. Other than estrogen, progesterone also has a profound influence on the immune system. Progesterone was found to have an antiviral effect against SARS-CoV-2 in vitro. Mature NK CD56dimCD16+KIR+ cells overexpress the progesterone receptor and thus are hormone-sensitive. Though there are conflicting reports regarding the association of disease severity and mortality with estrogen levels, it is plausible that drastic alteration of these hormones at menopause could perturb the delicate balance creating an environment that enhances the immune response fueling the cytokine storm, the hallmark for COVID complications. Further research in this area is needed to decipher the intricate molecular details of this process for future risk mitigation and disease management.

Assessment of asthma control in users of oral anti-asthma medications

BACKGROUND: Despite guidelines recommending inhalation therapy as the preferred choice, oral therapy is still widely used in the treatment of asthma in India. However, data about the level of asthma control and healthcare use in patients on oral anti-asthma medications are scarce.METHODS: A retrospective study was conducted to assess the level of asthma control and healthcare use in patients taking oral anti-asthma medications.RESULTS: The study population consisted of 381 adults randomly selected from health screening programmes. All subjects were already receiving oral anti-asthma medications; however, up to 72% had not been diagnosed with asthma by their treating doctors prior to the screening programmes. The cohort had a mean age of 48.26 ± 13.83 years (70% males) and mean peak expiratory flow of 245 ± 78.93 mL/sec. The mean Asthma Control Questionnaire 5 (ACQ-5) score was 2.53 ± 1.15, with respectively 33%, 49.3% and 32.6% reporting at least one episode of breathlessness, one emergency doctor visit and one hospitalisation due to asthma or its symptoms in the past year.CONCLUSION: Underdiagnosis and inappropriate management, as indicated by the poor asthma control and increased hospitalisations seen in this study, is probably a key contributor to the increased burden of the disease in India.

The curious case of COVID-19: Its murky origin, negligence and a botched international attempt for a cover-up

COVD-19 caused due to SARS-CoV2, family of Coronaviridae, the order Nidovirales, and the genus Coronavirus. A zoonotic spillover infection from bats to humans through some intermediate host was proposed to be responsible for its origin. This theory gained traction and raised no concern because our experience with other pathogenic viruses with humans in the past followed a similar trajectory. However, what caught the attention are few missing pieces of the jigsaw puzzle that seems to defy logic. A detailed investigation revealed a trail of deception, negligence, and blotched attempt of cover-up.

Non Government Organizations (NGO)-The gap fillers during COVID-19 lockdown in Assam, India

COVID-19 pandemic caused due to SARS-CoV2 has disrupted the spectrum of health care.  The wide arrays of supportive and palliative care needed for patients with ailments were grossly neglected, due to the diversion of resources and healthcare professionals in COVID management. This deficiency was further exaggerated by extended lockdown and closure of outdoor patient care services resulting in unprecedented crisis in disease management. Further, COVID-19 has been associated with increased risk of morbidity and mortality arising from associated risk factors in geriatric subjects and those with other high risk co-morbidities like hypertension, COPD, diabetes and cancer. North East Indian states and the adjoining regions seem to have suffered substantially during the COVID-19 crisis due to their pre-existing vulnerabilities and under developed health care infrastructure and logistics.  This deficiency, however, seems to have been fulfilled substantially by the participation of NGO (Non-Government Organizations) and other volunteer services who has actively participated to provide basic healthcare and other life support to cancer patients in this crisis.

Heat Shock Proteins and Their Role in Pregnancy: Redefining the Function of "Old Rum in a New Bottle"

Pregnancy in humans is a multi-step complex physiological process comprising three discrete events, decidualization, implantation and placentation. Its overall success depends on the incremental advantage that each of the preceding stages passes on to the next. The success of these synchronized sequels of events is an outcome of timely coordination between them. The pregnancy events are coordinated and governed primarily by the ovarian steroid hormones, estrogen and progesterone, which are essentially ligand-activated transcription factors. It's well known that intercellular signaling of steroid hormones engages a plethora of adapter proteins that participate in executing the biological functions. This involves binding of the hormone receptor complex to the DNA response elements in a sequence specific manner. Working with Drosophila melanogaster, the heat shock proteins (HSPs) were originally described by Ferruccio Ritossa back in the early 1960s. Over the years, there has been considerable advancement of our understanding of these conserved families of proteins, particularly in pregnancy. Accumulating evidence suggests that endometrial and uterine cells have an abundance of HSP27, HSP60, HSP70 and HSP90, implying their possible involvement during the pregnancy process. HSPs have been found to be associated with decidualization, implantation and placentation, with their dysregulation associated with implantation failure, pregnancy loss and other feto-maternal complications. Furthermore, HSP is also associated with stress response, specifically in modulating the ER stress, a critical determinant for reproductive success. Recent advances suggest a therapeutic role of HSPs proteins in improving the pregnancy outcome. In this review, we summarized our latest understanding of the role of different members of the HSP families during pregnancy and associated complications based on experimental and clinical evidences, thereby redefining and exploring their novel function with new perspective, beyond their prototype role as molecular chaperones.

COPD exacerbation rates are higher in non-smoker patients in India

BACKGROUND: Chronic obstructive pulmonary disease (COPD) is common among non-smokers exposed to solid fuel combustion at home. Different clinical characteristics in these patients may have significant therapeutic and prognostic implications.METHODS: We used medical record review and a questionnaire among COPD patients at 15 centres across India to capture data on demographic details, different types of exposures and clinical characteristics. Chest radiography and pulmonary function testing were performed in all 1984 cases; C-reactive protein and exhaled breath nitric oxide were measured wherever available.RESULTS: There were 1388 current or ex-smokers and 596 (30.0%) non-smokers who included 259 (43.5%) male and 337 (56.5%) female patients. Sputum production was significantly more common in smokers with COPD (P < 0.05). The frequency of acute symptomatic worsening, emergency visits and hospitalisation were significantly higher (P < 0.05) in non-smokers with COPD; however, intensive care unit admissions were similar in the two groups. There was no significant difference with respect to the use of bronchodilators, inhalational steroids or home nebulisation among smoker and non-smoker patients. The mean predicted forced expiratory volume in 1 sec in smokers (43.1%) was significantly lower than in non-smokers (46.5%).CONCLUSION: Non-smoker COPD, more commonly observed in women exposed to biomass fuels, was characterised by higher rate of exacerbations and higher healthcare resource utilisation.

Balancing Healthcare and Economy Amidst the COVID-19 Pandemic: An Indian Experience

With its 1.3 billion population and faced with the COVID-19 pandemic, India is at the junction of two crucial decisions, balancing healthcare and the economy. To prevent the community spread of the virus, the Indian Government imposed a nationwide lockdown. Though initially successful to some extent in containing the disease spread, the extended lockdown eventually leads to a spiraling out effect resulting in the slowdown of the economy, which, in turn, lead to widespread consequences affecting the lives of millions of people, mostly those at the base of the social pyramid. We investigated the implications of few government policies taken during this pandemic and their impact on society, thereby suggesting short-term crisis management with long-term solutions. Here, we present a comprehensive account of Indian policy in dealing with the COVID-19 crisis, balancing both economic and public health. We also explored a future contingency plan for risk mitigation along with few recommendations. This viewpoint will be useful for effective healthcare management and the economy in Asia's populous nation in the COVID-19 and prepare for a future crisis of this nature.

Exploring the Role of Gut Microbiome in Colon Cancer

Dysbiosis of the gut microbiome has been associated with the development of colorectal cancer (CRC). Gut microbiota is involved in the metabolic transformations of dietary components into oncometabolites and tumor-suppressive metabolites that in turn affect CRC development. In a healthy colon, the major of microbial metabolism is saccharolytic fermentation pathways. The alpha-bug hypothesis suggested that oncogenic bacteria such as enterotoxigenic Bacteroides fragilis (ETBF) induce the development of CRC through direct interactions with colonic epithelial cells and alterations of microbiota composition at the colorectal site. Escherichia coli, E. faecalis, F. nucleatum, and Streptococcus gallolyticus showed higher abundance whereas Bifidobacterium, Clostridium, Faecalibacterium, and Roseburia showed reduced abundance in CRC patients. The alterations of gut microbiota may be used as potential therapeutic approaches to prevent or treat CRC. Probiotics such as Lactobacillus and Bifidobacterium inhibit the growth of CRC through inhibiting inflammation and angiogenesis and enhancing the function of the intestinal barrier through the secretion of short-chain fatty acids (SCFAs). Crosstalk between lifestyle, host genetics, and gut microbiota is well documented in the prevention and treatment of CRC. Future studies are required to understand the interaction between gut microbiota and host to the influence and prevention of CRC. However, a better understanding of bacterial dysbiosis in the heterogeneity of CRC tumors should also be considered. Metatranscriptomic and metaproteomic studies are considered a powerful omic tool to understand the anti-cancer properties of certain bacterial strains. The clinical benefits of probiotics in the CRC context remain to be determined. Metagenomic approaches along with metabolomics and immunology will open a new avenue for the treatment of CRC shortly. Dietary interventions may be suitable to modulate the growth of beneficial microbiota in the gut.

Effects of 469 E/K polymorphism of ICAM1 gene in ischemic stroke and its association with stroke severity and outcome

Background: Stroke is the second leading cause of death globally and it is a major cause of long-term, physical, psychological, and social disability among the elderly. Increasing evidence shows that ischemic injury and inflammation account for its pathogenic progression. So, we studied the association of Intercellular Adhesion Molecule 1 (ICAM1) polymorphism with ischemic stroke, stroke severity, and outcome. Aims and Objectives: To compare ICAM1 469 E/K polymorphism in ischemic stroke patients with healthy controls, and to study its association with stroke severity and outcome. Materials and Methods: Fifty patients of ischemic stroke and hundred healthy individuals were included. The stroke severity was assessed clinically and radiologically. Outcome was measured at three and six months of stroke onset. Genomic DNA was used for Allele-Specific PCR to detect ICAM1 469 E/K polymorphism. The subjects were categorized into EE, EK, and KK genotypes. Results: The odds of EK genotype to develop stroke was 0.41 (95 % CI; 0.17 - 0.92) (p = 0.07) and of KK genotype was 0.41 (95 % CI; 0.11 - 0.87) (p = 0.04) compared to EE genotype. Subjects with ICAM1K allele had significantly reduced risk of stroke compared with those with E allele. (RR: 0.55; 95% CI: 0.35-0.87) (p=0.03). Conclusion: Subjects with ICAM1K allele had significantly reduced the risk of developing stroke. 469 E/K polymorphism of the ICAM1 gene does not significantly affect stroke severity, mortality, and outcome.

EMTiness in pseudo-malignant behavior of trophoblasts during embryo implantation

Implantation in humans is a multistep process that involves apposition, adhesion, and invasion of the developing blastocyst into the receptive maternal endometrium. Though significant volume of research in this direction has identified important players orchestrating this delicate process, there are still gaps in our understanding of all the sequence of events during embryo implantation. Also, the early pregnancy-related complications that lead to fetal loss and miscarriage often occur in this critical window of implantation, which is primarily defined as the time when the maternal endometrium is supposed to be most receptive to the free blastocyst that emerges out from the zona pellucida. Studies in humans and rodents have identified several mediators like folliculin, LIF, IL11Ra, splicing factor SC35, etc. to be essential for early implantation. Trophoblasts, that form the outer epithelial layer of the blastocyst, participate in the formation of the placenta. During placentation, invasive extravillous trophoblasts (EVTs), migrate into the endometrium, and a transient epithelial to mesenchymal transition (EMT) and remodel the uterine arteries for blood and nutrient exchange.

The scars of COVID19: Preparing for the collateral damages

COVID-19 is a pandemic of disproportionate magnitude. Its devastating effect seems to have a more significant impact on the emerging economies like India and the rest of SE Asia, which also has regions harbouring some of the world's highest population density living under poor socio-economic condition. What seems to have originated from one just one province in China, rapidly speard like wildfire across international territories, affecting millions and crippling the health care system. After about eight months into COVID-19, we realized that the fallout is not only humongous but also stretched across multiple avenues of the society and different aspects of our life. The scars of COVID-19 are much more than the virus itself. With a global shutdown in business and financial institutions, the economy is in free fall. Markets plummeted, stocks crashed and unemployment numbers skyrocketed. Apart from the economy, COVID-19 related shutdown has a tremendous impact on the healthcare system for those with preventable ailments, which were either compromised or delayed affecting millions who need hospitalization for non-COVID causes. COVID crisis also seems responsible for the emergence of a new culture system and mindset that was unprecedented before. With schools and other academic institutions closed, online teaching through electronic media and work from home became the new normal. In this editorial, we summarized the collateral damage on society, economy, and human health in the COVID crisis and few suggestions to chalk out a new plan and strategy to address the challenges for a future episode of similar nature. Though we could still remain vulnerable against similar contagious agents, an advanced planning strategy and preparedness will surely help us better in effective damage control and risk mitigation, not only to reduce mortality, but also from  economic downfall.

Potential SARS-CoV-2 interactions with proteins involved in trophoblast functions - An in-silico study

BACKGROUND

Though a large number of pregnant females have been affected by COVID-19, there is a dearth of information on the effects of SARS-CoV-2 infection on trophoblast function. We explored in silico, the potential interactions between SARS-CoV-2 proteins and proteins involved in the key functions of placenta.

METHODS

Human proteins interacting with SARS-CoV-2 proteins were identified by Gordon et al. (2020). Genes that are upregulated in trophoblast sub-types and stages were obtained by gene-expression data from NCBI-GEO and by text-mining. Genes altered in pathological states like pre-eclampsia and gestational diabetes mellitus were also identified. Genes crucial in placental functions thus identified were compared to the SARS-CoV-2 interactome for overlaps. Proteins recurring across multiple study scenarios were analyzed using text mining and network analysis for their biological functions.

RESULTS

The entry receptors for SARS-CoV-2 - ACE2 and TMPRSS2 are expressed in placenta. Other proteins that interact with SARS-CoV-2 like LOX, Fibulins-2 and 5, NUP98, GDF15, RBX1, CUL3, HMOX1, PLAT, MFGE8, and MRPs are vital in placental functions like trophoblast invasion and migration, syncytium formation, differentiation, and implantation. TLE3, expressed across first trimester placental tissues and cell lines, is involved in formation of placental vasculature, and is important in SARS-CoV (2003) budding and exit from the cells by COPI vesicles.

CONCLUSION

SARS-CoV-2 can potentially interact with proteins having crucial roles in the placental function. Whether these potential interactions identified in silico have effects on trophoblast functions in biological settings needs to be addressed by further in vitro and clinical studies.

Abstract 3127: To investigate the role of BRAF V600E co-occurring mutations in Langerhans cell histiocytosis (LCH)

a. Introduction :

Langerhans cell histiocytosis (LCH) is an inflammatory myeloid neoplasia caused by alterations of several genes in the MAPKinase pathway. The cell of origin is a white blood cell known as a dendritic cell priviously called as histiocyte characterized by a unique cytoplasmic organelle, the Birbeck granule, and the expression of CD1a and class II major histocompatibility complex molecules . The mutations cause these dendritic cells to attract other white blood cells and cause a “lesion” in any organ of the body. LCH has multi-orgnan involvement affecting skin bones, lymph nodes, brain etc. Systemic symptoms may include fever, bone pain, weight loss, jaundice, diabetes insipidus.

b. Description:

LCH is a rare sporadic, non-hereditary and non-malignant disease with unknown etiology characterized with a clonal proliferation of pathologic cells.Recent discovery of recurrent somatic mutations, BRAFV600E in MAPK pathway genes at critical stages of myeloid hematopoietic differentiation in LCH patients supports redefinition of the disease as a myeloproliferative disorder and provides opportunities to develop novel approaches to diagnosis and therapy. In the present proposal, we intend to analyze the BRAFV600E status along with other co-occurring mutations in a cohort of pediatric LCH patients by DNA sequencing in bone marrow samples or Peripheral Blood. Additionally we approach the above unanswered questions by applying an improved machine learning approach for classification and defining an algorithm for disease into different clusters for immediate clinical implication and to address its clinical heterogeneity.

c. Results :

We screened about 5 LCH patients and performed tageted exome seq to asertain the mutational profile of these patients. Sequencing detected BRAF V600E mutation in 3 of 5 samples for a mutation frequency of 60%. IHC based immunofloroscence shows that the intensity of phospho-MEK and phospho-ERK staining shows no significant alterations samples with mutation in BRAF. We are currently investigating mutations in other members of MAK pathways

d. Conclusion :

BRAF-V600E mutations were detected in few of our LCH patients. Neverless seeing the disease heterogeneity, we expect additionall mutations. More studies are needed to investigate mutations in the MAPK pathways that could efffect the course of disease management.We further plan to integrate the clinical and genomic findings to design a predictive model for the disease outcome.

Citation Format: Subhradip Karmakar, R Dhar, K Purkayastha, R Seth, S Karmakar. To investigate the role of BRAF V600E co-occurring mutations in Langerhans cell histiocytosis (LCH) [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3127.

Outcomes and risk factors of cholecystectomy in high risk patients: A case series

Introduction

Many studies looked at outcomes and risk factors in laparoscopic cholecystectomies in general, including a few studies on risk factors and scoring systems in predicting conversion to open surgery. Little data has been produced on high-risk patients undergoing cholecystectomy. Identifying risk factors in this group could help stratify decision making regarding best management strategies.

The aim of this study was to investigate outcomes of laparoscopic cholecystectomies in patients with ASA 3 and 4.

Methods

Data was collected and collated from a prospectively maintained database of all laparoscopic cholecystectomies performed by 13 general surgeons in a single unit. Case notes were reviewed for all patients with ASA 3 and 4 between 2013 and 2017. Data analysis was performed using R studio v 3.4.

Results

244 cases were reviewed. Common bile duct was dilated in 52 cases (21.31%). Gall bladder wall was thick in 102 (41.8%) of the patients. Surgery was elective in 203 (83.2%) of the patients. ERCP was performed in 41 (16.9%) of the patients prior to surgery. 150 patients (62.2%) stayed for 1 day while 36 (14.9%) stayed for 2 days and the remaining 55 (22.9%) stayed for 3 days or more. Complications occurred in 37 (15.16%) of the patients while 23 (9.43%) of the patients were readmitted. 7 patients (2.87%) returned to theatre and 8 (3.28%) stayed in ITU post-op. Two patients died (0.82%).

Conclusion

Laparoscopic cholecystectomies in higher risk populations are safe. Alternative methods such as cholecystostomy and ERCP may be of benefit in these patients.

•

Gallstone disease represents a significant volume of elective and emergency work in the United Kingdom.

•

The primary aim of the study was to explore the factors that lead to complications in high risk patients (ASA 3-4).

•

Histological gallbladder thickness and emergency surgery were the factors most strongly associated with negative outcomes.

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Age greater than 65 as an independent variable does not lead to an increase in negative outcomes.

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Cholecystectomy is a relatively safe procedure in what is typically considered higher risk patients.

Draft genome of Ompok bimaculatus (Pabda fish)

OBJECTIVE

Pabda (Ompok bimaculatus) is a freshwater catfish, largely available in Asian countries, especially in Bangladesh, India, Pakistan and Nepal. This fish is highly valued for its fabulous taste and high nutritional value and is very popular as a rich source of proteins, omega-3 and omega-6 fatty acids, vitamins and mineral for growing children, pregnant females and elders. We performed de-novo sequencing of Ompok bimaculatus using a hybrid approach and present here a draft assembly for this species for the first time.

DATA DESCRIPTION

The genome of Ompok bimaculatus (Fig. 1: Table 1, Data file 3) from Ganges river, has been sequenced by hybrid approach using Illumina short reads and PacBio long reads followed by structural annotations. The draft genome assembly was found to be 718 Mb with N50 size of 81 kb. MAKER gene annotation tool predicted 21,371 genes.

Elucidation of the de Vries behavior in terms of the orientational order parameter, apparent tilt angle, and field-induced tilt angle for smectic liquid crystals by polarized infrared spectroscopy

We report experimental results of the orientational order parameter, the apparent tilt angle, and the field-induced tilt angle for three chiral smectic liquid crystalline materials investigated using infrared (IR) polarized spectroscopy. The common feature in these materials is use of the core 5-methyl-2- pyrimidine benzoate as the central part of the mesogen. This core is terminated by siloxane or carbosilane chains on one of the ends and by the chiral alkoxy chains on the opposite. These compounds exhibit low concomitant layer shrinkage at the smectic A^{*} (SmA^{*}) to smectic C^{*} (SmC^{*}) transition temperature and within the SmC^{*} phase itself. The maximum layer shrinkage in SmC^{*} is observed as ∼1.5%. We calculate the apparent orientational order parameter, S_{app} in the laboratory reference frame from the observed IR absorbance for homeotropic aligned samples, and the true order parameter, S, is calculated using the measured tilt angle and is also interpolated from Iso-SmA^{*} transition temperature closer to SmC^{*} phase. The apparent tilt angle in the SmA^{*} phase calculated from a comparison of order parameters S and S_{app} is found to be significantly large. A low magnitude of S_{app} found for homeotropic aligned samples in the SmA^{*} phase indicates that the order parameter plays a vital role in determining the de Vries characteristics, especially of exhibiting larger apparent tilt angles. Furthermore there is a significant increase in the true order parameter at temperatures close to SmA^{*} to SmC^{*} transition temperature in all three compounds. The planar-aligned samples are used to study the dependence of induced tilt angle on the applied electric field. The generalized Langevin-Debye model given by Shen et al. reasonably fits the experimental data on the field-induced tilt angle. The results show that the dipole moment of the tilt correlated domain in SmA^{*} diverges as temperature is lowered to the SmA^{*}-SmC^{*} transition temperature. The generalized Langevin-Debye model is also found to be extremely effective in confirming some of the conclusions of the de Vries behavior.

De novo assembly of the Indian blue peacock (Pavo cristatus) genome using Oxford Nanopore technology and Illumina sequencing

Background

The Indian peafowl (Pavo cristanus) is native to South Asia and is the national bird of India. Here we present a draft genome sequence of the male blue peacock using Illumina and Oxford Nanopore technology (ONT).

Results

ONT sequencing gave ∼2.3-fold sequencing coverage, whereas Illumina generated 150–base pair paired-end sequence data at 284.6-fold coverage from 5 libraries. Subsequently, we generated a 0.915-gigabase pair de novo assembly of the peacock genome with a scaffold N50 of 0.23 megabase pairs (Mb). We predict that the peacock genome contains 23,153 protein-coding genes and 75.3 Mb (7.33%) of repetitive sequences.

Conclusions

We report a high-quality assembly of the peacock genome using a hybrid approach of sequences generated by both Illumina and ONT. The long-read chemistry generated by ONT was useful for addressing challenges related to de novo assembly, particularly at regions containing repetitive sequences spanning longer than the read length, and which could not be resolved with only short-read–based assembly. Contig assembly of Illumina short reads gave an N50 of 1,639 bases, whereas with ONT, the N50 increased by >9-fold to 14,749 bases. The initial contig assembly based on Illumina sequencing reads alone gave 685,241 contigs. Further scaffolding on assembled contigs using both Illumina and ONT sequencing reads resulted in a final assembly of 15,025 super-scaffolds, with an N50 of ∼0.23 Mb. Ninety-five percent of proteins predicted by homology matched with those in a public repository, verifying the completeness of our assembly. Like other phylogenetic studies of avian conserved genes, we found P. cristatus to be most closely related to Gallus gallus, followed by Meleagris gallopavo and Anas platyrhynchos. Compared with the recently published peacock genome assembly, the current, superior, hybrid assembly has greater sequencing depth, fewer non-ATGC sequences, and fewer scaffolds.

FBXO4 as a novel ubiquitin ligase that targets Cyclin D in the pathogenesis of breast cancer

e14722

Background: Members of ubiquitin ligase family are reported to be associated with cancer. Genome wide RNAi screen using Dharmacon on target Plus RNAi library identified FBXO4 as one of the potential hit . We therefore aimed to study its detailed role on proliferation of MCF7 breast cancer cells with special focus on cell cycle genes. We want to expand it further and study its involvement in context to E2 signaling in breast cancer. We hypothesized that increase in CCND1 expression, could mimic some of the E2 transcriptional regulation and that CCND1 overexpression could lead to E2 independent ER alpha binding to estrogen response element (ERE). Methods: Cell lines: MCF7 grown in MEM alpha supplemented with 10% FBS . For stimulation studies, cells were maintained in phenol free MEM alpha supplemented with 10% FBS and 10 nM estradiol. RNAi knockdown studies: On-target plus siRNA were used to knockdown FBXO4 in MCF7 cells. Western Blot: Western Blot was performed following standard protocols. IHC/Tissue Array: Paraffin embedded malignant breast cancer (ER/PR/EGFR +ve) tissue samples that are scored by pathologist were used for the study. Gene Expression Studies: Microarray and NGS based approach. Results: FBXO4 has been identified as a potential hit in our RNAi screen showing a hyper-proliferative phenotype in MCF7 cellsupon its knockdown. Western blot and ubiquitination assay identified cyclin D (CCND1) as a dedicated FBXO4 target as revealed by confocal microscopy where FBXO4 knockdown showed an enrichment of CCND1 in cytoplasm. Ingenuity pathway analysis and ChIP assay revealed an exploitation of E2 signaling and enhanced recruitment of ER alpha to estrogen response element (ERE) in FBXO4 depleted cells. CCND1 further seems to co-occupy ESR binding motifs thereby representing ER functions. These effects were observed even in absence of any E2 stimulation. Further we observed a significant overlap of differentially expressed genes in E2 stimulated and FBXO4 knockdown cells that were nullified by CCND1 siRNA. Conclusions: Our study elucidated that CCND1 is spared from degradation following loss of FBXO4 which in turn leads to a hyper-proliferative state. Our findings co-related with TCGA and METABRIC databases indicating a poor patient survival and relapse in FBXO4 low and CCND1 high cohorts of ER +ve breast cancer thereby implying a diagnostic value. Along with traditional hormonal therapy, an effective targeted therapy in breast cancer should be aimed to restore FBXO4 levels.

Chiral smectic-A and smectic-C phases with de Vries characteristics

Infrared and dielectric spectroscopic techniques are used to investigate the characteristics of two chiral smectics, namely, 1,1,3,3,5,5,5-heptamethyltrisiloxane 1-[4^{'}-(undecyl-1-oxy)-4-biphenyl(S,S)-2-chloro-3-methylpentanoate] (MSi_{3}MR_{11}) and tricarbosilane-hexyloxy-benzoic acid (S)-4'-(1-methyl-hexyloxy)-3'-nitro-biphenyl-4-yl ester (W599). The orientational features and the field dependencies of the apparent tilt angle and the dichroic ratio for homogeneous planar-aligned samples were calculated from the absorbance profiles obtained at different temperatures especially in the smectic-A* phase of these liquid crystals. The dichroic ratios of the C-C phenyl ring stretching vibrations were considered for the determination of the tilt angle at different temperatures and different voltages. The low values of the order parameter obtained with and without an electric field applied across the cell in the Sm-A^{*} phase for both smectics are consistent with the de Vries concept. The generalized Langevin-Debye model introduced in the literature for explaining the electro-optical response has been applied to the results from infrared spectroscopy. The results show that the dipole moment of the tilt-correlated domain diverges as the transition temperature from Sm-A^{*} to Sm-C^{*} is approached. The Debye-Langevin model is found to be extremely effective in confirming some of the conclusions of the de Vries chiral smectics and gives additional results on the order parameter and the dichroic ratio as a function of the field across the cell. Dielectric spectroscopy finds large dipolar fluctuations in the Sm-A^{*} phase for both compounds and again these confirm their de Vries behavior.

Neurologic complications of transplantation

Major neurologic morbidity, such as seizures and encephalopathy, complicates 20-30% of organ and stem cell transplantation procedures. The majority of these disorders occur in the early posttransplant period, but recipients remain at risk for opportunistic infections and other nervous system disorders for many years. These long-term risks may be increasing as acute survival increases, and a greater number of "sicker" patients are exposed to long-term immunosuppression. Drug neurotoxicity accounts for a significant proportion of complications, with posterior reversible leukoencephalopathy syndrome, primarily associated with calcineurin inhibitors (i.e., cyclosporine and tacrolimus), being prominent as a cause of seizures and neurologic deficits. A thorough evaluation of any patient who develops neurologic symptoms after transplantation is mandatory, since reversible and treatable conditions could be found, and important prognostic information can be obtained.