Diagnostic Relevance of Primary Investigations in Early Referral and Management of Colorectal Cancer Patients

Aim: Colorectal cancers are largely considered as curable yet the high mortality rates associated with it points out at deficiency in early management of the disease. The aim of this study was to analyze the diagnostic potential of routine primary investigations with an attempt to categorize symptoms for early referral of colorectal cancers patients.Methods: This study involved retrospective analysis of a cohort of 85 patients diagnosed with colorectal cancer that underwent surgery in a period of one year. The patients were arranged into different age-groups to analyze the relative incidence and prognosis of the disease with respect to generalized symptoms and clinicopathological details. Multinomial Logistic Regression analysis was employed to predict the most effective set of parameter combinations for primary prognosis of the diseased state.Results: Abdominal pain, rectal bleeding and change in bowel habits were predominantly reported symptoms; however, these were imprecise with age, sex or stage of cancer. Interestingly, almost 85% of the patients were reported anemic, with a majority of them (41.7%) having Hb 10. Anaemic patients showed significantly higher frequency of symptoms viz. change in bowel habits (p 0.023), rectal bleeding (p 0.035) and/or abdominal pain (p 0.039) compared to non-anaemic ones. The co-occurrence of any two of the symptoms further increased the likelihood of the disease in anaemic patients.Conclusion: A substantial decrease in hemoglobin count with concomitant change in bowel habits, rectal bleeding, and/or abdominal pain could be considered as potential referral markers for early management of suspected colorectal cancers patients

Angiogenesis in Control and Progression of Lung Cancer (This article was withdrawn as requested by the authors at March 24, 2015))

Lung cancer is the major cause of cancer-related mortality worldwide owing to its late-stage detection and aggressive behavior. Epidemiologically, several genetic and epigenetic factors contribute to the development of lung cancer. Angiogenesis, a critical process in tumor progression has become an important target for anti-cancer therapy particularly in lung cancer. Besides commercially available angiogenic inhibitors, numerous anti-angiogenic therapies have been developed to limit tumor growth, although, most of them have not proved beneficial in terms of long-term survival. Despite, logical advances in treatment strategies, NSCLC still remains a major health concern due to poor prognosis of the diseases state. This calls for a comprehensive analysis of signaling processes governing tumor angiogenesis and treatment options available thereof for development of a sustainable strategy to control cancer. In this review, several aspects of lung cancer have been discussed starting from its pathological characterization to the development of modern therapeutics

PD-1 signaling uncovers a pathogenic subset of T cells in inflammatory arthritis

Abstract Background PD-1 is an immune checkpoint on T cells, and interventions to block this receptor result in T cell activation and enhanced immune response to tumors and pathogens. Reciprocally, despite a decade of research, approaches to treat autoimmunity with PD-1 agonists have only had limited successful. To resolve this, new methods must be developed to augment PD-1 function beyond engaging the receptor. Methods We conducted a flow cytometry analysis of T cells isolated from the peripheral blood and synovial fluid of patients with rheumatoid arthritis. In addition, we performed a genome-wide CRISPR/Cas9 screen to identify genes associated with PD-1 signaling. We further analyzed genes involved in PD-1 signaling using publicly available bulk and single-cell RNA sequencing datasets. Results Our screen confirmed known regulators in proximal PD-1 signaling and, importantly, identified an additional 1112 unique genes related to PD-1 ability to inhibit T cell functions. These genes were strongly associated with the response of cancer patients to PD-1 blockades and with high tumor immune dysfunction and exclusion scores, confirming their role downstream of PD-1. Functional annotation revealed that the most significant genes uncovered were those associated with known immune regulation processes. Remarkably, these genes were considerably downregulated in T cells isolated from patients with inflammatory arthritis, supporting their overall inhibitory functions. A study of rheumatoid arthritis single-cell RNA sequencing data demonstrated that five genes, KLRG1, CRTAM, SLAMF7, PTPN2, and KLRD1, were downregulated in activated and effector T cells isolated from synovial fluids. Backgating these genes to canonical cytotoxic T cell signatures revealed PD-1+ HLA-DRHIGH KLRG1LOW T cells as a novel inflammatory subset of T cells. Conclusions We concluded that PD-1+ HLA-DRHIGH KLRG1LOW T cells are a potential target for future PD-1 agonists to treat inflammatory diseases. Our study uncovers new genes associated with PD-1 downstream functions and, therefore, provides a comprehensive resource for additional studies that are much needed to characterize the role of PD-1 in the synovial subset of T cells

PD-1 signaling uncovers a pathogenic subset of T cells in inflammatory arthritis

Background: PD-1 is an immune checkpoint on T cells, and interventions to block this receptor result in T cell activation and enhanced immune response to tumors and pathogens. Reciprocally, despite a decade of research, approaches to treat autoimmunity with PD-1 agonists have only had limited successful. To resolve this, new methods must be developed to augment PD-1 function beyond engaging the receptor. Methods: We conducted a flow cytometry analysis of T cells isolated from the peripheral blood and synovial fluid of patients with rheumatoid arthritis. In addition, we performed a genome-wide CRISPR/Cas9 screen to identify genes associated with PD-1 signaling. We further analyzed genes involved in PD-1 signaling using publicly available bulk and single-cell RNA sequencing datasets. Results: Our screen confirmed known regulators in proximal PD-1 signaling and, importantly, identified an additional 1112 unique genes related to PD-1 ability to inhibit T cell functions. These genes were strongly associated with the response of cancer patients to PD-1 blockades and with high tumor immune dysfunction and exclusion scores, confirming their role downstream of PD-1. Functional annotation revealed that the most significant genes uncovered were those associated with known immune regulation processes. Remarkably, these genes were considerably downregulated in T cells isolated from patients with inflammatory arthritis, supporting their overall inhibitory functions. A study of rheumatoid arthritis single-cell RNA sequencing data demonstrated that five genes, KLRG1, CRTAM, SLAMF7, PTPN2, and KLRD1, were downregulated in activated and effector T cells isolated from synovial fluids. Backgating these genes to canonical cytotoxic T cell signatures revealed PD-1+ HLA-DRHIGH KLRG1LOW T cells as a novel inflammatory subset of T cells. Conclusions: We concluded that PD-1+ HLA-DRHIGH KLRG1LOW T cells are a potential target for future PD-1 agonists to treat inflammatory diseases. Our study uncovers new genes associated with PD-1 downstream functions and, therefore, provides a comprehensive resource for additional studies that are much needed to characterize the role of PD-1 in the synovial subset of T cells

SAP-expressing T peripheral helper cells identify systemic lupus erythematosus patients with lupus nephritis

IntroductionT follicular (TFH) and peripheral helper (TPH) cells have been increasingly recognized as a pathogenic subset of CD4 T cells in systemic lupus erythematosus (SLE). The SLAM Associated Protein (SAP) regulates TFH and TPH function by binding to the co-stimulatory signaling lymphocyte activation molecule family (SLAMF) receptors that mediate T cell - B cell interactions. SAP and SLAMF are critical for TPH-dependent B cell maturation into autoantibody-producing plasma cells that characterize SLE pathogenesis. We hypothesized that SAP-expressing TPH cells are involved in the pathogenesis of lupus nephritis (LN).MethodsPeripheral blood mononuclear cells (PBMC) were isolated using density gradient separation from whole blood. Cells were stained for cell surface markers, followed by permeabilization and staining of intracellular SAP for spectral flow cytometry analysis. We also analyzed SAP expression from renal infiltrating LN T cells using the available single-cell RNA sequencing (scRNA seq) Accelerated Medicines Partnership (AMP) SLE dataset.ResultsPBMC from 30 patients with SLE (34 ± 10 years old, 83% female), including 10 patients with LN, were analyzed. We found an increase in total SAP-positive CD4 and CD8 T cells in SLE compared with controls (55.5 ± 2.6 vs. 41.3 ± 3.4, p=0.007, and 52.5 ± 3.0 vs. 39.2 ± 2.8, p=0.007 respectively). In CD4 T cells, the highest SAP expression was in the TPH subset. The frequency of SAP+TPH in circulation correlated with disease activity; SLE patients with renal disease had higher levels of circulating SAP+TPH that remained significant after adjusting for age, sex, race, low complements, and elevated anti-dsDNA (p=0.014). scRNA-seq data of renal infiltrating T cells in LN identified SAP expression to localize to the TFH-like CD4 cluster and GZMK+ CD8 cluster. Increased SAP expression in LN was associated with the differential expression of SLAMF3 and SLAMF7 and granzyme K and EOMES. The existence of two predominant SAP-expressing subsets, the TFH-like CD4 T cells, and GZMK+ effector CD8 T cells, was verified using scRNA-seq data from a human transcriptomic atlas of fifteen major organs.ConclusionThe expansion of SAP-expressing T helper cells was associated with LN in our cohort and verified using scRNA-seq data of renal infiltrating T cells. Improved SLAM and SAP signaling understanding can identify new therapeutic targets in LN

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Not AvailableCrocussativus,amonocottriploidspeciesbelonging totheIridaceaefamily,iscultivatedforitsredstigmaticlobesof the carpel that constitute saffron. Flower development has been extensively studied in different plants. Different floral developmental pathways have been deciphered in many plants. In Crocussativus,floweristhemostimportantpartandunderstanding the pathway underlying the flower development can pave the way for new avenues to improve its productivity and quality. The combination of class A genes (including APETALA1; CsAP1 and APETALA2; CsAP2), class B genes (including APETALA3; CsAP3 and PISTILLATA; CsPI) and class C genes (including AGAMOUS; CsAG) that are active in each whorl,determinestheidentityoftheorgansthatwilllaterdevelop in that whorl. CsAP3 is a class B homeotic gene which promotes petal and stamen formation and has a very important roleinflowerdevelopment.Italsoactivatesothergenesplaying pivotal role in flower development. It has been earlier reported that CsAP3 gene has direct role in activation of CsNAP gene whichpromotessenescenceinplants.Presentworkwasfocused on study of relative gene expression changes of CsAP3 and CsNAP gene during different stages of flower development. CsAP3 gene expression was found maximum during latepreanthesis stages of stigma development. Expression increases from stage5 tostage 6offlower development and then reduces again from stage 6 to stage 7. CsNAP gene had moderate expression during stage 3 to stage 4 transition and its expression increased abruptly from stage 6 to stage 7 of flower development. There is no direct concordance in the expression of CsAP3 and CsNAP gene expression in saffron. We may conclude that some other factor(s) may be responsible for initiation of CsNAP expression and CsAP3 gene may directly/indirectly be involved in regulating the factors responsible for CsNAP activation.Not Availabl

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Not AvailableSaffron, the desiccated stigmas of Crocus sativus, is recognized for its attractive color, flavor, and aroma which are due to the accumulation of crocin, picrocrocin, and safranal, respectively. HPLC analysis demonstrated maximum apocarotenoid accumulation during the fully developed scarlet stage of stigma development followed by the orange and yellow stages of stigma development. Reverse Transcription-PCR analysis revealed a concurrent expression pattern of CsZCD and CsLYC genes in a developmental stagespecific manner. However, CsBCH and CsGT2 genes were specifically expressed during the mature, scarlet stage of stigma development. Real-Time PCR analysis showed a sharp increase in gene expression of CsLYC gene during stigma development indicative of its possible regulatory role in apocarotenoid biosynthesis or stigma development. Results suggest that genetic manipulation of this gene can help to improve the quality of stigma in saffron; besides highlighting its potential to monitor stigma development during in vitro experimentation.Not Availabl

Molecular Characterization of Saffron-Potential Candidates for Crop Improvement

In this study, thirty one (31) morphologically distinct selections of saffron crop were used for molecular characterization. Molecular characterization was done through SSR, ISSR and RAPD markers. RAPD and ISSR markers showed significant variation; however, SSR markers did not reveal any variation between the selected clones. The Jaccard’s similarity coefficient ranged from 0.94 to 1.00 with an average of 0.98 among all 31 selections used. Minimum similarity value (0.94) was observed between CITH-S-107 and PAM-S-116 selections. The study provides sufficient knowledge to identify clones with better stigma characteristics for further crop improvement programs

Root-associated fungi of Pinus wallichiana A. B. Jackson in Kashmir Himalaya

An important factor in the performance of out-planted conifers is the association of plant roots with ectomycorrhizal (EcM) fungi. However, limited information is available about the diversity of root associated EcM fungi of Pinus wallichiana A. B. Jackson, a coniferous species endemic to Himalayan forests, which has hampered the reforestation programs in the area. The study was carried at three major forest areas of the Kashmir Himalaya believed to be pure stands of Pinus wallichiana. Fine root-tips harbouring EcM were collected and processed for extraction of fungal DNA which were subsequently subjected to ITS rDNA targeted PCR/ RFLP profiling. DNA sequencing analysis of the overlapping ITS amplifications followed by global nucleotide-blast analyses of the assembled nuclear ribosomal DNA (rDNA) revealed a total of 33 fungal taxa associated with P. wallichiana, out of which 23 species were EcM fungi. Out of the 10 non-EcM fungi, we found a peculiar saprophytic wood decaying fungus, Chalara microchona associated with P. wallichiana for the first time. The study not only reveals the species richness of fungi associated with this conifer but also documents new fungal associations with it, which have not been reported so far. The results in the study set a baseline for the broad association of ectomycorrhizal fungi with P. wallichiana which may serve as guiding cue to design reforestation programs in the Kashmir Himalaya.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

A novel kinase mutation in VEGFR-1 predisposes its alpha C-helix/activation loop towards allosteric activation: Atomic insights from protein simulation

Vascular endothelial growth factor receptor 1 (VEGFR-1) has been implicated in diverse pathologies, including cancers. Although VEGFR-1 is considered as functionally impaired kinase, its decoy characteristics make it an important regulator of VEGFR-mediated signaling, particularly in tumor angiogenesis. VEGFR-1 conveys signaling via its tyrosine kinase (TK) domain whose activation is regulated by phosphorylation of specific tyrosine residues. Thus dysregulation of VEGFR-1 signaling, as reported in most of the cancers, might be a consequence of altered phosphorylation that could be attributed to genotypic variations in its TK domain. Considering the importance of TK domain of VEGFR-1, we carried out its mutational screening in 84 clinically validated and histopathologically confirmed colorectal cancer patients. By means of direct DNA sequencing and SNP analyses, eight novel variations, including one synonymous, two deletion, one missense and four intronic variations, were reported in the TK domain of VEGFR-1. rs730882263:C>G variation specifically reported in colon cancer, representing a single-atomic change (Sulfur to Oxygen) in the predicted (p.Cys1110Ser) protein, was observed as potentially deleterious variation as assessed by multiple single-nucleotide polymorphism prediction servers. Molecular dynamics simulations of VEGFR-1 Wt and (p.Cys1110Ser) variant models revealed major conformational changes in variant protein presumptuously generating an open conformation thereby exposing the activation domain and consequently increasing the probability of phosphorylation events: a condition frequently reported in cancers