Publications by authors named "Roshan Sharma"

21 Publications

  • Page 1 of 1

Machine learning integration of scleroderma histology and gene expression identifies fibroblast polarisation as a hallmark of clinical severity and improvement.

Ann Rheum Dis 2021 02 7;80(2):228-237. Epub 2020 Oct 7.

Department of Medicine, Division of Rheumatology, Hospital for Special Surgery, New York, New York, USA.

Objective: We sought to determine histologic and gene expression features of clinical improvement in early diffuse cutaneous systemic sclerosis (dcSSc; scleroderma).

Methods: Fifty-eight forearm biopsies were evaluated from 26 individuals with dcSSc in two clinical trials. Histologic/immunophenotypic assessments of global severity, alpha-smooth muscle actin (aSMA), CD34, collagen, inflammatory infiltrate, follicles and thickness were compared with gene expression and clinical data. Support vector machine learning was performed using scleroderma gene expression subset (normal-like, fibroproliferative, inflammatory) as classifiers and histology scores as inputs. Comparison of w-vector mean absolute weights was used to identify histologic features most predictive of gene expression subset. We then tested for differential gene expression according to histologic severity and compared those with clinical improvement (according to the Combined Response Index in Systemic Sclerosis).

Results: aSMA was highest and CD34 lowest in samples with highest local Modified Rodnan Skin Score. CD34 and aSMA changed significantly from baseline to 52 weeks in clinical improvers. CD34 and aSMA were the strongest predictors of gene expression subset, with highest CD34 staining in the normal-like subset (p<0.001) and highest aSMA staining in the inflammatory subset (p=0.016). Analysis of gene expression according to CD34 and aSMA binarised scores identified a 47-gene fibroblast polarisation signature that decreases over time only in improvers (vs non-improvers). Pathway analysis of these genes identified gene expression signatures of inflammatory fibroblasts.

Conclusion: CD34 and aSMA stains describe distinct fibroblast polarisation states, are associated with gene expression subsets and clinical assessments, and may be useful biomarkers of clinical severity and improvement in dcSSc.
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http://dx.doi.org/10.1136/annrheumdis-2020-217840DOI Listing
February 2021

Unmasking Arrhythmogenic Hubs of Reentry Driving Persistent Atrial Fibrillation for Patient-Specific Treatment.

J Am Heart Assoc 2020 10 2;9(19):e017789. Epub 2020 Oct 2.

Department of Physiology & Cell Biology and Frick Center for Heart Failure and Arrhythmia The Ohio State University Wexner Medical Center Columbus OH.

Background Atrial fibrillation (AF) driver mechanisms are obscured to clinical multielectrode mapping approaches that provide partial, surface-only visualization of unstable 3-dimensional atrial conduction. We hypothesized that transient modulation of refractoriness by pharmacologic challenge during multielectrode mapping improves visualization of hidden paths of reentrant AF drivers for targeted ablation. Methods and Results Pharmacologic challenge with adenosine was tested in ex vivo human hearts with a history of AF and cardiac diseases by multielectrode and high-resolution subsurface near-infrared optical mapping, integrated with 3-dimensional structural imaging and heart-specific computational simulations. Adenosine challenge was also studied on acutely terminated AF drivers in 10 patients with persistent AF. Ex vivo, adenosine stabilized reentrant driver paths within arrhythmogenic fibrotic hubs and improved visualization of reentrant paths, previously seen as focal or unstable breakthrough activation pattern, for targeted AF ablation. Computational simulations suggested that shortening of atrial refractoriness by adenosine may (1) improve driver stability by annihilating spatially unstable functional blocks and tightening reentrant circuits around fibrotic substrates, thus unmasking the common reentrant path; and (2) destabilize already stable reentrant drivers along fibrotic substrates by accelerating competing fibrillatory wavelets or secondary drivers. In patients with persistent AF, adenosine challenge unmasked hidden common reentry paths (9/15 AF drivers, 41±26% to 68±25% visualization), but worsened visualization of previously visible reentry paths (6/15, 74±14% to 34±12%). AF driver ablation led to acute termination of AF. Conclusions Our ex vivo to in vivo human translational study suggests that transiently altering atrial refractoriness can stabilize reentrant paths and unmask arrhythmogenic hubs to guide targeted AF driver ablation treatment.
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http://dx.doi.org/10.1161/JAHA.120.017789DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7792422PMC
October 2020

L1CAM defines the regenerative origin of metastasis-initiating cells in colorectal cancer.

Nat Cancer 2020 Jan 13;1(1):28-45. Epub 2020 Jan 13.

Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

Metastasis-initiating cells with stem-like properties drive cancer lethality, yet their origins and relationship to primary-tumor-initiating stem cells are not known. We show that L1CAM cells in human colorectal cancer (CRC) have metastasis-initiating capacity, and we define their relationship to tissue regeneration. L1CAM is not expressed in the homeostatic intestinal epithelium, but is induced and required for epithelial regeneration following colitis and in CRC organoid growth. By using human tissues and mouse models, we show that L1CAM is dispensable for adenoma initiation but required for orthotopic carcinoma propagation, liver metastatic colonization and chemoresistance. L1CAM cells partially overlap with LGR5 stem-like cells in human CRC organoids. Disruption of intercellular epithelial contacts causes E-cadherin-REST transcriptional derepression of L1CAM, switching chemoresistant CRC progenitors from an L1CAM to an L1CAM state. Thus, L1CAM dependency emerges in regenerative intestinal cells when epithelial integrity is lost, a phenotype of wound healing deployed in metastasis-initiating cells.
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http://dx.doi.org/10.1038/s43018-019-0006-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7351134PMC
January 2020

Adult Human Glioblastomas Harbor Radial Glia-like Cells.

Stem Cell Reports 2020 02 30;14(2):338-350. Epub 2020 Jan 30.

Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Electronic address:

Radial glia (RG) cells are the first neural stem cells to appear during embryonic development. Adult human glioblastomas harbor a subpopulation of RG-like cells with typical RG morphology and markers. The cells exhibit the classic and unique mitotic behavior of normal RG in a cell-autonomous manner. Single-cell RNA sequencing analyses of glioblastoma cells reveal transcriptionally dynamic clusters of RG-like cells that share the profiles of normal human fetal radial glia and that reside in quiescent and cycling states. Functional assays show a role for interleukin in triggering exit from dormancy into active cycling, suggesting a role for inflammation in tumor progression. These data are consistent with the possibility of persistence of RG into adulthood and their involvement in tumor initiation or maintenance. They also provide a putative cellular basis for the persistence of normal developmental programs in adult tumors.
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http://dx.doi.org/10.1016/j.stemcr.2020.01.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7014025PMC
February 2020

Impaired neuronal sodium channels cause intranodal conduction failure and reentrant arrhythmias in human sinoatrial node.

Nat Commun 2020 01 24;11(1):512. Epub 2020 Jan 24.

Department of Physiology and Cell Biology, The Ohio State University Wexner Medical Center, Columbus, OH, USA.

Mechanisms for human sinoatrial node (SAN) dysfunction are poorly understood and whether human SAN excitability requires voltage-gated sodium channels (Nav) remains controversial. Here, we report that neuronal (n)Nav blockade and selective nNav1.6 blockade during high-resolution optical mapping in explanted human hearts depress intranodal SAN conduction, which worsens during autonomic stimulation and overdrive suppression to conduction failure. Partial cardiac (c)Nav blockade further impairs automaticity and intranodal conduction, leading to beat-to-beat variability and reentry. Multiple nNav transcripts are higher in SAN vs atria; heterogeneous alterations of several isoforms, specifically nNav1.6, are associated with heart failure and chronic alcohol consumption. In silico simulations of Nav distributions suggest that I is essential for SAN conduction, especially in fibrotic failing hearts. Our results reveal that not only cNav but nNav are also integral for preventing disease-induced failure in human SAN intranodal conduction. Disease-impaired nNav may underlie patient-specific SAN dysfunctions and should be considered to treat arrhythmias.
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http://dx.doi.org/10.1038/s41467-019-14039-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6981137PMC
January 2020

Combination anti-CTLA-4 plus anti-PD-1 checkpoint blockade utilizes cellular mechanisms partially distinct from monotherapies.

Proc Natl Acad Sci U S A 2019 11 21;116(45):22699-22709. Epub 2019 Oct 21.

Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030;

Immune checkpoint blockade therapy targets T cell-negative costimulatory molecules such as cytotoxic T lymphocyte antigen-4 (CTLA-4) and programmed cell death-1 (PD-1). Combination anti-CTLA-4 and anti-PD-1 blockade therapy has enhanced efficacy, but it remains unclear through what mechanisms such effects are mediated. A critical question is whether combination therapy targets and modulates the same T cell populations as monotherapies. Using a mass cytometry-based systems approach, we comprehensively profiled the response of T cell populations to monotherapy and combination anti-CTLA-4 plus anti-PD-1 therapy in syngeneic murine tumors and clinical samples. Most effects of monotherapies were additive in the context of combination therapy; however, multiple combination therapy-specific effects were observed. Highly phenotypically exhausted cluster of differentiation 8 (CD8) T cells expand in frequency following anti-PD-1 monotherapy but not combination therapy, while activated terminally differentiated effector CD8 T cells expand only following combination therapy. Combination therapy also led to further increased frequency of T helper type 1 (Th1)-like CD4 effector T cells even though anti-PD-1 monotherapy is not sufficient to do so. Mass cytometry analyses of peripheral blood from melanoma patients treated with immune checkpoint blockade therapies similarly revealed mostly additive effects on the frequencies of T cell subsets along with unique modulation of terminally differentiated effector CD8 T cells by combination ipilimumab plus nivolumab therapy. Together, these findings indicate that dual blockade of CTLA-4 and PD-1 therapy is sufficient to induce unique cellular responses compared with either monotherapy.
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http://dx.doi.org/10.1073/pnas.1821218116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6842624PMC
November 2019

Engineering γδT cells limits tonic signaling associated with chimeric antigen receptors.

Sci Signal 2019 09 10;12(598). Epub 2019 Sep 10.

Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.

Despite the benefits of chimeric antigen receptor (CAR)-T cell therapies against lymphoid malignancies, responses in solid tumors have been more limited and off-target toxicities have been more marked. Among the possible design limitations of CAR-T cells for cancer are unwanted tonic (antigen-independent) signaling and off-target activation. Efforts to overcome these hurdles have been blunted by a lack of mechanistic understanding. Here, we showed that single-cell analysis with time course mass cytometry provided a rapid means of assessing CAR-T cell activation. We compared signal transduction in expanded T cells to that in T cells transduced to express second-generation CARs and found that cell expansion enhanced the response to stimulation. However, expansion also induced tonic signaling and reduced network plasticity, which were associated with expression of the T cell exhaustion markers PD-1 and TIM-3. Because this was most evident in pathways downstream of CD3ζ, we performed similar analyses on γδT cells that expressed chimeric costimulatory receptors (CCRs) lacking CD3ζ but containing DAP10 stimulatory domains. These CCR-γδT cells did not exhibit tonic signaling but were efficiently activated and mounted cytotoxic responses in the presence of CCR-specific stimuli or cognate leukemic cells. Single-cell signaling analysis enabled detailed characterization of CAR-T and CCR-T cell activation to better understand their functional activities. Furthermore, we demonstrated that CCR-γδT cells may offer the potential to avoid on-target, off-tumor toxicity and allo-reactivity in the context of myeloid malignancies.
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http://dx.doi.org/10.1126/scisignal.aax1872DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7055420PMC
September 2019

Natural Genetic Variation Reveals Key Features of Epigenetic and Transcriptional Memory in Virus-Specific CD8 T Cells.

Immunity 2019 05 23;50(5):1202-1217.e7. Epub 2019 Apr 23.

Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA. Electronic address:

Stable changes in chromatin states and gene expression in cells of the immune system form the basis for memory of infections and other challenges. Here, we used naturally occurring cis-regulatory variation in wild-derived inbred mouse strains to explore the mechanisms underlying long-lasting versus transient gene regulation in CD8 T cells responding to acute viral infection. Stably responsive DNA elements were characterized by dramatic and congruent chromatin remodeling events affecting multiple neighboring sites and required distinct transcription factor (TF) binding motifs for their accessibility. Specifically, we found that cooperative recruitment of T-box and Runx family transcription factors to shared targets mediated stable chromatin remodeling upon T cell activation. Our observations provide insights into the molecular mechanisms driving virus-specific CD8 T cell responses and suggest a general mechanism for the formation of transcriptional and epigenetic memory applicable to other immune and non-immune cells.
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http://dx.doi.org/10.1016/j.immuni.2019.03.031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7023907PMC
May 2019

The emergent landscape of the mouse gut endoderm at single-cell resolution.

Nature 2019 05 8;569(7756):361-367. Epub 2019 Apr 8.

Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

Here we delineate the ontogeny of the mammalian endoderm by generating 112,217 single-cell transcriptomes, which represent all endoderm populations within the mouse embryo until midgestation. We use graph-based approaches to model differentiating cells, which provides a spatio-temporal characterization of developmental trajectories and defines the transcriptional architecture that accompanies the emergence of the first (primitive or extra-embryonic) endodermal population and its sister pluripotent (embryonic) epiblast lineage. We uncover a relationship between descendants of these two lineages, in which epiblast cells differentiate into endoderm at two distinct time points-before and during gastrulation. Trajectories of endoderm cells were mapped as they acquired embryonic versus extra-embryonic fates and as they spatially converged within the nascent gut endoderm, which revealed these cells to be globally similar but retain aspects of their lineage history. We observed the regionalized identity of cells along the anterior-posterior axis of the emergent gut tube, which reflects their embryonic or extra-embryonic origin, and the coordinated patterning of these cells into organ-specific territories.
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http://dx.doi.org/10.1038/s41586-019-1127-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6724221PMC
May 2019

Negative Co-stimulation Constrains T Cell Differentiation by Imposing Boundaries on Possible Cell States.

Immunity 2019 04 26;50(4):1084-1098.e10. Epub 2019 Mar 26.

Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Parker Institute for Cancer Immunotherapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address:

Co-stimulation regulates T cell activation, but it remains unclear whether co-stimulatory pathways also control T cell differentiation. We used mass cytometry to profile T cells generated in the genetic absence of the negative co-stimulatory molecules CTLA-4 and PD-1. Our data indicate that negative co-stimulation constrains the possible cell states that peripheral T cells can acquire. CTLA-4 imposes major boundaries on CD4 T cell phenotypes, whereas PD-1 subtly limits CD8 T cell phenotypes. By computationally reconstructing T cell differentiation paths, we identified protein expression changes that underlied the abnormal phenotypic expansion and pinpointed when lineage choice events occurred during differentiation. Similar alterations in T cell phenotypes were observed after anti-CTLA-4 and anti-PD-1 antibody blockade. These findings implicate negative co-stimulation as a key regulator and determinant of T cell differentiation and suggest that checkpoint blockade might work in part by altering the limits of T cell phenotypes.
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http://dx.doi.org/10.1016/j.immuni.2019.03.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6664799PMC
April 2019

Simulating urban expansion in a rapidly changing landscape in eastern Tarai, Nepal.

Environ Monit Assess 2019 Mar 28;191(4):255. Epub 2019 Mar 28.

Cultural and Spatial Ecology, Department of Geosciences, Florida Atlantic University, Boca Raton, FL, 33431, USA.

Understanding the spatiotemporal dynamics of urbanization and predicting future growth is now essential for sustainable urban planning and policy making. This study explores future urban expansion in the rapidly growing region of eastern lowland Nepal. We used the hybrid cellular automata-Markov (CA-Markov) model, which utilizes historical land use and land cover (LULC) maps and several biophysical change driver variables to predict urban expansion for the years 2026 and 2036. Transitional area matrices were generated based on historical LULC data from 1996 to 2006, from 2006 to 2016, and from 1996 to 2016. The approach was validated by cross comparing the actual and simulated maps for 2016. Evaluation gave satisfactory values of Kno (0.89), Kstandard (0.84), and Klocation (0.89) which verifies the accuracy of the model. Hence, the CA-Markov model was utilized to simulate the LULC map for the years 2026 and 2036. The study area experienced rapid peri/urban expansion and sharp decline in area of cultivated land during 1989-2016. Built-up area increased by 110.90 km over a period of 27 years at the loss of 87.59 km cultivated land. Simulation analysis indicates that urban expansion will continue with urban cover increasing to 230 km (8.95%) and 318.51 km (12.45%) by 2026 and 2036, respectively, with corresponding declines in cultivated land to 1453.83 km (56.86%) and 1374.93 km (53.77%) for the same years. The alarming increase in urban areas coupled with loss of cultivated land will have negative implications for food security and environmental equilibrium in the region.
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http://dx.doi.org/10.1007/s10661-019-7389-0DOI Listing
March 2019

The Combination of MEK Inhibitor With Immunomodulatory Antibodies Targeting Programmed Death 1 and Programmed Death Ligand 1 Results in Prolonged Survival in Kras/p53-Driven Lung Cancer.

J Thorac Oncol 2019 06 13;14(6):1046-1060. Epub 2019 Feb 13.

Section of Medical Oncology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale School of Medicine, New Haven, Connecticut; Developmental Therapeutics Translational Research Program, Yale Comprehensive Cancer Center, New Haven, Connecticut. Electronic address:

Introduction: This study aimed to characterize the tumor-infiltrating immune cells population in Kras/tumor protein 53 (Trp53)-driven lung tumors and to evaluate the combinatorial antitumor effect with MEK inhibitor (MEKi), trametinib, and immunomodulatory monoclonal antibodies (mAbs) targeting either programmed death -1 (PD-1) or programmed cell death ligand 1 (PD-L1) in vivo.

Methods: Trp53;Kras;Rosa26 (PKL) genetically engineered mice were used to develop autochthonous lung tumors with intratracheal delivery of adenoviral Cre recombinase. Using these tumor-bearing lungs, tumor-infiltrating immune cells were characterized by both mass cytometry and flow cytometry. PKL-mediated immunocompetent syngeneic and transgenic lung cancer mouse models were treated with MEKi alone as well as in combination with either anti-PD-1 or anti-PD-L1 mAbs. Tumor growth and survival outcome were assessed. Finally, immune cell populations within spleens and tumors were evaluated by flow cytometry and immunohistochemistry.

Results: Myeloid-derived suppressor cells (MDSCs) were significantly augmented in PKL-driven lung tumors compared to normal lungs of tumor-free mice. PD-L1 expression appeared to be highly positive in both lung tumor cells and, particularly MDSCs. The combinatory administration of MEKi with either anti-PD-1 or anti-PD-L1 mAbs synergistically increased antitumor response and survival outcome compared with single-agent therapy in both the PKL-mediated syngeneic and transgenic lung cancer models. Theses combinational treatments resulted in significant increases of tumor-infiltrating CD8 and CD4 T cells, whereas attenuation of CD11b/Gr-1 MDSCs, in particular, Ly6G polymorphonuclear-MDSCs in the syngeneic model.

Conclusions: These findings suggest a potential therapeutic approach for untargetable Kras/p53-driven lung cancers with synergy between targeted therapy using MEKi and immunotherapies.
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http://dx.doi.org/10.1016/j.jtho.2019.02.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6542636PMC
June 2019

Combined Aurora Kinase A (AURKA) and WEE1 Inhibition Demonstrates Synergistic Antitumor Effect in Squamous Cell Carcinoma of the Head and Neck.

Clin Cancer Res 2019 06 12;25(11):3430-3442. Epub 2019 Feb 12.

Section of Medical Oncology, Department of Internal Medicine and Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut.

Purpose: Human papillomavirus (HPV)-negative head and neck squamous cell carcinomas (HNSCC) commonly bear disruptive mutations in , resulting in treatment resistance. In these patients, direct targeting of p53 has not been successful, but synthetic lethal approaches have promise. Although Aurora A kinase (AURKA) is overexpressed and an oncogenic driver, its inhibition has only modest clinical effects in HPV-negative HNSCC. We explored a novel combination of AURKA and WEE1 inhibition to overcome intrinsic resistance to AURKA inhibition. AURKA protein expression was determined by fluorescence-based automated quantitative analysis of patient specimens and correlated with survival. We evaluated treatment with the AURKA inhibitor alisertib (MLN8237) and the WEE1 inhibitor adavosertib (AZD1775), alone or in combination, using and HNSCC models.

Results: Elevated nuclear AURKA correlated with worse survival among patients with p16(-) HNSCC. Alisertib caused spindle defects, G-M arrest and inhibitory CDK1 phosphorylation, and cytostasis in mutant HNSCC FaDu and UNC7 cells. Addition of adavosertib to alisertib instead triggered mitotic entry and mitotic catastrophe. Moreover, in FaDu and Detroit 562 xenografts, this combination demonstrated synergistic effects on tumor growth and extended overall survival compared with either vehicle or single-agent treatment.

Conclusions: Combinatorial treatment with adavosertib and alisertib leads to synergistic antitumor effects in and HNSCC models. These findings suggest a novel rational combination, providing a promising therapeutic avenue for mutated cancers.
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http://dx.doi.org/10.1158/1078-0432.CCR-18-0440DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6548643PMC
June 2019

Learning time-varying information flow from single-cell epithelial to mesenchymal transition data.

PLoS One 2018 29;13(10):e0203389. Epub 2018 Oct 29.

Institute for Molecular Life Sciences, University of Zurich, Zurich, Switzerland.

Cellular regulatory networks are not static, but continuously reconfigure in response to stimuli via alterations in protein abundance and confirmation. However, typical computational approaches treat them as static interaction networks derived from a single time point. Here, we provide methods for learning the dynamic modulation of relationships between proteins from static single-cell data. We demonstrate our approach using TGFß induced epithelial-to-mesenchymal transition (EMT) in murine breast cancer cell line, profiled with mass cytometry. We take advantage of the asynchronous rate of transition to EMT in the data and derive a pseudotime EMT trajectory. We propose methods for visualizing and quantifying time-varying edge behavior over the trajectory, and a metric of edge dynamism to predict the effect of drug perturbations on EMT.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0203389PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6205587PMC
March 2019

CD49b defines functionally mature Treg cells that survey skin and vascular tissues.

J Exp Med 2018 11 24;215(11):2796-2814. Epub 2018 Oct 24.

Howard Hughes Medical Institute, Immunology Program, and Ludwig Center, Memorial Sloan Kettering Cancer Center, New York, NY

Regulatory T (Treg) cells prevent autoimmunity by limiting immune responses and inflammation in the secondary lymphoid organs and nonlymphoid tissues. While unique subsets of Treg cells have been described in some nonlymphoid tissues, their relationship to Treg cells in secondary lymphoid organs and circulation remains unclear. Furthermore, it is possible that Treg cells from similar tissue types share largely similar properties. We have identified a short-lived effector Treg cell subset that expresses the α integrin, CD49b, and exhibits a unique tissue distribution, being abundant in peripheral blood, vasculature, skin, and skin-draining lymph nodes, but uncommon in the intestines and in viscera-draining lymph nodes. CD49b Treg cells, which display superior functionality revealed by in vitro and in vivo assays, appear to develop after multiple rounds of cell division and TCR-dependent activation. Accordingly, single-cell RNA-seq analysis placed these cells at the apex of the Treg developmental trajectory. These results shed light on the identity and development of a functionally potent subset of mature effector Treg cells that recirculate through and survey peripheral tissues.
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http://dx.doi.org/10.1084/jem.20181442DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6219731PMC
November 2018

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion.

Cell 2018 07 28;174(3):716-729.e27. Epub 2018 Jun 28.

Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA. Electronic address:

Single-cell RNA sequencing technologies suffer from many sources of technical noise, including under-sampling of mRNA molecules, often termed "dropout," which can severely obscure important gene-gene relationships. To address this, we developed MAGIC (Markov affinity-based graph imputation of cells), a method that shares information across similar cells, via data diffusion, to denoise the cell count matrix and fill in missing transcripts. We validate MAGIC on several biological systems and find it effective at recovering gene-gene relationships and additional structures. Applied to the epithilial to mesenchymal transition, MAGIC reveals a phenotypic continuum, with the majority of cells residing in intermediate states that display stem-like signatures, and infers known and previously uncharacterized regulatory interactions, demonstrating that our approach can successfully uncover regulatory relations without perturbations.
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http://dx.doi.org/10.1016/j.cell.2018.05.061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6771278PMC
July 2018

Comparative evaluation of different strengths of electrical current in the management of dentinal hypersensitivity.

Indian J Dent Res 2010 Apr-Jun;21(2):207-12

Department of Periodontics, S.G.T Dental College, Hospital and Research Institute, Budhera, Gurgaon, Haryana, India.

Background: Dentinal hypersensitivity is a commonly occurring but less understood and poorly managed problem of the teeth. Iontophoresis is a technique wherein desensitizing agents can be transferred under electrical pressure into the tooth structure to manage hypersensitivity.

Aim: The purpose of present study is to compare the effect of different strengths of electrical current used for varying lengths of time, keeping the electrical dosage constant with the iontophoretic unit in the management of dentinal hypersensitivity.

Materials And Methods: This study was conducted among the patients attending the Periodontal Department of the Government Dental College and Hospital, Patiala, Punjab, specifically complaining of tooth hypersensitivity. The Verbal Rating Scale (VRS) was used to record scores pre-, during, and post-treatment. Ten percent SrCl2 solution was applied with an iontophoretic unit. Three applications were performed at weekly intervals, up to the second week, using the same electric current dosage. The data compiled was statistically analyzed.

Results: A remarkable reduction in dentinal hypersensitivity to both air blast and cold water stimuli was noted at the end of two months after iontophoresis with each current group/method, namely, I (0.25 mA for 4 minutes), II (0.5 mA for 2 minutes), and III (1 mA for 1 minute). However, the differences in effectiveness/improvement within the three current groups during the entire duration of the study were found to be statistically insignificant.

Conclusion: Within the limits of this study, it could be implied that for relieving hypersensitivity, iontophoresis for all three current groups was almost equally effective, and it was found that repeated applications (up to three) gave good relief. Iontophoresis was found to be effective and safe.
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http://dx.doi.org/10.4103/0970-9290.66643DOI Listing
November 2010

Duration of reappearance of gingival melanin pigmentation after surgical removal - A clinical study.

J Indian Soc Periodontol 2010 Apr;14(2):101-5

Department of Periodontology and Oral Implantology, Guru Nanak Dev Dental College and Research Institute, Sunam, India.

Background: In dentistry, esthetics has a special place. Although gingival melanin pigmentation does not present a medical problem, clinicians are often faced with a challenge of achieving gingival esthetics.

Materials And Methods: A method of de-epithelialization of the pigmented gingiva using Kirkland's gingivectomy knife is described. Twenty patients who were conscious about their gingival melanin pigmentation were selected. The gingiva of the whole of the arch was abraded until the entire visible pigmentation was removed. Clinical observations for intensity of pigmentation were recorded at baseline and then after surgery at monthly intervals over a period of 9 months according to Dummett-Gupta Oral Pigmentation Index scoring criteria proposed by Dummett C. O. in 1964.

Results: The mean gingival melanin pigmentation score came down to 0.407 after 9 months as compared to preoperative score, which was 2.24. No repigmentation occurred in fair-complexioned persons. In persons with wheatish complexion, repigmentation was seen in 85.71% of the cases, but scores came down to 0.38 postoperatively as compared to 2.27 preoperatively. In dark-complexioned persons, repigmentation occurred in all cases, but the mean scores were 0.93 as compared to 2.40 preoperatively. The difference between preoperative and postoperative mean scores for each segment was put to statistical analysis by applying paired t test and was found to be significant.

Conclusion: As this method has shown statistically significant results, it can be used in patients who are conscious of pigmented gingiva and want an esthetically satisfactory color.
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http://dx.doi.org/10.4103/0972-124X.70828DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3110462PMC
April 2010

Biochemical abnormalities in neonatal seizures.

Indian J Pediatr 2003 Mar;70(3):221-4

Department of Pediatrics, Indira Gandhi Medical College, Shimla, India.

Objective: The presence of seizure does not constitute a diagnoses but it is a symptom of an underlying central nervous system disorder due to systemic or biochemical disturbances. Biochemical disturbances occur frequently in the neonatal seizures either as an underlying cause or as an associated abnormality. In their presence, it is difficult to control seizure and there is a risk of further brain damage. Early recognition and treatment of biochemical disturbances is essential for optimal management and satisfactory long term outcome.

Methods: The present study was conducted in the department of pediatrics in IGMC Shimla on 59 neonates. Biochemical abnormalities were detected in 29 (49.15%) of cases.

Result: Primary metabolic abnormalities occurred in 10(16.94%) cases of neonatal seizures, most common being hypocalcaemia followed by hypoglycemia, other metabolic abnormalities include hypomagnesaemia and hyponateremia. Biochemical abnormalities were seen in 19(38.77%) cases of non metabolic seizure in neonates. Associated metabolic abnormalities were observed more often with Hypoxic-ischemic-encephalopathy (11 out of 19) cases and hypoglycemia was most common in this group.

Conclusion: No infant had hyponateremia, hyperkelemia or low zinc level.
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http://dx.doi.org/10.1007/BF02725588DOI Listing
March 2003