Clinical Focus

  • Molecular Genetics
  • Clinical Pathology
  • Pathology


All Publications

  • A predictive tool for identification of SARS-CoV-2 PCR-negative emergency department patients using routine test results. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology Joshi, R. P., Pejaver, V., Hammarlund, N. E., Sung, H., Lee, S. K., Furmanchuk, A., Lee, H. Y., Scott, G., Gombar, S., Shah, N., Shen, S., Nassiri, A., Schneider, D., Ahmad, F. S., Liebovitz, D., Kho, A., Mooney, S., Pinsky, B. A., Banaei, N. 2020; 129: 104502


    Testing for COVID-19 remains limited in the United States and across the world. Poor allocation of limited testing resources leads to misutilization of health system resources, which complementary rapid testing tools could ameliorate.To predict SARS-CoV-2 PCR positivity based on complete blood count components and patient sex.A retrospective case-control design for collection of data and a logistic regression prediction model was used. Participants were emergency department patients > 18 years old who had concurrent complete blood counts and SARS-CoV-2 PCR testing. 33 confirmed SARS-CoV-2 PCR positive and 357 negative patients at Stanford Health Care were used for model training. Validation cohorts consisted of emergency department patients > 18 years old who had concurrent complete blood counts and SARS-CoV-2 PCR testing in Northern California (41 PCR positive, 495 PCR negative), Seattle, Washington (40 PCR positive, 306 PCR negative), Chicago, Illinois (245 PCR positive, 1015 PCR negative), and South Korea (9 PCR positive, 236 PCR negative).A decision support tool that utilizes components of complete blood count and patient sex for prediction of SARS-CoV-2 PCR positivity demonstrated a C-statistic of 78 %, an optimized sensitivity of 93 %, and generalizability to other emergency department populations. By restricting PCR testing to predicted positive patients in a hypothetical scenario of 1000 patients requiring testing but testing resources limited to 60 % of patients, this tool would allow a 33 % increase in properly allocated resources.A prediction tool based on complete blood count results can better allocate SARS-CoV-2 testing and other health care resources such as personal protective equipment during a pandemic surge.

    View details for DOI 10.1016/j.jcv.2020.104502

    View details for PubMedID 32544861

  • Targeted deep sequencing of cell-free DNA in serous body cavity fluids with malignant, suspicious, and benign cytology. Cancer cytopathology Yang, S., Mooney, K. L., Libiran, P., Jones, C. D., Joshi, R., Lau, H. D., Stehr, H., Berry, G. J., Zehnder, J. L., Long, S. R., Kong, C. S., Kunder, C. A. 2019


    BACKGROUND: Liquid biopsy using cell-free DNA (cfDNA) presents new opportunities for solid tumor genotyping. While studies have demonstrated the utility of cfDNA from plasma, cfDNA from other body fluids remains underexplored.METHODS: We evaluated the molecular features and clinicopathologic correlates of cfDNA from serous body cavity fluids by performing hybrid capture-based next-generation sequencing (NGS) on cfDNA isolated from residual effusion supernatants. Twenty-one serous effusions from pleural (n=15), peritoneal (n=5), and pericardial (n=1) cavity were analyzed.RESULTS: The supernatants provided a median cfDNA concentration of 10.3ng/L. Notably, all effusions were sequenced successfully to a median depth >1000*, revealing a broad range of genetic alterations including single nucleotide variants, small insertions and deletions, amplifications, and fusions. Specifically, pathogenic alterations were identified in all malignant fluids (13/13), all fluids suspicious for malignancy (2/2), and 1 benign fluid (1/6) from a patient with metastatic cancer. To validate our findings, we examined matching results from 11 patients who underwent additional testing using formalin-fixed, paraffin-embedded (FFPE) specimens. In 8 patients, the paired results between FFPE and supernatant testing were concordant, whereas in the remaining 3 patients, supernatant analysis identified additional variants likely associated with resistance to targeted therapies. Additional comparison between FFPE and supernatant testing showed no difference in DNA concentration (P=.5), depth of coverage (P=.6), or allele frequency of pathogenic mutations (P=.7).CONCLUSION: cfDNA isolated from serous body cavity fluids represents a promising source of genomic input for targeted NGS.

    View details for DOI 10.1002/cncy.22205

    View details for PubMedID 31751001

  • A Survey of Somatic Mutations in 41 Genes in a Cohort of T-Cell Lymphomas Identifies Frequent Mutations in Genes Involved in Epigenetic Modification APPLIED IMMUNOHISTOCHEMISTRY & MOLECULAR MORPHOLOGY Fernandez-Pol, S., Ma, L., Joshi, R. P., Arber, D. A. 2019; 27 (6): 416?22
  • Pharma-Oncogenomics in theEra of Personal Genomics: A Quick Guide to Online Resources and Tools. Advances in experimental medicine and biology Joshi, R. P., Steiner, D. F., Konnick, E. Q., Suarez, C. J. 2019; 1168: 103?15


    The past two decades have seen unprecedented advances in the field of oncogenomics. The ongoing characterization of neoplastic tissues through genomic techniques has transformed many aspects of cancer research, diagnosis, and treatment. However, identifying sequence variants with biological and clinical significance is a challenging endeavor. In order to accomplish this task, variants must be annotated and interpreted using various online resources. Data on protein structure, functional prediction, variant frequency in relevant populations, and multipleother factors have beencompiled in usefuldatabasesfor this purpose.Thus, understanding the available online resourcesfor the annotation and interpretationof sequencevariantsis critical to aid molecular pathologistsand researchers working in this space.

    View details for DOI 10.1007/978-3-030-24100-1_7

    View details for PubMedID 31713167

  • Transfusion Management of Conjoined Twins Undergoing Surgical Separation: A Single Center Experience with Three Sets of Thoraco-Omphalopagus Twins over Ten Years Tsang, H., Kuan, C., Boltz, M., Hartman, G., Joshi, R. P., Panigrahi, A., Andrews, J. WILEY. 2018: 122A?123A
  • The Brief Case: Confirmed Positive HIV-1 Serologic Screening but Undetectable RNA Virus Load in a Pregnant Woman. Journal of clinical microbiology Joshi, R. P., Gomez, C. A., Steiner, D., Aziz, N., Pinsky, B. A. 2017; 55 (12): 3316?20

    View details for PubMedID 29180504

  • Falsely high sirolimus concentrations due to everolimus cross-reactivity in the Siemens sirolimus immunoassay: Corrective actions implemented. Clinica chimica acta; international journal of clinical chemistry Bowen, R., Rieta, R., Joshi, R., Lee, R. C. 2017

    View details for PubMedID 29080689

  • Closing the Brief Case: Confirmed Positive HIV-1 Serological Screening but Undetectable RNA Virus Load in a Pregnant Woman. Journal of clinical microbiology Joshi, R. P., Gomez, C. A., Steiner, D., Aziz, N., Pinsky, B. A. 2017; 55 (12): 3566?67

    View details for PubMedID 29180505

  • Multiplexed detection of viral infections using rapid in situ RNA analysis on a chip LAB ON A CHIP Shaffer, S. M., Joshi, R. P., Chambers, B. S., Sterken, D., Biaesch, A. G., Gabrieli, D. J., Li, Y., Feemster, K. A., Hensley, S. E., Issadore, D., Raj, A. 2015; 15 (15): 3170?82


    Viral infections are a major cause of human disease, but many require molecular assays for conclusive diagnosis. Current assays typically rely on RT-PCR or ELISA; however, these tests often have limited speed, sensitivity or specificity. Here, we demonstrate that rapid RNA FISH is a viable alternative method that could improve upon these limitations. We describe a platform beginning with software to generate RNA FISH probes both for distinguishing related strains of virus (even those different by a single base) and for capturing large numbers of strains simultaneously. Next, we present a simple fluidic device for reliably performing RNA FISH assays in an automated fashion. Finally, we describe an automated image processing pipeline to robustly identify uninfected and infected samples. Together, our results establish RNA FISH as a methodology with potential for viral point-of-care diagnostics.

    View details for DOI 10.1039/c5lc00459d

    View details for Web of Science ID 000358022900010

    View details for PubMedID 26113495

    View details for PubMedCentralID PMC4670042

  • Loss of PIKfyve in platelets causes a lysosomal disease leading to inflammation and thrombosis in mice NATURE COMMUNICATIONS Min, S. H., Suzuki, A., Stalker, T. J., Zhao, L., Wang, Y., McKennan, C., Riese, M. J., Guzman, J. F., Zhang, S., Lian, L., Joshi, R., Meng, R., Seeholzer, S. H., Choi, J. K., Koretzky, G., Marks, M. S., Abrams, C. S. 2014; 5: 4691


    PIKfyve is essential for the synthesis of phosphatidylinositol-3,5-bisphosphate [PtdIns(3,5)P2] and for the regulation of endolysosomal membrane dynamics in mammals. PtdIns(3,5)P2 deficiency causes neurodegeneration in mice and humans, but the role of PtdIns(3,5)P2 in non-neural tissues is poorly understood. Here we show that platelet-specific ablation of PIKfyve in mice leads to accelerated arterial thrombosis, and, unexpectedly, also to inappropriate inflammatory responses characterized by macrophage accumulation in multiple tissues. These multiorgan defects are attenuated by platelet depletion in vivo, confirming that they reflect a platelet-specific process. PIKfyve ablation in platelets induces defective maturation and excessive storage of lysosomal enzymes that are released upon platelet activation. Impairing lysosome secretion from PIKfyve-null platelets in vivo markedly attenuates the multiorgan defects, suggesting that platelet lysosome secretion contributes to pathogenesis. Our findings identify PIKfyve as an essential regulator for platelet lysosome homeostasis, and demonstrate the contributions of platelet lysosomes to inflammation, arterial thrombosis and macrophage biology.

    View details for DOI 10.1038/ncomms5691

    View details for Web of Science ID 000342838800001

    View details for PubMedID 25178411

    View details for PubMedCentralID PMC4369914

  • Diacylglycerol Kinase zeta Limits the Generation of Natural Regulatory T Cells SCIENCE SIGNALING Schmidt, A. M., Zou, T., Joshi, R. P., Leichner, T. M., Pimentel, M. A., Sommers, C. L., Kambayashi, T. 2013; 6 (303): ra101


    Natural regulatory T (nT(reg)) cells are important for maintaining tolerance to self- and foreign antigens, and they are thought to develop from thymocytes that receive strong T cell receptor (TCR)-mediated signals in the thymus. TCR engagement leads to the activation of phospholipase C-?1, which generates the lipid second messenger diacylglycerol (DAG) from phosphatidylinositol 4,5-bisphosphate. We used mice that lack the ? isoform of DAG kinase (DGK?), which metabolizes DAG to terminate its signaling, to enhance TCR-mediated signaling and identify critical signaling events in nT(reg) cell development. Loss of DGK? resulted in increased numbers of thymic CD25(+)Foxp3(-)CD4(+) nT(reg) cell precursors and Foxp3(+)CD4(+) nT(reg) cells in a cell-autonomous manner. DGK?-deficient T cells exhibited increased nuclear translocation of the nuclear factor ?B subunit c-Rel, as well as enhanced extracellular signal-regulated kinase (ERK) phosphorylation in response to TCR stimulation, suggesting that these downstream pathways may contribute to nT(reg) cell development. Indeed, reducing c-Rel abundance or blocking ERK phosphorylation abrogated the increased generation of nTreg cells by DGK?-deficient thymocytes. The extent of ERK phosphorylation correlated with TCR-mediated acquisition of Foxp3 in immature thymocytes in vitro. Furthermore, the development of nT(reg) cells was augmented in mice in which ERK activation was selectively enhanced in T cells. Together, these data suggest that DGK? regulates the development of nT(reg) cells by limiting the extent of activation of the ERK and c-Rel signaling pathways.

    View details for DOI 10.1126/scisignal.2004411

    View details for Web of Science ID 000327730000001

    View details for PubMedID 24280042

    View details for PubMedCentralID PMC4103616

  • The zeta Isoform of Diacylglycerol Kinase Plays a Predominant Role in Regulatory T Cell Development and TCR-Mediated Ras Signaling SCIENCE SIGNALING Joshi, R. P., Schmidt, A. M., Das, J., Pytel, D., Riese, M. J., Lester, M., Diehl, J., Behrens, E. M., Kambayashi, T., Koretzky, G. A. 2013; 6 (303): ra102


    Diacylglycerol (DAG) is a critical second messenger that mediates T cell receptor (TCR)-stimulated signaling. The abundance of DAG is reduced by the diacylglycerol kinases (DGKs), which catalyze the conversion of DAG to phosphatidic acid (PA) and thus inhibit DAG-mediated signaling. In T cells, the predominant DGK isoforms are DGK? and DGK?, and deletion of the genes encoding either isoform enhances DAG-mediated signaling. We found that DGK?, but not DGK?, suppressed the development of natural regulatory T (T(reg)) cells and predominantly mediated Ras and Akt signaling downstream of the TCR. The differential functions of DGK? and DGK? were not attributable to differences in protein abundance in T cells or in their localization to the contact sites between T cells and antigen-presenting cells. RasGRP1, a key DAG-mediated activator of Ras signaling, associated to a greater extent with DGK? than with DGK?; however, in silico modeling of TCR-stimulated Ras activation suggested that a difference in RasGRP1 binding affinity was not sufficient to cause differences in the functions of each DGK isoform. Rather, the model suggested that a greater catalytic rate for DGK? than for DGK? might lead to DGK? exhibiting increased suppression of Ras-mediated signals compared to DGK?. Consistent with this notion, experimental studies demonstrated that DGK? was more effective than DGK? at catalyzing the metabolism of DAG to PA after TCR stimulation. The enhanced effective enzymatic production of PA by DGK? is therefore one possible mechanism underlying the dominant functions of DGK? in modulating T(reg) cell development.

    View details for DOI 10.1126/scisignal.2004373

    View details for Web of Science ID 000327730000002

    View details for PubMedID 24280043

    View details for PubMedCentralID PMC4096120

  • Enhanced Effector Responses in Activated CD8(+) T Cells Deficient in Diacylglycerol Kinases CANCER RESEARCH Riese, M. J., Wang, L. S., Moon, E. K., Joshi, R. P., Ranganathan, A., June, C. H., Koretzky, G. A., Albelda, S. M. 2013; 73 (12): 3566?77


    Recent clinical trials have shown promise in the use of chimeric antigen receptor (CAR)-transduced T cells; however, augmentation of their activity may broaden their clinical use and improve their efficacy. We hypothesized that because CAR action requires proteins essential for T-cell receptor (TCR) signal transduction, deletion of negative regulators of these signaling pathways would enhance CAR signaling and effector T-cell function. We tested CAR activity and function in T cells that lacked one or both isoforms of diacylglycerol kinase (dgk) expressed highly in T cells, dgk? and dgk?, enzymes that metabolize the second messenger diacylglycerol (DAG) and limit Ras/ERK activation. We found that primary murine T cells transduced with CARs specific for the human tumor antigen mesothelin showed greatly enhanced cytokine production and cytotoxicity when cocultured with a murine mesothelioma line that stably expresses mesothelin. In addition, we found that dgk-deficient CAR-transduced T cells were more effective in limiting the growth of implanted tumors, both concurrent with and after establishment of tumor. Consistent with our studies in mice, pharmacologic inhibition of dgks also augments function of primary human T cells transduced with CARs. These results suggest that deletion of negative regulators of TCR signaling enhances the activity and function of CAR-expressing T cells and identify dgks as potential targets for improving the clinical potential of CARs.

    View details for DOI 10.1158/0008-5472.CAN-12-3874

    View details for Web of Science ID 000320380300010

    View details for PubMedID 23576561

    View details for PubMedCentralID PMC3686869

  • Diacylglycerol Kinases: Regulated Controllers of T Cell Activation, Function, and Development INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES Joshi, R. P., Koretzky, G. A. 2013; 14 (4): 6649?73


    Diacylglycerol kinases (DGKs) are a diverse family of enzymes that catalyze the conversion of diacylglycerol (DAG), a crucial second messenger of receptor-mediated signaling, to phosphatidic acid (PA). Both DAG and PA are bioactive molecules that regulate a wide set of intracellular signaling proteins involved in innate and adaptive immunity. Clear evidence points to a critical role for DGKs in modulating T cell activation, function, and development. More recently, studies have elucidated factors that control DGK function, suggesting an added complexity to how DGKs act during signaling. This review summarizes the available knowledge of the function and regulation of DGK isoforms in signal transduction with a particular focus on T lymphocytes.

    View details for DOI 10.3390/ijms14046649

    View details for Web of Science ID 000318017100008

    View details for PubMedID 23531532

    View details for PubMedCentralID PMC3645659

  • AKT1 and AKT2 maintain hematopoietic stem cell function by regulating reactive oxygen species BLOOD Juntilla, M. M., Patil, V. D., Calamito, M., Joshi, R. P., Birnbaum, M. J., Koretzky, G. A. 2010; 115 (20): 4030?38


    Although AKT is essential for multiple cellular functions, the role of this kinase family in hematopoietic stem cells (HSCs) is unknown. Thus, we analyzed HSC function in mice deficient in the 2 isoforms most highly expressed in the hematopoietic compartment, AKT1 and AKT2. Although loss of either isoform had only a minimal effect on HSC function, AKT1/2 double-deficient HSCs competed poorly against wild-type cells in the development of myeloid and lymphoid cells in in vivo reconstitution assays. Serial transplantations revealed an essential role for AKT1 and AKT2 in the maintenance of long-term HSCs (LT-HSCs). AKT1/2 double-deficient LT-HSCs were found to persist in the G(0) phase of the cell cycle, suggesting that the long-term functional defects are caused by increased quiescence. Furthermore, we found that the intracellular content of reactive oxygen species (ROS) is dependent on AKT because double-deficient HSCs demonstrate decreased ROS. The importance of maintaining ROS for HSC differentiation was shown by a rescue of the differentiation defect after pharmacologically increasing ROS levels in double-deficient HSCs. These data implicate AKT1 and AKT2 as critical regulators of LT-HSC function and suggest that defective ROS homeostasis may contribute to failed hematopoiesis.

    View details for DOI 10.1182/blood-2009-09-241000

    View details for Web of Science ID 000277923600007

    View details for PubMedID 20354168

    View details for PubMedCentralID PMC2875090

  • Lytic Granule Loading of CD8(+) T Cells Is Required for HIV-Infected Cell Elimination Associated with Immune Control IMMUNITY Migueles, S. A., Osborne, C. M., Royce, C., Compton, A. A., Joshi, R. P., Weeks, K. A., Rood, J. E., Berkley, A. M., Sacha, J. B., Cogliano-Shutta, N. A., Lloyd, M., Roby, G., Kwan, R., McLaughlin, M., Stallings, S., Rehm, C., O'Shea, M. A., Mican, J., Packard, B. Z., Komoriya, A., Palmer, S., Wiegand, A. P., Maldarelli, F., Coffin, J. M., Mellors, J. W., Hallahan, C. W., Follman, D. A., Connors, M. 2008; 29 (6): 1009?21


    Virus-specific CD8+ T cells probably mediate control over HIV replication in rare individuals, termed long-term nonprogressors (LTNPs) or elite controllers. Despite extensive investigation, the mechanisms responsible for this control remain incompletely understood. We observed that HIV-specific CD8+ T cells of LTNPs persisted at higher frequencies than those of treated progressors with equally low amounts of HIV. Measured on a per-cell basis, HIV-specific CD8+ T cells of LTNPs efficiently eliminated primary autologous HIV-infected CD4+ T cells. This function required lytic granule loading of effectors and delivery of granzyme B to target cells. Defective cytotoxicity of progressor effectors could be restored after treatment with phorbol ester and calcium ionophore. These results establish an effector function and mechanism that clearly segregate with immunologic control of HIV. They also demonstrate that lytic granule contents of memory cells are a critical determinant of cytotoxicity that must be induced for maximal per-cell killing capacity.

    View details for DOI 10.1016/j.immuni.2008.10.010

    View details for Web of Science ID 000262012400019

    View details for PubMedID 19062316

    View details for PubMedCentralID PMC2622434

  • Pretreatment photosensitizer dosimetry reduces variation in tumor response INTERNATIONAL JOURNAL OF RADIATION ONCOLOGY BIOLOGY PHYSICS Zhou, X. D., Pogue, B. W., Chen, B., Demidenko, E., Joshi, R., Hoopes, J., Hasan, T. 2006; 64 (4): 1211?20


    To compensate for photosensitizer uptake variation in photodynamic therapy (PDT), via control of delivered light dose through photodynamic dose calculation based on online dosimetry of photosensitizer in tissue before treatment.Photosensitizer verteporfin was quantified via multiple fluorescence microprobe measurements immediately before treatment. To compensate individual PDT treatments, photodynamic doses were calculated on an individual animal basis, by matching the light delivered to provide an equal photosensitizer dose multiplied by light dose. This was completed for the lower quartile, median, and upper quartile of the photosensitizer distribution. PDT-induced tumor responses were evaluated by the tumor regrowth assay.Verteporfin uptake varied considerably among tumors and within a tumor. The coefficient of variation in the surviving fraction was found significantly decreased in groups compensated to the lower quartile (CL-PDT), the median (CM-PDT), and the upper quartile (CU-PDT) of photosensitizer distribution. The CL-PDT group was significantly less effective compared with NC-PDT (Noncompensated PDT), CM-PDT, and CU-PDT treatments. No significant difference in effectiveness was observed between NC-PDT, CM-PDT, and CU-PDT treatment groups.This research suggests that accurate quantification of tissue photosensitizer levels and subsequent adjustment of light dose will allow for reduced subject variation and improved treatment consistency.

    View details for DOI 10.1016/j.ijrobp.2005.11.019

    View details for Web of Science ID 000235897100032

    View details for PubMedID 16504761

  • Photosensitizer dosimetry controlled PDT treatment planning reduces inter-individual variability in response to PDT Zhou, X., Pogue, B. W., Chen, B., Demidenko, E., Joshi, R., Hoopes, J., Hasan, T., Kessel, D. SPIE-INT SOC OPTICAL ENGINEERING. 2006: 157-+

    View details for DOI 10.1117/12.647439

    View details for Web of Science ID 000237680100018

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