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Provocateurs of autoimmunity within the gut microbiota

Upadhyay, Rabi; Littman, Dan R
An arthritogenic strain of Subdoligranulum in the gut elicits a local immune response, a precursor to systemic autoimmunity (Chriswell et al.).
PMID: 36288277
ISSN: 1946-6242
CID: 5348492

Multimodal single-cell datasets characterize antigen-specific CD8+ T cells across SARS-CoV-2 vaccination and infection

Zhang, Bingjie; Upadhyay, Rabi; Hao, Yuhan; Samanovic, Marie I; Herati, Ramin S; Blair, John D; Axelrad, Jordan; Mulligan, Mark J; Littman, Dan R; Satija, Rahul
The immune response to SARS-CoV-2 antigen after infection or vaccination is defined by the durable production of antibodies and T cells. Population-based monitoring typically focuses on antibody titer, but there is a need for improved characterization and quantification of T cell responses. Here, we used multimodal sequencing technologies to perform a longitudinal analysis of circulating human leukocytes collected before and after immunization with the mRNA vaccine BNT162b2. Our data indicated distinct subpopulations of CD8+ T cells, which reliably appeared 28 days after prime vaccination. Using a suite of cross-modality integration tools, we defined their transcriptome, accessible chromatin landscape and immunophenotype, and we identified unique biomarkers within each modality. We further showed that this vaccine-induced population was SARS-CoV-2 antigen-specific and capable of rapid clonal expansion. Moreover, we identified these CD8+ T cell populations in scRNA-seq datasets from COVID-19 patients and found that their relative frequency and differentiation outcomes were predictive of subsequent clinical outcomes.
PMID: 37735591
ISSN: 1529-2916
CID: 5606242

Efficacy and Safety of COVID-19 Convalescent Plasma in Hospitalized Patients: A Randomized Clinical Trial

Ortigoza, Mila B; Yoon, Hyunah; Goldfeld, Keith S; Troxel, Andrea B; Daily, Johanna P; Wu, Yinxiang; Li, Yi; Wu, Danni; Cobb, Gia F; Baptiste, Gillian; O'Keeffe, Mary; Corpuz, Marilou O; Ostrosky-Zeichner, Luis; Amin, Amee; Zacharioudakis, Ioannis M; Jayaweera, Dushyantha T; Wu, Yanyun; Philley, Julie V; Devine, Megan S; Desruisseaux, Mahalia S; Santin, Alessandro D; Anjan, Shweta; Mathew, Reeba; Patel, Bela; Nigo, Masayuki; Upadhyay, Rabi; Kupferman, Tania; Dentino, Andrew N; Nanchal, Rahul; Merlo, Christian A; Hager, David N; Chandran, Kartik; Lai, Jonathan R; Rivera, Johanna; Bikash, Chowdhury R; Lasso, Gorka; Hilbert, Timothy P; Paroder, Monika; Asencio, Andrea A; Liu, Mengling; Petkova, Eva; Bragat, Alexander; Shaker, Reza; McPherson, David D; Sacco, Ralph L; Keller, Marla J; Grudzen, Corita R; Hochman, Judith S; Pirofski, Liise-Anne; Parameswaran, Lalitha; Corcoran, Anthony T; Rohatgi, Abhinav; Wronska, Marta W; Wu, Xinyuan; Srinivasan, Ranjini; Deng, Fang-Ming; Filardo, Thomas D; Pendse, Jay; Blaser, Simone B; Whyte, Olga; Gallagher, Jacqueline M; Thomas, Ololade E; Ramos, Danibel; Sturm-Reganato, Caroline L; Fong, Charlotte C; Daus, Ivy M; Payoen, Arianne Gisselle; Chiofolo, Joseph T; Friedman, Mark T; Wu, Ding Wen; Jacobson, Jessica L; Schneider, Jeffrey G; Sarwar, Uzma N; Wang, Henry E; Huebinger, Ryan M; Dronavalli, Goutham; Bai, Yu; Grimes, Carolyn Z; Eldin, Karen W; Umana, Virginia E; Martin, Jessica G; Heath, Timothy R; Bello, Fatimah O; Ransford, Daru Lane; Laurent-Rolle, Maudry; Shenoi, Sheela V; Akide-Ndunge, Oscar Bate; Thapa, Bipin; Peterson, Jennifer L; Knauf, Kelly; Patel, Shivani U; Cheney, Laura L; Tormey, Christopher A; Hendrickson, Jeanne E
Importance/UNASSIGNED:There is clinical equipoise for COVID-19 convalescent plasma (CCP) use in patients hospitalized with COVID-19. Objective/UNASSIGNED:To determine the safety and efficacy of CCP compared with placebo in hospitalized patients with COVID-19 receiving noninvasive supplemental oxygen. Design, Setting, and Participants/UNASSIGNED:CONTAIN COVID-19, a randomized, double-blind, placebo-controlled trial of CCP in hospitalized adults with COVID-19, was conducted at 21 US hospitals from April 17, 2020, to March 15, 2021. The trial enrolled 941 participants who were hospitalized for 3 or less days or presented 7 or less days after symptom onset and required noninvasive oxygen supplementation. Interventions/UNASSIGNED:A unit of approximately 250 mL of CCP or equivalent volume of placebo (normal saline). Main Outcomes and Measures/UNASSIGNED:The primary outcome was participant scores on the 11-point World Health Organization (WHO) Ordinal Scale for Clinical Improvement on day 14 after randomization; the secondary outcome was WHO scores determined on day 28. Subgroups were analyzed with respect to age, baseline WHO score, concomitant medications, symptom duration, CCP SARS-CoV-2 titer, baseline SARS-CoV-2 serostatus, and enrollment quarter. Outcomes were analyzed using a bayesian proportional cumulative odds model. Efficacy of CCP was defined as a cumulative adjusted odds ratio (cOR) less than 1 and a clinically meaningful effect as cOR less than 0.8. Results/UNASSIGNED:Of 941 participants randomized (473 to placebo and 468 to CCP), 556 were men (59.1%); median age was 63 years (IQR, 52-73); 373 (39.6%) were Hispanic and 132 (14.0%) were non-Hispanic Black. The cOR for the primary outcome adjusted for site, baseline risk, WHO score, age, sex, and symptom duration was 0.94 (95% credible interval [CrI], 0.75-1.18) with posterior probability (P[cOR<1] = 72%); the cOR for the secondary adjusted outcome was 0.92 (95% CrI, 0.74-1.16; P[cOR<1] = 76%). Exploratory subgroup analyses suggested heterogeneity of treatment effect: at day 28, cORs were 0.72 (95% CrI, 0.46-1.13; P[cOR<1] = 93%) for participants enrolled in April-June 2020 and 0.65 (95% CrI, 0.41 to 1.02; P[cOR<1] = 97%) for those not receiving remdesivir and not receiving corticosteroids at randomization. Median CCP SARS-CoV-2 neutralizing titer used in April to June 2020 was 1:175 (IQR, 76-379). Any adverse events (excluding transfusion reactions) were reported for 39 (8.2%) placebo recipients and 44 (9.4%) CCP recipients (P = .57). Transfusion reactions occurred in 2 (0.4) placebo recipients and 8 (1.7) CCP recipients (P = .06). Conclusions and Relevance/UNASSIGNED:In this trial, CCP did not meet the prespecified primary and secondary outcomes for CCP efficacy. However, high-titer CCP may have benefited participants early in the pandemic when remdesivir and corticosteroids were not in use. Trial Registration/ Identifier: NCT04364737.
PMID: 34901997
ISSN: 2168-6114
CID: 5084962

Endoscopic photoconversion reveals unexpectedly broad leukocyte trafficking to and from the gut

Morton, Angela M; Sefik, Esen; Upadhyay, Rabi; Weissleder, Ralph; Benoist, Christophe; Mathis, Diane
Given mounting evidence of the importance of gut-microbiota/immune-cell interactions in immune homeostasis and responsiveness, surprisingly little is known about leukocyte movements to, and especially from, the gut. We address this topic in a minimally perturbant manner using Kaede transgenic mice, which universally express a photoconvertible fluorescent reporter. Transcutaneous exposure of the cervical lymph nodes to violet light permitted punctual tagging of immune cells specifically therein, and subsequent monitoring of their immigration to the intestine; endoscopic flashing of the descending colon allowed specific labeling of intestinal leukocytes and tracking of their emigration. Our data reveal an unexpectedly broad movement of leukocyte subsets to and from the gut at steady state, encompassing all lymphoid and myeloid populations examined. Nonetheless, different subsets showed different trafficking proclivities (e.g., regulatory T cells were more restrained than conventional T cells in their exodus from the cervical lymph nodes). The novel endoscopic approach enabled us to evidence gut-derived Th17 cells in the spleens of K/BxN mice at the onset of their genetically determined arthritis, thereby furnishing a critical mechanistic link between the intestinal microbiota, namely segmented filamentous bacteria, and an extraintestinal autoinflammatory disease.
PMID: 24753589
ISSN: 1091-6490
CID: 3983422

Efficient 18F-Labeling of Synthetic Exendin-4 Analogues for Imaging Beta Cells

Keliher, Edmund J; Reiner, Thomas; Thurber, Greg M; Upadhyay, Rabi; Weissleder, Ralph
A number of exendin derivatives have been developed to target glucagon-like peptide 1 (GLP-1) receptors on beta cells in vivo. Modifications of exendin analogues have been shown to have significant effects on pharmacokinetics and, as such, have been used to develop a variety of therapeutic compounds. Here, we show that an exendin-4, modified at position 12 with a cysteine conjugated to a tetrazine, can be labeled with 18F-trans-cyclooctene and converted into a PET imaging agent at high yields and with good selectivity. The agent accumulates in beta cells in vivo and has sufficiently high accumulation in mouse models of insulinomas to enable in vivo imaging.
PMID: 23997998
ISSN: 2191-1363
CID: 3983412

Accurate measurement of pancreatic islet beta-cell mass using a second-generation fluorescent exendin-4 analog

Reiner, Thomas; Thurber, Greg; Gaglia, Jason; Vinegoni, Claudio; Liew, Chong Wee; Upadhyay, Rabi; Kohler, Rainer H; Li, Li; Kulkarni, Rohit N; Benoist, Christophe; Mathis, Diane; Weissleder, Ralph
The hallmark of type 1 diabetes is autoimmune destruction of the insulin-producing β-cells of the pancreatic islets. Autoimmune diabetes has been difficult to study or treat because it is not usually diagnosed until substantial β-cell loss has already occurred. Imaging agents that permit noninvasive visualization of changes in β-cell mass remain a high-priority goal. We report on the development and testing of a near-infrared fluorescent β-cell imaging agent. Based on the amino acid sequence of exendin-4, we created a neopeptide via introduction of an unnatural amino acid at the K(12) position, which could subsequently be conjugated to fluorophores via bioorthogonal copper-catalyzed click-chemistry. Cell assays confirmed that the resulting fluorescent probe (E4(×12)-VT750) had a high binding affinity (~3 nM). Its in vivo properties were evaluated using high-resolution intravital imaging, histology, whole-pancreas visualization, and endoscopic imaging. According to intravital microscopy, the probe rapidly bound to β-cells and, as demonstrated by confocal microscopy, it was internalized. Histology of the whole pancreas showed a close correspondence between fluorescence and insulin staining, and there was an excellent correlation between imaging signals and β-cell mass in mice treated with streptozotocin, a β-cell toxin. Individual islets could also be visualized by endoscopic imaging. In short, E4(×12)-VT750 showed strong and selective binding to glucose-like peptide-1 receptors and permitted accurate measurement of β-cell mass in both diabetic and nondiabetic mice. This near-infrared imaging probe, as well as future radioisotope-labeled versions of it, should prove to be important tools for monitoring diabetes, progression, and treatment in both experimental and clinical contexts.
PMID: 21768367
ISSN: 1091-6490
CID: 3983402

Bone marrow stromal cell transplants prevent experimental enterocolitis and require host CD11b+ splenocytes

Parekkadan, Biju; Upadhyay, Rabi; Dunham, Joshua; Iwamoto, Yoshiko; Mizoguchi, Emiko; Mizoguchi, Atsushi; Weissleder, Ralph; Yarmush, Martin L
BACKGROUND & AIMS/OBJECTIVE:Bone marrow stromal cells (MSCs) are being evaluated as a cellular therapeutic for immune-mediated diseases. We investigated the effects of MSCs in mice with chemically induced colitis and determined the effects of CD11b(+) cells based on the hypothesis that MSCs increase numbers of regulatory T cells. METHODS:Colitis was induced in mice using trinitrobenzene sulfonic acid; symptoms were monitored as a function of MSC delivery. An immunomodulatory response was determined by measuring numbers of regulatory T cells in mesenteric lymph nodes. In vitro cocultures were used to assess the interaction of MSCs with regulatory T cells and CD11b(+) cells; findings were supported using near-infrared tracking of MSCs in vivo. We chemically and surgically depleted splenic CD11b(+) cells before colitis was induced with trinitrobenzene sulfonic acid to monitor the effects of MSCs. We adoptively transferred CD11b(+) cells that were cocultured with MSCs into mice with colitis. RESULTS:Intravenous grafts of MSCs prevented colitis and increased survival times of mice. Numbers of Foxp3(+) regulatory T cells increased in mesenteric lymph nodes in mice given MSCs. MSCs increased the numbers of Foxp3(+) splenocytes in a CD11b(+) cell-dependent manner. Transplanted MSCs colocalized near splenic CD11b(+) cells in vivo. Loss of CD11b(+) cells eliminated the therapeutic effect of MSCs. MSCs increased the anticolitis effects of CD11b(+) cells in mice. CONCLUSIONS:MSC transplants, delivered by specific parameters, reduce colitis in mice. Interactions between MSC and CD11b(+) regulatory T cells might be used to develop potency assays for MSCs, to identify nonresponders to MSC therapy, and to create new cell grafts that are composed of CD11b(+) cells preconditioned by MSCs.
PMID: 20955701
ISSN: 1528-0012
CID: 3983392

Bioorthogonal turn-on probes for imaging small molecules inside living cells

Devaraj, Neal K; Hilderbrand, Scott; Upadhyay, Rabi; Mazitschek, Ralph; Weissleder, Ralph
Glowing tags: a series of activatable ("turn-on") tetrazine-conjugated fluorescent probes was developed, which react rapidly in an inverse-electron-demand [4+2] cycloaddition with strained dienophiles such as trans-cyclooctene, thereby strongly increasing the fluorescence intensity. The novel turn-on probes were applied for intracellular live-cell imaging of a microtubuli-binding trans-cyclooctene modified taxol.
PMID: 20306505
ISSN: 1521-3773
CID: 3983382

Systems-level modeling of cancer-fibroblast interaction

Wadlow, Raymond C; Wittner, Ben S; Finley, S Aidan; Bergquist, Henry; Upadhyay, Rabi; Finn, Stephen; Loda, Massimo; Mahmood, Umar; Ramaswamy, Sridhar
Cancer cells interact with surrounding stromal fibroblasts during tumorigenesis, but the complex molecular rules that govern these interactions remain poorly understood thus hindering the development of therapeutic strategies to target cancer stroma. We have taken a mathematical approach to begin defining these rules by performing the first large-scale quantitative analysis of fibroblast effects on cancer cell proliferation across more than four hundred heterotypic cell line pairings. Systems-level modeling of this complex dataset using singular value decomposition revealed that normal tissue fibroblasts variably express at least two functionally distinct activities, one which reflects transcriptional programs associated with activated mesenchymal cells, that act either coordinately or at cross-purposes to modulate cancer cell proliferation. These findings suggest that quantitative approaches may prove useful for identifying organizational principles that govern complex heterotypic cell-cell interactions in cancer and other contexts.
PMID: 19727395
ISSN: 1932-6203
CID: 3983372

Improved detection of ovarian cancer metastases by intraoperative quantitative fluorescence protease imaging in a pre-clinical model

Sheth, Rahul Anil; Upadhyay, Rabi; Stangenberg, Lars; Sheth, Rucha; Weissleder, Ralph; Mahmood, Umar
OBJECTIVES/OBJECTIVE:Cytoreductive surgery is a cornerstone of therapy in metastatic ovarian cancer. While conventional white light (WL) inspection detects many obvious tumor foci, careful histologic comparison has shown considerable miss rates for smaller foci. The goal of this study was to compare tumor detection using WL versus near infrared (NIR) imaging with a protease activatable probe, as well as to evaluate the ability to quantify NIR fluorescence using a novel quantitative optical imaging system. METHODS:A murine model for peritoneal carcinomatosis was generated and metastatic foci were imaged using WL and NIR imaging following the i.v. administration of the protease activatable probe ProSense750. The presence of tumor was confirmed by histology. Additionally, the ability to account for variations in fluorescence signal intensity due to changes in distance between the catheter and target lesion during laparoscopic procedures was evaluated. RESULTS:NIR imaging with a ProSense750 significantly improved upon the target-to-background ratios (TBRs) of tumor foci in comparison to WL imaging (minimum improvement was approximately 3.5 fold). Based on 52 histologically validated samples, the sensitivity for WL imaging was 69%, while the sensitivity for NIR imaging was 100%. The effects of intraoperative distance changes upon fluorescence intensity were corrected in realtime, resulting in a decrease from 89% to 5% in signal variance during fluorescence laparoscopy. CONCLUSIONS:With its molecular specificity, low background autofluorescence, high TBRs, and quantitative signal, optical imaging with NIR protease activatable probes greatly improves upon the intraoperative detection of ovarian cancer metastases.
PMID: 19135233
ISSN: 1095-6859
CID: 3983352