Ani Baghdasaryan

All Publications

• A human autoimmune organoid model reveals IL-7 function in coeliac disease. Nature Santos, A. J., van Unen, V., Lin, Z., Chirieleison, S. M., Ha, N., Batish, A., Chan, J. E., Cedano, J., Zhang, E. T., Mu, Q., Guh-Siesel, A., Tomaske, M., Colburg, D., Varma, S., Choi, S. S., Christophersen, A., Baghdasaryan, A., Yost, K. E., Karlsson, K., Ha, A., Li, J., Dai, H., Sellers, Z. M., Chang, H. Y., Dunn, J. C., Zhang, B. M., Mellins, E. D., Sollid, L. M., Fernandez-Becker, N. Q., Davis, M. M., Kuo, C. J. 2024

  Abstract

  In vitro models of autoimmunity are constrained by an inability to culture affected epithelium alongside the complex tissue-resident immune microenvironment. Coeliac disease (CeD) is an autoimmune disease in which dietary gluten-derived peptides bind to the major histocompatibility complex (MHC) class II human leukocyte antigen molecules (HLA)-DQ2 or HLA-DQ8 to initiate immune-mediated duodenal mucosal injury1-4. Here, we generated air-liquid interface (ALI) duodenal organoids from intact fragments of endoscopic biopsies that preserve epithelium alongside native mesenchyme and tissue-resident immune cells as a unit without requiring reconstitution. The immune diversity of ALI organoids spanned T cells, B and plasma cells, natural killer (NK) cells and myeloid cells, with extensive T-cell and B-cell receptor repertoires. HLA-DQ2.5-restricted gluten peptides selectively instigated epithelial destruction in HLA-DQ2.5-expressing organoids derived from CeD patients, and this was antagonized by blocking MHC-II or NKG2C/D. Gluten epitopes stimulated a CeD organoid immune network response in lymphoid and myeloid subsets alongside anti-transglutaminase 2 (TG2) autoantibody production. Functional studies in CeD organoids revealed that interleukin-7 (IL-7) is a gluten-inducible pathogenic modulator that regulates CD8+ T-cell NKG2C/D expression and is necessary and sufficient for epithelial destruction. Furthermore, endogenous IL-7 was markedly upregulated in patient biopsies from active CeD compared with remission disease from gluten-free diets, predominantly in lamina propria mesenchyme. By preserving the epithelium alongside diverse immune populations, this human in vitro CeD model recapitulates gluten-dependent pathology, enables mechanistic investigation and establishes a proof of principle for the organoid modelling of autoimmunity.

  View details for DOI 10.1038/s41586-024-07716-2

  View details for PubMedID 39048815

• Intratumor injected gold molecular clusters for NIR-II imaging and cancer therapy. Proceedings of the National Academy of Sciences of the United States of America Baghdasaryan, A., Liu, H., Ren, F., Hsu, R., Jiang, Y., Wang, F., Zhang, M., Grigoryan, L., Dai, H. 2024; 121 (5): e2318265121

  Abstract

  Surgical resections of solid tumors guided by visual inspection of tumor margins have been performed for over a century to treat cancer. Near-infrared (NIR) fluorescence labeling/imaging of tumor in the NIR-I (800 to 900 nm) range with systemically administrated fluorophore/tumor-targeting antibody conjugates have been introduced to improve tumor margin delineation, tumor removal accuracy, and patient survival. Here, we show Au25 molecular clusters functionalized with phosphorylcholine ligands (AuPC, ~2 nm in size) as a preclinical intratumorally injectable agent for NIR-II/SWIR (1,000 to 3,000 nm) fluorescence imaging-guided tumor resection. The AuPC clusters were found to be uniformly distributed in the 4T1 murine breast cancer tumor upon intratumor (i.t.) injection. The phosphocholine coating afforded highly stealth clusters, allowing a high percentage of AuPC to fill the tumor interstitial fluid space homogeneously. Intra-operative surgical navigation guided by imaging of the NIR-II fluorescence of AuPC allowed for complete and non-excessive tumor resection. The AuPC in tumors were also employed as a photothermal therapy (PTT) agent to uniformly heat up and eradicate tumors. Further, we performed in vivo NIR-IIb (1,500 to 1,700 nm) molecular imaging of the treated tumor using a quantum dot-Annexin V (QD-P3-Anx V) conjugate, revealing cancer cell apoptosis following PTT. The therapeutic functionalities of AuPC clusters combined with rapid renal excretion, high biocompatibility, and safety make them promising for clinical translation.

  View details for DOI 10.1073/pnas.2318265121

  View details for PubMedID 38261618

• Shortwave-infrared-light-emitting probes for the in vivo tracking of cancer vaccines and the elicited immune responses. Nature biomedical engineering Ren, F., Wang, F., Baghdasaryan, A., Li, Y., Liu, H., Hsu, R., Wang, C., Li, J., Zhong, Y., Salazar, F., Xu, C., Jiang, Y., Ma, Z., Zhu, G., Zhao, X., Wong, K. K., Willis, R., Christopher Garcia, K., Wu, A., Mellins, E., Dai, H. 2023

  Abstract

  Tracking and imaging immune cells in vivo non-invasively would offer insights into the immune responses induced by vaccination. Here we report a cancer vaccine consisting of polymer-coated NaErF4/NaYF4 core-shell down-conversion nanoparticles emitting luminescence in the near-infrared spectral window IIb (1,500-1,700 nm in wavelength) and with surface-conjugated antigen (ovalbumin) and electrostatically complexed adjuvant (class-B cytosine-phosphate-guanine). Whole-body wide-field imaging of the subcutaneously injected vaccine in tumour-bearing mice revealed rapid migration of the nanoparticles to lymph nodes through lymphatic vessels, with two doses of the vaccine leading to the complete eradication of pre-existing tumours and to the prophylactic inhibition of tumour growth. The abundance of antigen-specific CD8+ T lymphocytes in the tumour microenvironment correlated with vaccine efficacy, as we show via continuous-wave imaging and lifetime imaging of two intravenously injected near-infrared-emitting probes (CD8+-T-cell-targeted NaYbF4/NaYF4 nanoparticles and H-2Kb/ovalbumin257-264 tetramer/PbS/CdS quantum dots) excited at different wavelengths, and by volumetrically visualizing the three nanoparticles via light-sheet microscopy with structured illumination. Nanoparticle-based vaccines and imaging probes emitting infrared light may facilitate the design and optimization of immunotherapies.

  View details for DOI 10.1038/s41551-023-01083-5

  View details for PubMedID 37620621

  View details for PubMedCentralID 7157724

• Phosphorylcholine-conjugated gold-molecular clusters improve signal for Lymph Node NIR-II fluorescence imaging in preclinical cancer models. Nature communications Baghdasaryan, A., Wang, F., Ren, F., Ma, Z., Li, J., Zhou, X., Grigoryan, L., Xu, C., Dai, H. 2022; 13 (1): 5613

  Abstract

  Sentinel lymph node imaging and biopsy is important to clinical assessment of cancer metastasis, and novel non-radioactive lymphographic tracers have been actively pursued over the years. Here, we develop gold molecular clusters (Au25) functionalized by phosphorylcholine (PC) ligands for NIR-II (1000-3000nm) fluorescence imaging of draining lymph nodes in 4T1 murine breast cancer and CT26 colon cancer tumor mouse models. The Au-phosphorylcholine (Au-PC) probes exhibit 'super-stealth' behavior with little interactions with serum proteins, cells and tissues in vivo, which differs from the indocyanine green (ICG) dye. Subcutaneous injection of Au-PC allows lymph node mapping by NIR-II fluorescence imaging at an optimal time of ~ 0.5 - 1hour postinjection followed by rapid renal clearance. Preclinical NIR-II fluorescence LN imaging with Au-PC affords high signal to background ratios and high safety and biocompatibility, promising for future clinical translation.

  View details for DOI 10.1038/s41467-022-33341-6

  View details for PubMedID 36153336

• In vivo non-invasive confocal fluorescence imaging beyond 1,700 nm using superconducting nanowire single-photon detectors. Nature nanotechnology Wang, F., Ren, F., Ma, Z., Qu, L., Gourgues, R., Xu, C., Baghdasaryan, A., Li, J., Zadeh, I. E., Los, J. W., Fognini, A., Qin-Dregely, J., Dai, H. 2022

  Abstract

  Light scattering by biological tissues sets a limit to the penetration depth of high-resolution optical microscopy imaging of live mammals in vivo. An effective approach to reduce light scattering and increase imaging depth is to extend the excitation and emission wavelengths to the second near-infrared window (NIR-II) at >1,000 nm, also called the short-wavelength infrared window. Here we show biocompatible core-shell lead sulfide/cadmium sulfide quantum dots emitting at ~1,880 nm and superconducting nanowire single-photon detectors for single-photon detection up to 2,000 nm, enabling a one-photon excitation fluorescence imaging window in the 1,700-2,000 nm (NIR-IIc) range with 1,650 nm excitation-the longest one-photon excitation and emission for in vivo mouse imaging so far. Confocal fluorescence imaging in NIR-IIc reached an imaging depth of ~1,100 μm through an intact mouse head, and enabled non-invasive cellular-resolution imaging in the inguinal lymph nodes of mice without any surgery. We achieve in vivo molecular imaging of high endothelial venules with diameters as small as ~6.6 μm, as well as CD169 + macrophages and CD3 + T cells in the lymph nodes, opening the possibility of non-invasive intravital imaging of immune trafficking in lymph nodes at the single-cell/vessel-level longitudinally.

  View details for DOI 10.1038/s41565-022-01130-3

  View details for PubMedID 35606441

• Molecule-like and lattice vibrations in metal clusters PHYSICAL CHEMISTRY CHEMICAL PHYSICS Ramankutty, K., Yang, H., Baghdasaryan, A., Teyssier, J., Nicu, V., Buergi, T. 2022; 24 (22): 13848-13859

  Abstract

  We report distinct molecule-like and lattice (breathing) vibrational signatures of atomically precise, ligand-protected metal clusters using low-temperature Raman spectroscopy. Our measurements provide fingerprint Raman spectra of a series of noble metal clusters, namely, Au25(SR)18, Ag25(SR)18, Ag24Au1(SR)18, Ag29(S2R)12 and Ag44(SR)30 (-SR = alkyl/arylthiolate, -S2R = dithiolate). Distinct, well-defined, low-frequency Raman bands of these clusters result from the vibrations of their metal cores whereas the higher-frequency bands reflect the structure of the metal-ligand interface. We observe a distinct breathing vibrational mode for each of these clusters. Detailed analyses of the bands are presented in the light of DFT calculations. These vibrational signatures change systematically when the metal atoms and/or the ligands are changed. Most importantly, our results show that the physical, lattice dynamics model alone cannot completely describe the vibrational properties of ligand-protected metal clusters. We show that low-frequency Raman spectroscopy is a powerful tool to understand the vibrational dynamics of atomically precise, molecule-like particles of other materials such as molecular nanocarbons, quantum dots, and perovskites.

  View details for DOI 10.1039/d1cp04708f

  View details for Web of Science ID 000801987400001

  View details for PubMedID 35616625

• High-precision tumor resection down to few-cell level guided by NIR-IIb molecular fluorescence imaging. Proceedings of the National Academy of Sciences of the United States of America Wang, F., Qu, L., Ren, F., Baghdasaryan, A., Jiang, Y., Hsu, R., Liang, P., Li, J., Zhu, G., Ma, Z., Dai, H. 2022; 119 (15): e2123111119

  Abstract

  SignificanceSurgical removal of tumors has been performed to combat cancer for over a century by surgeons relying on visual inspection and experience to identify margins between malignant and healthy tissues. Herein, we present a rare-earth down-conversion nanoparticle-anti-CD105 conjugate for cancer targeting and a handheld imager capable of concurrent photographic imaging and fluorescence/luminescence imaging. An unprecedented tumor-to-muscle ratio was achieved by near-infrared-IIb (NIR-IIb, 1,500 to 1,700 nm) imaging during surgery, 100 times higher than previous organic dyes for unambiguous determination of tumor margin. The sensitivity/biocompatibility/safety of the probes and instrumentation developed here open a paradigm of imaging-guided surgery at the single-cell level, meeting all major requirements for clinical translation to combat cancer and save human lives.

  View details for DOI 10.1073/pnas.2123111119

  View details for PubMedID 35380898