Formula: C1195H1863N337O388S8
Molecular Weight: 27415.44 Da
ɛ280 = 37150 M-1 cm-1
Expression and Purification of Proteins. 5 µL of Kanamycin (stocked at 50 mg/mL) was added to a culture tube containing 5 mL 2xYT media and inoculated with a stab of protein (cloned into a NEB T7 Shuffle Express cell line). The culture was incubated at 30 ºC, with shaking at 250 RPM, for 16 hours. Each culture was transferred to a 2 L baffled flask containing 500 mL of autoclaved 2xYT media and 500 µL of Kanamycin (25 mg) and shaken at 30 ºC in an Innova 42R (New Brunswick Scientific) incubator for 4.5-5 hours (until the OD600 reached ~ 0.8). The cultures were then cooled to ~ 16°C and induced with IPTG (2.5 mM final concentration). The induced cultures were shaken overnight (20–24 hours) at 16 ºC. The bacteria were harvested the next day by centrifugation (3900 rpm for 10 min) and the pellet was reconstituted in 1x PBS with Dnase I and a tablet of protease inhibitor cocktail (EDTA free). The cells were lysed by sonication on an ice bath in 5 second increments over 10 minutes. The resulting bacterial lysate was centrifuged (11000 rpm for 20 min) to remove cellular debris. The supernatant was added to a 50 mL Kontes Flex column (Kimbal Kontes Glassware) containing 3 mL of Nickel-NTA histidine binding resin that was preequilibrated with 1x PBS buffer. This column was placed on a rotating shaker at room temperature for 1–2 hrs. After this period, the supernatant was drained from the column using gravity and the column washed with 1x PBS buffer twice. Weakly bound proteins were first washed off the resin using a low concentration elution buffer (2x 10 mL, 10 mM imidazole, 1x PBS pH 7.4 @ 25 ºC). The bound protein was then eluted from the resin using elution buffer (15 mL, 150 mM imidazole, 1x PBS pH 7.4 @ 25 ºC). The eluate was then concentrated to 0.5 mL in a 15 mL Microcon 10 kDa Centrifugal Filter Unit (Millipore) and subsequently purified by size exclusion chromatography (SEC) via an Akta FPLC (Cytiva), on a Hi-Load 16/60 Superdex 200 column using 1x PBS, pH 7.4 as the running buffer at 4 ºC. Pure fractions were determined by SDS-PAGE, pooled together with buffer exchange to 1x PBS, and stocked at either − 20 ºC or 4 ºC.
Enzymatic Bioconjugation and Click Chemistry Reactions. Bioconjugation reactions occurred in mild conditions (20 mM HEPES at pH 7.4, 150 mM NaCl, and 10 mM CaCl2) between eSrtA (100 µM) and a nanobody containing a C-terminal ligation tag (75 µM) using a primary amine containing functional group (20 mM). Reactions occurred with mixing by a rotary shaker overnight (16 h) and were quenched by the addition of a 1:1 volume of a chelating agent EDTA containing solution (20 mM HEPES at pH 7.4, 300 mM NaCl, and 10 mM EDTA) under rotation for one hour. After the reaction was stopped, the solution was concentrated and buffer exchanged to 1x PBS (without NaCl or MgCl2) three times by centrifugal dialysis. The protein solution was then immobilized to Nickel-NTA histidine binding resin at least 2 hours, and unbound protein was collected by washing the resin with 1x PBS. For nanobodies that contain a histidine in the native sequence, proteins were eluted in mild conditions (10 mM Imidazole in 1x PBS). Collected protein was concentrated and buffer exchanged to 1x PBS by centrifugal dialysis and verified by ESI-MS and SDS-PAGE. Click chemistry reactions proceeded by the addition of 5 eq. (molar) of the complementary handle (e.g. if an azide was placed on the nanobody, the click chemistry reaction would proceed with the addition of 5 eq. of DBCO-containing moiety). For Cy5 conjugations, sulfo-Cy5 was used from Sigma Aldrich, and Cy5 was also used from Broadpharm. After 48 hours of reaction between the protein-azide and the DBCO-moiety under rotation at room temperature, the mixture was purified by centrifugal dialysis four times with 1x PBS, and verified for purity by UV-VIS, ESI-MS, and SDS-PAGE.
Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis (SDS-PAGE). Protein samples were diluted in 1x PBS to 10 µM before analysis. 10 µL of the protein sample was mixed with 10 µL of reducing Laemmli buffer. Samples were boiled at 95 ºC for 5 minutes, and 15 µL of each sample was loaded into a 15-well, 4–15% Tris-glycine precast polyacrylamide gel (Biorad) and ran at a constant 150 V with 343 mA for 30 minutes. The gel was then either first imaged for fluorescence on a UV-transilluminator or directly stained using Coomassie-B-250.
Electrospray Ionization Liquid Chromatography Mass Spectrometry (ESI-MS). Proteins were buffer exchanged into ammonium acetate (pH 5.5) and concentrated to approximately 100 µM. ESI-MS data were collected using an Agilent 6210A time-of-flight (TOF) mass spectrometer at a range of 50 − 20,000 m/z over a period of two minutes. Data were analyzed with Agilent MassHunter IM-MS Acquisition Data software to reveal m/z data, where files were condensed across the two-minute run. These m/z data were deconvoluted using a maximum entropy deconvolution calculation using UniDec to give the deconvoluted mass spectra using background subtraction between a range of 1,000–5,000 m/z and with an export range of 5,000–50,000 Da.
Computational Modeling and Analysis of nAlb Nanobody. nAlb was modeled in silico using RoseTTAFold (GitHub; RosettaCommons) and binding between HSA (PDB: 1AO6) and nAlb was predicted using RosettaDock through ROSIE (Rosetta Online Server that Includes Everyone; Pittsburgh). After an initial screening for best fits of the docking between HSA (receptor) and nAlb (ligand), the best fit model was then returned for rescreening to confirm an optimal energy conformation between the structures. The final structures of nAlb and the bound nAlb-HSA complex were exported to PyMOL for generating a figure of the structure.
Isothermal Titration Calorimetry. All proteins used were equilibrated in buffer at indicated pH values by titration using HCl (aq.) or NaOH (aq.) in PBST, 150 mM NaCl, 3 mM EDTA, 0.05% Tween 20. Albumin (HSA and rMSA) and PD-L1 receptor titrations were run on the TA Instruments Affinity ITC instrument (TA Instruments, New Castle, DE). 350 µL of albumin or the PD-L1 receptor was added to the sample cell (10–20 µM), and either the nAlb nanobody (125–250 µM) or nPD-L1 nanobody (250 µM) was loaded into the injection syringe, respectively. The reference cell contained ultrapure water and was changed after each titration experiment. All runs used the following instrument settings: cell temperature 298 K, reference power 10 µCal/second, initial delay 240 seconds, stirring speed 75 rpm, feedback mode/gain high, and injection volume 2 µL for 10 seconds, titration spacings at 120 second intervals, and a filter period of 10 seconds. Data were analyzed using the provided NanoAnalyze software for the instrument to determine thermodynamics of binding from an independent model.
Tritosome Degradation Assay and MALDI-TOF MS. Tritosomes (BioIVT) were prepared and activated by combining 70 µL of nuclease-free water, 10x of catabolic buffer (K5200, BioIVT), and 100 µL of pure lysosomes (H0610.L, BioIVT) and incubating the mixture at 37 ºC for 15 minutes. Samples for lysosomal degradation were added at 0.5 µM (10 µL) with the tritosome mixture and incubated at 37 ºC over a period of 48 hours. Aliquots were taken from the reaction mixture at distinct time points and flash frozen with liquid nitrogen and stored at -80 ºC to stop the reaction. Activity was determined by observing molecular weight shifts in the substrate using matrix assisted laser desorption and ionization time-of-flight mass spectrometry (MALDI-TOF MS). 3 µL of matrix (15 mg mL-1 THAP in dry acetone) was combined with 1 µL of aliquoted sample and spotted on a stainless steel MALDI-MS plate (Bruker). Matrix was evaporated using compressed-air, read on a Bruker AutoFlex MALDI-TOF, and processed with the FlexControl software (Bruker Daltonics). The laser pulse rate was 500 Hz and spectra were obtained with a mass window of 400–4000 m/z at the highest resolution for the instrument (4.00 GS/s). FlexAnalysis software (Bruker Daltonics) was used to obtain baseline spectra for all samples. Data were exported and plotted using MATLAB to generate figures showing m/z spectra at distinct time points.
Synthesis and NMR Verification of DBCO-PEG11 -diABZI. Synthesis of the DBCO conjugated STING agonist (diABZI) is reported in Fig. S2, with NMR verification in Fig. S3-4. We first generated a STING agonist that features a reactive amine handle, which was synthesized in four steps. Briefly: Aryl amination of an aryl chloride 1 with an amine 2 gave a di-nitro analog, compound 3. The di-nitro compound 3 was subjected to reduction using sodium dithionite in methanol, generating a di-amine moiety 4. Compound 4 was then treated with isothiocyanate, followed by EDC coupling, to reveal a boc-protected analog, compound 5. Next, the boc-group from compound 5 was deprotected by treating with TFA:DCM. To a stirred solution of amine 6 (100 mg, 0.089 mmol, 1 eq.) in 5 mL DMF, hunig’s base was added (77 µL, 0.44 mmol, 5 eq.) under argon atmosphere at room temperature. After stirring for 5 min, a solution of activated NHS ester (98 mg, 0.098 mmol, 1.1 eq.) in DMF (5 mL) was added dropwise and stirred overnight (16 h). The solvent was evaporated to get crude product 7, which was purified by silica gel column chromatography using a mixture of Methanol/Dichloromethane as an eluent (5–25% MeOH) to get the desired product as a solid (70mg, 0.042mmol, yield 43%). (Rf = 0.5 in 20% MeOH in DCM). 1H NMR (400 MHz, DMSO) δ 8.01–7.93 (m, 2H), 7.88 (t, J = 5.7 Hz, 1H), 7.75 (t, J = 5.7 Hz, 1H), 7.67–7.60 (m, 4H), 7.49–7.42 (m, 3H), 7.38–7.27 (m, 7H), 6.49 (d, J = 7.1 Hz, 2H), 5.88–5.79 (m, 2H), 5.01 (d, J = 13.9 Hz, 1H), 4.91 (dd, J = 29.6, 4.2 Hz, 4H), 4.53–4.49 (m, 4H), 3.98 (t, J = 6.0 Hz, 2H), 3.72 (s, 3H), 3.60–3.57 (m, 2H), 3.54 (t, J = 6.5 Hz, 2H), 3.47 (broads, 46H), 3.30–3.26 (m, 2H), 3.14–3.05 (m, 4H), 2.26 (t, J = 6.5 Hz, 2H), 2.09 (s, 3H), 2.08 (s, 3H), 2.01–1.96 (m, 1H), 1.78–1.72 (m, 1H), 1.68 (p, J = 6.5 Hz, 2H), 1.28–1.27 (m, 6H). 13C NMR (151 MHz, DMSO) δ 171.57, 171.50, 170.52, 168.06, 167.33, 152.50, 152.45, 152.06, 148.88, 145.50, 145.28, 144.65, 140.37, 140.33, 132.87, 130.54, 130.49, 130.07, 129.37, 128.62, 128.58, 128.44, 128.25, 128.13, 127.24, 125.60, 122.99, 121.86, 120.11, 120.04, 114.67, 109.72, 108.61, 106.00, 105.83, 105.58, 70.21, 70.14, 70.10, 70.00, 69.94, 69.45, 67.26, 56.45, 55.34, 53.85, 46.05, 45.05, 42.12, 38.95, 36.57, 35.61, 30.80, 30.17, 29.13, 18.46, 17.17, 16.58, 13.57, 12.74. HRMS (ESMS) Calculated for C84H111N15O21 [M + Na]+: 1688.7977, found 1688.7982.
Synthesis and NMR Verification of Amine-PEG3 -Triazole-PEG11 -diABZI. To a stirred solution of amine-PEG3-azide (3.14 mg, 14.4 µmol, 3 eq) in a 1:1 MeCN:H2O mixture (4 mL), hunig’s base (3.10 mg, 24.0 µmol, 5 eq) and 450 µL of a stock solution of 10.8 millimolar DBCO-PEG11-diABZI in DMSO (8.0 mg, 4.8 µmol, 1 eq) were added and stirred overnight. Acetonitrile was removed by slowly passing an air stream through the reaction flask. When the reaction mixture reduced to half, the aqueous mixture was frozen at -80 ºC for 8 h and then lyophilized. Diethyl ether was added (×3) and vigorously shaken with diethyl ether. The mixture was decanted to remove excess amine-PEG3-azide. After three washes with diethyl ether, it was dried overnight in a vacuum chamber to obtain the desired compound (7 mg, 3.7 µmol, 77% yield). 1H NMR (400 MHz, DMSO) δ 8.03–7.95 (m, 2H), 7.90 (t, J = 5.7 Hz, 1H), 7.85–7.74 (m, 2H), 7.67 (d, J = 3.8 Hz, 1H), 7.65–7.62 (m, 2H), 7.59–7.52 (m, 2H), 7.51–7.45 (m, 1H), 7.40–7.26 (m, 7H), 6.50 (d, J = 7.1 Hz, 2H), 5.88–5.78 (m, 2H), 5.01–4.86 (m, 4H), 4.63–4.45 (m, 6H), 4.10–4.02 (m, 2H), 3.99 (t, J = 6.0 Hz, 2H), 3.76 (t, J = 5.5 Hz, 2H), 3.73 (s, 3H), 3.47 (broads, 60H), 2.96–2.88 (m, 5H), 2.27 (t, J = 6.0 Hz, 2H), 2.20–2.13 (m, 2H), 2.10 (s, 3H), 2.09 (s, 3H), 2.03–1.91 (m, 3H), 1.79–1.66 (m, 2H), 1.57–1.44 (m, 1H), 1.37–1.31 (m, 1H), 1.28–1.22 (m, 6H). MALDI-TOF MS Calculated for C92H129N19O24 [M + H]+: 1884.9458, found 1884.150.
In Vitro Reporter Cell Assays. Cell reporter assays were utilized in THP1-Dual and A549-Dual cell lines, as adapted from the manufacture protocols. Briefly, cells were plated at a density of 50,000 cells/well in a total volume of 180 µL of supplemented media in cell-culture treated 96-well plates overnight. After 24 h, cells were dosed with 20 µL of treatment groups (for a total volume of 200 µL/well in a 10:1 dilution, with either a 1:1 or 2:1 dilution down the plate) overnight. After 24 h of treatment, cells were pelleted at 1500 RPM for 5 minutes in the centrifuge, and 20 µL of supernatant was plated in a white-walled 96-well plate for analysis by QUANTI-Luc™ (InvivoGen) assay. After loading in a plate reader, 50 µL of QUANTI-Luc reagent was added to each well and luminescence was measured for determination of cell-based activity. To the remaining cells in the cell-culture treated 96-well plate, 30 µL of Cell-Titer Glo reagent (Promega) was added and the plate was incubated at 37 ºC for 1 h. After incubation, the plate was loaded into the plate reader and luminescence was measured to determine cell-mediated toxicity. Data were recorded in triplicate and analyzed in GraphPad PRISM (Version 10), with data reported with standard error of the mean (SEM).
In Vitro BMDC/BMDM Maturation and Activity. Bone marrow primary cells were harvested from both the femur and tibia of female C57BL/6 mice, aged between 6–8 weeks. After harvesting, cells were flushed with cold 1x PBS, centrifuged at 1500 rpm for 5 min, and resuspended in complete media (RPMI 1640 supplemented with 10% HI-FBS (Gibvo), 100 U ml − 1 penicillin, 100 µg ml − 1 streptomycin (Gibco), 2 mM L-glutamine, 10 mM HEPES, 1 mM sodium pyruvate, 1x non-essential amino acids, and 50 µM ß-mercaptoethanol. 20 ng/mL GM-CSF was added to culture BMDCs, and 20 ng/mL of M-CSF was added to culture BMDMs. A single cell suspension was generated by passing the collected cells through a 70 µm sterile cell strainer (Fisherbrand™; Thermo Fisher Scientific) and cells were then plated in non-tissue-culture-treated petri dishes (REF 351029; Corning) and incubated at 37°C with 5% CO2. Cells were provided with fresh culture media – supplemented with growth factors as described above – on days 3, 5, and 7. On day 8, the cells were collected and confirmed for either CD11c+ expression (BMDCs) or CD11b+F4/80+ expression (BMDM) using flow cytometry with fluorescent anti-CD11c (Clone N418; BioLegend), anti-CD11b (Clone M1/70, BioLegend), and anti-F4/80 (Clone BM8, BioLegend) antibodies. Primary cells were seeded into 12-well plates for analysis by qPCR or 96-well plates for in vitro flow cytometry.
Quantitative RT-PCR (qPCR). RNA was extracted either from animal tissue (by TissueLyser II, Qiagen) or from in vitro cell cultures using the RNeasy® Plus Mini Kit (Qiagen) according to the manufacturer’s protocol. cDNA was generated through a reverse transcriptase reaction using the iScript cDNA synthesis kit (Bio-Rad), by following the manufacturer’s instructions. To run the qPCR, cDNA was mixed with TaqMan gene expression kits (primer and master mix) to a final volume of 20 µL and run on the Bio-Rad CFX Connect Real-time System, with a threshold cycle number determination made by the Bio-Rad CFX manager software V.3.0. Primers used included: mouse Ifnb1 (Mm00439552_s1), mouse Tnf (Mm00443258_m1), mouse Cxcl10 (Mm00445235_m1), mouse Cxcl1 (Mm04207460_m1), and mouse Hmbs (Mm01143545_m1). Gene expression was first normalized to the housekeeping gene, Hmbs, and then normalized to the PBS treatment within groups using the 2− ddCt analysis method.
Colocalization Analysis. A density of 10 x 103 EMT6 and RAW 264.7 cells per well was plated in a glass bottom 96-well plate. After culturing for 12 h, cells were treated for 1.5 h. nAlb-Cy5 (2 µM) and nGFP-Cy5 (2 µM) were added to each well and further incubated for 4 h. Cells were treated with 50 nM of Lysotracker Green (Invitrogen) and 2 µM Hoechst (Invitrogen) for 10 min after the end of the incubation period. Wells were washed three times with phenol red free medium and visualized under confocal microscope (Zeiss LSM880). High-magnification images were obtained using the 40x objective lens. Manders’ coefficient calculated by using Image J Software for colocalization analysis.
Flow cytometry for In Vitro Uptake Studies. EMT-6 and RAW 264.7 cells were seeded in 6 well-plates at 5×105 cells per well. After 24 h, cells were treated with and without 5-(N-Ethyl-N-isopropyl) amiloride (EIPA, 50 µM) for 1.5 h. nAlb-Cy5 (2 µM) and nGFP-Cy5 (2 µM) were added to each well and further incubated for 4 hours. EMT6 Cells were digested with 0.25% trypsin. RAW 264.7 cells were collected by scraping. Both cells were washed three times with cold 1x PBS (1ml), and stained with DAPI for live/dead staining. Cells were washed and suspended in a Staining buffer (1x PBS, 2.5% FBS, 2.5 mM EDTA), and detected by flow cytometry. Bone marrow-derived macrophages (BMDMs) were isolated from 6- to 8-week-old female C57BL/6 mice. Cells were collected and BMDMs (CD11b+/F4/80+) were confirmed by flow cytometry. Fluorescence acquisition was carried out on Cytek Aurora spectral flow cytometer and analyzed on FlowJo V.10.8.1.
Evaluation of Nanobodies in Tumor Models. For B16.F10, B16.F10-LUC, or B16.F10-OVA tumor models, 6–8 week old C57BL/6 mice (The Jackson Laboratory) were used. For EMT6 tumor models, 6–8 week old Balb/C female mice (The Jackson Laboratory) were used. Tumors were generated in B16.F10 and B16.F10-OVA models by subcutaneous injection of 5 x 105 cancer cells, suspended in 100 µL of PBS, at the right flank of the mouse. B16.F10-LUC inoculations were performed by intravenous (I.V.) injection at a volume of 100 µL and using 1 x 106 cancer cells. EMT6 inoculations were orthotopic and placed at the left-side 4th mammary fat pad at a volume of 100 µL and using 5 x 105 cancer cells. When the volume of tumors reached ~ 75–100 mm3, mice were treated by I.V. injection of nanobodies or free diABZI compound 3 (using 40% PEG400 as an excipient for free diABZI, Sigma), or intraperitoneal (I.P) injection of commercial anti-PD-L1 IgG (Clone BE0101, Bio X Cell) (100 µL per injection). For MDSC inhibition studies with the SX-682 inhibitor (CXCL1/2 inhibitor, MedChemExpress), control high fat chow and SX-682 formulated chow (Research Diets, Inc.) were fed to mice at day 4 after tumor inoculation and continued through the course of the study. For studies evaluating the effects of MDSC, NK cell, CD4+ T cell, and CD8+ T cell depletion, mice (n = 6–8/group) with either EMT6 or B16.F10 tumors were intraperitoneally administered anti-Ly6G/Gr-1 (RB6-8C5; 200 µg), anti-asialo-GM1 (Poly21460; 100 µL for EMT6), anti-NK1.1 (PK136; 200 µL for B16.F10), anti-CD4+ (YTS-191; 200 µg), or anti-CD8+ (2.43; 200 µg) antibodies one day prior to each treatment with nanobody conjugates. Tumor volume calculations were calculated using Vtumor = L × W2 × 0.5, in which Vtumor is tumor volume, L is tumor length, and W is tumor width. Tumor volume, total murine mass, and murine well-being were recorded for the duration of the study. The endpoint for maximum tumor volume (i.e. survival) during studies was 1500 mm3.
Nanobodies in Spontaneous Tumor Model Studies. A cohort of female FVB/N-Tg (MMTV-PyVT)634Mul mice, bred in house, was used for these studies. Study animals were weighed, and mammary glands palpated twice weekly starting at 6 weeks of age. Tumor diameters in two dimensions were obtained using calipers. Treatment for the full cohort was initiated when first palpable tumors appeared at approximately 8–10 weeks of age. The mice received the nanobody-STING agonist conjugate or vehicle control for a total of 3 treatments at 7 day intervals. The study was terminated 22 days after the first treatment. At necropsy, tumors were removed and a wet weight obtained for each. One tumor was fixed in 10% buffered formalin for histological analysis. All tumor measurements and analysis were performed by individuals blinded to treatment group.
Adoptive OT-I T Cell Transfer in B16.F10-OVA Tumor Model. CD45.1+/− OT-I mice were a gift of Y. Kim at Vanderbilt University Medical Center. 6–8 week C57BL/6 CD45.1+/− OT-I mice were euthanized and spleens were harvested using EasySep Mouse CD8+ T Cell Isolation Kit (STEMCELL Technologies). Briefly, T cells were activated in vitro in supplemented RPMI 1640 (Gibco) with 10% HI-FBS (Gibco), 1% penicillin/streptomycin (Gibco), 50 µM ß-mercaptoethanol (MilliporeSigma), 1 mM sodium pyruvate, minimum essential medium NEAA (non-essential amino acids) (Gibco), 10 mM HEPES (Gibco), recombinant mouse interleukin-2 (10 U/ml; MilliporeSigma), and Dynabeads Mouse T-Activator CD3/CD28 (at a bead-to-cell ratio of 1:1; Gibco) at 37 ºC in a CO2 incubator (5%). After 5 days, T cells were magnetically separated from Dynabeads and allowed to rest for 24 h before use. The following day, in the B16.F10-OVA model, 5 x 105 OT-I CD8+ T cells were adoptively transferred by retro-orbital injection.
Western Blot Analysis. Mice were euthanized and tumors (EMT6 and B16.F10) were harvested and 500 µl RIPA buffer (Sigma) supplemented with protease inhibitors (Sigma) was added in approximately 10 mg of tissue. Tissue was homogenized using a bead mill tissue homogenizer (TissueLyser II; Qiagen) and kept the on ice for 30 min. For in vitro analysis of STING expression in EMT6 cells were incubated in RIPA buffer for 10 minutes on ice. Protein concentration was measured using a BCA protein assay kit (Thermo Scientific). Equal amount of protein (30 µg) was subjected to SDS-PAGE and transferred onto nitrocellulose membranes using the semi-dry transfer protocol (Bio-Rad). After transfer, membranes were probed with each respective primary antibody (anti-SPARC, anti-TBK1, anti-p-TBK1, anti-sting, anti Hsp-90 and anti-β-actin) overnight at 4°C. Following incubation, the membranes were probed with HRP-conjugated secondary antibodies. All antibodies were purchased from Cell signaling. Protein bands were visualized using ECL western blotting substrate (Thermo scientific). Images of immunoblots were obtained using a LI-COR Odyssey Imaging System.
Immunofluorescent analysis of EMT6 Tumors. 5-micron Paraffin-embedded tissue sections were prepared for immunofluorescence and stained with anti-CD31 (cell signaling #77699; 1:500), anti-SPARC (cell signaling #5420, 1:500), and anti-CD45 (cell signaling #70257; 1:500). Tissue slides were deparaffined in xylene and rehydrated in serial ethanol dilutions. Antigen retrieval was performed by heating slides for 17 minutes in Tris EDTA buffer, pH 9 in a pressure cooker at 110 ºC. Slides were cooled to room temperature and then blocked with 2.5% horse serum (vector labs). After blocking, slides were incubated overnight at 4 ºC with primary antibody in horse serum. Slides were then incubated in anti-rabbit HRP secondary (vector labs) for 1 h at room temperature the following day and subsequently incubated in 1:500 Opal 520 (green) or Opal 570 (red) (Akoya) for 10 minutes. For serial staining, slides were stripped using Citric Acid buffer, pH 6.1 in a pressure cooker at 110 ºC for 2 minutes and then staining was repeated using different antibody and Opal fluorophore. After the last Opal staining, slides were mounted using antifade gold mount with DAPI (Invitrogen). Stained images were acquired using a Keyence digital microscope system. Images were analyzed with Fiji software. Quantification of markers was done by measuring total amount of fluorescence divided by total number of cells (DAPI).
Flow Cytometric Experiments and Analysis. EMT6 tumor bearing Balb/c and B16.F10-OVA bearing C57BL/6 mice were euthanized either 24 h or 48 h after final treatment. Spleens and tumors were harvested, weighed, and placed on ice. Tumors were digested in RPMI 1640 media containing a tumor dissociation kit (collagenase III and deoxyribonuclease I, Miltenyi Biotech). Tumors were further dissociated using an OctoMACS separator (Miltenyi Biotech) and incubated for 30 min at 37 ºC for complete digestion. Tumors and spleens were mashed and separated into single cell suspensions using a 70 µm cell strainer (Fisherbrand™; Thermo Fisher Scientific) and red blood cells were lysed twice using ACK lysis buffer (Gibco). Cells were resuspended in flow buffer (1x PBS supplemented with 2% FBS and 50µM dasatinib), counted, and stained with Fc-block (aCD16/32, 2.4G2, Tonbo) for 15min at 4 ºC, and then stained with the appropriate antibodies for 1hr at 4 ºC (found below and in Tables S1-S2). After staining, cells were then washed again with FACS buffer, fixed with 2% paraformaldehyde for 10min, washed again with FACS buffer containing AccuCheck counting beads, and analyzed on a Cytek Aurora flow cytometer. All flow cytometry data were analyzed using FlowJo software (version 10; Tree Star; https://www.flowjo.com/solutions/flowjo). Representative flow cytometry plots and gating schemes are shown in Fig. S34-41.
Antibodies for Immune Cell Memory in B16.F10-OVA Tumor Model. The antibodies used were eFluor 780 viability dye (eBioscience), anti-CD3e (145-2C11, BV510, BioLegend), anti-CD8a (KT15, FITC, Invitrogen), anti-CD4 (RM4-5, violetFluor™ 450 Anti-Mouse CD4, FisherScientific), anti-CD69 (H1.2F3, PE/Cy7, BioLegend), anti-CD44 (IM7, PE/Cy5, BioLegend), and anti-CD62L (MEL-14, BV711, BioLegend), and PE-labeled pOVA/H-2Kb tetramer.
Pharmacokinetics and Ex Vivo Imaging Experiments. Healthy (Balb/c or C57BL/6) and EMT6 tumor bearing (Balb/c) mice were injected with 100 µL of Cy5 (either as free dye or as a nanobody conjugate) at a dose of 2 mg/kg intravenously. For pre-treatment with the diABZI conjugated nanobody, a dose was prepared at 1.25 µg diABZI in 100 µL total and injected 3 days prior to Cy5 dosing. Blood draws were taken using heparinized capillary tubes (DWK Life Sciences) at discrete time points up to five days after injection. 1 µL of blood was mixed with 50 µL of PBS, centrifuged, and the diluted plasma was collected for analysis. Prescence of Cy5 was determined by fluorescence intensity using a plate reader, with an excitation wavelength of 645 nm and an emission wavelength of 675 nm. Pharmacokinetic analysis was performed in GraphPad Prism (V10) using either a one-phase decay or two-phase decay, in which the reported half-life is the second phase (elimination). Biodistribution studies were performed by excising and weighing hearts, lungs, livers, spleens, kidneys, and tumors. Tissues were washed in 1x PBS and transferred to the stage of the IVIS Lumina III (PerkinElmer). After IVIS, tissue were homogenized using cell disruption in a volume of 200 µL 1x PBS. Homogenized tissue were centrifuged and the supernatant containing the Cy5 dye was quantified for the tissue was determined by fluorescence intensity using a plate reader. A standard curve was generated of free DBOC-Cy5 dye in 1x PBS and concentrations of Cy5 in tissue were calculated by fitting the standard curve to a linear regression. Fluorescence (radiant efficiency) was measured with a maximum value of 1.56 x 1010, and a minimum of 8.21 x 108, and areas were drawn manually for organs to generate average radiant efficiency values (per cm2) using the Living Image software (version 4.5). For B16.F10-LUC studies, lungs were placed in black 12-well plates (Cellvis) and incubated for 5 min in a solution of 1 mg/mL Pierce™ D-Luciferin, Monopotassium Salt (Thermo Fisher Scientific) in 1x PBS. Images were taken on the IVIS and luminescence was quantified as total radiant flux (p/s) for each set of lungs
Serum Analysis for Anti-VHH Antibodies. Mice were pre-treated with PBS or nAlb-diABZI (1.25 µg dose of diABZI) three times every three days, or treated once with nAlb-diABZI (1.25 µg dose of diABZI). 14 days after the first dose, blood was collected by cardiac puncture in and allowed to clot to extract serum. Tubes were centrifuged at 2000 x g for 15 min at 4 ºC, and the serum was then collected and diluted directly in PBS (1:4 to 1:8192) for analysis. MonoRab rabbit anti-camelid VHH antibody plates (GenScript) were used to determine anti-VHH antibodies in mouse serum. 3 µg in 100 µL of anti-albumin nanobody were loaded into each well of the 96 well plate and allowed to incubate in the pre-coated antibody plate, sealed, and incubated at 37 ºC for 30 minutes. The plate was washed with 200 µL of PBST four times. Either the diluted mouse serum or a commercial Rabbit anti-Camelid VHH antibody (Genscript; A01860) were added in serial dilutions to the wells of the plate at a volume of 100 µL. The plate was sealed and incubated at 37 ºC for 30 minutes, followed by washing four times with 200 µL of PBST. A commercial secondary Goat anti-Mouse IgG-FITC conjugate (Invitrogen; 31547) or secondary anti-Rabbit IgG-FITC conjugate (Sigma; F9887) was added to the mouse serum or commercial anti-VHH, respectively, at 100 µL and incubated for 30 minutes at 37 ºC before washing with PBST four times (200 µL). The plate was quantified using the fluorescence intensity of FITC (ex: 495 nm, em: 515 nm) using a plate reader.
Ex VivoPlasma Analyte Analysis. Blood was collected by either cheek bleed or cardiac puncture in K2EDTA-coated tubes (BD Biosciences). Tubes were centrifuged at 2000 x g for 15 min at 4 ºC, and the plasma was collected for analysis. Cytokine levels were evaluated using either the LEGENDplex™ Mouse Anti-Virus Response Panel (BioLegend) or the LEGENDplex™ Mouse Cytokine Panel 2 (BioLegend), both with V-bottom plates, according to manufacturer’s instructions, and data were collected using flow cytometry. Cytokine concentrations were interpolated from standard curves using an asymmetric sigmoidal 5-paramater logistic curve fits (GraphPad Prism V10). Bar plots comparing groups and heat maps of averaged values for groups were generated to analyze results.
NanoString nCounter Analysis of EMT6 Tumors. After three treatments of nAlb-diABZI (1.25 µg, n = 3–4), AP-diABZI (1.25 µg, n = 3–4), or PBS (n = 3–4) in EMT6 bearing female Balb/c mice, tumors were isolated, digested, and 100 ng of RNA was isolated, as described in the qPCR section. RNA was hybridized to the IO360 PanCancer panel, as well as through a selected gene panel, of target-specific fluorescent barcodes and analyzed using NanoString nCounter MAX Analysis system. The fold change for genes within groups was calculated by comparing against the average normalized gene expression values within PBS treated mice. All statistical significance, and clustering analysis, was performed in R (http://cran.r-project.org) based on the genes provided in the IO360 PanCancer panel.
Safety Statement. All research performed in this study was done so with careful consideration of any risks that are inherent to the materials, instruments, and experiments performed. All research safety guidelines and considerations as provided by the safety data sheets (SDS) and university guides were adhered to for the duration of this study.
Statistics. All data were plotted and statistical analysis performed using Prism 10 (GraphPad) software. Unless indicated in the figures, all data are presented as mean ± SEM. For comparisons between two groups, unpaired two-tailed Student’s t-tests were performed as indicated. For multiple comparisons a one-way ANOVA was performed with post-hoc Tukey’s correction for multiple comparisons. For tumor volume, statistically significance was examined through a two-way ANOVA followed by Tukey’s adjustment for multiple comparisons. A Log-rank (Mantel-Cox) test was used to compare Kaplan-Meyer survival data.