Synthesis and characterization of novel ssDNA X-aptamers targeting Growth Hormone Releasing Hormone (GHRH)

Burcu Ayhan-Sahin; Zeynep-Elif Apaydın; Pınar Obakan-Yerlikaya; Elif-Damla Arisan; Ajda Coker-Gurkan

doi:10.1371/journal.pone.0260144

. 2022 Jan 21;17(1):e0260144. doi: 10.1371/journal.pone.0260144

Synthesis and characterization of novel ssDNA X-aptamers targeting Growth Hormone Releasing Hormone (GHRH)

Burcu Ayhan-Sahin ^1,^#, Zeynep-Elif Apaydın ^1,^#, Pınar Obakan-Yerlikaya ², Elif-Damla Arisan ³, Ajda Coker-Gurkan ^4,^*

Editor: Paulo Lee Ho⁵

PMCID: PMC8782341 PMID: 35061691

Abstract

Background

Growth Hormone Releasing Hormone (GHRH), 44 amino acids containing hypothalamic hormone, retains the biological activity by its first 29 amino acids. GHRH (NH2 1–29) peptide antagonists inhibit the growth of prostate, breast, ovarian, renal, gastric, pancreatic cancer in vitro and in vivo. Aptamers, single-strand RNA, or DNA oligonucleotides are capable of binding to target molecules with high affinity. Our aim in this study is to synthesize and select X-aptamers against both GHRH NH2 (1–29) and GHRH NH2 (1–44) and demonstrate synthesized aptamers’ target binding activity as well as serum stability.

Methods and results

Aptamers against GHRH NH2 (1–44) and NH2 (1–29) peptides were synthesized, and binding affinity (K_d) of 24 putative X-aptamers was determined by the dot-blot method, co-immunofluorescence staining and, SPR analysis. The serum stability of TKY.T1.08, TKY1.T1.13, TKY.T2.08, TKY.T2.09 X-aptamers was 90–120 h, respectively. The dose-dependent binding of TKY1.T1.13, TKY.T2.08, TKY.T2.09 X-aptamers on GHRHR in MIA PaCa-2 was approved by co-IF assay results. Moreover, SPR analysis indicated the K_d (4.75, 1.21, and 4.0 nM) levels of TKY2.T1.13, TKY.T2.08, TKY.T2.09 putative X-aptamers, respectively.

Conclusion

Our results illustrate the synthesis of 24 putative X-aptamers against both GHRH NH2 (1–44) and NH2 (1–29) peptides and TKY1.T1.13, TKY.T2.08, TKY.T2.09 X-aptamers have high serum stability, high target binding potential with low K_d levels.

Introduction

Cancer is a complex disease in which cells undergo malignant transformation via various genomic and proteomic alterations, leading to uncontrollable cellular growth and proliferation [1]. Globally, it is foreseen that one in eight men and one in ten women will die due to cancer in the 2020s [2]. Sustaining proliferation, inducing angiogenesis, and activating invasion/metastasis is essential hallmarks of cancer, according to Hanahan and Weinberg [3]. Many growth factors are involved in these processes, such as Insulin-like growth factor-I (IGF1), Epidermal Growth Factor (EGF), Transforming Growth Factor Beta (TGF-ß), Vascular Endothelial Growth Factor (VEGF) [4]. In addition, cancer cells are known to produce growth factors that induce their proliferation, and thus cell division is continually stimulated in these cells [5].

Growth Hormone Releasing Hormone (GHRH) is a hypothalamic neuropeptide that stimulates the pituitary gland for the production and secretion of Growth Hormone (GH) [6]. Although a full-size GHRH peptide comprises 44 amino acids, its biological activity resides in the first 29 amino acids in the N-terminal [7]. Instead of the neuroendocrine function, the peripheral expression of GHRH and its receptor is evident in various surgical samples of the prostate, breast, ovarian, and endometrial cancers [8]. The expression and secretion of GHRH in non-pituitary cell types imply the effect of GHRH on the regulation of cell proliferation, differentiation, and carcinogenesis [9]. GHRH peptide antagonists have been shown to trigger apoptotic cell death via inhibiting the GHRH signaling in the prostate, endometrial, colon, lung cancer in vitro and in vivo [6, 10]. In order to generate GHRH antagonists, we select aptamers due to their excessive specificity, high binding affinity, low toxicity, and non-immunogenic properties [11].

Aptamers are single-strand nucleic acid molecules (DNA or RNA) that can bind to target molecules such as proteins, peptides, carbohydrates, bacteria, viruses, and cancer cells for detection and diagnosis [11]. However, they are generally used as biosensors for detecting and diagnosing target molecules. VEGF aptamer (Macugen) is used for the treatment of macular degeneration [12]. The synthesis of aptamers is commonly performed by the SELEX (systemic evolution of ligands by exponential enrichment) method, a repeating amplification of nucleic acid with high binding affinity against the target molecule [13]. Nucleic acid modifications, truncations, labeling of aptamers increased the binding affinity of aptamers [11]. Recently, new generation aptamer synthesis has been performed using a magnetic bead-dependent modified ssDNA library for target binding and amplifying candidate sequences termed X-aptamer technology [14]. The most improved advantage of X-aptamer technology is synthesizing up to 5 different targets simultaneously with one SELEX method. Besides, modified nucleotides are included in the X-aptamer library to increase the stability and specificity of aptamers. However, the limitation of X-aptamer technology is that the molecular size of the target molecule or targets longer than 10 amino acid is assumed to be more preferred [14]. As there is no GHRH antagonist aptamer, we preferred to synthesize aptamers against GHRH 1–44 and 1–29. To synthesize X-aptamers that can capture every epitopic region, we selected full GHRH protein NH2 (1–44). Besides, as GHRH peptide antagonist select 1–29 region, we used GHRH NH2 (1–29) peptide as a target to synthesize X-aptamers. To illustrate, by comparing the binding affinity of GHRH antagonist X-aptamers, we aimed to synthesize, select X-aptamers against both GHRH NH2 (1–44) and NH2 (1–29) peptides.

Materials and methods

Cell lines and antibodies

HEK293 (CRL-1573), MIA PaCa-2 (CRL-1429), HT-29 (HTB-38), PC3 (CRL-1435), LNCaP (CRL-1740), and PNT1a (CRL-11609) cells were purchased from American Type Culture Collection (ATCC, Manassas, VA, USA). Each cell line was grown in MEM, DMEM, McCoy’s 5A, and RPMI medium (PAN Biotech, Aidenbach, Germany) completed by 10% fetal bovine serum (Gibco, Paisley, PA4, United Kingdom), 10000 U/mL penicillin, and 10 mg/mL streptomycin (PAN Biotech, Aidenbach, Germany) at 37°C in 5% CO₂ incubator (HERAcell 150, Thermo Scientific (Paisley, PA4, United Kingdom), respectively. Anti-His tag (1:1000), anti-GAPDH (1:1000) primary antibodies, HRP-conjugated anti-rabbit secondary antibody (1:3000), and HRP-conjugated anti-goat secondary antibody (1:3000) were obtained from Cell Signaling Technologies (Danvers, MA, USA). Anti-GHRH primary antibody (1:500) and anti-GHRHR antibody (1:1000) were purchased from Origene (Rockville, USA) and Santa Cruz Biotechnology (Dallas, Texas, USA), respectively. His-tagged (pCMV3-SP-N-His-NCV; CV023) and His-tagged GHRH (pCMV3-SP-His-ORF His-GHRH) plasmids were purchased from Sino Biological (Wayne, PA, USA).

Bacterial His-GHRH (1–44) protein isolation and purification

1.5 x 10⁸ cells/mL E. coli HB101 become competent by the CaCl₂ method [15] and then 500 μg/mL His-tagged and His-tagged GHRH plasmids transformed by the heat shock method [16]. Following the transformation, His- and His-GHRH expressing selective positive controls were grown at 37°C overnight; the pellets were obtained by centrifugation and resuspended in lysis buffer (20 mM Tris-HCl pH: 7.5, 300 mM NaCl, 2M Urea, 2% Triton X-100, 1 mg/mL lysozyme and 1X EDTA-free Protease Inhibitor Cocktail). After the sonication step, the pellets were resuspended in the inclusion body solubilization solution (20 mM Tris-HCl, 0.5 M NaCl, 5 mM imidazole, and 6 M guanidine hydrochloride), and His-GHRH protein was purified by Dynabeads^™ His-Tag Isolation and Pulldown magnetic beads (Invitrogen, Paisley, UK) according to the manufacturer’s instructions [17].

Expression of His-tagged GHRH peptide in HEK293 cells

HEK293 cells were seeded at 6-well plates with a seeding density of 1 x 10⁵ cells/well. Following cell attachment overnight, cells were transfected with 1 μg/mL His tagged (pCMV3-SP-N-His-NCV) and His-GHRH (pCMV3-SP-His-ORF) plasmids and 6 μL ScreenFect A (ScreenFect, Eggenstein-Leopoldshafen) for 48 h. After incubation, cells were selected by hygromycin (Neofroxx, Einhausen, Germany) with increasing concentration for two weeks.

RNA isolation and real-time PCR

Total RNA was extracted in HEK293 cells and putative His, His-GHRH expressing HEK293 cells by PureZol RNA isolation reagent (Bio-Rad, Hercules, California, USA). The first-strand cDNA was synthesized by the iScript cDNA synthesis kit (Bio-Rad). Primers for the GHRH gene were 5’-TATGCAGATGCCATCTTCAC-3’ and 5’- TCATCCCTGGGAGTTCCTGC-3’, and the 18S gene were 5’-CTACCACATCCAAGGAAGGCA-3’ and 5’-TTTTTCGTCACTACCTCCCCG-3’, respectively. Real-time PCR was performed in Bio-Rad CFX Connect Real-Time PCR Detection System with SYBR Green Supermix (Bio-Rad). 18S was used as a normalization control. The fold of change was calculated according to the PFAFFL method [18]. All reactions were run in triplicate.

GHRH ELISA assay

wt, His, His-GHRH expressing HEK293 cells, MIA PaCa-2, HT-29, LNCaP, PC3, PNT1A cells were seeded at 100 mm Petri dishes with a seeding density of 3 x 10⁶ cells/dish. Following overnight cell attachment, the media were concentrated via filtering by Amicon Ultra centrifugal filter (Merck, Massachusetts, USA). 100 μL of concentrated cellular media were used for GHRH ELISA assay (Elabscience, E-EL-H1146) according to the manufacturer’s instructions and were measured at 450 nm wavelength by a microplate reader (Multiskan, Thermo Scientific). The secreted levels of GHRH concentration were calculated according to standards. Since we do not have unlabeled aptamers to compete with labeled aptamers, we used labeled aptamers in competitive ELISA Assay instead of detection antibodies.

Immunoblotting

Total proteins were extracted using M-PER Mammalian protein extraction reagent (Thermo Fisher Scientific). Concentrations of total proteins were quantified by Bradford assay [19]. 80 μg cellular proteins were separated on 15% SDS-PAGE and transferred to the PVDF membrane (Thermo Fisher Scientific). Membranes were blocked by 5% non-fat dried milk in TBS-T solution (1X TBS, 0.1% Tween-20) and probed with primary antibodies against GHRH and His-tag, then incubated with secondary anti-goat horseradish peroxidase-conjugated IgG, and developed with enhanced chemiluminescence solutions, images were taken by ChemiDoc Imaging System (BioRad, Hercules, California, USA).

Immunofluorescence staining

wt, His-, His-GHRH expressing HEK293 cells, and MIA PaCa-2, HT-29, LNCaP, PC3, PNT1A cells were seeded with a seeding density of 1 x 10⁵ cells/well. Following the 48 h incubation period, cells were fixed (ice-cold methanol), permeabilized (0.1% Triton-X-100 in PBS), blocked (2% BSA in PBS) and probed with anti-rabbit anti-GHRH primary antibody (1:50), then incubated with anti-rabbit Alexa Fluor 488-conjugated Ig (1:250 dilution). Nuclear staining performed by 1 μg/mL DAPI and GHRH localization was observed fluorescence microscopy (Olympus, Japan). 1 x 10⁵ cells/well MIA PaCa-2 cells were seeded with a seeding density, incubated with selected x-aptamers (500 nM) for 72 h. Cells were fixed (ice-cold methanol), permeabilized (0.1% Triton-X-100 in PBS), and blocked (2% BSA in PBS), probed with appropriate primary antibodies (anti-mouse anti-GH primary or anti-goat anti-GHRHR primary antibody), then incubated with anti-mouse Alexa Fluor 555-conjugated secondary antibody or FITC-conjugated anti-goat secondary antibody, respectively. Cellular GH or GHRHR expressions were visualized by fluorescence microscopy (Olympus, Japan).

X-aptamer selection and synthesis

According to the instruction, X-aptamer selection was performed by the X-aptamer selection kit (AM Biotechnologies, Houston, USA). At the first step, the X-aptamer library was prepared as follows: the library resuspended in a selection buffer [1X PBS pH:7.4, 1 mM MgCl₂, 0.05% Tween20, 0.02% BSA], incubated at 95°C water bath for 5 minutes, and cooled down slowly to room temperature. We performed two a bead based aptamer selection; first a bead based aptamer selection, we used bacterial/eukaryotic GHRH 1–44 His-tagged peptides, and second a bead based aptamer selection used GHRH 1–29 peptide (Sigma, G6771) as a target. Due to kit instructions, for the first a bead based aptamer selection, 10 μg His-tagged bacterial and 10 μg eukaryotic His-tagged GHRH 1–44 peptide was used to pulldown by magnetic beads. In addition, for the second bead based aptamer selection, biotinylated GHRH 1–29 peptide was used for streptavidin magnetic bead isolation. Next, His-tag/biotinylated isolation and pulldown magnetic beads were prepared for negative selection by washing with a selection buffer and incubated with the prepared library for one hour at room temperature. After incubation, the library which did not bind to magnetic beads (i.e., negatively selected library) was transferred to a clean tube with the aid of a magnetic stand. Then, his-tagged target protein [GHRH 1–44 (bacterial and eukaryotic)] or biotinylated GHRH 1–29 was mixed with His-tag/streptavidin coated-magnetic beads, incubated for 30 minutes at room temperature, and target protein-bound magnetic beads were washed with a selection buffer. Next, negatively selected library and target-bound magnetic beads were incubated at room temperature for 90 minutes. Magnetic beads were washed with a selection buffer and resuspended in the selection buffer. Putative aptamers were cleaved by incubating with NaOH at 65°C for 30 minutes and neutralizing with Tris-HCl. Cleaved putative aptamers were transferred to a clean tube. Spin column buffer exchange was performed to eliminate NaOH, and a “cleaved oligonucleotide pool” was obtained. For the secondary selection process, four 1.5 mL centrifuge tubes were labeled Tube 1, Tube 2, Tube 3, Tube 7. Cleaved oligonucleotide pools and selection buffers were added to all four tubes. His-GHRH (1–44) protein was added to Tube 2 and Tube 3 and incubated with rotation at room temperature for one hour. His magnetic beads were added to Tube 2, Tube 3, and Tube 7 and incubated with rotation at room temperature for 30 minutes. 10 μL from the tubes used as a template for PCR reaction. The forward primer was common for all; however for tube 1, reverse primer 1, tube 2 reverse primer 2, tube 3 reverse primer 3, and tube 7 reverse primer 7 was used. PCR reaction prepared in total 100 μL volume as follows: 1X PCR Buffer, 2.5 mM MgCl₂, 0.2 mM dNTP, 0.4 μM forward primer, 0.4 μM indicated reverse primer, 1U Taq polymerase. The temperature condition was 94°C 1 minute, cycles of 94°C 30 seconds, 50°C 30 seconds, 72°C 1 minute, and the last extension at 72°C for 3 minutes. For each tube, 14, 18, 22 cycles of PCR were performed. PCR products were run on agarose gel, and images were obtained by UV Imaging System. For the four tubes, 25 cycles were performed, and all PCR products were mixed in one tube and resent back to the manufacturer for Illumina next-generation sequencing (AM Biotechnology, Texas, Huston, USA). Next-generation sequencing and synthesis of candidate x-aptamers with 5’ biotin tag were performed by the corresponding company (AM Biotechnology, Texas, Huston, USA) [14].

Dot-blot assay

Putative 24 X-aptamers were renaturated (95°C for 10 min), incubated with either GHRH NH2 (1–29) or GHRH NH2 (1–44) peptide in dot blot binding buffer (15 mM Tris, 100 mM NaCl, 1 mM MgCl₂) overnight at +4°C, blotted to nitrocellulose membrane (Invitrogen) as a small spot. As a negative control we used scramble aptamer which has a ΔG: -27.621 kJ (5’-TTTTTTTCAGACCAGCCGTGCACGACGAACCACAAGCAGGTGGGCCCA-3’) Following air dry of the membrane, HRP-Streptavidin conjugate (Thermo Fisher Scientific) was added onto each membrane spot, incubated for two hours at room temperature in dark, TMB substrate solution (Thermo Fisher Scientific) added, and images were taken by LCD Camera. The same protocol was performed for K_d determination of each putative aptamers by the dot-blot method. The K_d levels were determined in each aptamer dot spot intensity level by Sigma Plot v14.0 (https://systatsoftware.com/products/sigmaplot/) program.

Serum stability of putative X-aptamers

5 μL from each 100 μM putative X-aptamer against GHRH was mixed with 5 μL human serum (Sigma Aldrich, P2918, Massachusetts, USA) for 0–120 h at 37°C. Following each incubation period, 10 μL of the mixture loaded at 12% polyacrylamide gel electrophoresis and was visualized under the ChemiDoc MP imaging system (Bio-Rad Laboratories, Hercules, USA). DNaseI digested aptamers were used as positive controls.

Cyclic AMP assay analysis

To determine the impact of aptamers on cAMP levels, we performed Cyclic AMP XP® Assay Kit (CST, 4339). Both HT29 colon cancer and MIA Paca-2 pancreatic cancer cells were seeded at 12 well-plate with a density of 2 x 10⁴. Following cell attachment, adherent cells treated with selected X-aptamers for 72 h, and cAMP assay performed according to the manufacturer’s instructions.

GH and GHRHR expression profile by immunofluorescence

1 x 10⁵ cells/coverslip of MIA Paca-2 cells were seeded on coverslips at 6 wells. After cell attachment, 500 nM selected X-aptamers were treated. Following fixation, permeabilization, blocking and probing anti-goat anti-GH primary antibody (1:50 dilution) at +4°C overnight, anti-goat Alexa flour 555-conjugated secondary antibody (1:250) applied at +4°C for 1 h. Following washing, blocking, cells probed with anti-mouse anti-GHRHR primary antibody (1:50 dilution) at +4°C overnight. Then, anti-mouse FITC conjugated secondary antibody (1:250 dilution) was applied at +4°C for one hour. The nucleus was stained with DAPI and images visualized by fluorescence microscopy (Olympus, Japan).

Dose-dependent X-aptamer binding affinity by immunofluorescence

MIA PaCa-2 pancreatic cancer cells were seeded on coverslips with a density of 1 x 10⁵ cells/coverslip. Following cell attachment, x-aptamers were applied in a dose-dependent manner (0–500 nM), cells were fixed, permeabilized, blocked, and probed with anti-rabbit anti-GHRH primary antibody (1:50 dilution) at +4°C overnight. Then, the anti-rabbit Alexa Fluor 568-conjugated secondary antibody (1:250 dilution) was applied at +4°C for one hour, 1 μL streptavidin solution added, and incubated at 37°C for 30 min, and probed with Streptavidin-Alexa fluor 488 conjugate (1:1000 dilution) for one hour at RT. The nucleus was stained with DAPI and images were visualized by fluorescence microscopy (Olympus, Japan). GHRH siRNA silencing with/without aptamer treatment was used as a negative control for aptamer binding affinity. 50 nM GHRH siRNA (Ambion, AM16708) with 6 μL FuGENE 6 (Promega, E2691) transfection reagent for 48 h performed in MIA Paca-2 cells. Following siRNA incubation period 500 nM aptamer treated and aptamers probed with Streptavidin-Alexa fluor 488 conjugate and GHRH probed with anti-rabbit Alexa Fluor 568-conjugated secondary antibody.

SPR analysis

The CM-5 chip was loaded with the dose-dependent (250 nM-4000 nM) GHRH NH2 1–29 peptide (Sigma, G6771) in acetic acid solution. Following the incubation period, every three selected aptamers (TKY2.T1.13, TKY.T2.08, and TKY.T2.09 X-aptamers) with three repeats were run in BiaCore T200 (GE Healthcare Life Sciences, Uppsala, Sweden) for 120–12000 sec. Single Cycle Kinetics parameters were analyzed, and modeling was performed by kinetic analyses-heterogeneous ligands. SPR analysis was performed in SUNUM Center at SABANCI University (Istanbul-TURKEY).

Statistical analysis

All the experiments were analyzed statistically by two-way ANOVA using GraphPad Prism 8 (GraphPad Software, La Jolla, CA, USA). p-values considered statistically significant were given as *p<0.05, ** p < 0.01, *** p < 0.001, respectively. Error bars in the graphs generated using ± standard deviation (SD) values. The mean ± SD of the data representing ELISA assay and the qRT-PCR analysis was achieved from at least two experiments with three replicates.

Results

Purification of His-tagged GHRH peptide

To obtain a target for X-aptamer selection, both bacterial and eukaryotic His-GHRH NH2 (1–44) expressing cellular models were generated. To yield a high range of GHRH 1–44 peptide, we selected E.coli HB101 cells and for post-transcriptional modifications of GHRH 1–44, we used HEK293 cells. E.coli HB101 cells expressing His-tagged and His-tagged GHRH protein determined by immunoblotting following plasmids transformed by heat-shock method (Fig 1a). Solubilized inclusion bodies and His-magnetic bead pull-down extracts containing His-GHRH determined by immunoblotting, respectively (Fig 1b). Since the bacterial protein synthesis mechanism lacks post-translational modifications, HEK293 cells were used for target protein production. For this purpose, His tagged (pCMV3-SP-N-His-NCV) and His-tagged GHRH (pCMV3-SP-His-ORF) plasmids were transfected to HEK293 human embryonic kidney cells, and stable His-tagged and His-GHRH-tagged expressing HEK293 cells generated following increased concentration of hygromycin application for selection. Transcriptional and translational GHRH 1–44 expression was determined by RT-PCR (Fig 1c), and immunoblotting (Fig 1d). Besides, the immunofluorescence method was confirmed the intracellular expression of GHRH majorly in HEK293-His-tagged GHRH stable cell line (Fig 1e). Moreover, the HEK293-His-GHRH stable cell line secreted 685,38 pg/mL GHRH was determined by the ELISA method (Fig 1f).

Fig 1 — A GHRH (1–44) expression of bacterial colonies expressing His- and His-GHRH vectors demonstrated by immunoblotting. 1 E. *coli* HB101 His vector clone, 2 E. *coli* HB101 His-GHRH vector clone. B Purified His tagged bacterial GHRH 1–44 ligand was demonstrated by immunoblotting *via* anti-GHRH and anti-His tag antibodies, respectively. 1 His-GHRH expressing total bacterial lysate, 2 His-GHRH expressing solubilized pellets. Eukaryotic GHRH NH2 (1–44) expression in His-GHRH vector-transfected HEK293 cells was identified by C qRT-PCR, D immunoblotting, and E immunofluorescence. 1 HEK293 wt 2 HEK293 His-transfected 3 HEK293 His-GHRH transfected. F GHRH 1–44 concentration in the media of HEK293 cells was measured by Human GHRH ELISA. GAPDH was used as a loading control. 18S was used as an internal control. DAPI was used to indicate the nuclei of the cells.

Synthesis and selection of x-aptamers against GHRH peptide

To synthesize and select X-aptamers against both GHRH NH2 (1–44) and NH2 (1–29), we performed two a bead based aptamer selection according to the kit protocol. First bead based aptamer selection, purified 10 μg bacterial and 10 μg eukaryotic His-tagged GHRH used, cycle-course PCR performed as 14 cycles, 18 cycles, 22 cycles, and 25 cycles of last PCR performed to obtain samples for sequencing (Fig 2a). As bacterial and eukaryotic His-tagged GHRH protein has 10 Histidine amino acids at N terminal region, GHRH 1–29 peptide also used as a target for second bead based aptamer selection cycle-course and last PCR was also performed for GHRH (1–29) target (Fig 2b). All the samples were sequenced by Illumina next-generation sequencing via aligning 3’ conserved sequences and putative x-aptamers were synthesized with a 5’-biotin tag by a commercial company, AM Biotechnologies (Houston, USA). The sequences of putative x-aptamers were given in Fig 2c. Aptamers against bacterial His-tagged GHRH were TKY2.T1.01, TKY2.T1.02, TKY2.T1.03, TKY2.T1.04, TKY2.T1.05, TKY2.T1.06, TKY2.T1.08, TKY2.T1.10, TKY2.T1.11, TKY2.T1.12, TKY2.T1.13, TKY2.T1.15, TKY2.T1.16, TKY2.T1.17. TKY.T1.01, TKY.T1.02, TKY.T1.03, TKY.T1.04, TKY.T1.05 aptamers were against eukaryotic GHRH NH2 (1–44) peptide. Putative X-aptamers against GHRH 1–29 target named as TKY.T2.02, TKY.T2.06, TKY.T2.07, TKY.T2.08, TKY.T2.09.

Fig 2 — A First bead based aptamer selection against GHRH NH2 (1–44) target and B second bead based aptamer selection against GHRH NH2 (1–29) target was performed by using the X-aptamer kit. Tube #1: Cleaved oligunucleotide pool, Tube #2: Cleaved oligonucleotide pool+Magnetic beads+Prokaryotic GHRH (1–44) target, Tube #3: Cleaved oligonucleotide pool+Magnetic beads+Eukaryotic GHRH (1–44) target, Tube #7: Cleaved oligonucleotide pool+Magnetic beads. Cycle course PCR (up) and last PCR (down) amplification of the x-aptamer selection process were given. C Sequences of putative x-aptamers were determined by next-generation sequencing. D. Analysis for all 24 putative aptamers were performed by using MEME program (https://meme-suite.org/meme/).

Screening the binding affinity of putative X-aptamers to the target protein by dot blot assay and SPR analysis and illustrating the serum stability of each X-aptamer

To observe the binding affinity of X-aptamers to the target protein, the dot blot assay was performed. The dot intensities measured and fold of change of band intensities calculated by Graphpad Prism 8 program via using spot intensity. According to calculations, putative x-aptamers against GHRH 1–44 target TKY2.T1.01, TKY2.T1.02, TKY2.T1.03, TKY2.T1.04, TKY2.T1.05, TKY2.T1.08, TKY2.T1.10, TKY2.T1.12, TKY2.T1.13, TKY2.T1.15, TKY2.T1.17, TKY.T1.01, TKY.T1.02 and putative X-aptamers against GHRH 1–29 target TKY.T2.02, TKY.T2.06, TKY.T2.07, TKY.T2.08, TKY.T2.09 showed statistically significance in binding affinity (Fig 3a and 3b). Then binding affinity of X-aptamers to target assessed in increasing aptamer doses. The fold of change was calculated according to the dot intensities and dissociation constant (K_d) was calculated by nonlinear regression in GraphPad Prism software (https://www.graphpad.com/scientific-software/prism/) (Fig 3c). TKY2.T1.08, TKY2.T1.13, TKY.T2.08, and TKY.T2.09 were selected for further experiments according to obtained data. To determine the non-specific binding of selected X-aptamers against its target, we performed GHRH competitive ELISA assay and dot-blot analysis (Fig 3d). According to GHRH ELISA results, instead of using detection antibody, we used x-aptamers to competitively capture GHRH peptide. Dose-dependent X-aptamer exposure increases the absorbance of GHRH ELISA results in each aptamer. To confirm the ELISA results, we performed a dot-blot analysis in a dose-dependent manner. As we do not have any unlabeled aptamers, the GHRH antibody is used as a competitor for GHRH X-aptamers against GHRH peptide binding. Thus, we performed a GHRH ELISA assay. X-aptamers specifically bind to GHRH peptide like GHRH antibody and this effect sharply increased in a dose-dependent manner by both GHRH ELISA assay and dot-blot analysis (Fig 3d). To evaluate the serum stability of each putative aptamer, 0–120 h incubation of each aptamer with human serum at 37°C, the mixture visualized by polyacrylamide gel electrophoresis. According to the serum stability results, TKY2.T1.02, TKY2.T1.04, TKY2.T1.05, TKY2.T1.08, TKY2.T1.13, TKY2.T1.17, TKY.T2.05, TKY.T1.05, TKY.T2.02, TKY.T2.07, TKY.T2.08 and TKY.T2.09 X-aptamers were stable in human serum within 120 h period at 37°C (Fig 4a and 4b). To confirm the K_d levels for selected TKY2.T1.13, TKY.T2.08 and TKY.T2.09 X-aptamers, we performed SPR analysis. According to SPR analysis, K_d levels for TKY2.T1.13, TKY.T2.08, and TKY.T2.09 were determined as 4.75, 1.21, and 4.0 nM, respectively (Fig 4c).

Fig 3 — The binding affinity of putative X-aptamers was determined by dot blot assay against A GHRH NH2 (1–44) target and B GHRH NH2 (1–29) target. C Dose-dependent dot blot assay was performed in increasing doses (0–1000 nM) of X-aptamers. The scramble aptamer was used a negative control for dot-blot analysis. Dot intensities were measured by Image J (imagej.nih.gov/ij/) and analyzed by GraphPad Prism 8.0. Nonlinear regression analysis was performed by Sigma Plot v14.0 and K_d was calculated. D. The specific binding affinity of selected aptamers against GHRH peptide was determined by both GHRH sandwich ELISA assay (left panel) and dot-blot analysis (right panel) in a dose-dependent manner.

Fig 4 — A. Stability of each putative aptamer detected by polyacrylamide gel electrophoresis of serum and aptamer mixture at 37°C in time-dependent (0–120 h) manner. Each experiment was performed and repeated at least three times, given figures are the representative figure of one of the three assay repeat results. ns nonspecific, *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001 B. Binding affinity of selected x-aptamers to their specific target was demonstrated by Surface Plasmon Resonance analysis. After loading the CM-5 chip with the dose-dependent target molecule and incubation period, each aptamer was run in BiaCore T200 in triplicate for 120–12000 seconds.

GHRH expression and secretion profile of MIA PaCa-2, HT-29, PC3 cancer cells and PNT1A epithelial derived normal cell

To determine the binding affinity of X-aptamers on cellular GHRH target, at first, GHRH-expressing cells were determined. Pancreatic cancer cell line MIA PaCa-2, colorectal cancer cell line HT-29, prostate cancer cell line PC3 and LNCaP, and normal human prostate epithelial cell line PNT1a used for this purpose. Primarily, GHRH expression in these cell lines determined by immunofluorescence assay with anti-GHRH antibody and it was observed that all these cell lines expressed GHRH endogenously (Fig 5a). GHRH expression of these cells was also investigated by immunoblotting (Fig 5b). GHRH concentration in media was also calculated by human GHRH ELISA assay. GHRH concentration in media was about 1500 pg/mL in MIA PaCa-2, HT-29, and PC3 cells while the value is about 700 pg/mL in PNT1a cells (Fig 5c).

Fig 5 — A GHRH expression was figured out in MIA PaCa-2 pancreatic cancer, HT-29 colorectal cancer, PC3 prostate cancer, and PNT1a normal prostate epithelium cell lines by immunofluorescence. DAPI was used to observe the nuclei of the cells. B Translational expression of GHRH in MIA PaCa-2, HT-29, PC3, and PNT1a cells was determined by immunoblotting. ß-actin was used as a loading control. C. GHRH concentrations in media of MIA PaCa-2, HT-29, PC3, and PNT1a cells determined by Human GHRH ELISA.

Determination of dose-dependent binding affinity of x-aptamers on MIA PaCa-2 cells by immunofluorescence staining

To screen the dose-dependent binding affinity of TKY2.T1.08, TKY2.T1.13, TKY.T2.08, and TKY.T2.09 X-aptamers on MIA PaCa-2 cells, immunofluorescence was performed by using streptavidin-Alexa Fluor-488 as selected aptamers labeled with biotin at 5’-end. Due to immunofluorescence staining, both TKY2.T1.08 and TKY.T2.08 x-aptamers binding on MIA PaCa-2 membrane determined only after 50 nM X-aptamer treatment, and binding affinity increased in a dose-dependent manner [Fig 6a and 6e (left panel)]. However, significant binding was observed after 250 nM TKY2.T1.13, and 100 nM TKY.T2.09 X-aptamer treatments (Fig 6c and 6g). To demonstrate the binding of X-aptamers with GHRH ligand, we performed co-immunofluorescence staining with both Streptavidin-488 (aptamer detection) and Alexa-Fluor 565 (GHRH detection) [Fig 6b, 6d, 6f and 6h (right panel)]. Similar to screening immunofluorescence staining, each aptamer binding was determined on MIA PaCa-2 cells simultaneously with GHRH co-staining. Moreover, we demonstrated that silencing of GHRH expression inhibited X-aptamer binding by immunofluorescence assay (Fig 6b, 6d, 6f and 6h).

Fig 6 — The binding position of A TKY2.T1.08, C TKY2.T1.13, E TKY.T2.08, G TKY.T2.09 x-aptamers were investigated by immunofluorescence. Streptavidin-Alexa Fluor 488 conjugate was used to specify biotin-labelled x-aptamers. Cells were treated with X-aptamers in a dose-dependent manner (0–500 nM). Following incubation, cells were examined under a fluorescence microscope (Olympus) and images were taken and analyzed. The binding position of B TKY2.T1.08, D TKY2.T1.13, F TKY.T2.08, H TKY.T2.09 x-aptamers investigated by co-immunofluorescence. Streptavidin-Alexa Fluor 488 conjugate was used to specify biotin-labelled X-aptamers. Streptavidin-Alexa Fluor 588 conjugated anti-GHRH was used to specify GHRH. Cells were treated with x-aptamers in a dose-dependent manner (0–500 nM). Following incubation, cells were examined under a fluorescence microscope (Olympus) and images were taken and analyzed. GHRH siRNA was used as a negative control.

Blocking activity of GHRH signaling of selected aptamers

To evaluate the selected aptamers’ effect on GHRH signaling, we performed cAMP assay analysis and GH/GHRHR co-immunofluorescence staining (Fig 7a and 7b). Due to cAMP assay analysis, both TKY2.T1.08 and TKY2.T1.13 X-aptamers significantly depleted intracellular cAMP concentration as compared to untreated control cells in HT-29 cells. When we checked the results, no significant effect was observed for cAMP levels for TKY2.T1.08 and TKY2.T1.13 X-aptamers application in MIA Paca-2 cells. In addition, we measured a statistically significant decline in cAMP levels following TKY.T2.08 and TKY.T2.09 X-aptamers treatment in MIA Paca-2 cells (Fig 7a). To demonstrate the blocking activity of selected aptamers on GHRH signaling, we performed GH/GHRHR co-immunofluorescence staining (Fig 7b). Active GHRH signaling due to GH and GHRHR expression profile was detected in untreated and GHRH peptide treated MIA Paca-2 cells. However, a significant downregulation on GH/GHRHR expression demonstrated following TKY2.T1.08, TKY.T2.08, and TKY.T2.09 treatment in MIA Paca-2 cells (Fig 7b).

Discussion

GHRH is a neuropeptide that is known to be ectopically expressed in many cancer types such as the pancreas [20], prostate [21], ovarian [22] and lung cancer [23]. Due to the expression of GHRH/GHRHR and biologically active signaling leads the potential essential role of therapeutic regimes targeting GHRH. For this purpose, many GHRH peptide antagonists have been designed and synthesized by modifications on GHRH NH2 (1–29) peptide [24]. It was shown that these antagonists compete with GHRH for binding to the GHRH receptor and block receptor activation [25]. In this way, these antagonists were demonstrated to inhibit proliferation and induce apoptosis, via a direct effect on tumor cells in many cancer types such as lung, breast, prostate, ovarian, colorectal, and pancreas cancers [6, 10]. With a similar strategy, we tried to target GHRH by synthesizing capturing aptamer as a ligand to block the GHRH signaling. Although GHRH antagonists were studied to block GHRH signaling, the peptide nature of these antagonists limits their use in vivo. Also, there are no reported aptamers against GHRH in literature, thus in this study, we aimed to select an aptamer against GHRH NH2 (1–44) and NH2 (1–29) peptide as a GHRH antagonist and characterize its binding affinities to target.

Aptamers can be easily degraded by plasma nucleases because of their oligonucleotide structure. This challenge may be overcome by some modifications to different positions of nucleotides, phosphodiester bonds, or oligomerization by using L-conformation nucleotides which are not recognized by endonucleases [11]. Aptamers are selected conventionally by a method called SELEX (systemic evolution of ligands by exponential expansion) [26, 27]. Nucleic acid aptamers are single-stranded synthetic DNA or RNA oligonucleotides that may fold into three-dimensional structures and interact with many types of targets with a high affinity and specificity [11, 13]. Many molecules including small molecules, proteins, peptides, toxins, and even cells can be targets of aptamers [28]. Although generally aptamers were preferred as a capturing key molecule in a biosensor and conjugated with chemotherapeutic agents, aptamer-based hormone targeting technology approaches still maintained. As aptamers are smaller, less immunogenic, with low cost, more stable, more prone to chemical modifications, and renaturation capability after non-physiological conditions, they are more preferable to peptides or antibodies [29]. Due to their structural advantages, aptamers against some target molecules were preferred for metabolic disease treatment. Among these aptamers, Macugen is the first FDA-approved VEGF targeting RNA-aptamer for age-related macular degeneration treatment [12].

Aptamers selected by the SELEX method might be assumed as a time-consuming method due to having a limited number of modifications, and also performing 8–15 selection rounds [29]. Therefore, new methods providing more functional groups and more stability have been developed. One of the newly-developed technologies is X-aptamers, which contain protein-like or drug-like side chains providing both more stability against nucleases and more affinity to target molecules [14]. Although X-aptamer technology and selection is a newly-emerged system, it is being used in different studies. Recently, potential biomarkers have been identified for schizophrenia by using X-aptamer technology [30]. X-aptamers against two immune checkpoint proteins PD-1 and PD-L1 have also been selected by this technology [31]. In this study, we selected x-aptamers against the growth hormone-releasing hormone by using an X-aptamer selection kit.

In the case of GHRH, it was indicated that, N-terminal 29 amino acids of the 44 amino acids-long GHRH peptide show full biological activity [7]. To study the difference, if any, we used both GHRH NH₂ (1–44) and GHRH NH2 (1–29) peptides for aptamer selection. Further, for purification of the target protein, we needed large-scale protein synthesis in the cells and we used E. coli expressing His-tagged GHRH protein for large-scale protein isolation. Also, since the bacterial protein synthesis system lacks post-translational modifications, we transfected human embryonic kidney HEK293 cells with His-GHRH vector stably and used the protein isolated from these cells as a target. Moreover, increasing technology on nucleic acid-based drug discovery, new generation aptamers synthesis by magnetic bead loaded DNA library was designed. The trademark name for this biotechnological approach was X-aptamer. Thus, we synthesized X-aptamers via targeting both GHRH NH2 (1–44) and NH2 (1–29) by using an X-Aptamer selection kit. Following cloning and sequencing of magnetic bead-based PCR products, 24 putative X-aptamers were synthesized by AM BioTechnologies (Houston, USA) (Fig 2c). Mfold program is generally preferred for the determination of ssDNA Aptamer’s schematic profiles and ΔG levels under physiological conditions. As we used new generation technology for synthesizing aptamers; X-aptamer, they are containing modified nucleotides such as phosphorodithioate, indole- or phenol-modified deoxyuridine. So there is not any tool that illustrates the potential secondary structure predictions of X-aptamers. To determine the binding affinity of aptamers against its synthesized ligands, Sypabekova et. al, 2017 and Li et. al, 2017 preferred dot-blot methods [32, 33]. As our 24 putative X-aptamers have 5’ biotinylated labeling, we performed the dot-blot method via targeting GHRH NH2 (1–44) and GHRH NH2 (1–29) peptide (Fig 3a and 3b). According to the dot-blot spot intensity relative folding with aptamer absent spot intensity, TKY2.T1.01, TKY2.T1.02, TKY2.T1.03, TKY2.T1.04, TKY2.T1.05, TKY2.T1.08, TKY2.T1.10, TKY2.T1.12, TKY2.T1.13, TKY2.T1.15, TKY2.T1.17, TKY.T1.01, TKY.T1.02, TKY.T2.02, TKY.T2.06, TKY.T2.07, TKY.T2.08 and TKY.T2.09 X-aptamers were significantly high binding affinity against target peptide. When we compared the binding affinity of GHRH NH2 (1–44) x-aptamers with GHRH NH2 (1–29) peptide, similar binding potential illustrated by GHRH NH2 (1–44) X-aptamers against GHRH (1–44) peptide in dot-blot analysis. Although aptamers against luteinizing hormone [34], thyroxine hormone [35], cortisol hormone [36] synthesized and characterized, there is not any study on GHRH aptamer synthesis. Thus, this is the first study reporting the X-aptamer synthesizing against both GHRH NH2 (1–44) and GHRH NH2 (1–29) peptide and also characterize each synthesized GHRH X-aptamers by dot-blot, immunofluorescence and, SPR analysis.

To evaluate the efficiency of aptamer and the incline impact of aptamers against their target molecules, the selection of appropriate targets is one of the most important steps in the aptamer selection process [29]. Generally, the dot-blot technique is used to determine the K_d levels of aptamers with ligands [32]. Besides the dose-dependent aptamer-ligand dot blot analysis, SPR analysis is also preferred to determine the dissociation fold of aptamers. From this point of view, for each putative X-aptamer dose-dependent dot-blot performed. Following GraphPad Prism non-linear regression analysis, TKY2.T1.01, TKY2.T1.02, TKY2.T1.03, TKY2.T1.04, TKY2.T1.05, TKY2.T1.08, TKY2.T1.11, TKY2.T1.13, TKY2.T1.15, TKY2.T1.17, TKY.T1.03, TKY.T1.04 X-aptamers has 21.60, 19.42, 21.45, 32.91, 139, 31.18, 28.91, 41.07, 131.3, 7.974, 46.40, 101.5, 21.60, 19.42, 21.45, 32.91, 5.139, 31.18, 28.91, 41.07, 131.3, 7.974, 46.40, 101.5 nM K_d levels, respectively (Fig 3c). To confirm the results of the dot-blot technique, SPR analysis was performed for selected three putative aptamers (TKY2.T1.13, TKY.T1.08, and TKY.T1.09). SPR mediated K_d determination was generally preferred for illustrating the aptamer-ligand binding affinity [37]. In our study, three novel putative X-aptamers against GHRH were TKY2.T1.13, TKY.T2.08, TKY.T2.09 before SPR analysis (Fig 3f). Even if, aptamers are used as a therapeutic agent, the stability of aptamers under specific conditions such as temperature and nuclease-containing conditions. Generally, the serum stability of aptamers was evaluated by mixing an equal volume of aptamer and human serum in a time-dependent manner [38]. TKY2.T1.02, TKY2.T1.03, TKY2.T1.04, TKY2.T1.05, TKY2.T1.13, TKY2.T1.15, TKY2.T1.17, TKY.T1.05, TKY.T2.02, TKY.T2.07, TKY.T2.08, TKY.T2.09 X-aptamers serum stability was prolonged to 120 h time points (Fig 3e). From so on, when we combine the K_d level, co-immunofluorescence profile, and putative secondary structure, TKY2. T1.08, TKY2.T1.13, TKY.T1.08, and TKY.T1.09 X-aptamers selected for the competitive targeting of GHRH-GHRHR or GHRH-aptamer heterocomplexes. Co-immunofluorescence techniques are generally preferred for the binding profile of two ligands. As our putative X-aptamers were synthesized with 5’-biotinylated labeling, we can use streptavidin Alexa Fluor 488 to demonstrate the cell surface binding of X-aptamers on MIA PaCa-2 pancreatic cancer cell line (Fig 5). Co-immunofluorescence results illustrate the membrane binding of TKY2.T1.08, TKY2.T1.13, and TKY.T2.08 X-aptamers starting from the 50 nM concentrations. Concomitantly, this effect was increased by dose-dependent X-aptamers. However, clear fluorescence intensity was performed following 100 nm TKY.T2.09 treatment in MIA PaCa-2 cell by immunofluorescence staining. These results guide us to confirm the GHRH binding with GHRHR simultaneously with cell surface attachment of X-aptamers. According to co-immunofluorescence results, merge figures illustrate the aptamer binding with GHRH on the surface of MIA PaCa-2 cells. Especially, a significant binding profile was detected for TKY2.T1.08, TKY.T2.08, and TKY.T2.09 only after 250 nM aptamer treatment. Following the binding affinity of GHRH X-aptamers against GHRH secreted from MIA PaCa-2 cells, we demonstrate the blocking impact of GHRH signaling via cAMP levels and GH/GHRHR expression profile. Due to cAMP assay kit results, both TKY2.T1.08 and TKY2.T1.13 X-aptamers declined cAMP levels compared to untreated controls in HT-29 colon cancer cells. In MIA PaCa-2 cells, both TKY.T2.08 and TKY.T2.09 X-aptamers decreased cAMP levels (Fig 6a). Moreover, each selected X-aptamer treatment sharply decreased the expression of both GH and GHRHR expressions as compared to untreated control cells in MIA Paca-2 cells (Fig 6b). Thus, TKY2.T1.08, TKY2.T1.13, TKY.T208, and TKY.T209 X-aptamers block GHRH signaling through suppression cAMP levels and inhibition on GH/GHRHR expression profiles. Finally, further studies may need to figure out the binding site of TKY2.T1.08, TKY2.T1.13, and TKY.T2.08 aptamers on GHRH epitope regions and determine the docking site for GHRHR and GHRH during GHRH-aptamer complex formation. Besides, in silico analysis, in vitro analysis might highlight the inhibitive effect of TKY2.T1.08, TKY2.T1.13, and TKY.T2.08, TKY.T2.09 X-aptamers on GHRH signaling.

In conclusion, this is the first report demonstrating the synthesis, selection, and characterization of four putative X-aptamers against GHRH peptide. Although various peptide antagonists targeting GHRH developed, there is not any X-aptamer targeting GHRH. We synthesized anti-GHRH aptamers by using X-aptamer technology via targeting both GHRH NH2 (1–44) and NH2 (1–29). Due to new generation sequencing, 24 putative X-aptamer against GHRH synthesized. Among these x-aptamers, TKY2.T1.01, TKY2.T1.02, TKY2.T1.03, TKY2.T1.04, TKY2.T1.05, TKY2.T1.12, TKY2.T1.13, TKY.T1.01, TKY.T1.02, TKY.T2.07, TKY.T2.08, TKY.T2.09 were demonstrated to be a high binding affinity and low K_d levels by dot-blot analysis. Due to serum stability and potential K_d levels predictions; TKY2.T1.13, TKY.T2.08, TKY.T2.09 were selected for SPR analysis. In addition, novel two anti-GHRH NH2 (1–44) and two anti-GHRH NH2 (1–29) X-aptamers were characterized according to their binding ability on in vitro systems by using high GHRH expressing and secreting cell lines. Two anti-GHRH NH2 (1–29) x-aptamers have a high binding affinity, low K_d levels, and elevated binding potential in low doses compared to anti-GHRH NH2 (1–44) x-aptamers. Similar to GHRH peptide antagonists, 1–29 amino acid residue of GHRH peptide is more essential for the targeting and synthesizing efficient GHRH binding aptamers. However, new studies might be performed to determine the potential inhibitive effect of these x-aptamers on GHRH signaling and the determination of docking sites for x-aptamers on GHRH ligands. In addition, further in vitro, in vivo, and in silico analysis may need to highlight the impact of these three-novel X-aptamers efficiencies on GHRH signaling.

Supporting information

S1 Raw images

(PDF)

Click here for additional data file.^{(65MB, pdf)}

Acknowledgments

Ethical statement: This article does not involve any study with human participants or animals performed by any of the authors. The research performed on commercially available cell lines.

Data Availability

All relevant data are within the paper and its Supporting information files.

Funding Statement

The project was funded by Scientific and Technological Research Council of Turkey (TUBİTAK) with a project number 117Z254.

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PLoS One. doi: 10.1371/journal.pone.0260144.r001

Decision Letter 0

Paulo Lee Ho

3 Mar 2021

PONE-D-21-00439

Synthesis and characterization of novel ssDNA X-Aptamers Targeting Growth Hormone Releasing Hormone (GHRH)

PLOS ONE

Dear Dr. GURKAN,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

1) It is missing some importante controls (blockage of GHRH signalling, competitor in excess concentration to correct for unspecific binding at all aptamer doses, negative controls of the imune reactions);

2) Please, see the comments raised by both the reviewers.

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Reviewer #1: Yes

Reviewer #2: Partly

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: No

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Reviewer #1: Yes

Reviewer #2: Yes

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: This work focuses on the synthesis and purification of X-aptamers against Growth Hormone Releasing Hormone (GHRH), which was expressed in HEK293 and bacteria cells. GHRH is a hypothalamic neuropeptide that stimulates the production of growth factor GH, which in turn stimulates cell proliferation and division in different types of cancer.

24 X-aptamers were synthesized and 3 of them (TKY1.T1.13, TKY.T2.08, TKY.T2.09) had the best stability in serum and the highest binding potential by GHRH with low levels of Kd.

The work carried out is original, it has great relevance. It is well written and in my opinion meets the requirements to be accepted. However, some minor details need to be corrected.

>the quality of the figures must be corrected

>figure 2E does not match between title and file. There is no mention of this figure in the text. It also seems unnecessary to me since it is redundant with the 3D figure

>Figure 5a-5h should be considered as supplementary material since the main purpose of the work is not to determine the ability of aptamers to bind to the cell lines studied

>Additional experiments are necessary to determine the ability of the obtained aptamers to block GHRH signaling. or at least make it clear that these experiments were not done (Page 19, lines 304-305 it is mentioned that aptamers are used to block GHRH).

>make clear the limitations of the study

Reviewer #2: The authors report the development of aptamers selectively binding to the GHRH peptide and show binding efficiency by dot blot and SPR assays as well as by immunofluorescence assays with cells.

Issues to be addressed:

1. Overall: Image quality is low

2. Where should be an explanation for X-aptamers, and not just a reference. Can X aptamer sequences by modeled by using the mFOLD software?

3. How many SELEX cycles were performed? Why so many PCR cycles were performed, which indeed lead to the accumulation of PCR artefacts and not of selected aptamers. Was there any problem with the efficiency of the PCR reaction? The sequenced aptamers have a long 5` terminal T extension, I would guess that this an artefact. I suggest to align the aptamer consensus sequences in Figure 2C and make sure, which sequences belong to constant and variable sequences of the aptamers. Figure 2D should show, where in the loop region the consensus sequences can be found, and most importantly, the sequences should be readable. Figure 2E shows the stability of DNA aptamers along time. As this figure stands, it is not worth anything. First DNA needs to be resolved in a high-resolution denaturing polyacrylamide gel (which could distinguish between different sizes of aptamers); second, I do not see any positive controls for this assay (i.e. nuclease, which should degrade the aptamers).

4. The following experiment has a problem: "Then binding affinity of X-aptamers to target was assessed in increasing aptamer doses. Fold of change was calculated according to the dot intensities and dissociation constant (Kd) was calculated by nonlinear regression". Such binding data contain specific and unspecific binding. A competitor in excess concentration needs to be used in order to correct for unspecific binding at all aptamer doses.

5. A two or three of change of binding is very little, assuming that the unselected aptamer library shows unspecific binding in the mM range. Binding affinities of aptamers should increase at least 1,000 fold, reflected by more than of a two or three fold amount of target bound aptamers.

6. Negative controls of immune reactions, including those with aptamers are missing.

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Reviewer #1: Yes: Ospina-Villa Juan David

Reviewer #2: No

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PLoS One. 2022 Jan 21;17(1):e0260144. doi: 10.1371/journal.pone.0260144.r002

Author response to Decision Letter 0

15 Apr 2021

Review Comments to the Author

24 X-aptamers were synthesized and 3 of them (TKY1.T1.13, TKY.T2.08, TKY.T2.09) had the best stability in serum and the highest binding potential by GHRH with low levels of Kd.

The work carried out is original, it has great relevance. It is well written and in my opinion meets the requirements to be accepted. However, some minor details need to be corrected.

Comment 1: the quality of the figures must be corrected.

Response to comment : All the figures quality is corrected

Comment 2 : figure 2E does not match between title and file. There is no mention of this figure in the text. It also seems unnecessary to me since it is redundant with the 3D figüre

Response to comment : According to reviewer’s comment about the figure 2e that was not matched with the title the mentioned figure was discarded from the revised version of the manuscript.

Comment 3: Figure 5a-5h should be considered as supplementary material since the main purpose of the work is not to determine the ability of aptamers to bind to the cell lines studied

Response to comment : According to other reviewer’s comment about figure 5a-5h, these figures couldn’t substituted to supplementary material. We performed GHRH siRNA transfection assays for this figure in order to demonstrate the effective binding of aptamers with GHRH ligand.

Comment 4: Additional experiments are necessary to determine the ability of the obtained aptamers to block GHRH signaling. or at least make it clear that these experiments were not done (Page 19, lines 304-305 it is mentioned that aptamers are used to block GHRH).

Response to comment : According to reviewer’s comment, the cAMP assay and coimmunofluorescence assays were performed. As the major downstream target of GHRH signaling were cAMP levels and target gene expressions (GH, GHRHR), we selected these experiments. Due to cAMP assay, significant decrease in cAMP levels were observed following selected aptamer treatment in HT29 and MIA Paca2 cells. Moreover, both GH and GHRHR expression profile after aptamers treatment was determined in MIA Paca-2 cells. All the results were inserted in the revised manuscript.

Comment 5: make clear the limitations of the study

Response to comment : In our previous version we tried to make clear the limitations of study by giving as “Finally, further studies may need to figure out the binding site of TKY2.T1.08, TKY2.T1.13, and TKY.T2.08 aptamers on GHRH epitope regions and determine the docking site for GHRHR and GHRH during GHRH-aptamer complex formation. Besides, in silico analysis, in vitro analysis might highlight the inhibitive effect of TKY2.T1.08, TKY2.T1.13, and TKY.T2.08, TKY.T2.09 X-aptamers on GHRH signaling.” And also in conclusion part we added “However, new studies might be performed in order to figure out the potential inhibitive effect of these x-aptamers on GHRH signaling and determination of docking sites for x-aptamers on GHRH ligands. In addition, further in vitro, in vivo and in silico analysis may need to highlight the impact of these three-novel x-aptamers efficiency on GHRH signaling.”

Issues to be addressed:

Comment 1. Overall: Image quality is low

Response to comment : Low quality images were corrected.

Comment 2. Where should be an explanation for X-aptamers, and not just a reference. Can X aptamer sequences by modeled by using the mFOLD software?

Response to comment : According to reviewer’s comment, instead of giving explanation for X-aptamer, we gave also reference in the revised version of the manuscript. Due to first reviewer the secondary structure of aptamers is not linked with the title so we discarded the 3D structure figures.

Comment 3. How many SELEX cycles were performed? Why so many PCR cycles were performed, which indeed lead to the accumulation of PCR artefacts and not of selected aptamers. Was there any problem with the efficiency of the PCR reaction? The sequenced aptamers have a long 5` terminal T extension, I would guess that this an artefact. I suggest to align the aptamer consensus sequences in Figure 2C and make sure, which sequences belong to constant and variable sequences of the aptamers. Figure 2D should show, where in the loop region the consensus sequences can be found, and most importantly, the sequences should be readable. Figure 2E shows the stability of DNA aptamers along time. As this figure stands, it is not worth anything. First DNA needs to be resolved in a high-resolution denaturing polyacrylamide gel (which could distinguish between different sizes of aptamers); second, I do not see any positive controls for this assay (i.e. nuclease, which should degrade the aptamers).

Response to comment : Due to X-aptamer synthesis kit instructions we performed increasing number of PCR amplifications in order to increase the yield of aptamers that are specific to GHRH peptide. So we performed 14, 22, 25 cycle of binding the magnetic bead based library with GHRH peptide. As this is a patented technology for generation of X-aptamers by kit based selection so accumulation of PCR artifacts were get rid of by each step washing procedure as every PCR cycle product was used as a template library for each following SELEX step. (https://www.youtube.com/watch?v=CgfX-KmXdA0). After amplifications, AM Biotechnologies were generated NGS in order to determine the novel putative sequences instead the ones similar with the 5’ and 3’ library linker sequences. (https://www.genomeweb.com/resources/new-product/am-biotechnologies-x-aptamer-selection-kit). All the sequences aligned and T rich 5’ region with “CACGAC” repeats were named as 5’ constant sequence and “GTGGGGCCCATG” sequence repeat at the 3’ region were named as 3’ constant sequence. The sequences between these fixed sequences were named as “variable sequence” . For the figure 2d, according to valuable contribution, we changed the figure to more readable one in the revised version of the text. According to comment on figure 2e, we performed polyacrylamide gel electrophoresis for serum stability of each aptamer and changed all the figures with the new results. Moreover, in each serum stability gel results, we added positive control as DNase I digested aptamers.

Comment 4. The following experiment has a problem: "Then binding affinity of X-aptamers to target was assessed in increasing aptamer doses. Fold of change was calculated according to the dot intensities and dissociation constant (Kd) was calculated by nonlinear regression". Such binding data contain specific and unspecific binding. A competitor in excess concentration needs to be used in order to correct for unspecific binding at all aptamer doses.

Response to comment : According to valuable contribution, we performed GHRH sandwich ELISA assay and dot blot analysis in order to detect the specifity of x-aptamers in dose-dependent manner for selected aptamers. The performed experiment results were given in Figure 3d. As one of most effective competitor for aptamer is antibody, we preffer to perform GHRH ELISA assay. GHRH ELISA is a sandwich ELISA and wells were coated with GHRH antibody. 500 nM GHRH peptide is applied to wells and dose-dependent aptamers was used as they are 5’ biotinylated in order to determine the colorimetric analysis. And we performed dot-blot from supernatant of GHRH-aptamer complex in dose-dependent manner for selected x-aptamers. Thus, we demonstrated dose-dependent x-aptamer is a competitor for GHRH antibody and x-aptamers bind to target GHRH peptide with a high binding affinity.

Comment 5. A two or three of change of binding is very little, assuming that the unselected aptamer library shows unspecific binding in the mM range. Binding affinities of aptamers should increase at least 1,000 fold, reflected by more than of a two or three fold amount of target bound aptamers.

Response to comment : According to valuable contribution, we repeated dot-blot analysis for all aptamers. And then calculated the fold of change due to colorimetric analysis of each spot comparing with the negative control as only GHRH ligand was used. The repeated experiment results and fold of change in GHRH binding affinity due to dot-blot analysis was replaced in the revised version of the manuscript.

Comment 6. Negative controls of immune reactions, including those with aptamers are missing.

Response to comment : According to valuable contribuition, we applied GHRH siRNA as a negative control of immune reactions. Beside dose-dependent aptamer applications, we also apply aptamers in MIA Paca-2 cells with blocked GHRH signaling by siRNA. Due to experiments GHRH silencing as a negative control for immune reactions demonstrated that aptamers didn’t bind to MIA Paca-2 cells. The new experiment results were replaced in the figure 5b-d-f-h in the revised version of the figures.

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PLoS One. doi: 10.1371/journal.pone.0260144.r003

Decision Letter 1

Paulo Lee Ho

10 Jun 2021

PONE-D-21-00439R1

Synthesis and characterization of novel ssDNA X-Aptamers Targeting Growth Hormone Releasing Hormone (GHRH)

PLOS ONE

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

Reviewer #2: (No Response)

Reviewer #3: (No Response)

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2. Is the manuscript technically sound, and do the data support the conclusions?

Reviewer #1: Yes

Reviewer #2: No

Reviewer #3: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: No

Reviewer #3: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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5. Is the manuscript presented in an intelligible fashion and written in standard English?

Reviewer #1: Yes

Reviewer #2: No

Reviewer #3: Yes

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6. Review Comments to the Author

Reviewer #1: All comments were resolved and incorporated in the new version of the manuscript. Additional experiments were carried out that clearly dispel the initial doubts of the reviewers

Reviewer #2: Authors showed some new data, but the paper remains unacceptable for publication. Besides the authors did not respond satisfactorily to my queries, the manuscript is full of grammar errors, making it almost impossible to understand the messages, which the authors would like to transmit.

Examples for poor English, sometimes together with conceptional errors.

“x-aptamers was used as a detection antibody in order to detect GHRH peptide that applied on GHRH antibody coated plates. “ An aptamer is not an antibody

“To confirm the ELISA results, we performed dot-blot analysis of upper phase of GHRH peptide 296 and X-aptamer combination in dose-dependent manner by dot-blot analysis. “

“As there is not any competitor for GHRH X-aptamers except antibody against GHRH peptide, we performed GHRH ELISA 298 assay. “ Not true, unlabeled aptamers in excess can be used to compete with binding of labeled aptamers.

“According to the serum stability results, TKY2.T1.02, TKY2.T1.04, TKY2.T1.05, 304 TKY2.T1.08, TKY2.T1.13, TKY2.T1.17, TKY.T2.05, TKY.T1.05, TKY.T2.02, TKY.T2.07, TKY.T2.08 and TKY.T2.09 X-aptamers were seems to be stable in human serum within 120 h period at 37o “

“X-aptamers were significantly deplete intracellular cAMP 338 concentration as compared to untreated control cells in HT-29 cells. When we checked the results, no significant effect was observed for cAMP levels for TKY2.T1.08 and TKY2.T1.13 X-aptamers application 340 in HT-29 cells“. Contradictory!

Scientific issues:

PCR cycles: I did not mean SELEX cycles, but PCR cycles needed for amplification of recovered DNA. If i.e. 1 % of the material was recovered following selection, a number of PCR cycles needed to restore 100% can be calculated and certainly will not give 25 cycles.

I know that the technique is patented, but nether the less technical details need to be given, that any researcher can repeat experiments.

Regression plots in Figure 3 are not readable and they seem to rely on a single measurement.

I asked the authors to provide an alignment of variable sequences, which allows the definition of structural classes. Authors just listed the sequences without any bioinformatical analysis.

I asked the authors to adequately introduce X-DNA aptamers (why authors select X-aptamers). This should be done in more detail and not by just citing a reference. The message is confusingly diluted along the paper. However, it should be clearly cited in the introduction.

Reviewer #3: The anuscript revision was attached as a word doc file, since it exceeded the limit of 20000 characters

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Reviewer #1: Yes: Ospina-Villa Juan

Reviewer #2: No

Reviewer #3: No

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PLoS One. 2022 Jan 21;17(1):e0260144. doi: 10.1371/journal.pone.0260144.r004

Author response to Decision Letter 1

8 Jul 2021

Introduction

The study presents the synthesis of 24 putative X-aptamers against GHRH peptides with high serum stability, target binding, and low Kd levels.

Overall:

English needs proofreading.

- Manuscript English was corrected and some sentences were rewritten.

Figure legends should be more informative, otherwise, the reader has to look back and forth to find the information scattered in the manuscript.

- Figure legends were detailed and altered to more informative.

Specific questions:

Comment#1 Introduction does not present clear information regarding the goal of making those aptamers. Do authors want to make GHRH antagonists? Authors want to make new therapeutic agents or diagnostic tools? It’s not clear and should be clarified in the Introduction section.

Reply to comment 1: According to valuable comment, we explained in the introduction part that we want to make GHRH aptamer antagonists. And we added “In order to generate GHRH antagonists, we select aptamers due to their high binding affinity, low toxicity, non-immunogenic properties (11)” sentense after GHRH peptide antagonists in the revised text.

Comment#2 Why authors want to make aptamers against 1-44 and/or 1-29 peptides? Are there any advantages/differences of using each peptide target for selection? A better explanation in the Introduction regarding the reasons for testing both targets is desirable. The only thing that is mentioned is the fact that biological activity is observed in the 1-29 sequence. If so, why not only 1-29 protein was used as a target? Also, I could not find in the Discussion section, whether 1-44 targeting aptamers were also able to detect 1-29 protein and vice versa. I believe this should be addressed in the discussion.

Rept to comment 2: We rewrote the introduction and discussion parts to explain why we use both peptides for aptamer synthesis. This is the first report demonstrating the synthesis of aptamers against GHRH so we want to generate SELEX against both 1-44 and 1-29. Like the same strategy with Macugen (anti-VEGF), we preferred to synthesize X-aptamers against GHRH full length protein which is 44 amino acid long. Moreover, this will give us to detect every epitopic part of GHRH variants when we synthesized aptamers. In addition, due to GHRH peptide antagonist that targets GHRH 1-29, we used 1-29 peptide as a target to demonstrate the impact of aptamers by comparing every epitopic region. We inserted “As there is not any GHRH antagonist aptamer, we preferred to synthesize aptamers against both GHRH 1-44 and 1-29. In order to synthesize X-aptamers that can capture every epitopic region, we selected full GHRH protein NH2 (1-44). Besides, as GHRH peptide antagonist select 1-29 region, we used GHRH NH2 (1-29) as a target in order to synthesize X-aptamers. In order to illustrate by comparing the binding affinity of GHRH antagonist X-aptamers, we aimed to synthesize, select X-aptamers against both GHRH NH2 (1-44) and NH2 (1-29) peptides.” Due to dot blot analysis, both GHRH NH2 (1-44) X-aptamers and GHRH NH2 (1-29) aptamers have similar binding affinity against GHRH peptide target. Thus, in discussion section we added “When we compared the binding affinity of GHRH NH2 (1-44) x-aptamers with GHRH NH2 (1-29) peptide, similar binding potential illustrated by GHRH NH2 (1-44) X-aptamers against GHRH (1-44) peptide in dot-blot analysis.”

Comment#3 X-aptamer technology was recently developed. The advantages and limitations of this SELEX procedure need to be further explored in the Introduction section.

Reply to comment 3: The advantages and limitations of this SELEX procedure were given in the introduction part as “The most important advantage of X-aptamer technology is to synthesize up to 5 different target at the same time by one SELEX method. However, the limitation of X-aptamer technology is molecular size of target molecule, targets longer than 10 amino acids is assumed to be more preferred (14).”

Comment#4 Line 99, “Expression of bacterial His” needs to be further explained. Is it the control of the experiment? Also, plasmids pCMV3-SP-N-His-NCV and pCMV3-SP-His-ORF His-GHRH are not defined. Which proteins are coded by these plasmids? A detailed explanation of each construct is desirable.

Rept to comment 4: The expression of bacterial His performed as a control in order to determine the His-tagged protein expression in HEK293 cells. His tagged protein synthesized by pCMV3-SP-N-His-NCV plasmid and His-tagged GHRH peptide expressed from pCMV3-SP-His-ORF His-GHRH plasmid. This explanation was given in the revised version of the manuscript.

Comment#5 Line 160. What is the composition of the selection buffer?

Reply to comment 5: The composition of the selection buffer is given in the revised version of the manuscript. The content of selection buffer is 1X PBS pH:7.4, 1 mM MgCl2, 0.05% Tween20, 0.02% BSA.

Comment#6 Line 173 “4 1.5 ml tubes”…needs improvement

Reply to comment 6: “4 1.5 ml tubes” was changed to “four 1.5 mL tubes” in the revised manuscript.

Comment#7 Units are wrong throughout the whole manuscript ….for example μl needs to be replaced by μL, ml by mL, etc.

Reply to comment 7: We changed them all in the revised text.

Comment# 8 Line 248-249. The sentence appears incomplete.

Reply to comment 8: According to valuable comment, the sentence appears to be incomplete was changed to “Purification of His-tagged GHRH peptide “ as a title for result section.

Comment#9 Line 253…” HEK293 cells were used…”

Reply to comment 9: According to valuable comment, “HEK293 cells were used” changed the revised manuscript.

Comment#10 Methodology of aptamer selection is very confusing. Author state: “Our aim in this study is to synthesize and purify GHRH (1-44) protein in HEK293 cells, synthesize and select X-aptamers against GHRH peptide both 1-29 and 1-44, and demonstrate synthesized aptamers’ target binding activity as well as serum stability.”

If only purification of GHRH 1-44 protein was performed, how the selection was performed using both proteins (1-29 and 1-44) as targets? There were two different Selex procedures, each one using one protein as the target? That is not clear. If authors claim that will select aptamers against both 1-29 and 1-44 peptides, the methodology should provide a detailed description of which peptide was used target for selection.

Also, seems strange that authors tried to express in E.coli since it’s widely known that bacteria lack a posttranscriptional modification mechanism. Line 252-254 says “Since the bacterial protein synthesis mechanism lacks post-translational modifications, HEK293 cells were used…” this information was already available before the bacterial expression was performed in this article, therefore, I wonder why bacterial expression was tested and included in the study…

Although using HEK293 for protein expression, it is not clear if 1-29 or 1-44 peptides were expressed.

Reply to comment 10: We realized that we didn’t write in the material method section that we used bacterial and eukaryotic GHRH NH2 (1-44) peptide and also GHRH NH2 (1-29) peptide as a target for X-aptamer SELEX. We performed two SELEX; first SELEX; bacterial/eukaryotic SELEX (Figure 2a) and second SELEX: GHRH 1-29 (figure 2b). As X-aptamer synthesing kit targets up to 5 targets, we used purified bacterial and eukaryotic GHRH 1-44 peptide for the first SELEX and also GHRH 1-29 peptide for the second SELEX. According to manufacturers instructions, target must be magnetically labelled with either his or streptavidin magnetic beads. Thus, we have to use His-tagged GHRH protein for his-magnetic beads and also biotinylated GHRH for streptavidin magnetic bead. Thus, in order to compare the binding affinity of X-aptamers against each target we prefer to use GHRH 1-44 and GHRH 1-29 peptides whether first 1-29 peptide or full length peptide epitopic regions determine the binding affinity of X-aptamers. To synthesize aptamers against GHRH 1-44 full length target, we used both E.coli HB101 cells to gain high yield of His-GHRH protein. However to compare the binding affinity of x-aptamers against bacterial and eukaryotic GHRH 1-44 peptide, we performed purification from each host. In addition, as HEK293 cells has no expression for GHRH, they express what we transfected through a plasmid and the plasmid has full length GHRH peptide with His-tagged. Thus, HEK293 cells express GHRH 1-44 peptide and this was confirmed by the immunoblotting results.

Comment#11 Sequences provided in Figure 2 are aptamers obtained from which selection (1-29 or 1-44)? What is the difference between sequences named TKY2 and TKY?

Reply to comment 11: The sequences provided in Figure 2 are aptamers obtained from both bacterial/eukaryotic GHRH 1-44 and GHRH 1-29 peptides. Names for TKY2 belongs to bacterial/eukaryotic GHRH 1-44 peptide and TKY belongs to GHRH 1-29 peptide. The detailed explanation was given as “Aptamers against bacterial His-tagged GHRH were TKY2.T1.01, TKY2.T1.02, TKY2.T1.03, TKY2.T1.04, TKY2.T1.05, TKY2.T1.08, TKY2.T1.10, TKY2.T1.12, TKY2.T1.13, TKY2.T1.15, TKY2.T1.17. TKY.T1.01, TKY.T1.02, TKY.T1.03, TKY.T1.04, TKY.T1.05 aptamers were against eukaryotic GHRH NH2 (1-44) peptide. Putative X-aptamers against GHRH 1-29 target named as TKY.T2.02, TKY.T2.06, TKY.T2.07, TKY.T2.08, TKY.T2.09.” in the results section of the revised manuscript.

Comment#12 Figure 1 shows expression and purification of NH2 (1-44) target or GHRH NH2 (1-29) target? Figure legends should be more informative, otherwise, the reader has to look back and forth to find the information scattered in the manuscript.

Reply to comment 12: We only purified GHRH 1-44 from bacterial and eukaryotic host origin, we bought the GHRH 1-29 peptide from Sigma G6771 as a product. Thus, the figure 1 represents the expression and purification of GHRH 1-44 target. It is mentioned in the figure legend 1 in the revised manuscript.

Comment#13. Bacterially expressed His-GHRH protein was expressed as inclusion bodies and denatured using Guanidine. No protocol for protein refolding was presented.

Reply to comment 13: Protein refolding by bacterial expressed His-GHRH protein as inclusion bodies and denatured using Guanidine, we gave reference in the revised manuscript. (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2324003/)

Review Comments to the Author

Reviewer #1: All comments were resolved and incorporated in the new version of the manuscript. Additional experiments were carried out that clearly dispel the initial doubts of the reviewers

Examples for poor English, sometimes together with conceptional errors.

- All the grammar errors were corrected, manuscript English is proofread and some sentences were rewritten again in order to transmit the messages.

Comment 1: “x-aptamers was used as a detection antibody in order to detect GHRH peptide that applied on GHRH antibody coated plates. “ An aptamer is not an antibody

Reply to comment: We changed the sentence as “ According to GHRH ELISA results, instead of using detection antibody, we used x-aptamers to competitively capture GHRH peptide. “ We know that an aptamer is not an antibody but as we dont have any unlabelled aptamers we prefered to use GHRH competitive ELISA in order to demonstrate the specificity of x-aptamers through their binding affinity against target molecule.

Comment 2: “To confirm the ELISA results, we performed dot-blot analysis of upper phase of GHRH peptide 296 and X-aptamer combination in dose-dependent manner by dot-blot analysis.

Reply to comment 2: According to valueable contribution, we changed the sentence as “To confirm the ELISA results, we performed dot-blot analysis in dose-dependent manner“.

Comment 3: “As there is not any competitor for GHRH X-aptamers except antibody against GHRH peptide, we performed GHRH ELISA 298 assay. “ Not true, unlabeled aptamers in excess can be used to compete with binding of labeled aptamers.

Reply to comment 3: According to valueable contributions, we changed the sentence as “As we do not have any unlabeled aptamers, GHRH antibody is used as a competitor for GHRH X-aptamers against GHRH peptide binding“. We know unlabelled excess aptamer will be used for competitive for GHRH binding to determine specifity of aptamers. However, we synthesized only 5’ biotin labeled aptamers from AM Biochemicals. As we couldn’t purchase both labelled and unlabelled 24 putative aptamers, we can only demonstrate by competitive ELISA Assay in dose-dependent manner.

Comment 4: “According to the serum stability results, TKY2.T1.02, TKY2.T1.04, TKY2.T1.05, 304 TKY2.T1.08, TKY2.T1.13, TKY2.T1.17, TKY.T2.05, TKY.T1.05, TKY.T2.02, TKY.T2.07, TKY.T2.08 and TKY.T2.09 X-aptamers were seems to be stable in human serum within 120 h period at 37o “

Reply to comment 4: We changed the sentence as “According to the serum stability results, TKY2.T1.02, TKY2.T1.04, TKY2.T1.05, TKY2.T1.08, TKY2.T1.13, TKY2.T1.17, TKY.T2.05, TKY.T1.05, TKY.T2.02, TKY.T2.07, TKY.T2.08 and TKY.T2.09 X-aptamers were stable in human serum within 120 h period at 37oC (Fig 3e).”

Comment 5: “X-aptamers were significantly deplete intracellular cAMP 338 concentration as compared to untreated control cells in HT-29 cells. When we checked the results, no significant effect was observed for cAMP levels for TKY2.T1.08 and TKY2.T1.13 X-aptamers application 340 in HT-29 cells“. Contradictory!

Reply to comment 5: The sentence was changed to “Due to cAMP assay analysis, both TKY2.T1.08 and TKY2.T1.13 X-aptamers significantly depleted intracellular cAMP concentration as compared to untreated control cells in HT-29 cells. When we checked the results, no significant effect observed for cAMP levels for TKY2.T1.08 and TKY2.T1.13 X-aptamers application in MIA Paca-2 cells. In addition, we measured statistically significant decline in cAMP levels following TKY.T2.08 and TKY.T2.09 X-aptamers treatment in MIA Paca-2 cells (Fig 6a).”

Scientific issues:

Comment 6: PCR cycles: I did not mean SELEX cycles, but PCR cycles needed for amplification of recovered DNA. If i.e. 1 % of the material was recovered following selection, a number of PCR cycles needed to restore 100% can be calculated and certainly will not give 25 cycles.

I know that the technique is patented, but nether the less technical details need to be given, that any researcher can repeat experiments.

Reply to comment 6: In the method, we do not aim to recover 100% DNA. Instead, the company requested the gel image and informed that it is sufficient for Next Generation Sequencing.

Comment 7: Regression plots in Figure 3 are not readable and they seem to rely on a single measurement.

Reply to comment 7: We changed figure as dot-blot analysis and also regression plots in order to increase its readability. The experiment was repeated three times and given figures illustrates the representative of one of the experiment.

Comment 8: I asked the authors to provide an alignment of variable sequences, which allows the definition of structural classes. Authors just listed the sequences without any bioinformatical analysis.

Reply to comment 8: According to comment, we align the variable sequences by bioinformatic analysis and given in the revised version of the manuscript.

Comment 9: I asked the authors to adequately introduce X-DNA aptamers (why authors select X-aptamers). This should be done in more detail and not by just citing a reference. The message is confusingly diluted along the paper. However, it should be clearly cited in the introduction.

Reply to comment 9: We explained in detail the X-aptamer technology, advantages and limitations of aptamers. Moreover, we clearly cited why we select X-aptamers in the introduction part.

Reviewer #3: The manuscript revision was attached as a word doc file, since it exceeded the limit of 20000 characters

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PLoS One. doi: 10.1371/journal.pone.0260144.r005

Decision Letter 2

Paulo Lee Ho

26 Aug 2021

PONE-D-21-00439R2

Synthesis and characterization of novel ssDNA X-Aptamers Targeting Growth Hormone Releasing Hormone (GHRH)

PLOS ONE

Dear Dr. GURKAN,

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

Reviewer #2: (No Response)

Reviewer #3: All comments have been addressed

**********

2. Is the manuscript technically sound, and do the data support the conclusions?

Reviewer #2: (No Response)

Reviewer #3: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #2: No

Reviewer #3: N/A

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

Reviewer #2: Yes

Reviewer #3: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

Reviewer #2: Yes

Reviewer #3: Yes

**********

6. Review Comments to the Author

Reviewer #2: I agree that the authors made some progress, but I have yet serious reservations regarding the scientific quality of this manuscript.

1. Authors did not understand the point of my concerns of a large number of PCR cycles for reestablishing the X-DNA pool. The point is that over amplification, i.e. by 25 cycles, for reestablishing 100 % from 1 % results in a loss of pool and sequence heterogeneity and selection of artefacts. This is shown in the alignment analysis that authors now provided. It is expected that there are conserved consensus motifs within a part of the previous random region, but not that practically the entire random region makes part of the random regions. If this would be like that, how authors explain the differences in binding affinities.

2. Figure 3c: Where is the control (scrambled sequence aptamer) for these assays. Increase of an unspecific aptamer concentration will augment binding, however cannot be saturated. This needs to be shown. I understand that a non-linear curve using a zero point needs to be performed. Please, check for that TKY2.T1.T2, TKY.T1.01 and TKY.T1.02. The fittings are just wrong. Are these just one-point measurements without any relevance?

3. Aptamer alignment by Clustal: So, which is the proposed consensus sequence? Analysis softwares for aptamers are available, including MEME, which are much more suitable than Clustal is.

Reviewer #3: The authors replied to all my comments, the paper appears more straightforward and can be accepted for publication.

**********

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Reviewer #3: No

PLoS One. 2022 Jan 21;17(1):e0260144. doi: 10.1371/journal.pone.0260144.r006

Author response to Decision Letter 2

7 Oct 2021

Response to reviewers comments:

Reviewer #2: I agree that the authors made some progress, but I have yet serious reservations regarding the scientific quality of this manuscript.

Comment 1. Authors did not understand the point of my concerns of a large number of PCR cycles for reestablishing the X-DNA pool. The point is that over amplification, i.e. by 25 cycles, for reestablishing 100 % from 1 % results in a loss of pool and sequence heterogeneity and selection of artefacts. This is shown in the alignment analysis that authors now provided. It is expected that there are conserved consensus motifs within a part of the previous random region, but not that practically the entire random region makes part of the random regions. If this would be like that, how authors explain the differences in binding affinities.

Reply to comment 1: Due to valuable comment, we understand that there is a misleading for the selection of aptamers. We didn’t use SELEX for the aptamer selection, we used X-aptamer kit and perform according to manifacturer instructions. The SELEX refers to a different process which itself implies multiple rounds of selection process by using PCR. We did not use SELEX which is a round of PCR amplification. We performed a bead-based aptamer selection. For more information we kindly advise you to watch the process from the following link. (https://www.youtube.com/watch?v=CgfX-KmXdA0). Therefore, we decided to mention the process in the manuscript in a more appropriate way as “We performed a bead-based aptamer selection against two targets, bacterial /eukaryotic GHRH 1-44 and GHRH 1-29 peptide. In addition we replaced “first SELEX” with “first aptamer selection”, and replace “second SELEX” with “second aptamer selection”. The different cycle numbers of PCR were only to determine the proper cycle number for each fraction to send clean product to sequencing with no overamplification.

Comment 2. Figure 3c: Where is the control (scrambled sequence aptamer) for these assays. Increase of an unspecific aptamer concentration will augment binding, however cannot be saturated. This needs to be shown. I understand that a non-linear curve using a zero point needs to be performed. Please, check for that TKY2.T1.T2, TKY.T1.01 and TKY.T1.02. The fittings are just wrong. Are these just one-point measurements without any relevance?

Reply to comment 2: According to valuable comment, we synthesized scramble sequence aptamer that has similar �G value. The sequence was given in the revised manuscript. We performed again dot-blotting with scramble sequence aptamer. Due to new dot-blot results, we analyze the Kd levels again and fit the results at GraphPad prism program. All the new results were given in the revised version of the manuscript. Although it is not a single measurement, we repeat dot-blot via using scramble aptamer.

Comment 3. Aptamer alignment by Clustal: So, which is the proposed consensus sequence? Analysis softwares for aptamers are available, including MEME, which are much more suitable than Clustal is.

Reply to comment 3: In our previous revision, we performed Cluster alignment program to determine the consensus sequence. However, due to comment we performed MEME analysis for all aptamers instead of Clustal analysis. According to MEME analysis 5’ and 3’ constant sequences and random sequence was given in the revised version of the manuscript.

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PLoS One. doi: 10.1371/journal.pone.0260144.r007

Decision Letter 3

Paulo Lee Ho

4 Nov 2021

Synthesis and characterization of novel ssDNA X-Aptamers Targeting Growth Hormone Releasing Hormone (GHRH)

PONE-D-21-00439R3

Dear Dr. GURKAN,

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

Reviewer #2: All comments have been addressed

**********

2. Is the manuscript technically sound, and do the data support the conclusions?

Reviewer #2: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #2: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

Reviewer #2: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

Reviewer #2: Yes

**********

6. Review Comments to the Author

Reviewer #2: My comments were addresssed, and the paper is ready for publication. All criteria for publication in PloS ONE have been met.

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PLoS One. doi: 10.1371/journal.pone.0260144.r008

Acceptance letter

Paulo Lee Ho

10 Jan 2022

PONE-D-21-00439R3

Synthesis and characterization of novel ssDNA X-Aptamers Targeting Growth Hormone Releasing Hormone (GHRH)

Dear Dr. Coker-Gurkan:

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Data Availability Statement

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PERMALINK

Synthesis and characterization of novel ssDNA X-aptamers targeting Growth Hormone Releasing Hormone (GHRH)

Burcu Ayhan-Sahin

Zeynep-Elif Apaydın

Pınar Obakan-Yerlikaya

Elif-Damla Arisan

Ajda Coker-Gurkan

Roles

Abstract

Background

Methods and results

Conclusion

Introduction

Materials and methods

Cell lines and antibodies

Bacterial His-GHRH (1–44) protein isolation and purification

Expression of His-tagged GHRH peptide in HEK293 cells

RNA isolation and real-time PCR

GHRH ELISA assay

Immunoblotting

Immunofluorescence staining

X-aptamer selection and synthesis

Dot-blot assay

Serum stability of putative X-aptamers

Cyclic AMP assay analysis

GH and GHRHR expression profile by immunofluorescence

Dose-dependent X-aptamer binding affinity by immunofluorescence

SPR analysis

Statistical analysis

Results

Purification of His-tagged GHRH peptide

Fig 1. Obtaining and purification of His-tagged GHRH (1–44) ligand for the aptamer selection.

Synthesis and selection of x-aptamers against GHRH peptide

Fig 2. Synthesis, selection of putative x-aptamers against Growth Hormone Releasing Hormone.

Screening the binding affinity of putative X-aptamers to the target protein by dot blot assay and SPR analysis and illustrating the serum stability of each X-aptamer

Fig 3. Determination of binding affinity, dissociation constant (Kd) of putative x-aptamers.

Fig 4. Determination of dissociation constant (Kd), and serum stability of putative x-aptamers.

GHRH expression and secretion profile of MIA PaCa-2, HT-29, PC3 cancer cells and PNT1A epithelial derived normal cell

Fig 5. Demonstration of GHRH expression in different cancer cell lines.

Determination of dose-dependent binding affinity of x-aptamers on MIA PaCa-2 cells by immunofluorescence staining

Fig 6. Investigation of the binding location of X-aptamers in MIA PaCa-2 cells.

Blocking activity of GHRH signaling of selected aptamers

Fig 7. Blockage of GHRH signaling by selected aptamers.

Discussion

Supporting information

Acknowledgments

Data Availability

Funding Statement

References

Decision Letter 0

Paulo Lee Ho

Roles

Author response to Decision Letter 0

Decision Letter 1

Paulo Lee Ho

Roles

Author response to Decision Letter 1

Decision Letter 2

Paulo Lee Ho

Roles

Author response to Decision Letter 2

Decision Letter 3

Paulo Lee Ho

Roles

Acceptance letter

Paulo Lee Ho

Roles

Associated Data

Supplementary Materials

Data Availability Statement

ACTIONS

PERMALINK

RESOURCES

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Fig 3. Determination of binding affinity, dissociation constant (K_d) of putative x-aptamers.

Fig 4. Determination of dissociation constant (K_d), and serum stability of putative x-aptamers.