DOI: 10.5061/dryad.dr7sqvb8w
title: Architecture mechanics mediated osteogenic progression in bone regeneration of artificial scaffolds

description: Scaffold architecture exerts a considerable influence on the osteogenic
 effect through stress transmission, as the deformation of scaffolds alters
 the mechanical microenvironment of cells adhering to scaffold surface.
 Despite extensive researches on bone regeneration influenced by scaffold
 architecture, present studies have not addressed the biological mechanism
 underlying scaffold architecture-induced stress stimulation (SASS) on
 cells yet, posing a great challenge in revealing the biomechanical cues
 between scaffold architecture and osteogenic progression. Therefore,
 Graphite (GP), Fullerene (FL), and Diamond (DM) scaffolds with gradient
 stress-stimulation to cells after deformation were prepared. Moreover, we
 analyzed the results of the finite element simulation of the compression
 and recovery process of the three types of scaffolds, and tested the
 macroscopic mechanical and viscoelastic properties. The cellular
 biomechanical mechanisms of SASS through single-cell RNA sequencing
 indicated that architectures providing SASS can induce the enrichment of
 focal adhesion and osteogenic differentiation pathways of bone mesenchymal
 stem cells, and balance bone resorption of osteoclasts and bone formation
 of osteoblasts. Besides, SASS enhances bone regeneration for repairing
 critical-sized defects in vivo. These results provide insights for
 artificial bone scaffold design and clarify the biomechanical cues between
 SASS and osteogenic progression.
description: # Architecture mechanics mediated osteogenic progression in bone
 regeneration of artificial scaffolds Dataset DOI:
 [10.5061/dryad.dr7sqvb8w](10.5061/dryad.dr7sqvb8w) ## Description of the
 data and file structure We summarized the finite element simulation of the
 micro-strain distribution, macro-mechanical, and viscoelastic properties
 of GP, FL, and DM scaffolds during the compression and recovery process.
 One month after implantation in the femur of rats, the new bone at the
 defect was removed, and single-cell sequencing was performed. The KEGG, GO
 enrichment, and gene expression differences of mesenchymal stem cells
 (MSCs), osteoclasts (OCs), and osteoblasts (OBs) cell clusters in the
 three scaffolds were analyzed. In the *in vivo* experiments, the
 parameters of new bone, semi-quantitative analysis of IHC and IF were
 analyzed. ### Files and variables #### File: Data\_files.zip
 **Description:**  **Porosity&surface-volume ratio.xlsx**: Porosity and
 surface-volume ratio of GP, FL, and DM scaffolds. **Step1_Element
 proportion-strain curves.csv, Step1.5_Element proportion-strain
 curves.csv, Step2_Element proportion-strain curves.csv, Step3_Element
 proportion-strain curves.csv, Step3.5_Element proportion-strain
 curves.csv, Step4_Element proportion-strain curves.csv**: Element
 proportion-strain curves at six time points (step 1, 1.5, 2, 3, 3.5, 4)
 for GP, FL, DM scaffolds and Bone (Step 1: Compress to 10N; Step 2:
 Maintain the gap for 10 minutes; Step 3: Return to the force of 0.05N;
 Step 3.5: Step 4: Maintain the gap for 5 minutes). "Start" and
 "end" refer to the range of strain, that is, the initial value
 and the final value. "Count" refers to the number of elements.
 "Ratio" refers to the proportion of the number of elements to
 the total number of elements. "Ratio(*100)" means
 "ratio" multiplied by 100. Step 1, 2, 3, and 4 refer to the end
 time points of each step, Step 1.5 is at the midpoint between Step 1 and
 Step 2, and Step 3.5 is at the midpoint between Step 3 and Step 4. **Mode,
 average, SD, peak width at half height.xlsx**: The strain analysis on the
 elements proportion-strain curves of the mode, the average, the standard
 deviation, the peak width at half-height for GP, FL, DM scaffolds, and
 Bone. **Stress, total strain, elastic strain and creep strain curves for
 the elements with the mode&max strain in the process of step
 1-4.xlsx**: Stress, total strain, elastic strain and creep strain curves
 for the elements with the mode proportion of strain and the elements with
 the largest strain in the process of step 1-4. **Compressive
 curves&strength&modulus.xlsx**: Compressive curves, strength, and
 modulus of the GP, FL, and DM scaffolds. **Macroscopic
 viscoelasticity.xlsx**: The stress-time curves of the four-step process
 (Step 1: Compress to 10N; Step 2: Maintain the gap for 10 minutes; Step 3:
 Return to the force of 0.05N; Step 4: Maintain the gap for 5 minutes) of
 the GP, FL, DM scaffolds and the cancellous bones of pigs. The relaxation
 curves of step 2 and the recovery curves of step 4 are shown after
 normalizing the initial point. The creep curves of the GP, FL, DM
 scaffolds, and Bone. Compression cycle of the GP, FL, DM scaffolds, and
 Bone. **Gene expression.xlsx**: The transcript levels of cell markers in
 the mesenchymal stem cell (MSCs), osteoclasts (OCs), osteoblasts (OBs),
 and osteocytes subtypes expressing these marker genes. The transcript
 levels of related genes in GP, FL, and DM scaffolds in MSCs, OCs, and OBs.
 **Cell ratio.xlsx**: Cell ratio in the MSCs, OCs, OBs, and osteocytes
 subtypes from DM, FL, and GP scaffolds. The proportion of immune cells in
 the GP, FL, and DM groups. **KEGG enrichment.xlsx, GO enrichment.xlsx**:
 KEGG pathway enrichment analyses of all differentially expressed genes by
 scRNA-seq in DM vs. GP scaffolds, DM vs. FL scaffolds, and FL vs. GP
 scaffolds in MSCs, OCs, OBs. GO pathway enrichment analyses of all
 differentially expressed genes by scRNA-seq in DM vs. GP scaffolds, DM vs.
 FL scaffolds, and FL vs. GP scaffolds in MSCs, OCs, and OBs. **RT
 PCR.xlsx**: Real-time PCR of BMSCs, OBs, and OCs under dynamic compression
 in vitro (The expression levels of Fn1 and Ibsp in BMSCs, the expression
 levels of Fn1 and Ibsp in OBs, and the expression levels of Spp1 and Acp5
 in OCs). **Routine blood tests.xlsx**: Routine blood tests for white blood
 cell count (WBC), lymphocyte count (Lymph), Monocyte count (Mon),
 neutrophil granulocyte count (Gran), red blood cell count (RBC),
 hemoglobin (HGB), platelet count (PLT) and mean platelet volume (MPV) of
 control group and critical defect healing 2 days and 2 weeks after GP, FL,
 DM scaffolds implantation in rats.
 **BV_TV&BMD&Tb.Th.&Tb.N.&Bending strength.xlsx**: Micro-CT
 quantification of critical defect femur in rats and Bamapigs healing 4
 weeks and 12 weeks after surgery for GP, FL and DM groups. BV/TV, BMD,
 Tb.N., Tb.Th.. Bending strength of critical defect femurs in rats at 4
 weeks and 12 weeks after implantation in the Bone, Blank, GP, FL, and DM
 groups. **Sirius red.xlsx**: Semi-quantitative positive area results of
 Sirius red staining. **Statistics of IHC&IF.xlsx**: Semi-quantitative
 mean optical density results of immunohistochemistry (IHC) staining.
 Semi-quantitative positive area results of immunofluorescence (IF)
 staining.