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1.
Cancer Sci ; 114(9): 3636-3648, 2023 Sep.
Article in English | MEDLINE | ID: mdl-37357017

ABSTRACT

The bone morphogenetic protein (BMP) pathway promotes differentiation and induces apoptosis in normal colorectal epithelial cells. However, its role in colorectal cancer (CRC) is controversial, where it can act as context-dependent tumor promoter or tumor suppressor. Here we have found that CRC cells reside in a BMP-rich environment based on curation of two publicly available RNA-sequencing databases. Suppression of BMP using a specific BMP inhibitor, LDN193189, suppresses the growth of select CRC organoids. Colorectal cancer organoids treated with LDN193189 showed a decrease in epidermal growth factor receptor, which was mediated by protein degradation induced by leucine-rich repeats and immunoglobulin-like domains protein 1 (LRIG1) expression. Among 18 molecularly characterized CRC organoids, suppression of growth by BMP inhibition correlated with induction of LRIG1 gene expression. Notably, knockdown of LRIG1 in organoids diminished the growth-suppressive effect of LDN193189. Furthermore, in CRC organoids, which are susceptible to growth suppression by LDN193189, simultaneous treatment with LDN193189 and trametinib, an FDA-approved MEK inhibitor, resulted in cooperative growth inhibition both in vitro and in vivo. Taken together, the simultaneous inhibition of BMP and MEK could be a novel treatment option in CRC cases, and evaluating in vitro growth suppression and LRIG1 induction by BMP inhibition using patient-derived organoids could offer functional biomarkers for predicting potential responders to this regimen.


Subject(s)
Colorectal Neoplasms , ErbB Receptors , Humans , Down-Regulation , ErbB Receptors/genetics , Bone Morphogenetic Proteins/metabolism , Colorectal Neoplasms/drug therapy , Colorectal Neoplasms/genetics , Colorectal Neoplasms/pathology , Mitogen-Activated Protein Kinase Kinases/metabolism , Cell Line, Tumor
2.
J Cell Sci ; 133(24)2020 11 16.
Article in English | MEDLINE | ID: mdl-33199519

ABSTRACT

During the transition from pluripotency to a lineage-committed state, chromatin undergoes large-scale changes in structure, involving covalent modification of histone tails, use of histone variants and gene position changes with respect to the nuclear periphery. Here, using high-resolution microscopy and quantitative image analysis, we surveyed a panel of histone modifications for changes in nuclear peripheral enrichment during differentiation of human embryonic stem cells to a trophoblast-like lineage. We found two dynamic modifications at the nuclear periphery, acetylation of histone H2A.Z (H2A.Zac), and dimethylation of histone H3 at lysine 9 (H3K9me2). We demonstrate successive peripheral enrichment of these markers, with H2A.Zac followed by H3K9me2, over the course of 4 days. We find that H3K9me2 increases concomitantly with, but independently of, expression of lamin A, since deletion of lamin A did not affect H3K9me2 enrichment. We further show that inhibition of histone deacetylases causes persistent and increased H2A.Z acetylation at the periphery, delayed H3K9me2 enrichment and failure to differentiate. Our results show a concerted change in the nature of peripheral chromatin occurs upon differentiation into the trophoblast state.


Subject(s)
Human Embryonic Stem Cells , Cell Differentiation , Chromatin , Histones/genetics , Humans , Trophoblasts
3.
Cancer Sci ; 111(8): 2837-2849, 2020 Aug.
Article in English | MEDLINE | ID: mdl-32539229

ABSTRACT

Accumulating evidence on the association of VEGF-C with lymphangiogenesis and lymph node metastasis implicates lymphatic vessels as a potential target in anti-cancer therapy. To evaluate whether blocking VEGF-C and VEGFR-3 signaling can inhibit multi-organ metastases, a mouse metastatic mammary cancer model was subjected to gene therapy using a soluble VEGFR-3 expression vector (psVEGFR-3). We showed that psVEGFR-3 significantly diminished cell growth in vitro with or without added VEGF-C, and significantly reduced primary tumor growth and tumor metastases to wide-spectrum organs in vivo. Although apoptotic cell death and angiogenesis levels did not differ between the control and psVEGFR-3 groups, cell proliferation and lymphangiogenesis in the mammary tumors were significantly decreased in the psVEGFR-3 group. Furthermore, lymphatic vessel invasion was significantly inhibited in this group. Real-time RT-PCR analysis revealed significantly high expression of the Vegfr3 gene due to gene therapy, and the transcriptional levels of Pcna and Lyve1 tended to decrease in the psVEGFR-3 group. Immunofluorescence staining indicated that phospho-tyrosine expression was considerably lower in tumor cells of psVEGFR-3-treated mammary carcinomas than those of control tumors. Double immunofluorescence staining indicated that phospho-tyrosine+ /LYVE-1+ (a lymphatic vessel marker) tended to decrease in psVEGFR-3-treated mammary carcinomas compared with control mice, indicating a decline in the activity of the VEGF-C/VEGFR-3 axis. These findings showed that a blockade of VEGF-C/VEGFR-3 signaling caused by sVEGFR-3 sequestered VEGF-C and prevented the side-effects of anti-angiogenesis and suppressed overall metastases, suggesting their high clinical significance.


Subject(s)
Genetic Therapy/methods , Mammary Neoplasms, Experimental/therapy , Neoplasm Metastasis/therapy , Vascular Endothelial Growth Factor C/metabolism , Vascular Endothelial Growth Factor Receptor-3/genetics , Animals , Cell Line, Tumor/transplantation , Female , Lymphatic Vessels/pathology , Mammary Glands, Animal/pathology , Mammary Neoplasms, Experimental/genetics , Mammary Neoplasms, Experimental/pathology , Mice , Neoplasm Invasiveness/genetics , Neoplasm Invasiveness/prevention & control , Neoplasm Metastasis/genetics , Vascular Endothelial Growth Factor C/antagonists & inhibitors , Vascular Endothelial Growth Factor Receptor-3/metabolism
4.
Knee Surg Sports Traumatol Arthrosc ; 28(12): 3888-3898, 2020 Dec.
Article in English | MEDLINE | ID: mdl-32030501

ABSTRACT

PURPOSE: Medial release during total knee arthroplasty (TKA) is used to correct ligament imbalance in knees with varus deformity. However, questions remain on whether residual ligament imbalance would be related to inferior clinical results. The purposes of the present study were to measure the intraoperative joint gap and to evaluate the effect of intraoperative soft tissue condition on the new Knee Society Score (KSS 2011) at 2-year follow-up, without the maneuver of additional medial release to correct the asymmetrical gap balance. METHODS: Varus-valgus gap angle and joint gap were measured using a tensor device without medial release for 100 knees with preoperative varus deformity. The knees were categorized according to the varus-valgus gap angle and the laxity. The preoperative and postoperative clinical outcomes using KSS 2011 were compared between the groups. RESULTS: The average varus-valgus angles had a residual imbalance of 2.8° varus and 1.3° varus in extension and flexion, respectively. In comparison, according to varus-valgus joint gap angle and knee laxity in extension and flexion, no significant differences were found in postoperative range of motion and subscale of KSS 2011 among the groups. CONCLUSION: Intraoperative asymmetrical joint gap and physiological laxity do not affect early clinical results after TKA. LEVEL OF EVIDENCE: III.


Subject(s)
Arthroplasty, Replacement, Knee , Joint Instability/physiopathology , Joint Instability/surgery , Knee Joint/physiopathology , Knee Joint/surgery , Osteoarthritis, Knee/physiopathology , Osteoarthritis, Knee/surgery , Patient Satisfaction , Aged , Arthroplasty, Replacement, Knee/methods , Female , Humans , Intraoperative Period , Ligaments/physiopathology , Ligaments/surgery , Male , Range of Motion, Articular , Treatment Outcome
5.
Knee Surg Sports Traumatol Arthrosc ; 28(5): 1568-1578, 2020 May.
Article in English | MEDLINE | ID: mdl-31227865

ABSTRACT

PURPOSE: The purpose of this study was to determine the ideal coronal alignment under dynamic conditions after open-wedge high tibial osteotomy (OWHTO). It was hypothesised that, although the classical target alignment was based on experimental evidence, it would demonstrate biomechanical validity. METHODS: Musculoskeletal computer models were analysed with various degrees of coronal correction in OWHTO during gait and squat, specifically with the mechanical axis passing through points at 40%, 50%, 60%, 62.5%, 70%, and 80% of the tibial plateau from the medial edge, defined as the weight-bearing line percentage (WBL%). The peak load on the lateral tibiofemoral (TF) joint, the medial collateral ligament (MCL), and anterior cruciate ligament (ACL) tensions, and knee kinematics with or without increased posterior tibial slope (PTS) were evaluated. RESULTS: The classical alignment with WBL62.5% achieved sufficient load on the lateral TF joint and maintained normal knee kinematics after OWHTO. However, over-correction with WBL80% caused an excessive lateral load and non-physiological kinematics. Increased WBL% resulted in increased MCL tension due to lateral femoral movement against the tibia. With WBL80%, abnormal contact between the medial femoral condyle and the medial intercondylar eminence of the tibia occurred at knee extension. The screw-home movement around knee extension and the TF rotational angle during flexion were reduced as WBL% increased. Increased PTS was associated with increased ACL tension and decreased TF rotation angle because of ligamentous imbalance. CONCLUSIONS: The classical target alignment demonstrated validity in OWHTO, and over-correction should be avoided as it negatively impacts clinical outcome. LEVEL OF EVIDENCE: IV.


Subject(s)
Bone Malalignment/surgery , Knee Joint/surgery , Osteotomy/methods , Tibia/surgery , Biomechanical Phenomena , Bone Malalignment/diagnostic imaging , Bone Malalignment/physiopathology , Computer Simulation , Humans , Knee Joint/diagnostic imaging , Knee Joint/physiopathology , Range of Motion, Articular , Tibia/diagnostic imaging , Tibia/physiopathology , Weight-Bearing
6.
Knee Surg Sports Traumatol Arthrosc ; 25(11): 3459-3466, 2017 Nov.
Article in English | MEDLINE | ID: mdl-28484791

ABSTRACT

PURPOSE: Abnormal knee motion under various conditions has been described after total knee arthroplasty (TKA). However, differences in kinematics and kinetics of knees with varus femoral versus varus tibial alignment have not been evaluated. It was hypothesized that varus femoral and tibial alignments have the same impact on knee motion. METHODS: A musculoskeletal computer simulation was used. Femoral and tibial alignment in the coronal plane was each varied from neutral to 5° of varus in 1° increments. Lift-off, defined as an intercomponent distance of >2 mm, and tibiofemoral contact forces were evaluated during gait up to 60° of knee flexion. Knee kinematics and contact stresses were also examined during squat, with up to 130° of knee flexion. RESULTS: During gait, lift-off occurred readily with more than 3° of varus tibial alignment and slight lateral joint laxity. In contrast, lift-off did not occur with varus femoral or tibial alignment of up to 5° during squat. Peak medial contact forces with varus femoral alignment were approximately twice those observed with varus tibial alignment. The lowest points of the femoral condyles moved internally with varus femoral alignment, contrary to the kinematics with neutral or varus tibial alignment. On the other hand, there was femoral medial sliding and edge loading against the tibia in mid-flexion with varus tibial alignment. CONCLUSION: Varus femoral alignment affects the non-physiological rotational movement of the tibiofemoral joint, whereas varus tibial alignment causes medial-lateral instability during mid-flexion. Varus femoral and tibial alignments might lead to post-TKA discomfort and unreliability.


Subject(s)
Arthroplasty, Replacement, Knee/adverse effects , Bone Malalignment/physiopathology , Femur/surgery , Tibia/surgery , Aged , Biomechanical Phenomena , Bone Malalignment/etiology , Computer Simulation , Female , Femur/physiopathology , Gait/physiology , Humans , Kinetics , Knee Joint/physiopathology , Knee Joint/surgery , Knee Prosthesis , Male , Range of Motion, Articular/physiology , Tibia/physiopathology
7.
Int J Mol Sci ; 18(5)2017 May 15.
Article in English | MEDLINE | ID: mdl-28505146

ABSTRACT

This study was conducted to investigate the autophagic response of Sertoli cells (SCs) to acute ethanol toxicity using in vivo and in vitro models. Adult Wistar rats were intraperitoneally injected with either 5 g/kg ethanol or phosphate-buffered saline (for the control group) and sacrificed 0, 3, 6 and 24 h after injection. Compared to the control group, enhanced germ cell apoptosis was observed in the ethanol-treated rats (ETRs) in association with upregulation of iNOS and reduced expression of androgen receptor protein levels in SCs, which were resistant to apoptosis. Meanwhile, autophagy was upregulated in ETR SCs (peaking at 24 h) compared to the control group, as evidenced by transcription factor EB (TFEB) nuclear translocation, enhanced expression of microtubule-associated protein 1 light chain3-II (LC3-II), lysosome-associated membrane protein-2 (LAMP-2), pan cathepsin protein levels and reduced expression of p62. This upregulation of SC autophagy was confirmed ultrastructurally by enhanced formation of autophagic vacuoles and by immunofluorescent double labelling of autophagosomal and lysosomal markers. Study of cultured SCs confirmed enhanced autophagic response to ethanol toxicity, which was cytoprotective based on decreased viability of SCs upon blocking autophagy with 3-methyladenine (3-MA). The results highlighted the molecular mechanisms of prosurvival autophagy in ETR SCs for the first time, and may have significant implications for male fertility.


Subject(s)
Apoptosis/genetics , Nitric Oxide Synthase Type II/genetics , Receptors, Androgen/genetics , Sertoli Cells/metabolism , Animals , Apoptosis/drug effects , Autophagy/drug effects , Autophagy/genetics , Cathepsins/genetics , Ethanol/administration & dosage , Ethanol/toxicity , Gene Expression Regulation/drug effects , Germ Cells/drug effects , Germ Cells/metabolism , Lysosomal-Associated Membrane Protein 2/genetics , Male , Microtubule-Associated Proteins/genetics , Rats , Sequestosome-1 Protein/genetics , Sertoli Cells/drug effects
9.
Biosci Biotechnol Biochem ; 79(7): 1111-8, 2015.
Article in English | MEDLINE | ID: mdl-25754602

ABSTRACT

A novel O-methyltransferase gene was isolated from Flammulina velutipes. The isolated full-length cDNA was composed of a 690-nucleotide open reading frame encoding 230 amino acids. A database search revealed that the deduced amino acid sequence was similar to those of other O-methyltransferases; the highest identity was only 61.8% with Laccaria bicolor. The recombinant enzyme was expressed by Escherichia coli. BL21 (DE3) was assessed for its ability to methylate (-)-epigallocatechin-3-O-gallate (EGCG). LC-TOF-MS and NMR revealed that the enzyme produced five kinds of O-methylated EGCGs: (-)-epigallocatechin-3-O-(3-O-methyl)gallate, (-)-epigallocatechin-3-O-(4-O-methyl)gallate, (-)-epigallocatechin-3-O-(3,4-O-dimethyl)gallate, (-)-epigallocatechin-3-O-(3,5-O-dimethyl)gallate, and (-)-4'-O-methylepigallocatechin-3-O-(3,5-O-dimethyl)gallate. The substrate specificity of the enzyme for 20 kinds of polyphenols was assessed using the crude recombinant enzyme of O-methyltransferase. This enzyme introduced methyl group(s) into polyphenols with pyrocatechol and pyrogallol structures.


Subject(s)
Flammulina/enzymology , Methyltransferases/metabolism , Pyrogallol/metabolism , Amino Acid Sequence , Catechin/analogs & derivatives , Catechin/chemistry , Catechin/metabolism , Catechol O-Methyltransferase/genetics , Catechol O-Methyltransferase/metabolism , Catechols/chemistry , Catechols/metabolism , Cloning, Molecular , Escherichia coli/genetics , Flammulina/genetics , Fungal Proteins/genetics , Fungal Proteins/metabolism , Gallic Acid/analogs & derivatives , Gallic Acid/metabolism , Methylation , Methyltransferases/genetics , Molecular Sequence Data , Molecular Structure , Polyphenols/chemistry , Polyphenols/metabolism , Pyrogallol/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Substrate Specificity
10.
Biosci Biotechnol Biochem ; 78(5): 806-11, 2014.
Article in English | MEDLINE | ID: mdl-25035983

ABSTRACT

An enzyme catalyzing the methylation of phenolic hydroxyl groups in polyphenols was identified from mycelial cultures of edible mushrooms to synthesize O-methylated polyphenols. Enzyme activity was measured to assess whether methyl groups were introduced into (-)-epigallocatechin-3-O-gallate (EGCG) using SAM as a methyl donor, and (-)-epigallocatechin-3-O-(3-O-methyl)-gallate (EGCG3″Me), (-)-epigallocatechin-3-O-(4-O-methyl)-gallate (EGCG4″Me), and (-)-epigallocatechin-3-O-(3,5-O-dimethyl)-gallate (EGCG3″,5″diMe) peaks were detected using crude enzyme preparations from mycelial cultures of Flammulina velutipes. The enzyme was purified using chromatographic and two-dimensional electrophoresis. The purified enzyme was subsequently analyzed on the basis of the partial amino acid sequence using LC-MS/MS. Partial amino acid sequencing identified the 17 and 12 amino acid sequences, VLEVGTLGGYSTTWLAR and TGGIIIVDNVVR. In database searches, these sequences showed high identity with O-methyltransferases from other mushroom species and completely matched 11 of 17 and 9 of 12 amino acids from five other mushroom O-methyltransferases.


Subject(s)
Flammulina/enzymology , Methyltransferases/isolation & purification , Methyltransferases/metabolism , Amino Acid Sequence , Catechin/analogs & derivatives , Catechin/metabolism , Hydrogen-Ion Concentration , Methyltransferases/chemistry , Molecular Sequence Data , Sequence Analysis , Temperature
11.
Biosci Biotechnol Biochem ; 78(7): 1140-6, 2014.
Article in English | MEDLINE | ID: mdl-25229848

ABSTRACT

Seven new O-methylated theaflavins (TFs) were synthesized by using O-methyltransferase from an edible mushroom. Using TFs and O-methylated TFs, metabolic stability in pooled human liver S9 fractions and inhibitory effect on H(2)O(2)-induced oxidative damage in human HepG2 cells were investigated. In O-methylation of theaflavin 3'-O-gallate (TF3'G), metabolic stability was potentiated by an increase in the number of introduced methyl groups. O-methylation of TF3,3'G did not affect metabolic stability, which was likely because of a remaining 3-O-galloyl group. The inhibitory effect on oxidative damage was assessed by measuring the viability of H(2)O(2)-damaged HepG2 cells treated with TFs and O-methylated TFs. TF3,3'G and O-methylated TFs increased cell viabilities significantly compared with DMSO, which was the compound vehicle (p < 0.05), and improved to approximately 100%. Only TF3'G did not significantly increase cell viability. It was suggested that the inhibitory effect on H(2)O(2)-induced oxidative damage was potentiated by O-methylation or O-galloylation of TFs.


Subject(s)
Biflavonoids/chemistry , Biflavonoids/pharmacology , Catechin/chemistry , Catechin/pharmacology , Hydrogen Peroxide/pharmacology , Oxidative Stress/drug effects , Oxygen/chemistry , Biflavonoids/chemical synthesis , Biflavonoids/metabolism , Catechin/chemical synthesis , Catechin/metabolism , Drug Stability , Hep G2 Cells , Humans , Methylation
12.
J Knee Surg ; 36(7): 731-737, 2023 Jun.
Article in English | MEDLINE | ID: mdl-34991175

ABSTRACT

Tunnel position during anterior cruciate ligament (ACL) reconstruction is considered as an important factor to restore normal knee kinematics and to gain better clinical outcomes. It is still unknown where the optimal femoral and tibial tunnel position is located in single-bundle (SB) ACL reconstruction. The purposes of this study were to analyze the knee kinematics with various graft positions and to propose the optimal graft position during SB ACL reconstruction. A musculoskeletal computer simulation was used to analyze knee kinematics. Four attachments on the femoral side (anteromedial [AM], mid, posterolateral [PL], and over-the-top positions) and three attachments on the tibial side (AM, middle, and PL positions) were determined. The middle-bundle attachment was placed at the midpoint of the AM and PL bundle attachments for the femoral and tibial attachments. SB ACL reconstruction models were constructed to combine each of the four femoral attachments with each of three tibial attachments. Kinematic comparison was made among a double-bundle (DB) model and 12 SB reconstruction models during deep knee bend and stair descent activity. The tunnel position of the tibia had greater effect of knee kinematics than that of the femur. AM tibial attachment models showed similar medial and lateral anteroposterior positions to the DB model for both activities. Axial rotation in the AM tibial attachment models was similar to the DB model regardless of the femoral attachment, whereas greater maximum axial rotation was exhibited in the PL tibial attachment models, especially during stair descent activity. AM tibial attachment can represent normal knee kinematics, whereas the PL tibial attachment can induce residual rotational instability during high-demand activities. The AM tibial tunnel is recommended for SB ACL reconstruction.


Subject(s)
Anterior Cruciate Ligament Reconstruction , Tibia , Humans , Tibia/surgery , Anterior Cruciate Ligament/surgery , Biomechanical Phenomena , Computer Simulation , Knee Joint/surgery , Femur/surgery
13.
iScience ; 26(2): 105962, 2023 Feb 17.
Article in English | MEDLINE | ID: mdl-36718360

ABSTRACT

Dynamic changes in cell properties lead to intratumor heterogeneity; however, the mechanisms of nongenetic cellular plasticity remain elusive. When the fate of each cell from colorectal cancer organoids was tracked through a clonogenic growth assay, the cells showed a wide range of growth ability even within the clonal organoids, consisting of distinct subpopulations; the cells generating large spheroids and the cells generating small spheroids. The cells from the small spheroids generated only small spheroids (S-pattern), while the cells from the large spheroids generated both small and large spheroids (D-pattern), both of which were tumorigenic. Transition from the S-pattern to the D-pattern occurred by various extrinsic triggers, in which Notch signaling and Musashi-1 played a key role. The S-pattern spheroids were resistant to chemotherapy and transited to the D-pattern upon drug treatment through Notch signaling. As the transition is linked to the drug resistance, it can be a therapeutic target.

14.
Knee ; 39: 185-196, 2022 Dec.
Article in English | MEDLINE | ID: mdl-36209651

ABSTRACT

BACKGROUND: Asymmetric tibial insert design is expected to restore normal knee kinematics better than symmetric design. A tri-condylar implant has asymmetric and symmetric tibial inserts with a ball-and-socket joint to replace the post-cam mechanism. The purpose of this study was to compare the knee kinematics of the two designs and to measure tibiofemoral contact stresses, including that of the ball-and-socket joint. METHODS: Using a computer simulation, the anteroposterior position and axial rotation of the femoral component were simulated during a weight-bearing deep knee bend for six validated models. Contact forces were simultaneously simulated in the medial, lateral, and ball-and-socket compartments. The relative position and the magnitude and direction of each contact force were applied to aforce/displacement control knee simulator. The contact stresses were measured individually using a pressure sensor. RESULTS: The asymmetric tibial insert demonstrated a more posterior position of the femoral component in the lateral compartment during the entire range of motion and greater external rotation of the femoral component, compared to the symmetrical tibial insert. The mean peak contact stress of the medial and lateral compartments was < 9 Mpa, with no significant differences between the two designs except at 0°. The contact stress of the ball-and-socket joint was < 5 MPa. CONCLUSIONS: Asymmetry of the tibial insert shows significant kinematic difference and has little influence on the peak contact stress, which is considerably lower than the yield strength of polyethylene. The asymmetric tibial insert can lead to clinical benefits owing to its kinematic and kinetic properties.


Subject(s)
Arthroplasty, Replacement, Knee , Knee Prosthesis , Humans , Tibia/surgery , Computer Simulation , Femur/surgery , Knee Joint/surgery , Biomechanical Phenomena , Range of Motion, Articular
15.
J Am Soc Mass Spectrom ; 32(2): 606-610, 2021 Feb 03.
Article in English | MEDLINE | ID: mdl-33331152

ABSTRACT

A moving string sampling probe and a new ESI based ionization source that can be readily incorporated into the existing endoscopes are developed for performing in vivo mass spectrometry during the endoscopic procedure. The medical-grade silk suture driven by a stepping motor is used to perform the sampling on the region of interest when the probe head is brought gently into contact with the surface of the gastrointestinal tissue. The tissues and the compounds adhered to the sampling string are transported to an ionization region inside the ion inlet tube in which they are extracted and ionized by the charging droplets generated from an electrospray outside the ion inlet. Since the extraction/ionization and sampling processes are isolated, organic solvents, high voltage (HV), and heating can be used for the optimization of ionization without compromising the biocompatibility of the sampling probe. The demonstration of the in vivo analysis of the gastric mucosa of a mouse is performed using a 2 m long gastrointestinal endoscope.

16.
Sci Rep ; 11(1): 23653, 2021 12 08.
Article in English | MEDLINE | ID: mdl-34880275

ABSTRACT

The identification of cancer subtypes is important for the understanding of tumor heterogeneity. In recent years, numerous computational methods have been proposed for this problem based on the multi-omics data of patients. It is widely accepted that different cancer subtypes are induced by different molecular regulatory networks. However, only a few incorporate the differences between their molecular systems into the identification processes. In this study, we present a novel method to identify cancer subtypes based on patient-specific molecular systems. Our method realizes this by quantifying patient-specific gene networks, which are estimated from their transcriptome data, and by clustering their quantified networks. Comprehensive analyses of The Cancer Genome Atlas (TCGA) datasets applied to our method confirmed that they were able to identify more clinically meaningful cancer subtypes than the existing subtypes and found that the identified subtypes comprised different molecular features. Our findings also show that the proposed method can identify the novel cancer subtypes even with single omics data, which cannot otherwise be captured by existing methods using multi-omics data.


Subject(s)
Gene Regulatory Networks , Neoplasms/genetics , Cluster Analysis , Datasets as Topic , Female , Humans , Kaplan-Meier Estimate , Male , Neoplasms/pathology , Sequence Analysis, RNA , Transcriptome
17.
Sci Rep ; 11(1): 11241, 2021 05 27.
Article in English | MEDLINE | ID: mdl-34045524

ABSTRACT

The current pandemic of SARS-CoV-2 has caused extensive damage to society. The characterization of SARS-CoV-2 profiles has been addressed by researchers globally with the aim of resolving this disruptive crisis. This investigation process is indispensable to understand how SARS-CoV-2 behaves in human host cells. However, little is known about the systematic molecular mechanisms involved in the effects of SARS-CoV-2 infection on human host cells. Here, we present gene-to-gene regulatory networks in response to SARS-CoV-2 using a Bayesian network. We examined the dynamic changes in the SARS-CoV-2-purturbated networks established by our proposed framework for gene network analysis, thus revealing that interferon signaling gradually switched to the subsequent inflammatory cytokine signaling cascades. Furthermore, we succeeded in capturing a COVID-19 patient-specific network in which transduction of these signals was concurrently induced. This enabled us to explore the local regulatory systems influenced by SARS-CoV-2 in host cells more precisely at an individual level. Our panel of network analyses has provided new insights into SARS-CoV-2 research from the perspective of cellular systems.


Subject(s)
COVID-19/metabolism , Gene Regulatory Networks , SARS-CoV-2/metabolism , Signal Transduction/genetics , Bayes Theorem , COVID-19/genetics , COVID-19/virology , Cell Line , Computational Biology , Databases, Genetic , Humans , RNA-Seq , SARS-CoV-2/genetics , Viral Load
18.
Biomolecules ; 10(2)2020 02 14.
Article in English | MEDLINE | ID: mdl-32075209

ABSTRACT

Gene network estimation is a method key to understanding a fundamental cellular system from high throughput omics data. However, the existing gene network analysis relies on having a sufficient number of samples and is required to handle a huge number of nodes and estimated edges, which remain difficult to interpret, especially in discovering the clinically relevant portions of the network. Here, we propose a novel method to extract a biomedically significant subnetwork using a Bayesian network, a type of unsupervised machine learning method that can be used as an explainable and interpretable artificial intelligence algorithm. Our method quantifies sample specific networks using our proposed Edge Contribution value (ECv) based on the estimated system, which realizes condition-specific subnetwork extraction using a limited number of samples. We applied this method to the Epithelial-Mesenchymal Transition (EMT) data set that is related to the process of metastasis and thus prognosis in cancer biology. We established our method-driven EMT network representing putative gene interactions. Furthermore, we found that the sample-specific ECv patterns of this EMT network can characterize the survival of lung cancer patients. These results show that our method unveils the explainable network differences in biological and clinical features through artificial intelligence technology.


Subject(s)
Computational Biology/methods , Gene Expression Profiling/methods , Gene Regulatory Networks/physiology , Algorithms , Bayes Theorem , Epithelial-Mesenchymal Transition/genetics , Gene Expression Regulation, Neoplastic/genetics , Humans , Lung Neoplasms/genetics , Prognosis , Unsupervised Machine Learning
19.
Knee ; 27(5): 1385-1395, 2020 Oct.
Article in English | MEDLINE | ID: mdl-33010752

ABSTRACT

BACKGROUND: Bicruciate-retaining total knee arthroplasty (BCR-TKA) was developed to maintain anterior cruciate ligament function and thus reproduce natural knee kinematics postoperatively. Traditional surgical techniques, however, may cause several complications secondary to kinematic conflict and ligament overtension. The objective of this study was to use a computer simulation of symmetric BCR-TKA to evaluate the effects of alternative surgical techniques on knee kinematics and ligaments. METHODS: A musculoskeletal computer model of a healthy knee was constructed and was used to simulate a BCR model with mechanical alignment (MA). Five adjusted models were investigated, characterized, respectively, by kinematic alignment (KA), two degrees increased tibial slope, two-millimeter distal setting of the tibial component, and an undersized femoral component with either MA or KA. RESULTS: All models exhibited a normal femoral position against the tibia at knee extension, with no anterior paradoxical motion during mid-flexion. The healthy knee model showed medial pivot motion and rollback. In contrast, the BCR MA model demonstrated abnormal bi-condylar rollback with excessive tensions of the lateral collateral ligament and posterior cruciate ligament during knee flexion, whereas the undersized femoral model with MA partly reduced both tensions. The BCR KA model retained relatively physiological kinematics and suppressed excessive ligament tensions. However, no adjusted model completely reproduced healthy knee conditions. CONCLUSIONS: The BCR MA model showed abnormal biomechanics due to kinematic conflict between the retained ligaments and the replaced joint surface. Surgeons using symmetric BCR-TKA should consider using the KA method to achieve sufficient ligament laxity throughout knee flexion.


Subject(s)
Arthroplasty, Replacement, Knee/methods , Biomechanical Phenomena/physiology , Computer Simulation , Knee Joint/physiology , Humans , Knee Joint/surgery
20.
J Orthop ; 21: 370-374, 2020.
Article in English | MEDLINE | ID: mdl-32904327

ABSTRACT

INTRODUCTION: The tension of anterior cruciate ligament (ACL) graft has an important role in antero-posterior (AP) and rotational stability of the knee. The purposes of this study were to analyze the kinematics and kinetics of normal knee models with loose and tight ACL tension, and to evaluate the effect of the tension of ACL on knee kinematics and kinetics. MATERIALS AND METHODS: Slack and tight ACL models were constructed in a musculoskeletal computer simulation. The effect of ACL tension on kinematics, and femorotibial contact force during various activities was analyzed. RESULTS: During stair descent activity in the slack ACL models, the lateral femoral condyles were positioned posterior, and more external rotation of the femur was observed in comparison with the normal model. The contact forces at the lateral compartment in the tight models increased during all activities, and the tension of the medial collateral ligament (MCL) in the slack models increased during the stair descent activity, compared with the normal knee model. CONCLUSION: AP and rotational instability and excessive MCL tension were observed in the ACL slack knees especially during stair descent movement, whereas the tibiofemoral contact force of the lateral compartment increased in the tight ACL knees.

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