Single-cell and WGCNA uncover a prognostic model and potential oncogenes in colorectal cancer

Background

Colorectal cancer (CRC) is one of the leading causes of cancer-related death worldwide. Single-cell transcriptome sequencing (scRNA-seq) can provide accurate gene expression data for individual cells. In this study, a new prognostic model was constructed by scRNA-seq and bulk transcriptome sequencing (bulk RNA-seq) data of CRC samples to develop a new understanding of CRC.

Methods

CRC scRNA-seq data were downloaded from the GSE161277 database, and CRC bulk RNA-seq data were downloaded from the TCGA and GSE17537 databases. The cells were clustered by the FindNeighbors and FindClusters functions in scRNA-seq data. CIBERSORTx was applied to detect the abundance of cell clusters in the bulk RNA-seq expression matrix. WGCNA was performed with the expression profiles to construct the gene coexpression networks of TCGA-CRC. Next, we used a tenfold cross test to construct the model and a nomogram to assess the independence of the model for clinical application. Finally, we examined the expression of the unreported model genes by qPCR and immunohistochemistry. A clone formation assay and orthotopic colorectal tumour model were applied to detect the regulatory roles of unreported model genes.

Results

A total of 43,851 cells were included after quality control, and 20 cell clusters were classified by the FindCluster () function. We found that the abundances of C1, C2, C4, C5, C15, C16 and C19 were high and the abundances of C7, C10, C11, C13, C14 and C17 were low in CRC tumour tissues. Meanwhile, the results of survival analysis showed that high abundances of C4, C11 and C13 and low abundances of C5 and C14 were associated with better survival. The WGCNA results showed that the red module was most related to the tumour and the C14 cluster, which contains 615 genes. Lasso Cox regression analysis revealed 8 genes (PBXIP1, MPMZ, SCARA3, INA, ILK, MPP2, L1CAM and FLNA), which were chosen to construct a risk model. In the model, the risk score features had the greatest impact on survival prediction, indicating that the 8-gene risk model can better predict prognosis. qPCR and immunohistochemistry analysis showed that the expression levels of MPZ, SCARA3, MPP2 and PBXIP1 were high in CRC tissues. The functional experiment results indicated that MPZ, SCARA3, MPP2 and PBXIP1 could promote the colony formation ability of CRC cells in vitro and tumorigenicity in vivo.

Conclusions

We constructed a risk model to predict the prognosis of CRC patients based on scRNA-seq and bulk RNA-seq data, which could be used for clinical application. We also identified 4 previously unreported model genes (MPZ, SCARA3, MPP2 and PBXIP1) as novel oncogenes in CRC. These results suggest that this model could potentially be used to evaluate the prognostic risk and provide potential therapeutic targets for CRC patients.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12575-022-00175-x.

DOCK4 regulates ghrelin production in gastric X/A-like cells

PURPOSE

Ghrelin, a gastric hormone, provides a hunger signal to the central nervous system to stimulate food intake. Ghrelin also modulates neuroinflammatory and apoptotic processes. Dedicator of cytokinesis 4 (DOCK4), a guanine nucleotide exchange factor (GEF), is involved in the regulation of neuronal polarization and axon regeneration. However, the effect of DOCK4 on ghrelin production has not been explored.

METHODS

The expression of DOCK4 in human and mouse stomach was examined by immunohistochemical staining. The synthesis and secretion of ghrelin in Dock4 null mice were evaluated by real-time quantitative PCR, Western blot and ELISA. The effects of DOCK4 on ghrelin production in mHypoE-42 cells were measured by real-time quantitative PCR and Western blot.

RESULTS

We showed that DOCK4 was expressed in both human and mouse gastric ghrelin cells. The mRNA and protein levels of gastric ghrelin, as well as ghrelin secretion, were remarkably diminished in Dock4 null mice. Furthermore, we showed that overexpression of Dock4 significantly stimulated ghrelin expression, while siRNA knockdown of endogenous Dock4 resulted in a marked decrease of ghrelin in mHypoE-N42 cells.

CONCLUSIONS

Our results identify DOCK4 as a critical regulator for ghrelin production in gastric X/A-like cells.

Total thyroidectomy versus hemithyroidectomy with intraoperative radiofrequency ablation for unilateral thyroid cancer with contralateral nodules: A propensity score matching study

Background

For unilateral papillary thyroid carcinoma (PTC) patients with contralateral benign nodules, optimal treatment decisions are made according to patient preference and the disease’s pathological features. This study was performed to evaluate the efficacy and complications of hemithyroidectomy with intraoperative radiofrequency ablation (RFA) compared with total thyroidectomy.

Methods

Patients with unilateral PTC and cytologically benign contralateral nodules were enrolled from 2014 to 2018. Total thyroidectomy or hemithyroidectomy with intraoperative RFA of the contralateral nodule was offered to patients who had anxiety regarding their disease. The operation-related parameters, transient or permanent nerve injury, hypocalcemia and disease recurrence, were recorded and compared between the two groups.

Results

After propensity score matching, 191 patients who underwent total thyroidectomy and 224 contralateral nodules in 191 patients underwent hemithyroidectomy with intraoperative RFA (HTRFA) were included. The volume reduction ratios of the contralateral nodules were 67.7% at 12 months and 95.8% at 24 months. The total thyroidectomy group reported significantly higher hypocalcemia than HTRFA within one year (7.8% vs. 2.6%, p = 0.022). Supplemental levothyroxine was not required in 28.3% (54/191) of the patients one year after HTRFA. With a median follow-up of 4.1 years, three recurrences (1.6%) were observed in the HTRFA, and no recurrence occurred in the total thyroidectomy group (p = 0.246).

Conclusions

Hemithyroidectomy for unilateral PTC and intraoperative RFA for contralateral nodules were acceptable and effective treatment approaches and did not increase the risk of complications.

Graphical Abstract

A seven-autophagy-related gene signature for predicting the prognosis of differentiated thyroid carcinoma

Background

Numerous studies have implicated autophagy in the pathogenesis of thyroid carcinoma. This investigation aimed to establish an autophagy-related gene model and nomogram that can help predict the overall survival (OS) of patients with differentiated thyroid carcinoma (DTHCA).

Methods

Clinical characteristics and RNA-seq expression data from TCGA (The Cancer Genome Atlas) were used in the study. We also downloaded autophagy-related genes (ARGs) from the Gene Set Enrichment Analysis website and the Human Autophagy Database. First, we assigned patients into training and testing groups. R software was applied to identify differentially expressed ARGs for further construction of a protein-protein interaction (PPI) network for gene functional analyses. A risk score-based prognostic risk model was subsequently developed using univariate Cox regression and LASSO-penalized Cox regression analyses. The model’s performance was verified using Kaplan-Meier (KM) survival analysis and ROC curve. Finally, a nomogram was constructed for clinical application in evaluating the patients with DTHCA. Finally, a 7-gene prognostic risk model was developed based on gene set enrichment analysis.

Results

Overall, we identified 54 differentially expressed ARGs in patients with DTHCA. A new gene risk model based on 7-ARGs (CDKN2A, FGF7, CTSB, HAP1, DAPK2, DNAJB1, and ITPR1) was developed in the training group and validated in the testing group. The predictive accuracy of the model was reflected by the area under the ROC curve (AUC) values. Univariate and multivariate Cox regression analysis indicated that the model could independently predict the prognosis of patients with THCA. The constrained nomogram derived from the risk score and age also showed high prediction accuracy.

Conclusions

Here, we developed a 7-ARG prognostic risk model and nomogram for differentiated thyroid carcinoma patients that can guide clinical decisions and individualized therapy.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12957-022-02590-6.

[SARS-CoV-2 with transcription regulatory sequence motif mutation poses a greater threat]

OBJECTIVE

To analyze the mutations in transcription regulatory sequences (TRSs) of coronaviruss (CoV) to provide the basis for exploring the patterns of SARS-CoV-2 transmission and outbreak.

METHODS

A combined evolutionary and molecular functional analysis of all sets of publicly available genomic data of viruses was performed.

RESULTS

A leader transcription regulatory sequence (TRS-L) usually comprises the first 60-70 nts of the 5' UTR in a CoV genome, and the body transcription regulatory sequences (TRS-Bs) are located immediately upstream of the genes other than ORF1a and 1b. In each CoV genome, the TRS-L and TRS-Bs share a specific consensus sequence, namely the TRS motif. Any changes of nucleotide residues in the TRS motifs are defined as TRS motif mutations. Mutations in the TRS-L or multiple TRS-Bs result in superattenuated variants. The spread of super-attenuated variants may cause an increase in asymptomatic or mild infections, prolonged incubation periods and a decreased detection rate of the viruses, thus posing new challenges to SARS-CoV-2 prevention and control. The super-attenuated variants also increase their possibility of long-term coexistence with humans. The Delta variant is significantly different from all the previous variants and may lead to a large-scale transmission. The Delta variant (B.1.617.2) with TRS motif mutation has already appeared and shown signs of spreading in Singapore, which, and even the Southeast Asia, may become the new epicenter of the next wave of SARS-CoV-2 outbreak.

CONCLUSION

TRS motif mutation will occur in all variants of SARS-CoV-2 and may result in super-attenuated variants. Only super-attenuated variants with TRS motif mutations will eventually lose the abilities of cross-species transmission and causing outbreaks.

The initial expression alterations occurring to transcription factors during the formation of breast cancer: Evidence from bioinformatics

Background

Breast cancer (BC) is the leading malignancy among women worldwide.

Aim

This work aimed to present a comprehensively bioinformatic analysis of gene expression profiles and to identify the hub genes during BC tumorigenesis, providing potential biomarkers and targets for the diagnosis and therapy of BC.

Materials & Methods

In this study, multiple public databases, bioinformatics approaches, and online analytical tools were employed and the real‐time reverse transcription polymerase chain reaction was implemented.

Results

First, we identified 10, 107, and 3869 differentially expressed genes (DEGs) from three gene expression datasets (GSE9574, GSE15852, and GSE42568, covering normal, para‐cancerous, and BC samples, respectively), and investigated different biological functions and pathways involved. Then, we screened out 8, 16, and 29 module genes from these DEGs, respectively. Next, 10 candidate genes were determined through expression and survival analyses. We noted that seven candidate genes JUN, FOS, FOSB, EGR1, ZFP36, CFD, and PPARG were downregulated in BC compared to normal tissues and lower expressed in aggressive types of BC (basal, HER2⁺, and luminal B), TP53 mutation group, younger patients, higher stage BC, and lymph node metastasis BC, while CD27, PSMB9, and SELL were upregulated. The present study discovered that the expression levels of these candidate genes were correlated with the infiltration of immune cells (CD8⁺ T cell, macrophage, natural killer [NK] cell, and cancer‐associated fibroblast) in BC, as well as biomarkers of immune cells and immune checkpoints. We also revealed that promoter methylation, amplification, and deep deletion might contribute to the abnormal expressions of candidate genes. Moreover, we illustrated downstream‐targeted genes of JUN, FOS, FOSB, EGR1, and ZFP36 and demonstrated that these targeted genes were involved in “positive regulation of cell death”, “pathways in cancer”, “PI3K‐Akt signaling pathway”, and so on.

Discussion & Conclusion

We presented differential gene expression profiles among normal, para‐cancerous, and BC tissues and further identified candidate genes that might contribute to tumorigenesis and progression of BC, as potential diagnostic and prognostic targets for BC patients.

Caloric restriction and Roux-en-Y Gastric Bypass promote white adipose tissue browning in mice

PURPOSE

Caloric restriction (CR) and Roux-en-Y Gastric Bypass (RYGB) are considered effective means of body weight control, but the mechanism by which CR and RYGB protect against high-fat diet (HFD)-induced obesity remains elusive. The browning of white adipose tissue (WAT) is a potential approach to combat obesity. Here we assess whether browning of WAT is involved in CR- and RYGB-treatment.

METHODS

The average size of adipocytes was determined by histological analysis. Expression of thermogenic genes in both human subjects and mice were measured by quantitative real-time PCR and immunohistochemical staining.

RESULTS

The average size of adipocytes was bigger, while the expression of thermogenic genes such as uncoupling protein 1 (UCP1), nuclear factor erythroid-2 like 1 (NRF1) and PPARγ coactivator-1 α (PGC1α) were lower in the WAT of obese subjects when compared to lean controls. Both CR and RYGB promoted weight and fat loss. Increment of the average adipocytes size and down-regulation of thermogenic genes were significantly reversed by both CR and RYGB in the WAT of obese mice.

CONCLUSIONS

Our findings showed that CR and RYGB significantly improved high-fat diet-induced lipid accumulation by promoting the browning of WAT.

Immunohistochemical Characterization of H3K4Me3 in Reactive Lymph Nodes and Follicular Lymphoma

Introduction/Objective

Genes involved in histone methylation are frequently mutated in non-Hodgkin’s lymphomas. For instance, frequent mutations in genes encoding histone methytransferases MML2 and EZH2 are present in diffuse large B cell lymphoma (DLBCL) and follicular lymphoma (FL). The aim of this study was to characterize the immunohistochemical expression of H3K4Me3 in benign/reactive lymph nodes (LNs) with comparison to follicular lymphoma (FL).

Methods/Case Report

Immunohistochemical staining with an anti-H3K4Me3 antibody was performed on FFPE whole slide section from patients with benign/reactive LNs (n=21), low grade (grade 1-2) FL (n=21). H3K4Me3 reactivity was scored for staining intensity and percentage of lymphocytes showing reactivity.

Results (if a Case Study enter NA)

The majority of the reactive LN sections (15 out of 21 cases) showed a distinct distribution of H3K4Me3 staining, with the majority of cells in the mantle zone and the interfollicular zones showing moderate-strong staining, whereas reactive germinal centers (GCs) showed significantly decreased or close to negative staining. Neoplastic follicles in all the FL cases contained positive cells with significantly stronger staining compared to that in the germinal centers in benign lymph nodes. The interfollicular zones, while diminished in FL due to expanded neoplastic follicles, showed retained H3K4Me3 staining. The difference in staining intensity between follicles and mantle/interfollicular zones became indistinct in FL.

Conclusion

H3K4Me3 expression in benign/reactive LNs is characterized by positive expression in lymphocytes in interfollicular and mantle zones and significantly decreased in GCs. However, the expression pattern is different in FL, which showed significantly increased expression in the follicles compared to that in reactive GCs. In FL, the expression in GCs is similar to that in the interfollicular and mantle zone lymphocytes. It is reported that about 90% of FL have MLL2 mutation and MLL2 is the enzyme responsible for the methylation of H3K4. So far, it is unclear whether the mutation of MLL2 in FL affects the overall methylation activity of the enzyme. In our study, there is increased methylation of H3K4 in the follicles of FL, which raises the possibility that MLL2 mutation somehow increases H3K4 methylation.

E_{8} Spectra of Quasi-One-Dimensional Antiferromagnet BaCo_{2}V_{2}O_{8} under Transverse Field

We report ^{51}V NMR and inelastic neutron scattering (INS) measurements on a quasi-1D antiferromagnet BaCo_{2}V_{2}O_{8} under transverse field along the [010] direction. The scaling behavior of the spin-lattice relaxation rate above the Néel temperatures unveils a 1D quantum critical point (QCP) at H_{c}^{1D}≈4.7  T, which is masked by the 3D magnetic order. With the aid of accurate analytical analysis and numerical calculations, we show that the zone center INS spectrum at H_{c}^{1D} is precisely described by the pattern of the 1D quantum Ising model in a magnetic field, a class of universality described in terms of the exceptional E_{8} Lie algebra. These excitations are nondiffusive over a certain field range when the system is away from the 1D QCP. Our results provide an unambiguous experimental realization of the massive E_{8} phase in the compound, and open a new experimental route for exploring the dynamics of quantum integrable systems as well as physics beyond integrability.

Visual identification and neuromonitoring vs. no sighting the external branch of the superior laryngeal nerve in thyroid surgery: a randomized clinical trial

To evaluate the incidence of external branch of the superior laryngeal nerve (EBSLN) injuries after thyroid surgical procedures with or without the functional and visual identification of the EBSLN before ligation at the superior thyroid pole. Patients with papillary thyroid carcinoma (PTC) enrolled from a single tertiary referral academic medical center were assigned to functional and visual identification of EBSLN group (study group) or no identification of EBSLN group (controlled group). The main outcome measures were the incidence of EBSLN injury detected by the intraoperative neuromonitoring and Voice Handicap Index-10 (VHI-10) and Impairment Index-5 (VII-5) valuation questionnaires. Postoperative complications were recorded. A total of 140 (50.4%) patients were enrolled in study group and 138 (49.6%) in controlled group. In the study group, 110 (39.3%) EBSLNs were direct visual recognized and 170 (60.7%) nerves were visually identified with the help of neuromonitoring. Three patients in the study group and two patients in the controlled group were diagnosed with vocal cord paralysis. Six (4.4%) patients in the identification group and 37 (27.2%) patients in the no identification group presented no response from the stimulation of sternothyroid-laryngeal triangle. The VII-5 scores of the study group were significantly higher than those of the controlled group at one and three months postoperatively (P = 0.024 and P = 0.034). With significant lower scores of VII-5 and VHI-10, functional and visual identification of EBSLN might be necessary during thyroid surgery to protect the structural integrity and motor activity of the nerve.

Vibration modes of a transportable optical cavity

Many factors still need to be evaluated to fully understand the physical mechanisms determining optical cavity vibration, which are crucial for designing and constructing a transportable ultra-stable laser. Herein, a detailed dynamic analysis is used to characterize the vibration modes of a transportable optical cavity. The first five resonance modes are identified in the presence of a cavity support, and the guidelines to achieve a high first-order resonance frequency are proposed; thereby, high robustness is described using a 50 mm length optical cavity. The results demonstrate that the first-order resonance of up to 681 Hz with a gross weight of 2.51 kg can be achieved using an optimization strategy for given cavity support. The theoretical results are consistent with simulation and experiment. With the optimal group, a 1.34 Hz linewidth transportable ultra-stable laser at 1550 nm is established, and a linewidth of 1.5 Hz and frequency instability of 9.5×10^-15@1s are obtained after the test including 100 km actual road transportation and 34 min continuous vibration. The test condition is equivalent to ∼ 1000 km road transportation. Our method can be readily extended to other transportable optical cavities, providing a powerful tool for improving the robustness of vibration, particularly important for transportable environments.

[Otological and hearing characteristics in children with Turner syndrome]

Objective: To explore the otological and hearing characteristics in children with Turner syndrome (TS), to determine risk factors of hearing loss, and to discuss algorithms for future surveillance. Methods: The clinical data of otolaryngology in children with TS from January 2018 to April 2020 were reviewed retrospectively. A total of 46 female children with TS, aged from 5 to 18 years were enrolled. Karyotypes included 17 cases (37.0%) of monosomy, 16 cases (34.7%) of mosaicism, and 13 cases (28.3%) of abnormal X chromosome structures. The otoscopic characteristics, audiological performance, and otologic diagnoses were evaluated. Multivariate logistic regression and Mann-Whitney U test were used for statistical analysis. Results: The most common otologic comorbidity was otitis media with effusion (OME), including 20 cases (43.5%) with 33 ears (35.9%). 14 cases (30.4%) were diagnosed with hearing loss. The regression analysis revealed that the age (OR=1.345, 95%CI: 1.072-1.760) and comorbidity of OME (OR=9.460, 95%CI: 2.065-60.350) were risk factors associated with hearing loss. In TS with OME, when compared with the mean air conduction threshold, the hearing loss of the group with pars flaccida retractions was significantly higher ((24.3±13.8) dB HL vs. (14.4±4.2) dB HL, U=59.500, P=0.008) than that of the group with none retractions. Conclusion: OME and hearing loss are common in children with TS. As age increases or suffers from OME, the risk of hearing loss increases.

The interface between paediatrics and camhs (child and adolescent psychiatry): Mental state examination teaching for paediatric trainees

Introduction

During an out-of-hours shift, the initial assessment of a CAMHS patient is performed by the paediatric trainee, usually the paediatric SHO (senior-house-officer). During my placement as a paediatric SHO, I was aware of a gap in formalised metal state examination teaching for paediatric juniors, which would be crucial for a thorough assessment of these patients, and to better guarantee they are safely managed until further assessment.

Objectives

The aim is to provide a short teaching session on mental state examining of the CAMHS patent to paediatric SHOs in order to improve their confidence in assessment.

Methods

In order to assess initial confidence in assessing the mental-state of a CAMHS patient, a pre-teaching questionnaire was given to the paediatric SHOs. A 30-minute teaching session on the mental state exam was then carried out and a post-teaching questionnaire was then given to the same trainees.

Results

Paired sample Wilcoxons signed rank test found that training significant improved trainees’ confidence in taking a psychiatric mental state exam (p= 0.005, r = 0.628), and improved their confidence in presenting a mental state exam (p = 0.0041, r = 0.6420).

Conclusions

Being able to confidently assess the mental state of a CAMHS patient in an on call shift is important for the initial assessing paediatric trainee. However this is often not taught in the paediatric curriculum and trainees have expressed some anxiety in performing this assessment overnight, before a more comprehensive assessment by a CAMHS professional. A simple teaching session may help to reduce this anxiety and improve trainees’ confidence.

The role of miRNA, lncRNA and circRNA in the development of intervertebral disk degeneration (Review)

Intervertebral disc degeneration (IVDD) is a degenerative musculoskeletal disorder with multiple causative factors, such as age, genetics, mechanics and life style. IVDD contributes to non-specific lower back pain (NLBP), which is a globally prevalent and debilitating musculoskeletal disorder. NLBP has a substantial impact on medical resources and creates an economic burden for the public. Dysregulated phenotypes of nucleus pulposus (NP) cells and endplate chondrocytes, such as proliferation, senescence and apoptosis, along with aberrant expression of extracellular matrix components, including type II collagen and aggrecan, are involved in the pathological process of IVDD. Evidence indicates that non-coding RNAs, mainly microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), play a vital role in the development of IVDD. In the present review, the potential molecular mechanisms of miRNAs, lncRNAs and circRNAs in the initiation and progression of IVDD were described based on the latest literature. Furthermore, ways to influence the functions of NP cells and endplate chondrocytes in IVDD were also summarized. The presented insights suggested that non-coding RNAs may function as potential targets for the treatment of IVDD.