Animal models of inflammatory bowel disease: category and evaluation indexes

Inflammatory bowel disease (IBD) research often relies on animal models to study the etiology, pathophysiology, and management of IBD. Among these models, rats and mice are frequently employed due to their practicality and genetic manipulability. However, for studies aiming to closely mimic human pathology, non-human primates such as monkeys and dogs offer valuable physiological parallels. Guinea pigs, while less commonly used, present unique advantages for investigating the intricate interplay between neurological and immunological factors in IBD. Additionally, New Zealand rabbits excel in endoscopic biopsy techniques, providing insights into mucosal inflammation and healing processes. Pigs, with their physiological similarities to humans, serve as ideal models for exploring the complex relationships between nutrition, metabolism, and immunity in IBD. Beyond mammals, non-mammalian organisms including zebrafish, Drosophila melanogaster, and nematodes offer specialized insights into specific aspects of IBD pathology, highlighting the diverse array of model systems available for advancing our understanding of this multifaceted disease. In this review, we conduct a thorough analysis of various animal models employed in IBD research, detailing their applications and essential experimental parameters. These include clinical observation, Disease Activity Index score, pathological assessment, intestinal barrier integrity, fibrosis, inflammatory markers, intestinal microbiome, and other critical parameters that are crucial for evaluating modeling success and drug efficacy in experimental mammalian studies. Overall, this review will serve as a valuable resource for researchers in the field of IBD, offering insights into the diverse array of animal models available and their respective applications in studying IBD.

Dietary Zinc Ameliorates TNBS-Induced Colitis in Mice Associated with Regulation of Th1/Th2/Th17 Balance and NF-κB/NLRP3 Signaling Pathway

Inflammatory bowel diseases (IBDs), including Crohn's disease and ulcerative colitis, are chronic relapsing inflammatory gastrointestinal tract diseases of uncertain origin, which are frequently associated with zinc deficiency. Animal models have a considerable value in elucidating the process of IBD. In this study, 50 male C57BL/6 J mice were randomly assigned to five groups: control group (Con), 2,4,6-trinitrobenzenesulfonic acid (TNBS) group, and three zinc supplementation groups, namely 160 ppm group, 400 ppm group, and 1000 ppm group. The results showed that supplementation of dietary zinc with zinc oxide could effectively relieve the severity of ulcerative colitis induced by TNBS in mice. We demonstrate that the protective mechanism involves the immunomodulation of dietary zinc by increasing CD3+, CD3+CD8+, and Th2 cells, suppressing Th1 and Th17 cells, and decreasing the production of serum IL-1β and IL-18. The dietary zinc oxide seems to be able to suppress the NF-κB/NLRP3 signaling pathway by downregulating the mRNA and protein expression of NIK, IKK, NF-κB, and NLRP3. The results suggest that dietary supplementation of zinc oxide may protect against colitis, and proper daily zinc supplementation may reduce the risk of IBD.

Tumor Treatment Response Assessed During the Concurrent Chemoradiotherapy for Nasopharyngeal Patients

PURPOSE/OBJECTIVE(S)

To evaluate intratumoral treatment response distribution with using FDG-PET/CT during the chemoradiotherapy of nasopharyngeal patients (NPC).

MATERIALS/METHODS

A total of 5 of 30 patients with stage III-IVA NPC were enrolled in the institutional protocol for induction/concurrent chemoradiotherapy with radiation dose of 70 Gy in 33 fractions. For each patient, a pre-radiation treatment FDG-PET/MRI image (SUV0) and a mid-treatment image (SUVm) at the treatment dose of 31.8 Gy were obtained. Followed by deformable PET/MRI registration between SUV0 and SUVm, the tumor voxel SUV reduction ratio was obtained to construct a tumor dose response matrix (DRM). Tumor SUVavid was also constructed by limiting tumor voxel SUVm > a given value. Spatial correlations of the tumor SUV0, SUVm, SUVavid and DRM were determined.

RESULTS

The mean and coefficient variation (CV) of the SUV0, SUVm and DRM for all tumors were 5.05 (52%), 2.72 (49%) and 0.64 (63%) (Table contains the individual data), which were smaller than those on the SUVs of head-n-neck HPV+ patients reported previously due to the induction chemotherapy, but had much larger DRM mean and CV. The inter-tumoral CVs of SUV0 and DRM were 29% and 27%, which were much lower than those of the intra-tumoral CVs 43% and 57%. Meanwhile, the intra-tumoral variations on SUV0 was smaller than the one of head-neck HPV+ patients, but the DRM intra-variation was much larger. There was a weak correlation between SUV0 and SUVm with the correlation coefficient 0.13, a medium correlation of -0.55 between SUV0 and DRM, but a strong correlation, 0.72, between SUVm and DRM. However, the spatial correlation between tumor DRM and SUVavid was getting weaker as the SUVavid value increasing and equal 0.47 with SUVavid value > 3.

CONCLUSION

The spatial dose response DRM for NPC in the concurrent chemoradiotherapy was relatively high, while had relatively low baseline tumor metabolic activity SUV0. It was most likely due to the induction chemotherapy. In addition, the tumor dose response showed vary large intra-tumoral variation. The high correlations between DRM and SUVm imply that SUVavid could be used partially to guide adaptive modification of NPC treatment with carefully selected boundary value.

Tumor Treatment Response Assessed During the Chemo-Radiotherapy for Locally Advanced NSCLC

PURPOSE/OBJECTIVE(S)

To evaluate the capability of assessing intratumoral treatment response distribution with using FDG-PET/CT during the chemoradiotherapy of locally advanced NSCLC.

MATERIALS/METHODS

Twelve of total 50 patients with stage III NSCLC were enrolled in the institutional protocol for concurrent chemoradiotherapy with treatment dose of 54-60 Gy in 27-30 fractions. For each patient, a pre-treatment FDG-PET/CT image (SUV0) and a mid-treatment image (SUVm) obtained within the treatment dose of 24 ∼ 46 Gy were obtained. Followed by deformable PET/CT registration between SUV0 and SUVm, the tumor voxel SUV reduction ratio was obtained to construct a tumor dose response matrix (DRM). Tumor SUVavid was also constructed by limiting tumor voxel SUVm > a given value. Spatial correlations of the tumor SUV0, SUVm, SUVavid and DRM were determined.

RESULTS

The mean and coefficient variation (CV) of the SUV0, SUVm and DRM for all tumors were 6.56(64%), 2.82(59%) and 0.52(70%) (Table contains the individual data), which were like those on the SUVs and the mean DRM of head-neck HPV- patients reported previously, but much larger on the DRM variation. The inter-tumoral CVs of SUV0 and DRM were 17% and 43%, which were much smaller than those of the intra-tumoral CVs 61% and 55%. Meanwhile, the intra-tumoral variations on both SUV0 and DRM were much larger than those of head-neck HPV- patients. There was a weak correlation between SUV0 and SUVm with the correlation coefficient 0.32, a medium correlation of -0.51 between SUV0 and DRM; 0.58 between SUVm and DRM. It implies that the rule of tumor dose response DRM on treatment modification decision cannot be fully replaced by either SUV0 or SUVm. The spatial correlation between tumor DRM and SUVavid was 0.23 with SUVavid value > 3, which was getting weaker when increasing SUVavid value.

CONCLUSION

Spatial dose response for NSCLC assessed using FDG-PET/CT feedback demonstrated high treatment resistant patterns, which had a large intra-tumoral variation. In addition, the medium correlations of DRM vs SUV0 and DRM vs SUVm imply that all these factors could be used to guide adaptive modification of NSCLC treatment.

Hybrid Immuno-RT for Bulky Tumors: Standard Fractionation with Partial Tumor SBRT

PURPOSE/OBJECTIVE(S)

Bulky tumors remain challenging to be treated. Stereotactic body radiation therapy (SBRT) is effective against radioresistant tumor cells and can induce immunogenic cell death (ICD) that leads to T-cell-mediated antitumor effects. Low-dose radiation (LDRT) can inflame the tumor microenvironment (TME) by recruiting T cells. We designed a novel radiotherapy technique (RT, ERT) whose dose distribution map resembles the "eclipse" by concurrently delivering LDRT to the whole tumor, meanwhile SBRT to only a part of the same tumor. This study examined the safety and efficacy of ERT to bulky lesions with PD-1 inhibitors in mice and patients.

MATERIALS/METHODS

In mice with CT26 colon or LLC1 lung bulky tumors (400 - 500 cm3), the whole tumor was irradiated by LDRT (2 Gy x 3), meanwhile the tumor center was irradiated by SBRT (10 Gy x 3); αPD-1 was given weekly. The dependence of therapeutic effects on CD8+ T cells was determined using depleting antibodies. Frequencies of CD8+ T cells and M1 macrophages (Mφ) were determined by flow cytometry. Multiplex Immunohistochemistry (mIHC) was applied to analyze the number and the location of CD8+ T cells and their subpopulations, as well as the phospho-eIF2α level (the ICD marker) of tumor cells in TME. Patients with advanced lung or liver bulky tumors who failed standard treatment or with oncologic emergencies were treated. Kaplan-Meier method was applied to estimate patients' progression-free survival (PFS) and overall survival (OS).

RESULTS

ERT/αPD-1 is superior to SBRT/αPD-1 or LDRT/αPD-1 in controlling bulky tumors in both mouse models in a CD8+ T-cell dependent manner. In the CT26 model, ERT/αPD-1 resulted in complete tumor regression in 3/11 mice and induced more CD8+ T cells and M1 Mφ in TME compared to other groups. mIHC analysis showed that ERT/αPD-1 induced higher bulk, stem-like (TCF1+ TIM3- PD-1+), and more differentiated (TCF1- TIM3+ PD-1+) CD8+ T cells infiltration into the tumor center and periphery compared to other groups. Compared to untreated or LDRT-treated tumor centers, tumor centers irradiated with ERT or SBRT showed elevated phospho-eIF2α accompanied by higher dendritic cell infiltration. In total, 39 advanced cancer patients were treated with ERT/αPD-1 or plus chemotherapy. Radiation-induced pneumonitis occurred in 1 of 26 patients receiving thoracic ERT. There were two cases of grade III toxicity associated with PD-1 inhibitors. No toxicity above grade III was observed. The objective response rate was 38.5%. The median PFS was 5.6 months and median OS was not reached at a median follow-up of 11.7 months.

CONCLUSION

ERT/αPD-1 showed superior efficacy in controlling bulky tumor in two mouse models. The hybrid immuno-RT (ERT) combing PD-1 inhibitors was safe and effective in patients with bulky tumors. Further clinical trials in combination with bioimaging to identify the optimal SBRT target region for the bulky tumor are warranted.

Safety and efficacy of dendritic cell-based immunotherapy (DCVAC/LuCa) combined with carboplatin/pemetrexed for patients with advanced non-squamous non-small-cell lung cancer without oncogenic drivers

Background

Our prospective, open-label, single-arm phase II study investigated the safety and efficacy of DCVAC/LuCa (dendritic cell vaccines for lung cancer) combined with standard carboplatin/pemetrexed in advanced non-squamous (nsq) non-small-cell lung cancer (NSCLC).

Patients and methods

Eligible patients had stage IV nsq NSCLC without oncogenic drivers and had not received prior systemic cancer therapy. Treatment consisted of carboplatin/pemetrexed for up to 6 cycles followed by 21 cycles of pemetrexed maintenance or until progression or intolerance. Non-progression patients after two cycles of chemotherapy started to receive DCVAC/LuCa subcutaneously (s.c.) on day 15 of cycle 3, and thereafter q3w (day 15 of chemotherapy cycles) for up to 15 doses. Dosing of DCVAC/LuCa s.c. varied among patients depending on the baseline number of leucocytes but remained constant for each single patient. Safety was assessed by adverse events (AEs), treatment-related adverse events (TRAEs), serious adverse events (SAEs), and adverse events of special interest (AESIs). Efficacy was measured by overall survival (OS), progression-free survival (PFS), time to progression (TTP), and objective response rate (ORR).

Results

Sixty-one patients were enrolled. In the safety population (n = 60), eight patients (13.33%) had grade 3 or greater TRAEs, and six patients (10.0%) showed SAEs which were not related to leukapheresis or DC vaccination. Six grade 1 AEs were considered to be related to leukapheresis. No AESIs or DCVAC/LuCa-induced AEs were observed. The 2-year survival rate in the modified intention-to-treat population (n = 44) was 52.57%. Median OS was not reached. Median PFS was 8.0 months, median TTP was 10.2 months, and the ORR was 31.82%.

Conclusion

In treatment-naïve stage IV nsq NSCLC patients without oncogenic drivers, the combination of carboplatin/pemetrexed and DCVAC/LuCa was well tolerated and showed promising efficacy. Therefore, a study to prove our immunotherapeutic concept in a randomized phase III trial is planned.

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We investigated the safety and efficacy of DCVAC/LuCa combined with standard carboplatin/pemetrexed in nsq NSCLC.

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The combination therapy showed a favorable tolerability profile in a selected Chinese population.

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The 2-year survival rate in the modified intention-to-treat population (n = 44) was 52.57%.

Gen-editing to model Short QT syndrome type 5 using human-induced pluripotent stem cell-derived cardiomyocytes

Aims

Short QT syndrome (SQTS), a disorder associated with characteristic electrocardiogram QT-segment abbreviation, predisposes afflicted patients to sudden cardiac death. Despite some progress in assessing the organ level pathophysiology and genetic changes of the disorder, the understanding of the human cellular phenotype and discovering of an optimal therapy has lagged due to a lack of appropriate human cellular models of the disorder. The aim of this study was to establish a cellular model of SQTS type 5 using human-induced pluripotent stem cell–derived cardiomyocytes (hiPSC-CMs) and gene-edited cell line using CRISPR/CAS9.

Methods and results

This study recruited one patient with short QT syndrome type 5 carrying a mutation in CACNb2 gene as well as one healthy control subject. We generated hiPSCs from their skin fibroblasts, and differentiated hiPSCs into cardiomyocytes (hiPSC-CMs) for physiological. Isogenic control hiPSC-CMs generated by the CRISPR/CAS9 technique were also used for the study.

The hiPSC-CMs from the patient showed a reduced calcium current (ICa-L) density and shortened action potential duration (APD) compared with healthy control hiPSC-CMs and isogenic hiPSC-CMs. Furthermore, they demonstrated abnormal rhythmic activities. Carbachol increased the arrhythmic events in SQTS significantly but not in healthy and isogenic control cells. Gene and protein expression profiling showed a decreased CACNb2 expression in SQTS cells. Quinidine prolonged the APD and abolished arrhythmic activity.

Conclusions

Patient-specific hiPSC-CMs are able to recapitulate single-cell phenotype features of SQTS type 5 and provide novel opportunities to further elucidate the cellular disease mechanism and test drug effects.

Funding Acknowledgement

Type of funding source: None

Immune cell infiltration features and related marker genes in lung cancer based on single-cell RNA-seq

PURPOSE

Immune cells in the immune microenvironment of lung cancer have a great impact on the development of lung cancer. Our purpose was to analyze the immune cell infiltration features and related marker genes for lung cancer.

METHODS

Single cell RNA sequencing data of 11,485 lung cancer cells were retrieved from the Gene Expression Omnibus. After quality control and data normalization, cell clustering was performed using the Seurat package. Based on the marker genes of each cell type from the CellMarker database, each cell was divided into G1, G2M, and S phases. Then, differential expression and functional enrichment analyses were performed. CIBERSORT was used to reconstruct immune cell types.

RESULTS

Following cell filtering, highly variable genes were identified for all cells. 14 cell types were clustered. Among them, CD4 + T cell, B cell, plasma cell, natural killer cell and cancer stem cell were the top five cell types. Up-regulated genes were mainly enriched in immune-related biological processes and pathways. Using CIBERSORT, we identified the significantly higher fractions of naïve B cell, memory CD4 + T cell, T follicular helper cell, T regulatory helper cell and M1 macrophage in lung cancer tissues compared to normal tissues. Furthermore, the fractions of resting NK cell, monocyte, M0 macrophage, resting mast cell, eosinophil and neutrophil were significantly lower in tumor tissues than normal tissues.

CONCLUSION

Our findings dissected the immune cell infiltration features and related marker genes for lung cancer, which might provide novel insights for the immunotherapy of lung cancer.

A polymorphic MYC response element in KBTBD11 influences colorectal cancer risk, especially in interaction with an MYC-regulated SNP rs6983267

Background

MYC is a well-established cancer driver gene regulating the expression of numerous genes, indicating that polymorphisms in MYC response elements could affect tumorigenesis through altering MYC regulation. We performed integrative multistage study to evaluate the effects of variants in MYC response elements and colorectal cancer (CRC) risk.

Patients and methods

We systematically integrated ChIP-Seq, DNase-Seq and transcription factor motif data to screen variants with potential ability to affect the MYC binding affinity. Then, we conducted a two-stage case-control study, totally consisting of 4830 CRC cases and 4759 controls in Chinese population to identify risk polymorphisms and interactions. The effects of risk variants were confirmed by functional assays in CRC LoVo, SW480 and HCT15 cells.

Results

We identified a novel polymorphism rs11777210 in KBTBD11 significantly associated with CRC susceptibility (P = 2.43 × 10-12). Notably, we observed a significant interaction between rs11777210 and MYC nearby rs6983267 (P-multi = 0.003, P-add = 0.005), subjects carrying rs6983267 GG and rs11777210 CC genotypes showing higher susceptibility to CRC (2.83-fold) than those carrying rs6983267 TT and rs11777210 TT genotypes. We further demonstrated that rs6983267 T > G increased MYC expression, and MYC bound to and negatively regulated KBTBD11 expression when the rs11777210 C risk allele was present. KBTBD11 was downregulated in tumor tissues, and KBTBD11 knockdown promoted cell proliferation and inhibited cell apoptosis.

Conclusion

The rs11777210 is a potential predictive biomarker of CRC susceptibility, and KBTBD11 functions as a putative tumor suppressor in tumorigenesis. Our study highlighted the high CRC risk of people carrying rs6983267 G and rs11777210 C alleles, and provided possible biological mechanism of the interaction.

Effects of online cone-beam computed tomography with active breath control in determining planning target volume during accelerated partial breast irradiation

PURPOSE

To test if active breath control during cone-beam computed tomography (CBCT) could improve planning target volume during accelerated partial breast radiotherapy for breast cancer.

METHODS

Patients who were more than 40 years old, underwent breast-conserving dissection and planned for accelerated partial breast irradiation, and with postoperative staging limited to T1-2 N0 M0, or postoperative staging T2 lesion no larger than 3cm with a negative surgical margin greater than 2mm were enrolled. Patients with lobular carcinoma or extensive ductal carcinoma in situ were excluded. CBCT images were obtained pre-correction, post-correction and post-treatment. Set-up errors were recorded at left-right, anterior-posterior and superior-inferior directions. The differences between these CBCT images, as well as calculated radiation doses, were compared between patients with active breath control or free breathing.

RESULTS

Forty patients were enrolled, among them 25 had active breath control. A total of 836 CBCT images were obtained for analysis. CBCT significantly reduced planning target volume. However, active breath control did not show significant benefit in decreasing planning target volume margin and the doses of organ-at-risk when compared to free breathing.

CONCLUSION

CBCT, but not active breath control, could reduce planning target volume during accelerated partial breast irradiation.

Surface Collective Modes in the Topological Insulators Bi_{2}Se_{3} and Bi_{0.5}Sb_{1.5}Te_{3-x}Se_{x}

We used low-energy, momentum-resolved inelastic electron scattering to study surface collective modes of the three-dimensional topological insulators Bi_{2}Se_{3} and Bi_{0.5}Sb_{1.5}Te_{3-x}Se_{x}. Our goal was to identify the "spin plasmon" predicted by Raghu and co-workers [Phys. Rev. Lett. 104, 116401 (2010)]. Instead, we found that the primary collective mode is a surface plasmon arising from the bulk, free carriers in these materials. This excitation dominates the spectral weight in the bosonic function of the surface χ^{"}(q,ω) at THz energy scales, and is the most likely origin of a quasiparticle dispersion kink observed in previous photoemission experiments. Our study suggests that the spin plasmon may mix with this other surface mode, calling for a more nuanced understanding of optical experiments in which the spin plasmon is reported to play a role.

Investigation of polymorphisms in exon7 of the NSUN7 gene among Chinese Han men with asthenospermia

Previous studies have shown that genetic polymorphisms in exon7 of the NSUN7 gene can be used as an infertility marker in Iranian men with asthenospermia. However, there have been no equivalent studies in China. In the present study, we investigated the possible association between the genetic polymorphisms in exon7 of NSUN7 and asthenospermia in a Chinese Han population. We recruited 240 asthenospermic men as a patient group and 256 normospermic men as a control group, and analyzed the semen parameters on the basis of World Health Organization (WHO) guidelines. The genetic polymorphisms in exon7 of NSUN7 were detected by DNA sequence analysis. The results were analyzed statistically and a P value < 0.05 was considered significant. There were two genetic polymorphisms, c.906C>T and c.922T>G, in exon7 of NSUN7. We found relatively similar genotypes and allele frequencies between the two groups (P = 0.928, P = 0.928, respectively). The combined genotypes of the two polymorphisms did not identify a haplotype associated with asthenospermia (P = 0.824, P = 0.824, respectively). Our findings revealed that genetic polymorphisms in exon7 of the NSUN7 gene are not associated with asthenospermia in Chinese Han men.

DIGRE: Drug-Induced Genomic Residual Effect Model for Successful Prediction of Multidrug Effects

Multidrug regimens are a promising strategy for improving therapeutic efficacy and reducing side effects, especially for complex disorders such as cancer. However, the use of multidrug therapies is very challenging, due to a lack of understanding of the mechanisms of drug interactions. We herein present a novel computational approach-Drug-Induced Genomic Residual Effect (DIGRE) Computational Model-to predict drug combination effects by explicitly modeling drug response curves and gene expression changes after drug treatments. The prediction performance of DIGRE was evaluated using two datasets: (i) OCI-LY3 B-lymphoma cells treated with 14 different drugs and (ii) MCF breast cancer cells treated with combinations of gefitinib and docetaxel at different doses. In both datasets, the predicted drug combination effects significantly correlated with the experimental results. The results indicated the model was useful in predicting drug combination effects, which may greatly facilitate the discovery of new, effective multidrug therapies.

An analysis of the small RNA transcriptome of four developmental stages of the citrus red mite (Panonychus citri)

The citrus red mite (Panonychus citri) can feed on more than 112 plant species around the world. Endogenous small RNAs (sRNAs) have proved to be important components of gene regulation in many eukaryotes. Recently, many sRNAs have been shown to be involved in various biological processes, such as development in many animals, including insects; however, to date, no sRNAs have been reported in the citrus red mite. Using Illumina sequencing, several categories of sRNAs were identified, including 594 known microRNAs (miRNAs) grouped into 206 families and 31 novel miRNAs in the four developmental stages of citrus red mite. In addition, according to bioinformatics analysis and S-Poly(T) miRNA assays, the expression level of many miRNAs varied among the developmental stages. Furthermore, the prediction of miRNAs target genes and their functional annotation indicated that miRNAs are involved in the regulation of multiple pathways in the citrus red mite. As the first report of the sRNA world in citrus red mite, the present study furthers our understanding of the roles played by sRNAs in the development of citrus red mite and the data may help to develop methods of controlling the pests in the field.