Comprehensive Gene Analysis of IgG4-Related Ophthalmic Disease Using RNA Sequencing

Stromal area differences with epithelial-mesenchymal transition gene changes in conjunctival and orbital mucosa-associated lymphoid tissue lymphoma

Purpose

To examine the molecular biological differences between conjunctival mucosa-associated lymphoid tissue (MALT) lymphoma and orbital MALT lymphoma in ocular adnexa lymphoma.

Methods

Observational case series. A total of 129 consecutive, randomized cases of ocular adnexa MALT lymphoma diagnosed histopathologically between 2008 and 2020.Total RNA was extracted from formalin-fixed paraffin-embedded tissue from ocular adnexa MALT lymphoma, and RNA-sequencing was performed. Orbital MALT lymphoma gene expression was compared with that of conjunctival MALT lymphoma. Gene set (GS) analysis detecting for gene set cluster was performed in RNA-sequence. Related proteins were further examined by immunohistochemical staining. In addition, artificial segmentation image used to count stromal area in HE images.

Results

GS analysis showed differences in expression in 29 GS types in primary orbital MALT lymphoma (N=5,5, FDR q-value <0.25). The GS with the greatest difference in expression was the GS of epithelial-mesenchymal transition (EMT). Based on this GS change, immunohistochemical staining was added using E-cadherin as an epithelial marker and vimentin as a mesenchymal marker for EMT. There was significant staining of vimentin in orbital lymphoma (P<0.01, N=129) and of E-cadherin in conjunctival lesions (P=0.023, N=129). Vimentin staining correlated with Ann Arbor staging (1 versus >1) independent of age and sex on multivariate analysis (P=0.004). Stroma area in tumor were significant difference(P<0.01).

Conclusion

GS changes including EMT and stromal area in tumor were used to demonstrate the molecular biological differences between conjunctival MALT lymphoma and orbital MALT lymphoma in ocular adnexa lymphomas.

Proteotranscriptomics of ocular adnexal B-cell lymphoma reveals an oncogenic role of alternative splicing and identifies a diagnostic marker

Background

Ocular adnexal B-cell lymphoma (OABL) is a rare subtype of non-Hodgkin lymphoma. The molecular characteristics of OABL remain poorly understood. We performed an integrated study to investigate the proteotranscriptome landscape and identify novel molecular characteristics and biomarkers of OABL.

Methods

Integrated quantitative proteome and transcriptome were performed on 40 OABL 12 idiopathic orbital inflammation, 6 reactive lymphoid hyperplasia, and 13 aesthetic orbital plastic surgery specimens. Complete clinicopathologic and prognostic data of the patients were recorded.

Results

We identified high global protein-mRNA concordance as a novel characteristic of OABL. High concordance was related to OABL recurrence. By integrated expression profile, motif enrichment and trend analysis, we found that alternative splicing is inflammation-independently dysregulated in OABL. After portraying the aberrant alternative splicing event landscape, we demonstrated the oncogenic role of ADAR, a core splicing regulator that regulates the splicing of Rho GTPase and cell cycle members. We found that ADAR regulates cell proliferation and Rho GTPase inhibitor sensitivity of lymphoma. We identified DNAJC9 as a potential biomarker for OABL in proteomic analyses. Immunohistochemistry and immunofluorescent staining showed the nuclear staining of DNAJC9 was significantly higher in extranodal marginal zone lymphomas compared with inflammation specimens.

Conclusions

These results provide an integrated gene expression profiling and demonstrate that high global protein-mRNA concordance is a prognosis-related molecular characteristic of OABL. We portray the alternative splicing events landscape of OABL, and reveal the oncogenic role of ADAR. We identified strong nuclear staining of DNAJC9 as a promising pathology diagnostic biomarker for extranodal marginal zone lymphomas.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13046-022-02445-8.

Evaluation of Orbital Lymphoproliferative and Inflammatory Disorders by Gene Expression Analysis

Non-specific orbital inflammation (NSOI) and IgG4-related orbital disease (IgG4-ROD) are often challenging to differentiate. Furthermore, it is still uncertain how chronic inflammation, such as IgG4-ROD, can lead to mucosa-associated lymphoid tissue (MALT) lymphoma. Therefore, we aimed to evaluate the diagnostic value of gene expression analysis to differentiate orbital autoimmune diseases and elucidate genetic overlaps. First, we established a database of NSOI, relapsing NSOI, IgG4-ROD and MALT lymphoma patients of our orbital center (2000−2019). In a consensus process, three typical patients of the above mentioned three groups (mean age 56.4 ± 17 years) at similar locations were selected. Afterwards, RNA was isolated using the RNeasy FFPE kit (Qiagen) from archived paraffin-embedded tissues. The RNA of these 12 patients were then subjected to gene expression analysis (NanoString nCounter®), including a total of 1364 target genes. The most significantly upregulated and downregulated genes were used for a machine learning algorithm to distinguish entities. This was possible with a high probability (p < 0.0001). Interestingly, gene expression patterns showed a characteristic overlap of lymphoma with IgG4-ROD and NSOI. In contrast, IgG4-ROD shared only altered expression of one gene regarding NSOI. To validate our potential biomarker genes, we isolated the RNA of a further 48 patients (24 NSOI, 11 IgG4-ROD, 13 lymphoma patients). Then, gene expression pattern analysis of the 35 identified target genes was performed using a custom-designed CodeSet to assess the prediction accuracy of the multi-parameter scoring algorithms. They showed high accuracy and good performance (AUC ROC: IgG4-ROD 0.81, MALT 0.82, NSOI 0.67). To conclude, genetic expression analysis has the potential for faster and more secure differentiation between NSOI and IgG4-ROD. MALT-lymphoma and IgG4-ROD showed more genetic similarities, which points towards progression to lymphoma.

Transcriptional profiling and circRNA-miRNA-mRNA network analysis identify the biomarkers in Sheng-ji Hua-yu formula treated diabetic wound healing

ETHNOPHARMACOLOGICAL RELEVANCE

Sheng-ji Hua-yu (SJHY) formula is a traditional Chinese herbal which is effective in treating diabetic ulcers. It has been indicated to accelerate re-epithelialization and healing time of cutaneous wounds in a Streptozotocin (STZ)-induced diabetic mouse model. However, its mechanisms remain undetermined.

AIM OF THE STUDY

To reveal the molecular mechanisms of SJHY formula in treating diabetic wounds through transcriptional profiling and circRNA-miRNA-mRNA network analysis clues.

MATERIALS AND METHODS

Protein expressions of tumor necrosis factor (TNF-α), interleukin (IL)-6, IL-1β in skin tissues of wounds from SJHY formula-treated and untreated mice were analyzed by Bio-Plex assay. Differentially expressed (DE) genes were detected by whole transcriptome sequencing (RNA-seq). Using predicted miRNA targets, circRNA-miRNA-mRNA networks were constructed. Furthermore, quantitative real-time PCR (qRT-PCR) was utilized to validate the circRNA-miRNA-mRNA networks.

RESULTS

Bio-Plex assay illustrated that the protein expressions of TNF-α, IL-1β, IL-6 were downregulated in SJHY formula-treated diabetic wounds compared with untreated wounds. RNA-seq identified 11 DE circRNAs and 476 DE mRNAs between SJHY formula-treated and diabetic mice, including 4 upregulated and 7 downregulated circRNAs, 311 upregulated and 165 downregulated mRNAs. CircRNA-Krt13/miR-665-3p/Itga3 and circRNA-Krt14/miR-706/Mylk4 pathways were built, which may contribute to the healing of SJHY formula-treated diabetic wounds.

CONCLUSIONS

Overall, this study suggests that these 2 circRNA-miRNA-mRNA networks are potential biomarkers for evaluation of SJHY formula efficacy in diabetic wound healing, which provides evidence to support its clinical applications.