SNRPD1/E/F/G Serve as Potential Prognostic Biomarkers in Lung Adenocarcinoma

Identification of shared pathogenic signatures of multiple sclerosis and chronic obstructive pulmonary disease: an integrated transcriptomic analysis of blood specimens

Patients with multiple sclerosis (MS) face a heightened risk of developing chronic obstructive pulmonary disease (COPD). Despite this widely reported association, the pathogenic contributors and processes that may favor the development of COPD in MS patients have yet to be identified. Recent studies have suggested peripheral blood leukocytes as a potential link between COPD and autoimmune disorders. Therefore, this study aimed to unveil shared molecular signatures between MS and COPD using blood transcriptomes. To this end, gene expression datasets obtained from MS and COPD blood specimens were retrieved from the Gene Expression Omnibus (GEO) database. By integrating datasets belonging to each disorder, differentially expressed genes (DEGs) were determined for each disease. Then, the protein-protein interaction (PPI) network was constructed for shared DEGs between MS and COPD. Subsequently, the network was analyzed to identify hub genes and key regulatory miRNAs. The integrated data for MS encompassed 51 samples (28 from MS patients and 23 from controls), and the integrated data for COPD included 450 samples (275 from COPD patients and 175 from controls). A total of 246 genes were found to exhibit identical directions of expression in both MS and COPD. By applying a high confidence threshold (0.7), a PPI network with 74 nodes was constructed. TP53, H4C6, SNRPE, and RPS11 were identified as hub genes according to the degree measure. In addition, 8 miRNAs were identified as key regulators, each interacting with 6 mRNAs. Among these miRNAs, miR-218-5p and miR-142-5p have been previously reported to contribute to the pathogenesis of these diseases, and here they were identified as key regulators of the shared PPI network, suggesting a potential epigenetic link between MS and COPD. In conclusion, the results highlighted the potential role of peripheral blood leucocytes as a bridge between MS and COPD. These findings broaden our understanding of pathogenic contributors linking MS and COPD. While this transcriptomics study identified multiple key players, such as TP53, miR-218-5p, and miR-142-5p, the assessment of their therapeutic efficacy demands further experimental studies.

Evaluation of Spliceosome Protein SmD2 as a Potential Target for Cancer Therapy

The core spliceosome Sm proteins are gaining attention as potential targets for cancer treatment. Here, we evaluate this, with focus on SmD2. A pan-cancer analysis including 26 solid tumor types revealed that the SmD2-encoding SNRPD2 gene was overexpressed in almost all cancers. In several cancers, high SNRPD2 expression was associated with a poor prognosis. To investigate the vulnerability of human cells to the loss of SmD2 expression, we silenced SNRPD2 using a short hairpin-expressing lentiviral vector in established cancer cell lines; in short-term cultured melanoma cells; and in several normal cell cultures, including cancer-associated fibroblasts cultured from non-small cell lung cancer resections. Additionally, we analyzed publicly available cell viability datasets for the dependency of cancer cell lines to SmD2 expression. Together, these studies clearly established SmD2 as a cancer-selective lethal target. Delving into genes with similar essentiality profiles to SNRPD2, we uncovered the intersected lethal stress between the loss of SmD2 and the loss of gene products participating in not only different mRNA processing steps including mRNA splicing, but also processes for coordinated protein production, as well as mitosis. Furthermore, we could correlate SNRPD2 expression to the responses of cancer cells to several FDA-approved anti-tumor drugs, especially to drugs inhibiting the cell cycle. Overall, our study confirms the anticipated role for targeting SmD2 in cancer treatment and reveals non-canonical SmD2 functions beyond mRNA splicing that could contribute to the dependency of cancer cells to high SNRPD2 expression.

Single-cell dissection reveals immunosuppressive F13A1+ macrophage as a hallmark for multiple primary lung cancers

BACKGROUND

The increasing prevalence of multiple primarylung cancers (MPLCs) presents challenges to current diagnostic and clinicalmanagement approaches. However, the molecular mechanisms driving MPLCdevelopment and distinguishing it from solitary primary lung cancers (SPLCs)remain largely unexplored.

METHODS

We performed a comparative single-cell RNAsequencing (scRNA-seq) analysis on tumour and adjacent para-tumour tissues fromMPLC and SPLC patients to comparatively evaluate their immunological landscapes.Additionally, multiplex immunofluorescence (mIF) staining and independentvalidation datasets were used to confirm findings.

RESULTS

MPLCs and SPLCs share significant similarities in genetic, transcriptomic and immune profiles, suggesting common therapeutic strategies such as EGFR-TKIs andICIs. Notably, an immunosuppressive macrophage subtype, F13A1+ Macrophage (Mϕ), is specifically enriched in MPLCs. This subtype overexpresses M2 macrophagemarkers and exhibits up-regulation of SPP1-CD44/CCL13-ACKR1 interactions, indicatingits role in shaping the immunosuppressive tumour microenvironment and promotingtumour growth in MPLCs.

CONCLUSIONS

This study unveils shared molecular mechanismsbetween MPLCs and SPLCs, while identifying MPLC-specific cellular and molecularfeatures, such as the role of F13A1+ macrophages. The findings provide novelinsights into MPLC pathogenesis, supporting the development of targetedtherapeutic strategies.

KEY POINTS

Comparative scRNA-seq analysis reveals significant similarities in genetic, transcriptomicand immune profiles between MPLCs and SPLCs. Identification of a unique immunosuppressive F13A1+ macrophage subtype, preferentially enriched in MPLCs, linked to immune evasion and tumourprogression. SPP1-CD44/CCL13-ACKR1 interactions are crucial in MPLC tumour microenvironment, indicating potential targets for therapeutic intervention.

The Potential Role of SNRPD1 Stabilized by IGF2BP2 in the Progression of Triple-Negative Breast Cancer

Background

Insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2), an RNA-binding protein with N6-methyladenosine (m6A) reader function, is associated with the poor prognosis of various tumors, including triple-negative breast cancer (TNBC). Small nuclear ribonucleoprotein D1 polypeptide (SNRPD1), a spliceosome member, exerts diagnostic and therapeutic functions in breast cancer by regulating the cell cycle and is a potential therapeutic target. However, the interaction between IGF2BP2 and SNRPD1 in the progression of TNBC remain unclear.

Objective

This study aimed to investigate the interaction between IGF2BP2 and SNRPD1 in TNBC and elucidate the underlying mechanisms.

Methods

Quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot were used to detect the expression levels of SNRPD1 and IGF2BP2 in human normal breast cells (MCF10A) and TNBC cells (MDA-MB-231). MDA-MB-231 cells were transfected with SNRPD1 interference or overexpression vectors, or co-transfected with SNRPD1 interference and IGF2BP2 overexpression vectors simultaneously. Cell viability, apoptosis, and invasion were assessed using MTT, flow cytometry, and Transwell assays. RNA stability, m6A levels, and the interaction between SNRPD1 and IGF2BP2 were evaluated using qRT-PCR, methylated RNA immunoprecipitation, and RIP assays.

Results

SNRPD1 was significantly up-regulated in TNBC cells, promoting cell viability and invasion while inhibiting apoptosis. IGF2BP2 was also up-regulated in TNBC cells and enhanced SNRPD1 mRNA stability via m6A modification. Furthermore, IGF2BP2 overexpression reversed the anti-tumor effect of SNRPD1 knockdown.

Conclusion

IGF2BP2 and SNRPD1 were significantly highly expressed in TNBC cells. IGF2BP2 might enhance the stability and protein expression of SNRPD1 through m6A-dependent mechanisms, potentially contributing to the progression of TNBC.

Proteomic Profiles Associated With Postsurgical Progression in Nonfunctioning Pituitary Adenomas

CONTEXT

There is a lack of reliable biomarkers capable of predicting postoperative tumor progression of nonfunctioning pituitary adenomas (NFPAs).

OBJECTIVE

To discover proteomic profiles associated with postoperative tumor progression in patients with NFPAs. This was a case-controlled exploratory study at a tertiary university hospital. Tissue samples were obtained from 46 patients with residual tumor following surgery for NFPAs of gonadotroph lineage. Two patient groups were compared: patients requiring reintervention due to residual tumor progression (cases; reintervention group, n = 29) and patients with a residual tumor showing no progression for a minimum of 5 years (controls; radiologically stable group, n = 17). Differentially expressed proteins (DEPs) between patient groups were measured.

RESULTS

Global quantitative proteomic analysis identified 4074 proteins, of which 550 were differentially expressed between the 2 groups (fold change >80%, false discovery rate-adjusted P ≤ .05). Principal component analysis showed good separation between the 2 groups. Functional enrichment analysis of the DEPs indicated processes involving translation, ROBO-receptor signaling, energy metabolism, mRNA metabolism, and RNA splicing. Several upregulated proteins in the reintervention group, including SNRPD1, SRSF10, SWAP-70, and PSMB1, are associated with tumor progression in other cancer types.

CONCLUSION

This is the first exploratory study analyzing proteomic profiles as markers of postoperative tumor progression in NFPAs. The findings clearly showed different profiles between tumors with indolent postoperative behavior and those with postoperative tumor progression. Both enriched pathways involving DEPs and specific upregulated proteins have previously been associated with tumor aggressiveness. These results suggest the value of proteomic profiling for predicting tumor progression in patients with NFPAs.

Zearalenone exposure differentially affects the ovarian proteome in pre-pubertal gilts during thermal neutral and heat stress conditions

Zearalenone (ZEN), a nonsteroidal estrogenic mycotoxin, causes endocrine disruption and porcine reproductive dysfunction. Heat stress (HS) occurs when exogenous and metabolic heat accumulation exceeds heat dissipation. Independently, HS and ZEN both compromise swine reproduction; thus, the hypothesis investigated was two-pronged: that ZEN exposure would alter the ovarian proteome and that these effects would differ in thermal neutral (TN) and HS pigs. Pre-pubertal gilts (n = 38) were fed ad libitum and assigned to either (TN: 21.0 ± 0.1 °C) or HS (12 h cyclic temperatures of 35.0 ± 0.2 °C and 32.2 ± 0.1 °C). Within the TN group, a subset of pigs were pair-fed (PF) to the amount of feed that the HS gilts consumed to eliminate the confounding effects of dissimilar nutrient intake. All gilts orally received a vehicle control (CT) or ZEN (40 μg/kg/BW) resulting in six treatment groups: thermoneutral (TN) vehicle control (TC; n = 6); TN ZEN (TZ; n = 6); PF vehicle control (PC; n = 6); PF ZEN (PZ; n = 6); HS vehicle control (HC; n = 7); or HS ZEN (HZ; n = 7) for 7 d. When compared to the TC pigs, TZ pigs had 45 increased and 39 decreased proteins (P ≤ 0.05). In the HZ pigs, 47 proteins were increased and 61 were decreased (P ≤ 0.05). Exposure to ZEN during TN conditions altered sec61 translocon complex (40%), rough endoplasmic reticulum membrane (8.2%), and proteasome complex (5.4%), asparagine metabolic process (0.60%), aspartate family amino acid metabolic process (0.14%), and cellular amide metabolic process (0.02%) pathways. During HS, ZEN affected cellular pathways associated with proteasome core complex alpha subunit complex (0.23%), fibrillar collagen trimer (0.14%), proteasome complex (0.05%), and spliceosomal complex (0.03%). Thus, these data identify ovarian pathways altered by ZEN exposure and suggest that the molecular targets of ZEN differ in TN and HS pigs.

Carcinogenesis and Prognostic Utility of Arginine Methylation-Related Genes in Hepatocellular Cancer

Protein arginine methylation is among the most important post-translational modifications and has been studied in cancers such as those of the lung and breast. However, comparatively less has been investigated regarding hepatocellular carcinoma, with an annual incidence of almost one million cases. Through using in silico methods, this study examined arginine methylation-related gene expression and methylation levels, and alongside network and enrichment analysis attempted to find how said genes can drive tumorigenesis and offer possible therapeutic targets. We found a robust relationship among the selected methylation genes, with ⅞ showing prognostic value regarding overall survival, and a medley of non-arginine methylation pathways also being highlighted through the aforementioned analysis. This study furthers our knowledge of the methylation and expression patterns of arginine histone methylation-related genes, offering jumping points for further wet-lab studies.