Gene Reports

Background: Uveal melanoma (UM) and cutaneous melanoma (CM) both originate from the same cell line. This proposes the possibility of a shared mechanism between entities, requiring explicit investigation. Methods: Data from GWAS Catalog and DisGeNET were used to identify shared variation-disease associations (VDAs) between UM and CM. The results were validated using the Ensembl database. In the next step, the STRING database was used to identify the protein-protein interaction. Results: Subsequently, 109 unique VDAs were identified for UM and 880 for CM. However, only 2 VDAs were found to be shared among UM and CM in different ethnic groups. These shared VDAs were rs12203592 of the IRF4 gene, rs12913832 of the HECT and RLD domain-containing E3 ubiquitin protein ligase 2 (HERC2) gene. Notably, PPI network assessment through STRING showcased that OCA2 and IRF4 directly interacted with HERC2. Conclusion: While HERC2 acts as a poor prognostic factor in uveal melanoma, IRF4 status is a key prognostic indicator in both UM and CM. Identifying IRF4 allele contributions enables a better understanding of melanoma pathogenesis and fosters the development of disease-specific approaches.

Objective -- To analyze the incidence dynamics of uveal melanoma (UM) in Irkutsk Oblast over the period 2023 -- 2025, assess the structure of newly diagnosed cases by territory and stage, and compare the outcomes of anticancer care with those of other constituent entities of the Russian Federation that lead in registered prevalence of malignant neoplasms (MN) of the eye and adnexa. Materials and Methods. Data from the cancer registry of the Irkutsk Regional Oncology Dispensary (IROD) for 2023 -- 2025 and information from the state reference book "The State of Cancer Care for the Population of Russia in 2025" (P.A. Herzen Moscow Oncology Research Institute) were used. The analysis included cases of MN of the eye and adnexa (ICD - 10 code C69) of uveal localization. Incidence rates per 100,000 population, stage distribution, proportion of morphological verification, mortality, and the cohort of patients under follow-up were calculated. Results. Over three years, 112 new cases of UM were registered in Irkutsk Oblast (37, 36, and 39, respectively), corresponding to a crude incidence rate of approximately 1.6 per 100,000 population per year. In 2025, the region ranked 3rd in the Russian Federation for the number of newly registered patients with MN of the eye (45 individuals) and 1st for the registered prevalence rate (15.6 per 100,000). The highest proportion of stage I disease (58.3 %) and one of the lowest mortality rates (1.9 %) were observed. Conclusions. Irkutsk Oblast is characterized by a consistently high incidence of UM, accompanied by a favorable stage distribution and low mortality, reflecting both the biological and geographic features of the region and an adequate level of organization of ophthalmic oncology care.

Background: Pulmonary arterial hypertension (PAH) is a serious disease with poor prognosis, especially in infants or preterm babies and there is still no optimal treatment for this disease. Noradrenalin (NE) is a vasoactive mediator which is released by sympathetic ganglion. According to previous studies, NE/1-adrenoreceptors is not only in regulating normal physiologic responses, but also in the pathogenesis of PAH. However, the mechanisms of NE in PAH are not fully understood. Methods: Human PASMC (PASMC) was used in this study. Cell viability assay and Wound healing assay were used to evaluate the proliferation and migration of PASMC. Immunoprecipitation and western blots analysis were used to investigate the mechanisms which involved in NE-induced PASMC proliferation. Results: We investigated that NE could induce human PASMC proliferation and migration. Furthermore, we first find that endothelin 1 (ET-1) signaling pathway plays an important role in NE-induced PASMC proliferation. ET1 is a critical molecular which is known for regulating cell growth and migration. We investigated that NE could increase NE-1 secretion, further enhancing ET-1 bind to its receptors. For further clarifying the downstream signals in NE/ET-1 induced PASMC proliferation, we detected the phosphorylation and expression levels of ERK and JNK. Conclusions: By combining the results from ours and previous studies, we believed that JNK/c-jun pathway may play an important role in NE-induced PASMC proliferation. Key Words: Noradrenaline; Pulmonary Arterial Hypertension; Pulmonary Artery Smooth Muscle Cells; Endothelin-1; JNK/c-Jun Signaling.

It has been previously shown that chronic social defeat stress caused by paired agonistic interactions between male mice is accompanied by the development of depression-like state and immune deficiency. The aim of this study was to investigate changes in the expression of C1qtnf superfamily genes (encoding the complement component related with tumor necrosis factor) in the hypothalamus, thymus and lungs against the background of the Lewis lung adenocarcinoma growth. In the experiments, on the 5th day of social stress, male mice were injected with tumor cells into the tail vein. Chronic social stress continued for the next two weeks. The transcriptomes of the hypothalamus, thymus and lungs of mice were sequenced at the Genoanalytica Collective Center (http://genoanalytica.ru/, Moscow). Changes in the expression of the C1qtnf genes in the tissues of stressed mice were studied compared with the control and mice that were additionally injected with tumor cells. Overall, significant correlations were found between expression of most genes in each tissue of the experimental groups. In the hypothalamus of stressed animals, when tumor cells were introduced, an increase in the expression of the genes C1qtnf1, C1qtnf2, C1qtnf3, C1qtnf6 and C1qtnf7 was observed compared to controls. In the thymus of these animals, tumor cell injection increased expression of the C1qtnf1, C1qtnf5, and C1qtnf6 genes. In the lung of tumor-injected stressed mice, expression of the C1qtnf1, C1qtnf2, C1qtnf7, and C1qtnf9 genes was decreased relative to controls and non-tumor-injected depressed mice, reaching near-zero levels in some mice. Analysis of C1qtnf superfamily gene expression in the all tissues revealed negative correlations between the expression of the C1qtnf1, C1qtnf2, and C1qtnf7 genes in the hypothalamus and lungs indicating synchronization of processes against the background of social stress and Levis lung adenocarcinoma.

Purpose: To identify transcript-level variants in crystallin genes in paediatric patients with unilateral cataracts. Methods: Anterior capsulorhexis (n=12) from patients underwent surgical management of congenital unilateral cataracts was collected. Total RNA was isolated from lens epithelial cells, and complementary DNA (cDNA) was synthesized. Full-length RNA transcripts of 10 lens-specific crystallin genes were PCR-amplified and analysed via Sanger sequencing. Identified transcript variants were further validated using genomic DNA (gDNA) through Sanger sequencing. In addition, the full-length (~7,535 bp) CRYBA1 genomic region was sequenced using Oxford Nanopore Technology. Results: Aberrant low molecular weight (LMW) amplicons (~370 bp) of the CRYBA1 transcript were identified in three patients presented with unilateral cataract. Of 3 patients, 2 had persistent fetal vasculature (PFV) and 1 had pre-existing posterior capsular defect (PPCD). Sanger sequencing revealed a precise loss of exons 2 to 4 in the CRYBA1 RNA transcript. No coding, splice-site, or large deletion variants were detected in the genomic DNA of the patients or their parents. In silico analysis predicted two possible truncated proteins arising from these alternatively spliced transcripts: one comprising the first 11 amino acids of the N-terminal region with a loss of all Greek key motifs, and another comprising 90 amino acids encoded by exons 5 and 6, initiated from an alternative start codon in exon 5, and loss of Greek key motifs 1 & 2. Conclusion: The precise skipping of exons 2 to 4, consistent with canonical splicing signals (5-prime-GU...AG-3-prime), in the absence of genomic alterations, suggests the presence of alternatively spliced (AS) CRYBA1 transcripts in human lenses. This is the first report documenting AS-CRYBA1 transcripts in association with childhood cataracts with PFV and PPCD.

Analyses of human breast carcinomas (BCs) and premalignant breast lesions show that the loss of RASSF1A is an early event in the development of ER+ BCs, which correlates linearly with malignant progression. This observation suggests that RASSF1A inhibition is important for the development and progression of ER+ BCs. In addition to RASSF1A, concurrent caveolin-1 (Cav-1) inhibition may further promote ER+ breast carcinogenesis. In the present study, transgenic Rassf1a-/- and Cav-1(-/-) single as well as Rassf1a-/-, Cav-1(-/-) double knockout mice were used to investigate the impact of single or combined Rassf1a and Cav-1 inactivation on BC initiation. Loss of either one or both proteins led to different, pre-malignant histopathological alterations within the mammary glands of the mice, but not to fully developed BC, confirming that Rassf1a and Cav-1 are both important for maintaining the integrity of mammary gland epithelial structure, but suggesting that further intracellular changes or extracellular factors are required for the development of luminal BC when both genes are lost.

Introduction. Hypertrophic cardiomyopathy (HCM) is characterized by clinical and genetic heterogeneity. Age of manifestation, clinical and anatomical phenotypes of HCM vary significantly. This study discusses genetic causes and reconstructive surgery results for patients with particular intracardiac phenotype - diffused generalized HCM (DG-HCM). Methods: personal and familial medical history, general examination, 12-lead resting ECG, 24-hour ECG Holter monitoring, transthoracic and transesophageal EchoCG, cardiac MRI with gadolinium enhancement. A ten-gene panel was sequenced by IonTorrent PGM. Mutational screening in patients with suspected multisystemic diseases was performed by Sanger sequencing. Results: 170 patients with obstructive HCM (oHCM) requesting genetic counseling and surgical correction of HCM were evaluated. We distinguished particular DG-HCM subtype of oHCM (diffuse hypertrophy of IVS, LV free walls, papillary muscles displaced towards the LV apex) in 34 patients; 31 out of 34 underwent open heart reconstructive surgery. Patients with DG-HCM were younger at the time of surgery, had higher risk of SCD, and connective tissue dysplasia of the mitral valve. Hemodynamics normalization was observed in 1, 3, and 5 years after surgery. Eighteen ICDs were implanted; five patients experienced appropriate shocks. The genetic spectrum was enriched up to 30% by multisystem disorders. Mutations in "sarcomeric" genes were detected in 15%. Conclusion: Intracardiac phenotype of HCM may correlate with genetic cause and long-term prognosis. DG-HCM phenotype accounts for 20% oHCM patients and indications for open-heart surgery. Extended myectomy with parietal resection of papillary muscles and correction of mitral valve insufficiency provides long-term benefits for DG-HCM patients. Multisystem disorders in patients with DG-HCM should be of special attention. Study was supported by research project FURG-2024-0004.

BackgroundReactive Oxygen Species (ROS) are the small, unstable and highly reactive species, having DNA oxidizing ability. Oxidation of the DNAs purine and pyrimidine bases can lead to single or double strands in this macromolecule. In this situation, the ATM molecule, a serine-threonine kinase, targets several proteins for phosphorylation, which causes the cell cycle to stop and the DNA damage repair begins. It has previously been proven that natural polyphenols have the cancer inhibiting properties due to their high efficacy and low side effects. Silibinin is the main herbal and medical ingredient in Milk Thistle (Silybum marianum) is a polyphenol flavonolignan, which has been widely considered as an antioxidant and anticancer agent. The purpose of the present study was to investigate the ATM gene expression and measurement of reactive oxygen species (ROS) in SKBR3 cell line, treated with Silibinin. Materials and MethodsAt first, the SKBR3 cell line was cultured in RPMI1640 culture medium and MTT assay was carried out to evaluate the Silibinin cytotoxicity. Flow Cytometry was carried out for cell cycle analysis, apoptotic induction, and ROS detection. While, Real Time PCR was used to evaluate the ATM gene expression in the Silibinin-treated and un-treated SKBR3 cells. ResultsPresent results have shown that 150 {micro}M Silibinin had the most significant cytotoxicity and apoptotic induction influence after the treatment period of 48 h. Flow cytometry data have shown that Silibinin induced considerable amount of apoptosis and caused cell cycle arrest at G1/S phase and induced production of ROS. Real-time PCR results have revealed that Silibinin increased the ATM expression in SKBR3 cell line. ConclusionSilibinin causes increased ATM gene expression by inducing ROS production, which initiates cell cycle arrest and apoptotic induction in SKBR3 cells line.

Gene model for the ortholog of Insulin-like peptide 3 (Ilp3) in the D. pseudoobscura Apr. 2013 (BCM-HGSC Dpse_3.0/DpseGB3) Genome Assembly (GenBank Accession: GCA_000001765.2) of Drosophila pseudoobscura. This ortholog was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila using the Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.

Abstract Aim: Low chemotherapy response is a major risk factor for early mortality in cancer patients; it is one of the biggest challenges in cancer treatment. Main aim of this study is to identify chemotherapy non-responder, prognostic significance of pre-chemotherapy baseline variables in survival, distinguish most effective anti-cancer drug classes and formulation. Methods: In this multi-center retrospective cohort (n=2459) patients deceased with NSCLC and received anti-cancer drugs were included for analyses. To identify chemotherapy non-responder, patient population was divided into three sub-groups based on chemotherapy prescription frequency [1-15] as group-A, [16-30] as group-B, and [[&ge;]31] as group-C. Multivariate analysis was performed to identify risk of 1-year mortality in these groups. To prognose chemotherapy response in resected and unresected NSCLC patients, 0-7 days pre-chemotherapy white blood cell (WBC) count total five-ranges were compared as per overall survival in abnormal Vs normal WBC counts. Results: Post-stratification in group-A there were (n=1289) patients, in group-B (n=648) patients, and in group-C (n=522) patients. In group-A (n=301) patients 23% were found to have no new metastasis post-diagnosis significantly less p-value (0.004) compared to Group-B (n=125) 19.3%, and group-C (n=110) 19.2% patients p-value (0.008). Metastasis during chemotherapy was found significantly less in 20% patients of group-A, compared to (33%) in group-B, and (43%) in group-C p-value (<0.001). Post-chemotherapy initiation OS in group-A patients were significantly less 9 months (95% CI 9.3 - 9.6) compared to group-B 19 months (95% CI 17.7 - 20.2) and group-C 36.6 months (95% CI 34.6 - 38.5) patients p-value (<0.0001). Despite of low new metastasis and post chemo metastasis, group-A patients survived significantly less based on these outcomes group-A patients were considered as chemotherapy non-responder. Males and NSCLC stage III/IV patients were at higher risk; clinical benefits are corelated to surgery and radiotherapy for chemotherapy non-responder. Leukocytosis in both resected/unresected NSCLC group-A (13%) patients were found to be bad prognostic factor of survival in unresected group-B (5%) patients. Oral formulation of receptor tyrosine kinase inhibitors (RTKI) was effective in non-responders. Conclusion: Stratification of patient population based on chemotherapy prescriptions could be a useful method to find chemotherapy response in retrospective analysis. Patients with pre-chemotherapy leukocytosis should be closely monitored prior to selection of chemotherapy dose and formulation.

Background and PurposePARP inhibitors have been evaluated in clinical trials for several cancers and Olaparib is FDA approved for treating BRCA deficient ovarian cancer. Numerous reports have suggested Poly(ADP-ribose) polymerase1(PARP1) overexpression in a variety of cancers including breast carcinomas and proposed the role of PARP1 in metastasis. However, the mechanism of PARP1 in regulating metastatic process in BRCA proficient and deficient TNBC is not studied thoroughly. In this study, we propose that PARP1 mediated breast carcinoma progression is gene transcription mediated, where it regulates several steps of pro-metastasis. Experimental ApproachPARP inhibitors effect on metastasis was monitored by migration and invasion assay, modulation in protein expression was assessed by proteomic analysis and further confirmed by immunoblotting. Chromatin immunoprecipitation was performed to study the transcriptional role of PARP1. Ectopic expression and siRhoGDI, and immunofluorescence assessed the cytoskeleton changes. PARP inhibitor was administered in xenograft mice to study metastasis. Immunohistochemical analysis was done on patient and mice tissues. Key resultsBreast cancer cells exhibited reduced migration and invasion due to PARP1 inhibition. PARP1 regulates expression of vimentin and RhoGDI and hence cytoskeletal rearrangement causing a change in migrating potential of a cell. Metastasis in mice was reduced upon PARP inhibition. PARP1 was identified to be a novel transcriptional regulator of RhoGDI. Furthermore, RhoGDI ectopic expression substantiated the PARP inhibitor effects, suggesting the PARP inhibitor downstream signaling to be mediated through RhoGDI. Conclusions and ImplicationsWe identified a novel aspect of PARP1 as promoter of metastasis via transcriptional regulation of RhoGDI. Assessing RhoGDI levels in TNBC patients might be useful to predict sensitivity to PARP inhibitors.

Long COVID (LC) is a complex condition characterized by persistent, chronic multisystem manifestations, with a significant proportion of patients exhibiting neurological symptoms. Human ion channels (HICs), particularly potassium channels, are abundantly expressed in the nervous system and linked to key metabolic processes, making them potential candidates for understanding LC pathophysiology and drug repurposing. Meta-analysis of RNA-Seq datasets from COVID-19 recovered and LC patients was performed to identify altered HICs in LC. Differential gene expression analysis, functional enrichment analysis, and weighted gene co-expression network analysis (WGCNA) were performed to uncover key genes, pathways, and co-expression modules consisting of HICs, lipid metabolism-, and immune signaling-related genes. Drug-gene interaction analysis was performed to identify approved drugs targeting potential HICs. A total of 715 dysregulated genes, including eighteen HICs were identified, among which seven were potassium channels. Three significant modules containing HICs, lipid metabolism-, and immune signaling-related genes were identified and found to be associated with antigen processing and presentation, complement and coagulation cascades, and cytokine-related pathways. Approved drugs targeting KCNA6, KCNJ10, KCNN3, and KCNH4 were identified. With further experimental validation, these dysregulated potassium channels, supported by their co-expression networks and pathway associations, may act as potential candidates for drug repurposing in LC patients.

Background: Pancreatic ductal adenocarcinoma (PDAC) has remained one of the most serious malignancies and is still a leading cause of cancer-related deaths worldwide. Great attention has been paid to the relationship between diabetes mellitus and PDAC. The aim of our study was to analyse the mutual association of PDAC and diabetes mellitus in the entire population of the Czech Republic within a 5-year period. Methods: The incidence of PDAC in 2018-2022 was estimated based on the individual population data from the Czech National Cancer Registry. Another data source, the National Registry of Reimbursed Health Services that collects data from health insurance companies, was used to identify individuals recently diagnosed with diabetes mellitus. For the purpose of this study, diagnosis of new-onset of diabetes mellitus was defined as the time of the first prescription of any antidiabetic drug or another related health care service. Subsequently, patients diagnosed with PDAC in 2022 were followed retrospectively to see if they had been diagnosed with diabetes mellitus in the last five years before diagnosis of pancreatic cancer. Results: In 2022, 2,189 patients aged 60 years or older were diagnosed with pancreatic cancer. New-onset diabetes was observed in 17.4% within five years prior to diagnosis, with the highest occurrence (12.4%) within the last three years. Among patients aged 60-74 years, the respective proportions were 14.4% within three years and 5.7% four to five years prior to pancreatic cancer diagnosis. Conclusion: The incidence of pancreatic cancer in the Czech Republic is among the highest in Europe. One-fifth of PDAC cases are diagnosed following new-onset diabetes mellitus in patients over sixty. Unintended significant weight loss combined with new-onset diabetes thus must not be overlooked, as these can be early signs of PDAC. An individualised diagnostic work-up should follow without any unnecessary delay.

Long non-coding RNAs (lncRNAs) and single nucleotide polymorphisms (SNPs) within them play crucial role in cancer susceptibility and disease outcomes. Breast and ovarian cancers, characterized by genetic heterogeneity, present significant challenges for precise diagnosis and treatment. Despite recent advancements in personalized medicine, inclusion of lncRNA-SNP (LSNP) markers into cancer risk detection panels remains limited. In this work, we put forward lncRNA-SNP regulated gene expression-based breast and ovarian cancer risk prediction model LsGCRPred (LSNP-Gene Interaction Based Cancer Risk Prediction Model). Notably, our approach accounts for the tissue-specificity of lncRNAs as well the benefit for individuals with predisposing conditions. Additionally, pathway analysis revealed the involvement of the LSNP interacting genes in key cancer regulating pathways. TaqMan genotyping and qPCR were performed to confirm the presence of selected LSNPs in ovarian and breast cancer cell lines along with the significant expression of the lncRNA and associated gene transcripts. These findings highlight previously overlooked genetic variants within lncRNA loci and their regulatory impact on disease outcomes, providing insights into personalized cancer diagnosis and treatment strategies. The tool LsGCRPred can be accessed as a standalone version on GitHub. Github Link: https://github.com/zglabDIB/LsGCRPred

BackgroundHeterochromatic long arm of mouse Y chromosome harbors the multicopy species-specific sequences Ssty, Sly, Asty and Orly that are transcribed in testis and have known functions in male fertility. Of these Ssty and Sly encode proteins - yet all the transcripts are not translated. To investigate the roles of these Y-heterochromatic transcripts further, we analyzed them. MethodsMice with 2/3rd deletion of the Y-chromosome (XYRIIIqdel) and its wild type (XYRIII) were used in this study. Bioinformatic approaches, small RNA northern blots, Electrophoretic Mobility Shift Assays, Luciferase reporter assays, dPCR analysis, RT-qPCR assays and western blotting techniques were used to identify piRNAs that regulate autosomal genes. ResultsWe demonstrate that the multicopy gene families from mouse Y-long arm generate piRNAs predominantly in testis. We observed sequences homologous to these piRNAs in the UTRs of a few autosomal genes, which are differentially expressed in the sperms of XYRIIIqdel mice. Furthermore, the Endogenous Retrovirus Element (ERV) LTR, found in the Orly1 transcript identified piRNAs in the database, showed homology to UTRs and associated genomic regions of a few autosomal genes. Orly1 showed a reduction in genomic copy number by digital PCR in XYRIIIqdel mice. One of the four autosomal genes containing the ERV segment in their UTRs, showed a differential testicular protein expression in the mutant mice. ConclusionsThus, we further elucidate that different classes of repeats from Y-chromosome regulate autosomal gene expression via piRNAs. Besides, this study also identified novel roles for a Y-derived ERV in autosomal gene regulation in testis.

Background: Although the lung is of low biomass, it harbors a diverse and dynamic microbiome that may influence disease and healing. Existing studies have used diverse sampling methods with high propensities for contamination and sampling error, leading to diverse and unclear results. Here, we characterized the lung microbiome via airway and parenchymal samples to determine variation across patients and sampling methods. Methods: We recruited adult patients undergoing lung resection for suspected or confirmed malignancy. After resection and under sterile conditions, a 1 cm cubic piece of non-cancerous lung parenchyma and a swab from the specimen's bronchus were collected and sent for microbiome analysis via 16S rRNA gene amplicon (V4) sequencing on an Illumina platform. An established bioinformatics pipeline was used to determine taxonomic identification. Baseline clinical and demographic data were compared to microbiome composition. Results: A total of 86 patients were included in the study. Beta diversity (microbial composition) varied significantly by sampling method (biopsy of lung parenchyma versus airway swabs), so all further results were analyzed within sample types. Further analyses revealed significant differences in beta diversity by lobe of the lung, indicating a different microbial composition by anatomic location. Analyses of patient demographics revealed significant differences by age and comorbidities, including chronic obstructive pulmonary disease and atrial fibrillation. Conclusions: The lung harbors a diverse microbiome that differs by anatomic location and patient characteristics. This study provides a framework for more accurate future lung microbiome sampling and characterization.

Purpose: Autosomal Dominant Polycystic Kidney Disease is the most common monogenic kidney disease and largely due to variants in PKD1. We aimed to assess pathogenicity evidence for PKD1 missense variants in disease databases and evaluate in silico pathogenicity prediction tool performance. Methods: PKD1 missense variants reported as pathogenic, likely pathogenic or likely benign were extracted from ClinVar and PKDB. Variants were re-classified using ACMG/AMP criteria to identify "truth sets" of pathogenic and benign variants. In silico scores were obtained from five tools (SIFT, PolyPhen-2, CADD, REVEL, AlphaMissense) and evaluated using established thresholds. A Receiver Operating Characteristic curve analysis was performed using the PKD1 variant truth sets. Results: 346/389 (89%) reported disease-causing missense variants in PKD1 were downgraded to Variants of Unknown Significance (VUS) using current classification criteria. Based on current thresholds, REVEL achieved the highest sensitivity of 62%, with specificity of 79%. AlphaMissense was the only tool not to misclassify any truth set variants, but many of the variant scores were between the pathogenic and benign thresholds. Conclusion: A large majority of PKD1 missense variants are classified as VUS with current pathogenicity criteria. Commonly used in silico tools, applied with established genome-wide thresholds, do not reliably distinguish pathogenic and benign missense variants in PKD1.

ObjectiveBone morphogenetic protein-3b (BMP-3b), also known as growth differentiation factor 10, has been implicated in tumor suppression; however, its role in breast cancer and its interaction with transforming growth factor-{beta}1 (TGF-{beta}1) signaling remain incompletely understood. MethodsPublicly available datasets were used to examine BMP-3b expression in breast lesions and its association with overall survival in patients with stage III or IV breast cancer. Human MCF-7 and murine 4T1 breast cancer cells were treated with recombinant BMP-3b. Cell proliferation, migration, invasion, epithelial-mesenchymal transition-related proteins, and TGF-{beta}1-induced Smad3 phosphorylation were assessed using Cell Counting Kit-8, scratch wound-healing, Transwell invasion, and Western blot assays. ResultsBMP-3b expression was lower in ductal carcinoma in situ than in normal mammary tissue. Low BMP-3b expression was associated with poorer overall survival in patients with stage III or IV breast cancer. BMP-3b reduced proliferation of MCF-7 and 4T1 cells and inhibited migration and invasion of 4T1 cells. BMP-3b increased E-cadherin and decreased vimentin expression in both cell lines. It also attenuated TGF-{beta}1-induced migration, invasion, and Smad3 phosphorylation in 4T1 cells. ConclusionsBMP-3b suppresses malignant phenotypes of breast cancer cells and modulates TGF- {beta}1/Smad3 signaling. These findings identify BMP-3b as a potential endogenous regulator of breast cancer progression.

Bioactive vitamin D (1,25-dihydoxyvitamin D or 1,25(OH)2D) is synthesized from its inert circulating form 25-hydroxyvitamin D (25(OH)D) by the enzyme 1--hydroxylase in the kidneys and in other tissues including breast. Because breast cancer is associated with changes in intra-tumoral lipid composition and vitamin D is known to affect lipid metabolism, we investigated the potential role of tumor-produced 1,25(OH)2D on lipid profile expression during breast tumor progression. For that purpose, we used the MMTV-PyMT mouse model which mimics the four phases of tumor progression seen in human breast cancer (hyperplasia, adenoma/mammary intraepithelial neoplasia (MIN), early carcinoma and late carcinoma). In previous studies we showed that conditional ablation of the gene encoding 1--hydroxylase (Cyp27b1), specifically in the mammary epithelium of this MMTV-PyMT mouse model, resulted in enhanced spontaneous tumor initiation and progression. In the present study, we used mass spectrometry imaging to compare lipid composition in the mammary glands of Cyp27b1 ablated and non-ablated MMTV-PyMT mice. In non-ablated control animals, we observed changes to specific lipid signals linked to stages of tumor progression. In particular, several discriminatory lipid signals were significantly up regulated throughout tumor progression. In ablated mice, absence of Cyp27b1 in the mammary epithelium was accompanied by different lipid signals in hyperplastic lesions. Several lipid signals were exclusively detected in non-ablated tumors but absent in hyperplasia. Our findings suggest that the tumor-produced 1,25(OH)2D known to play a key role in mammary tumor progression is mechanistically related to early changes in lipid composition seen prior to the development of hyperplasia.

Hurthle cell carcinoma (HCC) is an aggressive form of thyroid cancer. While mitochondrial DNA mutations and chromosomal losses have been identified in HCC, isoform switching, and its functional consequences remain uncharacterized. This study reanalyzed NCBI GEO dataset GSE228870 (n = 32), using Salmon and IsoformSwitchAnalyzeR() to identify isoform switching. The analysis resulted in 371 switches across 335 genes showing functional consequences including loss of protein domains, shorter open reading frames (ORFs), loss of signal peptides and novel sub-cellular localizations. Most significant isoform switches (q-value < 0.05, |dIF| > 0.1) were observed in LAMA2, LSP1, MAD2L2, FBLN2 and CXCL12, implicating extracellular matrix dysregulation, DNA damage response, immune signaling and cytoskeleton regulation. These genes are expressed in normal thyroid (median TPM 20.69, 11.66, 14.79, 134.1 & 80.76). However, specific isoforms of LAMA2 and MAD2L2 are not expressed in normal thyroid, explaining tumor-specific expression in HCC. Alternative transcription termination site (ATTS) gain was significant, suggesting altered 3 end in HCC transcripts. TCGA SpliceSeq showed LSP1, FBLN2 and CXCL12 undergo alternative promoter (LSP1 exon1 PSI=94.5%, FBLN2 exon2 PSI=99.0%) and alternative termination (CXCL12 exon3.3 PSI=53.9%) in thyroid cancer, suggesting ATTS and alternative transcription start site (ATSS) as shared splicing dysregulation mechanisms. This is the first systematic characterization of isoform-level dysregulation in HCC.