Histopathological assessment of melanocytic proliferations remains the gold standard for their correct classification. The most recent 5th edition of the World Health Organization (WHO) classification of melanocytic tumours incorporates cumulative sun damage and, in particular, molecular genetic changes to achieve this task, and recognizes nine different genetic pathways leading to melanoma development. Melanoma is therefore not a single disease genetically, but rather represents nine different well-defined clinicopathological entities that differ in terms of biological behaviour and their response to various treatment modalities. In this article, genetic pathways in the development of cutaneous melanoma are reviewed, and practical recommendations for pathologists with regards to molecular testing are provided.

OBJECTIVES:Due to its progressive fibro-inflammatory nature and frequent delays in diagnosis, IgG4-related disease (IgG4-RD) carries a significant risk of permanent organ damage. An index to evaluate the damage in IgG4-RD has been developed recently. The aim of this follow-up study was to assess the prognosis of IgG4-RD, with a focus on damage progression. METHODS:Data on IgG4-RD baseline characteristics, treatment, relapses, damage progression and deaths during follow-up were retrospectively extracted from electronic medical records of patients with IgG4-RD diagnosed and monitored at our rheumatology centre. Damage was assessed using the CIC IgG4-RD Damage Index (CIC IgG4-RD DI) at baseline, 12 months, 24 months and at the last follow-up visit. Risk factors for damage at the last visit and for death were evaluated by Cox proportional-hazards regression analysis. RESULTS:Of 59 patients diagnosed between January 2012 and December 2024, 55 were followed for a median (IQR) of 44.7 (20.4; 81.2) months (37/55 patients were followed for more than 24 months), while 4 were lost to follow-up. At diagnosis, 36 patients (65.5%) had already developed damage. At the 12-, 24-month visits and last follow-up visit of a subgroup followed-up for more than 24 months, 37/50 (74%), 29/37 (78.4%) and 32/37 (86.5%) patients had developed damage, respectively. A relapsing disease course was identified as a factor associated with damage at the last patient's visit (HR 5.3 (95%CI 1.1; 24,4), p=0.035). Eight patients (14.5%) died during follow-up, with 4 deaths related to IgG4-RD or its treatment. Damage at the last visit emerged as a risk factor for death (HR 1.5 (95%CI 1.0; 2.2), p=0.036). CONCLUSIONS:At diagnosis, damage was already present in nearly two-thirds of our patients. During follow-up, damage progressively accumulated and was associated with patient death.

Recommendations for the management and treatment of patients with soft tissue sarcoma emphasize the importance of individualized treatment in a referral center with a multidisciplinary sarcoma team. The only referral sarcoma center in Slovenia is the Institute of Oncology Ljubljana. Key components include imaging diagnostics using MRI and CT scans and a core needle biopsy. Surgical treatment remains the cornerstone of therapy, while radiotherapy reduces the risk of local recurrence. Systemic treatment with chemotherapy or targeted drugs is primarily considered for advanced, metastatic disease. The 2026 recommendations are available at the Institute of Oncology Ljubljana website.

Abstract Glioblastoma (GBM) is an aggressive brain tumour with limited responsiveness to current immunotherapeutic approaches, partly due to its low mutational burden and intra-tumour heterogeneity. A systematic understanding of the tumour antigen landscape is therefore essential for advancing tumour immunology and supporting rational development of immunotherapeutic strategies. In this study, we performed whole-transcriptome sequencing of RNA extracted from 79 formalin-fixed paraffin-embedded (FFPE) IDH-wildtype GBM samples to systematically identify and prioritise candidate tumour antigens derived from three sources: single-nucleotide variants (SNVs), overexpressed tumour-associated antigens (TAAs), and gene fusion events. Candidate peptides were evaluated using integrated computational criteria, including transcript expression, predicted antigen processing features, peptide–HLA binding affinity and stability. Across the cohort, mutation-derived tumor-specific antigens (TSAs) were largely private to individual samples, whereas TAAs constituted a larger and more recurrent candidate pool. Despite comparable predicted binding characteristics across antigen classes, recurrence patterns differed substantially, reflecting their distinct biological origins. Fusion-derived candidates were rare and sample-specific. Predicted peptide presentation was disproportionately associated with a limited subset of HLA class I alleles. Collectively, this study provides a systematically prioritized catalogue of transcriptionally expressed GBM antigen candidates and offers a comparative evaluation of mutation-, expression-, and fusion-derived antigen sources within a unified transcriptome-based framework.

Background: Data on the incidence of IgG4-related disease (IgG4-RD) are scarce. Our aim was to determine the incidence of IgG4-RD in a well-defined region. Methods: This retrospective study covered the Ljubljana region over the period from January 2012 to December 2024. A review of cases diagnosed with IgG4-RD was performed at several departments of the University Medical Centre Ljubljana—an integrated secondary/tertiary university teaching hospital (rheumatology, nephrology, angiology, gastroenterology, abdominal surgery, ENT surgery, ophthalmology). While IgG4-RD cases at the Department of Rheumatology were collected prospectively, potential cases at other departments were retrieved by searching electronic medical database for the keyword “IgG4”. In addition, the Institute of Pathology, Faculty of Medicine, University of Ljubljana, provided a list of patients with histological features consistent with IgG4-RD. Year-specific incidence rates and an average incidence rate over the 13-year period were determined. Clinical features of patients were analysed. Results: During the observation period, 58 cases of IgG4-RD were diagnosed. Of these, 35 patients were residents of the Ljubljana region, which had an average adult population of 541,600. The estimated average annual incidence rate of IgG4-RD was 5.0 per million (95% confidence interval: 3.5; 6.9), with year-specific incidence rates fluctuating between 1.8 and 9.3 per million adults. The cases were stratified into four phenotypic categories: pancreato-hepato-biliary (17%), retroperitoneal fibrosis-aortitis (43%), head and neck-limited (14%), and Mikulicz syndrome with systemic involvement (26%). Conclusions: The average annual incidence rate of IgG4-RD was 5 per million adults, with the retroperitoneal fibrosis-aortitis phenotype predominating in our cohort.

Craniopharyngiomas (CPs) are rare benign brain tumors that are classified as WHO grade I, with two subtypes: adamantinomatous craniopharyngioma (ACP) and papillary craniopharyngioma (PCP). ACP is caused by somatic mutations in exon 3 of the CTNNB1 gene activating the Wnt signaling pathway. PCP is associated with somatic BRAF p.V600E mutations activating the MAPK signaling pathway. Understanding their molecular differences is crucial for diagnosis and treatment. This study aimed to analyze common somatic alterations in ACP and PCP using bulk transcriptome sequencing and in situ spatial transcriptomics. RNA sequencing and high-resolution spatial profiling were used to detect mutations and examine gene expression differences among ACP, PCP, and healthy pituitary tissue. Whole transcriptome sequencing was performed on 24 tumor samples, with healthy pituitary data from the GTEx portal. Bioinformatics analysis utilized the CTAT mutation pipeline, with Sanger sequencing for validation. Results confirmed BRAF p.V600E mutations in all PCP samples and CTNNB1 mutations in all ACP samples. Differential gene expression analysis highlighted distinct molecular profiles and reinforced the involvement of Wnt and MAPK signaling. Spatial profiling identified 41 differentially expressed genes between ACP and PCP. This study provides critical insights into CP biology, supporting improved diagnostics and potential therapeutic strategies.

BACKGROUND:There is growing evidence that the Spitz group of melanocytic neoplasms should be restricted to those harboring kinase receptor fusions and HRAS mutations/11p15 amplification. The presence of genomic alterations characteristic of conventional melanomas (BRAF and NRAS mutations) precludes a diagnosis of a Spitz neoplasm. It is often challenging to distinguish Spitz neoplasms from conventional melanomas with spitzoid morphology on histopathological grounds alone. METHODS:We report a series of 70 consecutive melanocytic tumors in which targeted sequencing was indicated to distinguish Spitz from spitzoid neoplasms and to classify Spitz neoplasms along the biological spectrum. RESULTS:Final diagnoses incorporating molecular results included 12 conventional melanomas (nine of which with NRAS mutations), five Spitz melanomas, 35 atypical Spitz tumors, eight Spitz nevi, three melanocytic tumors with a MAP2K1 mutation, and seven desmoplastic Spitz nevi/tumors. There were significant discrepancies between initial diagnoses and final diagnoses after incorporating molecular results in 24 (34%) cases, including nine conventional melanomas favored to be Spitz neoplasms and nine Spitz neoplasms favored to be conventional melanomas. CONCLUSIONS:It is often not possible to reliably distinguish Spitz neoplasms from spitzoid melanocytic tumors without identifying their driver genomic alterations. Applying next-generation sequencing in diagnostically problematic tumors improves diagnostic accuracy.

BACKGROUND:To review the characteristics of all Slovenian patients with ocular adnexal lymphoma (OAL) in the period of 24 years with the aim of evaluating demographic data, lymphoma location and type, disease stage, treatment modality, local control rate and survival rate. PATIENTS AND METHODS:All patients with histologically diagnosed OAL in the main tertiary centre of Slovenia, Eye Hospital, University Medical Centre Ljubljana, who were treated at Institute of Oncology Ljubljana were included in the study. Patients' data were collected from October 1995 through April 2019. RESULTS:Seventy-four patients were included in the study having a median age of 68 years at diagnosis. The majority of lymphomas were of B-cell origin (98.6%). The most frequent type was the extranodal marginal zone B-cell lymphoma (MALT) (71.6%). Orbital lymphomas were diagnosed in 56 cases (75.7%) and conjunctival in 18 cases (24.3%). Ocular manifestation was the first sign of the disease in 78.4% of patients and in 67.6% of patients ocular adnexa were the only disease location. Fifty-one patients (68.9%) were treated with radiotherapy, 7 patients (9.4%) with systemic treatment, 5 patients (6.8%) with combined radiotherapy and systemic treatment and in 11 patients, biopsy and active surveillance strategy was applied (14.9%). Local control of the disease was achieved in 96.6% of treated patients. Median overall survival of the whole study group has not been reached yet. Five-year overall survival rate was 80.1% (95% CI 68.1% - 88.5%) and 5-year lymphoma specific survival rate was 87.2% (95% CI 83.2%-91.2%). CONCLUSIONS:OALs comprise a group of heterogeneous diseases with variable outcomes depending predominately on the patient's age and lymphoma type, with low grade lymphomas carrying good prognosis even in elderly patients.

There is an emerging group of distinct vascular neoplasms with NFATC1/2 fusions, involving bones and soft tissues and often displaying focal epithelioid morphology, variable atypia of endothelial cells, predominantly vasoformative and in some cases focal solid growth. Although they may show aggressive local growth and may recur locally, malignant behaviour has not been documented. We present a case of a 35-year-old woman with multiple vascular neoplasms with a EWSR1::NFATC2 fusion involving the lungs, multiple bones (vertebra, femurs, tibia, pelvis) and probably the liver. The bone lesions were locally aggressive and recurred after surgical treatment. Nine years after the first manifestation, there was progression to an epithelioid angiosarcoma. The patient died 3 months after the diagnosis of epithelioid angiosarcoma with massive lung and liver involvement(metastases). In addition to the EWSR1::NFATC2 fusion, an activating PIK3CA gene mutation was identified in the angiosarcoma but not in the previously diagnosed bone tumours. To the best of our knowledge, this is the first documentation of malignant progression of a vascular neoplasm with NFATC1/2 fusion as well as visceral (lung) involvement.

Semen cryopreservation is an important approach for preserving male fertility, and thawed semen is often used in in vitro fertilization/intracytoplasmic sperm injection (IVF/ICSI) procedures. This process has been used for decades and seems both safe and efficient, despite causing cryodamage to spermatozoa, including the impairment of sperm functions, with decreased viability and motility being the main indicators of poor sperm quality post-thawing. Although an increase in sperm DNA fragmentation is common during cryopreservation, data on how cryopreservation affects sperm at the molecular level are scarce. There are especially limited data on the influence of sperm cryopreservation on spermatozoa non-coding RNA (ncRNA) stability and expression. To date, only three publications have explored this issue in human sperm samples, and there have been only a few more studies in animals, including mouse, bull, ram, boar and giant panda. The results of studies on human and animal semen indicate that cryopreservation affects ncRNA expression, which could crucially affect fertilization and embryonic development. Moreover, a study employing boar spermatozoa further showed that alterations in ncRNA expression also depend on the sperm cryopreservation protocol used, and a study employing human spermatozoa showed that microRNA (miRNA) expression changes during cryostorage. Therefore, the effects of cryopreservation on ncRNA expression in spermatozoa should be studied more thoroughly, mostly because sperm cryopreservation is important for medically assisted reproduction. Furthermore, despite the wide usage of sperm cryopreservation, how cryopreservation changes sperm at the molecular level and whether these changes have any effect on future generations have not been determined.

Semen cryopreservation has played an important role in medically assisted reproduction for decades. In addition to preserving male fertility, it is sometimes used for overcoming logistical issues. Despite its proven clinical usability and safety, there is a lack of knowledge of how it affects spermatozoa at the molecular level, especially in terms of non-coding RNAs. Therefore, we conducted this study, where we compared slow freezing and vitrification of good- and poor-quality human semen samples by analyzing conventional sperm quality parameters, performing functional tests and analyzing the expression of miRNAs. The results revealed that cryopreservation of normozoospermic samples does not alter the maturity of spermatozoa (protamine staining, hyaluronan binding), although cryopreservation can increase sperm DNA fragmentation and lower motility. On a molecular level, we revealed that in both types of cryopreservation, miRNAs from spermatozoa are significantly overexpressed compared to those in the native semen of normozoospermic patients, but in oligozoospermic samples, this effect is observed only after vitrification. Moreover, we show that expression of selected miRNAs is mostly overexpressed in native oligozoospermic samples compared to normozoospermic samples. Conversely, when vitrified normozoospermic and oligozoospermic samples were compared, we determined that only miR-99b-5p was significantly overexpressed in oligozoospermic sperm samples, and when comparing slow freezing, only miR-15b-5p and miR-34b-3p were significantly under-expressed in oligozoospermic sperm samples. Therefore, our results imply that cryopreservation of normozoospermic sperm samples can modulate miRNA expression profiles in spermatozoa to become comparable to those in oligozoospermic samples.

The incidence of cutaneous melanoma in the world and in Slovenia is still increasing, but survival has improved in the last 20 years, mainly due to earlier detection of melanoma and uniform approaches in primary treatment. The updated Recommendations in 2024 bring a lot of novelties, especially in diagnostic procedures for detecting the early stages of melanoma, as well as precise follow-up recommendations after primary treatment, in the field of surgical treatment, and especially in the field of systemic treatment, both, of metastatic disease, and in adjuvant systemic treatment in high -risk stage II, also neoadjuvant systemic treatment of operable cutaneous melanoma. We have also included chapters on the nutrition and palliative care in this Recommendations.

The increasing availability of RNA sequencing data has opened up numerous opportunities to analyze various RNA interactions, including microRNA-target interactions (MTIs). In response to the necessity for a specialized tool to study MTIs in cancer and normal tissues, we developed AmiCa (https://amica.omics.si/), a web server designed for comprehensive analysis of mature microRNA (miRNA) and gene expression in 32 cancer types. Data from 9,498 tumor samples and 626 normal samples from The Cancer Genome Atlas were obtained through the Genomic Data Commons and used to calculate differential expression and miRNA-target gene (MTI) correlations. AmiCa provides data on differential expression of miRNAs/genes for cancers for which normal tissue samples were available. In addition, the server calculates and presents correlations separately for tumor and normal samples for cancers for which normal samples are available. Furthermore, it enables the exploration of miRNA/gene expression in all cancer types with different miRNA/gene expression. In addition, AmiCa includes a ranking system for genes and miRNAs that can be used to identify those that are particularly highly expressed in certain cancers compared to other cancers, facilitating targeted and cancer-specific research. Finally, the functionality of AmiCa is illustrated by two case studies.

Incidenca melanoma v svetu in Sloveniji še vedno narašča, se je pa preživetje v zadnjih 20 letih izboljšalo, predvsem zaradi zgodnejšega odkrivanja melanoma in enotnih pristopov v primarnem zdravljenju. Posodobljena Priporočila v letu 2024 prinašajo precej novosti, predvsem v diagnostičnih postopkih odkrivanja in zamejitve zgodnjih stadijev melanoma, kot tudi natančnih priporočil sledenja po primarnem zdravljenju, na področju kirurškega zdravljenja in pa predvsem sistemskega zdravljenja, tako metastatske bolezni, predvsem pa v adjuvan- tnem sistemskem zdravljenju v visoko rizičnem stadiju II, in neo- adjuvantnem sistemskem zdravljenju operabilnega melanoma. V tokratna Priporočila smo vključili tudi poglavji prehranskega in paliativnega tima.

Chondromyxoid fibroma (CMF) is a rare benign bone tumour. While CMF located entirely on the surface of a bone (i.e. juxtacortical CMF) has been well characterised, CMF has not so far been convincingly documented to arise in soft tissues without connection to an underlying bone. We report a subcutaneous CMF in a 34-year-old male, located on the distal medial aspect of the right thigh without any connection with the femur. The tumour measured 15 mm, it was well-circumscribed and displayed typical morphological features of a CMF. At the periphery, there was a small area of metaplastic bone. Immunohistochemically, the tumour cells were diffusely positive for smooth muscle actin and GRM1, and negative for S100 protein, desmin and cytokeratin AE1AE3. Whole transcriptome sequencing revealed a novel PNISR::GRM1 gene fusion. Our case indicates that CMF should be included in the differential diagnosis of soft tissue (including subcutaneous) tumours composed of spindle/ovoid cells, with a lobular architecture and chondromyxoid matrix. The diagnosis of CMF arising in soft tissues can be confirmed by identifying a GRM1 gene fusion or GRM1 expression by immunohistochemistry.

To report a patient with a very rare variant of iris melanoma that grows in the shape of a ring (ring melanoma). A 65-year-old patient was examined because of a pigmented lesion on the sclera. After a complete ophthalmic and ultrasound examination, a ring melanoma was diagnosed. Enucleation of the affected eye was performed, and histology report confirmed iris ring melanoma. This type of malignancy represents an exceedingly rare variant of uveal melanoma, and because of atypical clinical picture, it can be easily overlooked or misdiagnosed, which often delays adequate treatment. Gonioscopy, transillumination, and ultrasound help us to recognize and diagnose ring melanoma. Suspicion should be raised with a clinical picture that shows unilateral pigmentary glaucoma. The objective of this presentation is to describe and outline the challenging diagnosis and management of this rare disease entity.