Gene Rearrangement Research Articles

Some Tumours Can Drive You Nuts: An Enigmatic Case of Metastatic Lymph Node

Introduction: NUT carcinoma (NC) is a rare aggressive undifferentiated malignant neoplasm. It can arise from midline and non-midline structures with no predilection for age and gender. NC is due to NUT gene rearrangement (Chromosomal translocation). The diagnosis is established by NUTM1 protein expression by IHC / FISH / NGS RNA sequencing Given the rarity and novelty, herein we discuss our case of NC. Aim: To establish a diagnosis of NUT carcinoma and its diagnostic challenges. Clinical History: A 23-year-old young male presented with complaints of right neck swelling. Results: Histopathology revealed a poorly differentiated malignant neoplasm. Immunohistochemistry showed diffuse positivity for NUTM1 protein, hence was reported as NUT carcinoma. Conclusion: It is an aggressive malignant neoplasm with a dismal prognosis. An integrated approach by clinicians, radiologists and pathologists is required for accurate diagnosis and timely management.

LUNG CANCER IN THE NORTHEAST MICROREGION OF RIO GRANDE DO SUL: EPIDEMIOLOGICAL ASPECTS, MOLECULAR AND IMMUNOHISTOCHEMICAL PROFILE

Objective: To analyze the epidemiological profile of patients affected by lung cancer between 2005 and 2021 in the northeastern microregion of Rio Grande do Sul and to describe the molecular and immunohistochemical profile through the EGFR, PD-L1 and ALK biomarkers. Methods: This was a cross-sectional, retrospective study with quantitative and qualitative analysis carried out by the access to the Hospital Cancer Registry (RHC) database of a High Complexity Oncology Unit located in the northeast microregion of RS. Epidemiological parameters were histological type, age, gender, stage at diagnosis, family history, smoking and alcohol consumption, as well as data on PD-L1, ALK and EGFR biomarkers. Results: For the epidemiological profile, 1139 records were analyzed. Adenocarcinoma was the most frequent histological type (43.9%), the median age of patients was 65 years and men were more affected than women, corresponding to 66.4%. The most prevalent staging was IV (metastatic) and most patients were smokers, non-alcoholics and had a family history of cancer. Regarding the biomarkers, only 49 requests were made during the period. PD-L1 positivity, EGFR alterations and ALK gene rearrangements were observed in 43.8%, 20% and 7.5% of the cases, respectively. Conclusion: The epidemiological data cover 17 years of cases and corroborate previous studies evaluating lung cancer profile. Some variations of the analyzed biomarkers were verified in comparison to other national and international studies; however, more investigation is necessary to better assess the profile of biomarkers in the region.

ALK-positive large B-cell lymphoma: A study of six cases from an oncopathology center in North India.

ALK-positive large B-cell lymphoma (ALK+ LBCL) is a rare neoplasm with an aggressive course and poor therapeutic response to the standard R-CHOP regimen. Owing to its negativity for usual B- and T-cell markers and immunopositivity for epithelial markers, it can be easily misdiagnosed if it is not contemplated. To study the clinicopathological parameters of cases of ALK+ LBCL diagnosed at our institution. A retrospective observational study of ALK+ LBCL was conducted at a tertiary cancer center of North India with cases diagnosed over a period of 3 years. Six cases of ALK+ LBCL were identified. The clinical findings at presentation included mean age of 38.8 years, male-to-female ratio of 5:1, extranodal presentation (1/6 cases), concurrent extranodal and nodal involvement (3/6), nodal presentation (2/6), high serum LDH (5/5), and bone marrow involvement (1/5). Histomorphology of diffuse (100%), alveolar/nested (16.6%), and sinusoidal pattern (1 case upon relapse) and immunoblastic and plasmablastic morphology (100%) and immunopositivity in all cases for ALK-1 protein (100%), CD138 (100%), MUM1 (100%), LCA (100%) along with negativity for EBER-ISH/EBV-LMP1 immunohistochemistry clinched the diagnosis. Fluorescence in situ hybridization analysis for ALK gene rearrangement was detected in 4/4 cases. Four patients received chemotherapy demonstrating relapse in 2 cases: residual disease and no response in one case each, along with death in 2 cases. A high degree of diagnostic suspicion is required for accurate recognition of ALK+ LBCL. Awareness of its histology, immunohistochemistry, and cytogenetics is pivotal for precise identification of this rare entity.

Genomic and Transcriptomic Profiling of Digital Papillary Adenocarcinomas Reveals Alterations in MatrixRemodeling and Metabolic Genes.

Digital papillary adenocarcinoma (DPAC) is a rare but aggressive cutaneous malignant sweat gland neoplasm that occurs on acral sites. Despite its clinical significance, the cellular and genetic characteristics of DPAC remain incompletely understood. We conducted a comprehensive genomic and transcriptomic analysis of DPAC (n = 14) using targeted next-generation DNA and RNA sequencing, along with gene expression profiling employing the Nanostring Technologies nCounter IO 360 Panel. Gene expression in DPAC was compared to that in hidradenoma (n = 10). Immunohistochemistry was employed to validate gene expression. Two out of eight DPACs showed fusion gene rearrangements (CRTC3::MAML2 and TRPS1::PLAG1). No uniform mutational signature was detected in DPAC. Comparative gene expression analysis revealed an enrichment of genes related to matrix remodeling, metabolism, and DNA damage repair. Hallmark pathway analysis demonstrated significant upregulation of E2F target genes in DPAC compared to hidradenoma (p = 0.00710). Human papillomavirus-42 was found to be positive in all of our tested DPAC cases. Immunohistochemistry confirmed increased protein expression of CD56, CDC20, and SOX10 in DPAC. Notably, most DPAC tumors also exhibited B-cell infiltration, as indicated by CD20 staining. Our findings reveal novel fusions and validate altered replication pathways related to HPV42 in DPAC.

Stereotyped B-Cell Receptor Immunoglobulins in B-Cell Lymphomas.

Thorough examination of clonotypic B-cell receptor immunoglobulin (BcR IG) gene rearrangement sequences in patients with mature B-cell malignancies has revealed significant repertoire restrictions, leading to the identification of subsets of patients expressing highly similar, stereotyped BcR IG. This discovery strongly suggests selection by common epitopes or classes of structurally similar epitopes in the development of these tumors. Initially observed in chronic lymphocytic leukemia (CLL), where the stereotyped fraction accounts for a substantial fraction of patients, stereotyped BcR IGs have also been identified in other mature B-cell malignancies, including mantle cell lymphoma (MCL) and splenic marginal zone lymphoma (SMZL).Further comparisons across different entities have indicated that stereotyped IGs are predominantly "disease-biased," indicating distinct immune pathogenetic trajectories. Notably, accumulating evidence suggests that molecular subclassification of mature B-cell malignancies based on BcR IG stereotypy holds biological and clinical relevance. Particularly in CLL, patients belonging to the same subset due to the expression of a specific stereotyped BcR IG exhibit consistent biological backgrounds and clinical courses, especially for major and extensively studied subsets. Therefore, robust assignment to stereotyped subsets may aid in uncovering mechanisms underlying disease initiation and progression, as well as refining patient risk stratification. In this chapter, we offer an overview of recent studies on BcR IG stereotypy in mature B-cell malignancies and delineate past and present methodological approaches utilized for the identification of stereotyped BcR IG.

Construction of a fusant bacterial strain simultaneously degrading atrazine and acetochlor and its application in soil bioremediation.

Application of herbicide-degrading bacteria is an effective strategy to remove herbicide in soil. However, the ability of bacteria to degrade a herbicide is often severely limited in the presence of other pesticide. In this study, the atrazine-degrading strain Klebsiella varicola FH-1 and acetochlor-degrading strain Bacillus Aryabhatti LY-4 were used as parent strains to construct the recombinant RH-92 strain through protoplast fusion technology. Compared with the parent strains, RH-92 exhibited enhanced ability to degrade herbicide mixture containing atrazine and acetochlor, exhibiting 63.16% and 68.48% higher degradation rates, respectively. RAPD analysis showed that gene rearrangement occurred during protoplast fusion, and the genetic similarity indexes of the fused strain RH-92 and the two parent strains were 0.5853 and 0.4240, respectively. HPLC-MS analysis confirmed that RH-92 shared similar degradation products and pathways with both parent strains but exhibited a novel metabolic pathway for the continuous degradation of CMEPA (degradation product of acetochlor) into MEA through amide bond hydrolysis. The activities of GSH, GST and SOD of RH-92 increased and the level of MDA decreased under the stress of compound herbicides. Strain RH-92 did not show a large number of bacterial apoptosis, and maintained good cell membrane integrity and permeability. The half-lives of atrazine and acetochlor were 4.9 d and 7.6 d when the parent strains FH-1 and LY-4 were applied in unsterilized soil containing herbicide mixture treatment,the application fusant RH-92 strain significantly reduced the half-life to 1.6 and 1.8 d, respectively. Furthermore, 16S rRNA sequencing indicated that RH-92 application effectively restored bacterial taxa with diminished relative abundances under herbicide mixture treatment, ameliorated phytotoxicity in soybean seedlings, and promoted enhanced vegetative growth in the roots and plant height. This study highlighted the application of fusant strains as a bioremediation strategy for combatting atrazine and acetochlor pollution in soil and provided theoretical insights.

Clustering Algorithm-Driven Detection of TRBC1-Restricted Clonal T-Cell Populations Produces Better Results than Manual Gating Analysis.

Flow cytometric (FC) immunophenotyping and T-cell receptor (TCR) gene rearrangement studies are essential ancillary methods for the characterisation of T-cell lymphomas. Traditional manual gating and polymerase chain reaction (PCR)-based analyses can be labour-intensive, operator-dependent, and have limitations in terms of sensitivity and specificity. The objective of our study was to investigate the efficacy of the Phenograph and t-SNE algorithms together with an antibody specific for the TCR β-chain constant region 1 (TRBC1) to identify monoclonal T-cell populations. FC- and PCR-based clonality analyses were performed on 275 samples of T-cell lymphomas, B-cell lymphomas, and reactive lymphocytic proliferations. Monotypic T-cell populations were identified in 65.1% of samples by manual gating and 72.4% by algorithm-driven analysis, while PCR-based analysis detected clonal T cells in 68.0%. Of the 262 monotypic populations identified, 46.6% were classified as T-cell lymphomas and 53.4% as T-cell populations of uncertain significance (T-CUS). Algorithm-driven gating identified monotypic populations that were overlooked by manual gating or PCR-based methods. The study highlights the difficulty in distinguishing monotypic populations as T-cell lymphoma or T-CUS. Further research is needed to establish criteria for distinguishing between these populations and to improve FC diagnostic accuracy.

Genomic investigation of plant secondary metabolism: insights from synteny network analysis of oxidosqualene cyclase flanking genes.

The clustered distribution of genes involved in metabolic pathways within the plant genome has garnered significant attention from researchers. By comparing and analyzing changes in the flanking regions of metabolic genes across a diverse array of species, we can enhance our understanding of the formation and distribution of biosynthetic gene clusters (BGCs). In this study, we have designed a workflow that uncovers and assesses conserved positional relationships between genes in various species by using synteny neighborhood networks (SNN). This workflow is then applied to the analysis of flanking genes associated with oxidosqualene cyclases (OSCs). The method allows for the recognition and comparison of homologous blocks with unique flanking genes accompanying different subfamilies of OSCs. The examination of the flanking genes of OSCs in 122 plant species revealed multiple genes with conserved positional relationships with OSCs in angiosperms. Specifically, the earliest adjacency of OSC genes and CYP716 genes first appeared in basal eudicots, and the nonrandom occurrence of CYP716 genes in the flanking region of OSC persists across different lineages of eudicots. Our study showed the substitution of genes in the flanking region of the OSC varies across different plant lineages, and our approach facilitates the investigation of flanking gene rearrangements in the formation of OSC-related BGCs.

Analysis and reflections on the current status of diagnosis and treatment of marginal zone lymphoma

The current study aimed to understand the current status and problems of marginal zone lymphoma (MZL) in the diagnosis and treatment of hospitals at all levels in China. A multi-center questionnaire survey was conducted in a number of medical institutions across the country. A combination of online questionnaire survey and face-to-face interview was adopted. (1)Pathologists paid more attention than clinicians to distinguish MALT from chronic inflammation (86.3% vs 32.1%, P<0.01) and plasma cell tumor (51.8% vs 23.1%, P<0.01). A total of 21% pathologists never performed B-cell gene rearrangement, 67.6% of clinicians and 69.0% of pathologists would not recommend splenic puncture to diagnose SMZL.(2)In terms of treatment indications, 40.0% of clinicians mistakenly believed that stage Ⅲ-Ⅳ was also a treatment indication. Seventy percent of clinicians reported confusion about treatment indications. (3) In staging and efficacy evaluation, 63.3% of physicians performed PET-CT testing for patients, mainly for resolving clinical staging (89.0%), identifying histologically transformation (79.6%), and determining the site of radiotherapy or biopsy (66.2%). (4) In terms of treatment choice, only 32.2% of patients with indications were recommended for radiotherapy, and the proportion of hematologists choosing radiotherapy was significantly lower than that of oncologists (42.6% vs 71.7%, P<0.01); In the anti-HP indications, 53.1% of physicians will perform anti-HP therapy regardless of Hp positive or not; For advanced MZL, first-line immunochemotherapy was selected by 62.7% of clinicians, compared with 37.3% for targeted therapy. (5)15.3% of clinicians believed that the current prognostic evaluation system could not guide the selection of treatment options after initial treatment and recurrence. At present, there are still some cognitive deviations in the disease cognition and treatment indication of MZL among clinicians at all levels of hospitals in China. Likewise, there are still many unmet needs in MZL staging, efficacy evaluation, treatment selection and prognosis evaluation.

Efficacy and safety of lorlatinib as first-line treatment for advanced ALK-mutated non-small cell lung cancer: A clinical case study

In recent years, approaches to the pharmacological treatment of non-small cell lung cancer (NSCLC) have significantly evolved due to a deeper understanding of tumor biology and, consequently, the active development of personalized medicine and the introduction of targeted therapies. The identification of activating mutations, including ALK gene rearrangements, enables long-term objective control, which is particularly crucial in young patients with extensive metastatic disease and brain metastases (BM). The high rate of central nervous system (CNS) metastases characteristic of ALK-positive NSCLC underscores the importance of selecting therapeutic agents with high intracranial activity. Lorlatinib, a third-generation ALK tyrosine kinase inhibitor (TKI), is capable of crossing the blood-brain barrier and effectively suppressing resistance mutations that may develop during treatment with crizotinib or second-generation TKIs. Initially, lorlatinib was used in the second-line and subsequent lines of therapy; however, updated results from the CROWN study have demonstrated its unprecedented efficacy as a first-line treatment, including in patients with BM. Currently, lorlatinib is approved in the Russian Federation for the treatment of ALK-positive advanced NSCLC in both previously treated patients and as a first-line therapy. This paper presents a clinical case of a 49-yearold patient with advanced ALK-positive NSCLC and brain metastases. Following the diagnostic phase, which included videoassisted thoracoscopy and morphological verification, the patient underwent a course of chemotherapy with cisplatin and pemetrexed. Subsequently, based on the results of molecular genetic testing, lorlatinib was initiated at a dose of 100 mg/day. Within a month, a significant regression of CNS metastases was observed. Therapy was accompanied by minimal side effects, including hypercholesterolemia and elevated liver enzymes, which were successfully managed with lipid-lowering agents and physical activity. During targeted therapy, the patient has maintained stable disease for 26 months, showing a strong clinical response without the need for dose reduction. This case report highlights the efficacy and tolerability of lorlatinib in the treatment of ALK-positive NSCLC with BM and underscores its potential in clinical practice.

Molecular measurable residual disease by immunoglobulin gene rearrangements on circulating tumor DNA predicts outcome in diffuse large B-cell lymphoma.

In diffuse large B-cell lymphoma (DLBCL) treatment response relies on imaging. We investigated the potential value of molecular measurable residual disease (MRD) on circulating tumor DNA (ctDNA) to predict patient outcomes. We retrospectively evaluated 73 patients. Analyses were conducted on 57 tumor biopsies, based on sample availability. At baseline, next-generation sequencing was used to detect clonal immunoglobulin (IG) gene rearrangements on tumor biopsies and ctDNA. MRD monitoring was applied by tracking the IG clones in ctDNA samples collected during treatment (interim) and at the end of treatment (EOT). MRD results were correlated with clinical data and radiologic disease assessment. Before treatment, clonal IG were found in 91.2% (52/57) of tumor biopsies and in 93.2% (68/73) of ctDNA samples. In paired samples, the same clonotype was found in 69.2% (36/52) of cases. At the interim analysis, ctDNA MRD was negative in 32/45 evaluable patients and positive in 13/45, correlating significantly with progression-free survival (PFS) (78.1% MRD- vs 30.8% MRD+; p.

EXPRESSION OF IMMUNOGLOBULIN LIGHT CHAIN GENES IN STEREOTYPED CASES FROM UKRAINIAN COHORT OF CHRONIC LYMPHOCYTIC LEUKEMIA PATIENTS.

Analysis of immunoglobulin heavy chain gene (IGHV) rearrangements expressed in chronic lymphocytic leukemia (CLL) cells has provided insights into the B-cell receptor (BCR) repertoire in CLL. In more than 40% of CLL patients, (quasi)identical or stereotyped BCR is expressed. The recent data point at the non-stochastic expression of immunoglobulin light lambda (IGLV) or kappa (IGKV) chains as well. Several pairs of IGHV and IGK/LV have been described for some major stereotyped subsets, but most subsets have not been characterized. To study the IGK/LV gene expression in stereotyped CLL cases. Analysis was performed in a group of 105 CLL patients with stereotyped BCR. The cases with stereotyped BCRs were identified according to Agathangelidis et al. (2021). The IGHV and IGK/LV gene expressions were studied by a polymerase chain reaction followed by direct sequencing. The expression of the IGK/LV genes in the most presented major stereotyped subsets (#1, #2, #3C3, #4, #6, #28а) was in agreement with the data reported by other authors. For the cases of subsets #5b, #9D1, #9D4, #16, #50, #59, and #77, differences were found. The new data on the IGK/LV gene expression in 55 minor clusters were presented. A number of patterns of the IGK/LV gene expression depending on the phylogenetic clan and mutational status of the IGHV genes have been described. The non-stochastic distribution of the IGKV/LV gene expression in the individual stereotyped subsets was confirmed. Taking into account the complementary role of the light chains in antigen recognition by the clonotypic BCRs, it was suggested that the subsets with the heterogeneous IGK/LV expression might be reclassified and divided into separate subgroups based on the IGHV and IGK/LV association.

Immunoglobulin light chain mutational status refines IGHV prognostic value in identifying chronic lymphocytic leukemia patients with early treatment requirement.

The mutational status of immunoglobulin (IG) light chain genes in chronic lymphocytic leukemia (CLL) and its clinical impact have not been extensively studied. To assess their prognostic significance, the IG light chain gene repertoire in CLL patients has been evaluated using a training-validation approach. In the training cohort (N = 573 CLL), 92.5% showed productive IG light chain genes rearrangements, with IGKV4-1 (20.5%) and IGLV3-21 (19.0%) being the most common. A 99.0% somatic hypermutation cut-off was identified as the best predictor for time to first treatment (TTFT) in 414 Binet A CLL patients of the training cohort. Patients with unmutated (UM) light chain genes displayed a 10-year treatment free probability of 32.4% versus 73.2% for those with mutated (M) genes (p < 0.0001). Importantly, UM light chain genes maintained an independent association with a shorter TTFT when adjusted for the IPS-E prognostic model variables, that also includes IGHV mutational status. The validation cohort of 343 Rai 0 patients confirmed these findings, with UM light chain genes predicting a 7-year treatment free probability of 42.0% versus 73.7% for M genes (p < 0.0001). These results indicate that the mutational status of the light chain genes is an independent predictor of shorter TTFT in early-stage CLL patients.

Intraarticular Nodular Fasciitis of the Elbow Confirmed by UPS6::MYH9 Gene Fusion.

Nodular fasciitis is a benign, usually self-limiting myofibroblastic proliferation with a predilection for the upper extremities, trunk, and head and neck, and almost all of which harbor the USP6::MYH9 fusion. Since nodular fasciitis is not widely recognized to arise within the joints, it may therefore cause diagnostic confusion in this uncommon setting. We report an unusual tumor of an 11-year-old patient who presented with a 6-month history of right elbow swelling and pain. Histology revealed that the tumor was composed solely of proliferating bland spindle cells with osteoclast-like giant cells and scattered foam cells. There was only a focal area of immature granulation-like myxoid change, which suggested nodular fasciitis. Molecular analysis using next-generation sequencing revealed gene rearrangement involving USP6 and MYH9, supporting the diagnosis of nodular fasciitis within the elbow joint. This is the first of intraarticular nodular fasciitis within the elbow joint in which USP6::MYH9 gene fusion was identified by molecular analysis.

Characterization of the Mitochondrial Genome of Cambaroides schrenckii (Astacidea: Cambaridae) and Its Phylogenetic Implications.

Cambaroides schrenckii is an endangered freshwater crayfish in China, belonging to the genus Cambaroides, that can act as a complementary host for paragonimus. The objective of this study was to examine the complete mitochondrial genome characteristics and their evolutionary relationships within the Astacidea. The analysis of gene rearrangements and evolutionary relationships was conducted through the sequencing of the mitochondrial genome of C. schrenckii. C. schrenckii mitochondrial genome length was 15,572, comprising thirteen PCGs, two rRNAs, 22 tRNAs, and one d-loop region of C. schrenckii. The mitochondrial genome of C. schrenckii exhibits an A + T content of 69.61% and a G + C content of 30.39%. Among the thirteen PCGs, cytb, nad3, and nad6 have a start codon of ATT, while the other ten PCGs have ATC, ATA, and ATG start codons. All 22 tRNA genes displayed a typical cloverleaf secondary structure. Gene rearrangement analysis showed that seven gene arrangements were identified based on PCGs in the infraorder Astacidea, with type I being the most common. The relationship between the American Cambaridae is closer to Astacidae than the Asian Cambaridae. The present study provides a theoretical basis for further discussions of developmental relationships in the infraorder Astacidea.

YAP1::KMT2A-rearranged sarcomas harbor a unique methylation profile and are distinct from sclerosing epithelioid fibrosarcoma and low-grade fibromyxoid sarcoma.

Sclerosing epithelioid fibrosarcoma (SEF) was originally described as a peculiar variant of fibrosarcoma in 1995. Subsequent studies showed that conventional SEF was associated with both immunohistochemical expression of MUC4 and EWSR1/FUS gene rearrangements with CREB3L1 as the predominant fusion partner. Since then, a distinct group of fibrous tumors characterized by YAP1::KMT2A and KMT2A::YAP1 gene rearrangements and SEF-like morphology has been described. These YAP1::KMT2A-rearranged sarcomas were further shown to lack both immunohistochemical expression of MUC4 and canonical EWSR1/FUS gene rearrangements. To better understand whether the YAP1::KMT2A-rearranged sarcomas represent a subset of MUC4-negative SEF or a distinct entity, we studied 22 cases of YAP1::KMT2A-rearranged sarcomas, the largest series to date, and performed a literature review of all previously reported next-generation sequencing (NGS)-confirmed cases. These sarcomas often arose in young adults with a median age of 38 years and a male to female (M:F) ratio of 1.4:1. They predominantly involved somatic soft tissue; however, we report the first case of a tumor that primarily developed inside bone. Immunohistochemical studies showed that the tumors often demonstrated expression of YAP1 and EMA, while all tested cases were negative for MUC4. NGS confirmed the presence of YAP1::KMT2A gene fusions in all cases, some of which initially had false negative results with targeted FISH and solid tumor panel testing. Clinical follow-up information was available in 14 patients with a median follow-up of 25 months (range 1 to 170 months). Local recurrence occurred in three patients (21%) and metastasis developed in seven patients (50%). DNA methylation analysis further showed that YAP1::KMT2A-rearranged sarcomas formed a distinct cluster, which was clearly separate from both conventional SEF and low-grade fibromyxoid sarcoma (LGFMS). These results suggest that YAP1::KMT2A-rearranged sarcomas likely represent a unique sarcoma subtype with propensity for aggressive behavior.

Targeted RNA sequencing in diagnostically challenging head and neck carcinomas identifies novel MON2::STAT6, NFATC2::NUTM2B, POC5::RAF1, and NSD3::NCOA2 gene fusions.

Although molecular tests developed for a growing list of oncogenic alterations have significantly aided in the classification of head and neck carcinomas, tumours in which prototypical histologic and immunophenotypic features are lacking or only partially developed continue to pose diagnostic challenges. Searching for known diagnostic and therapeutic targets by clinical next-generation sequencing (NGS) assays can often lead to new discoveries. We present our institutional experience in applying targeted RNA NGS in 36 head and neck carcinomas that were morphologically difficult to classify between 2016 and 2023. The patients ranged in age from 5 to 83 years (median, 64), with the majority of tumors occurring in the major salivary glands and the sinonasal tract. Overall, seven (19%) cases showed unusual gene rearrangements, including five novel alterations: MON2::STAT6 in a hard palate adenocarcinoma with mucinous features, POC5::RAF1 in apocrine intraductal carcinoma of the lacrimal gland, EWSR1::CDADC1 fusion in a basaloid carcinoma of the submandibular gland, NFATC2::NUTM2B in myoepithelial carcinoma, and NSD3::NCOA2 fusion in a peculiar high-grade carcinoma with a peritheliomatous growth pattern, and focal myogenic differentiation. Potential therapeutic actionability was identified in three cases (RAF1 and FGFR2 fusions). These findings broaden the current spectrum of gene rearrangements in head and neck carcinomas and support the utility of clinical NGS in identifying unusual, actionable alterations in diagnostically challenging cases.

Clinicopathologic Features of Breast Tumors in Germline TP53 Variant-Associated Li-Fraumeni Syndrome.

We present one of the largest cohorts of TP53-pathogenic germline variants (PGVs) associated with patients with Li-Fraumeni syndrome (n = 82) with breast tumors (19 to 76y; median age: 35). Most had missense variants (77%), followed by large gene rearrangements (LGRs; 12%), truncating (6%), and splice-site (5%) variants. Twenty-one unique germline missense variants were found, with hotspots at codons 175, 181, 245, 248, 273, 334, and 337. Of 100 total breast tumors, 63% were invasive (mostly ductal), 30% pure ductal carcinoma in situ, 4% fibroepithelial lesions, and 3% with unknown histology. Unlike BRCA-associated tumors, approximately half of the breast cancers exhibited HER2-positivity, of which ~50% showed estrogen receptor coexpression. Pathology slides were available for review for 61 tumors (44 patients), and no significant correlation between the type of TP53 PGVs and histologic features was noted. High p53 immunohistochemistry expression (>50%) was seen in 67% of tumors tested (mostly missense variant). Null pattern (<1% cells) was seen in 2 (LGR and splicing variants carriers). Surprisingly, 2 tumors from patients with an LGR and 1 tumor from a patient with a truncating variant showed p53 overexpression (>50%). The subset of patients with the Brazilian p.R337H variant presented at a higher age than those with non-p.R337H variant (46 vs 35y) though statistically insignificant (P = 0.071) due to an imbalance in the sample size, and were uniquely negative for HER2-overexpressing tumors. To conclude, breast cancer in carriers of TP53 PGVs has some unique clinicopathological features that suggest differential mechanisms of tumor formation. p53 immunohistochemistry cannot be used as a surrogate marker to identify germline TP53-mutated breast cancers.

Dynamic O-GlcNAcylation governs long-range chromatin interactions in V(D)J recombination during early B-cell development.

V(D)J recombination secures the production of functional immunoglobulin (Ig) genes and antibody diversity during the early stages of B-cell development through long-distance interactions mediated by cis-regulatory elements and trans-acting factors. O-GlcNAcylation is a dynamic and reversible posttranslational modification of nuclear and cytoplasmic proteins that regulates various protein functions, including DNA-binding affinity and protein-protein interactions. However, the effects of O-GlcNAcylation on proteins involved in V(D)J recombination remain largely unknown. To elucidate this relationship, we downregulated O-GlcNAcylation in a mouse model by administering an O-GlcNAc inhibitor or restricting the consumption of a regular diet. Interestingly, the inhibition of O-GlcNAcylation in mice severely impaired Ig heavy-chain (IgH) gene rearrangement. We identified several factors crucial for V(D)J recombination, including YY1, CTCF, SMC1, and SMC3, as direct targets of O-GlcNAc modification. Importantly, O-GlcNAcylation regulates the physical interaction between SMC1 and SMC3 and the DNA-binding patterns of YY1 at the IgH gene locus. Moreover, O-GlcNAc inhibition downregulated DDX5 protein expression, affecting the functional association of CTCF with its DNA-binding sites at the IgH locus. Our results showed that locus contraction and long-range interactions throughout the IgH locus are disrupted in a manner dependent on the cellular O-GlcNAc level. In this study, we established that V(D)J recombination relies on the O-GlcNAc status of stage-specific proteins during early B-cell development and identified O-GlcNAc-dependent mechanisms as new regulatory components for the development of a diverse antibody repertoire.

Retrospective research: identifying and conducting phylogenetic analyses on four Orf virus strains isolated in Yunnan province between 2021 and 2023-revealing their significance and characteristic features.

Contagious Eczema (CE), caused by ORFV, impacts sheep and goats globally, with severe symptoms and economic losses. The ORFV situation in Yunnan, China, was unclear before 2021-2023 study. Eleven scab samples from goats on small farms in three Yunnan municipalities were collected. Four ORFV strains were isolated and characterized using scanning electron microscopy, cytopathic effect observation, and PCR. Phylogenetic analyses of ORFV011 and ORFV059 genes showed significant results. For ORFV011, the nucleotide similarity of the four strains to D1701 strain was 98.4-99%. For ORFV059, it was 97.2-97.9% with OV-SA00 strain. These findings suggest gene rearrangements and interactions among strains during Yunnan's ORFV outbreak, forming a unique evolutionary lineage. Our study is the first comprehensive one on Yunnan's ORFV prevalence with in-depth phylogenetic analysis. It has important implications. In vaccine development, understanding genetic variances helps create better vaccines. For disease control, customized strategies like targeted quarantine and disinfection can be designed based on strain characteristics. From a public health aspect, as CE is zoonotic, closely monitoring ORFV in goats aids in predicting and preventing human infections, thus being significant for protecting goats against CE in Yunnan.