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Bacteria of clinical importance, such as Pseudomonas aeruginosa, can become hypermutators upon loss of DNA mismatch repair (MMR) and are clinically correlated with high rates of multidrug resistance (MDR). Here, we demonstrate that hypermutated MMR-deficient P. aeruginosa has a unique mutational signature and rapidly acquires MDR upon repeated exposure to first-line or last-resort antibiotics. MDR acquisition was irrespective of drug class and instead arose through common resistance mechanisms shared between the initial and secondary drugs. Rational combinations of drugs having distinct resistance mechanisms prevented MDR acquisition in hypermutated MMR-deficient P. aeruginosa. Mutational signature analysis of P. aeruginosa across different human disease contexts identified appreciable quantities of MMR-deficient clinical isolates that were already MDR or prone to future MDR acquisition. Mutational signature analysis of patient samples is a promising diagnostic tool that may predict MDR and guide precision-based medical care., Competing Interests: Competing interests: K.M.H., L.G.W., Z.F.P., and L.A.M. are inventors of patent application #PCT/US2024/014280. K.M.H. and L.G.W. are employed by and are shareholders of Informuta, Inc. The remaining authors declare no competing interests., (© 2024. The Author(s).)

Aim: Autosomal recessive primary hyperoxalurias (PH) are genetic disorders characterised by elevated oxalate production. Mutations in genes involved in glycoxylate metabolism are the underlying cause of PH. Type 1 PH (PH1) results in malfunctioning of alanine-glyoxylate aminotransferase enzymes of liver due to a change in the genetic sequence of alanine-glyoxylate aminotransferase (AGXT) gene. We encountered a large family segregating genetic disease of high oxalate kidney stones. A genetic analysis was carried out with the aim to identify underlying genetic defect., Methods: A large family with multiple affected individuals was recruited for this study. An extensive clinical evaluation, followed by genetic analysis, was carried out. Due to the heterogeneous nature of the disease, two members of the family having disease symptoms were subjected to whole exome sequencing (WES). Variants were annotated, filtered, and prioritised using various bioinformatic tools to detect disease associated genetic defects., Results: Unbiased and hypothesis-free WES data analysis was performed. Raw reads (fastq files) were mapped to the reference genome and duplicates were removed. Variants were annotated, filtered, and prioritised. A low-frequency missense variant (c. 1049G>A) in the AGXT gene was considered the candidate variant. This variant replaces the highly conserved glycine amino acid with aspartate (p.Gly350Asp). The variant is destabilising for protein-protein interaction based on predicted change in binding free energy (ΔΔG). All members having disease phenotype were found homozygous to the mutation. Both parents and unaffected individuals in a family are heterozygous for the variant., Conclusion: Identification of pathogenic variant in the AGXT gene, in this family, provides genotype-phenotype correlation and permits accurate clinical diagnosis as well as carrier detection. Moreover, this variant extends the AGXT mutation spectrum in a different population and highlights the clinical significance and diagnostic relevance of the variant., (© 2025 Asian Pacific Society of Nephrology.)

Abstract: Regression (total or partial) is a common phenomenon in melanoma. From a pathogenic perspective, it is highly complex and only partially understood, involving aspects of both the tumor and the individual. One of the determining factors is the clonal selection of the tumor, wherein some clones within the tumor survive while others perish. This clonal selection can sometimes occur as a selective mechanism after the initiation of a therapeutic intervention. In many of these cases, the effect is detrimental, because the surviving clone is resistant to the applied therapy. However, occasionally, the therapy can successfully select the less harmful clone. We present an example of the latter, where therapy with interferon induced regression of the metastatic-capable melanocytic population, with only the primary tumor melanocytic population persisting. To confirm this, we demonstrated BRAF mutational similarity between the 2 populations, and an additional NRAS mutation in the metastatic population, which was absent in the primary tumor., Competing Interests: The authors declare no conflicts of interest., (Copyright © 2024 Wolters Kluwer Health, Inc. All rights reserved.)

A subset of desmoplastic melanomas (DMs) can show extensive morphologic and immunohistochemical overlap with cutaneous diffuse-type neurofibroma. Neurofibroma-like desmoplastic melanoma (NFLDM) thus poses a significant diagnostic pitfall because the clinical implications of these 2 entities differ dramatically. A series of 17 DMs, including 5 cases of NFLDM, were compared with a cohort of 53 cutaneous diffuse-type neurofibromas to explore the utility of molecular testing in the differential diagnosis between NFLDM and neurofibroma and to determine potentially useful morphologic features in this differential diagnosis. Unlike NFLDM, cutaneous diffuse-type neurofibromas: (1) rarely feature intratumoral or peritumoral lymphoid aggregates, (2) consistently harbor an intrinsic stromal support vasculature composed of evenly spaced capillary-sized vessels, and (3) infiltrate adjacent adipose tissue in a dermatofibrosarcoma protuberans-like manner with a complete lack of chronic inflammation or fat necrosis at the leading edge of the tumor. Conversely, DMs, including NFLDM: (1) do not contain Wagner-Meissner bodies, (2) often induce fat necrosis and/or chronic inflammation at the interface with adjacent fibroadipose tissue, (3) lack the intrinsic capillary-sized stromal vasculature observed in most neurofibromas, and (4) may harbor foci of perineuriomatous differentiation, mimicking a hybrid nerve sheath tumor. Any deviation from the expected clinical or morphologic features of cutaneous diffuse-type neurofibroma should raise suspicion for NFLDM. Although not entirely sensitive or specific, molecular testing can help to support the diagnosis of NFLDM by demonstrating genetic abnormalities associated with melanoma, including a UV-light-induced mutational signature, high tumor mutational burden, and/or chromosomal copy number alterations typical of melanoma., Competing Interests: ​Conflicts of Interest and Source of Funding: J.C.D. is a co-founder of Belay Diagnostics and holds stock in the company. For the remaining authors, none were declared., (Copyright © 2024 Wolters Kluwer Health, Inc. All rights reserved.)

Sialadenoma papilliferum is a tumor characterized by surface papillary projections and glandular/microcystic proliferation at the lesion base. Cases in which surface involvement is absent have been termed "sialadenoma papilliferum-like intraductal papillary tumor." Similar tumors that are present in the mandible have been termed "tubulopapillary hidradenoma-like tumor of the mandible." While previously considered benign, these tumors demonstrate variable clinical behavior and likely exist on a spectrum, rather than as discrete entities. In this study, we present a detailed clinicopathologic and molecular analysis of these lesions and propose a unifying diagnostic term: sialadenopapillary ductal tumor (SDT). Twenty-two cases with similar histologic features were reviewed, with special attention being paid to the clinicopathologic features. Immunohistochemistry for BRAF V600E and molecular testing were performed where material was available. The cases had varying diagnoses, ranging from benign to malignant. Six cases involved bone, 1 of which metastasized to a local lymph node. Of the 20 cases tested for BRAF V600E by immunohistochemistry, 18 were positive. Molecular testing was performed in 5 cases, where BRAF, PTPN11, and PIK3CA mutations were identified, predominantly members of the RAS-RAF-MEK-ERK pathway. In addition, 1 case was reclassified as an intraductal carcinoma after the identification of an NCOA4::RET gene fusion. Tumors on the SDT spectrum all share morphologic and molecular commonalities with unreliable distinguishing features. These tumors demonstrate the potential for aggressive local growth and regional metastasis. We propose a unifying diagnostic term for these lesions to reflect their common morphologic and molecular features and, most importantly, low malignant potential., Competing Interests: Conflicts of Interest and Source of Funding: The authors have disclosed that they have no significant relationships with, or financial interest in, any commercial companies pertaining to this article., (Copyright © 2024 Wolters Kluwer Health, Inc. All rights reserved.)

Background: The American Association of Endocrine Surgeons suggests screening for familial hypocalciuric hypercalcemia for 24-hour urine calcium <100 mg and for calcium to creatinine clearance ratio <1%. We explored the biochemical and clinical profiles of genetically tested patients to determine the usefulness of these recommendations., Methods: This was a retrospective review of patients who underwent analysis of the calcium-sensing receptor gene., Results: In total, 401 patients were identified between 2005 and 2024; 332 (83%) were negative for a mutation, 44 (11%) were positive, and 25 (6%) had variants of unknown significance. Median serum calcium was lower in patients who were negative (negative 10.1 mg/dL, variants of unknown significance 10.6 mg/dL, positive 10.9 mg/dL). Median urine calcium was lower in patients who were positive (negative 110 mg, variants of unknown significance 149 mg, positive 82 mg). Median parathyroid hormone levels were comparable between groups (negative 65 pg/mL, variants of unknown significance 58 pg/mL, positive 60 pg/mL). Eight of 21 (38%) patients who tested positive had urine calcium >100 mg and 5 of 21 (24%) had urine calcium >200 mg. Eight of 35 (23%) patients who were positive had a calcium to creatinine clearance ratio >1%. Urine calcium and calcium to creatinine clearance ratio receiver operating characteristic curves showed poor performance in identifying patients with familial hypocalciuric hypercalcemia (area under the curve [95% confidence interval]): 0.55 [0.45-0.65] and 0.63 [0.57-0.7], respectively. For positive patients with imaging, sestamibi was inconclusive or nonlocalizing for 13 of 23 and showed multiglandular disease for localizing scans in 7 of 10. Ultrasound was nonlocalizing or equivocal for 11 of 13. In total, 212 of 401 patients (53%) underwent surgery; 100 of 212 were tested preoperatively (0/100 positive, 5/100 variants of unknown significance) and 112 of 212 patients were tested postoperatively (15/112 positive, 10/112 variants of unknown significance)., Conclusion: Familial hypocalciuric hypercalcemia demonstrates non-negligible biochemical overlap with primary hyperparathyroidism, with many patients having a urine calcium value greater than the American Association of Endocrine Surgeons suggested threshold for considering genetic evaluation. More frequent genetic testing beyond urine measurements may help identify more patients with familial hypocalciuric hypercalcemia., Competing Interests: Conflict of Interest/Disclosure The authors have no related conflicts of interest to declare., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Foveal hypoplasia, optic nerve decussation, and anterior segment dysgenesis (FHONDA) is a rare recessively inherited syndrome first described in 2013. FHONDA is associated with biallelic disease-causing variants in the SLC38A8 gene, which has a strong expression in the photoreceptor layer. To date, 60 different disease-causing variants in the SLC38A8 gene have been described. In this cross-sectional case series, we included three unrelated female patients with FHONDA syndrome who presented with congenital nystagmus and decreased visual acuity from infancy. Best-corrected visual acuity was 20/100 OD and 20/60 OS for Patient 1 (P1) (72 years old); light perception OD and hand motion OS for Patient 2 (P2) (66 years old); and 20/100 OD and 20/100 OS for Patient 3 (P3) (25 years old). While normal retinal pigmentation was seen on P1 and P3, P2 presented retinal features of retinitis pigmentosa, including a pale optic nerve head, vessel thinning, and 360° dense bone spicule hyperpigmentation OU. Spectral-domain optical coherence tomography revealed grade 4 foveal hypoplasia in all patients. In P1 and P2, the novel class IV c.388 + 1G > T p.? variant in SLC38A8 was present in homozygosity; while P3 harboured the novel c.214G > C p.(Gly72Arg) variant in homozygosity, classified as class III. Thus, we expand the mutational spectrum of FHONDA by reporting two novel variants. In addition, we describe features of retinitis pigmentosa for the first time in a patient with biallelic homozygous S LC38A8 variants, thus broadening our understanding of the clinical phenotype associated with this rare syndrome., Competing Interests: Declaration of conflicting interestsThe authors declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.

Background: A liquid biopsy is a test that evaluates the status of a disease by analyzing a sample of bodily fluid, most commonly blood. In recent years, there has been progress in the development and clinical application of liquid biopsy methods to identify blood-based, tumor-specific biomarkers for many cancer types. However, the implementation of these technologies to aid in the treatment of patients who have a sarcoma remains behind other fields of cancer medicine. For this study, we chose to evaluate a sarcoma liquid biopsy based on circulating tumor DNA (ctDNA). All human beings have normal cell-free DNA (cfDNA) circulating in the blood. In contrast with cfDNA, ctDNA is genetic material present in the blood stream that is derived from a tumor. ctDNA carries the unique genomic fingerprint of the tumor with changes that are not present in normal circulating cfDNA. A successful ctDNA liquid biopsy must be able to target these tumor-specific genetic alterations. For instance, epidermal growth factor receptor (EGFR) mutations are common in lung cancers, and ctDNA liquid biopsies are currently in clinical use to evaluate the status of disease in patients who have a lung cancer by detecting EGFR mutations in the blood. As opposed to many carcinomas, sarcomas do not have common recurrent mutations that could serve as the foundation to a ctDNA liquid biopsy. However, many sarcomas have structural changes to their chromosomes, including gains and losses of portions or entire chromosomes, known as copy number alterations (CNAs), that could serve as a target for a ctDNA liquid biopsy. Murine double minute 2 (MDM2) amplification in select lipomatous tumors or parosteal osteosarcoma is an example of a CNA due to the presence of extra copies of a segment of the long arm of chromosome 12. Since a majority of sarcomas demonstrate a complex karyotype with numerous CNAs, a blood-based liquid biopsy strategy that searches for these CNAs may be able to detect the presence of sarcoma ctDNA. Whole-genome sequencing (WGS) is a next-generation sequencing technique that evaluates the entire genome. The depth of coverage of WGS refers to how detailed the sequencing is, like higher versus lower power on a microscope. WGS can be performed with high-depth sequencing (that is, > 60×), which can detect individual point mutations, or low-depth sequencing (that is, 0.1× to 5×), referred to as low-passage whole-genome sequencing (LP-WGS), which may not detect individual mutations but can detect structural chromosomal changes including gains and losses (that is, CNAs). While similar strategies have shown favorable early results for specific sarcoma subtypes, LP-WGS has not been evaluated for applicability to the broader population of patients who have a sarcoma., Questions/purposes: Does an LP-WGS liquid biopsy evaluating for CNAs detect ctDNA in plasma samples from patients who have sarcomas representing a variety of histologic subtypes?, Methods: This was a retrospective study conducted at a community-based, tertiary referral center. Nine paired (plasma and formalin-fixed paraffin-embedded [FFPE] tissue) and four unpaired (plasma) specimens from patients who had a sarcoma were obtained from a commercial biospecimen bank. Three control specimens from individuals who did not have cancer were also obtained. The paired and unpaired specimens from patients who had a sarcoma represented a variety of sarcoma histologic subtypes. cfDNA was extracted, amplified, and quantified. Libraries were prepared, and LP-WGS was performed using a NextSeq 500 next-generation sequencing machine at a low depth of sequencing coverage (∼1×). The ichorCNA bioinformatics algorithm, which was designed to detect CNAs from low-depth genomic sequencing data, was used to analyze the data. In contrast with the gold standard for diagnosis in the form of histopathologic analysis of a tissue sample, this test does not discriminate between sarcoma subtypes but detects the presence of tumor-derived CNAs within the ctDNA in the blood that should not be present in a patient who does not have cancer. The liquid biopsy was positive for the detection of cancer if the ichorCNA algorithm detected the presence of ctDNA. The algorithm was also used to quantitatively estimate the percent ctDNA within the cfDNA. The concentration of ctDNA was then calculated from the percent ctDNA relative to the total concentration of cfDNA. The CNAs of the paired FFPE tissue and plasma samples were graphically visualized using aCNViewer software., Results: This LP-WGS liquid biopsy detected ctDNA in 9 of 13 of the plasma specimens from patients with a sarcoma. The other four samples from patients with a sarcoma and all serum specimens from patients without cancer had no detectable ctDNA. Of those 9 patients with positive liquid biopsy results, the percent ctDNA ranged from 6% to 11%, and calculated ctDNA quantities were 0.04 to 5.6 ng/mL, which are levels to be expected when ctDNA is detectable., Conclusion: In this small pilot study, we were able to detect sarcoma ctDNA with an LP-WGS liquid biopsy searching for CNAs in the plasma of most patients who had a sarcoma representing a variety of histologic subtypes., Clinical Relevance: These results suggest that an LP-WGS liquid biopsy evaluating for CNAs to identify ctDNA may be more broadly applicable to the population of patients who have a sarcoma than previously reported in studies focusing on specific subtypes. Large prospective clinical trials that gather samples at multiple time points during the process of diagnosis, treatment, and surveillance will be needed to further assess whether this technique can be clinically useful. At our institution, we are in the process of developing a large prospective clinical trial for this purpose., Competing Interests: Each author certifies that there are no funding or commercial associations (consultancies, stock ownership, equity interest, patent/licensing arrangements, etc.) that might pose a conflict of interest in connection with the submitted article related to the author or any immediate family members. All ICMJE Conflict of Interest Forms for authors and Clinical Orthopaedics and Related Research® editors and board members are on file with the publication and can be viewed on request., (Copyright © 2024 by the Association of Bone and Joint Surgeons.)

Introduction: Pseudoxanthoma Elasticum (PXE) is a rare autosomal recessive disorder originated by disease-causing variants in ABCC6 gene. The purpose of this study was to characterize the genetic landscape, phenotypic spectrum and genotype-phenotype correlations in a Portuguese cohort of PXE patients., Methods: Multicentric cross-sectional study conducted in patients with a clinical and genetic diagnosis of PXE. Patients were identified using the IRD-PT registry (www.retina.com.pt). Genotypes were classified into 3 groups: (1) two truncating variants, (2) two non-truncating variants, or (3) mixed variants. Deep phenotyping comprised a comprehensive ophthalmologic and systemic evaluation using the updated Phenodex Score (PS)., Results: Twenty-seven patients (23 families) were included. Sixteen different ABCC6 variants were identified, 7 of which are novel. The most prevalent variant was the nonsense variant c.3421C > T p.(Arg1141*) with an allele frequency of 18.5%. All patients exhibited ocular manifestations. Cutaneous manifestations were present in most patients (88.9%, n = 24/27). A PS score > E2 was strongly associated with worse visual acuity (B = -29.02; p  = 0.001). No association was found between genotypic groups and cutaneous, vascular or cardiac manifestations., Conclusions: This study describes the genetic spectrum of patients with PXE for the first time in a Portuguese cohort. A total of 16 different variants in ABCC6 were found (7 of which are novel), thus highlighting the genotypic heterogeneity associated with this condition and expanding its mutational spectrum. Still, no major genotype-phenotype associations could be established., Competing Interests: Declaration of conflicting interestsThe authors declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.