Rare Cells Research Articles

Leveraging gene correlations in single cell transcriptomic data

BackgroundMany approaches have been developed to overcome technical noise in single cell RNA-sequencing (scRNAseq). As researchers dig deeper into data—looking for rare cell types, subtleties of cell states, and details of gene regulatory networks—there is a growing need for algorithms with controllable accuracy and fewer ad hoc parameters and thresholds. Impeding this goal is the fact that an appropriate null distribution for scRNAseq cannot simply be extracted from data in which ground truth about biological variation is unknown (i.e., usually).ResultsWe approach this problem analytically, assuming that scRNAseq data reflect only cell heterogeneity (what we seek to characterize), transcriptional noise (temporal fluctuations randomly distributed across cells), and sampling error (i.e., Poisson noise). We analyze scRNAseq data without normalization—a step that skews distributions, particularly for sparse data—and calculate p values associated with key statistics. We develop an improved method for selecting features for cell clustering and identifying gene–gene correlations, both positive and negative. Using simulated data, we show that this method, which we call BigSur (Basic Informatics and Gene Statistics from Unnormalized Reads), captures even weak yet significant correlation structures in scRNAseq data. Applying BigSur to data from a clonal human melanoma cell line, we identify thousands of correlations that, when clustered without supervision into gene communities, align with known cellular components and biological processes, and highlight potentially novel cell biological relationships.ConclusionsNew insights into functionally relevant gene regulatory networks can be obtained using a statistically grounded approach to the identification of gene–gene correlations.

DEPICT-seq: Single-Cell Transcriptomic Analysis of Rare Cell Subsets Isolated via Nucleic Acid Cytometry.

The ability to dive deep into specific rare cell populations is critical for understanding tissue physiology and pathology across various biological domains. As single-cell RNA-seq flourishes, many newly discovered cell subtypes are defined by their transcriptomic markers. However, our ability to retrieve and analyze cells based on their nucleic acid markers remains underdeveloped. Here, we present Double Emulsion PCR-Initiated Cell sorting and Transcriptomic Sequencing (DEPICT-seq), a high-throughput droplet nucleic acid cytometry method that integrates batch cell fixation for cellular information preservation, double emulsion digital PCR-based cell sorting to target nucleic acid markers of interest, and in-depth full-length transcriptomic analyses at single-cell resolution. We utilize DEPICT-seq to isolate and characterize T cell receptor (TCR)-engineered T cells within a mixed population and also demonstrate a variation of the workflow by incorporating an RNase H-dependent PCR step to enrich full-length TCR sequences for paired single-cell TCR sequencing and transcriptomic profiling.

Abstract C069: A conserved reepithelialization program driven by FOSL1 underlies malignancy in pancreatic ductal adenocarcinoma

Abstract Benign lesions named pancreatic intraepithelial neoplasia (PanIN) are frequent in the healthy population but are precursors to deadly pancreatic ductal adenocarcinoma (PDAC). Conversion of PanINs to PDAC is poorly understood. Here we harness high resolution spatial transcriptomics to identify a core transcriptional program associated with invasive growth across human PDAC and required for PanIN-to-PDAC progression in mice. The malignancy program is lineage restricted, and predominantly comprised of transcripts activated to drive reepithelialization during skin wound healing. This wound-like program appears in rare PanIN cells that also activate tumor suppressor genes (TSGs), which keep the incipient malignant cells in check. TSG KO in PanINs leads to rapid outgrowth of the wound-like population, unleashing invasive growth, driven by the wound-induced TF FOSL1. Bidirectional interactions between malignant epithelial cells and wound-like CTHRC1-expressing CAFs enforce the malignant state. Our results suggest that wound recapitulation drives the highly invasive properties of PDAC. Citation Format: Charles David, Melian Zhuo, Yong Li, Yifeng Zhang, Chenlu Yang, Ziqing Deng, Yupei Zhao, Wennming Wu, Junya Peng, Mo Chen. A conserved reepithelialization program driven by FOSL1 underlies malignancy in pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr C069.

Context-aware single-cell multiomics approach identifies cell-type-specific lung cancer susceptibility genes

Genome-wide association studies (GWAS) identified over fifty loci associated with lung cancer risk. However, underlying mechanisms and target genes are largely unknown, as most risk-associated variants might regulate gene expression in a context-specific manner. Here, we generate a barcode-shared transcriptome and chromatin accessibility map of 117,911 human lung cells from age/sex-matched ever- and never-smokers to profile context-specific gene regulation. Identified candidate cis-regulatory elements (cCREs) are largely cell type-specific, with 37% detected in one cell type. Colocalization of lung cancer candidate causal variants (CCVs) with these cCREs combined with transcription factor footprinting prioritize the variants for 68% of the GWAS loci. CCV-colocalization and trait relevance score indicate that epithelial and immune cell categories, including rare cell types, contribute to lung cancer susceptibility the most. A multi-level cCRE-gene linking system identifies candidate susceptibility genes from 57% of the loci, where most loci display cell-category-specific target genes, suggesting context-specific susceptibility gene function.

The role of the haematopoietic stem cell niche in development and ageing.

Blood production depends on rare haematopoietic stem cells (HSCs) and haematopoietic stem and progenitor cells (HSPCs) that ultimately take up residence in the bone marrow during development. HSPCs and HSCs are subject to extrinsic regulation by the bone marrow microenvironment, or niche. Studying the interactions between HSCs and their niche is critical for improving ex vivo culturing conditions and genetic manipulation of HSCs, which is pivotal for improving autologous HSC therapies and transplantations. Additionally, understanding how the complex molecular network in the bone marrow is altered during ageing is paramount for developing novel therapeutics for ageing-related haematopoietic disorders. HSCs are unique amongst stem and progenitor cell pools in that they engage with multiple physically distinct niches during their ontogeny. HSCs are specified from haemogenic endothelium in the aorta, migrate to the fetal liver and, ultimately, colonize their final niche in the bone marrow. Recent studies employing single-cell transcriptomics and microscopy have identified novel cellular interactions thatgovern HSC specification and engagement with their niches throughout ontogeny. New lineage-tracing models and microscopy tools have raised questions about the numbers of HSCs specified, as well as the functional consequences of HSCs interacting with each developmental niche. Advances have also been made in understanding how these niches are modified and perturbed during ageing, and the role of these altered interactions in haematopoietic diseases. In this Review, we discuss these new findings and highlight the questions that remain to be explored.

IL-13 induces loss of CFTR in ionocytes and reduces airway epithelial fluid absorption.

The airway surface liquid (ASL) plays a crucial role in lung defense mechanisms, and its composition and volume are regulated by the airway epithelium. The cystic fibrosis transmembrane conductance regulator (CFTR) is abundantly expressed in a rare airway epithelial cell type called an ionocyte. Recently, we demonstrated that ionocytes can increase liquid absorption through apical CFTR and basolateral barttin/chloride channels, while airway secretory cells mediate liquid secretion through apical CFTR channels and basolateral NKCC1 transporters. Th2-driven (IL-4/IL-13) airway diseases, such as asthma, cause goblet cell metaplasia, accompanied by increased mucus production and airway secretions. In this study, we investigate the effect of IL-13 on chloride and liquid transport performed by ionocytes. IL-13 treatment of human airway epithelia was associated with reduced epithelial liquid absorption rates and increased ASL volume. Additionally, IL-13 treatment reduced the abundance of CFTR-positive ionocytes and increased the abundance of CFTR-positive secretory cells. Increasing ionocyte abundance attenuated liquid secretion caused by IL-13. Finally, CFTR-positive ionocytes were less common in asthma and chronic obstructive pulmonary disease and were associated with airflow obstruction. Our findings suggest that loss of CFTR in ionocytes contributes to the liquid secretion observed in IL-13-mediated airway diseases.

A case of paraprotein-negative POEMS syndrome: Case report and literature review.

POEMS syndrome is a rare monoclonal plasma cell disease. The diagnosis of POEMS requires polyradiculoneuropathy and monoclonal plasma proliferating as 2 mandatory criteria, at least 1 of the major criteria (Castleman disease, elevated vascular endothelial growth factor level, and sclerotic bone lesion), and at least 1 of the minor criteria (organomegaly, extravascular volume overload, endocrinopathy, skin changes, papilledema, and thrombocytosis/polycythemia). This multisystem disorder is of high heterogeneity, and few variants of POEMS with no evidence of monoclonal gammopathy have been described, which further complicates the diagnosis in clinical practice. Now, we report a case of paraprotein-negative POEMS syndrome. A 45-year-old woman complained of lower extremity edema, shortness of breath, abdominal distension, and lymphadenopathy for few years. Finally, she was diagnosed with paraprotein-negative POEMS syndrome. With the lenalidomide-based regimen, the symptoms were all relieved. Paraprotein-negative POEMS syndrome. Lenalidomide-based regimen and some supportive therapy. All symptoms were relieved after 1 year of treatment. Physicians should pay more attention to the POEMS syndrome, especially the POEMS syndrome variants, which are absence of paraprotein; probably, these variants are just "on the way" to classic POEMS syndrome antiplasma cell therapy, which remains the treatment of choice.

A RARE CASE OF COEXISTING BLADDER SMALL CELL NEUROENDOCRINE CARCINOMA AND PROSTATE ADENOCARCINOMA: CASE REPORT AND LITERATURE REVIEW

Objective: We present a case of synchronous malignancies of rare bladder small cell neuroendocrine carcinoma (SCNC) and prostate adenocarcinoma and provide literature review of bladder SCNC. Case(s) presentation: A 72-year-old male smoker presented with 3 months history of gross hematuria. Ultrasonography showed a large hypoechoic mass in the right bladder. TURBT was performed and histopathology of the TURBT specimen showed a high-grade papillary urothelial carcinoma. Abdominal contrast-enhanced computed tomography (CECT) demonstrated an isodense heterogenous undefined mass, with irregular border at right anterolateral side of bladder wall. Radical cystoprostatectomy, bilateral radical lymph node dissection and bilateral ureterocutaneostomy was performed. Histopathology and immunohistochemical examination after radical cystoprostatectomy revealed bladder small cell neuroendocrine carcinoma coexisting with prostate adenocarcinoma (Gleason score 3+3=6, group 1). The patient eventually succumbed to disease after having symptomatic disease progression and metastatic disease five months after the surgery. Discussion: Bladder SCNC is a rare malignancy with an incidence of 1–9/1,000,000 reported. This tumor has an aggressive clinical course with high incidence of metastasis, and it tends to confer dismal prognosis. No specific clinical symptom exists. Histopathological recognition and immunohistochemistry is required to differentiate this rare entity. Conclusion: Clinicians and pathologists should be alert to the possibility of bladder SCNC despite extremely scarce incidence. Keywords: Bladder cancer, small cell neuroendocrine carcinoma, synchronous malignancy, case report.

Concurrent delayed recurrence of peripheral primitive neuroectodermal tumors in orbital and sellar/suprasellar regions in an older adult.

Peripheral primitive neuroectodermal tumors (pPNETs) are rare and aggressive small round cell tumors, tending to occur in the thoracic and paravertebral soft tissues in children and young adults. This report describes an exceptionally rare case of concurrent delayed recurrence of pPNET in the orbital and sellar/suprasellar regions in an older adult, with a discussion supported by a literature review. We report an 82-year-old woman with a history of orbital pPNETs resection at age 62, followed by gamma knife radiosurgery for local recurrence at age 66. She presented left eye pain, left eye protrusion, decreased vision in the right eye, and right homonymous hemianopia. MRI revealed extensive lesions in the left orbital cavity and sellar/suprasellar region, contiguous through the optic canal. The recurrent tumor was treated through a two-stage resection via transcranial and transsphenoidal approaches, which resulted in symptom improvement and a pathologic diagnosis of pPNETs. This case highlights a highly rare instance of late-onset orbital pPNETs recurrence in an elderly patient, with evidence suggesting tumor progression into the sellar/suprasellar regions through the optic canal.

VICTOR: Validation and inspection of cell type annotation through optimal regression

Single-cell RNA sequencing provides unprecedent opportunities to explore the heterogeneity and dynamics inherent in cellular biology. An essential step in the data analysis involves the automatic annotation of cells. Despite development of numerous tools for automated cell annotation, assessing the reliability of predicted annotations remains challenging, particularly for rare and unknown cell types. Here, we introduce VICTOR: Validation and inspection of cell type annotation through optimal regression. VICTOR aims to gauge the confidence of cell annotations by an elastic-net regularized regression with optimal thresholds. We demonstrated that VICTOR performed well in identifying inaccurate annotations, surpassing existing methods in diagnostic ability across various single-cell datasets, including within-platform, cross-platform, cross-studies, and cross-omics settings.

Abstract P433: Impaired Renin Activity in a Bicistronic Ren1 c -T2A-tdTomato Reporter Mouse

The study of renin cell identity and function often requires the isolation of this rare cell type –0.01% of the kidney cells. Multicistronic constructs are commonly used to express reporter genes in mice. They consist of two or more genes linked by 2A peptide sequences, which produce separate proteins through a ribosomal skipping mechanism. Here, we report on the generation of a mouse model to label renin-expressing cells with a bright fluorescent reporter for the tracking and isolation of renin cells. Ren1 ctdTomato mice were generated by inserting a bicistronic T2A-tdTomato knock-in cassette upstream of the TGA stop codon of the Ren1 c gene. Kidneys from adult heterozygous (het) Ren1 ctdTomat o mice showed tdTomato signal confined to the JG area under basal conditions, and extending along the afferent arterioles and in the intraglomerular mesangium upon treatment with captopril + low-salt diet to induce the endocrine transformation of renin cells. Unexpectedly, homozygous (homo) mice exhibited increased tdTomato signal that extended in the afferent arterioles and the mesangium even under normal physiological conditions, and progressive thickening of the kidney arterioles with age. Despite reduced Renin immunostaining in the renal cortex, homo mice exhibited significantly higher kidney Ren1 mRNA (7.9 ± 1.2 vs 1.2 ± 0.6, p< 0.0001) and circulating Renin levels (121.7 ± 44.0 vs 66.7 ± 29.4 ng/ml, p< 0.003) when compared to het controls. Moreover, homo mice showed significantly lower blood pressure measured under anesthesia (62.3 ± 5.9 vs 90.0 ± 5.7 mmHg, p< 0.0001), and Ang I plasma levels (159.3 ± 34.8 vs 500.0 ± 184.1 pmol/L, p< 0.05), indicating compromised Renin activity. The concentric arteriolar hypertrophy phenotype observed in these mice is identical to that described when RAS is genetically or pharmacologically inhibited, including the presence of mutations in the renin gene. Unlike mice with global deletion of renin, these animals did not require neonatal saline injections to survive and did not develop other kidney abnormalities, indicating that the bicistronic approach rendered a renin hypomorphic mouse. Ren1 ctdTomato mice constitute an excellent model for the labeling of renin-expressing cells and for the study of the mechanisms involved in the development of concentric vascular hypertrophy under RAS inhibition. In addition, this model may provide a better understanding of factors controlling renin protein folding, stability, packaging, and release.

Recovering single-cell expression profiles from spatial transcriptomics with scResolve.

Many popular spatial transcriptomics techniques lack single-cell resolution. Instead, these methods measure the collective gene expression for each location from a mixture of cells, potentially containing multiple cell types. Here, we developed scResolve, a method for recovering single-cell expression profiles from spatial transcriptomics measurements at multi-cellular resolution. scResolve accurately restores expression profiles of individual cells at their locations, which is unattainable with cell type deconvolution. Applications of scResolve on human breast cancer data and human lung disease data demonstrate that scResolve enables cell-type-specific differential gene expression analysis between different tissue contexts and accurate identification of rare cell populations. The spatially resolved cellular-level expression profiles obtained throughscResolve facilitate more flexible and precise spatial analysis that complements raw multi-cellular level analysis.

ScRNA-seq reveals the spatiotemporal distribution of camptothecin pathway and transposon activity in Camptotheca acuminata shoot apexes and leaves.

Camptotheca acuminata Decne., a significant natural source of the anticancer drug camptothecin (CPT), synthesizes CPT through the monoterpene indole alkaloid (MIA) pathway. In this study, we used single-cell RNA sequencing (scRNA-seq) to generate datasets encompassing over 60,000 cells from C. acuminata shoot apexes and leaves. After cell clustering and annotation, we identified five major cell types in shoot apexes and four in leaves. Analysis of MIA pathway gene expression revealed that most of them exhibited heightened expression in proliferating cells (PCs) and vascular cells (VCs). In contrast to MIA biosynthesis in Catharanthus roseus, CPT biosynthesis in C. acuminata did not exhibit multicellular compartmentalization. Some putative genes encoding enzymes and transcription factors (TFs) related to the biosynthesis of CPT and its derivatives were identified through co-expression analysis. These include 19 cytochrome P450 genes, 8 O-methyltransferase (OMT) genes, and 62 TFs. Additionally, these pathway genes exhibited dynamic expression patterns during VC and EC development. Furthermore, by integrating gene and transposable element (TE) expression data, we constructed novel single-cell transcriptome atlases for C. acuminata. This approach significantly facilitated the identification of rare cell types, including peripheral zone cells (PZs). Some TE families displayed cell type specific, tissue specific, or developmental stage-specific expression patterns, suggesting crucial roles for these TEs in cell differentiation and development. Overall, this study not only provides novel insights into CPT biosynthesis and spatial-temporal TE expression characteristics in C. acuminata, but also serves as a valuable resource for further comprehensive investigations into the development and physiology of this species.

ScCAD: Cluster decomposition-based anomaly detection for rare cell identification in single-cell expression data

Single-cell RNA sequencing (scRNA-seq) technologies have become essential tools for characterizing cellular landscapes within complex tissues. Large-scale single-cell transcriptomics holds great potential for identifying rare cell types critical to the pathogenesis of diseases and biological processes. Existing methods for identifying rare cell types often rely on one-time clustering using partial or global gene expression. However, these rare cell types may be overlooked during the clustering phase, posing challenges for their accurate identification. In this paper, we propose a Cluster decomposition-based Anomaly Detection method (scCAD), which iteratively decomposes clusters based on the most differential signals in each cluster to effectively separate rare cell types and achieve accurate identification. We benchmark scCAD on 25 real-world scRNA-seq datasets, demonstrating its superior performance compared to 10 state-of-the-art methods. In-depth case studies across diverse datasets, including mouse airway, brain, intestine, human pancreas, immunology data, and clear cell renal cell carcinoma, showcase scCAD’s efficiency in identifying rare cell types in complex biological scenarios. Furthermore, scCAD can correct the annotation of rare cell types and identify immune cell subtypes associated with disease, thereby offering valuable insights into disease progression.

Epidemiological estimates of paroxysmal nocturnal hemoglobinuria in Bulgaria.

Paroxysmal nocturnal hemoglobinuria is a rare clonal hematopoietic stem cell disorder with debilitating health consequences if untreated. Although cases have been described globally, precise epidemiological distribution is difficult to assess due to geographical underrepresentation in disease reporting. Evaluation of the burden of paroxysmal nocturnal hemoglobinuria in Bulgaria is currently missing. To provide epidemiological estimates, a systematic literature search for publications in the Bulgarian language or by Bulgarian authors was performed for a ten-year period (2013-2022), and clinically relevant information on case presentation was collected. Additionally, data was retrieved from the National Health Insurance Fund and National Statistical Institute on the count of registered cases with ICD-10 code "D59.5" and census for the same period. The estimated prevalence of paroxysmal nocturnal hemoglobinuria is relatively lower in the Bulgarian population than in other countries, and it is estimated to be 2.77 cases per 1,000,000 patient years. The treatment pattern mainly shows conventional blood product support use and is consistent with the pre-complement inhibition era. Underdiagnosis, lack of a reliable disease reporting system, and, until recently, restricted access to complement inhibitor therapy are significant impediments to the management of paroxysmal nocturnal hemoglobinuria in Bulgaria.

Challenges in diagnosis of Erdheim-chester disease: a case report

Background: Erdheim-Chester disease is a rare non-Langerhans cell histiocytosis characterized by the infiltration of lipid-laden macrophages into various tissues, leading to diverse clinical manifestations. Case Presentation: A 53-year-old male presented with a history of recurrent flank pain and obstructive uropathy over seven years, which led to multiple imaging studies and treatments for bilateral renal stones. Recent imaging, including a CT scan of the abdomen and pelvis, revealed bilateral perirenal soft tissue thickening extending into the renal sinus and pelvicalyceal systems, moderate hydronephrosis, and bilateral renal stones, suggestive of ECD. A CT-guided biopsy of the perinephric soft tissue confirmed the diagnosis. Histopathological analysis showed fibrofatty tissue with histiocytes exhibiting foamy cytoplasm, lymphocytes, plasma cells, and Touton cells. Immunohistochemistry stains were positive for Factor 13A and CD68 in histiocytes, confirming ECD. Conclusion: This case underscores the importance of considering ECD in patients with unexplained recurrent flank pain and renal abnormalities. Early recognition and biopsy are crucial for accurate diagnosis and management of this rare disease. The successful identification of ECD in this patient illustrates the critical role of advanced imaging and histopathological evaluation in diagnosing rare conditions.

Label-Free Microfluidic Apheresis of Circulating Tumor Cell Clusters.

Screening liters of blood (i.e., apheresis) represents a generalized approach to promote the reliable access to circulating tumor cell clusters (CTCCs), which are known to be highly metastasis-competent, yet ultrarare. However, no existing CTCC sorting technology has demonstrated high throughput, high yield, low shear stress, and minimal blood dilution simultaneously as required in apheresis. Here, a label-free method is introduced termed Precision Apheresis for Non-invasive Debulking of cell Aggregates (PANDA) to continuously isolate CTCCs from undiluted blood to clean buffer through size sorting, processing 1.4 billion cells per second. The cell focusing is optimized within whole blood leveraging secondary transverse flow and margination. The PANDA chip recovers >90% of spiked ≈24 rare HeLa cell clusters from 100mL undiluted blood samples (equivalent to ≈500 billion blood cells) at 1 Lh-1 throughput, with ≤20s device residence time, ≤15Pa shear stress, and >99.9% return of blood components. The technology lays the groundwork for future routine isolation to increase the recovery of these ultrarare yet clinically significant tumor cell populations from large volumes of blood to advance cancer research, early detection, and treatment.

Connectivity Network Feature Sharing in Single-Cell RNA Sequencing Data Identifies Rare Cells.

Single-cell RNA sequencing is a valuable technique for identifying diverse cell subtypes. A key challenge in this process is that the detection of rare cells is often missed by conventional methods due to low abundance and subtle features of these cells. To overcome this, we developed SCLCNF (Local Connectivity Network Feature Sharing in Single-Cell RNA sequencing), a novel approach that identifies rare cells by analyzing features uniquely expressed in these cells. SCLCNF creates a cellular connectivity network, considering how each cell relates to its neighbors. This network helps to pinpoint coexpression patterns unique to rare cells, utilizing a rarity score to confirm their presence. Our method performs better in detecting rare cells than existing techniques, offering enhanced robustness. It has proven to be effective in human gastrula data sets for accurately pinpointing rare cells, and in sepsis data sets where it uncovers previously unidentified rare cell populations.

ScDiffusion: conditional generation of high-quality single-cell data using diffusion model.

Single-cell RNA sequencing (scRNA-seq) data are important for studying the laws of life at single-cell level. However, it is still challenging to obtain enough high-quality scRNA-seq data. To mitigate the limited availability of data, generative models have been proposed to computationally generate synthetic scRNA-seq data. Nevertheless, the data generated with current models are not very realistic yet, especially when we need to generate data with controlled conditions. In the meantime, diffusion models have shown their power in generating data with high fidelity, providing a new opportunity for scRNA-seq generation. In this study, we developed scDiffusion, a generative model combining the diffusion model and foundation model to generate high-quality scRNA-seq data with controlled conditions. We designed multiple classifiers to guide the diffusion process simultaneously, enabling scDiffusion to generate data under multiple condition combinations. We also proposed a new control strategy called Gradient Interpolation. This strategy allows the model to generate continuous trajectories of cell development from a given cell state. Experiments showed that scDiffusion could generate single-cell gene expression data closely resembling real scRNA-seq data. Also, scDiffusion can conditionally produce data on specific cell types including rare cell types. Furthermore, we could use the multiple-condition generation of scDiffusion to generate cell type that was out of the training data. Leveraging the Gradient Interpolation strategy, we generated a continuous developmental trajectory of mouse embryonic cells. These experiments demonstrate that scDiffusion is a powerful tool for augmenting the real scRNA-seq data and can provide insights into cell fate research. scDiffusion is openly available at the GitHub repository https://github.com/EperLuo/scDiffusion or Zenodo https://zenodo.org/doi/10.5281/zenodo.13268742.

TFE3-rearranged nonmelanotic renal PEComa: a case series expanding their phenotypic and fusion landscape.

A subset of exceptionally rare primary renal perivascular epithelioid cell tumours (PEComas) that harbour Xp11.2 translocation have been reported, but no larger series devoted to this topic have been published. We describe the clinicopathological and molecular features of 10 renal PEComas, collected from our routine and consultation files. There were five female and five male patients aged 14-65 (median: 32 years). One patient had a history of childhood neuroblastoma, but no patients were known to have a tuberous sclerosis complex or other hereditary disorder. Complete surgical excision was the treatment for all patients. The available follow-up in five patients indicated a favourable outcome in 4/5 cases. Tumour size ranged from 2.8 to 15.2 cm (median, 5.2 cm). Immunohistochemistry revealed consistently strong TFE3 expression in all tumours, whereas PAX8 and keratin cocktails were uniformly negative. Other positive markers included HMB45 (7/9 tumours), CathepsinK (7/9 tumours), and CD117 (KIT) (3/5 tumours). TFE3 rearrangements were detected in 8/9 tumours (by targeted RNA sequencing in seven and by FISH in one). The identified fusion partners included SFPQ (n = 2) and one tumour each with ASPSCR1, ZC3H4, MED15, RBMX, and PRCC. One tumour that lacked TFE3 rearrangement by next-generation sequencing (NGS) and fluorescence in situ hybridization (FISH) revealed a large intrachromosomal deletion involving PKD1 and TSC2 by DNA-based NGS. This study highlights the morphologic and genetic diversity of TFE3-rearranged primary renal PEComas and underlines the value of surrogate TFE3 immunohistochemistry in identifying them. The lack of PAX8 and keratin expression represents the mainstay for distinguishing these tumours from MiTF-associated renal cell carcinomas. In addition, we report rare (ZC3H4, RBMX) and novel (MED15) TFE3 fusion partners in PEComa.