OBJECTIVE

To evaluate anti-cancer activity of Asparagus racemosus (AR) leaf extract on UOK146, a renal cell carcinoma cell line, and explore its mechanism of action.

METHODS

Dried AR leaves were extracted with chloroform and dissolved in DMSO. This extract was applied to UOK146 and cell death was estimated by MTT assay. In addition PRCC-TFE3 fusion transcripts were detected by real time PCR.

RESULTS

Extract was found to be cytotoxic with an IC50 of 0.9 mg/ml as estimated by dose response curve. Antitumor activity of the permissible doses of the extract was assessed by the down regulation of PRCC-TFE3 fusion transcript (38%) responsible for oncogenicity of the UOK146 cell line. No increment in the BAX, a proapoptotic marker level was observed.

CONCLUSIONS

Evidence of antiproliferative effect, PRCC-TFE3 fusion transcript inhibition and static BAX level clearly indicate that AR extract provides or elicits an apoptosis independent anticancer effect on RCC cells by some specific mechanism of regulation.

Monensin is a metal ionophore used as anticancer agent in many types of cancer cells. In this study, therapeutic potential of monensin was evaluated in TFE3 translocated renal cell carcinoma (RCC) cell line UOK146. UOK146 cells were treated with different concentrations of monensin, and cell death was induced as shown by MTT assay. Autophagy was studied by LC3 western, FACS and LC3 puncta formation after monensin treatment. Mitochondrial potential was studied by staining with TMRM and FACS. Antimetastatic potential of monensin was checked by inhibition of wound closure and MMP7 expression at RNA level. Dead and floating cells after the 10 μM monensin treatment were observed under phase contrast microscope. FACS analysis following TMRM staining showed that mitochondrial membrane gets depolarized after monensin treatment. FACS analysis after acridine orange staining showed increased double positive (green and red) cells, and LC3 upregulation and increased LC3 punta displayed autophagy activation in UOK146 cell line after monensin treatment. These findings showed that monensin acts as antiproliferative agent, activating autophagy and downregulates PRCC-TFE3 fusion transcript in Xp11.2 translocated tumor cell line.

Xp11 translocation renal cell carcinoma (RCC), a member of the microphthalmia-associated transcription factor (MiTF) family, is a rare renal tumor characterized by different translocations involving the TFE3 gene. Here, we reported a case of Xp11 translocation RCC with a rare MED15-TFE3 gene fusion by RNA sequencing. Morphologically, the tumor cells were arranged in a solid and small nest pattern. The cytoplasm was voluminous, flocculent eosinophilic, and vacuolated. The nuclei were round or polygon with fine granular chromatin, and the nucleoli were unconspicuous. Psammoma bodies were observed in mesenchyma. Immunohistochemically, the tumor cells were diffuse moderately or strongly positive for CD10, P504S, vimentin, PAX8, RCC, AE1/AE3, and SDHB and focally positive for CK7 and CA IX while negative for cathepsin K, HMB45, Melan-A, Ksp-cadherin, and CD117. The Ki67 proliferation index was approximately 3%. However, TFE3 labeling showed an uncertainly weak nuclear staining and been considered negative. Fluorescence in situ hybridization (FISH) demonstrated a positive result that splits signals with a distance of > 2 signal diameters. Subsequently, RNA sequencing confirmed a fusion of MED15 gene exon 11 on chromosome 22 with TFE3 gene exon 6 in the tumor. The patient was alive with no evidence of recurrence. Our report contributes to the understanding on MED15-TFE3 RCC.

OBJECTIVE

To investigate the significance of detecting chimeric mRNA resulting from t(X;17)(p11.2;q25) in paraffin-embedded tumor tissues of alveolar soft part sarcoma (ASPS).

METHODS

Formalin-fixed, paraffin-embedded tumor tissues from 8 cases of alveolar soft part sarcoma and 15 cases of controls (including 6 alveolar rhabdomyosarcomas, 6 renal cell carcinomas, 2 paragangliomas and 1 granular cell myoblastoma) were retrieved from the archival materials. ASPL-TFE3 fusion transcripts were analyzed in all samples by reverse transcriptase-polymerase chain reaction (RT-PCR). The quality of the mRNA was assessed using the house-keeping gene beta-actin.

RESULTS

ASPL-TFE3 fusion transcripts were detected in 6 of the 8 ASPS cases (4 being type 2 and 2 being type 1). The remaining 2 cases were negative for both beta-actin and ASPL-TFE3. No ASPL-TFE3 mRNA expression was detected in all the controls. PAX3/7-FKHR fusion transcripts were also detected in 4 of the 6 alveolar rhabdomyosarcoma samples.

CONCLUSIONS

The expression of ASPL-TFE3 fusion transcripts in paraffin-embedded tumor tissues can serve as an useful molecular marker in the diagnosis of ASPS. It may also be helpful in elucidating the underlying pathogenesis of ASPS in subsequent retrospective studies.

Alveolar soft part sarcoma (ASPS) that originates from the uterine cervix is extremely rare, with only thirteen cases reported. The participation of the ASPL-TFE3 chimeric gene, translocation (X; 17) (p11; q25), has been demonstrated in ASPS. Here, we report a case of cervical ASPS, along with a review of the literature. The patient, a 56-year-old woman, was referred for a 70 × 80 mm cervical tumor. She underwent a hysterectomy and bilateral salpingo-oophorectomy, and remained disease free for 66 months without adjuvant therapy. Pathological examination revealed features consistent with ASPS. In addition, the present case demonstrated strong positive nuclear staining for TFE3, and ASPL-TFE3 fusion gene type 1 was detected by RT-PCR. In a review of fourteen cases of this tumor (including the present case), the immunohistochemical expression patterns of myogenic or neuroendocrine markers were somewhat varied among cases. In all cases except for the present case, the patients were under 40 years of age, and the tumor sizes were under 5 cm. The prognosis of ASPS in the cervix was considerably better than that of ASPS in soft tissues. Complete resection with adequate margins is thought to be important, although the appropriate surgical method, including lymph node dissection, is uncertain. The role of chemotherapy or radiotherapy as adjuvant therapy has not been defined. Cervical ASPS is extremely rare, making case series the most viable option for understanding their natural history and for developing a treatment strategy, including an optimal surgical procedure and adjuvant therapy.

Alveolar soft part sarcoma (ASPS) is an uncommon neoplasm of uncertain histogenesis that usually behaves as a painless, slow-growing mass that metastasizes early. We report a 21-year-old woman with cutaneous metastases of ASPS, whose histologic characteristics gave rise to a wide range of differential diagnoses of both primary and metastatic cutaneous neoplasms. The tumor failed to show a characteristic immunoprofile using routine immunohistochemical procedures, but was strongly and diffusely positive for the TFE3 antibody. The molecular study identified a type 2 alveolar soft part locus-transcription factor E3 (ASPL-TFE3) fusion, secondary to der(17)t(X;17)(p11.2;q25) translocation. A computed tomography scan performed after the diagnosis was made disclosed a 13-cm primary tumor in the left buttock. Cutaneous metastases presenting as the first sign of ASPS have not been reported previously. We emphasize the difficulties in making the diagnosis of ASPS when it presents in an unusual manner.

We have carried out cytogenetic studies on a series of ten synovial sarcomas. Five of these tumours contained the characteristic reciprocal translocation t(X;18) (p11.2;q11.2) and a further two tumours contained complex rearrangements involving chromosomes X and 18. Secondary clonal alterations were seen in four tumours. Candidate genes at Xp11.2-p11.3 have been assessed for involvement in the translocation by Northern and Southern analysis: genes encoding transcription factors (ELK1 and TFE3), a metalloproteinase inhibitor (TIMP-1), a ubiquitin-activating enzyme (UBE1), a serine-threonine kinase (ARAF1) and the neural cell phosphoprotein synapsin 1 (SYN1). We found no evidence of abnormal transcription or rearrangements of these genes in a panel of synovial sarcoma biopsies and cell lines, indicating that they are not directly involved in the t(X;18) chromosome translocation.

Sarcomas encompass a broad group of malignant mesenchymal neoplasms, whose accurate diagnosis and classification relies on the integration of clinical, histopathological and molecular features. Our understanding of the latter has increased dramatically in recent years with the widespread application of high-throughput sequencing. Concomitantly, the role of immunohistochemistry has continued to expand, as many genomic alterations have been exploited by the development of novel diagnostic markers that act as surrogates for their detection. Herein, we review selected immunohistochemical markers that can infer the presence of diverse molecular events. These include gene fusions in vascular neoplasms (FOSB, CAMTA1 and TFE3), round cell sarcomas (BCOR, DUX4 and WT1), and fibroblastic/myofibroblastic tumors (STAT6, ALK and Pan-TRK); amplifications in well-differentiated and dedifferentiated liposarcomas (MDM2 and CDK4); and deletions in several aggressive neoplasms (SMARCB1 and SMARCA4). Protein correlates of single nucleotide variants (beta-catenin in desmoid fibromatosis) and epigenetic alterations (histone H3K27me3 in malignant peripheral nerve sheath tumor), as well as markers discovered through gene expression profiling (NKX2.2 and MUC4) are also discussed. While many of these new markers are transforming the practice of bone and soft tissue pathology, they are not without their own pitfalls and limitations, which are also highlighted. This article is protected by copyright. All rights reserved.

Alveolar soft part sarcoma (ASPS) is a rare malignant soft-tissue neoplasm of unknown histogenesis. The two main sites of occurrence are the lower extremities in adults and the head and neck in children. We report the first case of pleural ASPS occurring in a 58-yr-old man who presented with progressive dyspnea. A computed tomographic scan of the thorax revealed a large enhancing pleural mass with pleural effusion in the left hemithorax. Wide excision of the pleural mass was performed. Histologically, the tumor consisted of organoid nests of large polygonal cells, the cytoplasm of which had eosinophilic and D-PAS positive granules. Immunohistochemical staining showed that the tumor cell nuclei were positive for transcription factor 3 (TFE3). The pleural ASPS with multiple bone metastases recurred 1 yr after surgery and the patient died of acute pulmonary embolism 1.5 yr after diagnosis.

Only a few cases of sarcomatoid renal cell carcinomas (RCCs) with squamous differentiation have been published. We present 2 RCCs exhibiting a hitherto not reported biphasic neoplastic cell population exhibiting a predominantly alveolar architecture where squamoid differentiation was identified in one of the neoplastic cell populations. None of the tumors showed chromophobe features or any evidence of sarcomatoid transformation. The tumors arose in 2 adult patients and were characterized by routine histology, immunohistochemistry, ultrastructure, array comparative genomic hybridization, confirmatory fluorescent in situ hybridization, and loss of heterozygosity analysis. Tumors measured 3 and 4 cm and were located within the renal parenchyma and had no pelvicalyceal connection. Both tumors were composed of a distinctly dual-cell population. The larger tumor cells displayed squamoid features and formed round well-demarcated solid alveolated islands that, in large parts, were surrounded by a smaller neoplastic cell component. The squamoid cells were immunoreactive for cytokeratins (CKs) (AE1-AE3, Cam 5.2, CK5/6, CK7, and CK20), epithelial membrane antigen, racemase/AMACR, and carboanhydrase IX (in 1 case focally). The small cell population was positive for CK7, epithelial membrane antigen, and racemase/AMACR, whereas CK20, AE1-3, and carboanhydrase IX were negative. CD10 was focally positive in the large squamoid cells in 1 case. Cathepsin K, E-cadherin, and CD117 displayed focal positivity in 1 case. Vimentin, RCC marker, parvalbumin, S100 protein, S100 A1, p63, p53, CDX2, uroplakin III, HMB45, TFE3, WT1, synaptophysin, chromogranin A, thyroglobulin, and TTF1 were negative. The proliferative activity (Ki-67) was low (1%) in the small cell component in both cases, whereas the large neoplastic tumor cells displayed a significantly higher proliferation (20%-35%). Ultrastructurally, desmosomes and tonofilaments were identified in the large tumor cells, confirming squamoid differentiation in a subset of tumor cells. Array comparative genomic hybridization of 1 analyzable case (confirmed with fluorescent in situ hybridization and loss of heterozygosity analysis) revealed partial or complete losses of chromosomes 2, 5, 6, 9, 12, 15, 16, 17, 18 and 22, (including biallelic loss of CDKN2A locus) and partial gains of chromosomes 1, 5, 11, 12 and 13. Follow-up at 6 years showed no recurrence or metastasis in 1 patient. The other (male) patients had a subcutaneous metastasis at presentation, but during a 1-year follow-up no evidence of recurrence or further metastatic events have been documented. Our data indicate that biphasic alveolosquamoid renal carcinoma is a unique and distinctive tumor. The large squamoid and small tumor cells have overlapping but still distinctive immunohistochemical patterns of protein expression. Multiple chromosomal aberrations were identified, some of them located in regions with known tumor suppressor genes and oncogenes.

The Microphthalmia-associated transcription factor (MITF) is at the core of melanocyte and melanoma fate specification. The related factors TFEB and TFE3 have been shown to be instrumental for transcriptional regulation of genes involved in lysosome biogenesis and autophagy, cellular processes important for mediating nutrition signals and recycling of cellular materials, in many cell types. The MITF, TFEB, TFE3 and TFEC proteins are highly related. They share many structural and functional features and are targeted by the same signaling pathways. However, the existence of several isoforms of each factor and the increasing number of residues shown to be post-translationally modified by various signaling pathways poses a difficulty in indexing amino acid residues in different isoforms across the different proteins. Here we provide a resource manual to cross-reference amino acids and post-translational modifications in all isoforms of the MiT-TFE family in humans, mice and zebrafish and summarize the protein accession numbers for each isoform of these factors in the different genomic databases. This will facilitate future studies on the signaling pathways that regulate different isoforms of the MiT-TFE transcription factor family.

Clear cell renal cell carcinoma (ccRCC), the most common histologic subtype of RCCs, demonstrates a wide spectrum of morphologic features (i.e., low-grade spindle cell, syncytial giant cells, and mucin-producing cells). However, papillary growth pattern in ccRCCs is rather a rare finding, which can present challenges in differential diagnostic work up. The aim of this study was to investigate ccRCCs with predominant papillary features from morphologic, immunohistochemical and molecular genetic perspectives. 23 clear cell renal cell carcinomas with papillary architecture were selected. Tumors were evaluated morphologically, immunohistochemically, and molecularly by next-generation sequencing (NGS). The diagnosis of MiT family translocation RCC was excluded by TFE3 immunohistochemistry. Mean age of patients was 65.2 years (range 42-81 years), and 19/23 were male. Tumor size ranged from 1.6 to 12.8 cm (median 6.5 cm). At a median follow-up of 2.5 years (range 1.5-9 years), 2 patients (8.7%) died of disease, 2 developed metastasis. Areas of papillary pattern accounted for approximately 40-100% of the tumor. CK7 was negative in non-papillary areas in majority of cases (20/23, 87%), and was only focally positive in 3/23 cases (13%). In papillary areas, AMACR was positive/focally positive in 17/23 (73.9%) cases and in the non-papillary areas it was positive/focally positive in 22/23 (95.6%) cases. CAIX was mainly negative in both non-papillary and papillary areas (15/23 [65%] and 16/23 [69.5%], respectively). Molecular analysis of 15 analyzable cases revealed the most frequently mutated gene to be VHL (in 9 cases), followed by PRBM1 (in 2 cases) and 29 other different mutations in various genes. Papillary growth pattern in ccRCC is not an uncommon situation. Papillary RCC with clear cells and MiT family (TFE3) translocation RCCs are the major differential diagnostic considerations in such scenarios. Our NGS molecular analysis supported classifying such tumors as a morphologic variant of ccRCC.

Juxtaglomerular cell tumor (JGCT) is a rare tumor, with approximately 100 cases reported in the literature. The authors respectively studied the clinical data of 11 patients diagnosed with JGCT in Peking Union Medical College Hospital from 2004 to 2014, and investigated the immunohistochemical profiles in 10 tumors. Nine of the 11 patients were diagnosed before the age of 40 years. Hypertension was present in all patients, while hypokalemia occurred in seven of 11 patients. Computed tomography detected JGCTs with a sensitivity of 100%. Immunoreactivities for CD34 and vascular endothelial growth factor were observed in most tumor specimens, suggesting that JGCTs express a variety of vessel-related immunohistochemical markers, although JGCTs are considered a tumor without abundant blood supply. Nuclear accumulation of cyclin D1 was common in JGCTs. Results from immunohistochemistry were negative for BRAF, HER2, and TFE3, suggesting that BRAF, HER2, and TFE3 genes might not play a part in tumorigenesis in JGCTs.

Increasing evidence indicates that pyroptosis, a new type of programmed cell death, may participate in random flap necrosis and play an important role. ROS-induced lysosome malfunction is an important inducement of pyroptosis. Transcription factor E3 (TFE3) exerts a decisive effect in oxidative metabolism and lysosomal homeostasis. We explored the effect of pyroptosis in random flap necrosis and discussed the effect of TFE3 in modulating pyroptosis. Histological analysis via hematoxylin-eosin staining, immunohistochemistry, general evaluation of flaps, evaluation of tissue edema, and laser Doppler blood flow were employed to determine the survival of the skin flaps. Western blotting, immunofluorescence, and enzyme-linked immunosorbent assays were used to calculate the expressions of pyroptosis, oxidative stress, lysosome function, and the AMPK-MCOLN1 signaling pathway. In cell experiments, HUVEC cells were utilized to ensure the relationship between TFE3, reactive oxygen species (ROS)-induced lysosome malfunction and cell pyroptosis. Our results indicate that pyroptosis exists in the random skin flap model and oxygen and glucose deprivation/reperfusion cell model. In addition, NLRP3-mediated pyroptosis leads to necrosis of the flaps. Moreover, we also found that ischemic flaps can augment the accumulation of ROS, thereby inducing lysosomal malfunction and finally initiating pyroptosis. Meanwhile, we observed that TFE3 levels are interrelated with ROS levels, and overexpression and low expression of TFE3 levels can, respectively, inhibit and promote ROS-induced lysosomal dysfunction and pyroptosis during in vivo and in vitro experiments. In conclusion, we found the activation of TFE3 in random flaps is partially regulated by the AMPK-MCOLN1 signal pathway. Taken together, TFE3 is a key regulator of ROS-induced pyroptosis in random skin flaps, and TFE3 may be a promising therapeutic target for improving random flap survival.

Keywords: AMPK-MCOLN1 signaling pathway; ROS; TFE3; pyroptosis; random skin flap.

Perivascular epithelioid cell tumors (PEComas) are rarely found in the urinary tract. The clinicopathologic characteristics of 10 cases, retrospectively collected from 5 medical institutions in 3 different European countries, are presented in this study. Male/female ratio was 3:7 and the average age at diagnosis was 62.7 years. Nine cases were sporadic and 1 showed germline mutation of the TSC2 gene. Eight cases were located in the kidney, 1 in the left adrenal and 1 in the right ureter. All of the patients were alive and free of disease at the time of last contact (mean follow-up, 14.1 mo). Four cases displayed a conventional morphology and 6 showed a prominent sclerotic stroma. By immunohistochemistry, melanocytic markers were consistently expressed, especially HMB-45 (10 cases), MiTF (9 cases), and Melan-A (6 cases). Desmin was expressed in 6 cases; 2 cases were positive for CD117; a single case showed TFE3 expression. pMAPK, mTOR, and pAKT demonstrated variable immunostaining with focal positivity in 7, 4, and 2 cases, respectively. Cytokeratins were repeatedly negative in all cases. PEComas in the urinary tract, especially in the renal region, may show a relatively high frequency of the sclerosing histologic subtype. Knowledge of the distinct histology and immunohistochemical profile is vital to correctly diagnose this rare entity.

Alveolar soft part sarcoma (ASPS) is a rare, malignant mesenchymal tumor of distinctive clinical, morphologic, ultrastructural, and cytogenetical characteristics. It typically arises in the extremities of adolescents and young adults, but has also been documented in a number of unusual sites, thus causing diagnostic confusions both clinically and morphologically. The molecular signature of ASPS is a specific der(17)t(X;17)(p11.2;q25) translocation, which results in the fusion of TFE3 transcription factor gene at Xp11.2 with ASPL at 17q25. Recent studies have shown that the ASPL-TFE3 fusion transcript can be identified by reverse-transcriptase polymerase chain reaction analysis and TFE3 gene rearragement can be detected using a dual-color, break apart fluorescence in situ hybridization assay in paraffin-embedded tissue, and the resultant fusion protein can be detected immunohistochemically with antibody directed to the carboxy terminal portion of TFE3. Herein, we report a unique case of ASPS presenting as an asymptomatic mass in the lung of a 48 year-old woman without evidence of a primary soft tissue tumor elsewhere at the time of initial diagnosis. To the best of our knowledge, this is the third report of such cases appearing in the English language literature to date. We emphasize the differential diagnoses engendered by ASPS including a series of tumors involving the lung that have nested and alveolar growth patterns, and both clear and eosinophilic cytoplasm, and demonstrate the utility of molecular genetic analysis for TFE3 rearrangement and immunohistochemistry for TFE3 antigen expression for arriving at accurate diagnosis.

Ossifying fibromyxoid tumor (OFMT) is a rare soft tissue neoplasm of uncertain differentiation and intermediate biologic potential. Up to 85% of OFMTs, including benign, atypical and malignant forms, harbor fusion genes. Most commonly, the PHF1 gene localized to 6p21 is fused with EP400, but other fusion partners such as MEAF6, EPC1, and JAZF1 have also been described. Herein, we present two rare cases of superficial OFMTs with ZC3H7B-BCOR and the very recently described PHF1-TFE3 fusions. The latter also exhibited moderate to strong diffuse immunoreactivity for TFE3. Reciprocally this finding expands the entities with TFE3 rearrangements. Accumulation of additional data is necessary to determine if OFMTs harboring these rare fusions feature any reproducible clinicopathologic findings or carry prognostic and/or predictive implications. This article is protected by copyright. All rights reserved.

Alveolar soft-part sarcoma (ASPS) is a rare malignant soft tissue tumor of uncertain cellular origin. We reported the case of a 21-year-old man with ASPS presenting itself as a markedly vascular tumor of the prostate. Immunohistochemistry showed positive nuclear staining for TFE3, positive cytoplasm staining for MyoD1 and neuron-specific enolase, and negative for S100, CK, synaptophysin, chromogranin A, myogenin and PSA. A dual-color, break-apart fluorescence in situ hybridization (FISH) assay identified the presence of a TFE3 gene fusion in the tumor cells. RT-PCR was performed to confirm the ASPSCR1 (ASPL)/TFE3 fusion transcript product in the tumor tissue. The patient suffered bone metastases 8 months after surgery and died of cachexia 14 months later. ASPS of the prostate should be discussed in terms of differential diagnosis from clinicopathological characteristics, immunophenotypes, and molecular genetic features.

The tuberous sclerosis genes and MTOR are increasingly being found to have important roles in novel subtypes of renal cancer, particularly emerging entities eosinophilic solid and cystic renal cell carcinoma (RCC) and high-grade oncocytic renal tumor (HOT) / RCC with eosinophilic and vacuolated cytoplasm. We report a unique renal neoplasm in a 66 year-old woman that initially mimicked MITF family translocation RCC due to mixed clear and eosinophilic cells, extensive stromal hyalinization, and psammoma bodies, yet which was negative for TFE3 and TFEB fluorescence in situ hybridization (FISH) and a next generation sequencing (NGS) gene fusion assay. Cytoplasmic stippling triggered consideration of TSC-associated neoplasms, and a targeted next generation sequencing assay revealed a variant in exon 21 of TSC1 resulting in c.2626G > T p.(Glu876*) truncating mutation. This report adds to the morphologic spectrum of TSC-related renal neoplasms, including prominent stromal hyalinization as a potentially deceptive pattern. Due to the overlap in cytoplasmic stippling between eosinophilic solid and cystic RCC and HOT / RCC with eosinophilic and vacuolated cytoplasm, it is debatable which category this example would best fit. Further understanding of these entities and other renal neoplasms with alterations in the TSC genes will elucidate whether they should be considered a family of tumors. This article is protected by copyright. All rights reserved.

A distinct renal tumor has recently been described as "high-grade oncocytic renal tumor" and "sporadic renal cell carcinoma with eosinophilic and vacuolated cytoplasm". The Genitourinary Pathology Society (GUPS) consensus proposed a unifying name "eosinophilic vacuolated tumor" (EVT) for this emerging entity. In this multi-institutional study, we evaluated 19 EVTs, particularly their molecular features and mutation profile, using next-generation sequencing. All cases were sporadic and none of the patients had a tuberous sclerosis complex. There were 8 men and 11 women, with a mean age of 47 years (median 50; range 15-72 years). Average tumor size was 4.3 cm (median 3.8 cm; range 1.5-11.5 cm). All patients with available follow-up data (18/19) were alive and without evidence of disease recurrence or progression during the follow-up, ranging from 12 to 198 months (mean 56.3, median 41.5 months). The tumors were well circumscribed, but lacked a well-formed capsule, had nested to solid growth, focal tubular architecture, and showed ubiquitous, large intracytoplasmic vacuoles, round to oval nuclei, and prominent nucleoli. Immunohistochemically, cathepsin K, CD117, CD10, and antimitochondrial antigen were expressed in all cases. Other positive stains included: PAX8, AE1/AE3 and CK18. CK7 was typically restricted only to rare scattered cells. Vimentin, HMB45, melan-A, and TFE3 were negative in all cases. All tumors showed retained SDHB. All cases (19/19) showed non-overlapping mutations of the mTOR pathway genes: TSC1 (4), TSC2 (7), and MTOR (8); one case with MTOR mutation showed a coexistent RICTOR missense mutation. Low mutational rates were found in all samples (ranged from 0 to 6 mutations/Mbp). Microsatellite instability and copy number variations were not found in any of the 17 analyzable cases. EVT represents an emerging renal entity that shows a characteristic and readily identifiable morphology, consistent immunohistochemical profile, indolent behavior, and mutations in either TSC1, TSC2, or MTOR genes.

Aims: Translocation-associated renal cell carcinomas (RCCs) have been extensively subcharacterized in recent years, such that each is largely recognized by the 2016 World Health Organization as categorical neoplastic entities in the genitourinary tract. Those belonging to the t(6;11) family of tumors classically have a fusion between TFEB and MALAT1/α, and display a particular histomorphology. Specifically, they show a biphasic population of both small and large epithelioid cells, the smaller component of which surrounds basement membrane-type material. Despite this apt description, the tumors have variable morphology and mimic other RCCs including those with TFE3 translocations. Therefore, a high degree of suspicion is required to make the correct diagnosis.

Methods: The 2 cases described in this article were of strikingly different appearance, and initially considered consistent with other non-translocation-associated renal tumors. These included clear cell RCC (CCRCC), perivascular epithelioid cell tumor (PEComa), and other eosinophilic RCCs (mainly papillary RCC type 2).

Results: Using RNA sequencing techniques, they were found to harbor distinct pathogenic rearrangements involving the TFEB gene, namely, fusions with CLTC and NEAT1 (the latter partnering heretofore never reported).

Conclusions: These alterations manifested in 2 notably dissimilar lesions, underscoring the importance of including this family of carcinomas in the differential of any renal neoplasm that does not display immunophenotypic characteristics consistent with its morphology.

Keywords: CLTC; MiTF; NEAT1; TFE3; TFEB; renal cell carcinoma; translocation; α/MALAT1.

MiT family translocation renal cell carcinoma (MiT-RCC) harbors translocations involving the TFE3 or TFEB genes. RCC with TFEB amplification is also identified and is associated with a more aggressive clinical course. Accurate diagnosis of MiT-RCC is crucial for patient management. In this study, we evaluated the performance of the Archer FusionPlex assay for detection of MiT-RCC with TFE3 or TFEB translocations and TFEB amplifications. RNA was extracted from 49 RCC FFPE tissue samples with known TFE3/TFEB status (26 TFE3 FISH positive, 12 TFEB FISH positive, 4 TFEB amplified (1 case both split and amplified), and 8 FISH negative) using the Covaris extraction kit. Target enriched cDNA libraries were prepared using the Archer FusionPlex kit and sequenced on the Illumina NextSeq 550. We demonstrate that the age of the specimen, quality of RNA, and sequencing metrics are important for fusion detection. Fusions were identified in 20 of 21 cases less than 2 years old, and TFE3/TFEB rearrangements were detected in all cases with Fusion QC ≥ 100. The assay identified intrachromosomal inversions in two cases (TFE3-RBM10 and NONO-TFE3), usually difficult to identify by FISH assays. TFEB mRNA expression and the TFEB/TFE3 mRNA expression ratio were significantly higher in RCCs with TFEB fusion and TFEB gene amplification compared to tumors without TFEB fusion or amplification. A cutoff TFEB/TFE3 ratio of 0.5 resulted in 97.3% concordance to FISH results with no false negatives. Our study demonstrates that the FusionPlex assay successfully identifies TFE3 and TFEB fusions including intrachromosomal inversions. Age of the specimen and certain sequencing metrics are important for successful fusion detection. Furthermore, mRNA expression levels may be used for predicting cases harboring TFEB amplification, thereby streamlining testing. This assay enables accurate molecular detection of multiple subtypes of MiT-RCCs in a convenient workflow.

Macroautophagy/autophagy is a cellular catabolic process that results in lysosome-mediated recycling of organelles and protein aggregates, as well as the destruction of intracellular pathogens. Its role in the maintenance of the intestinal epithelium is of particular interest, as several autophagy-related genes have been associated with intestinal disease. Autophagy and its regulatory mechanisms are involved in both homeostasis and repair of the intestine, supporting intestinal barrier function in response to cellular stress through tight junction regulation and protection from cell death. Furthermore, a clear role has emerged for autophagy not only in secretory cells but also in intestinal stem cells, where it affects their metabolism, as well as their proliferative and regenerative capacity. Here, we review the physiological role of autophagy in the context of intestinal epithelial maintenance and how genetic mutations affecting autophagy contribute to the development of intestinal disease.Abbreviations: AKT1S1: AKT1 substrate 1; AMBRA1: autophagy and beclin 1 regulator 1; AMPK: AMP-activated protein kinase; APC: APC regulator of WNT signaling pathway; ATF6: activating transcription factor 6; ATG: autophagy related; atg16l1[ΔIEC] mice: mice with a specific deletion of Atg16l1 in intestinal epithelial cells; ATP: adenosine triphosphate; BECN1: beclin 1; bsk/Jnk: basket; CADPR: cyclic ADP ribose; CALCOCO2: calcium binding and coiled-coil domain 2; CASP3: caspase 3; CD: Crohn disease; CDH1/E-cadherin: cadherin 1; CF: cystic fibrosis; CFTR: CF transmembrane conductance regulator; CGAS: cyclic GMP-AMP synthase; CLDN2: claudin 2; CoPEC: colibactin-producing E. coli; CRC: colorectal cancer; CYP1A1: cytochrome P450 family 1 subfamily A member 1; DC: dendritic cell; DDIT3: DNA damage inducible transcript 3; DEPTOR: DEP domain containing MTOR interacting protein; DSS: dextran sulfate sodium; EGF: epidermal growth factor; EGFR: epidermal growth factor receptor; EIF2A: eukaryotic translation initiation factor 2A; EIF2AK3: eukaryotic translation initiation factor 2 alpha kinase 3; EIF2AK4/GCN2: eukaryotic translation initiation factor 2 alpha kinase 4; ER: endoplasmic reticulum; ERN1: endoplasmic reticulum to nucleus signaling 1; GABARAP: GABA type A receptor-associated protein; HMGB1: high mobility group box 1; HSPA5/GRP78: heat shock protein family A (Hsp70) member 5; IBD: inflammatory bowel disease; IEC: intestinal epithelial cell; IFN: interferon; IFNG/IFNγ:interferon gamma; IL: interleukin; IRGM: immunity related GTPase M; ISC: intestinal stem cell; LGR5: leucine rich repeat containing G protein-coupled receptor 5; LRRK2: leucine rich repeat kinase 2; MAP1LC3A/LC3: microtubule associated protein 1 light chain 3 alpha; MAPK/JNK: mitogen-activated protein kinase; MAPK14/p38 MAPK: mitogen-activated protein kinase 14; MAPKAP1: MAPK associated protein 1; MAVS: mitochondrial antiviral signaling protein; miRNA: microRNA; MLKL: mixed lineage kinase domain like pseudokinase; MLST8: MTOR associated protein, LST8 homolog; MNV: murine norovirus; MTOR: mechanistic target of rapamycin kinase; NBR1: NBR1 autophagy cargo receptor; NLRP: NLR family pyrin domain containing; NOD: nucleotide binding oligomerization domain containing; NRBF2: nuclear receptor binding factor 2; OPTN: optineurin; OXPHOS: oxidative phosphorylation; P: phosphorylation; Patj: PATJ crumbs cell polarity complex component; PE: phosphatidyl-ethanolamine; PI3K: phosphoinositide 3-kinase; PIK3C3/VPS34: phosphatidylinositol 3-kinase catalytic subunit type 3; PIK3R4: phosphoinositide-3-kinase regulatory subunit 4; PPARG: peroxisome proliferator activated receptor gamma; PRR5: proline rich 5; PRR5L: proline rich 5 like; PtdIns3K: phosphatidylinositol 3-kinase; PtdIns3P: phosphatidylinositol 3-phosphate; RB1CC1/FIP200: RB1 inducible coiled-coil 1; RER: rough endoplasmic reticulum; RHEB: Ras homolog, MTORC1 binding; RICTOR: RPTOR independent companion of MTOR complex 2; RIPK1: receptor interacting serine/threonine kinase 1; ROS: reactive oxygen species; RPTOR: regulatory associated protein of MTOR complex 1; RPS6KB1: ribosomal protein S6 kinase B1; SH3GLB1: SH3 domain containing GRB2 like, endophilin B1; SNP: single-nucleotide polymorphism; SQSTM1: sequestosome 1; STAT3: signal transducer and activator of transcription 3; STING1: stimulator of interferon response cGAMP interactor 1; TA: transit-amplifying; TFEB: transcription factor EB; TFE3: transcription factor binding to IGHM enhancer 3; TGM2: transglutaminase 2; TJ: tight junction; TJP1/ZO1: tight junction protein 1; TNBS: 2,4,6-trinitrobenzene sulfonic acid; TNF/TNFα: tumor necrosis factor; Tor: target of rapamycin; TRAF: TNF receptor associated factor; TRIM11: tripartite motif containing 11; TRP53: transformation related protein 53; TSC: TSC complex subunit; Ub: ubiquitin; UC: ulcerative colitis; ULK1: unc-51 like autophagy activating kinase 1; USO1/p115: USO1 vesicle transport factor; UVRAG: UV radiation resistance associated; WIPI: WD repeat domain, phosphoinositide interacting; WNT: WNT family member; XBP1: X-box binding protein 1; ZFYVE1/DFCP1: zinc finger FYVE-type containing 1.

Keywords: Autophagy; Crohn disease; IBD; MTOR; intestinal epithelium; intestinal stem cells.