Alveolar soft part sarcoma (ASPS) is a very rare sarcoma, report <1% of all soft tissue tumor. Majority of cases were young adult and tumor occurred in lower extremities and trunk. Here, we present a case of 53-year-old Thai female with rapidly glowing mass over her right forearm. The magnetic resonance imaging scan demonstrated a hypervascular mass with multiple feeding vessels located in flexure tendon of right forearm. Ultrasound-guided biopsy revealed malignant poorly differentiated epithelioid neoplasm with clear cell feature and focal necrosis. Surgery may be considered the first-line treatment in localized ASPS and may potentially increase long-term survival. Complete surgical excision is the mainstay of treatment. TFE3 and Cathepsin K immunohistochemistry are useful in confirming a diagnosis of ASPS with a distinctive clinicopathologic features.

Immunosenescence in monocytes has been shown to be associated with several biochemical and functional changes, including development of senescence-associated secretory phenotype (SASP), which may be inhibited by klotho protein. To date, it was believed that SASP activation is associated with accumulating DNA damage. However, some literature data suggest that endoplasmic reticulum and Golgi stress pathways may be involved in SASP development. Thus, the aim of this study was to investigate the role of klotho protein in the regulation of immunosenescence-associated Golgi apparatus and ER stress response induced by bacterial antigens in monocytes. We provide evidence that initiation of immunosenescent-like phenotype in monocytes is accompanied by activation of CREB34L and TFE3 Golgi stress response and ATF6 and IRE1 endoplasmic reticulum stress response, while klotho overexpression prevents these changes. Further, these changes are followed by upregulated secretion of proinflammatory cytokines, which final modification takes place exclusively in the Golgi apparatus. In conclusion, we provide for the first time evidence of klotho involvement in the crosstalk on the line ER-Golgi, which may, in turn, affect activation of SASP. This data may be useful for a novel potential target for therapy in age-related and chronic inflammatory conditions.

Alveolar soft-part sarcoma is a rare neoplasm of unknown histogenesis that accounts for less than 1% of all soft-tissue sarcomas. The tumor is highly vascularized with small vascular spaces separating nests of cells, and from cytogenetic point of view, is characterized by chromosome rearrangement der(17)t(X:17)(p11:q25) that results in the ASPL-TFE3 translocation. It can occur at any age, but it is most common between 15 and 35 years of age. The prognosis is poor, despite the relatively slow growth of the tumor. We present here an atypical case of alveolar soft-part sarcoma in which the age of the patient, the location, and the histopathologic characteristics of the lesion represented a diagnostic challenge.

Alveolar soft part sarcoma (ASPS) is an exceptionally rare non-rhabdomyosarcomatous soft tissue sarcoma (NRSTS), characterized by the translocation t(X;17) p(11.2;q25). This translocation results in the chimeric ASPSCR1-TFE3 transcription factor which drives tumorigenesis. Complete surgical resection is crucial in allowing a successful outcome in these cases. Here, we describe an 11-month-old female infant who presented with a well-circumscribed lesion of the tongue, with the clinical and radiologic appearances of an infantile hemangioma. This led to an initial plan for surveillance management. However, the mass continued to enlarge and the lesion was therefore biopsied when the infant was 17 months old. Histology showed plump epithelioid tumor cells, in many places lining pseudoalveolar spaces. Occasional Pas-D inclusions were present in the cytoplasm. Immunostaining showed nuclear positivity for TFE-3. Real-time quantitative polymerase chain reaction testing confirmed the presence of ASPSCR1-TFE3 fusion transcripts, characteristic of the translocation t(X;17) p(11.2;q25) observed in ASPS. This represents the youngest reported ASPS case with a confirmed molecular diagnosis. Complete surgical resection was undertaken and a surveillance imaging schedule implemented. This case highlights the need for regular review of the initial diagnosis and the importance of multidisciplinary discussion and early biopsy where the clinical course does not follow that expected for the putative (nonhistologically confirmed) diagnosis.

GGGGCC repeat expansion in C9orf72 is the most common genetic cause in both frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS), two neurodegenerative disorders in association with aging. Bidirectional repeat expansions in the noncoding region of C9orf72 have been shown to produce dipeptide repeat (DPR) proteins through repeat-associated non-ATG (RAN) translation and to reduce the expression level of the C9orf72 gene product, C9orf72 protein. Mechanisms underlying C9orf72-linked neurodegeneration include expanded RNA repeat gain of function, DPR toxicity, and C9orf72 protein loss of function. In the current study, we focus on the cellular function of C9orf72 protein. We report that C9orf72 can regulate lysosomal biogenesis and autophagy at the transcriptional level. We show that loss of C9orf72 leads to striking accumulation of lysosomes, autophagosomes, and autolysosomes in cells, which is associated with suppressed mTORC1 activity and enhanced nuclear translocation of MiT/TFE family members MITF, TFE3, and TFEB, three master regulators of lysosomal biogenesis and autophagy. We demonstrate that the DENN domain of C9orf72 specifically binds to inactive Rag GTPases, but not active Rag GTPases, thereby affecting the function of Rag/raptor/mTOR complex and mTORC1 activity. Furthermore, active Rag GTPases, but not inactive Rag GTPases or raptor rescued the impaired activity and lysosomal localization of mTORC1 in C9orf72-deficient cells. Taken together, the present study highlights a key role of C9orf72 in lysosomal and autophagosomal regulation, and demonstrates that Rag GTPases and mTORC1 are involved in C9orf72-mediated autophagy.

Differentiating neutrophils undergo large-scale changes in nuclear morphology. How such alterations in structure are established and modulated upon exposure to microbial agents is largely unknown. Here, we found that prior to encounter with bacteria, an armamentarium of inflammatory genes was positioned in a transcriptionally passive environment suppressing premature transcriptional activation. Upon microbial exposure, however, human neutrophils rapidly (<3 h) repositioned the ensemble of proinflammatory genes toward the transcriptionally permissive compartment. We show that the repositioning of genes was closely associated with the swift recruitment of cohesin across the inflammatory enhancer landscape, permitting an immediate transcriptional response upon bacterial exposure. We found that activated enhancers, marked by increased deposition of H3K27Ac, were highly enriched for cistromic elements associated with PU.1, CEBPB, TFE3, JUN, and FOSL2 occupancy. These data reveal how upon microbial challenge the cohesin machinery is recruited to an activated enhancer repertoire to instruct changes in chromatin folding, nuclear architecture, and to activate an inflammatory gene program.

Renal cell carcinoma (RCC) is rare in children. Unlike nephroblastoma, however, it does not respond well to chemoradiotherapy. Its treatment is therefore based on surgical removal of the tumour. However, lymphadenectomy for RCC is controversial, and its prognosis is unclear. The authors report a case of RCC with MiTF/TFE3 translocation at the stage of lymph node involvement without metastasis in a boy of age 12, who was treated with radical nephrectomy and limited lymphadenectomy. This tumour constitutes a newly individualised entity in the World Health Organization's 2004 classification. Eighteen months after the operation, the patient was presented with no sign of recurrence. This case aids in showing that lymph node involvement in RCC with translocation in children is not associated with a poor prognosis and that lymphadenectomy during surgery for enlarged nephrectomy is essential.

Background: Non-small cell lung carcinoma (NSCLC) is often fatal; advanced NSCLC has a 5-year survival rate less than 20%. Platinum-based chemotherapy, in particular, cis-diamminedichloroplatinum (II) (cisplatin or DDP), is employed for the treatment of NSCLC; however, the drug resistance occurs frequently. Autophagy is defined as the process of intracellular degradation of cytoplasmic materials in the lysosome; however, the correlation between autophagy and drug resistance remains controversial. Herein, we investigated the correlation between autophagy and cisplatin resistance and also explored the underlying mechanisms.

Methods and results: We demonstrated that DDP-resistant NSCLC A549 (A549/DDP) cells had higher autophagy activity in comparison with its parental A549 cells; DDP treatment induced a time- and dose-dependent decrease of autophagy. Intriguingly, inhibition of autophagy with pharmacological drugs or knockdown of ATG5 or Beclin-1 aggravated cell death induced by DDP treatment, indicating that autophagy played protective roles during DDP treatment. Further mechanistic investigation revealed that DDP treatment could decrease the mRNA expression level of key autophagy-related genes, such as ATG5, Beclin-1, and ATG7, suggesting DDP repressed autophagy at the transcriptional level. The MiTF/TFE family (including TFEB, TFE3, TFEC, and MiTF) were involved in nutrient sensing and organelle biogenesis, and specifically, the lysosomal biogenesis. We found that only MiTF was dramatically decreased upon DDP treatment, and also a profound decrease of lysosomal markers, LAMP-1 or LAMP-2, suggesting that MiTF was involved in the modulation of lysosomal biogenesis and, consequently, the autophagy. Moreover, the knockdown of MiTF resulted in more severe cell death in A549/DDP cells, indicting the substantial correlation between MiTF and cisplatin chemoresistance.

Conclusion: Our study provides novel insights into the association between MiTF and DDP chemoresistance in NSCLC cells, and suggests targeting MiTF and/or autophagy might be a potential strategy for the reversal of DDP chemoresistance for NSCLC treatment.

Keywords: MiTF; NSCLC; autophagy; chemoresistance; cisplatin.

Aims: Xp11 translocation renal cell carcinoma (RCC) is a distinctive subtype of RCC with TFE3 (Transcription Factor Binding to IGHM Enhancer 3) gene rearrangement. The gross features in most Xp11 translocation RCCs closely resemble clear cell RCCs. In this study, we report six cases of Xp11 translocation RCCs with a unique multicystic architecture, reminiscent of multilocular cystic renal cell neoplasm of low malignant potential (MCRN-LMP).

Methods and results: Microscopically, the renal mass was well circumscribed with multilocular cystic architecture. The cyst walls and septa were mostly lined by a single layer of cells with clear cytoplasm and low-grade nuclei, reminiscent of MCRN-LMP. Psammoma bodies were detected in four cases. One particular patient was misdiagnosed with benign cysts in local hospitals and led to second operation. Tumour cells were settled according to the track of the first surgical procedure. TFE3 fluorescence in situ hybridization (FISH) assay confirmed the diagnosis of Xp11 translocation RCCs. FISH and RNA sequencing analyses confirmed MED15-TFE3 gene fusion in all six cases. Respective patients were alive, without any recent evidence of disease recurrence and/or metastasis.

Conclusions: Here, we introduce a relatively inertia-variant of Xp11 translocation RCC which mimics MCRN-LMP. The distinctive morphological condition is linked to MED15-TFE3 gene fusion. In fact, renal neoplasms with morphological features of MCRN-LMP, especially those containing psammoma bodies, should be routinely evaluated for evidence of TFE3 gene rearrangements.

Keywords: genetics; kidney neoplasms; morphological and microscopic findings.

The microphthalmia of bHLH-LZ transcription factor (MiT/TFE) family chromosomal translocation or overexpression is linked with a poor prognosis in clear cell renal cell carcinoma (ccRCC) with elevated recurrence and drug resistance, but the molecular mechanism is not fully understood. Here, we investigated whether the resistance to sunitinib (Sun), the standard treatment for metastatic ccRCC, is due to up-regulation of programmed death ligand 1 (PD-L1) by the transcription factor E3 (TFE3). In this study, we propose that TFE3 but not TFEB is essential for tumour survival which was associated with the poorer survival of cancer patients. We also found a positive correlation between TFE3 and PD-L1 expression in ccRCC cells and tissues. Sun treatment led to enhanced TFE3 nuclear translocation and PD-L1 expression. Finally, we observed the therapeutic benefit of Sun plus PD-L1 inhibition which enhanced CD8+ cytolytic activity and thus tumour suppression in a xenografted mouse model. These data revealed that TFE3 is a potent tumour promoting gene and it mediates resistance to Sun by induction of PD-L1 in ccRCC. Our data provide a strong rationale to apply Sun and PD-L1 inhibition jointly as a novel immunotherapeutic approach for ccRCC treatment.

Keywords: PD-L1; TFE3; clear cell renal cell carcinoma; sunitinib.

The autophagy-lysosome pathway is a major protein degradation pathway stimulated by multiple cellular stresses, including nutrient or growth factor deprivation, hypoxia, misfolded proteins, damaged organelles, and intracellular pathogens. Recent studies have revealed that transcription factor EB (TFEB) and transcription factor E3 (TFE3) play a pivotal role in the biogenesis and functions of autophagosome and lysosome. Here we report that three translation inhibitors (cycloheximide, lactimidomycin, and rocaglamide A) can facilitate the nuclear translocation of TFEB/TFE3 via dephosphorylation and 14-3-3 dissociation. In addition, the inhibitor-mediated TFEB/TFE3 nuclear translocation significantly increases the transcriptional expression of their downstream genes involved in the biogenesis and function of autophagosome and lysosome. Furthermore, we demonstrated that translation inhibition increased autophagosome biogenesis but impaired the degradative autolysosome formation because of lysosomal dysfunction. These results highlight the previously unrecognized function of the translation inhibitors as activators of TFEB/TFE3, suggesting a novel biological role of translation inhibition in autophagy regulation.

Keywords: TFEB; TFEB nuclear translocation; autophagy-lysosome pathway; calcineurin; eIF4A helicase; mTOR; ribosome; translation inhibitor.

Lysosomes have recently been implicated in regulation of quiescence in adult neural stem cells (NSCs). Whether lysosomes regulate the differentiation of neural stem-progenitor cells (NPCs) in the embryonic brain has remained unknown, however. We here show that lysosomes are more abundant in rapidly dividing NPCs than in differentiating neurons in the embryonic mouse neocortex and ganglionic eminence. The genes for TFEB and TFE3, master regulators of lysosomal biosynthesis, as well as other lysosome-related genes were also expressed at higher levels in NPCs than in differentiating neurons. Anatomic analysis revealed accumulation of lysosomes at the apical and basal endfeet of NPCs. Knockdown of TFEB and TFE3, or that of the lysosomal transporter Slc15a4, resulted in premature differentiation of neocortical NPCs. Conversely, forced expression of an active form of TFEB (TFEB-AA) suppressed neuronal differentiation of NPCs in association with up-regulation of NPC-related genes. These results together point to a previously unappreciated role for TFEB and TFE3, and possibly for lysosomes, in maintenance of the undifferentiated state of embryonic NPCs. We further found that lysosomes are even more abundant in an NPC subpopulation that rarely divides and includes the embryonic origin of adult NSCs than in the majority of NPCs that divide frequently for construction of the embryonic brain, and that overexpression of TFEB-AA also suppressed the cell cycle of neocortical NPCs. Our results thus also implicate lysosomes in establishment of the slowly dividing, embryonic origin of adult NSCs. © AlphaMed Press 2021 SIGNIFICANCE STATEMENT: Regulation of adult tissue stem cells by organelles has recently received much attention, but the developmental functions of lysosomes have been less studied. We now reveal the importance of lysosomes for suppression of premature differentiation of mouse embryonic neural stem-progenitor cells (NPCs). Our data also implicate Slc15a4, a lysosomal histidine and short-peptide transporter that is associated with systemic lupus erythematosus (SLE), in NPC maintenance. These findings shed light on the role of lysosomes in regulation of neural development and tissue stem cells, and they may therefore provide insight into the pathogenesis of lysosome-related diseases such as SLE.

Keywords: TFE3; TFEB; adult neural stem cell; lysosome; neural stem-progenitor cell; neurogenesis.

Growing tumors exist in metabolically compromised environments that require activation of multiple pathways to scavenge nutrients to support accelerated rates of growth. The folliculin (FLCN) tumor suppressor complex (FLCN, FNIP1, FNIP2) is implicated in the regulation of energy homeostasis via 2 metabolic master kinases: AMPK and mTORC1. Loss-of-function mutations of the FLCN tumor suppressor complex have only been reported in renal tumors in patients with the rare Birt-Hogg-Dube syndrome. Here, we revealed that FLCN, FNIP1, and FNIP2 are downregulated in many human cancers, including poor-prognosis invasive basal-like breast carcinomas where AMPK and TFE3 targets are activated compared with the luminal, less aggressive subtypes. FLCN loss in luminal breast cancer promoted tumor growth through TFE3 activation and subsequent induction of several pathways, including autophagy, lysosomal biogenesis, aerobic glycolysis, and angiogenesis. Strikingly, induction of aerobic glycolysis and angiogenesis in FLCN-deficient cells was dictated by the activation of the PGC-1α/HIF-1α pathway, which we showed to be TFE3 dependent, directly linking TFE3 to Warburg metabolic reprogramming and angiogenesis. Conversely, FLCN overexpression in invasive basal-like breast cancer models attenuated TFE3 nuclear localization, TFE3-dependent transcriptional activity, and tumor growth. These findings support a general role of a deregulated FLCN/TFE3 tumor suppressor pathway in human cancers.

Keywords: Angiogenesis; Breast cancer; Cancer; Metabolism.

Transcription factor E3-rearranged renal cell carcinoma (TFE3-RCC) has heterogenous morphologic and immunohistochemical (IHC) features.131 pathologists with genitourinary expertise were invited in an online survey containing 23 questions assessing their experience on TFE3-RCC diagnostic work-up.Fifty (38%) participants completed the survey. 46 of 50 participants reported multiple patterns, most commonly papillary pattern (almost always 9/46, 19.5%; frequently 29/46, 63%). Large epithelioid cells with abundant cytoplasm were the most encountered cytologic feature, with either clear (almost always 10/50, 20%; frequently 34/50, 68%) or eosinophilic (almost always 4/49, 8%; frequently 28/49, 57%) cytology. Strong (3+) or diffuse (>75% of tumour cells) nuclear TFE3 IHC expression was considered diagnostic by 13/46 (28%) and 12/47 (26%) participants, respectively. Main TFE3 IHC issues were the low specificity (16/42, 38%), unreliable staining performance (15/42, 36%) and background staining (12/42, 29%). Most preferred IHC assays other than TFE3, cathepsin K and pancytokeratin were melan A (44/50, 88%), HMB45 (43/50, 86%), carbonic anhydrase IX (41/50, 82%) and CK7 (32/50, 64%). Cut-off for positive TFE3 fluorescent in situ hybridisation (FISH) was preferably 10% (9/50, 18%), although significant variation in cut-off values was present. 23/48 (48%) participants required TFE3 FISH testing to confirm TFE3-RCC regardless of the histomorphologic and IHC assessment. 28/50 (56%) participants would request additional molecular studies other than FISH assay in selected cases, whereas 3/50 participants use additional molecular cases in all cases when TFE3-RCC is in the differential.Optimal diagnostic approach on TFE3-RCC is impacted by IHC and/or FISH assay preferences as well as their conflicting interpretation methods.

Keywords: genitourinary pathology; immunohistochemistry; kidney neoplasms.

Objective: To analyze the clinico pathological features, differential diagnosis and prognosis of metastatic renal cell carcinomas. Methods: The clinical data, histology, immunophenotype and follow-up data of 196 patients with metastatic renal cell carcinoma diagnosed from 1994 to 2017 at the Department of Pathology, Changhai Hospital, Naval Military Medical University, Shanghai, China were analyzed retrospectively. Results: There were 142 males and 54 females, with a median age of 61 years. The top three metastatic sites for the 196 cases of metastatic renal cell carcinoma were lung (31.1%, 61/196), bone (29.1%, 57/196) and digestive system (19.4%, 38/196). Among the pathological subtypes of metastasis, the proportion of clear cell renal cell carcinoma was 94.4% (185/196) and that of type II papillary renal cell carcinoma was 3.6% (7/196). The TFE3 translocated renal cell carcinoma and congestive tubular carcinoma were rare, with 3 cases and 1 case, respectively. CK, vimentin, CAⅨ and CD10 were expressed in all metastatic clear cell renal cell carcinomas. CK7, CD10 and P504s were expressed in papillary renal cell carcinomas. TFE3 was expressed in TFE3 translocated renal cell carcinoma. The collecting duct carcinoma was positive for HCK. Conclusions: Lung metastasis and bone metastasis are still the most frequent metastatic sites of renal cell carcinoma. Five years after primary lesion resection may be the high risk time for metastasis. Most of the metastases are solitary when they are first identified. To better diagnose and identify the renal origin of a metastatic renal cell carcinoma, one should consider morphological characteristics, clinical history information of the metastasis and the combined immunohistochemistry of CK, vimentin, CD10, CK7, TFE3, PAX2 and PAX8.

目的： 探讨转移性肾细胞癌的临床病理学特征、鉴别诊断及预后。 方法： 回顾性分析海军军医大学长海医院病理科1994—2017年196例转移性肾细胞癌患者的临床资料、组织形态学、免疫表型及随访数据，并进行文献复习。 结果： 患者男性142例、女性54例，年龄19~81岁，中位年龄61岁。肿瘤转移部位位居前三者依次为肺（31.1%，61/196）、骨（29.1%，57/196）及消化系统（19.4%，38/196）。转移灶病理类型中，透明细胞性肾细胞癌最多见（94.4%，185/196）；其次为Ⅱ型乳头状肾细胞癌（3.6%，7/196）；TFE3易位性肾细胞癌和集合管癌罕见，分别为3例和1例。在转移性透明细胞性肾细胞癌病例中，多表达广谱细胞角蛋白（CKpan）、波形蛋白、碳酸酐酶Ⅸ（CAⅨ）、CD10；乳头状肾细胞癌中，多表达细胞角蛋白7（CK7）、CD10、P504s；TFE3易位性肾细胞癌表达TFE3；集合管癌表达高分子质量细胞角蛋白（HCK）。 结论： 肺转移、骨转移仍是肾癌最易发生转移的远隔部位；原发病灶切除术后5年内可能是发生转移的高危风险时间，且转移病灶首次发现时多为单发病灶。重视转移灶的形态学特征和临床病史信息，结合免疫组织化学CKpan、波形蛋白、CD10、CK7、TFE3、PAX2、PAX8，有助于正确诊断及判明肿瘤原发部位。.

Keywords: Prognosis; Renal cell carcinoma; Tumor metastasis.

Perivascular epithelioid cell tumor (PEComa), mesenchymal tumors morphologically characterized by epithelioid cells, coexpress melanocytic and muscle markers. Herein, we describe a heretofore-undescribed tuberous sclerosis complex (TSC)-related neoplasm, morphologically resembling a soft tissue fibroma-like lesion, but showing an immunophenotype resembling PEComa. We identified 3 soft tissue fibroma-like lesions in individuals with TSC. We also evaluated 6 TSC-related periungual fibroma as well as a range of non-TSC fibroma-like lesions (n=19). Immunohistochemistry for HMB-45, desmin, smooth muscle actin, TFE3, and S100 was performed on the TSC-related fibromas. Periungual fibromas and non-TSC fibroma-like lesions were also stained for HMB-45. All 3 TSC patients were female, ranging in age from 4 to 51 years (mean, 26.7 y). Two tumors were located in extremities and 1 on the chest wall. The tumors showed elongated to stellate spindle-shape cells, prominent collagenous background, and lacked mitotic activity and cytologic atypia. Immunohistochemically, all 3 tumors were positive for HMB-45; smooth muscle actin or desmin was positive in both tumors tested. TFE3 was negative. All patients were alive with no evidence of disease with median follow-up of 55 months (range, 6 to 131 mo). Non-TSC fibroma-like lesions and oral and periungual fibromas were negative for HMB-45. Fibroma-like PEComa, a newly recognized soft tissue tumor with a strong association with TSC, mimics soft tissue fibroma but shows reactivity with melanocytic markers.

Background: Ulcerative colitis-associated colorectal cancer (UC-CRC) is a life-threatening complication of ulcerative colitis (UC). The mechanisms underlying UC-CRC remain to be elucidated. The purpose of this study was to explore the key genes and biological processes contributing to colitis-associated dysplasia (CAD) or carcinogenesis in UC via database mining, thus offering opportunities for early prediction and intervention of UC-CRC.

Methods: Microarray datasets (GSE47908 and GSE87466) were downloaded from Gene Expression Omnibus (GEO). Differentially expressed genes (DEGs) between groups of GSE47908 were identified using the "limma" R package. Weighted gene co-expression network analysis (WGCNA) based on DEGs between the CAD and control groups was conducted subsequently. Functional enrichment analysis was performed, and hub genes of selected modules were identified using the "clusterProfiler" R package. Single-gene gene set enrichment analysis (GSEA) was conducted to predict significant biological processes and pathways associated with the specified gene.

Results: Six functional modules were identified based on 4929 DEGs. Green and blue modules were selected because of their consistent correlation with UC and CAD, and the highest correlation coefficient with the progress of UC-associated carcinogenesis. Functional enrichment analysis revealed that genes of these two modules were significantly enriched in biological processes, including mitochondrial dysfunction, cell-cell junction, and immune responses. However, GSEA based on differential expression analysis between sporadic colorectal cancer (CRC) and normal controls from The Cancer Genome Atlas (TCGA) indicated that mitochondrial dysfunction may not be the major carcinogenic mechanism underlying sporadic CRC. Thirteen hub genes (SLC25A3, ACO2, AIFM1, ATP5A1, DLD, TFE3, UQCRC1, ADIPOR2, SLC35D1, TOR1AIP1, PRR5L, ATOX1, and DTX3) were identified. Their expression trends were validated in UC patients of GSE87466, and their potential carcinogenic effects in UC were supported by their known functions and other relevant studies reported in the literature. Single-gene GSEA indicated that biological processes and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to angiogenesis and immune response were positively correlated with the upregulation of TFE3, whereas those related to mitochondrial function and energy metabolism were negatively correlated with the upregulation of TFE3.

Conclusions: Using WGCNA, this study found two gene modules that were significantly correlated with CAD, of which 13 hub genes were identified as the potential key genes. The critical biological processes in which the genes of these two modules were significantly enriched include mitochondrial dysfunction, cell-cell junction, and immune responses. TFE3, a transcription factor related to mitochondrial function and cancers, may play a central role in UC-associated carcinogenesis.

Keywords: Colitis associated dysplasia; Ulcerative colitis; Ulcerative colitis associated colorectal cancer; Weighted gene co-expression network analysis.

Organelle stress and Liver injuries often occur in human immunodeficiency virus (HIV) infected patients under anti-HIV therapies, yet few molecular off-targets of anti-HIV drugs have been identified in the liver. Here, we found through total RNA sequencing that the transcription of a host protease Ras converting CAAX endopeptidase 1 (RCE1) was altered in HepG2 cells treated with anti-HIV protease inhibitors, ritonavir and lopinavir. Levels of RCE1 protein were inhibited in HepG2 and primary mouse hepatocytes and in the liver of mice treated with the anti-HIV drugs, which were accompanied with inhibition of two potential substrates of RCE1, small GTP binding protein Rab13 and Rab18, which are with a common CAAX motif and known to regulate the ER-Golgi traffic or lipogenesis. Neither Rce1 transcription nor RCE1 protein level was inhibited by Brefeldin A, which is known to interfere with the ER-Golgi traffic causing Golgi stress. Knocking down Rce1 with RNA interference increased ritonavir and lopinavir-induced cell death as well as expression of Golgi stress response markers, TFE3, HSP47 and GCP60, in both primary mouse hepatocytes and mouse liver, and deteriorated alcohol-induced alanine aminotransferase (ALT) and fatty liver injury in mice. In addition, overexpressing Rab13 or Rab18 in primary human hepatocytes reduced partially the anti-HIV drugs and alcohol-induced Golgi fragmentation, Golgi stress response, and cell death injury. Conclusion: We identified a mechanism linking a host protease and its substrates, small guanosine triphosphate-binding proteins, to the anti-HIV drug-induced Golgi dysfunction, organelle stress response, and fatty liver injury.

TFE3 is accepted as a good marker for the diagnosis of Xp11 translocation renal cell carcinoma. However, the significance of TFE3 in other types of renal cell carcinomas remains unclear. We examined the expression of TFE3 using immunohistochemistry by automated Ventana BenchMark XT system in 1818 consecutive renal cell carcinomas and verified the strong positive cases with TFE3 break-apart fluorescence in situ hybridization and RNA sequencing. Among the 27 renal cell carcinomas with TFE3 strong positive immunostaining, 20 cases were diagnosed as Xp11 translocation renal cell carcinoma, and seven cases were diagnosed as clear cell renal cell carcinoma. We further analyzed the morphology, clinicopathological features, and immunohistochemistry markers (CK7, CD117, CD10, P504s, vimentin, CA-IX, AE1/AE3, EMA, HMB45, Melan-A, and cathepsin K) of them. Pale to eosinophilic flocculent cytoplasm and psammomatous calcification were seen only in Xp11 translocation renal cell carcinomas (P < 0.05). Tumor necrosis occurred in all four cases of Xp11 translocation renal cell carcinomas with pT3a stage, which had local recurrence and distant metastasis (two of them died) within 3 years. The expressions of Vimentin, CA-IX, AE1/AE3, and EMA were significantly different between them (P < 0.05). CA-IX was diffusely strong positive in clear cell renal cell carcinomas but negative or focally mild positive in Xp11 translocation renal cell carcinomas. Our study first demonstrates that a very small minority (0.4%) of clear cell renal cell carcinomas with TFE3 strong positive immunostaining, which points out a potential pitfall in diagnosis of Xp11 translocation renal cell carcinomas by TFE3 immunohistochemistry. CA-IX is a good marker to distinguish clear cell renal cell carcinoma with TFE3 strong positive immunostaining from Xp11 translocation renal cell carcinoma. Tumor necrosis could be a potential factor relevant to pT3a stage, which may be a high-risk factor for the patients with Xp11 translocation renal cell carcinomas.

Lysosome is the principal organelle for the ultimate degradation of cellular macromolecules, which are delivered through endocytosis, phagocytosis, and autophagy. The lysosomal functions have been found to be impaired by fatty foods and aging, and more importantly, the lysosomal dysfunction in macrophages has been reported as a risk of atherosclerosis development. In this study, we searched for dietary polyphenols which possess the activity for enhancing the lysosomal degradation in J774.1, a murine macrophage-like cell line. Screening test utilizing DQ-BSA digestion identified isorhamnetin (3'-O-methylquercetin) as an active compound. Interestingly, structural comparison to inactive flavonols revealed that the chemical structure of the B-ring moiety in isorhamnetin is the primary determinant of its lysosome-enhancing activity. Unexpectedly isorhamnetin failed to inhibit mTORC1-TFEB signaling, a master regulator of lysosomal biogenesis and function. Our data suggested that the other molecular mechanism might be critical for the regulation of lysosomes in macrophages.Abbreviations: ANOVA: analysis of variance; ApoE: apolipoprotein E; ATP6V0D2: ATPase H⁺ transporting V0 subunit d2; BAF: bafilomycin A1; BODIPY: boron dipyrromethene; BSA: bovine serum albumin; CTSD: cathepsin D; CTSF: cathepsin F; DMEM: Dulbecco's modified eagle medium; DMSO: dimethyl sulfoxide; EGCG: epigallocatechin-3-gallate; FBS: fetal bovine serum; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; HPLC: high-performance liquid chromatography; LAMP1: lysosomal-associated membrane protein 1; LAMP2A: lysosomal-associated membrane protein 2A; LC-MS/MS: liquid chromatography tandem mass spectrometry; MITF: microphthalmia-associated transcription factor; MRM: multiple reaction monitoring; mTORC1: mechanistic target of rapamycin complex 1; PBS: phosphate-buffered saline; PPARγ: peroxisome proliferator-activated receptor γ; RT-qPCR: reverse transcription quantitative polymerase chain reaction; SDS: sodium dodecyl sulfate; SNARE: soluble N-ethylmaleimide-sensitive-factor attachment protein receptor; TBS: Tris-buffered saline; TFA: trifluoroacetic acid; TFE3: transcription factor binding to IGHM enhancer 3; TFEB: transcriptional factor EB; TFEC: transcription factor EC; V-ATPase: vacuolar-type proton ATPase.

Autophagy plays an essential role in cell survival/death and functioning. Modulation of autophagy has been recognized as a promising therapeutic strategy against diseases/disorders associated with uncontrolled growth or accumulation of biomolecular aggregates, organelles, or cells including those caused by cancer, aging, neurodegeneration, and liver diseases such as α1-antitrypsin deficiency. Numerous pharmacological agents that enhance or suppress autophagy have been discovered. However, their molecular mechanisms of action are far from clear. Here, we collected a set of 225 autophagy modulators and carried out a comprehensive quantitative systems pharmacology (QSP) analysis of their targets using both existing databases and predictions made by our machine learning algorithm. Autophagy modulators include several highly promiscuous drugs (e.g., artenimol and olanzapine acting as activators, fostamatinib as an inhibitor, or melatonin as a dual-modulator) as well as selected drugs that uniquely target specific proteins (~30% of modulators). They are mediated by three layers of regulation: (i) pathways involving core autophagy-related (ATG) proteins such as mTOR, AKT, and AMPK; (ii) upstream signaling events that regulate the activity of ATG pathways such as calcium-, cAMP-, and MAPK-signaling pathways; and (iii) transcription factors regulating the expression of ATG proteins such as TFEB, TFE3, HIF-1, FoxO, and NF-κB. Our results suggest that PKA serves as a linker, bridging various signal transduction events and autophagy. These new insights contribute to a better assessment of the mechanism of action of autophagy modulators as well as their side effects, development of novel polypharmacological strategies, and identification of drug repurposing opportunities.

Introduction: Perivascular epithelioid cell tumors (PEComas) are a family of mesenchymal tumors that rarely arise as a primary bone tumor.

Material and methods: We report a case of primary malignant bone PEComa. A literature review via PubMed, Embase and Web of Science databases with the keyword "PEComa" and "bone" was performed.

Results: We reported a 33-year-old female with primary malignant bone PEComa in right distal humerus. The patient received an inhibitor of the mammalian target of rapamycin (mTOR) protein based on negative molecular investigation result of transcription factor E3 (TFE3) rearrangement, and additional therapies including palliative radiotherapy, anti-angiogenics and immunotherapy when the disease progression was detected. The patient was alive with the disease twenty-three months postoperatively. A total of nineteen related literature cases were retrieved and reviewed. Taking current case into account, ten males and ten females with median age of 24 years (range, 3-93 years) were identified, who were most frequently affected in tibia. The median follow-up duration of 24 months (range, 3-96 months). One patient died due to this disease, and six patients showed metastases. Three patients experienced recurrence, and two of them experienced twice and three times, respectively.

Conclusion: To our knowledge, this is the first case of primary malignant bone PEComa arising in humerus. Clinicopathological and radiological correlation is mandatory to the correct diagnosis and to determine its malignancy. More studies are required to understand the role of molecular test and imaging in selecting suitable treatment and mechanisms of treatment resistance.

Keywords: 18F-FDG, fluorine-18-fluorodeoxyglucose positron; ASPS, alveolar soft part sarcoma; Bone neoplasm; CT, computed tomography; ECT, emission computed tomography; EMA, membrane antigen; HMB 45, human melanoma black 45; HPF, high-power fields; Humerus; MITF, microphthalmia-associated transcription factor; MRI, magnetic resonance imaging; Malignant; Metastasis; PEComa, perivascular epithelioid cell tumor; PET/CT, positron emission tomography/computed tomography; Perivascular epithelioid cell tumor (PEComa); SMA, smooth muscle actin; SUVmax, maximum standard uptake value; TFE3, transcription factor E3; mTOR, mammalian target of rapamycin.

Perivascular epithelioid cell neoplasms (PEComas) are a family of mesenchymal neoplasms with features of both melanotic and smooth muscle differentiation. PEComa morphology is highly variable and encompasses epithelioid to spindle cells often with clear cytoplasm and prominent nucleoli. Molecularly, most PEComas are defined by a loss of function of the TSC1/TSC2 complex. Additionally, a distinct small subset of PEComas harboring rearrangements of the TFE3 (Xp11) gene locus has been identified. By presenting a series of three case reports with distinct features, we demonstrate diagnostic pitfalls as well as the importance of molecular work-up of PEComas because of important therapeutic consequences.