Research progress on the application of 16S rRNA gene sequencing and machine learning in forensic microbiome individual identification.

Forensic microbiome research is a field with a wide range of applications and a number of protocols have been developed for its use in this area of research. As individuals host radically different microbiota, the human microbiome is expected to become a new biomarker for forensic identification. To achieve an effective use of this procedure an understanding of factors which can alter the human microbiome and determinations of stable and changing elements will be critical in selecting appropriate targets for investigation. The 16S rRNA gene, which is notable for its conservation and specificity, represents a potentially ideal marker for forensic microbiome identification. Gene sequencing involving 16S rRNA is currently the method of choice for use in investigating microbiomes. While the sequencing involved with microbiome determinations can generate large multi-dimensional datasets that can be difficult to analyze and interpret, machine learning methods can be useful in surmounting this analytical challenge. In this review, we describe the research methods and related sequencing technologies currently available for application of 16S rRNA gene sequencing and machine learning in the field of forensic identification. In addition, we assess the potential value of 16S rRNA and machine learning in forensic microbiome science.

Primary adenomatoid tumor of the adrenal gland: A case report and literature review.

RATIONALE: Adenomatoid tumors are rare benign tumors, mainly involving the reproductive tract, such as the epididymis in men and the uterus and fallopian tubes in women. However, a few cases can occur outside the reproductive tract. Herein, we report a rare case of a primary adenomatoid tumor of the adrenal gland. PATIENT CONCERNS: A 50-year-old man underwent ultrasound examination and was found to have a right adrenal mass without elevated blood pressure, weakness after fatigue, frequent nocturnal urination urgency, pain, or a history of hematuria. The patient's general health was normal. Computed tomography revealed a polycystic mixed-density lesion in the right adrenal region, approximately 7.3 × 4.5 cm in size. DIAGNOSES: Based on the clinical information, morphological features, and immunohistochemistry results, a pathological diagnosis of primary adenomatoid tumor of the adrenal gland was made. INTERVENTION: Excision of the right adrenal gland and tumor through the 11 ribs. OUTCOMES: The patient's postoperative course was uneventful. LESSONS: Preventing misdiagnosis adenomatoid tumors with other types of adrenal gland tumors or metastatic tumors is imperative. Morphological and immunohistochemical features can help diagnose primary adenomatoid tumors of the adrenal gland.

Warthin-like papillary renal cell carcinoma: A case report.

BACKGROUND: Warthin-like papillary renal cell carcinoma (WPRCC) has been described as a rare pathological subtype of papillary renal cell carcinoma in the 2022 World Health Organization Classification of the Urinary and Male Reproductive System. Herein we report a case of WPRCC in the left kidney. CASE SUMMARY: Physical examination of a previously healthy 47-year-old woman revealed a lump in her left kidney, 4.5 cm × 3.5 cm × 3.5 cm in size. Based on the clinical information, imaging data, histmorphological features, and immunohistochemistry results, the pathological diagnosis was WPRCC in left kidney. CONCLUSION: Resection of the mass in the left kidney was performed and her postoperative course was uneventful.

Primary acinic cell carcinoma of the trachea: A case report and literature review.

RATIONALE: Salivary gland-type acinic cell carcinoma (ACC) is a low-grade malignancy. Primary ACC of the trachea and lungs is rare; here, we describe 1 such case. The histological morphology of tracheal ACC was similar to that of its salivary gland-associated equivalent. Because of its rarity, it is easily misdiagnosed as another type of tracheal or lung tumor. Microscopic analysis of pathological features and immunohistochemistry help diagnose primary ACC of the trachea and lungs. PATIENT CONCERNS: A 33-year-old female complained of shortness of breath and hemoptysis for 2 years, and reported the symptoms to have aggravated over the last 4 months. The patient was admitted to our hospital for further treatment. Enhanced computed tomography revealed a soft tissue density nodule shadow in the trachea, which was approximately 1.3 × 1.2 cm in size. DIAGNOSES: Based on the clinical information, morphological features, and immunohistochemistry, the pathological diagnosis was primary ACC of the trachea. INTERVENTION: The tracheal lesion was resected with an electric snare, electrotomy, freezing, and an argon knife using a rigid bronchoscope. OUTCOMES: The patient's postoperative course was uneventful. LESSONS: It is important to prevent misdiagnosis of this type of tumor as another type of lung tumor. Morphological and immunohistochemical features can be useful in diagnosing primary ACC of the trachea and lungs.

Thymic lipofibroadenomas: Three case reports.

BACKGROUND: Thymic lipofibroadenomas are extremely rare. In this study, we investigated the clinicopathological characteristics of thymic lipofibroadenomas. CASE SUMMARY: This study included three patients with thymic lipofibroadenomas. We retrospectively analyzed the patient data to determine the clinicopathological characteristics of thymic lipofibroadenomas. The study included one man and two women [mean age, 43 (33-59) years]. All patients were non-smokers and presented with well-defined anterior mediastinal tumors. The cut surfaces of the tumors were solid, with a mixture of yellow and white areas. Microscopic evaluation of resected specimens showed scattered cord-like structures of epithelial cells embedded within abundant fibrotic and hyaline stroma admixed with variable quantities of adipose tissue. One patient showed hyperplastic thymic tissue in a part of the tumor. CONCLUSION: Thymic lipofibroadenomas are an extremely rare type of benign thymic tumor. Surgical removal of lipofibroadenomas is usually curative.

Primary salivary gland-type polymorphous adenocarcinoma in the lung: A case report and literature review.

RATIONALE: Polymorphous low-grade adenocarcinoma is a low-risk infiltrative malignant tumor of the salivary glands. However, some of these tumors are more malignant than the low-grade tumors and therefore, according to the most recent recommendation of the World Health Organization, they are renamed as polymorphous adenocarcinomas (PACs). Primary polymorphous low-grade adenocarcinomas/PACs of the lungs are rare. Herein, we report a case of primary PAC of the lung with bronchial cartilage and perineural invasion, and lymph node metastasis. PATIENT CONCERNS: A 58-year-old man had developed fever half a month prior, without chills or other accompanying symptoms, and the underlying reasons were unknown. His self-measured temperature was up to 39°C, accompanied by cough and expectoration, yellow and thin sputum, and shortness of breath. The patient's general state was normal, and respiratory sounds originating from the right lung were weak. Enhancement computed tomography revealed that the bronchial lumen of the basal segment of the lower lobe of the right lung was narrow; soft tissue density nodules were seen, with a range of approximately 2.4 cm × 1.3 cm. DIAGNOSIS: Based on clinical information, morphological features, and immunohistochemistry results, the pathological diagnosis was primary PAC of the lungs. INTERVENTION: Thoracoscopic resection of the middle and lower lobes of the right lung was performed, further extended dissection of the mediastinal lymph nodes was performed. OUTCOMES: The postoperative course was uneventful. LESSONS: Primary PAC of the lung is rare and may cause misdiagnosis. When encountering a lung tumor with diverse tissue structures, uniform cell type and nerve invasion, we should consider the possibility of PAC. Morphological and immunohistochemical features can be useful for diagnosing primary PAC of the lungs.

PHLDA3 promotes lung adenocarcinoma cell proliferation and invasion via activation of the Wnt signaling pathway.

The PHLDA3 gene encodes a small 127 amino acid protein with a pleckstrin homology (PH)-only domain. The expression and significance of PHLDA3 in lung cancer remain unclear. Here, we investigated the role of PHLDA3 in tumor proliferation and invasion in lung adenocarcinoma. Immunohistochemistry and immunoblotting analyses were used to assess PHLDA3 expression in lung cancer tissues, and its correlation with clinicopathological factors in lung cancer. Plasmids encoding PHLDA3 and small interfering RNA against PHLDA3 were used to regulate the expression of PHLDA3 in lung cancer cells. Furthermore, the effects of PHLDA3 on lung cancer cell proliferation and invasion were investigated using the MTS, colony formation, Matrigel invasion, and wound healing assays. Co-immunoprecipitation analysis and inhibitors of both the Wnt signaling pathway and GSK3ß were used to explore the regulatory mechanisms underlying the role of PHLDA3 in lung cancer cells. PHLDA3 was found to be overexpressed in lung cancer tissues, and its expression was correlated with poor outcomes in lung adenocarcinoma patients. PHLDA3 expression promoted the proliferation, invasion, and migration of lung cancer cells. Overexpression of PHLDA3 activated the Wnt signaling pathway and facilitated epithelial-mesenchymal transition. Inhibition of Wnt signaling pathway activity, using XAV-939, reversed the effects of PHLDA3 overexpression in lung cancer cells; moreover, PHLDA3 could bind to GSK3ß. Inhibition of GSK3ß activity, using CHIR-99021, restored the proliferative and invasive abilities of PHLDA3 knockdown cells. Our findings demonstrate that PHLDA3 is highly expressed in lung adenocarcinomas and is correlated with poor outcomes. Furthermore, it promotes the proliferation and invasion of lung cancer cells by activating the Wnt signaling pathway.

DEK is highly expressed in breast cancer and is associated with malignant phenotype and progression.

DEK proto-oncogene (DEK) has been demonstrated as an oncogene and is associated with the development of many types of tumor; however, the expression and role of DEK in breast cancer remain unknown. The present study aimed to determine the role of DEK in the progression of breast cancer. The expression of DEK in 110 breast cancer tissues and 50 adjacent normal breast tissues was examined using immunohistochemistry. Furthermore, DEK expression was upregulated by DEK transfection or downregulated by DEK shRNA interference in MCF7 cells. Proliferative and invasive abilities were examined in MCF7 cells using MTT assay, colony-formation assay and transwell invasion assays. The results demonstrated that DEK expression level was significantly increased in breast cancer tissues compared with normal breast tissues. Furthermore, high DEK expression was associated with high histological grade, lymph node metastasis, advanced Tumor-Node-Metastasis stage and high Ki-67 index; however, DEK expression was not associated with the expression level of estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2. High DEK expression indicated poor prognosis in patients with breast cancer. DEK overexpression upregulated the protein expression of ß-catenin and Wnt and increased the proliferative and invasive abilities of breast cancer cells. DEK downregulation had the opposite effect. Taken together, the results from the present study demonstrated that high expression of DEK was common in patients with breast cancer and was associated with progression of the disease and poor prognosis, and that DEK overexpression promoted the proliferative and invasive abilities of breast cancer cells.

TRIP13 promotes the proliferation and invasion of lung cancer cells via the Wnt signaling pathway and epithelial-mesenchymal transition.

Thyroid hormone receptor interactor 13 (TRIP13) is an ATPase that has been found to be overexpressed in many tumors. The aim of this study was to investigate the role of TRIP13 and its mechanism of action in lung cancer. The expression of TRIP13 was examined in lung cancer tissues and corresponding normal lung tissues by western blotting. TRIP13 was overexpressed or knocked down by transient transfection or siRNA interference in lung cancer cells, respectively. The expression of key proteins associated with the Wnt signaling pathway and epithelial-mesenchymal transition (EMT) was assessed. The interaction between TRIP13 and low-density lipoprotein receptor-related protein 6 (LRP6) was examined by co-immunoprecipitation and laser confocal immunofluorescence. Moreover, this study determined the proliferative and invasive ability of cells through colony formation, cell proliferation, and Matrigel invasion assays. The expression of TRIP13 was higher in lung cancer tissues than in normal lung tissues (p = 0.002), and this correlated with poor patient prognosis (p < 0.001). In addition, overexpression of TRIP13 enhanced the levels of active ß-catenin and target proteins of the Wnt signaling pathways (p < 0.05). This study found that TRIP13 can co-localize and bind with LRP6. Furthermore, overexpression of TRIP13 caused the upregulation of N-cadherin, Snail, and vimentin, and the downregulation of E-cadherin (p < 0.05). The aforementioned results were reversed after knocking down the expression of TRIP13 (p < 0.05). TRIP13 is highly expressed in lung cancers, indicating poor prognosis. overexpression of TRIP13 promotes the proliferative and invasive ability of lung cancer cells via the activation of Wnt signaling pathway and EMT.

Primary thymic carcinoma with adenoid cystic carcinoma-like features: A case report and literature review.

RATIONALE: Thymic carcinoma with adenoid cystic carcinoma-like features is a special subtype of thymic adenocarcinoma, and the occurrence of this condition is extremely rare. Herein, we report a case of primary thymic carcinoma with adenoid cystic carcinoma-like features in a young man. PATIENT CONCERNS: A 38-year-old man had an incidental finding of space-occupying lesion in the anterior mediastinum during a routine health examination. The patient complained of occasional mild chest tightness during hot weather but had no obvious cough, sputum, chest pain, or fever. Contrast-enhanced computed tomography scan of the chest revealed a space-occupying lesion in the anterior mediastinum, which is likely benign. DIAGNOSIS: The lesion was diagnosed as a primary thymic carcinoma with adenoid cystic carcinoma-like features. INTERVENTION: The patient underwent thoracoscopic resection of left anterior mediastinal mass and enlarged resection of thymectomy and mediastinal fat in our hospital. OUTCOMES: The postoperative course was uneventful. LESSONS: The tissue characteristic of this tumor was extremely similar to that of adenoid cystic carcinoma. A precise pathological examination is extremely important to prevent misdiagnoses of the lesion as adenoid cystic carcinoma or other thymic tumors. Immunohistochemical staining is extremely useful for the pathological and differential diagnoses of this tumor.

FAM83A Promotes Lung Cancer Progression by Regulating the Wnt and Hippo Signaling Pathways and Indicates Poor Prognosis.

FAM83A (family with sequence similarity 83, member A) has been found to be highly expressed in cancers. The purpose of this study was to clarify the role and mechanism of FAM83A in lung cancers. The expression of FAM83A in lung cancer cells was enhanced by gene transfection or knocked down by small interfering RNA interference. The key proteins of the Wnt signaling pathway, the Hippo signaling pathway, and epithelial-mesenchymal transition (EMT) were examined using Western blot. The proliferation and invasion of lung cancer cells were examined using cell proliferation, colony formation, and invasion assays. The expression of FAM83A in lung cancer tissues was significantly increased and was correlated with advanced tumor-node-metastasis (TNM) stage and poor prognosis. Overexpression of FAM83A enhanced the proliferation, colony formation, and invasion of lung cancer cells. Meanwhile, FAM83A overexpression increased the expression of active ß-catenin and Wnt target genes and the activity of EMT. Furthermore, in FAM83A-overexpressed cells, the activity of Hippo pathway was downregulated, whereas the expression of yes-associated protein (YAP) and its downstream targets cyclin E and CTGF were upregulated. The inhibitor of the Wnt signaling pathway, XAV-939, reversed the promoting effect of FAM83A on YAP, cyclin E, and CTGF. On knocking down the expression of FAM83A, we obtained the opposite results. However, the inhibitor of GSK3ß, CHIR-99021, restored the expression of YAP, cyclin E, and CTGF after FAM83A was knocked down. FAM83A is highly expressed in lung cancers and correlated with advanced TNM stage and poor prognosis. FAM83A promotes the proliferation and invasion of lung cancer cells by regulating the Wnt and Hippo signaling pathways and EMT process.

DEK promotes the proliferation and invasion of lung cancers and indicates poor prognosis in lung adenocarcinomas.

DEK has been revealed to be overexpressed in many cancers and associated with cancer progression. The aim of the present study was to elucidate the role of DEK with a specific focus on its underlying mechanism in lung cancers. DEK expression in lung cancers and normal lung tissues and the correlations between DEK expression and clinicopathological parameters of lung cancers were investigated using the data from The Cancer Genome Atlas (TCGA). DEK expression was upregulated by DEK transfection or downregulated by DEK shRNA interference in A549 and H1299 cells. The effects of DEK on the Wnt signaling pathway and epithelial­mesenchymal transition (EMT) were examined using western blotting. Proliferative and invasive abilities were observed in A549 and H1299 cells treated with DEK using an MTT assay, colony formation assay, and Transwell migration and invasion assays. The expression of DEK was higher in lung cancer tissues than that in normal lung tissues. DEK expression was positively correlated with the expression of epidermal growth factor receptor (EGFR) and KRAS in lung adenocarcinomas. High expression of DEK indicated poor prognosis in lung adenocarcinomas (P=0.018). Enhanced expression of DEK upregulated the levels of active­ß­catenin and Wnt target genes, such as cyclin D1, c­Myc and MMP7 and increased the proliferative and invasive abilities of lung cancer cells. Enhanced expression of DEK in A549 and H1299 cells also increased the levels of EGFR, KRAS, vimentin, Snail, and N­cadherin, and decreased the level of E­cadherin. The opposite results were obtained with knockdown of DEK expression. DEK was highly expressed in lung cancers and indicated poor prognosis in lung adenocarcinomas. DEK expression activated the Wnt signaling pathway and EMT process and promoted the proliferation and invasion of lung cancers.

Overexpression of KRT17 promotes proliferation and invasion of non-small cell lung cancer and indicates poor prognosis.

PURPOSE: Keratin 17 (KRT17) is a 48 KDa type I intermediate filament, which is mainly expressed in epithelial basal cells. KRT17 has been shown to be overexpressed in many malignant tumors and play an important role in the occurrence and development of tumors. Therefore, this study explored the role and underlying mechanism of KRT17 in non-small cell lung cancers (NSCLC). METHODS: KRT17 expression and its correlations with clinicopathological factors were examined in lung cancer tissues by immunohistochemistry. The prognosis value of KRT17 in NSCLCs was retrieved from The Cancer Genome Atlas (TCGA) online databases. The expression level of KRT17 was increased or decreased by KRT17 gene transfection or small RNA interference in lung cancer cells, respectively. Further, proliferation and invasiveness of lung cancer cells were determined by cell proliferation and invasion assays, respectively. Finally, expression levels of proteins related to Wnt signaling pathways and epithelial mesenchymal transition (EMT) were detected by Western blot. RESULTS: The expression level of KRT17 in NSCLCs was significantly higher than normal lung tissues. High expression of KRT17 predicted poor prognosis of patients with NSCLCs, especially lung adenocarcinomas, and was correlated with poor differentiation and lymphatic metastasis. Overexpression of KRT17 enhanced, while KRT17 knockdown inhibited, the proliferation and invasiveness of lung cancer cells. Overexpression of KRT17 up-regulated ß-catenin activity and levels of Wnt target genes, such as cyclin D1, c-Myc, and MMP7. Moreover, KRT17 promoted EMT by up-regulating Vimentin, MMP-9, and Snail expression and down-regulating E-cadherin expression. CONCLUSION: Overexpression of KRT17 is common in NSCLCs and indicates poor prognosis. Overexpression of KRT17 enhances the proliferation and invasiveness of NSCLC cells by activating the Wnt signaling pathway and EMT process. KRT17 is a potential indicator of NSCLC progression and poor survival.

Primary malignant mesothelioma of the diaphragm with liver invasion: A case report and review of literature.

RATIONALE: Malignant mesothelioma is a malignant tumor with poor prognosis, which usually originates in the pleura, peritoneum, and pericardial cavity. Mesotheliomas that originate from the diaphragm are very rare. Here, we report a case of primary malignant mesothelioma of the diaphragm with liver invasion. PATIENT CONCERNS: A 66-year-old woman was admitted to our hospital because of a "liver space-occupying lesion," without any special clinical symptoms. Imaging examinations suggested a cystic-solid mixed lesion in the right lobe of the liver. DIAGNOSIS: The tumor was diagnosed as epithelioid mesothelioma of the diaphragm with liver invasion. INTERVENTION: The patient underwent abdominal surgery in our hospital to remove the diaphragmatic mass, liver mass, and part of the diaphragm. OUTCOMES: The postoperative course was uneventful. LESSONS: Primary diaphragmatic malignant mesothelioma is very rare and may involve liver or lung tissue and be mistaken for liver or lung tumor. Accurate diagnosis depends on careful pathological examination. Immunohistochemical staining is very useful to distinguish this tumor from other liver or diaphragmatic tumors.

Sclerosing pneumocytoma mixed with a typical carcinoid tumor: A case report and review of literature.

RATIONALE: Sclerosing pneumocytoma accompanied with other type of tumor in one patient is very rare. Here, we report a case of a sclerosing pneumocytoma mixed with a typical carcinoid tumor in a same neoplasm. PATIENT CONCERNS: A 55-year-old woman incidentally detected a space-occupying lesion of right lung in routine health examination. The patient was asymptomatic and there were no positive findings in routine laboratory examination, physical examination, and pulmonary function test. Computed tomography revealed a solitary round mass in the middle lobe of the right lung. DIAGNOSIS: The lesion was diagnosed as a sclerosing pneumocytoma accompanied with a typical carcinoid tumor of the right lung. INTERVENTION: The patient underwent thoracoscopic lobectomy in our hospital. OUTCOMES: The postoperative course was uneventful. LESSONS: This case is rare and noteworthy for a lesion containing two different types of neoplasms, which may cause diagnostic difficulties.

PRDM16 functions as a suppressor of lung adenocarcinoma metastasis.

BACKGROUND: The transcription factor PR domain containing 16 (PRDM16) is known to play a significant role in the determination and function of brown and beige fat. However, the role of PRDM16 in tumor biology has not been well addressed. Here we investigated the impact of PRDM16 on tumor growth and metastasis in lung cancer. METHODS: UALCAN database, immunoblotting and immunohistochemistry analysis were used to assess PRDM16 expression in lung cancer patients. Kaplan-Meier plotter database was used to analyze the overall survival of patients with lung cancer stratified by PRDM16 expression. PRDM16 overexpression and knockdown experiments were conducted to assess the effects of PRDM16 on growth and metastasis in vitro and in vivo, and its molecular mechanism was investigated in lung adenocarcinoma cells by chromatin immunoprecipitation-sequencing (ChIP-Seq), real time-quantitative PCR (RT-qPCR), luciferase assay, xenograft models and rescue experiments. RESULTS: PRDM16 was downregulated in lung adenocarcinomas, and its expression level correlated with key pathological characteristics and prognoses of lung adenocarcinoma patients. Overexpressing PRDM16 inhibited the epithelial-to-mesenchymal transition (EMT) of cancer cells both in vivo and in vitro by repressing the transcription of Mucin-4 (MUC4), one of the regulators of EMT in lung adenocarcinomas. Furthermore, deleting the PR domain from PRDM16 increased the transcriptional repression of MUC4 by exhibiting significant differences in histone modifications on its promoter. CONCLUSIONS: Our findings demonstrate a critical interplay between transcriptional and epigenetic modifications during lung adenocarcinoma progression involving EMT of cancer cells and suggest that PRDM16 is a metastasis suppressor and potential therapeutic target for lung adenocarcinomas.