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1.
Semin Diagn Pathol ; 41(2): 95-107, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38238218

ABSTRACT

With the growing recognition of IgG4-related hepatobiliary disease, establishing a definitive diagnosis relies mainly on a combination of clinical findings, serological markers, and imaging modalities. However, the role of histopathological evaluation remains indispensable, particularly in cases necessitating differential diagnosis or malignancy exclusion. While diagnosing IgG4-related hepatobiliary disease through surgical resection specimens is often straightforward, pathologists encounter substantial challenges when evaluating biopsies. The increasing rarity of surgical interventions exacerbates this due to improved disease recognition and suspicion. Numerous confounding factors, including the absence of the characteristic histologic features, limited tissue sample size, biopsy artifacts, and the limited value of IgG4 counts, further complicate the diagnostic process. Additionally, many other disorders exhibit clinical and histological features that overlap with IgG4-related disease, intensifying the complexity of interpreting biopsy specimens. This article explores the clinical and histomorphologic features of IgG4-related hepatobiliary disease and its potential mimickers. It offers valuable insights for pathologists and clinicians when confronted with biopsy specimens from hepatobiliary organs.


Subject(s)
Autoimmune Diseases , Cholangitis, Sclerosing , Immunoglobulin G4-Related Disease , Humans , Cholangitis, Sclerosing/diagnosis , Cholangitis, Sclerosing/pathology , Autoimmune Diseases/diagnosis , Autoimmune Diseases/pathology , Biopsy , Immunoglobulin G , Diagnosis, Differential
2.
Gastroenterology ; 166(5): 826-841.e19, 2024 May.
Article in English | MEDLINE | ID: mdl-38266738

ABSTRACT

BACKGROUND & AIMS: Incapacitated regulatory T cells (Tregs) contribute to immune-mediated diseases. Inflammatory Tregs are evident during human inflammatory bowel disease; however, mechanisms driving the development of these cells and their function are not well understood. Therefore, we investigated the role of cellular metabolism in Tregs relevant to gut homeostasis. METHODS: Using human Tregs, we performed mitochondrial ultrastructural studies via electron microscopy and confocal imaging, biochemical and protein analyses using proximity ligation assay, immunoblotting, mass cytometry and fluorescence-activated cell sorting, metabolomics, gene expression analysis, and real-time metabolic profiling utilizing the Seahorse XF analyzer. We used a Crohn's disease single-cell RNA sequencing dataset to infer the therapeutic relevance of targeting metabolic pathways in inflammatory Tregs. We examined the superior functionality of genetically modified Tregs in CD4+ T-cell-induced murine colitis models. RESULTS: Mitochondria-endoplasmic reticulum appositions, known to mediate pyruvate entry into mitochondria via voltage-dependent anion channel 1 (VDAC1), are abundant in Tregs. VDAC1 inhibition perturbed pyruvate metabolism, eliciting sensitization to other inflammatory signals reversible by membrane-permeable methyl pyruvate supplementation. Notably, interleukin (IL) 21 diminished mitochondria-endoplasmic reticulum appositions, resulting in enhanced enzymatic function of glycogen synthase kinase 3 ß, a putative negative regulator of VDAC1, and a hypermetabolic state that amplified Treg inflammatory response. Methyl pyruvate and glycogen synthase kinase 3 ß pharmacologic inhibitor (LY2090314) reversed IL21-induced metabolic rewiring and inflammatory state. Moreover, IL21-induced metabolic genes in Tregs in vitro were enriched in human Crohn's disease intestinal Tregs. Adoptively transferred Il21r-/- Tregs efficiently rescued murine colitis in contrast to wild-type Tregs. CONCLUSIONS: IL21 triggers metabolic dysfunction associated with Treg inflammatory response. Inhibiting IL21-induced metabolism in Tregs may mitigate CD4+ T-cell-driven chronic intestinal inflammation.


Subject(s)
Colitis , Mitochondria , Animals , Humans , Mice , CD4-Positive T-Lymphocytes/immunology , CD4-Positive T-Lymphocytes/metabolism , Chronic Disease , Colitis/immunology , Colitis/metabolism , Colitis/pathology , Crohn Disease/immunology , Crohn Disease/metabolism , Crohn Disease/pathology , Interleukins/metabolism , Interleukins/pharmacology , Mice, Inbred C57BL , Mitochondria/metabolism , T-Lymphocytes, Regulatory/immunology , Voltage-Dependent Anion Channel 1/metabolism , Voltage-Dependent Anion Channel 1/genetics
3.
Am J Gastroenterol ; 119(4): 662-670, 2024 Apr 01.
Article in English | MEDLINE | ID: mdl-37795907

ABSTRACT

INTRODUCTION: Endoscopic eradication therapy (EET) is standard of care for T1a esophageal adenocarcinoma (EAC). However, data on outcomes in high-risk T1a EAC are limited. We assessed and compared outcomes after EET of low-risk and high-risk T1a EAC, including intraluminal EAC recurrence, extraesophageal metastases, and overall survival. METHODS: Patients who underwent EET for T1a EAC at 3 referral Barrett's esophagus endotherapy units between 1996 and 2022 were included. Patients with submucosal invasion, positive deep margins, or metastases at initial diagnosis were excluded. High-risk T1a EAC was defined as T1a EAC with poor differentiation and/or lymphovascular invasion, with low-risk disease being defined without these features. All pathology was systematically assessed by expert gastrointestinal pathologists. Baseline and follow-up endoscopy and pathology data were abstracted. Time-to-event analyses were performed to compare outcomes between groups. RESULTS: One hundred eighty-eight patients with T1a EAC were included (high risk, n = 45; low risk, n = 143) with a median age of 70 years, and 84% were men. Groups were comparable for age, sex, Barrett's esophagus length, lesion size, and EET technique. Rates of delayed extraesophageal metastases (11.1% vs 1.4%) were significantly higher in the high-risk group ( P = 0.02). There was no significant difference in the rates of intraluminal EAC recurrence ( P = 0.79) and overall survival ( P = 0.73) between the 2 groups. DISCUSSION: Patients with high-risk T1a EAC undergoing successful EET had a substantially higher rate of extraesophageal metastases compared with those with low-risk T1a EAC on long-term follow-up. These data should be factored into discussions with patients while selecting treatment approaches. Additional prospective data in this area are critical.


Subject(s)
Adenocarcinoma , Barrett Esophagus , Esophageal Neoplasms , Male , Humans , Aged , Female , Barrett Esophagus/surgery , Barrett Esophagus/pathology , Prospective Studies , Esophageal Neoplasms/pathology , Adenocarcinoma/pathology , Endoscopy, Gastrointestinal
4.
Mol Genet Metab ; 138(4): 107559, 2023 04.
Article in English | MEDLINE | ID: mdl-36965289

ABSTRACT

Phosphomannomutase-2-congenital disorder of glycosylation (PMM2-CDG) is the most common CDG and presents with highly variable features ranging from isolated neurologic involvement to severe multi-organ dysfunction. Liver abnormalities occur in in almost all patients and frequently include hepatomegaly and elevated aminotransferases, although only a minority of patients develop progressive hepatic fibrosis and liver failure. No curative therapies are currently available for PMM2-CDG, although investigation into several novel therapies is ongoing. We report the first successful liver transplantation in a 4-year-old patient with PMM2-CDG. Over a 3-year follow-up period, she demonstrated improved growth and neurocognitive development and complete normalization of liver enzymes, coagulation parameters, and carbohydrate-deficient transferrin profile, but persistently abnormal IgG glycosylation and recurrent upper airway infections that did not require hospitalization. Liver transplant should be considered as a treatment option for PMM2-CDG patients with end-stage liver disease, however these patients may be at increased risk for recurrent bacterial infections post-transplant.


Subject(s)
Congenital Disorders of Glycosylation , Liver Transplantation , Phosphotransferases (Phosphomutases) , Female , Humans , Child, Preschool , Glycosylation , Follow-Up Studies , Phosphotransferases (Phosphomutases)/genetics , Congenital Disorders of Glycosylation/complications , Congenital Disorders of Glycosylation/genetics , Liver/metabolism , Immunoglobulin G
5.
Cell Rep ; 42(1): 112003, 2023 01 31.
Article in English | MEDLINE | ID: mdl-36641749

ABSTRACT

Linear nevus sebaceous syndrome (LNSS) is a neurocutaneous disorder caused by somatic gain-of-function mutations in KRAS or HRAS. LNSS brains have neurodevelopmental defects, including cerebral defects and epilepsy; however, its pathological mechanism and potentials for treatment are largely unclear. We show that introduction of KRASG12V in the developing mouse cortex results in subcortical nodular heterotopia and enhanced excitability, recapitulating major pathological manifestations of LNSS. Moreover, we show that decreased firing frequency of inhibitory neurons without KRASG12V expression leads to disrupted excitation and inhibition balance. Transcriptional profiling after destabilization domain-mediated clearance of KRASG12V in human neural progenitors and differentiating neurons identifies reversible functional networks underlying LNSS. Neurons expressing KRASG12V show molecular changes associated with delayed neuronal maturation, most of which are restored by KRASG12V clearance. These findings provide insights into the molecular networks underlying the reversibility of some of the neuropathologies observed in LNSS caused by dysregulation of the RAS pathway.


Subject(s)
Epilepsy , Nevus, Sebaceous of Jadassohn , Mice , Animals , Humans , Proto-Oncogene Proteins p21(ras)/genetics , Nevus, Sebaceous of Jadassohn/genetics , Nevus, Sebaceous of Jadassohn/pathology , Neuropathology , Mutation/genetics
6.
Hum Pathol ; 131: 108-115, 2023 01.
Article in English | MEDLINE | ID: mdl-36470475

ABSTRACT

Large B-cell lymphoma (LBL) with interferon regulatory factor 4 (IRF4) rearrangement (LBL-IRF4), a provisional entity in the 2017 WHO classification, primarily arises in children and young adults and has a favorable prognosis. However, few studies have addressed the clinicopathologic and cytogenetic features of older adults with IRF4-rearranged B-cell lymphomas. From a database of all internal and external cases (08/01/2015 to 12/01/2020) on which interphase fluorescence in situ hybridization was performed at the Mayo Clinic, we identified 43 patients with B-cell lymphoma and IRF4 rearrangements. Consistent features included large cell morphology, expression of CD20, BCL6, and MUM1, and absence of MYC-R. All pediatric cases (n = 12) arose in Waldeyer's ring (WR), cervical lymph node (CLN), or bowel, and lacked BCL6-R and BCL2-R, and all but one showed classic morphology. Adults with WR, CLN, or bowel involvement (n = 22) were younger (median 32 years). Their lymphomas resembled pediatric cases morphologically and lacked BCL2-R, although 30% harbored BCL6-R (P = 0.043). Lymphomas that involved other anatomic sites (n = 9) arose in older adults (median 68 years; P = 0.002) and often showed atypical morphology (P < 0.001). All lacked BCL6-R and 2 of 4 harbored BCL2-R (P < 0.001). LBL-IRF4 - arising in WR, CLN, or bowel may represent a distinct clinicopathologic entity characterized by pediatric/younger adult age, classic morphology, and lack of BCL2-R. In contrast, B-cell lymphomas with IRF4-R that arise in other sites usually involve older adults, are often morphologically atypical and/or harbor BCL2-R, and may be more akin to diffuse LBL, not otherwise specified.


Subject(s)
Lymphoma, Large B-Cell, Diffuse , Aged , Child , Humans , Young Adult , Gene Rearrangement , In Situ Hybridization, Fluorescence , Lymphoma, Large B-Cell, Diffuse/pathology , Prognosis , Proto-Oncogene Proteins c-bcl-2/genetics , Proto-Oncogene Proteins c-bcl-6/genetics , Proto-Oncogene Proteins c-myc/genetics
7.
Mol Psychiatry ; 28(2): 856-870, 2023 02.
Article in English | MEDLINE | ID: mdl-36357673

ABSTRACT

Although large-scale genome-wide association studies (GWAS) have identified an association between MAD1L1 (Mitotic Arrest Deficient-1 Like 1) and the pathology of schizophrenia, the molecular mechanisms underlying this association remain unclear. In the present study, we aimed to address these mechanisms by examining the role of MAD1 (the gene product of MAD1L1) in key neurodevelopmental processes in mice and human organoids. Our findings indicated that MAD1 is highly expressed during active cortical development and that MAD1 deficiency leads to impairments in neuronal migration and neurite outgrowth. We also observed that MAD1 is localized to the Golgi apparatus and regulates vesicular trafficking from the Golgi apparatus to the plasma membrane, which is required for the growth and polarity of migrating neurons. In this process, MAD1 physically interacts and collaborates with the kinesin-like protein KIFC3 (kinesin family member C3) to regulate the morphology of the Golgi apparatus and neuronal polarity, thereby ensuring proper neuronal migration and differentiation. Consequently, our findings indicate that MAD1 is an essential regulator of neuronal development and that alterations in MAD1 may underlie schizophrenia pathobiology.


Subject(s)
Neocortex , Schizophrenia , Animals , Humans , Mice , Cell Cycle Proteins/genetics , Genome-Wide Association Study , Kinesins/genetics , Kinesins/metabolism , Neocortex/metabolism , Neurons/metabolism , Schizophrenia/genetics , Schizophrenia/metabolism
8.
Hum Pathol ; 132: 20-30, 2023 02.
Article in English | MEDLINE | ID: mdl-35932826

ABSTRACT

Celiac disease (CD) is an immunoallergic enteropathy affecting genetically susceptible individuals upon dietary exposure to gluten. In current clinical practice, the diagnosis of CD is based on a combination of clinical, serologic, and histologic factors with the possible exception of pediatric patients. Histopathologic evaluation of small intestinal tissue plays a critical role in the disease diagnosis and management, despite many practical challenges. Recently published best practice guidelines help to standardize biopsy sample procurement, tissue preparation, histology interpretation, and reporting, to optimize patient care. In addition, an increasing demand for monitoring the disease course, particularly demonstrating the efficacy of dietary and nondietary interventions for disease management, calls for the use of quantitative histology. With the advent of a gradual transition toward digital pathology in routine diagnostic practice, quantitative histopathologic evaluation in CD shows a promising future.


Subject(s)
Celiac Disease , Humans , Child , Celiac Disease/diagnosis , Celiac Disease/therapy , Genetic Predisposition to Disease
9.
Am J Case Rep ; 23: e937628, 2022 Nov 21.
Article in English | MEDLINE | ID: mdl-36404611

ABSTRACT

BACKGROUND Langerhans cell histiocytosis (LCH) is a rare condition caused by a neoplastic proliferation of myeloid cells. It can present as a single-system or multi-system disorder. Worse prognosis is associated with the hematopoietic system (spleen, liver, bone marrow), which is routinely observed in multi-system disease. Because of the varied presentation of this disorder, diagnosis can be difficult, and therefore suitable treatment can be delayed. CASE REPORT We report a case of hepatic LCH in a 51-year-old man who presented with epigastric abdominal pain, with imaging demonstrating a hepatic nodule. A low ejection fraction on hepatobiliary iminodiacetic acid scan suggested chronic cholecystitis. Therefore, the patient underwent a cholecystectomy for biliary dyskinesia, in which liver nodules were noted, and biopsies were taken. The biopsies demonstrated characteristic findings of LCH along with positive immunohistochemical markers and negative BRAF V600E mutation. Radiologic and pathologic findings were consistent with LCH within the liver, associated with bile duct injury and mild biliary obstruction. The patient was placed on a cladribine regimen. His abdominal pain improved. CONCLUSIONS LCH limited to the liver is uncommon and can appear as chronic biliary disease, as was suspected in this case. Despite the poor prognosis of hematopoietic LCH, early recognition can lead to better outcome and chemotherapy susceptibility. This patient was most likely in the first stage of liver LCH, given his presentation, which could have aided his response to chemotherapy. The lack of BRAF V600E mutation could have contributed to a positive prognosis and more possibilities for treatment.


Subject(s)
Histiocytosis, Langerhans-Cell , Proto-Oncogene Proteins B-raf , Male , Humans , Middle Aged , Proto-Oncogene Proteins B-raf/genetics , Mutation , Histiocytosis, Langerhans-Cell/diagnosis , Liver , Abdominal Pain
10.
Nat Commun ; 13(1): 6750, 2022 11 08.
Article in English | MEDLINE | ID: mdl-36347849

ABSTRACT

Magnetically responsive composites can impart maneuverability to miniaturized robots. However, collective actuation of these composite robots has rarely been achieved, although conducting cooperative tasks is a promising strategy for accomplishing difficult missions with a single robot. Here, we report multimodal collective swimming of ternary-nanocomposite-based magnetic robots capable of on-demand switching between rectilinear translational swimming and rotational swimming. The nanocomposite robots comprise a stiff yet lightweight carbon nanotube yarn (CNTY) framework surrounded by a magnetic polymer composite, which mimics the hierarchical architecture of musculoskeletal systems, yielding magnetically articulated multiple robots with an agile above-water swimmability (~180 body lengths per second) and modularity. The multiple robots with multimodal swimming facilitate the generation and regulation of vortices, enabling novel vortex-induced transportation of thousands of floating microparticles and heavy semi-submerged cargos. The controllable collective actuation of these biomimetic nanocomposite robots can lead to versatile robotic functions, including microplastic removal, microfluidic vortex control, and transportation of pharmaceuticals.


Subject(s)
Nanocomposites , Robotics , Swimming/physiology , Plastics , Biomimetics
11.
Mol Cells ; 45(7): 465-478, 2022 Jul 31.
Article in English | MEDLINE | ID: mdl-35444070

ABSTRACT

MicroRNAs (miRNAs) are a class of small non-coding RNAs that regulate the expression of target messenger RNA (mRNA) complementary to the 3' untranslated region (UTR) at the post-transcriptional level. Hsa-miR-422a, which is commonly known as miRNA derived from transposable element (MDTE), was derived from short interspersed nuclear element (SINE). Through expression analysis, hsa-miR-422a was found to be highly expressed in both the small intestine and liver of crab-eating monkey. AT-Rich Interaction Domain 5 B (ARID5B) was selected as the target gene of hsa-miR-422a, which has two binding sites in both the exon and 3'UTR of ARID5B. To identify the interaction between hsa-miR-422a and ARID5B, a dual luciferase assay was conducted in HepG2 cell line. The luciferase activity of cells treated with the hsa-miR-422a mimic was upregulated and inversely downregulated when both the hsa-miR-422a mimic and inhibitor were administered. Nuclear factor erythroid-2 (NF-E2) was selected as the core transcription factor (TF) via feed forward loop analysis. The luciferase expression was downregulated when both the hsa-miR-422a mimic and siRNA of NF-E2 were treated, compared to the treatment of the hsa-miR-422a mimic alone. The present study suggests that hsa-miR-422a derived from SINE could bind to the exon region as well as the 3'UTR of ARID5B. Additionally, hsa-miR-422a was found to share binding sites in ARID5Bwith several TFs, including NF-E2. The hsa-miR-422a might thus interact with TF to regulate the expression of ARID5B, as demonstrated experimentally. Altogether, hsa-miR-422a acts as a super enhancer miRNA of ARID5Bby collaborating with TF and NF-E2.


Subject(s)
MicroRNAs , 3' Untranslated Regions/genetics , Gene Expression Regulation , Luciferases/genetics , MicroRNAs/metabolism , RNA, Messenger
12.
Insights Imaging ; 12(1): 110, 2021 Aug 09.
Article in English | MEDLINE | ID: mdl-34370093

ABSTRACT

MRI is routinely used for rectal cancer staging to evaluate tumor extent and to inform decision-making regarding surgical planning and the need for neoadjuvant and adjuvant therapy. Extramural venous invasion (EMVI), which is intravenous tumor extension beyond the rectal wall on histopathology, is a predictor for worse prognosis. T2-weighted images (T2WI) demonstrate EMVI as a nodular-, bead-, or worm-shaped structure of intermediate T2 signal with irregular margins that arises from the primary tumor. Correlative diffusion-weighted images demonstrate intermediate to high signal corresponding to EMVI, and contrast enhanced T1-weighted images demonstrate tumor signal intensity in or around vessels. Diffusion-weighted and post contrast images may increase diagnostic performance but decrease inter-observer agreement. CT may also demonstrate obvious EMVI and is potentially useful in patients with a contraindication for MRI. This article aims to review the spectrum of imaging findings of EMVI of rectal cancer on MRI and CT, to summarize the diagnostic accuracy and inter-observer agreement of imaging modalities for its presence, to review other rectal neoplasms that may cause EMVI, and to discuss the clinical significance and role of MRI-detected EMVI in staging and restaging clinical scenarios.

13.
Int J Surg Pathol ; 29(6): 606-614, 2021 Sep.
Article in English | MEDLINE | ID: mdl-33736504

ABSTRACT

Aims. Mucinous cystic neoplasms (MCNs) are cystic neoplasms with mucinous epithelium surrounded by ovarian-like stroma. Extraovarian MCN occurring in the liver and pancreas have been well characterized. However, only rare case reports of MCN arising outside of these locations have been reported. MCNs arising in unusual locations should enter the differential diagnosis of mucinous intra-abdominal tumors and must be distinguished from more common mimics. Therefore, we aimed to examine a series of MCNs of the retroperitoneum and mesentery to characterize the clinicopathologic features of this entity. Methods and results. Seven MCNs arising in the abdominal mesentery or retroperitoneum were retrospectively identified. A clinicopathologic, histologic, and immunohistochemical (keratin 7, keratin 19, keratin 20, calretinin, inhibin-α, steroidogenic factor-1 (SF-1), estrogen receptor (ER), progesterone receptor (PR), PAX8, CDX2, and CD10) analysis was performed. All 7 MCNs were from females with a median age of 41 years old and a median size of 8 cm. All cases demonstrated mucinous with or without concomitant non-mucinous epithelium overlying spindle cell ovarian-like stroma. Luteinized cells were noted. The epithelium was positive for keratin 7 and keratin 19 in all 7 cases, while the stroma expressed ER, PR, and SF-1 in all cases stained. Calretinin was focally positive in the stroma of 3 of 7 cases, while inhibin-α was focally expressed in 5 of 6 cases. Conclusions. These results highlight the clinicopathologic, histologic, and immunophenotypic similarities between MCNs of the mesentery, retroperitoneum, pancreas, and liver. Overlapping features suggest a common histogenesis for all MCNs, which could include periductal fetal mesenchyme, aberrant migration of primordial germ cells, or abnormal differentiation or metaplasia of the embryonic coelomic epithelium.


Subject(s)
Cystadenocarcinoma, Mucinous/diagnosis , Mesentery/pathology , Retroperitoneal Neoplasms/diagnosis , Adult , Aged , Biomarkers, Tumor/analysis , Biomarkers, Tumor/metabolism , Cystadenocarcinoma, Mucinous/pathology , Diagnosis, Differential , Female , Humans , Immunohistochemistry , Male , Middle Aged , Retroperitoneal Neoplasms/pathology , Retroperitoneal Space/pathology , Retrospective Studies
14.
Sci Rep ; 11(1): 3139, 2021 02 04.
Article in English | MEDLINE | ID: mdl-33542430

ABSTRACT

Transposable elements (TEs) are DNA sequences that cut or introduced into the genome, and they represent a massive portion of the human genome. TEs generate a considerable number of microRNAs (miRNAs) are derived from TEs (MDTEs). Numerous miRNAs are related to cancer, and hsa-miRNA-625 is a well-known oncomiR derived from long interspersed nuclear elements (LINEs). The relative expression of hsa-miRNA-625-5p differs in humans, chimpanzees, crab-eating monkeys, and mice, and four primers were designed against the 3'UTR of GATAD2B to analyze the different quantities of canonical binding sites and the location of miRNA binding sites. Luciferase assay was performed to score for the interaction between hsa-miRNA-625 and the 3'UTR of GATAD2B, while blocking NF-κB. In summary, the different numbers of canonical binding sites and the locations of miRNA binding sites affect gene expression, and NF-κB induces the enhancer activity of hsa-miRNA-625-5p by sharing the binding sites.


Subject(s)
DNA Transposable Elements , Enhancer Elements, Genetic , Genome , Long Interspersed Nucleotide Elements , MicroRNAs/genetics , NF-kappa B/genetics , Repressor Proteins/genetics , 3' Untranslated Regions , A549 Cells , Animals , Base Pairing , Computational Biology/methods , DNA Primers/chemical synthesis , DNA Primers/metabolism , Genes, Reporter , Humans , Luciferases/genetics , Luciferases/metabolism , Macaca fascicularis , Mice , MicroRNAs/metabolism , NF-kappa B/metabolism , Pan troglodytes , Repressor Proteins/metabolism
15.
Sci Rep ; 11(1): 3665, 2021 02 11.
Article in English | MEDLINE | ID: mdl-33574427

ABSTRACT

Transposable elements cause alternative splicing (AS) in different ways, contributing to transcript diversification. Alternative polyadenylation (APA), one of the AS events, is related to the generation of mRNA isoforms in 70% of human genes. In this study, we tried to investigate AluYRa1s located at the terminal region of cynomolgus monkey genes, utilizing both computational analysis and molecular experimentation. We found that ten genes had AluYRa1 at their 3' end, and nine of these AluYRa1s were sense-oriented. Furthermore, in seven genes, AluYRa1s were expected to have a similar consensus sequence for polyadenylation cleavage. Additional computational analysis using the annotation files from the UCSC database showed that AluYRa1 was more involved in polyadenylation than in open reading frame exon splicing. To examine the extent of AluYRa1 involvement in polyadenylation, RNA-seq data from 30 normal cynomolgus monkeys were analyzed using TAPAS, a recently devised software that detects all the promising polyadenylation sites including APA sites. We observed that approximately 74% of possible polyadenylation sites in the analyzed genes were provided by sense-oriented AluYRa1. In conclusion, AluYRa1 is an Old-World monkey-specific TE, and its sense-oriented insertion at the 3'UTR region tends to provide a favorable environment for polyadenylation, diversifying gene transcripts.


Subject(s)
Alu Elements/genetics , Evolution, Molecular , Polyadenylation/genetics , Transcription, Genetic , 3' Untranslated Regions/genetics , Alternative Splicing/genetics , Animals , Cell Lineage/genetics , Humans , Macaca fascicularis/genetics , RNA Isoforms/genetics , RNA Splicing/genetics , Software
16.
Orphanet J Rare Dis ; 16(1): 20, 2021 01 07.
Article in English | MEDLINE | ID: mdl-33413482

ABSTRACT

BACKGROUND: The congenital disorders of glycosylation (CDG) are a heterogeneous group of rare metabolic diseases with multi-system involvement. The liver phenotype of CDG varies not only according to the specific disorder, but also from patient to patient. In this study, we sought to identify common patterns of liver injury among patients with a broad spectrum of CDG, and to provide recommendations for follow-up in clinical practice. METHODS: Patients were enrolled in the Frontiers in Congenital Disorders of Glycosylation natural history study. We analyzed clinical history, molecular genetics, serum markers of liver injury, liver ultrasonography and transient elastography, liver histopathology (when available), and clinical scores of 39 patients with 16 different CDG types (PMM2-CDG, n = 19), with a median age of 7 years (range: 10 months to 65 years). For patients with disorders which are treatable by specific interventions, we have added a description of liver parameters on treatment. RESULTS: Our principal findings are (1) there is a clear pattern in the evolution of the hepatocellular injury markers alanine aminotransferase and aspartate aminotransferase according to age, especially in PMM2-CDG patients but also in other CDG-I, and that the cholangiocellular injury marker gamma-glutamyltransferase is not elevated in most patients, pointing to an exclusive hepatocellular origin of injury; (2) there is a dissociation between liver ultrasound and transient elastography regarding signs of liver fibrosis; (3) histopathological findings in liver tissue of PMM2-CDG patients include cytoplasmic glycogen deposits; and (4) most CDG types show more than one type of liver injury. CONCLUSIONS: Based on these findings, we recommend that all CDG patients have regular systematic, comprehensive screening for liver disease, including physical examination (for hepatomegaly and signs of liver failure), laboratory tests (serum alanine aminotransferase and aspartate aminotransferase), liver ultrasound (for steatosis and liver tumors), and liver elastography (for fibrosis).


Subject(s)
Congenital Disorders of Glycosylation , Phosphotransferases (Phosphomutases) , Congenital Disorders of Glycosylation/genetics , Follow-Up Studies , Glycosylation , Humans , Infant , Liver/diagnostic imaging , Liver/metabolism
17.
Am J Clin Pathol ; 155(3): 397-404, 2021 02 11.
Article in English | MEDLINE | ID: mdl-33145590

ABSTRACT

OBJECTIVES: Sclerosing pneumocytomas are rare pulmonary neoplasms that are typically benign. However, rare patients experience progressive disease, and therapy targeting specific genetic underpinnings could be an attractive therapeutic option. Recent studies have found recurrent AKT 1 mutations in sclerosing pneumocytoma, but little is known about whether oncogenic fusion genes may also be present. METHODS: To better understand the genetic background, 10 sclerosing pneumocytomas were subjected to next-generation sequencing cancer mutation panel testing (n = 9) and/or RNA sequencing (n = 3). The patients were all women (average age, 47 years; range, 17-74 years). RESULTS: Eight patients had solitary sclerosing pneumocytomas, while one had two tumors, and one had many bilateral tumors. Recurrent mutations were noted in genes involved in the mTOR pathway, including AKT1, PIK3R1, and PTEN. AKT1 alterations were particularly common, present in 78%. No recurrent genetic fusions were identified. The patient in our study with multiple bilateral lesions was treated with the mammalian target of rapamycin (mTOR) inhibitor everolimus, with no objective radiographic evidence of treatment response after 4 months. CONCLUSIONS: Our data further support that abnormal activation of the mTOR pathway is a consistent genetic event in sclerosing pneumocytoma. This warrants further exploration to determine if mTOR pathway inhibitors may be effective in patients with metastatic or recurrent disease.


Subject(s)
Pulmonary Sclerosing Hemangioma/genetics , TOR Serine-Threonine Kinases/genetics , Adolescent , Adult , Aged , Biomarkers, Tumor/genetics , Female , High-Throughput Nucleotide Sequencing , Humans , Middle Aged , Retrospective Studies , Sequence Analysis, RNA , Signal Transduction/physiology , Translocation, Genetic , Young Adult
18.
Case Rep Transplant ; 2020: 8894922, 2020.
Article in English | MEDLINE | ID: mdl-33381347

ABSTRACT

Herein we present a patient that underwent a liver transplant due to primary biliary cholangitis (PBC) and after 9 years developed multiple myeloma. Following the cessation of mycophenolate mofetil and 2 weeks after lenalidomide treatment was started, the patient experienced acute cellular rejection. The patient recovered after treatment with corticosteroids, resumption of mycophenolate mofetil, and cessation of lenalidomide. Lenalidomide-associated allograft rejection has been reported in other organs. However, this is the first case report of liver rejection induced by lenalidomide.

19.
Aging (Albany NY) ; 13(1): 846-864, 2020 12 03.
Article in English | MEDLINE | ID: mdl-33290253

ABSTRACT

African green monkeys (AGMs, Chlorocebus aethiops) are Old World monkeys which are used as experimental models in biomedical research. Recent technological advances in next generation sequencing are useful for unraveling the genetic mechanisms underlying senescence, aging, and age-related disease. To elucidate the normal aging mechanisms in older age, the blood transcriptomes of nine healthy, aged AGMs (15‒23 years old), were analyzed over two years. We identified 910‒1399 accumulated differentially expressed genes (DEGs) in each individual, which increased with age. Aging-related DEGs were sorted across the three time points. A major proportion of the aging-related DEGs belonged to gene ontology (GO) categories involved in translation and rRNA metabolic processes. Next, we sorted common aging-related DEGs across three time points over two years. Common aging-related DEGs belonged to GO categories involved in translation, cellular component biogenesis, rRNA metabolic processes, cellular component organization, biogenesis, and RNA metabolic processes. Furthermore, we identified 29 candidate aging genes that were upregulated across the time series analysis. These candidate aging genes were linked to protein synthesis. This study describes a changing gene expression pattern in AGMs during aging using longitudinal transcriptome sequencing. The candidate aging genes identified here may be potential targets for the treatment of aging.


Subject(s)
Aging/genetics , Mitochondrial Membranes/metabolism , Proteasome Endopeptidase Complex/genetics , Ribosomes/genetics , Spliceosomes/genetics , Animals , Chlorocebus aethiops , Gene Expression Profiling , Gene Ontology , Longitudinal Studies , Protein Biosynthesis/genetics , Protein Folding , RNA/metabolism , RNA Splicing/genetics , RNA, Ribosomal/metabolism , RNA-Seq , Ribosome Subunits/genetics
20.
Ann Diagn Pathol ; 49: 151589, 2020 Dec.
Article in English | MEDLINE | ID: mdl-32947230

ABSTRACT

Malignant vascular neoplasms such as epithelioid hemangioendothelioma (EHE) and angiosarcoma (AS) can arise within the liver. The aim of this study was to study the expression of keratins CK7, AE1/AE3 and OSCAR in primary hepatic EHE and AS. 9 cases of hepatic EHE and 13 cases of hepatic AS were stained with ERG, CK7, keratin AE1/AE3 and keratin OSCAR. Their expression was graded as 1+ (1-25% of tumor cells positive), 2+ (26-50%), 3+ (51-75%) or 4+ (>75%). ERG was positive in all 9 (100%) EHEs and all 13 (100%) ASs. CK7 was positive in 5/9 (56%) EHEs (2, 1+; 1, 2+; 1, 3+; 1, 4+) and 1/13 (8%) AS (2+). Keratin OSCAR was positive in 6/9 (67%) EHEs (5, 1+; 1, 2+) and 4/13 (31%) ASs (2, 1+; 1, 2+; 1, 4+). Keratin AE1/AE3 was positive in 6/9 (67%) EHEs (3, 1+; 3; 2+) and 4/13 (31%) ASs (2, 1+; 1, 2+; 1, 4+). Overall, 6/ 9 (67%) EHEs were positive for at least one keratin marker, of which 5 were positive for all 3 keratins (AE1/AE3, OSCAR and CK7) while 1 was positive only for 2 keratins (OSCAR and AE1/AE3). 4/13 (31%) of ASs were positive for both keratins OSCAR and AE1/AE3, of which 1 case was also positive for CK7. Aberrant keratin expression is common in primary hepatic EHEs (67%) and ASs (31%). Awareness of this diagnostic pitfall is important for avoiding misdiagnosis of these primary hepatic malignant vascular tumors as carcinomas.


Subject(s)
Hemangioendothelioma, Epithelioid/diagnosis , Hemangiosarcoma/diagnosis , Keratins/metabolism , Liver Neoplasms/diagnosis , Adolescent , Adult , Aged , Aged, 80 and over , Biomarkers, Tumor/analysis , Carcinoma/diagnosis , Diagnosis, Differential , Female , Hemangioendothelioma, Epithelioid/metabolism , Hemangiosarcoma/metabolism , Humans , Keratins/analysis , Liver Neoplasms/metabolism , Male , Middle Aged , Young Adult
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