A STUDY ON CORRELATION BETWEEN ELECTROMYOGRAPHICAL AND MORPHOLOGICAL FINDINGS OF BACK MUSCLES IN SCOLIOSIS, ESPECIALLY CHANGES IN THE INTRAMUSCULAR NERVE ENDINGS.

3. In the cases of neurofibromatosis with scoliosis, intramuscular nerve endings showed almost normal morphological appearances but, comparative histograms of the diameters of the end-plates in each 5μ. group showed 2 peak formations.. One of these cases recorded fibrillation voltage at the concave side showed abnormal staining of terminal filamints of the end-plates in deep back muscles at the same side. The sensory nerve endings showed perfectly preserved histological appearances. 4. In cases of rachitogenic scoliosis, motor end-plates of the back muscles were observed using the histochemical method of cholinesterase staining and vital staining with methylene blue. Histograms of the diameters of the end-plates showed a noted reduction in size and in number of units, but no apparent degenerative changes in sensory and motor endings or in terminal axons were seen. 5. In a case of discogenic scoliosis, silver impregnation was applied on the back muscles at both sides of the curvature. In the convex side, collateral branching and swelling of the nerve fibers was observed and also the motor end-plates showed an abnormality of staining in terminal arborization, but, fibrillation voltage was not recorded. 6. In congenital scoliosis, electromyographic findings failed to trace fibrillation voltage, but, terminal axons in deep muscles, showed collateral branchig and an increased terminal innervation ratio in a highly affected case. In slightly curved cases, atrophic changes, and intramuscular fibers and endings appeared almost normal. 7. In the so-called idiopathic scoliosis , about 50% had not traced fibrillation voltage in the paravertebral back muscles. Degenerative findings.of the intramuscular nerve fibers and endings were not observed, but comparative histograms of the diameters of the end -plates showed 2 peak formations in the convex side of the back muscles. Innervation ratio was not changed and sensory nerve endings showed normal appearances.8. In idiopathic scoliosis, characterised by fibrillation voltage which was traced in the paravertebral back muscles, intramuscular motor nerve endings were degenerated in deep muscles of the convex side, and disseminated muscle atrophy in the concave side. In deep muscles of the convex side, terminal axons showed collateral branching and motor endplates, club-like swelling, and 2 peak formations of the histograms of the diameters. However, sensory nerve endings were normal in appearance. These findings lead to a conclusion that changes in the motor endings observed in paralytic scoliosis differed from histological changes in the cases of idiopathic scoliosis, in which fibrillation voltage had been traced. In paralytic scoliosis, histological changes of the back muscles showed various kinds of degenerative findings, but, in cases of idiopathic scoliosis with fibrillation voltage they showed collateral branching and degenerative changes of the end-plates, respectively, in deep back muscles especially in the convex side. In other kinds of scoliosis, neuromuscular changes were largely influenced by their own basic disorders such as, degeneration of discs, abnormality of vertebral bodies, nutritional deficiencies and metablic disorders. In the cases of idiopathic scoliosis without fibrillation voltage intramuscular nerve endings were preserved in good condition, but almost all of the cases of non-paralytic scoliosis showed an abnormality of the histograms of the endplates, or atrophic changes in deep muscles. Prophylactic treatment must be employed on the back muscles for the prevention of further deformity and progression of scoliosis.An electromyographical and histological study on 20 cases of various kinds of scoliosis was carried out. In particular, a biopsy of the back muscles at the apex of the primary curve was performed using the methods of gold chloride staining, silver impregnation modified by Seto, vital staining with methylene blue, and the histochemical demonstration of cholinesterase on the subneural apparatuses of the endplates. Specimens were taken from superficial (M. longissimus dorsi) and deep (M. multifidus) back muscles of scoliosis patients and in all cases, an electromyographic fibrillation voltage was picked up under deep general anesthesia with ether. This was done from the paravertebral back muscles and a comparison of histologic and electromyographic findings was performed. The results obtained are summarized as follows : 1. Motor end-plates of normal back muscles, dissected at autopsy from adults were found to be concentrated in band-like narrow zones and situated at the mid-point of the muscle fibers. Through comparative histograms of the diameters of subneural apparatuses and those of the end-plates of gold chloride staining showed a close correlation. 2. Intramuscular endings in the cases of paralytic scoliosis showed remarkable collateral axonic sprouting and various kinds of pathological changes of the end-plates, multiple innervation, large and and small end-plates, thickened terminal filaments, failure to stain, irregular swelling, and abnormal terminal expansion. The motor endings of the musclespindle were also remarkably degenerated but sensory nerve fibers and endings remained undisturbed. In neuromuscular endings, pathological changes of the back muscles at the apex of the primary curve, displayed a distinguishing feature in a lack of uniformity in the degree of alignment and curvature, but, compared with superficial muscles, the deep muscles were significantly involved. In all cases a giant spike and fibrillation voltage was recorded from wide-spread various parts of the back muscles

Genomic and transcriptomic analyses of thyroid cancers identify DICER1 somatic mutations in adult follicular-patterned RAS-like tumors

BackgroundPapillary thyroid carcinoma (PTC) is the most common type of thyroid cancer (TC). Several genomic and transcriptomic studies explored the molecular landscape of follicular cell-derived TCs, and BRAFV600E, RAS mutations, and gene fusions are well-established drivers. DICER1 mutations were described in specific sets of TC patients but represent a rare event in adult TC patients.MethodsHere, we report the molecular characterization of 30 retrospective follicular cell-derived thyroid tumors, comprising PTCs (90%) and poorly differentiated TCs (10%), collected at our Institute. We performed DNA whole-exome sequencing using patient-matched control for somatic mutation calling, and targeted RNA-seq for gene fusion detection. Transcriptional profiles established in the same cohort by microarray were investigated using three signaling-related gene signatures derived from The Cancer Genome Atlas (TCGA).ResultsThe occurrence of BRAFV600E (44%), RAS mutations (13%), and gene fusions (13%) was confirmed in our cohort. In addition, in two patients lacking known drivers, mutations of the DICER1 gene (p.D1709N and p.D1810V) were identified. DICER1 mutations occur in two adult patients with follicular-pattern lesions, and in one of them a second concurrent DICER1 mutation (p.R459*) is also observed. Additional putative drivers include ROS1 gene (p.P2130A mutation), identified in a patient with a rare solid-trabecular subtype of PTC. Transcriptomics indicates that DICER1 tumors are RAS-like, whereas the ROS1-mutated tumor displays a borderline RAS-/BRAF-like subtype. We also provide an overview of DICER1 and ROS1 mutations in thyroid lesions by investigating the COSMIC database.ConclusionEven though small, our series recapitulates the genetic background of PTC. Furthermore, we identified DICER1 mutations, one of which is previously unreported in thyroid lesions. For these less common alterations and for patients with unknown drivers, we provide signaling information applying TCGA-derived classification

The genomics of desmoplastic small round cell tumor reveals the deregulation of genes related to DNA damage response, epithelial–mesenchymal transition, and immune response

Abstract Background Desmoplastic small round cell tumor (DSRCT) is a rare, aggressive, and poorly investigated simple sarcoma with a low frequency of genetic deregulation other than an Ewing sarcoma RNA binding protein 1 (EWSR1)-Wilm’s tumor suppressor (WT1) translocation. We used whole-exome sequencing to interrogate six consecutive pre-treated DSRCTs whose gene expression was previously investigated. Methods DNA libraries were prepared from formalin-fixed, paraffin-embedded archival tissue specimens following the Agilent SureSelectXT2 target enrichment protocol and sequenced on Illumina NextSeq 500. Raw sequence data were aligned to the reference genome with Burrows–Wheeler Aligner algorithm. Somatic mutations and copy number alterations (CNAs) were identified using MuTect2 and EXCAVATOR2, respectively. Biological functions associated with altered genes were investigated through Ingenuity Pathway Analysis (IPA) software. Results A total of 137 unique somatic mutations were identified: 133 mutated genes were case-specific, and 2 were mutated in two cases but in different positions. Among the 135 mutated genes, 27% were related to two biological categories: DNA damage-response (DDR) network that was also identified through IPA and mesenchymal–epithelial reverse transition (MErT)/epithelial–mesenchymal transition (EMT) already demonstrated to be relevant in DSRCT. The mutated genes in the DDR network were involved in various steps of transcription and particularly affected pre-mRNA. Half of these genes encoded RNA-binding proteins or DNA/RNA-binding proteins, which were recently recognized as a new class of DDR players. CNAs in genes/gene families, involved in MErT/EMT and DDR, were recurrent across patients and mostly segregated in the MErT/EMT category. In addition, recurrent gains of regions in chromosome 1 involving many MErT/EMT gene families and loss of one arm or the entire chromosome 6 affecting relevant immune-regulatory genes were recorded. Conclusions The emerging picture is an extreme inter-tumor heterogeneity, characterized by the concurrent deregulation of the DDR and MErT/EMT dynamic and plastic programs that could favour genomic instability and explain the refractory DSRCT profile

DataSheet_1_Genomic and transcriptomic analyses of thyroid cancers identify DICER1 somatic mutations in adult follicular-patterned RAS-like tumors.pdf

BackgroundPapillary thyroid carcinoma (PTC) is the most common type of thyroid cancer (TC). Several genomic and transcriptomic studies explored the molecular landscape of follicular cell-derived TCs, and BRAFV600E, RAS mutations, and gene fusions are well-established drivers. DICER1 mutations were described in specific sets of TC patients but represent a rare event in adult TC patients.MethodsHere, we report the molecular characterization of 30 retrospective follicular cell-derived thyroid tumors, comprising PTCs (90%) and poorly differentiated TCs (10%), collected at our Institute. We performed DNA whole-exome sequencing using patient-matched control for somatic mutation calling, and targeted RNA-seq for gene fusion detection. Transcriptional profiles established in the same cohort by microarray were investigated using three signaling-related gene signatures derived from The Cancer Genome Atlas (TCGA).ResultsThe occurrence of BRAFV600E (44%), RAS mutations (13%), and gene fusions (13%) was confirmed in our cohort. In addition, in two patients lacking known drivers, mutations of the DICER1 gene (p.D1709N and p.D1810V) were identified. DICER1 mutations occur in two adult patients with follicular-pattern lesions, and in one of them a second concurrent DICER1 mutation (p.R459*) is also observed. Additional putative drivers include ROS1 gene (p.P2130A mutation), identified in a patient with a rare solid-trabecular subtype of PTC. Transcriptomics indicates that DICER1 tumors are RAS-like, whereas the ROS1-mutated tumor displays a borderline RAS-/BRAF-like subtype. We also provide an overview of DICER1 and ROS1 mutations in thyroid lesions by investigating the COSMIC database.ConclusionEven though small, our series recapitulates the genetic background of PTC. Furthermore, we identified DICER1 mutations, one of which is previously unreported in thyroid lesions. For these less common alterations and for patients with unknown drivers, we provide signaling information applying TCGA-derived classification.</p

Table_2_Genomic and transcriptomic analyses of thyroid cancers identify DICER1 somatic mutations in adult follicular-patterned RAS-like tumors.xlsx

BackgroundPapillary thyroid carcinoma (PTC) is the most common type of thyroid cancer (TC). Several genomic and transcriptomic studies explored the molecular landscape of follicular cell-derived TCs, and BRAFV600E, RAS mutations, and gene fusions are well-established drivers. DICER1 mutations were described in specific sets of TC patients but represent a rare event in adult TC patients.MethodsHere, we report the molecular characterization of 30 retrospective follicular cell-derived thyroid tumors, comprising PTCs (90%) and poorly differentiated TCs (10%), collected at our Institute. We performed DNA whole-exome sequencing using patient-matched control for somatic mutation calling, and targeted RNA-seq for gene fusion detection. Transcriptional profiles established in the same cohort by microarray were investigated using three signaling-related gene signatures derived from The Cancer Genome Atlas (TCGA).ResultsThe occurrence of BRAFV600E (44%), RAS mutations (13%), and gene fusions (13%) was confirmed in our cohort. In addition, in two patients lacking known drivers, mutations of the DICER1 gene (p.D1709N and p.D1810V) were identified. DICER1 mutations occur in two adult patients with follicular-pattern lesions, and in one of them a second concurrent DICER1 mutation (p.R459*) is also observed. Additional putative drivers include ROS1 gene (p.P2130A mutation), identified in a patient with a rare solid-trabecular subtype of PTC. Transcriptomics indicates that DICER1 tumors are RAS-like, whereas the ROS1-mutated tumor displays a borderline RAS-/BRAF-like subtype. We also provide an overview of DICER1 and ROS1 mutations in thyroid lesions by investigating the COSMIC database.ConclusionEven though small, our series recapitulates the genetic background of PTC. Furthermore, we identified DICER1 mutations, one of which is previously unreported in thyroid lesions. For these less common alterations and for patients with unknown drivers, we provide signaling information applying TCGA-derived classification.</p

MOESM6 of Whole exome sequencing and single nucleotide polymorphism array analyses to identify germline alterations in genes associated with testosterone metabolism in a patient with androgen insensitivity syndrome and early-onset colorectal cancer

Additional file 6: Table S6. Chromosomal rearrangements of cancer function-related genes detected in the proband through single nucleotide polymorphism

MOESM1 of Whole exome sequencing and single nucleotide polymorphism array analyses to identify germline alterations in genes associated with testosterone metabolism in a patient with androgen insensitivity syndrome and early-onset colorectal cancer

Additional file 1: Table S1. Variants of tumor genes detected by Sanger sequencing in the proband

Whole-exome sequencing in radically resected gastric cancer (GC): Analysis of patients (pts) with poor prognostic factors from the Italian Trial of Adjuvant Chemotherapy Adenocarcinoma (ITACA-S) trial

64 Background: At present, the clinical management of resected GC is only based on risk stratification according to the AJCC staging. This project evaluates molecular factors on formalin-fixed, paraffin-embedded (FFEP) specimens of the primary tumor radically resected in an omogeneous group patients considered at poor prognosis according by nodal involvement (pN3a/b AJCC 7th edition) and included in the ITACA-S trial. Methods: Matched pairs of tumor-normal GC FFPE specimens collected from 15 patients were subjected to whole-exome sequencing using TruSeq Exome technology and NextSeq500 (Illumina). Somatic mutations (single-nucleotide variants) were identified, filtered and then searched for recurrently mutated genes and pathways. Patients with recurrence (cases) were compared to an equally-sized sample of patients without recurrence (controls) with the same follow up time (60 months). Results: Clinical characteristics of 15 pts: median age 61 (41-71) yrs. Nodal involvement: pN3a( 5); pN3b (10). Histotype: Intestinal (4); diffuse (8); mixed (3). Primary site: gastroesophageal junction (1); gastric (14). Patients with GC relapse (8) and without relapse (7). Whole exome sequencing revealed the presence of an average of 553 somatic mutations (range: 197 - 1318) following removal of not exonic/silent variants and of variants with an alternative allele depth &lt; 5. Among a list of 48 genes, reported as mutated in some GC studies, we found that CDH1, GNAS and DCC were mutated in 57% of patients, whereas CTNNB1, LRP1B, LRRK2, NOTCH1, and TRRAP were mutated in 42%. Furthermore RHOA, KRAS, FGFR2, PDGFRA and PRKDC showed mutation in 28% of cases. We are currently evaluating the presence of mutual exclusive relationships mechanisms, functions and molecular pathways in “cases” versus “controls”. Conclusions: Our findings confirm a relevant role of disregulation of cell adhesion pathway involving CDH1 and DCC in GC. However, a validation analysis with an independent and bigger cohort of GC patients is ongoing, in order to find outcome-related mutational patterns that could be relevant for the selection of treatment in GC. </jats:p