Molecular Genetic Findings Research Articles

Total thyroidectomy can still remain the method of choice in some Bethesda III cases.

The latest WHO classification of tumours of endocrine organs defines new units of borderline thyroid tumours (BTT). The aim of our study was to evaluate ultrasonographic and cytological features, mutation profile and surgery treatment in rare thyroid tumours. An analysis of 8 BTT out of 487 patients, who underwent thyroid surgery between June 2016 and June 2020. The definitive diagnosis was made postoperatively by extensive histopathological examination. Molecular genetic analysis of genes associated with thyroid oncology (BRAF, HRAS, KRAS, NRAS, TERT, TP53, fused genes) were performed from one FNAB, and 7 formalin-fixed paraffin-embedded (FFPE) samples. BTT were found in a total of 8 patients (1.6%), with a predominance of men with respect to other operated patients. FNAB samples were classified in the Bethesda system as Bethesda I, Bethesda II and Bethesda III in one, four and three cases, respectively. Hemithyroidectomy and total thyroidectomy were performed equally in four patients. The histopathological diagnosis revealed non-invasive encapsulated follicular neoplasm with papillary-like nuclear features (NIFTP) in three patients, follicular tumour of uncertain malignant potential (FT-UMP) in three patients, well differentiated tumour of uncertain malignant potential (WDT-UMP) in one patient, and hyalinizing trabecular tumour (HTT) in one case. In NIFTP cases mutation in HRAS gene in one patient together with probable pathogenic variant in TP53 gene and in NRAS gene in two patients were detected. In HTT patient PAX8/GLIS3 fusion gene was detected. The surgical treatment of BTT is necessarily individual influenced by preoperative clinical, ultrasonographic, cytological and molecular genetic findings, and the presence of other comorbidities.

Deep Learning Algorithms Depict New Subgroups of AML and MDS Based on Genetics Only and Allow Distinction of Both Entities with High Accuracy of 90%

Since 45 years MDS and AML are separated according to the percentage of bone marrow blasts. Although this is an arbitrary threshold, it led to different therapeutic strategies and the discovery of more or less directly related cytogenetic changes. The last decade added a lot of molecular genetic information for diagnosis, prognosis and increasingly targeted treatment options. The vast majority of cytogenetic and molecular genetic findings however are common in both diseases, irrespective of blast count. However, the classification of myeloid neoplasms is still based on morphology. Therefore, we analyzed for the first time a large cohort of morphologically defined de novo AML (n=901) and MDS (n=2,097) patients (pts), all characterized by gene panel sequencing and cytogenetics, and applied deep learning algorithms to differentiate AML versus MDS based on genetics only. Mutation status of 22 recurrently mutated genes as well as 23 recurrent cytogenetic aberrations, including fusion transcripts and copy number variations, were used as markers.The dataset was initially filtered to exclude pts and genes with a large number of missing values, which would otherwise hamper the computational analysis of the cohort. The filtered dataset was randomly divided into a training (90%) and validation (10%) set. Subsequently we applied Lasso regression to classify AML versus MDS with 10-fold cross-validation. The whole procedure was repeated 1,000 times. We were able to classify AML versus MDS with an accuracy of 83%. Misclassification of 17% of pts indicated that these pts exhibited a genetic profile that could not be matched to the learned patterns of the two entities. Interestingly, the only cytogenetic markers that impacted classification at all but on a low level were PML - RARA and CBFB - MYH11, while 19 gene mutations were of high impact.Hence, we applied unsupervised k-modes clustering to partition the pts into k groups per entity. Here the dissimilarity of two gene profiles was determined by simple-matching distance and the optimal k was chosen based on internal measures and biological relevance of the groups using the 19 most relevant gene mutations as markers only.The analysis revealed 4 genetically distinct clusters for both the AML and MDS cohorts. Within AML 158 pts were grouped in one cluster, dominated by mutations in ASXL1, RUNX1, and SRSF2 . A second cluster (n=160) was mainly set up by pts with NPM1, IDH, and DNMT3A mutations, while a third cluster consisted of 41 pts with ASXL1, NRAS, and TET2 mutations. The remaining pts (n=541) grouped in cluster 4 showed no obvious pattern. 242 MDS pts were grouped in one cluster with also ASXL1, RUNX1, and SRSF2 mutations. A second cluster contained 216 MDS pts with mainly ASXL1, SRSF2, and TET2 mutations. A third cluster was dominated by pts with SF3B1 mutation (n=382), while cluster 4 again was a cluster with no obvious pattern (n=1,257).We performed the same analysis for both entities together and identified 6 different clusters (Fig.). The distribution of AML and MDS to the 6 clusters differed significantly, one cluster each was dominated by AML and MDS, respectively, although each cluster contained pts from both entities. Cluster 2 represented cases with SF3B1 and RUNX1 mutation, while cluster 3 was dominated by NPM1, IDH, and DNMT3A mutated AML pts. Cluster 4 contained preferentially pts with NPM1 and TET2 mutations and cluster 6 ASXL1, RUNX1, and TET2 mutated pts. Cluster 1 and 5 showed no obvious pattern. Interestingly, these 6 clusters showed different outcome within the AML and MDS subgroups, respectively (range median OS AML: 12 to 46 months, MDS: 9 months to not reached; p<0.001 for both groups).Using the 19 highly relevant genetic markers now for Lasso regression to classify AML versus MDS with 10-fold cross-validation we reached an accuracy of 90%.In conclusion, we here challenged arbitrary disease defining thresholds (20% of bone marrow blasts) and applied deep learning approaches and artificial intelligence to a cohort of AML and MDS pts. 1) We reproduced only on 19 molecular markers the standard diagnoses with an accuracy of 90%. 2) We detected specific molecular patterns shared from AML and MDS cases that were irrespective of the original WHO diagnoses. 3) The respective new patterns demonstrated different outcome within AML and MDS subgroups. This might be a first proof how future classification systems might be based on molecular data and deep learning algorithms. [Display omitted] DisclosuresMeggendorfer:MLL Munich Leukemia Laboratory: Employment. Walter:MLL Munich Leukemia Laboratory: Employment. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Kern:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership.

Mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes (MELAS) syndrome: frequency, clinical features, imaging, histopathologic and molecular genetic findings in a third-level healthcare center in Mexico. (1280)

Mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes (MELAS) syndrome: frequency, clinical features, imaging, histopathologic and molecular genetic findings in a third-level healthcare center in Mexico. (1280)

New Honorary Member of the BSPP

Jonathan D. G. Jones grew up in London and graduated in Botany from Cambridge University followed by graduate work at the PBI, Cambridge. His career in plant–microbe interactions began with Ausubel at Harvard, studying Rhizobium–legume associations. He then worked at Advanced Genetic Sciences Inc. where his expertise using broad host-range plasmids underpinned the development of plant genetic engineering tools using Agrobacterium. Since 1988, he has led a research team at The Sainsbury Lab (TSL), Norwich, where he isolated the tomato Cf-9 gene for resistance to the fungus Cladosporium fulvum. Cf-9 encodes a pioneer cell surface “receptor-like protein” immune receptor, with extracellular leucine-rich repeats (LRRs). He isolated six such genes, each recognizing different fungal virulence factors. These preceded the Nobel prize-winning discoveries of similar Toll-like receptors in animal innate immunity. He went on to characterize complex immune receptor-encoding haplotypes with multiple paralogs and infer their evolutionary trajectories. He discovered that solvent-exposed amino acids in plant immune receptor LRRs are hypervariable and under diversifying selection for specific recognition of distinct pathogen molecules, and that unequal crossing over between paralogous genes at complex loci also contributes to receptor diversification. In a Cf-2 resistance gene suppressor screen, he discovered Rcr3, a cysteine protease required for Cf-2 to recognize the Avr2. In collaboration with the de Wit laboratory in Wageningen, he showed that Cf-2 “guards” Rcr3, activating defence when Rcr3 is inhibited by the Avr2 protease inhibitor. The resulting guard hypothesis was the subject of an influential paper with Dangl in 2001. He also identified several protein kinases and E3 ubiquitin ligases involved in Cf-dependent immunity, verifying their requirement for defence activation, and was first to show the role of receptor-like cytoplasmic kinases in cell surface receptor-mediated immunity. Most plant resistance genes encode intracellular nucleotide-binding LRR (NLR) immune receptors. He cloned one of the earliest (RPP5) and has defined >12 more. He was first to reveal the extreme haplotype diversity at the RPP5 locus between Arabidopsis accessions, again verifying extreme diversity in solvent-exposed amino acids of the LRRs of different paralogs, and unequal crossovers between paralogs in their evolution. In an influential 2006 paper with Dangl, he articulated the roles of cell surface “pattern-triggered immunity” and intracellular “effector-triggered immunity” in plant defence, integrating them for the first time. He has led discoveries on cross-talk between various hormone signalling pathways, in pathogen effector mechanisms, and in the role of variation in detection capacity in population resistance to disease. Some NLR receptors carry integrated domains (IDs) and are encoded adjacent in the genome to another NLR gene. Arabidopsis RPS4 and RRS1 are a paradigmatic example; RRS1 carries a WRKY transcription factor domain and the pair creates an immune receptor that detects pathogen effectors that act on WRKY domains. His work provided the first demonstration that NLRs can evolve to be immune receptors that contain IDs that mimic authentic pathogen targets. His fascination with genetic variation in host–pathogen interactions led him to develop sequence capture-based methods to interrogate plant immune receptor diversity. Resistance gene enrichment sequencing (RenSeq) has greatly accelerated our understanding of plant immune receptor repertoires. He also developed capture-based methods to investigate the genetic diversity of obligate parasites growing on hosts (PenSeq). He used RenSeq to address nonhost resistance (NHR) and defined the genetic basis of Arabidopsis NHR to Brassica-infecting races of white rust, revealing the crucial role of NLR receptors. Solanum americanum shows NHR to the potato late blight pathogen Phytophthora infestans. By isolating two NLR immune receptors, Rpi-amr1 and Rpi-amr3, from S. americanum, defining their recognized effectors from P. infestans, and verifying the efficacy of Rpi-amr1, Rpi-amr3, and Rpi-vnt1 in transgenic potato field experiments, he showed that their deployment might enable NHR to control blight in the field. He has played a key role in making the case that this approach to controlling crop disease is useful, safe, and sustainable. His discoveries in plant molecular genetics earned him election as Professor at UEA (1996), EMBO member (1998), Royal Society Fellow (2003), and International Member of US National Academy of Sciences (2015). He served in Royal Society working groups on food security and coauthored the Royal Society’s 2009 “Reaping the Benefits” report.

Identification of Two Dysfunctional Variants in the ABCG2 Urate Transporter Associated with Pediatric-Onset of Familial Hyperuricemia and Early-Onset Gout.

The ABCG2 gene is a well-established hyperuricemia/gout risk locus encoding a urate transporter that plays a crucial role in renal and intestinal urate excretion. Hitherto, p.Q141K—a common variant of ABCG2 exhibiting approximately one half the cellular function compared to the wild-type—has been reportedly associated with early-onset gout in some populations. However, compared with adult-onset gout, little clinical information is available regarding the association of other uricemia-associated genetic variations with early-onset gout; the latent involvement of ABCG2 in the development of this disease requires further evidence. We describe a representative case of familial pediatric-onset hyperuricemia and early-onset gout associated with a dysfunctional ABCG2, i.e., a clinical history of three generations of one Czech family with biochemical and molecular genetic findings. Hyperuricemia was defined as serum uric acid (SUA) concentrations 420 μmol/L for men or 360 μmol/L for women and children under 15 years on two measurements, performed at least four weeks apart. The proband was a 12-year-old girl of Roma ethnicity, whose SUA concentrations were 397–405 µmol/L. Sequencing analyses focusing on the coding region of ABCG2 identified two rare mutations—c.393G>T (p.M131I) and c.706C>T (p.R236X). Segregation analysis revealed a plausible link between these mutations and hyperuricemia and the gout phenotype in family relatives. Functional studies revealed that p.M131I and p.R236X were functionally deficient and null, respectively. Our findings illustrate why genetic factors affecting ABCG2 function should be routinely considered in clinical practice as part of a hyperuricemia/gout diagnosis, especially in pediatric-onset patients with a strong family history.

A novel compound heterozygous mutation in MYSM1 gene in a 1-month-old girl: a bone marrow failure syndrome 4 family survey and literature review

目的报道1例MYSM1基因复合杂合变异致骨髓衰竭综合征4型患儿临床表现及全外显子检测结果，同时报道其家系全外显子检测结果，为早期诊断此类骨髓衰竭综合征提供典型案例。方法报道1例1月龄骨髓衰竭综合征4型患儿临床诊断过程，并对患儿及其家系成员外周血DNA进行全外显子测序，使用BWA、GATK等软件对测序结果进行注释分析。结果本例1月龄骨髓衰竭综合征4型患儿，表现为全血细胞减少、多指畸形，影像学示非特异性脑白质改变及囊肿，淋巴细胞亚群分类示CD3−CD19+ B细胞降低。通过家系全外显子测序检测，鉴定患儿携带分别遗传自父母的MYSM1基因复合杂合性变异NM_001085487.2:c.1607_c.1611delAAGAG和c.1432C>T。家系验证证实先证者父亲携带的c.1432C>T突变来源于先证者祖父，先证者母亲携带的c.1607_c.1611delAAGAG突变来自于先证者外祖父，其他家系成员均不携带突变。结论本研究新发现MYSM1致病性变异c.1607_c.1611delAAGAG，国内外尚未见报道。本例为BMFS4的早期诊断提供了典型案例，并扩展了MYSM1基因致病性变异谱和表型谱。

The revised pancreatitis etiology-based classification system TIGAR-O, version 2: adaptation for the Russian clinical practice

The discoveries in molecular genetics and breakthrough visualization techniques in the last 20 years have changed our understanding of the pancreatitis causes and biomarkers, expanded our knowledge on the pathophysiology of the disease, and promoted the development of new additional conservative treatments. From the practical perspective, the physician's comprehension of the etiology is of particular importance. It is for this reason that the activities to elaborate an etiology-based classification of pancreatitis have been already started since long ago. The first internationally acknowledged system was TIGAR-O checklist, introduced in 2001. Being innovative at the time, it structured our understanding of the etiology of chronic pancreatitis. The revised version (version 2) was published in 2019 and is less known to the Russian medical community, although from the authors' point of view, it has been substantially extended and structured to be maximally convenient and useful for physicians in routine medical practice. The review presents key provisions of the TIGAR-O, version 2 and recommendations for its adaption to the Russian clinical setting.

Clinicopathological features of polymorphous low-grade neuroepithelial tumor of the young

Objective: To investigate the clinicopathological features, diagnosis and prognosis of polymorphous low-grade neuroepithelial tumor of the young (PLNTY). Methods: Two cases of PLNTY diagnosed during January 2016 to December 2019 were collected from Ningbo Diagnostic Pathology Center, Zhejiang, China. The clinical features, histopathological characteristics, immunohistochemical and molecular genetic findings were analyzed and the relevant literature was reviewed. Results: The two patients were both female, at the ages of 14 and 25 years, respectively. Both patients presented with seizure attacks. The imaging study showed a mixed signal in the cerebral cortex, located in the occipital and temporal lobes, respectively. Microscopically, the tumors were characterized by the invariable presence of oligodendroglioma-like appearance, often with calcification. Immunohistochemically, the tumors were diffusely and intensely CD34 positive with ramified, CD34-expressing neural elements in regional cortex. The tumors were positive for GFAP, Olig2 and ATRX, and negative for IDH1, Neu N, nestin and EMA. The Ki-67 labeling index was less than 2%. The case number 2 harbored the BRAF V600E mutation, while the case number 1 was negative for both the BRAF V600E mutation and 1p/19q codeletion. Both patients recovered very well and were free of seizures after the following-up of 2 and 24 months, respectively. Conclusions: PLNTY is an uncommon neuroepithelial tumor. Histopathologic and immunohistochemical examinations are necessary for establishing the diagnosis and for excluding oligodendroglioma. PLNTY should be considered as a benign tumor corresponding to WHO Grade I. The prognosis is overall good after complete tumor-resection.

IDH2 Inhibitor Therapy in Relapsed and Refractory Acute Myeloid Leukemia: A Single Institution Experience

Introduction: Mutations in the gene isocitrate dehydrogenase 2 (IDH2) occur in ~12-15% of patients with acute myeloid leukemia (AML). Enasidenib, an oral small molecule selective targeted inhibitor of IDH2 enzymes, was approved forIDH2mutated relapsed/refractory AML (RR-AML) in 2017 (Stein et. al., 2017). There is limited data regarding its efficacy and toxicity outside the context of clinical trials. Using Mayo Clinic's cohort of AML patients, we provide a real-world look at outcomes forIDH2mutated RR-AML patients treated with enasidenib. Methods: A total of 13 patients treated with enasidenib for RR-AML were identified, all of which experienced at least one relapse following induction chemotherapy. Response assessment was based on European Leukemia Net (ELN) 2017 response criteria.Complete blood counts including blast percentage and transfusion dependency were obtained at AML diagnosis, initiation of enasidenib, 2 months and 6 months following initiation of therapy. Transfusion dependency was defined by the need for either a red cell or platelet transfusion within 4 weeks of the designated time frame. We compared the clinical characteristics of patients who achieved complete response (CR) (n=4) to those not achieving CR (n=9), using the Mann-Whitney U test for numerical variables and the Fischer's Exact test for quantitative data. Results: The median age at diagnosis of our 13 patients was 68 years (range 60-82), with a male predilection (n=11) (Table 1). Cytogenetic and molecular genetic findings are provided in Table 2. Complete response (CR) was achieved in 4 (30.7%) patients by cycle 2 and 2 of those patients (50%) proceeded to an allogeneic hematopoietic stem cell transplant (AHSCT). The median time from diagnosis to initiation of treatment for patients in CR was 3.5 months (range 1-7), and for patients not achieving CR was 13 months (range 6-53; p=0.048), with median time of follow up after treatment initiation of 23.5 months (range, 5-36) and 7 months (range, 1-14), respectively. Among 8 patients who were transfusion dependent at baseline, all the CR patients (2/2) achieved red blood cell and platelet transfusion independence 6 months after treatment, instead only (3/6) 50% of those not in CR achieved transfusion independence (p=0.028). An initial trajectory of improvement in counts is noted from the time of diagnosis to the 2 month mark post treatment with 75% of the responder cohort showing improvement in counts which was durable through the 6 month mark, whereas 55% of those that did not respond had worsening counts at month 2 and died prior to 6 month follow up. At the time of data cut-off, the median duration of CR was 14 months (range, 2-33), with 3 of 4 (75%) of responders maintaining CR. Figure 1 details overall responses and outcomes in all 13 patients. None of the patients in our study experienced differentiation syndrome. Five patients were hospitalized in the course of treatment for infectious complications. Two patients were noted to have hyperbilirubinemia however there was no clear indication that this was secondary to enasidenib Median overall survival for all 13 patients was 21 months (range, 6-53 months) with leukemia free survival of 7 months (range, 5-19 months). Furthermore, median overall survival for patients in CR was 27 months (range, 6-42), and those not in CR was 16 months (range, 6-53) (p=0.20). In addition, we observed that 75% of patients who attained CR are alive compared to 11.1% of those not in CR (p = 0.052). Conclusion: We demonstrate a superior CR rate of 30.7% with enasidenib amongstIDH2mutated RR-AML patients compared with clinical trial data showing CR rate of 19.6% (Stein et. al., 2019) despite our patients being heavily pre-treated with median number of two prior therapies (range; 1-5) including prior AHSCT in 2 patients. Moreover, a subset of patients (2 of 4 in CR) were able to undergo ASCHT. Finally, the achievement of CR at 2 months after initiation of therapy serves as an appropriate time point for response assessment. Disclosures No relevant conflicts of interest to declare.

Analysis of XX SRY-Negative Sex Reversal Dogs.

Simple SummaryThe study of XX SRY-negative sex reversal cases is of great interest because testicular tissue develops in these subjects in the absence of SRY gene, thus allowing us to deepen the knowledge of all the other genes involved in the development of testes and the structures related to the male reproductive apparatus. This paper reports the results of the study of four new canine disorders of sex development (DSDs) XX SRY-negative cases in which 11 copy number variations (CNVs) are observed, five of which are never described. Impaired fertility associated with disorders of sex development (DSDs) due to genetic causes in dogs are more and more frequently reported. Affected dogs are usually of specific breeds thus representing a cause of economic losses for breeders. The aim of this research is to report the clinical, cytogenetic and molecular genetic findings of four XX SRY-negative DSD dog cases. All the subjects showed a female aspect and the presence of an enlarged clitoris with a penis bone. Morphopathological analyses performed in three of the four cases showed the presence of testes in two cases and ovotestis in another. Conventional and R-banded cytogenetic techniques were applied showing that no chromosome abnormalities were involved in these DSDs. CGH arrays show the presence of 11 copy number variations (CNVs), one of which is a duplication of 458 Kb comprising the genomic region between base 17,503,928 and base 17,962,221 of chromosome 9 (CanFam3 genome assembly). This CNV, confirmed also by qPCR, includes the promoter region of SOX9 gene and could explain the observed phenotype.

Early-onset of Frontotemporal Dementia and Amyotrophic Lateral Sclerosis in an Albanian Patient with a c.1319C&gt;T Variant in the UBQLN2 Gene

Background: Frontotemporal Dementia (FTD) is the second most common cause of dementia under 65 years of age; it has a prevalence of 4-15 per 100,000 persons. The overt disease usually manifests in the sixth decade, and it is extremely rare to find affected patients in their twenties. Objective: Here, we present the clinical and molecular genetic findings of an Albanian family with a patient with early-onset FTD and Amyotrophic Lateral Sclerosis (ALS). Methods: Given the great variability of clinical presentation of FTD and the number of genes involved, targeted Next Generation Sequencing (NGS) was used to screen the DNA of the 27-year-old male patient. Segregation analysis was performed in available family members. Results and Discussion: A variant, consisting of a proline-leucine amino acid substitution in position 440, was identified in the UBQLN2 gene on the X-chromosome. This variant was previously reported as a variant of unknown significance in a 30-year-old female patient with amyotrophic lateral sclerosis. With the description of our case, we add evidence on its involvement, also in ALS-FTD. The variant is in a functional domain important for interaction with HSP70 and this, in turn, may impair the shuttling of proteins to the proteasome leading to an accumulation of protein aggregates. The variant was inherited from the unaffected mother, in line with the fact that incomplete penetrance has been widely described for this gene. Conclusion:The present report adds information regarding one of 34 variants in the UBQLN2 gene reported so far in association with neurodegeneration and proposes a molecular pathogenesis of ALS-FTD in this patient.

The 2020 WHO Classification

The fifth edition of the World Health Organization Classification of Tumors of Soft Tissue and Bone was published in early 2020. The revisions reflect a consensus among an international expert editorial board composed of soft tissue and bone pathologists, geneticists, a medical oncologist, surgeon, and radiologist. The changes in the soft tissue tumor chapter notably include diverse, recently described tumor types (eg, atypical spindle cell/pleomorphic lipomatous tumor, angiofibroma of soft tissue, and CIC-rearranged sarcoma), new clinically significant prognostic information for a variety of existing entities (eg, dedifferentiated liposarcoma and solitary fibrous tumor), and a plethora of novel genetic alterations, some of practical diagnostic relevance (eg, NAB2-STAT6 in solitary fibrous tumor, FOSB rearrangements in epithelioid hemangioma and pseudomyogenic hemangioendothelioma, and SUZ12 or EED mutations in malignant peripheral nerve sheath tumor, leading to loss of H3K27 trimethylation). In this review, we highlight the major changes to the soft tissue chapter in the 2020 World Health Organization Classification, as well as the new chapter on undifferentiated small round cell sarcomas, with a focus on updates in diagnostic categories, prognostication, and novel markers. Recent discoveries in molecular genetics are also discussed, particularly those of immediate utility in differential diagnosis, including protein correlates detectable using immunohistochemistry.

Clinical features and blood iron metabolism markers in children with beta-propeller protein associated neurodegeneration.

Neurodegeneration with brain iron accumulation constitutes a group of rare progressive movement disorders sharing intellectual disability and neuroimaging findings as common denominators. Beta-propeller protein-associated neurodegeneration (BPAN) represents approximately 7% of the cases, and its first signs are typically epilepsy and developmental delay. We aimed to describe in detail the phenotype of BPAN with a special focus on iron metabolism. We present a cohort of paediatric patients with pathogenic variants of WD-Repeat Domain 45 gene (WDR45). The diagnosis was established by targeted panel sequencing of genes associated with epileptic encephalopathies (n=9) or by Sanger sequencing of WDR45 (n=1). Data on clinical characteristics, molecular-genetic findings and other performed investigations were gathered from all participating centres. Markers of iron metabolism were analysed in 6 patients. Ten children (3 males, 7 females, median age 8.4 years) from five centres (Prague, Berlin, Vogtareuth, Tubingen and Cologne) were enrolled in the study. All patients manifested first symptoms (e.g. epilepsy, developmental delay) between 2 and 31 months (median 16 months). Seven patients were seizure-free (6 on antiepileptic medication, one drug-free) at the time of data collection. Neurological findings were non-specific with deep tendon hyperreflexia (n=4) and orofacial dystonia (n=3) being the most common. Soluble transferrin receptor/log ferritin ratio was elevated in 5/6 examined subjects; other parameters of iron metabolism were normal. Severity of epilepsy often gradually decreases in BPAN patients. Elevation of soluble transferrin receptor/log ferritin ratio could be another biochemical marker of the disease and should be explored by further studies.

Non-Conventional Treatments for Conventional Chondrosarcoma.

Chondrosarcomas are the most common malignant tumors of the cartilage, are seen predominantly in adults, and have varied clinical behavior. The majority of them affect the medullary canal of long bones and pelvic bones. The prognosis of chondrosarcoma is closely related to histological grading; however, the grading is subject to interobserver variability. Conventional chondrosarcomas are overall considered to be chemotherapy- and radiation-resistant, resulting in limited treatment options. The majority of advanced conventional chondrosarcomas are treated with chemotherapy without any survival benefit. Recent studies have evaluated molecular genetic findings which have improved the understanding of chondrosarcoma biology. Newer therapeutic targets are desperately needed. In this review article, we explore ongoing clinical trials evaluating novel ways of treating advanced conventional chondrosarcoma.

Fatal outcome of autosomal recessive polycystic kidney disease in neonates with recessive PKHD1 mutations.

Autosomal recessive polycystic kidney disease (ARPKD) is the most common inherited childhood-onset renal disease, with underlying ciliopathy, and varies widely in clinical severity. The aim of this study was to describe the most severe form of ARPKD, with a fatal clinical course, and its association with mutations in polycystic kidney and hepatic disease 1 (fibrocystin) (PKHD1). Clinical, imaging, pathological, and molecular genetic findings were reviewed in patients prenatally affected with ARPKD and their families.Five unrelated Korean families, including 9 patients, were analyzed. Among the 9 patients, 2 fetuses died in utero, 6 patients did not survive longer than a few days, and 1 patient survived for 5 months with ventilator support and renal replacement therapy. A total of 6 truncating mutations (all nonsense) and 4 missense mutations were detected in a compound heterozygous state, including 4 novel mutations. The most severe phenotypes were shared among all affected patients in each family, irrespective of mutation types.Our data suggest a strong genotype–phenotype relationship in ARPKD, with minimal intra-familial heterogeneity. These findings are important for informing future reproductive planning in affected families.

Cerebellar ataxia, neuropathy, hearing loss, and intellectual disability due to AIFM1 mutation.

ObjectiveTo describe the clinical and molecular genetic findings in a family segregating a novel mutation in the AIFM1 gene on the X chromosome.MethodsWe studied the clinical features and performed brain MRI scans, nerve conduction studies, audiometry, cognitive testing, and clinical exome sequencing (CES) in the proband, his mother, and maternal uncle. We used in silico tools, X chromosome inactivation assessment, and Western blot analysis to predict the consequences of an AIFM1 variant identified by CES and demonstrate its pathogenicity.ResultsThe proband and his maternal uncle presented with childhood-onset nonprogressive cerebellar ataxia, hearing loss, intellectual disability (ID), peripheral neuropathy, and mood and behavioral disorder. The proband's mother had mild cerebellar ataxia, ID, and mood and behavior disorder, but no neuropathy or hearing loss. The 3 subjects shared a variant (c.1195G>A; p.Gly399Ser) in exon 12 of the AIFM1 gene, which is not reported in the exome/genome sequence databases, affecting a critical amino acid for protein function involved in NAD(H) binding and predicted to be pathogenic with very high probability by variant analysis programs. X chromosome inactivation was highly skewed in the proband's mother. The mutation did not cause quantitative changes in protein abundance.ConclusionsOur report extends the molecular and phenotypic spectrum of AIFM1 mutations. Specific findings include limited progression of neurologic abnormalities after the first decade and the coexistence of mood and behavior disorder. This family also shows the confounding effect on the phenotype of nongenetic factors, such as alcohol and drug use and side effects of medication.

Nitrate in 2020: Thirty Years from Transport to Signaling Networks.

Nitrogen (N) is an essential macronutrient for plants and a major limiting factor for plant growth and crop production. Nitrate is the main source of N available to plants in agricultural soils and in many natural environments. Sustaining agricultural productivity is of paramount importance in the current scenario of increasing world population, diversification of crop uses, and climate change. Plant productivity for major crops around the world, however, is still supported by excess application of N-rich fertilizers with detrimental economic and environmental impacts. Thus, understanding how plants regulate nitrate uptake and metabolism is key for developing new crops with enhanced N use efficiency and to cope with future world food demands. The study of plant responses to nitrate has gained considerable interest over the last 30 years. This review provides an overview of key findings in nitrate research, spanning biochemistry, molecular genetics, genomics, and systems biology. We discuss how we have reached our current view of nitrate transport, local and systemic nitrate sensing/signaling, and the regulatory networks underlying nitrate-controlled outputs in plants. We hope this summary will serve not only as a timeline and information repository but also as a baseline to define outstanding questions for future research.

Osteoid-forming bone tumors : Morphology and current translational cell biology

Osteoid osteoma and osteoblastoma are the most important benign osteoid-forming tumors. They grow slowly and are well differentiated. Histologically, the tumor cells show no atypia and no increased mitoses. In typical cases, they can be clearly diagnosed. However, the rare cases on the dividing line between osteoblastoma and osteosarcoma are extremely problematic. In these cases, molecular genetic investigations should contribute to finding the correct diagnosis in the future.Juvenile highly malignant osteosarcoma is the most important malignant osteoid-forming tumor. About 40years ago, neoadjuvant chemotherapy was introduced for the mostly young patients. This therapy highly significantly improved prognosis. However, aplateau phase was quickly reached and the last several decades have seen no further progress in conventional therapeutic approaches. There is no doubt that further progress can only be achieved on the basis of new molecular genetic and cell biological findings. The target-therapeutic strategies derived from these findings will be discussed in this review.The rare parosteal osteosarcoma and the even rarer periosteal osteosarcoma are mostly not highly malignant tumors that are located on the surface of bone. The parosteal osteosarcoma is usually G1 and the periosteal osteosarcoma G2. Occasionally, the differential diagnosis between aparosteal osteosarcoma and afibrous dysplasia is difficult. In such rare cases, the detection of GNAS mutations in fibrous dysplasia can prove useful. In contrast to chondromas and chondrosarcomas, periosteal osteosarcomas do not contain IDH1 and IDH2 mutations.

Genetic associations with mathematics tracking and persistence in secondary school

Maximizing the flow of students through the science, technology, engineering, and math (STEM) pipeline is important to promoting human capital development and reducing economic inequality. A critical juncture in the STEM pipeline is the highly cumulative sequence of secondary school math courses. Students from disadvantaged schools are less likely to complete advanced math courses. Here, we conduct an analysis of how the math pipeline differs across schools using student polygenic scores, which are DNA-based indicators of propensity to succeed in education. We integrated genetic and official school transcript data from over 3000 European-ancestry students from U.S. high schools. We used polygenic scores as a molecular tracer to understand how the flow of students through the high school math pipeline differs in socioeconomically advantaged versus disadvantaged schools. Students with higher education polygenic scores were tracked to more advanced math already at the beginning of high school and persisted in math for more years. Analyses using genetics as a molecular tracer revealed that the dynamics of the math pipeline differed by school advantage. Compared to disadvantaged schools, advantaged schools buffered students with low polygenic scores from dropping out of math. Across all schools, even students with exceptional polygenic scores (top 2%) were unlikely to take the most advanced math classes, suggesting substantial room for improvement in the development of potential STEM talent. These results link new molecular genetic discoveries to a common target of educational-policy reforms.

Current classification of lung carcinoma. Histological, immunophenotypic, molecular and clinical considerations

In recent years, the rapid technological development and the better knowledge of genetic and molecular aspects in medicine have allowed a better approach to understand, diagnose and treat various oncological diseases. Regarding lung carcinoma, there has been a remarkable evolution from the first classifications, which were purely morphological, to the last one issued in 2015. This last classification includes histological, immunophenotypic, molecular genetics, clinical and radiological information, which allows a better evaluation and therapeutic management of these patients. In the present article, the first classifications of lung carcinoma to the last one are reviewed, and the most relevant changes and the importance of the molecular genetics findings are examined for a better clinical and therapeutic approach.