Updating genome annotation for the microbial cell factory Aspergillus niger using gene co-expression networks.

A significant challenge in our understanding of biological systems is the high number of genes with unknown function in many genomes. The fungal genus Aspergillus contains important pathogens of humans, model organisms, and microbial cell factories. Aspergillus niger is used to produce organic acids, proteins, and is a promising source of new bioactive secondary metabolites. Out of the 14,165 open reading frames predicted in the A. niger genome only 2% have been experimentally verified and over 6,000 are hypothetical. Here, we show that gene co-expression network analysis can be used to overcome this limitation. A meta-analysis of 155 transcriptomics experiments generated co-expression networks for 9,579 genes (∼65%) of the A. niger genome. By populating this dataset with over 1,200 gene functional experiments from the genus Aspergillus and performing gene ontology enrichment, we could infer biological processes for 9,263 of A. niger genes, including 2,970 hypothetical genes. Experimental validation of selected co-expression sub-networks uncovered four transcription factors involved in secondary metabolite synthesis, which were used to activate production of multiple natural products. This study constitutes a significant step towards systems-level understanding of A. niger, and the datasets can be used to fuel discoveries of model systems, fungal pathogens, and biotechnology.

MRI cT1-2 rectal cancer staging accuracy: a population-based study.

BACKGROUND: Adequate MRI-based staging of early rectal cancers is essential for decision-making in an era of organ-conserving treatment approaches. The aim of this population-based study was to determine the accuracy of routine daily MRI staging of early rectal cancer, whether or not combined with endorectal ultrasonography (ERUS). METHODS: Patients with cT1-2 rectal cancer who underwent local excision or total mesorectal excision (TME) without downsizing (chemo)radiotherapy between 1 January 2011 and 31 December 2018 were selected from the Dutch ColoRectal Audit. The accuracy of imaging was expressed as sensitivity, specificity, and positive predictive value (PPV) and negative predictive value. RESULTS: Of 7382 registered patients with cT1-2 rectal cancer, 5539 were included (5288 MRI alone, 251 MRI and ERUS; 1059 cT1 and 4480 cT2). Among patients with pT1 tumours, 54·7 per cent (792 of 1448) were overstaged by MRI alone, and 31·0 per cent (36 of 116) by MRI and ERUS. Understaging of pT2 disease occurred in 8·2 per cent (197 of 2388) and 27·9 per cent (31 of 111) respectively. MRI alone overstaged pN0 in 17·3 per cent (570 of 3303) and the PPV for assignment of cN0 category was 76·3 per cent (2733 of 3583). Of 834 patients with pT1 N0 disease, potentially suitable for local excision, tumours in 253 patients (30·3 per cent) were staged correctly as cT1 N0, whereas 484 (58·0 per cent) and 97 (11·6 per cent) were overstaged as cT2 N0 and cT1-2 N1 respectively. CONCLUSION: This Dutch population-based analysis of patients who underwent local excision or TME surgery for cT1-2 rectal cancer based on preoperative MRI staging revealed substantial overstaging, indicating the weaknesses of MRI and missed opportunities for organ preservation strategies.

ANTECEDENTES: Una adecuada estadificación mediante resonancia magnética nuclear (RMN) de los cánceres de recto en estadios precoces es esencial para la toma de decisiones en una era en la existen diferentes opciones de tratamiento preservadoras del recto. El objetivo de este estudio de base poblacional fue determinar la precisión de la estadificación mediante RMN del cáncer de recto precoz en la práctica diaria, ya sea combinada o no con la ecografía endorectal (endorectal ultrasound, ERUS). MÉTODOS: Los pacientes con cáncer de recto en estadio cT1-2 que se sometieron a resección local o resección total del mesorrecto (total mesorectal excision, TME) sin (quimio) radioterapia neoadyuvante fueron seleccionados a partir del registro auditado ColoRectal holandés, entre el 1 de enero de 2011 y el 31 de diciembre de 2018. La precisión de las imágenes se expresó como sensibilidad, especificidad y valores predictivos positivo y negativo (positive- and negative predicting value, PPV / NPV). RESULTADOS: De un total de 7.382 pacientes registrados con cáncer de recto en estadio cT1-2, se incluyeron 5.539 pacientes (5.288 solamente RMN, 251 RMN + ERUS; 1.059 cT1 y 4.480 cT2). Los pacientes pT1 fueron sobreestadificados cuando se utilizó únicamente la RMN en un 54,7% de los casos (792/1.448) y cuando se combinó RMN y ERUS en un 31,0% (36/116). La infraestadificación de pT2 ocurrió en un 8,2% (197/2.388) y en un 27,9% (31/111), respectivamente. La RMN utilizada como única prueba sobreestadificó los casos pN0 en el 17,3% (570/3.303) y el VPP del estadio cN0 fue del 76,3% (2.733/3.583). De los 834 pacientes con estadio pT1N0, potencialmente adecuado para la resección local, 253 pacientes (30,3%) se clasificaron correctamente como cT1N0, y 484 (58,8%) y 97 (11,6%) pacientes se sobreestadificaron como cT2N0 y cT1-2N1, respectivamente. CONCLUSIÓN: Este estudio de base poblacional holandés en pacientes que se sometieron a una resección local o a cirugía TME por cáncer de recto cT1-2 con estadificación preoperatoria mediante RMN, muestra una considerable sobreestadificación, lo que indica las debilidades y oportunidades en las estrategias de preservación del recto.

17q21.31 duplication causes prominent tau-related dementia with increased MAPT expression.

To assess the role of rare copy number variations in Alzheimer's disease (AD), we conducted a case-control study using whole-exome sequencing data from 522 early-onset cases and 584 controls. The most recurrent rearrangement was a 17q21.31 microduplication, overlapping the CRHR1, MAPT, STH and KANSL1 genes that was found in four cases, including one de novo rearrangement, and was absent in controls. The increased MAPT gene dosage led to a 1.6-1.9-fold expression of the MAPT messenger RNA. Clinical signs, neuroimaging and cerebrospinal fluid biomarker profiles were consistent with an AD diagnosis in MAPT duplication carriers. However, amyloid positon emission tomography (PET) imaging, performed in three patients, was negative. Analysis of an additional case with neuropathological examination confirmed that the MAPT duplication causes a complex tauopathy, including prominent neurofibrillary tangle pathology in the medial temporal lobe without amyloid-ß deposits. 17q21.31 duplication is the genetic basis of a novel entity marked by prominent tauopathy, leading to early-onset dementia with an AD clinical phenotype. This entity could account for a proportion of probable AD cases with negative amyloid PET imaging recently identified in large clinical series.

Novel mutations in DNAJB6 cause LGMD1D and distal myopathy in French families.

BACKGROUND AND PURPOSE: The aim was to determine the genetic background of unknown muscular dystrophy in five French families. METHODS: Twelve patients with limb girdle muscular dystrophy or distal myopathy were clinically evaluated. Gene mutations were identified using targeted exon sequencing and mutated DNAJB6 was tested in vitro. RESULTS: Five patients presented with distal lower limb weakness whilst others had proximal presentation with a variable rate of progression starting at the mean age of 38.5 years. Two novel mutations (c.284A>T, p.Asn95Ile, two families; and c.293_295delATG, p.Asp98del, one family) as well as the previously reported c.279C>G (p.Phe93Leu, two families) mutation in DNAJB6 were identified. All showed a reduced capacity to prevent protein aggregation. CONCLUSIONS: The mutational and phenotypical spectrum of DNAJB6-caused muscle disease is larger than previously reported, including also dysphagia. The originally reported c.279C>G (p.Phe93Leu) mutation is now identified in four different populations and appears to be a mutational hotspot. Our report confirms that some DNAJB6 mutations cause distal-onset myopathy and hence DNAJB6 defects should be considered broadly in dominant muscular dystrophy families.

[Pilomatrixoma in a tattoo]. / Pilomatrixom in einem Tattoo.

A 31-year-old man developed a fast-growing tumor on the right upper arm within a black tattoo, which could be classified histologically as pilomatrixoma. While the age of the patient and the rapid growth of the tumor cannot be regarded as typical findings of pilomatrixomas, the localization on the upper arm is one of their predilection points. Despite the wide spread use of tattoos in the last few decades, tumor development in tattooed skin is rarely reported. It is still controversial whether the ingredients of the tattoo agents can be responsible for tumor induction.

[Bullosis diabeticorum : Two case studies]. / Bullosis diabeticorum : Zwei Kasuistiken.

We report two cases of patients with diabetes mellitus who developed bullae measuring 2 cm in diameter on the fingers or toes, which could be classified as bullosis diabeticorum after excluding several differential diagnoses that are discussed. Bullosis diabeticorum is a rare blister formation located on the palmoplantar region, which is mainly observed in the case of diabetic patients. The clinical picture is characterized by tense bullae measuring up to 10 cm in diameter, containing clear to hemorrhagic fluid. Generally, lesions heal without residual scarring, less frequently with residual postinflammatory pigmentation or tender scars. On histopathological examination, both intraepidermal and subepidermal bullae are found without any significant inflammatory infiltrate. The etiopathogenesis of bullosis diabeticorum has not yet been clarified.

[Segmental neurofibromatosis]. / Segmentale Neurofibromatose.

Thirteen years ago, a 48-year-old man developed numerous neurofibromas in a circumscribed area on the right chest. At the same time, a bilateral seminoma was diagnosed and treated curatively. There was no evidence for other complications of neurofibromatosis. The family history was inconspicuous. The segmental neurofibromatosis (SN) presented in this patient is the result of a mosaic formation resulting from a mutation of the NF1 gene, a tumor suppressor gene. Concomitant, typical diseases of neurofibromatosis generalisata (NFG), including malignant neoplasms, are the exception to SN.

Clinical validation of a prognostic tool in a population of outpatients treated for incurable cancer undergoing anticancer therapy: PRONOPALL study.

BACKGROUND: In 2008, a study of the characteristics of hospitalised patients led to the development of a prognostic tool that distinguished three populations with significantly different 2-month survival rates. The goal of our study aimed at validating prospectively this prognostic tool in outpatients treated for cancer in terminal stage, based on four factors: performance status (ECOG) (PS), number of metastatic sites, serum albumin and lactate dehydrogenase. PATIENTS AND METHODS: PRONOPALL is a multicentre study of current care. About 302 adult patients who met one or more of the following criteria: life expectancy under 6 months, performance status ≥ 2 and disease progression during the previous chemotherapy regimen were included across 16 institutions between October 2009 and October 2010. Afterwards, in order to validate the prognostic tool, the score was ciphered and correlated to patient survival. RESULTS: Totally 262 patients (87%) were evaluable (27 patients excluded and 13 unknown score). Median age was 66 years [37-88], and women accounted for 59%. ECOG PS 0-1 (46%), PS 2 (37%) and PS 3-4 (17%). The primary tumours were: breast (29%), colorectal (28%), lung (13%), pancreas (12%), ovary (11%) and other (8%). About 32% of patients presented one metastatic site, 35% had two and 31% had more than two. The median lactate dehydrogenase level was 398 IU/l [118-4314]; median serum albumin was 35 g/l [13-54]. According to the PRONOPALL prognostic tool, the 2-month survival rate was 92% and the median survival rate was 301 days [209-348] for the 130 patients in population C, 66% and 79 days [71-114] for the 111 patients in population B, and 24% and 35 days for [14-56] the 21 patients in population A. These three populations survival were statistically different (P <0.0001). CONCLUSION: PRONOPALL study confirms the three prognostic profiles defined by the combination of four factors. This PRONOPALL score is a useful decision-making tool in daily practice.

SORL1 rare variants: a major risk factor for familial early-onset Alzheimer's disease.

The SORL1 protein plays a protective role against the secretion of the amyloid ß peptide, a key event in the pathogeny of Alzheimer's disease. We assessed the impact of SORL1 rare variants in early-onset Alzheimer's disease (EOAD) in a case-control setting. We conducted a whole exome analysis among 484 French EOAD patients and 498 ethnically matched controls. After collapsing rare variants (minor allele frequency ≤1%), we detected an enrichment of disruptive and predicted damaging missense SORL1 variants in cases (odds radio (OR)=5.03, 95% confidence interval (CI)=(2.02-14.99), P=7.49.10(-5)). This enrichment was even stronger when restricting the analysis to the 205 cases with a positive family history (OR=8.86, 95% CI=(3.35-27.31), P=3.82.10(-7)). We conclude that predicted damaging rare SORL1 variants are a strong risk factor for EOAD and that the association signal is mainly driven by cases with positive family history.

[Generalized circumscribed scleroderma with blisters]. / Generalisierte zirkumskripte Sklerodermie mit Blasenbildung.

The patient suffered from a 20-year course of generalized circumscribed scleroderma and presented with blisters in circumscribed areas of the affected skin. The development of subepidermal blisters has been described in all clinical forms of circumscribed scleroderma. Aetiology and pathogenesis of blister formation have not yet been clarified. An obstruction of the lymphatic vessels due to the present sclerosis is favoured. Treatment of bullous circumscribed scleroderma is considered to be difficult. Oral steroids, methotrexate, hydroxychloroquine and PUVA methods have been used with varying success.

[Frontal fibrosing alopecia]. / Frontal fibrosierende Alopezie Kossard.

Within the group of cicatricial alopecias, Kossard first described frontal fibrosing alopecia (FFA) in 1994 as a variant of lichen planopilaris (LPP). This classification is based on the histopathological findings of FFA and LPP, which are identical and therefore not separable. The clinical picture of FFA, however, is very characteristic and marked by regionally distinct structures of the skin. Typically, postmenopausal women present with a band-shaped atrophy that is several centimeters wide located in the frontotemporal area. Adjacent to the hairline, perifollicular erythema and papules can be found. In the majority of patients there is a loss of the eyebrows. Circumscribed alopecia and perifollicular papules occur only rarely on the extremities or the trunk. Etiology and pathogenesis of FFA are unclear. Hormone-related involutionary phenomena of the follicle, genetic factors, disruption of lipid homeostasis, and in accordance with the lichen planus associated T­cell cytotoxic autoimmune response are discussed. Treatment of FFA is difficult. Atrophy cannot be influenced by the currently available treatment options. With regard to the follicular inflammation, topical steroids and systemic hydroxychloroquine, antiandrogens, and tetracyclines are mainly used on a topical basis.

[Verrucous variant of porokeratosis of Mibelli as a differential diagnosis of psoriasis vulgaris]. / Verruköse Variante der Porokeratosis Mibelli als Differenzialdiagnose der Psoriasis vulgaris.

In a 37-year-old man, diagnosis of verrucous porokeratosis could only be made by histological examination. Previously, the skin lesions on the right buttock had been treated by several dermatologists as psoriasis vulgaris. The clinical picture of both dermatoses was characterized by sharply defined, erythematous papules and plaques. Precise evaluation of the clinical morphology was key for diagnosis. Moreover, in contrast to psoriasis, verrucous porokeratosis is characterized by a high degree of treatment resistance.

[Tattooing agents and adverse reactions]. / Tätowiermittel und ihre Unverträglichkeitsreaktionen.

BACKGROUND: Tattoos are regarded as body jewelry and have become widespread in all parts of society. Despite introduction of the tattooing agents' regulation (Tätowiermittelverordnung) in Germany in 2009, consumer protection is incomplete. OBJECTIVES: Prevalence of tattoos and their legal basis, ingredients of tattooing agents, clinical findings of adverse reactions, pathogenesis and therapy. METHODS: The work is based on a selective literature search in PubMed and on the clinical experience of the authors. RESULTS: Adverse reactions by tattooing are a particular problem, because the causing substances are not biodegradable within the tissue. In addition to an agonizing pruritus, the clinical picture is characterized by erythematous plaques. Histopathology reveals different patterns of inflammation, including pseudolymphomatous reactions. Treatment is problematic. In many cases, extensive surgical excision is necessary, which is associated with cosmetic consequences. CONCLUSION: A regulation to assess the safety of tattooing does not exist.

[Leukonychia totalis]. / Leukonychia totalis.

Our patient presented with leukonychia totalis at the age of 15 years. Other malformations such as syndromes or underlying internal diseases did not exist. The patient's family history was unremarkable. In the classification of leukonychias, the real, usually hereditary leukonychia can be distinguished from the acquired form. The white color of the nails can be isolated, depending on its present form, appear as part of a syndrome, or as a result of internal disease. An effective treatment of hereditary leukonychia is not known.

[Subcutaneous panniculitis-like T-cell lymphoma : Two case reports]. / Subkutanes pannikulitisartiges T-Zell-Lymphom : Zwei Kasuistiken.

Histopathology, immunohistochemical, and molecular genetic findings revealed the diagnosis of subcutaneous panniculitis-like T-cell-lymphoma in two patients, aged 44 and 70 years. The clinical morphology of the lymphoma manifestations showed varied significantly. One patient presented with a singular erythematous nodule in the chin region. The other patient suffered from extended plate-like resistances and atrophy of the face, upper arms and left breast. Hemophagocytic syndrome was not present in either patient. Prognosis of subcutaneous panniculitis-like T-cell lymphoma without associated hemophagocytic syndrome is reported to be favorable. Radiotherapy of the singular lesion on the chin and systemic corticosteroids of the extended plaques induced complete remission in both patients.

Postoperative irinotecan in resected stage II-III rectal cancer: final analysis of the French R98 Intergroup trial†.

BACKGROUD: The R98 trial explores the addition of irinotecan to a 5-fluorouracil (5-FU) plus leucovorin (5-FU/LV) adjuvant regimen in optimally resected stages II-III rectal cancers. We report the updated long-term results. Disease-free survival (DFS) was the primary end point. PATIENST AND METHODS: Between March 1999 and December 2005, 357 patients were randomized: 178 in 5-FU/LV and 179 in LV5-FU2 + irinotecan arm. The trial was stratified by control arm: Mayo Clinic regimen or LV5-FU2 regimen. RESULTS: Three hundred and fifty-seven randomized patients were evaluable for efficacy. With a follow-up of 156 months, the DFS was in favour of experimental arm but did not reach statistical significance [hazard ratio (HR) = 0.80, P = 0.154]. The same was observed for overall survival (OS) (HR = 0.87, P = 0.433). The 5-year DFS was 58% in the control arm and 63% in the experimental arm. The 5-year OS was 74% in the control arm and 75% in the experimental arm. Patients allocated to the experimental arm had more grade 3-4 neutropenia when compared with the LV5-FU2 arm (33% versus 6%, P = 0.03), but not when compared with the Mayo Clinic arm (33% versus 36%, P = 0.84). Grade 3-4 diarrhoea tended to be higher in the experimental arm, but analyses stratified by control arm or by radiotherapy failed to show significant differences across strata (test for interaction P = 0.44). CONCLUSION: Even though a benefit of irinotecan in subgroups of patients cannot be excluded, due to early termination and lack of power, the study does not support the addition of irinotecan to 5-FU/LV in routine in patients with resected stage II-III rectal cancer.

[Chronic venous insufficiency: Update on pathophysiology, diagnosis and treatment]. / Chronische venöse Insuffizienz: Aktuelles zur Pathophysiologie, Diagnostik und Therapie.

Chronic venous insufficiency is very common and has an important socioeconomic impact. It is associated with a high morbidity for the patients and causes high costs for the healthcare systems. In recent years novel treatment modalities have evolved and their efficacy has been evaluated in many studies. Knowledge of pathophysiology, the diagnostic procedures and therapeutic options for chronic venous insufficiency is important for effective treatment of affected patients.

[Impact of neoadjuvant chemotherapy on therapeutic management of muscle-invasive bladder cancer]. / Impact de la chimiothérapie néoadjuvante sur la prise en charge des tumeurs de vessie infiltrant le muscle.

OBJECTIVE: Assess the toxicity of neoadjuvant chemotherapy (NAC), its impact on surgical schedule and postoperative morbidity of cystectomy for muscle-invasive bladder cancer (MIBC). PATIENTS AND METHODS: Retrospective multicentric study of 78 patients who underwent a cystectomy from January 2009 to March 2012 for MIBC. The following criteria have been studied: toxicity of NC (WHO classification), precystectomy interval, postoperative morbidity (Clavien), duration of stay, downsizing on CT-scan before cystectomy, and free of cancer pathology (pT0). RESULTS: Seventy-eight patients had been included, thirty-nine had a NAC. Thirty-three percent had a incomplete chemotherapy because of toxicity. Forty-eight percent had a significant toxicity and grade ≥ 3 toxicity was 33%. Median time between diagnosis and cystectomy was 12.6 weeks (0.7-38), 18 weeks with NAC (group 1) versus eight weeks without NAC (group 2) (P=0.01). In case of toxicity, the delay was 3.5 weeks longer (P=0.12). After cystectomy, 60% of patients had at least one postoperative complication; including 23% had major morbidity. NAC did not increase neither postoperative morbidity (P=0.15) nor duration of stay (18 vs 20 days; P=0.2). Radiological response rate to NC was 38%. pT0 rate was 79 vs 7.7%. The increase of precystectomy interval after NC did not worsen the pathological stage (P=0.5). CONCLUSION: NC had a high toxicity, but without impact on postoperative morbidity, and precystectomy interval did not have any impact on the prognosis. LEVEL OF EVIDENCE: 5.

Evaluation in usual practice of the bevacizumab-FOLFIRI combination for the first-line treatment of patients with unresectable metastatic colorectal cancer treated in 2006: focus on resected patients and oncogeriatrics: AVASTIN OUEST cohort of the Observatory of Cancer of the Brittany and Pays de la Loire Areas (Observatoire dédié au Cancer Bretagne / Pays de la Loire).

BACKGROUND: In 2006, bevacizumab, a targeted therapy agent was combined with FOLFIRI for the firstline treatment of patients with unresectable metastatic colorectal cancer. METHODS/RESULTS: A study on a homogenous series of 111 patients from the Brittany and Pays de la Loire areas who received bevacizumab-FOLFIRI as first-line treatment in 2006 showed the following results: 51 responses, 29 stabilisations, 21 progressions and 10 cases of toxicity prior to assessment. Median overall survival (OS) was 25.1 months and median progression-free survival was 10.2 months. Surgery secondary to treatment tripled median OS which reached 59.2 months in resected patients versus 18.8 months in unresected patients. Comparison of patients aged more or less than 70 years showed no differences in terms of benefits or risks. CONCLUSION: Bevacizumab-FOLFIRI could be administered as part of a routine care protocol to elderly patients previously evaluated by a geriatric assessment and validated by a multidisciplinary staff.

En 2006, bevacizumab-FOLFIRI représente la thérapie ciblée administrable dès la première ligne chez les patients porteurs d'un cancer colorectal métastatique non opérable. Une série homogène de 111 patients colligés en région Bretagne et Pays de la Loire ayant reçu du bevacizumab- FOLFIRI en première ligne en 2006 révèle les résultats suivants: 51 réponses, 29 stabilités, 21 progressions et 10 toxicités avant évaluation. La médiane de survie globale (OS) est de 25,1 mois et la médiane de survie sans progression (PFS) de 10,2 mois. Dans le cas d'une chirurgie secondaire, l'OS médian triple de 18,8 mois chez les patients non réséqués versus 59,2 mois ceux réséqués. En comparant les sujets âgés de plus et de moins de 70 ans, aucune différence n'a été mise en évidence en termes de bénéfice ou de risque. Bevacizumab-FOLFIRI pourrait être administré en pratique courante chez les personnes âgées sous couvert d'une évaluation gériatrique et d'une approche multidisciplinaire.

Long-Term Functional Outcome After Early vs. Late Stoma Closure in Rectal Cancer Surgery: Sub-analysis of the Multicenter FORCE Trial.

PURPOSE: The aim of this study was to assess the effect of early stoma closure on bowel function after low anterior resection (LAR) for rectal cancer. METHODS: Patients participating in the FORCE trial who underwent LAR with protective stoma were included in this study. Patients were subdivided into an early closure group (< 3 months) and late closure group (> 3 months). Endpoints of this study were the Wexner Incontinence, low anterior resection syndrome (LARS), EORTC QLQ-CR29, and fecal incontinence quality of life (FIQL) scores at 1 year. RESULTS: Between 2017 and 2020, 38 patients had received a diverting stoma after LAR for rectal cancer and could be included. There was no significant difference in LARS (31 vs. 30, p = 0.63) and Wexner score (6.2 vs. 5.8, p = 0.77) between the early and late closure groups. Time to stoma closure in days was not a predictor for LARS (R2 = 0.001, F (1,36) = 0.049, p = 0.83) or Wexner score (R2 = 0.008, F (1,36) = 0.287, p = 0.60) after restored continuity. There was no significant difference between any of the FIQL domains of lifestyle, coping, depression, and embarrassment. In the EORTC QLQ-29, body image scored higher in the late closure group (21.3 vs. 1.6, p = 0.004). CONCLUSION: Timing of stoma closure does not appear to affect long-term bowel function and quality of life, except for body image. To improve functional outcome, attention should be focused on other contributing factors.