A natural antisense RNA derived from the HIV-1 env gene encodes a protein which is recognized by circulating antibodies of HIV+ individuals

AbstractA naturally occurring antisense RNA, transcribed in the opposite direction and complementary to the envelope transcript,was identified in various cell lines chronically infected with HIV-1. In T cells, the antisense transcript is constitutively expressed and enhanced by activation with phorbol myristate acetate. The open reading frame corresponding to the antisense transcript, when expressed in vitro, encodes a protein with an apparent molecular mass of 19 kDa. Antibodies against this protein have been detected in several sera of HIV+ individuals and not in any of the noninfected control sera. These results indicate, for the first time, that expression of an antisense open reading frame most likely accompanies the HIV infection cycle in humans

Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons

10.1371/journal.pone.0046152PLoS ONE79

Innovations 2022 en chirurgie orthopédique et traumatologie

La limitation des moyens financiers en soins de Santé nous appelle à justifier de nos choix en apportant la preuve d’une amélioration réelle pour le patient, traduite par sa capacité à réintégrer rapidement le circuit économique et le retour à une vie sociale active, ou encore en développant des techniques moins invasives qui permettent de réduire la période d’incapacité ou les complications auxquelles le patient est exposé. Le service de Chirurgie Orthopédique et Traumatologie a choisi de mettre en évidence différentes approches dans ce cadre : le bénéfice d’une évaluation fonctionnelle en chirurgie de la main quant à l’objectivation du bénéfice de différentes modalités thérapeutiques, les perspectives, encore précoces, de traitement par phages dans les infections d’implants orthopédiques par des bactéries multirésistantes, sans devoir recourir à des chirurgies lourdes, et deux approches biologiques et bio-technologiques pour obtenir la guérison des défauts de consolidation des fractures, sans exposer le patient aux complications d’un prélèvement osseux autologue

Chirurgie orthopédique et traumatologie: que retenir en 2021?

L’année 2021 nous permet d’éclairer l’impact des techniques mini-invasives en chirurgie d’arthroplastie de hanche, la poursuite des progrès dans l’arthroplastie du genou, la place de stratégies non conventionnelles dans le contrôle des infections d’implants et l’intérêt d’une nouvelle installation pour la réalisation des techniques d’arthroscopie de l’épaule. L’optimisation des techniques chirurgicales en arthroplastie de hanche permet d’identifier les patients pour lesquels un contrôle sanguin postopératoire s’avère nécessaire mais aussi, dès lors d’optimiser les patients avant l’intervention afin de réduire le risque d’anémie postopératoire et la nécessité d’une transfusion. Le bénéfice de l’arthroplastie du genou n’a jusqu’à présent pas égalé celui de la hanche. Néanmoins, le développement des stratégies de resurfaçage respectant l’anatomie individuelle du patient soutenu par la technologie moderne et particulièrement la robotisation et le recours aux implants sur mesures laisse augurer de progrès significatifs. L’infection constitue une complication redoutable de la chirurgie d’arthroplastie. Aux stratégies classiques viennent s’ajouter de nouvelles approches thérapeutiques comme la chirurgie deux temps en un et une meilleure définition de la place de l’antibiothérapie suppressive au long cours. Enfin, Il semble qu’une position optimale pour les patients qui bénéficient d’arthroscopies de l’épaule soit celle en décubitus dorsal, évitant les inconvénients des positions semi-assise et en décubitus latéral, la première étant associée à un risque anesthésique accru et la deuxième à des difficultés chirurgicales en cas de conversion vers une voie ouverte et un risque de lésion du plexus brachial.[2021 innovations in orthopedic surgery and traumatology] The year 2021 enabled us to shed light on the impact of minimally invasive techniques in hip arthroplasty surgery, continued progress in knee arthroplasty, place of unconventional strategies in the control of implant infections, and interest of a new surgical positioning for performing shoulder arthroscopy techniques. The optimization of surgical techniques in hip arthroplasty renders it now possible to identify those patients for whom a postoperative blood control proves necessary but also, therefore, for optimizing the patients before the intervention in order to reduce the risk of postoperative anemia and transfusion requirement. The benefit of knee replacement surgery has so far not matched that of hip replacement. Nevertheless, the development of resurfacing strategies respecting the individual anatomy of the patient, supported by modern technology and particularly robotization and using custom-made implants, augurs well for significant progress. Infection is a serious complication of arthroplasty surgery. To the classic strategies were added new therapeutic approaches, such as two-stage surgery in one stage and a better definition of the place of long-term suppressive antibiotic therapy. Finally, an optimal position for patients benefitting from shoulder arthroscopy is that in the supine position, avoiding the disadvantages of semi-sitting and lateral decubitus positions, with the first associated with increased anesthetic risks and the second with surgical difficulties in the event of conversion to an open approach, with a risk of injury to the brachial plexus

Clinical presentation, course, and prognosis of patients with mixed connective tissue disease : a multicenter retrospective cohort

International audienceObjectives: The objective of this study is to better characterize the features and outcomes of a large population of patients with mixed connective tissue disease (MCTD). Methods: We performed an observational retrospective multicenter cohort study in France. Patients who fulfilled at least one diagnostic criterion set for MCTD and none of the criteria for other differentiated CTD (dCTD) were included. Results: Three hundred and thirty patients (88% females, median [interquartile range] age of 35 years [26–45]) were included. The diagnostic criteria of Sharp or Kasukawa were met by 97.3% and 93.3% of patients, respectively. None met other classification criteria without fulfilling Sharp or Kasukawa criteria. After a median follow-up of 8 (3–14) years, 149 (45.2%) patients achieved remission, 92 (27.9%) had interstitial lung disease, 25 (7.6%) had pulmonary hypertension, and 18 (5.6%) died. Eighty-five (25.8%) patients progressed to a dCTD, mainly systemic lupus erythematosus (15.8%) or systemic sclerosis (10.6%). Median duration between diagnosis and progression to a dCTD was 5 (2–11) years. The presence at MCTD diagnosis of an abnormal pattern on nailfold capillaroscopy (odds ratio [OR] = 2.44, 95% confidence interval [95%CI] [1.11–5.58]) and parotid swelling (OR = 3.86, 95%CI [1.31–11.4]) were statistically associated with progression to a dCTD. Patients who did not progress to a dCTD were more likely to achieve remission at the last follow-up (51.8% vs. 25.9%). Conclusions: This study shows that MCTD is a distinct entity that can be classified using either Kasukawa or Sharp criteria, and that only 25.8% of patients progress to a dCTD during follow-up

Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes

Somatic genome rearrangements are thought to play important roles in cancer development. We optimized a long-span paired-end-tag (PET) sequencing approach using 10-Kb genomic DNA inserts to study human genome structural variations (SVs). The use of a 10-Kb insert size allows the identification of breakpoints within repetitive or homology-containing regions of a few kilobases in size and results in a higher physical coverage compared with small insert libraries with the same sequencing effort. We have applied this approach to comprehensively characterize the SVs of 15 cancer and two noncancer genomes and used a filtering approach to strongly enrich for somatic SVs in the cancer genomes. Our analyses revealed that most inversions, deletions, and insertions are germ-line SVs, whereas tandem duplications, unpaired inversions, interchromosomal translocations, and complex rearrangements are over-represented among somatic rearrangements in cancer genomes. We demonstrate that the quantitative and connective nature of DNA–PET data is precise in delineating the genealogy of complex rearrangement events, we observe signatures that are compatible with breakage-fusion-bridge cycles, and we discover that large duplications are among the initial rearrangements that trigger genome instability for extensive amplification in epithelial cancers

SV identification based on the mapping pattern of dPET clusters.

<p>The dark red and pink arrows represent the 5′ and 3′ anchor regions of the dPET cluster, respectively. Black, white and blue horizontal lines represent chromosome segments. The red track represents the coverage of cPETs. The dotted lines indicate the connections between the two dPET clusters. The sub-types of insertions are as follows: (1) Intra-chromosomal direct forward insertion. (2) Intra-chromosomal direct backward insertion. (3) Intra-chromosomal inverted forward insertion. (4) Intra-chromosomal inverted backward insertion. (5) Deletion plus intra-chromosomal direct forward insertion. (6) Deletion plus intra-chromosomal inverted forward insertion. (7) Inter-chromosomal direct insertion. (8) Inter chromosome inverted insertion.</p

DNA-PET library construction, sequencing and mapping.

<p>(A) The genomic DNA was randomly sheared to different size range. (B) The very narrow region DNA fragments were obtained after size selection. (C) The purified DNA fragments were circularized, <i>EcoP15I</i> digested, sequencing adaptor ligated, and finally sequenced by SOLiD sequencer. (D) PET mapping span distribution of 1 kb (blue), 10 kb (red) and 20 kb (green) libraries. Based on the mapping pattern, PETs can be distinguished as concordant PETs and discordant PETs.</p

Reconstruction of the <i>BCR-ABL1</i> amplicon of K562.

<p>(A) Concordant tag distributions representing copy number are shown for amplified genomic regions (top, green track). Genomic segments between predicted breakpoints are indicated by colored arrows and dPET clusters with cluster sizes greater than 35 of predicted somatic rearrangements are represented by horizontal lines flanked by dark red and pink arrows indicating 5′ and 3′ anchor regions (middle). Small to large dPET clusters are arranged from top to bottom. Cluster sizes are indicated. High dPET cluster size of the CML causing <i>BCR-ABL1</i> translocation suggests that the rearrangement occurred early and that it has subsequently been amplified. Fusion points I–III correspond to panels C–D. (B) Fluorescence <i>in situ</i> hybridization (FISH) of <i>BCR-ABL1</i> rearrangement (fusion point I with cluster size 692). Yellow spots represent fusion signals and illustrate the amplification of <i>BCR-ABL1</i>. (C) FISH analysis of metaphase chromosomes of three high copy fusion points: I) probes used in B show fusion signals on two marker chromosomes and on chromosome 2q and normal localization on both rearranged chromosomes 9 and normal chromosome 22; the fusion on chromosome 2 has not been identified by DNA-PET most likely due to low sequence complexity at the break point or complex rearrangements, II) probes spanning the fusion point II (cluster size 259) show fusion signals on the same marker chromosomes and normal localization on both normal and rearranged chromosomes 9 and 13, III) probes spanning fusion point III (cluster size 218) show fusion signals on the same marker chromosomes and normal localization on both normal chromosome 22 and rearranged chromosomes 9. (D) Contigs (indicated by boxes) which were covered by PET mapping were concatenated by fusion-point-guided-concatenation method. The length of a contig is represented by the length of the box. Because of the size difference between chromosomes 1, 3, 9, 13, and 22, the length of chromosome 22 is represented by the length of contig/10,000 while the lengths of chromosomes 1, 3, 9, and 13 are represented by the length of contig/100,000. Any value less than 0.1 is rounded to 0.1; any value larger than 6 is rounded to 6. The thickness of borders of each contig represents the coverage (copy number). Red dashed edges represent dPET edges, while black bold edges represent cPET edges. The thickness of dPET edges represents the size of the corresponding dPET cluster. cPET edges have uniform thickness. Arrow heads pointing towards a contig indicate connections with the lower coordinates, arrow heads pointing away from a contig indicate connections with the higher coordinates.</p

Statistics of PET sequencing.

1)<p>non-redundant.</p>2)<p>physical coverage.</p>3)<p>concordant PET.</p>4)<p>proportion of cPET to total NR PET.</p>5)<p>discordant PET.</p>6)<p>proportion of dPET to total NR PET.</p>7)<p>number of dPET involved in the dPET clusters with cluster count ≥3.</p