CTLA4 protects against maladaptive cytotoxicity during the differentiation of effector and follicular CD4+ T cells.

As chronic antigenic stimulation from infection and autoimmunity is a feature of primary antibody deficiency (PAD), analysis of affected patients could yield insights into T-cell differentiation and explain how environmental exposures modify clinical phenotypes conferred by single-gene defects. CD57 marks dysfunctional T cells that have differentiated after antigenic stimulation. Indeed, while circulating CD57+ CD4+ T cells are normally rare, we found that they are increased in patients with PAD and markedly increased with CTLA4 haploinsufficiency or blockade. We performed single-cell RNA-seq analysis of matched CD57+ CD4+ T cells from blood and tonsil samples. Circulating CD57+ CD4+ T cells (CD4cyt) exhibited a cytotoxic transcriptome similar to that of CD8+ effector cells, could kill B cells, and inhibited B-cell responses. CTLA4 restrained the formation of CD4cyt. While CD57 also marked an abundant subset of follicular helper T cells, which is consistent with their antigen-driven differentiation, this subset had a pre-exhaustion transcriptomic signature marked by TCF7, TOX, and ID3 expression and constitutive expression of CTLA4 and did not become cytotoxic even after CTLA4 inhibition. Thus, CD57+ CD4+ T-cell cytotoxicity and exhaustion phenotypes are compartmentalised between blood and germinal centers. CTLA4 is a key modifier of CD4+ T-cell cytotoxicity, and the pathological CD4cyt phenotype is accentuated by infection.

Clinical predictors of survival in real world practice in stage IV melanoma.

BACKGROUND AND AIM: While studies continually identify new clinical prognostic factors in stage IV melanoma, the introduction of targeted and immunotherapies have revolutionised the prognosis of advanced melanoma since 2011. The study aims to investigate the prognostic significance of past and newly identified clinical factors in a contemporary cohort. METHODS: A retrospective analysis of The Canberra Hospital melanoma database identified 161 patients with Stage IV melanoma between 2011 and 2017. Survival was analysed by demographics and clinical factors with chi-square tests to determine significance. Logistic binary regression was performed to test the independence of the clinical factors on predicting the survival outcome. RESULTS: Overall, the 3-month, 6-month, 9-month, and 12-month stage IV melanoma survival rate of our cohort was 79%, 67%, 55%, and 45%, respectively. Age, sex, and BRAF mutation status were found to have no impact on survival, whereas M1d category of the American Joint Committee on Cancer (AJCC) staging (8th edition), neutrophil-lymphocyte ratio (NLR) >3, elevated serum LDH, more than three metastatic sites, brain metastases, poorer Eastern cooperative oncology group (ECOG) status were associated with poorer survival. Binary logistic regression test identified AJCC staging, NLR (cutoff score 3), LDH, and brain metastases as independent prognostic factors. CONCLUSION: Most clinical factors investigated in this study were found to have a statistically significant impact on survival, with AJCC (8th edition) staging M1a-M1d, NLR (cutoff score 3), LDH, and brain metastases identified as independent prognostic factors in stage IV melanoma from a contemporary cohort treated with targeted therapies and immunotherapies.

Atezolizumab and bevacizumab as first line therapy in advanced hepatocellular carcinoma: Practical considerations in routine clinical practice.

Hepatocellular carcinoma (HCC) is the most common primary liver cancer. For advanced HCC, sorafenib was considered the standard of care for more than ten years. Recently the atezolizumab and bevacizumab combination has become standard of care for these patients without contraindications to either immune checkpoint inhibitors or antiangiogenic therapy. We now review the practical aspects of the atezolizumab and bevacizumab combination, including current evidence, indications, contraindications, management of adverse events, sequencing of this combination, areas of current knowledge gaps and future areas of active clinical research of this combination for busy clinicians in clinical practice.

NTRK and ALK rearrangements in malignant pleural mesothelioma, pulmonary neuroendocrine tumours and non-small cell lung cancer.

OBJECTIVES: Gene rearrangements involving NTRK1, NTRK2, NTRK3, ROS1 and ALK have been identified in many types of cancer, including non-small cell lung cancer (NSCLC). Data in malignant pleural mesothelioma (MPM), lung neuroendocrine tumors (NETs) and small-cell lung cancer (SCLC) are lacking. Given the activity of NTRK, ROS-1 and ALK inhibitors in tumors harboring gene fusions, we sought to explore such rearrangements in these less common tumors in addition to NSCLC. METHODS: Archival tumor tissue from patients with MPM, lung NETs, SCLC and NSCLC were used to create tissue microarrays. Immunohistochemistry (IHC) was performed using a cocktail of antibodies against TRK, ROS1 and ALK. IHC positive samples underwent RNA sequencing using the ArcherDX FusionPlex CTL diagnostic assay. Clinical data were obtained through retrospective chart review. RESULTS: We performed IHC on 1116 samples: 335 MPMs, 522 NSCLCs, 105 SCLCs and 154 lung NETs. There were 23 IHC positive cases (2.1%) including eight MPMs (2.4%), eight NETs (5.2%), five SCLC (4.8%) and two NSCLC (0.4%). The following fusions were detected: one MPM with an NTRK ex10-TPM3 ex8, another MPM with an ALK ex20-EML4ex13, one lung intermediate-grade NET (atypical carcinoid) with an ALK ex20-EML4 ex6/intron6, and two NSCLCs with an ALK ex20-EML4 ex6/intron6 rearrangement. None of the patients received targeted treatment. CONCLUSIONS: To our knowledge, we report for the first time NTRK and ALK rearrangements in a small subset of MPM. An ALK rearrangement was also detected in lung intermediate-grade NET (or atypical carcinoid). Our data suggest that IHC could be a useful screening test in such patients to ensure that all therapeutic strategies including targeted therapy are utilized.

Acquired lipodystrophy associated with immune checkpoint inhibitors.

Immune checkpoint inhibitors have become the mainstay of treatment for metastatic melanoma. This article presents a new case of acquired generalised lipodystrophy (AGL) during anti-programmed cell death-1 (anti-PD-1) therapy and a systematic review of the literature with an aim to further understand the pathogenesis. A comprehensive search was conducted using PubMed, Embase, MEDLINE and Cochrane Central databases. We identified four cases of lipodystrophy associated with anti-PD-1 immunotherapy, including our own. Of these, three were associated with nivolumab, and one with pembrolizumab. Body composition changes occurred at a median of 7 months after anti-PD-1 initiation. All cases reported AGL, with subcutaneous fat loss affecting majority of the body. There were three reported cases of insulin resistance associated with AGL. AGL should be a recognised adverse event associated with anti-PD-1 therapy.

Whole-Genome Sequences of Four Corynebacterium CDC Group F-1 Strains Isolated from Urine.

Three draft and one complete genome sequence from strains isolated from urine and consistent with Corynebacterium CDC group F-1 were assembled and studied. Genome sizes ranged between 2.3 and 2.44 Mb, with G+C content between 60.4% and 60.7%.

Posterior Reversible Encephalopathy Syndrome in Early-Stage Breast Cancer.

Wider use of chemotherapy and targeted agents can be associated with posterior reversible encephalopathy syndrome (PRES). This syndrome is most commonly found in metastatic adenocarcinoma treated with platinum-based analogs and is managed with cessation of the precipitating medication. We present the first case of PRES in early-stage breast cancer and discuss the further management of this condition. Recognition of this condition and correction of identifiable precipitating factor including cessation of relevant medications remains important in its management.

Genome sequence of a chimpanzee herpesvirus and its relation to other primate alphaherpesviruses.

This study reports the complete genome sequence of chimpanzee herpesvirus (ChHV), an alphaherpesvirus isolated from a chimpanzee. Although closely related to human herpes simplex virus type 2 (HSV2), the level of sequence diversity confirms that ChHV is sufficiently distinct to be considered a member of a different virus species rather than a variant strain of HSV2. Phylogenetic comparison with other simplexviruses at several levels supports the hypothesis that HSV2 and ChHV co-evolved with their respective human and chimpanzee hosts and raises questions regarding the evolutionary origins of HSV1.

The attenuated genotype of varicella-zoster virus includes an ORF0 transitional stop codon mutation.

Varicella-zoster virus (VZV) is the first of the human herpesviruses to be attenuated and subsequently approved as a live vaccine to prevent varicella and herpes zoster. Both the attenuated VZV vaccine, called vaccine Oka or vOka, and the parental strain pOka have been completely sequenced. Yet the specific determinants of attenuation are uncertain. The open reading frame (ORF) with the most single nucleotide polymorphisms (SNPs), ORF62, encodes the regulatory protein IE62, but IE62 studies have failed to define a specific SNP associated with attenuation. We have completed next-generation sequencing of the VZV Ellen genome, a strain known to be highly attenuated by its very limited replication in human skin xenografts in the SCID mouse model of VZV pathogenesis. A comparative analysis of the Ellen sequence with all other complete VZV sequences was extremely informative. In particular, an unexpected finding was a stop codon mutation in Ellen ORF0 (herpes simplex virus UL56 homolog) identical to one found in vOka, combined with the absence of polymorphisms in most Ellen ORFs that were known to be mutated in vOka. The mutated ORF0 protein was also imaged in both two dimensions and three dimensions by confocal microscopy. The probability of two VZV strains not connected by a recent common ancestor having an identical ORF0 SNP by chance would be 1 × 10(-8), in other words, extremely unlikely. Taken together, these bioinformatics analyses strongly suggest that the stop codon ORF0 SNP is one of the determinants of the attenuation genotype of live VZV vaccines.

Mucosal melanoma of the middle ear cavity and Eustachian tube: a case report, literature review, and focus on surgical technique.

OBJECTIVE: To present a case of mucosal melanoma of the Eustachian tube with a focus on surgical technique and to review the literature on treatment of mucosal melanoma of the head and neck, and review cases involving the middle ear and/or Eustachian tube. PATIENT: A 67-year-old man was diagnosed with mucosal melanoma of the middle ear and Eustachian tube. INTERVENTION: The patient underwent primary surgical resection including transtemporal/transpetrosal approach, endoscopic nasopharyngectomy, infratemporal fossa dissection, temporomandibular joint resection, ipsilateral neck dissection (levels II-IV), and superficial parotidectomy. RESULTS: The patient was discharged on postoperative Day 7 with a very good functional status. He did have early dysphagia and dysarthria as a result of the VII to XII anastomosis for facial nerve reconstruction, which did require PEG tube placement. However, at 4 months after surgery, the patient was eating solid foods and returning to normal activities. He received radiation therapy postoperatively. There has been no evidence of tumor recurrence at 8 months after treatment. CONCLUSION: The standard treatment of head and neck mucosal melanoma is primarily surgical. Surgical removal of mucosal melanoma in the Eustachian tube/middle ear can present challenges in achieving microscopically negative margins. However, gross tumor resection with postoperative radiotherapy has been shown to improve locoregional control.

Robotic-assisted transoral removal of a bilateral floor of mouth ranulas.

OBJECTIVE: To describe the management of bilateral oral ranulas with the use of the da Vinci Si Surgical System and discuss advantages and disadvantages over traditional transoral resection. STUDY DESIGN: Case Report and Review of Literature. RESULTS: A 47 year old woman presented to our service with an obvious right floor of mouth swelling. Clinical evaluation and computerized tomography scan confirmed a large floor of mouth ranula on the right and an incidental asymptomatic early ranula of the left sublingual gland. After obtaining an informed consent, the patient underwent a right transoral robotic-assisted transoral excision of the ranula and sublingual gland with identification and dissection of the submandibular duct and lingual nerve. The patient had an excellent outcome with no evidence of lingual nerve paresis and a return to oral intake on the first postoperative day. Subsequently, the patient underwent an elective transoral robotic-assisted excision of the incidental ranula on the left sublingual gland. CONCLUSION: We describe the first robotic-assisted excision of bilateral oral ranulas in current literature. The use of the da Vinci system provides excellent visualization, magnification, and dexterity for transoral surgical management of ranulas with preservation of the lingual nerve and Wharton's duct with good functional outcomes. However, the use of the robotic system for anterior floor of mouth surgery in terms of improved surgical outcomes as compared to traditional transoral surgery, long-term recurrence rates, and cost effectiveness needs further validation.

Molecular definition of vaginal microbiota in East African commercial sex workers.

Resistance to HIV infection in a cohort of commercial sex workers living in Nairobi, Kenya, is linked to mucosal and antiinflammatory factors that may be influenced by the vaginal microbiota. Since bacterial vaginosis (BV), a polymicrobial dysbiosis characterized by low levels of protective Lactobacillus organisms, is an established risk factor for HIV infection, we investigated whether vaginal microbiology was associated with HIV-exposed seronegative (HESN) or HIV-seropositive (HIV(+)) status in this cohort. A subset of 44 individuals was selected for deep-sequencing analysis based on the chaperonin 60 (cpn60) universal target (UT), including HESN individuals (n = 16), other HIV-seronegative controls (HIV-N, n = 16), and HIV(+) individuals (n = 12). Our findings indicate exceptionally high phylogenetic resolution of the cpn60 UT using reads as short as 200 bp, with 54 species in 29 genera detected in this group. Contrary to our initial hypothesis, few differences between HESN and HIV-N women were observed. Several HIV(+) women had distinct profiles dominated by Escherichia coli. The deep-sequencing phylogenetic profile of the vaginal microbiota corresponds closely to BV(+) and BV(-) diagnoses by microscopy, elucidating BV at the molecular level. A cluster of samples with intermediate abundance of Lactobacillus and dominant Gardnerella was identified, defining a distinct BV phenotype that may represent a transitional stage between BV(+) and BV(-). Several alpha- and betaproteobacteria, including the recently described species Variovorax paradoxus, were found to correlate positively with increased Lactobacillus levels that define the BV(-) ("normal") phenotype. We conclude that cpn60 UT is ideally suited to next-generation sequencing technologies for further investigation of microbial community dynamics and mucosal immunity underlying HIV resistance in this cohort.

Pyrosequencing of chaperonin-60 (cpn60) amplicons as a means of determining microbial community composition.

The chaperonin-60 universal target (cpn60 UT) is generated from a set of PCR primers and provides a universally conserved, phylogenetically informative sequence signature for determining the composition of microbial communities by DNA sequencing. Pyrosequencing of cpn60 UT amplicons is emerging as a next-generation tool for providing unprecedented sequencing depth and resolution of microbial communities in individual samples. Owing to the increase in sequencing depth, the dynamic range across which the presence and abundance of individual species can be sampled experimentally also increases, significantly improving our ability to investigate microbial community richness and diversity. The flexible format of the pyrosequencing reaction setup combined with the ability to pool samples through the use of multiplexing IDs makes the generation of microbial profiles based on the cpn60 UT both feasible and cost-effective. We describe here the methods we have developed for determining microbial community profiles by pyrosequencing of cpn60 UT amplicons, from generating amplicons to sequencing and data analysis.

Robotic-assisted transoral removal of a submandibular megalith.

The majority of salivary stones are less than 8 mm in size and most frequently occur in the submandibular gland. Traditional management of larger stones involves gland resection. Sialendoscopy combined with an external or a transoral sialolithotomy, also called the combined approach technique, permits stone removal and gland preservation. A 31-year-old male presented to our service with a 20-mm megalith in the left submandibular gland. Here we report the first description of a combined approach using the da Vinci Si Surgical System to facilitate transoral stone removal and salivary duct repair.

Treatment of nasopharyngeal papillomatosis with coblation: a case series.

BACKGROUND: Nasopharyngeal papillomatosis is uncommon. Access and visualization make excision difficult, increasing the risk for recurrence. We present a novel technique for excision of nasopharyngeal papillomatosis. METHODS: A case series of 3 patients with recurrent papilloma of the nasopharynx (NP) were treated with endoscopic transnasal coblation. We used an Arthrocare EVac 70 Coblator (setting: coblation-9, coagulation-5). RESULTS: Using transnasal endoscopic coblation, we performed complete excision in 3 patients with recurrent papilloma of the NP (4 total procedures). There were no complications. One patient had a minor recurrence, which was successfully re-excised with the same technique. CONCLUSION: Nasopharyngeal papillomas can be difficult to excise. Multiple techniques have been described using a transoral approach, with no reported complications. However, surgical access to the entire NP is more challenging with a transoral approach. Also, bleeding and poor visualization secondary to bleeding can be encountered with these techniques. These problems were not encountered with transnasal coblation. The absence of eschar and decreased collateral thermal damage make coblation preferable to cauterization or laser excision. This proposed technique enables more complete visualization and removal of disease, which may reduce recurrence rates.

Middle ear endoscopy and trans-tympanic drug delivery using an interventional sialendoscope: a feasibility study in human cadaveric temporal bones.

OBJECTIVES: The aim of our study was to assess feasibility of using a 1.3mm semi-rigid interventional salivary endoscope for middle ear endoscopy and as a route for trans-tympanic delivery of medication in human cadaveric temporal bones. METHODS: Five temporal bones harvested from human cadavers were examined. A 1.3mm diameter 0 degree. Marchal interventional sialendoscope equipped with an interventional channel (0.4 mm) and an irrigation/suction channel was used. Middle ear endoscopy was performed via endoscopic guided postero-inferior and antero-superior myringotomies. The round window niche (RWN) was easily identified, and a guide wire was placed within the RWN. Also, the Eustachian tube orifice was identified and cannulated with a guide wire. RESULTS: Access to the RWN was obtained via a postero-inferior myringotomy in all five temporal bones (100%). A guide wire could be navigated to the RWN without difficulty in all patients. The opening to the ET was visualized and could be cannulated with a guide wire in all patients where it was attempted (N=3). CONCLUSION: The 1.3 mm interventional sialendoscope allowed adequate visualization of the ET, middle ear space, and the RWN with interventional capabilities in a cadaveric model. Our result validates the feasibility of its use for trans-tympanic drug delivery. However, the proposed indication for the use of the sialendoscope needs to be evaluated in a clinical setting. Additional cadaveric and human studies are necessary to further investigate additional applications for its use in the field of otolaryngology.

Pyrosequencing of the chaperonin-60 universal target as a tool for determining microbial community composition.

We compared dideoxy sequencing of cloned chaperonin-60 universal target (cpn60 UT) amplicons to pyrosequencing of amplicons derived from vaginal microbial communities. In samples pooled from a number of individuals, the pyrosequencing method produced a data set that included virtually all of the sequences that were found within the clone library and revealed an additional level of taxonomic richness. However, the relative abundances of the sequences were different in the two datasets. These observations were expanded and confirmed by the analysis of paired clone library and pyrosequencing datasets from vaginal swabs taken from four individuals. Both for individuals with a normal vaginal microbiota and for those with bacterial vaginosis, the pyrosequencing method revealed a large number of low-abundance taxa that were missed by the clone library approach. In addition, we showed that the pyrosequencing method generates a reproducible profile of microbial community structure in replicate amplifications from the same community. We also compared the taxonomic composition of a vaginal microbial community determined by pyrosequencing of 16S rRNA amplicons to that obtained using cpn60 universal primers. We found that the profiles generated by the two molecular targets were highly similar, with slight differences in the proportional representation of the taxa detected. However, the number of operational taxonomic units was significantly higher in the cpn60 data set, suggesting that the protein-encoding gene provides improved species resolution over the 16S rRNA target. These observations demonstrate that pyrosequencing of cpn60 UT amplicons provides a robust, reliable method for deep sequencing of microbial communities.

A full-genome phylogenetic analysis of varicella-zoster virus reveals a novel origin of replication-based genotyping scheme and evidence of recombination between major circulating clades.

Varicella-zoster virus (VZV) is a remarkably stable virus that until recently was thought to exhibit near-universal genetic homogeneity among circulating wild-type strains. In recent years, the expanding knowledge of VZV genetics has led to a number of groups proposing sequence-based typing schemes, but no study has yet examined the relationships between VZV genotypes at a full-genome level. A central hypothesis of this study is that VZV has coevolved with humankind. In this study, 11 additional full VZV genomic sequences are presented, bringing the current number of complete genomic sequences publicly available to 18. The full-genome alignment contained strains representing four distinct clades, but the possibility exists that a fifth clade comprised of African and Asian-like isolates was not represented. A consolidated VZV genotyping scheme employing the origin-associated region between reiteration region R4 and open reading frames (ORFs) 63 and 70 is described, one which accurately categorizes strains into one of four clades related to the geographic origin of the isolates. The full-genome alignment also provided evidence for recombination having occurred between the major circulating VZV clades. One Canadian clinical isolate was primarily Asian-like in origin, with most of the genome showing strong sequence identity to the Japanese-like clade B, with the exceptions being two putative recombination regions, located in ORFs 14 to 17 and ORFs 22 to 26, which showed clear similarity to the European/North American clade A. The very low rate of single-nucleotide polymorphisms scattered across the genome made full-genome sequencing the only definitive method for identifying specific VZV recombination events.

Complete genome sequence of cercopithecine herpesvirus 2 (SA8) and comparison with other simplexviruses.

We have obtained the complete sequence of the herpesvirus simian agent 8 (SA8; cercopithecine herpesvirus 2) a baboon simplexvirus closely related to the monkey B virus and herpes simplex virus types 1 and 2. The genome of SA8 is 150,715 bp long, with an overall G/C content of 76%, the highest among the simplexviruses sequenced so far. The sequencing has confirmed that the genomic arrangement of SA8 is similar to that of other simplexviruses: unique long and unique short regions bordered by two sets of inverted repeats. All genes identified in SA8 are homologous and collinear with those of the monkey B virus, including the lack of the RL1 open reading frame, a gene responsible for neurovirulence in human herpes simplex viruses. This latter finding supports the hypothesis that a different pathogenetic mechanism may have developed in human simplexviruses, after their divergence from monkey simplexviruses.