Peripheral T-cell lymphomas expressing CD30 and CD15 expand the spectrum of anaplastic large cell lymphoma, ALK-negative.

Peripheral T-cell lymphomas (PTCL) are morphologically and biologically heterogeneous and a subset expresses CD30, including anaplastic large cell lymphomas (ALCL) and a minority of PTCL, not otherwise specified (PTCL, NOS). ALCL with ALK translocations (ALCL, ALK+) are readily identified by routine diagnostic methods, but differentiating ALCL without ALK translocation (ALCL, ALK-) and PTCL, NOS expressing CD30 (PTCL CD30+) can be challenging. Furthermore, rare PTCL co-express CD30 and CD15 (PTCL CD30+CD15+); some resemble ALCL, ALK- while others resemble classic Hodgkin lymphoma. To explore the relationship between PTCL CD30+CD15+ and ALCL, ALK-, we analysed 19 cases of PTCL with CD30 expression, previously diagnosed as ALCL, ALK- (nine cases) and PTCL CD30+CD15+ (10 cases) for DUSP22/IRF4 rearrangements, coding RNA expression and selected transcriptome analysis using the NanoString nCounter gene expression analysis platform. Unsupervised clustering showed no clear segregation between ALCL, ALK- and PTCL CD30+CD15+. Three cases previously classified as PTCL CD30+CD15+ showed DUSP22/IRF4 rearrangements, favouring a diagnosis of ALCL, ALK-. Our results suggest that cases previously designated PTCL CD30+CD15+, likely fall within the spectrum of ALCL, ALK-; additionally, a subset of ALCL, ALK- with DUSP22/IRF4 rearrangement expresses CD15, consistent with previous reports and expands the immunophenotypic spectrum of this lymphoma subgroup.

Comparison of lung aeration loss in open abdominal oncologic surgeries after ventilation with electrical impedance tomography-guided PEEP versus conventional PEEP: a pilot feasibility study.

Background: Existing literature lacks high-quality evidence regarding the ideal intraoperative positive end-expiratory pressure (PEEP) to minimize postoperative pulmonary complications (PPCs). We hypothesized that applying individualized PEEP derived from electrical impedance tomography (EIT) would reduce the severity of postoperative lung aeration loss, deterioration in oxygenation, and PPC incidence. Methods: A pilot feasibility study was conducted on 36 patients who underwent open abdominal oncologic surgery. The patients were randomized to receive individualized PEEP or conventional PEEP at 4 cm H2O. The primary outcome was the impact of individualized PEEP on changes in the modified lung ultrasound score (MLUS) derived from preoperative and postoperative lung ultrasonography. A higher MLUS indicated greater lung aeration loss. The secondary outcomes were the PaO2/FIO2 ratio and PPC incidence. Results: A significant increase in the postoperative MLUS (12 ± 3.6 vs 7.9 ± 2.1, P < 0.001) and a significant difference between the postoperative and preoperative MLUS values (7.0 ± 3.3 vs 3.0 ± 1.6, P < 0.001) were found in the conventional PEEP group, indicating increased lung aeration loss. In the conventional PEEP group, the intraoperative PaO2/FIO2 ratios were significantly lower but not the postoperative ratios. The PPC incidence was not significantly different between the groups. Post-hoc analysis showed the increase in lung aeration loss and deterioration of intraoperative oxygenation correlated with the deviation from the individualized PEEP. Conclusions: Individualized PEEP appears to protect against lung aeration loss and intraoperative oxygenation deterioration. The advantage was greater in patients whose individualized PEEP deviated more from the conventional PEEP.

A "Cool" extraction technique for difficult pediatric airway foreign bodies: Report of two cases.

Foreign body (FB) aspiration is a potentially life-threatening accident in children. Traditionally, rigid bronchoscopy has been the procedure of choice for FB removal, however it may miss distally lodged FBs. We report two pediatric cases with distal impacted FBs that could not be retrieved by rigid bronchoscopy (RB) and were mobilised using Fogarty balloon followed by flexible bronchoscopic cryoextraction. The advantage of a cryoprobe is lower risk of fragmentation of FB that may occur with forceps. Cryoextraction is particularly advantageous for removing water-containing FBs. In both patients, FB was removed more than 2 weeks following aspiration, leading to the formation of granulation tissue around the FB, which considerably hampered the process. Using a laryngeal mask airway to secure the airway, FB removal by flexible bronchoscopy may be a safe and effective technique in skilled hands, especially for FBs impacted in distal airways with granulation tissue where RB fails.

Polygenic architecture of rare coding variation across 394,783 exomes.

Both common and rare genetic variants influence complex traits and common diseases. Genome-wide association studies have identified thousands of common-variant associations, and more recently, large-scale exome sequencing studies have identified rare-variant associations in hundreds of genes1-3. However, rare-variant genetic architecture is not well characterized, and the relationship between common-variant and rare-variant architecture is unclear4. Here we quantify the heritability explained by the gene-wise burden of rare coding variants across 22 common traits and diseases in 394,783 UK Biobank exomes5. Rare coding variants (allele frequency < 1 × 10-3) explain 1.3% (s.e. = 0.03%) of phenotypic variance on average-much less than common variants-and most burden heritability is explained by ultrarare loss-of-function variants (allele frequency < 1 × 10-5). Common and rare variants implicate the same cell types, with similar enrichments, and they have pleiotropic effects on the same pairs of traits, with similar genetic correlations. They partially colocalize at individual genes and loci, but not to the same extent: burden heritability is strongly concentrated in significant genes, while common-variant heritability is more polygenic, and burden heritability is also more strongly concentrated in constrained genes. Finally, we find that burden heritability for schizophrenia and bipolar disorder6,7 is approximately 2%. Our results indicate that rare coding variants will implicate a tractable number of large-effect genes, that common and rare associations are mechanistically convergent, and that rare coding variants will contribute only modestly to missing heritability and population risk stratification.

Systematically characterizing the roles of E3-ligase family members in inflammatory responses with massively parallel Perturb-seq.

E3 ligases regulate key processes, but many of their roles remain unknown. Using Perturb-seq, we interrogated the function of 1,130 E3 ligases, partners and substrates in the inflammatory response in primary dendritic cells (DCs). Dozens impacted the balance of DC1, DC2, migratory DC and macrophage states and a gradient of DC maturation. Family members grouped into co-functional modules that were enriched for physical interactions and impacted specific programs through substrate transcription factors. E3s and their adaptors co-regulated the same processes, but partnered with different substrate recognition adaptors to impact distinct aspects of the DC life cycle. Genetic interactions were more prevalent within than between modules, and a deep learning model, comßVAE, predicts the outcome of new combinations by leveraging modularity. The E3 regulatory network was associated with heritable variation and aberrant gene expression in immune cells in human inflammatory diseases. Our study provides a general approach to dissect gene function.

Treatment-associated remodeling of the pancreatic cancer endothelium at single-cell resolution.

Pancreatic ductal adenocarcinoma (PDAC) is one of the most treatment refractory and lethal malignancies. The diversity of endothelial cell (EC) lineages in the tumor microenvironment (TME) impacts the efficacy of antineoplastic therapies, which in turn remodel EC states and distributions. Here, we present a single-cell resolution framework of diverse EC lineages in the PDAC TME in the context of neoadjuvant chemotherapy, radiotherapy, and losartan. We analyzed a custom single-nucleus RNA-seq dataset derived from 37 primary PDAC specimens (18 untreated, 14 neoadjuvant FOLFIRINOX + chemoradiotherapy, 5 neoadjuvant FOLFIRINOX + chemoradiotherapy + losartan). A single-nucleus transcriptome analysis of 15,185 EC profiles revealed two state programs (ribosomal, cycling), four lineage programs (capillary, arterial, venous, lymphatic), and one program that did not overlap significantly with prior signatures but was enriched in pathways involved in vasculogenesis, stem-like state, response to wounding and hypoxia, and endothelial-to-mesenchymal transition (reactive EndMT). A bulk transcriptome analysis of two independent cohorts (n = 269 patients) revealed that the lymphatic and reactive EndMT lineage programs were significantly associated with poor clinical outcomes. While losartan and proton therapy were associated with reduced lymphatic ECs, these therapies also correlated with an increase in reactive EndMT. Thus, the development and inclusion of EndMT-inhibiting drugs (e.g., nintedanib) to a neoadjuvant chemoradiotherapy regimen featuring losartan and/or proton therapy may be most effective in depleting both lymphatic and reactive EndMT populations and potentially improving patient outcomes.

SAIGE-GENE+ improves the efficiency and accuracy of set-based rare variant association tests.

Several biobanks, including UK Biobank (UKBB), are generating large-scale sequencing data. An existing method, SAIGE-GENE, performs well when testing variants with minor allele frequency (MAF) ≤ 1%, but inflation is observed in variance component set-based tests when restricting to variants with MAF ≤ 0.1% or 0.01%. Here, we propose SAIGE-GENE+ with greatly improved type I error control and computational efficiency to facilitate rare variant tests in large-scale data. We further show that incorporating multiple MAF cutoffs and functional annotations can improve power and thus uncover new gene-phenotype associations. In the analysis of UKBB whole exome sequencing data for 30 quantitative and 141 binary traits, SAIGE-GENE+ identified 551 gene-phenotype associations.

Identifying disease-critical cell types and cellular processes by integrating single-cell RNA-sequencing and human genetics.

Genome-wide association studies provide a powerful means of identifying loci and genes contributing to disease, but in many cases, the related cell types/states through which genes confer disease risk remain unknown. Deciphering such relationships is important for identifying pathogenic processes and developing therapeutics. In the present study, we introduce sc-linker, a framework for integrating single-cell RNA-sequencing, epigenomic SNP-to-gene maps and genome-wide association study summary statistics to infer the underlying cell types and processes by which genetic variants influence disease. The inferred disease enrichments recapitulated known biology and highlighted notable cell-disease relationships, including γ-aminobutyric acid-ergic neurons in major depressive disorder, a disease-dependent M-cell program in ulcerative colitis and a disease-specific complement cascade process in multiple sclerosis. In autoimmune disease, both healthy and disease-dependent immune cell-type programs were associated, whereas only disease-dependent epithelial cell programs were prominent, suggesting a role in disease response rather than initiation. Our framework provides a powerful approach for identifying the cell types and cellular processes by which genetic variants influence disease.

Comments on "Optimal control analysis of a COVID-19 and tuberculosis co-dynamics model".

Study of dynamics of COVID-19 and its co-infection with other diseases through mathematical models is the major focus of recent advancement in mathematical modeling of infectious diseases. There are numerous mathematical models on COVID-19 which describe its dynamics for different geographic regions. However, there are very few research papers dealing with co-infection of COVID-19 and TB. As both TB and COVID-19 are infectious diseases of same nature it becomes very difficult to predict the co-dynamics of these two diseases. The formulation of a correct mathematical model is very important in any kind of modeling and if the mathematical model is not proper then any prediction based on this may not be valid. This letter highlights the important limitations in the proposed mathematical model of co-dynamics of COVID-19 and TB by [1].

Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data.

Single-cell RNA sequencing (scRNA-seq) provides unique insights into the pathology and cellular origin of disease. We introduce single-cell disease relevance score (scDRS), an approach that links scRNA-seq with polygenic disease risk at single-cell resolution, independent of annotated cell types. scDRS identifies cells exhibiting excess expression across disease-associated genes implicated by genome-wide association studies (GWASs). We applied scDRS to 74 diseases/traits and 1.3 million single-cell gene-expression profiles across 31 tissues/organs. Cell-type-level results broadly recapitulated known cell-type-disease associations. Individual-cell-level results identified subpopulations of disease-associated cells not captured by existing cell-type labels, including T cell subpopulations associated with inflammatory bowel disease, partially characterized by their effector-like states; neuron subpopulations associated with schizophrenia, partially characterized by their spatial locations; and hepatocyte subpopulations associated with triglyceride levels, partially characterized by their higher ploidy levels. Genes whose expression was correlated with the scDRS score across cells (reflecting coexpression with GWAS disease-associated genes) were strongly enriched for gold-standard drug target and Mendelian disease genes.

Institutional end-of-life care policy for inpatients at a tertiary care centre in India: A way forward to provide a system for a dignified death.

India has a high share in the global burden of chronic terminal illnesses. However, there is a lack of a uniform system in providing better end-of-life care (EOLC) for large patients in their terminal stage of life. Institutional policies can be a good alternative as there is no national level policy for EOLC. This article describes the important aspects of the EOLC policy at one of the tertiary care institutes of India. A 15 member institutional committee including representatives from various departments was formed to develop this institutional policy. This policy document is aimed at helping to recognize the potentially non-beneficial or harmful treatments and provide transparency and accountability of the process of limitation of treatment through proper documentation that closely reflects the Indian legal viewpoint on this matter. Four steps are proposed in this direction: (i) recognition of a potentially non-beneficial or harmful treatment by the physicians, (ii) consensus among all the caregivers on a potentially non-beneficial or harmful treatment and initiation of the best supportive care pathway, (iii) initiation of EOLC pathways, and (iv) symptom management and ongoing supportive care till death. The article also focuses on the step-by-step process of formulation of this institutional policy, so that it can work as a blueprint for other institutions of our country to identify the infrastructural needs and resources and to formulate their own policies.

Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment.

Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal and treatment-refractory cancer. Molecular stratification in pancreatic cancer remains rudimentary and does not yet inform clinical management or therapeutic development. Here, we construct a high-resolution molecular landscape of the cellular subtypes and spatial communities that compose PDAC using single-nucleus RNA sequencing and whole-transcriptome digital spatial profiling (DSP) of 43 primary PDAC tumor specimens that either received neoadjuvant therapy or were treatment naive. We uncovered recurrent expression programs across malignant cells and fibroblasts, including a newly identified neural-like progenitor malignant cell program that was enriched after chemotherapy and radiotherapy and associated with poor prognosis in independent cohorts. Integrating spatial and cellular profiles revealed three multicellular communities with distinct contributions from malignant, fibroblast and immune subtypes: classical, squamoid-basaloid and treatment enriched. Our refined molecular and cellular taxonomy can provide a framework for stratification in clinical trials and serve as a roadmap for therapeutic targeting of specific cellular phenotypes and multicellular interactions.

Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity.

Disease-associated single-nucleotide polymorphisms (SNPs) generally do not implicate target genes, as most disease SNPs are regulatory. Many SNP-to-gene (S2G) linking strategies have been developed to link regulatory SNPs to the genes that they regulate in cis. Here, we developed a heritability-based framework for evaluating and combining different S2G strategies to optimize their informativeness for common disease risk. Our optimal combined S2G strategy (cS2G) included seven constituent S2G strategies and achieved a precision of 0.75 and a recall of 0.33, more than doubling the recall of any individual strategy. We applied cS2G to fine-mapping results for 49 UK Biobank diseases/traits to predict 5,095 causal SNP-gene-disease triplets (with S2G-derived functional interpretation) with high confidence. We further applied cS2G to provide an empirical assessment of disease omnigenicity; we determined that the top 1% of genes explained roughly half of the SNP heritability linked to all genes and that gene-level architectures vary with variant allele frequency.

Interplay of vascular endothelial growth factor receptors in organ-specific vessel maintenance.

Vascular endothelial growth factors (VEGFs) and their receptors (VEGFRs) are quintessential for the development and maintenance of blood and lymphatic vessels. However, genetic interactions between the VEGFRs are poorly understood. VEGFR2 is the dominant receptor that is required for the growth and survival of the endothelium, whereas deletion of VEGFR1 or VEGFR3 was reported to induce vasculature overgrowth. Here we show that vascular regression induced by VEGFR2 deletion in postnatal and adult mice is aggravated by additional deletion of VEGFR1 or VEGFR3 in the intestine, kidney, and pancreas, but not in the liver or kidney glomeruli. In the adult mice, hepatic and intestinal vessels regressed within a few days after gene deletion, whereas vessels in skin and retina remained stable for at least four weeks. Our results show changes in endothelial transcriptomes and organ-specific vessel maintenance mechanisms that are dependent on VEGFR signaling pathways and reveal previously unknown functions of VEGFR1 and VEGFR3 in endothelial cells.

Anterolateral thigh osteomyocutaneous flap in head and neck: Lessons learned.

BACKGROUND: Concerns regarding iatrogenic femur fracture may deter adoption of the anterolateral thigh osteomyocutaneous (ALTO) flap as an alternative reconstructive technique for large composite defects of the head and neck. We describe the evolution of our experience with this flap and the lessons learned in femur management. METHODS: Records from a prospective database (July 2009-January 2020) were reviewed to identify patients with composite osseous free tissue reconstructions. Venous thromboembolic events (VTE), femur fracture, estimated blood loss (EBL), procedure time, blood transfusions, and length of stay (days) were compared for ALTO flaps prior to and after the adoption of intramedullary fixation protocol. RESULTS: ALTO represented 10.5% (n = 23) of total osseus (n = 219) flaps. For large composite reconstructions with either ALTO flap, double flap (n = 2), or subscapular mega flaps (n = 14), ALTO flaps were most frequently used (59%, n = 23/59). There were no differences in operative time prior to and after implementation of prophylactic fixation [median (range): 5.4 (1.7-19.2) vs. 5.8 (1.7-15.0), p = .574]. Additionally, there were no differences in VTE, femur fracture, EBL, blood transfusion, or length of stay (p > .05) with adoption of prophylactic intramedullary fixation. CONCLUSIONS: The ALTO flap represents a useful tool to consider in the armamentarium of reconstructive options for large through and through defects of the head and neck. In our experience, the ALTO flap is a reasonable alternative to subscapular or double flap reconstructions and especially in the setting of unusable fibular flaps or when bone need exceeds that available from the scapula.

Awake Proning for Nonintubated Adult Hypoxic Patients with COVID-19: A Systematic Review of the Published Evidence.

Objective: Awake proning is an intervention that is being advocated for COVID-19 patients and has been suggested to improve the oxygenation, thereby decreasing oxygen requirements. We performed this systematic review with the aim of appraising the latest published evidence on the clinical effectiveness of awake proning in COVID-19 patients. Data sources: PubMed, EMBASE, The Cochrane Central Register of Controlled Trials (CENTRAL), Web of Science, Google Scholar, and one trial registry were searched until September 23, 2020, for studies on the use of awake proning for nonintubated COVID-19 patients. Study selection: Published or in-press peer-reviewed randomized control trials, case-control trials, and prospective or retrospective cohort studies in English language only were sought, assessing the effectiveness of awake proning for nonintubated patients diagnosed with COVID-19. Data results: We included 21 published studies (19 single arm and 2 with comparison group). Twenty-three registered clinical trials were identified. No randomized clinical trial has been published so far. Conclusions: Awake proning is probably safe and effective in enhancing oxygenation in nonintubated COVID-19 patients; however, there is insufficient evidence. Further high-quality clinical trials are urgently needed to assess the effectiveness of awake proning on a variety of patient-centered outcomes. How to cite this article: Parashar S, Karthik AR, Gupta R, Malviya D. Awake Proning for Nonintubated Adult Hypoxic Patients with COVID-19: A Systematic Review of the Published Evidence. Indian J Crit Care Med 2021;25(8):906-916.

Identifying disease-critical cell types and cellular processes across the human body by integration of single-cell profiles and human genetics.

Genome-wide association studies (GWAS) provide a powerful means to identify loci and genes contributing to disease, but in many cases the related cell types/states through which genes confer disease risk remain unknown. Deciphering such relationships is important for identifying pathogenic processes and developing therapeutics. Here, we introduce sc-linker, a framework for integrating single-cell RNA-seq (scRNA-seq), epigenomic maps and GWAS summary statistics to infer the underlying cell types and processes by which genetic variants influence disease. We analyzed 1.6 million scRNA-seq profiles from 209 individuals spanning 11 tissue types and 6 disease conditions, and constructed gene programs capturing cell types, disease progression, and cellular processes both within and across cell types. We evaluated these gene programs for disease enrichment by transforming them to SNP annotations with tissue-specific epigenomic maps and computing enrichment scores across 60 diseases and complex traits (average N= 297K). Cell type, disease progression, and cellular process programs captured distinct heritability signals even within the same cell type, as we show in multiple complex diseases that affect the brain (Alzheimer’s disease, multiple sclerosis), colon (ulcerative colitis) and lung (asthma, idiopathic pulmonary fibrosis, severe COVID-19). The inferred disease enrichments recapitulated known biology and highlighted novel cell-disease relationships, including GABAergic neurons in major depressive disorder (MDD), a disease progression M cell program in ulcerative colitis, and a disease-specific complement cascade process in multiple sclerosis. In autoimmune disease, both healthy and disease progression immune cell type programs were associated, whereas for epithelial cells, disease progression programs were most prominent, perhaps suggesting a role in disease progression over initiation. Our framework provides a powerful approach for identifying the cell types and cellular processes by which genetic variants influence disease.