Identifying the genetic associations among the psoriasis patients in eastern India.

Psoriasis is a multifactorial genetic disorder manifested by hyperproliferation and abnormal differentiation of epidermal keratinocytes, along with the infiltration of inflammatory cells into the skin. Although ~80 genetic susceptibility variants were reported in psoriasis, many loci showed population-specific associations, warranting the need for more population-specific association studies in psoriasis. We determined the association of forty single nucleotide polymorphisms (SNPs) among 2136 psoriasis patients and normal individuals from eastern India. We investigated the expression of corresponding genes and evaluated the protein structure stability for the genes with susceptible coding variants. We found fifteen SNPs significantly associated with psoriasis, while additional three SNPs showed significant association when we classified the patients based on the presence of HLA-Cw6 allele. Epistatic interaction between HLA-Cw6 and other associated loci showed significant association with the SNPs at PSORS1 region, along with other five SNPs outside PSORS1. Three genes showed significant differential expression in psoriatic tissues compared to the adjacent normal skin tissues but were not differential when classified the patients based on their genotypes. SNP rs495337 at SPATA2 (Spermatogenesis Associated 2) showed a 1.2-fold increased risk among the HLA-Cw6 patients compared to combined samples. We found significant downregulation of SPATA2 among the patients with risk genotypes and HLA-Cw6 allele compared to the non-risk genotypes. Protein structure stability analysis showed reduced structural stability for all the mutant residues caused by the associated coding variants. Our study evaluated the genetic associations of psoriasis-susceptible variants in India and evaluated the possible functional significance of these associated variants in psoriasis.

Intrinsically disordered domain of transcription factor TCF-1 is required for T cell developmental fidelity.

In development, pioneer transcription factors access silent chromatin to reveal lineage-specific gene programs. The structured DNA-binding domains of pioneer factors have been well characterized, but whether and how intrinsically disordered regions affect chromatin and control cell fate is unclear. Here, we report that deletion of an intrinsically disordered region of the pioneer factor TCF-1 (termed L1) leads to an early developmental block in T cells. The few T cells that develop from progenitors expressing TCF-1 lacking L1 exhibit lineage infidelity distinct from the lineage diversion of TCF-1-deficient cells. Mechanistically, L1 is required for activation of T cell genes and repression of GATA2-driven genes, normally reserved to the mast cell and dendritic cell lineages. Underlying this lineage diversion, L1 mediates binding of TCF-1 to its earliest target genes, which are subject to repression as T cells develop. These data suggest that the intrinsically disordered N terminus of TCF-1 maintains T cell lineage fidelity.

High-throughput Oligopaint screen identifies druggable 3D genome regulators.

The human genome functions as a three-dimensional chromatin polymer, driven by a complex collection of chromosome interactions1-3. Although the molecular rules governing these interactions are being quickly elucidated, relatively few proteins regulating this process have been identified. Here, to address this gap, we developed high-throughput DNA or RNA labelling with optimized Oligopaints (HiDRO)-an automated imaging pipeline that enables the quantitative measurement of chromatin interactions in single cells across thousands of samples. By screening the human druggable genome, we identified more than 300 factors that influence genome folding during interphase. Among these, 43 genes were validated as either increasing or decreasing interactions between topologically associating domains. Our findings show that genetic or chemical inhibition of the ubiquitous kinase GSK3A leads to increased long-range chromatin looping interactions in a genome-wide and cohesin-dependent manner. These results demonstrate the importance of GSK3A signalling in nuclear architecture and the use of HiDRO for identifying mechanisms of spatial genome organization.

Quantitative control of Ets1 dosage by a multi-enhancer hub promotes Th1 cell differentiation and protects from allergic inflammation.

Multi-enhancer hubs are spatial clusters of enhancers present across numerous developmental programs. Here, we studied the functional relevance of these three-dimensional structures in T cell biology. Mathematical modeling identified a highly connected multi-enhancer hub at the Ets1 locus, comprising a noncoding regulatory element that was a hotspot for sequence variation associated with allergic disease in humans. Deletion of this regulatory element in mice revealed that the multi-enhancer connectivity was dispensable for T cell development but required for CD4+ T helper 1 (Th1) differentiation. These mice were protected from Th1-mediated colitis but exhibited overt allergic responses. Mechanistically, the multi-enhancer hub controlled the dosage of Ets1 that was required for CTCF recruitment and assembly of Th1-specific genome topology. Our findings establish a paradigm wherein multi-enhancer hubs control cellular competence to respond to an inductive cue through quantitative control of gene dosage and provide insight into how sequence variation within noncoding elements at the Ets1 locus predisposes individuals to allergic responses.

Multiscale 3D genome organization underlies ILC2 ontogenesis and allergic airway inflammation.

Innate lymphoid cells (ILCs) are well-characterized immune cells that play key roles in host defense and tissue homeostasis. Yet, how the three-dimensional (3D) genome organization underlies the development and functions of ILCs is unknown. Herein, we carried out an integrative analysis of the 3D genome structure, chromatin accessibility and gene expression in mature ILCs. Our results revealed that the local 3D configuration of the genome is rewired specifically at loci associated with ILC biology to promote their development and functional differentiation. Importantly, we demonstrated that the ontogenesis of ILC2s and the progression of allergic airway inflammation are determined by a unique local 3D configuration of the region containing the ILC-lineage-defining factor Id2, which is characterized by multiple interactions between the Id2 promoter and distal regulatory elements bound by the transcription factors GATA-3 and RORα, unveiling the mechanism whereby the Id2 expression is specifically controlled in group 2 ILCs.

Diagnostic performance and survival outcome following sentinel lymph node biopsy in breast cancer patients from a tertiary cancer centre in India.

Background: Sentinel lymph node biopsy (SLNB) has replaced axillary lymph node dissection (ALND) for axillary staging in early node-negative breast cancer (BC) patients in developed countries. However, in resource-constrained developing countries, adoption of SLNB is slow due to logistic issues and lack of outcome data from non-screened BC cohort. Therefore, we aim to report diagnostic performance, surgical morbidity and survival outcome of SLNB in BC patients from a tertiary care cancer centre in India. Methodology: 1,521 consecutive early node-negative T1-3N0 BC patients having SLNB from 2011 to 2020 were included in the study. Data were retrieved from the institutional Redcap database and electronic medical records. Analysis was done using Stata14. Results: SLNB was done by dual dye (methylene blue (MB) + radioisotope (RI)/indo cyanine green (ICG)) in 57.7%, MB only in 39.3%, and RI alone in 3% of patients. The identification rate (IR) and SLNB positivity rate were 96% and 27.7%, respectively. IR was highest (98%) with MB + ICG and lowest (94%) with MB alone SLNB. UltraSonoGraphy guided fine needle aspiration cytology of radiological suspicious nodes has significantly reduced the SLNB positivity rate from 34.6% to 26.4% (p < 0.01). One patient had skin necrosis, and 16 had persistent blue staining of the skin in the MB injection site. All were managed conservatively. The lymphedema rate was significantly higher (5.2%) in the ALND versus 0.5% in the SLNB alone patients (p < 0.05). In a median follow up of 27 months, the axillary recurrence rate was 0.04% (4/1,023), and false-negative rate was 0.9% in SLNB negative patients. There were 35 recurrences and 25 deaths in SLNB negative patients, with 10 years predicted disease-free survival of 81% (95% CI 66% to 89%) and overall survival of 79% (95% CI 59% to 90%). Conclusions: SLNB should be offered as an axillary staging procedure to all eligible BC patients from developing countries to avoid the morbidity associated with ALND. Fluorescent dye can be used as an alternative for RI in a resource-constrained setup.

TCF-1 promotes chromatin interactions across topologically associating domains in T cell progenitors.

The high mobility group (HMG) transcription factor TCF-1 is essential for early T cell development. Although in vitro biochemical assays suggest that HMG proteins can serve as architectural elements in the assembly of higher-order nuclear organization, the contribution of TCF-1 on the control of three-dimensional (3D) genome structures during T cell development remains unknown. Here, we investigated the role of TCF-1 in 3D genome reconfiguration. Using gain- and loss-of-function experiments, we discovered that the co-occupancy of TCF-1 and the architectural protein CTCF altered the structure of topologically associating domains in T cell progenitors, leading to interactions between previously insulated regulatory elements and target genes at late stages of T cell development. The TCF-1-dependent gain in long-range interactions was linked to deposition of active enhancer mark H3K27ac and recruitment of the cohesin-loading factor NIPBL at active enhancers. These data indicate that TCF-1 has a role in controlling global genome organization during T cell development.

Stripenn detects architectural stripes from chromatin conformation data using computer vision.

Architectural stripes tend to form at genomic regions harboring genes with salient roles in cell identity and function. Therefore, the accurate identification and quantification of these features are essential for understanding lineage-specific gene regulation. Here, we present Stripenn, an algorithm rooted in computer vision to systematically detect and quantitate architectural stripes from chromatin conformation measurements using various technologies. We demonstrate that Stripenn outperforms existing methods and highlight its biological applications in the context of B and T lymphocytes. By comparing stripes across distinct cell types and different species, we find that these chromatin features are highly conserved and form at genes with prominent roles in cell-type-specific processes. In summary, Stripenn is a computational method that borrows concepts from widely used image processing techniques to demarcate and quantify architectural stripes.

Evaluating Quality Indicators of Glioblastoma Care: Audit Results From an Indian Tertiary Care Cancer Center.

PURPOSE: There are limited reports of quality metrics in glioblastoma. We audited our adherence to quality indicators as proposed in the PRIME Quality Improvement study. METHODS: This is a retrospective audit of patients treated between 2017 and 2020. After postsurgical integrated diagnosis, patients received radiotherapy (RT) with concurrent and adjuvant temozolomide (TMZ). Multiparametric magnetic resonance imaging at predefined times guided management. Numbers with proportions for indices were calculated. Survival was estimated using the Kaplan-Meier method. RESULTS: One hundred six patients were consecutively treated. The median age was 55 years (interquartile range of 47-61 years) with a male preponderance (68%). Ninety-six (90.6%) patients underwent subtotal resection, and 10 (9.4%) biopsy alone. Isocitrate dehydrogenase was wild-type in 96 (91%), and O6-methylguanine-DNA methyltransferase was unmethylated in 70 (66.0%) patients. Telomerase reverse transcriptase promoter was mutated in 64 (60.4%), and TP53 was mutated in 22 (20.8%). Concurrent radiation and TMZ were planned for 104 (98.1%), and radiation alone for 2 (1.9%). The median time to concurrent RT-TMZ was 36 days (interquartile range 30-44 days). All patients planned for RT-TMZ completed treatment, but only 81 (76%) completed adjuvant TMZ. Sixty-three (59%) completed six cycles, 18 (17%) received less than six cycles, and 25 (24%) did not receive adjuvant TMZ. At a median follow-up of 24 months (range 21-31 months), the median (95% CI) progression-free survival and overall survival were 11 (95% CI, 9.4 to 13.0) and 20.0 (95% CI, 15 to 26) months, respectively. CONCLUSION: Our patients met quality indices in most domains; outcomes are comparable with global results. Metrics will be periodically evaluated to include new standards and assess continuous service appropriateness.

Inflammatory Lesions Mimicking Chest Malignancy: CT, Bronchoscopy, EBUS, and PET Evaluation From an Oncology Referral Center.

Infective and inflammatory diseases can mimic malignancy of the lung. Granulomatous inflammations are common causes of pulmonary nodule, mass, or nodal disease. Systemic infection or inflammation also commonly involves the lung that may raise suspicion of a malignant process. Even in patients with a known malignancy, inflammatory diseases can simulate new metastasis or disease progression. Knowledge of the imaging features of these diseases is essential to prevent missed or overdiagnosis of malignancy. Radiologists also need to be familiar with the scope and limitations of bronchoscopy, endobronchial ultrasound, PET-CT, and biopsy to guide clinical management. In this review, we discuss the imaging features and diagnostic approach of common mimickers of chest malignancy that involve the chest wall, pleura, lung parenchyma, and mediastinal nodes.

MICaps: Multi-instance capsule network for machine inspection of Munro's microabscess.

Munro's Microabscess (MM) is the diagnostic hallmark of psoriasis. Neutrophil detection in the Stratum Corneum (SC) of the skin epidermis is an integral part of MM detection in skin biopsy. The microscopic inspection of skin biopsy is a tedious task and staining variations in skin histopathology often hinder human performance to differentiate neutrophils from skin keratinocytes. Motivated from this, we propose a computational framework that can assist human experts and reduce potential errors in diagnosis. The framework first segments the SC layer, and multiple patches are sampled from the segmented regions which are classified to detect neutrophils. Both UNet and CapsNet are used for segmentation and classification. Experiments show that of the two choices, CapsNet, owing to its robustness towards better hierarchical object representation and localisation ability, appears as a better candidate for both segmentation and classification tasks and hence, we termed our framework as MICaps. The training algorithm explores both minimisation of Dice Loss and Focal Loss and makes a comparative study between the two. The proposed framework is validated with our in-house dataset consisting of 290 skin biopsy images. Two different experiments are considered. Under the first protocol, only 3-fold cross-validation is done to directly compare the current results with the state-of-the-art ones. Next, the performance of the system on a held-out data set is reported. The experimental results show that MICaps improves the state-of-the-art diagnosis performance by 3.27% (maximum) and reduces the number of model parameters by 50%.

Transcription factors combine to paint the methylation landscape.

There is paucity of information about DNA methylation dynamics in immune cells. Roy et al. mapped the DNA methylation status of several thousand differentially methylated CpGs in human immune cells. They reported that the extent of cell type-specific hypermethylation is intriguingly most prevalent in adaptive immune cells rather than innate cells.

Accuracy of MRI without intracavernosal prostaglandin E1 injection in staging, preoperative evaluation, and operative planning of penile cancer.

PURPOSE: To evaluate the performance of non-erectile MRI in staging and preoperative evaluation of penile carcinomas, compared to postoperative histopathology. METHODS: In this retrospective study, MRI scans of patients who had undergone surgery for penile carcinoma (n = 54) between January 2012 and April 2018 were read by two radiologists; and disagreement was solved in the presence of a third experienced radiologist. Data necessary for preoperative evaluation and staging were collected and compared with final postoperative histology and the type of surgery performed. All MRI had been performed without intracavernosal injection of prostaglandin E1 and with IV Gadolinium, as per local protocol. RESULTS: 54 patients were included in the study (mean age 57.52 ± 12.78). The number of patients with T1, T2, and T3 staging in histopathology were 32, 14, and 8. Moderate interobserver agreement was found for staging, disease-free penile length, and all subsites except urethra, which had weak agreement. Strong agreement of consensus MRI with final histopathological staging was found (49/54, weighted κ = 0.85), with high sensitivity and specificity. Sensitivity and specificity for involvement of corpus spongiosum, corpora cavernosa, and urethra were 95.5% and 93.8%, 87.5% and 97.8%, and 90.9% and 86.1%, respectively. Sensitivity (89.6%) and specificity (100%) of MRI for predicting adequate disease-free penile length were high. CONCLUSION: There were acceptable interobserver agreement and good diagnostic performance of MRI for staging and preoperative assessment without intracavernosal injection, especially for higher stages and higher degrees of invasion which require more extensive surgery.

Functional Mapping of Genetic Interactions between HLA-Cw6 and LCE3A in Psoriasis.

Functional studies to delineate the molecular mechanisms of causal genetic variants are the main focus in the post-GWAS era. Previous GWASs have identified >50 susceptibility loci associated with psoriasis. Functional understanding of the biology underlying the disease risk of most of these associated loci is unclear. In this study, we identified a regulatory SNP at the putative enhancer of the LCE3A gene within the epidermal differentiation complex that showed epistatic interaction with HLA-Cw6. The variant allele disrupted signal transducer and activator of transcription 3 binding to the region, thereby regulating the expression of the downstream LCE3A gene. Electrophoretic mobility shift and pulldown assay confirmed the preferential binding of signal transducer and activator of transcription 3 to the DNA with a wild-type allele compared with the DNA with a variant allele. The reporter assay further validated the IL-6‒stimulated phosphorylated signal transducer and activator of transcription 3‒mediated LCE3A activation in the presence of the wild-type allele. Interestingly, the presence of the HLA-Cw6 allele leads to IL-6‒mediated phosphorylation of signal transducer and activator of transcription 3, followed by its nuclear localization in the epidermal keratinocytes of psoriatic skin, suggesting indirect interaction of the HLA-Cw6 allele and a regulatory SNP upstream of the LCE3A gene. This study reflects an interesting approach to dissecting the molecular mechanism underlying the genetic interaction observed between HLA-Cw6 and LCE3A in psoriasis pathogenesis.

Foxp3 Re-distributes Its Heavy Lifting.

Understanding the mechanisms that establish regulatory T (Treg) cell identity is central to understanding Treg cell function. van der Veeken et al. now show that the lineage-determining transcription factor Foxp3 establishes Treg-cell-specific chromatin architecture indirectly, mostly by decreasing the expression of other transcriptional regulators, including TCF1.

Human Papillomavirus (HPV)-Associated Squamous Cell Carcinoma In situ With Positive p16 and Ki-67 Immunohistochemical Stains in a Young Immunocompetent Patient.

There is an oncogenic role of human papillomavirus (HPV) in the development of premalignant and malignant skin cancers, especially squamous cell carcinomas (SCCs). Some of the major risk factors for SCC include older age, fair skin types, immunosuppression, ultraviolet radiation (UVR), history of epidermodysplasia verruciformis (EV), and co-carcinogenesis by the HPV. Our case report exemplifies a unique case of a low-risk, 34-year-old female who developed an HPV-associated squamous cell carcinoma in situ (SCCIS) on her left palmar hand, despite having none of the contributing risk factors. The biopsy also showed full-thickness keratinocyte atypia and increased mitotic activity throughout all the layers of the epidermis. Immunohistochemical stains showed strong and diffuse nuclear staining of p16 and Ki-67 throughout the SCCIS, confirming HPV etiology. We speculate that tumor development in our patient relied on the combined effects of UVR exposure, localized immunosuppression, and the co-carcinogenic effects of HPV infection.

Genetic Variation in Type 1 Diabetes Reconfigures the 3D Chromatin Organization of T Cells and Alters Gene Expression.

Genetics is a major determinant of susceptibility to autoimmune disorders. Here, we examined whether genome organization provides resilience or susceptibility to sequence variations, and how this would contribute to the molecular etiology of an autoimmune disease. We generated high-resolution maps of linear and 3D genome organization in thymocytes of NOD mice, a model of type 1 diabetes (T1D), and the diabetes-resistant C57BL/6 mice. Multi-enhancer interactions formed at genomic regions harboring genes with prominent roles in T cell development in both strains. However, diabetes risk-conferring loci coalesced enhancers and promoters in NOD, but not C57BL/6 thymocytes. 3D genome mapping of NODxC57BL/6 F1 thymocytes revealed that genomic misfolding in NOD mice is mediated in cis. Moreover, immune cells infiltrating the pancreas of humans with T1D exhibited increased expression of genes located on misfolded loci in mice. Thus, genetic variation leads to altered 3D chromatin architecture and associated changes in gene expression that may underlie autoimmune pathology.