Targeted Intraoperative Radiotherapy (TARGIT-IORT) for Early-Stage Invasive Breast Cancer: A Single Institution Experience.

Purpose/Objective: We present our single-institution experience in the management of invasive breast cancer with targeted intraoperative radiotherapy (TARGIT-IORT), focusing on patient suitability for IORT determined by the American Society for Radiation Oncology (ASTRO) Accelerated Partial Breast Irradiation (APBI) consensus guidelines. Materials/Methods: We identified 237 patients treated for biopsy-proven early-stage invasive breast cancer using low energy x-ray TARGIT-IORT at the time of lumpectomy between September 2013 and April 2020 who were prospectively enrolled in an institutional review board (IRB) approved database. We retrospectively reviewed preoperative and postoperative clinicopathologic factors to determine each patient's ASTRO APBI suitability (suitable, cautionary or unsuitable) according to the 2017 consensus guidelines (CG). Change in suitability group was determined based on final pathology. Kaplan-Meier methods were used to estimate the survival probability and recurrence probability across time. Results: 237 patients were included in this analysis, based on preoperative clinicopathologic characteristics, 191 (80.6%) patients were suitable, 46 (19.4%) were cautionary and none were deemed unsuitable. Suitability classification changed in 95 (40%) patients based on final pathology from lumpectomy. Increasing preoperative lesion size or a body mass index (BMI) ≥ 30 kg/m2 were significant predictors for suitability group change. Forty-one (17.3%) patients received additional adjuvant whole breast radiotherapy after TARGIT-IORT. At a median follow up of 38.2 months (range 0.4 - 74.5), five (2.1%) patients had ipsilateral breast tumor recurrences (IBTR), including two (0.8%) true local recurrences defined as a recurrence in the same quadrant as the initial lumpectomy bed with the same histology as the initial tumor. IBTR occurred in 1/103 (0.09%) patient in the post-op suitable group, 4/98 (4.08%) patients in the post-op cautionary group, and no patients in the post-op unsuitable group. At 3-years, the overall survival rate was 98.4% and the local recurrence free survival rate was 97.1%. Conclusion: There is a low rate of IBTR after TARGIT-IORT when used in appropriately selected patients. Change in suitability classification pre to postoperatively is common, highlighting a need for further investigation to optimize preoperative patient risk stratification in this setting. Patients who become cautionary or unsuitable based on final pathology should be considered for additional adjuvant therapy.

Computational Genomics in the Era of Precision Medicine: Applications to Variant Analysis and Gene Therapy.

Rapid methodological advances in statistical and computational genomics have enabled researchers to better identify and interpret both rare and common variants responsible for complex human diseases. As we continue to see an expansion of these advances in the field, it is now imperative for researchers to understand the resources and methodologies available for various data types and study designs. In this review, we provide an overview of recent methods for identifying rare and common variants and understanding their roles in disease etiology. Additionally, we discuss the strategy, challenge, and promise of gene therapy. As computational and statistical approaches continue to improve, we will have an opportunity to translate human genetic findings into personalized health care.

Genetics of symptom remission in outpatients with COVID-19.

We conducted a genome-wide association study of time to remission of COVID-19 symptoms in 1723 outpatients with at least one risk factor for disease severity from the COLCORONA clinical trial. We found a significant association at 5p13.3 (rs1173773; P = 4.94 × 10-8) near the natriuretic peptide receptor 3 gene (NPR3). By day 15 of the study, 44%, 54% and 59% of participants with 0, 1, or 2 copies of the effect allele respectively, had symptom remission. In 851 participants not treated with colchicine (placebo), there was a significant association at 9q33.1 (rs62575331; P = 2.95 × 10-8) in interaction with colchicine (P = 1.19 × 10-5) without impact on risk of hospitalisations, highlighting a possibly shared mechanistic pathway. By day 15 of the study, 46%, 62% and 64% of those with 0, 1, or 2 copies of the effect allele respectively, had symptom remission. The findings need to be replicated and could contribute to the biological understanding of COVID-19 symptom remission.

A long isoform of GIV/Girdin contains a PDZ-binding module that regulates localization and G-protein binding.

PDZ domains are one of the most abundant protein domains in eukaryotes and are frequently found on junction-localized scaffold proteins. Various signaling molecules bind to PDZ proteins via PDZ-binding motifs (PBM) and fine-tune cellular signaling. However, how such interaction affects protein function is difficult to predict and must be solved empirically. Here we describe a long isoform of the guanine nucleotide exchange factor GIV/Girdin (CCDC88A) that we named GIV-L, which is conserved throughout evolution, from invertebrates to vertebrates, and contains a PBM. Unlike GIV, which lacks PBM and is cytosolic, GIV-L localizes onto cell junctions and has a PDZ interactome (as shown through annotating Human Cell Map and BioID-proximity labeling studies), which impacts GIV-L's ability to bind and activate trimeric G-protein, Gαi, through its guanine-nucleotide exchange modulator (GEM) module. This GEM module is found exclusively in vertebrates. We propose that the two functional modules in GIV may have evolved sequentially: the ability to bind PDZ proteins via the PBM evolved earlier in invertebrates, whereas G-protein binding and activation may have evolved later only among vertebrates. Phenotypic studies in Caco-2 cells revealed that GIV and GIV-L may have antagonistic effects on cell growth, proliferation (cell cycle), and survival. Immunohistochemical analysis in human colon tissues showed that GIV expression increases with a concomitant decrease in GIV-L during cancer initiation. Taken together, these findings reveal how regulation in GIV/CCDC88A transcript helps to achieve protein modularity, which allows the protein to play opposing roles either as a tumor suppressor (GIV-L) or as an oncogene (GIV).

Tyrosine-Based Signals Regulate the Assembly of Daple⋠PARD3 Complex at Cell-Cell Junctions.

Polarized distribution of organelles and molecules inside a cell is vital for a range of cellular processes and its loss is frequently encountered in disease. Polarization during planar cell migration is a special condition in which cellular orientation is triggered by cell-cell contact. We demonstrate that the protein Daple (CCDC88C) is a component of cell junctions in epithelial cells which serves like a cellular "compass" for establishing and maintaining contact-triggered planar polarity. Furthermore, these processes may be mediated through interaction with the polarity regulator PARD3. This interaction, mediated by Daple's PDZ-binding motif (PBM) and the third PDZ domain of PARD3, is fine-tuned by tyrosine phosphorylation on Daple's PBM by receptor and non-receptor tyrosine kinases, such as Src. Hypophosphorylation strengthens the interaction, whereas hyperphosphorylation disrupts it, thereby revealing an unexpected role of Daple as a platform for signal integration and gradient sensing for tyrosine-based signals within the planar cell polarity pathway.

Connectedness to Nature and to Humanity: their association and personality correlates.

People differ in the extent to which they identify with humans beyond their ingroup and with non-human living things. We refer to the former as the Connectedness to Humanity (CH) and to the latter as the Connectedness to Nature (CN). In a sample of 324 undergraduate students, CH and CN were operationalized using the Identification with All Humanity Scale (McFarland et al., 2012) and the CN Scale (Mayer and Frantz, 2004), respectively. These variables correlated moderately with each other (r = 0.44) and shared Openness to Experience and Honesty-Humility as their primary personality correlates. CN was found to play an important role in mediating the relationships between the two personality variables and some specific pro-environmental/pro-animal attitudes and ecological behaviors.

Expression and localization of an ice nucleating protein from a soil bacterium, Pseudomonas borealis.

An ice nucleating protein (INP) coding region with 66% sequence identity to the INP of Pseudomonas syringae was previously cloned from P. borealis, a plant beneficial soil bacterium. Ice nucleating activity (INA) in the P. borealis DL7 strain was highest after transfer of cultures to temperatures just above freezing. The corresponding INP coding sequence (inaPb or ina) was used to construct recombinant plasmids, with recombinant expression visualized using a green fluorescent protein marker (gfp encoding GFP). Although the P. borealis strain was originally isolated by ice-affinity, bacterial cultures with membrane-associated INP-GFP did not adsorb to pre-formed ice. Employment of a shuttle vector allowed expression of ina-gfp in both Escherichia coli and Pseudomonas cells. At 27 °C, diffuse fluorescence appeared throughout the cells and was associated with low INA. However, after transfer of cultures to 4 °C, the protein localized to the poles coincident with high INA. Transformants with truncated INP sequences ligated to either gfp, or an antifreeze protein-gfp fusion showed that the repetitive ice-nucleation domain was not necessary for localization. Such localization is consistent with the flanking residues of the INP associating with a temperature-dependent secretion apparatus. A polar location would facilitate INP-INP interactions resulting in the formation of larger aggregates, serving to increase INA. Expression of INPs by P. borealis could function as an efficient atmospheric dispersal mechanism for these soil bacteria, which are less likely to use these proteins for nutrient procurement, as has been suggested for P. syringae.

Where to locate the isocenter? The treatment strategy for repeat trigeminal neuralgia radiosurgery.

PURPOSE: The purpose of this study is to investigate how the spatial relationship between the isocenters of the first and second radiosurgeries affects the overall outcome. METHODS AND MATERIALS: We performed a retrospective study on 40 patients who had repeat gamma knife radiosurgery for trigeminal neuralgia. Only one 4-mm isocenter was applied in both first and second radiosurgeries, with a maximum radiation dose of 75 Gy and 40 Gy, respectively. The MR scan of the first radiosurgery was registered to that of the second radiosurgery by a landmark-based registration algorithm. The spatial relationship between the isocenter of the first and the second radiosurgeries was thus determined. The investigating parameters were the distance between the isocenters of the two separate radiosurgeries and isocenter proximity to the brainstem. The outcome end points were pain relief and dysesthesias. The median follow-up for the repeat radiosurgery was 28 months (range, 6-51 months). RESULTS: Pain relief was complete in 11 patients, nearly complete (> or =90%) in 7 patients, partial (> or =50%) in 8 patients, and minimal (<50%) or none in another 14 patients. The mean distance between the two isocenters was 2.86 mm in the complete or nearly complete pain relief group vs. 1.93 mm in the others. Farther distance between isocenters was associated with a trend toward better pain relief (p = 0.057). The proximity of the second isocenter to the brainstem did not affect pain relief, and neither did placing the second isocenter proximal or distal to the brainstem compared with the first one. Three patients developed moderate dysesthesias (score of 4 on a 0-10 scale), and 2 other patients developed more significant dysesthesias (score of 7) after the second radiosurgery. Dysesthesias related neither to distance between isocenters nor to which isocenter was closer to the brainstem. CONCLUSIONS: Image registration between MR scans of the first and second radiosurgeries helps target delineation and radiosurgery treatment planning. Increasing the isocenter distance between the two radiosurgeries treated a longer segment of the trigeminal neuralgia nerve and was associated with a trend toward improved pain relief.

Cost-effectiveness analysis of biological treatments for rheumatoid arthritis.

This review compares the cost-effectiveness of four biologics - adalimumab (Humira, Abbott Laboratories), anakinra (Kineret, Amgen Inc.), etanercept (Enbrel, Wyeth) and infliximab (Remicade, Schering-Plough) - used in the treatment of rheumatoid arthritis. A decision analytic model was constructed to estimate the costs and effectiveness of these biologics used alone or in combination with methotrexate during 1 year, from the perspective of a managed care organization. The direct costs consisted of drugs and healthcare resources. Effectiveness was measured by quality-adjusted life years based on preference weights and health states in which patients achieved one out of four levels of response according to the American College of Rheumatology (ACR) response criteria (No ACR, ACR20, ACR50 and ACR70), and experienced one of the four levels of adverse events (e.g., no, mild, moderate and severe) due to their treatments. Results were sensitive to changes in treatment costs and probabilities of health states in directions as predicted. For monotherapy and combination therapy regimens, anakinra was the least expensive option while etanercept dominated other treatments.

SNP and haplotype variation in the human genome.

We have surveyed and summarized several aspects of DNA variability among humans. The variation described is the result of mutation followed by a combination of drift, migration and selection bringing the frequencies high enough to be observed. This paper describes what we have learned about how DNA variability differs among genes and populations. We sequenced functional regions of a set of 3950 genes. DNA was sampled from 82 unrelated humans: 20 African-Americans, 20 East Asians, 21 Caucasians, 18 Hispanic-Latinos and 3 Native Americans. Different aspects of variability showed a great deal of concordance. In particular, we studied patterns of single nucleotide polymorphism (SNP) allele and haplotype sharing among the four, large sample populations. We also examined how linkage disequilibrium (LD) between SNPs relates to physical distance in the different populations. It is clear from our findings that while many variants are common to all populations, many others have a more restricted distribution. Research that attempts to find genetic variants that explain phenotypic variants must be careful in their choice of study population.

DNA variability of human genes.

We have investigated the level of DNA-based variation (both SNPs and haplotypes) for several thousand human genes. In addition, we have characterized how this variation is distributed in a number of biologically and clinically important ways. First, we have determined how SNPs are distributed within human genes: where they occur relative to various functional regions; levels of variability of human SNPs; pattern of the molecular sequence of SNPs; and how these compare with the corresponding sequence of a chimpanzee. Second, we have determined how these aspects of SNP distribution vary among four human population samples. All genes were sequenced on DNA obtained from 82 unrelated individuals: 20 African-Americans, 20 East Asians, 21 European-Americans, 18 Hispanic-Latinos and three Native Americans. In particular, we looked at patterns of SNP and haplotype sharing among the four larger population samples. Third, we have determined the patterns of linkage disequilibrium among SNPs, which also determines the haplotype variability of each gene. These characteristics also vary substantially among populations. A deeper understanding of these aspects of human genetic variation will be of vital importance when trying to identify the genetic contribution to complex phenotypes such as aging.