Brahma safeguards canalization of cardiac mesoderm differentiation.

Differentiation proceeds along a continuum of increasingly fate-restricted intermediates, referred to as canalization1,2. Canalization is essential for stabilizing cell fate, but the mechanisms that underlie robust canalization are unclear. Here we show that the BRG1/BRM-associated factor (BAF) chromatin-remodelling complex ATPase gene Brm safeguards cell identity during directed cardiogenesis of mouse embryonic stem cells. Despite the establishment of a well-differentiated precardiac mesoderm, Brm-/- cells predominantly became neural precursors, violating germ layer assignment. Trajectory inference showed a sudden acquisition of a non-mesodermal identity in Brm-/- cells. Mechanistically, the loss of Brm prevented de novo accessibility of primed cardiac enhancers while increasing the expression of neurogenic factor POU3F1, preventing the binding of the neural suppressor REST and shifting the composition of BRG1 complexes. The identity switch caused by the Brm mutation was overcome by increasing BMP4 levels during mesoderm induction. Mathematical modelling supports these observations and demonstrates that Brm deletion affects cell fate trajectory by modifying saddle-node bifurcations2. In the mouse embryo, Brm deletion exacerbated mesoderm-deleted Brg1-mutant phenotypes, severely compromising cardiogenesis, and reveals an in vivo role for Brm. Our results show that Brm is a compensable safeguard of the fidelity of mesoderm chromatin states, and support a model in which developmental canalization is not a rigid irreversible path, but a highly plastic trajectory.

Characterising plasmacytoid and myeloid AXL+ SIGLEC-6+ dendritic cell functions and their interactions with HIV.

AXL+ Siglec-6+ dendritic cells (ASDC) are novel myeloid DCs which can be subdivided into CD11c+ and CD123+ expressing subsets. We showed for the first time that these two ASDC subsets are present in inflamed human anogenital tissues where HIV transmission occurs. Their presence in inflamed tissues was supported by single cell RNA analysis of public databases of such tissues including psoriasis diseased skin and colorectal cancer. Almost all previous studies have examined ASDCs as a combined population. Our data revealed that the two ASDC subsets differ markedly in their functions when compared with each other and to pDCs. Relative to their cell functions, both subsets of blood ASDCs but not pDCs expressed co-stimulatory and maturation markers which were more prevalent on CD11c+ ASDCs, thus inducing more T cell proliferation and activation than their CD123+ counterparts. There was also a significant polarisation of naïve T cells by both ASDC subsets toward Th2, Th9, Th22, Th17 and Treg but less toward a Th1 phenotype. Furthermore, we investigated the expression of chemokine receptors that facilitate ASDCs and pDCs migration from blood to inflamed tissues, their HIV binding receptors, and their interactions with HIV and CD4 T cells. For HIV infection, within 2 hours of HIV exposure, CD11c+ ASDCs showed a trend in more viral transfer to T cells than CD123+ ASDCs and pDCs for first phase transfer. However, for second phase transfer, CD123+ ASDCs showed a trend in transferring more HIV than CD11c+ ASDCs and there was no viral transfer from pDCs. As anogenital inflammation is a prerequisite for HIV transmission, strategies to inhibit ASDC recruitment into inflamed tissues and their ability to transmit HIV to CD4 T cells should be considered.

Next-generation characterization of the Cancer Cell Line Encyclopedia.

Large panels of comprehensively characterized human cancer models, including the Cancer Cell Line Encyclopedia (CCLE), have provided a rigorous framework with which to study genetic variants, candidate targets, and small-molecule and biological therapeutics and to identify new marker-driven cancer dependencies. To improve our understanding of the molecular features that contribute to cancer phenotypes, including drug responses, here we have expanded the characterizations of cancer cell lines to include genetic, RNA splicing, DNA methylation, histone H3 modification, microRNA expression and reverse-phase protein array data for 1,072 cell lines from individuals of various lineages and ethnicities. Integration of these data with functional characterizations such as drug-sensitivity, short hairpin RNA knockdown and CRISPR-Cas9 knockout data reveals potential targets for cancer drugs and associated biomarkers. Together, this dataset and an accompanying public data portal provide a resource for the acceleration of cancer research using model cancer cell lines.

Functionalizing Yeast Lipid Droplets as Versatile Biomaterials.

Lipid droplets (LD) are dynamic cellular organelles of ≈1 µm diameter in yeast where a neutral lipid core is surrounded by a phospholipid monolayer and attendant proteins. Beyond the storage of lipids, opportunities for LD engineering remain underdeveloped but they show excellent potential as new biomaterials. In this research, LD from yeast Saccharomyces cerevisiae is engineered to display mCherry fluorescent protein, Halotag ligand binding protein, plasma membrane binding v-SNARE protein, and carbonic anhydrase enzyme via linkage to oleosin, an LD anchoring protein. Each protein-oleosin fusion is coded via a single gene construct. The expressed fusion proteins are specifically displayed on LD and their functions can be assessed within cells by fluorescence confocal microscopy, TEM, and as isolated materials via AFM, flow cytometry, spectrophotometry, and by enzyme activity assay. LD isolated from the cell are shown to be robust and stabilize proteins anchored into them. These engineered LD function as reporters, bind specific ligands, guide LD and their attendant proteins into union with the plasma membrane, and catalyze reactions. Here, engineered LD functions are extended well beyond traditional lipid storage toward new material applications aided by a versatile oleosin platform anchored into LD and displaying linked proteins.

OMIP-103: A 35-marker imaging mass cytometry panel for the co-detection of HIV and immune cell populations in human formalin fixed paraffin embedded intestinal tissue.

We introduce a 35-marker imaging mass cytometry (IMC) panel for a detailed examination of immune cell populations and HIV RNA in formalin fixed paraffin embedded (FFPE) human intestinal tissue. The panel has broad cell type coverage and particularly excels in delineating subsets of mononuclear phagocytes and T cells. Markers for key tissue structures are included, enabling identification of epithelium, blood vessels, lymphatics, and musculature. The described method for HIV RNA detection can be generalized to other low abundance RNA targets, whether endogenous or pathogen derived. As such, the panel presented here is useful for high parameter spatial mapping of intestinal immune cells and their interactions with pathogens such as HIV.

Sports participation after craniosynostosis repair: the critical role of post-operative guidance in parental decision-making.

PURPOSE: Despite previous research supporting patient safety in sports after craniosynostosis surgery, parental anxiety remains high. This study sought to evaluate the role of healthcare providers in guiding patients and families through the decision-making process. METHODS: Parents of children with repaired craniosynostosis were asked to assess sports involvement and parental decision-making in children ages 6 and older. Questions were framed primarily on 5-point Likert scales. Sport categorizations were made in accordance with the American Academy of Pediatrics. Chi-squared, linear regression, and Pearson correlation tests were used to analyze associations between the questions. RESULTS: Forty-three complete parental responses were recorded. Mean ages at surgery and time of sports entry were 7.93 ± 4.73 months and 4.76 ± 2.14 years, respectively. Eighty-two percent of patients participated in a contact sport. Discussions with the primary surgeon were more impactful on parental decisions about sports participation than those with other healthcare providers (4.04 ± 1.20 vs. 2.69 ± 1.32). Furthermore, children whose parents consulted with the primary surgeon began participating in sports at a younger age (4.0 ± 1.0 vs. 5.8 ± 2.7 years, p = 0.034). The mean comfort level with contact sports (2.8 ± 1.4) was lower than that with limited-contact (3.8 ± 1.1, p = 0.0001) or non-contact (4.4 ± 1.3, p < 0.0001) sports. CONCLUSION: This study underscores the critical role that healthcare professionals, primarily surgeons, have in guiding families through the decision-making process regarding their children's participation in contact sports.

A diffusion tensor imaging comparison of white matter development in nonsyndromic craniosynostosis to neurotypical infants.

PURPOSE: Nonsyndromic craniosynostosis (NSC) is associated with neurocognitive deficits, and intervention at infancy is standard of care to limit the negative effects of NSC on brain development. In this study, diffusion tensor imaging (DTI) was implemented to investigate white matter microstructure in infants with NSC undergoing cranial vault remodeling, and a comparison was made with white matter development in neurotypical controls. METHODS: Infants presenting with NSC (n = 12) underwent DTI scans before and after cranial vault remodeling. Neurotypical infants (n = 5), age matched to NSC patients at preoperative scans, were compared to preoperative DTI scans. Pre- and postoperative NSC scans were compared in aggregate, and the sagittal synostosis (n = 8) patients were evaluated separately. Finally, neurotypical infants from the University of North Carolina/University of New Mexico Baby Connectome Project (BCP), who underwent DTI scans at timepoints matching the NSC pre- and postoperative DTI scans, were analyzed (n = 9). Trends over the same time period were compared between NSC and BCP scans. RESULTS: No significant differences were found between preoperative NSC scans and controls. White matter development was more limited in NSC patients than in BCP patients, with microstructural parameters of the corpus body and genu and inferior and superior longitudinal fasciculi consistently lagging behind developmental changes observed in healthy patients. CONCLUSION: Infant white matter development appears more limited in NSC patients undergoing cranial vault remodeling relative to that in neurotypical controls. Further investigation is needed to explore these differences and the specific effects of early surgical intervention.

Quantification of Cephalometric Changes in Gonial Angle Morphology Following Facial Feminization Surgery.

Facial feminization surgery (FFS) is a type of gender-affirming surgery aimed at bringing masculine facial features more in line with typically feminine characteristics. Specifically, mandibular contouring can create a softer jawline and help create a more round, feminine face. As the popularity of FFS continues to increase, improving surgical techniques and patient satisfaction is imperative. However, no quantitative measurement system currently exists to measure these changes. In this study, the authors describe the use of a novel segmentation technique using computerized tomography imaging to quantify the bony changes that occur during gonial angle reduction. Further, authors utilize this technique to describe changes in a cohort of 13 patients, and how these changes correlate with patient satisfaction. The authors found that gonial angle volume and surface area significantly decreased, as well as the intergonial:interzygomatic ratio, with a smaller ratio associated with more feminine features. In addition, patient satisfaction significantly increased post-operatively both specifically regarding jawline appearance (P = 0.0014) and regarding overall social and psychological function (P = 0.0021 and P = 0.0032, respectively), as captured by the FACE-Q and World Health Organization Quality of Life (WHOQOL) surveys. Patients with greater changes in surface area reported greater improvements in WHOQOL psychological scores (P = 0.0086), and patients with greater changes in the intergonial:interzygomatic ratio reported greater improvements in WHOQOL social scores (P = 0.0299). Overall, our novel technique captures significant changes in gonial angle shape and can be applied to a wide range of future studies to improve the quality and accessibility of FFS.

Perceived Age and Gender Perception Using Facial Recognition Software Following Facial Feminization Surgery.

Measures of success for facial feminization surgery (FFS) have previously included improved rates of external gender perception as female and patient-reported outcome measures. In this study, we used artificial intelligence facial recognition software to objectively evaluate the effects of FFS on both perceived gender and age among male-to-female transgender patients, as well as their relationship with patient facial satisfaction. Standardized frontal preoperative and postoperative images of 27 transgender women undergoing FFS were analyzed by Amazon's AI facial recognition software to determine gender, femininity confidence score, and perceived age. Female gender-typing, improvement in gender-typing (preoperatively to postoperatively), and femininity confidence scores were analyzed. To assess patient satisfaction, FACE-Q modules were completed postoperatively. Preoperatively, FFS images were perceived as female 48.1% of the time, and postoperatively, this improved to 74.1% ( P =0.05). Femininity confidence scores improved from a mean score of 0.04 preoperatively to 0.39 postoperatively ( P =0.003). FFS was associated with a decrease in perceived age relative to the patient's true age (-2.4 y, P <0.001), with older patients experiencing greater reductions. Pearson correlation matrix found no significant relationship between improved female gender typing and patient facial satisfaction. Undergoing surgery at a younger age was associated with higher overall facial satisfaction ( r =-0.6, P =0.01). Transfeminine patients experienced improvements in satisfaction with facial appearance, perceived gender, and decreases in perceived age following FFS. Notably, patient satisfaction was not directly associated with improved AI-gender typing, suggesting that other factors may influence patient satisfaction.

Evolution of Virtual Surgical Planning Use Among Craniofacial Surgeons.

Virtual surgical planning (VSP) has benefits in craniofacial surgery with growing popularity. However, while specific use cases are highlighted in the literature, no studies exist providing an overview of VSP use among craniofacial surgeons, and little is known about the extent of exposure to VSP during plastic surgery training. This study surveyed members of The American Society of Maxillofacial Surgeons (ASMS) to better characterize both the landscape of VSP use among practicing craniofacial surgeons and the extent of exposure to VSP throughout surgical training. An electronic survey was administered in the fall of 2023. Response data included surgeon demographics, VSP usage, including the use in residency/fellowship, procedures for which VSP is used, and assessment of VSP's impact on the surgeon's practice. Demographics and VSP use were analyzed using descriptive statistics, while categorical and continuous variables were analyzed using χ2 tests and t-tests, respectively. Of the 44 respondents, 40 (90.9%) completed a craniofacial surgery fellowship, and 18 (40.9%) utilized VSP in either residency or fellowship. In respondents' current practice, VSP is utilized most commonly for orthognathic surgery (n=32, 91.4%), postablative reconstruction (n=23, 82.1%), and facial feminization (n=11, 73.3%). Shorter operative time and improved esthetic outcomes were frequently reported as benefits derived from VSP use. Finally, surgeons in practice for less than 10 years were significantly more likely to have used VSP in both residency (OR=20.3, P<0.01) and in fellowship (OR=40.6, P<0.01) than those practicing for more than 10 years. These findings suggest that craniofacial surgeons apply VSP more commonly for certain procedure types. Our results additionally suggest that incorporation of VSP into residency and fellowship training has become significantly more common over time, with a pivot towards integration in the last decade.

Interpretation of Cardiac Standstill in Children Using Point-of-Care Ultrasound.

STUDY OBJECTIVE: This study aimed to determine the level of agreement among pediatric emergency medicine (PEM) physicians in whether various point-of-care ultrasound (POCUS) video clips represent cardiac standstill in children and to highlight the factors that may be associated with the lack of agreement. METHODS: A single, online, cross-sectional, convenience sample survey was administered to PEM attendings and fellows with variable ultrasound experience. PEM attendings with an experience of 25 cardiac POCUS scans or more were the primary subgroup based on ultrasound proficiency set by the American College of Emergency Physicians. The survey contained 11 unique, 6-second video clips of cardiac POCUS performed during pulseless arrest in pediatric patients and asked the respondent if the video clip represented a cardiac standstill. The level of interobserver agreement was determined using the Krippendorff's α (Kα) coefficient across the subgroups. RESULTS: A total of 263 PEM attendings and fellows completed the survey (9.9% response rate). Of the 263 total responses, 110 responses were from the primary subgroup of experienced PEM attendings with at least 25 previously seen cardiac POCUS scans. Across all video clips, PEM attendings with 25 scans or more had an acceptable agreement (Kα=0.740; 95% CI 0.735 to 0.745). The agreement was the highest for video clips wherein the wall motion corresponded to the valve motion. However, the agreement fell to unacceptable levels (Kα=0.304; 95% CI 0.287 to 0.321) across video clips wherein the wall motion occurred without the valve motion. CONCLUSION: There is an overall acceptable interobserver agreement when interpreting cardiac standstill among PEM attendings with an experience of at least 25 previously reported cardiac POCUS scans. However, factors that may influence the lack of agreement include discordances between the wall and valve motion, suboptimal views, and the lack of a formal reference standard. More specific consensus reference standards of pediatric cardiac standstill may help to improve interobserver agreement moving forward and should include more specific details regarding the wall and valve motion.

Extracorporeal membrane oxygenator as a bridge to definitive treatment in patients with persistent infective endocarditis.

Considering the worsening opioid epidemic, complicated infective endocarditis (IE) secondary to intravenous drug use (IVDU) that fails medical management is increasingly common. We present a 31-year-old patient post tricuspid valve replacement who relapsed with recurrent IE and secondary complications of severe tricuspid stenosis and regurgitation, ventricular septal defect (VSD), pulmonary emboli, right-sided heart failure with severe hepatic congestion, and cardiogenic shock. Despite maximal medical management, the patient remained in septic and cardiogenic shock with a potential disposition to hospice care. Upon consulting cardiothoracic surgery, she underwent a first-stage valvectomy with central Extracorporeal Membrane Oxygenation (ECMO) as a bridge to definitive treatment. After clearance of infection, she underwent a second-stage valve replacement, VSD repair, and final ECMO decannulation. Our case alludes to ECMO as a potential bridge for patients with complicated infective endocarditis who fail medical management and are high-risk candidates for immediate definitive surgical management.

Modular tissue-specific regulation of doublesex underpins sexually dimorphic development in Drosophila.

The ability of a single genome to produce distinct and often dramatically different male and female forms is one of the wonders of animal development. In Drosophila melanogaster, most sexually dimorphic traits are controlled by sex-specific isoforms of the doublesex (dsx) transcription factor, and dsx expression is mostly limited to cells that give rise to sexually dimorphic traits. However, it is unknown how this mosaic of sexually dimorphic and monomorphic organs arises. Here, we characterize the cis-regulatory sequences that control dsx expression in the foreleg, which contains multiple types of sex-specific sensory organs. We find that separate modular enhancers are responsible for dsx expression in each sexually dimorphic organ. Expression of dsx in the sex comb is co-regulated by two enhancers with distinct spatial and temporal specificities that are separated by a genitalia-specific enhancer. The sex comb-specific enhancer from D. willistoni, a species that primitively lacks sex combs, is not active in the foreleg. Thus, the mosaic of sexually dimorphic and monomorphic organs depends on modular regulation of dsx transcription by dedicated cell type-specific enhancers.

Genomic evidence suggests that cutaneous neuroendocrine carcinomas can arise from squamous dysplastic precursors.

Merkel cell carcinoma (MCC) is an aggressive cutaneous neuroendocrine carcinoma without a known dysplastic precursor. In some cases, MCC is associated with SCCIS in the overlying epidermis; however, the MCC and SCCIS populations display strikingly different morphologies, and thus far a relationship between these components has not been demonstrated. To better understand the relationship between these distinct tumor cell populations, we evaluated 7 pairs of MCC-SCCIS for overlapping genomic alterations by cancer profiling panel. A subset was further characterized by transcriptional profiling and immunohistochemistry. In 6 of 7 MCC-SCCIS pairs there was highly significant mutational overlap including shared TP53 and/or RB1 mutations. In some cases, oncogenic events previously implicated in MCC (MYCL gain, MDM4 gain, HRAS mutation) were detected in both components. Although FBXW7 mutations were enriched in MCC, no gene mutation was unique to the MCC component across all cases. Transcriptome analysis identified 2736 differentially expressed genes between MCC and SCCIS. Genes upregulated in the MCC component included Polycomb repressive complex targets; downregulated transcripts included epidermal markers, and immune genes such as HLA-A. Immunohistochemical studies revealed increased expression of SOX2 in the MCC component, with diminished H3K27Me3, Rb, and HLA-A expression. In summary, MCC-SCCIS pairs demonstrate clonal relatedness. The shift to neuroendocrine phenotype is associated with loss of Rb protein expression, decrease in global H3K27Me3, and increased expression of Merkel cell genes such as SOX2. Our findings suggest an epidermal origin of MCC in this setting, and to our knowledge provide the first molecular evidence that intraepithelial squamous dysplasia may represent a direct precursor for small cell carcinoma.

Aging accelerates while multiparity delays tumorigenesis in mouse models of high-grade serous carcinoma.

OBJECTIVES: The "incessant ovulation" hypothesis links increased risk for tubo-ovarian high-grade serous carcinoma (HGSC) due to more ovulations and reduced risk conferred by pre-menopausal exposures like oral contraceptive use, multiparity, and breastfeeding. However, most women diagnosed with HGSC are postmenopausal, implying age is a major risk factor for HGSC. Our mouse model for HGSC, based on tamoxifen (TAM)-induced somatic inactivation of the Brca1, Trp53, Rb1, and Nf1 (BPRN) tumor suppressor genes in oviductal epithelium, recapitulates key genetic, histopathologic, and biological features of human HGSCs. We aimed to credential the model for future efforts to define biological and risk modification factors in HGSC pathogenesis. METHODS: BPRN mice were treated with TAM to induce tumors at defined ages and parity status. RESULTS: BPRN mice aged 9-months prior to tumor induction had markedly shorter survival than 6-8 week old mice induced to form tumors (median 46.5 weeks versus 61.5 weeks, log-rank test P = 0.0006). No significant differences in cancer phenotypes were observed between multiparous versus nulliparous BPRN mice. However, using a modified tumor model with one wild-type Nf1 allele (BPRNfl/+), nulliparous mice had more advanced tumors than multiparous mice (Mantel-Haenszel Chi-square test of association, P = 0.01). CONCLUSIONS: Our findings show aging is associated with significantly shortened survival post tumor induction in the BRPN model and multiparity delays development and/or progression of HGSC in certain genetic contexts. The findings support relevance of our mouse model to gain mechanistic insights into how known factors exert their protective effects and to test novel approaches for HGSC prevention.

Spatial-temporal trends in the risk of illicit drug toxicity death in British Columbia.

BACKGROUND: Illicit drug poisoning (overdose) continues to be an important public health problem with overdose-related deaths currently recorded at an unprecedented level. Understanding the geographic variations in fatal overdose mortality is necessary to avoid disproportionate risk resulting from service access inequity. METHODS: We estimated the odds of fatal overdose per event from all cases captured by the overdose surveillance system in British Columbia (2015 - 2018), using both conventional logistic regression and Generalized Additive Models (GAM). The results of GAM were mapped to identify spatial-temporal trends in the risk of fatal overdose. RESULTS: We found that the odds of fatal overdose were about 30% higher in rural areas than in large urban centers, with some regions reporting odds 50% higher than others. Temporal variations in fatal overdose revealed an increasing trend over the entire province. However, the increase occurred earlier and faster in the Interior and Northern regions. CONCLUSION: Rural areas were disproportionately affected by fatal overdose; lack of access to harm reduction services may partly explain the elevated risk in these areas.

The role of shape-dependent flight stability in the origin of oriented meteorites.

The atmospheric ablation of meteoroids is a striking example of the reshaping of a solid object due to its motion through a fluid. Motivated by meteorite samples collected on Earth that suggest fixed orientation during flight-most notably the conical shape of so-called oriented meteorites-we hypothesize that such forms result from an aerodynamic stabilization of posture that may be achieved only by specific shapes. Here, we investigate this issue of flight stability in the parallel context of fluid mechanical erosion of clay bodies in flowing water, which yields shapes resembling oriented meteorites. We conduct laboratory experiments on conical objects freely moving through water and fixed within imposed flows to determine the dependence of orientational stability on shape. During free motion, slender cones undergo postural instabilities, such as inversion and tumbling, and broad or dull forms exhibit oscillatory modes, such as rocking and fluttering. Only intermediate shapes, including the stereotypical form carved by erosion, achieve stable orientation and straight flight with apex leading. We corroborate these findings with systematic measurements of torque and stability potentials across cones of varying apex angle, which furnish a complete map of equilibrium postures and their stability. By showing that the particular conical form carved in unidirectional flows is also posturally stable as a free body in flight, these results suggest a self-consistent picture for the origin of oriented meteorites.

Sample Preparation and Imaging Conditions Affect mEos3.2 Photophysics in Fission Yeast Cells.

Photoconvertible fluorescent proteins (PCFPs) are widely used in super-resolution microscopy and studies of cellular dynamics. However, our understanding of their photophysics is still limited, hampering their quantitative application. For example, we do not know the optimal sample preparation methods or imaging conditions to count protein molecules fused to PCFPs by single-molecule localization microscopy in live and fixed cells. We also do not know how the behavior of PCFPs in live cells compares with fixed cells. Therefore, we investigated how formaldehyde fixation influences the photophysical properties of the popular green-to-red PCFP mEos3.2 in fission yeast cells under a wide range of imaging conditions. We estimated photophysical parameters by fitting a three-state model of photoconversion and photobleaching to the time course of fluorescence signal per yeast cell expressing mEos3.2. We discovered that formaldehyde fixation makes the fluorescence signal, photoconversion rate, and photobleaching rate of mEos3.2 sensitive to the buffer conditions likely by permeabilizing the yeast cell membrane. Under some imaging conditions, the time-integrated mEos3.2 signal per yeast cell is similar in live cells and fixed cells imaged in buffer at pH 8.5 with 1 mM DTT, indicating that light chemical fixation does not destroy mEos3.2 molecules. We also discovered that 405-nm irradiation drove some red-state mEos3.2 molecules to enter an intermediate dark state, which can be converted back to the red fluorescent state by 561-nm illumination. Our findings provide a guide to quantitatively compare conditions for imaging mEos3.2-tagged molecules in yeast cells. Our imaging assay and mathematical model are easy to implement and provide a simple quantitative approach to measure the time-integrated signal and the photoconversion and photobleaching rates of fluorescent proteins in cells.

Molecular Characterization of a Rare Case of Bilateral Vitreoretinal T Cell Lymphoma through Vitreous Liquid Biopsy.

Vitreoretinal lymphoma (VRL) is an uncommon eye malignancy, and VRLs of T cell origin are rare. They are difficult to treat, and their molecular underpinnings, including actionable genomic alterations, remain to be elucidated. At present, vitreous fluid liquid biopsies represent a valuable VRL sample for molecular analysis to study VRLs. In this study, we report the molecular diagnostic workup of a rare case of bilateral T cell VRL and characterize its genomic landscape, including identification of potentially targetable alterations. Using next-generation sequencing of vitreous-derived DNA with a pan-cancer 126-gene panel, we found a copy number gain of BRAF and copy number loss of tumor suppressor DNMT3A. To the best of our knowledge, this represents the first exploration of the T cell VRL cancer genome and supports vitreous liquid biopsy as a suitable approach for precision oncology treatments.

Comparative Molecular Analysis of Primary Central Nervous System Lymphomas and Matched Vitreoretinal Lymphomas by Vitreous Liquid Biopsy.

Primary Central Nervous System Lymphoma (PCNSL) is a lymphoid malignancy of the brain that occurs in ~1500 patients per year in the US. PCNSL can spread to the vitreous and retina, where it is known as vitreoretinal lymphoma (VRL). While confirmatory testing for diagnosis is dependent on invasive brain tissue or cerebrospinal fluid sampling, the ability to access the vitreous as a proximal biofluid for liquid biopsy to diagnose PCNSL is an attractive prospect given ease of access and minimization of risks and complications from other biopsy strategies. However, the extent to which VRL, previously considered genetically identical to PCNSL, resembles PCNSL in the same individual with respect to genetic alterations, diagnostic strategies, and precision-medicine based approaches has hitherto not been explored. Furthermore, the degree of intra-patient tumor genomic heterogeneity between the brain and vitreous sites has not been studied. In this work, we report on targeted DNA next-generation sequencing (NGS) of matched brain and vitreous samples in two patients who each harbored VRL and PCSNL. Our strategy showed enhanced sensitivity for molecular diagnosis confirmation over current clinically used vitreous liquid biopsy methods. We observed a clonal relationship between the eye and brain samples in both patients, which carried clonal CDKN2A deep deletions, a highly recurrent alteration in VRL patients, as well as MYD88 p.L265P activating mutation in one patient. Several subclonal alterations, however, in the genes SETD2, BRCA2, TERT, and broad chromosomal regions showed heterogeneity between the brain and the eyes, between the two eyes, and among different regions of the PCNSL brain lesion. Taken together, our data show that NGS of vitreous liquid biopsies in PCNSL patients with VRL highlights shared and distinct genetic alterations that suggest a common origin for these lymphomas, but with additional site-specific alterations. Liquid biopsy of VRL accurately replicates the findings for PCNSL truncal (tumor-initiating) genomic alterations; it can also nominate precision medicine interventions and shows intra-patient heterogeneity in subclonal alterations. To the best of our knowledge, this study represents the first interrogation of genetic underpinnings of PCNSL with matched VRL samples. Our findings support continued investigation into the utility of vitreous liquid biopsy in precision diagnosis and treatment of PCNSL/VRL.