An in vitro CRISPR screen of cell-free DNA identifies apoptosis as the primary mediator of cell-free DNA release

ABTRACT

Clinical circulating cell-free DNA (cfDNA) testing is now routine, however test accuracy remains limited. By understanding the life-cycle of cfDNA, we might identify opportunities to increase test performance. Here, we profile cfDNA release across a 24-cell line panel and utilize a cell-free CRISPR screen (cfCRISPR) to identify mediators of cfDNA release. Our panel outlines two distinct groups of cell lines: one which releases cfDNA fragmented similarly to clinical samples and purported as characteristic of apoptosis, and another which releases larger fragments associated with vesicular or necrotic DNA. Our cfCRISPR screens reveal that genes mediating cfDNA release are primarily involved with apoptosis, but also identify other subsets of genes such as RNA binding proteins as potential regulators of cfDNA release. We observe that both groups of cells lines identified primarily produce cfDNA through apoptosis. These results establish the utility of cfCRISPR, genetically validate apoptosis as a major mediator of DNA release in vitro, and implicate ways to improve cfDNA assays.

Correlates of Taxane-Induced Neuropathy, an Electronic Health Record Based Observational Study

BACKGROUND

Chemotherapy-induced peripheral neuropathy (CIPN) is a common therapeutic complication affecting cancer patients' quality-of-life. We evaluated clinical characteristics, demographics, and lifestyle factors in association with CIPN following taxane treatment.

METHODS

Data were extracted from the electronic health record of 3387 patients diagnosed with a primary cancer and receiving taxane (i.e., paclitaxel or docetaxel) at Vanderbilt University Medical Center. Neuropathy was assessed via a validated computer algorithm. Univariate and multivariate regression models were applied to evaluate odds ratios (ORs) and 95% confidence intervals (CIs) of CIPN-associated factors.

RESULTS

Female sex (OR = 1.28, 95% CI = 1.01-1.62), high body-mass index (BMI) (OR = 1.31, 95% CI = 1.06-1.61 for overweight, and OR = 1.49, 95% CI = 1.21-1.83 for obesity), diabetes (OR = 1.66, 95% CI = 1.34-2.06), high mean taxane dose (OR = 1.05, 95% CI = 1.03-1.08 per 10 mg/m2), and more treatment cycles (1.12, 95% CI = 1.10-1.14) were positively associated with CIPN. Concurrent chemotherapy (OR = 0.74, 95% CI = 0.58-0.94) and concurrent radiotherapy (OR = 0.77, 95% CI = 0.59-1.00) were inversely associated with CIPN. Obesity and diabetes both had a stronger association with docetaxel CIPN compared to paclitaxel, although interaction was only significant for diabetes and taxane (p = 0.019). Increased BMI was associated with CIPN only among non-diabetic patients (OR:1.34 for overweight and 1.68 for obesity), while diabetes increased CIPN risk across all BMI strata (ORs were 2.65, 2.41, and 2.15 for normal weight, overweight, and obese, respectively) compared to normal-weight non-diabetic patients (p for interaction = 0.039).

CONCLUSIONS

Female sex, obesity, and diabetes are significantly associated with taxine-induced CIPN. Further research is needed to identify clinical and pharmacologic strategies to prevent and mitigate CIPN in at-risk patient populations.

Insights From Dynamic Neuro-Immune Imaging on Murine Immune Responses to CNS Damage

Evolving technologies and increasing understanding of human physiology over the past century have afforded our ability to intervene on human diseases using implantable bio-materials. These bio-electronic devices present a unique challenge through the creation of an interface between the native tissue and implantable bio-materials: the generation of host immune response surrounding such devices. While recent developments in cancer immunology seek to stimulate the immune system against cancer, successful long-term application of implantable bio-material devices need to durably minimize reactive immune processes at involved anatomical sites. Peripheral immune system response has been studied extensively for implanted bio-materials at various body sites. Examples include tooth composites (Gitalis et al., 2019), inguinal hernia repair (Heymann et al., 2019), and cardiac stents and pacemaker leads (Slee et al., 2016). Studies have also been extended to less well-studied immune reactivity in response to CNS neural-electronic implant devices. Recent technological advances in 2-Photon Laser Scanning Microscopy (2P-LSM) have allowed novel insights into in vivo immune response in a variety of tissue microenvironments. While imaging of peripheral tissues has provided an abundance of data with regards to immune cell dynamics, central nervous system (CNS) imaging is comparatively complicated by tissue accessibility and manipulation. Despite these challenges, the results of dynamic intravital neuro-immune imaging thus far have provided foundational insights into basic CNS biology. Utilizing a combination of intravital and ex vivo 2P-LSM, we have observed novel pathways allowing immune cells, stromal cells, cancer cells and proteins to communicate between the CNS parenchyma and peripheral vasculature. Similar to what has been reported in the intestinal tract, we have visualized myeloid cells extend dendritic processes across the blood brain barrier (BBB) into pial blood vessels. Furthermore, transient vessel leaks seen during systemic inflammation provide opportunities for cellular protein to be exchanged between the periphery and CNS. These insights provide new, visual information regarding immune surveillance and antigen presentation within the CNS. Furthermore, when combining intravital 2P-LSM and microfluidic devices complexed with mathematical modeling, we are gaining new insights into the intravascular behavior of circulating immune cells. This new knowledge into the basic mechanisms by which cells migrate to and interact with the CNS provide important considerations for the design of neuro-electronic biomaterials that have the potential to connect the peripheral-neural microenvironments into a unique, artificial interface.

Cdk5 disruption attenuates tumor PD-L1 expression and promotes antitumor immunity

Cancers often evade immune surveillance by adopting peripheral tissue- tolerance mechanisms, such as the expression of programmed cell death ligand 1 (PD-L1), the inhibition of which results in potent antitumor immunity. Here, we show that cyclin-dependent kinase 5 (Cdk5), a serine-threonine kinase that is highly active in postmitotic neurons and in many cancers, allows medulloblastoma (MB) to evade immune elimination. Interferon-γ (IFN-γ)-induced PD-L1 up-regulation on MB requires Cdk5, and disruption of Cdk5 expression in a mouse model of MB results in potent CD4(+) T cell-mediated tumor rejection. Loss of Cdk5 results in persistent expression of the PD-L1 transcriptional repressors, the interferon regulatory factors IRF2 and IRF2BP2, which likely leads to reduced PD-L1 expression on tumors. Our finding highlights a central role for Cdk5 in immune checkpoint regulation by tumor cells.

Multiple Administrations of Viral Nanoparticles Alter in Vivo Behavior-Insights from Intravital Microscopy

Multiple administrations of nanoparticle-based formulations are often a clinical requirement for drug delivery and diagnostic imaging applications. Steady pharmacokinetics of nanoparticles is desirable to achieve efficient therapeutic or diagnostic outcomes over such repeat administrations. While clearance through mononuclear phagocytic system is a key determinant of nanoparticle persistence in vivo, multiple administrations could potentially result in altered pharmacokinetics by evoking innate or adaptive immune responses. Plant viral nanoparticles (VNPs) represent an emerging class of programmable nanoparticle platform technologies that offer a highly organized proteinaceous architecture and multivalency for delivery of large payloads of drugs and molecular contrast agents. These very structural features also render them susceptible to immune recognition and subsequent accelerated systemic clearance that could potentially affect overall efficiency. While the biodistribution and pharmacokinetics of VNPs have been reported, the biological response following repeat administrations remains an understudied area of investigation. Here, we demonstrate that weekly administration of filamentous plant viruses results in the generation of increasing levels of circulating, carrier-specific IgM and IgG antibodies. Furthermore, PVX specific immunoglobulins from the serum of immunized animals quickly form aggregates when incubated with PVX in vitro. Such aggregates of VNP-immune complexes are also observed in the mouse vasculature in vivo following repeat injections when imaged in real time using intravital two-photon laser scanning microscopy (2P-LSM). The size of aggregates diminishes at later time points, coinciding with antibody class switching from IgM to IgG. Together, our results highlight the need for careful in vivo assessment of (viral) nanoparticle-based platform technologies, especially in studying their performance after repeat administration. We also demonstrate the utility of intravital microscopy to aid in this evaluation.

Transient Surface CCR5 Expression by Naive CD8+ T Cells within Inflamed Lymph Nodes Is Dependent on High Endothelial Venule Interaction and Augments Th Cell-Dependent Memory Response

In inflamed lymph nodes, Ag-specific CD4(+) and CD8(+) T cells encounter Ag-bearing dendritic cells and, together, this complex enhances the release of CCL3 and CCL4, which facilitate additional interaction with naive CD8(+) T cells. Although blocking CCL3 and CCL4 has no effect on primary CD8(+) T cell responses, it dramatically impairs the development of memory CD8(+) T cells upon Ag rechallenge. Despite the absence of detectable surface CCR5 expression on circulating native CD8(+) T cells, these data imply that naive CD8(+) T cells are capable of expressing surface CCR5 prior to cognate Ag-induced TCR signaling in inflamed lymph nodes; however, the molecular mechanisms have not been characterized to date. In this study, we show that CCR5, the receptor for CCL3 and CCL4, can be transiently upregulated on a subset of naive CD8(+) T cells and that this upregulation is dependent on direct contact with the high endothelial venule in inflamed lymph node. Binding of CD62L and CD11a on T cells to their ligands CD34 and CD54 on the high endothelial venule can be enhanced during inflammation. This enhanced binding and subsequent signaling promote the translocation of CCR5 molecules from intracellular vesicles to the surface of the CD8(+) T cell. The upregulation of CCR5 on the surface of the CD8(+) T cells increases the number of contacts with Ag-bearing dendritic cells, which ultimately results in increased CD8(+) T cell response to Ag rechallenge.

Focal transient CNS vessel leak provides a tissue niche for sequential immune cell accumulation during the asymptomatic phase of EAE induction

Peripheral immune cells are critical to the pathogenesis of neurodegenerative diseases including multiple sclerosis (MS) (Hendriks et al., 2005; Kasper and Shoemaker, 2010). However, the precise sequence of tissue events during the early asymptomatic induction phase of experimental autoimmune encephalomyelitis (EAE) pathogenesis remains poorly defined. Due to the spatial-temporal constrains of traditional methods used to study this disease, most studies had been performed in the spine during peak clinical disease; thus the debate continues as to whether tissue changes such as vessel disruption represent a cause or a byproduct of EAE pathophysiology in the cortex. Here, we provide dynamic, high-resolution information on the evolving structural and cellular processes within the gray matter of the mouse cortex during the first 12 asymptomatic days of EAE induction. We observed that transient focal vessel disruptions precede microglia activation, followed by infiltration of and directed interaction between circulating dendritic cells and T cells. Histamine antagonist minimizes but not completely ameliorates blood vessel leaks. Histamine H1 receptor blockade prevents early microglia function, resulting in subsequent reduction in immune cell accumulation, disease incidence and clinical severity.

Comparison of intravital thinned skull and cranial window approaches to study CNS immunobiology in the mouse cortex

Fluorescent imaging coupled with high-resolution femto-second pulsed infrared lasers allows for interrogation of cellular interactions deeper in living tissues than ever imagined. Intra-vital imaging of the central nervous system (CNS) has provided insights into neuronal development, synaptic transmission, and even immune interactions. In this review we will discuss the two most common intravital approaches for studying the cerebral cortex in the live mouse brain for pre-clinical studies, the thinned skull and cranial window techniques, and focus on the advantages and drawbacks of each approach. In addition, we will discuss the use of neuronal physiologic parameters as determinants of successful surgical and imaging preparation.

Confirmation of proximal 1q duplication using fluorescence in situ hybridization

We report on a boy with excessively wrinkled skin, mild micro/brachycephaly with mild hydrocephalus and slightly small temporal lobes, apparently low-set ears, retro/micrognathia and cleft soft palate (Pierre-Robin anomaly), patent ductus arteriosus and foramen ovale, pulmonary hypoplasia, eventration of the left hemidiaphragm, right cryptorchidism, a sacral dimple, flexion contractures of fingers and knees, and equinovarus deformities of both feet. The infant had a de novo dir dup(1)(pter-->q25::q12-->qter). Partial duplications involving proximal 1q have rarely been reported. Furthermore, this is the first case of proximal duplication of chromosome 1q with unequivocal identification using fluorescence in situ hybridization (FISH) with a chromosome 1 painting probe.

Rickets in premature infants fed different formulas

To study the role of formula as a cause of rickets, we randomly assigned 46 very-low-birth-weight (VLBW) infants (less than or equal to 1,500 gm) to one of three groups receiving either Isomil, a soy isolate formula, Similac with Iron, a common milk-based formula, or Similac 24 LBW, a hypercaloric milk-based formula designed for low-birth-weight infants during the first three to four months of life. Postnatal changes in serum calcium, phosphorus, alkaline phosphatase, and albumin were monitored during this study. Radiologic diagnosis of rickets was made in 60% of infants fed Isomil and 5% fed Similac with Iron. Significantly low levels of serum phosphorus and high levels of serum alkaline phosphatase were also seen in infants fed Isomil. The exact cause of the biochemical changes and the high incidence of rickets among infants fed Isomil is not clear. Poor solubility and possibly the decreased bioavailability of minerals in soy isolate formula may be important. We conclude that rickets occurs with high frequency among VLBW infants fed soy isolate, but not milk-based formulas. We suggest that prolonged feeding of soy isolate formulas should be avoided in VLBW infants.

Incidence of sepsis in neonates with clinical respiratory distress

Respiratory distress is the most frequent symptom initiating referral to neonatal intensive care centers. Previous reports have indicated that 40% of infants with sepsis proved by blood culture had respiratory symptoms as their clinical presentation. In this prospective study there were 145 consecutive infants referred because of respiratory distress. Two-site blood cultures were collated with all other clinical and laboratory data to confirm a diagnosis of septicemia. There was a 4.8% incidence of bacteremia, and clinical and laboratory parameters confirmed septicemia in 3.5% of infants studied. Sixty percent of these infants had group B streptococcal sepsis, and 80% had leukopenia. The low incidence of confirmed septicemia in infants referred because of respiratory distress suggests that antibiotic therapy should not be routine.

Phencyclidine ingestion: therapy review

The case of a 2 1/2-year-old comatose white boy successfully treated for acute phencyclidine poisoning has been reported with a brief review of symptoms and therapy. Supportive treatment consisted of maintaining intravascular volume; giving diuretics as needed to insure an adequate urinary output; controlling excessive secretions and seizure activity; and providing respiratory support. The patient recovered over a ten-day period of treatment without neurologic or psychologic sequelae.