A Case Report of Refractory Graft-Versus-Host Disease Colitis Managed With Robotic Total Abdominal Colectomy.

Graft-versus-host disease (GvHD) is a common complication following hematopoietic stem cell transplant (HSCT) and has protean manifestations. It results from the activation of transplanted T lymphocytes against the HLA antigens of recipient cells, resulting in tissue destruction. The most commonly involved sites of acute GvHD are the skin and gut, with high mortality reported in the latter. Historically, surgery for gut GvHD has been reserved for those with frank perforations or uncontrolled hemorrhage. Here, we present a case of steroid and ruxolitinib refractory colonic GvHD in a 41-year-old female, which was ultimately managed with robotic-assisted total abdominal colectomy with resolution of enteric symptoms. This case highlights the role of surgical management in gut GvHD in patients who are refractory to the growing arsenal of immunomodulating agents. Given the rarity of surgical intervention in this population, more data are needed to minimize morbidity in this setting.

Characteristics and variations in young adults with cutaneous melanoma: A national cancer database analysis.

BACKGROUND AND OBJECTIVES: Many cancers in young adulthood differ in terms of biology, histologic variation, and prognosis compared to cancer in other older age groups. Differences in cutaneous melanoma among young adults compared to other older age groups, as well as between sexes in young adults are not well studied. METHODS: The National Cancer Database was queried for patients diagnosed with cutaneous melanoma between 2004 and 2017. Patient characteristics, disease factors, and treatment were stratified by age-based cohorts and compared using standard univariate statistics. The Kaplan-Meier method and log-rank tests were used to evaluate overall survival (OS) between age-based cohorts and young adult sexes. RESULTS: Of the 329 765 patients identified, 10.5% were between 18 and 39 years of age at diagnosis. Compared with other older age groups, young adult patients were more likely to be female and uninsured with higher proportions of superficial spreading melanoma, melanoma of the trunk and extremities, and earlier-stage disease. Young adults had improved OS compared to other older age groups. Young male patients had a greater proportion of no insurance, nodular melanoma, higher-stage disease, and decreased OS compared to young female patients. Additionally, while the 5-year OS difference was statistically significant across all stages of disease between young males and females, the clinical significance is likely limited to later stages. CONCLUSIONS: Age and sex-specific differences in cutaneous melanoma highlight distinct patterns and characteristics, emphasizing the need for tailored approaches to screening, diagnosis, and treatment.

Data-Driven Surveillance Protocol for Patients at Risk for Peritoneal Recurrence of Primary Colon Cancer: Surveillance for Peritoneal Carcinomatosis.

Peritoneal carcinomatosis (PC) is rarely discovered early due to low sensitivity of screening imaging and tumor markers, however, earlier identification may improve outcomes. This study assesses risk factors and time to recurrence of PC and implementation of a surveillance system. Patients with stage II-III colon adenocarcinoma undergoing curative colectomy between 2005-2022 were retrospectively reviewed at a single tertiary care institution. Patients were divided into three cohorts: no recurrence (NR), PC, and other types of recurrence (OTR). Baseline characteristics between cohorts were compared with univariate analysis. Overall survival and PC risk were assessed using multivariate analysis with Cox's proportional-hazard modelling. 412 patients were included; 78.4% had NR, 7.8% had PC, and 13.8% had OTR. Patient demographics, comorbidities, tumor side, and histologic features were similar between cohorts. Patients with PC were more likely to have microscopic tumor perforation (25% vs. 8.8% vs. 6.8%, p = 0.002), margin involvement (25% vs. 8.8% vs. 4.6%, p < 0.001), lymphovascular invasion (56.2% vs. 33.3%, vs. 24.5%, p < 0.001), perineural invasion (28.1% vs. 15.8% vs. 11.5%, p = 0.026) compared to OTR or NR. Median time to PC after colectomy was 11 months. Tumor characteristics of stage II-III colon cancer define a high-risk profile for PC. An early surveillance program sensitive for peritoneal disease should be adopted for these patients.

Association between Medicaid Expansion and Cutaneous Melanoma Diagnosis and Outcomes: Does Where You Live Make a Difference?

BACKGROUND: Early detection and standardized treatment are crucial for enhancing outcomes for patients with cutaneous melanoma, the commonly diagnosed skin cancer. However, access to quality health care services remains a critical barrier for many patients, particularly the uninsured. Whereas Medicaid expansion (ME) has had a positive impact on some cancers, its specific influence on cutaneous melanoma remains understudied. METHODS: The National Cancer Database identified 87,512 patients 40-64 years of age with a diagnosis of non-metastatic cutaneous melanoma between 2004 and 2017. In this study, patient demographics, disease characteristics, and treatment variables were analyzed, and ME status was determined based on state policies. Standard univariate statistics were used to compare patients with a diagnosis of non-metastatic cutaneous melanoma between ME and non-ME states. The Kaplan-Meier method and log-rank tests were used to evaluate overall survival (OS) between ME and non-ME states. Multivariable Cox regression models were used to examine associations with OS. RESULTS: Overall, 28.6 % (n = 25,031) of the overall cohort was in ME states. The patients in ME states were more likely to be insured, live in neighborhoods with higher median income quartiles, receive treatment at academic/research cancer centers, have lower stages of disease, and receive surgery than the patients in non-ME states. Kaplan-Meier analysis found enhanced 5-year OS for the patients in ME states across all stages. Cox regression showed improved survival in ME states for stage II (hazard ratio [HR], 0.84) and stage III (HR, 0.75) melanoma. CONCLUSIONS: This study underscores the positive association between ME and improved diagnosis, treatment, and outcomes for patients with non-metastatic cutaneous melanoma. These findings advocate for continued efforts to enhance health care accessibility for vulnerable populations.

Genitourinary complications in orthopaedic surgery.

Genitourinary complications following orthopaedic intervention are uncommon but well-described occurrences and exist on a spectrum of severity. These complications vary depending on the anatomic location and surgical approach, with surgery of the spine, hip, and pelvis of particular concern. Injuries to the urinary tract may present acutely with urinary retention or hematuria. However, they often have a delayed presentation with severe complications such as urinary fistula and recurrent infection. Delayed presentations may place the onus of timely and proper diagnosis on the orthopaedic provider, who may serve as the patient's primary source of long-term follow-up. Detailed knowledge of anatomy and at-risk structures is key to both preventing and identifying injury. Although iatrogenic injury is not always avoidable, early identification can help to facilitate timely evaluation and management to prevent long-term complications such as bladder dysfunction, obstructive renal injury, sexual dysfunction, and chronic pain.  Keywords: urologic injury, bladder injury, genitourinary injury, hip arthroplasty, pelvic ring injuries, spine surgery.

The cardiac molecular setting of metabolic syndrome in pigs reveals disease susceptibility and suggests mechanisms that exacerbate COVID-19 outcomes in patients.

Although metabolic syndrome (MetS) is linked to an elevated risk of cardiovascular disease (CVD), the cardiac-specific risk mechanism is unknown. Obesity, hypertension, and diabetes (all MetS components) are the most common form of CVD and represent risk factors for worse COVID-19 outcomes compared to their non MetS peers. Here, we use obese Yorkshire pigs as a highly relevant animal model of human MetS, where pigs develop the hallmarks of human MetS and reproducibly mimics the myocardial pathophysiology in patients. Myocardium-specific mass spectroscopy-derived metabolomics, proteomics, and transcriptomics enabled the identity and quality of proteins and metabolites to be investigated in the myocardium to greater depth. Myocardium-specific deregulation of pro-inflammatory markers, propensity for arterial thrombosis, and platelet aggregation was revealed by computational analysis of differentially enriched pathways between MetS and control animals. While key components of the complement pathway and the immune response to viruses are under expressed, key N6-methyladenosin RNA methylation enzymes are largely overexpressed in MetS. Blood tests do not capture the entirety of metabolic changes that the myocardium undergoes, making this analysis of greater value than blood component analysis alone. Our findings create data associations to further characterize the MetS myocardium and disease vulnerability, emphasize the need for a multimodal therapeutic approach, and suggests a mechanism for observed worse outcomes in MetS patients with COVID-19 comorbidity.

SnRNA sequencing defines signaling by RBC-derived extracellular vesicles in the murine heart.

Extracellular vesicles (EVs) mediate intercellular signaling by transferring their cargo to recipient cells, but the functional consequences of signaling are not fully appreciated. RBC-derived EVs are abundant in circulation and have been implicated in regulating immune responses. Here, we use a transgenic mouse model for fluorescence-based mapping of RBC-EV recipient cells to assess the role of this intercellular signaling mechanism in heart disease. Using fluorescent-based mapping, we detected an increase in RBC-EV-targeted cardiomyocytes in a murine model of ischemic heart failure. Single cell nuclear RNA sequencing of the heart revealed a complex landscape of cardiac cells targeted by RBC-EVs, with enrichment of genes implicated in cell proliferation and stress signaling pathways compared with non-targeted cells. Correspondingly, cardiomyocytes targeted by RBC-EVs more frequently express cellular markers of DNA synthesis, suggesting the functional significance of EV-mediated signaling. In conclusion, our mouse model for mapping of EV-recipient cells reveals a complex cellular network of RBC-EV-mediated intercellular communication in ischemic heart failure and suggests a functional role for this mode of intercellular signaling.

Mir-30d Regulates Cardiac Remodeling by Intracellular and Paracrine Signaling.

RATIONALE: Previous translational studies implicate plasma extracellular microRNA-30d (miR-30d) as a biomarker in left ventricular remodeling and clinical outcome in heart failure (HF) patients, although precise mechanisms remain obscure. OBJECTIVE: To investigate the mechanism of miR-30d-mediated cardioprotection in HF. METHODS AND RESULTS: In rat and mouse models of ischemic HF, we show that miR-30d gain of function (genetic, lentivirus, or agomiR-mediated) improves cardiac function, decreases myocardial fibrosis, and attenuates cardiomyocyte (CM) apoptosis. Genetic or locked nucleic acid-based knock-down of miR-30d expression potentiates pathological left ventricular remodeling, with increased dysfunction, fibrosis, and cardiomyocyte death. RNA sequencing of in vitro miR-30d gain and loss of function, together with bioinformatic prediction and experimental validation in cardiac myocytes and fibroblasts, were used to identify and validate direct targets of miR-30d. miR-30d expression is selectively enriched in cardiomyocytes, induced by hypoxic stress and is acutely protective, targeting MAP4K4 (mitogen-associate protein kinase 4) to ameliorate apoptosis. Moreover, miR-30d is secreted primarily in extracellular vesicles by cardiomyocytes and inhibits fibroblast proliferation and activation by directly targeting integrin α5 in the acute phase via paracrine signaling to cardiac fibroblasts. In the chronic phase of ischemic remodeling, lower expression of miR-30d in the heart and plasma extracellular vesicles is associated with adverse remodeling in rodent models and human subjects and is linked to whole-blood expression of genes implicated in fibrosis and inflammation, consistent with observations in model systems. CONCLUSIONS: These findings provide the mechanistic underpinning for the cardioprotective association of miR-30d in human HF. More broadly, our findings support an emerging paradigm involving intercellular communication of extracellular vesicle-contained miRNAs (microRNAs) to transregulate distinct signaling pathways across cell types. Functionally validated RNA biomarkers and their signaling networks may warrant further investigation as novel therapeutic targets in HF.

CITED4 Protects Against Adverse Remodeling in Response to Physiological and Pathological Stress.

RATIONALE: Cardiac CITED4 (CBP/p300-interacting transactivators with E [glutamic acid]/D [aspartic acid]-rich-carboxylterminal domain4) is induced by exercise and is sufficient to cause physiological hypertrophy and mitigate adverse ventricular remodeling after ischemic injury. However, the role of endogenous CITED4 in response to physiological or pathological stress is unknown. OBJECTIVE: To investigate the role of CITED4 in murine models of exercise and pressure overload. METHODS AND RESULTS: We generated cardiomyocyte-specific CITED4 knockout mice (C4KO) and subjected them to an intensive swim exercise protocol as well as transverse aortic constriction (TAC). Echocardiography, Western blotting, qPCR, immunohistochemistry, immunofluorescence, and transcriptional profiling for mRNA and miRNA (microRNA) expression were performed. Cellular crosstalk was investigated in vitro. CITED4 deletion in cardiomyocytes did not affect baseline cardiac size or function in young adult mice. C4KO mice developed modest cardiac dysfunction and dilation in response to exercise. After TAC, C4KOs developed severe heart failure with left ventricular dilation, impaired cardiomyocyte growth accompanied by reduced mTOR (mammalian target of rapamycin) activity and maladaptive cardiac remodeling with increased apoptosis, autophagy, and impaired mitochondrial signaling. Interstitial fibrosis was markedly increased in C4KO hearts after TAC. RNAseq revealed induction of a profibrotic miRNA network. miR30d was decreased in C4KO hearts after TAC and mediated crosstalk between cardiomyocytes and fibroblasts to modulate fibrosis. miR30d inhibition was sufficient to increase cardiac dysfunction and fibrosis after TAC. CONCLUSIONS: CITED4 protects against pathological cardiac remodeling by regulating mTOR activity and a network of miRNAs mediating cardiomyocyte to fibroblast crosstalk. Our findings highlight the importance of CITED4 in response to both physiological and pathological stimuli.

Younger age is associated with greater early neurocognitive decline postcardiopulmonary bypass.

Objective: To examine the effect of aging on postoperative neurocognitive decline (NCD) in cardiac surgery patients. Methods: Patients undergoing coronary artery bypass graft or open aortic valve replacement were administered the Repeatable Battery for the Assessment of Neuropsychological Status at preoperative, postoperative day (POD) 4, and 1 month. Blood samples were collected at preoperative, 6 hours postoperative, and POD 4. Plasma interleukin (IL)-6, tumor necrosis factor-α, and C-reactive protein (CRP) levels were quantified. Quality of life was measured with the 12-Item Short Form Health Survey. Data were analyzed using paired ratio and unpaired t tests with Welch's correction, and linear regression for cytokine levels. Results: NCD occurred in 15 patients (N = 33, 45.5%). Dichotomized at age extremes (<60 years; ≥75 years), youngest patients had greater preoperative scores (P = .02) with lower scores by POD 4 (P = .03). There was no NCD in the oldest patients, and scores were not different between age groups on POD 4 (P = .08). Regression at 1 month showed NCD scores again declined by age (n = 15), with younger scores returning toward baseline (P = .008). Regression analyses showed decline by age at 6 hours postoperative and POD 4 in plasma CRP levels (P = .05 6 hours, P = .02 POD 4). Dichotomizing IL-6 levels by age (<70 years, ≥70 years) demonstrated that levels were greater in younger versus older patients at 6 hours postoperative (P = .03), but not on POD 4. Conclusions: Younger patients tend to have better cognitive scores before surgery but scores at POD 4 are similar to those of older patients, with this trend disappearing at 1 month. IL-6 and CRP upregulation is greater in younger patients, suggesting that a robust perioperative inflammatory response may be associated with reduction in neurocognitive function, and this may be greater in younger versus older patients.

Skeletal muscle microvasculature response to ß-adrenergic stimuli is diminished with cardiac surgery.

BACKGROUND: Cardiac surgery and cardiopulmonary bypass are associated with alterations in blood pressure in the perioperative period, which, if uncontrolled, can result in end organ damage or dysfunction. Microvessels, significant contributors to blood pressure, both in the myocardium and peripheral skeletal muscle, have diminished responsiveness to major mediators of vascular tone, including thromboxane and serotonin after cardiopulmonary bypass. Responsiveness of these vessels to ß-adrenergic stimulation, a major mediator of vascular tone, has not yet been studied. In this report, we investigated the role of ß-adrenergic receptors in vascular tone regulation in human skeletal muscle microvessels before and after ß-adrenergic stimulation. METHODS: Skeletal muscle microvessels were isolated from patients undergoing cardiac surgery before and after cardiopulmonary bypass. Vessels were exposed in an ex vivo model to the ß-adrenergic agonist isoproterenol, or the direct adenylyl cyclase activator, forskolin, and the selective ß-receptor antagonist ICI18.551 hydrochloride plus isoproterenol. Immunofluorescence of ß receptors and Western blotting were also performed. RESULTS: Microvessels showed diminished responsiveness to isoproterenol (10-6 to 10-4M) after cardiopulmonary bypass (n = 8/group, P = .01). Pretreatment with the selective ß-2 blocker ICI18.551 (10-6M) prevented isoproterenol-induced microvascular relaxation (P = .001). Forskolin-induced relaxation response was also significantly diminished after cardiopulmonary bypass (n = 4/group, P < .05 versus before cardiopulmonary bypass). No significant changes in the total protein expression of ß-1, ß-2, and ß-3 receptors were detected by western blotting or immunofluorescence. CONCLUSION: Microvessels isolated from human skeletal muscle show diminished responsiveness to isoproterenol and its downstream activator forskolin after cardiopulmonary bypass, suggesting there is an alteration in ß-adrenergic receptor responsive in adenylate cyclase. The relaxation response to isoproterenol was via activation ß-2 receptors without changes in ß-adrenergic receptor abundance.

Robust effect of metabolic syndrome on major metabolic pathways in the myocardium.

Although the high-fat-diet-induced metabolic syndrome (MetS) is a precursor of human cardiac pathology, the myocardial metabolic state in MetS is far from clear. The discrepancies in metabolite handling between human and small animal models and the difficulties inherent in obtaining human tissue complicate the identification of the myocardium-specific metabolic response in patients. Here we use the large animal model of swine that develops the hallmark criteria of human MetS. Our comparative metabolomics together with transcriptomics and computational nonnegative matrix factorization (NMF) interpretation of the data exposes significant decline in metabolites related to the fatty acid oxidation, glycolysis, and pentose phosphate pathway. Behind the reversal lies decreased expression of enzymes that operate in the pathways. We showed that diminished glycogen deposition is a metabolic signature of MetS in the pig myocardium. The depletion of glycogen arises from disbalance in expression of genes that break down and synthesize glycogen. We show robust acetoacetate accumulation and activated expression of key enzymes in ketone body formation, catabolism and transporters, suggesting a shift in fuel utilization in MetS. A contrasting enrichment in O-GlcNAcylated proteins uncovers hexosamine pathway and O-GlcNAcase (OGA) expression involvement in the myocardial response to MetS. Although the hexosamine biosynthetic pathway (HBP) activity and the availability of the UDP-GlcNAc substrate in the MetS myocardium is low, the level of O-GlcNacylated proteins is high as the O-GlcNacase is significantly diminished. Our data support the perception of transcriptionally driven myocardial alterations in expression of standard fatty acids, glucose metabolism, glycogen, and ketone body related enzymes and subsequent paucity of their metabolite products in MetS. This aberrant energy metabolism in the MetS myocardium provide insight into the pathogenesis of CVD in MetS.

Impact of Variations in PACKRAT Administration: A Retrospective Review.

The Physician Assistant Clinical Knowledge Rating and Assessment Tool (PACKRAT) was developed to be an objective, comprehensive self-assessment tool for students. When the PACKRAT exam was initially developed, its goal was to help students determine what level of knowledge they currently possessed and what they had to learn prior to graduation. The purpose of this study was to review PACKRAT test-taker scores over the past 5 years and analyze the variations in test administration. Deidentified PACKRAT scores, exam length in minutes, and proctored or unproctored status, along with time extensions were analyzed from 2013 to 2018. Descriptive statistics and frequency counts were used to summarize the data. An independent samples t-test was used to determine if there was a difference in test-taker scores between proctored and unproctored exams. The 83,271 student test-taker exam data were analyzed, and time ranged from 180 to 360 minutes with a mean of 226.5 minutes. When comparing test-taker scores between proctored and unproctored exams, the mean scores were 145.02 and 144.77, respectively, with no significant difference. The Physician Assistant Clinical Knowledge Rating and Assessment Tool can be confidently used and compared to national scores whether a program administers the exam proctored or without a proctor. The average time taken for exam completion is close to the recommended 225 minutes that is suggested by Physician Assistant Education Association PACKRAT exam developers.

Comparison of treatment options for depression in heart failure: A network meta-analysis.

BACKGROUND: Depression independently predicts poor outcomes in heart failure (HF) patients, including increased mortality, morbidity and 30-day re-hospitalization. In this network meta-analysis, we compared different interventions designed to treat depression in HF. MATERIALS AND METHODS: Electronic searches were conducted using Ovid MEDLINE, EMBASE, CINAHL, Web of Science, and PsycINFO up to November 2016. Included randomized clinical trials (RCTs) compared interventions (Exercise therapy (ET), cognitive behavioral therapy (CBT) or antidepressant (AD) medications) for depression in heart failure patients. The primary outcome was change in depressive symptoms based on validated measures of depression. Network meta-analysis based on random effects model estimating standardized mean difference (SMD) with 95% confidence interval (CI), compared the effects of the 3 classes of interventions with respect to usual care or placebo control conditions. RESULTS: A total of 21 RCTs (including 4563 HF patients) reporting the effects of treating depression in HF patients were included in the analysis. In comparison to placebo or usual standard of care, ET (SMD -0.38; 95% CI -0.54 to -0.22) and CBT (SMD -0.29; 95% CI -0.58 to -0.01) were associated with reduction in depressive symptoms whereas AD (SMD -0.16; 95% CI -0.44 to 0.11) was less effective. CONCLUSIONS: This meta-analysis is suggestive of therapeutic benefit of ET and CBT in comparison to usual standard of care in treating depression in HF patients. However, comparison among the three interventions was not conclusive. Future randomized clinical trials are warranted to compare the therapeutic effects of ET, CBT and AD in such patients.

Associations of Circulating Extracellular RNAs With Myocardial Remodeling and Heart Failure.

Importance: Mortality is high among patients heart failure (HF) who are receiving treatment, and therefore identifying new pathways rooted in preclinical cardiac remodeling phenotypes may afford novel biomarkers and therapeutic avenues. Circulating extracellular RNAs (ex-RNAs) are an emerging class of biomarkers with target-organ epigenetic effects relevant to myocardial biology, although large human investigations remain limited. Objective: To measure the association of highly expressed circulating ex-RNAs with left ventricular remodeling and incident HF in a community-based cohort. Design, Setting, and Participants: This is a prospective observational cohort study of individuals who were included in the eighth examination of the Framingham Offspring Cohort (2005-2008). Collected data include measurements of the left ventricle via electrocardiography, determination of circulating ex-RNAs in plasma, and incidence of heart failure. Data analysis was completed from December 2016 to June 2018. Exposures: A total of 398 circulating ex-RNA molecules in plasma were measured by reverse transcription polymerase chain reaction; disease ontology analysis was also performed. Main Outcomes and Measures: Echocardiographic indices of left ventricular (LV) remodeling and incident heart failure. Results: A total of 2763 participants of the Framingham Heart Study with measured ex-RNAs (mean [SD] age, 66.3 [9.0] years; 1499 [54.3%] female) were included in this study. Of this sample, 2429 to 2432 individuals had echocardiographic measures recorded (depending on the measurement). A total of 2681 individuals had HF status determined, of whom 116 (4.3%) experienced HF (median [interquartile range] follow-up, 7.7 [6.6-8.6] years). We identified 12 ex-RNAs associated with LV mass and at least 1 other echocardiographic phenotype (LV end-diastolic volume or left atrial dimension). Of these 12 ex-RNAs, 3 micro RNAs (miR-17, miR-20a, and miR-106b) were associated with a 15% reduction in long-term incident HF per 2-fold increase in circulating level during the follow-up period, after adjustments for age, sex, established HF risk factors, and prevalent or interim myocardial infarction. These 3 RNAs shared sequence homology and targeted a shared group of messenger RNAs that specified pathways relevant to HF (eg, transforming growth factor-ß signaling, growth/cell cycle, and apoptosis), and shared a disease association with hypertension in disease ontology analysis. Conclusions and Relevance: This study identifies a group of circulating, noncoding RNAs associated with echocardiographic phenotypes, long-term incident HF, and pathways relevant to myocardial remodeling in a large community-based sample. Further investigations into the functional biology of these ex-RNAs are warranted for surveillance for HF prevention.

A Retrospective Review of Physician Assistant Education Association End of Rotation Examinations.

The PAEA End of Rotation™ exams were developed to assess medical knowledge of the 7 core supervised clinical practice experiences, including Emergency Medicine, Family Medicine, Internal Medicine, General Surgery, Pediatrics, Women's Health, and Psychiatry and Behavioral Health. The examinations were created by experienced PA educators and national exam experts with continual review and content updates. This paper summarizes changes since the inception of the exam program, including test construction and development, reliability, validity, and scale scoring. They are built using content blueprints and topic lists that were developed by experienced PA educators and national examination experts. All examination items are peer reviewed by PA educators and statistically validated for accuracy and consistency by psychometricians who specialize in examination development. This article will review the changes since the inception of the exam program including test construction and development, reliability, validity and scale scoring. Also addressed is an update on the PAEA End of Curriculum™ examination.

Evaluation of commercially available small RNASeq library preparation kits using low input RNA.

BACKGROUND: Evolving interest in comprehensively profiling the full range of small RNAs present in small tissue biopsies and in circulating biofluids, and how the profile differs with disease, has launched small RNA sequencing (RNASeq) into more frequent use. However, known biases associated with small RNASeq, compounded by low RNA inputs, have been both a significant concern and a hurdle to widespread adoption. As RNASeq is becoming a viable choice for the discovery of small RNAs in low input samples and more labs are employing it, there should be benchmark datasets to test and evaluate the performance of new sequencing protocols and operators. In a recent publication from the National Institute of Standards and Technology, Pine et al., 2018, the investigators used a commercially available set of three tissues and tested performance across labs and platforms. RESULTS: In this paper, we further tested the performance of low RNA input in three commonly used and commercially available RNASeq library preparation kits; NEB Next, NEXTFlex, and TruSeq small RNA library preparation. We evaluated the performance of the kits at two different sites, using three different tissues (brain, liver, and placenta) with high (1 µg) and low RNA (10 ng) input from tissue samples, or 5.0, 3.0, 2.0, 1.0, 0.5, and 0.2 ml starting volumes of plasma. As there has been a lack of robust validation platforms for differentially expressed miRNAs, we also compared low input RNASeq data with their expression profiles on three different platforms (Abcam Fireplex, HTG EdgeSeq, and Qiagen miRNome). CONCLUSIONS: The concordance of RNASeq results on these three platforms was dependent on the RNA expression level; the higher the expression, the better the reproducibility. The results provide an extensive analysis of small RNASeq kit performance using low RNA input, and replication of these data on three downstream technologies.