Circulating, cell-free methylated DNA indicates cellular sources of allograft injury after liver transplant.

Post-transplant complications reduce allograft and recipient survival. Current approaches for detecting allograft injury non-invasively are limited and do not differentiate between cellular mechanisms. Here, we monitor cellular damages after liver transplants from cell-free DNA (cfDNA) fragments released from dying cells into the circulation. We analyzed 130 blood samples collected from 44 patients at different time points after transplant. Sequence-based methylation of cfDNA fragments were mapped to patterns established to identify cell types in different organs. For liver cell types DNA methylation patterns and multi-omic data integration show distinct enrichment in open chromatin and regulatory regions functionally important for the respective cell types. We find that multi-tissue cellular damages post-transplant recover in patients without allograft injury during the first post-operative week. However, sustained elevation of hepatocyte and biliary epithelial cfDNA beyond the first week indicates early-onset allograft injury. Further, cfDNA composition differentiates amongst causes of allograft injury indicating the potential for non-invasive monitoring and timely intervention.

Deconvolution of immune cell composition and biological age of hepatocellular carcinoma using DNA methylation.

Hepatocellular carcinoma (HCC) has been an approved indication for the administration of immunotherapy since 2017, but biomarkers that predict therapeutic response have remained limited. Understanding and characterizing the tumor immune microenvironment enables better classification of these tumors and may reveal biomarkers that predict immunotherapeutic efficacy. In this paper, we applied a cell-type deconvolution algorithm using DNA methylation array data to investigate the composition of the tumor microenvironment in HCC. Using publicly available and in-house datasets with a total cohort size of 57 patients, each with tumor and matched normal tissue samples, we identified key differences in immune cell composition. We found that NK cell abundance was significantly decreased in HCC tumors compared to adjacent normal tissue. We also applied DNA methylation "clocks" which estimate phenotypic aging and compared these findings to expression-based determinations of cellular senescence. Senescence and epigenetic aging were significantly increased in HCC tumors, and the degree of age acceleration and senescence was strongly associated with decreased NK cell abundance. In summary, we found that NK cell infiltration in the tumor microenvironment is significantly diminished, and that this loss of NK abundance is strongly associated with increased senescence and age-related phenotype. These findings point to key interactions between NK cells and the senescent tumor microenvironment and offer insights into the pathogenesis of HCC as well as potential biomarkers of therapeutic efficacy.

Circulating cell-free methylated DNA reveals tissue-specific, cellular damage from radiation treatment.

Radiation therapy is an effective cancer treatment, although damage to healthy tissues is common. Here we analyzed cell-free, methylated DNA released from dying cells into the circulation to evaluate radiation-induced cellular damage in different tissues. To map the circulating DNA fragments to human and mouse tissues, we established sequencing-based, cell-type-specific reference DNA methylation atlases. We found that cell-type-specific DNA blocks were mostly hypomethylated and located within signature genes of cellular identity. Cell-free DNA fragments were captured from serum samples by hybridization to CpG-rich DNA panels and mapped to the DNA methylation atlases. In a mouse model, thoracic radiation-induced tissue damage was reflected by dose-dependent increases in lung endothelial and cardiomyocyte methylated DNA in serum. The analysis of serum samples from patients with breast cancer undergoing radiation treatment revealed distinct dose-dependent and tissue-specific epithelial and endothelial responses to radiation across multiple organs. Strikingly, patients treated for right-sided breast cancers also showed increased hepatocyte and liver endothelial DNA in the circulation, indicating the impact on liver tissues. Thus, changes in cell-free methylated DNA can uncover cell-type-specific effects of radiation and provide a readout of the biologically effective radiation dose received by healthy tissues.

Cell-type Deconvolution and Age Estimation Using DNA Methylation Reveals NK Cell Deficiency in the Hepatocellular Carcinoma Microenvironment.

Hepatocellular carcinoma (HCC) has been an approved indication for the administration of immunotherapy since 2017, but biomarkers that predict therapeutic response have remained limited. Understanding and characterizing the tumor immune microenvironment enables better classification of these tumors and may reveal biomarkers that predict immunotherapeutic efficacy. In this paper, we applied a cell-type deconvolution algorithm using DNA methylation array data to investigate the composition of the tumor microenvironment in HCC. Using two publicly available datasets with a total cohort size of 57 patients, each with tumor and matched normal tissue samples, we identified key differences in immune cell composition. We found that NK cell abundance was significantly decreased in HCC tumors compared to adjacent normal tissue. We also applied DNA methylation "clocks" which estimate phenotypic aging and compared these findings to expression-based determinations of cellular senescence. Senescence and epigenetic aging was significantly increased in HCC tumors, and the degree of age acceleration and senescence was strongly associated with decreased NK cell abundance. In summary, we found that NK cell infiltration in the tumor microenvironment is significantly diminished, and that this loss of NK abundance is strongly associated with increased senescence and age-related phenotype. These findings point to key interactions between NK cells and the senescent tumor microenvironment and offer insights into the pathogenesis of HCC as well as potential biomarkers of therapeutic efficacy.

Paralog knockout profiling identifies DUSP4 and DUSP6 as a digenic dependence in MAPK pathway-driven cancers.

Although single-gene perturbation screens have revealed a number of new targets, vulnerabilities specific to frequently altered drivers have not been uncovered. An important question is whether the compensatory relationship between functionally redundant genes masks potential therapeutic targets in single-gene perturbation studies. To identify digenic dependencies, we developed a CRISPR paralog targeting library to investigate the viability effects of disrupting 3,284 genes, 5,065 paralog pairs and 815 paralog families. We identified that dual inactivation of DUSP4 and DUSP6 selectively impairs growth in NRAS and BRAF mutant cells through the hyperactivation of MAPK signaling. Furthermore, cells resistant to MAPK pathway therapeutics become cross-sensitized to DUSP4 and DUSP6 perturbations such that the mechanisms of resistance to the inhibitors reinforce this mechanism of vulnerability. Together, multigene perturbation technologies unveil previously unrecognized digenic vulnerabilities that may be leveraged as new therapeutic targets in cancer.

Low Dose Chronic Angiotensin II Induces Selective Senescence of Kidney Endothelial Cells.

Angiotensin II can cause oxidative stress and increased blood pressure that result in long term cardiovascular pathologies. Here we evaluated the contribution of cellular senescence to the effect of chronic exposure to low dose angiotensin II in a model that mimics long term tissue damage. We utilized the INK-ATTAC (p16Ink4a-Apoptosis Through Targeted Activation of Caspase 8) transgenic mouse model that allows for conditional elimination of p16Ink4a -dependent senescent cells by administration of AP20187. Angiotensin II treatment for 3 weeks induced ATTAC transgene expression in kidneys but not in lung, spleen and brain tissues. In the kidneys increased expression of ATM, p15 and p21 matched with angiotensin II induction of senescence-associated secretory phenotype genes MMP3, FGF2, IGFBP2, and tPA. Senescent cells in the kidneys were identified as endothelial cells by detection of GFP expressed from the ATTAC transgene and increased expression of angiopoietin 2 and von Willebrand Factor, indicative of endothelial cell damage. Furthermore, angiotensin II induced expression of the inflammation-related glycoprotein versican and immune cell recruitment to the kidneys. AP20187-mediated elimination of p16-dependent senescent cells prevented physiologic, cellular and molecular responses to angiotensin II and provides mechanistic evidence of cellular senescence as a driver of angiotensin II effects.

Integrative Analysis of DNA Methylation and microRNA Expression Reveals Mechanisms of Racial Heterogeneity in Hepatocellular Carcinoma.

Pathologic alterations in epigenetic regulation have long been considered a hallmark of many cancers, including hepatocellular carcinoma (HCC). In a healthy individual, the relationship between DNA methylation and microRNA (miRNA) expression maintains a fine balance; however, disruptions in this harmony can aid in the genesis of cancer or the propagation of existing cancers. The balance between DNA methylation and microRNA expression and its potential disturbance in HCC can vary by race. There is emerging evidence linking epigenetic events including DNA methylation and miRNA expression to cancer disparities. In this paper, we evaluate the epigenetic mechanisms of racial heterogenity in HCC through an integrated analysis of DNA methylation, miRNA, and combined regulation of gene expression. Specifically, we generated DNA methylation, mRNA-seq, and miRNA-seq data through the analysis of tumor and adjacent non-tumor liver tissues from African Americans (AA) and European Americans (EA) with HCC. Using mixed ANOVA, we identified cytosine-phosphate-guanine (CpG) sites, mRNAs, and miRNAs that are significantly altered in HCC vs. adjacent non-tumor tissue in a race-specific manner. We observed that the methylome was drastically changed in EA with a significantly larger number of differentially methylated and differentially expressed genes than in AA. On the other hand, the miRNA expression was altered to a larger extent in AA than in EA. Pathway analysis functionally linked epigenetic regulation in EA to processes involved in immune cell maturation, inflammation, and vascular remodeling. In contrast, cellular proliferation, metabolism, and growth pathways are found to predominate in AA as a result of this epigenetic analysis. Furthermore, through integrative analysis, we identified significantly differentially expressed genes in HCC with disparate epigenetic regulation, associated with changes in miRNA expression for AA and DNA methylation for EA.

Molecular basis for substrate recruitment to the PRMT5 methylosome.

PRMT5 is an essential arginine methyltransferase and a therapeutic target in MTAP-null cancers. PRMT5 uses adaptor proteins for substrate recruitment through a previously undefined mechanism. Here, we identify an evolutionarily conserved peptide sequence shared among the three known substrate adaptors (CLNS1A, RIOK1, and COPR5) and show that it is necessary and sufficient for interaction with PRMT5. We demonstrate that PRMT5 uses modular adaptor proteins containing a common binding motif for substrate recruitment, comparable with other enzyme classes such as kinases and E3 ligases. We structurally resolve the interface with PRMT5 and show via genetic perturbation that it is required for methylation of adaptor-recruited substrates including the spliceosome, histones, and ribosomal complexes. Furthermore, disruption of this site affects Sm spliceosome activity, leading to intron retention. Genetic disruption of the PRMT5-substrate adaptor interface impairs growth of MTAP-null tumor cells and is thus a site for development of therapeutic inhibitors of PRMT5.

Immune characterization and profiles of SARS-CoV-2 infected patients reveals potential host therapeutic targets and SARS-CoV-2 oncogenesis mechanism.

The spread of SARS-CoV-2 and the increasing mortality rates of COVID-19 create an urgent need for treatments, which are currently lacking. Although vaccines have been approved by the FDA for emergency use in the U.S., patients will continue to require pharmacologic intervention to reduce morbidity and mortality as vaccine availability remains limited. The rise of new variants makes the development of therapeutic strategies even more crucial to combat the current pandemic and future outbreaks. Evidence from several studies suggests the host immune response to SARS-CoV-2 infection plays a critical role in disease pathogenesis. Consequently, host immune factors are becoming more recognized as potential biomarkers and therapeutic targets for COVID-19. To develop therapeutic strategies to combat current and future coronavirus outbreaks, understanding how the coronavirus hijacks the host immune system during and after the infection is crucial. In this study, we investigated immunological patterns or characteristics of the host immune response to SARS-CoV-2 infection that may contribute to the disease severity of COVID-19 patients. We analyzed large bulk RNASeq and single cell RNAseq data from COVID-19 patient samples to immunoprofile differentially expressed gene sets and analyzed pathways to identify human host protein targets. We observed an immunological profile of severe COVID-19 patients characterized by upregulated cytokines, interferon-induced proteins, and pronounced T cell lymphopenia, supporting findings by previous studies. We identified a number of host immune targets including PERK, PKR, TNF, NF-kB, and other key genes that modulate the significant pathways and genes identified in COVID-19 patients. Finally, we identified genes modulated by COVID-19 infection that are implicated in oncogenesis, including E2F transcription factors and RB1, suggesting a mechanism by which SARS-CoV-2 infection may contribute to oncogenesis. Further clinical investigation of these targets may lead to bonafide therapeutic strategies to treat the current COVID-19 pandemic and protect against future outbreaks and viral escape variants.

Immune characterization and profiles of SARS-CoV-2 infected patients reveals potential host therapeutic targets and SARS-CoV-2 oncogenesis mechanism.

The spread of SARS-CoV-2 and the increasing mortality rates of COVID-19 create an urgent need for treatments, which are currently lacking. Although vaccines have been approved by the FDA for emergency use in the U.S., patients will continue to require pharmacologic intervention to reduce morbidity and mortality as vaccine availability remains limited. The rise of new variants makes the development of therapeutic strategies even more crucial to combat the current pandemic and future outbreaks. Evidence from several studies suggests the host immune response to SARS-CoV-2 infection plays a critical role in disease pathogenesis. Consequently, host immune factors are becoming more recognized as potential biomarkers and therapeutic targets for COVID-19. To develop therapeutic strategies to combat current and future coronavirus outbreaks, understanding how the coronavirus hijacks the host immune system during and after the infection is crucial. In this study, we investigated immunological patterns or characteristics of the host immune response to SARS-CoV-2 infection that may contribute to the disease severity of COVID-19 patients. We analyzed large bulk RNASeq and single cell RNAseq data from COVID-19 patient samples to immunoprofile differentially expressed gene sets and analyzed pathways to identify human host protein targets. We observed an immunological profile of severe COVID-19 patients characterized by upregulated cytokines, interferon-induced proteins, and pronounced T cell lymphopenia, supporting findings by previous studies. We identified a number of host immune targets including PERK, PKR, TNF, NF-kB, and other key genes that modulate the significant pathways and genes identified in COVID-19 patients. Finally, we identified genes modulated by COVID-19 infection that are implicated in oncogenesis, including E2F transcription factors and RB1, suggesting a mechanism by which SARS-CoV-2 infection may contribute to oncogenesis. Further clinical investigation of these targets may lead to bonafide therapeutic strategies to treat the current COVID-19 pandemic and protect against future outbreaks and viral escape variants.

GEMINI: a variational Bayesian approach to identify genetic interactions from combinatorial CRISPR screens.

Systems for CRISPR-based combinatorial perturbation of two or more genes are emerging as powerful tools for uncovering genetic interactions. However, systematic identification of these relationships is complicated by sample, reagent, and biological variability. We develop a variational Bayes approach (GEMINI) that jointly analyzes all samples and reagents to identify genetic interactions in pairwise knockout screens. The improved accuracy and scalability of GEMINI enables the systematic analysis of combinatorial CRISPR knockout screens, regardless of design and dimension. GEMINI is available as an open source R package on GitHub at https://github.com/sellerslab/gemini .

TCF7L1 Modulates Colorectal Cancer Growth by Inhibiting Expression of the Tumor-Suppressor Gene EPHB3.

Dysregulation of the Wnt pathway leading to accumulation of ß-catenin (CTNNB1) is a hallmark of colorectal cancer (CRC). Nuclear CTNNB1 acts as a transcriptional coactivator with TCF/LEF transcription factors, promoting expression of a broad set of target genes, some of which promote tumor growth. However, it remains poorly understood how CTNNB1 interacts with different transcription factors in different contexts to promote different outcomes. While some CTNNB1 target genes are oncogenic, others regulate differentiation. Here, we found that TCF7L1, a Wnt pathway repressor, buffers CTNNB1/TCF target gene expression to promote CRC growth. Loss of TCF7L1 impaired growth and colony formation of HCT116 CRC cells and reduced tumor growth in a mouse xenograft model. We identified a group of CTNNB1/TCF target genes that are activated in the absence of TCF7L1, including EPHB3, a marker of Paneth cell differentiation that has also been implicated as a tumor suppressor in CRC. Knockdown of EPHB3 partially restores growth and normal cell cycle progression of TCF7L1-Null cells. These findings suggest that while CTNNB1 accumulation is critical for CRC progression, activation of specific Wnt target genes in certain contexts may in fact inhibit tumor growth.

To evaluate the effect of various surface treatments on the shear bond strength of three different intraoral ceramic repair systems: an in vitro study.

Fractures of metal-ceramic restoration pose an esthetic and functional dilemma both for patient and the dentist. Intraoral repair systems eliminate the remake and removal of restoration. Many intraoral repair materials and surface treatments are available to repair intraorally fractured metal-ceramic restoration. Bond strength data of various materials and specific technique used for repair are necessary for predicting the success of a given repair system. This study evaluated the shear bond strength of three different intraoral repair systems for metal-ceramic restorations applied on exposed metal and porcelain surface. One hundred and twenty metal discs (20 mm in diameter × 0.7 mm thick) were fabricated with nickel-chromium alloy (Mealloy, Dentsply, USA). Feldspathic porcelain (Duceram, Degudent, Germany) were applied over one test surface of the discs in the thickness of 1.8 mm followed by conventional firing. The defect, which simulates clinical failures were created in 1/4th area of the metal-ceramic discs. The metal-ceramic discs samples were divided into ceramic substrate (Group I, n = 60) and metal substrate (Group II, n = 60), according to the defect location. Then, samples of ceramic substrate (Group I) and metal substrate (Group II) were subdivided into A, B according to the surface treatments (A; roughening with diamond bur and B; abraded with 50 µ Al2O3) and repaired with one of the intraoral repair systems tested (a. Ceramic repair system, Ivoclar Vivadent; b. Clearfil repair system, Kurary, c; Porcelain repair system, 3 M ESPE). All the repaired samples were stored in distilled water at 37 °C for 24 h. After thermocycling at 6-60° C, all the samples were stored at 37 °C for additional 7 days. Shear bond strength of all the samples were calculated by using Universal testing machine. The mean shear bond strength values for the group I (A/B) were as follows: Ceramic repair system (9.47 ± 1.41/14.03 ± 2.54 MPa), Clearfil repair system (14.03 ± 2.32/14.64 ± 2.28 MPa), and Porcelain repair system (14.41 ± 3.96/14.86 ± 3.10 MPa). The mean shear bond strength values for the group II (A/B) were as follows: Ceramic repair system (9.42 ± 1.44/18.61 ± 2.60 MPa), Clearfil repair system (14.44 ± 3.23/14.98 ± 2.73 MPa), and Porcelain repair system (11.86 ± 2.24/13.24 ± 2.72 MPa). Air abrasion with 50 µm aluminum oxide particles is the preferred surface treatment. Porcelain repair system showed the highest shear bond with air abrasion for ceramic substrate and for metal substrate Ceramic repair system showed the highest bond strength with air abrasion as a surface treatment. This study suggest that the three repair systems tested are adequate for intraoral chairside repair of metal-ceramic restoration when air abrasion is used for surface treatment of the substrate (Ceramic repair system, Ivoclar Vivadent, Germany; Clearfil repair system, Kurary, Japan; Porcelain repair system, 3M ESPE, Germany).

Attenuation of the side effect profile of regadenoson: a randomized double-blinded placebo-controlled study with aminophylline in patients undergoing myocardial perfusion imaging. "The ASSUAGE trial".

BACKGROUND: It is unknown whether the standardized intravenous aminophylline administration following regadenoson-stress can prevent the gastrointestinal and other adverse effects associated with regadenoson. METHODS: In a randomized, double-blinded, placebo-controlled clinical trial we compared the frequency and severity of regadenoson adverse effects in those who received 75 mg of intravenous aminophylline versus a matching placebo administered 2 minutes after regadenoson or 90 seconds post-radioisotope injection. RESULTS: 248 patients [44.8% women, mean age 62.2 (± 13.3) years] were randomized to receive aminophylline (124) or placebo (124). In the aminophylline arm, there was 50% reduction in the incidence of the primary endpoint of diarrhea and abdominal discomfort [11 (8.9%) vs 22 (17.7%), P = .04] and 70% reduction in the incidence of diarrhea [4 (3.2%) vs 13 (10.5%), P = .02]. Additionally, aminophylline use was associated with 34% reduction in the secondary endpoint of any regadenoson adverse effects [55 (44.4%) vs 83 (66.9%), P < .001] and 71% reduction in headache [9 (7.3%) vs 31 (25%), P < .001]. The stress protocol was better tolerated in the aminophylline group (P = .007). The quantitative summed difference score was similar in both study groups (P = .92). There were no excess adverse events in the aminophylline arm. CONCLUSIONS: This trial supports the routine administration of IV-aminophylline to reduce the frequency and severity of adverse effects associated with regadenoson-stress.

Patient and provider delays in breast cancer patients attending a tertiary care centre: a prospective study.

OBJECTIVES: To find out factors that are responsible for the patient or provider delays in the diagnosis of breast cancer in India. DESIGN: This prospective study was designed to be conducted over a period of two years including a cohort of 100 patients with locally advanced breast cancer. The delays were assessed using questionnaires prepared according to the Indian scenario. SETTING: A prospective study in an Indian setting. PARTICIPANTS: One hundred patients with locally advanced breast cancer receiving neoadjuvant chemotherapy were included after providing informed consent and receiving ethical committee clearance. MAIN OUTCOME MEASURES: The most common factor responsible for delays in diagnosis was observed to be the health providers, although illiteracy and lack of adequate healthcare services also contributed significantly. Unregistered medical practitioners or quacks contributed significantly to the delays in reporting and diagnosis of the disease. RESULTS: One hundred patients of locally advanced breast cancer were evaluated using standardized questionnaires to assess the delays in diagnosis. Provider delays were found to be significant (the unregistered doctors or quacks being a significant cause of delays).The average time lapse before diagnosis for rural patients was higher (67.5 days) compared to urban patients (53.7 days). The literacy levels of the patients also had a significant impact on the delays at diagnosis. The delay in illiterates was 60.6 days compared to 49.5 days for literates. CONCLUSIONS: The most common factor responsible for delays in reporting and diagnosis was observed to be at the end of the health providers, although illiteracy and lack of adequate healthcare services also contributed significantly. Unregistered medical practitioners or quacks contributed significantly to the delays in reporting and diagnosis of the disease.

The correlation of anxiety and depression levels with response to neoadjuvant chemotherapy in patients with breast cancer.

BACKGROUND: The aim was to evaluate and correlate anxiety and depression levels with response to neoadjuvant chemotherapy in patients with breast cancer. The study also assessed the effects of family support on distress levels. DESIGN: It was a prospective study in a cohort of 84 patients with locally advanced breast cancer. These assessments were done using the Hospital Anxiety and Depression Scale (HADS). SETTING: A prospective study in a developing world setting. PARTICIPANTS: Eighty-four patients with locally advanced breast cancer receiving neoadjuvant chemotherapy were included after taking an informed consent and ethical committee clearance. MAIN OUTCOME MEASURES: A significant correlation was observed between response to neoadjuvant chemotherapy and depression levels in breast cancer patients. Joint family and literacy levels also had an impact on the levels of depression observed. RESULTS: A total of 84 patients receiving neoadjuvant chemotherapy for breast cancer were evaluated using HADS. The effect of family support, literacy levels and employment on the psychological status of these patients were also assessed. CONCLUSIONS: The response to neoadjuvant chemotherapy had a direct correlation with the levels of depression, the distress levels being lower in responders. This was found to be the most important variable determining the psychological status of the patients. It was also observed that Indian patients in comparison to their Western counterparts react differently to cancer-related stress.

Vulval elephantiasis as a result of tubercular lymphadenitis: two case reports and a review of the literature.

INTRODUCTION: Elephantiasis as a result of chronic lymphedema is characterized by gross enlargement of the arms, legs or genitalia, and occurs due to a variety of obstructive diseases of the lymphatic system. Genital elephantiasis usually follows common filariasis and lymphogranuloma venereum. It may follow granuloma inguinale, carcinomas, lymph node dissection or irradiation and tuberculosis but this happens rarely. Vulval elephantiasis as a consequence of extensive lymph node destruction by tuberculosis is very rare. We present two very unusual cases of vulval elephantiasis due to tuberculous destruction of the inguinal lymph nodes. CASE PRESENTATION: Two Indian women - one aged 40 years and the other aged 27 years, with progressively increasing vulval swellings over a period of five and four years respectively - presented to our hospital. In both cases, there was a significant history on presentation. Both women had previously taken a complete course of anti-tubercular treatment for generalized lymphadenopathy. The vulval swellings were extremely large: in the first case report, measuring 35 × 25 cm on the right side and 45 × 30 cm on the left side, weighing 20 lb and 16 lb respectively. Both cases were managed by surgical excision with reconstruction and the outcome was positive. Satisfactory results have been maintained during a follow-up period of six years in both cases. CONCLUSIONS: Elephantiasis of the female genitalia is unusual and it has rarely been reported following tuberculosis. We report two cases of vulval elephantiasis as a consequence of extensive lymph node destruction by tuberculosis, in order to highlight this very rare clinical scenario.