Clinical application of whole-genome sequencing of solid tumors for precision oncology.

Genomic alterations in tumors play a pivotal role in determining their clinical trajectory and responsiveness to treatment. Targeted panel sequencing (TPS) has served as a key clinical tool over the past decade, but advancements in sequencing costs and bioinformatics have now made whole-genome sequencing (WGS) a feasible single-assay approach for almost all cancer genomes in clinical settings. This paper reports on the findings of a prospective, single-center study exploring the real-world clinical utility of WGS (tumor and matched normal tissues) and has two primary objectives: (1) assessing actionability for therapeutic options and (2) providing clarity for clinical questions. Of the 120 patients with various solid cancers who were enrolled, 95 (79%) successfully received genomic reports within a median of 11 working days from sampling to reporting. Analysis of these 95 WGS reports revealed that 72% (68/95) yielded clinically relevant insights, with 69% (55/79) pertaining to therapeutic actionability and 81% (13/16) pertaining to clinical clarity. These benefits include the selection of informed therapeutics and/or active clinical trials based on the identification of driver mutations, tumor mutational burden (TMB) and mutational signatures, pathogenic germline variants that warrant genetic counseling, and information helpful for inferring cancer origin. Our findings highlight the potential of WGS as a comprehensive tool in precision oncology and suggests that it should be integrated into routine clinical practice to provide a complete image of the genomic landscape to enable tailored cancer management.

CHMP2A regulates broad immune cell-mediated antitumor activity in an immunocompetent in vivo head and neck squamous cell carcinoma model.

BACKGROUND: Natural killer (NK) cells are key effector cells of antitumor immunity. However, tumors can acquire resistance programs to escape NK cell-mediated immunosurveillance. Identifying mechanisms that mediate this resistance enables us to define approaches to improve immune-mediate antitumor activity. In previous studies from our group, a genome-wide CRISPR-Cas9 screen identified Charged Multivesicular Body Protein 2A (CHMP2A) as a novel mechanism that mediates tumor intrinsic resistance to NK cell activity. METHODS: Here, we use an immunocompetent mouse model to demonstrate that CHMP2A serves as a targetable regulator of not only NK cell-mediated immunity but also other immune cell populations. Using the recently characterized murine 4MOSC model system, a syngeneic, tobacco-signature murine head and neck squamous cell carcinoma model, we deleted mCHMP2A using CRISPR/Cas9-mediated knock-out (KO), following orthotopic transplantation into immunocompetent hosts. RESULTS: We found that mCHMP2A KO in 4MOSC1 cells leads to more potent NK-mediated tumor cell killing in vitro in these tumor cells. Moreover, following orthotopic transplantation, KO of mCHMP2A in 4MOSC1 cells, but not the more immune-resistant 4MOSC2 cells enables both T cells and NK cells to better mediate antitumor activity compared with wild type (WT) tumors. However, there was no difference in tumor development between WT and mCHMP2A KO 4MOSC1 or 4MOSC2 tumors when implanted in immunodeficient mice. Mechanistically, we find that mCHMP2A KO 4MOSC1 tumors transplanted into the immunocompetent mice had significantly increased CD4+T cells, CD8+T cells. NK cell, as well as fewer myeloid-derived suppressor cells (MDSC). CONCLUSIONS: Together, these studies demonstrate that CHMP2A is a targetable inhibitor of cellular antitumor immunity.

Population-level call properties of endangered Dryophytes suweonensissensu lato (Anura: Amphibia) in South Korea.

Calling is one of the unique amphibian characteristics that facilitates social communication and shows individuality; however, it also makes them vulnerable to predators. Researchers use amphibian call properties to study their population status, ecology, and behavior. This research scope has recently broadened to species identification and taxonomy. Dryophytes flaviventris has been separated from the endangered anuran species, D. suweonensis, based on small variations in genetic, morphometric, and temporal call properties observed in South Korea. The Chilgap Mountain (CM) was considered as the potential geographic barrier for the speciation. However, it initiated taxonomic debates as CM has been hardly used and is considered a potential barrier for other species. The calls of populations from both sides are also apparently similar. Thus, to verify the differences in call properties among populations of D. suweonensis sensu lato (s.l.; both of the species), we sampled and analyzed call data from five localities covering its distribution range, including the southern (S) and northern (N) parts of CM. We found significant differences in many call properties among populations; however, no specific pattern was observed. Some geographically close populations, such as Iksan (S), Wanju (S), and Gunsan (S), had significant differences, whereas many distant populations, such as Pyeongtaek (N) and Wanju (S), had no significant differences. Considering the goal of this study was only to observe the call properties, we cautiously conclude that the differences are at the population level rather than the species level. Our study indicates the necessity of further investigation into the specific status of D. flaviventris using robust integrated taxonomic approaches, including genetic and morphological parameters from a broader array of localities.

Diffuse Large B-Cell lymphoma Misdiagnosed as a Hematoma: Case Report.

Background: Diffuse large B-cell lymphoma (DLBCL), the most common subtype of non-Hodgkin's lymphoma, often presents diagnostic challenges due to its diverse clinical presentation. We present a case of DLBCL that was initially misdiagnosed as a hematoma, highlighting the importance of considering malignancy when faced with unresponsive soft tissue swelling. Methods: A 76-year-old man presented to the emergency department with right periorbital swelling and ecchymosis following a traumatic injury. Despite ongoing anticoagulant therapy (warfarin) for atrial fibrillation, the symptoms persisted. A CT scan of the facial bones revealed a large, irregular, homogeneous mass. Initially, the clinical history and radiologic findings suggested an extraconal hematoma. As a result, an incision and drainage procedure was performed, and the old blood was evacuated. However, the patient's symptoms continued to worsen. A follow-up CT scan showed enlargement of the lesion, prompting a surgical excisional biopsy. Results: Pathologic examination of the excised mass revealed a diffuse infiltrate of lymphocytes surrounding the tissue, confirming the diagnosis of diffuse large B-cell lymphoma (DLBCL). The patient was subsequently referred to hematology for further management. Conclusions: Although rare, DLBCL is associated with a challenging prognosis. This case highlights the diagnostic complexities that can arise, particularly when factors such as prior injury and anticoagulant therapy confound the clinical picture. The initial misclassification of the condition as a hematoma led to a delay in diagnosis and the subsequent initiation of treatment. Therefore, it is imperative to remain vigilant and consider malignancy as a potential underlying cause of unresponsive soft tissue swelling. Timely recognition and accurate diagnosis are paramount to improving patient outcomes in DLBCL, an aggressive lymphoma with a diverse clinical presentation.

Identification of cell division cycle protein 20 in various forms of acute and chronic kidney injury in mice.

Tubular epithelial cell fate following exposure to various types of injurious stimuli can be decided at distinct cell cycle checkpoints. One such checkpoint occurs during mitosis, known as the spindle assembly checkpoint, and is tightly regulated through the actions of cell division cycle protein 20 (CDC20). Due to our paucity of knowledge about the role of CDC20 in the kidney, the present study was designed to investigate the expression levels and distribution of CDC20 within the kidney and how pharmacological inhibition of CDC20 function affects kidney recovery using various rodent models of kidney injury. CDC20 is normally detected in distal tubules, but upon injury by either cisplatin administration or ureter obstruction, CDC20 accumulation is considerably elevated. Blockade of CDC20 activity using a selective pharmacological inhibitor, Apcin, lowered serum creatinine, tubular damage, and DNA injury following acute kidney injury compared with vehicle-treated mice. In unilateral ureteral obstruction, Apcin reduced tissue kidney injury molecule-1 levels, sirius red staining, and tubulointerstitial α-smooth muscle actin staining in the tissue. The findings in the present study demonstrated that elevations in CDC20 levels in the kidney are associated with kidney injury and that inhibition of CDC20 can alleviate and reverse some of the pathological effects on the architecture and function of kidney.NEW & NOTEWORTHY To our knowledge, this is the first study to characterize the expression and localization of cell division cycle 20 protein (CDC20) in normal and acute, and chronically injured kidneys. Tubular epithelial cell damage was markedly reduced through the administration of a selective inhibitor of CDC20, Apcin. This study provides new evidence that CDC20 can be induced in damaged kidney cells and negatively impact the recovery of the kidney following acute kidney injury.

The impact of anti-Asian racism on routine activities and mental health among Korean American older adults and their caregivers.

Introduction: Reported anti-Asian discrimination has been on the rise since the COVID-19 pandemic. Nevertheless, limited research addresses the health impact of perceived anti-Asian racism on Asian Americans, especially among older adults, during COVID-19. To address the gap, we examined how the novel coronavirus pandemic affected Korean American older adults, one of the largest Asian subgroups. Specifically, this study addressed the magnitude of racism or discrimination related to the pandemic and impact of anti-Asian racism on negative mental health symptoms among Korean American older adults and their caregivers. Methods: We used survey data collected from 175 Korean American older adults with probable dementia and their primary caregivers (female = 62%, mean age = 71 years) who went through eligibility screening for an ongoing randomized controlled trial involving dyads in the Baltimore-Washington and the New York Metropolitan areas (ClinicalTrials.gov Identifier: NCT03909347). Results: Nearly a quarter of the survey sample reported they were fearful for their safety due to anti-Asian racism related to the pandemic. Additionally, 47% of the respondents indicated changes to routine activities due to anti-Asian racism or discrimination related to COVID-19. The most common changes included avoiding walking alone or physical activities outside, followed by avoiding public transportation or leaving the house to go to any public places such as grocery stores, churches, or schools, not carrying out usual social activities, and avoiding going to health care appointments. Multinomial logistic regression revealed that people who reported changes to routine activities were at least five times more likely (adjusted odds ratio = 5.017, 95% confidence interval = 1.503, 16.748) to report negative mental health symptoms than those who did not. Being fearful for their own safety was not associated with experiencing negative mental health symptoms in the survey sample. Discussion: Study findings indicate that the increased reporting of anti-Asian racism during the COVID-19 pandemic has substantially affected Korean American older adults and their caregivers. The mechanism by which changes to routine activities is related to negative mental health symptoms is unclear, future research is needed to elucidate this pathway. Furthermore, our findings highlight the importance of identifying multi-level strategies to raise awareness of and to mitigate the reported surge of racism.

Efficacy of Polydeoxyribonucleotide in Promoting the Healing of Diabetic Wounds in a Murine Model of Streptozotocin-Induced Diabetes: A Pilot Experiment.

We assessed the efficacy of polydeoxyribonucleotide (PDRN) in accelerating the healing of diabetic wounds in a murine model of streptozotocin (STZ)-induced diabetes. After the creation of diabetic wounds, the mice of the PDRN SC, PDRN IP and PBS groups received a subcutaneous, an intra-peritoneal injection of PDRN and a subcutaneous injection of PBS, respectively. After euthanasia, time-dependent changes in the wound diameter and histologic scores were measured and vascular endothelial growth factor (VEGF), transforming growth factor-ß1 (TGF-ß1) and collagen types I and III were assessed for their expression levels. The PDRN SC and the PDRN IP groups showed a significantly smaller diameter of diabetic wounds, significantly higher histologic scores, a significantly greater expression of VEGF, a significantly lower expression of TGF-ß1 and a significantly greater expression of collagen types I and III as compared with the PBS group (p < 0.05 or 0.0001). In conclusion, PDRN might be effective in promoting the healing of diabetic wounds in a murine model of STZ-induced diabetes.

CHMP2A regulates tumor sensitivity to natural killer cell-mediated cytotoxicity.

Natural killer (NK) cells are known to mediate killing of various cancer types, but tumor cells can develop resistance mechanisms to escape NK cell-mediated killing. Here, we use a "two cell type" whole genome CRISPR-Cas9 screening system to discover key regulators of tumor sensitivity and resistance to NK cell-mediated cytotoxicity in human glioblastoma stem cells (GSC). We identify CHMP2A as a regulator of GSC resistance to NK cell-mediated cytotoxicity and we confirm these findings in a head and neck squamous cells carcinoma (HNSCC) model. We show that deletion of CHMP2A activates NF-κB in tumor cells to mediate increased chemokine secretion that promotes NK cell migration towards tumor cells. In the HNSCC model we demonstrate that CHMP2A mediates tumor resistance to NK cells via secretion of extracellular vesicles (EVs) that express MICA/B and TRAIL. These secreted ligands induce apoptosis of NK cells to inhibit their antitumor activity. To confirm these in vitro studies, we demonstrate that deletion of CHMP2A in CAL27 HNSCC cells leads to increased NK cell-mediated killing in a xenograft immunodeficient mouse model. These findings illustrate a mechanism of tumor immune escape through EVs secretion and identify inhibition of CHMP2A and related targets as opportunities to improve NK cell-mediated immunotherapy.

Sphingosine 1-Phosphate Receptor 4 Promotes Nonalcoholic Steatohepatitis by Activating NLRP3 Inflammasome.

BACKGROUND & AIMS: Sphingosine 1-phosphate receptors (S1PRs) are a group of G-protein-coupled receptors that confer a broad range of functional effects in chronic inflammatory and metabolic diseases. S1PRs also may mediate the development of nonalcoholic steatohepatitis (NASH), but the specific subtypes involved and the mechanism of action are unclear. METHODS: We investigated which type of S1PR isoforms is activated in various murine models of NASH. The mechanism of action of S1PR4 was examined in hepatic macrophages isolated from high-fat, high-cholesterol diet (HFHCD)-fed mice. We developed a selective S1PR4 functional antagonist by screening the fingolimod (2-amino-2-[2-(4- n -octylphenyl)ethyl]-1,3- propanediol hydrochloride)-like sphingolipid-focused library. RESULTS: The livers of various mouse models of NASH as well as hepatic macrophages showed high expression of S1pr4. Moreover, in a cohort of NASH patients, expression of S1PR4 was 6-fold higher than those of healthy controls. S1pr4+/- mice were protected from HFHCD-induced NASH and hepatic fibrosis without changes in steatosis. S1pr4 depletion in hepatic macrophages inhibited lipopolysaccharide-mediated Ca++ release and deactivated the Nod-like receptor pyrin domain-containning protein 3 (NLRP3) inflammasome. S1P increased the expression of S1pr4 in hepatic macrophages and activated NLRP3 inflammasome through inositol trisphosphate/inositol trisphosphate-receptor-dependent [Ca++] signaling. To further clarify the biological function of S1PR4, we developed SLB736, a novel selective functional antagonist of SIPR4. Similar to S1pr4+/- mice, administration of SLB736 to HFHCD-fed mice prevented the development of NASH and hepatic fibrosis, but not steatosis, by deactivating the NLRP3 inflammasome. CONCLUSIONS: S1PR4 may be a new therapeutic target for NASH that mediates the activation of NLRP3 inflammasome in hepatic macrophages.

Sphingomyelin synthase 1 mediates hepatocyte pyroptosis to trigger non-alcoholic steatohepatitis.

OBJECTIVE: Lipotoxic hepatocyte injury is a primary event in non-alcoholic steatohepatitis (NASH), but the mechanisms of lipotoxicity are not fully defined. Sphingolipids and free cholesterol (FC) mediate hepatocyte injury, but their link in NASH has not been explored. We examined the role of free cholesterol and sphingomyelin synthases (SMSs) that generate sphingomyelin (SM) and diacylglycerol (DAG) in hepatocyte pyroptosis, a specific form of programmed cell death associated with inflammasome activation, and NASH. DESIGN: Wild-type C57BL/6J mice were fed a high fat and high cholesterol diet (HFHCD) to induce NASH. Hepatic SMS1 and SMS2 expressions were examined in various mouse models including HFHCD-fed mice and patients with NASH. Pyroptosis was estimated by the generation of the gasdermin-D N-terminal fragment. NASH susceptibility and pyroptosis were examined following knockdown of SMS1, protein kinase Cδ (PKCδ), or the NLR family CARD domain-containing protein 4 (NLRC4). RESULTS: HFHCD increased the hepatic levels of SM and DAG while decreasing the level of phosphatidylcholine. Hepatic expression of Sms1 but not Sms2 was higher in mouse models and patients with NASH. FC in hepatocytes induced Sms1 expression, and Sms1 knockdown prevented HFHCD-induced NASH. DAG produced by SMS1 activated PKCδ and NLRC4 inflammasome to induce hepatocyte pyroptosis. Depletion of Nlrc4 prevented hepatocyte pyroptosis and the development of NASH. Conditioned media from pyroptotic hepatocytes activated the NOD-like receptor family pyrin domain containing 3 inflammasome (NLRP3) in Kupffer cells, but Nlrp3 knockout mice were not protected against HFHCD-induced hepatocyte pyroptosis. CONCLUSION: SMS1 mediates hepatocyte pyroptosis through a novel DAG-PKCδ-NLRC4 axis and holds promise as a therapeutic target for NASH.

Nonlocal Network Coding in Interference Channels.

In a network, a channel introduces correlations to the parties that aim to establish a communication protocol. We present a framework of nonlocal network coding by exploiting a Bell scenario and show the usefulness of nonlocal and quantum resources in network coding. Two-sender and two-receiver interference channels are considered, for which network coding is characterized by two-input and four-outcome Bell scenarios. It is shown that nonsignaling correlations lead to strictly higher channel capacities than quantum correlations in general. This also holds true for quantum and local correlations: network coding with quantum resources shows a strictly higher channel capacity than local ones. It turns out, however, that more nonlocality does not necessarily imply a higher channel capacity. The framework can be generally applied to network communication protocols.

Virus Isolation from the First Patient with SARS-CoV-2 in Korea.

Novel coronavirus (SARS-CoV-2) is found to cause a large outbreak started from Wuhan since December 2019 in China and SARS-CoV-2 infections have been reported with epidemiological linkage to China in 25 countries until now. We isolated SARS-CoV-2 from the oropharyngeal sample obtained from the patient with the first laboratory-confirmed SARS-CoV-2 infection in Korea. Cytopathic effects of SARS-CoV-2 in the Vero cell cultures were confluent 3 days after the first blind passage of the sample. Coronavirus was confirmed with spherical particle having a fringe reminiscent of crown on transmission electron microscopy. Phylogenetic analyses of whole genome sequences showed that it clustered with other SARS-CoV-2 reported from Wuhan.

The clinical impact of family history of cancer in female never-smoker lung adenocarcinoma.

OBJECTIVES: Accumulating evidence reveals the association between the risk of never-smoker lung cancer and family history of cancer. However, the clinicogenomic effect of family history of cancer in never-smoker lung cancer remains unknown. MATERIAL AND METHODS: We screened 3,241 lung cancer patients who (a) underwent curative resection at National Cancer Center (Goyang, Korea) between 2001-2014, and (b) completed a pre-designed interview about family/smoking history at the time of diagnosis and identified 604 female never smoker lung adenocarcinoma. A positive family history of cancer [categorized as pulmonary cancer (FH-PC) or non-pulmonary cancer (FH-NPC)] was defined as a self-reported history of cancer in first-degree relatives. Survival data were followed up until January 2017. Multiplexed targeted next-generation sequencing was performed for genetic profiling. RESULTS: Of 604 patients, 29.1% (n = 176) had a FH, including 132 (21.9%) with FH-NPC and 44 (7.3%) with FH-PC. Patients with the FH-NPC had a higher proportion of young patients (≤45 years) than those without the FH-NPC (FH-NPC, FH-PC, and no FH; 13.6%, 2.3%, and 8.2%, respectively; P = 0.032). Patients with the FH-NPC had an increased risk of recurrence (hazard ratio [HR]: 1.90; 95% confidence interval [CI]: 1.40-2.56; P<0.001) and death (HR: 1.67; 95% CI: 1.18-2.37; P=0.004). In contrast, the FH-PC had no prognostic effect on recurrence (HR: 1.23; 95% CI: 0.71-2.15; P = 0.456) and death (HR: 0.93; 95% CI: 0.45-1.91; P=0.838). Among three driver oncogene alterations, EGFR mutation was significantly associated with the FH-PC (53.8%, 84.1%, and 65.8%, respectively; P = 0.016), ALK/ROS1/RET fusions was significantly associated with the FH-NPC (13.7%, 0.0%, and 5.0%, respectively; P = 0.004), but KRAS mutation was not associated with any type of the FH (13.8% vs. 6.0% vs. 7.8%, respectively; P = 0.288). CONCLUSION: The type of family history of cancer was associated with distinct clinocogenomic subtypes and prognosis of never-smoker lung adenocarcinoma.

Whole Exome and Transcriptome Analyses Integrated with Microenvironmental Immune Signatures of Lung Squamous Cell Carcinoma.

The immune microenvironment in lung squamous cell carcinoma (LUSC) is not well understood, with interactions between the host immune system and the tumor, as well as the molecular pathogenesis of LUSC, awaiting better characterization. To date, no molecularly targeted agents have been developed for LUSC treatment. Identification of predictive and prognostic biomarkers for LUSC could help optimize therapy decisions. We sequenced whole exomes and RNA from 101 tumors and matched noncancer control Korean samples. We used the information to predict subtype-specific interactions within the LUSC microenvironment and to connect genomic alterations with immune signatures. Hierarchical clustering based on gene expression and mutational profiling revealed subtypes that were either immune defective or immune competent. We analyzed infiltrating stromal and immune cells to further characterize the tumor microenvironment. Elevated expression of macrophage 2 signature genes in the immune competent subtype confirmed that tumor-associated macrophages (TAM) linked inflammation and mutation-driven cancer. A negative correlation was evident between the immune score and the amount of somatic copy-number variation (SCNV) of immune genes (r = -0.58). The SCNVs showed a potential detrimental effect on immunity in the immune-deficient subtype. Knowledge of the genomic alterations in the tumor microenvironment could be used to guide design of immunotherapy options that are appropriate for patients with certain cancer subtypes. Cancer Immunol Res; 6(7); 848-59. ©2018 AACR.

Weight analysis of mastectomy specimens and abdominal flaps used for breast reconstruction in Koreans.

BACKGROUND: Slim patients or those with large breasts may be ineligible for breast reconstruction with an abdominal flap, as the volume of the flap may be insufficient. This study aimed to establish that abdominal tissue-based breast reconstruction can be well suited for Korean patients, despite their thin body habitus. METHODS: A total of 252 patients who underwent postmastectomy breast reconstruction with an abdominal flap from October 2006 to May 2013 were retrospectively reviewed. The patients' age and body mass index were analyzed, and a correlation analysis was performed between the weight of the mastectomy specimen and that of the initial abdominal flap. RESULTS: The average weights of the mastectomy specimen and initial abdominal flap were 451.03 g and 644.95 g, respectively. The ratio of the weight of the mastectomy specimen to that of the initial flap was 0.71±0.23. There was a strong positive linear relationship between the weight of the mastectomy specimen and that of the initial flap (Pearson correlation coefficient, 0.728). Thirty nulliparous patients had a final-to-initial flap weight ratio of 0.66±0.11. The 25 patients who underwent a contralateral procedure had a ratio of 0.96±0.30. The adjusted ratio of the final flap weight to the initial flap weight was 0.66±0.12. CONCLUSIONS: Breast weight had a strong positive relationship with abdominal flap weight in Koreans. Abdominal flaps provided sufficient soft tissue for breast reconstruction in most Korean patients, including nulliparous patients. However, when the mastectomy weight is estimated to be >700 g, a contralateral reduction procedure may be considered.

Transcriptome analyses of chronic traumatic encephalopathy show alterations in protein phosphatase expression associated with tauopathy.

Chronic traumatic encephalopathy (CTE) is a progressive neurodegenerative disorder that is associated with repetitive head injury and has distinctive neuropathological features that differentiate this disease from other neurodegenerative diseases. Intraneuronal tau aggregates, although they occur in different patterns, are diagnostic neuropathological features of CTE, but the precise mechanism of tauopathy is not known in CTE. We performed whole RNA sequencing analysis of post-mortem brain tissue from patients with CTE and compared the results to normal controls to determine the transcriptome signature changes associated with CTE. The results showed that the genes related to the MAP kinase and calcium-signaling pathways were significantly downregulated in CTE. The altered expression of protein phosphatases (PPs) in these networks further suggested that the tauopathy observed in CTE involves common pathological mechanisms similar to Alzheimer's disease (AD). Using cell lines and animal models, we also showed that reduced PPP3CA/PP2B phosphatase activity is directly associated with increases in phosphorylated (p)-tau proteins. These findings provide important insights into PP-dependent neurodegeneration and may lead to novel therapeutic approaches to reduce the tauopathy associated with CTE.

De novo assembly and phasing of a Korean human genome.

Advances in genome assembly and phasing provide an opportunity to investigate the diploid architecture of the human genome and reveal the full range of structural variation across population groups. Here we report the de novo assembly and haplotype phasing of the Korean individual AK1 (ref. 1) using single-molecule real-time sequencing, next-generation mapping, microfluidics-based linked reads, and bacterial artificial chromosome (BAC) sequencing approaches. Single-molecule sequencing coupled with next-generation mapping generated a highly contiguous assembly, with a contig N50 size of 17.9 Mb and a scaffold N50 size of 44.8 Mb, resolving 8 chromosomal arms into single scaffolds. The de novo assembly, along with local assemblies and spanning long reads, closes 105 and extends into 72 out of 190 euchromatic gaps in the reference genome, adding 1.03 Mb of previously intractable sequence. High concordance between the assembly and paired-end sequences from 62,758 BAC clones provides strong support for the robustness of the assembly. We identify 18,210 structural variants by direct comparison of the assembly with the human reference, identifying thousands of breakpoints that, to our knowledge, have not been reported before. Many of the insertions are reflected in the transcriptome and are shared across the Asian population. We performed haplotype phasing of the assembly with short reads, long reads and linked reads from whole-genome sequencing and with short reads from 31,719 BAC clones, thereby achieving phased blocks with an N50 size of 11.6 Mb. Haplotigs assembled from single-molecule real-time reads assigned to haplotypes on phased blocks covered 89% of genes. The haplotigs accurately characterized the hypervariable major histocompatability complex region as well as demonstrating allele configuration in clinically relevant genes such as CYP2D6. This work presents the most contiguous diploid human genome assembly so far, with extensive investigation of unreported and Asian-specific structural variants, and high-quality haplotyping of clinically relevant alleles for precision medicine.

Nitric Oxide Produced by Macrophages Inhibits Adipocyte Differentiation and Promotes Profibrogenic Responses in Preadipocytes to Induce Adipose Tissue Fibrosis.

Fibrosis of adipose tissue induces ectopic fat accumulation and insulin resistance by inhibiting adipose tissue expandability. Mechanisms responsible for the induction of adipose tissue fibrosis may provide therapeutic targets but are poorly understood. In this study, high-fat diet (HFD)-fed wild-type (WT) and iNOS(-/-) mice were used to examine the relationship between nitric oxide (NO) produced by macrophages and adipose tissue fibrosis. In contrast to WT mice, iNOS(-/-) mice fed an HFD were protected from infiltration of proinflammatory macrophages and adipose tissue fibrosis. Hypoxia-inducible factor 1α (HIF-1α) protein level was increased in adipose tissue of HFD-fed WT mice, but not iNOS(-/-) mice. In contrast, the expression of mitochondrial biogenesis factors was decreased in HFD-fed WT mice, but not iNOS(-/-) mice. In studies with cultured cells, macrophage-derived NO decreased the expression of mitochondrial biogenesis factors, and increased HIF-1α protein level, DNA damage, and phosphorylated p53 in preadipocytes. By activating p53 signaling, NO suppressed peroxisome proliferator-activated receptor γ coactivator 1α expression, which induced mitochondrial dysfunction and inhibited preadipocyte differentiation in adipocytes. The effects of NO were blocked by rosiglitazone. The findings suggest that NO produced by macrophages induces mitochondrial dysfunction in preadipocytes by activating p53 signaling, which in turn increases HIF-1α protein level and promotes a profibrogenic response in preadipocytes that results in adipose tissue fibrosis.

Intraoperative venous congestion in free transverse rectus abdominis musculocutaneous and deep inferior epigastric artery perforator flaps during breast reconstruction: A systematic review.

BACKGROUND: Even with patent deep inferior epigastric vein anastomoses, venous congestion can occur during free transverse rectus abdominis musculocutaneous (TRAM) or deep inferior epigastric artery perforator (DIEP) flap surgery and lead to flap compromise if not recognized and managed. OBJECTIVES: To identify the incidence of intraoperative venous congestion and describe the best available prevention and treatment methods. METHODS: Systematic electronic searches of the PubMed database including Medline were performed to identify studies published until 2014. The following keywords were used: "DIEP" or "free TRAM" and "venous insufficiency" or "venous congestion". Supplemental searches were conducted to identify referenced studies. Statistical analysis using the χ(2) test was performed. RESULTS: Nine studies representing 4747 free abdominal flaps cases were included and demonstrated an overall incidence of intraoperative venous congestion of 2.8%. The incidence in DIEP flaps (3.3%) was significantly higher than that in the free TRAM flaps (1.0%). All nine articles reported using the superficial inferior epigastric vein to treat venous insufficiency. CONCLUSION: The risk for developing intraoperative venous congestion following free abdominal flap breast reconstruction is influenced by inadequate perforator selection and persistent dominance in the superficial venous system. The solution is establishing another venous draining route using the superficial inferior epigastric vein.

HISTORIQUE: Malgré des anastomoses de la veine épigastrique inférieure profonde perméable, une congestion veineuse peut survenir pendant une chirurgie par lambeau libre musculocutané du grand droit transverse (MGDT) ou par lambeau perforant de l'artère épigastrique inférieure profonde (AEIP) et compromettre le lambeau si elle n'est pas décelée et prise en charge. OBJECTIFS: Déterminer l'incidence de congestion veineuse peropératoire et décrire les meilleures méthodes préventives et thérapeutiques en place. MÉTHODOLOGIE: Les chercheurs ont effectué des recherches virtuelles systématiques dans la base de données PubMed, y compris dans Medline, pour extraire les études publiées jusqu'en 2014. Ils ont utilisé les mots-clés suivants : DIEP ou free TRAM et venous insufficiency ou venous congestion. Ils ont mené d'autres recherches pour extraire les études des références. Ils ont effectué une analyse statistique au moyen du test du chi carré. RÉSULTATS: Neuf études représentant 4 747 cas de lambeaux abdominaux libres ont été incluses, pour démontrer une incidence globale de congestion veineuse peropératoire de 2,8 %. L'incidence de lambeaux AEIP (3,3 %) était considérablement plus élevée que celle de lambeaux libres MGDT (1,0 %). Dans les neuf articles, la veine épigastrique inférieure profonde était utilisée pour traiter l'insuffisance veineuse. CONCLUSION: Le risque de congestion veineuse peropératoire après une reconstruction mammaire par lambeaux abdominaux libres est influencé par une mauvaise sélection du lambeau perforant et une dominance persistante du système veineux superficiel. La solution consiste à établir une autre voie de drainage veineux au moyen de la veine épigastrique inférieure superficielle.