Domain generalization enables general cancer cell annotation in single-cell and spatial transcriptomics.

Single-cell and spatial transcriptome sequencing, two recently optimized transcriptome sequencing methods, are increasingly used to study cancer and related diseases. Cell annotation, particularly for malignant cell annotation, is essential and crucial for in-depth analyses in these studies. However, current algorithms lack accuracy and generalization, making it difficult to consistently and rapidly infer malignant cells from pan-cancer data. To address this issue, we present Cancer-Finder, a domain generalization-based deep-learning algorithm that can rapidly identify malignant cells in single-cell data with an average accuracy of 95.16%. More importantly, by replacing the single-cell training data with spatial transcriptomic datasets, Cancer-Finder can accurately identify malignant spots on spatial slides. Applying Cancer-Finder to 5 clear cell renal cell carcinoma spatial transcriptomic samples, Cancer-Finder demonstrates a good ability to identify malignant spots and identifies a gene signature consisting of 10 genes that are significantly co-localized and enriched at the tumor-normal interface and have a strong correlation with the prognosis of clear cell renal cell carcinoma patients. In conclusion, Cancer-Finder is an efficient and extensible tool for malignant cell annotation.

Endolymphatic sac tumor misdiagnosed as metastatic renal cell carcinoma: Pitfalls in morphology and immunohistochemistry.

Endolymphatic sac tumor (ELST) is a rare disease that originates from the endolymphatic sac system of the inner ear. Being a low-grade malignant tumor, ELST has a mild morphology and is characterized by a slow but aggressive growth. Most clinicians and pathologists are unfamiliar with this disease. ELST can be misdiagnosed as metastatic renal cancer because of the similarity in morphology and expression of nephrogenic markers such as PAX8. The presented case of a 27-year-old man revealed that observing the characteristic location and confirming the absence of renal neoplasm to rule out the possibility of metastasis are critical for obtaining an accurate final diagnosis.

Clear cell renal cell carcinoma with syncytial giant cells: Not that rare.

Syncytial giant cells (SGCs) are neoplastic giant cells of epithelial origin. The nuclear morphology of SGCs is uniform and similar to those of adjacent mononuclear tumor cells. Clear cell renal cell carcinoma (ccRCC) with SGCs is a rare microscopic morphology. In this study, the clinical and pathological data of 16 ccRCC cases with SGCs were retrospectively reviewed. The incidence of SGCs in pathological stages pT3 and above (12.1%, 8/66) was significantly higher than that in pT1 and pT2 (2.6%, 8/306) (P = 0.002). The incidence of SGCs in the WHO/ISUP nuclear grade 3 or 4 ccRCC (12.4%, 14/113) was significantly higher than that in grade 1 or 2 (0.8%, 2/259) (P < 0.001). Two forms of SGCs were observed, some exhibited nuclear pyknosis and degeneration. Of the 16 cases, eight cases were accompanied by necrosis and seven cases had lymphovascular invasion. Both SGCs and mononuclear tumor cells were positive for ccRCC markers (PAX8, CAIX, CD10 and Vimentin). None of the SGC nuclei were positive for Ki-67. Follow-up information was available on 14 patients, with a median follow-up time of 27.5 months. Ten patients were alive without disease, three were alive with metastatic disease, and one patient died 10 months after surgery. These findings indicated that SGCs are not rare, especially in ccRCC with high nuclear grade and pathological stage, and often co-exist with other adverse prognostic features. SGCs may be senescent tumor cells, the presence of SGCs should not be considered as Fuhrman and WHO/ISUP nuclear grading 4.

Dynamic RBM47 ISGylation confers broad immunoprotection against lung injury and tumorigenesis via TSC22D3 downregulation.

ISGylation is a well-established antiviral mechanism, but its specific function in immune and tissue homeostasis regulation remains elusive. Here, we reveal that the RNA-binding protein RBM47 undergoes phosphorylation-dependent ISGylation at lysine 329 to regulate immune activation and maintain lung homeostasis. K329R knockin (KI) mice with defective RBM47-ISGylation display heightened susceptibility to LPS-induced acute lung injury and lung tumorigenesis, accompanied with multifaceted immunosuppression characterized by elevated pro-inflammatory factors, reduced IFNs/related chemokines, increased myeloid-derived suppressor cells, and impaired tertiary lymphoid structures. Mechanistically, RBM47-ISGylation regulation of the expression of TSC22D3 mRNA, a glucocorticoid-inducible transcription factor, partially accounts for the effects of RBM47-ISGylation deficiency due to its broad immunosuppressive activity. We further demonstrate the direct inhibitory effect of RBM47-ISGylation on TSC22D3 expression in human cells using a nanobody-targeted E3 ligase to induce site-specific ISGylation. Furthermore, epinephrine-induced S309 phosphorylation primes RBM47-ISGylation, with epinephrine treatment exacerbating dysregulated cytokine expression and ALI induction in K329R KI mice. Our findings provide mechanistic insights into the dynamic regulation of RBM47-ISGylation in supporting immune activation and maintaining lung homeostasis.

Male-Biased Gut Microbiome and Metabolites Aggravate Colorectal Cancer Development.

Men demonstrate higher incidence and mortality rates of colorectal cancer (CRC) than women. This study aims to explain the potential causes of such sexual dimorphism in CRC from the perspective of sex-biased gut microbiota and metabolites. The results show that sexual dimorphism in colorectal tumorigenesis is observed in both ApcMin/ + mice and azoxymethane (AOM)/dextran sulfate sodium (DSS)-treated mice with male mice have significantly larger and more tumors, accompanied by more impaired gut barrier function. Moreover, pseudo-germ mice receiving fecal samples from male mice or patients show more severe intestinal barrier damage and higher level of inflammation. A significant change in gut microbiota composition is found with increased pathogenic bacteria Akkermansia muciniphila and deplets probiotic Parabacteroides goldsteinii in both male mice and pseudo-germ mice receiving fecal sample from male mice. Sex-biased gut metabolites in pseudo-germ mice receiving fecal sample from CRC patients or CRC mice contribute to sex dimorphism in CRC tumorigenesis through glycerophospholipids metabolism pathway. Sexual dimorphism in tumorigenesis of CRC mouse models. In conclusion, the sex-biased gut microbiome and metabolites contribute to sexual dimorphism in CRC. Modulating sex-biased gut microbiota and metabolites could be a potential sex-targeting therapeutic strategy of CRC.

Primary angiomatoid fibrous histiocytoma of the mandible with EWSR1-ATF1 fusion in an adult patient: case report and review of literature.

OBJECTIVE: We report our diagnosis of a rare case of primary angiomatoid fibrous histiocytoma in the mandible of a 42-year-old male using next-generation sequencing to detect disease-specific EWSR1-ATF1 fusion. STUDY DESIGN: After the initial cone beam computerized tomography scan and reconstruction, we performed immunohistochemical staining and fluorescence in situ hybridization analysis on tissue samples to detect EWSR1 gene rearrangement. For the final diagnosis, we performed next-generation sequencing to detect disease-specific EWSR1-ATF1 fusion. RESULTS: FISH analysis showed approximately 55% of tumor cells with mostly isolated red signals, as well as several split red-green signals, indicating the presence of EWSR1 gene rearrangement. Next-generation sequencing analysis identified an EWSR1 exon9-ATF1 exon4 fusion, a diagnostic biomarker of angiomatoid fibrous histiocytoma (AFH). Based on the findings, we diagnosed primary AFH derived from the mandible. CONCLUSIONS: Next-generation sequencing is a powerful methodology for detecting disease-specific EWSR1-ATF1 fusion and diagnosing primary angiomatoid fibrous histiocytoma.

Loss of renal tubular G9a benefits acute kidney injury by lowering focal lipid accumulation via CES1.

Surgery-induced renal ischemia and reperfusion (I/R) injury and nephrotoxic drugs like cisplatin can cause acute kidney injury (AKI), for which there is no effective therapy. Lipid accumulation is evident following AKI in renal tubules although the mechanisms and pathological effects are unclear. Here, we report that Ehmt2-encoded histone methyltransferase G9a is upregulated in patients and mouse kidneys after AKI. Renal tubular specific knockout of G9a (Ehmt2Ksp ) or pharmacological inhibition of G9a alleviates lipid accumulation associated with AKI. Mechanistically, G9a suppresses transcription of the lipolytic enzyme Ces1; moreover, G9a and farnesoid X receptor (FXR) competitively bind to the same promoter regions of Ces1. Ces1 is consistently observed to be downregulated in the kidney of AKI patients. Pharmacological inhibition of Ces1 increases lipid accumulation, exacerbates renal I/R-injury and eliminates the beneficial effects on AKI observed in Ehmt2Ksp mice. Furthermore, lipid-lowering atorvastatin and an FXR agonist alleviate AKI by activating Ces1 and reducing renal lipid accumulation. Together, our results reveal a G9a/FXR-Ces1 axis that affects the AKI outcome via regulating renal lipid accumulation.

Tumor-infiltrating lymphocytes status, programmed death-ligand 1 expression, and clinicopathological features of 41 cases of pure apocrine carcinoma of the breast: a retrospective study based on clinical pathological analysis and different immune statuses.

Background: Pure apocrine carcinoma (AC) of the breast can be divided into human epidermal growth factor receptor-2 (HER2)-positive and triple-negative apocrine carcinoma (TNAC). Some studies showed that triple negative breast cancer with low tumor-infiltrating lymphocytes (TILs) and high programmed death-ligand 1 (PD-L1) status may be a therapeutic target for immune checkpoint inhibitors. However, the clinicopathological features of different HER2 expression, TILs status and PD-L1 expression in AC are not clear. Therefore, we investigate the status of TILs and PD-L1, as well as the clinicopathological features of pure apocrine carcinoma of the breast. Methods: We retrospectively analyzed the clinicopathological data, and prognosis of 41 cases of pure apocrine carcinoma of the breast that underwent surgical resection from January 2014 to November 2020. TILs were evaluated. Immunohistochemistry (IHC) staining was applied to detect PD-L1 protein expression in 14 of these samples from January 2019 to November 2020. The expression and correlation of HER2, TILs, PD-L1 and clinicopathological features and prognoses were analyzed. Results: A total of 80.5% (33/41) of patients had TILs <50%, and 19.5% (8/41) had TILs ≥50%. The expression of TILs and the Ki-67 proliferation index were significantly higher in the HER2-positive group (41.5%, 17/41) compared to the HER2-negative group (58.5%, 24/41) (P<0.05). Approximately 52.9% (9/17) of HER2-positive patients treated with Trastuzumab targeted therapy, overall survival was higher in HER2-positive patients than in HER2-negative patients (P=0.211). The PD-L1 positivity rate was 50% (7/14) in the 14 pure apocrine carcinoma of the breast samples, and 66.7% (4/6) and 37.5% (3/8) in the HER2-negative and HER2-positive groups, respectively, with no significant difference (P=0.592). Among these 14 cases, two samples had TILs ≥50%, both of which were positive for PD-L1 and Ki67 >20%; and 12 cases had TILs <50%, of which 41.7% (5/12) were PD-L1-positive and 58.3% (7/12) were PD-L1-negative. All 14 cases with PD-L1-negative had TILs <50%. There was no significant difference in overall survival between TILs and Ki67 co-expression (P=0.452). Conclusions: Pure AC HER2-positive patients have higher levels of TILs and Ki67, HER2 negative and TILs ≥50% patients may have higher PD-L1 expression, which may be helpful for screening patients with different immune statuses to guide effective clinical treatment combinations.

Mecp2 protects kidney from ischemia-reperfusion injury through transcriptional repressing IL-6/STAT3 signaling.

Rationale: Ischemia-reperfusion (IR) induced acute kidney injury (AKI) causes serious clinical problems associated with high morbidity and mortality. Mecp2 is a methyl-CpG binding protein, its mutation or deletion causes a neurodevelopment disease called Rett syndrome. Notably, some Rett syndrome patients present urological dysfunctions. It remains unclear whether and how Mecp2 affects AKI. Methods: Renal tubular cell specific Mecp2 deletion mice challenged with IR injury were used to investigate the effects of Mecp2 on renal tubular damage, function, cell death, fibrosis and inflammation. Cultured renal epithelial cell lines were transfected with wildtype or different domain-deletion mutants of Mecp2 to study the effects of Mecp2 on Il-6/STAT3 signaling. Results: Our results indicated rapidly upregulated Mecp2 upon acute in vivo and in vitro renal injury. Notably, increased tubular MeCP2 staining was also found in the renal sections of AKI patients. Furthermore, ablation of Mecp2 aggravated renal injury, and promoted renal cell death, inflammation, and fibrosis. Mechanistically, through its transcriptional repression domain, Mecp2 bound to the promoter of proinflammatory cytokine Il-6 to negatively regulate its expression, thus inhibiting STAT3 activation. Conclusions: A novel protective role of Mecp2 against AKI via repressing the Il-6/STAT3 axis was suggested.

Identification of clinical and molecular features of recurrent serous borderline ovarian tumour.

Background: Serous borderline ovarian tumour (SBOT) is the most common type of BOT. Fertility sparing surgery (FSS) is an option for patients with SBOT, though it may increase the risk of recurrence. The clinical and molecular features of its recurrence are important and need to be investigated in detail. Methods: An internal cohort of 319 patients with SBOT was collected from Aug 1, 2009 to July 31, 2019 from the Obstetrics and Gynecology Hospital of Fudan University in China. An external cohort of 100 patients with SBOT was collected from Aug 1, 2009 to Nov 30, 2019 from the Shandong Provincial Hospital in China. The risk factors for the recurrence were identified by multivariate cox analysis. Several computational methods were tested to establish a prediction tool for recurrence. Whole genome sequencing, RNA-seq, metabolomics and lipidomics were used to understand the molecular characteristics of the recurrence of SBOT. Findings: Five factors were significantly correlated with SBOT recurrence in a Han population: micropapillary pattern, advanced stage, FSS, microinvasion, and lymph node invasion. A random forest-based online recurrence prediction tool was established and validated using an internal cohort and an independent external cohort for patients with SBOT. The multi-omics analysis on the original SBOT samples revealed that recurrence is related to metabolic regulation of immunological suppression. Interpretation: Our study identified several important clinical and molecular features of recurrent SBOT. The prediction tool we established could help physicians to estimate the prognosis of patients with SBOT. These findings will contribute to the development of personalised and targeted therapies to improve prognosis. Funding: JL was funded by MOST 2020YFA0803600, 2018YFA0801300, NSFC 32071138, and SKLGE-2118 to Jin Li; JY was funded by the Initial Project for Young and Middle-aged Medical Talents of Wuhan City, Hubei Province ([2014] 41); HH was funded by MOST 2019YFA0801900 and 2020YF1402600 to He Huang; JS was funded by NSFC 22,104,080; CG was funded by Natural Science Foundation of Shanghai 20ZR1408800 and NSFC82171633; BL was funded by Natural Science Foundation of Shanghai 19ZR1406800.

Gene Expression Profiling for Differential Diagnosis of Liver Metastases: A Multicenter, Retrospective Cohort Study.

BACKGROUND: Liver metastases (LM) are the most common tumors encountered in the liver and continue to be a significant cause of morbidity and mortality. Identification of the primary tumor of any LM is crucial for the implementation of effective and tailored treatment approaches, which still represents a difficult problem in clinical practice. METHODS: The resection or biopsy specimens and associated clinicopathologic data were archived from seven independent centers between January 2017 and December 2020. The primary tumor sites of liver tumors were verified through evaluation of available medical records, pathological and imaging information. The performance of a 90-gene expression assay for the determination of the site of tumor origin was assessed. RESULT: A total of 130 LM covering 15 tumor types and 16 primary liver tumor specimens that met all quality control criteria were analyzed by the 90-gene expression assay. Among 130 LM cases, tumors were most frequently located in the colorectum, ovary and breast. Overall, the analysis of the 90-gene signature showed 93.1% and 100% agreement rates with the reference diagnosis in LM and primary liver tumor, respectively. For the common primary tumor types, the concordance rate was 100%, 95.7%, 100%, 93.8%, 87.5% for classifying the LM from the ovary, colorectum, breast, neuroendocrine, and pancreas, respectively. CONCLUSION: The overall accuracy of 93.8% demonstrates encouraging performance of the 90-gene expression assay in identifying the primary sites of liver tumors. Future incorporation of the 90-gene expression assay in clinical diagnosis will aid oncologists in applying precise treatments, leading to improved care and outcomes for LM patients.

MET Amplification Attenuates Lung Tumor Response to Immunotherapy by Inhibiting STING.

Immune checkpoint blockade (ICB) has revolutionized cancer therapy. However, the response of patients to ICB is difficult to predict. Here, we examined 81 patients with lung cancer under ICB treatment and found that patients with MET amplification were resistant to ICB and had a poor progression-free survival. Tumors with MET amplifications had significantly decreased STING levels and antitumor T-cell infiltration. Furthermore, we performed deep single-cell RNA sequencing on more than 20,000 single immune cells and identified an immunosuppressive signature with increased subsets of XIST- and CD96-positive exhausted natural killer (NK) cells and decreased CD8+ T-cell and NK-cell populations in patients with MET amplification. Mechanistically, we found that oncogenic MET signaling induces phosphorylation of UPF1 and downregulates tumor cell STING expression via modulation of the 3'-UTR length of STING by UPF1. Decreased efficiency of ICB by MET amplification can be overcome by inhibiting MET. SIGNIFICANCE: We suggest that the combination of MET inhibitor together with ICB will overcome ICB resistance induced by MET amplification. Our report reveals much-needed information that will benefit the treatment of patients with primary MET amplification or EGFR-tyrosine kinase inhibitor resistant-related MET amplification.This article is highlighted in the In This Issue feature, p. 2659.

A fast and effective detection framework for whole-slide histopathology image analysis.

Pathologists generally pan, focus, zoom and scan tissue biopsies either under microscopes or on digital images for diagnosis. With the rapid development of whole-slide digital scanners for histopathology, computer-assisted digital pathology image analysis has attracted increasing clinical attention. Thus, the working style of pathologists is also beginning to change. Computer-assisted image analysis systems have been developed to help pathologists perform basic examinations. This paper presents a novel lightweight detection framework for automatic tumor detection in whole-slide histopathology images. We develop the Double Magnification Combination (DMC) classifier, which is a modified DenseNet-40 to make patch-level predictions with only 0.3 million parameters. To improve the detection performance of multiple instances, we propose an improved adaptive sampling method with superpixel segmentation and introduce a new heuristic factor, local sampling density, as the convergence condition of iterations. In postprocessing, we use a CNN model with 4 convolutional layers to regulate the patch-level predictions based on the predictions of adjacent sampling points and use linear interpolation to generate a tumor probability heatmap. The entire framework was trained and validated using the dataset from the Camelyon16 Grand Challenge and Hubei Cancer Hospital. In our experiments, the average AUC was 0.95 in the test set for pixel-level detection.

Direct Evidence of Active SARS-CoV-2 Replication in the Intestine.

BACKGROUND: Currently, there is no direct evidence to prove the active replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the intestinal tract and relevant pathological changes in the colon and rectum. We investigated the presence of virions and pathological changes in surgical rectal tissues of a patient with clinically confirmed coronavirus disease 2019 (COVID-19) with rectal adenocarcinoma. METHODS: The clinical data were collected during hospitalization and follow-up of this patient. Quantitative reverse transcriptase-polymerasechain reaction (RT-PCR) was performed on the rectal tissue specimens obtained from surgical resection, succus entericus and intestinal mucosa of ileostomy, and rectal mucosa during follow-up after recovery. Ultrathin sections of surgical samples were observed for SARS-CoV-2 virions using electron microscopy. Histopathological examination was performed using hematoxylin-eosin stain. Immunohistochemical analysis and immunofluorescence were carried out on rectal tissues to evaluate the distribution of SARS-CoV-2 antigen and immune cell infiltrations. RESULTS: The patient had fever and cough on day 3 postoperatively, was diagnosed with COVID-19 on day 7, and was discharged from the hospital on day 41. RNA of SARS-CoV-2 was detected in surgically resected rectal specimens but not in samples collected 37 days after discharge. Notably, coincident with rectal tissues of surgical specimens testing nucleic acid positive for SARS-CoV-2, typical coronavirus virions in rectal tissue were observed under electron microscopy. Moreover, abundant lymphocytes and macrophages (some were SARS-CoV-2 positive) infiltrating the lamina propria were found with no significant mucosal damage. CONCLUSIONS: We first report the direct evidence of active SARS-CoV-2 replication in a patient's rectum during the incubation period, which might explain SARS-CoV-2 fecal-oral transmission.

Clinicopathological and genetic characteristics of diffuse large B-cell lymphoma of the oropharyngeal and maxillofacial region.

OBJECTIVES: The study was aimed to analyze the clinicopathological and molecular pathological features of diffuse large B-cell lymphoma (DLBCL) in the oropharyngeal and maxillofacial region. SUBJECTS AND METHODS: A retrospective review was performed with 36 patients who were diagnosed with primary DLBCL of the oropharyngeal and maxillofacial region from 2009 to 2017 in the Department of Pathology at the Hospital of Stomatology, Wuhan University. Immunohistochemistry and fluorescence in situ hybridization were performed. RESULTS: Gene rearrangements of BCL2, BCL6, and MYC were observed in 5.6%, 33.3%, and 22.2%, respectively, including two double-hit and one triple-hit DLBCL (8.3%). There was a significant correlation between MYC protein expression and gene translocation (rs = 0.679, p < .001). However, 25% of cases with MYC rearrangement showed low MYC protein expression. In univariate analysis, MYC protein expression, BCL2 rearrangement, MYC rearrangement, and double/triple-hit DLBCL were associated with shorter overall survival, whereas only MYC protein expression was an independent prognostic value in multivariate model. CONCLUSIONS: MYC protein expression was an essential prognostic marker of DLBCL in the oropharyngeal and maxillofacial region. Notably, immunohistochemical staining of MYC, BCL2, and BCL6 could not predict their gene rearrangements, although MYC protein expression was correlated with gene translocation.

Multigenerational maternal obesity increases the incidence of HCC in offspring via miR-27a-3p.

BACKGROUND & AIMS: Obesity is an independent risk factor for malignancies, including hepatocellular carcinoma (HCC). However, it remains unknown whether maternal obesity affects the incidence of HCC in offspring. Thus, we aimed to investigate this association and its underlying mechanisms. METHODS: Diethylnitrosamine (DEN) was used to induce HCC in a high-fat diet (HFD)-induced multigenerational obesity model. RNA-sequencing was performed to identify the genes and microRNAs (miRNAs) that were altered over generations. The role of the miR-27a-3p-Acsl1/Aldh2 axis in HCC was evaluated in cell lines and HCC-bearing nude mice, and its intergenerational impact was studied in pregnant mice and their offspring. RESULTS: Under HFD stress, maternal obesity caused susceptibility of offspring to DEN-induced HCC, and such susceptibility was cumulative over generations. We identified that Acsl1 and Aldh2, direct targets of miR-27a-3p, were gradually changed over generations. Under hyperlipidemic conditions, downregulation of Acsl1 and Aldh2 increased cell proliferation (in vitro) or tumor growth (in vivo) in synergy. Intratumor injection of an miR-27a-3p agomir exacerbated tumor growth by downregulating Acsl1 and Aldh2; while intratumor injection of an miR-27a-3p antagomir had the opposite effect. Moreover, serum miR-27a-3p levels gradually increased in the HFD-fed maternal lineage over generations. Injecting pregnant mice with an miR-27a-3p agomir not only upregulated hepatic miR-27a-3p and downregulated Acsl1/Aldh2 in offspring (fetus, young and adult stages), but also exacerbated HCC development in DEN-treated offspring. In human HCC, upregulated miR-27a-3p and downregulated Acsl1/Aldh2 were negatively correlated with survival on TCGA analysis; while, hepatic miR-27a-3p was negatively correlated with Acsl1/Aldh2 expression in tumor/non-tumor tissues from fatty/non-fatty livers. CONCLUSIONS: Maternal obesity plays a role in regulating cumulative susceptibility to HCC development in offspring over multiple generations through the miR-27a-3p-Acsl1/Aldh2 axis. LAY SUMMARY: It is not currently known how maternal obesity affects the incidence of liver cancer in offspring. In this study, we identified a microRNA (miR-27a-3p) that was upregulated in obese mothers and could be passed on to their offspring. This microRNA enhanced the risk of liver cancer in offspring by regulating 2 genes (Acsl1 and Aldh2). This mechanism could be a future therapeutic target.

Comprehensive mutanome analysis of Lewis lung cancer reveals immunogenic neoantigens for therapeutic vaccines.

Personalized neoantigen vaccines are capable of eliciting vigorous T-cell responses and have been demonstrated to achieve striking therapeutic effects against cancer. Here we performed comprehensive mutanome analysis of the mouse Lewis lung cancer cells to identify tumor neoantigens followed by prediction of their MHC affinity and immunogenicity. We adopted a strategy that enables us to select neoantigens that were predicted to have high affinity to both MHC I and MHC II. Ten neoantigens were selected to synthesize peptide vaccines and tested in vivo for immunogenicity. Four neoantigen peptide vaccines were found to elicit robust immune reactivity and were further examined for tumor inhibition in mice with xenografted LLC tumors. Two neoantigen peptide vaccines showed significant inhibition on tumor growth and prolonged the survival of tumor-bearing mice. Our studies explored the neoantigen peptide vaccines to treat lung cancer and provide rationale for the optimization of tumor neoantigen selection for therapeutic vaccines.

The anatomy and metabolome of the lymphatic system in the brain in health and disease.

Recent studies have demonstrated that the brain is equipped with a lymphatic drainage system that is actively involved in parenchymal waste clearance, brain homeostasis and immune regulation. However, the exact anatomic drainage routes of brain lymph fluid (BLF) remain elusive, hampering the physiological study and clinical application of this system. In this study, we systematically dissected the anatomy of the BLF pathways in a rat model. Moreover, we developed a protocol to collect BLF from the afferent lymphatic vessels of deep cervical lymph nodes (dcLNs) and cerebrospinal fluid (CSF) from the fourth ventricle. Nuclear magnetic resonance spectroscopy showed that BLF contains more metabolites than CSF, suggesting that BLF might be a more sensitive indicator of brain dynamics under physiological and pathological conditions. Finally, we identified several metabolites as potential diagnostic biomarkers for glioma, Parkinson's disease and CNS infectious diseases. Together, these data may provide insight into the physiology of the lymphatic system in the brain and into the clinical diagnosis of CNS disorders.

DBS: a fast and informative segmentation algorithm for DNA copy number analysis.

BACKGROUND: Genome-wide DNA copy number changes are the hallmark events in the initiation and progression of cancers. Quantitative analysis of somatic copy number alterations (CNAs) has broad applications in cancer research. With the increasing capacity of high-throughput sequencing technologies, fast and efficient segmentation algorithms are required when characterizing high density CNAs data. RESULTS: A fast and informative segmentation algorithm, DBS (Deviation Binary Segmentation), is developed and discussed. The DBS method is based on the least absolute error principles and is inspired by the segmentation method rooted in the circular binary segmentation procedure. DBS uses point-by-point model calculation to ensure the accuracy of segmentation and combines a binary search algorithm with heuristics derived from the Central Limit Theorem. The DBS algorithm is very efficient requiring a computational complexity of O(n*log n), and is faster than its predecessors. Moreover, DBS measures the change-point amplitude of mean values of two adjacent segments at a breakpoint, where the significant degree of change-point amplitude is determined by the weighted average deviation at breakpoints. Accordingly, using the constructed binary tree of significant degree, DBS informs whether the results of segmentation are over- or under-segmented. CONCLUSION: DBS is implemented in a platform-independent and open-source Java application (ToolSeg), including a graphical user interface and simulation data generation, as well as various segmentation methods in the native Java language.

Mycobacterium tuberculosis Erdman infection of cynomolgus macaques of Chinese origin.

BACKGROUND: Nearly one-third of the population worldwide is estimated to have latent tuberculosis infection (LTBI), which represents a vast reservoir for a constant source of tuberculosis (TB) transmission. It has been suggested that cynomolgus macaques are less susceptible to Mycobacterium tuberculosis (M.tb) infection than rhesus macaques, we examined M.tb infection of Chinese cynomolgus macaques. METHODS: Eight Chinese cynomolgus macaques were infected with M.tb Erdman strain with a small [25 colony forming unit (CFU)] or large dose (500 CFU) via bronchoscopy. The infected animals were monitored for symptoms and examined by chest X-ray, computed tomography (CT), tuberculin skin test (TST), and enzyme-linked immunospot (ELISPOT). RESULTS: Based on TST conversion and the specific immune responses to M.tb antigens, all animals were successfully infected. Half of the animals developed active infection and died within 15 months postinfection. The other four animals were grouped with latent M.tb infection because of positive TST but few clinical signs and pathological changes of TB during the course of this study. Interestingly, a challenge with a large dose of M.tb also induced latent infection. Similar to the changes that occur with human TB patients, the animals with active infection exhibited weight loss, cough and typical TB pathological changes, including caseous granulomas, cavities, consolidation, lipid pneumonia, pleural effusion, lymphadenopathy and bacterial burden in lungs and other organs. CONCLUSIONS: The low dose of M.tb was sufficient to cause both active and latent M.tb infection in cynomolgus macaques of Chinese origin.