Therapeutic single-cell landscape: methotrexate exacerbates interstitial lung disease by compromising the stemness of alveolar epithelial cells under systemic inflammation.

BACKGROUND: Interstitial lung disease (ILD) poses a serious threat in patients with rheumatoid arthritis (RA). However, the impact of cornerstone drugs, including methotrexate (MTX) and TNF inhibitor, on RA-associated ILD (RA-ILD) remains controversial. METHODS: Using an SKG mouse model and single-cell transcriptomics, we investigated the effects of MTX and TNF blockade on ILD. FINDINGS: Our study revealed that MTX exacerbates pulmonary inflammation by promoting immune cell infiltration, Th17 activation, and fibrosis. In contrast, TNF inhibitor ameliorates these features and inhibits ILD progression. Analysis of data from a human RA-ILD cohort revealed that patients with ILD progression had persistently higher systemic inflammation than those without progression, particularly among the subgroup undergoing MTX treatment. INTERPRETATION: These findings highlight the need for personalized therapeutic approaches in RA-ILD, given the divergent outcomes of MTX and TNF inhibitor. FUNDING: This work was funded by GENINUS Inc., and the National Research Foundation of Korea, and Seoul National University Hospital.

Chemoembolization as first-line treatment for hepatocellular carcinoma invading segmental portal vein with tumour burden limited to a monosegmental level.

OBJECTIVES: To evaluate the safety and effectiveness of chemoembolization for hepatocellular carcinoma (HCC) with portal vein tumour thrombosis (PVTT) confined to a monosegment of the liver. METHODS: A total of 192 treatment-naive patients who received chemoembolization between March 2008 and January 2023 as a first-line treatment for locally advanced HCC with PVTT limited to a monosegment were retrospectively analysed. Overall survival (OS) and the identification of pretreatment risk factors related to OS were investigated using Cox regression analysis. Complications, radiologic tumour response, and progression-free survival (PFS) following chemoembolization were investigated. RESULTS: After chemoembolization, the 1-, 3-, and 5-year OS rates were 86%, 48%, and 39%, respectively, and the median OS was 33 months. Multivariable analyses revealed four significant pretreatment risk factors: infiltrative HCC (P = .02; HR, 1.60), beyond the up-to-11 criteria (P = .002; HR, 2.26), Child-Pugh class B (P = .01; HR, 2.35), and serum AFP ≥400 ng/mL (P = .01; HR, 1.69). The major complication rate was 5%. Of the 192 patients, 1 month after chemoembolization, 35% achieved a complete response, 47% achieved a partial response, 11% had stable disease, and 7% showed progressive disease. The median PFS after chemoembolization was 12 months. CONCLUSIONS: Chemoembolization shows high safety and efficiency, and contributes to improved survival in patients with HCC with PVTT confined to a monosegment. Four risk factors were found to be significantly associated with improved survival rates after chemoembolization in patients with HCC with PVTT confined to a monosegment. ADVANCES IN KNOWLEDGE: (1) Although systemic therapy with a combination of atezolizumab and bevacizumab (Atezo-Bev) is recommended as the first-line treatment when HCC invades the portal vein, chemoembolization is not infrequently performed in HCC cases in which tumour burden is limited. (2) Our study cohort (n=192) had a median OS of 33 months and a 5% major complication rate following chemoembolization, findings in the range of candidates typically accepted as ideal for chemoembolization. Thus, patients with HCC with PVTT confined to a monosegment may be good candidates for first-line chemoembolization.

Genomic hypomethylation in cell-free DNA predicts responses to checkpoint blockade in lung and breast cancer.

Genomic hypomethylation has recently been identified as a determinant of therapeutic responses to immune checkpoint blockade (ICB). However, it remains unclear whether this approach can be applied to cell-free DNA (cfDNA) and whether it can address the issue of low tumor purity encountered in tissue-based methylation profiling. In this study, we developed an assay named iMethyl, designed to estimate the genomic hypomethylation status from cfDNA. This was achieved through deep targeted sequencing of young LINE-1 elements with > 400,000 reads per sample. iMethyl was applied to a total of 653 ICB samples encompassing lung cancer (cfDNA n = 167; tissue n = 137; cfDNA early during treatment n = 40), breast cancer (cfDNA n = 91; tissue n = 50; PBMC n = 50; cfDNA at progression n = 44), and ovarian cancer (tissue n = 74). iMethyl-liquid predicted ICB responses accurately regardless of the tumor purity of tissue samples. iMethyl-liquid was also able to monitor therapeutic responses early during treatment (3 or 6 weeks after initiation of ICB) and detect progressive hypomethylation accompanying tumor progression. iMethyl-tissue had better predictive power than tumor mutation burden and PD-L1 expression. In conclusion, our iMethyl-liquid method allows for reliable noninvasive prediction, early evaluation, and monitoring of clinical responses to ICB therapy.

Risk of venous thromboembolism in Korean patients with rheumatoid arthritis treated with Janus kinase inhibitors: A nationwide population-based study.

OBJECTIVE: There was a safety concern about an increased risk of thromboembolic events in patients with rheumatoid arthritis (RA) treated with Janus kinase inhibitors (JAKis). This study aimed to determine the risk of venous thromboembolism (VTE) in Korean patients with RA treated with JAKis compared with tumour necrosis factor (TNF) inhibitors. METHODS: Using the National Health Insurance Service database between 2015 and 2019, patients with prevalent RA who started JAKi or TNF inhibitor were selected as the study population. All participants were naïve to targeted therapy. Patients that had experienced any VTE event or used anticoagulant agents within 30 days were excluded. Demographic and clinical characteristics were all balanced by stabilised inverse probability of treatment weighting (sIPTW) using propensity score. The Cox proportional hazard model considering death as a competing risk was used to evaluate the risk of VTE in JAKi users compared with TNF inhibitor users. RESULTS: A total of 4,178 patients were included: 871 JAKi users and 3,307 TNF inhibitor users were followed up for 1,029.2 person-years (PYs) and 5,940.3 PYs, respectively. With a balanced sample after sIPTW, the incidence rates (IR) of VTE were 0.06 per 100 PYs (95% confidence interval [CI] 0.00-1.23) in JAKi users and 0.38 per 100 PYs (95% CI 0.25-0.58) in TNF inhibitor users. The hazard ratio was 0.18 (95% CI 0.01-3.47) after adjusting for unbalanced variables after performing sIPTW. CONCLUSION: There is no increased risk of VTE in RA patients treated with JAKis compared with TNF inhibitors in Korea.

Widespread somatic L1 retrotransposition in normal colorectal epithelium.

Throughout an individual's lifetime, genomic alterations accumulate in somatic cells1-11. However, the mutational landscape induced by retrotransposition of long interspersed nuclear element-1 (L1), a widespread mobile element in the human genome12-14, is poorly understood in normal cells. Here we explored the whole-genome sequences of 899 single-cell clones established from three different cell types collected from 28 individuals. We identified 1,708 somatic L1 retrotransposition events that were enriched in colorectal epithelium and showed a positive relationship with age. Fingerprinting of source elements showed 34 retrotransposition-competent L1s. Multidimensional analysis demonstrated that (1) somatic L1 retrotranspositions occur from early embryogenesis at a substantial rate, (2) epigenetic on/off of a source element is preferentially determined in the early organogenesis stage, (3) retrotransposition-competent L1s with a lower population allele frequency have higher retrotransposition activity and (4) only a small fraction of L1 transcripts in the cytoplasm are finally retrotransposed in somatic cells. Analysis of matched cancers further suggested that somatic L1 retrotransposition rate is substantially increased during colorectal tumourigenesis. In summary, this study illustrates L1 retrotransposition-induced somatic mosaicism in normal cells and provides insights into the genomic and epigenomic regulation of transposable elements over the human lifetime.

Intravenous patient-controlled analgesia regimen in postoperative pain management following elective cesarean section: A single-center retrospective evaluation.

Intravenous patient-controlled analgesia (IV PCA; IVA) is the most widely used method for postoperative pain management. An appropriate IVA regimen is required, depending on the expected intensity of pain after surgery. This study expected that a decrease in the second prescription rate of IVA after elective cesarean section (CS) would help establish an appropriate regimen for the initial IVA. We retrospectively reviewed the records of 632 patients who were prescribed IVA after CS. We classified patients into phase 1 (basal rate 15.00 mcg/hours, bolus dose 15.00 mcg, total volume 100 mL) and phase 2 (basal rate 31.25 mcg/hours, bolus dose 31.25 mcg, nefopam 60 mg, paracetamol 3 g, total volume 160 mL) according to the IVA regimen, and patients in phase 2 were classified into the basal 15 group and basal 30 group according to the basal rate of IVA. We compared the rates of second prescription, drug removal, and side effects of IVA between the 2 phases and the 1 group. We analyzed the data of 631 eligible patients. The second prescription rate of IVA in phase 2 was 3.77%, a significant decrease compared to that in phase 1 (27.48%); however, the incidence of complications in phase 2 was 6.92%, a significant increase compared to that in phase 1 (0.96%). Within phase 2, in the basal 30 group, the basal rate was almost double that in the basal 15 group. However, there were no significant differences in the rate of second prescription, removed drug IVA, or adverse events between the basal 15, and 30 groups. In the case of CS, which has a high degree of postoperative pain, it is beneficial to control acute pain by properly setting the regimen of the initial IVA with a basal rate infusion to nullify a second prescription.

DeepNeo: a webserver for predicting immunogenic neoantigens.

Non-self epitopes, whether originated from foreign substances or somatic mutations, trigger immune responses when presented by major histocompatibility complex (MHC) molecules and recognized by T cells. Identification of immunogenically active neoepitopes has significant implications in cancer and virus medicine. However, current methods are mostly limited to predicting physical binding of mutant peptides and MHCs. We previously developed a deep-learning based model, DeepNeo, to identify immunogenic neoepitopes by capturing the structural properties of peptide-MHC pairs with T cell reactivity. Here, we upgraded our DeepNeo model with up-to-date training data. The upgraded model (DeepNeo-v2) was improved in evaluation metrics and showed prediction score distribution that better fits known neoantigen behavior. The immunogenic neoantigen prediction can be conducted at https://deepneo.net.

Self-expandable metallic stents as a bridge to surgery in obstructive right- and left-sided colorectal cancer: a multicenter cohort study.

The insertion of a self-expandable metal stent (SEMS) has been proposed as an alternative to emergent surgery (ES) for obstructive colorectal cancer (CRC). We aimed to evaluate the perioperative and oncologic outcomes of SEMS as a bridge to surgery in obstructive CRC, as compared with ES. We retrospectively reviewed the medical records of patients who underwent curative resection of obstructive CRC at four Hallym University-affiliated hospitals between January 2010 and December 2019. All patients were analyzed overall colon, then according to the side of obstruction (overall, right or left). Of 167 patients, 52 patients underwent ES and 115 underwent SEMS insertion and surgery (SEMS group). The postoperative hospital stay and time to soft diet were shorter in the SEMS group than in the ES group for overall and both sided cancer. The SEMS group had lower rates of stoma formation and severe complications for overall and for left-sided cancer. The 5-year overall survival (P = 0.682) and disease-free survival (P = 0.233) rates were similar in both groups. SEMS insertion as a bridge to surgery was associated with faster recovery, a lower rate of stoma formation with similar oncologic outcomes to those of ES.

MHC II immunogenicity shapes the neoepitope landscape in human tumors.

Despite advances in predicting physical peptide-major histocompatibility complex I (pMHC I) binding, it remains challenging to identify functionally immunogenic neoepitopes, especially for MHC II. By using the results of >36,000 immunogenicity assay, we developed a method to identify pMHC whose structural alignment facilitates T cell reaction. Our method predicted neoepitopes for MHC II and MHC I that were responsive to checkpoint blockade when applied to >1,200 samples of various tumor types. To investigate selection by spontaneous immunity at the single epitope level, we analyzed the frequency spectrum of >25 million mutations in >9,000 treatment-naive tumors with >100 immune phenotypes. MHC II immunogenicity specifically lowered variant frequencies in tumors under high immune pressure, particularly with high TCR clonality and MHC II expression. A similar trend was shown for MHC I neoepitopes, but only in particular tissue types. In summary, we report immune selection imposed by MHC II-restricted natural or therapeutic T cell reactivity.

Association between malignancy risk and Janus kinase inhibitors versus tumour necrosis factor inhibitors in Korean patients with rheumatoid arthritis: a nationwide population-based study.

OBJECTIVE: To determine the risk of malignancy in Korean patients with rheumatoid arthritis (RA) receiving Janus kinase inhibitors (JAKis) compared with tumour necrosis factor inhibitors (TNFis). METHODS: A retrospective cohort of patients with RA initiating their first JAKi or TNFi was established using the Korean National Health Insurance database between 2015 and 2019. They were followed up from treatment initiation to the occurrence of malignancy, drug discontinuation, death or until December 2019. Baseline features of the patients were balanced through inverse probability of treatment weighting (IPTW) using a propensity score. A Cox proportional hazard model was established to estimate the HR for malignancy risk in JAKi users compared with TNFi users. RESULTS: A total of 4929 patients (1064 JAKi-treated and 3865 TNFi-treated patients) were included, and the observation periods were 1288.6 person-years (PYs) for JAKi users and 6823.8 PYs for TNFi users. The incidence rates of overall malignancy were 0.54 per 100 PYs (95% CI 0.26 to 1.14) in JAKi users and 0.85 per 100 PYs (95% CI 0.66 to 1.10) in TNFi users. In IPTW analysis with a balanced sample (4101 JAKi-treated and 5131 TNFi-treated patients), HR was 0.83 (95% CI 0.55 to 1.27) for overall malignancy: 0.77 (95% CI 0.50 to 1.19) for solid malignancy and 2.86 (95% CI 0.41 to 20.00) for haematological malignancy. CONCLUSION: Malignancy risk in Korean patients with RA was not increased with JAKi use compared with TNFi use.

Identification of Metabolic Signature Associated with Idiopathic Inflammatory Myopathy Reveals Polyamine Pathway Alteration in Muscle Tissue.

Idiopathic inflammatory myopathy (IIM) is hard to diagnose without a muscle biopsy. We aimed to identify a metabolite panel for IIM detection by metabolomics approach in serum samples and to explore the metabolomic signature in tissue samples from a mouse model. We obtained serum samples from IIM patients, ankylosing spondylitis (AS) patients, healthy volunteers and muscle tissue samples from IIM murine model. All samples were subjected to a targeted metabolomic approach with various statistical analyses on serum and tissue samples to identify metabolic alterations. Three machine learning methods, such as logistic regression (LR), support vector machine (SVM), and random forest (RF), were applied to build prediction models. A set of 7 predictive metabolites was calculated using backward stepwise selection, and the model was evaluated within 5-fold cross-validation by using three machine algorithms. The model produced an area under the receiver operating characteristic curve values of 0.955 (LR), 0.908 (RF) and 0.918 (SVM). A total of 68 metabolites were significantly changed in mouse tissue. Notably, the most influential pathways contributing to the inflammation of muscle were the polyamine pathway and the beta-alanine pathway. Our metabolomic approach offers the potential biomarkers of IIM and reveals pathologically relevant metabolic pathways that are associated with IIM.

Recurrence-Free Survival Outcomes Based on Novel Classification Combining Lymphovascular Invasion, Perineural Invasion, and T4 Status in Stage II-III Colon Cancer.

Background: T4 tumor, lymphovascular invasion (LVI) and perineural invasion (PNI) are regarded as one of risk factors and associated with poor outcomes in colorectal cancer. The relationship between these three combined risk factors and the prognosis for colon cancer is not yet clear. The purpose of this study was to evaluate the prognostic value of combining the risk factors T4 tumor, LVI, and PNI in stage II-III colon cancer. Methods: Between January 2011 and December 2019, we retrospectively reviewed the medical records of patients who underwent curative resection for stage II-III colon cancer at four Hallym University-affiliated hospitals. These patients are categorized into three groups based on T4, LVI and PNI: no-risk group (no risk factors), low-risk group (one risk factor), and high-risk group (two or more risk factors). Results: Of 1684 patients, the incidence of no-, low-, and high-risk group were 49.3%, 32.6%, 18.0%, respectively. The median follow-up period was 48.9 months, and the 5-year recurrence-free survival (RFS) rate decreased from 78.5% to 58.7% as the number of risk factors increased (P < 0.001). Cox's proportional hazard regression models showed that T4 (P < 0.001), LVI (P = 0.043), and PNI (P = 0.018) were independent prognostic factors for poor RFS. In subgroup analysis in stage II colon cancer, patients with one or more risk factors showed the better 5-year RFS rate when they received adjuvant chemotherapy than in those who did not (P < 0.001). Poor/mucinous differentiation, obstruction, and lymph-node positivity were independent predictors in the high risk group. Conclusion: The present study showed the histological combination of LVI, PNI, and T4 indicates a poor prognosis for RFS in patients with stage II-III colon cancer. Therefore, patients with one of these risk factors should be considered for chemotherapy and have close follow-up.

Erratum: Isolated Vestibular Syndrome With "Double-Panda" Sign in CNS Lymphoma.

This corrects the article on p. 111 in vol. 18, PMID: 35021288.

Clinical and oncologic outcomes of laparoscopic versus open surgery in elderly patients with colorectal cancer: a retrospective multicenter study.

BACKGROUND: Laparoscopic surgery is commonly used in elderly patients over 80 years old. The purpose of this study was to compare the perioperative and oncologic outcomes between laparoscopic surgery and open surgery in elderly patients with colorectal cancer. METHODS: We retrospectively analyzed the medical records of patients aged ≥ 80 years who underwent curative resection of colorectal cancer at six Hallym University-affiliated hospitals. The perioperative outcomes and oncologic outcomes were compared between laparoscopic and open surgery RESULTS: Of 294 elderly patients, 104 (35.3%) underwent open surgery and 190 (64.7%) underwent laparoscopic surgery. The postoperative hospital stay (P = 0.019) and time to soft diet (P = 0.009) were shorter in the laparoscopic group than in the open group. Postoperative complications were less frequent in the laparoscopic group than in the open group (P < 0.001), including wound infection (P = 0.005), ileus (P = 0.005), and pneumonia (P = 0.001). The 3-year overall survival (OS) (P = 0.982) and recurrence-free survival rates (RFS) (P = 0.532) were similar in both groups. In multivariable analyses, positive lymph node status was the only independent factor associated with OS (P = 0.019) and RFS (P = 0.012). Laparoscopic surgery was not associated with OS (P = 0.874) and RFS (P = 0.772). CONCLUSION: Laparoscopic surgery offers several perioperative advantages over open surgery and similar long-term oncological outcomes for elderly patients with colorectal cancer. Therefore, we suggest that laparoscopic surgery can be safely performed for the treatment of elderly patients (≥ 80 years old) with colorectal cancer.

Circulating mitochondrial N-formyl peptides contribute to secondary nosocomial infection in patients with septic shock.

Secondary infections typically worsen outcomes of patients recovering from septic shock. Neutrophil [polymorphonuclear leukocytes (PMNs)] migration to secondarily inoculated sites may play a key role in inhibiting progression from local bacterial inoculation to secondary infection. Mitochondrial N-formyl peptide (mtFP) occupancy of formyl peptide receptor-1 (FPR1) has been shown to suppress PMN chemotaxis. Therefore, we studied the association between circulating mtFPs and the development of secondary infection in patients with septic shock. We collected clinical data and plasma samples from patients with septic shock admitted to the intensive care unit for longer than 72 h. Impacts of circulating nicotinamide adenine dinucleotide dehydrogenase subunit-6 (ND6) upon clinical outcomes were analyzed. Next, the role of ND6 in PMN chemotaxis was investigated using isolated human PMNs. Studying plasma samples from 97 patients with septic shock, we found that circulating ND6 levels at admission were independently and highly associated with the development of secondary infection (odds ratio = 30.317, 95% CI: 2.904 to 316.407, P = 0.004) and increased 90-d mortality (odds ratio = 1.572, 95% CI: 1.002 to 2.465, P = 0.049). In ex vivo experiments, ND6 pretreatment suppressed FPR1-mediated PMN chemotactic responses to bacterial peptides in the presence of multiple cytokines and chemokines, despite increased nondirectional PMN movements. Circulating mtFPs appear to contribute to the development of secondary infection and increased mortality in patients with septic shock who survive their early hyperinflammatory phase. The increased susceptibility to secondary infection is probably partly mediated by the suppression of FPR1-mediated PMN chemotaxis to secondary infected sites.

Anesthetic considerations of Joubert syndrome in patients with mitochondrial disease - A case report.

BACKGROUND: Joubert syndrome and mitochondrial disease are rare congenital diseases in which a wide range of symptoms affects multiple organs. Patients with these diseases present characteristic symptoms related to the musculoskeletal, respiratory, and neurological systems, which make it difficult for anesthesiologists to manage the patient's airway and choose appropriate anesthetic drugs. CASE: A 13-year-old male patient with Joubert syndrome and mitochondrial disease underwent elective surgery to insert a continuous ambulatory peritoneal dialysis catheter. Anesthesia was induced and maintained with propofol, remifentanil, and rocuronium. An I-gel was inserted to secure the airway; however, the fitting did not work properly, so the patient was intubated. The operation was completed without any major problems, and the intubated patient was transferred to the intensive care unit. CONCLUSIONS: Anesthesiologists should determine the method of anesthesia and prepare for unintended complications based on a full understanding of these congenital diseases.

Renovascular hypertension and RNF213 p.R4810K variant in Korean children with Moyamoya disease.

Moyamoya disease (MMD) is the most common underlying disease in Korean pediatric renovascular hypertension (RVH). The ring finger protein 213 (RNF213) p.R4810K variant is reported to be a pathologic variant in East Asian MMD. The purpose of this study was to evaluate hypertension (HTN) prevalence and clinical manifestations as well as RNF213 p.R4810K variant prevalence in Korean pediatric MMD patients. The medical records of pediatric MMD patients from January 2000 to June 2018 were retrospectively reviewed. RVH was confirmed by computer tomography angiography or renal Doppler ultrasonography. The American Academy of Pediatrics 2017 guideline for sex-, age-, and height-related blood pressure standards was used to define HTN. Of 706 patients with MMD, 40 (5.7%) had HTN. Among these patients, 22 had RVH and 12 had HTN with no evidence of renal artery stenosis (non-RVH). Patients with MMD and RVH had an MMD onset at a younger age and lower body mass index compared to those with MMD and non-RVH. Among the patients with MMD and HTN, 4 presented with HTN before developing MMD. Genetic testing for the RNF213 p.R4810K variant was performed in 32 patients with MMD and HTN. When the patient had a homozygous RNF213 p.R4810K variant, the odds ratio of RVH to non-RVH was 8.3. Our study suggests that RVH is more prevalent than non-RVH in pediatric MMD patients. Furthermore, RNF213 p.R4810K may be the cause of RVH in Korean children with MMD.