CTCF organizes inter-A compartment interactions through RYBP-dependent phase separation

Chromatin is spatially organized into three-dimensional structures at different levels including A/B compartments, topologically associating domains and loops. The canonical CTCF-mediated loop extrusion model can explain the formation of loops. However, the organization mechanisms underlying long-range chromatin interactions such as interactions between A-A compartments are still poorly understood. Here we show that different from the canonical loop extrusion model, RYBP-mediated phase separation of CTCF organizes inter-A compartment interactions. Based on this model, we designed and verified an induced CTCF phase separation system in embryonic stem cells (ESCs), which facilitated inter-A compartment interactions, improved self-renewal of ESCs and inhibited their differentiation toward neural progenitor cells. These findings support a novel and non-canonical role of CTCF in organizing long-range chromatin interactions via phase separation.

POS0370 COMPARATIVE RETINOPATHY RISK OF HIGH- VS LOW-DOSE HYDROXYCHLOROQUINE AMONG 4,677 INCIDENT LONG-TERM USERS: EMULATED TARGET TRIAL ANALYSES

Background

Hydroxychloroquine (HCQ) is a key treatment for patients with lupus, but the major long-term toxicity is HCQ retinopathy. A large cross-sectional study found a prevalence of HCQ retinopathy of 7.5% overall and 5 times higher odds associated with HCQ dose >5 mg/kg/day, which led to ophthalmology guidelines recommending the avoidance of HCQ dosing >5 mg/kg.1 However, whether this dosing recommendation is applicable to the future risk of HCQ retinopathy is unknown, as is the incidence of severe bullseye retinopathy vs. the mild, pre-symptomatic stage. Furthermore, recent studies have indicated that the use of lower doses of HCQ may increase the risk of lupus flares and hospitalizations.2

Objectives

To determine the incidence of HCQ retinopathy associated with long-term HCQ use and compare them according to HCQ dose.

Methods

We emulated a hypothetical target trial using observational data3 from the US integrated health network Kaiser Permanente Northern California to compare two HCQ weight-based dosing strategies, >5 vs ≤5 mg/kg/day, based on dispensed tablets per year. A secondary analysis evaluated >80% of prescription days covered by dispensed tablets per year with HCQ dose >5 vs ≤5 mg/kg. We included 4,677 patients who initiated and continued HCQ for at least 5 years between 1997-2020. We emulated randomization of treatment strategy by cloning each subject and assigning a replicate to each treatment group.3 We censored replicates if and when they deviated from the assigned treatment group, assessed as the average dose in the first 5 years and annually thereafter. We used inverse probability weighting to account for censoring. The primary outcome was HCQ retinopathy, assessed by expert adjudication of spectral domain-optical coherence tomography (SD-OCT) and graded by severity. All SD-OCTs were prospectively reviewed by an expert ophthalmologist (RM), and a second expert ophthalmologist (MM) reviewed all abnormal scans and a random subset of normal scans. We assessed intra-rater reliability of SD-OCT findings. We used pooled logistic regression to estimate the cumulative incidence of HCQ retinopathy for each HCQ dose strategy from initiation. The odds ratios approximated hazard ratios (HRs) because the outcome at each one-year time block is <5%.

Results

Among 4,677 patients, the mean age at HCQ initiation was 52 years; 83% were female. The racial/ethnic composition included 51% non-Hispanic White, 19% Hispanic, 14% Asian, and 11% Black patients. 756 (16.2%) and 3,921 (83.8%) patients initiated HCQ with the primary definition of the treatment strategies >5 and ≤5 mg/kg/day, respectively. The weighted kappa was 0.80 for SD-OCT reliability. 164 patients developed HCQ retinopathy (100 mild, 38 moderate, and 26 severe cases). The cumulative incidence of retinopathy over 18 years was 37.6% for >5 and 5.7% for ≤5mg/kg of HCQ in our primary analysis. The corresponding risk was 26.5% for >5 and 3.2% for ≤5 mg/kg in our secondary analysis using >80% of prescription days. Compared with ≤5 mg/kg of HCQ, the HRs of retinopathy were 9.65 (95% CI 5.73-16.65) and 10.79 (95% CI 6.40-20.07) for >5 mg/kg using the primary and secondary definitions of HCQ dose categories, respectively (Figure 1).

Conclusion

The risk of HCQ retinopathy associated with long-term adherence to >5 mg/kg dosing was high, approximately 10 times that of ≤5 mg/kg dosing. However, most cases identified during the study were mild and pre-symptomatic, supporting the value of regular screening. These data should be incorporated into individualized decisions about long-term use of HCQ.

References

[1]Melles RB, Marmor MF. The risk of toxic retinopathy in patients on long-term hydroxychloroquine therapy. JAMA Ophthalmol 2014;132(12):1453-60

[2]Almeida-Brasil CC et al. Flares after hydroxychloroquine reduction or discontinuation: results from the SLICC inception cohort. Ann Rheum Dis 2021 Dec 15, epub ahead of print

[3]Hernán MA, Robins JM. Using Big Data to Emulate a Target Trial When a Randomized Trial Is Not Available. Am J Epidemiol 2016;183(8):758-64

Disclosure of Interests

April Jorge: None declared, Ronald Melles: None declared, Michael Marmor: None declared, Carol Conell: None declared, Baijun Zhou: None declared, Jingbo Niu: None declared, Yuqing Zhang: None declared, Hyon Choi Consultant of: Ironwood, Selecta, Horizon, Takeda, Kowa, and Vaxart., Grant/research support from: Ironwood and Horizon

Implementation of network information security monitoring system based on adaptive deep detection

For a better detection in Network information security monitoring system, the author proposes a method based on adaptive depth detection. A deep belief network (DBN) was designed and implemented, and the intrusion detection system model was combined with a support vector machine (SVM). The data set adopts the NSL-KDD network communication data set, and this data set is authoritative in the security field. Redundant cleaning, data type conversion, normalization, and other processing operations are performed on the data set. Using the data conversion method based on the probability mass function probability mass function coding, a standard data set with low redundancy and low dimensionality can be obtained. Research indicates that when the batch size reaches 64, the accuracy of the test set reaches its maximum value. As the batch size increases, the accuracy first increases and then decreases. When the batch size continues to increase, the model will inevitably fall into the local optimal state, resulting in the degradation of the detection performance of the system. In terms of the false alarm rate, the DBN-SVM model is also the highest; however, it is only 10.73%. Under the premise of increasing the detection rate, the false alarm rate is improved; for the overall detection performance of the model, it is within an acceptable range. In terms of accuracy, the DBN-SVM model also scored the highest. The accuracy rate is the ratio of normal and correct classification for intrusion detection. It can explain the detection ability of the model. In summary, the overall detection ability of the DBN-SVM model is the best. The good classification ability to use SVM is proved, and the classification of low-dimensional features is expected to increase the detection rate of the system.

Optimal time point of response assessment for predicting survival is associated with tumor burden in hepatocellular carcinoma receiving repeated transarterial chemoembolization

OBJECTIVES

Objective response rate (ORR) under mRECIST criteria after transarterial chemoembolization (TACE) is a well-perceived surrogate endpoint of overall survival (OS). However, its optimal time point remains controversial and may be influenced by tumor burden. We aim to investigate the surrogacy of initial/best ORR in relation to tumor burden.

METHODS

A total of 1549 eligible treatment-naïve patients with unresectable hepatocellular carcinoma (HCC), Child-Pugh score ≤ 7, and performance status score ≤ 1 undergoing TACE between January 2010 and May 2016 from 17 academic hospitals were retrospectively analyzed. Based on "six-and-twelve" criteria, tumor burden was graded as low, intermediate, and high if the sum of the maximum tumor diameter and tumor number was ≤ 6, > 6 but ≤ 12, and > 12, respectively.

RESULTS

Both initial and best ORRs interacted with tumor burden. Initial and best ORRs could equivalently predict and correlate with OS in low (adjusted HR, 2.55 and 2.95, respectively, both p < 0.001; R = 0.84, p = 0.035, and R = 0.97, p = 0.002, respectively) and intermediate strata (adjusted HR, 1.81 and 2.22, respectively, both p < 0.001; R = 0.74, p = 0.023, and R = 0.9, p = 0.002, respectively). For high strata, only best ORR exhibited qualified surrogacy (adjusted HR, 2.61, p < 0.001; R = 0.70, p = 0.035), whereas initial ORR was not significant (adjusted HR, 1.08, p = 0.357; R = 0.22, p = 0.54).

CONCLUSIONS

ORR as surrogacy of OS is associated with tumor burden. For patients with low/intermediate tumor burden, initial ORR should be preferred in its early availability upon similar sensitivity, whereas for patients with high tumor burden, best ORR has optimal sensitivity. Timing of OR assessment should be tailored according to tumor burden.

KEY POINTS

• This is the first study utilizing individual patient data to comprehensively analyze the surrogacy of ORR with a long follow-up period. • Optimal timing of ORR assessment for predicting survival should be tailored according to tumor burden. • For patients with low and intermediate tumor burden, initial ORR is optimal for its timeliness upon similar sensitivity with best ORR. For patients with high tumor burden, best ORR has optimal sensitivity.

The Status of Iodine Nutrition after Removing Iodized Salt in High Water Iodine Regions: a Cross-sectional Study in China

Currently, the removal of iodized salt is carried out in high water iodine regions. The present situation of iodine nutrition and the prevalence of thyroid diseases in such regions have not been clearly elucidated. This study aimed to figure out these problems to help render effective measures for cases of abnormal iodine nutrition status. A cross-sectional study was carried out in four areas of Jining and Heze, Shandong Province, China, with different water iodine concentrations (WIC). In total, 1344 adults were enrolled in this study, and data related to their iodine nutrition, thyroid function, and thyroid ultrasonography were collected. Subjects were grouped according to WIC, urine iodine concentration (UIC), serum iodine concentration (SIC), and combined UIC and SIC for analysis. Iodine levels were in excess in the 100 μg/L ≤ WIC < 300 μg/L and WIC ≥ 300 μg/L areas. Compared with the control WIC group (10-100 μg/L), the WIC ≥ 300 μg/L group had a higher prevalence of thyroid autoimmunity (TAI, 21.25% vs. 13.19%, P <0.05), subclinical hypothyroidism (SH, 20.20% vs. 11.96%, P < 0.05), thyroid nodules (TN, 31.75% vs. 18.71%, P < 0.05), and thyroid dysfunction (23.62% vs. 12.26%, P < 0.05). Compared with the UIC control group (100-300 μg/L), high UIC group (≥ 800 μg/L) had a higher prevalence of TN (33.75% vs. 21.14%, P < 0.05) and thyroid dysfunction (25% vs. 14.47%, P < 0.05). Next, compared with the control SIC group (50-110 μg/L), high SIC group (≥ 110 μg/L) had a higher prevalence of TAI (33.80% vs. 14.47%, P < 0.05), SH (23.94% vs. 14.30%, P < 0.05), and thyroid dysfunction (33.80% vs. 15.29%, P < 0.05). Finally, subjects with the highest UIC and the highest SIC also had a higher prevalence of TAI (25.92% vs. 10.97%, P < 0.05), SH (23.45% vs. 10.97%, P < 0.05), TN (34.56% vs. 15.85%, P < 0.05), and thyroid dysfunction (27.16% vs. 13.41%, P < 0.05) than subjects with middle iodine levels. The iodine nutrition of subjects in the WIC ≥ 300 μg/L areas was still in excess after removing iodized salt from their diets. High levels of iodine also increased the prevalence of TAI, SH, TN, and thyroid dysfunction in those areas. Simply removing iodized salt may not be sufficient for high water iodine regions.

Rational Design for Nitroreductase (NTR)-Responsive Proteolysis Targeting Chimeras (PROTACs) Selectively Targeting Tumor Tissues

The catalytic properties of proteolysis targeting chimeras (PROTACs) may lead to uncontrolled off-tissue target degradation that causes potential toxicity, limiting their clinical applications. The precise control of this technology in a tissue-selective manner can minimize the potential toxicity. Hypoxia is a hallmark of most solid tumors, accompanied by elevated levels of nitroreductase (NTR). Based on this character, we presented a type of NTR-responsive PROTACs to selectively degrade proteins of interest (POI) in tumor tissues. Compound 17-1 was the first NTR-responsive PROTAC synthesized by incorporating the caging group on the Von Hippel-Lindau (VHL) E3 ubiquitin ligase ligand. It could be activated by NTR to release the active PROTAC 17 to efficiently degrade the EGFR protein and subsequently exert antitumor efficacy. Thus, a general strategy for the precise control of PROTAC to induce POI degradation in tumor tissues by NTR was established, which provided a generalizable platform for the development of NTR-controlled PROTACs to achieve selective degradation.

SY-707, an ALK/FAK/IGF1R inhibitor, suppresses growth and metastasis of breast cancer cells

Focal adhesion kinase (FAK), a multi-functional cytoplasmic tyrosine kinase, plays a critical role in cancer migration, proliferation and metastasis via regulating multiple signaling pathways. SY-707 is an anaplastic lymphoma kinase (ALK)/FAK/type 1 insulin-like growth factor receptor (IGF1R) multi-kinase inhibitor which is now being evaluated in phase II clinical trials for ALK positive non-small cell lung cancer (NSCLC). However, the effect of SY-707 on breast cancer is unknown. In this study, we assessed preclinical the anti-growth and anti-metastasis potency of SY-707 in breast cancer cells. ATP content, PE-Annexin V, and would healing assays were used to examine cell proliferation, cell cycle and migration. Then, SD rat and beagle dog models were used to evaluate the pharmacokinetics profile of SY-707, and mouse xenograft model was used to evaluate the anti-cancer activities of SY-707 . We found that breast cancer cells apoptosis were induced by SY-707. Moreover, SY-707 exerted inhibition on cell migration and adhesion in a dose-dependent manner. In T47D xenograft mice, SY-707 had significant anti-tumor activities alone or synergistically with Paclitaxel. Meanwhile, SY-707 also displayed significant suppression on spontaneous metastasis of tumor to the lung in 4T1 murine breast cancer xenograft model. In conclusion, SY-707 has potent anti-proliferation and anti-migration potential in breast cancer and , implying its therapeutic application for the treatment of breast cancer in future clinical trials.

Restoration of the gut microbiota is associated with a decreased risk of hepatic encephalopathy after TIPS

Background & Aims

Hepatic encephalopathy (HE) is a major complication after transjugular intrahepatic portosystemic shunt (TIPS) and is primarily influenced by the gut microbiota. We aimed to evaluate alterations in the microbiota after TIPS and the association between such alterations and HE.

Methods

We conducted a prospective longitudinal study of 106 patients with cirrhosis receiving TIPS. Faecal samples were collected before and after TIPS, and the gut microbiota was analysed by 16S ribosomal RNA sequencing.

Results

Among all patients, 33 developed HE (HE+ group) within 6 months after TIPS and 73 did not (HE- group), and 18 died during follow-up. After TIPS, the autochthonous taxa increased, whereas the potential pathogenic taxa decreased in the HE- group, and the autochthonous taxon Lachnospiraceae decreased in the HE+ group. Furthermore, synergism among harmful bacteria was observed in all patients, which was weakened in the HE- group (p <0.001) but enhanced in the HE+ group (p <0.01) after TIPS. Variations of 5 autochthonous taxa, namely, Coprococcus, Ruminococcus, Blautia, Ruminococcaceae_uncultured, and Roseburia, were negatively correlated with the severity of HE. Notably, increased abundances of Coprococcus and Ruminococcus were protective factors against HE, and the incidences of HE in patients with improved, stable, and deteriorated microbiota after TIPS were 13.3, 25.9, and 68.2%, respectively. Higher total bilirubin level, Child–Pugh score, model for end-stage liver disease score, Granulicatella, and Alistipes and lower Subdoligranulum before TIPS were the independent risk factors for death.

Conclusions

Alterations in gut dysbiosis were negatively related to the occurrence and severity of post-TIPS HE, and the pre-TIPS microbiota were associated with death, suggesting the gut microbiota could be a promising potential biological target for screening suitable patients receiving TIPS and prevention and treatment of post-TIPS HE.

Lay summary

Alterations in the gut microbiota after transjugular intrahepatic portosystemic shunt (TIPS) and the relationship between such alterations and post-TIPS hepatic encephalopathy (HE) remain unclear. We therefore performed this study and found that after TIPS, restoration of the gut microbiota, mainly characterised by expansion of autochthonous taxa, depletion of harmful taxa, and weakening of synergism among harmful bacteria, was inversely related to the occurrence and severity of post-TIPS HE.

•

Gut dysbiosis of the patients without HE showed significant improvement after TIPS.

•

Expansion of autochthonous taxa after TIPS was negatively correlated with the occurrence and severity of HE.

•

The changes of relationship among the microbiota in different prognostic groups were opposite.

•

Pre-TIPS gut microbiota and certain clinical indices were associated with survival.

Mediating Effects of Malnutrition on the Relationship between Depressive Symptoms Clusters and Muscle Function Rather than Muscle Mass in Older Hemodialysis Patients

OBJECTIVES

The purpose of this study was to investigate the association and mediation pathways among muscle mass, muscle function (muscle strength and physical performance), and malnutrition with depressive symptoms clusters in the older hemodialysis patients.

DESIGN

A multi-center cross-sectional study.

SETTING AND PARTICIPANTS

A total of 499 patients aged ≥ 60 on hemodialysis from seven facilities in Shanghai of China from 2020 to 2021.

MEASUREMENTS

Muscle mass was assessed by skeletal muscle index(SMI). Muscle strength was measured by handgrip strength, and physical performance was measured via gait speed and Timed Up and Go Test (TUGT). Nutritional status was assessed by Malnutrition Inflammation Score (MIS). Depressive symptoms were evaluated by the Patient Health Questionnaire-9 (PHQ-9). Logistic regression and mediation analyses fully adjusted for all potential confounding factors.

RESULTS

Among 499 participants (312 men, mean age 69.2±6.6 years), 108 (21.6%) had depressive symptoms. The muscle strength, physical performance and malnutrition were associated with depressive symptoms. Furthermore, malnutrition significantly mediated the association of muscle function with total, cognitive-affective symptoms. The association of the muscle function with somatic symptoms were mediated by the nutritional status. The mediated proportions of malnutrition in the relationship between physical performance and depressive symptoms clusters were stronger in somatic symptoms than in cognitive-affective symptoms.

CONCLUSIONS

Our findings suggest that muscle function rather than muscle mass may contribute substantially to the development of depressive symptoms clusters in the hemodialysis via malnutrition. The malnutrition mediated stronger in the association of muscle function with somatic symptoms. These findings may help guide clinicians to better diagnose and manage depression in the context of concomitant muscle function and malnutrition.

Polarization modulation with optical lock-in detection reveals universal fluorescence anisotropy of subcellular structures in live cells

The orientation of fluorophores can reveal crucial information about the structure and dynamics of their associated subcellular organelles. Despite significant progress in super-resolution, fluorescence polarization microscopy remains limited to unique samples with relatively strong polarization modulation and not applicable to the weak polarization signals in samples due to the excessive background noise. Here we apply optical lock-in detection to amplify the weak polarization modulation with super-resolution. This novel technique, termed optical lock-in detection super-resolution dipole orientation mapping (OLID-SDOM), could achieve a maximum of 100 frames per second and rapid extraction of 2D orientation, and distinguish distance up to 50 nm, making it suitable for monitoring structural dynamics concerning orientation changes in vivo. OLID-SDOM was employed to explore the universal anisotropy of a large variety of GFP-tagged subcellular organelles, including mitochondria, lysosome, Golgi, endosome, etc. We found that OUF (Orientation Uniformity Factor) of OLID-SDOM can be specific for different subcellular organelles, indicating that the anisotropy was related to the function of the organelles, and OUF can potentially be an indicator to distinguish normal and abnormal cells (even cancer cells). Furthermore, dual-color super-resolution OLID-SDOM imaging of lysosomes and actins demonstrates its potential in studying dynamic molecular interactions. The subtle anisotropy changes of expanding and shrinking dendritic spines in live neurons were observed with real-time OLID-SDOM. Revealing previously unobservable fluorescence anisotropy in various samples and indicating their underlying dynamic molecular structural changes, OLID-SDOM expands the toolkit for live cell research.

Development trajectory for the temporal and spatial evolution of the resilience of regional tourism environmental systems in 14 cities of Gansu Province, China

The rapid development of the urban economy in China and the accompanying income growth experienced by urban residents have increased demand for tourism and leisure, which has brought pressure on the urban tourism environment system (UTES), making the contradiction between tourism economic development and the ecological environment increasingly acute. While seeking to rationalize the economic, social, and ecological benefits of tourism, reducing the fragility of the UTES and improving its anti-interference and recovery capabilities have become attracted significant attention from scholars in China and elsewhere. This paper establishes a definition of resilience for an UTES and constructs an evaluation index system for it in terms of the social, economic, and ecological environments. It also establishes an entropy weight-TOPSIS resilience evaluation model to measure resilience in regional systems, using ArcGIS to analyze the standard deviation ellipse and center of the gravity track of the resilience. System dynamics was used to construct diagrams of causal relationships and stock flow for the constituent elements of UTES to show the mechanisms that promote its resilience. This paper investigates 14 cities of Gansu Province in particular to simulate the resilience model of a regional system.

First-in-human phase 1 study of the anti-TIGIT antibody vibostolimab as monotherapy or with pembrolizumab for advanced solid tumors, including non-small cell lung cancer

BACKGROUND

In this first-in-human phase 1 study, we investigated the safety and efficacy of the anti-TIGIT antibody vibostolimab as monotherapy or in combination with pembrolizumab.

METHODS

Part A enrolled patients with advanced solid tumors and part B enrolled patients with non-small cell lung cancer (NSCLC). Patients received vibostolimab 2.1-700 mg alone or with pembrolizumab 200 mg in part A and vibostolimab 200 mg alone or with pembrolizumab 200 mg in part B. Primary end points were safety and tolerability. Secondary end points included pharmacokinetics and objective response rate (ORR) per RECIST v1.1.

RESULTS

Part A enrolled 76 patients (monotherapy, 34; combination therapy, 42). No dose-limiting toxicities were reported. Across doses, 56% of patients receiving monotherapy and 62% receiving combination therapy had treatment-related adverse events (TRAEs); grade 3-4 TRAEs occurred in 9% and 17% of patients, respectively. The most common TRAEs were fatigue (15%) and pruritus (15%) with monotherapy and pruritus (17%) and rash (14%) with combination therapy. Confirmed ORR was 0% with monotherapy and 7% with combination therapy. In part B, 39 patients had anti-PD-1/PD-L1-naïve NSCLC (all received combination therapy) and 67 had anti-PD-1/PD-L1-refractory NSCLC (monotherapy, 34; combination therapy, 33). In patients with anti-PD-1/PD-L1-naive NSCLC: 85% had TRAEs-the most common were pruritus (38%) and hypoalbuminemia (31%); confirmed ORR was 26%, with responses occurring in both PD-L1-positive and PD-L1-negative tumors. In patients with anti-PD-1/PD-L1‒refractory NSCLC: 56% receiving monotherapy and 70% receiving combination therapy had TRAEs-the most common were rash and fatigue (21% each) with monotherapy and pruritus (36%) and fatigue (24%) with combination therapy; confirmed ORR was 3% with monotherapy and 3% with combination therapy.

CONCLUSION

Vibostolimab plus pembrolizumab was well tolerated and demonstrated antitumor activity in patients with advanced solid tumors, including patients with advanced NSCLC.

Social distancing during COVID-19: threat and efficacy among university students in seven nations

COVID-19 has been spreading fast worldwide, and until effective and safe vaccines have been widely adopted, preventive measures such as social distancing are crucial to keep the pandemic under control. The study's research questions asked which psychosocial factors predict social distancing behavior and whether there are country-level differences in social distancing? Using the Extended Parallel Process Model (EPPM) as a theoretical lens, we examined the predictive effects of threat and efficacy and demographic variables on adherence to the COVID-19 preventive behavior of social distancing using a survey among an international sample of university students. Using path modeling and analysis of covariance, we confirmed the predictive effects of the EPPM on social distancing behavior. Our final model showed that perceived susceptibility to COVID-19 was both directly and indirectly (through response efficacy) associated with social distancing behavior; that perceived severity of COVID-19 yielded a significant indirect effect on social distancing behavior through both self-efficacy and response efficacy; that perceived susceptibility is indirectly and positively associated with social distancing behavior through response efficacy; and that self-efficacy and response efficacy were directly associated with social distancing behavior. Additionally, there were country-level differences in social distancing. Possible explanations for and implications of these findings are discussed.

A new least‐squares‐based reproducing kernel method for solving regular and weakly singular Volterra‐Fredholm integral equations with smooth and nonsmooth solutions

Based on the least‐squares method, we proposed a new algorithm to obtain the solution of the second kind of regular and weakly singular Volterra‐Fredholm integral equations in reproducing kernel spaces. The stability and uniform convergence of the algorithm are investigated in detail. Numerical experiments verify the theoretical findings. Meanwhile, this method is also applicable to the nonlinear Volterra integral equations. Test problems which have non‐smooth solutions are also considered, and our proposed method is efficient as some recent Krylov subspace methods such as LSQR and LSMR.

The loss of heterochromatin is associated with multiscale three-dimensional genome reorganization and aberrant transcription during cellular senescence

Heterochromatin remodeling is critical for various cell processes. In particular, the "loss of heterochromatin" phenotype in cellular senescence is associated with the process of aging and age-related disorders. Although biological processes of senescent cells, including senescence-associated heterochromatin foci (SAHF) formation, chromosome compaction, and redistribution of key proteins, have been closely associated with high-order chromatin structure, the relationship between the high-order chromatin reorganization and the loss of heterochromatin phenotype during senescence has not been fully understood. By using senescent and deep senescent fibroblasts induced by DNA damage harboring the "loss of heterochromatin" phenotype, we observed progressive 3D reorganization of heterochromatin during senescence. Facultative and constitutive heterochromatin marked by H3K27me3 and H3K9me3, respectively, show different alterations. Facultative heterochromatin tends to switch from the repressive B-compartment to the active A-compartment, whereas constitutive heterochromatin shows no significant changes at the compartment level but enhanced interactions between themselves. Both types of heterochromatin show increased chromatin accessibility and gene expression leakage during senescence. Furthermore, increased chromatin accessibility in potential CTCF binding sites accompanies the establishment of novel loops in constitutive heterochromatin. Finally, we also observed aberrant expression of repetitive elements, including LTR (long terminal repeat) and satellite classes. Overall, facultative and constitutive heterochromatin show both similar and distinct multiscale alterations in the 3D map, chromatin accessibility, and gene expression leakage. This study provides an epigenomic map of heterochromatin reorganization during senescence.