bluuebunny/crossref_metadata_2025 huggingface dataset:
Two Cases of Breakthrough Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infections Caused by the Omicron Variant (B.1.1.529 Lineage) in International Travelers to Japan
Authors: Maruki Taketomo , Iwamoto Noriko , Kanda Kohei , Okumura Nobumasa , Yamada Gen , Ishikane Masahiro , Ujiie Mugen , Saito Masumichi , Fujimoto Tsuguto , Kageyama Tsutomu , Saito Tomoya , Saito Shinji , Suzuki Tadaki , Ohmagari Norio
Published: January 2022

In November 2021, the World Health Organization designated a new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant of concern, Omicron (PANGO lineage B.1.1.529). We report on the first 2 cases of breakthrough coronavirus disease 2019 (COVID-19) caused by Omicron in Japan among international travelers returning from the country with undetected infection. The spread of infection by Omicron were considered.
Developing Transitional Justice for Youth: An Assessment of Youth Reintegration Programmes in Colombia
Authors: Mitra Arpita
Published: January 2022

ABSTRACT∞

Young people, or ‘youth’ are one of the key groups affected by armed conflict as well as in the process of transitioning from it. This article explores what a youth-inclusive process of transitional justice may entail. It looks at the reintegration of youth, who were previously associated with armed groups, into civilian lives through Disarmament, Demobilisation and Reintegration (DDR) programmes and broader community-based initiatives with a prevention focus that lie outside a traditional transitional justice framework. The article scopes the study to the context in Colombia. A selection of programmes is assessed alongside international standards on youth reintegration, particularly the UN Integrated DDR Standards on Youth and complemented with empirical evidence that attests the ways in which youth experience these interventions. In doing so, the article analyzes potential ‘blueprints’ for the programmatic response to youth reintegration and contribute to an under-researched area that links youth, transitional justice and guarantees of non-recurrence.
SARS-CoV-2 Variant Exposures Elicit Antibody Responses With Differential Cross-Neutralization of Established and Emerging Strains Including Delta and Omicron
Authors: Laurie Matthew T , Liu Jamin , Sunshine Sara , Peng James , Black Douglas , Mitchell Anthea M , Mann Sabrina A , Pilarowski Genay , Zorn Kelsey C , Rubio Luis , Bravo Sara , Marquez Carina , Sabatino Joseph J , Mittl Kristen , Petersen Maya , Havlir Diane , DeRisi Joseph
Published: January 2022

The wide spectrum of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with phenotypes impacting transmission and antibody sensitivity necessitates investigation of immune responses to different spike protein versions. Here, we compare neutralization of variants of concern, including B.1.617.2 (delta) and B.1.1.529 (omicron), in sera from individuals exposed to variant infection, vaccination, or both. We demonstrate that neutralizing antibody responses are strongest against variants sharing certain spike mutations with the immunizing exposure, and exposure to multiple spike variants increases breadth of variant cross-neutralization. These findings contribute to understanding relationships between exposures and antibody responses and may inform booster vaccination strategies.
Proteus, Matrine, and Pyridalyl Toxicity and Their Sublethal Effects on Orius laevigatus (Hemiptera: Anthocoridae)
Authors: Kordestani Mona , Mahdian Kamran , Baniameri Valiollah , Garjan Aziz Sheikhi
Published: January 2022

Proteus, matrine, and pyridalyl were tested in the laboratory for their effects upon Orius laevigatus (Fieber), which is a polyphagous predator used for IPM programs of Frankliniella occidentalis (Pergande). Against female adults, the most toxic insecticide was Proteus (LC50 = 44.3 µl L–1), followed by pyridalyl (LC50 = 83.8 µl L–1) and matrine (LC50 = 102.7 µl L–1). The mortality of female adults was checked 24, 48, 72, and 96 h after exposure to 14-d residues of the treatments on strawberry leaves. The residual of Proteus was less toxic; the remaining products caused the lowest mortality at different times after exposure. Sublethal treatments (LC25) significantly prolonged the developmental duration of total immature stages from 17.6 d in control to 21.6 and 20.0 d in Proteus and pyridalyl treatments, respectively. Also, the fecundity of O. laevigatus treated with Proteus, pyridalyl, and matrine decreased to 58.8%, 75.6%, and 96.7%, respectively, in comparison to the control. Compared with the control population (0.118 d–1), the intrinsic rate of increase (r) of F1 generation decreased by 0.053, 0.095, and 0.110 d–1 in Proteus, pyridalyl, and matrine treatments, respectively. The consumption rate of control bugs reached 14.0 thrips during 24 h. The adults fed on Proteus treatment had the lowest consumption rate in this period (9.4 preys). Overall, matrine proved to be harmless with reproductive capacity and r similar to what was recorded in control bugs. We concluded that matrine can be used as an alternative for the synthetic insecticide to integrate with O. laevigatus.
Exploiting non-linear scales in galaxy–galaxy lensing and galaxy clustering: A forecast for the dark energy survey
Authors: Salcedo Andrés N , Weinberg David H , Wu Hao-Yi , Wibking Benjamin D
Published: January 2022

The combination of galaxy–galaxy lensing (GGL) and galaxy clustering is a powerful probe of low-redshift matter clustering, especially if it is extended to the non-linear regime. To this end, we use an N-body and halo occupation distribution (HOD) emulator method to model the redMaGiC sample of colour-selected passive galaxies in the Dark Energy Survey (DES), adding parameters that describe central galaxy incompleteness, galaxy assembly bias, and a scale-independent multiplicative lensing bias Alens. We use this emulator to forecast cosmological constraints attainable from the GGL surface density profile ΔΣ(rp) and the projected galaxy correlation function wp, gg(rp) in the final (Year 6) DES data set over scales $r_p=0.3\!-\!30.0\, h^{-1} \, \mathrm{Mpc}$. For a $3{{\ \rm per\ cent}}$ prior on Alens we forecast precisions of $1.9{{\ \rm per\ cent}}$, $2.0{{\ \rm per\ cent}}$, and $1.9{{\ \rm per\ cent}}$ on Ωm, σ8, and $S_8 \equiv \sigma _8\Omega _m^{0.5}$, marginalized over all halo occupation distribution (HOD) parameters as well as Alens. Adding scales $r_p=0.3\!-\!3.0\, h^{-1} \, \mathrm{Mpc}$ improves the S8 precision by a factor of ∼1.6 relative to a large scale ($3.0\!-\!30.0\, h^{-1} \, \mathrm{Mpc}$) analysis, equivalent to increasing the survey area by a factor of ∼2.6. Sharpening the Alens prior to $1{{\ \rm per\ cent}}$ further improves the S8 precision to $1.1{{\ \rm per\ cent}}$, and it amplifies the gain from including non-linear scales. Our emulator achieves per cent-level accuracy similar to the projected DES statistical uncertainties, demonstrating the feasibility of a fully non-linear analysis. Obtaining precise parameter constraints from multiple galaxy types and from measurements that span linear and non-linear clustering offers many opportunities for internal cross-checks, which can diagnose systematics and demonstrate the robustness of cosmological results.
Translating the Biology of Diffuse Large B-cell Lymphoma Into Treatment
Authors: Danilov Alexey V , Magagnoli Massimo , Matasar Matthew J
Published: January 2022

Diffuse large B-cell lymphoma (DLBCL) is characterized by clinical and molecular heterogeneity; however, this heterogeneity is rarely taken into account by standard-of-care treatment approaches. While the disease was traditionally classified based on transcriptome signatures purporting the tumor cell of origin, recent classification systems have further differentiated these subtypes into clusters based on molecular and genetic features. Alongside a better understanding of the biology of the disease and the signaling pathways involved, emerging therapeutic agents may be better aimed at attacking distinct disease subsets. It is hoped that molecular subtyping at diagnosis will allow patients to be allocated to the appropriate treatment that targets their specific disease subtype, thus advancing the promise of precision medicine in lymphoma, an approach that is most needed. For high-risk disease subsets, this is particularly important, and much research is still needed to develop agents effective in this population. Here, we review recent advances in DLBCL biology and how they can be translated into clinical care.
Definitive Intensity-Modulated Chemoradiation for Anal Squamous Cell Carcinoma: Outcomes and Toxicity of 428 Patients Treated at a Single Institution
Authors: Holliday Emma B , Morris Van K , Johnson Benny , Eng Cathy , Ludmir Ethan B , Das Prajnan , Minsky Bruce D , Taniguchi Cullen , Smith Grace L , Koay Eugene J , Koong Albert C , Delclos Marc E , Skibber John M , Rodriguez-Bigas Miguel A , You Y Nancy , Bednarski Brian K , Tillman Mathew M , Chang George J , Jennings Kristofer , Messick Craig A
Published: January 2022

Background

Although intensity-modulated radiation therapy (IMRT) is considered the standard of care for the treatment of squamous cell carcinoma of the anus (SCCA), few large series have reported oncologic outcomes and toxicities. In this retrospective report, we aim to describe outcomes and toxicities after IMRT-based chemoradiation (CRT) for the treatment of SCCA, evaluate the impact of dose escalation (>54 Gy), and compare concurrent fluoropyrimidine in combination with either mitomycin or with cisplatin as chemosensitizers.

Methods

Patients treated at The University of Texas MD Anderson Cancer Center between January 1, 2003 and December 31, 2018 with IMRT-based CRT were included. Median time to locoregional recurrence, time to colostomy, and overall survival were estimated using the Kaplan–Meier method.

Results

A total of 428 patients were included; median follow-up was 4.4 years. Three hundred and thirty-four patients (78.0%) were treated with concurrent cisplatin and fluoropyrimidine, and 160 (37.4%) with >54 Gy. Two- and 5-year freedom from locoregional failure, freedom from colostomy failure, and overall survival were 86.5% and 81.2%, respectively, 90.0% and 88.3%, respectively, and 93.6% and 85.8%, respectively. Neither dose escalation nor mitomycin-based concurrent chemotherapy resulted in improved outcomes. Mitomycin-based concurrent chemotherapy was associated with in approximately 2.5 times increased grade 3 or greater acute toxicity. Radiation dose >54 Gy was associated with approximately 2.6 times increased Grade 3 or greater chronic toxicity.

Conclusions

Our results suggest IMRT-based CRT with concurrent fluoropyrimidine and cisplatin is a safe and feasible option for patient with SCCA and may cause less acute toxicity. The role for radiation dose escalation is unclear and requires further study.
Phase I Trial of a Third Generation EGFR Mutant-Selective Inhibitor (D-0316) in Patients with Advanced Non-Small Cell Lung Cancer
Authors: Jian Hong , Wang Kai , Cheng Ying , Ding Lieming , Wang Yang , Shi Zhe , Zhang Ling , Wang Yaolin , Lu Shun
Published: January 2022

Background

D-0316 is a third-generation epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) developed for patients with locally advanced or metastatic non-small cell lung cancer (NSCLC) with EGFR T790M mutation that progressed after prior treatment with the first- or second-generation EGFR-TKI.

Methods

This phase I, open-label, multicenter clinical trial evaluated daily oral D-0316 administration in dose-escalation (25 to 150 mg; 17 patients) and dose-expansion (50, 100 mg; 67 patients) cohorts for safety, tolerability, anti-tumor activity, and pharmacokinetics.

Results

D-0316 was well tolerated at daily doses of 25 to 150 mg and the maximum tolerated dose (MTD) was not reached. The most common treatment-related adverse events (AEs) were platelet count decreased, electrocardiogram QT corrected interval prolonged, anemia, rash, low white blood cell count, hypertriglyceridemia, high cholesterol, headache, pruritus, cough, and aspartate transaminase (AST) or alanine transaminase (ALT) increased. Most of AEs were grade 1 or 2. In the 50 and 100 mg group, the overall response rate (ORR) was 33.3% and 45.5%, the disease control rate (DCR) was 86.7% and 93.9%, and the median PFS was 8.3 and 9.6 months, respectively. D-0316 exposure increased in proportion to dose from 25 to 150 mg. The recommended phase II dose (RP2D) was 100 mg.

Conclusion

D-0316 is safe, tolerable, and effective for patients with locally advanced/metastatic NSCLC with the EGFR T790M mutation who previously received EGFR-TKI.

ClinicalTrials.gov Identifier

NCT03452150.
Cetuximab and Irinotecan With or Without Bevacizumab in Refractory Metastatic Colorectal Cancer: BOND-3, an ACCRU Network Randomized Clinical Trial
Authors: Lipsyc-Sharf Marla , Ou Fang-Shu , Yurgelun Matthew B , Rubinson Douglas A , Schrag Deborah , Dakhil Shaker R , Stella Philip J , Weckstein Douglas J , Wender Donald B , Faggen Meredith , Zemla Tyler J , Heying Erica N , Schuetz Samantha R , Noble Stephanie , Meyerhardt Jeffrey A , Bekaii-Saab Tanios , Fuchs Charles S , Ng Kimmie
Published: January 2022

Background

Combination irinotecan and cetuximab is approved for irinotecan-refractory metastatic colorectal cancer (mCRC). It is unknown if adding bevacizumab improves outcomes.

Patients and Methods

In this multicenter, randomized, double-blind, placebo-controlled phase II trial, patients with irinotecan-refractory RAS-wildtype mCRC and no prior anti-EGFR therapy were randomized to cetuximab 500 mg/m2, bevacizumab 5 mg/kg, and irinotecan 180 mg/m2 (or previously tolerated dose) (CBI) versus cetuximab, irinotecan, and placebo (CI) every 2 weeks until disease progression or intolerable toxicity. The primary endpoint was progression-free survival (PFS). Secondary endpoints included overall survival (OS), objective response rate (ORR), and adverse events (AEs).

Results

The study closed early after the accrual of 36 out of a planned 120 patients due to changes in funding. Nineteen patients were randomized to CBI and 17 to CI. Baseline characteristics were similar between arms. Median PFS was 9.7 versus 5.5 months for CBI and CI, respectively (1-sided log-rank P = .38; adjusted hazard ratio [HR] = 0.64; 95% confidence interval [CI], 0.25-1.66). Median OS was 19.7 versus 10.2 months for CBI and CI (1-sided log-rank P = .02; adjusted HR = 0.41; 95% CI, 0.15-1.09). ORR was 36.8% for CBI versus 11.8% for CI (P = .13). Grade 3 or higher AEs occurred in 47% of patients receiving CBI versus 35% for CI (P = .46).

Conclusion

In this prematurely discontinued trial, there was no significant difference in the primary endpoint of PFS between CBI and CI. There was a statistically significant improvement in OS in favor of CBI compared with CI. Further investigation of CBI for the treatment of irinotecan-refractory mCRC is warranted.

Clinical Trial Registration: NCT02292758
FDA Approval Summary: Revised Indication and Dosing Regimen for Ponatinib Based on the Results of the OPTIC Trial
Authors: Pulte E Dianne , Chen Haiyan , Price Lauren S L , Gudi Ramadevi , Li Hongshan , Okusanya Olanrewaju O , Ma Lian , Rodriguez Lisa , Vallejo Jonathon , Norsworthy Kelly J , de Claro R Angelo , Theoret Marc R , Pazdur Richard
Published: January 2022

On December 18, 2020, US Food and Drug Administration (FDA) approved a supplemental application for ponatinib extending the indication in patients with chronic-phase chronic myeloid leukemia (CP-CML) to patients with resistance or intolerance of at least 2 prior kinase inhibitors. Ponatinib was initially approved in December 2012 but was briefly voluntarily withdrawn due to serious safety concerns including the risk of arterial occlusive events (AOE). It returned to the market in December 2013 with an indication limited to patients with T315I mutation or for whom no other tyrosine kinase inhibitor (TKI) therapy was indicated with revised warnings and precautions. A post-marketing requirement was issued to identify the optimal safe and effective dose for CP-CML. Thus, the OPTIC trial was performed, which randomized patients to 1 of 3 doses, 45 mg, 30 mg, or 15 mg, with a dose reduction to 15 mg on achievement of MR2 (BCR-ABLIS ≤1%). Patients enrolled were treated with at least 2 prior TKIs or had a T315I mutation. Patients with a history of clinically significant, uncontrolled, or active cardiovascular disease were excluded. Efficacy was established on an interim analysis based on the rate of MR2 at 12 months in the modified intent-to-treat population of 261 patients, with 88, 86, and 87 patients in the 45, 30, and 15 mg cohorts, respectively. With a median follow-up of 28 months, the rate of achievement of MR2 at 12 months was 42%, 28%, and 24% in the respective cohorts. The safety profile was consistent with that observed in prior evaluations of ponatinib with notable adverse reactions including pancreatitis, hypertension, hyperlipidemia, liver dysfunction, and AOE. Of patients treated at the 45/15 mg dose, AOEs were seen in 13%, with a higher rate being observed in patients age 65 or older compared to younger patients. A readjudication of AOEs seen on the prior pivotal phase 2 study resulted in a rate of 26%. Overall, the results supported a modification of the recommended dose for patients with CP-CML to 45 mg until the achievement of MR2 followed by a reduction to 15 mg. The expansion of the indication to patients with exposure to 2 prior TKIs was approved given data showing that ponatinib could be successfully used for the treatment of this population with appropriate monitoring and screening for risk factors.
Rational Second-Generation Antiandrogen Use in Prostate Cancer
Authors: Orme Jacob J , Pagliaro Lance C , Quevedo J Fernando , Park Sean S , Costello Brian A
Published: January 2022

The second-generation antiandrogens have achieved an ever-growing list of approvals and indications in subsets of prostate cancer. Here, we provide an overview of second-generation antiandrogen trials and FDA approvals and outline a rational sequencing approach for the use of these agents as they relate to chemotherapy and other available treatment modalities in advanced prostate cancer. All published phase II-III randomized controlled trials reporting outcomes with the use of second-generation antiandrogens in prostate cancer are included as well as all published trials and retrospective studies of second-generation antiandrogen sequencing and/or combinations. Complete tabular and graphical representation of all available evidence is provided regarding the use and sequencing of second-generation antiandrogens in prostate cancer. In metastatic castration-resistant prostate cancer, evidence suggests prioritization of abiraterone before chemotherapy, chemotherapy after second-generation antiandrogen failure, and postchemotherapy enzalutamide in select patients to maximize agent efficacy and tolerability. We conclude that a rational, optimized sequencing of second-generation antiandrogens with other treatment options is feasible with present data.
Phase II Study of Continued Trastuzumab Plus Irinotecan in Patients with HER2-positive Gastric Cancer Previously Treated with Trastuzumab (HGCSG 1201)
Authors: Kawamoto Yasuyuki , Yuki Satoshi , Meguro Takashi , Hatanaka Kazuteru , Uebayashi Minoru , Nakamura Michio , Okuda Hiroyuki , Iwanaga Ichiro , Kato Takashi , Nakano Shintaro , Sato Atsushi , Harada Kazuaki , Oba Koji , Sakata Yuh , Sakamoto Naoya , Komatsu Yoshito
Published: January 2022

Background

The efficacy of irinotecan plus continuous trastuzumab beyond progression in patients with gastric cancer previously treated with trastuzumab plus standard first-line chemotherapy has not been reported.

Methods

Patients with human epidermal growth factor receptor 2 (HER2)-positive advanced gastric cancer who were previously treated with trastuzumab received trastuzumab every 3 weeks and irinotecan every 2 weeks. The primary endpoint was the overall response rate (ORR), and the secondary endpoints included progression-free survival (PFS), 6-month survival rates, safety, and subgroup analysis by HER2 status.

Results

Sixteen patients were enrolled in a 3-year pre-planned registration period. This study was prematurely closed due to poor patient accrual. The ORR and disease control rate were 6.7% (95% CI, 0.2-32.0) and 53.3% (95% CI, 26.6-78.7). The median PFS and overall survival (OS) were 2.4 months (95% CI, 0.0-5.2) and 9.7 months (95% CI, 8.2-11.2), respectively. The most frequently reported grades 3-4 adverse events were neutropenia (40%), anemia (27%), anorexia (33%), and fatigue (33%).

Conclusion

With only 16 patients enrolled, the present study has very low power to detect any clinical benefit of trastuzumab plus irinotecan beyond disease progression in patients with HER2-positive advanced gastric cancer who previously received trastuzumab.

Trial Identifier: UMIN000007636.
Combining Analysis of Tumor-infiltrating Lymphocytes (TIL) and PD-L1 Refined the Prognostication of Breast Cancer Subtypes
Authors: Ni Yunbi , Tsang Julia Y , Shao Yan , Poon Ivan K , Tam Fiona , Shea Ka-Ho , Tse Gary M
Published: January 2022

Background

PD-L1 has been used as a biomarker to select patients for treatment of PD-1/PD-L1 inhibitors.

Materials and Methods

In this study, we assessed the clinicopathological features of breast cancers that are associated with PD-L1 expression, as well as its relationship with other immune components and its prognostic significance.

Results

Totally 1752 cases were included in this cohort. PD-L1 expression in tumor-infiltrating immune cells (PD-L1-IC) expression and in tumor cells (PD-L1-TC) expression were identified in 34.2% and 10.1% of cases, respectively, and they showed a positive correlation with higher tumor grade, morphological apocrine features, presence of necrosis, and higher stromal tumor-infiltrating lymphocytes (sTIL). PD-L1-IC and PD-L1-TC expression correlated positively with each other, and both of them were negatively associated with estrogen receptor and progesterone receptor and positively associated with Ki67, HER2, EGFR, p63, and p-cadherin. In survival analysis, PD-L1-IC expression was associated with better disease-free survival (DFS) and breast cancer-specific survival (BCSS) in HER2-overexpressed (HER2-OE) cancers and high–grade luminal B cancers. In triple–negative breast cancers (TNBC) and HER2–OE cancers, compared with sTIL low PD-L1-IC negative cases, sTIL high cases showed significantly better DFS independent of PD-L1-IC status. sTIL low PD-L1-IC positive cases also demonstrated a better DFS in HER2–OE cancers. In high–grade luminal B cancers, sTIL high PD-L1-IC positive cases showed the best BCSS.

Conclusion

The data suggested that the combining analysis of sTIL and PD-L1-IC expression refined the prognostication of breast cancer subtypes. Cases with high TIL and PD-LI-IC expression appear to be more immune active.
Inventory-Constrained Underwriters and Corporate Bond Offerings
Authors: Nagler Florian , Ottonello Giorgio
Published: January 2022

We empirically study how inventory constraints of underwriters affect corporate bond offerings. Using underwriter-insurer-level transaction data, we find that a more constrained underwriter is more likely to place a bond and increases the allocation in the primary market to an insurer with a stronger preexisting relationship. The same underwriter is also more likely to buy back part of an allocation from the same insurer within 6 to 12 months after an offering. Overall, by “parking” inventory to relationship investors in the primary market, underwriters mitigate the effect of their inventory constraints on firms’ bond financing costs. (JEL G12, G32)
Human Mesenchymal Stem/Stromal Cells in Immune Regulation and Therapy
Authors: Mezey Éva
Published: January 2022

Studies of mesenchymal stem (or stromal) cells (MSCs) have moved from bedside to bench and back again. The stromal cells or fibroblasts are found in all tissues and participate in building the extracellular matrix (ECM). Bone marrow (BM)-derived MSCs have been studied for more than 50 years and have multiple roles. They function as stem cells and give rise to bone, cartilage, and fat in the BM (these are stem cells); support hematopoiesis (pericytes); and participate in sensing environmental changes and balancing pro- and anti-inflammatory conditions. In disease states, they migrate to sites of injury and release cytokines, hormones, nucleic acids depending on the microenvironment they find. Clinicians have begun to exploit these properties of BM, adipose tissue, and umbilical cord MSCs because they are easy to harvest and expand in culture. In this review, I describe the uses to which MSCs have been put, list ongoing clinical trials by organ system, and outline how MSCs are thought to regulate the innate and adaptive immune systems. I will discuss some of the reasons why clinical applications are still lacking. Much more work will have to be done to find the sources, doses, and culture conditions needed to exploit MSCs optimally and learn their healing potential. They are worth the effort.
Otic Organoids Containing Spiral Ganglion Neuron-like Cells Derived from Human-induced Pluripotent Stem Cells as a Model of Drug-induced Neuropathy
Authors: Kurihara Sho , Fujioka Masato , Hirabayashi Motoki , Yoshida Tomohiko , Hosoya Makoto , Nagase Masashi , Kato Fusao , Ogawa Kaoru , Okano Hideyuki , Kojima Hiromi , Okano Hirotaka James
Published: January 2022

The spiral ganglion of the cochlea is essential for hearing and contains primary bipolar neurons that relay action potentials generated by mechanosensory hair cells. Injury to spiral ganglion neurons (SGNs) causes permanent hearing loss because these cells have limited regenerative capacity. Establishment of human cell-derived inner ear tissue in vitro could facilitate the development of treatments for hearing loss. Here, we report a stepwise protocol for differentiating human-induced pluripotent stem cells (hiPSCs) into otic organoids that contain SGN-like cells and demonstrate that otic organoids have potential for use as an experimental model of drug-induced neuropathy. Otic progenitor cells (OPCs) were created by 2D culture of hiPSCs for 9 days. Otic spheroids were formed after 2D culture of OPCs for 2 days in a hypoxic environment. Otic organoids were generated by 3D culture of otic spheroids under hypoxic conditions for 5 days and normoxic conditions for a further 30 days or more. The protein expression profile, morphological characteristics, and electrophysiological properties of SGN-like cells in otic organoids were similar to those of primary SGNs. Live-cell imaging of AAV-syn-EGFP-labeled neurons demonstrated temporal changes in cell morphology and revealed the toxic effects of ouabain (which causes SGN-specific damage in animal experiments) and cisplatin (a chemotherapeutic drug with ototoxic adverse effects). Furthermore, a cyclin-dependent kinase-2 inhibitor suppressed the toxic actions of cisplatin on SGN-like cells in otic organoids. The otic organoid described here is a candidate novel drug screening system and could be used to identify drugs for the prevention of cisplatin-induced neuropathy.
Site-Specific Integration of TRAIL in iPSC-Derived Mesenchymal Stem Cells for Targeted Cancer Therapy
Authors: Wang Zujia , Chen Hongting , Wang Peiyun , Zhou Miaojin , Li Guangxu , Hu Zhiqing , Hu Qian , Zhao Junya , Liu Xionghao , Wu Lingqian , Liang Desheng
Published: January 2022

Mesenchymal stem cells (MSCs) are a promising cellular vehicle for transferring anti-cancer factors to malignant tumors. Currently, a variety of anti-cancer agents, including the tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL), have been loaded into MSCs derived from a range of sources through different engineering methods. These engineered MSCs exhibit enormous therapeutic potential for various cancers. To avoid the intrinsic defects of MSCs derived from tissues and the potential risk of viral vectors, TRAIL was site-specifically integrated into the ribosomal DNA (rDNA) locus of human-induced pluripotent stem cells (iPSCs) using a non-viral rDNA-targeting vector and transcription activator-like effector nickases (TALENickases). These genetically modified human iPSCs were differentiated into an unlimited number of homogeneous induced MSCs (TRAIL-iMSCs) that overexpressed TRAIL in both culture supernatants and cell lysates while maintaining MSC-like characteristics over continuous passages. We found that TRAIL-iMSCs significantly induced apoptosis in A375, A549, HepG2, and MCF-7 cells in vitro. After intravenous infusion, TRAIL-iMSCs had a prominent tissue tropism for A549 or MCF-7 xenografts and significantly inhibited tumor growth through the activation of apoptotic signaling pathways without obvious side effects in tumor-bearing mice models. Altogether, our results showed that TRAIL-iMSCs have strong anti-tumor effects in vitro and in vivo on a range of cancers. This study allows for the development of an unlimited number of therapeutic gene-targeted MSCs with stable quality and high homogeneity for cancer therapy, thus highlighting a universal and safe strategy for stem cell-based gene therapy with high potential for clinical applications.
Microbial Sensing by Hematopoietic Stem and Progenitor Cells
Authors: Barman Pijus K , Goodridge Helen S
Published: January 2022

Balanced production of immune cells is critical for the maintenance of steady-state immune surveillance, and increased production of myeloid cells is sometimes necessary to eliminate pathogens. Hematopoietic stem and progenitor cell (HSPC) sensing of commensal microbes and invading pathogens has a notable impact on hematopoiesis. In this review, we examine how commensal microbes regulate bone marrow HSPC activity to maintain balanced hematopoiesis in the steady state, and how HSPCs proliferate and differentiate during emergency myelopoiesis in response to infection. HSPCs express a variety of pattern recognition receptors and cytokine receptors that they use to sense the presence of microbes, either directly via detection of microbial components and metabolites, or indirectly by responding to cytokines produced by other host cells. We describe direct and indirect mechanisms of microbial sensing by HSPCs and highlight evidence demonstrating long-term effects of acute and chronic microbial stimuli on HSPCs. We also discuss a possible connection between myeloid-biased hematopoiesis and elevated levels of circulating microbiome-derived components in the context of aging and metabolic stress. Finally, we highlight the prospect of trained immunity-based vaccines that could exploit microbial stimulation of HSPCs.
Generation of a Cone Photoreceptor-specific GNGT2 Reporter Line in Human Pluripotent Stem Cells
Authors: Nazlamova Liliya , Cassidy Emma-Jane , Sowden Jane C , Lotery Andrew , Lakowski Jörn
Published: January 2022

Fluorescent reporter lines generated in human pluripotent stem cells are a highly useful tool to track, isolate, and analyze cell types and lineages in live cultures. Here, we generate the first human cone photoreceptor reporter cell line by CRISPR/Cas9 genome editing of a human embryonic stem cell (hESC) line to tag both alleles of the Guanine nucleotide-binding protein subunit gamma-T2 (GNGT2) gene with a mCherry reporter cassette. Three-dimensional optic vesicle-like structures were produced to verify reporter fidelity and track cones throughout their development in culture. The GNGT2-T2A-mCherry hESC line faithfully and robustly labels GNGT2-expressing cones throughout the entirety of their differentiation in vitro, recapitulating normal fetal expression of this gene. Our observations indicate that human cones undergo significant migratory activity during the course of differentiation in vitro. Consistent with this, our analysis of human fetal retinae from different stages of development finds positional differences of the cone population depending on their state of maturation. This novel reporter line will provide a useful tool for investigating human cone development and disease.
Single-Cell RNA Sequencing-Based Characterization of Resident Lung Mesenchymal Stromal Cells in Bronchopulmonary Dysplasia
Authors: Mižíková Ivana , Lesage Flore , Cyr-Depauw Chanele , Cook David P , Hurskainen Maria , Hänninen Satu M , Vadivel Arul , Bardin Pauline , Zhong Shumei , Carpén Olli , Vanderhyden Barbara C , Thébaud Bernard
Published: January 2022

Late lung development is a period of alveolar and microvascular formation, which is pivotal in ensuring sufficient and effective gas exchange. Defects in late lung development manifest in premature infants as a chronic lung disease named bronchopulmonary dysplasia (BPD). Numerous studies demonstrated the therapeutic properties of exogenous bone marrow and umbilical cord-derived mesenchymal stromal cells (MSCs) in experimental BPD. However, very little is known regarding the regenerative capacity of resident lung MSCs (L-MSCs) during normal development and in BPD. In this study we aimed to characterize the L-MSC population in homeostasis and upon injury. We used single-cell RNA sequencing (scRNA-seq) to profile in situ Ly6a+ L-MSCs in the lungs of normal and O2-exposed neonatal mice (a well-established model to mimic BPD) at 3 developmental timepoints (postnatal days 3, 7, and 14). Hyperoxia exposure increased the number and altered the expression profile of L-MSCs, particularly by increasing the expression of multiple pro-inflammatory, pro-fibrotic, and anti-angiogenic genes. In order to identify potential changes induced in the L-MSCs transcriptome by storage and culture, we profiled 15 000 Ly6a+ L-MSCs after in vitro culture. We observed great differences in expression profiles of in situ and cultured L-MSCs, particularly those derived from healthy lungs. Additionally, we have identified the location of Ly6a+/Col14a1+ L-MSCs in the developing lung and propose Serpinf1 as a novel, culture-stable marker of L-MSCs. Finally, cell communication analysis suggests inflammatory signals from immune and endothelial cells as main drivers of hyperoxia-induced changes in L-MSCs transcriptome.
SARS-CoV-2 vaccination induces immunological memory able to cross-recognize variants from Alpha to Omicron
Authors: Tarke Alison , Coelho Camila H. , Zhang Zeli , Dan Jennifer M. , Yu Esther Dawen , Methot Nils , Bloom Nathaniel I. , Goodwin Benjamin , Phillips Elizabeth , Mallal Simon , Sidney John , Filaci Gilberto , Weiskopf Daniela , da Silva Antunes Ricardo , Crotty Shane , Grifoni Alba , Sette Alessandro
Published: January 2022

We address whether T cell responses induced by different vaccine platforms (mRNA-1273, BNT162b2, Ad26.COV2.S, NVX-CoV2373) cross-recognize SARS-CoV-2 variants. Preservation of at least 83% and 85% for CD4+and CD8+T cell responses was found, respectively, regardless of vaccine platform or variants analyzed. By contrast, highly significant decreases were observed for memory B cell and neutralizing antibody recognition of variants. Bioinformatic analyses showed full conservation of 91% and 94% of class II and class I spike epitopes. For Omicron, 72% of class II and 86% of class I epitopes were fully conserved, and 84% and 85% of CD4+and CD8+T cell responses were preserved. In-depth epitope repertoire analysis showed a median of 11 and 10 spike epitopes recognized by CD4+and CD8+T cells from vaccinees. Functional preservation of the majority of the T cell responses may play an important role as a second-level defense against diverse variants.
Cross reactivity of spike glycoprotein induced antibody against Delta and Omicron variants before and after third SARS-CoV-2 vaccine dose
Authors: Faustini Sian E , Shields Adrian M , Banham Gemma , Wall Nadezhda , Al-Taei Saly , Tanner Chloe , Ahmed Zahra , Efstathiou Elena , Townsend Neal , Plant Tim , Perez-Toledo Marisol , Jasiulewicz Aleksandra , Price Ruth , McLaughlin James , Farnan John , Moore Julie , Robertson Louise , Nesbit Andrew , Curry Grace , Black Amy , Cunningham Adam F , Harper Lorraine , Moore Tara , Drayson Mark T , Richter Alex G
Published: January 2022

Variants of SARS-CoV-2 may evade natural and vaccine induced immunity and monoclonal antibody immunotherapeutics. There is an urgent need to know how well antibodies, induced by healthy and Clinically Extremely Vulnerable (CEV) patients, will bind and thus help reduce transmission and severity of infection from variants of concern (VOC). This study determines the cross-reactive binding of serum antibodies obtained prior to and 28 days after a third vaccination in three cohorts; a health care worker cohort who received three doses of Pfizer-BioNtech (PPP), a cohort of CEV patients received two doses of the AstraZeneca-ChAdOx1-nCoV-19 (AAP) vaccine, followed by a third PFZ vaccine and a haemodialysis cohort that had a mixture of two AZ or PFZ vaccines followed by a PFZ booster. Six months post second vaccine there was evidence of antibody waning with 58.9% of individuals in the HD cohort seropositive against Wuhan, 34.4% Delta and 62.2% Omicron strains. For the AAP cohort, equivalent figures were 62.5%, 45.8% and 91.7% and the PPP cohort 92.2%, 90% and 91.1%. Post third dose vaccination there were universal increases in seropositivity and median optical density. For the HD cohort, 98.8% were seropositive to the Wuhan strain, 97.6% against Delta and 100% against Omicron strains. For the PPP and AAP cohorts, 100% were seropositive against all 3 strains. Lastly, we examined the WHO NIBSC 20/136 standard and there was no loss of antibody binding to either VOC. Similarly, a dilution series of Sotrovimab (GSK) found this therapeutic monoclonal antibody bound similarly to all VOC.

Highlights

IgG anti-SARS-CoV-2 Omicron spike glycoprotein antibody levels were high in 100% of health care workers (HCW), a general practice population considered clinically extremely vulnerable (CEV) and haemodialysis patients (HD) 4 weeks after a third SARS-CoV-2 vaccine dose (Pfizer-BioNtech-PFZ).

For both Delta and Omicron variant spike glycoproteins these antibody levels were highest in the CEV cohort who had previously received two doses of AstraZeneca ChAdOx1 nCoV-19 vaccine (AAP), lower in HCW who had previously received two doses of PFZ (PPP) and lowest in HD who had a mix of vaccines for the first and second dose

Prior to this third vaccine dose and 6 months post second vaccine dose there was evidence of significant waning of antibodies against VOC.
New 63 knot and other knots in human proteome from AlphaFold predictions
Authors: Perlinska Agata P. , Niemyska Wanda H. , Gren Bartosz A. , Rubach Pawel , Sulkowska Joanna I.
Published: January 2022

AlphaFold is a new, highly accurate machine learning protein structure prediction method that outperforms other methods. Recently this method was used to predict the structure of 98.5% of human proteins. We analyze here the structure of these AlphaFold-predicted human proteins for the presence of knots. We found that the human proteome contains 65 robustly knotted proteins, including the most complex type of a knot yet reported in proteins. That knot type, denoted 63 in mathematical notation, would necessitate a more complex folding path than any knotted proteins characterized to date. In some cases AlphaFold structure predictions are not highly accurate, which either makes their topology hard to verify or results in topological artifacts. Other structures that we found, which are knotted, potentially knotted, and structures with artifacts (knots) we deposited in a database available at: https://knotprot.cent.uw.edu.pl/alphafold.
Muscarinic acetylcholine receptors modulate HCN channel properties in vestibular ganglion neurons
Authors: Bronson Daniel , Kalluri Radha
Published: January 2022

Vestibular efferent neurons play an important role in shaping vestibular afferent excitability and, accordingly, on the information encoded by their spike patterns. Efferent- modulation is linked to muscarinic signaling cascades that affect ion channel conductances, most notably low-voltage gated potassium channels such as KCNQ. Here we tested and found that muscarinic signaling cascades also modulate hyperpolarization- activated cyclic-nucleotide gated channels (HCN). HCN channels play a key role in controlling spike-timing regularity and a non-chemical form of transmission between type I hair cells and vestibular afferents. The impact of cholinergic efferent input on HCN channels was assessed using voltage-clamp methods, which measure currents in the disassociated cell bodies of vestibular ganglion neurons (VGN). Membrane properties in VGN were characterized before and after administration of the muscarinic acetylcholine receptor (mAChR) agonist oxotremorine-M (Oxo-M). We found that Oxo-M shifted the voltage-activation range of HCN channels in the positive direction by 3.2 ± 0.7 mV, which more than doubled the available current when held near rest at -70 mV (a 139 ± 43% increase, n=12). This effect was not blocked by pre-treating the cells with a KCNQ channel blocker, linopirdine, which suggests that this effect is not dependent on KCNQ currents. We also found that HCN channel properties in the baseline condition and sensitivity to mAChR activation depended on cell size and firing patterns. Large-bodied neurons with onset firing patterns had the most depolarized activation range and least sensitivity to mAChR activation. Together, our results highlight the complex and dynamic regulation of HCN channels in VGN.

Significance Statement

Vestibular afferents express a diverse complement of ion channels. This diversity is key to shaping their various response properties, allowing them to encode both fast and slow head movements. In vitro studies that characterized afferent diversity identified low-voltage activated potassium channels and hyperpolarization-activated cyclic- nucleotide gated (HCN) channels as crucial for shaping the timing and sensitivity of afferent responses. Afferent excitability is known to be controlled by a network of acetylcholine-releasing efferent neurons that close a type of low-voltage activated potassium channel found on the afferent neuron. Here, we show that the same efferent signaling cascade that shuts these potassium channels also enhances the activation of HCN channels by depolarizing their voltage-activation range. The size of this effect varies from cell to cell depending on the endogenous properties of the HCN channel and on cell type (as determined by discharge patterns and cell size). Simultaneously controlling two ion-channel groups gives the vestibular efferent system robust and flexible control over the excitability and timing properties vestibular afferent activity.
Patterns of Arc mRNA expression in the rat brain following dual recall of fear- and reward-based socially acquired information
Authors: Agee Laura A. , Hilz Emily N. , Jun Dohyun , Nemchek Victoria , Lee Hongjoo J. , Monfils Marie-H.
Published: January 2022

The ability to learn new information and behaviors is a vital component of survival in most animal species. This learning can occur via direct experience or through observation of another individual (i.e., social learning). While research focused on understanding the neural mechanisms of direct learning is prevalent, less work has aimed at understanding the brain circuitry mediating the acquisition and recall of socially acquired information. We aimed to further elucidate the mechanisms underlying recall of socially acquired information by having rats sequentially recall a socially transmitted food preference (STFP) and a fear association via fear conditioning by-proxy (FCbP). Brain tissue was processed for mRNA expression of the immediate early gene (IEG) Arc, which reliably expresses in the cell nucleus following transcription before migrating to the cytoplasm over the next 25 minutes. Given this timeframe, we were able to identify whether Arc transcription was triggered by STFP recall, FCbP recall, or following recall of both memories. Surprisingly – and contrary to past research examining expression of other IEGs following STFP or FCbP recall separately – we found no differences in any of the Arc expression measures across a number of prefrontal regions and the vCA3 of the hippocampus between controls, demonstrators, and observers, though we did detect an overall effect of sex in a number of regions. We theorize that these results may indicate that relatively little Arc-dependent neural restructuring is taking place in the prefrontal cortices following recall of a recently socially acquired information or directly acquired fear associations in these areas.
High affinity enhancer-promoter interactions can bypass CTCF/cohesin-mediated insulation and contribute to phenotypic robustness
Authors: Chakraborty Shreeta , Kopitchinski Nina , Eraso Ariel , Awasthi Parirokh , Chari Raj , Rocha Pedro P
Published: January 2022

Transcriptional control by distal enhancers is an integral feature of gene regulation. To understand how enhancer-promoter interactions arise and assess the impact of disrupting 3D chromatin structure on gene expression, we generated an allelic series of mouse mutants that perturb the physical structure of the Sox2 locus. We show that in the epiblast and in neuronal tissues, CTCF-mediated loops are neither required for the interaction of the Sox2 promoter with distal enhancers, nor for its expression. Insertion of various combinations of CTCF motifs between Sox2 and its distal enhancers generated ectopic loops with varying degrees of insulation that directly correlated with reduced transcriptional output. Yet, even the mutants exhibiting the strongest insulation, with six CTCF motifs in divergent orientation, could not fully abolish activation by distal enhancers, and failed to disrupt implantation and neurogenesis. In contrast, cells of the anterior foregut were more susceptible to chromatin structure disruption with no detectable SOX2 expression in mutants with the strongest CTCF-mediated boundaries. These animals phenocopied loss of SOX2 in the anterior foregut, failed to separate trachea from esophagus and died perinatally. We propose that baseline transcription levels and enhancer density may influence the tissue-specific ability of distal enhancers to overcome physical barriers and maintain faithful gene expression. Our work suggests that high affinity enhancer-promoter interactions that can overcome chromosomal structural perturbations, play an essential role in maintaining phenotypic robustness.
Theta- and gamma-band oscillatory uncoupling in the macaque hippocampus
Authors: Abbaspoor S. , Hussin A.T. , Hoffman K.L.
Published: January 2022

Nested hippocampal oscillations in the rodent give rise to temporal dynamics that may underlie learning, memory, and decision making. Although theta/gamma coupling in rodent CA1 occurs during exploration, in contrast to sharp-wave ripples that emerge in quiescence, it is less clear that these oscillatory regimes extend to primates. We, therefore, sought to identify correspondences in frequency bands, nesting, and behavioral coupling taken from the macaque hippocampus. We found that, in contrast to rodent oscillations, theta and gamma frequency bands in macaque CA1 were segregated by behavioral states. Beta2/gamma (15-70 Hz) had greater power during visual search while the theta band (3-10 Hz; peak ∼8 Hz) dominated during quiescence. Moreover, theta band amplitude was strongest when beta2/slow gamma (20-35 Hz) amplitude was weakest, occurring instead concomitant with higher frequencies (60-150 Hz). Spike-field coherence was most frequently seen in these three bands, (3-10 Hz, 20-35 Hz, and 60-150 Hz); however, the theta-band coherence was largely due to spurious coupling during sharp-wave ripples. Accordingly, no intrinsic theta spiking rhythmicity was apparent. These results support a role for beta2/slow gamma modulation in CA1 during active exploration in the primate that is decoupled from theta oscillations. The apparent difference to the rodent oscillatory canon calls for a shift in focus of frequency when considering the primate hippocampus.