Biology subjects

Chi, M.

Publications and source records attributed to Chi, M..

7 recordsLinked to original sources

bioRxiv2026

Hemoglobin C is prone to oxidative denaturation, resulting in red blood cell membrane damage in HbSC disease

Sickle-hemoglobin-C (HbSC) sickle cell disease is characterized by RBC dehydration (xerocytosis), which promotes polymerization of HbS. HbSC causes substantial morbidity despite lower sickling potential than HbSS, suggesting a critical detrimental role of HbC in the disease pathophysiology. We derived HbCC mice by interbreeding our HbSC mice, which demonstrated a similar RBC phenotype of xerocytosis as humans with HbCC. We compared RBCs from HbCC, HbSC, and HbSS mice. Oxidized ferryl (Fe4+)-Hb, and its oxidative-denaturation, which results in hemichrome formation (Heinz-bodies), was most pronounced in HbCC>HbSC>HbSS, despite significantly higher reactive oxygen species in HbSS, illustrating a higher propensity of HbC to denaturation than HbS. RBC deformability followed a similar pattern, with Elongation Index lowest in HbCC<HbSC<HbSS. Next, we determined if RBC from HbSC patients on hydroxyurea showed improved membrane damage. Hydroxyurea treatment reduced Heinz-body formation and improved RBC deformability, despite negligible/modest fetal hemoglobin (HbF) induction, compared to non-hydroxyurea HbSC controls. The antioxidant quercetin showed a similar reduction in Heinz-body burden and improvement in RBC deformability as hydroxyurea, without affecting Hb or HbF concentration, reticulocyte count, or RBC xerocytosis. HbC-driven oxidative denaturation and membrane damage represent important contributors of RBC dysfunction in HbSC disease; hence, oxidative membrane injury could be targeted besides antisickling approaches.

cell biology↗

bioRxiv2026

Temporal structure of task engagement organizes infra-slow BOLD dynamics

Task-based fMRI has traditionally characterized cognitive engagement through spatial patterns of BOLD activation, leaving open whether tasks also organize activity along the frequency dimension. Here we tested whether temporally structured task engagement reshapes infra-slow BOLD dynamics, asking whether task responses are simply superimposed onto ongoing activity or instead redistribute power across the infra-slow spectrum. Across three independent fMRI datasets, task timing systematically reorganized the BOLD power spectrum. In the main visual attention dataset, periodic stimulation produced sharp stimulus-locked peaks at 0.083 and 0.125 Hz; critically, these gains were matched by a reduction concentrated within the dominant intrinsic infra-slow range (0.01-0.04 Hz), indicating redistribution rather than a simple local increase. Independent auditory and visual-motion datasets showed analogous task-frequency responses at their respective timescales, indicating that this reorganization generalizes across modalities and stimulation frequencies. The peaks were spatially related to GLM-derived activation but persisted after removal of the GLM-modeled response, indicating that this frequency-specific organization is not fully reducible to conventional task-evoked activation. These features were functionally informative: task-imposed frequencies distinguished cognitive states, predicted individual reaction time, and preserved subject-specific signatures across runs more effectively than broader spectral ranges or GLM-derived features. Finally, Jansen-Rit simulations coupled to a Balloon-Windkessel model reproduced the peaks, showing that their expression depends on balanced excitatory, inhibitory, and filter-gain regimes rather than simple amplification of input. Together, these findings indicate that task-fMRI reveals not only where cognition is localized, but how temporally structured engagement redistributes infra-slow dynamics across timescales.

neuroscience↗

bioRxiv2024

The S2 subunit of spike encodes diverse targets for functional antibody responses to SARS-CoV-2

The SARS-CoV-2 virus responsible for the COVID-19 global pandemic has exhibited a striking capacity for viral evolution that drives continued evasion from vaccine and infection-induced immune responses. Mutations in the receptor binding domain of the S1 subunit of the spike glycoprotein have led to considerable escape from antibody responses, reducing the efficacy of vaccines and monoclonal antibody (mAb) therapies. Therefore, there is a need to interrogate more constrained regions of Spike, such as the S2 subdomain. Here, we describe a collection of S2 mAbs from two SARS-CoV-2 convalescent individuals that target multiple regions in the S2 subdomain and can be grouped into at least five epitope classes. Most did not neutralize SARS-CoV-2 with the exception of C20.119, which bound to a highly conserved epitope in the fusion peptide and showed broad binding and neutralization activity across SARS-CoV-2, SARS-CoV-1, and closely related zoonotic sarbecoviruses. Several of the S2 mAbs tested mediated antibody-dependent cellular cytotoxicity (ADCC) at levels similar to the S1 mAb S309 that was previously authorized for treatment of SARS-CoV-2 infections. Three of the mAbs with ADCC function also bound to spike trimers from HCoVs, such as MERS-CoV and HCoV-HKU1. Our findings suggest there are diverse epitopes in S2, including functional S2 mAbs with HCoV and sarbecovirus breadth that likely target functionally constrained regions of spike. These mAbs could be developed for potential future pandemics, while also providing insight into ideal epitopes for eliciting a broad HCoV response. AUTHOR SUMMARYThe early successes of vaccines and antibody therapies against SARS-CoV-2, the virus responsible for the COVID-19 global pandemic, leveraged the considerable antibody response to the viral entry protein, spike, after vaccination or infection. These initial interventions were highly effective at protecting from infection and reducing severe disease or death. However, SARS-CoV-2 has shown no sign of abating, with the continued rise of new variants that have escaped some of the antibody defense due to distinct alterations most significantly in regions of the spike protein that elicit most of the anti-viral, functional antibody response. These findings suggest a critical need to identify vaccine approaches and therapies that provide the broadest possible antibody responses, focused on regions of spike critical for SARS-CoV-2 infection and, therefore, do not undergo changes that could lead to immune evasion. Our study describes a panel of functional antibodies, from individuals after SARS-CoV-2 infection, that recognize the S2 spike subdomain that is responsible for carrying out viral fusion with host cells. These regions in S2 are generally well conserved across SARS-CoV-2 variants and other closely related viruses and thus, could guide more effective vaccine design in the face of continued viral evolution.

immunology↗

bioRxiv2020

Sclerostin depletion induces inflammation in the bone marrow of mice

Romosozumab, a humanized monoclonal antibody specific for sclerostin, has been approved for treatment of post-menopausal women with osteoporosis at high risk for fracture. In several Phase III clinical trials, romosozumab decreased the risk of vertebral fractures up to 73% and increased total hip area bone mineral density by 3.2%. Previous work in 12 to 15-week-old sclerostin-knockout (Sost-/-) mice indicated that changes in immune cell development occur in the bone marrow (BM), which could be a possible side effect to follow in human patients. Our overall goal was to define the mechanisms that guide behavior of long-term hematopoietic stem cells (LT-HSCs) after exposure to an irregular BM microenvironment. SOST plays an important role in maintaining bone homeostasis, as demonstrated by the increased ratio of bone volume to total volume observed in Sost-/- mice. Here, we examined the effects of short-term sclerostin depletion in the BM on hematopoiesis in young (8 week-old) mice receiving sclerostin-antibody (Scl-Ab) treatment for 6 weeks, and the effects of long-term Sost-deficiency on wild-type (WT) LT-HSCs transplanted into older (16-22 week-old) cohorts of Sost-/- mice. Our analyses revealed an increased frequency of granulocytes and decreased frequency of lymphocytes in the BM of Scl-Ab treated mice and WT[->]Sost-/- hematopoietic chimeras, indicating myeloid-biased differentiation in Sost-deficient BM microenvironments. This myeloid bias extended to extramedullary hematopoiesis in the spleen and was correlated with an increase in inflammatory cytokines TNF, IL-1 and MCP-1 in the serum of the Sost-/- BM. Additionally, we observed alterations in erythrocyte differentiation in the BM and spleen of Sost-/- mice. Taken together, our current study indicates novel roles for Sost in the regulation of myelopoiesis and control of inflammation in the BM. Our animal studies strongly recommend tracking of hematopoietic function in patients treated with romosozumab.

immunology↗

bioRxiv2019

The Aging Microenvironment Shapes Alveolar Macrophage Identity in Aging

A dysfunctional response to inhaled pathogens and toxins drives a substantial portion of the susceptibility to acute and chronic lung disease in the elderly. We used transcriptomic profiling combined with genetic lineage tracing, heterochronic adoptive transfer, parabiosis and treatment with metformin to show that the lung microenvironment defines the phenotype of long-lived alveolar macrophages during aging. While tissue-resident alveolar macrophages persist in the lung without input from monocytes over the lifespan, severe lung injury results in their replacement with monocyte-derived alveolar macrophages. These monocyte-derived alveolar macrophages are also shaped by the microenvironment both during aging and in response to a subsequent environmental challenge to become transcriptionally and functionally similar to tissue-resident alveolar macrophages. These findings show that changes in alveolar macrophage phenotypes during injury and aging are not cell autonomous but instead are shaped by changes in the aging lung microenvironment.

immunology↗

bioRxiv2018

Transcriptome analysis of Culter alburnus gonad tissues for discovery of sex-related genes

Culter alburnus is an important commercially fish species for freshwater breeding in China, and the females grow faster than the males. However, the molecular genetic mechanism of sex determination in C.alburnus is still poorly characterized. Here, we performed de novo assembly of a transcriptome from adult fish tissues of different gender using short read sequencing technology (Illumina). Our results showed that a total of 364,650 unigenes using Trinity software were obtained, giving rise to an average of 561.92 bp per read. Among them, 70,215 sequences matched known genes, including 5,892 male-biased unigenes and 942 female-biased unigenes. Many sex-related genes and pathways were identified based on annotation information. These results would provide new insights into the genetic mechanism of C.alburnus sex determination and also establish an important foundation for further research on aquaculture breeding.

bioinformatics↗

bioRxiv2018

Single-Cell Transcriptomic Analysis of Human Lung Reveals Complex Multicellular Changes During Pulmonary Fibrosis

Pulmonary fibrosis is a devastating disorder that results in the progressive replacement of normal lung tissue with fibrotic scar. Available therapies slow disease progression, but most patients go on to die or require lung transplantation. Single-cell RNA-seq is a powerful tool that can reveal cellular identity via analysis of the transcriptome, but its ability to provide biologically or clinically meaningful insights in a disease context is largely unexplored. Accordingly, we performed single-cell RNA-seq on lung tissue obtained from eight transplant donors and eight recipients with pulmonary fibrosis and one bronchoscopic cryobiospy sample. Integrated single-cell transcriptomic analysis of donors and patients with pulmonary fibrosis identified the emergence of distinct populations of epithelial cells and macrophages that were common to all patients with lung fibrosis. Analysis of transcripts in the Wnt pathway suggested that within the same cell type, Wnt secretion and response are restricted to distinct non-overlapping cells, which was confirmed using in situ RNA hybridization. Single-cell RNA-seq revealed heterogeneity within alveolar macrophages from individual patients, which was confirmed by immunohistochemistry. These results support the feasibility of discovery-based approaches applying next generation sequencing technologies to clinically obtained samples with a goal of developing personalized therapies.\n\nOne Sentence SummarySingle-cell RNA-seq applied to tissue from diseased and donor lungs and a living patient with pulmonary fibrosis identifies cell type-specific disease-associated molecular pathways.

systems biology↗