Biology subjects

Cai, H.

Publications and source records attributed to Cai, H..

At least 91 records · Page 5Linked to original sources

bioRxiv2023

Brain Organoid Computing for Artificial Intelligence

Brain-inspired hardware emulates the structure and working principles of a biological brain and may address the hardware bottleneck for fast-growing artificial intelligence (AI). Current brain-inspired silicon chips are promising but still limit their power to fully mimic brain function for AI computing. Here, we develop Brainoware, living AI hardware that harnesses the computation power of 3D biological neural networks in a brain organoid. Brain-like 3D in vitro cultures compute by receiving and sending information via a multielectrode array. Applying spatiotemporal electrical stimulation, this approach not only exhibits nonlinear dynamics and fading memory properties but also learns from training data. Further experiments demonstrate real-world applications in solving non-linear equations. This approach may provide new insights into AI hardware.

bioengineering↗

bioRxiv2022

Transcriptomic landscape and potential therapeutic targets for human testicular aging revealed by single-cell RNA sequencing

BackgroundTesticular aging is known to cause male age-related fertility decline and hypogonadism, but the underlying molecular mechanisms remain unclear. MethodsWe survey the single-cell transcriptomic landscape of testes from young and old men and examine age-related changes in germline and somatic niche cells. ResultsIn-depth evaluation of the gene expression dynamics of germline cells reveals that disturbance of base-excision repair pathway is a major feature of aging spermatogonial stem cells (SSCs), suggesting that defective DNA repair of SSCs may serve as a potential driver for increased de novo germline mutations with age. Further analysis of aging-associated transcriptional changes shows that stress-related changes and apoptotic signaling pathway accumulate in aged somatic cells. We identify age-related impairment of redox homeostasis in aged Leydig cells and find that pharmacological treatment with antioxidants alleviate this cellular dysfunction of Leydig cells and promote testosterone production. Lastly, our results reveal that decreased pleiotrophin (PTN) signaling is a contributing factor for testicular aging. ConclusionsThese findings provide a comprehensive understanding of the cell-type-specific mechanisms underlying human testicular aging at a single-cell resolution, and suggest potential therapeutic targets that may be leveraged to address age-related male fertility decline and hypogonadism. FundingThis work was supported by the National Key Research and Development Program of China (2018YFA0107200, 2018YFA0801404), the National Natural Science Foundation of China (32130046, 82171564, 82101669, 81871110, 81971759), the Key Research and Development Program of Guangdong Province (2019B020234001), the Natural Science Foundation of Guangdong Province, China (2022A1515010371), the Major Project of Medical Science and Technology Development Research Center of National Health Planning Commission, China (HDSL202001000), the Open Project of NHC Key Laboratory of Male Reproduction and Genetics (Family Planning Research Institute of Guangdong Province) (KF202001), the Guangdong Province Regional Joint Fund-Youth Fund Project (2021A1515110921), the China Postdoctoral Science Foundation (2021M703736).

developmental biology↗

bioRxiv2022

Improved Neutralization of Omicron BA.4/5, BA.4.6, BA.2.75.2, BQ.1.1, and XBB.1 with Bivalent BA.4/5 Vaccine

The BNT162b2 bivalent BA.4/5 COVID-19 vaccine has been authorized to mitigate COVID-19 due to current Omicron and potentially future variants. New sublineages of SARS-CoV-2 Omicron continue to emerge and have acquired additional mutations, particularly in the spike protein, that may lead to improved viral fitness and immune evasion. The present study characterized neutralization activities against new Omicron sublineages BA.4.6, BA.2.75.2, BQ.1.1, and XBB.1 after a 4th dose (following three doses of BNT162b2) of either the original monovalent BNT162b2 or the bivalent BA.4/5 booster in individuals >55 years of age. For all participants, the 4th dose of monovalent BNT162b2 vaccine induced a 3.0x, 2.9x, 2.3x, 2.1x, 1.8x, and 1.5x geometric mean neutralizing titer fold rise (GMFR) against USA/WA1-2020 (a strain isolated in January 2020), BA.4/5, BA.4.6, BA.2.75.2, BQ.1.1, and XBB.1, respectively; the bivalent vaccine induced 5.8x, 13.0x, 11.1x, 6.7x, 8.7x, and 4.8x GMFRs. For individuals without SARS-CoV-2 infection history, BNT162b2 monovalent induced 4.4x, 3.0x, 2.5x, 2.0x, 1.5x, and 1.3x GMFRs, respectively; the bivalent vaccine induced 9.9x, 26.4x, 22.2x, 8.4x, 12.6x, and 4.7x GMFRs. These data suggest the bivalent BA.4/5 vaccine is more immunogenic than the original BNT162b2 monovalent vaccine against circulating Omicron sublineages, including BQ.1.1 that is becoming prevalent globally.

microbiology↗

bioRxiv2022

The GxcM-Fbp17/RacC-WASP signaling cascade regulates polarized cortex assembly in migrating cells

The actin-rich cortex plays a fundamental role in many cellular processes. Its architecture and molecular composition vary across cell types and physiological states. The full complement of actin assembly factors driving cortex formation and how their activities are spatiotemporally regulated remain to be fully elucidated. Using Dictyostelium as a model for polarized and rapidly migrating cells, we show that GxcM, a RhoGEF localized specifically in the rear of migrating cells, functions together with F-BAR protein Fbp17, a small GTPase RacC, and the actin nucleation-promoting factor WASP to coordinately promote Arp2/3 complex-mediated cortical actin assembly. Over-activation of this signaling cascade leads to excessive actin polymerization in the rear cortex, whereas its disruption causes defects in cortical integrity and function. Therefore, different from its well-defined role in the formation of the front protrusions, the Arp2/3 complex-based actin carries out a previously unappreciated function in building the rear cortical subcompartment in rapidly migrating cells.

cell biology↗

bioRxiv2022

Central extended amygdala neurons in the development of activity-based anorexia

Anorexia nervosa (AN) is a serious psychiatric disease characterized by restricted eating, fear of gaining weight, as well as excessive exercise, and also is often comorbid with emotional disorders such as anxiety and depression. However, the etiology of AN is unknown and the neural mechanism that leads to AN remains to be determined. Here, we show that a specific subpopulation of neurons, marked by the expression of protein kinase C-delta (PKC-{delta}), in two nuclei of the central extended amygdala (EAc)-- central nucleus (CeA) and oval region of bed nucleus of stria terminalis (ovBNST)--regulates development of activity-based anorexia (ABA), the current best animal model of AN. Specifically, simultaneous dual ablation of CeAPKC-{delta} and ovBNSTPKC-{delta} neurons prevents the key phenotypes of ABA: increases in wheel activity, decreases in food intake, and life-threatening body weight loss. However, ablating PKC-{delta} neurons in CeA or ovBNST alone is not sufficient to prevent ABA. Correspondingly, activation of PKC-{delta} neurons in one type of nuclei continues to suppress food intake even when PKC-{delta} neurons in the other nuclei are silenced. Consistent with their role in suppressing food intake when activated, these PKC-{delta} neurons show increased activity with ABA development. Together, our study illuminates how neurons in the amygdala regulate ABA development and supports the complex and heterogenous etiology of AN.

neuroscience↗

bioRxiv2022

Molecular Recognition of Itching Neuropeptides by Bombesin Receptors.

Neuromedin B (NMB) and gastrin-releasing peptide (GRP), two bombesin analogs, are endogenous itch-specific neuropeptides that induce histaminergic and nonhistaminergic itch, respectively. Their functions are mediated by two G protein-coupled bombesin receptors, NMBR and GRPR. Here we present cryo-electron microscopy(cryo-EM) structures of G protein coupled NMBR and GRPR bound to NMB and GRP, respectively. The structures reveal that both bombesin receptors contain an extended and deep pocket to adopt NMB and GRP, with the conserved C-terminal motif of GH(F/L)M from both peptides to contact the toggle switch residues for the receptor activation. Together with mutational and functional data, our structures reveal the mechanism of ligand selectivity and specific activation of the bombesin receptors. These findings also pave the way to facilitate rational design of therapies targeting bombesin receptors for the treatment of pruritus.

biophysics↗

bioRxiv2022

Engineering human spinal microphysiological systems to model opioid-induced tolerance

Opioids are commonly used for treating chronic pain. However, with continued use, they may induce tolerance and/or hyperalgesia, which limits therapeutic efficacy. The human mechanisms of opioid-induced hyperalgesia are significantly understudied, in part, because current models cannot fully recapitulate human pathology. Here, we engineered novel human spinal microphysiological systems (MPSs) integrated with plug-and-play neural activity sensing for modeling human nociception and opioid-induced tolerance. Each spinal MPS consists of a flattened human spinal cord organoid derived from human stem cells and a 3D printed organoid holder device for plug-and-play neural activity measurement. We found that the flattened organoid design of MPSs not only reduces hypoxia and necrosis in the organoids, but also promotes their neuron maturation, neural activity, and functional development. We further demonstrated that prolonged opioid exposure resulted in neurochemical correlates of opioid tolerance and hyperalgesia, as measured by altered neural activity, reduced densities of glutamate transporter levels and downregulation of -opioid receptor expression of human spinal MPSs. The MPSs are scalable, cost-effective, easy-to-use, and compatible with commonly-used well-plates, thus allowing plug-and-play measurements of neural activity. We believe the MPSs hold a promising translational potential for studying human pain etiology, screening new treatments, and validating novel therapeutics for human pain medicine.

bioengineering↗

bioRxiv2022

Exposure to BA.4/BA.5 Spike glycoprotein drives pan-Omicron neutralization in vaccine-experienced humans and mice

The SARS-CoV-2 Omicron variant and its sublineages show pronounced viral escape from neutralizing antibodies elicited by vaccination or prior SARS-CoV-2 variant infection owing to over 30 amino acid alterations within the spike (S) glycoprotein. We and others have recently reported that breakthrough infection of vaccinated individuals with Omicron sublineages BA.1 and BA.2 are associated with distinct patterns of cross-neutralizing activity against SARS-CoV-2 variants of concern (VOCs). BA.2 breakthrough infection mediated overall stronger cross-neutralization of BA.2 and its descendants (BA.2.12.1, BA.4, and BA.5) compared to BA.1 breakthrough infection. Here we characterized the effect of Omicron BA.4/BA.5 S glycoprotein exposure on the magnitude and breadth of the neutralizing antibody response upon breakthrough infection in vaccinated individuals and in mice upon booster vaccination. We show that immune sera from triple mRNA-vaccinated individuals with subsequent Omicron BA.4/BA.5 breakthrough infection display broad and robust neutralizing activity against Omicron BA.1, BA.2, BA.2.12.1, and BA.4/BA.5. Administration of a prototypic BA.4/BA.5-adapted mRNA booster vaccine to mice following SARS-CoV-2 wild-type strain-based primary immunization is associated with similarly broad neutralizing activity. Immunization of naive mice with a bivalent mRNA vaccine (wild-type + Omicron BA.4/BA.5) induces strong and broad neutralizing activity against Omicron VOCs and previous variants. These findings suggest that when administered as boosters, mono- and bivalent Omicron BA.4/BA.5-adapted vaccines may enhance neutralization breadth, and in a bivalent format may also have the potential to confer protection to individuals with no pre-existing immunity against SARS-CoV-2.

immunology↗

bioRxiv2022

Identification of GTF2IRD1 as a novel transcription factor essential for acute myeloid leukemia

Acute myeloid leukemia (AML) is an aggressive blood malignancy characterized by clonal accumulation of immature myeloid progenitors in the bone marrow and peripheral blood. Transcription factors are the most frequently mutated and dysregulated genes in AML, and they have critical roles in AML pathogenesis and progression. In this study, we performed large-scale RNA interference screens in MLL-AF9-transformed AML cells and identified GTF2IRD1 as a novel transcription factor essential for the survival of various types of myeloid leukemic cells in vitro and in vivo, but not for primary normal hematopoietic cells. Inhibition of GTF2IRD1 reduced the frequency of primary childhood and adult AML cells, including cell populations enriched for leukemia-initiating cells. In animal models for AML, inhibition of GTF2IRD1 significantly delayed the disease progression. Loss of GTF2IRD1 promoted accumulation of AML cells in the G0 phase of the cell cycle but caused minor effects in apoptosis induction. In line with this, RNA sequencing analysis revealed a significant downregulation of E2F targets as a consequence of genetic inhibition of GTF2IRD1. Taken together, we identified GTF2IRD1 as a transcription factor with a selective importance in AML, and our findings may contribute to the development of improved therapeutic inventions for the disease.

cancer biology↗

bioRxiv2022

An interpretable machine learning algorithm to predict disordered protein phase separation based on biophysicalinteractions

Protein phase separation is increasingly understood to be an important mechanism of biological organization and biomaterial formation. Intrinsically disordered protein regions (IDRs) are often significant drivers of protein phase separation. A number of protein phase separation prediction algorithms are available, with many specific for particular classes of proteins and others providing results that are not amenable to interpretation of contributing biophysical interactions. Here we describe LLPhyScore, a new predictor of IDR-driven phase separation, based on a broad set of physical interactions or features. LLPhyScore uses sequence-based statistics from the RCSB PDB database of folded structures for these interactions, and is trained on a manually curated set of phase separation driver proteins with different negative training sets including the PDB and human proteome. Competitive training for a variety of physical chemical interactions shows the greatest importance of solvent contacts, disorder, hydrogen bonds, pi-pi contacts, and kinked-beta structure, with electrostatics, cation-pi, and absence of helical secondary structure also contributing. LLPhyScore has strong phase separation prediction recall statistics and enables a quantitative breakdown of the contribution from each physical feature to a sequences phase separation propensity. The tool should be a valuable resource for guiding experiment and providing hypotheses for protein function in normal and pathological states, as well as for understanding how specificity emerges in defining individual biomolecular condensates. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/499043v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@151f0cdorg.highwire.dtl.DTLVardef@984335org.highwire.dtl.DTLVardef@645b3dorg.highwire.dtl.DTLVardef@a22b06_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2022

On-Demand Fully-Enclosed Superhydrophobic-Optofluidic Device Enabled by High Precision Microstereolithography

Superhydrophobic surface-based optofluidics have been introduced to biosensors and unconventional optics with unique advantages such as low light loss and power consumption. However, most of these platforms were made with planar-like micro- and nano-structures, which may cause bonding issues and resulting in significant waveguide loss. Here, we introduce a fully-enclosed superhydrophobic-based optofluidics system, enabled by a one-step high precision microstereolithography procedure. Various micro-structured cladding designs with a feature size down to 100 m were studied and a "T-type" overhang design exhibits the lowest optical loss, regardless of the excitation wavelength. Surprisingly, the optical loss of superhydrophobic-based optofluidics is not solely decided by the solid area fraction at the solid/water/air interface, but also the cross-section shape and the effective cladding layer composition. We show that this fully-enclosed optofluidic system can be used for CRISPR-labeled quantum dot quantification, intended for in vitro and in vivo CRISPR therapeutics.

bioengineering↗

bioRxiv2022

A Mesenchymal Cell Niche in Skin for Acute Myeloid Leukemia

Leukemia cutis or leukemic cell infiltration in skin is one of the common extramedullary manifestations of acute myeloid leukemia (AML) and signifies a poorer prognosis. However, its pathogenesis and maintenance remain understudied. Here, we report massive AML cell infiltration in the skin in a transplantation-induced MLL-AF9 AML mouse model. These AML cells could regenerate AML post-transplantation. Prospective niche characterization revealed that skin harbored mesenchymal progenitor cells (MPCs) with a similar phenotype as BM mesenchymal stem cells. These skin MPCs protected AML-initiating stem cells (LSCs) from chemotherapy in vitro partially via mitochondrial transfer. Furthermore, Lama4 deletion in skin MPCs promoted AML LSC proliferation and chemoresistance. Importantly, more chemoresistant AML LSCs appeared to be retained in Lama4-/- mouse skin post-cytarabine treatment. Our study reveals the characteristics and previously unrecognized roles of skin mesenchymal niches in maintaining and protecting AML LSCs during chemotherapy, meriting future exploration of their impact on AML relapse. A 40-word summary Sandhow et al have in transplantation-induced AML mouse models demonstrated the leukemia-regenerating capacity of AML cells infiltrated in the skin and the role of skin mesenchymal niches in maintaining/protecting AML cells, providing new insight into the pathology of leukemia cutis.

cancer biology↗

bioRxiv2022

Striosomes constrain locomotor vigor with respect to an innate valence differential

Survival demands that safe and unsafe contexts are met with different locomotor profiles, yet whether striatal microcircuitry links contextual valence to spontaneous locomotor vigor is unresolved. Here we test for striosome contributions to spontaneous locomotion using ablation, calcium imaging and chemogenetics in the context of a modified Light/Dark box test. We found that locomotor speed reflects the unlearned, external valence differential present in this test, and that striosomes gate valence-oriented speed selection. Our data suggest that striosomes dampen motor vigor associated with lesser valence, or elevated anxiety. HighlightsO_LIMice explore the light and dark zones in Light/Dark box with different walk speed C_LIO_LIStriosome ablation reduces restful slowing and elevates speed relative to zone C_LIO_LIMany striosome neurons exhibit light-zone preference and speed related activity C_LIO_LIStriosome enhancement slows mice and blunts zone discrimination by speed C_LI

neuroscience↗

bioRxiv2022

A multiplexed in vivo approach to identify driver genes in small cell lung cancer

Small cell lung cancer (SCLC) is a highly lethal form of lung cancer. The high mutation burden in SCLC cells makes it challenging to predict key drivers of SCLC from genome sequencing data, thereby hindering the identification of possible therapeutic targets. Here we develop a quantitative multiplexed approach based on lentiviral barcoding with somatic CRISPR/Cas9-mediated genome editing to functionally investigate candidate regulators of tumor initiation and growth in genetically engineered mouse models of SCLC. Lentiviral vector-mediated SCLC initiation was greatly enhanced by naphthalene pre-treatment, enabling high multiplicity of tumor clones for analysis through high-throughput sequencing methods. Based on a meta-analysis across multiple human SCLC genomic datasets, we quantified the impact of inactivating 39 genes across many candidate pathways and captured both positive and detrimental effects on SCLC initiation and progression upon gene inactivation. This analysis and subsequent validation in human SCLC cells identified TSC1 in the PI3K-AKT-mTOR pathway as a robust tumor suppressor in SCLC. This new approach should illuminate novel drivers of SCLC, facilitate the development of precision therapies for defined SCLC genotypes, and identify new therapeutic targets.

cancer biology↗

bioRxiv2022

Neutralization of Omicron BA.1, BA.2, and BA.3 SARS-CoV-2 by 3 doses of BNT162b2 vaccine

The newly emerged Omicron SARS-CoV-2 has 3 distinct sublineages: BA.1, BA.2, and BA.3. BA.1 accounts for the initial surge and is being replaced by BA.2, whereas BA.3 is at a low prevalence at this time. Here we report the neutralization of BNT162b2-vaccinated sera (collected at 1 month after dose 3) against the three Omicron sublineages. To facilitate the neutralization testing, we engineered the complete BA.1, BA.2, or BA.3 spike into an mNeonGreen USA-WA1/2020 SRAS-CoV-2. All BNT162b2-vaccinated sera neutralized USA-WA1/2020, BA.1-, BA.2-, and BA.3-spike SARS-CoV-2s with titers of >20; the neutralization geometric mean titers (GMTs) against the four viruses were 1211, 336, 300, and 190, respectively. Thus, the BA.1-, BA.2-, and BA.3-spike SARS-CoV-2s were 3.6-, 4.0-, and 6.4-fold less efficiently neutralized than the USA-WA1/2020, respectively. Our data have implications in vaccine strategy and understanding the biology of Omicron sublineages.

microbiology↗

bioRxiv2022

A Spatiotemporal Reconstruction of the C. elegans Pharyngeal Cuticle Reveals a Structure Rich in Phase-Separating Proteins

Roughly 4.5 million species of ecdysozoan animals repeatedly shed their old cuticle and construct a new one underneath to accommodate growth. How cuticles are constructed is not well understood. Here, we systematically mine gene expression datasets to uncover the spatiotemporal blueprint for how the chitin-based pharyngeal cuticle of the nematode Caenorhabditis elegans is built. We demonstrate that the blueprint correctly predicts expression patterns and functional relevance to cuticle development. We find that as larvae prepare to molt, catabolic enzymes are upregulated and the genes that encode chitin synthase, chitin cross-linkers, and homologs of amyloid regulators subsequently peak in expression. 48% of the gene products secreted during the molt are predicted to be intrinsically disordered proteins (IDPs), many of which belong to four distinct families that are expressed in overlapping waves. These include the IDPAs, IDPBs, and IDPCs that are introduced for the first time here. We find that all four families have sequence properties known to drive phase separation and show in vitro phase separation for one of these proteins. This systematic analysis reveals the massive contribution that IDPs make to the cuticle and highlights how reversibly phase-separating materials may facilitate cuticle disassembly and reassembly during the molt.

systems biology↗

bioRxiv2022

Atypical MAPK regulates translocation of GATA transcription factor in response to chemoattractant stimulation

The Dictyostelium atypical MAPK Erk2 (a.k.a. ErkB) is required for chemotactic responses to external cAMP as individual amoeba aggregate and undergo a multicellular developmental program. External cAMP also stimulates the translocation of the GATA transcription factor, GtaC, a key regulator of developmental gene expression and a developmental timer of repeated cAMP stimulation of developing cells. In this study, atypical MAPK Erk2 was found to be essential for the translocation of GtaC in response to external cAMP as indicated by the cellular distribution of GFP-GtaC reporters. Erk2 was also demonstrated to mediate the translocation of GtaC in response to external folate, a signal that directs the foraging of amoeba for bacterial food sources. Erk1, the only other Dictyostelium MAPK, was not required for the GtaC translocation to either chemoattractant, indicating that GFP-GtaC is a kinase translocation reporter specific for atypical MAPKs. The translocation of GFP-GtaC in response to folate was absent in mutants lacking the folate receptor, Far1 (a.k.a. GrlL) or the coupled G protein, G4 subunit. Loss of GtaC function resulted in enhanced chemotactic movement to folate. Inspection of the GtaC primary sequence revealed four sites recognized as Erk2 preferred phosphorylation sites. The creation and analysis of GFP-GtaC mutants with alterations at these sites determined that these sites are required for translocation in response to folate. Consistent with the role of translocation for GtaC function certain combinations of these phosphorylation site alterations interfered with the ability of GFP-GtaC reporter to rescue aggregation of gtaC- cells. These findings provide the first evidence that atypical MAPKs can regulate transcription factors through specific phosphorylation sites in response to chemoattractants. The ability of different stimuli to regulate GtaC translocation through Erk2 indicates atypical MAPKs can regulate different cell fates in part through the translocation of transcription factors.

developmental biology↗

bioRxiv2022

Understanding immune-driven brain aging by human brain organoid microphysiological analysis platform

The aging of the immune system drives systemic aging and the pathogenesis of age-related diseases. However, a significant knowledge gap remains in understanding immune-driven aging, especially in brain aging, due to the limited current in vitro models of neuro-immune interaction. Here we report the development of a human brain organoid microphysiological analysis platform (MAP) to discover the dynamic process of immune-driven brain aging. We create the organoid MAP by 3D printing that can confine organoid growth and perfuse oxygen and nutrients (and immune cells) to generate standardized human cortical organoids that promote viability, maturation, and commitment to human forebrain identity. Dynamic rocking flow is incorporated for the platform that allows us to perfuse primary monocytes from young (20 to 30-year-old) and aged (>60-year-old) donors and culture human cortical organoids for modeling and analyzing the aged immune cell interacting organoid tissues systematically. We discovered the aged monocytes had increased infiltration and promoted the expression of aging-related markers (e.g., p16 in astrocytes neighboring to monocytes) within human cortical organoids, indicating that aged monocytes may drive brain aging. We believe that our human brain organoid MAP provides promising solutions for basic research and translational applications in aging, neuroimmunological diseases, autoimmune disorders, and cancers.

bioengineering↗