Biology subjects

Shan, H.

Publications and source records attributed to Shan, H..

14 recordsLinked to original sources

bioRxiv2026

Biologically inspired alignment reveals distributed and directionally asymmetric correspondence between rat and human cortices

Rodent models enable causal interrogation of brain circuits, but translating their systems-level organization to humans requires correspondence beyond one-to-one anatomical homology. Guided by the view that cortical areas are characterized by their relationships within distributed functional networks, we developed BrainMapping, a biologically inspired framework for aligning rat and human cortex using resting-state functional MRI. The framework combined a shared representation with optimal transport to derive probabilistic, bidirectional maps. These alignments revealed distributed, many-to-many correspondences that generalized to held-out subjects and preserved functional connectivity architecture, cortical gradients, and graph topology. Organizational preservation was directionally asymmetric. Human-to-rat mapping preserved organization more uniformly across rat cortical systems, whereas rat-to-human mapping showed stronger preservation in human association-related networks than in primary sensory and motor networks. The maps recovered literature-consistent default-mode and salience-system correspondences and generated testable non-canonical predictions. These findings provide a framework for expressing rat functional organization in human functional-network coordinates.

neuroscience↗

bioRxiv2026

Plasma titration provides a physical ruler for cross-platform proteomics

Plasma proteomics is expanding across platforms and cohorts, and integrating these data for AI demands comparability at the protein level, not merely concordant associations1,2. Affinity and MS platforms use distinct probes (antibodies, aptamers, or peptides) and signal readouts, yielding contradictory cross-platform results3,4. Without a known quantitative truth, we cannot distinguish biology from measurement distortion, leaving no gold standard for integration. Here we introduce Plasmix--a plasma reference suite with predefined male:female ratios (M, 1:0; Y, 3:1; P, 1:1; X, 1:3; F, 0:1)--and show that preserving this quantitative titration gradient, not just technical repeatability, predicts cross-platform concordance and identifies protein measurements suitable for integration. Profiling Plasmix across five platforms (Olink, SomaScan, NULISA, AAgAtlas, and MS-DIA) and 12 protocols across 17 batches, we found discordance is dominated by signal generation, not sample identity, and platforms distort signals in a protein-specific manner. Crucially, proteins retaining the titration response showed stronger agreement in an independent cohort; anchoring to the Plasmix midpoint (P) via sample-to-reference ratios reduced distortions, extending harmonizable coverage by 10-20%. Plasmix thus provides a physical ruler to benchmark accuracy, identifying genuinely integrable measurements before pooling datasets or training AI models--a critical bottleneck for plasma proteomics.

molecular biology↗

bioRxiv2026

The genome of an aneuploid cultivar facilitates elucidating the genetic bases of trait polymorphisms in Phalaenopsis orchids

As an important ornamental crop, Phalaenopsis orchids exhibit extraordinary trait diversity with unclear genetic bases. Here, we present a haplotype-resolved, chromosome-level genome for an aneuploid cultivar Santiago. We reveal pervasive variation in the number and sequence among homoeologous genes. When serving as a reference, this genome facilitates the genetic understanding of trait variation in a hybrid population that is highly representative in trait polymorphisms. Specifically, nucleotide polymorphisms in a potential long-distance enhancer and the consequential expression variation of PsAGL6-2, presence/absence of PsMYB12 and b-type homoeologous gene of PsMYB2 determine lip morphology variation, presence/absence of venation-associated stripes and background pink color, respectively. Diverse functions of PsMYBx1 in repressing anthocyanin accumulation across different cultivars further enhances the color patterning diversity in Phalaenopsis. Our study provides a practical framework for using a highly heterogeneous, haplotype-resolved genome to decode phenotypic diversity and has the potential to promote marker-assisted breeding in Phalaenopsis.

genomics↗

bioRxiv2026

Discovery of potent oligopeptides for various metabolic diseases using deep learning

Artificial intelligence (AI)-based methods are increasingly critical in peptide drug discovery, but their applications are limited in a narrow scope such as antimicrobial peptides. For indications where peptide therapy inherently excels, such as metabolism, endocrinology, and tissue regeneration, AI-based pipeline for therapeutic peptide discovery is long awaited but still unmet. Here, we propose a deep learning-based pipeline, Deepeptide, capable of identifying therapeutic oligopeptides for various metabolism-related indications. Leveraging the intrinsical relationship of disease indication -- biological processes -- molecular functions, Deepeptide discovers oligopeptides with indication-ameliorating-related molecular functions as lead candidates for indication of interest. Deepeptide was applied in five representative indications of metabolism, endocrinology, and tissue regeneration: angiogenesis, lipid metabolism, osteogenesis, glucose metabolism, and anti-angiogenesis. Overall, 62% of the identified oligopeptide candidates demonstrated significant bioactivity in vitro, with most of them showing comparable potency to the first-line drugs. Notably, the heptapeptide AP7 exhibited angiogenic potency comparable to VEGF in excisional wound splinting mouse model by promoting cell migration rather than proliferation, and hexapeptide TP6 showed significant dual-efficacy against hyperlipidemia and obesity in high-fat diet mice by inhibiting lipid synthesis and regulating gut microbiota. These findings highlight the potential and generalizability of Deepeptide in therapeutic oligopeptide discovery for metabolic diseases.

bioinformatics↗

bioRxiv2025

Graph embeddings for identifying symmetries in connectomes

In many circuit models of neural computation, synaptic connections between neurons are organized according to their tuning to the variables being processed. The connectivities of canonical neural network models of head direction, spatial navigation, and orientation selectivity obey this principle and contain symmetries related to the angular and spatial variables they operate on. We develop a graph embedding algorithm to identify such symmetries. The algorithm segregates structure related to cell type from that related to the symmetries we seek to identify, distinguishing it from standard embedding methods. Our method successfully identifies rotational and translational symmetries in heading direction and visual projection neuron circuits using a connectome of the adult Drosophila brain, and it also identifies a toroidal symmetry in a synthetic connectome of grid cells in the medial entorhinal cortex. Such embedding geometries reveal the latent variables that are processed by a neural circuit and which cell types are responsible for this computation.

neuroscience↗

bioRxiv2025

Structural innovations and neurogenic continuity define avian brain development and evolution

Understanding how neurogenic diversity and brain architecture emerge is crucial for deciphering the mechanisms of brain plasticity and cognitive evolution. Here, we present a comprehensive single-cell and spatial transcriptomic atlas of the budgerigar brain, a highly cognitive avian species. We uncover a striking dorsoventral symmetry in excitatory neuron distribution, precisely organized along the lamina mesopallialis intermedia (LMI), a key boundary structure. Cross-species comparisons further reveal the origins of this unique avian pallial organization, offering new insight into avian brain evolution. Our study also highlights distinct developmental trajectories and asynchronous maturation patterns between telencephalic and optic tectum excitatory neurons, underscoring their contribution to innate circuit assembly. Furthermore, we identify adult neural stem cells (NSCs) with evolutionarily conserved transcriptomic signatures across avian species, emphasizing their role in brain plasticity and adaptation. These findings refine fundamental models of avian brain development and elucidate conserved principles of cognitive plasticity.

evolutionary biology↗

bioRxiv2025

CRISPR-Cas9 Screening Reveals Microproteins Regulating Adipocyte Proliferation and Lipid Metabolism

Small open reading frames (smORFs) encode microproteins that play crucial roles in various biological processes, yet their functions in adipocyte biology remain largely unexplored. In a previous study, we identified thousands of smORFs in white and brown adipocytes derived from the stromal vascular fraction (SVF) of mice using ribosome profiling (Ribo-Seq). Here, we expand on this work by identifying additional smORFs related to adipocytes using the in vitro 3T3-L1 preadipocyte model. To systematically investigate the functional relevance of these smORFs, we designed a custom CRISPR/Cas9 guide RNA (sgRNA) library and screened for smORFs influencing adipocyte proliferation and differentiation. Through a dropout screen and fluorescence-assisted cell sorting (FACS) of lipid droplets, we identified dozens of smORFs that regulate either cell proliferation or lipid accumulation. Among these, we validated a novel microprotein as a key regulator of adipocyte differentiation. These findings highlight the potential of CRISPR/Cas9-based screening to uncover functional smORFs and provide a framework for further exploration of microproteins in adipocyte biology and metabolic regulation. SignificanceObesity and its associated metabolic disorders pose significant public health challenges, yet the molecular mechanisms regulating adipocyte function remain incompletely understood. Small open reading frames (smORFs) and their encoded microproteins represent an emerging class of regulatory elements with potential roles in metabolism. Here, we leveraged CRISPR/Cas9 screening to functionally characterize smORFs in adipocytes, identifying novel regulators of cell proliferation and lipid metabolism. Our findings demonstrate that conservation is not a prerequisite for smORF function, as we validated a mouse-specific microprotein that modulates adipocyte differentiation. This work establishes a robust pipeline for unbiased smORF discovery and highlights the potential for species-specific microproteins to regulate adipose biology. Future studies in human adipocytes may uncover additional microproteins with therapeutic relevance for obesity and metabolic disease.

cell biology↗

bioRxiv2023

Mechanisms of ligand recognition and activation of melanin-concentrating hormone receptors

Melanin-concentrating hormone (MCH) is a cyclic neuropeptide that regulates food intake, energy balance, and other physiological functions by stimulating MCHR1 and MCHR2 receptors, both of which are class A G protein-coupled receptors. MCHR1 can couple with multiple G-proteins, including Gi/o, Gq/11, and Gs, while MCHR2 only couple to Gq/11. Here we present cryo-electron microscopy structures of MCH-activated MCHR1 with Gi and MCH-activated MCHR2 with Gq complexes, at the global resolutions of 3.01 [A] and 2.40 [A], respectively. These structures reveal that MCH adopts a consistent cysteine-mediated hairpin loop configuration in both receptors. A central arginine from the LGRVY core motif between the two cysteines of MCH penetrates deeply into the transmembrane pocket, triggering receptor activation. Integrated with mutational and functional insights, our findings elucidate the molecular underpinnings of ligand recognition and MCH receptor activation, offering a structured foundation for targeted drug design.

molecular biology↗

bioRxiv2023

A conserved and druggable pocket in class B G protein coupled receptors for orally active small molecule agonists

Class B G protein-coupled receptors (GPCRs), including glucagon-like receptor 1 (GLP-1R) and parathyroid hormone receptor 1 (PTH1R), are peptide hormone receptors and important drug targets. Injectable peptide drugs targeting class B GPCRs have been developed for the treatment of many diseases, including type 2 diabetes, obesity, and osteoporosis, but orally available small molecule drugs are hotly pursued in the field, especially small molecule agonists of GLP-1R and PTH1R. Here we report the first high-resolution structure of the human PTH1R in complex with the stimulatory G protein (Gs) and a small molecule agonist, PCO371, which reveals an unexpected binding mode of PCO371 at the interface of PTH1R and Gs. The binding site of PCO371 is totally different from all binding sites previously reported for small molecules or peptide ligands in GPCRs. Residues that make up the PCO371 binding pocket are mostly conserved in class B GPCRs and a single mutation in PTH type 2 receptor (PTH2R) and two residue mutations in GLP-1R convert these receptors to respond to PCO371 activation. Functional assays reveal that PCO371 is a G-protein biased agonist that is defective in promoting PTH1R-mediated arrestin signaling. Together, these results uncover a distinct binding site for designing small molecule agonists for PTH1R and possible other members of class B GPCRs and define a receptor conformation that is only specific for G protein activation but not arrestin signaling. These insights should facilitate the design of distinct types of class B GPCR small molecule agonists for various therapeutic indications.

biochemistry↗

bioRxiv2022

Helping can be driven by non-affective cues in rat

Helping another in distress can be motivated by either affective or cognitive empathy, with the latter commonly believed to be restricted to humans and possibly other apes. Here, we found evidence for rodent helping that occurs in the absence of affective cues. We employed a paradigm in which a free rat can open the door to a restrainer containing a trapped rat. When the trapped rat was treated with the anxiolytic midazolam, the helping behavior exhibited by the free rat was diminished but did not extinguish. Correspondingly, midazolam-treated trapped rats still released themselves when given the opportunity, albeit at longer latencies than controls, evidence that midazolam only partially reduced the distress experienced by trapped rats. To test whether helping could occur for a rat who exhibited no affect, trapped rats were immobilized by general anesthesia or heavy sedation. Surprisingly, rats opened the door to restrainers containing these immobilized rats and pulled the incapacitated rats out of the restrainer, pushing them away from the arena center. The same solicitous behavior was observed when an anesthetized rat was simply placed in the center of the arena, without being confined within a restrainer. We speculate that the cognitive dissonance of immobile rats, at odds with predictive expectations of rat behavior built up over a lifetime, motivated solicitous behavior including helping. To block affective behavioral displays without associated dissonant cues of immobility, metyrapone, a drug that selectively blocks corticosterone synthesis, was administered to trapped rats. Under such circumstances, little helping behavior occurred. In sum, rats may be motivated either by affect or by cognitive dissonance, the latter comprising a rudimentary form of cognitive empathy.

neuroscience↗

bioRxiv2021

A Minimum Perturbation Theory of Deep Perceptual Learning

Perceptual learning (PL) involves long-lasting improvement in perceptual tasks following extensive training and is accompanied by modified neuronal responses in sensory cortical areas in the brain. Understanding the dynamics of PL and the resultant synaptic changes is important for causally connecting PL to the observed neural plasticity. This is theoretically challenging because learning-related changes are distributed across many stages of the sensory hierarchy. In this work, we modeled the sensory hierarchy as a deep nonlinear neural network and studied PL of fine discrimination, a common and well-studied paradigm of PL. Using tools from statistical physics, we developed a mean-field theory of the network in the limit of large number of neurons and large number of examples. Our theory suggests that, in this "thermodynamic" limit, the input-output function of the network can be exactly mapped to that of a deep linear network, allowing us to characterize the space of solutions for the task. Surprisingly, we found that modifications of synaptic weights in lower levels of the hierarchy are both sufficient and necessary for PL. To address the degeneracy of the space of solutions, we postulate that PL dynamics are constrained by a normative "minimum perturbation" (MP) principle, which favors weight matrices with minimal changes relative to their pre-learning values. Interestingly, MP plasticity induces changes to weights and neural representations in all layers of the network, except for the readout weight vector. In addition, such plasticity can be learned simply through slow learning. We further elucidate the properties of MP changes and compare them against experimental findings. Overall, our statistical mechanics theory of PL provides mechanistic and normative understanding of several important empirical findings of PL.

neuroscience↗

bioRxiv2020

A COVID-19 antibody curbs SARS-CoV-2 nucleocapsid protein-induced complement hyper-activation

Although human antibodies elicited by severe acute respiratory distress syndrome coronavirus-2 (SARS-CoV-2) nucleocapsid (N) protein are profoundly boosted upon infection, little is known about the function of N-directed antibodies. Herein, we isolated and profiled a panel of 32 N protein-specific monoclonal antibodies (mAb) from a quick recovery coronavirus disease-19 (COVID-19) convalescent, who had dominant antibody responses to SARS-CoV-2 N protein rather than to Spike protein. The complex structure of N protein RNA binding domain with the highest binding affinity mAb nCoV396 reveals the epitopes and antigens allosteric changes. Functionally, a virus-free complement hyper-activation analysis demonstrates that nCoV396 specifically compromises N protein-induced complement hyper-activation, a risk factor for morbidity and mortality in COVID-19, thus paving the way for functional anti-N mAbs identification. One Sentence SummaryB cell profiling, structural determination, and protease activity assays identify a functional antibody to N protein.

molecular biology↗

bioRxiv2020

Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites

The outbreak of coronavirus disease (COVID-19) in China caused by SARS-CoV-2 virus continually lead to worldwide human infections and deaths. It is currently no specific viral protein targeted therapeutics yet. Viral nucleocapsid protein is a potential antiviral drug target, serving multiple critical functions during the viral life cycle. However, the structural information of SARS-CoV-2 nucleocapsid protein is yet to be clear. Herein, we have determined the 2.7 [A] crystal structure of the N-terminal RNA binding domain of SARS-CoV-2 nucleocapsid protein. Although overall structure is similar with other reported coronavirus nucleocapsid protein N-terminal domain, the surface electrostatic potential characteristics between them are distinct. Further comparison with mild virus type HCoV-OC43 equivalent domain demonstrates a unique potential RNA binding pocket alongside the {beta}-sheet core. Complemented by in vitro binding studies, our data provide several atomic resolution features of SARS-CoV-2 nucleocapsid protein N-terminal domain, guiding the design of novel antiviral agents specific targeting to SARS-CoV-2.

molecular biology↗

bioRxiv2019

Highly precise base editing with CC context-specificity using engineered human APOBEC3G-nCas9 fusions

Cytidine base editors, composed of a cytidine deaminase fused to Cas9 nickase, enable efficient C-to-T conversion in various organisms. However, current base editors can induce unwanted bystander C-to-T conversions when more than one C is present in the activity window of cytidine deaminase, which negatively affects the precision. Here, we develop a new base editor with CC context-specificity using rationally engineered human APOBEC3G, thus significantly reduce unwanted bystander activities. In addition, efficient C-to-T conversion that can further recognize relaxed NG PAMs is achieved by combining an engineered SpCas9-NG variant. These novel base editors with improved precision and targeting scope will expand the toolset for precise gene modification in organisms.

molecular biology↗