Biology subjects

Li, C. H.

Publications and source records attributed to Li, C. H..

At least 19 recordsLinked to original sources

bioRxiv2026

TMEM55B promotes anterograde transport and distal axonal distribution of LAMP1-positive organelles

Lysosomal function throughout life is vital for the proper functioning and survival of post-mitotic neurons by mediating cellular signaling, degradation, and recycling processes. Their intracellular transport relies on microtubule-dependent mechanisms involving kinesin and dynein motors. While lysosomes were long thought absent from axons, recent studies have demonstrated the importance of LAMP1-positive endo-/lysosomal organelles in axonal compartments. This study investigates the physiological role of TMEM55B, a lysosomal membrane protein involved in lysosome positioning and motor coupling in neurons. TMEM55B is highly expressed in LAMP1-positive organelles in cortical neurons. We generated viable Tmem55b knockout mice that exhibited altered lysosomal positioning in neurons. Lysosomes clustered abnormally in the pre-axonal exclusion zone and the proximal axon, with many forming elongated tubular structures. Similarly, in primary rat neurons, TMEM55B depletion resulted in lysosomal tubulation and impaired bidirectional lysosomal transport, particularly in distal axon segments, without affecting lysosome velocity in the proximal and mid-axon. These transport defects were consistent with disrupted JIP4 function, a scaffold linking TMEM55B to both dynein and kinesin motors. TMEM55B deficiency did not result in neurodegeneration, behavioral deficits, or reduced lifespan in mice. As an orthogonal approach, we analyzed TMEM55B function in C. elegans. Worms lacking the TMEM55B homolog Y71H2AM.2 showed altered lysosomal dynamics in cholinergic neurons, supporting an evolutionarily conserved role. To test the involvement of TMEM55B's paralog, TMEM55A, in regulating neuronal lysosome positioning, we generated Tmem55a/b double-knockout mice, which exhibit impaired growth, premature death, and an overall aggravated phenotype. Collectively, our findings demonstrate that both TMEM55B and TMEM55A regulate lysosome distribution in neurons, particularly in axons, by influencing JIP4-dependent retro- and, notably, anterograde motor protein-mediated transport. This function is critical for spatial lysosomal homeostasis. Our study underscores the importance of TMEM55A/TMEM55B in regulating neuronal organelle dynamics and may be a factor considered in neurodegenerative diseases involving lysosomal trafficking defects.

cell biology↗

bioRxiv2026

Integrative single cell analysis of CD8+ T-cells across early and advanced oral cancers reveals signatures of anti-tumour activity

Tumour-targeting CD8 T cells drive responses to every major form of cancer immunotherapy. Identifying them, however, remains an unsolved problem in solid tumours. The antigens they recognize are rarely defined and almost never shared between patients. We profiled 51,459 CD8+ T cells by paired single-cell RNA and T-cell receptor sequencing across 28 samples from 17 HPV-negative oral cancers spanning primary tumours, draining lymph nodes, metastases, and pembrolizumab-treated recurrences. We found that clonotypes that were expanded and shared across anatomical sites and timepoints were enriched within tumours and progressively selected over disease evolution and checkpoint blockade. Designating these shared-expanded clones as putative tumour-targeting cells, we trained a machine learning classifier that identifies them from transcriptome data alone. This 108-feature random forest signature recapitulated programmes of tumour reactivity and generalized to an integrated atlas of 89,318 CD8+ T cells from independent cohorts, showing progressive enrichment from normal to malignant tissue, and localized to tumour-proximal niches in spatial transcriptomics. By demonstrating that clonal behaviour across space and time encodes tumour reactivity in the transcriptome, this work establishes a generalizable framework for mapping tumour-engaged immunity without knowledge of the underlying antigen.

cancer biology↗

bioRxiv2026

Spatiotemporal proteomics elucidates trafficking and localization of Neuroligins to the axon initial segment plasma membrane

Neuronal development and function rely on precise sorting of membrane proteins to distinct neuronal domains, yet the underlying mechanisms remain incompletely understood. Here, we investigated the trafficking of two highly homologous NLGNs (NLGN1 and 2) which distinctly localize and function at excitatory and inhibitory synapses. By using spatiotemporal proteomics, genetic engineering and microscopy in CNS cultured neurons and organotypic slices, we dissected the itinerary of biosynthetic NLGNs, identifying co-cargoes and sorting routes to dendrites and the AIS. At the AIS, which contains only inhibitory synapses, both NLGN1 and NLGN2 are locally exocytosed. While NLGN2 is stably recruited to axo-axonic synapses by its extracellular domain and modulated by activity, NLGN1 is retrieved by endocytic mechanisms. We propose that biosynthetic NLGNs are co-sorted to the AIS PM where they detect pre-synaptic type. These findings may help to elucidate the role of AIS-localized NLGNs in shaping AIS structural and functional plasticity. HighlightsO_LISpatiotemporal proteomics elucidates interactome of biosynthetic NLGN1 in neurons C_LIO_LINLGN1 and NLGN2 are targeted to the AIS by kinesin-1 C_LIO_LINLGN2, but not NLGN1, is retained at axo-axonic synapses and modulated by activity C_LIO_LINLGN stability at the AIS plasma membrane is determined by the ectodomain C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=194 HEIGHT=200 SRC="FIGDIR/small/733123v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@a45909org.highwire.dtl.DTLVardef@1d171b0org.highwire.dtl.DTLVardef@17f132aorg.highwire.dtl.DTLVardef@1c33a8d_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

The axonal ER couples translation and secretion machineries for local delivery of axonal transmembrane proteins to promote axonal development

Neuronal development and function rely on the polarized sorting of transmembrane proteins (TMPs). Most TMPs follow a conventional secretory pathway confined to the cell soma, where ER-translated TMPs exit the ER through ERES to reach the Golgi, prior to PM delivery. We recently found that the axonal ER regulates local translation; however, how this is linked to secretion remains unknown. Here, we find that axonally translated TMPs exit the ER and reach the axonal PM via an ERES-dependent/Golgi-independent route. Intriguingly, we uncover a feedback loop linking translation and secretion at axonal ERES. HDLBP-dependent TMP synthesis regulates ERES formation, and axonal ERES in turn modulate TMP translation. Subsequently, the NRZ-SEC22B tethering complex links local TMP ER exit to PM delivery, dependent on ER-PM contacts. Axonal ERES and these associated molecular players support axon growth and bouton assembly. We propose a novel mechanism in which coupling of axonal TMP synthesis and secretion is essential for neuronal development.

cell biology↗

bioRxiv2025

Sex Differences in the Cancer Proteome

Proteins play a central role in cancer biology: they are the most common drug targets and biomarkers. Sex influences the proteome in many diseases, ranging from neurological to cardiovascular. In cancer, sex is associated with incidence, progression and therapeutic response, as well as characteristics of the tumour genome and transcriptome. The extent to which sex differences impact the cancer proteome remains largely unknown. To fill this gap, we quantified sex differences across 1,590 proteomes from eight cancer types, identifying 901 genes with sex-differential proteins abundance in adenocarcinomas of the lung, and 20 genes across five other tumour types: squamous cell carcinoma of the lung, hepatocellular carcinomas, clear cell cancers of the kidney, adenocarcinomas of the pancreas and glioblastoma. A subset of these protein differences could be rationalized by sex-differential copy number aberrations. Pathway analysis showed that male-biased proteins in lung adenocarcinoma were enriched in MYC and E2F target pathways. These findings highlight the modest impact of sex on the cancer proteome, but the very limited power of existing proteomics cohorts for these analyses.

cancer biology↗

bioRxiv2025

Sex Differences in Cancer Functional Genomics: Gene Dependency and Drug Sensitivity

Patient sex influences a wide range of cancer phenotypes, including prevalence, response to therapy and survival endpoints. Molecular sex differences across the central dogma have been identified that may drive these phenotypic differences. Despite a growing catalog of specific genomic, transcriptomic and proteomic sex differences in a range of cancer types, their functional consequences remain unclear. To assess how patient sex impacts cancer cell function, we evaluated 1,209 cell lines subjected to CRISPR knockout, RNAi knockdown or drug exposures. Despite limited statistical power, we identified pan- and per-cancer sex differences in gene essentiality in six sex-linked and fourteen autosomal genes, and in drug sensitivity for two compounds. These data expand our understanding of the propagation of sex-differing molecular features to functional outcomes, and their role in influencing patient phenotypes. They highlight the importance of considering sex-specific effects in mechanistic and functional studies.

cancer biology↗

bioRxiv2024

Spatiotemporal proteomics reveals the biosynthetic lysosomal membrane protein interactome in neurons

Lysosomes are membrane-bound organelles critical for maintaining cellular homeostasis. Delivery of biosynthetic lysosomal proteins to lysosomes is crucial to orchestrate proper lysosomal function. However, it remains unknown how the delivery of biosynthetic lysosomal proteins to lysosomes is ensured in neurons, which are highly polarized cells. Here, we developed Protein Origin, Trafficking And Targeting to Organelle Mapping (POTATOMap), by combining trafficking synchronization and proximity-labelling based proteomics, to unravel the trafficking routes and interactome of the biosynthetic lysosomal membrane protein LAMP1 at specified time points. This approach, combined with advanced microscopy, enabled us to identify the neuronal domain-specific trafficking machineries of biosynthetic LAMP1. We revealed a role in replenishing axonal lysosomes, in delivery of newly synthesized axonal synaptic proteins, and interactions with RNA granules to facilitate hitchhiking in the axon. POTATOMap offers a robust approach to map out dynamic biosynthetic protein trafficking and interactome from their origin to destination.

cell biology↗

bioRxiv2021

A distinct core regulatory module enforces oncogene expression in KMT2A-rearranged leukemia

A small set of lineage-restricted transcription factors (TFs), termed core regulatory circuitry (CRC), control cell identity and malignant transformation. Here, we integrated gene dependency, chromatin architecture and TF perturbation datasets to characterize 31 core TFs in acute myeloid leukemia (AML). Contrary to a widely accepted model, we detected a modular CRC structure with hierarchically organized, partially redundant and only sparsely interconnected modules of core TFs controlling distinct genetic programs. Rapid TF degradation followed by measurement of genome-wide transcription rates revealed that core TFs directly regulate dramatically fewer genes than previously assumed. Leukemias carrying KMT2A (MLL) rearrangements depend on the IRF8/MEF2 axis to directly enforce expression of the key oncogenes MYC, HOXA9 and BCL2. Our datasets provide an evolving model of CRC organization in human cells, and a resource for further inquiries into and therapeutic targeting of aberrant transcriptional circuits in cancer.

genomics↗

bioRxiv2021

iSubGen: Integrative Subtype Generation by Pairwise Similarity Assessment

There are myriad types of biomedical data- genetics, transcriptomics, clinical, imaging, wearable devices and many more. When a group of patients with the same underlying disease exhibit similarities across multiple types of data, this is called a subtype. Disease subtypes can reflect etiology and sometimes predict clinical behaviour. Existing subtyping approaches struggle to simultaneously handle multiple diverse data types, particularly when there is missing information, as is common in most real-world clinical datasets. To improve subtype discovery, we exploited changes in the correlation-structure between different data types to create iSubGen, an algorithm for integrative subtype generation. iSubGen can combine arbitrary data types for subtype discovery, such as merging molecular, mutational signature, pathway and micro-environmental data. iSubGen recapitulates known subtypes across multiple diseases, even in the face of substantial missing data. It identifies groups of patients with divergent clinical outcomes, and can combine arbitrary data types for subtype discovery, such as merging molecular, mutational signature, pathway and micro-environmental data. iSubGen can accommodate any feature that can be compared with a similarity-metric, and provides a versatile approach for creating subtypes. It is available at https://CRAN.R-project.org/package=iSubGen.

bioinformatics↗

bioRxiv2021

Real-Time Three-Dimensional Tracking of Single Vesicles Reveals the Abnormal Motion and Vesicle Pools of Synaptic Vesicles in Neurons of Huntington's Disease Mice

Although defective synaptic transmission was suggested to play a role in neurodegenerative diseases, the dynamics and vesicle pools of synaptic vesicles during neurodegeneration remain elusive. Here, we performed real-time three-dimensional tracking of single synaptic vesicles in cortical neurons from a mouse model of Huntingtons disease (HD). Vesicles in HD neurons had a larger net displacement and radius of gyration compared with wild-type neurons. Vesicles with a high release probability (Pr) were interspersed with low-Pr vesicles in HD neurons, whereas high-Pr and low-Pr vesicle pools were spatially separated in wild-type neurons. Non-releasing vesicles in HD neurons had an abnormally high prevalence of irregular oscillatory motion. These abnormal dynamics and vesicle pools were rescued by overexpressing Rab11, and the abnormal irregular motion was rescued by jasplakinolide. These results suggest the abnormal dynamics and vesicle pools of synaptic vesicles in the early stages of HD, suggesting a possible pathogenic mechanism of neurodegenerative diseases.

neuroscience↗

bioRxiv2020

Ancestry Influences on the Molecular Presentation of Tumours

Epidemiological studies have identified innumerable ways in which cancer presentation and behaviour is associated with patient ancestry. The molecular bases for these relationships remain largely unknown. We analyzed ancestry associations in the somatic mutational landscape of 12,774 tumours across 33 tumour-types, including 2,562 with whole-genome sequencing. Ancestry influences both the number of mutations in a tumour and the evolutionary timing of when they occur. Specific mutational signatures are associated with ancestry, reflecting potential differences in exogenous and endogenous oncogenic processes. A subset of known cancer driver genes was mutated in ancestry-associated patterns, with transcriptomic consequences. Cancer genome sequencing data is not well-balanced in epidemiologic factors; these data suggest ancestry strongly shapes the somatic mutational landscape of cancer, with potential functional implications.

cancer biology↗

bioRxiv2020

Auditory aversion in absolute pitch possessors

Absolute pitch (AP) refers to the ability of identifying the pitch of a given tone without reliance on any reference pitch. The downside of possessing AP may be the experience of disturbance when exposed to out-of-tune tones. Here, we investigated this so-far unexplored phenomenon in AP, which we refer to as auditory aversion. Electroencephalography (EEG) was recorded in a sample of AP possessors and matched control musicians without AP while letting them perform a task underlying a so-called affective priming paradigm: Participants judged valenced pictures preceded by musical primes as quickly and accurately as possible. The primes were bimodal, presented as tones in combination with visual notations that either matched or mismatched the actually presented tone. Regardless of the prime condition, AP possessors performed more poorly in judging pleasant pictures and their EEG revealed later peaks at around 200 ms (P200) after prime onset. Their performance dropped when responding to pleasant pictures preceded by incongruent primes, especially when mistuned by one semitone. This interference was also reflected in an EEG deflection at around 400 ms (N400) after picture onset, preceding the behavior responses. These findings suggest that AP possessors process mistuned musical stimuli and pleasant pictures as affectively unrelated with each other, supporting an aversion towards out-of-tune tones in AP possessors. The longer prime-related P200 latencies exhibited by AP possessors suggest a delay in integrating musical stimuli, underlying an altered affinity towards pitch-label associations.

neuroscience↗

bioRxiv2019

The Establishment of CDK9/ RNA PolII/H3K4me3/DNA Methylation Feedback Promotes HOTAIR Expression by RNA Elongation Enhancement in Cancer

Long non-coding RNA HOX Transcript Antisense RNA (HOTAIR) is overexpressed in multiple cancers with diverse genetic profiles, which heavily contributed to cancer progression. However, the underlying mechanism leading to HOTAIR deregulation is largely unexplored. Here, we revealed that gene body methylation promoted HOTAIR expression through enhancing the transcription elongation process in cancer. We linked up the aberrant gene body histone and DNA methylation in promoting transcription elongation via phosphorylation of Polymerase II Ser 2 by CDK7-CDK9, and elucidated the mechanism of a positive feedback loop involving CDK7, MLL1 and DNMT3A in promoting gene body methylation and overexpressing HOTAIR. To our knowledge, this is the first time to demonstrate that a positive feedback loop that involved CDK9-mediated phosphorylation of PolII and histone and gene body methylation induced robust transcriptional elongation, which heavily contributed to the upregulation of oncogenic lncRNA in cancer.

cancer biology↗

bioRxiv2019

Ectopic HOTTIP Expression Induces Non-canonical Transactivation Pathways to Promote Growth and Invasiveness in Pancreatic Ductal Adenocarcinoma

LncRNA HOTTIP (HOXA transcript at the distal tip) is upregulated in pancreatic ductal adenocarcinoma (PDAC). However, oncogenic pathway mediated by HOTTIP is not fully understood. We identified canonical HOTTIP-HOXA13 targets: CYP26B1, CLIC5, CHI3L1 and UCP2 which were responsible for cell growth and cell invasion. Importantly, genome-wide analysis revealed that 38% of the genes regulated by HOTTIP contained H3K4me3 and HOTTIP enrichment at their promoters, without HOXA13 binding. HOTTIP complexed with WDR5-MLL1 to trans-activate oncogenic proteins CYB5R2, SULT1A1, KIF26A, SLC1A4 and TSC22D1 through directly triggering H3K4me3 at their promoters. The WDR5, MLL1 and H3K4me3 levels at their promoters and their expression levels were sensitive to HOTTIP overexpression and knockdown. These suggested the importance of non-canonical trans-acting HOTTIP-WDR5-MLL1 pathway in HOTTIP-regulatory mechanism by promoting the expression of oncogenic proteins. Furthermore, we dissected the mechanism by which HOTTIP was regulated by miR-497 in PDAC. Analysis of PDAC human tissues also revealed that HOTTIP was negatively correlated with miR-497 level. Our findings demonstrated that HOTTIP, upregulated in PDAC due to the loss of inhibitory miR-497, promoted PDAC progression through canonical HOTTIP-HOXA13 axis and a novel non-canonical trans-acting HOTTIP-WDR5-MLL1-H3K4me3 pathway.

cancer biology↗

bioRxiv2019

Divergent mutational processes distinguish hypoxic and normoxic tumours

Many primary tumours have low levels of molecular oxygen (hypoxia). Hypoxic tumours are more likely to metastasize to distant sites and respond poorly to multiple therapies. Surprisingly, then, the pan-cancer molecular hallmarks of tumour hypoxia remain poorly understood, with limited understanding of its associations with specific mutational processes, non-coding driver genes and evolutionary features. To fill this gap, we quantified hypoxia in 1,188 tumours spanning 27 cancer types. We show that elevated hypoxia is associated with increased mutational load across cancers, irrespective of the underlying mutational class. The proportion of mutations attributed to several mutational signatures of unknown aetiology are directly associated with the level of hypoxia, suggesting underlying mutational processes for these signatures. At the gene level, driver mutations in TP53, MYC and PTEN are enriched in tumours with high hypoxia, and mutations in PTEN interact with hypoxia to direct the evolutionary trajectory of tumours. Overall, this work demonstrates that hypoxia plays a critical role in shaping the genomic landscape of cancer.

cancer biology↗

bioRxiv2019

Sex Differences in Mutational Processes

Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here, we describe the first pan-cancer analysis of sex differences in whole genomes of 1,983 tumours of 28 subtypes from the ICGC Pan-Cancer Analysis of Whole Genomes project. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in cancer research. Sex disparities in cancer epidemiology include an increased overall cancer risk in males corresponding with higher incidence in most tumor types, even after adjusting for known risk factors1,2. Cancer mortality is also higher in males, due in part to better survival for female patients in many cancer types, including those of the colon and head & neck3. Interestingly, female colorectal cancer patients respond better to surgery4 and adjuvant chemotherapy, though this is partially due to biases in tumour location and microsatellite instability5. Similarly, premenopausal female nasopharyngeal cancer patients have improved survival regardless of tumour stage, radiation or chemotherapy regimen6. There is a growing body of evidence for sex differences in cancer genomics7-13, but their molecular origins and clinical implications remain largely elusive. Previous studies have mostly focused on protein coding regions, leaving the vast majority of the genome unexplored. We hypothesized that there are uncharacterized sex differences in the non-coding regions of the genome. Using whole genome sequencing data from the Pan-cancer Analysis of Whole Genomes (PCAWG) project14, we performed a survey of sex-biased mutations in 1,983 samples (1,213 male, 770 female) from 28 tumour subtypes, excluding those of the sex organs (Supplementary Table 1). We also excluded the X and Y chromosomes to focus on autosomal sex differences in cancers affecting both men and women, but there are known to be significant X-chromosome mutational differences between tumours arising in men and women15. Our analysis revealed sex differences in both genome-wide phenomena and in specific genes. These sex-biases occur not only at the pan-cancer level across all 1,983 samples, but also in individual tumour subtypes.

cancer biology↗

bioRxiv2018

Accurate Reference-Free Somatic Variant-Calling by Integrating Genomic, Sequencing and Population Data

The detection of somatic single nucleotide variants (SNVs) is critical in both research and clinical applications. Studies of human cancer typically use matched normal (reference) samples from a distant tissue to increase SNV prediction accuracy. This process both doubles sequencing costs and poses challenges when reference samples are not readily available, such as for many cell-lines. To address these challenges, we created S22S: an approach for the prediction of somatic mutations without need for matched reference tissue. S22S takes underlying sequence data, augments them with genomic background context and population frequency information, and classifies SNVs as somatic or non-somatic. We validated S22S using primary tumor/normal pairs from four tumor types, spanning two different sequencing technologies. S22S robustly identifies somatic SNVs, with the area under the precision recall curve reaching 0.97 in kidney clear cell carcinoma, comparable to the best tumor/normal analysis pipelines. S22S is freely available at http://labs.oicr.on.ca/Boutros-lab/software/s22s.

bioinformatics↗

bioRxiv2017

A stable beneficial symbiotic relationship between endophytic fungus Schizophyllum commune and host plant Panax ginseng

Endophytes and plants can establish specific long-term symbiosis through the accumulation of secondary metabolites. Interactions between microbial inhabitants represent a novel area of study for natural products research. In this study, a strain of endophyte 3R-2 that can enhance the biomass and contents of ginsenoside Rc, ginsenoside Rg2 and ginsenoside Rg3 of Panax ginseng hairy roots was screened out via HPLC, which was identified as Schizophyllum commune through the morphological and molecular identification. On the base, we found the infection of the endophyte were obviously observed widely in the P. ginseng and the strain formed a stable relationship with P. ginseng hairy roots in parenchyma cells around through tissues embedding slicing, HE ammonium silver staining and immunofluorescence staining. On the other hand, elicitors of fungus 3R-2 can also significantly promote hairy root growth and contents of several ginsenosides, even several times higher than 3R-2 mycelium did. Moreover, S. commune 3R-2 mycelium and its elicitor could enhance the transcriptional activity of key genes during the ginsenosides biosynthetic pathway dramatically. Thus, endophyte S. commune 3R-2 and its elicitor change the chemical substance content by regulating the expression of genes involved in the secondary metabolite biosynthetic pathway.

plant biology↗