Biology subjects

Chang, J. S.

Publications and source records attributed to Chang, J. S..

8 recordsLinked to original sources

bioRxiv2025

Characterization of Clinical Fusobacterium nucleatum Isolates from Oral Squamous Cell Carcinoma Patients

Fusobacterium nucleatum (Fn), a Gram-negative anaerobe primarily residing in the oral cavity, has garnered increasing attention for its role in a broad spectrum of human diseases. While typically absent or rarely detected outside the oral cavity in healthy individuals, Fn is frequently found at extra-oral sites under disease conditions and has been implicated in cancer progression and prognosis1. In oral squamous cell carcinoma (OSCC), the abundance of Fn significantly increases as the disease progresses, promoting cell invasion and metastasis. Furthermore, substantial evidence links Fn to accelerated tumor growth and metastatic progression in colorectal cancer (CRC), where its presence is also associated with chemotherapy resistance and poor prognosis. Here, to further elucidate the pathogenic mechanisms of Fn in cancer progression, this study characterized the physiological traits, virulence factor expression, and impacts on cancer cells of 10 Fn strains, including two well-characterized ATCC strains and eight clinical isolates. The clinical isolates consisted of three strains from saliva samples of 117 OSCC patients and five strains from 160 non-cancer individuals. Results indicated that oral isolates, regardless of disease origin, all belong to Fn subspecies polymorphum. The ATCC strains (23726 and 25586) exhibited shorter cell lengths and faster growth rates compared to the clinical isolates. Both ATCC strains formed stable biofilms and expressed key virulence genes, including aim1, fadA, fomA, and radD. All isolates tested showed sensitivity to a panel of eight different antibiotics. Interestingly, only one clinical isolate displayed similar stimulation of CRC cell migration as the two ATCC strains, while the other seven displayed no such ability. Collectively, these findings suggest that the most virulent strains, in terms of biofilm formation and virulence gene expression, are not necessarily the most pathogenic in the context of cancer cell interactions. Future pan-genomic analyses, incorporating whole-genome sequencing of the clinical isolates, will aim to delineate the genetic determinants contributing to the carcinogenic potential of Fn.

microbiology↗

bioRxiv2024

Cold-inducible GOT1 activates the malate-aspartate shuttle in brown adipose tissue to support fuel preference for fatty acids

Brown adipose tissue (BAT) simultaneously metabolizes fatty acids (FA) and glucose under cold stress but favors FA as the primary fuel for heat production. It remains unclear how BAT steer fuel preference toward FA over glucose. Here we show that the malate-aspartate shuttle (MAS) is activated by cold in BAT and plays a crucial role in promoting mitochondrial FA utilization. Mechanistically, cold stress selectively induces glutamic-oxaloacetic transaminase (GOT1), a key MAS enzyme, via the {beta}-adrenergic receptor-PKA-PGC-1 axis. The increase in GOT1 activates MAS, transferring reducing equivalents from the cytosol to mitochondria. This process enhances FA oxidation in mitochondria while limiting glucose oxidation. In contrast, loss of MAS activity by GOT1 deficiency reduces FA oxidation, leading to increased glucose oxidation. Together, our work uncovers a unique regulatory mechanism and role for MAS in mitochondrial fuel selection and advances our understanding of how BAT maintains fuel preference for FA under cold conditions. HighlightsO_LIGot1 is markedly induced by cold in BAT via a {beta}-adrenergic receptor-PKA-PGC-1 axis C_LIO_LIThe increase in cytosolic GOT1 activates the malate-aspartate shuttle (MAS) C_LIO_LIMAS activation promotes fatty acid oxidation while reducing glucose oxidation C_LIO_LILoss of MAS activity in BAT by Got1 deletion shifts the fuel preference to glucose C_LI

cell biology↗

bioRxiv2024

Immunologic and Biophysical Features of the BNT162b2 JN.1- and KP.2-Adapted COVID-19 Vaccines

Vaccines remain a vital public health tool to reduce the burden of COVID-19. COVID-19 vaccines that are more closely matched to circulating SARS-CoV-2 lineages elicit more potent and relevant immune responses that translate to improved real-world vaccine effectiveness. The rise in prevalence of the Omicron JN.1 lineage, and subsequent derivative sublineages such as KP.2 and KP.3, coincided with reduced neutralizing activity and effectiveness of Omicron XBB.1.5-adapted vaccines. Here, we characterized the biophysical and immunologic attributes of BNT162b2 JN.1- and KP.2-adapted mRNA vaccine-encoded spike (S) protein immunogens. Biophysical interrogations of S revealed the structural consequences of hallmark amino acid substitutions and a potential molecular mechanism of immune escape employed by JN.1 and KP.2. The vaccine candidates were evaluated for their immunogenicity when administered as fourth or fifth doses in BNT162b2-experienced mice or as a primary series in naive mice. In both vaccine-experienced and naive settings, JN.1- and KP.2-adapted vaccines conferred improved neutralizing responses over the BNT162b2 XBB.1.5 vaccine against a broad panel of emerging JN.1 sublineages, including the predominant KP.3.1.1 and emerging XEC lineages. Antigenic mapping of neutralizing responses indicated greater antigenic overlap of JN.1- and KP.2-adapted vaccine responses with currently circulating sublineages compared to an XBB.1.5-adapted vaccine. CD4+ and CD8+ T cell responses were generally conserved across all three vaccines. Together, the data support the selection of JN.1- or KP.2-adapted vaccines for the 2024-25 COVID-19 vaccine formula. ONE-SENTENCE SUMMARYThe Omicron JN.1- and KP.2-adapted BNT162b2 mRNA vaccines encoding prefusion S proteins elicit similar preclinical neutralizing antibody responses against circulating JN.1 sublineage pseudoviruses that are more potent than those elicited by past iterations of BNT162b2 licensed vaccines, thus demonstrating the importance of annual strain changes to the COVID-19 vaccine.

immunology↗

bioRxiv2024

The protease interpain A of Prevotella intermedia promotes human OSCC cells proliferation and migration

Prevotella intermedia has been increasingly recognized as a potential contributor to oral squamous cell carcinoma (OSCC), yet the underlying mechanisms remain poorly defined. In this study, we identified interpain A (InpA), a cysteine protease secreted by P. intermedia, as a key virulence factor that promotes oral epithelial cell proliferation and OSCC cell migration. Conditioned medium (CM) derived from P. intermedia strain ATCC 25611 enhanced proliferation in both normal oral keratinocytes (SG cells) and OSCC cell lines (SCC-15, SAS). The pro-proliferative effect was abolished upon heat inactivation of the CM and inhibited by E64, a cysteine protease inhibitor, and FSLLRY-NH2, a PAR-2 antagonist, suggesting the involvement of protease-activated receptor-2 (PAR-2) signaling. InpA was highly secreted by strain ATCC 25611 but not by clinical isolates lacking proliferative effects, and RT-qPCR confirmed higher inpA expression in OSCC-derived strains compared to non-cancer controls. Recombinant InpA (rInpA) mimicked the effect of CM, inducing proliferation and migration, which were blocked by PAR-2 inhibition. Transcriptomic and protein-level screening in SG cells revealed activation of EGFR and downstream RAS-RAF-MEK-ERK signaling. Furthermore, in a colorectal cancer (CRC) mouse model, oral administration of P. intermedia led to increased tumor formation, suggesting a broader oncogenic potential. These findings highlight InpA as a PAR-2-activating protease that may contribute to OSCC and potentially other cancers associated with oral microbiota dysbiosis.

cancer biology↗

bioRxiv2024

Discovery of orally active SARS-CoV-2 papain-like protease (PLpro) inhibitors

Vaccines and first-generation antiviral therapeutics have provided important protection against coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, there remains a need for additional therapeutic options that provide enhanced efficacy and protection against potential viral resistance. The SARS-CoV-2 papain-like protease (PLpro) is one of two essential cysteine proteases involved in viral replication. While inhibitors of the SARS-CoV-2 main protease (Mpro) have demonstrated clinical efficacy, known PLpro inhibitors have to date lacked the inhibitory potency and requisite pharmacokinetics to demonstrate that targeting PLpro translates to in vivo efficacy in a preclinical setting. Herein, we report the machine learning-driven discovery of potent, selective, and orally available SARS-CoV-2 PLpro inhibitors, with lead compound PF-07957472 (4) providing robust efficacy in a mouse-adapted model of COVID-19 infection.

microbiology↗

bioRxiv2023

Preclinical Characterization of the Omicron XBB.1.5-Adapted BNT162b2 COVID-19 Vaccine

As SARS-CoV-2 continues to evolve, increasing in its potential for greater transmissibility and immune escape, updated vaccines are needed to boost adaptive immunity to protect against COVID-19 caused by circulating strains. Here, we report features of the monovalent Omicron XBB.1.5-adapted BNT162b2 vaccine, which contains the same mRNA backbone as the original BNT162b2 vaccine, modified by the incorporation of XBB.1.5-specific sequence changes in the encoded prefusion-stabilized SARS-CoV-2 spike protein (S(P2)). Biophysical characterization of Omicron XBB.1.5 S(P2) demonstrated that it maintains a prefusion conformation that adopts a flexible and predominantly open one-RBD-up state, with high affinity binding to the human ACE-2 receptor. When administered as a 4th dose in BNT162b2-experienced mice, the monovalent Omicron XBB.1.5 vaccine elicited substantially higher serum neutralizing titers against pseudotyped viruses of Omicron XBB.1.5, XBB.1.16, XBB.1.16.1, XBB.2.3, EG.5.1 and HV.1 sublineages and the phylogenetically distant BA.2.86 lineage than the bivalent Wild Type + Omicron BA.4/5 vaccine. Similar trends were observed against Omicron XBB sublineage pseudoviruses when the vaccine was administered as a 2-dose primary series in naive mice. Strong S-specific Th1 CD4+ and IFN{gamma}+ CD8+ T cell responses were also observed. These findings, together with prior experience with variant-adapted vaccine responses in preclinical and clinical studies, suggest that the monovalent Omicron XBB.1.5-adapted BNT162b2 vaccine is anticipated to confer protective immunity against dominant SARS-CoV-2 strains. ONE-SENTENCE SUMMARYThe monovalent Omicron XBB.1.5-adapted BNT162b2 mRNA vaccine encodes a prefusion-stabilized spike immunogen that elicits more potent neutralizing antibody responses against homologous XBB.1.5 and other circulating sublineage pseudoviruses compared to the bivalent Wild Type + Omicron BA.4/5 BNT162b2 vaccine, thus demonstrating the importance of annual strain changes to the COVID-19 vaccine.

immunology↗

bioRxiv2022

Accurate models of substrate preferences of post-translational modification enzymes from a combination of mRNA display and deep learning

Promiscuous post-translational modification (PTM) enzymes often display non-obvious substrate preferences by acting on diverse yet well-defined sets of peptides and/or proteins. Thorough understanding of substrate fitness landscapes for promiscuous PTM enzymes is important because they play key roles in many areas of contemporary science, including natural product biosynthesis, molecular biology and biotechnology. Here, we report the development of an integrated platform for accurate profiling of substrate preferences for PTM enzymes. The platform features a combination of i) mRNA display with next generation sequencing as an ultrahigh throughput technique for data acquisition and ii) deep learning for data analysis. The high accuracy (>0.99 in each of two studies) and generalizability of the resulting deep learning models enables comprehensive analysis of enzymatic substrate preferences. The models can be utilized to quantify fitness across sequence space, map modification sites, and identify important amino acids in the substrate. To benchmark the platform, we perform substrate specificity profiling of a Ser dehydratase (LazBF) and a Cys/Ser cyclodehydratase (LazDEF), two enzymes from the lactazole biosynthesis pathway. In both studies, our results point to highly complex enzymatic preferences, which, particularly for LazBF, cannot be reduced to a set of simple rules. The ability of the constructed models to dissect and analyze such complexity suggests that the developed platform can facilitate the wider study of PTM enzymes.

biochemistry↗

bioRxiv2021

A chemical-genetic map of the pathways controlling drug potency in Mycobacterium tuberculosis

Mycobacterium tuberculosis (Mtb) infection is notoriously difficult to treat. Treatment efficacy is limited by Mtbs intrinsic drug resistance, as well as its ability to evolve acquired resistance to all antituberculars in clinical use. A deeper understanding of the bacterial pathways that govern drug efficacy could facilitate the development of more effective therapies to overcome resistance, identify new mechanisms of acquired resistance, and reveal overlooked therapeutic opportunities. To define these pathways, we developed a CRISPR interference chemical-genetics platform to titrate the expression of Mtb genes and quantify bacterial fitness in the presence of different drugs. Mining this dataset, we discovered diverse and novel mechanisms of intrinsic drug resistance, unveiling hundreds of potential targets for synergistic drug combinations. Combining chemical-genetics with comparative genomics of Mtb clinical isolates, we further identified numerous new potential mechanisms of acquired drug resistance, one of which is associated with the emergence of a multidrug-resistant tuberculosis (TB) outbreak in South America. Lastly, we make the unexpected discovery of an "acquired drug sensitivity." We found that the intrinsic resistance factor whiB7 was inactivated in an entire Mtb sublineage endemic to Southeast Asia, presenting an opportunity to potentially repurpose the macrolide antibiotic clarithromycin to treat TB. This chemical-genetic map provides a rich resource to understand drug efficacy in Mtb and guide future TB drug development and treatment.

microbiology↗