multi-omics-and-integrative-analytics-in-natural-products-discovery

Multi-Omics and Integrative Analytics in Natural Products Discovery

Natural products (NPs) have long been an essential source of new bioactive compounds for drug discovery; however, traditional methods for screening and ...

Deyang People's Hospital of Chengdu University of Traditional Chinese Medicine

Inheritable colorectal cancers (CRC) accounted for about 20% of the CRC cases, such as hereditary nonpolyposis colorectal cancer (HNPCC), Gardner syndrome and familial adenomatous polyposis (FAP). A four-generation Han Chinese family was found affected with polyposis in colons. Inferred from the pedigree structure, the disease in this family showed an autosomal dominant inheritance model. To locate the causal mutations in this family, genomic DNAs were extracted and the next generation sequencing for 5 genes relating to colon cancer performed by Ion Torrent Personal Genome Machine with a 314 chip. The reads were aligned with human reference genome hg19 to call variants in the 5 genes. After analysis, 14 variants were detected in the sequenced sample and 13 been collected in dbSNP database and assigned with a rs identification number. In these variants, 9 were synonymous, 4 missense and 1 non-sense. In them, 2 rare variants (c.694C>T in APC and c.1690A>G in MSH2) might be the putative causal mutations for familial adenomatous polyposis (FAP) since the rarity of the mutated allele in normal controls. c.694C>T was detected in only affected members and generated a premature stop codon in APC. It should be a de novo germline mutation making APC containing this stop codon as targets for nonsense-mediated mRNA decay (NMD). c.1690A>G in MSH2 was not only detected in affected members, but also in normal ones in the family. Functional prediction revealed that the amino acid affected by this variant had no effect on the function of MSH2. Here, we report a de novo germline mutation of APC as the causal variant in a Chinese family with inheritable colon cancer by the next generation sequencing.

A de novo germline mutation of APC for inheritable colon cancer in a Chinese family using multigene next generation sequencing.

The large nuclear mitotic apparatus (NuMA) has been investigated for over 30years with functions related to the formation and maintenance of mitotic spindle poles during mitosis. However, the existence and functions of NuMA isoforms generated by alternative splicing remains unclear. In the present work, we show that at least seven NuMA isoforms (categorized into long, middle and short groups) generated by alternative splicing from a common NuMA mRNA precursor were discovered in HeLa cells and these isoforms differ mainly at the carboxyl terminus and the coiled-coil domains. Two "hotspot" exons with molecular mass of 3366-nt and 42-nt tend to be spliced during alternative splicing in long and middle groups. Furthermore, full-length coding sequences of long and middle NuMA obtained by using fusion PCR were constructed into GFP-tagged vector to illustrate their cellular localization. Long NuMA mainly localized in the nucleus with absence from nucleoli during interphase and translocated to the spindle poles in mitosis. Middle NuMA displayed the similar cell cycle-dependent distribution pattern as long NuMA. However, expression of NuMA short isoforms revealed a distinct subcellular localization. Short NuMA were present in the cytosol during the whole cycle, without colocalization with mitotic apparatus. These results have allowed us tentatively to explore a new research direction for NuMA's various functions.

Identification and characterization of novel NuMA isoforms.

Coffin-Siris syndrome (CSS) is a multiple malformation syndrome characterized by intellectual disability associated with coarse facial features, hirsutism, sparse scalp hair, and hypoplastic or absent fifth fingernails or toenails. CSS represents a small group of intellectual disability, and could be caused by at least twelve genes. The genetic background is quite heterogenous, making it difficult for clinicians and genetic consultors to pinpoint the exact disease types.

Identification of de novo mutations for ARID1B haploinsufficiency associated with Coffin-Siris syndrome 1 in three Chinese families via array-CGH and whole exome sequencing.

Tissue-resident memory T (T) cells are crucial components of the immune system that provide rapid, localized responses to recurrent pathogens at mucosal and epithelial barriers. Unlike circulating memory T cells, T cells are located within peripheral tissues, and they play vital roles in antiviral, antibacterial, and antitumor immunity. Their unique retention and activation mechanisms, including interactions with local epithelial cells and the expression of adhesion molecules, enable their persistence and immediate functionality in diverse tissues. Recent advances have revealed their important roles in chronic inflammation, autoimmunity, and cancer, illuminating both their protective and their pathogenic potential. This review synthesizes current knowledge on T cells' molecular signatures, maintenance pathways, and functional dynamics across different tissues. We also explore the interactions of T cells with other immune cells, such as B cells, macrophages, and dendritic cells, highlighting the complex network that underpins the efficacy of T cells in immune surveillance and response. Understanding the nuanced regulation of T cells is essential for developing targeted therapeutic strategies, including vaccines and immunotherapies, to enhance their protective roles while mitigating adverse effects. Insights into T cells' biology hold promise for innovative treatments for infectious diseases, cancer, and autoimmune conditions.

Tissue-resident memory T cells in diseases and therapeutic strategies.

Mutations at RNA splicing sites or regulatory elements can alter splicing efficiency or patterns, affecting RNA functionality and tissue-specific expression. Here, we present a protocol to study the impact of mutations near splicing sites on precursor mRNA (pre-mRNA) splicing. We describe steps for constructing plasmids by cloning the target gene into the pEGFP-N1 vector, performing site-directed mutagenesis, and transiently transfecting HEK293 cells. We then detail procedures for conducting mini-gene splicing assays to analyze splicing patterns influenced by mutations. For complete details on the use and execution of this protocol, please refer to Peng et al..

Protocol to study the effects of mutations near splicing sites on pre-mRNA splicing.

Tissue-resident memory T (T) cells are a specialized subset of memory T cells that permanently reside in non-lymphoid tissues, providing localized and long-lasting immune protection. In the urinary tract, T cells play critical roles in defending against infections, mediating tumor immunity, and influencing the pathogenesis of chronic inflammatory diseases. Their therapeutic potential is immense, with promising avenues for vaccine development, enhanced cancer immunotherapy, and targeted treatments for chronic inflammation. However, challenges remain in harnessing their protective roles while minimizing their pathological effects, particularly in immunosuppressive or inflammatory microenvironments. This review explores the diverse roles of T cells in urinary tract diseases, including infections, cancer, and chronic inflammation, and discusses therapeutic strategies and future directions for leveraging T cells to improve clinical outcomes. By advancing our understanding of T cell biology, we can develop innovative interventions that balance their immune-protective and regulatory functions.

Tissue-resident memory T cells in urinary tract diseases.

 The composition and metabolic activity of the gut microbiota play a crucial role in various health conditions, including the occurrence and development of chronic constipation. Recent metabolomic advances reveal that gut microbiota-derived metabolites-such as SCFAs, bile acids, neurotransmitters, and microbial gases-play critical roles in regulating intestinal function.  We systematically analyzed the current literature on microbial metabolomics in chronic constipation. This review consolidates findings from high-throughput metabolomic techniques (GC-MS, LC-MS, NMR) comparing metabolic profiles of constipated patients with healthy individuals. It also examines diagnostic improvements and personalized treatments, including fecal microbiota transplantation and neuromodulation, guided by these metabolomic insights.  This review shows that reduced SCFA levels impair intestinal motility and promote inflammation. An altered bile acid metabolism-with decreased secondary bile acids like deoxycholic acid-disrupts receptor-mediated signaling, further affecting motility. Additionally, imbalances in amino acid metabolism and neurotransmitter production contribute to neuromuscular dysfunction, while variations in microbial gas production (e.g., methane vs. hydrogen) further modulate gut transit.  Integrating metabolomics with gut microbiota research clarifies how specific microbial metabolites regulate gut function. These insights offer promising directions for precision diagnostics and targeted therapies to restore microbial balance and improve intestinal motility.

Article	Year
A de novo germline mutation of APC for inheritable colon cancer in a Chinese family using multigene next generation sequencing. Biochemical and biophysical research communications\| PubMed ID: 24735542	2014
Identification and characterization of novel NuMA isoforms. Biochemical and biophysical research communications\| PubMed ID: 25451259	2014
Identification of de novo mutations for ARID1B haploinsufficiency associated with Coffin-Siris syndrome 1 in three Chinese families via array-CGH and whole exome sequencing. BMC medical genomics\| PubMed ID: 34775996	2021
Tissue-resident memory T cells in diseases and therapeutic strategies. MedComm\| PubMed ID: 39802636	2025
Protocol to study the effects of mutations near splicing sites on pre-mRNA splicing. STAR protocols\| PubMed ID: 40048423	2025
Tissue-resident memory T cells in urinary tract diseases. Frontiers in immunology\| PubMed ID: 40066439	2025
Metabolomics Insights into Gut Microbiota and Functional Constipation. Metabolites\| PubMed ID: 40278398	2025

Guanting Lu

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