Complex cellular functions occur via the coordinated formation and dissociation of protein complexes. Functions such as the response to a signaling ligand can incorporate dozens of proteins and hundreds of complexes. Until recently, it has been difficult to measure multiple protein complexes at the single-cell level. Here, we present a step-by-step procedure for proximity sequencing, which enables the simultaneous measurement of proteins, mRNA and hundreds of protein complexes located on the outer membrane of cells. We guide the user through probe creation, sample preparation, staining, sequencing and computational quantification of protein complexes. This protocol empowers researchers to study, for example, the interplay between transcriptional states and cellular functions by coupling measurements of transcription to measurements of linked effector molecules, yet could be generalizable to other paired events. The protocol requires roughly 16 h spread over several days to complete by users with expertise in basic molecular biology and single-cell sequencing.
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http://dx.doi.org/10.1038/s41596-024-01030-x | DOI Listing |
Anal Bioanal Chem
December 2024
XJTLU Wisdom Lake Academy of Pharmacy-BEAVER Biomedical Joint Laboratory, Suzhou, 215123, China.
Protein glycosylation is one of the most important post-translational modifications, implicated in the development of various diseases, including neurodegenerative diseases, diabetes, and cancers. However, the low content of glycoproteins in biological samples, the diversity and heterogeneity of glycan structures, and insensitive detection methods make glycosylation analysis challenging. As a result, efficient enrichment of glycopeptides from complex samples is a critical step.
View Article and Find Full Text PDFTrials
December 2024
Liver Transplantation Center, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China.
Background: Indocyanine green (ICG) is a near-infrared fluorescent dye widely used for intraoperative navigation during liver surgeries because of its non-radioactive nature, high safety, and minimal impact on liver function. However, variability in its dosage and concentration and its low imaging success rates have limited its widespread application. To address these issues, we developed a novel ICG-human serum albumin (ICG-HSA) complex to enhance fluorescence visualization during laparoscopic anatomical liver resection.
View Article and Find Full Text PDFHum Exp Toxicol
December 2024
Department of neurology, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, China. Hubei Sizhen Laboratory, Affiliated Hospital of Hubei University of Chinese Medicine, Wuhan, China.
Introduction: The incidence of cerebral ischemia-reperfusion injury (I/R) is complex which seriously threatens the life safety of patients. Neither its prevention nor its treatment has been successful so far. Proteins that bind to DNA and belong to the C2/H2 zinc finger family are known as Krüppel-like factors (KLFs).
View Article and Find Full Text PDFESMO Open
December 2024
Cancer Institute and Blood Disorders, Hospital Clinic, Barcelona; Translational Genomics and Targeted Therapies in Solid Tumors, August Pi I Sunyer Biomedical Research Institute (IDIBAPS), Barcelona; Department of Medicine, University of Barcelona, Barcelona; Reveal Genomics, Barcelona; Breast Cancer Unit, IOB-QuirónSalud, Barcelona, Spain. Electronic address:
Therapies targeting human epidermal growth factor receptor 2 (HER2)-positive breast cancer significantly impact patient outcomes, quality of life, and health care systems. While chemotherapy and trastuzumab improve survival in early-stage HER2-positive breast cancer, variability in clinical and biological characteristics leads to different response to therapies and outcomes. Clinical guidelines provide general recommendations, but significant uncertainty persists in identifying an optimal treatment plan for individual patients.
View Article and Find Full Text PDFDrug Discov Today
December 2024
Cell Signaling and Cancer Biology Laboratory, Department of Biochemistry, Guindy Campus, University of Madras, Chennai 600025, India. Electronic address:
Salt-inducible kinases (SIKs), a group of serine/threonine kinases in the adenosine monophosphate-activated protein kinase (AMPK) family, exist in three isoforms: SIK1, SIK2 and SIK3. These kinases are crucial in various physiological processes. Emerging evidence indicates that dysregulation of SIK expression and activation significantly contributes to carcinogenesis by promoting cellular proliferation, metabolic dysregulation, metastasis and chemoresistance through the modulation of crucial signaling pathways.
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