E. J. Fertig

Immune landscape of tertiary lymphoid structures in hepatocellular carcinoma (HCC) treated with neoadjuvant immune checkpoint blockade

This study examines TLS in HCC treated with neoadjuvant immunotherapy, finding TLS correlate with better outcomes and show distinct morphological and functional features in tumor regression.

Informing virtual clinical trials of hepatocellular carcinoma with spatial multi-omics analysis of a human neoadjuvant immunotherapy clinical trial

The paper develops a spatial quantitative systems pharmacology model for virtual clinical trials in HCC, validated with spatial multi-omics data from a neoadjuvant immunotherapy trial.

SpliceMutr enables pan-cancer analysis of splicing-derived neoantigen burden in tumors

SpliceMutr quantifies splicing-derived neoantigens across cancers, finding correlations with immune biomarkers and treatment response.

Latent transcriptional programs reveal histology-encoded tumor features spanning tissue origins

This paper uses machine learning to identify latent transcriptional programs in squamous cell carcinomas from histology images, linking them to clinically relevant biological processes.

Spatial transcriptomics analysis of neoadjuvant cabozantinib and nivolumab in advanced hepatocellular carcinoma identifies independent mechanisms of resistance and recurrence

This study uses spatial transcriptomics to analyze HCC tumors treated with cabozantinib and nivolumab, identifying distinct immune and fibrotic mechanisms linked to response and recurrence.

MLL1 regulates cytokine-driven cell migration and metastasis

This study shows MLL1 promotes cancer metastasis by regulating cytokine secretion and actin dynamics, and its inhibition reduces metastasis when combined with chemotherapy.

PanIN and CAF Transitions in Pancreatic Carcinogenesis Revealed with Spatial Data Integration

This paper develops a new protocol for spatial transcriptomics analysis of FFPE PanIN specimens and integrates it with imaging and scRNA-seq to study the progression from PanIN to PDAC.

Inflammatory Signaling in Pancreatic Cancer Transfers Between a Single-cell RNA Sequencing Atlas and Co-Culture

This paper integrates single-cell RNA sequencing data with organoid co-cultures to study inflammatory signaling in pancreatic cancer and validates findings through transfer learning and mechanistic experiments.

Transfer learning of an in vivo-derived senescence signature identifies conserved and tissue-specific senescence across species and diverse pathologies

The paper develops a transfer learning approach to identify senescent cells across species and tissues using an in vivo-derived gene expression signature, revealing conserved and tissue-specific senescence features.

Using Mathematical Modeling to Distinguish Intrinsic and Acquired Targeted Therapeutic Resistance in Head and Neck Cancer

This study uses mathematical models to determine the timing and mechanism of cetuximab resistance in HNSCC using tumor volume data from xenografts.

Age-associated Senescent - T Cell Signaling Promotes Type 3 Immunity that Inhibits Regenerative Response

This study shows that age-related senescent T cells promote type 3 immunity, which inhibits tissue repair, and that blocking this pathway improves healing in older animals.

Fibroblast activation protein regulates natural killer cell migration, extravasation and tumor infiltration

This study shows that fibroblast activation protein (FAP) is expressed by human NK cells and promotes their migration, extravasation, and tumor infiltration, suggesting FAP as a target to enhance NK cell-based therapies.

Phenotypic shifts of tumor associated macrophages and STAT3 mediated suppression of myeloid derived suppressor cells drive sensitization of HER2+ tumor immunity.

The paper uses single-cell RNA-sequencing to show entinostat shifts tumor microenvironment cell states, reducing immunosuppression and enhancing immune checkpoint inhibitor responses in HER2+ breast tumors.

Immune Selection Pressure Contributes to Pancreatic Cancer Immune Evasion

This study shows immune selection pressure in pancreatic cancer drives myeloid mimicry and immune evasion, which can be counteracted by JAK/STAT pathway inhibition to enhance immunotherapy.

Aging interacts with tumor biology to produce major changes in the immune tumor microenvironment

The paper examines how aging interacts with tumor biology to alter the immune tumor microenvironment, identifying age-specific immune cell changes and immune checkpoint gene expression patterns.

Transfer learning between preclinical models and human tumors identifies conserved NK cell activation signature in anti-CTLA-4 responsive tumors

The paper uses transfer learning to identify a conserved NK cell activation signature in anti-CTLA-4 responsive tumors across preclinical models and humans, showing its clinical relevance.

Integrated single cell and bulk multi-omics reveals heterogeneity and early changes in pathways associated with cetuximab resistance in HNSCC sensitive cell lines

The paper uses single cell and bulk multi-omics to study early resistance mechanisms in HNSCC cells treated with cetuximab, identifying TFAP2A and EMT as independent pathways.