Biology subjects

Halper-Stromberg, E.

Publications and source records attributed to Halper-Stromberg, E..

3 recordsLinked to original sources

bioRxiv2023

Somatic protospacer adjacent motifs are numerous and selectively targetable in cancers

Somatic mutations are desirable targets for selective elimination of cancer, yet most are found within the noncoding regions. We propose a novel, cancer-specific killing approach using CRISPR-Cas9 which exploits the requirement of a protospacer adjacent motif (PAM) for Cas9 activity. Through whole genome sequencing (WGS) of paired tumor minus normal (T-N) samples from three pancreatic cancer patients (Panc480, Panc504, and Panc1002), we identified an average of 417 somatic PAMs per tumor produced from single base substitutions. We analyzed 591 paired T-N samples from The International Cancer Genome Consortium and discovered medians of [~]455 somatic PAMs per tumor in pancreatic, [~]2800 in lung, and [~]3200 in esophageal cancer cohorts. Finally, we demonstrated >80% selective cell death of two targeted pancreatic cancer cell lines in co-cultures using 4-9 sgRNAs, targeting noncoding regions, designed from the somatic PAM discovery approach. We also showed no off-target activity from these tumor-specific sgRNAs through WGS. Statement of significanceThis study demonstrates the potential of CRISPR-Cas9 as a novel and selective anti-cancer strategy. It requires just a few targets to induce double strand breaks for significant cytotoxicity. Our findings markedly expand the repertoire of targetable mutations in cancers and support genetically targeting other adult solid tumor types.

cancer biology↗

bioRxiv2023

Mechanism of delayed cell death following simultaneous CRISPR-Cas9 targeting in pancreatic cancers

While radiation is an effective oncologic therapy, killing cancer by inducing DNA double-strand breaks (DSBs), it lacks specificity for neoplastic cells. We have previously adapted the CRISPR-Cas9 gene-editing technology as a cancer-specific treatment modality targeting somatic mutations in pancreatic cancer (PC). However, its tumoricidal potential remains unclear, especially in comparison to therapeutic doses of radiation. Here, we demonstrate that CRISPR-Cas9-induced DSBs are more cytotoxic in PCs than a comparable number of radiation-induced DSBs. We observed >90% tumor growth inhibition by targeting 9 sites with cancer-specific single-guide RNAs (sgRNAs). Through both bioinformatics and cytogenetics analyses, we found that CRISPR-Cas9-induced DSBs triggered ongoing chromosomal rearrangements, with 87% of structural variants not directly produced from the initial CRISPR-Cas9-induced DSBs, and chromosomal instability (CIN) peaking before cell death. By comparing the cytotoxicity of CRISPR-Cas9- to radiation-induced DSBs, we demonstrate that the number of DSBs required to achieve equitoxic effects was [~]3 times higher for radiation than CRISPR-Cas9. Finally, we show that PC cells that had survived CRISPR-Cas9 targeting retained susceptibility to subsequent CRISPR-Cas9-induced DSBs at different genomic sites with >87% growth inhibition. Together, our data support the therapeutic potential of CRISPR-Cas9 as an anti-cancer strategy.

cancer biology↗

bioRxiv2017

Systemic Markers of Adaptive and Innate Immunity Are Associated with COPD Severity and Spirometric Disease Progression

The progression of chronic obstructive pulmonary disease (COPD) is associated with marked alterations in circulating immune cell populations, but no studies have characterized alterations in these cell types across the full spectrum of lung function impairment in current and former smokers. In 6,299 subjects from the COPDGene and ECLIPSE studies, we related Coulter blood counts and proportions to cross-sectional FEV1 adjusting for current smoking status. We also related cell count measures to three-year change in FEV1 in ECLIPSE subjects. In a subset of subjects with blood gene expression data, we used cell type deconvolution methods to infer the proportions of immune cell subpopulations, and we related these to COPD clinical status. We observed that FEV1 levels are positively correlated with lymphocytes and negatively correlated with myeloid populations such as neutrophils and monocytes. In multivariate models, absolute cell counts and proportions were associated with cross-sectional FEV1, and lymphocytes, monocytes, and eosinophil counts were predictive of three-year change in lung function. Using cell type deconvolution to study immune cell subpopulations, we observed that subjects with COPD had a lower proportion of CD4+ resting memory cells and naive B cells compared to non-COPD smokers. Alterations in circulating immune cells in COPD support a mixed pattern of lymphocyte suppression and an enhanced myeloid cell immune response. Cell counts and proportions contribute independent information to models predicting lung function suggesting a critical role for immune response in long-term COPD outcomes. Cell type deconvolution is a promising method for immunophenotyping in large cohorts.

genomics↗