SMARCAL1 is a dual regulator of innate immune signaling and PD-L1 expression that promotes tumor immune evasion

Genomic instability can trigger cancer-intrinsic innate immune responses that promote tumor rejection. However, cancer cells often evade these responses by overexpressing immune checkpoint regulators, such as PD-L1. Here, we identify the SNF2-family DNA translocase SMARCAL1 as a factor that favors tumor immune evasion by a dual mechanism involving both the suppression of innate immune signaling and the induction of PD-L1-mediated immune checkpoint responses. Mechanistically, SMARCAL1 limits endogenous DNA damage, thereby suppressing cGAS-STING-dependent signaling during cancer cell growth. Simultaneously, it cooperates with the AP-1 family member JUN to maintain chromatin accessibility at a PD-L1 transcriptional regulatory element, thereby promoting PD-L1 expression in cancer cells. SMARCAL1 loss hinders the ability of tumor cells to induce PD-L1 in response to genomic instability, enhances anti-tumor immune responses and sensitizes tumors to immune checkpoint blockade in a mouse melanoma model. Collectively, these studies uncover SMARCAL1 as a promising target for cancer immunotherapy.

Towards a CRISPeR understanding of homologous recombination with high-throughput functional genomics

CRISPR-dependent genome editing enables the study of genes and mutations on a large scale. Here we review CRISPR-based functional genomics technologies that generate gene knockouts and single nucleotide variants (SNVs) and discuss how their use has provided new important insights into the function of homologous recombination (HR) genes. In particular, we highlight discoveries from CRISPR screens that have contributed to define the response to PARP inhibition in cells deficient for the HR genes BRCA1 and BRCA2, uncover genes whose loss causes synthetic lethality in combination with BRCA1/2 deficiency, and characterize the function of BRCA1/2 SNVs of uncertain clinical significance. Further use of these approaches, combined with next-generation CRISPR-based technologies, will aid to dissect the genetic network of the HR pathway, define the impact of HR mutations on cancer etiology and treatment, and develop novel targeted therapies for HR-deficient tumors.

Functional interrogation of DNA damage response variants with base editing screens

Mutations in DNA damage response (DDR) genes endanger genome integrity and predispose to cancer and genetic disorders. Here, using CRISPR-dependent cytosine base editing screens, we identify > 2,000 sgRNAs that generate nucleotide variants in 86 DDR genes, resulting in altered cellular fitness upon DNA damage. Among those variants, we discover loss- and gain-of-function mutants in the Tudor domain of the DDR regulator 53BP1 that define a non-canonical surface required for binding the deubiquitinase USP28. Moreover, we characterize variants of the TRAIP ubiquitin ligase that define a domain, whose loss renders cells resistant to topoisomerase I inhibition. Finally, we identify mutations in the ATM kinase with opposing genome stability phenotypes and loss-of-function mutations in the CHK2 kinase previously categorized as variants of uncertain significance for breast cancer. We anticipate that this resource will enable the discovery of additional DDR gene functions and expedite studies of DDR variants in human disease.

MCM8IP activates the MCM8-9 helicase to promote DNA synthesis and homologous recombination upon DNA damage

Homologous recombination (HR) mediates the error-free repair of DNA double-strand breaks to maintain genomic stability. Here we characterize C17orf53/MCM8IP, an OB-fold containing protein that binds ssDNA, as a DNA repair factor involved in HR. MCM8IP-deficient cells exhibit HR defects, especially in long-tract gene conversion, occurring downstream of RAD51 loading, consistent with a role for MCM8IP in HR-dependent DNA synthesis. Moreover, loss of MCM8IP confers cellular sensitivity to crosslinking agents and PARP inhibition. Importantly, we report that MCM8IP directly associates with MCM8-9, a helicase complex mutated in primary ovarian insufficiency, and RPA1. We additionally show that the interactions of MCM8IP with MCM8-9 and RPA facilitate HR and promote replication fork progression and cellular viability in response to treatment with crosslinking agents. Mechanistically, MCM8IP stimulates the helicase activity of MCM8-9. Collectively, our work identifies MCM8IP as a key regulator of MCM8-9-dependent DNA synthesis during DNA recombination and replication.

Detection of Marker-Free Precision Genome Editing and Genetic Variation through the Capture of Genomic Signatures

Genome editing technologies have transformed our ability to engineer desired genomic changes within living systems. However, detecting precise genomic modifications often requires sophisticated, expensive, and time-consuming experimental approaches. Here, we describe DTECT (Dinucleotide signaTurE CapTure), a rapid and versatile detection method that relies on the capture of targeted dinucleotide signatures resulting from the digestion of genomic DNA amplicons by the type IIS restriction enzyme AcuI. DTECT enables the accurate quantification of marker-free precision genome editing events introduced by CRISPR-dependent homology-directed repair, base editing, or prime editing in various biological systems, such as mammalian cell lines, organoids, and tissues. Furthermore, DTECT allows the identification of oncogenic mutations in cancer mouse models, patient-derived xenografts, and human cancer patient samples. The ease, speed, and cost efficiency by which DTECT identifies genomic signatures should facilitate the generation of marker-free cellular and animal models of human disease and expedite the detection of human pathogenic variants.

Stimulation of CRISPR-mediated homology-directed repair by an engineered RAD18 variant

Precise editing of genomic DNA can be achieved upon repair of CRISPR-induced DNA double-stranded breaks (DSBs) by homology-directed repair (HDR). However, the efficiency of this process is limited by DSB repair pathways competing with HDR, such as non-homologous end joining (NHEJ). Here we individually express in human cells 204 open reading frames involved in the DNA damage response (DDR) and determine their impact on CRISPR-mediated HDR. From these studies, we identify RAD18 as a stimulator of CRISPR-mediated HDR. By defining the RAD18 domains required to promote HDR, we derive an enhanced RAD18 variant (e18) that stimulates CRISPR-mediated HDR in multiple human cell types, including embryonic stem cells. Mechanistically, e18 induces HDR by suppressing the localization of the NHEJ-promoting factor 53BP1 to DSBs. Altogether, this study identifies e18 as an enhancer of CRISPR-mediated HDR and highlights the promise of engineering DDR factors to augment the efficiency of precision genome editing.

CRISPR-Mediated Base Editing Enables Efficient Disruption of Eukaryotic Genes through Induction of STOP Codons

Standard CRISPR-mediated gene disruption strategies rely on Cas9-induced DNA double-strand breaks (DSBs). Here, we show that CRISPR-dependent base editing efficiently inactivates genes by precisely converting four codons (CAA, CAG, CGA, and TGG) into STOP codons without DSB formation. To facilitate gene inactivation by induction of STOP codons (iSTOP), we provide access to a database of over 3.4 million single guide RNAs (sgRNAs) for iSTOP (sgSTOPs) targeting 97%-99% of genes in eight eukaryotic species, and we describe a restriction fragment length polymorphism (RFLP) assay that allows the rapid detection of iSTOP-mediated editing in cell populations and clones. To simplify the selection of sgSTOPs, our resource includes annotations for off-target propensity, percentage of isoforms targeted, prediction of nonsense-mediated decay, and restriction enzymes for RFLP analysis. Additionally, our database includes sgSTOPs that could be employed to precisely model over 32,000 cancer-associated nonsense mutations. Altogether, this work provides a comprehensive resource for DSB-free gene disruption by iSTOP.

Preclinical development and qualification of ZFN-mediated CCR5 disruption in human hematopoietic stem/progenitor cells

Gene therapy for HIV-1 infection is a promising alternative to lifelong combination antiviral drug treatment. Chemokine receptor 5 (CCR5) is the coreceptor required for R5-tropic HIV-1 infection of human cells. Deletion of CCR5 renders cells resistant to R5-tropic HIV-1 infection, and the potential for cure has been shown through allogeneic stem cell transplantation with naturally occurring homozygous deletion of CCR5 in donor hematopoietic stem/progenitor cells (HSPC). The requirement for HLA-matched HSPC bearing homozygous CCR5 deletions prohibits widespread application of this approach. Thus, a strategy to disrupt CCR5 genomic sequences in HSPC using zinc finger nucleases was developed. Following discussions with regulatory agencies, we conducted IND-enabling preclinical in vitro and in vivo testing to demonstrate the feasibility and (preclinical) safety of zinc finger nucleases-based CCR5 disruption in HSPC. We report here the clinical-scale manufacturing process necessary to deliver CCR5-specific zinc finger nucleases mRNA to HSPC using electroporation and the preclinical safety data. Our results demonstrate effective biallelic CCR5 disruption in up to 72.9% of modified colony forming units from adult mobilized HSPC with maintenance of hematopoietic potential in vitro and in vivo. Tumorigenicity studies demonstrated initial product safety; further safety and feasibility studies are ongoing in subjects infected with HIV-1 (NCT02500849@clinicaltrials.gov).

Highly efficient homology-driven genome editing in human T cells by combining zinc-finger nuclease mRNA and AAV6 donor delivery

The adoptive transfer of engineered T cells for the treatment of cancer, autoimmunity, and infectious disease is a rapidly growing field that has shown great promise in recent clinical trials. Nuclease-driven genome editing provides a method in which to precisely target genetic changes to further enhance T cell function in vivo. We describe the development of a highly efficient method to genome edit both primary human CD8 and CD4 T cells by homology-directed repair at a pre-defined site of the genome. Two different homology donor templates were evaluated, representing both minor gene editing events (restriction site insertion) to mimic gene correction, or the more significant insertion of a larger gene cassette. By combining zinc finger nuclease mRNA delivery with AAV6 delivery of a homologous donor we could gene correct 41% of CCR5 or 55% of PPP1R12C (AAVS1) alleles in CD8⁺ T cells and gene targeting of a GFP transgene cassette in >40% of CD8⁺ and CD4⁺ T cells at both the CCR5 and AAVS1 safe harbor locus, potentially providing a robust genome editing tool for T cell-based immunotherapy.

Location of platinum binding sites on bacteriorhodopsin by electron diffraction

A platinum-containing derivative of bacteriorhodopsin has been prepared by treating purple membranes with glycyl-L-methionatoplatinum. Low-dose electron diffraction was used to identify Pt binding sites in the 5.6 A resolution reconstruction of the bacteriorhodopsin unit cell in projection. This is a necessary first step in the use of the Pt derivative for identifying the parts of the amino acid sequence corresponding to the alpha helices in the bacteriorhodopsin structure and for obtaining phases for reflections out to 3.5 A resolution by the method of heavy-atom isomorphous replacement. The largest peak in a Fourier difference map between platinum-labeled and native purple membrane is larger than the spurious features expected to arise from errors in measurements of diffraction intensities.

Unintentional carbon monoxide deaths in California from charcoal grills and hibachis

This study was carried out to determine the annual incidence rate of and factors associated with unintentional deaths due to carbon monoxide (CO) poisoning from charcoal grills/hibachis in California during 1979-1988. A search through the California Master Mortality File was conducted to identify all cases with ICD-9 codes related to unintentional CO deaths. Individual coroners' investigation reports were obtained from 42 counties and evaluated by three evaluators. After excluding miscoded and misclassified cases, 444 deaths were judged to be authentic cases of unintentional CO poisoning. Among them, 59 deaths found to be due to the improper use of charcoal grills/hibachis. An increasing but not statistically significant trend was observed over the 10-year period. The highest rates occurred among males, asians, blacks, and middle-aged (20-39) people. Fifty-four percent of the deaths occurred in motor vehicles and 46% in residential structures.

Causes of unintentional deaths from carbon monoxide poisonings in California

The purpose of this study was to determine the annual number and incidence of unintentional deaths from carbon monoxide (CO) poisonings in California and to identify specific factors that caused or contributed to the deaths. Unintentional CO deaths in California over a ten-year period (1979 to 1988) were identified from the database of the California Master Mortality File and coroners' investigation reports. Factors associated with unintentional CO deaths were determined based on the information from the investigation reports. The annual number of unintentional CO deaths varied from 27 to 58 over the ten years examined, with an average annual death incidence of 1.7 x 10(-6). Death rates were high among males and African-Americans. Alcohol appeared to be a factor in 31% of the cases. The types of combustion sources associated with unintentional CO deaths were: heating or cooking appliances; motor vehicles; charcoal grills and hibachis; small engines; and camping equipment. Factors associated with unintentional CO deaths interact in a complex way. To reduce the rate of unintentional CO deaths effectively, joint efforts involving several prevention methods are suggested.

The distribution of lifetime cumulative exposures to radon for California residents

The distribution of individual lifetime exposures to radon was estimated using data from studies on radon concentrations, mobility, and time-activity patterns in the state of California. The distributions of radon concentrations in various geographic regions were obtained from the results of year-long radon measurements of 310 residences. The mobility patterns were acquired through a survey of the moving histories of the members of 507 households. The indoor and outdoor time-activity data were collected for 1,780 individuals in 1,596 households. Based on these data, a computer simulation technique was used to estimate the distribution of radon exposures with a parametric (lognormal model) and a nonparametric approach (bootstrap method). The estimated average lifetime exposure for radon was 2,448 Bq.m-3.yr for the lognormal model and 2,487 Bq.m-3.yr for the bootstrap method. The standard deviation was 1,130 and 1,145 Bq.m-3.yr respectively. Assuming no move over the lifetime, the estimated average lifetime exposure to radon was 2,052 Bq.m-3.yr for the lognormal model and 2,078 Bq.m-3.yr for the bootstrap method, while the standard deviation increased to 1,378 Bq.m-3.yr for the lognormal model and 1,514 Bq.m-3.yr for the bootstrap method.

Irritant effects of formaldehyde exposure in mobile homes

This paper reports the irritant effects associated with formaldehyde exposures in mobile homes. Week-long, integrated formaldehyde concentrations were measured using passive monitors in summer and winter while the mobile home residents continued their normal activities. Information on acute health problems, chronic respiratory/allergic illnesses, smoking behavior, demographic variables, and time spent at home was obtained on over 1000 individuals during the sampling period. Measured formaldehyde concentrations varied from under the limit of detection (0.01 ppm) to 0.46 ppm. Formaldehyde exposure was estimated for each individual by multiplying the concentration measured in his or her home by the time he or she spent at home. Irritant effects were found to be associated with formaldehyde exposure after controlling for age, sex, smoking status, and chronic illnesses using a logistic procedure. Some of the interaction terms found to be significant indicated that there were synergistic effects between formaldehyde exposure and chronic health problems.

Public inquiries about indoor air quality in California

To identify the indoor air quality issues about which Californians most often sought advice from a health department or a public information agency and to evaluate how well these agencies met the public's needs, members of the California Interagency Working Group (IWG) on Indoor Air Quality kept records of inquiries they received over a 30-month period from mid-1985 through 1987. Members of the IWG answered calls from residents of a least 49 of California's 58 counties. IWG members received more public inquiries about residences than about offices, educational institutions, commercial buildings, or medical facilities. However, each call about a residence probably represented fewer people at risk of exposure to a real or a potential problem than did calls about other types of buildings. Homeowners themselves asked the majority of the questions about residences, whereas a large number of the inquiries about office buildings were made, not by affected office workers, but by building managers, contractors, consultants, or company health and safety officers. The leading topics of concern in the residences were asbestos, chemical and biological contamination, and radon. In offices, chemical contamination, the ventilation system, biological contamination, asbestos, and tobacco smoke were the most frequently mentioned sources of problems. Callers often reported experiencing headaches, allergy symptoms, nose or throat irritation, and respiratory tract problems in connection with their complaints. IWG members directed a third of the calls elsewhere, of which half were referred to consultants or testing laboratories. The IWG's experience in the State of California could help other health departments prepare to face the public's increasing concern about indoor air pollution.

Radon in California homes

Images

Location of an extrinsic label in the primary and tertiary structure of bacteriorhodopsin

We located a heavy metal label, mercurilated phenylglyoxal, in both the primary sequence and in the tertiary structure of bacteriorhodopsin. This label modified arginines 225 and 227, which are on the COOH-terminal helix (G). In the projected electron potential difference map, the major site is close to the central inner helix. From this result we conclude that helix 1 could not be the COOH-terminal helix G. We tested the multiple isomorphous replacement method for obtaining phases for purple membrane by electron diffraction.

Peptide-chain secondary structure of bacteriorhodopsin

Ultraviolet circular dichroism spectroscopy in the interval from 190 to 240 nm and infrared spectroscopy in the region of the amide I band (1,600 cm-1 to 1,700 cm-1) has been used to estimate the alpha-helix content and the beta-sheet content of bacteriorhodopsin. Circular dichroism spectroscopy strongly suggests that the alpha-helix content is sufficient for only five helices, if each helix is composed of 20 or more residues. It also suggests that there is substantial beta-sheet conformation in bacteriorhodopsin. The presence of beta-sheet secondary structure is further suggested by the presence of a 1,639 cm-1 shoulder on the amide I band in the infrared spectrum. Although a structural model consisting of seven alpha-helical rods has been generally accepted up to this point, the spectroscopic data are more consistent with a model consisting of five alpha-helices and four strands of beta-sheet. We note that the primary amino acid sequence can be assigned to segments of alpha-helix and beta-sheet in a way that does not require burying more than two charged groups in the hydrophobic membrane interior, contrary to the situation for any seven-helix model.

High resolution cold stage for the JEOL 100B and 100C electron microscopes

A high resolution, liquid nitrogen-cooled specimen stage has been designed and constructed for use on the JEOL 100B and 100C electron-microscopes. This stage will be useful for imaging biological macromolecular arrays in the frozen-hydrated or glucose-embedded states at low temperature. Images thus obtained should have an increased signal-to-noise ratio due to the radiation damage protection offered by low temperature.

Radiation damage of purple membrane at low temperature

The intensities of diffracted electron beams for the purple membrane of Halobacterium halobium are found to decay exponentially as a function of the accumulated electron exposure, both at room temperature and at -120 degrees C. This permits us to define the "critical dose" Ne(h,k) for the (h,k) diffracted beam, as being the electron exposure (electrons/A2) at which the diffracteed intensity has fallen to e-1 of its initial value. The critical of purple membrane is found to increase from the room temperature value by at least a factor of four when the specimen is maintained at a temperature of -120 degrees C on a liquid-nitrogen-cooled stage. A relationship derived between the critical dose, Ne, and the dose for optimum imaging, Nopt. Both Ne and Nopt depend, of course, upon the spatial frequency, or resolution. The derivation is valid only for the case in which all sources of noise other than quantum fluctuations are neglected. In this case, Nopt approximately equal to 2.5Ne. Finally, Nuclear Track Emulsion plates have been shown to be advantageous for recording high resolution electron diffraction patterns of small (1 micrometer 2) patches of crystalline biological materials.

Molecular orientation of bacteriorhodopsin within the purple membrane of Halobacterium halobium

The direction of orientation of the protein bacteriorhodopsin within the purple membrane of Halobacterium halobium has been determined by selected-area electron diffraction of membranes preferentially oriented by adsorption to polylysine. Purple membrane is known to adsorb preferentially to polylysine by its cytoplasmic surface at neutral pH and by its extracellular surface at low pH. To maintain the adsorbed membranes in a well-ordered state in the electron microscope, an improved technique of preparing frozen specimens was developed. Large areas of frozen-hydrated specimens, devoid of bulk water, were obtainable after the specimen was passed through a Ca stearate film at an air-water interface. High-resolution microscopy was used to relate the orientation observed in the electron diffraction patterns to the orientation of the projected structure that is obtained from images. We have found that the three-dimensional structure determined by Henderson and and Unwin [Henderson, R. & Unwin, P.N.T. (1975) Nature 257, 28--32] is oriented with the cytoplasmic side uppermost--i.e., the helices fan outward on the cytoplasmic side of the membrane.